SMAD4 Mutations Research Articles

Integrating cfDNA liquid biopsy and organoid-based drug screening reveals PI3K signaling as a promising therapeutic target in colorectal cancer

BackgroundThe current precision medicine relies on biomarkers, which are mainly obtained through next-generation sequencing (NGS). However, this model failed to find effective drugs for most cancer patients. This study tried to combine liquid biopsy with functional drug tests using organoid models to find potential drugs for cancer patients.MethodsColorectal cancer (CRC) patients were prospectively enrolled and blood samples were collected from patients before the start of treatment. Targeted deep sequencing of cfDNA samples was performed using a 14-gene panel. Gastrointestinal (GI) cancer organoids were established and PI3K and mTOR inhibitors were evaluated on organoid models.ResultsA total of 195 mutations were detected across 58 cfDNA samples. The most frequently mutated genes were KRAS, TP53, PIK3CA, and BRAF, all of which exhibited higher mutation rates than tissue biopsy. Although 81% of variants had an allele frequency of less than 1%, certain mutations in KRAS, TP53, and SMAD4 had high allele frequencies exceeding 10%. Notably, among the seven patients with high allele frequency mutations, six had metastatic tumors, indicating that a high allele frequency of ctDNA could potentially serve as a biomarker of later-stage cancer. A high rate of PIK3CA mutation (31 out of 67, or 46.3%) was discovered in CRC patients, suggesting possible tumor progression mechanisms and targeted therapy opportunities. To evaluate the value of anti PI3K strategy in GI cancer, different lines of GI cancer organoids were established. The organoids recapitulated the morphologies of the original tumors. Organoids were generally insensitive to PI3K inhibitors. However, CRC-3 and GC-4 showed response to mTOR inhibitor Everolimus, and GC-3 was sensitive to PI3Kδ inhibitor Idelalisib. The CRC organoid with a PIK3CA mutation showed greater sensitivity to the PI3K inhibitor Alpelisib than wildtype organoids, suggesting potential treatment options for the corresponding patients.ConclusionLiquid biopsy holds significant promise for improving precision treatment and tumor prognosis in colorectal cancer patients. The combination of biomarker-based drug prediction with organoid-based functional drug sensitivity assay may lead to more effective cancer treatment.

Correlation between TP53, KRAS, SMAD4 and other mutations profile and neoadjuvant therapy efficacy and prognosis in locally advanced rectal cancer.

186 Background: Locally advanced rectal cancer presents a poor prognosis due to the risk of local recurrence and distant metastasis. Neoadjuvant Chemotherapy (NAC) without radiation therapy for locally advanced rectal cancer holds the potential for both local control and reduced distant recurrence, but identifying cases where its efficacy can be expected remains challenging. To explore predictive factors for the efficacy of NAC and prognosis in locally advanced rectal cancer. Methods: We examined 43 cases of locally advanced rectal cancer (cT3 or deeper, or cN3) that underwent primary tumor resection after NAC between January 2013 and June 2021. Genomic profiles were analyzed by extracting DNA from formalin-fixed paraffin-embedded (FFPE) tumor tissues, including 42 pre-NAC biopsy samples and 39 surgical samples, excluding 4 cases with significant NAC response. Targeted sequencing was used for analysis, and mutations were considered positive if detected in either biopsy or surgical samples, with an allele frequency of 5% or higher and not classified as variants of unknown significance (VUS). Additionally, we examined 334 cases of locally advanced rectal cancer that underwent preoperative treatment using publicly available data in cBioPortal. Results: The median recurrence-free survival (RFS) was 1,415 days (range: 97-2,868) with 15 recurrences, and the median overall survival (OS) was 1,702 days (range: 97-2,868) with 8 deaths (6 from the original disease, 1 from other cancers, and 1 of unknown cause). Among the 4 cases that showed histological response to NAC (AJCC Tumor Regression Grade 0-1), there was 1 recurrence, but no deaths occurred. RFS and OS in TRG0-1 were favorable compared to TRG2-3, but the differences were not statistically significant (3-year RFS: 75% vs. 65%, P=0.557; 3-year OS: 100% vs. 92%, P=0.339). In targeted sequencing analysis, TP53 mutations were found in 32 cases, KRAS mutations in 19 cases, APC mutations in 14 cases, FBXW7 mutations in 5 cases, SMAD4 mutations in 4 cases, PIK3CA mutations in 3 cases, and NRAS mutations in 2 cases. Co-mutations were observed in 13 cases for TP53/KRAS, 8 cases for TP53/APC, and 5 cases for KRAS/APC. One case each of these co-mutations was observed in TRG0-1. FBXW7, SMAD4, PIK3CA, and NRAS mutations were not found in TRG0-1. In the publicly available database, TRG0-1 showed significantly better RFS and OS compared to TRG2-3 (RFS: P=0.002, OS: P=0.089). SMAD4 mutations were significantly more frequent in TRG3 (P=0.02). Co-mutations of TP53/SMAD4, KRAS/SMAD4, and TP53/KRAS/SMAD4 were associated with significantly worse OS compared to cases with no co-mutations (P=0.001, P=0.0002, P=0.003). Conclusions: Co-mutations in TP53, KRAS, and SMAD4 may serve as factors for predicting the effectiveness of preoperative treatment and prognosis in locally advanced rectal cancer.

