Association between hepatitis C virus genotype 4 and renal cell carcinoma: Molecular and virological studies

Hepatitis C virus (HCV) is the most common infection worldwide. The correlation between HCV and renal cell carcinoma (RCC) is still mysterious. Therefore, the relationship between HCV and RCC was investigated. The study included 100 patients with RCC; 32 with HCV infection, and 68 without HCV infection. Expressions of viral proteins (NS3 and NS5A) were tested using an immune electron-microscope (IEM) and immunohistochemistry (IHC). IHC and quantitative real time-PCR investigated the presentation of human proteins TP53 and p21 genes. Transmission electron (TEM) detected viral-like particles in infected RCC tissues. The gene and protein expression of P53 was higher in HCV positive versus HCV negative patients and p21 was lower in HCV positive versus HCV negative in both tumor and normal tissue samples. Viral like particles were observed by TEM in the infected tumor and normal portion of the RCC tissues and the plasma samples. The IEM showed the depositions of NS3 and NS5A in infected renal tissues, while in noninfected samples, were not observed. The study hypothesizes that a correlation between HCV and RCC could exist through successfully detecting HCV-like particles, HCV proteins, and (p53 and p21) in RCC-infected patients.

Stem cell therapy for hepatocellular carcinoma and end-stage liver disease

Hepatocellular carcinoma (HCC) is a major health problem worldwide, especially for patients who are suffering from end-stage liver disease (ESLD). The ESLD is considered a great challenge for clinicians due to the limited chance for liver transplantation, which is the only curative treatment for those patients. Stem cell-based therapy as a part of regenerative medicine represents a promising application for ESLD patients. Many clinical trials were performed to assess the utility of bone marrow-derived stem cells as a potential therapy for patients with liver diseases. The aim of the present study is to present and review the various types of stem cell-based therapy, including the mesenchymal stem cells (MSCs), BM-derived mononuclear cells (BM-MNCs), CD34 + hematopoietic stem cells (HSCs), induced pluripotent stem cells (iPSCs), and cancer stem cells.Though this type of therapy achieved promising results for the treatment of ESLD, however still there is a confounding data regarding its clinical application. A large body of evidence is highly required to evaluate the stem cell-based therapy after long-term follow-up, with respect to the incidence of toxicity, immunogenicity, and tumorigenesis that developed in many patients.

Genetic profiling of different phenotypic subsets of breast cancer stem cells (BCSCs) in breast cancer patients

BACKGROUND

Breast cancer stem cells (BCSCs) have a crucial role in breast carcinogenesis, development, and progression. The aim of the current study is to characterize the BCSCs through the genetic profiling of different BCSCs phenotypic subsets to determine their related genetic pathways.

METHODS

Fresh tumor tissue samples were obtained from 31 breast cancer (BC) patients for (1) Mammosphere culture. (2) Magnetic separation of the BCSCs subsets using CD24, CD44, and CD326 Microbeads. (3) Flow cytometry (FCM) assay using CD44, CD24, and EpCAM. (4) RT-PCR profiler Arrays using stem cell (SC) panel of 84 genes for four group of cells (1) CD44⁺/CD24^-/EpCAM^- BCSCs, (2) CD44⁺/CD24^- /EpCAM⁺ BCSCs, (3) mammospheres, and (4) normal breast tissues.

RESULTS

The BCSCs (CD44⁺/CD24^-/EpCAM^-) showed significant downregulation in 13 genes and upregulation in 15, where the CD44, GJB1 and GDF3 showed the maximal expression (P = 0.001, P = 0.003 and P = 0.007); respectively). The CD44⁺/CD24^-/EpCAM⁺ BCSCs showed significant upregulation in 28 genes, where the CD44, GDF3, and GJB1 showed maximal expression (P < 0.001, P = 0.001 and P = 0.003; respectively). The mammospheres showed significant downregulation in 9 genes and a significant upregulation in 35 genes. The maximal overexpression was observed in GJB1 and FGF2 (P = 0.001, P = 0.001; respectively). The genes which achieved significant overexpression in all SC subsets were CD44, COL9A1, FGF1, FGF2, GDF3, GJA1, GJB1, GJB2, HSPA9, and KRT15. While significant downregulation in BMP2, BMP3, EP300, and KAT8. The genes which were differentially expressed by the mammospheres compared to the other BCSC subsets were CCND2, FGF3, CD4, WNT1, KAT2A, NUMB, ACAN, COL2A1, TUBB3, ASCL2, FOXA2, ISL1, DTX1, and DVL1.

