Defective DNA Mismatch Repair Research Articles

Abstract PO1-13-05: Genomic characteristics and its therapeutic implications in breast cancer patients with detectable molecular residual disease

Abstract Background: Breast cancer constitutes approximately 30% of cancers in women, with a mortality-to-incidence ratio of 15%. While early and middle-stage breast cancer patients can undergo radical surgical resection, postoperative recurrence remains a significant challenge for clinicians. Molecular residual disease (MRD) is the main cause of postoperative recurrence of breast cancer. However, the baseline tumor genomic characteristics and therapeutic implications of breast cancer patients with detectable MRD are still unknown. Methods: In this study, we enrolled 80 patients with breast cancer who underwent next-generation sequencing (NGS)-based genetic testing of 1,021 cancer-related genes performed on baseline tumor and postoperative plasma from Army Specialty Medical Center between June 2017 and January 2023. The criteria for the patient’s enrollment were: (1) pathological diagnosis as breast cancer, (2) no distal metastasis, (3) radical surgery and R0 resection, (4) 1021 cancer-related gene testing of the tumor, (5) plasma MRD testing performed within 3 months after surgery and before adjuvant therapy. Results: A total of 18 patients in our cohort had detectable MRD. Baseline clinical characteristics found that patients with higher clinical stages were more likely to have detectable MRD. Analysis of single nucleotide variations and small insertions/deletions in baseline tumors showed that somatic mutations in MAP3K1, ATM, FLT1, GNAS, POLD1, SPEN, and WWP2 were significantly enriched in patients with postoperative MRD. Oncogenic signaling pathway analysis revealed that alteration of the Cell cycle pathway was more likely to occur in patients with detectable MRD (p=0.0125). Mutational signature analysis showed that defective DNA mismatch repair and activation-induced cytidine deaminase (AID) mediated somatic hypermutation (SHM) were associated with detectable MRD. Somatic copy number variation analysis found that amplification of CDKN2A, HOXB13, PPM1D, MPL, and VHL was significantly enriched in patients with detectable MRD. According to the OncoKB database, 77.8% (14/18) of patients with detectable MRD had U.S. Food and Drug Administration-approved mutational biomarkers and targeted therapy. Conclusion: For the first time, our study reports genomic characteristics of breast cancer patients with detectable MRD. The tumor biology is probably the main driver of detectable MRD. We also found the vast majority of patients with detectable MRD have the opportunity to access targeted therapy. Keywords: Breast cancer, MRD, Genomic character, Cell cycle pathway, Defective DNA mismatch repair, Activation-induced cytidine deaminase Figure 1. Somatic mutational landscape and clinical actionability of breast cancer patients with detectable MRD A. Oncoplot of top 20 genes altered in patients with detectable MRD. B. Forest plot of different mutant genes between patients with detectable and undetectable MRD. OR means odds ratio. Inf means infinity. ＊ means P-value < 0.05. C. The ten cancer-related signaling pathways were affected by somatic mutations both in patients with detectable and undetectable MRD. ＊ means P-value < 0.05. D&E. The fraction and etiology of each signature in patients with detectable (D) or undetectable (E) MRD. F. The number of patients with detectable MRD in different actionable alterations. gBRCA1 means germline BRCA1 mutation. sBRCA1 means somatic BRCA1 mutation. sBRCA2 means somatic BRCA2 mutation. TMB-H means TMB-High. Citation Format: Xu Yan, Shu Zhang, Lu zhou, Yan Jiang, Jing Xu, Gang Zhang, Lu Shen. Genomic characteristics and its therapeutic implications in breast cancer patients with detectable molecular residual disease [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-13-05.

Abstract PO2-07-06: Multimodal learning predictor of HER2-positive breast cancer therapy response in the randomized PREDIX HER2 trial