Pancreatic cancer and diabetes: The effects of race and genes.

627 Background: Pancreatic cancer and diabetes mellitus (DM) have been shown to be connected, but the genetic associations between the two have not been well characterized. The goal of this study was to identify racial and genomic patterns that relate the timing of DM onset with a pancreatic cancer diagnosis. Methods: Consecutive pancreatic cancer patients treated at the University of Cincinnati Cancer Center with available tumor genomic profiles were studied. Descriptive statistics for 133 genes, patient characteristics, cancer stage, treatment details, and family history were analyzed. Categorical variables were compared using the Pearson Chi-square test for contingency tables (or Fisher’s exact test when the expected frequency within any cell was less than 5 in the contingency table), and the t-test or ANOVA was used for continuous variables. For overall survival, we generated Kaplan-Meier curves by DM diagnosis, and fit univariable Cox Proportional-Hazard models for each interest variable for all patients, and multivariable Cox models, which included only significant variables. Results: Of 147 individuals with pancreatic cancer (median age 67 years, 49% female, 12% Black), 46.3% had a DM diagnosis. Of these, 62% had chronic DM, while 38% were diagnosed within one year of their pancreatic cancer diagnosis. Black individuals were more likely to have DM diagnosed (76.5% vs 41.7%, p = 0.007), and were more likely to have been diagnosed within a year of pancreatic cancer (69.2% vs 30.2%, p = 0.023), compared with White individuals. There were 15 genes found to be upregulated in those with DM and pancreatic cancer, and 11 genes found to be downregulated. RNF43 mutation was more prevalent in pancreatic cancer patients with chronic DM than those without DM (71.4% vs 32.5%, p = 0.048), although absolute number of individuals with the mutation were low. No other genomic association on the timing of DM and pancreatic cancer was found. A SMAD4 mutation was associated with a 121% increased risk of mortality (HR = 2.21, 95% CI 1.16-4.19, p=0.016). Conclusions: In a cohort of pancreatic cancer patients at a single center, Black individuals were more likely to have DM diagnosed closer to pancreatic cancer diagnosis (rather than earlier), compared with other races. No remarkable genomic association was found. This highlights that a diagnosis of diabetes may be related to inequities in healthcare, as opposed to true genomic differences, and needs to be explored in larger datasets.

Genomic alteration in sporadic adolescent and young adult-onset colorectal adenocarcinoma.

154 Background: Colorectal cancer (CRC) incidence is increasing in adults younger than 50 years. This study evaluated genomic alteration in adolescent and young adult (AYA)-onset sporadic CRC patients who aged between 15 and 39 years. Methods: DNA from 90 archived formalin-fixed, paraffin-embedded (FFPE) tissue samples that histologically confirmed adenocarcinoma with proficient mismatch repair tumors at Siriraj Hospital (Bangkok, Thailand) were extracted. Patients who clinically suspected familial adenomatous polyposis were excluded. Gene mutational analysis was performed by next-generation sequencing (NGS) using an Oncomine Comprehensive Assay Plus kit (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and compared with previous reported molecular data in adult-onset CRC from our group. Results: The top 5 mutations frequency observed were TP53, KRAS, FBXW7, PIK3CA, and SMAD4 mutations which were comparable to what reported in adult-onset CRC. However, FBXW7, PIK3CA, NOTCH1, FGFR3, ERBB2, and PTEN were reported more frequent in AYA group. No difference in number of KRAS, NRAS, and BRAF mutations among 2 groups. Table below shows key cancer genes mutation frequencies. Conclusions: This study is the comprehensive report hotspot mutations using NGS in sporadic AYA-onset sporadic CRC patients. The most commonly identified gene mutation frequencies among AYA-onset were similar to those reported in adult-onset, except for FBXW7, PIK3CA, NOTCH1, FGFR3, ERBB2, and PTEN mutations that had a slightly higher frequency. Further studies on larger sample set for genetic and epigenetic landscape are required. [Table: see text]

Impact of somatic genomic alterations in patients with metastatic colorectal cancer in a minority-rich academic medical center.

215 Background: Genomic alterations in metastatic colorectal cancer (mCRC) play a pivotal role in the clinical manifestations of the disease. Mutations have been associated with the age of onset of mCRC, tumor location, and metastatic sites. We conducted a retrospective study to explore the relationship between the genomic profile and clinical phenotype in a distinct patient population predominantly comprised of Hispanic and Black patients with mCRC. Methods: Patients with mCRC with available next-generation sequencing (NGS) treated at Montefiore Einstein Comprehensive Cancer Center (MECCC) who were diagnosed from January 2000 - January 2023 were included. Molecular testing was collected from: Perthera, Guardant, Caris, and Foundation One. The following parameters were collected: race, ethnicity, age of CRC diagnosis, age of metastatic diagnosis, metastatic sites, NGS profile, tumor location, and lines of treatment. Mutations were categorized into one of eight distinct pathways: cell cycle, MAP Kinase, WNT, homologous recombination, DNA damage repair, epigenetic modifications, transcription, & cell death. The primary endpoint was to examine the relationship between individual genetic alterations or any of these eight pathways and the clinical parameters. Results: 169 patients with microsatellite stable (MSS) mCRC were included (median age at diagnosis 59 years, 42% Hispanic, 38% Black). 148 distinct genetic alterations were discovered across our population, of which roughly half fit into one of eight clinical pathways. In concordance with previously published data, we found a significant association between PTEN and right-sided tumors (38% mutated in right-sided vs. 16% mutated in left-sided, p<.001). Cell cycle pathway mutations and SMAD4 mutations were associated with an earlier age of both primary CRC (p=.001 & p=.042, respectively) and metastatic diagnosis (p=<.001 & p=.013, respectively). CDK8 mutations were associated with atypical sites of metastases (p=.045). Conclusions: This analysis sought to deepen the understanding of how genomic alterations impacted the clinical phenotype in our population of mCRC patients. We identified previously undescribed associations between mutations in the cell cycle pathway and SMAD4 versus age of CRC diagnosis. As molecular sequencing in CRC continues to advance, these relationships may be further elucidated, which can potentially help guide treatment and identify higher-risk patients.

