Tumor Samples Research Articles

Identification of differentially expressed mRNAs as novel predictive biomarkers for gastric cancer diagnosis and prognosis

BACKGROUND Gastric cancer (GC) has a high mortality rate worldwide. Despite significant progress in GC diagnosis and treatment, the prognosis for affected patients still remains unfavorable. AIM To identify important candidate genes related to the development of GC and identify potential pathogenic mechanisms through comprehensive bioinformatics analysis. METHODS The Gene Expression Omnibus database was used to obtain the GSE183136 dataset, which includes a total of 135 GC samples. The limma package in R software was employed to identify differentially expressed genes (DEGs). Thereafter, enrichment analyses of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed for the gene modules using the clusterProfile package in R software. The protein-protein interaction (PPI) networks of target genes were constructed using STRING and visualized by Cytoscape software. The common hub genes that emerged in the cohort of DEGs that was retrieved from the GEPIA database were then screened using a Venn Diagram. The expression levels of these overlapping genes in stomach adenocarcinoma samples and non-tumor samples and their association with prognosis in GC patients were also obtained from the GEPIA database and Kaplan-Meier curves. Moreover, real-time quantitative polymerase chain reaction (RT-qPCR) and western blotting were performed to determine the mRNA and protein levels of glutamic-pyruvic transaminase (GPT ) in GC and normal immortalized cell lines. In addition, cell viability, cell cycle distribution, migration and invasion were evaluated by cell counting kit-8, flow cytometry and transwell assays. Furthermore, we also conducted a retrospective analysis on 70 GC patients diagnosed and surgically treated in Wenzhou Central Hospital, Dingli Clinical College of Wenzhou Medical University, The Second Affiliated Hospital of Shanghai University between January 2017 to December 2020. The tumor and adjacent normal samples were collected from the patients to determine the potential association between the expression level of GPT and the clinical as well as pathological features of GC patients. RESULTS We selected 19214 genes from the GSE183136 dataset, among which there were 250 downregulated genes and 401 upregulated genes in the tumor samples of stage III-IV in comparison to those in tumor samples of stage I-II with a P -value < 0.05. In addition, GO and KEGG results revealed that the various upregulated DEGs were mainly enriched in plasma membrane and neuroactive ligand-receptor interaction, whereas the downregulated DEGs were primarily enriched in cytosol and pancreatic secretion, vascular smooth muscle contraction and biosynthesis of the different cofactors. Furthermore, PPI networks were constructed based on the various upregulated and downregulated genes, and there were a total 15 upregulated and 10 downregulated hub genes. After a comprehensive analysis, several hub genes, including runt-related transcription factor 2 (RUNX2 ), salmonella pathogenicity island 1 (SPI1 ), lysyl oxidase (LOX ), fibrillin 1 (FBN1 ) and GPT , displayed prognostic values. Interestingly, it was observed that GPT was downregulated in GC cells and its upregulation could suppress the malignant phenotypes of GC cells. Furthermore, the expression level of GPT was found to be associated with age, lymph node metastasis, pathological staging and distant metastasis (P < 0.05). CONCLUSION RUNX2 , SPI1 , LOX , FBN1 and GPT were identified key hub genes in GC by bioinformatics analysis. GPT was significantly associated with the prognosis of GC, and its upregulation can effectively inhibit the proliferative, migrative and invasive capabilities of GC cells.

Transcript and protein signatures derived from shared molecular interactions across cancers are associated with mortality

BackgroundCharacterization of shared cancer mechanisms have been proposed to improve therapy strategies and prognosis. Here, we aimed to identify shared cell–cell interactions (CCIs) within the tumor microenvironment across multiple solid cancers and assess their association with cancer mortality.MethodsCCIs of each cancer were identified by NicheNet analysis of single-cell RNA sequencing data from breast, colon, liver, lung, and ovarian cancers. These CCIs were used to construct a shared multi-cellular tumor model (shared-MCTM) representing common CCIs across cancers. A gene signature was identified from the shared-MCTM and tested on the mRNA and protein level in two large independent cohorts: The Cancer Genome Atlas (TCGA, 9185 tumor samples and 727 controls across 22 cancers) and UK biobank (UKBB, 10,384 cancer patients and 5063 controls with proteomics data across 17 cancers). Cox proportional hazards models were used to evaluate the association of the signature with 10-year all-cause mortality, including sex-specific analysis.ResultsA shared-MCTM was derived from five individual cancers. A shared gene signature was extracted from this shared-MCTM and the most prominent regulatory cell type, matrix cancer-associated fibroblast (mCAF). The signature exhibited significant expression changes in multiple cancers compared to controls at both mRNA and protein levels in two independent cohorts. Importantly, it was significantly associated with mortality in cancer patients in both cohorts. The highest hazard ratios were observed for brain cancer in TCGA (HR [95%CI] = 6.90[4.64–10.25]) and ovarian cancer in UKBB (5.53[2.08–8.80]). Sex-specific analysis revealed distinct risks, with a higher mortality risk associated with the protein signature score in males (2.41[1.97–2.96]) compared to females (1.84[1.44–2.37]).ConclusionWe identified a gene signature from a comprehensive shared-MCTM representing common CCIs across different cancers and revealed the regulatory role of mCAF in the tumor microenvironment. The pathogenic relevance of the gene signature was supported by differential expression and association with mortality on both mRNA and protein levels in two independent cohorts.