Abstract Background: The PREDIX HER2 trial, compared six courses of docetaxel, trastuzumab, and pertuzumab (DTP) vs. trastuzumab emtansine (T-DM1) as neoadjuvant treatment for HER2-positive breast cancer (BC). Similar rates of pathologic complete response (pCR) were seen. Methods: Clinicopathological, shallow whole-genome sequencing (CUTseq, n=176), whole exome sequencing (WES, n=192), and RNA-sequencing (RNA-seq, n=187) data were generated using fresh-frozen baseline core biopsies. Potential tumor intrinsic resistance factors and microenvironment components were quantified by multi-omics analysis, including BC-specific somatic mutations and copy number alterations (CNA), COSMIC mutational signatures, CNA-based chromosomal instability signatures (CIN), subclone percentage, PAM50 subtype, GGI/PIK3CA score, HER2DX score, immune profiles (Danaher signature score, TIDE score and immune repertoires). We assessed the association of biomarkers with pCR in each treatment arm using logistic regression adjusting for hormone receptor (HR) status, and evaluated their predictive value by adding the interaction term (biomarker x treatment arm). In addition, a machine learning (ML) analysis was conducted from different classifiers, comprising unimodal ML-based models from clinical, RNA and DNA information, respectively. Model performance was assessed using the mean and standard deviation (mean ± std) of the area under receiver operator characteristic curve (AUC), positive predictive value (PPV) and negative predictive value (NPV) using a nested stratified cross-validation (CV) schema of 200 outer shuffle splits and 100 inner 5-fold CV to mitigate potential risk of overfitting. Results: In DTP arm, patients with higher ERBB2 copy ratio (ORadj=1.98, p=0.004) or mRNA (ORadj=3.08, p< 0.001) or HER2-enriched subtype (PAM50) (ORadj=1.78, p=0.02) had higher pCR rates, while ESR1 gene expression (ORadj=0.59, p=0.07) predicted treatment resistance despite adjustment for HR status. Conversely, response to T-DM1 was less likely to depend on ERBB2 profiles and only PAM50 HER2 enriched subtype (ORadj=1.53, p=0.1) showed higher pCR rate (52% vs. 25%) than other subtypes. Both ESR1 (ORadj=0.4, p=0.008) and PGR (ORadj=0.5, p=0.03) gene expression were independent predictors of T-DM1 resistance. Pre-treatment immune exclusion metrics could predict resistance to DTP (endothelial cell, ORadj=0.67, p=0.07) and T-DM1 (neutrophils, ORadj=0.54, p=0.02; mast cells, ORadj=0.57, p=0.02; cancer-associated fibroblasts, ORadj=0.67, p=0.09)), respectively. Predefined metrics such as PIK3CA signature score (ORadj =1.67, p=0.04) and Taxane response score (ORadj =1.64, p=0.03) were positively related to pCR in DTP arm. Genome instability, involving CIN CX2 signature (impaired homologous recombination) (ORadj=1.71, p=0.05), COSMIC signature6 (ORadj =1.53, p=0.07) and signature13 (ORadj =1.57, p=0.05), predicted benefit from DTP. The biomarker-treatment interaction tests were significant for HER2DX (pinteraction=0.004) and COSMIC signature15 (defective DNA mismatch repair) (pinteraction=0.007): lower HERDX score (ORadj =0.73, p=0.14) or higher COSMIC signature15 score (ORadj =1.51, p=0.1) could identify patients benefiting from T-DM1, while being resistant to DTP (HERDX: ORadj =1.46, p=0.13; signature15: ORadj =0.70, p=0.1). In the ML models, clinical information yielded an AUC=0.62±0.07, PPV=0.64±0.12 and NPV=0.64±0.06; for DNA data, AUC was equal to 0.70±0.08, PPV=0.72±0.09 and NPV=0.71±0.07; an adaptive boosting ensemble learning on RNA reported slightly increased pCR prediction performance (AUC=0.72±0.06, PPV=0.64±0.06, NPV=0.80±0.09). Conclusion: This study demonstrates that antibody–drug conjugates and standard treatment harbor strikingly distinctive biomarkers across tumor ecosystem. Further external validation and integrated ML model comprising all unimodal models are ongoing. Citation Format: Kang Wang, Yajing Zhu, Ioannis Zerdes, Emmanouil Sifakis, Georgios Manikis, Dimitrios Salgkamis, Nikolaos Tsiknakis, Luuk Harbers, Nicola Crosetto, Jonas Bergh, Alexios Matikas, Thomas Hatschek, Theodoros Foukakis. Multimodal learning predictor of HER2-positive breast cancer therapy response in the randomized PREDIX HER2 trial [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-07-06.

The immune response-related genomic alterations in patients with malignant melanoma.

Immune checkpoint inhibitors (ICIs) significantly improve the survival outcomes of patients with advanced melanoma. However, response varies among from patient to patient and predictive biomarkers are urgently needed. We integrated mutational profiles from next-generation sequencing (NGS) data and clinicopathologic characteristics of melanoma patients to investigate whether tumor genomic profiling contribute to clinical benefit of ICIs treatment. The majority of genes identified with high mutation frequency have all been reported as well-known immunotherapy-related genes. Thirty-five patients (43.2%) had at least 1 BRAF/RAS/NF1 mutation. The other 46 (56.8%) melanomas without BRAF/RAS/NF1 mutation were classified as Triple-WT. We identified mutational signature 6 (known as associated with defective DNA mismatch repair) among cases in this cohort. Compared to patients with PD-L1 expression (TPS < 1%), patients with PD-L1 expression (TPS ≥ 1%) had significantly higher median progression-free survival (mPFS), but no significantly higher durable clinical benefit (DCB) rate. In contrast, FAT1, ATM, BRCA2, LRP1B, and PBRM1 mutations only occurred frequently in patients with DCB, irrespective of PD-L1 expression status. Our study explored molecular signatures of melanoma patients who respond to ICIs treatment and identified a series of mutated genes that might serve as predictive biomarker for ICIs responses in melanoma.

Genomic Characteristics and Its Therapeutic Implications in Breast Cancer Patients with Detectable Molecular Residual Disease.

Molecular residual disease (MRD) is the main cause of postoperative recurrence of breast cancer. However, the baseline tumor genomic characteristics and therapeutic implications of breast cancer patients with detectable MRD after surgery are still unknown. In this study, we enrolled 80 patients with breast cancer who underwent next-generation sequencing-based genetic testing of 1,021 cancer-related genes performed on baseline tumor and postoperative plasma, among which 18 patients had detectable MRD after surgery. Baseline clinical characteristics found that patients with higher clinical stages were more likely to have detectable MRD. Analysis of single nucleotide variations and small insertions/deletions in baseline tumors showed that somatic mutations in MAP3K1, ATM, FLT1, GNAS, POLD1, SPEN, and WWP2 were significantly enriched in patients with detectable MRD. Oncogenic signaling pathway analysis revealed that alteration of the Cell cycle pathway was more likely to occur in patients with detectable MRD (p=0.012). Mutational signature analysis showed that defective DNA mismatch repair and activation-induced cytidine deaminase (AID) mediated somatic hypermutation (SHM) were associated with detectable MRD. According to the OncoKB database, 77.8% (14/18) of patients with detectable MRD had U.S. Food and Drug Administration-approved mutational biomarkers and targeted therapy. Our study reports genomic characteristics of breast cancer patients with detectable MRD. The cell cycle pathway, defective DNA mismatch repair, and AID-mediated SHM were found to be the possible causes of detectable MRD. We also found the vast majority of patients with detectable MRD have the opportunity to access targeted therapy.