LMTK3 gene expression and the molecular landscape of colorectal cancer (CRC).

172 Background: Lemur tail kinase 3 (LMTK3) plays a critical role in multiple cellular pathways such as Wnt signaling, KIT modulation, and the estrogen receptor pathway. We previously reported that LMTK3 gene polymorphisms are associated with clinical outcome in patients with CRC, and that LMTK3 and estrogen-mediated signaling play a crucial role in CRC tumorigenesis in vitro. Here, we aimed to characterize the molecular features associated with LMTK3 gene expression in CRC. Methods: 20,219 CRC were tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS). Top quartile transcripts per million (TPM) for LMTK3 expression (Q4) were considered high while bottom quartile (Q1) low. Consensus molecular subtypes (CMS) were assessed using RNAseq. Cell infiltration (CI) in the tumor microenvironment (TME) was estimated by QuantiSEQ. X2 and Fisher-Exact tests were used, and significance was determined as p-value adjusted for multiple comparisons ( q < 0.05). Gene expression profiles were analyzed for transcriptional signatures predictive of response to immunotherapy (interferon gamma [IFNγ] score; T-cell inflamed signature [TIS] score). Results: LMTK3 expression was highest in left-sided (0.98 median TPM) followed by right-sided (0.96) and lowest in rectal tumors (0.92). No difference in patient sex distribution was observed between Q1 and Q4 cohorts. Overall, LMTK3 Q1 was associated with TMB-high (≥ 10 Mut/Mb, 11.4 vs 8.7%) and dMMR/MSI-H (8.1 vs 4.6%) ( q < 0.0001); however, these associations were no longer significant in pMMR/MSS tumors. In the pMMR/MSS cohort, LMTK3 expression was highest in CMS4 (1.09 median TPM) followed by CMS2 (0.98), CMS1 (0.88), and lowest in CMS3 (0.70, all intergroup q < 0.05). LMTK3 high showed differential rates of mutations and copy number alterations (CNA) in several genes, including higher mutation rates of APC, TP53, and CDX2 CNA, while lower mutation rates of KMT2A/D, ASXL1, ATM, SMAD4, RNF43 and AMER1 in the overall cohort ( q < 0.05). In the pMMR/MSS cohort, the associations with APC, TP53, SMAD4 and ATM mutations and CDX2 CNA still held true ( q < 0.05). High LMTK3 was associated with higher immune CI in the TME, including B cells, neutrophils, NK cells, CD4+ T cells, monocytes and dendritic cells, while macrophages and Tregs were lower regardless of tumor MSI status (fold change: 0.83-2.4, all q < 0.0001). The IFNγ score was significantly lower in LMTK3 Q4 while the TIS score was significantly higher in LMTK3 Q4 ( q < 0.0001). Conclusions: Our data show a strong association between LMTK3 gene expression and distinct molecular features and TME immune cell infiltration in CRC. These findings suggest that LMTK3 may be an important molecular factor that plays a role in determining the composition of the TME, thus targeting LMTK3 could represent a novel strategy in selected CRC subgroups.

High-resolution transcriptional signature to predict survival benefit in colorectal cancer (CRC) treated with EGFR inhibitors (EGFRi) independent of RAS/BRAF mutation status or tumor sidedness.