CONCLUSION

BCSCs have specific molecular profiles that differ according to their phenotypes which could affect patients' prognosis and outcome.

Frequency of Pathogenic Germline Mutations in Early and Late Onset Familial Breast Cancer Patients Using Multi-Gene Panel Sequencing: An Egyptian Study

BACKGROUND

Precision oncology has been increasingly used in clinical practice and rapidly evolving in the oncology field. Thus, this study was performed to assess the frequency of germline mutations in early and late onset familial breast cancer (BC) Egyptian patients using multi-gene panel sequencing to better understand the contribution of the inherited germline mutations in BC predisposition. Moreover, to determine the actionable deleterious mutations associated with familial BC that might be used as biomarker for early cancer detection.

METHODS

Whole blood samples were collected from 101 Egyptian patients selected for BC family history, in addition to 50 age-matched healthy controls. A QIAseq targeted DNA panel (human BC panel) was used to assess the frequency of germline mutations.

RESULTS

A total of 58 patients (57.4%) out of 101 were found to have 27 deleterious germline mutations in 11 cancer susceptibility genes. Of them, 32 (31.6%) patients carried more than one pathogenic mutation and each one carried at least one pathogenic mutation. The major genes harboring the pathogenic mutations were: ATM, BRCA2, BRCA1, VHL, MSH6, APC, CHEK2, MSH2, MEN1, PALB2, and MUTYH. Thirty-one patients (30.6%) had BRCA2 mutations and twenty (19.8%) had BRCA1 mutations. Our results showed that exon 10 and exon 11 harbored 3 and 5 mutations, respectively, in BRCA1 and BRCA2 genes. Our analysis also revealed that the VHL gene significantly co-occurred with each of the BRCA2 gene (p = 0.003, event ratio 11/21), the MSH2 gene (p = 0.01, 4/10), the CHEK2 gene (p = 0.02, 4/11), and the MSH6 gene (p = 0.04, 4/12). In addition, the APC gene significantly co-occurred with the MSH2 gene (p = 0.01, 3/7). Furthermore, there was a significant mutually exclusive event between the APC gene and the ATM gene (p = 0.04, 1/36). Interestingly, we identified population specific germline mutations in genes showing potentials for targeted therapy to meet the need for incorporating precision oncology into clinical practice. For example, the mutations identified in the ATM, APC, and MSH2 genes.

CONCLUSIONS

Multi-gene panel sequencing was used to detect the deleterious mutations associated with familial BC, which in turns mitigate the essential need for implementing next generation sequencing technologies in precision oncology to identify cancer predisposing genes. Moreover, identifying DNA repair gene mutations, with focus on non-BRCA genes, might serve as candidates for targeted therapy and will be increasingly used in precision oncology.

Her2/EGFR-PDGFR pathway aberrations associated with tamoxifen response in metastatic breast cancer patients

Background

Metastatic breast cancer (MBC) is a major health problem worldwide. Some patients improve on tamoxifen and others do not respond to treatment. Therefore, the aim of the current study is to assess genetic aberrations in the Her2/EGFR-PDGFR pathway associated with tamoxifen response in MBC patients.

Methods

This is a retrospective cohort study, including 157 hormone receptors positive, locally recurrent inoperable and/or MBC patients on tamoxifen treatment. Patients were categorized into 78 (49.7%) tamoxifen responders and 79 (50.3%) tamoxifen non-responder patients. Genetic aberrations of 84 genes involved in the Her2/EGFR-PDGFR pathway were assessed in the tumor tissue samples obtained from the patients using SA-Bioscience assay. The identified panel was correlated to patients’ response to treatment, to detect the differentially expressed genes in tamoxifen responders and non-responders.