Comprehensive molecular profiling identifies actionable biomarkers for patients from Thailand and the United Arab Emirates with advanced malignancies

BackgroundComprehensive molecular profiling of tissue samples that can help guide therapy management is not widely available across the globe.MethodsComprehensive molecular profiling through Caris Molecular Intelligence involves the analysis of DNA through next-generation sequencing, chromogenic or fluorescent in situ hybridization, pyrosequencing, and copy number alterations; RNA through whole-transcriptome sequencing and multiplex PCR of RNA; and protein through immunohistochemistry.ResultsHere we describe the experience of molecular profiling of tumor tissue samples from patients diagnosed with advanced solid tumors and treated in two countries, the United Arab Emirates and Thailand. Tumor cancer cases submitted to Caris Life Sciences (Phoenix, Arizona, USA) for molecular profiling from the UAE and Thailand were retrospectively analyzed (data accessed between 2019 and 2020) for their molecular alterations and clinical biomarkers, without regard to ethnicity. A total of 451 samples from 35 distinct types of advanced cancers were examined for mutations, amplifications, overexpression, exon copy number alterations, microsatellite instability, deficient mismatch repair, tumor mutational burden, and fusions. Interrogating each step of the biological pathway, from DNA to RNA to distinct protein, identified an alteration with an associated therapy for 75% of these tumor samples. The most common alterations identified included elevated PDL-1 that can be targeted with an immune checkpoint inhibitors and amplification of HER2 for which a variety of anti HER2 therapies are available.ConclusionComprehensive molecular profiling in patients with advanced malignancies can help optimize therapeutic management allowing for improved prognostic outcome.

Characterization of innate lymphoid cell subsets infiltrating melanoma and epithelial ovarian tumors

ABSTRACT The innate lymphoid cell (ILC) family is composed of heterogeneous innate effector and helper immune cells that preferentially reside in tissues where they promote tissue homeostasis. In cancer, they have been implicated in driving both pro- and anti-tumor responses. This apparent dichotomy highlights the need to better understand differences in the ILC composition and phenotype within different tumor types that could drive seemingly opposite anti-tumor responses. Here, we characterized the frequency and phenotype of various ILC subsets in melanoma metastases and primary epithelial ovarian tumors. We observed high PD-1 expression on ILC subsets isolated from epithelial ovarian tumor samples, while ILC populations in melanoma samples express higher levels of LAG-3. In addition, we found that the frequency of cytotoxic ILCs and NKp46+ILC3 in tumors positively correlates with monocytic cells and conventional type 2 dendritic cells, revealing potentially new interconnected immune cell subsets in the tumor microenvironment. Consequently, these observations may have direct relevance to tumor microenvironment composition and how ILC subset may influence anti-tumor immunity.

The analysis of transcriptomic signature of TNBC—searching for the potential RNA-based predictive biomarkers to determine the chemotherapy sensitivity

AbstractNeoadjuvant chemotherapy is the foundation treatment for triple-negative breast cancer (TNBC) and frequently results in pathological complete response (pCR). However, there are large differences in clinical response and survival after neoadjuvant chemotherapy of TNBC patients. The aim was to identify genes whose expression significantly associates with the efficacy of neoadjuvant chemotherapy in patients with TNBC. Transcriptomes of 46 formalin-fixed paraffin-embedded (FFPE) tumor samples from TNBC patients were analyzed by RNA-seq by comparing 26 TNBCs with pCR versus 20 TNBCs with pathological partial remission (pPR). Subsequently, we narrowed down the list of genes to those that strongly correlated with drug sensitivity of 63 breast cancer cell lines based on Dependency Map Consortium data re-analysis. Furthermore, the list of genes was limited to those presenting specific expression in breast tumor cells as revealed in three large published single-cell RNA-seq breast cancer datasets. Finally, we analyzed which of the selected genes were significantly associated with overall survival (OS) in TNBC TCGA dataset. A total of 105 genes were significantly differentially expressed in comparison between pPR versus pCR. As revealed by PLSR analysis in breast cancer cell lines, out of 105 deregulated genes, 42 were associated with sensitivity to docetaxel, doxorubicin, paclitaxel, and/or cyclophosphamide. We found that 24 out of 42 sensitivity-associated genes displayed intermediate or strong expression in breast malignant cells using single-cell RNAseq re-analysis. Finally, 10 out of 24 genes were significantly associated with overall survival in TNBC TCGA dataset. Our RNA-seq-based findings suggest that there might be transcriptomic signature consisted of 24 genes specifically expressed in tumor malignant cells for predicting neoadjuvant response in FFPE samples from TNBC patients prior to treatment initiation. Additionally, nine out of 24 genes were potential survival predictors in TNBC. This group of 24 genes should be further investigated for its potential to be translated into a predictive test(s).

Long-term prospective outcome data using EndoPredict as risk stratification and chemotherapy decision biomarker in hormone receptor-positive, HER2-negative early breast cancer

Abstract Purpose To report the prospective long-term outcome data of patients whose chemotherapy decision was guided by the EndoPredict test. Methods Patients with hormone receptor-positive HER2-negative early breast cancer with 0–3 positive lymph nodes were enrolled. The EndoPredict test was carried out on all tumor samples. Treatment compliance, local recurrence, distant metastases, and survival were evaluated. Associations of EPclin risk stratification with 5-year disease-free survival and distant metastasis-free survival were evaluated by time-to-event analysis. Results 368 consecutive patients were included in the analysis. Median follow-up was 8.2 years. EndoPredict allocated 238 (65%) in the low-risk and 130 (35%) patients in the high-risk group. Risk for disease recurrence or death in EPclin high-risk patients was twofold higher than in EPclin low-risk patients (hazard ratio [HR] 2.08; 95% CI 1.26–3.44; p = 0.004). EPclin low-risk patients had a 5-year disease-free survival of 95.3% (95% CI 92.6–98.0%). EPclin high-risk patients were at higher risk of developing distant metastases or death (HR 2.21; 95% CI 1.27–3.88; p = 0.005). EPclin high-risk patients who underwent chemotherapy had a 5-year DFS of 89.1% (95% CI 82.7–96.1%) in contrast to high-risk patients without chemotherapy (68.9%; 95% CI 56.2–84.5%; HR 0.46; 95% CI 0.23–0.95; p = 0.036). EPclin high-risk patients were at higher risk of experiencing distant metastases or death than EPclin low-risk patients regardless of menopausal status (premenopausal: HR 3.55; 95% CI 1.17–12.32; p = 0.025; postmenopausal: HR 1.92; 95% CI 0.99–3.7; p = 0.054). Conclusion EndoPredict can guide decisions on adjuvant chemotherapy in early luminal breast cancer. EndoPredict risk stratification is also applicable in premenopausal women.

