HER2 Subtype Research Articles

Targeting HER2-positive metastatic breast cancer with ARX788, a novel anti-HER2 antibody-drug conjugate in patients whose disease is resistant or refractory to T-DM1, and/or T-DXd, and/or tucatinib-containing regimens.

TPS1112 Background: The overexpression and/or amplification of human epidermal growth factor receptor 2 (HER2) occurs in approximately 20% of breast cancers (BC) and is a major driver of tumor development and progression. This HER2 subtype confers aggressive tumor behavior and the HER2 receptor remains a valuable target for antibodies, bi-specifics, and antibody drug conjugates (ADC). With advances in targeted therapy, patients with HER2-positive breast cancer (HER2+ BC) may experience an improved prognosis, including survival. Novel HER2-targeted therapies are being investigated to overcome drug resistance and to help mitigate adverse events (e.g., cardiotoxicity). ARX788 is a next-generation ADC using a technology platform whereby a HER2 specific monoclonal antibody is conjugated with Amberstatin269 (AS269), a potent cytotoxic tubulin inhibitor. Site-specificity, high homogeneity, and stable covalent conjugation of ARX788 leads to its slow release and prolonged peak of serum pAF-AS269, which may contribute to the lower systemic toxicity and increased targeted delivery of payload to tumor cells at a lower effective dose compared to other HER2 ADCs. Clinical activity has been seen in Phase I HER2 breast and pan-tumor studies. Methods: Trial Design: ACE-Breast-03 (NCT04829604) is a global, phase 2 study designed to assess anticancer activity and safety of ARX788 in patients with metastatic HER2 positive breast cancer. Patients whose disease is resistant or refractory to T-DM1, and/or T-DXd, and/or tucatinib-containing regimens are eligible. Patients must have adequate organ function. Any brain metastases must be radiographically stable without steroid dependence. Efficacy will be assessed using Response Evaluation Criteria in Solid Tumors (RECIST) v1.1 by imaging every 6 weeks on study. Endpoints include objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), overall survival (OS), best overall response (BOR), duration of response (DOR), and time to response (TTR). The safety and tolerability profile will be evaluated. Blood samples will be collected at specified time points to determine serum concentrations of ARX788, total antibody, and metabolite pAF-AS269. Potential predictive and/or prognostic biomarkers at baseline and on-treatment will be analyzed for exploratory purposes. Descriptive statistics will be used to evaluate anticancer activity, safety, and tolerability. The study is currently recruiting patients. Please contact breast03trialinquiry@ambrx.com for additional information. Clinical trial information: NCT04829604.

Triple Negative Breast Cancer: An Analysis of the Subtypes and the Effects of Menopausal Status on Invasive Breast Cancer.

Background: Triple negative breast cancer (TNBC) is a subtype of breast cancer which lacks hormone receptor (HR) expression and HER2 gene amplification and is the most aggressive subtype, with a heterogeneous genetic profile. The aim of this retrospective study was to evaluate the clinical significance of menopausal status in breast cancer cases with TNBC. Methods: Primary breast cancer patients who underwent curative surgery were enrolled in this retrospective study. A total of 5153 invasive breast cancer cases with Stage I–III were analyzed. The distribution of cases according to the menopausal status and subtypes was investigated and the clinicopathological characteristics and prognosis were compared between pre- and postmenopausal TNBC patients. Results: TNBC was frequently seen in postmenopausal patients and Luminal B and Luminal/HER2 subtypes were more common in premenopausal patients. There was no difference in DFS in the Luminal A/B and HER2 subtypes, but a significant difference was seen in the TNBC patients. Premenopausal patients with TNBC frequently had an overexpression of the p53 protein, a significantly higher Ki-67 index value, and a higher nuclear grade. A multivariate analysis revealed that menopausal status, nodal status, and tumor size were significant factors for DFS in TNBC cases. Conclusion: Menopausal status significantly correlates with breast cancer subtypes. TNBC was often seen in postmenopausal patients and these patients tend to have more favorable factors and a better DFS than premenopausal patients. These findings suggest that menopausal status is an important factor for evaluating biology and prognosis in TNBC cases.

Tucatinib has Selective Activity in HER2-Positive Cancers and Significant Combined Activity with Approved and Novel Breast Cancer-Targeted Therapies.