Abstract LB395: NetraAI-driven discovery of novel biomarkers in MSI-high colon cancer for precision immunotherapy

Abstract By leveraging NetraAI, a novel machine learning (ML) approach, we identify potential biomarkers in microsatellite instability-high (MSI-H) colon cancer. MSI, marked by DNA mismatch repair (MMR) defects characterizes 5-20% of colorectal cancers (CRCs). MSI-H tumors harbor higher mutational burdens, produce neoantigens, and enhance immune recognition and responsiveness to immunotherapy. The innovative Sub-Insight Learning approach of NetraAI, allows us to overcome challenges associated with smaller data sets not reflecting the totality of the disease they represent. This approach utilizes a set of validated mathematical methods to identify sub-insights about patients even from small data sets. This allows the system to decompose the data sets into high and low confidence patient subpopulations, enhancing predictive model accuracy and reducing overfitting. Further, the system explains what variables are driving the etiology defining the subpopulations of patients. Utilizing a small data set consisting of 141 RNA expression profiles of CRC samples (E-GEOD-41258) with MSI-H and MSI-low colon cancer, we were able to derive several unique insights into patients’ molecular profiles. NetraAI analysis identified several unique variables, including CATSPERB, FUT8, PLLP, DUSP4, and MLPH that may play significant roles in MSI-H colon cancer pathology. These markers hold potential for personalizing clinical trials as well as potential therapeutic targets. Furthermore, protein-protein interaction (PPI) networks revealed co-expression and co-localizations that exist amongst these genes, suggesting a complex interplay among these genes, particularly in the context of spermatogenesis. The application of NetraAI and its Sub-Insight Learning paradigm has revealed novel insights into the molecular profile of MSI-H colon cancer. These findings pave the way for more targeted and effective precision immunotherapy strategies, demonstrating the power of AI in advancing the understanding and treatment of complex cancers. Citation Format: Bessi Qorri, Mike J. Tsay, Paul Leonchyk, Larry Alphs, Luca Pani, Joseph Geraci. NetraAI-driven discovery of novel biomarkers in MSI-high colon cancer for precision immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB395.

Abstract 6011: Pharmacological inhibition of PMS2 increases tumor mutational burden, induces microsatellite instability and elicits immune mediated rejection in vivo

Abstract Tumors carrying defects in DNA mismatch repair (MMR-d) display high tumor mutational burden (TMB) and increased tumor neoantigen levels. MMR-d leads to accumulation of single nucleotide variants (SNVs) and insertions or deletions (indels) amongst repetitive DNA sequences generating microsatellite instability (MSI). Cancers that harbor &amp;gt;40% microsatellite variations are described as MSI-high (MSI-H). These tumors display unique clinical features including better prognosis, increased immune infiltration and remarkable response to immune checkpoint blockade (ICB) therapy. Colorectal cancer (CRC) patients with MMR-d often respond to therapies based on immune checkpoint blockade, whilst those with mismatch repair proficient (MMR-p) tumors do not. Therefore, identifying strategies to enhance the efficacy of immunotherapeutic treatments and transform this prevalent subgroup of CRCs from immunologically cold to hot remains an urgent and an unmet clinical need. We discovered NP1867 a first-in-class, potent, selective, covalent small molecule inhibitor of the DNA Mismatch Repair protein PMS2. We show by biochemical, biophysical, and protein-ligand X-ray crystallographic methods that NP1867 binds irreversibly to the ATP binding site of the N-terminal ATPase domain of PMS2. NP1867 displays potent binding to PMS2 in a NanoBRET cellular target engagement assay and inhibits MMR activity in mechanistic and functional cell-based assays of MMR-dependent DNA repair. Continuous treatment of murine CRC cell line CT26 (MMR-p) with NP1867 increases TMB, specifically enriches gained mutations with typical MMR-d related COSMIC mutational signatures, and elicits MSI-H status in a time-dependent manner, demonstrating for the first time that inhibition of PMS2 with a small molecule phenocopies the inactivation of MMR observed in patients. Remarkably, inoculation of immune-competent mice with CT26 cells pre-treated with NP1867 elicits tumor regressions in anti-PD1-treated animals, recapitulating the unique clinical features of MMR-d/MSI-H tumors. Conversely, no response is observed in immune-competent animals inoculated with control-treated cells. The extent of in vivo response correlates with the duration of in vitro NP1867 treatment and with the MSI-H status of treated CT26 cells. In conclusion, small molecule NP1867 functionally inhibits DNA MMR by targeting PMS2, enriches gained mutations with MMR-d COSMIC signatures, elicits MSI-H status, and enhances immune surveillance in preclinical models. These findings pave the way for the development of orally bioavailable compounds suitable for long-term dosing in animal models. Citation Format: Eleonora Piumatti, Alexia Hervieu, Philippe Riou, Julian Blagg, Adam Peall, Sam Weeks, Maria T. Rodríguez-Plata, Giuseppe Rospo, Sasi Arunachalam, Bettina Meier, Paige Tongue, Tessa McLaren, Kalpesh Parmar, Pradip Patel, David Clark, Gareth Langley, Charles Nichols, Benoît Rousseau, Paul Winship, Matthew Baker, Martin Drysdale, Giovanni Germano, Alberto Bardelli. Pharmacological inhibition of PMS2 increases tumor mutational burden, induces microsatellite instability and elicits immune mediated rejection in vivo [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 6011.

