ERβ Expression Research Articles

A kinome drug screen identifies multi-TKI synergies and ERBB2 signaling as a therapeutic vulnerability in MYC/TYR subgroup atypical teratoid rhabdoid tumors.

Atypical teratoid rhabdoid tumor (ATRT) is a rare, devastating, and largely incurable pediatric brain tumor. Although recent studies have uncovered 3 molecular subgroups of ATRTs with distinct disease patterns, and signaling features, the therapeutic profiles of ATRT subgroups remain incompletely elucidated. We examined the effect of 465 kinase inhibitors on a panel of ATRT subgroup-specific cell lines. We then applied multiomics analyses to investigate the underlying molecular mechanism of kinase inhibitor efficacy in ATRT subgroups. We observed that ATRT cell lines are broadly sensitive to inhibitors of the PI3K and MAPK signaling pathways, as well as CDKs, AURKA/B kinases, and polo-like kinase 1. We identified 2 classes of multikinase inhibitors predominantly targeting receptor tyrosine kinases including PDGFR and EGFR/ERBB2 in MYC/TYR ATRT cells. The PDGFRB inhibitor, Dasatinib, synergistically affected MYC/TYR ATRT cell growth when combined with broad-acting PI3K and MAPK pathway inhibitors, including Rapamycin and Trametinib. We observed that MYC/TYR ATRT cells were also distinctly sensitive to various inhibitors of ERBB2 signaling. Transcriptional, H3K27Ac ChIPSeq, ATACSeq, and HiChIP analyses of primary MYC/TYR ATRTs revealed ERBB2 expression, which correlated with differential methylation and activation of a distinct enhancer element by DNA looping. Significantly, we show the brain penetrant EGFR/ERBB2 inhibitor, Afatinib, specifically inhibited in vitro and in vivo growth of MYC/TYR ATRT cells. Taken together, our studies suggest combined treatments with PDGFR and ERBB2-directed TKIs with inhibitors of the PI3K and MAPK pathways as an important new therapeutic strategy for the MYC/TYR subgroup of ATRTs.

Ellagic acid mitigates heat-induced testicular detriment in a mouse model

Heat stress has been shown to have a detrimental impact on testicular activity and spermatogenesis. Ellagic acid is a plant-derived organic compound that has a variety of biological functions. Thus, it is believed that ellagic acid may improve heat-stressed testicular dysfunction. There has been no research on the impact of ellagic acid on heat-stressed testicular dysfunction. The mice were divided into 4 groups. The first group was the normal control group (CN), and the second received heat stress (HS) by submerging the lower body for 15 min in a water bath with a thermostatically controlled temperature kept at 43°C (HS), and the third and fourth groups were subjected to heat-stress similar to group two and given two different dosages of ellagic acid (5 mg/kg (EH5) and 50 mg/kg (EH50) for 14 days. Ellagic acid at a dose of 50 mg/kg improved the level of circulating testosterone (increased 3βHSD) and decreases the oxidative stress. The testicular and epididymal architecture along with sperm parameters also showed improvement. Ellagic acid treatment significantly increases the germ cell proliferation (GCNA, BrdU staining) and Bcl2 expression and decreases active caspase 3 expression. Heat stress downregulated the expression of AR, ER-α and ER-β, and treatment with ellagic acid increased the expression of ER-α and ER-β markers in the 50 mg/kg treatment group. Thus, our finding suggests that ellagic acid ameliorates heat-induced testicular impairment through modulating testosterone synthesis, germ cell proliferation, and oxidative stress. These effects could be manifested by regulating androgen and estrogen receptors. However, the two doses showed differential effects of some parameters, which require further investigation.

Aging is associated with sex-specific alteration in the expression of genes encoding for neuroestradiol synthesis and signaling proteins in the mouse trigeminal somatosensory input

Pain perception is influenced by sex and aging, with previous studies indicating the involvement of aromatase, the estradiol synthase enzyme, in regulating pain perception. Previous research has established the presence of aromatase in dorsal root ganglia sensory neurons and its role in modulating pain perception. The present study aims to explore the implications of aging and sex on the expression of aromatase and estrogen receptors in the trigeminal ganglion. The study examined mRNA levels of aromatase, ERs, and the androgen receptor (AR) in the trigeminal ganglion of 3-month-old and 27-month-old male and female mice, as well as 3-month-old mice from the four-core genotype (FCG) transgenic model. The latter facilitates the assessment of gonadal hormone and sex chromosome implications for sex-specific traits. Aromatase localization in the ganglion was further assessed through immunohistochemistry. Aromatase immunoreactivity was observed for the first time in sensory neurons within the trigeminal ganglion. Trigeminal ganglion gene expressions were detected for aromatase, ERs, and AR in both sexes. Aromatase, ERβ, and GPER gene expressions were higher in young males versus young females. Analyses of the FCG model indicated that sex differences depended solely on gonadal sex. The aging process induced an enhancement in the expression of aromatase, ERs, and AR genes across both sexes, culminating in a reversal of the previously observed gender-based differences. the potential impact of estrogen synthesis and signaling in the trigeminal ganglion on age and sex differences warrants consideration, particularly in relation to trigeminal sensory functions and pain perception.Graphical abstractAge and gonadal sex influence ERs, AR, and ARO levels in the trigeminal ganglion. Although somatosensory perception shows a decline in the elderly, the incidence of trigeminal neuralgia intensifies in aged adults and is predominantly prevalent in women relative to men. The increased expression of aromatase and estrogen receptors in aged female animals suggests that the modulatory influence that neuroestradiol exerts over the trigeminal somatosensory input, inclusive of pain, undergoes changes in elderly male and female individuals in a sex-specific manner.

Retracing RAS signaling by correlating protein expression in different subtypes of neurofibromatosis 1-associated nerve sheath tumors.

Expression patterns of key proteins involved in RAS signaling and connected pathways were determined and correlated to possibly provide information for therapeutic application of RAS inhibitors in neurofibromatosis type 1 (NF1)-associated peripheral nerve sheath tumors (PNST). Clinical variables (age, sex), histological parameters (cell density, mitoses), and expression of immunohistochemically evaluated ligand and receptor proteins (neuregulin 1 (NRG1), ErbB2, ErbB3), RAS pathway proteins (mTor, Rho, phosphorylated MEK), transcription factors (Pax7, Sox9), and proliferation marker Ki-67, were correlated in cutaneous (CNF, n = 136), diffuse (DNF, n = 123)/diffuse plexiform (DPNF, n = 113), and plexiform neurofibroma (PNF, n = 126), and in malignant PNST (MPNST, n = 22). In CNF, NRG1 correlated with Ki-67 and Pax7. Further, mTOR correlated with ErbB3, Sox9, Pax7, and Ki-67. In DNF/DPNF, expression of NRG1 correlated with pMEK and Pax7. mTOR correlated with pMEK, Sox9, and Pax7. Noteworthy, pMEK was weakly expressed in some DNF but not in DPNF. ErbB3 correlated with mTor and Ki-67. Furthermore, Rho correlated with Pax7 and Ki-67. In PNF, ErbB3 expression was associated with Sox9, mTOR, pMEK, and Pax7 as well as mTOR with Sox9 and Pax7, Rho with pMEK and Pax7, and pMEK with Pax7 and Sox9. In MPNST, only few correlations were observed, ErbB2 correlated with Ki-67, and Rho with pMEK. Signaling networks of the RAS pathway could be retraced by correlation analysis of protein expression in subgroups of NF1 associated benign PNST. In regard to treatment of PNST, MEK inhibitors, which are presently evaluated for PNF, may possibly also be effective to some extent in DNF.