Pharmacologically targeting the HER2 oncoprotein with therapeutics such as the mAb, trastuzumab, provides clinical benefit for patients with HER2-positive (HER2+) cancers. However, a significant number of patients eventually progress on these therapies. Efforts to overcome therapeutic resistance through combination therapy with small-molecule inhibitors of HER2 have been limited by toxicities associated with off-target activity and/or limited efficacy. In this preclinical study, we explore single-agent and combined activity of tucatinib, a novel HER2-selective small-molecule inhibitor. Tucatinib demonstrated potent, selective activity in a panel of 456 human cancer cell lines, with activity restricted to cell lines (breast and non-breast) with HER2-amplification, including models of acquired resistance to trastuzumab. Within the HER2+ population, tucatinib response tracked strongly with HER2-driven signaling. Single-agent tucatinib induced tumor regressions in xenograft models of HER2+ breast cancer and combination with trastuzumab induced a complete and sustained blockade of HER2/PI3K/AKT signaling. Efficacy of the tucatinib/trastuzumab combination matched that induced by current standard-of-care trastuzumab/pertuzumab/docetaxel combination, with the exception that the chemotherapy-sparing tucatinib/trastuzumab combination did not require a dosing holiday to achieve the same efficacy. In xenograft models of HER2+ breast cancer that also express estrogen receptor (ER; HER2+/ER+), tucatinib showed combined efficacy with inhibitors of CDK4/6 and ER, indicating potential novel therapeutic strategies for difficult-to-treat subtypes of HER2+ breast cancer. These data support expanded clinical investigations of tucatinib as a combination partner for other novel and approved targeted therapies for HER2-driven malignancies.

A propensity score-matched analysis of breast-conserving surgery plus whole-breast irradiation versus mastectomy in breast cancer.

Recent observations regarding long-term outcomes among patients with early-stage breast cancer (BC) who underwent breast-conserving surgery (BCS) plus whole-breast irradiation (WBI) or mastectomy are from a small number of registry-based studies. Therefore, these findings may overestimate differences in survival between the two groups, compared with randomized controlled trials conducted in the 1980s. The aim of this study is to compare long-term outcomes and clinicopathologic characteristics between patients treated with BCS + WBI or mastectomy for BC. We performed a propensity score-matched analysis in a cohort of 9710 patients aged < 70years who underwent BCS + WBI or mastectomy without external radiotherapy for a first primary BC (pT1-2, N0-3a) at the European Institute of Oncology between 2000 and 2008. Patients were matched by propensity score. Median follow-up was 8.4years (interquartile range 6.5-10.2). The cumulative incidence of axillary lymph node recurrence at 10years was lower in the BCS + WBI group [2.4% (95% CI, 1.7-3.3%)] than in the mastectomy group [4.4% (95% CI, 3.5-5.5%)] (P = .0005), and the cumulative incidence of contralateral BC was higher in the BCS + WBI group [3.9% (95% CI, 2.8-5.1%)] than in the mastectomy group [2.5% (95% CI, 1.7-3.4%)] (P = .01). Among the 366 patients with HER2 subtype BC, BCS + WBI was associated with a fivefold higher risk [hazard ratio 4.97 (95% CI, 2.28-10.8)] of ipsilateral breast tumor recurrence (IBTR), compared with mastectomy (P < .0001); however, among patients with other BC subtypes, the rates of IBTR were not statistically significantly different. Patients with HER2 subtype BC (T1-2, N0-3) who underwent BCS + WBI had a statistically significantly higher risk of IBTR than patients who underwent mastectomy. Survival was not statistically significantly different between the groups.

Abstract P2-08-22: Correlation of ER (ESR1), PR (PGR), and HER2 (ERBB2) at protein and mRNA levels in operable breast cancer

Abstract Background:. We aimed to analyze the concordance between ER (ESR1), PR (PGR), and HER2 (ERBB2) levels and breast cancer subtyping results obtained by using the immunohistochemistry (IHC) and reverse transcriptase-polymerase chain reaction (RT-PCR) methods and to assess recurrence-free survival (RFS) between subtypes as determined by the two methods. Patients and Methods:. We included a total of 441 operable breast cancer patients, consisting of the training (n = 116), testing (n = 56) and validation (n = 269) cohorts in this study. Protein levels of estrogen receptor (ER) and progesterone receptor (PR) were obtained by using the IHC and that of human epidermal growth factor receptor 2 (HER2) by the IHC/FISH methods. Expression (mRNA) levels of the corresponding genes, ESR1, PGR, and ERBB2, respectively, were determined by the RT-PCR method. We then compared the status of ER (ESR1), PR (PGR), and HER2 (ERBB2) in the training, testing and validation cohorts. We categorized all validation cases into luminal (ER/PR-positive and HER2-negative), HER2 (HER2-positive regardless of ER/PR status), and triple negative (TN: ER-, PR-, and HER2-negative) subtypes accordingly. The concordance of the two methods and RFS estimated by the Kaplan-Meier methods of the three different subtypes were revealed to evaluate the clinical performance. Results:. The concordance rates between the two methods in the validation cohort were 95.1% (Kappa = 0.74) for ER (ESR1), 91.1% (Kappa = 0.67) for PR (PGR), and 93.6% (Kappa = 0.59) for HER2 (ERBB2). Kappa statistic was 0.66 for the resulting luminal, HER2 and TN subtypes. The 5-year RFS was 83.3% for luminal vs. 73.9% for HER2 vs. 48.4% for TN subtypes as determined by the IHC (p = 0.019), and 84.3% vs. 66.3% vs. 54.4% by the RT-PCR method (p = 0.016). Conclusions:. Whereas discordance existed for some cases between the IHC and RT-PCR methods for determination of the ER (ESR1), PR (PGR), and HER2 (ERBB2) status and the resulting subtypes; both the methods showed values in RFS prognosis of the population studied. It is arguable that supplementing the conventional IHC with the molecular method for subtyping of breast cancer may have beneficial clinical implications. Citation Format: Lei Lei, Xiaojia Wang, Skye Hung-Chun Cheng. Correlation of ER (ESR1), PR (PGR), and HER2 (ERBB2) at protein and mRNA levels in operable breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-08-22.