Comparative analysis of the tumor microbiome, molecular profiles, and immune cell abundances by HPV status in mucosal head and neck cancers and their impact on survival

ABSTRACT Head and Neck Squamous Cell Carcinoma (HNSCC) comprises a diverse group of tumors with variable treatment response and prognosis. The tumor microenvironment (TME), which includes microbiome and immune cells, can impact outcomes. Here, we sought to relate the presence of specific microbes, gene expression, and tumor immune infiltration using tumor transcriptomics from The Cancer Genome Atlas (TCGA) and associate these with overall survival (OS). RNA sequencing (RNAseq) from HNSCC tumors in TCGA was processed through the exogenous sequences in tumors and immune cells (exotic) pipeline to identify and quantify low-abundance microbes. The detection of the Papillomaviridae family of viruses assessed HPV status. All statistical analyses were performed using R. A total of 499 RNAseq samples from TCGA were analyzed. HPV was detected in 111 samples (22%), most commonly Alphapapillomavirus 9 (90.1%). The presence of Alphapapillomavirus 9 was associated with improved OS [HR = 0.60 (95%CI: 0.40–0.89, p = .01)]. Among other microbes, Yersinia pseudotuberculosis was associated with the worst survival (HR = 3.88; p = .008), while Pseudomonas viridiflava had the best survival (HR = 0.05; p = .036). Microbial species found more abundant in HPV- tumors included several gram-negative anaerobes. HPV- tumors had a significantly higher abundance of M0 (p < .001) and M2 macrophages (p = .035), while HPV+ tumors had more T regulatory cells (p < .001) and CD8+ T-cells (p < .001). We identified microbes in HNSCC tumor samples significantly associated with survival. A greater abundance of certain anaerobic microbes was seen in HPV tumors and pro-tumorigenic macrophages. These findings suggest that TME can be used to predict patient outcomes and may help identify mechanisms of resistance to systemic therapies.

Differential expression of angiogenesis-related genes ‘VEGF’ and ‘angiopoietin-1’ in metastatic and EMAST-positive colorectal cancer patients

Abnormal angiogenesis leads to tumor progression and metastasis in colorectal cancer (CRC). This study aimed to elucidate the association between angiogenesis-related genes, including VEGF-A, ANGPT-1, and ANGPT-2 with both metastatic and microsatellite alterations at selected tetranucleotide repeats (EMAST) subtypes of CRC. We conducted a thorough assessment of the ANGPT-1, ANGPT-2, and VEGF-A gene expression utilizing publicly available RNA sequencing and microarray datasets. Then, the experimental validation was performed in 122 CRC patients, considering their disease metastasis and EMAST+/− profile by using reverse transcription polymerase chain reaction (RT-PCR). Subsequently, a competing endogenous RNA (ceRNA) network associated with these angiogenesis-related genes was constructed and analyzed. The expression level of VEGF-A and ANGPT-2 genes were significantly higher in tumor tissues as compared with normal adjacent tissues (P-value < 0.001). Nevertheless, ANGPT-1 had a significantly lower expression in tumor samples than in normal colon tissue (P-value < 0.01). We identified a significantly increased VEGF-A (P-value = 0.002) and decreased ANGPT-1 (P-value = 0.04) expression in EMAST+ colorectal tumors. Regarding metastasis, a significantly increased VEGF-A and ANGPT-2 expression (P-value = 0.001) and decreased ANGPT-1 expression (P-value < 0.05) were established in metastatic CRC patients. Remarkably, co-expression analysis also showed a strong correlation between ANGPT-2 and VEGF-A gene expressions. The ceRNA network was constructed by ANGPT-1, ANGPT-2, VEGF-A, and experimentally validated miRNAs (hsa-miR-190a-3p, hsa-miR-374c-5p, hsa-miR-452-5p, and hsa-miR-889-3p), lncRNAs (AFAP1-AS1, KCNQ1OT1 and MALAT1), and TFs (Sp1, E2F1, and STAT3). Network analysis revealed that colorectal cancer is amongst the 82 significant pathways. We demonstrated a significant differential expression of VEGF-A and ANGPT-1 in colorectal cancer patients exhibiting the EMAST+ phenotype. This finding provides novel insights into the molecular pathogenesis of colorectal cancer, specifically in EMAST subtypes. Yet, the generalization of in silico findings to EMAST+ colorectal cancer warrants future experimental investigations. In the end, this study proposes that the EMAST biomarker could serve as an additional perspective on CMS4 biology which is well-defined by activated angiogenesis and worse overall survival.

CD163+ macrophages in the triple-negative breast tumor microenvironment are associated with improved survival in the Women’s Circle of Health Study and the Women’s Circle of Health Follow-Up Study