Promotion of stem cell-like phenotype of lung adenocarcinoma by FAM83A via stabilization of ErbB2

Lung cancer stands as the leading cause of mortality among all types of tumors, with over 40% of cases being lung adenocarcinoma (LUAD). Family with sequence similarity 83 member A (FAM83A) emerges as a notable focus due to its frequent overexpression in LUAD. Despite this, the precise role of FAM83A remains elusive. This study addresses this gap by unveiling the crucial involvement of FAM83A in maintaining the cancer stem cell-like (CSC-like) phenotype of LUAD. Through a global proteomics analysis, the study identifies human epidermal growth factor receptor 2 (HER2 or ErbB2) as a crucial target of FAM83A. Mechanistically, FAM83A facilitated ErbB2 expression at the posttranslational modification level via the E3 ubiquitin ligase STUB1 (STIP1-homologous U-Box containing protein 1). More importantly, the interaction between FAM83A and ErbB2 at Arg241 promotes calcineurin (CALN)-mediated dephosphorylation of ErbB2, followed by inhibition of STUB1-mediated ubiquitin-proteasomal ErbB2 degradation. The maintenance of the CSC-like phenotype by FAM83A, achieved through the posttranslational regulation of ErbB2, offers valuable insights for identifying potential therapeutic targets for LUAD.

HER2 overexpression in urothelial carcinoma with GATA3 and PPARG copy number gains.

HER2, encoded by the ERBB2 gene, is an important druggable driver of human cancer gaining increasing importance as a therapeutic target in urothelial carcinoma (UC). The genomic underpinnings of HER2 overexpression in ERBB2 nonamplified UC are poorly defined. To address this knowledge gap, we investigated 172 UC tumors from patients treated at the University of California San Francisco, using immunohistochemistry and next-generation sequencing. We found that GATA3 and PPARG copy number gains individually predicted HER2 protein expression independently of ERBB2 amplification. To validate these findings, we interrogated the Memorial Sloan Kettering/The Cancer Genome Atlas (MSK/TCGA) dataset and found that GATA3 and PPARG copy number gains individually predicted ERBB2 mRNA expression independently of ERBB2 amplification. Our findings reveal a potential link between the luminal marker HER2 and the key transcription factors GATA3 and PPARG in UC and highlight the utility of examining GATA3 and PPARG copy number states to identify UC tumors that overexpress HER2 in the absence of ERBB2 amplification. In summary, we found that an increase in copy number of GATA3 and PPARG was independently associated with higher ERBB2 expression in patient samples of UC. This finding provides a potential explanation for HER2 overexpression in UC tumors without ERBB2 amplification and a way to identify these tumors for HER2-targeted therapies.

Molecular characterization and expression profile of estrogen receptor subtypes in female hilsa (Tenualosa ilisha)

Hilsa (Tenualosa ilisha), a highly prized edible fish, is consumed by over 250 million people worldwide. Estrogens are essential hormones required during reproduction and bind with estrogen receptors in target organs for biological activity. The two unique subtypes of the estrogen receptor found in fish are alpha (α) and beta (β) and exhibit distinctive roles in reproduction. The present study aimed to understand the breeding physiology of hilsa during the seasonal gonadal cycles through GSI seasonal variation, histological study, and molecular identification, characterization, and transcriptional modification of estrogen receptors in hilsa. Monthly GSI analysis from females showed that during September, the GSI value was maximum (22.01 ± 0.68), followed by the May GSI value (18.78 ± 0.97). Histological observation showed the formation of asynchronous gametes during the development of ovaries. The histological analysis revealed the formation of developing oocytes, nucleus, presence of primary oogonia, secondary oogonia, chromatin nucleolar oocytes, and early perinucleolar oocytes in the ovary (January–early July). Progressively, formations of the yolk vesicles, yolk granule stage, premature stage, and mature stage with post-ovulatory follicles were also identified. Linear observation was recorded during the monsoon season from July to November. Furthermore, partial length cDNAs for estrogen receptors were characterized, and their mRNA expression patterns demonstrate that ER-α expression significantly increased in September, followed by April and August in the ovary and liver tissue. Both the liver and ovary showed the highest mRNA expression of ER-β in September. The study revealed that ER-α expression was higher in the ovary as compared with liver tissue. Furthermore, we introduce three-dimensional (3D) models depicting the hilsa estrogen receptors in complex with estradiol (E2), constructed through homology modeling. This investigation contributes valuable insights into the molecular characteristics of estrogen receptors in this teleost fish. Our present work provided preliminary evidence of estrogen receptors during reproduction in hilsa.

Defining low-HER2 cancers using RNA quantification by next generation sequencing.

