TEST:

nCounter® Breast Cancer 360™ Panel

Background TOPACIO was a phase I/II study evaluating the PARP inhibitor (PARPi) niraparib in combination with the anti-PD-1 antibody pembrolizumab in patients with locally advanced or metastatic triple-negative breast cancer (TNBC, n=55), irrespective of BRCA mutation status. The study protocol and/or other relevant documents received central approval by the Dana-Farber institutional review board and/or relevant competent authorities at each site. All patients supplied written informed consent for their participation in the study.

Median age was 62 (range 39-85); 6(50%) had grade 1, 3(25%) grade 2 and 3(25%) grade 3 tumors; 5 with known protein TP53 immunohistochemical status had wild type TP53. The majority (58%) had mismatch repair (MMR)-proficient disease. Median duration of 1st ET was 6 months (range 2-50 months).

PAM50 and immune-related signatures provide important prognostic information in patients with T1abN0 breast cancer, which may refine the risk assessment in these patients.

Our findings indicate higher AURKA expression in young breast cancer, and associations between high Aurora-A/AURKA and aggressive tumor features, including higher tumor cell proliferation, and shorter survival, in the young. Our findings point to AURKA as a marker for increased DNA damage and DNA repair deficiency and suggest AURKA as a biomarker of clinical relevance in young breast cancer.

Our study contributes new insights into biomarker utility for identifying suitable TNBC therapies and the intercorrelations between genomic, transcriptomic, protein, and cellular biomarkers. Additionally, our rich data resource can be used by other researchers to explore the interplay between DNA, RNA, and protein biomarkers in TNBC.

Exclusion of variants below 5% variant allele frequency was essential to overcome FFPE-induced artefacts. Targeted genomic analyses were feasible in simultaneously extracted DNA/RNA from FFPE material, providing insights for their implementation in clinical trials/cohorts.

The study highlights the potential of specific cytokines and chemokines, in conjunction with TILs, as predictive biomarkers for pCR in patients with TNBC undergoing NAC. Further validation of these results is needed to elucidate their clinical relevance and potential for personalized therapeutic interventions in TNBC.

Adding pertuzumab to neoadjuvant TCH does not significantly correlate with pCR in HER2E. Despite this lack of pCR improvement HER2E pts treated with TCHP showed better EFS irrespective of pathological response. EFS pertuzumab benefit was only observed in stage III or N(+) HER2E pts.

P2; N=46 --> 20 | Active, not recruiting --> Terminated; The enrollment was stopped prematurely due to the lack of funding

The patient clusters provided new insight in the immune cell distribution across tumor subtypes, potentially contributing to survival differences between the clusters and the molecular subtypes and indicating age-related mechanisms improving outcome. Our study confirms the applicability of ROR as a valid prognosticator also in a young breast cancer cohort.

Clinicopathologic features are prognostic beyond 10 years. Conversely, molecular features, such as copy number alterations, TP53 mutations and intrinsic subtype which have early prognostic significance, have little prognostic value after 10 years.

In this pilot study, the molecular and genetic differences suggest that the tumor microenvironment may play a role in treatment outcomes between NHPIs and Asians. Further analysis will be conducted to determine the differences in immune cell infiltration. >*Out of 7 samples.

P2; Trial completion date: Nov 2024 --> May 2024 | Trial primary completion date: Dec 2023 --> Apr 2024

Conclusions This comprehensive analysis strongly suggests that LP has as profound an effect on luminal tumours as chemotherapy, with regard to proliferation decrease, immune attraction and stromal changes associated with tumor response. These results provide rationale for future chemo-sparing studies in high-risk luminal breast cancer.

P=N/A; GEX of AR adds prognostic information for MBC. Our descriptive analyses illuminate the biological differences between MBCs in relation to outcome and metastatic site.

We are the first study to profile immune microenvironment using both transcriptomic and IHC methods. Our study is also unique in using NPBC and BC>2Y patients as control groups for PABC patients. CD8+ T cells are statistically higher in PABC patients than in NPBC patients using either transcriptomic profiling or multiplex IHC analysis.