Results

One hundred twenty-three (78.3%) patients were estrogen receptor (ER) and progesterone receptor (PR) positive, 108 (68.8%) were ER only positive, and 78 (49.7%) were PR only positive. There were 56 genes overexpressed in the refractory group compared to responders. However, only five out of these 56 genes, Janus kinase 1 (JAK1), collagen type I alpha 1 (COL1A1), GRB2-associated binding protein 1 (GAB1), fibronectin-1 (FN1), and MAP kinase-interacting serine/threonine-protein kinase (MKNK1), showed statistical significance between the two groups. Patients with bone metastasis showed a better response to treatment compared to those with metastatic deposits in other sites such as visceral metastasis (P < 0.005).

Conclusions

Genetic profiling using simple quantitative real-time polymerase chain reaction (qRT-PCR) protocols could be used to assess response to tamoxifen treatment in MBC patients. According to our data, a five-gene panel in the EGFR pathway (JAK1, COL1A1, GAB1, FN1 and MKNK1) could be used to categorize MBC patients into groups according to treatment response.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Estrogen Receptor Gene Polymorphism as a Possible Genetic Risk Factor for Treatment Response in ER-Positive Breast Cancer Patients

Estrogen receptor-α (ESR1) single nucleotide polymorphisms (SNPs) have been related to breast cancer (BC) susceptibility. In this retrospective study we investigated ESR1 SNPs in association with survival and treatment response in BC patients. Seven ESR1 SNPs were genotyped using TaqMan probe assay in 100 formalin-fixed paraffin embedded blocks of Egyptian ER⁺BC patients. Log-binomial regression was used to assess the association of 5 ESR1 SNPs with relative risk of non-response to adjuvant-hormonal treatment. We compared the performance of five machine learning classification models for prediction of treatment response. Predictive models were developed using rs1801132, rs2228480, and rs9322354 that were significantly associated with increased risk for non-response along with the relevant clinical features. Survival analysis was performed to detect prognostic significance of ESR1 SNPs in ESR⁺BC patients. rs1801132 (C), rs2228480 (A), and rs9322354 (G) minor alleles significantly increased the risk of non-response to tamoxifen by more than 81, 84, and 117%, respectively, in ER⁺BC patients on anthracycline/anthracycline-taxanes-based chemotherapy. Multivariate Cox regression survival analysis revealed that rs1801132 (C) and large tumor size were independent predictors for poor survival outcome in ER⁺BC. The best response predictive model was a combination random forest, K-nearest neighbor, and decision tree having an area under the curve of 0.94 and an accuracy of 90.8%. Our proposed predictive model based on ESR1 rs1801132, rs2228480, and rs9322354 SNPs represents a promising genetic risk stratification for selection patients who could benefit from tamoxifen therapy in such a way that might facilitate personalized medicine required to improve ER⁺BC patients' outcome.

Identification of Different miRNAs and Their Relevant miRNA Targeted Genes Involved in Sister Chromatid Cohesion and Segregation (SCCS)/chromatin Remodeling Pathway on T1G3 Urothelial Carcinoma (UC) Response to BCG Immunotherapy

BACKGROUND

Till now, no definite clinical or laboratory marker can predict the recurrence or progression of T1 G3 urothelial carcinoma (UC). Genetic aberrations of the chromatin remodeling genes and sister chromatid cohesion and segregation (SCCS) were identified in UC. Here we investigated the impact of novel miRNAs and their targeted expressed SCCS and chromatin remodeling genes on T1G3 UC response to Bacillus Calmette-Guérin (BCG) therapy.

METHODS

One hundred tissue samples were obtained from NMIBC patients. Gene expression and immunohistochemical assay of STAG2, ARID1A, NCOR1and UTX were assessed. MiRNA analysis for their targeting miRNAs (miR-21, miR-31, Let7a and miR-199a) was carried out. Assessed genes were compared between responders and no responders to BCG. Univariate and multivariate analysis of predictors of disease recurrence and progression were performed using cox regression analysis.

