Mutations In APC Gene Research Articles

8536 Unusual Finding of Familial Adenomatous Polyposis in a Patient with X Linked Adrenoleukodystrophy

Abstract Disclosure: A. Deswal: None. A. Dwarakanathan: None. Introduction: X Linked Adrenal Leukodystrophy (X-ALD) is a rare hereditary genetic disorder of impaired peroxisomal metabolism due to a defective transmembrane protein, ADLP. Defective ADLP impairs transport of VLCFA-CoA esters across cytosol into peroxisomes leading to build-up of toxic VLCFA in the cells. X-ALD is caused by mutation in ABCD1 gene, located on X chromosome, which codes for ADLP. It has a broad clinical spectrum including Cerebral ALD, Adrenomyeloneuropathy and Adrenocortical insufficiency. X-ALD has a general prevalence of 1 in 17,000 newborns. Approximately 80% of males with X-ALD develop primary adrenal insufficiency in their lifetime. It can be diagnosed by measuring VLCFA levels in plasma , checking for ABCD1 gene mutation or by doing Brain MRI (depending upon phenotypical presentation ). Case presentation: We report a case of a 23 year old man who had primary adrenocortical insufficiency subtype of X-ALD. His mother was a carrier of ABCD1 gene mutation. He himself tested hemizygous for ABCD1 gene. He came to our office for a follow up visit after an episode of adrenal crisis for which he was hospitalized. He was started on replacement therapy with prednisone and fludrocortisone. Over the next couple of years, he was diagnosed with diabetes mellitus with initial HbA1C of 8.8%. GAD antibody test for type I DM came out negative. His diabetes was managed with metformin and pioglitazone( later discontinued) .By the age of 25,he was found to have polyposis of colon. He tested positive for APC gene mutation . He underwent a J pouch surgery . He also developed PICA aneurysm. Discussion: X-ALD is a hereditary progressive disease with no association between genetic and phenotypic presentations. Adrenal insufficiency type is usually the first to present. Cerebral ALD is typically diagnosed between the ages of 3-18 presenting as psychiatric illness. Myelopathy typically starts by middle age and involves the spinal cord, causing the affected individuals to develop gait disturbances , bladder and bowel dysfunction, with severe mobility dysfunction by 5th-6th decade of life. We present a unique case of a young man with adrenal insufficiency type of X-ALD who also developed gastrointestinal pathology. Per our literature review, X-ALD has not been seen associated with APC gene mutations or colon carcinomas . Pathology behind XLD revolves around ABCD1 gene mutaion causing VLCFA accumulation in plasma, fibroblasts, adrenal glands, oligodendrocytes , astrocytes etc. Whereas FAP involves APC gene mutation which affects the intestinal epithelial cells leading to their apoptosis and polyp formation. X-ALD and FAP are disorders of two different gene mutations with varied clinical presentations. But the question arises regarding finding of APC gene mutation in a patient with ABCD1 gene mutation that if it is a mere co-incidence or common mutation pathway linking these two disorders exists. Presentation: 6/2/2024

6847 Poorly Differentiated Thyroid Cancer: A Rare Entity

Abstract Disclosure: S. Fatima: None. S. Ward: None. A. Champion: None. Introduction: Poorly differentiated thyroid carcinoma (PDTC) is a rare thyroid carcinoma originating from follicular epithelial cells. Regarding the degree of differentiation, PDTC ranks between differentiated thyroid cancer and anaplastic thyroid cancer. We hereby present a rare case of PDTC. Case: 29-year-old female with a history of metastatic papillary thyroid cancer (PTC) presented to the emergency department with shortness of breath. She initially noticed a left thyroid mass in 2021. CT neck in 1/2022 showed a 7 cm left thyroid mass with substernal extension, small right thyroid mass with tracheal compression, left bulky cystic nodal masses extending anterior and posterior to carotid and internal jugular vein. PET scan in 3/2022 showed left 7.6 cm thyroid mass SUV 12.1 with tracheal compression, left level II-IV adenopathy with level IV nodal masses 5.1 cm SUV 4.5. Ultrasound-guided FNA in 4/2022 showed PTC in left 8.7cm thyroid nodule; right 2.8 cm nodule showed Atypia of Undetermined Significance; Left 5.5 cm neck level III lymph node (LN) showed PTC metastasis; right 5.1 cm neck level III LN showed PTC metastasis (+ thyroglobulin and TTF-1). CT chest in 11/2022 showed additional involvement of manubrium. Repeat core needle biopsy of left thyroid mass showed left invasive thyroid carcinoma. She was started on neoadjuvant Lenvatinib in 1/2023. Follow-up CT neck in 5/2023 showed a reduction in the size of the left thyroid mass to 5.5cm x 5.8cm x 6.5cm. At this time, she had symptoms of dysphagia, orthopnea, weight loss of about 60 lbs and neck pain. In 11/2023 at time of current presentation she underwent total thyroidectomy, bilateral modified radical neck dissection and manubriectomy. Surgical pathology showed PDTC in left thyroid mass, PTC in right thyroid mass with metastatic PDTC in left proximal sternocleidomastoid, manubrium and LN involvement in neck and mediastinum. OmniSeq Insight testing showed APC and BRCA1 gene mutations, negative BRAF V600E, RET fusion, RET mutation, NTRK1/2/3 fusion and PD L1 immunohistochemistry score is <1%. The patient is planned to receive [1]3[1]I ablation therapy. Conclusion: PDTC accounts for 3–5% of all thyroid carcinomas. The 5, 10-, and 15-year survival rates of patients are 50–85%, 34–50%, and 0%, respectively. RAS gene alterations are found in 25–35%, BRAF mutation in 15–27%, TERT promoter mutation in 40% and mutant TP53 in 16–28% of PDTCs. TERT promoter gene and TP53 mutation usually indicate an aggressive phenotype and a dismal prognosis. Surgery, [1]3[1]I therapy, and external beam radiotherapy constitute the mainstay of traditional treatment for patients with advanced disease; however, treatment is challenging. Tyrosine kinase inhibitors i.e, sorafenib and lenvatinib, have been used in cases of progressive, recurrent, or metastatic disease not responsive to [1]3[1]I therapy. Immunotherapy may be an option in PD-L1-positive tumors. Presentation: 6/1/2024