Combination treatment with onalespib and paclitaxel had an acceptable toxicity profile and showed anti-tumor activity in patients with advanced TNBC. Gene expression analysis of patient tumor samples suggest that TNBCs with greater activation of immune checkpoint pathways and those with proteins dependent on HSP90 activity, including p53 and HER2, may be more susceptible to HSP90 inhibition.ClinicalTrials.gov study identification: NCT02474173

IL20RA and SOX10 represent potential biomarkers for TNBC risk that may serve as a stratification tool for NHB women. The results of this study have the potential to improve assessment and management of TNBC risk among NHB women, thereby contributing significantly to reducing health disparities in breast cancer outcomes.

Our findings reveal significant parallels between ARLI and PPI. Future research will assess how LIFR/pSTAT3 signaling is linked to induction of apoptotic markers in perimenopausal women and will investigate how anomalies in the LIFR/pSTAT3 pathway might contribute to heightened breast cancer risk in women with delayed or incomplete ARLI. This study not only sheds light on the complex biological processes of aging in breast tissue but also opens new avenues for breast cancer risk assessment and prevention strategies.

pILCs are morphologically distinct from cILCs, with higher histologic grade and higher average TILs. Genes more highly expressed in pILCs, including IDO1, GRB7 and CXCL9, have been associated with immune suppression and therapeutic resistance. These alterations are of interest as predictive markers and as potential targets for therapeutic intervention.

pILCs are morphologically distinct from cILCs, with higher histologic grade and higher average TILs. Genes more highly expressed in pILCs, including IDO1, GRB7 and CXCL9, have been associated with immune suppression and therapeutic resistance. These alterations are of interest as predictive markers and as potential targets for therapeutic intervention.

Breast cancers classified as basal-like by PAM50 comprise a histologically heterogeneous group of tumors. Tumors with infiltrating borders are much more likely to be associated with LVI and lymph node metastasis compared with pushing border tumors. Genes more highly expressed in tumors with infiltrative borders include a number of potential therapeutic targets, suggesting unique therapeutic strategies.

Findings from this study show a dynamic range of binding partners for aCT1, many of which regulate gene expression and RNA biology. nCounter analysis shows that a number of pathways are significantly impacted by aCT1, including upregulation of apoptotic factors, leading to the prediction and demonstration that aCT1 can boost the cell death effects of cisplatin and lapatinib in HER2+ breast cancer cells that have become resistant to HER2-targeted agents.

This exploratory analysis of the Neoadjuvant Carboplatin in Triple Negative Breast Cancer (NACATRINE) study aimed to identify the biomarkers of pathological complete response (pCR) in patients with triple-negative breast cancer (TNBC) treated with neoadjuvant chemotherapy (NAC) within the context of a clinical trial...We successfully identified gene expression signatures associated with pCR in pretreatment samples of patients with TNBC treated with NAC. Further investigation of these biomarkers is warranted.

Estrogen signaling may therefore serve as a surrogate to AR signaling during progression and in hormone-refractory disease, particularly in prostate cancer patients with stromal-rich tumors. Collectively, the use of agnostic biomarkers developed for breast cancer stratification has facilitated a precise clinical classification of patients undergoing radical prostatectomy and highlighted the therapeutic potential of targeting estrogen signaling in prostate cancer.

These results illuminate the biological differences between mBC in relation to outcome and metastatic site. Better understanding of the mBC GEX subtypes may open new venues for tailored treatment.

In this trastuzumab-treated early HER2-positive breast cancer cohort, we observed four subgroups with different biological pathway enrichment patterns. The subgroup with the combination of low stromal and low immune biological pathway enrichment was associated with a poorer prognosis than those mainly enriched with either stromal or immune pathways. This study shows the diversity of biological signatures within HER2-positive breast cancer, and results could potentially be used in future studies of HER2 target treatments.

Gene expression data determined using the nCounter BC360 panel was available at baseline from two patient cohorts: 1) the CORALLEEN phase II trial which evaluated neoadjuvant ribociclib plus letrozole vs multi-agent chemotherapy in postmenopausal patients with luminal B by PAM50, HR+/HER2- early BC (Prat et al. A mechanistic model was developed, trained on cell line data, and then used to predict treatment outcome of patients with HR+/HER2-/PAM50 Luminal B BC treated with CDK4/6i plus ET. This approach showed significant association with observed outcome and could be used to assign patients to different response groups, indicating the usefulness of the model as a potential marker for response.