Abstract 4096: Comparative molecular profiling of sporadic and Lynch syndrome MSI tumors: Unraveling insights for vaccine design

Abstract Lynch Syndrome (LS) is a hereditary syndrome that predisposes carriers to colorectal cancer (CRC). The hallmark of LS is microsatellite instability (MSI), resulting from a defective DNA mismatch repair (MMR) system. MSI cases have hyper-elevated frameshift mutation rates including “shared” hotspot mutations recurrently across patients. Frameshift mutations can generate neopeptides that activate the immune system. These open the door for preventive vaccines. However, preventive vaccines work best with neopeptides that happen early during tumorigenesis. Here we present 83 newly sequenced adenomas and carcinomas from Lynch syndrome carriers and combine them with previously published 68 Lynch cases and 133 Sporadic cases, thus generating the largest currently available colorectal neoplasia MSI cohort. We leveraged this large cohort to analyze the molecular landscape of adenomas vs carcinoma tumors and Lynch vs sporadic tumors. Employing our recently developed MSIDetect tool on our WGS samples, we identified microsatellite instability in 75% of adenomas, which is higher than previously reported. We found that about 30% of normal adjacent tissues showed MSI, suggesting early mismatch repair defects. This early MSI occurrence supports the potential effectiveness of preventive vaccines. We observed comparable levels of SNVs, microsatellite Indels, and single base signature activity among Lynch adenomas and carcinomas, as well as sporadic carcinomas while adjusting for variations in coverage across different datasets. Moreover, using RNA sequencing data and PCA analysis we found that adenoma and carcinoma cluster together. This large cohort enabled us to identify (as fast as we know for the first time) MS-indels that tend to have a second MS-indel in the same locus. The high similarities observed between Lynch and sporadic tumors allow for their combination in one vaccine. Using the combined MSI cohort we generated a set of about 300 neopeptides that emerged from frequent mutations (&amp;gt;5% in our cohort) with a strong binding affinity for at least one HLA type. We evaluated that a set of about 60 neopeptides per person from that list is predicted likely to initiate an immune response in ~99.5% of the carriers. These findings hold promise for the development of a preventive vaccine capable of targeting early tumorigenic stages. This work is approved under Weill Cornell IRB exemption 1810019672. Citation Format: Hagay Ladany, Mark Grossman, Julian Hess, Nicole Lu, Derin Keskin, Catherine J. Wu, Nir Hacohen, Richard Gallon, John Burn, Heather Hampel, Zsofia Stadler, Gad Getz, Yosef E. Maruvka, Steven Lipkin. Comparative molecular profiling of sporadic and Lynch syndrome MSI tumors: Unraveling insights for vaccine design [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 4096.

Abstract 2276: Comprehensive analysis of the genomic landscape of thyroid cancer

Abstract Thyroid cancer, the most common endocrine malignancy, has a high incidence worldwide. Meanwhile, the incidence of thyroid cancer ranks first in Korea. To assess the possible influence of ethnicity on the molecular profile of thyroid cancer, we compared the genomic features of South Korean thyroid cancer with European thyroid cancer. In this study, we performed whole genome sequencing profiling (WGS) for 459 Korean thyroid cancer patients, including papillary thyroid carcinoma (PTC, n = 274), noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP, n =18), follicular thyroid carcinoma (FTC, n = 16), follicular thyroid adenoma (FTA, n = 63), Hürthle cell adenoma (HCA, n = 22), and invasive encapsulated follicular variant papillary thyroid carcinoma (IEFVPTC, n = 19). We assessed the single nucleotide variant (SNV) and insertions and deletions using Mutect2, Varscan2, and Strelka2. For mutation signature and copy number alterations analysis, we used the Maftools and GISTIC2.0 packages, respectively. Our results revealed that most somatic mutations were similar between the Korean thyroid cancer dataset and the cancer genome atlas program (TCGA). However, the Korean cohort (1%) had a much lower NRAS mutation frequency than the TCGA cohort (8%). Mutation signature analysis showed that SBS6 and SBS2 were highly associated with the TCGA and Korean cohort. SBS6 is related to defective DNA mismatch repair, and SBS2 is characterized predominantly by CC &amp;gt; TT doublet base substitutions. In addition, we identified the NIFTP-specific somatic mutations such as KEAP1 and ZFP36L2. This study presents insights into the genomic landscape of Korean thyroid cancer and reveals some similarities and differences with European thyroid cancer at the molecular level. Citation Format: SooHyun Im, Jong-Lyul Park, Jae-Yoon Kim, Chan-Kwon Jung, Seon-Young Kim. Comprehensive analysis of the genomic landscape of thyroid 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 2276.