Gastric dysplastic lesions in Helicobacter pylori-naïve stomach: Foveolar-type adenoma and intestinal-type dysplasia.

Reports of Helicobacter pylori (Hp)-naïve gastric neoplasm (HpNGN) cases have been rapidly increasing due to the recent increase in the Hp-naïve population in Japan. Most HpNGNs exhibit the gastric immunophenotype and a low malignant potential regardless of histological type. Especially, foveolar-type gastric adenoma (FGA) and intestinal-type gastric dysplasia (IGD) rarely progress to invasive carcinoma. FGA is a foveolar epithelial neoplasm that occurs in the fundic gland (oxyntic gland) mucosa and is classified as the flat type or raspberry type (FGA-RA). The flat type is a large, whitish flatly elevated lesion while FGA-RA is a small reddish polyp. Genomically, the flat type is characterized by APC and KRAS gene mutations and FGA-RA by a common single nucleotide variant in the KLF4 gene. This KLF4 single-nucleotide variant reportedly induces gastric foveolar epithelial tumorigenesis and activates both cell proliferation and apoptosis, leading to its slow-growing nature. IGD consists of an intestinalized epithelial dysplasia that develops in the pyloric gland mucosa, characterized as a superficial depressed lesion surrounded by raised mucosa showing a gastritis-like appearance. Immunohistochemically, it exhibits an intestinal or gastrointestinal phenotype and, frequently, p53 overexpression. Thus, IGD shows unique characteristics in HpNGNs and a potential multistep tumorigenic process.

Liquid biopsy multiomics enable clinical triage for early colorectal cancer diagnosis.

e15599 Background: Colorectal cancer (CRC) is the second most common cause of cancer death in the United State. Despite advancements in screening, diagnosis, and treatment, the disease remains a formidable public health issue. In 2023, approximately 153020 individuals were diagnosed with CRC and 52550 will die from the disease. In order to meet early diagnostic, we developed this multiomics assay to enable clinical triage for liquid biopsy screening. Methods: Xenonucleic acid (XNAs) are artificial genetic polymers that retain the Watson-Crick base-pairing capability and exhibit high chemical and biological stability. They can be employed as molecular clamps in RT-qPCR due to the stronger hybridizing/binding capability seen in XNA/DNA duplexes than DNA/DNA duplexes. We are developing an XNA-based multiplex RT-qPCR assay for APC, BRAF, CTNNB1, KRAS, NRAS, PIK3CA, SMAD4 and TP53 gene mutation panel and CRC 9 genes methylation panel combined with multiplex protein panel, called ColoscapeTM Plus. We enrolled in FIT positive subjects of both genders, aged 50-74, attending the CRC screening program, we tested 152 plasma samples, 75 health, 50 AA and 27 early CRC with this multiomics assay. Results: The assay results showed that its sensitivity was about 44% (95% CI: 0.302- 0.587) and specificity about 80% (95%CI: 0.689- 0.880) for advanced adenoma (AA). For CRC stage I and II, its sensitivity is about 63% and 78% with 80% specificity separately. Conclusions: The primary data has shown that this low cost and rapid turnaround time multiomics assay has a comparable sensitivity for early colorectal cancer diagnostic.