BackgroundTumor-associated macrophages (TAMs) are a prominent immune subpopulation in the tumor microenvironment that could potentially serve as therapeutic targets for breast cancer. Thus, it is important to characterize this cell population across different tumor subtypes including patterns of association with demographic and prognostic factors, and breast cancer outcomes.MethodsWe investigated CD163+ macrophages in relation to clinicopathologic variables and breast cancer outcomes in the Women’s Circle of Health Study and Women’s Circle of Health Follow-up Study populations of predominantly Black women with breast cancer. We evaluated 611 invasive breast tumor samples (507 from Black women, 104 from White women) with immunohistochemical staining of tissue microarray slides followed by digital image analysis. Multivariable Cox proportional hazards models were used to estimate hazard ratios for overall survival (OS) and breast cancer-specific survival (BCSS) for 546 cases with available survival data (median follow-up time 9.68 years (IQR: 7.43–12.33).ResultsWomen with triple-negative breast cancer showed significantly improved OS in relation to increased levels of tumor-infiltrating CD163+ macrophages in age-adjusted (Q3 vs. Q1: HR = 0.36; 95% CI 0.16–0.83) and fully adjusted models (Q3 vs. Q1: HR = 0.30; 95% CI 0.12–0.73). A similar, but non-statistically significant, association was observed for BCSS. Macrophage infiltration in luminal and HER2+ tumors was not associated with OS or BCSS. In a multivariate regression model that adjusted for age, subtype, grade, and tumor size, there was no significant difference in CD163+ macrophage density between Black and White women (RR = 0.88; 95% CI 0.71–1.10).ConclusionsIn contrast to previous studies, we observed that higher densities of CD163+ macrophages are independently associated with improved OS and BCSS in women with invasive triple-negative breast cancer.Trial registrationNot applicable.

The Association between Mutational Signatures and Clinical Outcomes among Patients with Early-Onset Breast Cancer

Early-onset breast cancer (EoBC), defined by a diagnosis &lt;40 years of age, is associated with poor prognosis. This study investigated the mutational landscape of non-metastatic EoBC and the prognostic relevance of mutational signatures using 100 tumour samples from Alberta, Canada. The MutationalPatterns package in R/Bioconductor was used to extract de novo single-base substitution (SBS) and insertion–deletion (indel) mutational signatures and to fit COSMIC SBS and indel signatures. We assessed associations between these signatures and clinical characteristics of disease, in addition to recurrence-free (RFS) and overall survival (OS). Five SBS and two indel signatures were extracted. The SBS13-like signature had higher relative contributions in the HER2-enriched subtype. Patients with higher than median contribution tended to have better RFS after adjustment for other prognostic factors (HR = 0.29; 95% CI: 0.08–1.06). An unsupervised clustering algorithm based on absolute contribution revealed three clusters of fitted COSMIC SBS signatures, but cluster membership was not associated with clinical variables or survival outcomes. The results of this exploratory study reveal various SBS and indel signatures may be associated with clinical features of disease and prognosis. Future studies with larger samples are required to better understand the mechanistic underpinnings of disease progression and treatment response in EoBC.

Neoantigen Landscape Supports Feasibility of Personalized Cancer Vaccine for Follicular Lymphoma

Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that ‘polyvalent’ vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole exome sequencing (WES) and RNA sequencing (RNA-Seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-Seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by alignment of B-cell receptor (BCR) CDR3 regions from RNA-Seq data, grouping at the protein level, and comparison to the BCR repertoire from healthy individuals using RNA-Seq data. An average of 52 somatic mutations per patient (range: 2-172) were identified, and two or more (median: 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide (SLP) vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all four patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field.

Time-course RNAseq data of murine AB1 mesothelioma and Renca renal cancer following immune checkpoint therapy

Time-critical transcriptional events in the immune microenvironment are important for response to immune checkpoint blockade (ICB), yet these events are difficult to characterise and remain incompletely understood. Here, we present whole tumor RNA sequencing data in the context of treatment with ICB in murine models of AB1 mesothelioma and Renca renal cell cancer. We sequenced 144 bulk RNAseq samples from these two cancer types across 4 time points prior and after treatment with ICB. We also performed single-cell sequencing on 12 samples of AB1 and Renca tumors an hour before ICB administration. Our samples were equally distributed between responders and non-responders to treatment. Additionally, we sequenced AB1-HA mesothelioma tumors treated with two sample dissociation protocols to assess the impact of these protocols on the quality transcriptional information in our samples. These datasets provide time-course information to transcriptionally characterize the ICB response and provide detailed information at the single-cell level of the early tumor microenvironment prior to ICB therapy.

Comprehensive Genomic Characterization in Ovarian Low-Grade and chemosensitive and chemoresistant High-Grade Serous Carcinomas.

Genomic characterization of serous ovarian carcinoma (SOC), which includes low-grade serous carcinoma (LGSC) and high-grade serous carcinoma (HGSC), remains necessary to improve efficacy of platinum-based chemotherapy. The aim was to investigate the genomic variations in these SOC groups, also in relation to chemoresponse. 45 samples SOC were retrospectively analyzed by Next Generation Sequencing (NGS) on DNA/RNA extracts from formalin-fixed, paraffin-embedded (FFPE) tumor samples obtained at diagnosis. HGSCs were classified as platinum-resistant and platinum-sensitive. In the LGSC group, 44% of the carcinomas had mutually exclusive variants in the RAS/RAF pathway, while additional likely oncogenic variants in the CDKN2A, SMARCA4 and YAP1 genes were observed in the remaining LGSCs. Tumor mutation burden (TMB) was significantly lower in the intrinsically chemoresistant LGSC group than in the HGSC group. In the HGSC cohort, TP53 variants were found in 90% and homologous recombination repair (HRR) pathway variants in 41% of the neoplasms. HGSCs of the chemoresistant group without classic mutations in the HRR pathway were characterized by additional variants in FGFR2 and with a FGFR3::TACC3 fusion. In addition, HGSCs showed MYC, CCNE1 and AKT2 gains that were almost exclusively observed in the chemosensitive HGSC group. These results suggest that very low TMB and MYC, CCNE1 and AKT2 gains in SOC patients may be biomarkers related to platinum treatment efficacy. Thorough genomic characterization of SOCs prior to treatment might lead to more specific platinum-based chemotherapy therapy strategies.

