Egyptian Colorectal Cancer Patients Research Articles

Case-control study: Unveiling human polyomaviruses and papillomavirus in Egyptian colorectal cancer patients.

Colorectal cancer (CRC) is a cancer type that is thought to be influenced by human papillomaviruses (HPVs) and human polyomaviruses (HPyVs). In Egypt, CRC ranks as the 7th most common cancer, accounting for 3.47% of male cancers and 3% of female cancers. However, there is currently a lack of information regarding the presence of PyVs and HPVs co-infection specifically in CRC cases in Egypt. Therefore, the aim of this study was to investigate the occurrence of HPVs and HPyVs (JCPyV, BKPyV, and SV40) infections, as well as co-infections, among CRC patients in Egypt. Additionally, the study aimed to assess any potential association between these viral infections and tumor stages. In the present study, we analyzed a total of 51 tissue samples obtained from Egyptian CRC patients, along with 19 polyps' samples. Our investigation focused on the detection and genotyping of HPyVs using Real-Time PCR. Additionally, we employed real-time PCR for the detection of HPVs, and for their genotyping, we utilized a combination of PCR amplification followed by sequencing. In our study, we found evidence of HPyVs infection in the CRC patients, specifically SV40 (25.5%) and BKPyV (19.6%). However, JCPyV was not detected in the samples that were examined. Additionally, we discovered that HPV was present in 43.1% of the CRC patients. When considering viral co-infections, 19.6% of the CRC samples showed coexistence of multiple viruses, while no co-infections were found in the polyps samples. Importantly, we observed a significant correlation between the presence of HPVs and advanced colorectal tumor grades B2 and D. Our findings provide valuable data for the detection of oncogenic viruses in colorectal cancer (CRC) and underscore the association of viral co-infections with advanced tumor stages. However, further research with larger cohorts is necessary to validate these findings and strengthen their significance in the field of CRC.

Abstract 3854: Revealing mismatch repair deficiency in Egyptian colorectal cancer patients using next generation sequencing a predictive biomarker for immunotherapy efficacy

Abstract Background: The mismatch repair (MMR) deficiency is a potential predictive biomarker for immunotherapy efficacy, particularly in colorectal cancer (CRC), where alterations in various DNA polymerases and MMR genes are prevalent. The accumulation of these genetic aberrations may cause a subsequent neoantigen formation. study aimed to identify the mutational profile of DNA polymerases and MMR genes in Egyptian CRC patients', providing insights into colorectal carcinogenesis and potential implications for immunotherapy. Material and Methods: Thirty-nine blood samples from Egyptian patients with CRC and twenty-four blood samples from healthy controls were collected. The libraries were prepared by Qiaseq UMI-based targeted panel and sequenced via an Ion proton sequencer. The detected genetic variants with an average coverage of 500x were annotated against Cosmic, dbSNP, and ClinVar databases using Ingenuity Variant analysis (IVA). Results: Our results revealed that the POLD1andPOLE genes (DNA polymerases) in the CRC patients, when compared with healthy controls, harbored 10 and 13 pathogenic variants (PVs), respectively. These PVs cause a loss of their functionality. The most frequently detected PVs and likely to be novel in the POLD1gene werec.44delC(31%)andc.3008delG(31%), while c.3510delA(18%)andc.2793delT(15%) were detected in the POLE gene. As per MMR genes, our study showed that the MLH1, MLH3, MSH2, MSH3, MSH6, PMS1,and PMS2 harbored 8, 13, 23, 19, 22, 23, and 7 PVs, respectively. The highly frequent PV in the MLH1wasc.469delT (26%), while the novel most frequently detected PV in the MLH3 wasc.1467delA (23%). Moreover, the PVs found highly frequent are c.2647delA (36%) in MSH2,c.1148delA (41%)in the MSH3, and c.2079delA (44%) in the MSH6. RegardingPMS1/2, the most frequently detected PV and likely to be novel was c.1647delA (44%) in PMS1, while c.869delT (13%) was the most prevalent PV in PMS2. Conclusion: Our results revealed the MMR mechanism deficiency in Egyptian CRC patients offering crucial insights into colorectal carcinogenesis and neoantigen formation. These insights are pivotal for developing ethnic-based personalized immunotherapy strategies in Egyptian CRC patients, shedding light on their role in CRC. Interestingly, we have identified novel variants in the DNA repair enzymes. However, further investigations and validations are required to corroborate these findings and explore their clinical significance in the personalized medicine. Citation Format: Amira Salah El-Din Youssef, Mohamed Ragab, Heba Aly Ateya, Mostafa Elberry, Nasra Fathy, Asmaa Elleithy, Abdel Rahman Zekri, Ola Sayed Ahmed, Auhood Nassar. Revealing mismatch repair deficiency in Egyptian colorectal cancer patients using next generation sequencing a predictive biomarker for immunotherapy efficacy [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 3854.

