Breast Cancer Tissue Microarrays Research Articles

Knock-out of CD73 delays the onset of HR-negative breast cancer by reprogramming lipid metabolism and is associated with increased tumor mutational burden

ObjectiveCD73 (ecto-5′-nucleotidase, NT5E), a cell-surface enzyme converting 5′-AMP to adenosine, is crucial for cancer progression. However, its role in the tumorigenesis process remains mostly obscure. We aimed to demonstrate CD73's role in breast cancer (BC) tumorigenesis through metabolic rewiring of fatty acid metabolism, a process recently indicated to be regulated by BC major prognostic markers, hormone receptors (HR) for estrogen (ER), and progesterone (PR). MethodsA murine model of chemically induced mammary gland tumorigenesis was applied to analyze CD73 knock-out (KO)-induced changes at the transcriptome (RNA-seq), proteome (IHC, WB), and lipidome (GC-EI-MS) levels. CD73 KO-induced changes were correlated with scRNA-seq and bulk RNA-seq data for human breast tissues and BCs from public collections and confirmed at the proteome level with IHC or WB analysis of BC tissue microarrays and cell lines. ResultsCD73 KO delayed the onset of HR/PR-negative mammary tumors in a murine model. This delay correlated with increased expression of genes related to biosynthesis and β-oxidation of fatty acids (FAs) in the CD73 KO group at the initiation stage. STRING analysis based on RNA-seq data indicated an interplay between CD73 KO, up-regulated expression of PR-coding gene, and DEGs involved in FA metabolism, with PPARγ, a main regulator of FA synthesis, as a main connective node. In epithelial cells of mammary glands, PPARγ expression correlated with CD73 at the RNA level. With cancer progression, CD73 KO increased the levels of PUFAn3/6 (polyunsaturated omega 3/6 FAs), known ligands of PPARγ and target for lipid peroxidation, which may lead to oxidative DNA damage. It correlated with the downregulation of genes involved in cellular stress response (Mlh1, Gsta3), PR–or CD73-dependent changes in the intracellular ROS levels and expression or activation of proteins involved in DNA repair or oxidative stress response in mammary tumor or human BC cell lines, increased tumor mutational burden (TMB) and genomic instability markers in CD73 low HR-negative human BCs, and the prolonged onset of tumors in the CD73 KO HR/PR-negative group. ConclusionsCD73 has a significant role in tumorigenesis driving the reprogramming of lipid metabolism through the regulatory loop with PR and PPARγ in epithelial cells of mammary glands. Low CD73 expression/CD73 KO might enhance mutational burden by disrupting this regulatory loop, delaying the onset of HR-negative tumors. Our results support combining therapy targeting the CD73-adenosine axis and tumor lipidome against HR-negative tumors, especially at their earliest developmental stage.

Systematic characterization of the expression, prognosis and immune characteristics of PLOD family genes in breast cancer.

The expression patterns and prognostic value of Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD) family genes in breast cancer remain to be elucidated. The expression levels, prognostic value, and biological function of PLODs were determined using Oncomine, cBioPortal, GEPIA, Timer, UALCAN, PrognoScan, GeneMANIA, Metascape, and breast cancer tissue microarrays. The expressions of PLOD1 and PLOD3 were upregulated in breast cancer tissues, indicating worse clinical stages. High expression levels of PLOD family genes were associated with worse disease-free survival and distant metastasis-free survival, while high expression levels of PLOD1 and PLOD3 were related to worse overall survival in all breast cancer patients. The levels of PLOD family genes were all significantly higher in the age ≤51 y group, HR-negative patients, and triple negative breast cancer (TNBC) patients. They are associated with tumor-infiltrating immune cells (TIICs), including CD4+ T cells, CD8+ T cells, B cells, macrophages, neutrophils, and dendritic cells. According to co-expression gene analysis and functional enrichment, they are associated with protein hydroxylation, collagen biosynthesis and modifying enzymes, collagen metabolism, RNA splicing, extracellular matrix organization, VEGFA-VEGFR2 signaling pathway, and skeletal system development. Immunohistochemistry showed that the expressions of all PLOD family genes were significantly elevated in breast cancer tissues. PLOD1 expression was positively correlated with ER, TNBC status, and tumor grade. PLOD2 expression was positively connected with Ki-67 status. PLOD3 expression was positively related with age and tumor grade. PLOD family genes are novel potential prognostic biomarkers for breast cancer, and targeting PLOD inhibitors might be an effective strategy for breast cancer therapy.

TSP50 facilitates breast cancer stem cell-like properties maintenance and epithelial-mesenchymal transition via PI3K p110α mediated activation of AKT signaling pathway