Abstract P4-07-09: Triple negative breast cancer: An analysis of the subtypes and the effects of menopausal status on invasive breast cancer

Abstract Background: Triple negative breast cancer (TNBC) is a subtype of breast cancer which lacks hormone receptor (HR) expression and HER2 gene amplification, and is the most aggressive subtype with a heterogeneous genetic profile. Menopausal status is an important factor when considering endocrine therapy for patients with HR-positive tumors. Breast cancer in younger women can be more aggressive than in older women. Moreover, the menopausal status has limited predictive power for distant recurrence and overall survival (OS) in HR-positive cases. The aim of this retrospective study is to evaluate the clinical significance of menopausal status in breast cancer subtypes, especially TNBC. Methods: Primary breast cancer patients who underwent curative surgery from January 2002 to March 2021 were enrolled in this study. A total of 5153 invasive breast cancer cases with Stage I-III were analyzed. The distribution of cases according to the menopausal status was investigated according to each subtype, and the clinicopathological characteristics and prognosis were compared between pre- and postmenopausal TNBC patients. The factors investigated included nodal status, tumor size, nuclear grade, ER/PgR and HER2 status, p53 overexpression, and the Ki-67 index value. Breast cancer subtypes were categorized based on the immunohistochemistry (IHC) data derived from ER/PgR, HER2 and Ki-67 (cutoff: 20%) in invasive tumors. The disease-free survival (DFS) was compared between menopausal status in each subtype using the Kaplan-Meier and the log-rank test. Cox's proportional hazard model was used to perform univariate and multivariate analyses of the factors related to DFS. The median follow-up period was 95 months. Results:. 1. There were significant differences in menopausal status among the subtypes. TNBC was frequently seen in postmenopausal patients, and Luminal B and Luminal/HER2 subtypes were more common in premenopausal patients. 2. There was no difference in DFS in Luminal A/B and HER2 subtypes, but a significant difference was seen in the TNBC patients (premenopausal patients had a poorer DFS than the postmenopausal patients). 3. There was no significant correlation between menopausal status, tumor size and nodal status in TNBC. On the other hand, premenopausal patients significantly correlated with a higher Ki-67 index value, p53 overexpression and a higher nuclear grade. 4. Moreover, premenopausal patients often received (neo)adjuvant chemotherapy, but there was no significant difference in the pCR rate between the pre- and postmenopausal status. 5. A multivariate analysis revealed that menopausal status, nodal status and tumor size were significant factors for DFS in TNBC. Conclusion: Menopausal status significantly correlates with breast cancer subtypes. TNBC was often seen in postmenopausal patients, and these patients tend to have more favorable factors and a better DFS than premenopausal patients. These findings suggest that menopausal status is an important factor for evaluating the biology and prognosis in TNBC cases. Citation Format: Nobuyuki Arima, Reiki Nishimura, Tomofumi Osako, Yasuhiro Okumura, Masahiro Nakano, Mamiko Fujisue, Hiroko Otsuka. Triple negative breast cancer: An analysis of the subtypes and the effects of menopausal status on invasive breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-07-09.