Clinical utility of hsa-miR-181a-5p expression level in Egyptian colorectal cancer patients

Clinical utility of hsa-miR-181a-5p expression level in Egyptian colorectal cancer patients

Deleterious and ethnic-related BRCA1/2 mutations in tissue and blood of Egyptian colorectal cancer patients and its correlation with human papillomavirus

This study aimed to identify BRCA1/2 mutational patterns in the tissue and blood of Egyptian colorectal cancer (CRC) patients and to study the possible correlation of this mutational pattern with Human papillomavirus (HPV) infection. Eighty-two colonoscopic biopsies and forty-six blood samples were collected from Egyptian CRC patients, as well as blood samples of age and sex-matched healthy controls (n = 43) were enrolled. The libraries were performed using Qiaseq Human BRCA1 and BRCA2 targeted DNA panel and sequenced via Ion proton sequencer. Also, the CRC tissues were subjected to conventional PCR targeting the HPV Late 1 (L1) region. Our analysis revealed that the BRCA-DNA damage pathway had been altered in more than 65% of the CRC patients. Comparing tissue and blood samples from CRC patients, 25 somatic mutations were found exclusively in tissue, while 41 germline mutations were found exclusively in blood. Additionally, we identified 23 shared BRCA1/2 pathogenic (PVs) mutations in both blood and tissue samples, with a significantly higher frequency in blood samples compared to tissue samples. The most affected exon in BRCA1 was exon 10, while the most affected exons in BRCA2 were 11, 14, 18, 24, and 27 exons. Notably, we revealed an ethnic-related cluster of polymorphism variants in our population closely related to South Asian and African ethnicities. Novel PVs were identified and submitted to the ClinVar database. HPV was found in 23.8% of the CRC tissues, and 54% of HPV-positive cases had somatic BRCA1/2 PVs. The results of this research point to a possible connection between infection with HPV and BRCA1/2 mutations in the occurrence of colorectal cancer in the Egyptian population, which has a mixed ethnic background. Our data also indicate that liquid biopsy (blood samples) may be more representative than tissue samples for detecting BRCA1/2 mutations. These findings may have implications for cancer screening and the development of personalized, targeted therapies, such as PARP inhibitors, which can effectively target BRCA1/2 mutations.

Determination of Capecitabine and Its Metabolites in Plasma of Egyptian Colorectal Cancer Patients

The incidence of colorectal cancer (CRC) is increasing worldwide. It has variable signs and symptoms starting from changes in bowel habit to nausea and vomiting. Chemotherapeutic agents are often prescribed in CRC such as Capecitabine (CCB) and 5-Fluorouracil (FU). CCB is the prodrug of FU in oral dosage form, which makes it preferable by physicians, since no hospitalization is needed for drug administration. CCB is activated to FU in a three-step reaction producing 5′-deoxy-5-fluorocytidine (DFCR) (by carboxylesterase (CES) enzyme), then 5′-deoxy-5-fluorouridine (DFUR) (by cytidine deaminase (CDD) enzyme) and finally FU (by thymidine phosphorylase (TP) enzyme), the active form, which is later deactivated to give 5,6-dihydro-5-fluorouracil (DHFU). Different patients exhibit variable drug responses and adverse in response to CCB therapy, despite being treated by the same dose, which could be attributed to the occurrence of different possible enzyme single nucleotide polymorphisms (SNPs) along the activation and deactivation pathways of CCB. The most commonly occurring toxicities in CCB therapy are hand-foot syndrome and diarrhea. This study aims at developing and validating a new method for the simultaneous determination of CCB and its metabolites by HPLC-UV, followed by a correlation study with the toxicities occurring during therapy, where predictions of toxicity could be based on metabolites’ levels instead of the tedious process of genotyping. A new superior analytical method was optimized by a quality-by-design approach using DryLab® 2000 software achieving a baseline resolution of the six analytes within the least possible gradient time of 10 min. The method also showed linearity (in a range from 1 to 500 μg/mL), accuracy, precision and robustness upon validation: The LOD was found to be 3.0 ng/mL for DHFU and CCB, and 0.3 ng/mL for DFUR, DFCR and FU. The LOQ was found to be 10.0 ng/mL for DHFU and CCB, and 1.0 ng/mL for DFUR, DFCR and FU. The clinical results showed a positive correlation between the concentration of DFCR and mucositis and between the concentration of DFUR and hand-foot syndrome, confirming that this technique could be used for predicting such toxicities.