Abstract PO2-04-06: Investigation of the genomic evolution of HER2-positive breast cancer following progression on dual HER2-targetted therapy with Trastuzumab and Tucatinib

Abstract Background: Advanced HER2-positive breast cancer remains an incurable and highly morbid condition. One of the key challenges has been treatment of central nervous system (CNS) metastases, commonly seen in those with HER2-positive disease. Tucatinib is a recently approved treatment HER2-targetting tyrosine kinase inhibitor with proven CNS activity. There has been little analysis of potential genomic mechanisms of drug resistance. Method: We retrospectively identified patients that were treated with tucatinib, capecitabine and trastuzumab. We collated baseline clinical data and treatment history and all tumour and plasma samples available were obtained for testing. DNA was extracted from plasma samples using the QIAamp DNA Mini Kit (Qiagen) on 4ml plasma samples. Targeted next generation sequencing (NGS) of serial tumour and plasma samples was performed using a custom hybrid capture assay that covered 180 genes known to be recurrently mutated in breast cancer focusing on the known genomic landscape of metastatic disease as well as the inclusion of specific actionable targets. Survival analyses was performed using Cox regression models. Results: We identified 11 patients at our institution. Plasma samples were available for all 11 patients with a total of 107 serial samples across multiple time points, with a median of 8 (range 2-19) samples per patient. All 11 patients had baseline and End of Treatment (EOT) samples. In addition, 6/11 (54%) patients had tumour sequenced on the same NGS platform prior to commencement of therapy, with 12 individual tumour samples tested. The median PFS of our cohort was 9.6 months (4.0 - NR) with a median OS of 36.2 months (10.4-NR). 7/11 (64%) patients had CNS disease at baseline with their median PFS being 13.5 months (3.9-24.4) and median OS of 36.2months (10.4-NR). Overall, we observed an average of 18.4 (4-35) mutations per patient in tumour, 5.1 (1-15) in baseline plasma and 5.8 (2-14) in EOT plasma. The most frequent mutations seen in baseline tumour samples were ERBB2 (92%), KMT2C (67%) and NCOR1 (58%) compared with KMT2C (64%), NOTCH4 (36%) and PIK3CA (27%) in baseline plasma. Patients with a lower number of ctDNA mutations at baseline showed a trend towards improved survival (PFS 14 months vs 7.5 months). In this small cohort of patients we identified a higher than expected rates of KMT2C mutations. A KMT2C mutation was identified in 67% of samples which is higher than previously described rates of 7-15% in TCGA and METABRIC cohorts respectively. The presence of a concordant ctDNA KMT2C mutation in baseline and progression samples was a poor prognostic indicator (mPFS 7.5 months) when compared with no KMT2C mutation (mPFS 15.5 months) p =0.14 suggesting a possible mechanism of resistance to tucatinib. Conclusions: In this retrospective analysis of patients treated with Tucatinib, Trastuzumab and Capecitabine we established the genomic landscape of heavily pre-treated, advanced HER2-positive disease is complex. We observed there may be a correlation with KMT2C mutations and poorer clinical outcomes, however given the very small number of patients this data remains hypothesis generating, requiring validation with larger datasets. Citation Format: Elizabeth Blackley, Courtney van Geelen, Yi-An Ko, Stephen Wong, Miriam Yeung, Stephen Luen, Sarah-Jane Dawson, Sherene Loi. Investigation of the genomic evolution of HER2-positive breast cancer following progression on dual HER2-targetted therapy with Trastuzumab and Tucatinib [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-04-06.

Abstract PS12-07: Phase II clinical trial of palbociclib and binimetinib in advanced triple-negative breast cancer (TNBC) with hyperactivation of ERK and/or CDK4/6

Abstract Background: We previously demonstrated that a kinase-based taxonomy of TNBC was most parsimonious than next-generation sequencing in defining TNBC subtypes associated with prognostic categories in early disease. The most aggressive TNBC variants were driven by a heterogeneous set of genetic aberrations that converged in the increased activity of 6 kinases: KIT, PNKP, PRKCE, P70S6K, ERK and CDK6 (Nat Commun; 9:3501-18). The combined inhibition of these kinases in pairs led to potent tumor regression in preclinical models, being the most powerful combination that one directed against CDK6 and ERK. This prompted us to design a phase II trial testing the combination of palbociclib (against CDK6) and binimetinib (against the ERK upstream kinase MEK, since no ERK inhibitor was available at that moment outside phase I trials) in advanced TNBC. Hyperactivation of CDK6 and/or ERK was selected as entry criterion. Trial design: This was a single-arm, prospective, multicentric, open-label, phase II investigator-initiated trial. CDK6 and phosphor-ERK levels were measured in tumor samples by immunohistochemistry and normalized with a reference sample collection to a Z-score. Patients with scores for either kinase above the median were candidates for the trial. Key inclusion criteria included metastatic &amp;gt;18year-old TNBC, adequate organ function, measurable disease, and progression to 1-2 prior treatment lines (including immunotherapy, and a PARP inhibitor in case of germline BRCA1/2 mutation). Patients started continuous oral binimetinib at 45 mg/BID and palbociclib 100 mg/day from days 1 to 21, in 28-day cycles. Patients experiencing ≤ grade 1 tolerable side effects as the greatest toxicity were escalated to palbociclib to 125 in cycle 2. RECIST 1.1 and NCI CTC AE V 5.0 were used for assessing disease control (q8 weeks) and toxicity. The primary aims were to assess the efficacy and toxicity of this combination, and the secondary one to detect biomarkers of activity. At the time of trial design, in absence of available Sacituzumab for prescription, the reference PFS to beat in advanced lines for physician’s choice in TNBC was 1.7 month (NEJM; 384:1529-41, 2021). With alpha and beta errors of 0.05 and 0.2, the minimum number of patients to demonstrate a 30% improvement in PFS to 2.5 months was 25. Results: From November 2020 to April 2023, 69 patients were screened and 24 entered the trial (5 positive for phosphor-ERK; 2 for CDK6; 17 for both). Toxicity was generally mild and included grade 1-2 diarrhea (33% of the patients), grade 1-2 asthenia (50%), grade 1-3 neutropenia (75%), grade 2 retinal toxicity (8.3%) and grade 3 rash (4.2%); no grade 4/5 toxicities were observed. Median PFS was 1.83 months (range 0.3 to 11.3+). Phospho-ERK and CDK6 levels were not correlated (Pearson’s R= -0.089; P=0.68); CDK6 levels did not show association with PFS time (R = -0.120; P=0.58). Interestingly, however, phosphor-ERK levels in the baseline tumor sample showed correlation with PFS time (R = 0.428; P=0.037). Conclusion: The combination of palbociclib and binimetinib was generally safe, and PFS time showed correlation with baseline phosphorylation levels of ERK. However, the trial did not meet its primary endpoint. Citation Format: Rodrigo Sánchez-Bayona, Alfonso Cortes, Juan Miguel Cejalvo, Luis Manso, Serafin Morales, Jose A Garcia-Saenz, Jorge Silva, Juan A Guerra, Diego Malón-Giménez, Silvana Mouron, Eduardo Caleiras, Miguel Quintela-Fandino. Phase II clinical trial of palbociclib and binimetinib in advanced triple-negative breast cancer (TNBC) with hyperactivation of ERK and/or CDK4/6 [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 PS12-07.