Abstract P2-08-11: How reliable are biomarkers assessed on a core needle biopsy? A study of paired core needle biopsies and surgical specimens in early breast cancer

Abstract Background: The conventional biomarkers estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG) are used to classify breast cancer into its molecular subtypes, determine prognosis, and guide treatment. A preoperative core needle biopsy (CNB) is used to confirm the diagnosis and invasiveness of a breast lesion and forms the basis for characterizing the tumor in the case of neoadjuvant primary treatment, emphasizing the importance of obtaining reliable biomarker assessment from a diagnostic CNB. Aim: The aim of this study was to determine the similarity between biomarker status assessed on a CNB compared to a medically untreated surgical specimen. Methods: Paired CNB and surgical specimens from 267 patients that were part of the prospective Sweden Cancerome Analysis Network- Breast (SCAN-B) cohort were studied. The concordance for the five biomarkers: ER, PgR, Ki67, HER2 and molecular subtype, between paired CNB and surgical specimen were investigated using immunohistochemistry (IHC) and gene expression-based analytical methods (GEX). IHC data were collected from patient medical records and gene expression was measured by RNA sequencing. Cohen’s kappa and Mcnemar’s test were used to compare the concordance of biomarkers.Results: Moderate to very good levels of concordance were observed between the biomarker status obtained on a CNB compared with the paired surgical specimen for IHC (κappa range 0.474-0.917) and GEX (κappa range 0.528-0.776), respectively. However, a significant drift from low to high Ki67 status and from negative to positive HER2 status between the CNB and surgical specimen was observed when using IHC and GEX, respectively (McNemar p &amp;lt; 0.05 for both comparisons). Moderate to good concordance levels of biomarker status were generally obtained when comparing GEX and IHC status measured from the same type of sample (κappa range 0.484-0.649) except for Ki67 which consistently displayed poor concordance levels between IHC and GEX for both CNB and surgical specimen comparisons (κappa range 0.158-0.198). Notably, a significant shift from positive to negative ER status and high to low Ki67 status was observed when comparing IHC with GEX classification (McNemar p &amp;lt;0.001 for both comparisons). Conclusion: The tissue sampling and the method of biomarker analysis may affect the results of biomarker status and ultimately affect treatment decisions. The implications of using a preoperative CNB to determine biomarker status, prognosis, and treatment choice should be taken into consideration in neoadjuvant treatment settings. Citation Format: Hani Saghir, Srinivas Veerla, Martin Malmberg, Lisa Rydén, Anna Ehinger, Lao Saal, Johan Vallon-Christersson, Åke Borg, Cecilia Hegardt, Ingrid Hedenfalk, Susanne Dieroff-Hay, Christer Larsson, Niklas Loman, Siker Kimbung. How reliable are biomarkers assessed on a core needle biopsy? A study of paired core needle biopsies and surgical specimens in early breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-08-11.

Breast cancer stem cell population in different molecular subtypes of breast cancer.

Breast cancer heterogeneity is well documented and to some extent is attributed to the presence of cancer stem cells (CSCs). Breast cancer stem cells are identified by the presence of cell surface molecule CD44 and absence of CD24. In the present study a flowcytometric analysis was done to study the expression distribution of CSC phenotype of CD44+/CD24-/low, among different molecular subtypes of breast cancer and to find a correlation with clinicopathological features. CSCs were observed in all the molecular subtypes of breast cancer. The highest population of CSCs was noted in luminal B (3.4%), followed by TNBC (1.7%), and Her-2 subtype (1.6%). The least number of CD44+/CD24- cells were seen in Luminal A subgroup (1.3%). Existence of cancer stem cells in all the subtypes may suggest the possibility of failure of current therapies in treatment of patients.

Correlation of ER, PR, and HER2 at the protein and mRNA levels in Asian patients with operable breast cancer.

Breast cancer is the most common cancer and the leading cause of cancer-related deaths in women. The estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) are the important biomarkers in the prognosis of breast cancer, and their expression is used to categorize breast cancer into subtypes. We aimed to analyze the concordance among ER, PR, and HER2 expression levels and breast cancer subtyping results obtained by immunohistochemistry (IHC, for protein) and reverse transcriptase-polymerase chain reaction (RT-PCR, for mRNA) and to assess the recurrence-free survival (RFS) of the different subtypes as determined by the two methods. We compared biomarker expression by IHC and RT-PCR in 397 operable breast cancer patients and categorized all patients into luminal, HER2, and triple-negative (TN) subtypes. The concordance of biomarker expression between the two methods was 81.6% (κ = 0.4075) for ER, 87.2% (κ = 0.5647) for PR, and 79.1% (κ = 0.2767) for HER2. The κ-statistic was 0.3624 for the resulting luminal, HER2, and TN subtypes. The probability of 5-year RFS was 0.78 for the luminal subtype versus 0.77 for HER2 and 0.51 for TN, when determined by IHC (P=0.007); and 0.80, 0.71, and 0.61, respectively, when determined by the RT-PCR method (P=0.008). Based on the current evidence, subtyping by RT-PCR performs similar to conventional IHC with regard to the 5-year prognosis. The PCR method may thus provide a complementary means of subtyping when IHC results are ambiguous.

Obesity in Terms of BMI and BSA in Egyptian Breast Cancer Patients: Can Tumor Behavior Be Predicted?