Assessment of Quality of Life among Colorectal Cancer Survivors

Background The concepts of quality of life and patient-centered outcomes have become popular in medical communities; however, the wide application of Quality-of-life investigations remains an obstacle for most clinicians due to the limited validation studies performed to date and the lack of disease-specific measuring instruments. Health-related quality of life has become an indispensable component of research outcomes, particularly for cancer therapy. Colorectal cancer (CRC) ranks the third in terms of incidence, but second in terms of mortality, and its incidence is steadily rising in developing nations. The burden of colorectal cancer is rapidly increasing due to the high incidence and consequences of cancer therapy. Patients who survived colorectal cancer therapies may continue to suffer from physical or psychological problems. Objective Validating a tool for Assessment of quality of life among colorectal cancer survivors using EORTC CR29 questionnaire, by assessment of construct Validity of the Egyptian version of the questionnaire. Methods This is a cross-sectional study was held in Ain Shams University Hospitals and Nasser Institute Cancer Centre for 6 months between January 2020 and July 2020 on 85 patients with colorectal cancer, received neo- adjuvant, adjuvant or palliative Therapy (Chemo or Radiotherapy), underwent palliative or radical surgery and not on treatment at time of study. Results 85 patients (62.4% males and 37.6% females) participated in the study. All patients were diagnosed with colorectal cancer. Age was ≤ 60 years among 52.9% of patients while age was > 60 years among 47.1%. after assessing the quality of life (symptoms scale) in our studied patients using EORTC QLQ-CR29 scoring Manual, mean urinary frequency during day score was 28.47± 8 out of 100, mean Urinary Frequency during night score was 31.87 ± 10 out of 100, mean Urinary incontinence score was 32.94 ± 7 out of 100, mean Dysuria score was 16 ± 5 out of 100, mean Abdominal pain score was 25.86 ± 9 out of 100, mean Buttock pain score was 39 ± 12 out of 100, mean Bloated feeling score was 34 ± 11 out of 100, mean Blood and mucus in stool score was 18 ± 7 out of 100, mean Dry mouth score was 30.8 ± 5 out of 100, mean Trouble with taste score was 19.31 ±5.7 out of 100 & mean Hair loss score was 34.8 ± 16 out of 100. We assessed Quality of life (functional scale Table 5).Mean Anxiety for health in our studied patients was 70 ± 18 while Mean Anxiety for weight was 65.8 ± 9. Mean Body image - Attractive was 63.5 ± 8, Mean Body imageSatisfaction was 60.4 ± 12. Conclusion This study shows that the Egyptian version of the EORTC QLQ- CR29 is a valid tool for measuring QOL, as determined by application to a sample of Egyptian colorectal cancer patients.

Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients

PurposeAlthough there is an established role for microbiome dysbiosis in the pathobiology of colorectal cancer (CRC), CRC patients of various race/ethnicities demonstrate distinct clinical behaviors. Thus, we investigated microbiome dysbiosis in Egyptian, African American (AA), and European American (EA) CRC patients. Patients and methodsCRCs and their corresponding normal tissues from Egyptian (n = 17) patients of the Alexandria University Hospital, Egypt, and tissues from AA (n = 18) and EA (n = 19) patients at the University of Alabama at Birmingham were collected. DNA was isolated from frozen tissues, and the microbiome composition was analyzed by 16S rRNA sequencing. Differential microbial abundance, diversity, and metabolic pathways were identified using linear discriminant analysis (LDA) effect size analyses. Additionally, we compared these profiles with our previously published microbiome data derived from Kenyan CRC patients. ResultsDifferential microbiome analysis of CRCs across all racial/ethnic groups showed dysbiosis. There were high abundances of Herbaspirillum and Staphylococcus in CRCs of Egyptians, Leptotrichia in CRCs of AAs, Flexspiria and Streptococcus in CRCs of EAs, and Akkermansia muciniphila and Prevotella nigrescens in CRCs of Kenyans (LDA score >4, adj. p-value <0.05). Functional analyses showed distinct microbial metabolic pathways in CRCs compared to normal tissues within the racial/ethnic groups. Egyptian CRCs, compared to normal tissues, showed lower l-methionine biosynthesis and higher galactose degradation pathways. ConclusionsOur findings showed altered mucosa-associated microbiome profiles of CRCs and their metabolic pathways across racial/ethnic groups. These findings provide a basis for future studies to link racial/ethnic microbiome differences with distinct clinical behaviors in CRC.

The Clinical Significance of Septin 9 and Colon Cancer Specific Antigen-2 (CCSA-2) in Colorectal Cancer.

Colorectal cancer (CRC) is a major health problem Worldwide, Egypt shows a high rate of early CRC in the world as 35% of 1,600 Egyptian CRC patients were under 40 with threefold increased risk of death within 5 years. DNA methylation-based biomarkers as methylated Septin9 (mSEPT9) has a promising role for detecting CRC. As well as set of nuclear matrix proteins associated with changes in the nuclear structure/architecture. detection of these nuclear proteins resulted in identification of biomarkers that are specific for colon cancer. Particular interest has been placed on colon cancer specific antigen-2(CCSA-2). A total of 30 newly diagnosed CRC patients, 7 colonic adenoma patients, and 15 age- and sex-matched control subjects were recruited in this study. Plasma mSEPT9was assayed by Epi procolon kit, CCSA-2 by ELISA and, Occult blood in stool by Guaiac-based fecal occult blood test. The level of Colon Cancer mSEPT9 and CCSA-2 were carried on CRC patients both preoperatively and three months postoperatively. mSEPT9 has 96.7% sensitivity and 95.5% specificity in differentiating colorectal cancer patients from non-malignant cases. Also, our study showed a highly statistically significant difference between the pre and three months postoperative expression of mSEPT9 in colorectal cancer as there was a dramatically decrease in the expression of mSEPT9 postoperatively (p value < 0.001). The CCSA-2 at the cutoff level of >1.43 would provide 93.3% sensitivity and 90.9% specificity in differentiation between malignant and non-malignant cases. Also, the study showed that there is a statistically significant difference between colorectal cancer patients preoperatively and postoperatively according to CCSA-2 with dramatic decrease in its level postoperatively (p value > 0.001). The plasma SEPT9 DNA methylation level and Serum CCSA-2 could be used as promising non-invasive methods for observing the CRC patients postsurgical response to predict the occurrence of complete remission or relapses.

