HER2-enriched Molecular Subtypes Research Articles

Massively Invasive Ductal Breast Cancer: Association Between Mammographic Features and the HER2-enriched Molecular Subtype

Massively Invasive Ductal Breast Cancer: Association Between Mammographic Features and the HER2-enriched Molecular Subtype

Baseline [18F]FDG PET/CT and MRI first-order breast tumor features do not improve pathological complete response prediction to neoadjuvant chemotherapy.

To verify the ability of pretreatment [18F]FDG PET/CT and T1-weighed dynamic contrast-enhanced MRI to predict pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) in breast cancer (BC) patients. This retrospective study includes patients with BC of no special type submitted to baseline [18F]FDG PET/CT, NAC and surgery. [18F]FDG PET-based features reflecting intensity and heterogeneity of tracer uptake were extracted from the primary BC and suspicious axillary lymph nodes (ALN), for comparative analysis related to NAC response (pCR vs. non-pCR). Multivariate logistic regression was performed for response prediction combining the breast tumor-extracted PET-based features and clinicopathological features. A subanalysis was performed in a patients' subsample by adding breast tumor-extracted first-order MRI-based features to the multivariate logistic regression. A total of 170 tumors from 168 patients were included. pCR was observed in 60/170 tumors (20/107 luminal B-like, 25/45 triple-negative and 15/18 HER2-enriched surrogate molecular subtypes). Higher intensity and higher heterogeneity of [18F]FDG uptake in the primary BC were associated with NAC response in HER2-negative tumors (immunohistochemistry score 0, 1 + or 2 + non-amplified by in situ hybridization). Also, higher intensity of tracer uptake was observed in ALN in the pCR group among HER2-negative tumors. No [18F]FDG PET-based features were associated with pCR in the other subgroup analyses. A subsample of 103 tumors was also submitted to extraction of MRI-based features. When combined with clinicopathological features, neither [18F]FDG PET nor MRI-based features had additional value for pCR prediction. The only significant predictors were estrogen receptor status, HER2 expression and grade. Pretreatment [18F]FDG PET-based features from primary BC and ALN are not associated with response to NAC, except in HER2-negative tumors. As compared with pathological features, no breast tumor-extracted PET or MRI-based feature improved response prediction.

Clinicopathological Significance of Cyclin-Dependent Kinase 2 (CDK2) in Ductal Carcinoma In Situ and Early-Stage Invasive Breast Cancers.

Cyclin-dependent kinase 2 (CDK2) is a key cell cycle regulator, with essential roles during G1/S transition. The clinicopathological significance of CDK2 in ductal carcinomas in situ (DCIS) and early-stage invasive breast cancers (BCs) remains largely unknown. Here, we evaluated CDK2's protein expression in 479 BC samples and 216 DCIS specimens. Analysis of CDK2 transcripts was completed in the METABRIC cohort (n = 1980) and TCGA cohort (n = 1090), respectively. A high nuclear CDK2 protein expression was significantly associated with aggressive phenotypes, including a high tumour grade, lymph vascular invasion, a poor Nottingham prognostic index (all p-values < 0.0001), and shorter survival (p = 0.006), especially in luminal BC (p = 0.009). In p53-mutant BC, high nuclear CDK2 remained linked with worse survival (p = 0.01). In DCIS, high nuclear/low cytoplasmic co-expression showed significant association with a high tumour grade (p = 0.043), triple-negative and HER2-enriched molecular subtypes (p = 0.01), Comedo necrosis (p = 0.024), negative ER status (p = 0.004), negative PR status (p < 0.0001), and a high proliferation index (p < 0.0001). Tumours with high CDK2 transcripts were more likely to have higher expressions of genes involved in the cell cycle, homologous recombination, and p53 signaling. We provide compelling evidence that high CDK2 is a feature of aggressive breast cancers. The clinical evaluation of CDK2 inhibitors in early-stage BC patients will have a clinical impact.

Abstract PO1-16-01: Clinicopathological and global transcriptional complexity of estrogen receptor low positive breast cancers in a contemporary Swedish prospective population-based cohort