Elucidating immunological characteristics of the adenoma-carcinoma sequence in colorectal cancer patients in South Korea using a bioinformatics approach

Colorectal cancer (CRC) is one of the top five most common and life-threatening malignancies worldwide. Most CRC develops from advanced colorectal adenoma (ACA), a precancerous stage, through the adenoma-carcinoma sequence. However, its underlying mechanisms, including how the tumor microenvironment changes, remain elusive. Therefore, we conducted an integrative analysis comparing RNA-seq data collected from 40 ACA patients who visited Dongguk University Ilsan Hospital with normal adjacent colons and tumor samples from 18 CRC patients collected from a public database. Differential expression analysis identified 21 and 79 sequentially up- or down-regulated genes across the continuum, respectively. The functional centrality of the continuum genes was assessed through network analysis, identifying 11 up- and 13 down-regulated hub-genes. Subsequently, we validated the prognostic effects of hub-genes using the Kaplan–Meier survival analysis. To estimate the immunological transition of the adenoma-carcinoma sequence, single-cell deconvolution and immune repertoire analyses were conducted. Significant composition changes for innate immunity cells and decreased plasma B-cells with immunoglobulin diversity were observed, along with distinctive immunoglobulin recombination patterns. Taken together, we believe our findings suggest underlying transcriptional and immunological changes during the adenoma-carcinoma sequence, contributing to the further development of pre-diagnostic markers for CRC.

Abstract PO3-16-03: Investigating HER2DX genomic assay concordance within HER2-positive breast cancer

Abstract Background: The HER2DX genomic assay, encompassing a 27-gene panel, provides prognostic (risk-score) and predictive (pathological complete response [pCR]-score) information while quantifying ERBB2 mRNA expression (ERBB2-score). This study aims to explore the variability of HER2DX scores within tumor samples and between paired diagnostic biopsies and surgical specimens. Methods: The standardized HER2DX assay was conducted on pretreatment FFPE biopsies from two distinct geographical areas within tumors (i.e., two different core biopsies) of patients enrolled in the 14-409 phase II study. This study assessed the impact of HER2 heterogeneity on treatment response in stage II-III HER2+ breast cancer patients treated with neoadjuvant T-DM1 and pertuzumab. Additionally, HER2DX was evaluated on paired biopsy-surgery FFPE samples from 6 patients who underwent primary surgery without pre-operative treatment. Variability and concordance of the three HER2DX groups scores were calculated, and Pearson's correlation coefficient determined the correlation between scores at different sites/time points. Paired t-tests were performed between tumor samples for the HER2DX scores. Results: The HER2DX assay was evaluated in two different diagnostic pre-treatment core biopsies from 106 patients (n=212 HER2DX assays). Intra-tumor concordance rates of the three HER2DX groups (risk-score, pCR-score, and ERBB2-score) were 94.3%, 87.7%, and 91.5%, respectively. No significant differential expression of HER2DX scores was observed across paired core biopsies (p-values=0.327 [risk-score], 0.415 [pCR-score], and 0.451 [ERBB2-score]). The average score differences (core 1 - core 2 [scale from 0 to 100]) were 0.57 (risk-score), 0.63 (pCR score), and -0.63 (ERBB2-score). Correlation coefficients across paired core biopsies were 0.96 (risk-score), 0.91 (pCR-score), and 0.90 (ERBB2-score). Additionally, intra-patient variability of the HER2DX scores was evaluated. Average variability in risk-score was 3.38% (95% CI: 2.76-4.01), in pCR-score was 3.53% (95% CI: 2.84-4.23) and in ERBB2 was 3.87% (95% CI: 2.97-4.77). In 6 patients with cT1-2 cN0 disease, HER2DX was evaluated in a diagnostic core biopsy and a surgical specimen, with an average time interval of 8.5 weeks (range 4 to 12 weeks) between time points. The intra-patient concordance rates of the three HER2DX groups were 83.3%, 83.3%, and 100% for risk-score, pCR-score, and ERBB2-score, respectively. No significant differential expression of HER2DX scores was found across paired biopsy-surgery samples (p-values=0.814 [risk-score], 0.128 [pCR-score], and 0.607 [ERBB2-score]). The average score differences (core biopsy - surgical specimen [scale from 0 to 100]) were -0.67 (risk-score), -11.5 (pCR score), and 2 (ERBB2-score). Correlation coefficients across paired HER2DX assays were 0.97 (risk-score), 0.87 (pCR-score), and 0.94 (ERBB2-score). Conclusion: The HER2DX genomic assay demonstrates low variability within HER2+ breast cancer, supporting its reliability as a consistent tool for assessing prognosis, the probability of pCR and ERBB2 quantitative expression. Citation Format: Fara Brasó-Maristany, Laia Paré, Guillermo Villacampa, Mercedes Marín-Aguilera, Paul Spellman, Adrienne Waks, Ian Krop, Esther Sanfeliu, Zhequi Li, Patricia Galván, Eva Hernández-Illán, Pedro Jares, Joan Antón Puig-Butillé, Ana Vivancos, Patricia Villagrasa, Joel S. Parker, Charles M. Perou, Sara Tolaney, Otto Metzger, Kornelia Polyak, Aleix Prat. Investigating HER2DX genomic assay concordance within HER2-positive 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 PO3-16-03.