203 Background: Cetuximab (CTX) and Panitumumab (PMB) therapies directed at EGFR have been restricted to left-sided CRC harboring wild-type KRAS ( KRASWT), limiting their utility. Approximately 50% of mCRC fail to respond to EGFRi, thus identification of predictive biomarkers is an unmet need. Here we evaluate a CTX sensitivity score (CTX-S) that we previously reported (Yang M. et al., 2019), in a large, real-world population of RAS/BRAF mutant vs wild-type and in right- vs left-sided tumors. Methods: CTX/PMB-treated CRC specimens (n=1124) with clinical outcomes, NextGen Sequencing of DNA (592-gene panel or whole exome sequencing) and RNA (whole transcriptome sequencing) were tested at Caris Life Sciences (Phoenix, AZ). 1097 specimens were MSS as determined by IHC of MMR proteins and/or NGS. Association of CTX-S with RAS/BRAF mutation and tumor sidedness was performed in MSS tumors. Tumors with likely pathogenic mutations in KRAS, NRAS or BRAF were considered as RASMUT /BRAFMUT, or RASWT /BRAFWT if no mutation was detected for each gene. Samples were stratified based on CTX-S quintiles. Survival on EGFRi was calculated from the initiation of EGFRi to last contact using Kaplan-Meir method. Results: Higher CTX-S quintiles were significantly associated with longer survival on EGFRi in RAS/BRAF wild-type as well as -mutant subpopulations. Similar results were seen in left- vs. right-sided tumors (Table). Higher CTX-S quintiles were associated with a survival benefit in all CMS classes but CMS2; however, the vast majority of CMS2 tumors (460/467) were among the top 3 CTX-S quintiles. As the median survival among the top 3 quintiles was ~2-fold higher than the bottom 2 quintiles, we used stratification by the 40th percentile for the genomic analysis. CTX-S >40th percentile was associated with an increased prevalence in APC (91 vs 47%) and TP53 (93 vs 76%) mutations and decreased prevalence in BRAF (6 vs 32%), SMAD4 (8 vs 19%), RNF43 (1 vs 12%) and ATM (2 vs 5%) mutations (all q<0.05). Conclusions: Our data suggest that CTX-S may predict longer survival on EGFRi, surprisingly independent of RAS/BRAF mutation status as well as tumor sidedness. Patients with high CTX-S had increased prevalence of CMS2 and harbored more APC and TP53 mutations. A strong EGFRi biomarker would likely expand the utility of EGFRi to right-sided tumors and possibly to RASMUT tumors. Further validation of these biomarkers in a prospective clinical trial is warranted and could change our current standard of care for CRC.[Table: see text]

Abstract A044: Tumor-infiltrating lymphocyte density correlates with survival in pancreatic adenosquamous carcinoma

Abstract Background: Pancreatic adenosquamous carcinoma (PASC) is a rare and aggressive form of pancreatic cancer, representing only 1-5% of cases. Histologically, it is defined by the presence of at least 30% squamous differentiation mixed with ductal adenocarcinoma. No standard therapies or prognostic biomarkers have been validated to date in this understudied disease. Methods: All patients diagnosed with pancreatic cancer in the Johns Hopkins Cancer Registry from 2013 to 2018 were queried for adenosquamous histology. Archived slides of available tumor specimens were examined to quantify the percentage of squamous differentiation and tumor-infiltrating lymphocyte (TIL) density. Descriptive statistics were used to summarize clinical, pathologic, and molecular characteristics. Kaplan-Meier estimates and log-rank tests were used for survival analyses. Results: Among a total of 8,908 patients queried, 155 patients with adenosquamous histology were identified. Median overall survival (OS) was 14.2 months and 7.5 months for resectable and unresectable/metastatic disease, respectively. Molecular tumor testing revealed frequent somatic mutations in KRAS, TP53, and SMAD4 in addition to multiple DNA damage repair genes. The percentage of squamous differentiation and TIL density was correlated with survival outcomes in a subset of 28 patients with evaluable tumor specimens. No association between the percentage of squamous differentiation and OS was identified. Of note, compared to those with low TIL density (0-10%), patients with an intermediate/high TIL density (>10%) exhibited significantly improved survival (median OS 36.3 vs 14.2 months, p = 0.011). Conclusions: For the first time, intermediate/high TIL density is associated with prolonged OS in a single-institution cohort of PASC patients. Prospective validation in larger cohorts is needed to establish prognostic biomarkers that can guide therapeutic decision-making in this lethal and under-examined disease subtype. Citation Format: Saurav D. Haldar, Christopher D. Jakubowski, Su Jin Lim, Hao Wang, Richard A. Burkhart, Kelly Lafaro, William R. Burns III, Jin He, Daniel A. Laheru, Elizabeth D. Thompson, Nilofer S. Azad. Tumor-infiltrating lymphocyte density correlates with survival in pancreatic adenosquamous carcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A044.

Abstract A073: A link between the mitochondrial enzyme glutamic-oxaloacetic transaminase 2 (GOT2) and epigenetic dysregulation in pancreatic cancer

Abstract At present, pancreatic cancer stands as the 3rd cause of cancer-related fatalities in the US. The most common type of pancreatic cancer develops from the exocrine pancreas known as ductal adenocarcinoma (PDAC). PDAC exhibits a highly aggressive nature and carries a bleak prognosis, with a 5-year survival rate averaging below 10%. Moreover, the majority of patients receive their diagnosis at advanced stages of the disease. Compounding the issue, the emergence of resistance to modern first-line chemotherapies contributes to the progression of PDAC and exacerbates its overall high mortality rate. The specific cause of PDAC remains unknown, although lifestyle factors such as alcohol and tobacco use, along with genetic abnormalities, have been linked to its increasing incidence over the past decade. Mutations in KRAS, TP53, SMAD4, and CDKN2A are recognized as genetic drivers contributing to the progression of PDAC. Recently, research has shifted its focus to investigating the role of epigenetic dysregulation in PDAC advancement. Significant evidence suggests that remodeling of the epigenome plays a crucial role in the development and progression of PDAC, but the exact mediators responsible for these alterations remain largely unknown. Recent studies have indicated that mitochondrial enzymes may influence epigenetic modifications, thus contributing to the progression of tumorigenesis. In our previous work, we reported that the mitochondrial protein GOT2 (glutamic-oxaloacetic transaminase) supports PDAC development by promoting an immunosuppressive phenotype within the tumor microenvironment. Ongoing epigenetic studies following ChIP- and ATAC-seq (chromatin immunoprecipitation and assay for transposase-accessible chromatin with sequencing, respectively) experiments in mammalian PDAC cell lines have revealed that loss of GOT2 leads to genome-wide changes in histone acetylation and chromatin accessibility. These changes in acetylation and chromatin architecture imply a reconfiguration of the epigenetic landscape and subsequent alterations in the PDAC transcriptome, suggesting a potential role for GOT2 in maintaining epigenetic profiles within the context of pancreatic cancer. Further exploration of the genomic regions where these histone modification changes occur has implicated cis-regulatory regions and the expression of their target genes, which may be crucial for PDAC progression. Collectively, these epigenetic studies hold the potential to identify novel therapeutic targets that could address the urgent need for more effective antineoplastic treatments against this aggressive form of pancreatic cancer. Citation Format: Luis Francisco Diaz, Mara H. Sherman, Jonathan R. Brody. A link between the mitochondrial enzyme glutamic-oxaloacetic transaminase 2 (GOT2) and epigenetic dysregulation in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A073.