e13044 Background: The recent success of treatment with HER2-directed antibody-drug conjugate T-DXd (trastuzumab-deruxtecan) in treating low-HER2 expression breast cancer raises the possibility of similar success in other tumors that express similarly low levels of HER2. HER2 amplification has been reported in various types of tumors at relatively low frequency. However, “low-HER2” expression in various types of tumors remains undefined. In this study, we utilized next generation sequencing to explore the levels of ERBB2 (HER2), ERBB3, ERBB4, PIK3CA, and ERS1 mRNA in various types of cancers and attempted to set limits reflecting distinct biology of tumors based of level of ERBB2 expression. Methods: RNA was extracted from FFPE samples from patients with cancers of breast (N=203), ovary (N=95), endometrium (N=75), and esophagus/stomach (N=46). RNA was sequenced via a 1408 gene panel using a standard hybrid capture approach. Results: Based on previous data correlating gene amplification with gene expression (DOI: 10.1002/imed.1051), we defined ERBB2 expression as high, low, and very-low when ERBB2 expression measured >1500 TPM (transcripts per million), 800-1500 TPM, and <800 TPM, respectively. ERBB2 high, low, and very-low were detected in 20%, 32%, and 48% of breast cancer; 5%, 29%, and 65% of endometrial cancer; 9%, 26%, and 65% of ovarian cancer; 12%, 16%, and 72% of esophageal/stomach cancer; and 8%, 19%, and 73% of lung cancer. With minor exceptions, cases classified as ERBB2 high and low from the five tumor types showed no correlation with levels of PIK3CA, ESR1, or ERBB4 mRNA. In contrast, cases with relatively very-low ERBB2 showed significant correlation with PIK3CA, ESR1, and ERBB4 mRNA. Endometrial cancer was an exception and showed no correlation with PIK3CA mRNA in very-low ERBB2 cases. Activation of PIK3CA has been reported to be associated with resistance to anti-HER2 therapy. These findings suggest that cases showing high or low ERBB2 are independent of PIK3CA and likely less influenced by the negative effects of PIK3CA on response to HER2 inhibitors. Cases classified as ERBB2 high or low showed significantly higher (P<0.0001) PIK3CA mutations as compared with ERBB2 very-low cases (27% vs 14%). ERBB2 mutations were relatively rare, detected in only 7%, 8%, 14%, 1%, and 4% of breast, endometrial, esophageal/stomach, ovarian, and lung cancers, respectively. However, significantly (P=0.001) higher mutation rate is detected in ERBB2-high and -low as compared with very-low ERBB2 cases (8% vs 6%). Conclusions: ERBB2/HER2 RNA quantification in cancers can define a biologically distinct group of patients. Patients defined as very-low ERBB2 as classified in this approach appear to be biologically distinct and more likely to be resistant to anti-HER2 therapy. Clinical trials using this approach in selecting patients for treatment with antibody-drug conjugates are justified and needed.

Spatial transcriptomic and proteomic insight into Trop-2, HER2, and AR expression: A pathway to tailored therapies in triple-negative breast cancer.

e12576 Background: Triple-negative breast cancer’s (TNBC) dismal prognosis demands more effective therapy selection. Previously described molecular subtypes reveal its heterogeneity but lack spatial insight and are not currently used in clinical practice. Here, we aim to evaluate by immunohistochemistry (IHC) the expression of key biomarkers in TNBC and its correlation with spatial gene expression obtained by spatial transcriptomics (ST). Methods: We studied a retrospective cohort of 92 patients (pts) treated at the Institut Jules Bordet in Belgium with primary surgery for early TNBC. ST (Visium Spatial Gene Expression, 10X Genomics) was previously performed on fresh frozen surgical samples. Using serial sections of these samples, we performed duplex IHC staining for Trop-2/androgen receptor (AR) and HER2/Ki-67. IHC staining was scored using H-score (Trop-2), Allred score (AR), and current guidelines (Ki67/HER2), adding the ultra-low and null HER2 categories. Statistical analyses included descriptive statistics, Spearman correlation, Mann-Whitney test, and Kaplan-Meier with log-rank tests for estimating outcome distribution. Results: Of 92 pts included, 4 (4.3%), 25 (27.2%), 28 (30.4%), and 35 (38%) pts had HER2 2+, 1+, ultra-low, and null, respectively, tumors. Importantly, we observed a significant difference in tumor cell-derived ERBB2 gene expression of HER2 ultra-low versus HER2 null tumors ( p<0.0001), while there was no difference in ERBB2 expression between HER2 ultra-low and HER2 1+ tumors ( p=0.49). HER2 expression was not correlated with prognosis. Trop-2 expression by IHC was high, medium, and low in 67%, 23%, and 10% of pts, respectively. IHC expression correlated well with tumor-derived gene expression (r=0.54), with intrasample heterogeneity observed both in IHC and spatial gene expression. Trop-2 expression was prognostic, pts with high Trop-2 H-score tumors having significantly worse outcome ( p=0.021). In this cohort, 25%, 40.2%, and 34.8% of pts had AR Allred scores of 0-2, 3-5, and 6-8, respectively. Tumor AR gene expression was well correlated with IHC AR expression (67.7%). IHC AR expression was associated with the presence of adipose tissue in the stroma (r=0.23, p=0.025) but not with prognosis. Of note, we report for the first time, to our knowledge, for TNBC, AR expression both in tumor and stroma cells, both at the IHC and gene expression levels. Importantly, we could construct a classifier that identifies luminal androgen receptor tumors, using AR Allred score > 5 and Ki67 ≤ 40%, with a PPV of 93% and an NPV of 96%. Conclusions: ST data has the potential to improve easily accessible IHC classifiers, with the aim of refining patient selection for ADC and anti-AR therapies in TNBC.

Deciphering tumor microenvironment dynamics in HER2-amplified refractory metastatic colorectal cancer in the TRIUMPH trial.

3564 Background: Approximately 2-4% of patients with metastatic colorectal cancer (mCRC) harbor HER2 amplification, a subset notorious for poor response rates following conventional treatments. The TRIUMPH trial introduces anti-HER2 therapy, combining trastuzumab and pertuzumab. Despite its potential, the observed response rate stands at 30%, accompanied by an early recurrence within 3.5 months with acquired resistance, which emphasizes the need for further investigations into resistance mechanisms within this patient population. Here, we delineate the dynamic changes in both the tumor and its microenvironment in response to treatment and mechanisms of acquired resistance using spatial transcriptomics. Methods: Within the TRIUMPH trial, a total of 20 formalin-fixed paraffin-embedded (FFPE) biopsy slides from 13 patients were collected before and after treatment or at one time. Utilizing these FFPE slides, we employed imaging-based single-cell spatial transcriptomics, using a custom panel tailored for the tumor and its microenvironment. This panel includes gene sets related to tumor growth, drug resistance, and immune response. Results: To comprehend the complexities of the tumor and its surroundings, we categorized tumor tissue into distinct sections, encompassing tumor, stromal, and immune-enriched areas based on their neighbor cells. Remarkably, we noted a substantial rise in the infiltration of T cells and myeloid cells into tumor-enriched regions post-treatment. T cells increased from a median of 1.5% to 2.2%, and myeloid cells from 4.3% to 7.4%, particularly in patients showing a response. Additionally, ERBB2 expression in tumor cells was high, whereas the non-response group exhibited lower expression levels. Prior to treatment, fibroblast and endothelial cells were intricately intertwined with tumor cells. However, subsequent to treatment, these cells segregated into stromal regions, exhibiting an increase in their proportions. Notably, angiogenic tumor-associated macrophage (angio-TAM), expressing SPP1 and VEGFA, were localized at the interface of tumors and stromal cells and proliferated following disease progression. This spatial reorganization signifies dynamic alterations within the tumor microenvironment following treatment. Conclusions: Our study on HER2-amplified metastatic colorectal cancer in the TRIUMPH trial uncovers intriguing spatial changes post anti-HER2 therapy. Notably, dynamic reorganization of fibroblast and endothelial cells into stromal regions suggest complex treatment responses. Identification of angio-TAM expressing SPP1 and VEGFA adds depth to understanding the contribution of tumor microenvironment to the resistance mechanism. These findings highlight the intricate tumor microenvironment shifts, urging further exploration for optimized therapeutic strategies.