Abstract Background: Estrogen receptor (ER) expression is currently the most consequential biomarker for prognostic and therapeutic decision making in clinical management of early breast cancer. Endocrine therapy (ET) is an important part of standard of care in most cases with ER-positive disease, and an effective therapy for patients with endocrine-responsive tumors, decreasing the risk of recurrence and improving the rate of survival. Unfortunately, ET comes with frequently bothersome side-effects and tend to decrease quality of life. The threshold to define ER positivity as a marker of endocrine responsiveness is non-uniform between international and local guidelines. Among ER low positive tumors (ERlow ,1-10% expression) endocrine responsiveness is uncertain. Swedish national guidelines recommend a cut-off of ≥10% for ER positivity and ET prescriptions, thus patients with ERlow tumors are often exempted from adjuvant ET. This study explores the clinicopathological characteristics, global transcriptional complexity and clinical outcome of ERlow tumors to better understand their biology and response to therapy. Methods: 9138 patients diagnosed with early breast cancer between 2010 – 2021 in Sweden with available clinicopathological data and RNA sequencing data were included. Patients were classified according to ER expression: ERneg (&amp;lt; 1%; n=897), ERlow (1-10%, n=158) and ERhigh ( &amp;gt;10%, n=8083). Adjuvant ET was provided to 3.6%, 16.8% and 91.5% of patients with ERneg, ERlow, and ERhigh tumors, respectively. Clinicopathological characteristics, overall survival (OS) and global transcriptional profiles of ERlow tumors were compared with ERneg and ERhigh tumors, respectively. Results: Generally, ERlow and ERneg tumor pathological characteristics were more similar to each other but were significantly distinct compared to ERhigh tumors. However, among patients with HER2-negative disease only, significant differences related to tumor biology persisted between ERlow compared with ERneg tumors; ERlow was enriched with tumors displaying a lobular histology, NHG grades 1&amp;2, PgRlow/high expression, low proliferation and Luminal &amp; HER2-enriched molecular subtypes (p&amp;lt; 0.05 for all comparisons). Moreover, multivariable survival analyses revealed that the risk of dying was significantly lower for patients with ERlow tumors compared to patients with ERneg (p=0.005) or ERhigh tumors (p=0.011) in this cohort. The distribution of clinicopathological characteristics and overall survival between ERlow compared with ERneg or ERhigh tumors were similar among patients with HER2-positive tumors only. Global transcriptional comparisons identified only 42 genes to be differentially expressed between ERlow vs ERneg tumors (FDR&amp;lt; 0.05); but gene set enrichment analyses failed to identify any significantly enriched cancer-related processes/pathways within the queried databases. Conclusions: Identification of optimal therapies for all subsets of breast cancer is necessary in the pursuit of personalized medicine. These results confirm that ERneg and ERlow tumors are pathologically and transcriptionally distinct from ERhigh tumors. Although subtle differences exists in the underlying biology of ERlow compared to ERneg tumors, similar therapeutic management excluding ET for patients with ERlow and ERneg disease is recommended in the Swedish context. Omission of adjuvant ET did not seem to compromise overall survival for ERlow relative to ERneg or ERhigh tumors, urging the need for prospective studies investigating the true benefit of ET for ERlow tumors. Our results also raise reasonable clinical thoughts on the benefits of new treatment strategies such as cyclin-dependent kinase 4/6 inhibitors, immunotherapy and antibody-drug conjugates for patients with ERlow expressing tumors. Citation Format: Siker Kimbung, Srinivas Veerla, Anna Ehinger, Johan Vallon-Christersson, Martin Malmberg, Niklas Loman. Clinicopathological and global transcriptional complexity of estrogen receptor low positive breast cancers in a contemporary Swedish prospective population-based cohort [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 PO1-16-01.

Abstract PS09-08: Genomic characterization of endocrine resistance in ER+HER2+ breast cancers in the POETIC Trial