Clinical, genomic and immune microenvironmental determinants of nivolumab response in head and neck squamous cell carcinoma.

In view of improving biomarkers predicting the efficacy of immunotherapy for head and neck squamous cell carcinoma (R/M HNSCC), this multicenter retrospective study aimed to identify clinical, tumor microenvironmental, and genomic factors that are related to therapeutic response to the anti- Programmed cell death protein 1 (PD-1) antibody, nivolumab, in patients with R/M HNSCC. The study compared 53 responders and 47 non-responders, analyzing formalin-fixed paraffin-embedded samples using 14-marker multiplex immunohistochemistry and targeted gene sequencing. Of 100 patients included, responders had significantly lower smoking and alcohol index, higher incidence of immune related adverse events, and higher PD-1 ligand (PD-L1) expression in immune cells as well as PD-L1 combined positive score (CPS) than non-responders. The frequency of natural killer cells was associated with nivolumab response in patients with prior cetuximab use, but not in cetuximab-naïve status. Age-stratified analysis showed nivolumab response was linked to high CPS and lymphoid-inflamed profiles in patients aged ≥ 65. In contrast, lower NLR in peripheral blood counts was associated with response in patients aged < 65. Notably, TP53 mutation-positive group had lower CPS and T cell densities, suggesting an immune-excluded microenvironment. Patients with altered tumor suppressor gene pathways, including TP53, CDKN2A, and SMAD4 mutations, had lower CPS, higher smoking index, and were associated with poor responses. Nivolumab treatment efficacy in HNSCC is influenced by a combination of clinical factors, age, prior treatment, immune environmental characteristics, and gene mutation profiles.

Local Therapy Improves Survival for Early Recurrence After Resection of Colorectal Liver Metastases.

Early recurrence following hepatectomy for colorectal liver metastases (CLM) is associated with worse survival; yet, impact of further local therapy is unclear. We sought to evaluate whether local therapy benefits patients with early recurrence following hepatectomy for CLM. Clinicopathologic and survival outcomes of patients managed with hepatectomy for CLM (1/2001-12/2020) were queried from a prospectively maintained database. Timing of recurrence was stratified as early (recurrence-free survival [RFS] < 6months), intermediate (RFS 6-12months), and later (RFS > 12months). Local therapy was defined as ablation, resection, or radiation. Of 671 patients, 541 (81%) recurred with 189 (28%) early, 180 (27%) intermediate, and 172 (26%) later recurrences. Local therapy for recurrence resulted in improved survival, regardless of recurrence timing (early 78 vs. 32months, intermediate 72 vs. 39months, later 132 vs. 65months, all p < 0.001). Following recurrence, treatment with local therapy (hazard ratio [HR] = 0.24), liver and extrahepatic recurrence (HR = 1.81), RAS + TP53 co-mutation (HR = 1.52), and SMAD4 mutation (HR = 1.92) were independently associated with overall survival (all p ≤ 0.002). Among patients with recurrence treated by local therapy, patients older than 65years (HR 1.79), liver and extrahepatic recurrence (HR 2.05), primary site or other recurrence (HR 1.90), RAS-TP53 co-mutation (HR 1.63), and SMAD4 mutation (HR 2.06) had shorter post-local therapy survival (all p ≤ 0.04). While most patients recur after hepatectomy for CLM, local therapy may result in long-term survival despite early recurrence. Somatic mutational profiling may help to guide the multidisciplinary consideration of local therapy after recurrence.