Abstract 1964: The mutational pattern of cell cycle checkpoints and regulators in Egyptian colorectal cancer patients

Abstract Background: Uncontrolled proliferation is a hallmark of cancer cells. Many cell cycle checkpoints and regulators are altered in tumors which in turn results in the accumulation of genetic aberrations. So, this study aimed to identify the mutational profile of cell cycle checkpoints and regulators in tissue biopsies in Egyptian Colorectal Cancer patients. Material and Methods: Sixty two fresh tissues samples were collected from Egyptian patients with CRC. The libraries were performed using Qiaseq UMI-based targeted panel.The detected genetic variants with an average coverage of 500x were annotated using Ingenuity Variant analysis (IVA) and pathway analysis was performed using Ingenuity Pathway analysis (IPA). Results: Data analysis revealed that TP53&amp; ATM genes; the checkpoints at G1/S and G2/M phases, were highly mutated. They harbored 12 and 9 pathogenic mutations respectively, which cause loss of functionality. The most frequently detected pathogenic variants were c.121delG (58%) in the TP53 &amp; c.640delT (29%) in the ATM. While CHECK2; the checkpoint at G2/M phase, harbored 4 pathogenic variants; c.430delC (16%) was the most detected one. Also, two pathogenic variants were detected in the M phase checkpoint BUB1B and the most frequently detected one was c.1669delA (37%). We also detected pathogenic variants involved in the G1/S phase regulators; SMAD4 (c.1241delT (23%)), CDKN2A (c.238delG (18%)), STK11 (c.340delG (11%)), and CDH1 (c.1955delT (19%)). Other pathogenic variants involved in G2/M phase regulators were also detected; BRCA1 (c.3214delC (16%)) &amp; EP300 (c.4408delA (19%)). Moreover, we detected 2 pathogenic variants in M phase regulator; CDC27 (c.1998delA (7%) &amp; c.2070delA (5%)). Conclusion: Our data showed the deregulated pattern of cell cycle checkpoints and regulators that are crucial for understanding colorectal cancer progression in Egyptian patients. Also, it may help in developing personalized targeted therapies that efficiently target the cell cycle genes mutations, thereby limits the CRC progression in those patients. Citation Format: Amira Salah El-Din Youssef, Mai M. Lotfy, Auhood Nassar, Abdel-Rahman N. Zekri. The mutational pattern of cell cycle checkpoints and regulators in Egyptian colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1964.

Conventional peritoneal cytology lacks the prognostic significance of detecting local or peritoneal recurrence in colorectal cancer: An Egyptian experience.

Background and AimColorectal cancer (CRC) accounts for over 8% of all deaths each year, with 1.2 million new cases diagnosed annually worldwide. It represents the seventh most common cancer in Egypt. Early detection of peritoneal metastasis is a major challenge in such cases. It helps with the decision of the immediate application of intraperitoneal chemotherapy after resection. Meta‐analysis studies reported contrast evidence for a possible prognostic role of intraperitoneal free cancer cells (IPCCs) in peritoneal recurrence and survival after curative resection. In this work, we aim to evaluate the prevalence and impact of detecting free malignant cells in peritoneal fluid on survival and local recurrence and to estimate the incidence of peritoneal carcinomatosis (PC) during follow up.MethodsDesign: This was a prospective cohort study. Settings: From June 2016 to December 2018, samples were collected from 104 patients who underwent abdominal surgery for colorectal cancer in the Egyptian National Cancer Institute. A total of 96 Egyptian CRC patients who underwent curative resection were enrolled. Intraoperative peritoneal lavage was performed to detect IPCC by conventional cytology. Patients with no residual tumor after surgery and no evidence of PC were followed up for a median 14 months. The cumulative 12‐month overall survival rate for patients with IPCC was 100% versus 86% for patients with negative cytology.ResultsOur results demonstrated that the prevalence of IPCC in the peritoneal lavage was 11.5%. Peritoneal and local recurrence occurred at a higher rate in patients with cytology positive lavage (9.1% vs 6.3% and 9.1% vs 3.8%, respectively), although this was statistically insignificant. Distant metastasis occurred significantly in patients with positive cytology (45.5% vs 8.9%) with P‐value <0.001.The conventional cytology technique has a high specificity but less sensitivity.ConclusionsThe presence of IPCC using conventional cytology was not an independent prognostic factor for the development of PC or survival.

Differential Expression of miR-21, miR-23a, and miR-27a, and Their Diagnostic Significance in Egyptian Colorectal Cancer Patients.