Whole‑exome sequencing reveals Lewis lung carcinoma is a hypermutated Kras/Nras–mutant cancer with extensive regional mutation clusters in its genome

Lewis lung carcinoma (LLC), as a widely used preclinical cancer model, has still not been genetically and genomically characterized. Here, we performed a whole–exome sequencing analysis on the LLC cell line to elucidate its molecular characteristics and etiologies. Our data showed that LLC originated from a male mouse belonging to C57BL/6L (a transitional strain between C57BL/6J and C57BL/6N) and contains substantial somatic SNV and InDel mutations (> 20,000). Extensive regional mutation clusters are present in its genome, which were caused mainly by the mutational processes underlying the SBS1, SBS5, SBS15, SBS17a, and SBS21 signatures during frequent structural rearrangements. Thirty three deleterious mutations are present in 30 cancer genes including Kras, Nras, Trp53, Dcc, and Cacna1d. Cdkn2a and Cdkn2b are biallelically deleted from the genome. Five pathways (RTK/RAS, p53, cell cycle, TGFB, and Hippo) are oncogenically deregulated or affected. The major mutational processes in LLC include chromosomal instability, exposure to metabolic mutagens, spontaneous 5–methylcytosine deamination, defective DNA mismatch repair, and reactive oxygen species. Our data also suggest that LLC is a lung cancer similar to human lung adenocarcinoma. This study lays a molecular basis for the more targeted application of LLC in preclinical research.

Whole exome sequencing uncovers HRAS mutations as potential mediators of resistance to metronomic chemotherapy

ObjectivesThe aim of this pilot study is to identify the genetic factors that contribute to the response of metronomic chemotherapy in head and neck squamous cell carcinoma (HNSCC) patients using whole-exome sequencing (WES). This study would facilitate the identification of predictive biomarkers, which would enable personalized treatment strategies and improve treatment outcomes for patients with HNSCC. Materials and MethodsWe have selected patients with recurrent head and neck cancer who underwent metronomic chemotherapy. Sequential tumor biopsies were collected from the patients at different stages of treatment to capture the genomic alterations and tumor evolution during metronomic chemotherapy and sequenced using WES. ResultsWe identified several known HNSCC hallmark genes reported in COSMIC, including KMT2B, NOTCH1, FAT1, TP53, HRAS, CASP8, and CDKN2A. Copy number alteration analysis revealed amplifications and deletions in several oncogenic and tumor suppressor genes. COSMIC Mutational Signature 15 associated with defective DNA mismatch repair was enriched in 73% of HNSCC samples. Further, the comparison of genomic alterations between responders and non-responders identified HRAS gene uniquely mutated in non-responders that could potentially contribute to resistance against metronomic chemotherapy. DiscussionOur findings corroborate the molecular heterogeneity of recurrent HNSCC tumors and establish an association between HRAS mutations and resistance to metronomic chemotherapy, suggesting HRAS as a potential therapeutic target. Combining HRAS inhibitors with metronomic regimens could improve treatment sensitivity in HRAS-mutated HNSCC patients. Further studies are needed to fully elucidate the genomic mechanisms underlying the response to metronomic chemotherapy.

[Histology-agnostic tumor treatment - a farewell to tumor entities?]

Considerable efforts concerning the molecular characterization and targeted treatment of cancer have significantly improved treatment options and prognosis of tumor patients. Nevertheless, in tumor entities without recurrent genetic alterations the application of molecular testing for potentially targetable lesions remains heterogeneous and, in most cases, the approval of targeted therapies is still restricted to defined tumor entities harboring corresponding predictive biomarkers.The broad genomic analysis of different tumor entities including rare cancers within several genome sequencing initiatives and precision oncology programs has revealed the occurrence of addressable molecular alterations across many tumor entities, although their incidence may differ significantly in the context of the underlying cancer type. The treatment of molecularly defined patient cohorts demonstrated an impressive tumor-agnostic efficacy of certain therapeutics such as NTRK inhibitors, while the outcome of other targeted therapies, such as ERBB or BRAF inhibitors, varied in the context of the underlying disease.In the meantime, a handful targeted therapeutics addressing NRTK and RET fusions, the BRAF V600E mutation or different features of defective DNA mismatch repair and high tumor mutational burden has been approved for histology-agnostic treatment of tumors harboring these target lesions. Ongoing molecularly stratified basket trials will further investigate the tumor-agnostic efficacy of different targeted treatment approaches.

Genomic characteristics of triple negative apocrine carcinoma: a comparison to triple negative breast cancer.

Apocrine carcinoma is a rare breast cancer subtype. As such, the genomic characteristics of apocrine carcinoma with triple negative immunohistochemical results (TNAC), which has been treated as triple negative breast cancer (TNBC), have not been revealed. In this study, we evaluated the genomic characteristics of TNAC compared to TNBC with low Ki-67 (LK-TNBC). In the genetic analysis of 73 TNACs and 32 LK-TNBCs, the most frequently mutated driver gene in TNAC was TP53 (16/56, 28.6%), followed by PIK3CA (9/56, 16.1%), ZNF717 (8/56, 14.3%), and PIK3R1 (6/56, 10.71%). Mutational signature analysis showed enrichment of defective DNA mismatch repair (MMR)-related signatures (SBS6 and SBS21) and the SBS5 signature in TNAC, whereas an APOBEC activity-associated mutational signature (SBS13) was more prominent in LK-TNBC (Student's t test, p < 0.05). In intrinsic subtyping, 38.4% of TNACs were classified as luminal A, 27.4% as luminal B, 26.0% as HER2-enriched (HER2-E), 2.7% as basal, and 5.5% as normal-like. The basal subtype was the most dominant subtype (43.8%) in LK-TNBC (p < 0.001), followed by luminal B (21.9%), HER2-E (21.9%), and luminal A (12.5%). In the survival analysis, TNAC had a five-year disease-free survival (DFS) rate of 92.2% compared to 59.1% for LK-TNBC (P = 0.001) and a five-year overall survival (OS) rate of 95.3% compared to 74.6% for LK-TNBC (P = 0.0099). TNAC has different genetic characteristics and better survival outcomes than LK-TNBC. In particular, normal-like and luminal A subtypes in TNAC have much better DFS and OS than other intrinsic subtypes. Our findings are expected to impact medical practice for patients diagnosed with TNAC.