Abstract Background: Mechanisms of resistance to endocrine therapy are not well understood within ER+HER2+ breast cancer (BC). Our prior work suggested that intrinsic HER2-Enriched (HER2E) molecular subtype predicts early resistance to aromatase inhibitors (AI) (Bergamino eBioMedicine 2022) and high on-treatment (on-Txt) Ki67 levels predict poor survival (Smith Lancet Oncol 2020). Improved early detection of persistent proliferating tumor cells with endocrine resistance pathways could be targeted by pre-emptive personalized therapy and reduction in recurrence. In this study, we proposed to further identify additional alterations/features from genomic and spatial data to provide unprecedented new insight into intrinsic and adaptive resistant pathways in tumor cells that may assist to identify molecular targets for treatment. Materials: POETIC was a phase III trial of post-menopausal patients with ER/PR+ invasive BC (n = 4480) randomized 2:1 to 2 weeks of peri-operative AI (POAI) vs control, followed by standard-of-care treatment. Ki67 was assessed by IHC and intra-tumor heterogeneity was evaluated (5-15 regions) for all the POETIC POAI samples (N = 2487). ER+HER2+ samples were classified as good responders (GR) or poor responders (PR) based on a reduction in Ki67 between pre-treatment (pre-Txt) and 2-week on-Txt samples. Tumor-infiltrating lymphocytes were assessed; multiplex Immunofluorescence (mIF) was performed to measure immune cell densities in tumor and stroma compartments (CD3, CD20, CD68, FOXP3, and CD3 FOXP3 co-expression). Gene expression profiles by BC360™ (Nanostring) on all 210 pairs of POAI treated ER+/HER2+; whole exome sequencing (WES, 100X) were performed on pre-Txt tumor and blood samples from 13 GR, 17 PR, and 9 HER2E GR. We performed GeoMx Whole Transcriptome on 4 pairs (pre-Txt and on-Txt) of GR and GeoMx Proteins (77 including IO proteins) on 6 pairs of GRs and 6 pairs of PRs. Results: The most frequently mutated genes were TP53, PIK3CA, GATA3, and CHD4. Only TP53 was associated with PR (Fisher’s exact p=0.01). TP53 mutated cases had higher expression of TP53 mutant-like gene expression signature compared to wild-type cases (Wilcoxon test p=0.001), mIF FOXP3 (Wilcoxon test p = 0.0005), and CD68 (Wilcoxon test p = 0.019) density score. However, within the HER2-E subset, we found that TP53 mutations were associated with GR (Fisher’s exact p=0.02). We found spatial heterogeneity of Ki67 IHC levels across POAI samples. Examining IHC, while there was higher heterogeneity of Ki67 in the ER+HER2- samples (n = 2264) with 3% of pre-Txt and 9% on-Txt, 6% of ER+HER2+ samples (13/223, 6 LumA, 5 LumB, and 2 HER2E) showed heterogeneity of Ki67 exclusively on-Txt. Even in GR tumors with Ki67 &amp;lt; 10% on-Txt, we identified hotspots with retained proliferating Ki67+ cells after 2 weeks of POAI. The lobular tumors were GR and had characteristic CDH1 mutations. Importantly, cases with persistent areas of Ki67+ cells, regardless of Her2 status, were associated with late relapse. To further explore intratumoral heterogeneity, we performed spatial whole transcriptomics profiling on 95 regions from 4 pairs of GR samples (Ki67 &amp;gt; 10% at baseline and Ki67 &amp;lt; 10% on-Txt) and found low intratumoral heterogeneity in the pre-Txt samples that increased at 2 weeks on-Txt. In a larger set of samples including both GR and PR with the GeoMx protein method, we found increased intratumoral heterogeneity in the PR vs GR. Conclusion: While TP53 mutation was generally a predictor of poor response; in HER2-E it paradoxically was associated with a good early response to aromatase inhibitor which warrants further investigation. Ki67 levels in ER+HER2+ showed higher intratumoral heterogeneity in a subset of patients on treatment suggesting the potential of persistent, proliferating cells leading to later recurrence. Our spatial RNA and protein data further observe the intratumoral heterogeneity that identifies pathways for use as potential spatial biomarkers. Citation Format: Maggie Chon U Cheang, Xixuan Zhu, Orsolya Sipos, Anastasia Alataki, Mikayla Feldbauer, Elena López-Knowles, Holly Tovey, Lucy Kilburn, Milana Bergamino Sirvén, Dhrusti Patel, Hui Xiao, Perry Maxwell, Anthony Skene, Chris Holcombe, Manuel Salto-Tellez, Nicholas Turner, Andrew Dodson, Ian Smith, John Robertson, Judith Bliss, Gene Schuster, Roberto Salgado, Mitch Dowsett, Katherine A Hoadley. Genomic characterization of endocrine resistance in ER+HER2+ breast cancers in the POETIC Trial [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 PS09-08.

Abstract PO5-02-09: Discordance of the PAM50 intrinsic subtypes with the immunohistochemistry-based subtypes in HER2-negative early breast cancer treated with neoadjuvant chemotherapy

Abstract Background The PAM50 (Prosigna Breast Cancer Gene Signature Assay) can be used to assess the expression levels of 50 genes in early breast cancer biopsies, including formalin-fixed paraffin-embedded (FFPE) tissue from human epidermal growth factor receptor 2 (HER2)-negative patients. However, there is currently no practical molecular assay for intrinsic subtype in real-world practice that addresses the problems of cost and run-time. Methods In the phase 2 HER2E-PAM/PAMILIA study (NCT04817540), we prospectively analyzed molecular subtyping through the PAM50 test in low HER2 (HER2 IHC 1+ or 2+ SISH-) breast cancer patients. PAM50 intrinsic subtypes were determined according to 50 cancer genes using the NanoString nCounter Analysis System. This study was originally designed to determine whether adding HER2-targeted treatment in HER2 enriched molecular subtype increases the pathologic complete rate (pCR). We aimed to analyze the discordance between immunohistochemistry (IHC)-based surrogate subtyping of pre- &amp; post-operative tissues and PAM50 intrinsic subtypes, and to assess the pCR according to the discordance. Results In a total 82 patients, the proportions of HR+/HER2- and triple negative breast cancer (TNBC) in the preoperative tissue were 85.4% (n=70) and 14.6% (n=12), respectively. According to PAM50 intrinsic subtypes, 11.0% (n=9) were basal, 8.5% (n=7) were HER2-enriched, 34.1% (n=28) were luminal A, 36.6% (n=30) were luminal B, and 3.7% (n=3) were normal-like type. In total, 32 patients (41.5%) were discordant between IHC-based preoperative subtype and PAM50 intrinsic subtype. Among the 70 patients with HR+/HER2-, non-luminal A, B type was found in 12.9% with basal-like, 8.6% with HER2-enriched, and 4.3% with normal-like type, respectively. Of 12 TNBC patients, 83.3% were luminal A, B type, and 8.3% were HER2-enriched. In the other hands, 6 patients (13.0%) were discordant between IHC-based post-operative subtype and PAM50 intrinsic subtype. Among the 40 patients with HR+/HER2- postoperative subtype, non-luminal A, B type was found in 2.5% with basal-like, 2.5% with HER2-enriched, and 5.0% with normal-like type, respectively. Of 6 TNBC postoperative patients, 16.7% were normal-like. Most received anthracycline- and taxane-based neoadjuvant chemotherapy. During data analysis (June 2023), 54 cases underwent surgery after neoadjuvant chemotherapy. 4 of 54 patients (7.4%) achieved a pCR, of which one was HER2-enriched, one was luminal B-like, and two were basal-like PAM50 intrinsic subtype. However, discordance of IHC based subtype with intrinsic subtype was not considerable and was not correlated with pCR. Conclusion A substantial portion of patients showed discrepancy between preoperative and postoperative IHC subtype and PAM50 intrinsic subtype in our study. Citation Format: Jee Hung Kim, Soong June Bae, Sung Gwe Ahn, Jeonghee Lim, Min Hwan Kim, Gun Min Kim, Joo Hyuk Sohn, Joon Jeong. Discordance of the PAM50 intrinsic subtypes with the immunohistochemistry-based subtypes in HER2-negative early breast cancer treated with neoadjuvant chemotherapy [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 PO5-02-09.