Background: Colorectal cancer (CRC) rates are affected by genetics, ethnicity, and environmental factors; it is considered one of the most aggressive human malignancies with high mortality and morbidity rates worldwide due, in part, to its asymptomatic nature during the early stages of disease. Objective: Owing to the impact of microRNA (miRNA) dysregulation on CRC development and progression, this study was conducted to explore the expression levels of mir-21, -23a, and -27a in the sera and tissues of Egyptian CRC patients and to evaluate their diagnostic efficacy based on circulating levels. Methods: In the test phase, the relative expression levels of the studied miRNAs were evaluated in the sera of 70 participants (35 CRC patients and 35 healthy controls) using quantitative real-time-polymerase chain reaction and to verify their diagnostic value. The exploratory phase was designed to validate the tumor-derived trait by comparing the miRNA levels in the cancerous and adjacent noncancerous tissues. Results: The relative expression levels of the studied miRNAs were significantly upregulated in both serum and tumor tissues of the patients compared to their corresponding controls. In addition, significant positive correlations were found between the relative expression levels of the studied miRNAs in serum samples and their levels in the matched CRC tissues. The serum expression levels of mir-21 and -23a were more predictive of CRC than mir-27a. Conclusion: Circulating mir-21, -23a, and -27a expression levels appear to be valuable diagnostic biomarkers for CRC, especially when combined.

Abstract PO-124: Mutational profiling of DNA repair and mismatch repair genes in the Egyptian colorectal cancer patients using targeted DNA sequencing

Abstract Background: Colorectal cancer (CRC) remains one of the most prevalent and deadly tumor worldwide. DNA repair and mismatch repair (MMR) genes play an important role in the occurrence and development of colorectal cancer; however, there is insufficient knowledge of DNA repair and MMR mutational profile in the Egyptian Colorectal cancer (CRC) patients which limit our understanding of its progression. Aim: This study aimed to sequence DNA repair and mismatch repair (MMR) genes frequently associated with colorectal cancer (CRC) progression in order to identify their frequencies in the Egyptian CRC patients which may help in understanding colorectal carcinogenesis and developing personalized therapy. Material and methods: Biopsy samples were collected from 62 CRC Egyptian patients. The libraries were performed using Qiaseq UMI-based targeted panel and sequenced via Ion proton sequencer. The detected genetic variants with an average coverage of 500x were annotated against Cosmic and dbSNP and Clinvar databases using Ingenuity Variant analysis (IVA). Results: Regarding DNA repair genes, our results revealed that ATM &amp; CHEK2 genes harbored 19 and 4 variants, respectively. The most frequently detected pathogenic mutations in the ATM were COSM1350741 (29%), COSM1351020 (26%) &amp; COSM41596 (17%) while those pathogenic mutations detected in the CHEK2 were rs772683219 (2%) &amp; rs587780181 (2%). As per MMR genes, it has been shown that MLH1, MLH3, MSH2, MSH3, MSH6, PMS1 &amp; PMS2 harbored 6, 6, 8, 6, 7, 3 &amp; 4 variants, respectively. The identified pathogenic mutations in the MLH1 were COSM1131469 (32%) &amp; rs63750217 (2%), while those pathogenic mutations detected in the MSH2 were rs63749832 (7%), COSM26124 (5%), rs63750084 (2%). Moreover, the highly frequent detected pathogenic mutations were COSM1438892 (7%) in MSH3, &amp; rs267608093 (10%), COSM13395 (6%), COSM13394 (3%) in MSH6. Regarding PMS1, The most frequently detected pathogenic mutation was COSM1404081 (10%). However, no pathogenic mutations were detected in both PMS2 &amp; MLH3 genes. Conclusion: In this data set, we shed the light on the most frequently identified DNA repair and MMR genetic mutations that are crucial for understanding colorectal carcinogenesis and developing ethnic-based personalized therapies in the Egyptian CRC patients. Citation Format: Amira Salah El-Din Youssef, Mai M. Lotfy, Auhood Nassar, Abdel-Rahman N. Zekri. Mutational profiling of DNA repair and mismatch repair genes in the Egyptian colorectal cancer patients using targeted DNA sequencing [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-124.

Abstract PO-131: Therapeutic molecular targets in Egyptian colorectal cancer patients: Time for ethnic personalized medicine