Incidence of common gene mutations in early-onset colorectal cancer and the association with cancer survival: a meta-analysis

Objective: The incidence of early-onset colorectal cancer (EOCRC) is increasing globally; however, the molecular characteristics and prognosis of sporadic EOCRC are unclear. In this systematic review and meta-analysis, we aimed to investigate the incidence of gene mutations and their association with cancer survival in sporadic EOCRC, focusing on six common gene mutations (TP53, BRAF, KRAS, NRAS, PTEN, and APC). Methods: Ovid Embase and Ovid Medline electronic databases were searched for studies involving patients with sporadic EOCRC (i.e., diagnosed with colorectal cancer before the age of 50 years and with no evidence of hereditary syndromes predisposing to colorectal cancer). The included articles were evaluated using quality assessment tools. Meta-analysis was performed using random-effects and fixed-effects models. Cochran's Q statistic and the I2 index were used to assess heterogeneity. The incidence of the six common gene mutations listed above in sporadic EOCRC and their association with cancer survival were evaluated. Results: (1) Incidence of specific gene mutations in sporadic EOCRC. A total of 34 articles were included in this meta-analysis. The incidence of APC gene mutation was 36% (from 13 articles, 95%CI: 19%-55%, P=0.043); of KRAS gene mutation 30% (from 26 articles, 95%CI: 24%-35%, P=0.190); of BRAF gene mutation 7% (from 18 articles, 95%CI: 5%-11%, P=0.422); of NRAS gene mutation 4% (from five articles, 95%CI: 3%-5%, P=0.586); of PTEN gene mutation 6% (from six articles, 95%CI: 4%-10%, P=0.968); and of TP53 gene mutation 59% (from 13 articles, 95%CI: 49%-68%, P=0.164). (2) Association between gene mutations and survival in sporadic EOCRC. A total of six articles were included in this meta-analysis. Compared with wild-type BRAF, mutant BRAF was significantly associated with increased overall mortality risk in patients with EOCRC (pooled HR=2.85, 95%CI: 1.45-5.60, P=0.002). Subgroup analysis showed that the incidence of BRAF gene mutation was higher in Eastern than in Western countries, whereas the incidence of TP53, KRAS, NRAS, and APC gene mutations was lower. There was no significant difference in the incidence of PTEN gene mutation between different regions. Conclusion: Compared with colorectal cancer occurring in the general population, the incidence of APC and KRAS mutations is lower in EOCRC, whereas the incidence of TP53 mutation remains consistent. BRAF mutation is associated with increased overall mortality risk in patients with EOCRC.

Mutational analysis of pulmonary large cell neuroendocrine carcinoma: APC gene mutations identify a good prognostic factor

Pulmonary large cell neuroendocrine carcinoma (LCNEC) is a highly aggressive neoplasm with biological heterogeneity. Mutations in multiple genes have been identified in LCNEC. However, associations between gene alterations, histopathological characteristics, and prognosis remain ambiguous. Here, we investigated the clinicopathologic, immunohistochemical, and genomic characteristics of 19 patients with LCNEC and 9 patients with atypical carcinoid (AC). We revealed high mutation frequencies of TP53 (89.5 %), RB1 (42.1 %), APC (31.6 %), and MCL1 (31.6 %) in LCNEC, while genetic alterations were rarely found in AC. APC alterations mainly occurred to the exon 16 and were only identified in LCNEC with wild-type RB1. The 19 LCNEC were further subgrouped into APC wild-type (LCNEC-APCMT, 6/19) and APC-mutated (LCNEC-APCWT, 13/19) subgroups. In comparison with LCNEC-APCWT, LCNEC-APCMT displayed lower TMB (median: 12.64 vs 4.20, P = 0.045), and relatively mild cytologic atypia. In addition, LCNEC-APCMT distinguished itself from AC and LCNEC-APCWT by obviously downregulated expression of neuroendocrine markers (CD56 and Syn, P < 0.01) and significantly altered expression of genes downstream of APC (β-catenin migrating into the cytoplasm and nucleus, P < 0.001; c-Myc upregulating, P = 0.005). The OS of LCNEC-APCMT was numerically intermediate between AC and LCNEC-APCWT. We first proposed that APC alterations were common in LCNEC with wild-type RB1 and that LCNEC-APCMT was associated with lower TMB and better OS in comparison with LCNEC-APCWT.

Colorectal cancer cells secreting DKK4 transform fibroblasts to promote tumour metastasis

Wnt/β-catenin signalling is aberrantly activated in most colorectal cancer (CRC) and is one key driver involved in the initiation and progression of CRC. However, mutations of APC gene in CRC patients retain certain activity of APC protein with decreased β-catenin signalling and DKK4 expression significantly upregulates and represses Wnt/β-catenin signalling in human CRC tissues, suggesting that a precisely modulated activation of the Wnt/β-catenin pathway is essential for CRC formation and progression. The underlying reasons why a specifically reduced degree, not a fully activating degree, of β-catenin signalling in CRC are unclear. Here, we showed that a soluble extracellular inhibitor of Wnt/β-catenin signalling, DKK4, is an independent factor for poor outcomes in CRC patients. DKK4 secreted from CRC cells inactivates β-catenin in fibroblasts to induce the formation of stress fibre-containing fibroblasts and myofibroblasts in culture conditions and in mouse CRC xenograft tissues, resulting in restricted expansion in tumour masses at primary sites and enhanced CRC metastasis in mouse models. Reduced β-catenin activity by a chemical inhibitor MSAB promoted the CRC metastasis. Our findings demonstrate why reduced β-catenin activity is needed for CRC progression and provide a mechanism by which interactions between CRC cells and stromal cells affect disease promotion.