BackgroundStudies have confirmed that epithelial-mesenchymal transition (EMT) and cancer stem cell (CSC)-like properties are conducive to cancer metastasis. In recent years, testes-specific protease 50 (TSP50) has been identified as a prognostic factor and is involved in tumorigenesis regulation. However, the role and molecular mechanisms of TSP50 in EMT and CSC-like properties maintenance remain unclear.MethodsThe expression and prognostic value of TSP50 in breast cancer were excavated from public databases and explored using bioinformatics analysis. Then the expression of TSP50 and related genes was further validated by quantitative RT-PCR (qRT-PCR), Western blot, and immunohistochemistry (IHC). In order to investigate the function of TSP50 in breast cancer, loss- and gain-of-function experiments were conducted, both in vitro and in vivo. Furthermore, immunofluorescence (IF) and immunoprecipitation (IP) assays were performed to explore the potential molecular mechanisms of TSP50. Finally, the correlation between the expression of TSP50 and related genes in breast cancer tissue microarray and clinicopathological characteristics was analyzed by IHC.ResultsTSP50 was negatively correlated with the prognosis of patients with breast cancer. TSP50 promoted CSC-like traits and EMT in both breast cancer cells and mouse xenograft tumor tissues. Additionally, inhibition of PI3K/AKT partly reversed TSP50-induced activation of CSC-like properties, EMT and tumorigenesis. Mechanistically, TSP50 and PI3K p85α regulatory subunit could competitively interact with the PI3K p110α catalytic subunit to promote p110α enzymatic activity, thereby activating the PI3K/AKT signaling pathway for CSC-like phenotypes maintenance and EMT promotion. Moreover, IHC analysis of human breast cancer specimens revealed that TSP50 expression was positively correlated with p-AKT and ALDH1 protein levels. Notably, breast cancer clinicopathological characteristics, such as patient survival time, tumor size, Ki67, pathologic stage, N stage, estrogen receptor (ER) and progesterone receptor (PR) levels, correlated well with TSP50/p-AKT/ALDH1 expression status.ConclusionThe effects of TSP50 on EMT and CSC-like properties promotion were verified to be dependent on PI3K p110α. Together, our study revealed a novel mechanism by which TSP50 facilitates the progression of breast cancer, which can provide new insights into TSP50-based breast cancer treatment strategies.

Fit-for-Purpose Ki-67 Immunohistochemistry Assays for Breast Cancer

New therapies are being developed for breast cancer, and in this process, some “old” biomarkers are reutilized and given a new purpose. It is not always recognized that by changing a biomarker’s intended use, a new biomarker assay is created. The Ki-67 biomarker is typically assessed by immunohistochemistry (IHC) to provide a proliferative index in breast cancer. Canadian laboratories assessed the analytical performance and diagnostic accuracy of their Ki-67 IHC laboratory-developed tests (LDTs) of relevance for the LDTs’ clinical utility.Canadian clinical IHC laboratories enrolled in the Canadian Biomarker Quality Assurance Pilot Run for Ki-67 in breast cancer by invitation. The Dako Ki-67 IHC pharmDx assay was employed as a study reference assay. The Dako central laboratory was the reference laboratory. Participants received unstained slides of breast cancer tissue microarrays with 32 cases and performed their in-house Ki-67 assays. The results were assessed using QuPath, an open-source software application for bioimage analysis. Positive percent agreement (PPA, sensitivity) and negative percent agreement (NPA, specificity) were calculated against the Dako Ki-67 IHC pharmDx assay for 5%, 10%, 20%, and 30% cutoffs.Overall, PPA and NPA varied depending on the selected cutoff; participants were more successful with 5% and 10%, than with 20% and 30% cutoffs. Only 4 of 16 laboratories had robust IHC protocols with acceptable PPA for all cutoffs. The lowest PPA for the 5% cutoff was 85%, for 10% was 63%, for 20% was 14%, and for 30% was 13%. The lowest NPA for the 5% cutoff was 50%, for 10% was 33%, for 20% was 50%, and for 30% was 57%.Despite many years of international efforts to standardize IHC testing for Ki-67 in breast cancer, our results indicate that Canadian clinical LDTs have a wide analytical sensitivity range and poor agreement for 20% and 30% cutoffs. The poor agreement was not due to the readout but rather due to IHC protocol conditions. International Ki-67 in Breast Cancer Working Group (IKWG) recommendations related to Ki-67 IHC standardization cannot take full effect without reliable fit-for-purpose reference materials that are required for the initial assay calibration, assay performance monitoring, and proficiency testing.

Abstract PO3-13-11: Quantitative Multiplex Immunofluorescence Assay for TROP2 and HER2 Expression in Breast Cancer: Towards Guiding Patient Selection for Antibody Drug Conjugate Therapies

Abstract Emerging antibody drug conjugate (ADC) therapies targeting human trophoblast cell-surface antigen (TROP2) and human epidermal growth factor receptor 2 (HER2) are transforming the treatment landscape for breast cancer. Sacituzumab govitecan (SG) and trastuzumab deruxtecan (T-DXd) have gained approval for an overlapping set of "HER2-low" metastatic breast cancers, including hormone receptor (HR)-positive HER2 non-amplified and "triple-negative" subtypes. Nevertheless, the optimal selection of patients and treatment sequencing for these ADC therapies remains a clinical challenge. Clinical trial objective response rates to SG are approximately 30%, compared to 30-90% for T-DXd depending on HER2 expression levels. While both drugs are thought to be targeted therapies, the value of measuring the target and the best methods to do so are still not established. We believe that quantitative measurement of TROP2 and HER2 antigen expression levels could establish thresholds for responders, enabling more effective patient selection for ADC therapies. Here, we present a TROP2, high-sensitivity HER2, and cytokeratin (CK) quantitative immunofluorescence (QIF) multiplex assay. Using a ten-cell line standard array and proteomic mass spectrometry, we can convert tumor compartment QIF intensity to protein concentration in fmol/mm2 for tissue specimens. Anti-HER2, anti-TROP2 antibodies, and fluorescence detection systems were titrated and combined to maximize signal-to-noise ratio on our cell line standard array and breast cancer tissue microarrays (TMA). The multiplex assay was designed for automated slide stainers (Leica BOND Rx) and fluorescence slide scanning (Rarecyte CyteFinder II HT). We perform our analyses in QuPath using an image processing plugin developed for automated QIF/IHC analysis (Qymia). Reproducible TROP2 and HER2 QIF scoring (R² > 0.95) was achieved across multiple staining batches using serial sections of breast cancer TMAs and cell standard arrays. This assay has a TROP2 linear range between 0.63 - 9.17 fmol/mm2 (about 1 million TROP2 receptors/cell) and HER2 linear range between 0.09 - 0.565 fmol/mm2 (about 60,000 HER2 receptors/cell). We then applied this multiplex assay to two serial retrospective primary breast cancer cohorts from Yale University to quantitatively measure TROP2 and HER2 expression (338 clinical cases). We find a weak negative correlation between TROP2 and HER2 expression in our breast cancer cohorts (Pearson r = -0.14, p = 0.0097, n = 338). TROP2 expression levels were above the limit of detection (LOD) in 90.2% of cases, with 4.1% exceeding the limit of linearity (LOL), and a mean TROP2 expression of 4.05 fmol/mm2. For HER2, 67.2% of cases were above the LOD, with 7.1% exceeding the LOL, and a mean HER2 expression of 0.186 fmol/mm2. Both TROP2 and HER2 were below the LOD in 3.0% of cases, which we define as “negative”. We found 29.9% expressed TROP2 and were HER2-negative, and 6.8% expressed HER2 and were TROP2-negative. Our future studies will aim to quantitatively define expression thresholds for T-DXd and SG response with the goal to produce a clinical grade assay for ADC patient selection and determine the value of the assay to help select which ADC to give first. HER2 and TROP2 protein expression summary in Yale breast cancer cohort Table 1: Summary of HER2 and TROP2 protein expression levels in serial retrospective primary breast cancer cohort of 338 cases using our high-sensitivity HER2 and TROP2 multiplex immunofluorescent assay Citation Format: Charles Robbins, Mengni He, Revekka Khaimova, Katherine Bates, Nay Nwe Nyein Chan, Daniel Liebler, Regan Fulton, David Rimm. Quantitative Multiplex Immunofluorescence Assay for TROP2 and HER2 Expression in Breast Cancer: Towards Guiding Patient Selection for Antibody Drug Conjugate Therapies [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-13-11.