Abstract A176: Loss of SMAD4 unleashes mTOR and increases dependency on cap-dependent translation in esophageal tumorigenesis

Abstract Application of molecular targeted therapies for esophageal adenocarcinoma (EAC) has been limited by a lack of druggable oncogenic drivers. We propose that synthetic lethal interactions may provide new opportunities for targeted therapies in EAC. We have taken an integrated multi-omics approach incorporating Perturb-Seq (CRISPR editing combined with single cell RNA sequencing) and in vivo tumorigenesis assays to perform high-throughput characterisation of &amp;gt;70 high-confidence EAC driver genes, and genome-wide CRISPR-Cas9 knockout screens in isogenic models of EAC tumorigenesis to identify disease relevant synthetic lethal genetic interactions. MS-based proteomics, reverse phase protein arrays, polysome profiling and bulk RNA-sequencing of isogenic models were utilised to interrogate the biology of bona fide EAC drivers and associated driver specific gene dependencies. The overall goals were to (i) enhance our understanding of EAC tumorigenesis, (ii) identify potential opportunities for therapeutic interventions targeting EAC drivers via synthetic lethal-like approaches, and (iii) reduce the complexity of genetic heterogeneity by categorising EAC drivers with similar phenotypic outcomes. Through our approach we have identified complex crosstalk between the tumor suppressor SMAD4 and regulation of mTOR signaling, with specific downstream effects on translational reprogramming in EAC. Mutation or loss of SMAD4 occurs in up to 20% of EAC, but not pre-malignant tissue (Barrett’s esophagus), and is sufficient to promote transformation of pre-malignant cells in our in vivo tumorigenesis model. In this model, xenotransplanted SMAD4-deficient (via CRISPR-Cas9 knockout or shRNA knockdown) Barrett’s metaplasia cells formed invasive, metastatic tumors after a period of latency. SMAD4 deficient cells had downregulated expression of 4E-BP1, which inhibits EIF4E, the cap-dependent translation initiation factor. This was accompanied by increased mTOR activity, including phosphorylation and inactivation of 4EBP1. Moreover, we found that SMAD4-deficient cells preferentially upregulate cap-dependent translation and become addicted to translation of oncogenic mRNAs. Furthermore, perturbation of additional negative regulators of mTOR signaling in combination with SMAD4 knockout exacerbated these effects and accelerated tumorigenesis in vivo. We have extended these findings to a model of Barrett’s esophagus patient-derived organoids (PDOs) and observed increased proliferative potential of our genetically modified PDOs. Finally, analysing gene ontologies for differentially expressed genes from Perturb-seq revealed that driver-dependent transcriptional changes can be categorized into a smaller number of functional pathways allowing us to potentially consider groups of drivers as functional units. This work advances our understanding of EAC tumorigenesis, provides new mechanistic insights into SMAD4-driven transformation as well as novel potential therapeutic avenues for SMAD4-deficient EAC. Citation Format: Julia V Milne, Ebtihal Mustafa, Kenji Fujihara, Eric Kusnadi, Niko Thio, Maree Pechlivanis, Carlos Cabalag, Twishi Gulati, Kaylene Simpson, Cuong Duong, Luc Furic, Wayne Phillips, Nicholas J Clemons. Loss of SMAD4 unleashes mTOR and increases dependency on cap-dependent translation in esophageal tumorigenesis [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A176.

Association between SMAD4 Mutations and GATA6 Expression in Paired Pancreatic Ductal Adenocarcinoma Tumor Specimens: Data from Two Independent Molecularly-Characterized Cohorts.

Several molecular biomarkers have been identified to guide induction treatment selection for localized pancreatic ductal adenocarcinoma (PDAC). SMAD4 alterations and low GATA6 expression/modified "Moffitt" basal-like phenotype have each been associated with inferior survival uniquely for patients receiving 5-FU-based therapies. SMAD4 may directly regulate the expression of GATA6 in PDAC, pointing to a common predictive biomarker. To evaluate the relationship between SMAD4 mutations and GATA6 expression in human PDAC tumors, patients with paired SMAD4 mutation and GATA6 mRNA expression data in the TCGA and CPTAC were identified. In 321 patients (TCGA: n = 180; CPTAC: n = 141), the rate of SMAD4 alterations was 26.8%. The rate of SMAD4 alteration did not vary per tertile of normalized GATA6 expression (TCGA: p = 0.928; CPTAC: p = 0.828). In the TCGA, SMAD4 alterations and the basal-like phenotype were each associated with worse survival (log rank p = 0.077 and p = 0.080, respectively), but their combined presence did not identify a subset with uniquely inferior survival (p = 0.943). In the CPTAC, the basal-like phenotype was associated with significantly worse survival (p < 0.001), but the prognostic value was not influenced by the combined presence of SMAD4 alterations (p = 0.960). SMAD4 alterations were not associated with poor clinico-pathological features such as poor tumor grade, advanced tumor stage, positive lymphovascular invasion (LVI), or positive perineural invasion (PNI), compared with SMAD4-wildtype. Given that SMAD4 mutations were not associated with GATA6 expression or Moffitt subtype in two independent molecularly characterized PDAC cohorts, distinct biomarker-defined clinical trials are necessary.

Hereditary haemorrhagic telangiectasia and SMAD4 mutation in a patient with complex single ventricle heart disease.

We report a case of hypoplastic left heart syndrome and with subsequent aortopathy and then found to have hereditary haemorrhagic telangiectasia/juvenile polyposis syndrome due to a germline SMAD4 pathologic variant. The patient's staged palliation was complicated by the development of neoaortic aneurysms, arteriovenous malformations, and gastrointestinal bleeding thought to be secondary to Fontan circulation, but workup revealed a SMAD4 variant consistent with hereditary haemorrhagic telangiectasia/juvenile polyposis syndrome. This case underscores the importance of genetic modifiers in CHD, especially those with Fontan physiology.