The KENDO trial further supports CDK4/6i+ET use in aggressive CT-naïve HR+/HER2- MBC. Biomarkers of immune activation such as IF tumors, higher TILs and presence of TLS pointed towards better survival outcomes. Genomic immunological features also showed prognostic effect, with differences according to treatment arm and/or the immune process or cell line tracked.

Our study shows that PABC is potentially a clinical and molecular different entity with predominance of the basal-like subtype. Moreover, our results suggest the activation of oncogenic pathways related to cell proliferation, DNA damage repair and p53 mutations which may lead to a clinically more aggressive phenotype for PABC patients. Likewise, the enrichment of BRCAness and HRD signatures found in PABC patients in our study may suggest an increased genetic instability due to a breakdown in the DNA damage repair.

Our findings demonstrate that gene expression patterns can predict the response to neoadjuvant TCHP chemotherapy in HER2+ BC. The functional characterization of 39 DEGs suggests that the tumor microenvironment, including adjacent immune cells, plays a significant role in modulating the response to neoadjuvant chemotherapy in HER2+ BC. Table 1.

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.

Among patients with HER2-neg BC, gene-expression profiling is similar in ER-neg (i.e., < 1%) vs. ER-low tumors with a high prevalence of PAM50 Basal-like tumors and few differentially expressed genes. In both ER-low and ER-int HER2-neg BCs, PAM50 Basal-like subtype is also associated with higher TIL levels.

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. 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.

Expression of FOXA1 is a promising predictive biomarker for tamoxifen effect in ER+/HER2- premenopausal breast cancer. In addition, each of the signatures BC proliferation, Hypoxia, Mast cells, and the GEX of AR, ESR1, and PGR had prognostic value, also after adjusting for established prognostic factors. Trial registration This trial was retrospectively registered in the ISRCTN database the 6th of December 2019, trial ID: https://clinicaltrials.gov/ct2/show/ISRCTN12474687 .

Background Early metabolic change on FDG PET/CT was predictive of response to neoadjuvant trastuzumab/pertuzumab (HP) in TBCRC026, with high negative predictive value (NPV) suggesting a lack of decline in SULmax at cycle 1 day 15 (C1D15) best predicts those who will not achieve pathological complete response (pCR) with HP alone. Conclusions The composite HER2/PET biomarker had high prediction power for pCR, however was not superior to the prediction power of PET/CT alone. These data suggest clinical trials informed by early FDG PET/CT biomarkers warrant further evaluation to personalize breast cancer care.

Methods TACT2 was a phase 3, randomised trial testing adjuvant accelerated versus standard Epirubicin in early breast cancer...Table: 307P Comparing the goodness-of-fit of three mCox models using chi-square, brier score and integrated calibration index Conclusions We identified 4 eTNBC B-grp based on distinct biology which provided more accurate 5-year TTR prediction in addition to ClinPath than TNS. The association of the B-grp with survival for other treatments could be further evaluated.

The study has been conceived and will be conducted according to international and local agreements for ethical research. Ethical approval has been granted by two Ethics Committees in Chile.The results will be disseminated to scientific and lay audiences (publications in scientific journals and conferences, seminars and a website for plain language dissemination).

Our study reported unique characteristics between the four TNBC subgroups and showed the potential use of immune checkpoint and PARP inhibitors in subsets of Thai TNBC patients. Our findings warrant further clinical investigation to validate TNBC's sensitivity to these regimens.

ConclusionImmune function plays a key role in CDK4/6i treatment efficacy. Elevated inflammatory profiles within the tumor but also in the peripheric immune system are associated to limited CDK4/6i clinical efficacy, providing new tools for the clinical management of CDK4/6i treatment.

Our study suggests a key role of tumor immunity in resistance to CDK4/6i, with an additional association of macrophages with worse outcome. The correlation of poor response to CDK4/6i with worse survival suggests its utility as a surrogate biomarker. Further investigation of the use of immunotherapeutic agents in this setting is deserved to improve CDK4/6i response.

Gene-expression profiling of matched primary BCs and BMs shows recurrent gene expression modifications in metastatic samples which might have potential therapeutic implications (e.g. acquisition of HER2-E subtyping and increase in ERBB2 mRNA levels). >