Mutational pattern off homologous recombination repair (HRR)-related genes in upper tract urothelial carcinoma.

Homologous recombination (HR) repair (HRR) has been indicated to be a biomarker for immunotherapy, chemotherapy, and poly-ADP ribose polymerase inhibitors inhibitors (PARPis). Nonetheless, their molecular correlates in upper tract urothelial carcinoma (UTUC) have not been well studied. This study aimed to explore the molecular mechanism and tumor immune profile of HRR genes and the relevance of their prognostic value in patients with UTUC. One hundred and ninety-seven tumors and matched blood samples from Chinese UTUC were subjected to next-generation sequencing. A total of 186 patients from The Cancer Genome Atlas were included. Comprehensive analysis was performed. In Chinese patients with UTUC, 5.01% harbored germline HRR gene mutations, and 1.01% had Lynch syndrome-related genes. A total of 37.6% (74/197) of patients carried somatic or germline HRR gene mutations. There was marked discrepancy in the mutation landscapes, genetic interactions, and driver genes between the HRR-mut cohorts and HRR-wt cohorts. Aristolochic acid signatures and defective DNA mismatch repair signatures only existed in individuals in the HRR-mut cohorts. Inversely, the unknown signature (signature A) and signature SBS55 only existed in patients in the HRR-wt cohorts. HRR gene mutations regulated immune activities by NKT cells, plasmacytoid dendritic cells, hematopoietic stem cell, and M1 macrophages. In patients with local recurrence, patients with HRR gene mutations had poorer DFS rates than patients with wild-type HRR genes. Our results imply that the detection of HRR gene mutations can predict recurrence in patients with UC. In addition, this study provides a path to explore the role of HRR-directed therapies, including PARPis, chemotherapy, and immunotherapy.

Lynch screening and genetic testing in endometrial cancer in a diverse population.

e17619 Background: Lynch syndrome (LS) accounts for most of the inherited endometrial cancers. Universal screening of endometrial tumors for defects in DNA mismatch repair (MMR) is recommended using immunohistochemistry (IHC) to identify which patients qualify for genetic counseling and testing. We report Lynch screening and genetic testing rates at a New York City tertiary care center with a large minority population, while investigating any potential disparities. Methods: This is a retrospective cohort study of patients with newly diagnosed endometrial cancer between January 2014 and June 2022. Data were obtained from pathology and chemotherapy databases at the NewYork-Presbyterian Brooklyn Methodist Hospital. Variables including age, race, ethnicity, BMI, insurance, language, family history of cancer, date of diagnosis, stage, MMR IHC, and genetic counseling/testing status were manually extracted. Descriptive statistics were used. Chi-square/Fisher’s exact tests were used to examine the association between genetic counseling/testing and categorical variables. Wilcoxon rank-sum/t-tests were used for continuous factors. The Mann-Kendall trend test was used to determine the significance of time trends. Results: 373 patients were identified. 45% identified as white, 42% black, 1.3% Asian, 12% other/unknown; 8.3% were of Hispanic ethnicity and 18% were non-English speaking. Mean age at diagnosis was 66 years (SD:10). 207 (55%) patients were screened using MMR IHC. 82 (40%) of these patients had MMR deficiencies on IHC. Of these, 63 (77%) received genetic counseling. 62 (98%) of those counseled subsequently underwent genetic testing, and ultimately 7 (11%) were diagnosed with LS. The overall rate of LS detected was 1.9% in the study population. The rate of MMR IHC testing has been increasing, reaching 95% in 2021 and 100% in 2022. It was associated with significant differences in mean age at diagnosis (p &lt; 0.01) and insurance type (p = 0.04). 45% of patients that received MMR IHC had private insurance, compared to 34% of patients that did not. The rate was not influenced by race, language, BMI, family history of cancer, or stage. The proportion of patients that received genetic counseling and testing for endometrial cancer also showed a significant upwards trend over time (p &lt; 0.01). Genetic counseling and testing rates were significantly different by ethnicity (p = 0.03), with only 3.0% of patients receiving genetic counseling/testing identifying as Hispanic. 98% of genetic counseling was performed by a gynecologic oncologist, as opposed to a genetic counselor. Conclusions: There were no disparities in access to initial IHC screening in this diverse patient population, however more work must be done to reach all ethnicities for genetic counseling and testing. The rate of LS detected was less than the known prevalence in endometrial cancer, possibly indicating demographic differences or gaps in screening.