Abstract 866: Identification of survival-associated epithelial cell markers linked to TROP2 through single-cell and bulk sequencing analysis

Abstract Introduction: Colorectal Cancer (CRC) is known for its aggressiveness and drug resistance. This has increased the interest in antibody-drug conjugates (ADCs) as a possible therapy. In this study, we aim to investigate the effects of the ADC target TROP2, on the level of epithelial cells and its correlation with survival outcomes in CRC patients. Methods: Single-cell RNA (scRNA) data was downloaded from Gene Expression Omnibus (GEO) for CRC patients and evaluated for TROP2 expression. Patients were grouped into low and high-TROP2 based on median TROP2 expression, and pseudo-bulk analysis was used to find the differentially expressed genes (DEGs). The DEGs were used to find the survival association in the TCGA-CRC cohort. A risk score was built using principal component analysis (PCA) on the TROP2-DEGs and cutoff point was chosen based on survival. Kaplan-Meier curve was used to compare overall survival (OS), progression-free survival (PFS), and disease-free survival (DFS) risk groups. Gene Set Variation Analysis (GSVA) was used to identify the enriched pathways between low- and high-TROP2 in GSE using pseudo-bulk by pooling epithelial cells of individual patients. Results: Of the 10424 cells of 15 different types for 9 CRC patients retrieved from GSE146771, TROP2 was significantly expressed by epithelial cells (n = 766) with mean expression of 1.64 (SD: 1.96, P-value: 0.003) using pseudo-bulk analysis. Three significant DEGs were obtained which are: KIF13B, UCHL3, and PLAC8. These were evaluated for survival association in resectable stages (I-III) CRC patients (n = 419) using PCA to group the patients into low-risk (n = 88) and high-risk (n = 331), using -1.4 as the cutoff point. High risk group showed a better survival with a 1-year survival probability of 94% compared to 90% in the low group and a 5-year survival probability of 74% vs. 46% in the low group. The Kaplan-Meier curve showed that OS, PFS &amp; DFS were significantly better in the low-risk group (p-value = 0.004, 0, 04, and 0.024 respectively). TROP2 and PLAC8 were significantly associated with worse prognosis, whereas UCHL3 was associated with better prognosis (p-value = &amp;lt;0.001), however, KIF3B did not significantly affect the prognosis. APC gene mutation and TP53 were higher in the low-risk group (p-value = 0.004, 0.007 respectively). KRAS-signaling, IL-18-signaling, MET activation of PTK2-signaling were upregulated in high-TROP2 group, while MYC targets, MTORC1 signaling, DNA repair, reactive-oxygen-species signaling, and TCR-signaling were upregulated in low-TROP2. Conclusion: In this study we developed a TROP2-associated risk score that significantly predicted OS, PFS, and DFS in patients with resectable CRC by combining single-cell and bulk-RNA-seq datasets and showing predominant expression of TROP2 in epithelial cells. These findings support the development of TROP2 targeting therapeutics in this space. Citation Format: Noor Nedal Al-Bzour, Ayah Nedal Al-Bzour, Azhar Saeed, Lujia Chen, Anwaar Saeed. Identification of survival-associated epithelial cell markers linked to TROP2 through single-cell and bulk sequencing analysis [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 866.

Abstract 7487: Construction of a reliable CTC detection method and validity evaluation of CTC markers in colorectal cancer

Abstract Even in modern times when medical technology has advanced, cancer remains a life-threatening disease, and recurrence and metastasis are major issues in cancer treatment. The characteristics of cancer cells change with progression and treatment. Therefore, timely evaluation on their characteristics and decision on the treatment strategy are required. Circulating tumor cells (CTCs) are released into blood vessels in solid tumors and promote metastasis by circulating in the blood. CTCs are thus attractive targets for liquid biopsy and can provide useful information for selection of appropriate treatment. To obtain reliable results from CTC testing, it is important to prove that the detected cells are derived from cancerous tissue. In molecular tests targeting CTCs, it is still unclear whether the detected cells are derived from cancer tissue displaying genetic mutations. Aiming to establish reliable CTC testing, we have developed a simple method using molecular imaging flow cytometry to detect APC gene mutation together with Cytokeratin and Vimentin, which are epithelial-mesenchymal transition markers. Since, abnormalities in the APC gene are detected in 60-70% of colorectal cancer patients, detecting such mutations provides strong evidence that the detected cells are derived from cancerous tissue. Here, we show that upon evaluation of analytical performance of our method using cells isolated from cancerous tissue, our method showed high concordance rate against APC gene mutation. A clinical proof-of-concept using 5 mL of whole blood from colorectal cancer patients revealed that counts of cells with APC mutation in blood and cells with Cytokeratin and/or Vimentin expression in blood are highly correlated. Our results demonstrated a pathological stage-dependent increase in the count and frequency of Cytokeratin and/or Vimentin positive CTCs. We believe that our study not only establishes a practical approach for identifying CTCs in cancer patients but also provides potential implications in clinical practice, prognostic evaluation, and selection of treatment strategies. Citation Format: Yusuke Takahashi, Yuichi Ijiri, Shiki Fujino, Nakhaei Elnaz, Ayuko Kishimoto, Kentaro Shirai, Shigeki Iwanaga, Masatoshi Yanagida, Ali Asgar Bhagat, Norikatsu Miyoshi. Construction of a reliable CTC detection method and validity evaluation of CTC markers in colorectal 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 7487.