Background: Obesity is a major health problem worldwide and is involved in etiology of breast cancer. Egypt is ranked among the highest globally in obesity problem. Body mass index (BMI) is the most widely used tool to define obesity. Body surface area (BSA) is another measure used widely in clinical practice, particularly in calculating doses of chemotherapeutic agents. Both Body Surface Area (BSA) and Body Mass Index (BMI) rely on weight and height and can be used as indicators of obesity. Patients and Methods: This is a cross-sectional observational study that was carried out in the department of clinical oncology, Faculty of medicine, Ain Shams University Hospitals. Medical records of patients scheduled for adjuvant chemotherapy were revised regarding age, comorbidity, side of the tumor, stage, and type of the surgery performed. Immunohistochemistry (IHC) to detect ER, PR, and Her2 and molecular subtypes of the tumors was recorded. BMI and BSA were calculated for all patients. Inclusion Criteria: Female patients with newly diagnosed breast cancer, cases that didn’t start the adjuvant treatment, data for IHC available, weight, and height of the patients recorded in the files. Exclusion Criteria: Male breast cancer cases, bilateral cases, metastatic cases, age above 80 years, cases with multiple primaries. Results: The mean age of patients was 48 ± 11 years and 60% of them were premenopausal. The mean weight in Kgs was 81 ± 13 and the mean height in cm was 156 cm ± 5. Mean BMI was 33.8 ± 6.0 and mean BSA was 1.84 ± 0.15. Comorbidities were present in 10.6% of patients. In the studied group of patients, tumors were more common of right side (55.7%), T2 tumor (40%), N1 (40.9%), and stage III in 57.4%. Regarding the hormonal receptor status, most of the patients were ER+ (76.5%), PR+ (66.1%) and Her2? (73.9%). The molecular subtypes were also estimated with HR+ subtype most common in (60%) and Her2+ subtype least common in (10.4%). Neither BMI nor BSA was different based on menopausal status. Tumor characteristics were compared in relation to BMI and BSA, and none of the studied parameters regarding menopausal status, T staging, N staging, TNM staging, ER, PR, Her2 and molecular subtype were significantly associated with BMI or BSA. Receiver operating characteristic (ROC) curve was done for the poor prognostic variables. It was found that both BMI and BSA were poorly predictive for the prognostic tumor characteristics regarding T stage, N stage, Her2 overexpression and TN disease. Conclusion: Obesity is a major health problem among breast cancer patients in Egypt. Both BSA and BMI (as indicators of obesity) in Egyptian breast cancer patients are higher compared to other parts of the world. Both BMI and BSA were poorly predictive of prognostic parameters in breast cancer patients.

Targeting prooxidant MnSOD effect inhibits triple-negative breast cancer (TNBC) progression and M2 macrophage functions under the oncogenic stress

Triple-negative breast cancer (TNBC) has been shown with high mitochondrial oxidative phosphorylation and production of reactive oxygen species (ROS). MnSOD (SOD2) is a mitochondrial antioxidant defense that has been implicated in inhibition of human malignancies. However, the impact of MnSOD on immunosuppressive macrophage functions and TNBC aggressiveness has never been explored. We found here that SOD2high is primarily observed in the aggressive subtypes of HER2(+) breast cancers and TNBCs patients. Further analyses demonstrated that the oncoprotein multiple copies in T-cell malignancy-1 (MCT-1 or MCTS1) induces mitochondrial superoxide dismutase (MnSOD) in TNBC cells by stabilizing the transcription factor Nrf2. SOD2high/MCTS1high expression correlates with a poor prognosis in breast cancer patients. MnSOD in TNBC cells functions as a prooxidant peroxidase that increases mitochondrial ROS (mROS) and adaptation to oxidative stress under the oncogenic effect. Interleukin-6 (IL-6) in the MCT-1 pathway elevates Nrf2/MnSOD and mROS levels. Knockdown of MnSOD inhibits TNBC cell invasion, breast cancer stem cells (BCSCs), mROS, and IL-6 excretion promoted by MCT-1. TNBC cells deficient in MnSOD prevent the polarization and chemotaxis of M2 macrophages but improve the ability of M1 macrophages to engulf cancer cells. Quenching mROS with MitoQ, a mitochondria-targeted non-metal-based antioxidant MnSOD mimics, effectively suppresses BCSCs and M2 macrophage invasion exacerbated by MnSOD and MCT-1. Consistently, silencing MnSOD impedes TNBC progression and intratumoral M2 macrophage infiltration. We revealed a novel stratagem for TNBC management involving targeting the MCT-1 oncogene-induced mitochondrial prooxidant MnSOD pathway, which prevents the development of an immunosuppressive tumor microenvironment.

APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses.