RESULTS

Thirty-two and 22 patients developed recurrence and progression to MIBC (BCG non-responders). BCG non-responders showed statistically significant higher expression of miR-21 and their targeted STAG2, miR-199a and NCOR1 gene (P < .001), and lower expression of miR-31, Let7a, ARID1A and UTX genes (P < .001). Higher miR-199a (P = .006) and lower miR-31 (P = .01), ARID1A (P = .008) and UTX (P = .03) were independent predictor of higher tumor recurrence. Recurrent disease (P = .003), higher expression of STAG2 (P = .01), NCOR1 (P = .01) and miR-21 (P = .03) genes and lower expression of miR-31 (P = .02), Let7a (P = .04) and ARID1A (P = .04) genes were the independent predictor of disease progression.

CONCLUSION

Upregulation of STAG2 and NCOR1 and down regulation of ARID1A and UTX genes and their targeting miRNAs were associated with UC non-response to BCG.

Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection

At Wuhan, in December 2019, the SRAS-CoV-2 outbreak was detected and it has been the pandemic worldwide. This study aims to investigate the mutations in sequence of the SARS-CoV-2 genome and characterize the mutation patterns in Egyptian COVID-19 patients during different waves of infection. The samples were collected from 250 COVID-19 patients and the whole genome sequencing was conducted using Next Generation Sequencing. The viral sequence analysis showed 1115 different genome from all Egyptian samples in the second wave mutations including 613 missense mutations, 431 synonymous mutations, 25 upstream gene mutations, 24 downstream gene mutations, 10 frame-shift deletions, and 6 stop gained mutation. The Egyptian genomic strains sequenced in second wave of infection are different to that of the first wave. We observe a shift of lineage prevalence from the strain B.1 to B.1.1.1. Only one case was of the new English B.1.1.7. Few samples have one or two mutations of interest from the Brazil and South Africa isolates. New clade 20B appear by March 2020 and 20D appear by May 2020 till January 2021.

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.

Abstract 257: Tumor mutation burden of Egyptian breast cancer patients based on next generation sequencing

Tumor mutation burden of Egyptian breast cancer patients based on next generation sequencing Aim: This study aimed to identify the tumor mutation burden (TMB) value in Egyptian Breast cancer (BC) patients. Additionally, we aimed to find the best model to predict TMB value by the expression of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER-2), and proliferative index Ki-67, to help expecting the prognosis of patients and predicting the possible response to immunotherapy. Patients and methods: In 58 Egyptian patients with BC, the Ion AmpliSeq Comprehensive Cancer Panel based on NGS was used to determine the TMB value of primary tumor tissues of Egyptian BC patients. The predicted TMB value was divided into 4 groups: A (0.00-0.625), B (0.626-1.25), C (1.251-2.50), and D (&gt;2.50), according to the quartile method, with group A as reference level. Different machine learning models were used to select the optimal classification model. Results: The measured TMB value was between 0 and 8.12/Mb. The TMB distribution among the studied 58 cases was: 19 cases in group A, 12 cases in group B, 14 cases in group C, and 13 cases in group D. ER positive expression was significantly associated with TMB ≤ 1.25 (ER positive vs ER-negative, OR =0.35, 95% CI: 0.04-2.98, p= 0.001). TMB ≤1.25 was significantly distributed in patients with PR positive expression (PR positive versus PR negative, OR = 0.17, 95% CI= 0.02-0.44, p= 0.002). Ki67 expression positive was significantly associated with TMB &gt;1.25 than those who were Ki-67 expression negative (Ki67 positive versus Ki67 negative, OR = 9.33, 95% CI= 2.07-42.18, p= 0.004). Also, TMB &gt;1.25 was significantly distributed in triple negative (TN) patients than non-TN patients (OR=9.69, 95% CI: 1.05-89.9, p=0.045). However, no significant differences were observed between HER2 positive and HER2 negative group (OR = 2.47, 95% CI: 0.64-9.54, p =0.19). The adjusted Pseudo-R2 was 0.329 (P&lt;0.001). The optimized logistic regression model was TMB = -27.5 -1.82 ER - 0.73 PR + 0.826 HER2 + 2.08 Ki67. Conclusion: the preliminary findings of our studied sample set revealed that level of TMB in Egyptian BC patients is relatively low. Also, TMB value in hormone receptor positive and Ki-67 expression positive Egyptian BC patients is higher than hormone receptor negative and Ki-67 expression negative patients. Moreover, TMB value can be predicted based on the expression level of ER, PR, HER-2, and Ki-67. The optimized logistic regression model was TMB = -27.5 -1.82 ER - 0.73 PR + 0.826 HER2 + 2.08 Ki67.