Abstract 2182: 15-lipoxygenase-1 modulation of colonic resolvin production to suppress colorectal carcinogenesis

Abstract Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are widely used dietary supplements and FDA-approved treatments. The reported impacts of fish oil, DHA, and EPA on colorectal carcinogenesis (CRC) have spurred debates, as certain studies suggest promotional effects while numerous others emphasize suppressive effects. Nevertheless, resolvins, oxidative metabolites of EPA and DHA, exhibit the ability to inhibit crucial pathways (such as TNF-α and IL-1β) that contribute to CRC. 15-lipoxygenase-1 (ALOX15) plays a crucial role in the oxidative metabolism of DHA and EPA, ultimately leading to the formation of resolvins. However, ALOX15 expression is commonly lost during human CRC. Whether loss of ALOX15 expression modulates the effects of DHA and EPA on CRC remains to be elucidated. We therefore conducted the experiments in preclinical CRC mouse models induced by Azoxymethane or Apc gene mutation to explore the hypothesis that ALOX15 expression in colonic epithelial cells regulates DHA and EPA metabolism to generate resolvins, subsequently influencing CRC outcomes. We found that 1) DHA and EPA exert differential effects on CRC, which can be further modified by factors such as their formulation (e.g., ethyl ester versus triglyceride); 2) targeted transgenic expression of ALOX15 in the intestines of mice (referred to as ALOX15-Gut mice) markedly augmented the production of resolvins and concurrently suppressed CRC; 3) the predominant products from the expressed ALOX15 enzymatic activity were identified as 17-HDHA and resolvin D5; and 4) the effects ALOX15 on increasing resolvin generation and suppressing CRC were consistent across various promoters used to drive ALOX15 transgenic expression in mice. These findings collectively underscore the profound importance of ALOX15 intestinal expression as a host-related factor in resolvin generation from EPA and DHA, which subsequently contributes to the suppression of CRC. Citation Format: Xiangsheng Zuo, Yoshiyuki Kiyasu, Yi Liu, Micheline Moussalli, Bo Wei, Peiying Yang, Imad Shureiqi. 15-lipoxygenase-1 modulation of colonic resolvin production to suppress colorectal carcinogenesis [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 2182.

Immune landscape in APC and TP53 related tumor microenvironment in colon adenocarcinoma: A bioinformatic analysis.

APC and TP53 are the two most regularly mutated genes in colon adenocarcinoma (COAD), especially in progressive malignancies and antitumoral immune response. The current bioinformatics analysis investigates the APC and TP53 gene expression profile in colon adenocarcinoma as a prognostic characteristic for survival, particularly concentrating on the correlated immune microenvironment. Clinical and genetic data of colon cancer and normal tissue samples were obtainedfrom The Cancer Genome Atlas (TCGA)-COAD and Genotype-Tissue Expression (GTEx) online databases, respectively. The genetic differential expressions were analyzed in both groups via the one-way ANOVA test. Kaplan-Meier survival curves were applied to estimate the overall survival (OS). P < 0.05 was fixed as statistically significant. On Tumor Immune Estimation Resource and Gene Expression Profiling Interactive Analysis databases, the linkage between immune cell recruitment and APC and TP53 status was assessed through Spearman's correlation analysis. APC and TP53 were found mutated in 66.74% and 85.71% of the 454 and 7 TCGA-COAD patients in colon and rectosigmoid junction primary sites, respectively with a higher log2-transcriptome per million reads compared to the GTEx group (318 samples in sigmoid and 368 samples in transverse). Survival curves revealed a worse significant OS for the high-APC and TP53 profile colon. Spearman's analysis of immune cells demonstrated a strong positive correlation between the APC status and infiltration of Tcell CD4+, T cell CD8+, NK cell, and macrophages and also a positive correlation between status and infiltration of T cell CD4+, T cell CD8+. APC and TP53 gene mutations prevail in colon cancer and are extremely associated with poor prognosis and shortest survival. The infiltrating T cell CD4+, T cell CD8+, NK cell, and macrophages populate the colon microenvironment and regulate the mechanisms of tumor advancement, immune evasion, and sensitivity to standard chemotherapy. More comprehensive research is needed to demonstrate these results and turn them into new therapeutic outlooks.