Evaluating antitumor activity and response determinants to trastuzumab deruxtecan in pediatric solid tumors.

10049 Background: Trastuzumab deruxtecan (T-DXd) is an anti-HER2 antibody-drug conjugate (ADC) linked to a topoisomerase inhibitor FDA-approved for several indications, including the treatment of HER2+ breast and gastric cancer. Although HER2 amplification is uncommon in pediatric cancers, recent demonstration of T-DXd efficacy in HER2-low breast cancer patients prompted us to examine the potential clinical relevance of T-DXd in pediatrics by evaluating HER2 expression and activity of T-DXd in preclinical pediatric solid tumor models. Methods: Cell viability was assessed in a panel of histologically diverse pediatric solid tumor cell lines and 2 HER2-amplified adult cancer cell lines treated with T-DXd, payload (DXd), and a control IgG-ADC. HER2 protein expression in patient-derived xenograft (PDX) tumors was evaluated by immunohistochemistry (IHC) using 5 clinically validated anti-HER2 antibodies. RNAseq was performed on clinical (n=290) and PDX (n=184) tumors to determine relative expression of ERBB2. In vivo activity of T-DXd was evaluated in osteosarcoma (OS, n=10), Wilms tumor (WT, n=1) and malignant rhabdoid tumor (MRT, n=1) PDX models and a desmoplastic small round cell tumor (DSRCT) cell line xenograft model. Differences in tumor volume and time to disease progression was assessed and compared across treatments and models. Responses were correlated with HER2 expression by IHC. Results: In vitro, HER2-amplified control cell lines demonstrated a >30-fold reduction of IC50 when comparing T-DXd to ADC control. In contrast, the ADC control IC50 was nearly identical to T-DXd across all pediatric cancer cell lines, consistent with the absence of HER2 amplification in these models. We observed focal and membranous staining of HER2 by IHC in PDXs but was quite variable across antibodies tested: WT 0-17% HER2+ cases (n=6), MRT 0-40% (n=5), DSRCT 0-33% (n=24), OS 0-7% (n=30). ERBB2 gene expression was highest in DSRCT followed by WT, OS and MRT. In vivo efficacy studies demonstrated complete and partial responses in OS, WT, and DSRCT and improved disease control rates (OS: 67%, p=0.006, Mann-Whitney; WT: 100%; DSRCT: 100%). However, T-DXd and ADC control demonstrated similar activity in all tumor types with no consistent correlation between in vivo response and HER2 expression. Consistent with these preclinical studies, 4 patients with progressive DSRCT were treated with T-DXd via compassionate/off-label access with signs of clinical and radiographic responses. Conclusions: T-DXd shows significant preclinical antitumor activity across multiple pediatric solid tumors but little correlation with HER2 expression suggesting a mechanism of action similar to the clinical activity observed in HER2-low breast cancer. Xenograft efficacy studies and preliminary clinical experience with T-DXd in DSRCT patients warrant formal clinical trial investigation in this largely incurable disease.

Cabozantinib inhibits the growth of lenvatinib-resistant hepatoma cells restoring FTCD expression

Cabozantinib is a newly developed tyrosine kinase inhibitor, which is applied on patients with hepatocellular carcinoma (HCC) unresponsive to conventional tyrosine kinase inhibitors, including lenvatinib. However, the mechanism of cabozantinib efficacy for lenvatinib-resistant tumor cells has not been well established in basic studies. The purpose of this study is to elucidate the mechanisms by which cabozantinib inhibits tumor growth of lenvatinib-resistant hepatocellular carcinoma cell lines in vitro and in vivo. We established a lenvatinib-resistant Hep3B cell line (Hep3B-LR) and evaluated the inhibitory effect of cabozantinib on the growth of Hep3B-LR cells. Hep3B-LR exhibited approximately 20 times greater IC50 for lenvatinib than the wild type. Compared with wild-type Hep3B, Hep3B-LR was characterized by enhanced expression of EGFR, MET and ErbB2. Cabozantinib suppressed tumor growth of Hep3B-LR in vitro and in vivo. Microarray analysis and real-time qPCR using the xenografts revealed cabozantinib downregulated miR-126-3p, a tumor suppressor miRNA, suggesting that miR-126-3p did not contribute to tumor inhibitory effect of cabozantinib. Proteome analysis using xenograft tissues demonstrated an upregulation of FTCD, a tumor suppressor gene, by cabozantinib administration. The enhanced expression of FTCD by cabozantinib was confirmed by western blot and immunohistochemistry analysis. Furthermore, FTCD expression in Hep3B-LR before cabozantinib administration was weaker than that in wild-type Hep3B. FTCD expression was weakened along with acquisition of lenvatinib-resistance, and was restored by cabozantinib administration. FTCD may be a novel therapeutic target of cabozantinib in case of lenvatinib treatment failure.

Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells.

APOBEC-induced mutations occur in 50% of sequenced human tumors, with APOBEC3A (A3A) being a major contributor to mutagenesis in breast cancer cells. The mechanisms that cause A3A activation and mutagenesis in breast cancers are still unknown. Here, we describe factors that influence basal A3A mRNA transcript levels in breast cancer cells. We found that basal A3A mRNA correlates with A3A protein levels and predicts the amount of APOBEC signature mutations in a panel of breast cancer cell lines, indicating that increased basal transcription may be one mechanism leading to breast cancer mutagenesis. We also show that alteration of ERBB2 expression can drive A3A mRNA levels, suggesting the enrichment of the APOBEC mutation signature in Her2-enriched breast cancer could in part result from elevated A3A transcription. Hierarchical clustering of transcripts in primary breast cancers determined that A3A mRNA was co-expressed with other genes functioning in viral restriction and interferon responses. However, reduction of STAT signaling via inhibitors or shRNA in breast cancer cell lines had only minor impact on A3A abundance. Analysis of single cell RNA-seq from primary tumors indicated that A3A mRNA was highest in infiltrating immune cells within the tumor, indicating that correlations of A3A with STAT signaling in primary tumors may be result from higher immune infiltrates and are not reflective of STAT signaling controlling A3A expression in breast cancer cells. Analysis of ATAC-seq data in multiple breast cancer cell lines identified two transcription factor sites in the APOBEC3A promoter region that could promote A3A transcription. We determined that Rel-A, and Bach1, which have binding sites in these peaks, elevated basal A3A expression. Our findings highlight a complex and variable set of transcriptional activators for A3A in breast cancer cells.