Breast Carcinoma: Correlation of Molecular Subtypes with Histopathologic Characteristics

Context: Breast carcinoma is a heterogenous disease and similar histological subtypes may exhibit different behavior and treatment response. The molecular classification may provide better prognostic, predictive and therapeutic information than histological classification. The study aimed at evaluating the distribution of molecular subtypes of breast cancer and its association with prognostic factors. Method: This prospective cross-sectional study was conducted on breast cancer cases, over a period of 2 years, at M.S. Ramaiah Medical College and Hospitals, Bengaluru. The resection specimens were evaluated for histopathological features. Immunohistochemical analysis for ER, PR, Her2neu and Ki-67 expression was performed to identify molecular subtypes. Correlation of molecular subtypes with histopathological prognostic factors was done by Chi- square test or Fischer’s exact test. Results: A total of 85 cases were evaluated and classified into Luminal A (50.6%), Basal like (27%), Luminal B (11.8%) and HER-2 enriched (10.6%) molecular subtypes. Invasive ductal carcinoma was the commonest histologic type across all the molecular subtypes. Majority of low-grade tumors were Luminal A and most of high-grade tumors were Basal like (p= 0.004). HER-2 enriched and Basal like tumors were relatively more frequent in ≤ 50 years of age and Luminal A tumors exhibited less frequent lymph node metastasis. However, these associations fell short of statistical significance. Conclusion: Luminal A tumors are the most common molecular subtype. Statistically significant correlation exists between histologic grade and molecular subtype. There is no significant correlation between molecular subtype and age, tumor size, nodal metastasis, pathological T stage and TNM stage. Keywords: Basal like, Breast carcinoma, HER2­Enriched, Luminal A, Luminal­ B, Molecular subtypes

Preoperative Dynamic Contrast-Enhanced and Diffusion-Weighted Breast Magnetic Resonance Imaging Findings for Prediction of Lymphovascular Invasion of the Lesions in Node-Negative Invasive Breast Cancer.

Purpose: Our single-centre retrospective study aimed to investigate the relationship between preoperative dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) findings and apparent diffusion coefficient (ADC) values and lymphovascular invasion (LVI) status of the lesions in patients with clinically-radiologically lymph node-negative invasive breast cancer. Methods: A total of 250 breast lesions diagnosed in preoperative magnetic resonance imaging were identified. All patients were divided into 2 subgroups: LVI-negative and LVI-positive according to the pathological findings of surgical specimens. The 2 groups' DCE-MRI findings, ADC values, and histopathological results of lesions were compared. Results: LVI was detected in 100 of 250 lesions. Younger age than 45 years and larger lesion size than 20 mm were found to be associated with the presence of LVI (P < .001). High histological and nuclear grade (P = .001), HER2-enriched molecular subtype (P = .001), and Ki-67 positivity (P = .016) were significantly associated with LVI. The LVI positivity rate was significantly higher in the lesions with medium-rapid initial phase kinetic curve and washout delayed phase kinetic curve (P = .001). The presence of LVI was significantly associated with the presence of peritumoural edema, sentinel lymph node metastasis, adjacent vessel sign, and increased whole breast vascularity (P < .001). When diffusion-weighted imaging findings were evaluated, it was determined that tumoural ADC values lower than 1068 × 10-6 mm2/second (P = .002) and peritumoural-tumoural ADC ratios higher than 1.5 (P = .001) statistically increased the probability of LVI. Conclusion: The patient's age, various histopathological and DCE-MRI findings, tumoural ADC value, and peritumoural-tumoural ADC ratio may be useful in the preoperative prediction of LVI status in breast cancer lesions.