Molecular Spectrum and Determination of the Frequency and Distribution of APC, PIK3CA and SMAD4 Gene Mutations in Ugandan Patients with Colorectal Cancer

Molecular Spectrum and Determination of the Frequency and Distribution of APC, PIK3CA and SMAD4 Gene Mutations in Ugandan Patients with Colorectal Cancer

Genetic specificity study using next-generation sequencing (NGS) of peritoneal metastatic colorectal cancer compared to primary colorectal cancer.

In patients with colorectal cancer, peritoneal metastases are the second most frequent metastatic lesion after liver metastases. Peritoneal metastases have a very poor prognosis, with a median survival time of 5-7months. Currently, there is a lack of research on the genetic differences between primary colorectal cancer and peritoneal metastases. Therefore, we aimed to identify their genetic characteristics through a cancer panel test using next-generation sequencing. We aim to investigate the specificity of genetic variants in primary colorectal cancer and peritoneal metastases. We recruited patients with stage I, II, and III primary colorectal cancer and peritoneal metastases for genetic analysis using NGS. Samples were collected from patients who underwent surgery at Dankook University Hospital and consented to genetic testing. NGS was performed using a cancer panel. Among 36 patients with primary cancer, TP53 gene mutation was identified the most in 25 patients (69%), followed by APC gene mutation in 19 patients (53%), and KRAS gene mutation in 17 patients (47%). In the peritoneal metastasis patient group, unlike the primary cancer patient group, KRAS gene mutations were the most common 6 patients (55%), followed by TP53 gene mutations in 4 patients (36%) and PIK3CA gene mutations in 2 patients (18%). The small number of surgical cases of peritoneal metastases was a limitation of our sample size. Nevertheless, we identified differences in the alterations of specific genes between primary and peritoneal metastases. Acquiring additional cases and collecting more data will provide deeper insights into these cancers.

Cyclin D1 in various cancers: Mechanisms and clinical implications

Gastrointestinal cancers, including esophageal, gastric, hepatic, pancreatic, and colorectal malignancies, present a significant global health challenge. Their distinct characteristics characterized by abnormal cell proliferation, invasive behavior, and tumor formation make them highly aggressive and detrimental to human health. These diseases often lead to malnutrition, organ failure, and obstruction. Cyclin D1 protein is a critical regulator of cell cycle progression and an essential marker for comprehending the complex landscape of cancer biology. This research provides an in-depth exploration of gastrointestinal cancers by shedding light on their adverse effects on the human body while emphasizing the critical role played by cyclin D1 within this challenging disease context. Extensively studied in colorectal cancer as well as esophageal squamous cell carcinoma (ESCC), gastric cancer, and pancreatic cancer contexts. Cyclin D1 emerges as a key player. Specifically, in cases of colorectal cancer, overexpression of cyclin D1 is frequently linked to aggressive tumor behavior brought on by APC gene mutations and abnormal Wnt signalling pathway activation. Esophageal cancer patients especially those with ESCC frequently exhibit elevated levels of Cyclin D1 indicating poor prognosis. A similar trend is observed in gastric cancer where increased expression of cyclin D1 is linked to disease severity.

Commitment Complex Splicing Factors in Cancers of the Gastrointestinal Tract-An In Silico Study.

The initial step in pre-mRNA splicing involves formation of a spliceosome commitment complex (CC) or E-complex by factors that serve to bind and mark the exon-intron boundaries that will undergo splicing. The CC component U1 snRNP assembles at the 5'-splice site (ss), whereas SF1, U2AF2, and U2AF1 define the 3'-ss of the intron. A PRP40 protein bridges U1 snRNP with factors at the 3'-ss. To determine how defects in CC components impact cancers, we analyzed human gastrointestinal (GI) cancer patient tissue and clinical data from cBioPortal. cBioPortal datasets were analyzed for CC factor alterations and patient outcomes in GI cancers (bowel, stomach, esophagus, pancreas, and liver). In addition, co-expression datasets were used to determine the splicing targets of the CC. Our analysis found that frequency of genetic changes was low (1%-13%), but when combined with changes in expression levels, there was an overall surprisingly high incidence of CC component (>30%) alterations in GI cancers. Colon cancer patients carrying BRAF driver gene mutations had high incidences of CC alterations (19%-61%), whereas patients with APC, KRAS, or TP53 gene mutations had low (<5%) incidences of CC alterations. Most significantly, patients with mutations in CC genes exhibited a consistent trend of favorable survival rates, indicating that mutations that impair or lower CC component expression favor patient survival. Conversely, patients with high CC expression had worse survival. Pathway analysis indicates that the CC regulates specific metabolic and tumor suppressor pathways. Metabolic pathways involved in cell survival, nutrition, biosynthesis, autophagy, cellular movement (invasion), or immune surveillance pathways correlated with CC factor upregulation, whereas tumor suppressor pathways, which regulate cell proliferation and apoptosis, were inversely correlated with CC factor upregulation. This study demonstrates the versatility of in silico analysis to determine molecular function of large macromolecular complexes such as the spliceosome CC. Furthermore, our analysis indicates that therapeutic lowering of CC levels in colon cancer patients may enhance patient survival.