The Expression of Adipogenic Marker Is Significantly Increased in Estrogen-Treated Lipedema Adipocytes Differentiated from Adipose Stem Cells In Vitro.

Lipedema is a chronic, idiopathic, and painful disease characterized by an excess of adipose tissue in the extremities. The goal of this study is to characterize the gene expression of estrogen receptors (ERα and ERβ), G protein-coupled estrogen receptor (GPER), and ER-metabolizing enzymes: hydroxysteroid 17-beta dehydrogenase (HSD17B1, 7, B12), cytochrome P450 (CYP19A1), hormone-sensitive lipase (LIPE), enzyme steroid sulfatase (STS), and estrogen sulfotransferase (SULT1E1), which are markers in Body Mass Index (BMI) and age-matched non-lipedema (healthy) and lipedema ASCs and spheroids. Flow cytometry and cellular proliferation assays, RT-PCR, and Western Blot techniques were used to determine the expression of ERs and estrogen-metabolizing enzymes. In 2D monolayer culture, estrogen increased the proliferation and the expression of the mesenchymal marker, CD73, in hormone-depleted (HD) healthy ASCs compared to lipedema ASCs. The expression of ERβ was significantly increased in HD lipedema ASCs and spheroids compared to corresponding healthy cells. In contrast, ERα and GPER gene expression was significantly decreased in estrogen-treated lipedema spheroids. CYP19A1 and LIPE gene expressions were significantly increased in estrogen-treated healthy ASCs and spheroids, respectively, while estrogen upregulated the expression of PPAR-ϒ2 and ERα in estrogen-treated lipedema-differentiated adipocytes and spheroids. These results indicate that estrogen may play a role in adipose tissue dysregulation in lipedema.

Abstract PO4-02-02: Genomic Landscape of ER positive HER2-low early breast cancers in the FLEX Study: MammaPrint, BluePrint and whole transcriptome analysis

Abstract Background: Antibody-drug conjugates (ADCs) continue to emerge for the treatment of a new subset of patients with HER2-low breast cancer. There is limited evidence to demonstrate HER2-low tumors as a distinct biological subtype and why/if these tumors benefit from ADCs. To improve our understanding of this newly defined HER2 category of breast cancers, we evaluated clinical characteristics, MammaPrint (MP), BluePrint (BP), and the whole transcriptomic profile of HER2-low breast cancers in FLEX study. Methods: FLEX (NCT03053193) is a prospective, observational trial that includes stage I-III breast cancer patients who undergo MammaPrint testing (with or without BluePrint) as standard of care, and consent to full transcriptome and clinical data collection. In this study, clinically ER+/HER2- tumors were analyzed. The HER2-low cohort group (n=1698) was defined as HER2 IHC 1+ (ISH positive excluded) and IHC 2+, ISH Negative, and the HER2-0 group (n=1181) was defined as HER2 IHC 0. MP classified tumors as Low Risk or High Risk (further stratified as High 1 and High 2). MP together with BP categorized tumors as Luminal A (MP Low Risk), Luminal B (MP High Risk), HER2 or Basal. Two-tailed proportional z-test was used to compare clinical features and genomic subtypes of HER2-low vs. HER2-0 and the limma R package for differential gene expression analysis (DGEA). P-values were adjusted for multiple testing by Benjamini-Hochberg; significant differentially expressed genes (DEGs) had a p-value < 0.05 and a fold change >2. Results: In this FLEX study, clinically ER+/HER2- tumors showed that the clinical characteristics between HER2-low and HER2-0 did not differ significantly except higher percentage of premenopausal within HER2-low (23% vs 17%, p < 0.01). Of all HER2-low patients, 46% were MP High Risk as within HER2-0 patients (44%, p = 0.27). In both groups with MP High Risk tumors, there was a higher frequency of MP High 1 (83% in HER2-low, 80% in HER2-0) compared to MP High 2 (17% in HER2-low, 20% in HER2-0). BP subtyping showed similar distribution for Luminal subtype between HER2-low and HER2-0, but the frequency of ER+, Basal subtype was lower in HER2-low (2.5%), compared to HER2-0 (4.5%) (p=0.005). Principal component analysis (PCA) of the 500 most variable genes did not reveal a separation of HER2-low and -0 tumors, but clustering was apparent when tumors were classified by BP. DGEA within Basal tumors revealed no DEGs. Within Luminal A tumors, more than 1800 DEGs were identified, and within Luminal B tumors, nearly 300 DEGs were identified. However, all DEGs were < 1.5-fold change: mean, max (1.09, 1.38) for Luminal A and (1.12, 1.44) for Luminal B. In addition, a significant difference (p< 0.01) towards increased ERBB2 (HER2) expression was detected from HER2-0 to HER2-low, but there was a large overlap of expression between the 2 groups. Conclusion: Our study showed that HER2-low and HER2-0 tumors are clinically and biologically similar. The differences in ERBB2 and low-level genome wide expression detected between HER2-low and HER2-0 should be further investigated to determine how these changes affect tumor biology and treatment benefit. The biological heterogeneity among IHC-defined HER2-negative tumors was better captured by MammaPrint and BluePrint than IHC. MammaPrint identified 53% of HER2-low tumors as Low Risk, a subgroup of patients known to have good outcomes without chemotherapy. Our data suggest a subset of patients with HER2-low, MP Low Risk tumors could be spared from the potential toxicities of ADCs. Future studies will investigate the utility of MammaPrint and BluePrint in predicting chemosensitivity and benefit from ADCs, such as T-DXd, in patients with HER2-low tumors. Citation Format: Abirami Sivapiragasam, Adam Brufsky, Hannah Linden, Natasha Hunter, Cynthia Osborne, Sami Diab, Robert Maganini, Joyce O'Shaughnessy, Manojkumar Bupathi, Sung Ho Lee, Theodore Y Kim, William Audeh, Josien Haan, Andrea Menicucci, Lavanya Samraj, FLEX Investigators' Group. Genomic Landscape of ER positive HER2-low early breast cancers in the FLEX Study: MammaPrint, BluePrint and whole transcriptome analysis [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-02-02.