Characterization of DNA Damage Response-Associated Somatic Mutations in Borderline Resectable and Locally Advanced Pancreatic Cancer

The role of radiation for pancreatic cancer remains controversial, with recent studies showing conflicting results, highlighting the need to develop biomarkers of radiation response. Despite its potential utility in predicting radiosensitivity, the landscape of somatic mutations in borderline resectable pancreatic cancer (BRPC) and locally advanced pancreatic cancer (LAPC), as related to DNA damage response (DDR), has not been well characterized. This study aimed to characterize the frequency of such mutations in a cohort of patients with BRPC/LAPC treated with neoadjuvant chemotherapy and stereotactic body radiotherapy (SBRT). Mutational data was collected from patients with BRPC/LAPC treated at a single institution with neoadjuvant chemotherapy and SBRT, followed by surgical resection from 2016-2021. Chemotherapy consisted of modified FOLFIRINOX or gemcitabine/nab-paclitaxel, and patients were treated with SBRT in 33 Gy in 5 fractions. Genomic data was obtained from either endoscopic biopsy or surgical specimens, and next-generation sequencing was performed either in-house with a Solid Tumor Panel or with FoundationOne CDx. Specific emphasis was placed on the characterization of double-strand DNA break (DSB) repair genes, as this is the type of tumor cell damage traditionally induced by radiation therapy. Genes associated with the two main pathways of DSB repair, non-homologous end joining (NHEJ) and homologous repair (HR), were analyzed. Specific HR pathway mutations assessed were BLM, BRCA1/2, MRE11, NBN, PALB2, RAD50, RAD51B-D, and RAD54L, while PRKDC mutations were assessed for the NHEJ pathway. Mutations in ATM, an important initiator of DDR pathways, were also analyzed. Additionally, the frequency of mutations in TP53, CDKN2A and SMAD4 in patients with concomitant KRAS mutations was assessed. Eighty-five patients were included in the study. Five (5.9%) patients had mutations in the NHEJ pathway of the PRKDC gene. Twenty (23.5%) patients had mutations in the HR pathway, including BRCA2 (10/85; 11.8%), PALB2 (5/85; 5.9%), BRCA1 (3/85; 3.5%), and RAD50 (1/85; 1.2%). Six (7.1%) patients had mutations in ATM. No patients were found to have mutations in BLM, RAD51B-D, RAD54L, or NBN. Amongst patients with KRAS mutations (72/85), concomitant mutations were observed in TP53 (47/85; 55.3%), CDKN2A (16/85; 18.8%), and SMAD4 (9/85; 10.6%). Herein, we characterized the frequency of somatic mutations associated with DSB repair genes in patients with BRPC/LAPC. Data analysis on outcomes related to radiation response in patients with mutations in DDR pathways is ongoing, but will likely also benefit from multi-institutional efforts to increase the power to answer this question.

Roth spots in a Rendu-Osler-Weber syndrome.

To describe the molecular diagnosis and atypical ocular presentation of a patient who suffered for a Rendu-Osler-Weber syndrome associated with juvenile polyposis (JP) syndrome. This is a case report of a patient that underwent fundus examen, brain Magnetic Resonance Imaging (MRI) and arteriography. Genetic testing was performed by next-generation-sequencing (NGS). A 35-year-old woman presented with right hemiplegia with right homonymous lateral hemianopia and homolateral complete sensory deficit. She also had Roth spots in her left fundus. Genetic testing revealed a pathogenic variation in the heterozygous state in the SMAD-4 gene (c.1245_1248del). Hereditary Hemorrhagic Telangiectasia (HTT) also known as Rendu-Osler-Weber syndrome is a rare autosomal dominant disease which reveals mostly with epistaxis and cutaneous telangiectasias. Our clinical case reports Roth spots in the context of HTT associated with juvenile polyposis syndrome. SMAD-4 mutation may explain the presence of a carotid-ophthalmic aneurysm which is not a lesion usually found in HTT.

Impact of Smad4 and p53 mutations on the prognosis of patients with pancreatic ductal adenocarcinoma undergoing chemotherapy.

This prospective cohort study evaluated the feasibility of using endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) samples for comprehensive mutational analysis of cancer-related genes using microtissues. Fifty patients with suspected pancreatic cancer presenting consecutively at the Kindai University Hospital between January 2018 and January 2019 were enrolled. Cancerous tissues from EUS-FNB were obtained from each tumor and subjected to histological examination and mutational analysis. The primary endpoint was the collection rate of EUS-FNB specimens suitable for comprehensive cancer panels using deep sequencing. Clinical history and genetic variations between the disease control and progressive disease groups of patients on chemotherapy were evaluated as secondary endpoints. The collection rate of EUS-FNB specimens suitable for comprehensive cancer panels using deep sequencing was 93.6%. The cancer panel was sequenced for 25 patients with pancreatic cancer treated initially with systemic chemotherapy. Mutation in p53 and Smad4 were positively and negatively associated, respectively, with disease control at the initial evaluation. The median time to progression in 15 patients with p53 and without Smad4 mutations was 182.0days; whereas, it was 92.5days in other 10 patients; this difference was significant (p = 0.020). Tissue samples from EUS-FNB were suitable for mutational analysis. Pancreatic cancers with p53 and without Smad4 mutations responded better to chemotherapy and had a better prognosis than those others.