Abstract Background: Colorectal cancer (CRC) in Egypt is one of the most prevalent and deadly tumor. The pathogenesis of CRC is complex and affected by multiple factors: genetic, epigenetic and familial history of polyposis and long standing inflammatory condition. Aim: This study aimed to sequence custom panel consists of 96 tumor suppressor genes and oncogenes frequently associated with colorectal cancer (CRC) to identify the potential molecular therapeutic targets and their frequencies in the Egyptian CRC patients which may help in developing personalized therapy. Material and methods: Biopsy samples were collected from 62 CRC Egyptian patients. The libraries were performed using Qiaseq UMI-based targeted panel and sequenced via Ion proton sequencer. The detected genetic variants with an average coverage of 500x were annotated against Cosmic and dbSNP and Clinvar databases. Further Variant and Pathway analysis were performed using both Ingenuity Variant analysis (IVA) and Ingenuity Pathway analysis (IPA). Results: The Pathway Analysis revealed that Wnt-B-catenin, P53 signaling, RTK-RAS, TGF-beta signaling pathways were the most altered pathways in the CRC patients (73%. 72%, 38% &amp; 36%, respectively). Regarding P53 signaling pathway, it has been shown that TP53 variant (c.215C&amp;gt;G (44%)) was the most frequent single nucleotide polymorphism (SNP) and drug response variant involved in drug efflux resistance mechanism, this variant was found to be more related to the Europe, Jewish and Latino populations (0.73, 0.72 &amp; 0.71, respectively). In RTK-RAS signaling pathway, we identified many variants that are associated with resistant mechanism to anti EGFR therapy as well as drug efflux resistance mechanism; RET (c.2071G&amp;gt;A (37%)) &amp; KIT (c.1621A&amp;gt;C (13%)) SNPs were the most frequently detected variants among the studied groups while KRAS (c.35G&amp;gt;T(8%) &amp; c.38G&amp;gt;A(3%)), ERBB2(c.922G&amp;gt;A(2%) &amp; c.2690G&amp;gt;A(2%)), NRAS (c.35G&amp;gt;T(2%)) and BRAF(c.1781A&amp;gt;G(2%) &amp; c.1799T&amp;gt;A(3%)) were less frequent variants. Moreover, we identified many variants as molecular targets for PD-1 and PDL-1 immunotherapy; 8 variants in APC (c.3754delT (65%), c.1742delA (13%), c.1495C&amp;gt;T (2%), c.2055G&amp;gt;A (2%), c.2309C&amp;gt;G (2%), c.4588G&amp;gt;T (2%), c.8446C&amp;gt;T (2%) &amp;c.3856G&amp;gt;T (2%)), three in SMAD4 (c.1064A&amp;gt;G (2%), c.1081C&amp;gt;T (3%) &amp; c.1088G&amp;gt;A (2%)), two in PIK3CA (c.1173A&amp;gt;G (16%) &amp; c.3140A&amp;gt;G (2%)) and one in PIK3R1 (c.978G&amp;gt;A (23%)). The two variants PIK3CA (c.1173A&amp;gt;G) &amp; PIK3R1 (c.978G&amp;gt;A)) were found to be more related to the African ethnicity (0.21 &amp; 0.38, respectively). Conclusion: In this data set, we shed the light on the most frequently identified molecular therapeutic targets and the most altered pathways that are crucial for understanding cancer predisposition and developing ethnic-based personalized therapies in the Egyptian CRC patients. Citation Format: Amira Salah El-Din Youssef, Auhood Nassar, Mai M. Lotfy, Mohamed A. Abdel-Fattaf, Abdel-Rahman N. Zekri. Therapeutic molecular targets in Egyptian colorectal cancer patients: Time for ethnic personalized medicine [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-131.

The potential value of miRNA-223 as a diagnostic biomarker for Egyptian colorectal patients.

Colorectal cancer (CRC) is the third lethal malignancy worldwide. Dysregulation of microRNAs (miRNAs) mediates several growth factors signaling pathways and induces abnormal genes expression, which leads to colorectal carcinogenesis. We aimed to comprehensively assess the expression of miRNA-200c, miRNA-203a, miRNA-223 in Egyptian CRC tissue and their corresponding serum samples and to explore if they have any potential prognostic or diagnostic value for CRC patients. A total of 195 subjects (120 CRC patients and 75 healthy controls) participated in exploration and validation sets. The relative expression of miRNA-200c, miRNA-203a, and miRNA-223 was measured in both CRC tissue and serum samples, and the expressed miRNAs were compared in different CRC grades and types and the prognostic value was evaluated. The expression levels of miRNA-200c and miRNA-203a were reduced in CRC tissue samples than adjacent noncancerous tissues. miRNA-223 level was significantly upregulated in both CRC tissue and serum samples with a positive association between them (r = 0.85, P = 0.001). The miRNA-223 can effectively discriminate CRC patients from controls and can significantly differentiate between colon and rectal cancer patients. The association between serum miRNA-223 expression and CRC development was validated in the second set and the ROC curve showed highly significant prognostic value with 90.1% sensitivity, 87% specificity, and area under the curve of 0.914 (95% confidence interval: 0.830-0.978, P = 0.0001). These results showed the association between miRNA-223 upregulation and the CRC carcinogenesis. Circulating miRNA-223 can be a potential noninvasive prognostic biomarker for Egyptian CRC patients.

Detection of miR-1246, miR-23a and miR-451 in sera of colorectal carcinoma patients: a case-control study in Cairo University hospital.