Citation Format: Auhood Nassar, Ahmed M. Lymona, Mai M. Lotfy, Amira Salah El-Din Youssef, Abdel-Rahman N. Zekri. Tumor mutation burden of Egyptian breast cancer patients based on next generation sequencing [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 257.

BRCA1/2 Mutations and Long-Term Clinical Outcomes in Egyptian Breast Cancer Patients

Introduction:

Clinical findings regarding the impact of BRCA1/2 mutational status on the prognosis of breast cancer patients are still controversial. We aimed to investigate the prognostic relevance of BRCA1/ 2 mutations on recurrence and long-term survival, for the first time, in Egyptian female breast cancer patients.

Patients and Methods:

The study cohort comprised 103 Egyptian female breast cancer patients previously tested for BRCA1/2 mutations using HRM analysis and direct sequencing. Clinicopathological and long-term clinical follow-up data including date and site of disease progression, were retrieved from medical records until death or loss to follow-up. Outcome measures including overall survival (OS), disease-free survival (DFS), recurrence-free survival, and metastasis-free survival (MFS) were compared in all BRCA1/ 2 mutation carriers versus non-carriers at 2, 5, 10, and 15 years after diagnosis.

Results:

The profile of the detected variants was previously reported. The American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines were used to re-classify the variants. The median follow-up time was 6.9 years (range, 4.2-24.4 years). BRCA carriers had significantly worse DFS than non-carriers, at 2 years 86.7% vs 88.2%; at 5 years 38.1% vs 57.8%; and at 10 years 21.6% vs 34.1% ( P=0.024). Negative estrogen receptor (ER) status (HR=2.44, 95%CI=1.33-4.47) and large tumor size (HR=2.19, HR=1.21-3.98) were also significant factors for worse DFS. Recurrence-free survival was significantly worse in BRCA carriers compared to non-carriers, at 5 years: 95.2% vs 98.2%; at 10 years: 54.4% vs 79.8%; and at 15 years 34.6% vs 61.7% ( P=0.005). BRCA carriers showed poorer OS and MFS, though not statistically significant [OS in BRCA carriers and non-carriers at 5 years: 81.6% vs 89.3%; at 10 years: 59.2% vs 60.6%; and at 15 years: 36.3 vs 59.2% ( P=0.42); and MFS at 2 years 86.7% vs 88.1%; at 5 years 44.5% vs 61.1% ; and at 10 years: 25.3% vs 38.2% ( P=0.41)].

Conclusion:

To our knowledge, this is the first study in the Middle East to investigate long-term survival outcome of BRCA1/2 related breast cancer. We, herein, underline the necessity of implementing BRCA screening strategies and intensive surveillance in the mainstream oncology practice in Egypt.

Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes

Background

Severe acute respiratory syndrome-2 (SARS-CoV-2) exhibits a broad spectrum of clinical manifestations. Despite the fact that SARS-CoV-2 has slower evolutionary rate than other coronaviruses, different mutational hotspots have been identified along the SARS-CoV-2 genome.

Methods

We performed whole-genome high throughput sequencing on isolates from 50 Egyptian patients to see if the variation in clinical symptoms was related to mutations in the SARS-CoV-2 genome. Then, we investigated the relationship between the observed mutations and the clinical characteristics of the patients.

Results

Among the 36 most common mutations, we found two frameshift deletions linked to an increased risk of shortness of breath, a V6 deletion in the spike glycoprotein's signal peptide region linked to an increased risk of fever, longer fever duration and nasal congestion, and L3606-nsp6 deletion linked to a higher prevalence of cough and conjunctival congestion. S5398L nsp13-helicase was linked to an increased risk of fever duration and progression. The most common mutations (241, 3037, 14,408, and 23,403) were not linked to clinical variability. However, the E3909G-nsp7 variant was more common in children (2–13 years old) and was associated with a shorter duration of symptoms. The duration of fever was significantly reduced with E1363D-nsp3 and E3073A-nsp4.