Abstract PO3-13-03: RNAScope: a practical approach and promising alternative to immunohistochemistry to quantify HER2 expression in breast cancer

Abstract T-DXd has been approved by the FDA to treat patients with metastatic HER2-low and -positive breast cancer. The utility of current HER2 immunohistochemistry (IHC) assays in evaluating HER2-low tumors is not clear. A simple and objective method to evaluate HER2 expression in breast cancer is urgently needed. RNAScope can detect HER2 RNA levels by in situ hybridization using one regular unstained FFPE slide and processed using the Leica BOND-III autostainer that is readily available in many clinical laboratories. RNA level detected by RNAScope can be quantified by dots/cell using publicly available software. Therefore, RNAScope is a practical assay and could be a promising alternative to IHC to quantify HER2 levels in breast cancer. We evaluated HER2 levels in 605 breast cancer tissue microarray cores using RNAScope and the two most commonly used FDA approved HER2 IHC assays: Ventana PATHWAY (PATHWAY) and Dako HercepTest (HercepTest). Clinical data were available for 505 cores from 347 patients. RNA level (dots/cell) by RNAScope was quantified using publicly available software QuPath. IHC assays were scored as 0, ultralow (UL, >0% but ≤10% incomplete membranous staining), 1+, 2+ and 3+. In addition, HER2 protein levels (AQUA protein level) were quantified from 100 cores through regression analysis, using AQUA score against cell line arrays with pre-calibrated HER2 protein levels determined by mass spectrometry. We used ANOVA to assess the differences in RNAScope results among the five IHC scores, and linear regressions to correlate RNAScope with HER2 AQUA protein levels. We finally evaluated 41 RNAScope whole-slide images (IHC 1+: n=5; 2+: n=26; 3+: n=10) of metastatic tumors from 31 patients treated with T-DXd. No significant differences of RNAScope results were observed among the 0, UL, and 1+ cores in both IHC assays, indicating the current IHC assays cannot differentiate HER levels in HER2-low tumors. However, statistically significant differences (p < 0.0001) were found among the IHC 1+, 2+, and 3+ cores and higher RNAScope dots/cell was associated with higher stage of the tumors. There was a strong correlation (R2 = 0.610) between the RNAScope results and quantitative HER2 AQUA protein level in the 100 cores. There were significantly higher HER2 RNA levels in the 41 metastatic biopsies with higher IHC scores (p < 0.05). When we used RNAScope to measures HER2 levels in metastases right before T-DXd treatment, there was numerically (p=0.881) higher HER2 RNA levels in responders (5.60±8.82 dots/cell) vs non-responders (5.20±5.31). Interestingly, the HER2 RNA levels in bone metastases was statistically higher (p=0.030) in non-responders (5.24±2.87, n=3) than in responders (1.55±0.81, n=5); although number of patients was low. For the non-bone metastases (esophagus, lymph node, liver, brain, lung), HER2 RNAScope values were numerically higher (p=0.261) in responders (9.65±2.87, n=5) than non-responders (5.19±5.74, n=15). In these non-bone metastatic cases, the response rates by IHC scores were 100% in 1+ cases, 24% in 2+ and 33% in 3+. When we used AI assisted categories based on RNAScope results, the response rates were 20% in RNAScope 1+ cases, 20% in 2+, 50% in 3+ cases. Our study shows that current IHC assays are unable to differentiate HER2 levels between IHC 0 and 1+ breast cancer cases, which is a critical issue in properly identifying patients who will benefit from T-DXd treatment. RNAScope results strongly correlate with HER2 protein levels and showed similar RNA levels among IHC 0 and 1+ cases. RNAScope is a simple and objective assay to quantify HER2 levels by dots/cell using publicly available software and may help better identify which patients benefit from T-DXd treatment. Other factors besides HER2 level may also contribute to the response rate in patients treated with T-DXd. RNAScope results in association with immunohistochemistry (IHC) scores by PATHWAY, HercepTest, and in biopsies from patients treated with T-DXd (T-DXd cohort). XX XX No significant (ns) difference of RNAScope dots/cell were seen among 0, UL and 1+ cases by both PATHWAY and HercepTest assays. There were significant differences of dots/cell comparing 1+, 2+ and 3+ cases. Note: ns not significant (p>0.05), * p<0.05, *** p<0.001, **** p<0.0001 Citation Format: Xiaoxian Li, Ji-Hoon Lee, Yuan Gao, Jilun Zhang, Katherine Bates, David Rimm, Huina Zhang, Geoffrey Smith, Diane Lawson, Jane Meisel, Jenny Chang, Lei Huo. RNAScope: a practical approach and promising alternative to immunohistochemistry to quantify HER2 expression in breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-13-03.