The APOBEC family of cytidine deaminases is one of the most common endogenous sources of mutations in human cancer. Genomic studies of tumors have found that APOBEC mutational signatures are enriched in the HER2 subtype of breast cancer and are associated with immunotherapy response in diverse cancer types. However, the direct consequences of APOBEC mutagenesis on the tumor immune microenvironment have not been thoroughly investigated. To address this, we developed syngeneic murine mammary tumor models with inducible expression of APOBEC3B. We found that APOBEC activity induced antitumor adaptive immune responses and CD4+ T cell-mediated, antigen-specific tumor growth inhibition. Although polyclonal APOBEC tumors had a moderate growth defect, clonal APOBEC tumors were almost completely rejected, suggesting that APOBEC-mediated genetic heterogeneity limits antitumor adaptive immune responses. Consistent with the observed immune infiltration in APOBEC tumors, APOBEC activity sensitized HER2-driven breast tumors to anti-CTLA-4 checkpoint inhibition and led to a complete response to combination anti-CTLA-4 and anti-HER2 therapy. In human breast cancers, the relationship between APOBEC mutagenesis and immunogenicity varied by breast cancer subtype and the frequency of subclonal mutations. This work provides a mechanistic basis for the sensitivity of APOBEC tumors to checkpoint inhibitors and suggests a rationale for using APOBEC mutational signatures and clonality as biomarkers predicting immunotherapy response in HER2-positive (HER2+) breast cancers.

Bayesian multistudy factor analysis for high-throughput biological data

This paper analyzes breast cancer gene expression across seven studies to identify genuine and thus replicable gene patterns shared among these studies. Our premise is that genuine biological signal is more likely to be reproducibly present in multiple studies than spurious signal. Our analysis uses a new modeling strategy for the joint analysis of high-throughput biological studies which simultaneously identifies shared as well as study-specific signal. To this end, we generalize the multi-study factor analysis model to handle high-dimensional data and generalize the sparse Bayesian infinite factor model to this context. We provide strategies for the identification of the loading matrices, common and study-specific. Through extensive simulation analysis, we characterize the performance of the proposed approach in various scenarios and show that it outperforms standard factor analysis in identifying replicable signal in all scenarios considered. The analysis of breast cancer gene expression studies identifies clear replicable gene patterns. These patterns are related to well-known biological pathways involved in breast cancer, such as the ER, cell cycle, immune system, collagen, and metabolic pathways. Some of these patterns are also associated with existing breast cancer subtypes, such as LumA, Her2, and basal subtypes, while other patterns identify novel pathways active across subtypes and missed by hierarchical clustering approaches. The R package MSFA implementing the method is available on GitHub.

Aspects cliniques : Cancers HER2 et atteinte du système nerveux central, que faire en 2021 ?: Central nervous system metastases from HER2 positive breast cancers: what to do in 2021?

Metastatic breast cancer is the second most common cause of brain metastasis (BM), and this problem is particularly marked for the amplified HER2 subtype (HER2+), with a cumulative incidence reaching up to 49 % in the ER-/HER2+ subgroup. Literature review shows that therapeutic progress has been major since the marketing of systemic anti-HER2+ treatments, with life expectancies now relatively unaffected by brain development. The recommended treatments are, on the one hand, specific treatment for brain development and, on the other hand, appropriate systemic treatment. Regarding local treatments, we will always favor surgery when possible, especially for large metastases, and stereotaxic radiotherapy, possibly iterative. One should be wary of whole brain irradiation which has never been shown to improve overall survival, but which is clearly associated with more cognitive toxicities. All the systemic anti-HER2 treatments currently on the market have shown efficacy on BM from HER2+ breast cancer and must therefore be chosen above all on the basis of their potential activity on the systemic disease at the time of cerebral evolution. If BM evolution happen without concomitant systemic progression, and local treatment can control it, it is not recommended to change the current medical treatment. Finally, randomized clinical studies opened to patients with active brain disease are starting to be published. The first of them showed the benefit of the triple combination tucatinib-trastuzumab-capecitabine in this context.

GLO 1 and PKCλ Regulate ALDH1-positive Breast Cancer Stem Cell Survival.

We examined the inhibitory effects of both glyoxalase 1 (GLO 1) and protein kinase C (PKC)λ in aldehyde dehydrogenase 1 (ALDH1)-positive breast cancer stem cells (CSCs). Breast cancer genomics datasets (TCGA, n=593; METABRIC, n=1904) were downloaded and statistically analyzed. The effects of GLO 1 and PKCλ on trypan blue staining and tumor-sphere formation by ALDH1high cells derived from triple negative breast cancer (TNBC) and basal-like breast cancer were examined. GLO 1high, PKCλhigh, and ALDH1A3high tumors were enriched in stage I/II/III/IV samples, associated with the HER2 and TNBC subtypes according to receptor status, and associated with the HER2-enriched and basal-like subtypes according to PAM50. Inhibition of either GLO 1 (TLSC702) or PKCλ (ANF) suppressed tumor-sphere formation and enhanced death in ALDH1high cells. TLSC702 also effectively inhibited tumor-sphere formation and induced death in PKCλ knockout ALDH1high cells. GLO 1 and PKCλ are important for the survival of ALDH1-positive breast CSCs, and may represent potential therapeutic targets for the treatment of ALDH1-positive breast CSCs.