Correlation of the Pro-Inflammatory Cytokines IL-1β, IL-6, and TNF-α, Inflammatory Markers, and Tumor Markers with the Diagnosis and Prognosis of Colorectal Cancer.

Colorectal cancer (CRC) remains one of the most important global health problems, being in the top 3 neoplasms in terms of the number of cases worldwide. Although CRC develops predominantly from the adenoma-adenocarcinoma sequence through APC gene mutations, in recent years, studies have demonstrated the role of chronic inflammation in this neoplasia pathogenesis. Cytokines are important components of chronic inflammation, being some of the host regulators in response to inflammation. The pro-inflammatory cytokines IL-1β, IL-6, and TNF-α are involved in tumor cell proliferation, angiogenesis, and metastasis and seem to strengthen each other's mode of action, these being stimulated by the same mediators. In our study, we collected data on 68 patients with CRC and 20 healthy patients from the Gastroenterology Department of Craiova County Emergency Clinical Hospital, who were assessed between January 2022 and February 2023. The main purpose of this study was to investigate the correlation between increased plasma levels of the cytokines and the extent of the tumor, lymph nodes, and metastasis-(TNM stage), as well as the patients' prognoses. We also compared the plasma levels of cytokines and acute inflammatory markers, namely, the erythrocyte sedimentation rate (ESR), c-reactive protein (CRP), and fibrinogen, along with the tumor markers, carcinoembryonic antigen (CEA) and carbohydrate antigen 19.9 (CA 19.9), in CRC patients. We showed that all the pro-inflammatory cytokines studied had higher levels in patients with CRC in comparison with the control group. We also showed that the acute inflammatory markers of erythrocyte sedimentation rate, C-reactive protein, and fibrinogen, and the tumor markers of CEA and CA 19.9 can be useful in diagnosis and prognosis in patients with CRC. Considering the association between pro-inflammatory cytokines and CRC, the development of new targeted therapies against IL-1β, IL-6, and TNF-α can improve patient care and the CRC survival rate.

Surgical treatment of familial adenomatous polyposis in children: cross-sectional study

Familial adenomatous polyposis (FAP) is an autosomal dominant disease caused by the APC gene mutation, characterized by colon adenomas and colorectal cancer, including in children. The issue of timing and indications for surgical treatment of FAP in childhood remains debatable.AIM: to identify predictors of surgery for FAP in pediatric patients.PATIENTS AND METHODS: a retrospective case-control study was conducted. The results of treatment of 50 children with FAP who were in the surgical department of the Russian Children's Clinical Hospital from January 2000 to April 2023 were analyzed. Two groups were formed: patients who underwent surgery of FAP under the age of 18 (case), and patients who did not undergo surgery at this age (control). We analyzed potential predictors: the age of manifestation, the clinical, the characteristics of adenomas, the anemia and family history, polyposis of the upper gastrointestinal tract.RESULTS: in the surgical group, the proportion of patients with more than 100 adenomas was higher (23 (88%) versus 11 (45%) (p=0.002)). It was revealed that the number of adenomas was more than 100 at the time of the first colonoscopy (OR 12 (95% CI (3–80), p=0.02) and the presence of colon bleeding (OR 5.8 (95% CI 1–35, p=0 .03) are independent predictors of colproctectomy in children.CONCLUSION: the number of adenomas over 100 and colon bleeding are independent predictors of colproctectomy in childhood.

Novel deep learning–based prognostic prediction model for colorectal cancer using hematoxylin and eosin–stained whole slide images.

3119 Background: Previous studies have shown that the presence or absence of genetic mutations is critical for colorectal cancer prognosis. However, genomic testing can be expensive and difficult to perform on all samples. In contrast, hematoxylin and eosin (H&amp;E) staining is relatively inexpensive and can be performed on all tissue specimens. In this study, we designed a novel prognostic method using spatial image features extracted from H&amp;E–stained whole slide images (WSIs) and genetic mutation prediction neural networks. Methods: We obtained H&amp;E–stained WSIs and data on Microsatellite Instability ( MSI), BRAF, TTN and APC gene mutations from a clinical cohort of 548 patients with The Cancer Genome Atlas (TCGA) Colon adenocarcinoma and rectum adenocarcinoma. We divided them into training (n=361), validation (n=90), and test (n=115) groups. Classification models were trained to predict the presence or absence of MSI, BRAF, TTN, and APC mutations. The model input comprised features of the H&amp;E–stained WSIs, as obtained via a deep learning–based feature extractor. All resultant models were incorporated into a prognostic model (overall survival: &gt; 60 months (low risk)/&lt; 60 months (high risk)). Our prognostic model’s performance was evaluated against TCGA colorectal dataset, and a survival analysis was performed on the model using the Kaplan–Meier method. Finally, we compared our model’s performance with the end–to–end prognostic prediction of a convolutional neural network (CNN) that also used H&amp;E–stained WSIs as input and provided prognostic prediction as output. Results: Our deep learning–based prognostic prediction model achieved an AUC score of 0.834 with a 95% confidence interval (CI) of 0.734–1.000 alongside TCGA dataset; the survival analysis compared the survival distributions of low–risk and high–risk groups, as predicted by our model; a p–value &lt; 0.01 was obtained. The model could classify low– and high–risk patients and accurately predict patient status as alive (low risk) or deceased (high risk) at 60 months. In contrast, the CNN–based model achieved an AUC score of only 0.502 (95% CI: 0.315–0.690) on the same TCGA dataset, and the p–value obtained for it under the Kaplan–Meier log–rank test was greater than 0.5. The CNN–based method was unable to distinguish between low– and high–risk patients, confirming that our method using spatial imaging features extracted from WSIs was a more effective approach. Conclusions: We developed a novel prognostic prediction method using spatial image features extracted from WSIs and genetic mutation prediction neural networks. Our results demonstrated the advantage of using image features over gene mutation data for prognostic prediction in colorectal cancer patients.