Abstract PO4-03-08: Enhanced Assessment of Clinical Behavior of TNBC and TPBC using Quantified Levels of HER2, Estrogen and Progestin Receptor Proteins and Expression of Their Cognate Genes

Abstract Background: Renewed interest in clinical relevance of low-HER2 protein in breast cancer management prompted a retrospective investigation of a unique de-identified Database of quantified biomarkers associated with patient outcomes. Currently, IHC of ER, PR and HER2 proteins provides semi-quantitative results, at times complicated by variation in methods and interpretation (cf. ASCO/CAP Guidelines). Our goal was to ascertain relationships of these clinical analytes to predict cancer relapse when quantified for protein products and cognate gene expression. Methods: Database contained 2756 quantified HER2 results by ELISA (Oncogene Sciences) or by EIA (Triton Diagnostics) of which 198 patients had associated clinical outcomes. No definition of HER2-low has been accepted for IHC, although > 50% of biopsies may be categorized as HER2-low (cf. ASCP CE Programs). Microarray results obtained for ~ 22,000 genes using RNA purified from LCM-procured carcinoma cells of 247 primary breast biopsies were analyzed. ESR1, PGR and ERBB2 gene expression levels in 276 biopsies had been validated by RTqPCR. To assess distribution and dispersion of HER2 protein, cumulative relative frequency distribution analyses were employed, focusing on cut-offs within interquartile range. Permutations and combinations of the 3 biomarkers based on IHC definitions (cf. ASCO/CAP Guidelines) were examined. Tertiles and quartiles of data sets were used to explore association between biomarker levels and clinical outcomes. Box plots depicted protein and gene expression levels, Progression-Free Survival (PFS), or Overall Survival (OS) across ER/PR/HER2 categories and compared differences using a Kruskal-Wallis ANOVA Rank Test. Cox regressions were used to contrast hazard ratios among the ER/PR/HER2 groups. Kaplan-Meier plots visualized survival rates among groups and a log-rank test detected statistical discrepancies. We investigated differences between groups for categorical variables using chi-squared tests (Fisher's exact test for non-normally distributed data), while for ordinal variables, ANOVA tests were used (Kruskal-Wallis for non-normally distributed data). Categorical variables were summarized as count (%), and ordinal variables were summarized as median [IQR]. Analyses were performed using R version 4.2.2 (Innocent and Trusting). Results: Neither quantified ER or PR alone nor ER/PR collectively were related to HER2 oncoprotein levels. Influence of menopausal status on biopsy biomarker profiles was investigated. With a median cutoff for HER2 protein, patients with ER+/PR+/HER2+ (TPBC) exhibited increased OS, whereas those with TNBC had decreased OS, of 8 combinations possible. Using tertiles and quartiles, TPBC was exhibited by 34-37% of specimens compared to TNBC, which represented 9.1-12.7% of biopsies when biomarker proteins were quantified. After qPCR data were stratified by ER/PR/HER2 status with a 50% quantile cut for HER2, 39% were TPBC and 10% were TNBC. Using microarray data with the same cutoffs, only 14% were TPBC and 17% were TNBC. Once TPBC were identified by either microarray or by qPCR, increased ESR1, PGR and ERBB2 expression collectively was associated with increased PFS and OS of patients. In general, biopsies that were TNBC or other combinations of biomarker’s gene expression correlated with poorer prognosis and overall survival. Conclusions: Quantifying levels of ER, PR and HER2 proteins as well as of ESR1, PGR and ERBB2 expression were correlated with prediction of clinical outcomes of TNBC, TPBC and patients with other biomarker subsets. Results support quantitative assessment of these biomarkers in biopsies to assess utility of the HER2-low type in personalizing breast cancer management and prediction of risk of relapse. Citation Format: James Wittliff, Michael Daniels. Enhanced Assessment of Clinical Behavior of TNBC and TPBC using Quantified Levels of HER2, Estrogen and Progestin Receptor Proteins and Expression of Their Cognate Genes [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-03-08.

Abstract PO2-15-12: Novel Transcriptomic Classification System Unveils HER2-Low Breast Tumors

Abstract Breast cancers (BCs) are segregable into subtypes based on their intrinsic molecular features. When evaluating HER2 status, clinicians often rely on IHC, which is plagued by reproducibility issues. The widely used PAM50 transcriptomic system also does not include the HER2-low subtype. Addressing these limitations is particularly important given the recent approval of targeted therapy for HER2-low BCs. Here, we developed a unique transcriptomic classification system that can identify HER2-low BCs. Accurate identification of HER2-low BCs can help physicians navigate treatment selection and, in turn, allow patients to benefit from the new targeted therapy. We analyzed 6,361 BC samples with clinical and pathological annotation, including FISH and IHC data, from three public datasets (TCGA BRCA and SCAN-B [total n = 4,457]; METABRIC [n = 1,904]) for gene expression, differential expression, gene enrichment, copy number alterations, and mutations. An algorithm was applied to categorize samples from TCGA and SCAN-B into subtypes by customizing a gene set, employing UMAP dimensionality reduction, and utilizing clustering with the HDBSCAN algorithm. Each resulting cluster that was associated with a specific gene set was named and excluded from the next analysis. After four iterations, five subtypes were sequentially identified: Basal, HER2-high, HER2-low, Luminal B (LumB), and Luminal A (LumA). The Light GBM-based hierarchical classifier model was trained on the TCGA and SCAN-B cohorts and validated on the METABRIC dataset. Samples with high ERBB2 expression and copy number amplification were classified as HER2-high, and samples with similar PAM50 expression profiles but lacking ERBB2 expression were considered HER2-low. Luminal samples were grouped into two subtypes: LumA, characterized by low proliferation rates, and LumB, characterized by high proliferation rates. HER2-high, Basal, LumA, and LumB subtypes exhibited expected mutational and gene expression profiles. We observed ERBB2 copy number amplification and high gene expression in HER2-high samples from the TCGA and METABRIC cohorts, as confirmed by FISH and IHC in 97% and 93% of samples, respectively. Conversely, we did not see high ERBB2 expression or copy number amplification in the HER2-low samples, which was concordant with an absence of HER2 3+ expression by IHC. HER2-low samples had high mutational frequencies in PTEN, KMT2C, and ERBB2 (12%, 14%, and 8% respectively, adj. p < 0.005, chi-square test). HER2-low samples also showed increased EGFR (logFC = 2.8, adj. p < 0.001) and CLDN8 (logFC = 3.4, adj. p < 0.001) expression levels. The novel classifier identified 55% of the HER2-low samples as the luminal androgen receptor (LAR) Burstein subtype, as a result of higher AR expression than in HER2-high samples (logFC = 2.9, p = 0.04). Classification of SCAN-B luminal samples into the LumA and LumB subtypes also better predicted Ki-67 positivity (≥ 20% of Ki-67+ malignant cells by IHC, F1-score = 0.77) than the previously reported PAM50 classification (F1-score = 0.62). Our refined classifier effectively defined five breast cancer subtypes, including the HER2-low subtype, based on their molecular profiles. By determining HER2 status with transcriptomic data, our classifier may help minimize IHC-related reproducibility issues and, in turn, facilitate more precise treatment decision-making. Given its concordance with copy number amplification, IHC, and FISH data, our classification system can distinguish between HER2-high and HER2-low BCs. Since HER2-low BCs may represent a unique group that requires different treatment approaches, further optimization of our classifier may assist in identifying effective therapies for patients with HER2-low BCs. Citation Format: Polina Turova, Vladimir Kushnarev, Oleg Baranov, Anna Butusova, Sofia Menshikova, Sheila Yong, Anna Love, Konstantin Chernyshov, Nikita Kotlov. Novel Transcriptomic Classification System Unveils HER2-Low Breast Tumors [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-15-12.