Immune checkpoint inhibition in locally advanced rectal adenocarcinoma at Mayo Clinic.

e15626 Background: Studies have shown the effectiveness of immune checkpoint inhibition (ICI) in patients with tumors demonstrating microsatellite instability (MSI-H) and an associated defect in DNA mismatch repair (dMMR). In particular, KEYNOTE-177 demonstrated significant survival benefit for patients with unresectable or metastatic colorectal cancer with MSI-H or dMMR. Recently published case reports and series have demonstrated similar outcomes for patients with locally advanced and resectable rectal cancer. We report on the experience of patients with locally advanced, resectable rectal adenocarcinoma treated across the Mayo Clinic Health System. Methods: We conducted a retrospective analysis of patients treated at Mayo Clinic since 2015 A search of the Mayo Clinic database was done to include parameters for confirmed rectal adenocarcinoma, dMMR in pathology reports. Patients receiving ICI treatment including pembrolizumab, nivolumab/ipilimumab and durvalumab in any combination with chemotherapy and/or radiation were included. Patients with metastatic disease at the time of surgical intervention or ICI were excluded. Clinical data was assimilated. Results: Twenty-one patients met criteria for inclusion in our analysis. Fifteen patients had de novo disease. Six patients had local recurrence and had been treated previously with chemotherapy, radiation (RT) and surgery. None of the patients included had prior ICI therapy. Fifteen patients had Lynch syndrome. The median age of diagnosis was 41.5 years. Seven patients underwent surgical intervention. of the seven patients received surgery upfront followed by immunotherapy. The remaining six had neoadjuvant immunotherapy alone or in combination with chemotherapy and/or radiation. Prior to surgery, all patients demonstrated radiographic partial response (rPR). 67% of these demonstrated a pathologic complete response (pCR) while 33% had residual disease. The patient who received surgery upfront and adjuvant ICI continues to have radiographic stable disease after 1 year of treatment. For patients who did not have surgery, 50% had radiographic “complete or near complete” response (rCR), 43% had rPR and 7% had radiographic stable disease. Ten patients received RT and ICI with 70% demonstrating rCR and 30% rPR. Overall, the objective response rate was 90 Response to treatment was observed upwards of 75 months. Only 1 person in the study had progression of disease that occurred after 14 months of therapy. Conclusions: Similar to KEYNOTE-177, patients with locally advanced MSI-H/dMMR rectal cancer have significant and durable response to immunotherapy alone or in combination with chemotherapy, radiation and surgery. Further large prospective trials are needed to validate these findings and determine a standardized approach.

A pilot study evaluating somatic mutational burden and signatures among endometrial cancer patients: Is there prognostic benefit to whole genome sequencing?

e17629 Background: Whole genome sequencing (WGS) has emerged as a tool to characterize mutational burden and potentially identify new therapeutic targets and predictive biomarkers. In this study, we describe the mutational landscape of diverse patients with endometrial cancer using WGS and explore associations between mutations and clinicopathologic characteristics. Methods: Patients with endometrial cancer were prospectively consented and WGS was performed on tumors and blood. Using the the New York Genome Center Cancer pipeline, we identified high confidence somatic mutations in our patient cohort (identified by 2 or more variant callers). Somatic variants were categorized into mutational signatures based on the Catalog of Somatic Mutations in Cancer (COSMIC) v2. Associations between COSMIC signatures and clinicopathologic variables were evaluated using ANOVA tests. Results: Sixteen patients with endometrial cancer were enrolled; 10 (62.5%) self-identified as White, 4 (25.0%) as Black, and 2 (12.5%) as Asian. Tumor histology was endometrioid (13, 81.3%) or serous/clear cell (2, 12.5%), with both low grade (9, 56.3%) and high grade (7, 43.8%) tumors. The most frequently mutated genes were PTEN (15, 93.8%), ARID1A (9, 56.3%), PIK3CA (9, 56.3%), and TP53 (6, 37.5%). PIK3CA mutations were found in all mismatch repair (MMR) deficient tumors (5), compared to only 30.0% (3) of patients with intact MMR mechanisms (FDR p = 0.0256). Signature 3, associated with BRCA mutations and loss of DNA double-strand break-repair by homologous recombination, was enriched in p53 mutated tumors (p = 0.0036). Signature 1, associated with age, was enriched in patients with MMR intact tumors (p = 0.0475), while signatures 6 and 20, associated with defective DNA MMR and microsatellite unstable tumors, were enriched in patients with in MMR deficient tumors (p &lt; 0.0001 and p = 0.0022, respectively). Signature 8, of unknown etiology, was enriched in patients with MMR intact tumors, advanced disease (p = 0.0045), disease spread to lymph nodes (p = 0.0231), and disease recurrence (p = 0.0021). Signature 12, also of unknown etiology, was enriched in MMR deficient tumors (p = 0.0005) and stage 1 disease (p = 0.0235). Conclusions: WGS revealed distinct patterns of mutational burden associated with clinicopathologic variables. MMR status was associated with PIK3CA mutations and multiple mutational signatures. Mutational signature 8 was associated with multiple clinicopathologic characteristics associated with poor prognosis, suggesting utility as a biomarker. Further investigation regarding the mechanism of the mutational signatures and correlation with prognostic factors may shed light on disparate biologic endometrial cancer outcomes and serve as a source of hypothesis-generation for the development of targeted therapies.

Microsatellite Instability and Immune Response: From Microenvironment Features to Therapeutic Actionability-Lessons from Colorectal Cancer.

Microsatellite instability (MSI) can be found in 15-20% of all colorectal cancers (CRC) and is the key feature of a defective DNA mismatch repair (MMR) system. Currently, MSI has been established as a unique and pivotal biomarker in the diagnosis, prognosis, and treatment of CRC. MSI tumors display a strong lymphocytic activation and a shift toward a tumoral microenvironment restraining metastatic potential and ensuing in a high responsiveness to immunotherapy of MSI CRC. Indeed, neoplastic cells with an MMR defect overexpress several immune checkpoint proteins, such as programmed death-1 (PD-1) and programmed death-ligand 1(PD-L1), that can be pharmacologically targeted, allowing for the revival the cytotoxic immune response toward the tumor. This review aims to illustrate the role of MSI in the tumor biology of colorectal cancer, focusing on the immune interactions with the microenvironment and their therapeutic implications.