The impact of scan number and its preprocessing in micro-FTIR imaging when applying machine learning for breast cancer subtypes classification

The breast cancer molecular subtype is an important classification to outline the prognostic. Gold-standard assessing using immunohistochemistry adds subjectivity due to interlaboratory and interobserver variations. In order to increase the diagnosis confidence, other techniques need to be examined, where the FTIR spectroscopy imaging allied with machine learning techniques may provide additional and quantitative information regarding the molecular composition. However, the impact of co-added scans acquisition parameter into machine learning classifications still needs better evaluation. In this study, FTIR images of Luminal B and HER2 subtypes were acquired varying the scan number and preprocessing techniques. It was demonstrated a spectral quality improvement when the scan number was increased, decreasing the standard deviation and outliers. Six machine learning models were used to classify the subtypes: Linear Discriminant Analysis, Partial Least Squares Discriminant Analysis, K-Nearest Neighbors, Support Vector Machine, Random Forest and Extreme Gradient Boosting. Best mean accuracy of 0.995 was achieved by Extreme Gradient Boosting model. It was found that all models achieved similar high accuracies with groups b256_064 (256 background and 064 scans), b256_128 and b128_128. Besides assessing the performance of different models, the b256_064 was established as the optimal group due to the minimum acquisition time. Therefore, this work indicates b256_064 for breast cancer subtype classification and also as a basis for other studies using machine learning for cancer evaluation.

From Cellular Infiltration Assessment to a Functional Gene Set-Based Prognostic Model for Breast Cancer.

BackgroundCancer heterogeneity is a major challenge in clinical practice, and to some extent, the varying combinations of different cell types and their cross-talk with tumor cells that modulate the tumor microenvironment (TME) are thought to be responsible. Despite recent methodological advances in cancer, a reliable and robust model that could effectively investigate heterogeneity with direct prognostic/diagnostic clinical application remained elusive.ResultsTo investigate cancer heterogeneity, we took advantage of single-cell transcriptome data and constructed the first indication- and cell type-specific reference gene expression profile (RGEP) for breast cancer (BC) that can accurately predict the cellular infiltration. By utilizing the BC-specific RGEP combined with a proven deconvolution model (LinDeconSeq), we were able to determine the intrinsic gene expression of 15 cell types in BC tissues. Besides identifying significant differences in cellular proportions between molecular subtypes, we also evaluated the varying degree of immune cell infiltration (basal-like subtype: highest; Her2 subtype: lowest) across all available TCGA-BRCA cohorts. By converting the cellular proportions into functional gene sets, we further developed a 24 functional gene set-based prognostic model that can effectively discriminate the overall survival (P = 5.9 × 10−33, n = 1091, TCGA-BRCA cohort) and therapeutic response (chemotherapy and immunotherapy) (P = 6.5 × 10−3, n = 348, IMvigor210 cohort) in the tumor patients.ConclusionsHerein, we have developed a highly reliable BC-RGEP that adequately annotates different cell types and estimates the cellular infiltration. Of importance, the functional gene set-based prognostic model that we have introduced here showed a great ability to screen patients based on their therapeutic response. On a broader perspective, we provide a perspective to generate similar models in other cancer types to identify shared factors that drives cancer heterogeneity.

Drug repositioning based on gene expression data for human HER2-positive breast cancer

Human epidermal growth factor receptor 2 (HER2)-positive breast cancer represents approximately 15–30% of all invasive breast cancers. Despite the recent advances in therapeutic practices of HER2 subtype, drug resistance and tumor recurrence still have remained as major problems. Drug discovery is a long and difficult process, so the aim of this study is to find potential new application for existing therapeutic agents. Gene expression data for breast invasive carcinoma were retrieved from The Cancer Genome Atlas (TCGA) database. The normal and tumor samples were analyzed using Linear Models for Microarray Data (LIMMA) R package in order to find the differentially expressed genes (DEGs). These genes were used as entry for the library of integrated network-based cellular signatures (LINCS) L1000CDS2 software and suggested 24 repurposed drugs. According to the obtained results, some of these drugs including vorinostat, mocetinostat, alvocidib, CGP-60474, BMS-387032, AT-7519, and curcumin have significant functional similarity and structural correlation with FDA-approved breast cancer drugs. Based on the drug-target network, which consisted of the repurposed drugs and their target genes, the aforementioned drugs had the highest degrees. Moreover, the experimental approach verified curcumin as an effective therapeutic agent for HER2 positive breast cancer. Hence, our work suggested that some repurposed drugs based on gene expression data can be noticed as potential drugs for the treatment of HER2-positive breast cancer.