316P Comprehensive characterization of the HER2-enriched intrinsic molecular subtype in ER-positive HER2-negative breast cancer

316P Comprehensive characterization of the HER2-enriched intrinsic molecular subtype in ER-positive HER2-negative breast cancer

Immunohistochemical expression of Hairy and Enhancer of Split 1 (HES1) protein in breast carcinoma

Background Hairy and Enhancer of Split 1 (HES1) is a transcription factor involved in cell differentiation, proliferation, and in various cancer progression. Recently, HES1 was addressed as a potential biomarker that induces stem cell features in breast cancer and stimulates epithelial-mesenchymal transition in triple-negative breast cancer (TNBC). Aim This study aimed to assess HES1 immunohistochemical (IHC) expression in invasive breast carcinoma and correlate it with the clinicopathological variables and different molecular subtypes of the cases. Patients and methods IHC was conducted on 76 paraffin blocks with an anti-HES1 monoclonal antibody, and a final IHC score was calculated based on staining intensity and percentage of positively stained cells. A final IHC of greater than or equal to 4 was considered an HES1 positive expression. Results HES1 expression was positive in 18 (23.7%) cases and was significantly associated with breast cancer HER2-enriched molecular subtype, followed by triple-negative breast cancer (P&lt;0.05). HES1 expression was also significantly associated with estrogen and progesterone receptor negativity and HER2 overexpression (P&lt;0.05). Positive HES1 expression was associated with high tumor grade, advanced stage, high Ki-67 proliferation index, and presence of tumor vascular emboli, although it did not reach statistical significance (P&gt;0.05). Conclusion Our study demonstrated that the HES1 protein showed a significantly higher expression in nonluminal breast cancer subtypes. In addition, it could have a potential role in the growth and spread of breast cancer cells. These findings suggest that HES1 is a possible promising target for therapeutic interventions.

Intra- and Peritumoral Radiomics Model Based on Early DCE-MRI for Preoperative Prediction of Molecular Subtypes in Invasive Ductal Breast Carcinoma: A Multitask Machine Learning Study.

PurposeThe aim of this study is to investigate radiomics features extracted from the optimal peritumoral region and the intratumoral area on the early phase of dynamic contrast-enhanced MRI (DCE-MRI) for predicting molecular subtypes of invasive ductal breast carcinoma (IDBC).MethodsA total of 422 IDBC patients with immunohistochemical and fluorescence in situ hybridization results from two hospitals (Center 1: 327 cases, Center 2: 95 cases) who underwent preoperative DCE-MRI were retrospectively enrolled. After image preprocessing, radiomic features were extracted from the intratumoral area and four peritumoral regions on DCE-MRI from two centers, and selected the optimal peritumoral region. Based on the intratumoral, peritumoral radiomics features, and clinical–radiological characteristics, five radiomics models were constructed through support vector machine (SVM) in multiple classification tasks related to molecular subtypes and visualized by nomogram. The performance of radiomics models was evaluated by receiver operating characteristic curves, confusion matrix, calibration curves, and decision curve analysis.ResultsA 6-mm peritumoral size was defined the optimal peritumoral region in classification tasks of hormone receptor (HR)-positive vs others, triple-negative breast cancer (TNBC) vs others, and HR-positive vs human epidermal growth factor receptor 2 (HER2)-enriched vs TNBC, and 8 mm was applied in HER2-enriched vs others. The combined clinical–radiological and radiomics models in three binary classification tasks (HR-positive vs others, HER2-enriched vs others, TNBC vs others) obtained optimal performance with AUCs of 0.838, 0.848, and 0.930 in the training cohort, respectively; 0.827, 0.813, and 0.879 in the internal test cohort, respectively; and 0.791, 0.707, and 0.852 in the external test cohort, respectively.ConclusionRadiomics features in the intratumoral and peritumoral regions of IDBC on DCE-MRI had a potential to predict the HR-positive, HER2-enriched, and TNBC molecular subtypes preoperatively.

Abstract 464: AI-powered segmentation and analysis of nuclei morphology predicts genomic and clinical markers in multiple cancer types

Abstract Morphological features of cancer cell nuclei are linked to gene expression signatures and genomic alterations. In addition, pathologists have leveraged nuclear morphology as diagnostic and prognostic markers. To enable the use of nuclear morphology in digital pathology, we developed a pan-tissue, deep-learning-based digital pathology pipeline for exhaustive nucleus detection, instance segmentation, and classification. We collected &amp;gt; 29,000 manual nucleus annotations from hematoxylin and eosin (H&amp;E)-stained pathology images from 21 tumor types at 40x and 20x magnification from The Cancer Genome Atlas (TCGA) project, as well as a proprietary set of H&amp;E-stained tissue biopsies of skin, liver non-alcoholic steatohepatitis (NASH), colon inflammatory bowel disease (IBD), and kidney lupus. Annotations were used to train an object detection and segmentation model for identifying nuclei. Application of the model to held-out test data, including held-out tissue types, demonstrated performance comparable to state-of-the-art models described in the literature (mean Dice score = 0.80, aggregated Jaccard index = 0.60). We deployed our model to segment nuclei in H&amp;E slides from the breast cancer (BRCA, N = 941) and prostate adenocarcinoma (PRAD, N = 457) TCGA cohorts. We extracted interpretable features describing the shape (circularity, eccentricity), size, staining intensity (mean and standard deviation), and texture of each nucleus. Nuclei were assigned as cancer or other cell types using separately trained convolutional neural networks for BRCA and PRAD. We used the mean and standard deviation of each feature sampled from a random subset of cancer nuclei to summarize the nuclear morphology on each slide (mean (range) = 10,068 (5,981-10,452) cancer cells from each BRCA slide; mean (range) = 10,053 (5,029-10,495) cancer cells from each PRAD slide). We used nuclear features to construct random forest classification models for predicting markers of genomic instability and prognosis: whole-genome doubling (WGD) and homologous recombination deficiency (HRD) status separately in BRCA and PRAD, HER2 subtype in BRCA, and Gleason grade in PRAD. Nuclear features were predictive of WGD (area under the receiver operating characteristic curve (AUROC) = 0.78 BRCA, = 0.69 PRAD) and binarized HRD status (AUROC = 0.65 BRCA, = 0.68 PRAD) on held-out test sets. Nuclear features were predictive of HER2-enriched breast cancer vs. other molecular subtypes (AUROC = 0.72), and distinguished between low risk (6) and moderate/high risk (7-10) Gleason grade in PRAD (AUROC = 0.72). In summary, we present a powerful pan-tissue approach for nucleus segmentation and featurization, which enables the construction of predictive models and the identification of features linking nuclear morphology with clinically-relevant prognostic biomarkers across multiple cancer types. Citation Format: John Abel, Suyog Jain, Deepta Rajan, Ken Leidal, Harshith Padigela, Aaditya Prakash, Jake Conway, Michael Nercessian, Christian Kirkup, Robert Egger, Ben Trotter, Andrew Beck, Ilan Wapinski, Michael G. Drage, Limin Yu, Amaro Taylor-Weiner. AI-powered segmentation and analysis of nuclei morphology predicts genomic and clinical markers in multiple cancer types [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 464.