Abstract PO5-24-08: Differential exploitation of Cation Transport Regulator homolog 1 (CHAC1) by Wild-type and mutant p53

Abstract Background: Cancer cells are constantly exposed to harsh conditions like nutrient deprivation, hypoxia, and calcium imbalance leading to the induction of UPR. In its early phase, UPR aims to restore homeostasis while prolonged stress leads to induction of apoptosis. Thus, it is not surprising to observe that expression of the UPR components has been reported to both promote as well as suppress tumorigenesis. Studies have shown that Cation transport regulator homolog 1 (CHAC1) plays a dual role in cancer progression. The objective of the present study is to investigate the p53 mediated regulation of CHAC1 in breast cancer. Methods: We initially subjected a breast cancer tissue microarray (TMA) to immunohistochemistry (IHC) with p53 and CHAC1 specific antibody. We further did in vitro experiments like western blotting, qRT-PCR to see the expression of CHAC1 when wild type (WT) p53 was either induced using camptothecin (CPT) and Nutlin-3 in WT p53 expressing breast cancer cells or by the ectopic WT and mutant p53 transfection in null p53 breast cancer cells (MDA-MB-157). The Chromatin immunoprecipitation (ChIP) assay was done to find a potential binding site of p53 on CHAC1 promoter. Further, in vitro study was done to elucidate a potential role of CHAC1 in cell proliferation. Results: The IHC staining analysis revealed that there was no significant difference in the CHAC1 expression between high and low p53 staining tissue cores as high CHAC1 staining was observed in both cases. Further, in vitro analysis reinforced the findings of CHAC1 in TMAs as cell line studies showed that both forms of p53 had enhancing effect on CHAC1 levels. Upon induction of WT p53 and/or ectopic transfection of WT and mutant p53, we observed that CHAC1 levels were upregulated in a dose dependent manner. ChIP assay revealed that while WT p53 occupies the promoter region of the CHAC1 gene to induce its expression, mutant p53 may be inducing CHAC1 expression through an unknown mediator. These observations provide the basis that CHAC1 may be a novel transcriptional target of p53. Ectopic transfection of WT and mutant 53 showed opposite effect on cellular proliferation as evident from BrdU cellular proliferation assay in MDA-MB-157 cells. Further, we showed that CHAC1 enhanced breast cancer cell proliferation possibly via upregulation of PI3K/Akt/mTOR pathway and may likely be a player in angiogenesis as shown by in vitro angiogenesis assay. Conclusion: Taken together, the data from present study suggests that the effect of CHAC1 on cellular proliferation was associated with the status of p53 in breast cancer cells. The results suggest a plausible explanation for the differential behavior of CHAC1 in tumorigenesis. Citation Format: Vikrant Mehta, Harish Chander. Differential exploitation of Cation Transport Regulator homolog 1 (CHAC1) by Wild-type and mutant p53 [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 PO5-24-08.

IFI30 as a key regulator of PDL1 immunotherapy prognosis in breast cancer

BackgroundIFI30 is a lysosomal thiol reductase involved in antigen presentation and immune regulation in various cancers, including breast cancer. Despite its known involvement, the precise mechanism, function, and relationship with the PD-L1 axis and immune response remain unclear. MethodsWe conducted an extensive investigation into IFI30 mRNA expression in breast cancer utilizing data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Furthermore, we characterized IFI30 mRNA expression across various cell types using publicly available single-cell RNA sequencing datasets, and assessed protein expression through immunohistochemistry using an in-house breast cancer tissue microarray. Functional experiments were performed to elucidate the effects of IFI30 overexpression on PD-L1 expression and inhibitory efficacy in both macrophages and breast tumor cells. ResultsOur study unveiled a marked upregulation of IFI30 expression in breast cancer tissues compared to their normal counterparts, with notable associations identified with tumor stage and prognosis. Additionally, IFI30 expression demonstrated significant correlations with various immune-related signaling pathways, encompassing peptide antigen binding, cytokine binding, and MHC class II presentation. Notably, breast cancer samples exhibiting high IFI30 expression in tumor cells displayed high PD-L1 expression on corresponding cells, alongside a diminished ratio of CD8 + T cell infiltration within the tumor microenvironment. Furthermore, ectopic knockdown of IFI30 in both tumor cells and macrophages resulted in a reduction of PD-L1 expression, while conversely, overexpression of IFI30 led to an increase in PD-L1 expression. ConclusionsThis study offers new insights into the involvement of IFI30 in breast cancer, elucidating its interplay with the PD-L1 axis and immune response dynamics. Our findings suggest that modulation of the IFI30-PD-L1 axis could serve as a promising strategy for regulating T cells infiltration in breast cancer thus treating breast cancer.