Colorectal cancer (CRC) has high morbidity and mortality rates. Invasive techniques and other laboratory tests with variable sensitivity and specificity are currently used in diagnosis. Micro ribonucleic acids (miRNAs) have bio vital roles in cell proliferation and apoptosis. Dys-regulation of miRNAs is linked to tumour genesis. The objective of this study was to evaluate the specificity and sensitivity of serum non-invasive biomarkers (micro-RNAs), miR-1246, miR-23a, and miR-451in CRC patients. Peripheral expression of three miRNAs (miR-1246, miR-23a and miR-451) was investigated in sera of 37 CRC Egyptian patients and 30 healthy controls, using quantitative real-time polymerase chain reaction trying to reach the optimal non-invasive combination of miRNAs. Serum miR-1246 was up-regulated in sera of CRC patients compared to normal controls (fold change = 3.55; P<0.001) and showed 100% sensitivity and 80% specificity in diagnosis of CRC. Serum miR-451 was significantly down-regulated in CRC patients (fold change = -4.86; p= 0.014), whereas, miR-23a was down-regulated but this was not statistically significant. Up-regulation of miR-1246 and down-regulation of miR-451 in the sera of primary CRC Egyptian patients were confirmed with high sensitivity and specificity. Large-scale studies on a wider spectrum of miRNAs in Egyptian CRC patients are needed.

Abstract 3615: Profiling of BRCA1 &amp; BRCA2 mutations in Egyptian colorectal cancer patients via next generation sequencing

Abstract Aim: This study aimed to sequence BRCA1 &amp; BRCA2 genes to identify the frequency of the detected genetic mutations in the disease progression of colorectal cancer (CRC) and to estimate colorectal cancer risks in those BRCA mutation carriers. Material and methods: 140 biopsy samples were collected from Egyptian patients categorized into inflammatory bowel disease (IBD) (n=20), colonic polyp (CP) (n=38) and CRC (n=62) patients as well as subjects with chronic colitis served as a control group (n=20). The libraries were performed using Qiaseq UMI-based targeted panel and sequenced via Ion proton sequencer. The detected genetic variants at 500x were annotated against Cosmic, dbSNP, exac all, Polyphen2, Sift and Clinvar databases. Results: Analysis revealed that BRCA1 gene harbored 26, 19, 8 and 11 variants in the CRC, CP, IBD and control groups; respectively. Exon 10 was the most affected exon harbored 7 pathogenic variants in the CRC group. Two out of 7 were the most frequently detected common pathogenic variants associated with disease progression from colitis to CRC (c.1961delA (11%) &amp; c.3214delC (16%). Moreover, 3 common begnin SNP variants were found to be related to ethnicity (c.3548A&amp;gt;G (58%), c.2612C&amp;gt;T (60%), c.4900A&amp;gt;G (69%). Moreover, BRCA2 gene harbored 48, 29, 24 and 18 variants in the CRC, CP, IBD and control groups respectively. Exon 2, 11, 23 were the most affected exons harbored 12 pathogenic variants in the CRC group. Four out of 12 were the most frequently detected common pathogenic variants associated with disease progression from colitis to CRC (c.3860delA (8%), c.5351delA (18%), c.9097delA (24%) &amp; c.36delT (34%). Conclusion: Our data showed that BRCA1 &amp; BRCA2 genes analyzed by Next-Generation Sequencing (NGS) identifies large number of pathogenic and begnin variants that are crucial for understanding CRC predisposition and early detection. Also, developing personalized therapies that efficiently target the individual CRC-specific mutations. Key words: Egyptian Colorectal cancer, BRCA1, BRCA2, pathogenic, begnin, Next Generation Sequencing Citation Format: Amira Salah El-Din Youssef, Ahmed Osama Touny, Zeinab K. Hassan, Mohammed Mohey Eldin, Mai M. Lotfy, Auhood Nassar, Mohamed El-Hadidi, Ali Kishk, ola sayed, Abdel-Rahman N. Zekri. Profiling of BRCA1 &amp; BRCA2 mutations in Egyptian colorectal cancer patients via next generation sequencing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3615.

Abstract 3616: Somatic mutation profiling of colorectal cancer by targeted next generation sequencing