Retracted: Microcalcification-associated breast cancer: HER2-enriched molecular subtype is associated with mammographic features.

To investigate whether the mammographic features were different between breast cancer HER2-enriched molecular subtype and non-HER2-enriched molecular subtype. 283 microcalcification-associated breast cancers were identified (HER2-enriched: n = 57; non-HER2-enriched: n = 226). Mammographic tumor mass and calcification features in relation to HER2 molecular subtype were analyzed. On univariate analysis, HER2-enriched molecular subtype rates were significantly higher (a) in tumor size ≤2 cm [33 of 57 (57.9%)] than in tumor size >2 cm lesions [22 of 226 (9.7%)] (p = 0.007), (b) in non-spiculated mass [39 of 57 (68.4%)] than in spiculated mass lesions [18 of 226 (7.9%)] (p = 0.034)，(c) in calcifications extent >2 cm [41 of 57 (71.9%)] lesions than in calcifications extent ≤2 cm lesions [16 of 226 (7.1%)] (p < 0.001) and (d) in calcification density ＞20 cm-2 [44 of 57 (71.2%)] lesions than in calcification density ≤20 cm-2 lesions [13 of 226 (5.8%)] (p = 0.034).On multivariate analysis, three mammographic features [tumor size >2 cm vs size ≤2 cm odds ratio (OR): 0.415 95% confidence interval (CI) (0.215 to 0.802), p = 0.009, spiculated mass vs non-spiculated mass OR: 0.226 95% CI (0.114 to 0.446), p < 0.001 and calcifications extent >2 cm vs calcifications extent ≤2 cm OR: 7.754, 95% CI (3.100 to 19.339) p< 0.001] were independent predictors. Our results indicated that small tumor size, non-spiculated mass and calcification extent >2 cm are more likely to be HER2 molecular subtype. The discrimination of this model, as quantified by the area under the curve, was 0.751 [95% CI (0.701 to 0.854)]. Our study presents a prediction model that incorporates the mammographic features of tumor size, non-spiculated mass and calcification extent, which can potentially be used to preoperative predict breast cancer HER2-enriched subtype. Mammographic features can noninvasively visualize breast tumor phenotype characteristics.

Microcalcification-associated breast cancer: HER2-enriched molecular subtype is associated with mammographic features.

Microcalcification-associated breast cancer: HER2-enriched molecular subtype is associated with mammographic features.

Abstract 1977: Combined inhibition of EGFR and PI3Kinase signaling in EGFR amplified triple negative breast cancer cells induces apoptosis and reduces cancer stem cells