Abstract PO5-21-06: Pathway profiling for prediction of response to neoadjuvant Letrozole therapy in ER positive postmenopausal breast cancer: gaining new insights for targeted treatment

Abstract Introduction: The NEOLBC (NCT03283384) study included postmenopausal patients with hormone receptor positive (ER≥50%, PR any), HER2 negative, stage II/III breast cancer. A baseline biopsy was taken prior to start letrozole treatment and after two weeks of treatment. Based on the two week Ki67-IHC, patients were randomized (Ki67 ≥1%) to receive either Letrozole + Ribociclib or standard chemotherapy until surgery, or continued (Ki67 &amp;lt; 1%) Letrozole mono therapy. Here we describe the signal transduction pathway profiles to better understand the molecular mechanisms of response to neoadjuvant letrozole. Methods: Signal transduction pathway activities for the ER, AR, MAPK, PI3K, HH, TGFβ and Notch pathways were measured on baseline and two weeks samples using the OncoSIGNal qPCR test (InnoSIGN). High pathway activity in a tumor sample was defined as pathway activity value above the 95th percentile of reference normal epithelial breast tissue. The pathway activity patterns of the Ki67 &amp;lt; 1% (n=30) and Ki67 &amp;gt; 1% (n=63) groups were compared between baseline and two weeks of treatment. Results: Although all measured baseline samples (n=93) were ER IHC staining positive (≥50%), there is a large range in baseline ER signal transduction pathway activity (32 to 78 on a scale from 0 – 100) and 20% of the samples show an ER-activity range (32 - 45) that normally falls in the range of ER IHC stained negative breast tissue. The group with Ki67 &amp;gt; 1% after 2 weeks Letrozole treatment showed non elevated ER pathway activity at baseline more often (25%) compared to the Ki67 &amp;lt; 1% group (10%). 92% of the patients showed a decrease in ER pathway (11.6 ± 8.6) activity after 2 week letrozole treatment compared to baseline (p=8.5e-13). Interestingly, baseline AR pathway activity has a good differentiating predictive value for the two week response to letrozole treatment and the overall AR pathway activity score was higher in the low Ki67 group (51.4 ± 7.4) than in the Ki67 ≥ 1% group (46.7 ± 6.4; p=0.0053) and more often classified as high in 30% of the low Ki67 group vs. 13% of the Ki67 ≥ 1% group. The Ki67 &amp;gt; 1% group showed activation of non-hormonal pathways (PI3K, MAPK and/or HH) more frequent (38%) at baseline compared to the &amp;lt; 1% Ki67 group (19%). Conclusion: Positive ER staining does not always relate to a high ER pathway activity, possibly explaining that not all patients respond equally well to ER inhibition therapy. Activation of hormonal pathways (ER, but also AR) appear to be predictive for early (2 weeks) response towards Letrozole as assessed by Ki67 staining. Involvement of non-hormonal pathways is associated with less effective response towards Letrozole alone. Pathway activity patterns could improve insight to underlying hormonal treatment escape mechanisms which could lead to alternative treatment options in patients with ER-positive breast cancer. Citation Format: Nadia de Gruil, Anne Florine de Groot, Yvonne Wesseling-Rozendaal, Diederick Keizer, Sigi Neerken, Judith Kroep. Pathway profiling for prediction of response to neoadjuvant Letrozole therapy in ER positive postmenopausal breast cancer: gaining new insights for targeted treatment [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 PO5-21-06.

Abstract PO3-05-02: Impact of hormone receptor expression level in HR+/HER2- metastatic breast cancer in the large French ESME cohort

Abstract Background: In patients (pts) with early breast cancer (BC), the level of expression of estrogen receptor (ER) evaluated by immunohistochemistry is prognostic and predictive while progesterone receptor (PR) expression has an additional prognostic value. Allred scoring combines the percentage of positive cells and the intensity of staining. It is widely used for treatment choice for early BC. In metastatic setting, its role is less defined. Methods: The ESME database is a French National cohort of all consecutive pts who initiated a first-line treatment for metastatic BC (MBC) between January 2008 and December 2020 in one of the 18 French Comprehensive Cancer Centers (NCT03275311). For this study, we selected pts with HER2- MBC, known ER expression and intensity percentages, known PR status and who received endocrine-based therapy as first-line metastatic treatment. Primary objective was to evaluate the overall survival (OS) and first line progression-free survival (PFS1) under endocrine therapy according to ER and PR expression level. ER expression was defined using Allred score on the last available tumor sample. PR status was defined using a positive (≥10%)vs negative ( &amp;lt; 10%) threshold. Secondary objective was to evaluate clinical PFS1 whether de novo or recurrent MBC and according to type of first line therapy (mono- vs combined endocrine therapy). Results: In the ER+ ± PR+/HER2- population, 8269 pts had information on ER percentage and staining intensity. Median follow-up was 53.4 months (95%CI [51.9; 54.7]). Allred score distribution, OS and PFS1 are described in table 1. Median OS was 43.1 months [41.1; 45.0] for the PR- group compared with 52.3 months [50.5; 54.4] for the PR+ group. After adjustments, patients with a PR- tumour had still a worse prognosis (HR=1.20, 95%CI [1.12-1.28], p&amp;lt;0.001). Median PFS1 was 10.2 months[9.6; 10.8]and 14.8 months[14.2; 15.4] for pts with PR- vs PR+ tumour (HR=1.36 (1.29-1.43), p&amp;lt;0.001) and PR status remained significant prognostic factor independently of de novo or recurrent status and association or not with a targeted therapy. Conclusion: ER expression evaluated using the Allred scoring, as well as PR positivity, retain prognostic value in first-line MBC patients. Table 1 : OS and PFS according to Allred status, de novo status and type of endocrine therapy. * Selected variables on multivariate model include PR status, age, SBR grade, histological subtype, number of metastatic site, type of metastasis (non visceral, visceral, brain visceral), HER 2 (0 vs 1-2), metastatic-free interval, mono- vs combined endocrine therapy. Citation Format: Marie Alexandre, Florence Castan, Thibault De La Motte Rouge, Audrey Mailliez, Etienne Brain, Thomas Bachelot, Monica Arnedos, Florence Dalenc, Jean-Marc Ferrero, Vincent Massard, Isabelle Desmoulins, Marie-Ange Mouret-Reynier, Christelle Levy, Anthony Gonçalves, Anca Berghian, Aude-marie Savoye, Jean-Sébastien frenel, Lise Bosquet, Suzette Delaloge, William Jacot. Impact of hormone receptor expression level in HR+/HER2- metastatic breast cancer in the large French ESME cohort [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-05-02.