Elongin B promotes breast cancer progression by ubiquitinating tumor suppressor p14/ARF

Elongin B (ELOB), a pivotal element in the ELOB/c-Cullin2/5-SOCS-box E3 ubiquitin-protein ligase complex, plays a significant role in catalyzing the ubiquitination and subsequent degradation of a broad spectrum of target proteins. Notably, it is documented to facilitate these processes. However, the regulatory role of ELOB in breast cancer remains ambiguous. In this study, through bio-informatic analysis of The Cancer Genome Atlas and Fudan University Shanghai Cancer Center database, we demonstrated that ELOB was over-expressed in breast cancer tissues and was related to unfavorable prognosis. Additionally, pathway enrichment analysis illustrated that high expression of ELOB was associated with multiple cancer promoting pathways, like cell cycle, DNA replication, proteasome and PI3K − Akt signaling pathway, indicating ELOB as a potential anticancer target. Then, we confirmed that both in vivo and in vitro, the proliferation of breast cancer cells could be significantly suppressed by the down-regulation of ELOB. Mechanically, immunoprecipitation and in vivo ubiquitination assays prompted that, as the core element of Cullin2-RBX1-ELOB E3 ligase (CRL2) complex, ELOB regulated the ubiquitination and the subsequent degradation of oncoprotein p14/ARF. Moreover, the anticancer efficacy of erasing ELOB could be rescued by simultaneous knockdown of p14/ARF. Finally, through analyzing breast cancer tissue microarrays and western blot of patient samples, we demonstrated that the expression of ELOB in tumor tissues was elevated in compared to adjacent normal tissues. In conclusion, ELOB is identified to be a promising innovative target for the drug development of breast cancer by promoting the ubiquitination and degradation of oncoprotein p14/ARF.Graphical headlightsELOB is highly expressed in breast cancer.High ELOB levels were positively associated with poor prognosis.ELOB promotes p14/ARF degradation as part of the Cullin2-RBX1-ELOB E3 ligase complex.ELOB is a promising biomarker for breast cancer.Graphical

Abstract 5591: ARID domain containing BAF subunits exhibit neomorphism: Have we identified the new Achilles heel in cancer

Abstract The SWI/SNF chromatin remodeler utilizes energy of ATP hydrolysis to slide or evict nucleosomes or histones, respectively, thus enabling nuclear processes by driving an ‘open’ chromatin architecture. The mammalian SWI/SNF, also termed the BrG1/Brm associated factor (BAF) complex, is the major chromatin remodeler in ontogeny and adult life. Three major BAF complexes namely canonical (cBAF), polybromo (pBAF), and non-canonical (ncBAF) have been studied. BAF components, classified as a tumor suppressors, exhibit frequent mutations in cancers. Though, studies have evaluated functional roles of BAF subunits, very few attempted to study BAF mutations identified across cancer types. In our previous studies, we identified tumor specific mutations in the gene encoding ‘A-T rich interaction domain containing 1B’ (ARID1B), within its nuclear localization signal (NLS). NLS-inactivated ARID1B exhibited cytoplasmic localization and promoted tumorigenesis by activating the ERK and Wnt/β-catenin pathways. More recently, we detected inactivating mutations in the gene encoding ARID2, a component of the pBAF complex and an ARID1B paralogue. We now present detailed characterization of tumor-specific ARID2 truncations that were presumed to be inactivating in nature. One such truncation mutation viz. p.Ser989fsArg21*, identified in our previous study, is expected to yield an ARID2 protein truncating at amino acid position 1010 (as against the full length of 1835 amino acids). Scrutiny of The Cancer Genome Atlas cBioPortal and Cancer Cell Line Encyclopedia mutation data bases revealed several ARID2 mutations expected to truncate the protein around the 1010 position. Surprisingly, ectopic expression of truncated ARID2 forms promoted oncogenic function in both ARID2 proficient and deficient backgrounds, thus validating a neomorphic gain of function for the truncated protein. Fluorescence based intracellular localization assays revealed a surprising cytoplasmic localization of truncated ARID2. Further, we mapped the ARID2 NLS by in silico analysis followed by evaluation of several deletion constructs, to be located at 1488-1518 position; thus, explaining the cytoplasmic localization of ARID2 forms truncating around 1010 position. Further, truncated ARID2 was unable to bind other pBAF components and did not sequester other pBAF components to the cytoplasm, in both ARID2 proficient and deficient cells. Tandem Affinity Purification Mass-spectrometry revealed putative interaction partners for truncated ARID2; analysis is currently underway to reveal the mechanism of tumorigenic induction exhibited by truncated ARID2. Immunohistochemistry on colorectal and breast cancer tissue microarrays revealed ARID2 cytoplasmic localization in a significant fraction of samples. We have discovered a novel YIN-YANG function of BAF components expected to yield efficient therapeutic options in cancer. Citation Format: Sanjana Sarkar, Murali Dharan Bashyam. ARID domain containing BAF subunits exhibit neomorphism: Have we identified the new Achilles heel in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5591.

Evidence for the presence of Borrelia burgdorferi in invasive breast cancer tissues.