Abstract Aim: This study aimed to sequence custom 96 genes of tumor suppressor genes and oncogenes frequently associated with colorectal cancer (CRC) to identify the frequency of the detected genetic mutations in the disease progression of CRC patients and to develop personalized therapy in those somatic mutation carriers. Material and methods: Biopsy samples were collected from Egyptian patients classified into inflammatory bowel disease (IBD) (n=20), colonic polyp (CP) (n=38) and CRC (n=60) patients as well as subjects with chronic non-specific colitis served as a control group (n=20). The libraries were performed using Qiaseq UMI-based targeted panel and sequenced via Ion proton sequencer. The detected genetic variants with an average coverage of 500x were annotated against Cosmic and dbSNP and Clinvar databases. Results: Analysis revealed that 52 genes harbor 128, 47 genes harbor 111, 40 genes harbor 71 and 39 genes harbor 66 somatic variants were detected in the CRC, CP, IBD and control groups; respectively. ARID1A (c.5548dupG (5%)), ATM (c.2572T&amp;gt;C (10%)), AXIN2 (c.1975C&amp;gt;T (5%)), FLCN (c.1285dupC (8%)), KRAS (c.35G&amp;gt;T (8%)), MSH6 (c.3261dupC (5%)), SLC9A9 (c.1765A&amp;gt;G (10%)), TP53 (c.1024C&amp;gt;T (5%)) were found to be the highly frequently detected pathogenic CRC specific variants. We also identified 29 genes harbor 43 common variants. The highly frequently common detected variants were ACVR2A (c.1310delA), ATM (c.5557G&amp;gt;A), BRCA1 (c.3548A&amp;gt;G, c.2612C&amp;gt;T), BRCA2 (c.1114A&amp;gt;C), IGF2 (c.677delG), KIT (c.1621A&amp;gt;C), MLH1 (c.655A&amp;gt;G), MLK4 (c.2223G&amp;gt;T, c.2182G&amp;gt;A), PIK3CA (c.1173A&amp;gt;G), PTPN12 (c.964G&amp;gt;A), RET (c.2071G&amp;gt;A), TP53 (c.121delG, c.215C&amp;gt;G) Conclusion: Our data showed that our Egyptian genetic makeup is different from other population. Also, the identified somatic mutations are crucial for understanding cancer predisposition and developing personalized therapies for the Egyptian colorectal cancer patients. Citation Format: Amira Salah El-Din Youssef, Ahmed Moustafa, Ahmed Osama Touny, Zeinab K. Hassan, Mohammed Mohey Eldin, Mai M. Lotfy, Auhood Nassar, ola sayed, Abdel-Rahman N. Zekri. Somatic mutation profiling of colorectal cancer by targeted next generation sequencing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3616.

Clinicopathological Significance of BRAF V600E Mutation in Egyptian Colorectal Cancer Patients

Abstract Background: In Egypt, there is a rapid increase in Color-ectal Cancer (CRC) incidence with more aggressive course and younger age at presentation compared to western patients. Aim of Study: This study aimed to examine BRAF V600E mutation in Egyptian CRC patients. Material and Methods: This study is done by collaboration between Pathology and Clinical Oncology & Nuclear Medicine Departments, Faculty of Medicine, Menoufia University between January 2015 and August 2019 in which 81 CRC patients were studied. Expression of BRAF V600E protein was evaluated by immunohistochemistry. The results of the studied marker were correlated with different clinicopatho-logical parameters and survival data. Results: The frequency of BRAF V600E mutation was 51.9%. There was no statistical difference between different studied clinicopathological parameters including sidedness and BRAF V600E mutation. Regarding survival during this follow-up duration, no significant statistical differences were detected. Conclusion: In Egyptian CRC patients, BRAF V600E protein expression had no correlation with CRC prognosis. However, validation of our results in a larger sample size is necessary.

Circulating microRNA-944 and its target gene EPHA7 as a potential biomarker for colorectal cancer

MicroRNAs (miRNAs) have critical roles in colorectal cancer (CRC) tumorigenesis and development. It has been reported that Eph receptor A7 (EphA7) was a potential target of miR-944 which is transcriptionally activated in cancer. The aim of this study was to explore the expression profile of miR-944 and its target gene EPHA7 in the serum of Egyptian CRC patients. 150 CRC patients, 50 adenomatous polyps (AP) patients, and 100 healthy controls were included. Serum miR-944 was downregulated (0.304 ± 0.0512) while serum EPHA7 was upregulated (3.163 ± 0.610) in CRC and AP patients versus controls and discriminated aganst these groups by Receiver operating characteristic curve (ROC) analysis. miR-944 presented the highest diagnostic accuracy for CRC patients from control (AUC = 0.90). Moreover obvious prognostic power in distinguishing AP from CRC (AUC = 0.87). In conclusion, miR-944 and EPHA7 are potential genetic markers of CRC predisposition and novel potential non-invasive diagnostic biomarkers for CRC.

Role of the JC Polyomavirus (JCV) and BK Polyomavirus (BKV) in the colorectal cancer of some Egyptian patients

Although several cases and case-control studies reported the prevalence of JC polyomavirus (JCV) and BK polyomavirus (BKV) in tumor tissues of colorectal cancer (CRC) patients as well as in control samples; however, many recent studies did not show the prevalence of these viruses in the CRC patients. A total of 50 clinical biopsies samples were collected from patients with and without CRC in the General surgery department, Faculty of Medicine, Ain Shams University, Egypt, with the approval of the research ethics committee. Current results showed the absence of the genomic DNA of both JCV and BKV in the tumor tissue samples, adjacent-tumor normal mucosa samples from CRC patients, and also in the normal mucosa samples collected from the non-CRC patients. Moreover, results of the semi-nested PCR and real-time PCR are similar, and confirmed that JCV and BKV are not prevalent in the Egyptian CRC patients. There are no promising results for further investigation of the expression of the large T-Ag protein, and any other related proteins in the tumor cells. Based on the present results, no evidence supports the association between the JCV, BKV and CRC in the Egyptian patients. For the best of our knowledge, this is the first case-control study on the prevalence of JCV and BKV in the Egyptian CRC patients. The aim of the current study was to detect the presence of JCV and BKV genomic DNA in the tissue samples, to support further studies on the role of these viruses in the CRC etiology and development.