Abstract PO5-13-06: Classifying HER2-low breast cancer using a combination of ERBB2 mRNA expression and altered genes

Abstract Background It has been recently demonstrated that some HER2-low, defined as immunohistochemistry (IHC) 1+ or 2+ with no gene amplification by FISH, breast cancer (BC) patients respond to trastuzumab deruxtecan (T-DXd). Results of the DAISY trial also suggested clinical activity with T-DXd in some of those classified as HER2-0 cancers by IHC, indicating an unmet need to better identify cancers that may truly respond to T-DXd. We compared ERBB2 (HER2) mRNA expression obtained from whole-transcriptome sequencing with IHC/FISH assignment of HER2 status. Furthermore, we constructed a classifier using ERBB2 expression and alterations in other genes as a proof of concept to illustrate classification of BC samples into HER2-0 versus HER2-low status. Methods We chose consecutive HR positive/HER2-negative BC samples that were submitted for OncoExTraTM testing between April 2020 and October 2022. The OncoExTra test uses tumor-normal whole exome and whole transcriptome sequencing to detect somatic single base substitutions, indels, copy number alterations, gene fusions and alternative transcripts. In addition, we investigated the expression profile of select genes for this analysis. We utilized OncoExTra data to examine the relationship between HER2 IHC status and gene expression, mutation and copy number profiles of selected genes, and built a classifier to predict HER2 status. Results A total of 279 BC samples were analyzed, including 106 HER2-IHC 0, 120 HER2-IHC 1+ and 53 HER2-IHC 2+. Of these, 273 were primary and 6 were metastatic samples. The distributions of patient age and tumor fraction were similar among these categories (p=0.54 and p=0.41, respectively; one-way ANOVA). ERBB2 expression differed among all three HER2-IHC categories and was lowest in HER2-0 and highest in HER2-2+ (HER2-0 vs HER2-1+, p< 0.001; HER2-0 vs HER2-2+, p< 0.0001; HER2-1+ vs HER2-2+, p=0.011; HER2-0 vs HER2-low, p< 0.0001; Mann-Whitney U test in all comparisons). Five genes were mutated in more than 10% of samples: PIK3CA (45.5%), GATA3 (15.4%), CDH1 (12.5%), MAP3K1 (11.1%) and TP53 (10.8%). Mutations in two genes, GATA3 and PTEN, appeared to differ in frequency between the HER2-0 and HER2-low categories (Table 1). We selected 4 genes with mutations, 2 genes with copy number changes, and expression from ERBB2, ESR1, CD274, HLA-A, HLA-B and HLA-C to train a logistic regression classifier to predict HER2 IHC status. The classifier was trained on 163 samples, hyperparameter tuning was done using 55 samples, and testing was performed on 61 samples. Preliminary results indicated that of the 28 HER2-IHC 0 samples in the test set, 17 (65%) were classified as HER2-low. Further development and evaluation of the classifier using a blinded testing set is currently in progress. Conclusion In this cohort of BC samples, ERBB2 mRNA expression was positively associated with HER2 protein IHC status. Additional studies are required to determine whether a classifier including ERBB2 mRNA expression could be used to identify patients for T-DXd therapy. The relative enrichment of PTEN alterations in HER2-IHC 0 samples suggests that mTOR/AKT inhibitors may sometimes be appropriate in patients who are not eligible for T-DXd therapy, and further investigation should be considered. Table 1. Number (frequency) of altered genes by HER2 IHC status. Citation Format: Gargi Basu, Niru Chennagiri, Turgut Dogruluk, David Hall, Jess Hoag, Cynthia Flannery, Snehal Thakkar, Melanie Palomares, Frederick Baehner, Lajos Pusztai. Classifying HER2-low breast cancer using a combination of ERBB2 mRNA expression and altered genes [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-13-06.

Abstract PS09-01: Individual patient data meta-analysis of clinical and translational biomarkers for prediction of pathological complete response (pCR) after de-escalated therapy in HER2+ breast cancer in four trials of the West German Study Group