Abstract RF01-05: Functional assessment of RAD51 foci and replication fork dynamics in PARPi resistant BRCA1/2 mutated breast cancer

Abstract Background: Although platinum salts (Pt) or Poly (ADP-Ribose) Polymerase inhibitors (PARPi) are effective in treating homologous recombination defective (HRD) breast cancer, resistance often emerges, especially in advanced disease. Predicting response and relapse is complex, even in patients with germline BRCA1/2 mutations (gBRCA1/2m). Clinically approved HRD detection methods are limited to identification of pathogenic mutations in HR genes or mutational signatures in the genome of tumors caused by HRD. In PDX models derived from HRD breast cancer, the restoration of nuclear RAD51 foci formation, a key feature of functional HR, can predict resistance to HRD-targeted treatment.1 In addition, the restoration of replication fork stability, despite PARPi or induction of Pt adducts that induce replication fork arrest and collapse, confers resistance in pre-clinical models2; to date this resistance mechanism has not been clinically validated. Here we analyse RAD51 foci in FFPE samples and DNA replication fork dynamics, using DNA fibre combing assays, in patient derived organoids (PDO) relating these to clinical response to illustrate how such assays might predict clinical HRD-targeted therapy resistance in metastatic breast cancer (MBC). Patients and Methods: We used immunofluorescent detection of RAD51 foci as a marker for HR proficiency (HRP) in tumors from 29 patients with gBRCA1/2m with MBC treated with HRD-targeted treatment (n=6 PARPi, n=2 Pt and n=21 both agents in sequence). All patients developed resistance that was either de novo or acquired. RAD51 and BRCA1 foci were scored in a minimum of 50 geminin (a marker of S/G2 phase) positive tumor cells; cells with ≥5 foci were classified as positive, and tumours where ≤10% or &amp;gt;10% of cells were positive were considered HRD or HRP, respectively. DNA replication fork dynamics were assessed in with or without PARPi using thymidine analogue labelling. DNA fibre analysis was performed in PDOs developed from fresh tumor sampling of HRD-targeted treatment sensitive or resistant tumors, to determine the relationship between replication fork dynamics, stability and PARPi sensitivity. Results: RAD51 analysis was performed on 9 treatment naïve samples (n=9 patients), 8 samples obtained after HRD-targeted treatment resistance (n=8 patients) and 27 samples obtained pre and post HRD-targeted treatment resistance (n=12 patients). Functional HRD by RAD51 in treatment naive samples was seen in 100% (n=17) of patients with acquired resistance and 66% of patients with de novo resistance. All patients, whether with de novo or acquired resistance, exhibited high RAD51 scores in post-resistance tumour samples, suggesting restoration of HR function is the dominant mechanism of PARPi resistance. As such, RAD51 analysis shows potential as a biomarker of clinical PARPi resistance. Replication fork stability fibre was analysed after exposure to potent PARP1 trapping inhibitors or an ATRi control in 3 PDOs (2 gBRCA1m, 1 BRCAwt). As controls we used an isogenic 2D cell line with and without a CRISPR engineered BRCA1 reversion mutation (SUM149 parental BRCA1m and SUM149BS*1 revertant) or with a PARP1 mutation (SUM149 TR2 clone) that prevents PARP1 being trapped on DNA. These experiments indicate that replication fork dynamics can be assessed in “patient derived” models of breast cancer and that PARPi sensitivity was associated with PARPi induced replication fork instability (median ratio IdU:CldU in resistant lines: 0.98, sensitive lines: 0.60). Conclusion: We show that HRP restoration and RAD51 foci in advanced BRCA1/2m breast cancers is the dominant form resistance to HRD-targeted treatment. We also demonstrate for the first time that analysis of DNA replication fork dynamics can be carried out in breast cancer PDOs and could be further explored as a functional predictive biomarker of PARPi resistance. 1.Pellegrino et al, 2022 (PMID: 35425960) 2.Chaudhuri et al, 2016 (PMID: 27443740) Citation Format: Elizabeth Harvey-Jones, Maya Raghunandan, Luisa Robbez-Masson, Thanussuyah Alaguthurai, Alba Llop-Guevara, Jennifer Trendell, Olga Rodriguez, Marta Guzman, Daniel Weekes, Christelle deRenty, Eleanor Knight, Rebecca Marlow, Christopher Starling, Ruifang Liu, Nivedita Ravindran, Ioannis Roxanis, Natalia Lukashchuk, Violeta Serra, Stephen Pettitt, Christopher Lord, Andrew NJ Tutt. Functional assessment of RAD51 foci and replication fork dynamics in PARPi resistant BRCA1/2 mutated 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 RF01-05.