Borrelia burgdorferi, the causative agent of Lyme disease, has recently been demonstrated to infect andenhance the invasive properties of breast cancer cells, while also influencing the expression of inflammatory chemokines (CXCL8 and CXCL10). This study investigates the presence of B. burgdorferi in invasive breast cancer tissues using commercially available, FDA-approved breast cancer tissue microarrays consisting of 350 ductal, 32 lobular, and 22 intraductal invasive breast carcinomas, alongside 29 normal breast tissues. Employing fluorescent immunohistochemical staining and high-resolution imaging, the findings revealed that approximately 20% of invasive lobular and ductal carcinomas, followed by 14% of intraductal carcinomas, tested positive for B. burgdorferi, while all normal breast tissues tested negative. PCR analysis further confirmed the presence of B. burgdorferi DNA in breast cancer tissues. Moreover, 25% of B. burgdorferi-positive tissues exhibited expression of both chemokines, CXCL8 and CXCL10, which was not observed in B. burgdorferi-negative tissues. Analysis ofavailable patient data, including age, indicated a correlation between older patients and B. burgdorferi-positive tissues. This study validates the presence of B. burgdorferi in invasive breast cancer tissues andhighlights the involvement of key CXCL family members associated with inflammatory processes.

Expression and Clinical Significance of NUDCD1, PI3K/AKT/mTOR Signaling Pathway-Related Molecules and Immune Infiltration in Breast Cancer

BackgroundNUDCD1 (NudC Domain Containing 1) performs an essential function in biological processes such as cell progression, migration, cell cycle, and intracellular material transport. Many solid tumors express it highly, which is a prospective biomarker and therapeutic approach. However, the expression and clinical importance of NUDCD1 across breast cancer is unclear. MethodsThe expressions of NUDCD1 in breast cancers and normal breast tissues were studied utilizing the TIMER database and immunohistochemical analysis. Subsequently, we validate the association between the expression of NUDCD1 and clinicopathologic features and prognosis of breast cancer. The immunohistochemical experiments of pathway-related molecules were done on 214 breast cancer tissue microarrays. The investigation of correlation between NUDCD1 expression and tumor immune infiltration was subsequently conducted. ResultsThrough the utilization of bioinformatics analysis and immunohistochemical experiments, it was determined that NUDCD1 exhibited upregulation within breast cancer. Furthermore, it was discovered that an elevated expression of NUDCD1 may potentially be linked to a worse prognosis in breast cancer. Our study reveals that the PI3K/AKT/mTOR signaling pathway may perform a function in NUDCD1 regulating breast cancer progression via enrichment analysis. Furthermore, the expression of NUDCD1 may be associated with the degree of immunological infiltration. ConclusionThe expression of NUDCD1 was explored to be elevated in breast cancer and was observed to be correlated with a poorer prognosis. p-AKT, PI3K, AKT, mTOR, and p-mTOR expression levels underwent significant elevation in breast cancer. The function of NUDCD1 within breast cancer might be associated with the PI3K/AKT/mTOR signaling pathway.

AI improves accuracy, agreement and efficiency of pathologists for Ki67 assessments in breast cancer

The Ki-67 proliferation index (PI) guides treatment decisions in breast cancer but suffers from poor inter-rater reproducibility. Although AI tools have been designed for Ki-67 assessment, their impact on pathologists' work remains understudied. 90 international pathologists were recruited to assess the Ki-67 PI of ten breast cancer tissue microarrays with and without AI. Accuracy, agreement, and turnaround time with and without AI were compared. Pathologists’ perspectives on AI were collected. Using AI led to a significant decrease in PI error (2.1% with AI vs. 5.9% without AI, p < 0.001), better inter-rater agreement (ICC: 0.70 vs. 0.92; Krippendorff’s α: 0.63 vs. 0.89; Fleiss’ Kappa: 0.40 vs. 0.86), and an 11.9% overall median reduction in turnaround time. Most pathologists (84%) found the AI reliable. For Ki-67 assessments, 76% of respondents believed AI enhances accuracy, 82% said it improves consistency, and 83% trust it will improve efficiency. This study highlights AI's potential to standardize Ki-67 scoring, especially between 5 and 30% PI—a range with low PI agreement. This could pave the way for a universally accepted PI score to guide treatment decisions, emphasizing the promising role of AI integration into pathologist workflows.

Patient-derived tumor organoids with p53 mutations, and not wild-type p53, are sensitive to synergistic combination PARP inhibitor treatment

Poly (ADP-ribose) polymerase inhibitors (PARPi) are used for patients with BRCA1/2 mutations, but patients with other mutations may benefit from PARPi treatment. Another mutation that is present in more cancers than BRCA1/2 is mutation to the TP53 gene. In 2D breast cancer cell lines, mutant p53 (mtp53) proteins tightly associate with replicating DNA and Poly (ADP-ribose) polymerase (PARP) protein. Combination drug treatment with the alkylating agent temozolomide and the PARPi talazoparib kills mtp53 expressing 2D grown breast cancer cell lines. We evaluated the sensitivity to the combination of temozolomide plus PARPi talazoparib treatment to breast and lung cancer patient-derived tumor organoids (PDTOs). The combination of the two drugs was synergistic for a cytotoxic response in PDTOs with mtp53 but not for PDTOs with wtp53. The combination of talazoparib and temozolomide induced more DNA double-strand breaks in mtp53 expressing organoids than in wild-type p53 expressing organoids as shown by increased γ-H2AX protein expression. Moreover, breast cancer tissue microarrays (TMAs) showed a positive correlation between stable p53 and high PARP1 expression in sub-groups of breast cancers, which may indicate sub-classes of breast cancers sensitive to PARPi therapy. These results suggest that mtp53 could be a biomarker to predict response to the combination of PARPi talazoparib-temozolomide treatment.

Upregulated bone morphogenetic protein 8A (BMP8A) in triple negative breast cancer (TNBC) and its involvement in the bone metastasis.