Conclusions

The most common mutations, D614G/spike-glycoprotein and P4715L/RNA-dependent-RNA-polymerase, were linked to transmissibility regardless of symptom variability. E3909G-nsp7 could explain why children recover so quickly. Nsp6-L3606fs, spike-glycoprotein-V6fs, and nsp13-S5398L variants may be linked to clinical symptom worsening. These variations related to host-virus interactions might open new therapeutic avenues for symptom relief and disease containment.

Prevalence of MMTV-Like env Sequences and Its Association with BRCA1/2 Genes Mutations Among Egyptian Breast Cancer Patients

Background

Mouse mammary tumor virus (MMTV) is thought to have a role in human breast cancer (BC) pathogenesis. BRCA1 and 2 genes mutations are well-established risk factors for BC. The purpose of this study was to evaluate the presence of MMTV in familial and non-familial Egyptian breast cancer patients. We also aimed to establish a correlation between BRCAs genes mutations and MMTV infection in those patients.

Patients and Methods

The study was included 80 BC patients and 10 healthy women were included as a control group. We used PCR to amplify a 250-bp MMTV-like env sequence. We also used PCR followed by direct sequencing to identify the genetic variation of exons 2, 13, 19 of BRCA1 gene and exon 9 and region f of exon 11 of BRCA2 gene. High resolution melting (HRM) analysis was used to screen the selected exons of BRCA1/2 genes in order to detect different variants.

Results

MMTV DNA-like env sequences were detected in 70%, 76% of familial and non-familial BC patients, respectively, and it was not detected in any of the control subjects. The presence of viral sequences was associated with larger tumor size in the sporadic patients. Seventy BC patients showed variations in BRCA1/2 genes according to HRM analysis and sequencing analysis showed two different sequences of polymorphism among 22 familial and non-familial BC patients.

Conclusion

MMTV DNA was present among BC patients and it was associated with increased tumor growth. This indicates a potential role for MMTV in BC patients with and without deleterious mutation in BRCA1/2 genes.

Assessment of the Circulating Tumor Cells and Microsatellite Instability in Colorectal Cancer Patients: Prognostic and Diagnostic Value

Background

Microsatellite instability (MSI) and circulating tumor cells (CTCs) play important roles in the diagnosis, prognosis and management of colorectal cancer (CRC) patients.

Methods

CTCs and MSI were assessed in the blood and representative tumor tissues of 100 CRC patients by flow cytometry (FCM) and PCR amplification. The data were correlated to relevant clinicopathological features of the patients, progression-free survival (PFS) and overall survival (OS) rates.

Results

MSI-high was detected in 44 (44.0%) patients, MSI-low in 37 (37%), and microsatellite stable (MSS) in 19 (19.0%) patients (P=0.007). The baseline CTCs count (<4 cells/7mL blood) was reported in 39% of the patients, and CTCs ≥4 cells/7mL blood in 61% of the patients (P=0.028). Improved PFS and OS rates were associated significantly with MSI-high (P<0.001), decreased CTC levels during the course of treatment (P<0.001) and post-treatment CTCs (P=0.008). There was no significant association between MSI-high and PFS or OS in early-stage patients (P=0.187 and P=0.187; respectively); however, it was associated significantly with better PFS and OS in late-stage patients (P<0.001). Multivariate analysis showed that only a change in serial CTC levels is considered an independent prognostic factor for OS (P<0.012). Post-treatment CTCs level, serial CTCs level changes during the course of treatment, lymph nodes and distant metastasis were independent prognostic factors for PFS (P<0.001, P= 0.047, P=0.001 and P<0.001; respectively).

Conclusion

MSI and CTCs could be used as accurate, reliable and sensitive diagnostic and prognostic biomarkers for CRC patients’ survival rates and outcomes.

The Prognostic Significance of 5-Fluorouracil Induced Inflammation and Immuno-Modulation in Colorectal Cancer Patients

Aim

The change in the levels of peripheral inflammatory markers together with EGFR in relation to 5- fluorouracil (5-FU) therapy was evaluated for their prognostic significance in colorectal cancer (CRC) patients.