Abstract Signaling from the Epidermal Growth Factor Receptor (EGFR) family is commonly dysregulated in various cancer types by amplification or activating mutations. For example, HER2 amplification occurs in 15-20% of breast cancers, and is a well-defined driver of tumorigenesis. EGFR is amplified in approximately 2% of breast cancer patients with unknown significance. It is amplified more frequently in TNBC (5.7-6.7%) and ER-/HER2+ cancers (5.8-6.5%). Basal (4.3-8.1%) and HER2 enriched (3.9-45.4%) molecular subtypes show the highest amplification than other molecular subtypes. EGFR amplification leads to shorter overall survival among breast cancer patients compared to those without amplified EGFR. Approximately 71% of EGFR amplified tumors have activated PI3K signaling, indicating a possible dual-inhibition therapeutic approach targeting both EGFR and PI3K. In order to study the role of EGFR amplification and PI3K aberrations in TNBC, we used the TNBC cell lines BT20 (amplified EGFR, PIK3CA activating mutation), MDA-MB-468 (amplified EGFR, PTEN deletion), and MDA-MB-231 (no amplification of EGFR or PI3K pathway mutations). EGFR amplification in both MDA-MB-468 and BT20 cell lines was confirmed by western blotting and Fluorescent in situ Hybridization; MDA-MB-231 did not have EGFR amplification. Activating mutations in both alleles of PIK3CA in BT20 was confirmed by sequencing. Loss of PTEN in MDA-MB-468 was confirmed by immunoblotting. Inhibition of EGFR with erlotinib resulted in decreased ERK signaling in BT20 and MDA-MB-468, but not in MDA-MB-231. Inhibition of the PI3K with Ly294002 or BKM120 decreased activation of AKT and mTOR signaling in BT20 and MDA-MB-468, but not in MDA-MB-231. The combination of erlotinib and PI3K inhibitors more dramatically reduced mTOR and AKT signaling in the BT20 and MDA-MB-468 cells. Combination of erlotinib and PI3K inhibitors reduced cell viability in these 3 cell lines, but inhibition was greater in MDA-MB-468 and BT20 compared to MDA-MB-231, and only MDA-MB-468 and BT20 cells had an increased fraction of apoptotic cells, signifying that combination therapy is most effective in cells with amplified EGFR and aberrant PI3K. It has been previously shown that HER2/HER3 activation plays a role in self renewal of tumor initiating cells. We demonstrate that the combination of erlotinib and BKM120 reduced the cancer stem cell population as measured by an aldeflour assay and by mammosphere formation. In summary, these data demonstrate that EGFR amplification in TNBC drives cell viability through EGFR and PI3K signaling, and EGFR/PI3K inhibitor combination causes apoptosis as well as reduction in the cancer stem cell population. We present evidence therefore that dual inhibition of EGFR/PI3K presents as a potential targetable pathway in TNBC with EGFR amplification and aberrant PI3K signaling. Citation Format: David John Wisniewski, Donna Voeller, Stanley Lipkowitz. Combined inhibition of EGFR and PI3Kinase signaling in EGFR amplified triple negative breast cancer cells induces apoptosis and reduces cancer stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1977.

A Histone Acetylation Modulator Gene Signature for Classification and Prognosis of Breast Cancer.

Regulators of histone acetylation are promising epigenetic targets for therapy in breast cancer. In this study, we comprehensively analyzed the expression of histone acetylation modulator genes in breast cancer using TCGA data sources. A gene signature composed of eight histone acetylation modulators (HAMs) was found to be effective for the classification and prognosis of breast cancers, especially in the HER2-enriched and basal-like molecular subtypes. The eight genes consist of two histone acetylation writers (GTF3C4 and CLOCK), two erasers (HDAC2 and SIRT7) and four readers (BRD4, BRD7, SP100, and BRWD3). Both histone acetylation writer genes and eraser genes were found to be differentially expressed between the two groups indicating a close relationship exists between overall histone acetylation level and prognosis of breast cancer in HER2-enriched and basal-like breast cancer.

The importance of SUVmax in predicting prognosis of invasive breast carcinoma-no special types

Aim: We aimed to investigate the relationship between FDG uptake and clinicopathological characteristics of invasive breast carcinoma-no special type in the present study.Materials and Methods: One hundred seventy invasive breast carcinoma-no special type cases who underwent PET-CT before surgery between 2011-2019 were included in the study. The clinicopathological features and SUVmax of the patients were compared.Results: We observed a strong relationship between the size, grade, pathological stage groups and SUVmax of the tumors and revealed that the SUVmax increased as the size, grade, and pathological stage groups of the tumors increased (p0.001). Carcinomas with high Ki67 proliferation index and ER and PR negative carcinomas exhibited higher SUVmax (p0.001). Triple negative and HER2-enriched molecular subtypes had distinctly higher SUVmax than Luminal A and Luminal B ones (p0.001). HER2-enriched tumors, the cases that were 40 years old and advanced stage designated higher SUVmax (p0.05). Conclusion: It is observed that invasive breast carcinoma-no special type with good prognostic factors have low SUVmax, while carcinomas with poor prognostic features have high SUVmax. It can be suggested that PET/CT can be use to predict the prognosis of invasive breast carcinoma-no special type.

The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences

Molecular profiling of breast cancer has enabled the development of more robust molecular prognostic signatures and therapeutic options for breast cancer patients. However, non-Caucasian populations remain understudied. Here, we present the mutational, transcriptional, and copy number profiles of 560 Malaysian breast tumours and a comparative analysis of breast cancers arising in Asian and Caucasian women. Compared to breast tumours in Caucasian women, we show an increased prevalence of HER2-enriched molecular subtypes and higher prevalence of TP53 somatic mutations in ER+ Asian breast tumours. We also observe elevated immune scores in Asian breast tumours, suggesting potential clinical response to immune checkpoint inhibitors. Whilst HER2-subtype and enriched immune score are associated with improved survival, presence of TP53 somatic mutations is associated with poorer survival in ER+ tumours. Taken together, these population differences unveil opportunities to improve the understanding of this disease and lay the foundation for precision medicine in different populations.