Screening of Exosome-Derived Proteins and Their Potential as Biomarkers in Diagnostic and Prognostic for Pancreatic Cancer.

In the oncological area, pancreatic cancer is one of the most lethal diseases, with 5-year survival rising just 10% in high-development countries. This disease is genetically characterized by KRAS as a driven mutation followed by SMAD4, CDKN2, and TP53-associated mutations. In clinical aspects, pancreatic cancer presents unspecific clinical symptoms with the absence of screening and early plasmatic biomarker, being that CA19-9 is the unique plasmatic biomarker having specificity and sensitivity limitations. We analyzed the plasmatic exosome proteomic profile of 23 patients with pancreatic cancer and 10 healthy controls by using Nanoscale liquid chromatography coupled to tandem mass spectrometry (NanoLC-MS/MS). The pancreatic cancer patients were subdivided into IPMN and PDAC. Our findings show 33, 34, and 7 differentially expressed proteins when comparing the IPMN vs. control, PDAC-No treatment vs. control, and PDAC-No treatment vs. IPMN groups, highlighting proteins of the complement system and coagulation, such as C3, APOB, and SERPINA. Additionally, PDAC with no treatment showed 11 differentially expressed proteins when compared to Folfirinox neoadjuvant therapy or Gemcitabine adjuvant therapy. So here, we found plasmatic exosome-derived differentially expressed proteins among cancer patients (IPMN, PDAC) when comparing with healthy controls, which could represent alternative biomarkers for diagnostic and prognostic evaluation, supporting further scientific and clinical studies on pancreatic cancer.

The Mutation Portraits of Oncogenes and Tumor Supressor Genes in Predicting the Overall Survival in Pancreatic Cancer: A Bayesian Network Meta-Analysis.

In pancreatic cancer, the carcinogenesis can not be separated from genetics mutations. The portraits of genes alterations majorily including oncogenes (KRAS, HER2, PD-L1) and tumor supressor genes (P53, CDKN2A, SMAD4). Besides being notorious a screening marker, the genetic mutations were related to the prognosis of pancreatic cancer. The aim of this study is to determine the genetic mutations portrait in predicting the overall survival in pancreatic cancer. The network meta analysis (NMA) was registered in PROSPERO (CRD42023397976) and conducted in accordance with the PRISMA-P (Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols) in addition of NMA extension guidance. Comprehensive searches were done including all studies which reported the overall survival of pancreatic cancer subjects with KRAS, HER2, PD-L1, P53, CDKN2A, SMAD4. Data were collected and analysis will be done based on Bayesian method, Markov Chain Monte Carlo algorithm, using BUGSnet package in R studio. Transivity was controlled by methods and consistency of the NMA will be fitted by deviance information criterion. Data analysis in NMA were presented in Sucra plot, league table, and forest plot. Twenty-four studies were included in this NMA with 4613 total subjects. The NMA was conducted in random-effects, consistent, and convergence model. Relative to control, the genetic mutation of SMAD4 (HR 1.84; 95%CI 1.39-2.46), HER2 (HR 1.76; 95%CI 1.14-2.71), and KRAS (HR 1.7; 95%CI 1.19-2.48) were significant to have worse survival. The mutations of PD-L1, P53, and CDKN2A also showed poor survival, but not statistically significant compared to control. In pancreatic cancer, the mutation of SMAD4 predicted the worst overall survival, compared to control, also mutation of HER2, KRAS, PD-L1, P53, and CDKN2A.

Oncogenic Drivers and Therapeutic Vulnerabilities in KRAS Wild-Type Pancreatic Cancer.

Approximately 8% to 10% of pancreatic ductal adenocarcinomas (PDAC) do not harbor mutations in KRAS. Understanding the unique molecular and clinical features of this subset of pancreatic cancer is important to guide patient stratification for clinical trials of molecularly targeted agents. We analyzed a single-institution cohort of 795 exocrine pancreatic cancer cases (including 785 PDAC cases) with a targeted multigene sequencing panel and identified 73 patients (9.2%) with KRAS wild-type (WT) pancreatic cancer. Overall, 43.8% (32/73) of KRAS WT cases had evidence of an alternative driver of the MAPK pathway, including BRAF mutations and in-frame deletions and receptor tyrosine kinase fusions. Conversely, 56.2% of cases did not harbor a clear MAPK driver alteration, but 29.3% of these MAPK-negative KRAS WT cases (12/41) demonstrated activating alterations in other oncogenic drivers, such as GNAS, MYC, PIK3CA, and CTNNB1. We demonstrate potent efficacy of pan-RAF and MEK inhibition in patient-derived organoid models carrying BRAF in-frame deletions. Moreover, we demonstrate durable clinical benefit of targeted therapy in a patient harboring a KRAS WT tumor with a ROS1 fusion. Clinically, patients with KRAS WT tumors were significantly younger in age of onset (median age: 62.6 vs. 65.7 years; P = 0.037). SMAD4 mutations were associated with a particularly poor prognosis in KRAS WT cases. This study defines the genomic underpinnings of KRAS WT pancreatic cancer and highlights potential therapeutic avenues for future investigation in molecularly directed clinical trials. See related commentary by Kato et al., p. 4527.