Clustering subtypes of breast cancer by combining immunohistochemistry profiles and metabolism characteristics measured using FDG PET/CT

BackgroundThe aim of this study was to investigate the effect of combining immunohistochemical profiles and metabolic information to characterize breast cancer subtypes.MethodsThis retrospective study included 289 breast tumors from 284 patients who underwent preoperative 18 F-fluorodeoxyglucose (FDG) positron emission tomography/ computed tomography (PET/CT). Molecular subtypes of breast cancer were classified as Hormonal, HER2, Dual (a combination of both Hormonal and HER2 features), and triple-negative (TN). Histopathologic findings and immunohistochemical results for Ki-67, EGFR, CK 5/6, and p53 were also analyzed. The maximum standardized uptake value (SUV) measured from FDG PET/CT was used to evaluate tumoral glucose metabolism.ResultsOverall, 182, 24, 47, and 36 tumors were classified as Hormonal, HER2, Dual, and TN subtypes, respectively. Molecular profiles of tumor aggressiveness and the tumor SUV revealed a gradual increase from the Hormonal to the TN type. The tumor SUV was significantly correlated with tumor size, expression levels of p53, Ki-67, and EGFR, and nuclear grade (all p < 0.001). In contrast, the tumor SUV was negatively correlated with the expression of estrogen receptors (r = − 0.234, p < 0.001) and progesterone receptors (r = − 0.220, p < 0.001). Multiple linear regression analysis revealed that histopathologic markers explained tumor glucose metabolism (adjusted R-squared value 0.238, p < 0.001). Tumor metabolism can thus help define breast cancer subtypes with aggressive/adverse prognostic features.ConclusionsMetabolic activity measured using FDG PET/CT was significantly correlated with the molecular alteration profiles of breast cancer assessed using immunohistochemical analysis. Combining molecular markers and metabolic information may aid in the recognition and understanding of tumor aggressiveness in breast cancer and be helpful as a prognostic marker.

Chemotherapy of HER2- and MDM2-Enriched Breast Cancer Subtypes Induces Homologous Recombination DNA Repair and Chemoresistance.

Simple SummaryMDM2 is a protein responsible for negative regulation of the p53 tumor suppressor. In addition, MDM2 exhibits chaperone-like properties similar to the HSP90 molecular chaperone. Multiple studies revealed that MDM2 is deeply involved in cancer development and progression. Some recently published results indicate that the role of MDM2 in DNA repair inhibition is more complex than previously thought. We show that MDM2 is directly involved in the homologous recombination DNA repair, and its chaperone-like activity is crucial for this function. The DNA repair inhibition is a result of inefficient MDM2 dissociation from the NBN protein complex. When cancer cells are treated with chemotherapy, MDM2 can be easily released from the interaction and degraded, resulting in effective homologous recombination DNA repair, which translates into the acquisition of a chemoresistant phenotype by the tumor. This knowledge may allow for identification of the patients that are at particular risk of tumor chemoresistance. Analyzing the TCGA breast cancer database, we discovered that patients with the HER2 cancer subtype and overexpression of MDM2 exhibited decreased post-treatment survival. Inhibition of MDM2 expression in the SKBR3 cell line (HER2 subtype) diminished the survival of cancer cells treated with doxorubicin, etoposide, and camptothecin. Moreover, we demonstrated that inhibition of MDM2 expression diminished DNA repair by homologous recombination (HR) and sensitized SKBR3 cells to a PARP inhibitor, olaparib. In H1299 (TP53−/−) cells treated with neocarzinostatin (NCS), overexpression of MDM2 WT or E3-dead MDM2 C478S variant stimulated the NCS-dependent phosphorylation of ATM, NBN, and BRCA1, proteins involved in HR DNA repair. However, overexpression of chaperone-dead MDM2 K454A variant diminished phosphorylation of these proteins as well as the HR DNA repair. Moreover, we demonstrated that, upon NCS treatment, MDM2 K454A interacted with NBN more efficiently than MDM2 WT and that MDM2 WT was degraded more efficiently than MDM2 K454A. Using a proliferation assay, we showed that overexpression of MDM2 WT, but not MDM2 K454A, led to acquisition of resistance to NCS. The presented results indicate that, following chemotherapy, MDM2 WT was released from MDM2-NBN complex and efficiently degraded, hence allowing extensive HR DNA repair leading to the acquisition of chemoresistance by cancer cells.