Predictive and prognostic role of tumour-infiltrating lymphocytes in breast cancer patients with different molecular subtypes: a meta-analysis

BackgroundWhether tumour-infiltrating lymphocytes (TILs) play different roles in different molecular subtypes of breast cancer remains unknown. Additionally, their prognostic and predictive value in different molecular subtypes of breast cancer is still controversial. The aim of our meta-analysis was to assess the prognostic and predictive value of TILs in different molecular subtypes of breast cancer by summarizing all relevant studies performing multivariate analysis.MethodsPubMed, Embase, EBSCO, ScienceDirect, the Cochrane Database and Web of Science were comprehensively searched (until March 2020). Hazard ratios (HRs), odds ratios (ORs) and their 95% confidence intervals (CIs) were used as effect measures to perform our meta-analysis. A random effect model was used. Stata software, version 15 (2017) (StataCorp, College Station, TX, USA) was used to perform the statistical analysis.ResultsThirty-three studies including 18,170 eligible breast cancer patients were analysed. The meta-analysis showed that high TIL expression was significantly associated with increased pathological complete response (pCR) rates after neoadjuvant chemotherapy in patients with the HER2-enriched molecular subtype (OR = 1.137, 95% CI [1.061 ~ 1.218], p < 0.001) and triple-negative breast cancer (TNBC) subtype (OR = 1.120, 95% CI [1.061 ~ 1.182], p < 0.001). However, high TIL expression was not significantly associated with high pCR rates after neoadjuvant chemotherapy in patients with the luminal molecular subtype of breast cancer (OR = 1.154, 95% CI [0.789 ~ 1.690], p = 0.460). We carried out a meta-analysis on the HRs of overall survival (OS) and disease-free survival (DFS) to assess the prognostic value of TILs in breast cancer with different molecular subtypes more deeply. Our meta-analysis confirmed that high TILs were associated with significantly improved DFS in patients with the HER2-enriched molecular subtype [HR = 0.940, 95% CI (0.903 ~ 0.979), p = 0.003] and TNBC molecular subtype [HR = 0.907, 95% CI (0.862 ~ 0.954), p < 0.001]. However, high TILs were not associated with significantly better DFS in patients with the luminal molecular subtype of breast cancer [HR = 0.998, 95% CI (0.977 ~ 1.019), p = 0.840]. Furthermore, the results confirmed that high TILs were significantly related to better OS in patients with the HER2-enriched molecular subtype [HR = 0.910, 95% CI (0.866 ~ 0.957), p < 0.001] and TNBC molecular subtype [HR = 0.869, 95% CI (0.836 ~ 0.904), p < 0.001]. Conversely, the summarized results indicated that high TILs were significantly associated with poor OS in patients with the luminal molecular subtype of breast cancer [HR = 1.077, 95% CI (1.016 ~ 1.141), p = 0.012].ConclusionsOur meta-analysis confirms that high TILs are associated with favourable survival and predicts pCR in breast cancer patients with the TNBC and HER2-enriched molecular subtypes.

PIK3CA Mutation in the ShortHER Randomized Adjuvant Trial for Patients with Early HER2+ Breast Cancer: Association with Prognosis and Integration with PAM50 Subtype.

We explored the prognostic effect of PIK3CA mutation in HER2+ patients enrolled in the ShortHER trial. The ShortHER trial randomized 1,253 patients with HER2+ breast cancer to 9 weeks or 1 year of adjuvant trastuzumab combined with chemotherapy. PIK3CA hotspot mutations in exon 9 and 20 were analyzed by pyrosequencing. Expression of 60 genes, including PAM50 genes was measured using the nCounter platform. A mutation of the PIK3CA gene was detected in 21.7% of the 803 genotyped tumors. At a median follow-up of 7.7 years, 5-year disease-free survival (DFS) rates were 90.6% for PIK3CA mutated and 86.2% for PIK3CA wild-type tumors [HR, 0.84; 95% confidence interval (CI), 0.56-1.27; P = 0.417]. PIK3CA mutation showed a favorable prognostic impact in the PAM50 HER2-enriched subtype (n = 232): 5-year DFS 91.8% versus 76.1% (log-rank P = 0.049; HR, 0.46; 95% CI, 0.21-1.02). HER2-enriched/PIK3CA mutated versus wild-type tumors showed numerically higher tumor-infiltrating lymphocytes (TIL) and significant upregulation of immune-related genes (including CD8A, CD274, PDCD1, and MYBL2, a proliferation gene involved in immune processes). High TILs as well as the upregulation of PDCD1 and MYBL2 were associated with a significant DFS improvement within the HER2-enriched subtype (HR, 0.82; 95% CI, 0.68-0.99; P = 0.039 for 10% TILs increment; HR, 0.81; 95% CI, 0.65-0.99; P = 0.049 for PDCD1 expression; HR, 0.72; 95% CI, 0.53-0.99; P = 0.042 for MYBL2 expression). PIK3CA mutation showed no prognostic impact in the ShortHER trial. Within the HER2-enriched molecular subtype, patients with PIK3CA mutated tumors showed better DFS versus PIK3CA wild-type, which may be partly explained by upregulation of immune-related genes.