The present study aimed to investigate the involvement of aberrant BMP8A expression in TNBC and bone metastasis. Aberrant expression of BMP8A in breast cancer was first determined by analyzing The Cancer Genome Atlas breast cancer cohort (TCGA-BRCA) and an immunohistochemical (IHC) staining of BMP8A in a breast cancer tissue microarray (TMA). Clinical relevance of deregulated BMP8A in breast cancer was assessed using Kaplan-Meier online analysis. The influence of BMP8A on cellular functions of two TNBC cell lines was assessed using in vitro assays. Conditional medium (CM) collected from the supernatant of hFOB cells and bone matrix extract (BME) was applied to mimic the bone micro-environment to evaluate the role played by BMP8A in bone metastasis. Correlations with both osteolytic and osteoblastic markers were evaluated in the TCGA-BRCA cohort. Expression of certain responsive genes was quantified in the BMP8A overexpression cell lines. Additionally, signal transduction through both Smad-dependent and independent pathways was evaluated using Western blot assay. Compared to the adjacent normal tissues, BMP8A expression was significantly increased in primary tumors (p < 0.05) which was associated with shorter distant metastasis free survival (DMFS) in TNBC (p < 0.05). BMP8A was observed to enhance cell invasion and migration within TNBC cells. In the simulated bone milieu, both MDA-MB-231BMP8Aexp and BT549BMP8Aexp cells presented enhanced invasiveness. BMP8A level was strongly correlated with most osteolytic and osteoblastic markers, suggesting the potential involvement of BMP8A in bone metastasis in TNBC. Receptor activator of nuclear factor kappa-B ligand (RANKL) expression was significantly increased in BMP8A overexpressed triple-negative cell lines (MDA-MB-231 and BT549). Furthermore, enhanced phosphorylation of Smad3 and increased expression of epidermal growth factor receptor (EGFR) were observed in MDA-MB-231 cells overexpressing BMP8A. BMP8A was upregulated in TNBC which was associated with poorer DMFS. BMP8A overexpression enhanced the invasion and migration of TNBC cells. With a putative role in osteolytic bone metastasis in TNBC, BMP8A represents a promising candidate for further investigation into its therapeutic potential.

Correlation of HER2 Protein Level With mRNA Level Quantified by RNAscope in Breast Cancer

Trastuzumab deruxtecan (T-DXd) has been approved by the US Food and Drug Administration (FDA) to treat patients with metastatic HER2-positive and HER2-low breast cancer, and clinical trials are examining its efficacy against early-stage breast cancer. Current HER2 immunohistochemical (IHC) assays are suboptimal in evaluating HER2-low breast cancers and identifying which patients would benefit from T-DXd. HER2 expression in 526 breast cancer tissue microarray (TMA) cores was measured using the FDA-approved PATHWAY and HercepTest IHC assays, and the corresponding RNA levels were evaluated by RNAscope. HER2 protein levels by regression analysis using a quantitative immunofluorescence score against cell line arrays with known HER2 protein levels determined by mass spectrometry were available in 48 of the cores. RNAscope was also performed in 32 metastatic biopsies from 23 patients who were subsequently treated with T-DXd, and the results were correlated with response rate. HER2 RNA levels by RNAscope strongly correlated with HER2 protein levels (P < .0001) and with HER2 IHC H-scores from the PATHWAY and HercepTest assays (P < .0001). However, neither protein levels nor RNA levels significantly differed between cases scored 0, ultralow, and 1+ by PATHWAY and HercepTest. The RNA levels were significantly higher (P = .030) in responders (6.4 ± 8.2 dots/cell, n = 12) than those in nonresponders (2.6 ± 2.2, n = 20) to T-DXd. RNAscope is a simple assay that can be objectively quantified and is a promising alternative to current IHC assays in evaluating HER2 expression in breast cancers, especially HER2-low cases, and may identify patients who would benefit from T-DXd.

Automatically Score Tissue Images Like a Pathologist by Transfer Learning

Cancer is the second leading cause of death in the world. Diagnosing cancer early on can save many lives. Pathologists have to look at tissue microarray (TMA) images manually to identify tumors, which can be time-consuming, inconsistent and subjective. Existing automatic algorithms either have not achieved the accuracy level of a pathologist or require substantial human involvements. A major challenge is that TMA images with different shapes, sizes, and locations can have the same score. Learning staining patterns in TMA images requires a huge number of images, which are severely limited due to privacy and regulation concerns in medical organizations. TMA images from different cancer types may share certain common characteristics, but combining them directly harms the accuracy due to heterogeneity in their staining patterns. Transfer learning is an emerging learning paradigm that allows borrowing strength from similar problems. However, existing approaches typically require a large sample from similar learning problems, while TMA images of different cancer types are often available in small sample size and further existing algorithms are limited to transfer learning from one similar problem. We propose a new transfer learning algorithm that could learn from multiple related problems, where each problem has a small sample and can have a substantially different distribution from the original one. The proposed algorithm has made it possible to break the critical accuracy barrier (the 75% accuracy level of pathologists), with a reported accuracy of 75.9% on breast cancer TMA images from the Stanford Tissue Microarray Database. It is supported by recent developments in transfer learning theory and empirical evidence in clustering technology. This will allow pathologists to confidently adopt automatic algorithms in recognizing tumors consistently with a higher accuracy in real time.