Abstract Background Introduction of anti-HER2 therapies substantially improved outcomes for HER2-positive early breast cancer (HER2+ eBC). However, a considerable proportion of patients (pts) may still be overtreated with systemic chemotherapy (CTx) combinations. Establishing safe de-escalation strategies to avoid toxicities requires precise patient selection. Therefore, we set out to determine predictors for efficacy and survival in the unique setting of four de-escalation trials investigating short (12-week) neoadjuvant treatments (NAT) in HER2+ eBC. We investigated the prognostic ability of clinical and translational biomarkers for pCR to identify pts with the best prognosis after de-escalated systemic CTx-free NAT. Methods 756 pts who received de-escalated NAT were analyzed: trastuzumab + pertuzumab (T + P, n=92) and T + P + paclitaxel (pac, n=42) in ADAPT-HR-/HER2+ (NCT01817452); trastuzumab emtansine (T-DM1, n=118), T-DM1 + endocrine therapy (ET, n=125), and T + ET (n=129) in ADAPT-HR+/HER2+ (NCT01779206), T + P + pac (n=107) and T + P + ET (n=100) in TP-II (NCT03272477); and T + P + pembrolizumab (n=43) in Keyriched-1 (NCT03988036) in HER2-enriched (HER2-E) subtype by PAM50. The primary endpoint of each trial was pCR (ypT0/is ypN0). Survival was a secondary endpoint in all trials but Keyriched-1; survival data for TP-II are pending. Baseline gene expression was analyzed by BC360 assay; intrinsic molecular subtypes were determined using the PAM50 predictor. Stromal tumor infiltrating lymphocytes (sTILs) were evaluated at baseline and at week 3 of NAT. sTILs were categorized using a 30% threshold and the low cellularity category ( < 500 invasive tumor cells) at week 3. Prognostic markers for pCR were identified with univariate and multivariable logistic regression models with backstep algorithm excluding variables with p≥0.1; considered variables included age, sTILs (baseline, 3-weeks), cT, cN, grade, hormone receptor and HER2 status, intrinsic subtype, and standardized ERBB2 and ESR1 gene expression. These analyses were performed separately for NAT involving systemic CTx (i.e. containing pac, n=149) and systemic CTx-free NAT (n=607). Results Overall pCR rate was 39.1% (CTx: 66.4%; CTx-free: 32.5%). Multivariable analysis identified predictors of pCR after CTx-free NAT: low cellularity at week 3 (vs < 30% sTILs: OR 3.21, 95%CI 1.85-5.57), ERBB2 (OR 1.90, 95%CI 1.41-2.55), HER2 3+ (vs 1+/2+ and ISH+: OR 8.01, 95%CI 1.65-38.99), LumA/LumB/Basal subtype (vs HER2-E: OR 0.57, 95%CI 0.34-0.97), cT2 (vs 1: OR 0.54, 95%CI 0.33-0.89), and cN1-3 (vs 0, OR 0.46, 95%CI 0.27-0.78). In CTx-containing NAT, only ERBB2 (OR 2.08, 95%CI 1.28-3.40) and additionally ESR1 (OR 0.38, 95%CI 0.23-0.61) were prognostic for pCR. Updated analysis including expanded gene expression data from ADAPT-HR+/HER2+ and a prognostic score for pCR after CTx-free NAT developed using machine learning methods will be presented at the meeting. Conclusions This pooled analysis demonstrated a 66% pCR rate after a short (12-week) de-escalated NAT in HER2+ eBC. In one-third of patients (with mainly stage I cancer, higher HER2 expression by immunohistochemistry and gene expression analysis, and low cellularity at 3 weeks), pCR can be achieved without systemic CTx. Identified biomarkers could pave the way for developing new patient selection strategies to spare CTx-associated acute and late toxicities in a clinically meaningful number of patients. Citation Format: Monika Graeser, Oleg Gluz, Christine zu Eulenburg, Sherko Küemmel, Raquel von Schumann, Matthias Christgen, Rachel Wuerstlein, Enrico Pelz, Hans-Heinrich Kreipe, Peter Schmid, Marc Thill, Michael Braun, Jochem Potenberg, Claudia Schumacher, Joke Tio, Andreas Hartkopf, Marianne Just, Christian Schem, Kerstin Lüdtke-Heckenkamp, Eva-Maria Grischke, Felix Hilpert, Angela Kentsch, Ronald Kates, Ulrike Nitz, Nadia Harbeck. Individual patient data meta-analysis of clinical and translational biomarkers for prediction of pathological complete response (pCR) after de-escalated therapy in HER2+ breast cancer in four trials of the West German Study Group [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS09-01.

Abstract PO3-14-08: Metaplastic Breast Cancer: Whole Genome Sequencing Analysis and Emerging Therapeutic Targets

Abstract Background: Metaplastic breast cancer (MpBC) is a rare histologic subtype of triple negative breast cancer (TNBC) with an aggressive behavior and poor outcome. Previous studies by whole-exome and targeted sequencing showed that MpBCs display a dominant mutational signature 3, associated to homologous recombination (HR) deficiency (HRD). Tumors displaying HRD are associated with response to therapies causing double strand breaks. Nonetheless, MpBCs consistently display significantly lower rates of response to neoadjuvant chemotherapy than non-metaplastic TNBCs and effective therapeutic alternatives are an unmet clinical need. Here we sought to assess the HR features of MpBCs using whole-genome sequencing (WGS), and to evaluate the expression in MpBCs of antigens that are targets of novel antibody drug conjugates (ADCs) in common forms of breast cancer. In addition, we sought to assess the efficacy of ADCs and drugs targeting the DNA damage response (DDR) using preclinical MpBC models. Materials and Methods: We subjected 25 primary MpBC to WGS. HRDetect, the ‘gold standard’ tool for assessment of HRD, was utilized. Mutational signatures were inferred using Signal. 31 MpBCs were subjected to RNA-sequencing to assess the gene expression levels ADC targets compared to non-MpBCs from The Cancer Genome Atlas (TCGA). Efficiency of ADCs and DDR drugs was evaluated using the MpBC cell models HCC1806, BT549 and Hs578T in vitroand/or using HCC1806 xenografts in athymic mice in vivo. Results: Although the majority of MpBCs (13/25) displayed a dominant SBS mutational signature 3, only a small subset of cases (3/25) were classified as HRD by HRDetect. These three bona fide HRD cases were found to harbor bi-allelic inactivation of BRCA1 (n=2) or RAD51C (n=1), and displayed various genomic features of HRD, including deletions with microhomology, enrichment in tandem duplications, rearrangement signatures 3 and 5, and high large scale state transitions (LST) and telomeric allelic imbalance (NtAI) scores. Most MpBCs (22/25), however, were not classified as HRD by HRDetect displaying an incomplete HRD phenotype, with only partial genomic features of HRD. 52% of MpBCs (13/25) displayed APOBEC mutagenesis exposure, which was present in the three bona fide HRD MpBCs. RNA-sequencing analyses revealed detectable ERBB2 and TROP2 expression in all MpBCs interrogated, although at lower levels than in non-MpBCs from TCGA. The HCC1806, BT549 and Hs578T MpBC cell models were found to be sensitive to Sacituzumab Govitecan and Trastuzumab Deruxtecan (T-DXd) in cell viability and colony formation assays, and to T-DXd in vivo. These MpBC cell models were also found to be sensitive to DDR compounds, such as ATR, WEE1 and PKMYT1 inhibitors in vitro, alone and in combination with T-DXd or Sacituzumab Govitecan. Conclusions: Most MpBCs display an incomplete HRD genomic scar, except for those cases harboring bi-allelic inactivation of HRD genes. APOBEC mutagenesis is operative in MpBCs and co-exists with HRD. MpBCs express ERBB2 and TROP2, and MpBC cell models are sensitive to T-DXd and Sacituzumab govitecan, as well as DDR compounds, targeting the incomplete HRD phenotype of MpBCs, alone and in combination. Taken together, these findings warrant further studies in patients with MpBCs testing the therapeutic efficacy of agents targeting the incomplete HRD phenotype, as well as the expression of ADC targets in these aggressive rare forms of TNBCs. Citation Format: Fresia Pareja, Andrea Gazzo, Higinio Dopeso, David Brown, Pier Selenica, Yingjie Zhu, Juan Blanco-Heredia, Laxmi Gusain, Xin Pei, Giacomo Montagna, Nour Abuhadra, Hanna Y Wen, Edi Brogi, Nadeem Riaz, Sarat Chandarlapaty, Maurizio Scaltriti, Larry Norton, Simon Powell, Jorge Reis-Filho, Britta Weigelt. Metaplastic Breast Cancer: Whole Genome Sequencing Analysis and Emerging Therapeutic Targets [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-14-08.