A conserved motif in the disordered linker of human MLH1 is vital for DNA mismatch repair and its function is diminished by a cancer family mutation.

DNA mismatch repair (MMR) is essential for correction of DNA replication errors. Germline mutations of the human MMR gene MLH1 are the major cause of Lynch syndrome, a heritable cancer predisposition. In the MLH1 protein, a non-conserved, intrinsically disordered region connects two conserved, catalytically active structured domains of MLH1. This region has as yet been regarded as a flexible spacer, and missense alterations in this region have been considered non-pathogenic. However, we have identified and investigated a small motif (ConMot) in this linker which is conserved in eukaryotes. Deletion of the ConMot or scrambling of the motif abolished mismatch repair activity. A mutation from a cancer family within the motif (p.Arg385Pro) also inactivated MMR, suggesting that ConMot alterations can be causative for Lynch syndrome. Intriguingly, the mismatch repair defect of the ConMot variants could be restored by addition of a ConMot peptide containing the deleted sequence. This is the first instance of a DNA mismatch repair defect conferred by a mutation that can be overcome by addition of a small molecule. Based on the experimental data and AlphaFold2 predictions, we suggest that the ConMot may bind close to the C-terminal MLH1-PMS2 endonuclease and modulate its activation during the MMR process.

DNA Mismatch Repair Deficiency in Colorectal Adenocarcinoma by a Two-Antibody Immunohistochemical Approach and its Association with Clinicopathological Features among Bangladeshi Patients

Background: Defective DNA Mismatch Repair (dMMR) genes cause dMMR/Microsatellite Instability (MSI)-related Colorectal Cancers (CRC) in humans which are different from Microsatellite Stable (MSS) tumors in terms of biological behavior, therapeutic response, and prognosis. We aimed to determine the frequency of dMMR CRCs by a two-antibody (PMS2 and MSH6) immunohistochemical approach and to evaluate their association with clinicopathological parameters to document the ever first report of such cases in Bangladesh. Methods: Fifty histopathologically confirmed resected bowel specimens of CRC were studied over a period of two years at a tertiary-level hospital in Bangladesh. Histopathological parameters like morphologic variants, histologic subtypes, grade, stage, Lymphovascular Invasion (LVI), intratumoral lymphocytic infiltrate, and Crohn-like peritumoral reaction were assessed. Immunohistochemistry using PMS2 and MSH6 was performed on representative paraffin blocks by DAKO EnVision method. Expression of both of the markers was evaluated in classified groups. Results: Mean age of study population was 48.60±14.6 years with a male to female ratio of 1.8:1. dMMR was recorded in 32% of cases. Expression of PMS2 and MSH6 were lost in 20% and 12% of cases, respectively. dMMR status was significantly associated with mucinous histology (p=0.014), lower pN staging (p=0.042), low LVI (p=0.002), exhibited intra-tumoral lymphocytosis (p=0.001), and Crohn like peritumoral reaction (p=0.001). No significant association with gender, age, right-sided location, histologic type, pT stage or grade was observed. Conclusion: Frequency of dMMR CRCs was comparatively higher in the Bangladeshi population than in other races. Identification of dMMR tumors by their protein expression pattern using at least two, preferably four antibodies is proposed for routine screening of CRC cases.

High concordance rate of capillary electrophoresis workflow for microsatellite instability analysis and mismatch repair (MMR) immunostaining in colorectal carcinoma.

Microsatellite instability (MSI) is the primary predictive biomarker for therapeutic efficacies of cancer immunotherapies. Establishment of the MSI detection methods with high sensitivity and accessibility is important. Because MSI is mainly caused by defects in DNA mismatch repair (MMR), immunohistochemical (IHC) staining for the MMR proteins has been widely employed to predict the responses to immunotherapies. Thus, due to the high sensitivity of PCR, the MSI-PCR analysis has also been recommended as the primary approach as MMR IHC. This study aimed to develop a sensitive and convenient platform for daily MSI-PCR services. The routine workflow used a non-labeling QIAxcel capillary electrophoresis system which did not need the fluorescence labeling of the DNA products or usage of a multi-color fluorescence reader. Furthermore, the 15 and 1000 bp size alignment markers were used to precisely detect the size of the DNA product. A cohort of 336 CRC cases was examined by MSI-PCR on the five mononucleotide MSI markers recommended by ESMO. The PCR products were analyzed in the screening gels, followed by high-resolution gel electrophoresis for confirmation if needed. In the MSI-PCR tests, 90.1% (303/336) cases showed clear major shift patterns in the screening gels, and only 33 cases had to be re-examined using the high-resolution gels. The cohort was also analyzed by MMR IHC is, which revealed 98.5% (331/336) concordance with MSI-PCR. In the five discordant cases, 4 (3 MSI-L and 1 MSS) showed MSH6 loss. Besides, one case exhibited MSI-H but no loss in the MMR IHC. Further NGS analysis, in this case, found that missense and frameshift mutations in the PMS2 and MSH6 genes occurred, respectively. In conclusion, the non-labeling MSI-PCR capillary electrophoresis revealed high concordance with the MMR IHC analysis and is cost- and time-effective. Therefore, it shall be highly applicable in clinical laboratories.