Abstract B008: Machine-learning enabled quantification of colocalized multiplex IHC signals with spectral overlap

Abstract Background: Immunohistochemistry (IHC) is the gold standard for detecting protein biomarkers in cancer. In breast cancer, several nuclear biomarkers are relevant for guiding treatment decisions, including estrogen receptor (ER) and progesterone receptor (PR), indicative of response to endocrine therapy, and the proliferation marker Ki67, indicative of response to CDK inhibition1. However, these nuclear markers are detected using chromogens that colocalize and spectrally overlap with hematoxylin (HTX), the standard nuclear counterstain for IHC. Thus, the accurate detection and quantification of nuclear antigens is challenging. To overcome this limitation of IHC-based biomarker assays, we developed a method to identify colocalized signals after staining with chromophores with spectral overlap. Methods: Multiplex IHC (mIHC) using primary antibodies against Ki67, PR, and ER was performed on a breast cancer tissue microarray (N=65 cores). Antigens were detected by dabsyl-, tamra-, and Cy5-conjugated secondary antibodies, respectively, and slides were counterstained with HTX. The cores were scanned with brightfield imaging (Aperio AT2 and 3DHistech microscopes). The same cores were imaged on a custom brightfield microscope using an LED light source and 10 nm wide band-pass filters at 405, 450, 520, 550, 589, 632 and 660 nm. Images were spectrally unmixed using absorption spectra of the different chromophores and the background estimated based on the images themselves and aligned with the brightfield images. Pathologist-trained individuals collected exhaustive manual annotations in regions of interest for each marker and HTX using unmixed channels. A convolutional neural network (CNN) was trained using the annotations for each marker and HTX and applied to the WSI. Predicted cell locations were aggregated across the four channels to obtain an exhaustive “super-annotation” co-expression map of the WSI. Super-annotations were then used to train a CNN to detect ER/PR/Ki67/HTX colocalization in the aligned RBG image of the same slide. Predictions from the super-annotation model were compared to ER/PR/Ki67/HTX detection done via HALO (Indica Labs). Results: Our multi-spectral imaging pipeline allowed for comprehensive annotations of all nuclei positive for at least one of the three markers or HTX. Using our super-annotation model, the count error of nuclei that are positive for HTX and one, two, or three markers was reduced by 7.8%, 6.4%, and 0.03%, respectively, compared to HALO. Conclusions: We have developed a method to identify colocalized antigens after mIHC using chromogens with spectral overlap. Related work to extend this approach to membranous biomarkers is ongoing and will enable additional novel analyses (e.g., describing the precise spatial organization of PD-L1+ tumor cells relative to CD8+ tumor-infiltrating lymphocytes). The approach that we describe here has great potential to facilitate the utilization of mIHC for the clinical detection of biomarkers in oncology.

EXTH-10. QUAD-DM1: A HIGHLY POTENT DRUG CONJUGATE FOR BREAST CANCER AND BREAST CANCER BRAIN METASTASIS TREATMENT

Abstract Triple-negative breast cancer (TNBC) remains an unmet need in medicine. Previously, we and others found that interleukin 13 receptor alpha 2 (IL-13RA2), EphA2, EphA3 and EphB2 receptors are over-expressed in almost all patients with glioblastoma (GBM). We performed a first-of-a-kind Phase I clinical trial in dogs with spontaneous gliomas using a cocktail of cytotoxins targeting IL-13RA2 and EphA2 receptor. The majority of dogs experienced &amp;gt;50% of tumor regression; four dogs exhibited &amp;gt;92% tumor shrinkage and several dogs became long-term survivors. Next, we pursued the novel idea of targeting four tumor-associated receptors, instead of two, with one pharmaceutical compound. To this end, we produced a multivalent ligand, termed QUAD. More recently, we found that a conjugate of QUAD with emtansine (DM1), a microtubule-disrupting agent, demonstrated a specific killing potency on GBM cells, in low picomolar range. Unexpectedly, we observed that human breast cancer cells are also highly responsive to this drug candidate. We thus examined the presence of the four receptors in breast cancer cells and tissue micro-arrays, including involved lymph nodes, and in paired primary tumor - brain metastases, spanning two molecular subtypes of breast cancer: TNBC and HER2+. We found that the four targeted receptors are expressed in almost all breast cancer and related metastases to brain specimens, based on the expression levels for the genes and the gene products. Furthermore, the breast cancer cell lines like HC1806, MDA-MB-468, MDA-MB-231, BT549, and the breast metastatic cell line MDA-MB-231-BRM cells are killed at up to picomolar concentrations of QUAD-DM1. MDA-MB-231 tumors growing in mammary pads of athymic mice responded significantly to QUAD-DM1 given intravenously; QUAD recognizes murine receptors similarly to human. Thus, QUAD-DM1 is a novel type of a multivalent drug conjugate for the treatment of breast cancer and its brain metastases, which is applicable, but not exclusively, to TNBC.

Phosphorylation of EZH2 differs HER2-positive breast cancer invasiveness in a site-specific manner

HER2-positive breast cancer (BC) invasiveness and drug-resistance issue is the critical treatment obstacle recently. We investigated the total and phosphorylated status EZH2 expression in database and BC tissue microarray. We demonstrated for the first time that EZH2 is distributed both in cytoplasm and nucleus of breast cancer cells in a phosphorylation site-specific manner. High expressed-EZH2 cases more frequently had an advanced clinical stage (lymph node metastasis) and aggressive features than EZH2-low cases, potentially indicating the high risk of HER2-positive BC (p < 0.05). Notably, highly expressed phosphorylated EZH2 is differently located in cytoplasm or nucleus in a site-specific manner in breast cancer cells. Nucleus-located pEZH2-S21 is expressed in invasive and lymph node metastatic HER2-positive BC cases (p = 0.144, p = 0.001). Cytoplasmic pEZH2-T487 is correlated with HER2 positive status (p = 0.014).In conclusion, high expression of nucleus-located EZH2 might be a predictor of invasive BC. Activation of phosphorylated EZH2-S21 site in nucleus would be a potential predictor of HER2-positve BC and poor efficacy of HER2-target therapy. These results point to a PRC2-independent non-epigenetic mechanism and therapeutic strategy of EZH2 in HER2-positive BC.