Evaluation of genomic alterations in early-onset versus late-onset colorectal cancer.

3511 Background: The etiology of the rising incidence of early-onset colorectal cancer (EOCRC), defined as CRC in patients aged &lt; 50, remains unknown. In this study, we evaluated tumor genomic differences in patients with EOCRC versus average-onset CRC (AOCRC, age &gt; 60). Methods: The cohort included 13,262 patients diagnosed with stages I-III colon or rectal cancer who had whole exome sequencing as part of their ctDNA testing (Signatera, bespoke mPCR NGS assay). Tumor mutational burden (TMB) and microsatellite instability (MSI) status were derived from tumor whole exome sequencing analysis. The prevalence of somatic variants and mutations in known oncogenic pathways was compared between EOCRC and AOCRC groups, stratified by TMB and MSI status. Fisher’s exact test was used to test significance between the groups and p-values were adjusted using the FDR method for multiple test correction. Results: A total of 3,093 patients with EOCRC (70.8% colon, 27.4% rectal, 1.9% unknown) and 10,169 patients with AOCRC (79.9% colon, 18.3% rectal, 1.7% unknown) were included, where 9.0%/37.3%/53.7% were AJCC stages I, II, and III, respectively. Early-onset patients compared to average-onset patients had fewer cases of stage II CRC (30.7% vs. 39.3%, p &lt; 0.01) and more cases of stage III CRC (60.9% vs 51.6%, p &lt; 0.01). Patients with EOCRC were less commonly MSI-H compared to patients with AOCRC (10% vs. 17%, p &lt; 0.01), or have high tumor mutational burden (15% vs. 19%, p &lt; 0.01). The BRAF V600E mutation and truncated RNF43 mutations were less prevalent in EOCRC (3% vs. 15% and 2% vs. 9%, p &lt; 0.01), regardless of TMB and MSI status. Molecular alterations of the RTK-RAS pathway were less prevalent in the EOCRC cohort (p &lt; 0.01), while TP53 pathway alterations were more frequent in the EOCRC cohort (p &lt; 0.01). In the TMB-low/MSS group, TP53 mutations were more common in EOCRC (8% vs. 5%, p &lt; 0.01), but APC gene mutations were less common in EOCRC (56% vs. 66%, p &lt; 0.01). In the TMB-H/MSI-H group, BRAF V600E (4% vs. 60%), RNF43G659V (16% vs. 45%), and WNT1 G619A (6% vs. 20%) mutations were less prevalent in EOCRC (p &lt; 0.01 for all mutations); however, patients with EOCRC had more PIK3CA H1047R (22% vs. 9%) , APC R1468* (11% vs. 3%), and KRAS A146T (7% vs. 2%) variants (p &lt; 0.01 for all mutations). In the TMB-H/MSS group, EOCRC patients were more likely to have driver mutations in the PI3K pathway (74% vs. 56%, p &lt; 0.01). The POLE P286R mutation was more common in TMB-H/MSS patients with EOCRC (38% vs. 13%, p &lt; 0.01), whereas ACVR2A K437R was less common (11% vs. 30%, p &lt; 0.01). Prevalence of somatic variants and mutated oncogenic pathways did not vary significantly by tumor stage. Conclusions: Patients with AOCRC harbored more somatic variants and mutations in established pathways of CRC carcinogenesis. Tumors in EOCRC cases carried unique genomic alterations that varied across the TMB and microsatellite subpopulations. BRAF V600E and RNF43 truncating mutations were more frequent in AOCRC.

Reply to Kaminski, N.E.; Cohen, S.M. Comment on "Bischoff et al. The Effects of the Food Additive Titanium Dioxide (E171) on Tumor Formation and Gene Expression in the Colon of a Transgenic Mouse Model for Colorectal Cancer. Nanomaterials 2022, 12, 1256".

We appreciate the interest in our article describing transcriptome changes in a transgenic mouse model carrying an APC gene mutation and would like to reply to the reader [...].