Patients and Methods

Expression levels of COX2, IL6, IL1β, EGFR, IL10, and TNFα were determined with quantitative real-time PCR (qPCR) in the peripheral blood of 90 CRC patients. The inflammatory response was correlated with patients’ clinical features, disease-free survival (DFS), and overall survival (OS).

Results

After 6 months of 5-FU therapy, increased inflammatory response was found to be associated with smoking, T3 or T4 tumors, performance status (PS) III, positive lymph nodes, distant metastasis, and gastrointestinal (GIT) toxicity. The combination of COX2 with interleukins in a predictive equation for DFS was significant in patients with over-expression of EGFR. DFS and OS rates were reduced in patients with increased COX2, IL6, IL10, and TNFα expression with 5-FU therapy. Significant hazard of disease progression was associated with smoking (HR=1.27, P=0.004), 5-FU induction of COX2, and IL6 expression (HR=1.35, P=0.001 and HR=1.27, P=0.004, respectively). Moreover, smoking, 5-FU induction of IL6, TNFα, and IL10 expression are found to be independent prognostic factors for OS (P=0.003, 0.003, 0.002, and 0.002, respectively).

Conclusion

The peripheral effects of 5-FU therapy have shown a significant impact on the treatment outcome of CRC patients.

Cancer in Africa: Is It a Genetic or Environmental Health Problem?

Patients of African ancestry have the poorest outcome and the shortest survival rates from cancer globally. This could be attributed to many variables including racial, biological, socioeconomic and sociocultural factors (either single, multiple or combined), which may be responsible for this major health problem. We sought to assess the most common types of cancer that endanger the health of the African people, and tried to investigate the real differences between African and other Non-African patients regarding incidence, prevalence and mortality rates of different cancers. Therefore, identifying the underlying aetiological causes responsible for the increased incidence and mortality rates of African patients will allow for changing the current plans, to make optimized modalities for proper screening, diagnosis and treatment for those African patients, in order to improve their survival and outcomes.

BRCA1 and BRCA2 truncating mutations and variants of unknown significance in Egyptian female breast cancer patients

BACKGROUND

Breast cancer is the most common malignancy among women worldwide and the leading cause of cancer death in economically developing countries. We sought to study the contribution of BRCA1/2 mutations to the burden of breast cancer in Egypt.

PATIENTS AND METHODS

103 Egyptian female breast cancer patients, unselected for age of onset or family history, were included in the study. Mutational screening of some exons of BRCA1/2 genes was performed using High Resolution Melting analysis followed by direct sequencing of detected variants.

RESULTS

Twenty sequence variants were identified. According to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines, 8 variants were classified as pathogenic (Class 5), 1 as likely pathogenic and 11 as variants of unknown significance (Class 3). The pathogenic variants comprised 5 novel frameshift mutations; BRCA1 c.5205delA and BRCA2 (c.3641delT, c.3291dupT, c.3292delA, and c.787dupA) mutations; 1 novel nonsense mutation (BRCA2 c.3280A>T) and 2 previously described missense mutations (BRCA1 c.117T>G, c.110C>A).

CONCLUSION

This study provides the results of our attempt to delineate the genetic aspect of breast cancer among the Egyptian population and emphasizes the necessity of implementing screening strategies for early diagnosis and counseling for breast cancer in Egypt.

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

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% & 36%, respectively).

Regarding P53 signaling pathway, it has been shown that TP53 variant (c.215C&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 & 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&gt;A (37%)) & KIT (c.1621A&gt;C (13%)) SNPs were the most frequently detected variants among the studied groups while KRAS (c.35G&gt;T(8%) & c.38G&gt;A(3%)), ERBB2(c.922G&gt;A(2%) & c.2690G&gt;A(2%)), NRAS (c.35G&gt;T(2%)) and BRAF(c.1781A&gt;G(2%) & c.1799T&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&gt;T (2%), c.2055G&gt;A (2%), c.2309C&gt;G (2%), c.4588G&gt;T (2%), c.8446C&gt;T (2%) &c.3856G&gt;T (2%)), three in SMAD4 (c.1064A&gt;G (2%), c.1081C&gt;T (3%) & c.1088G&gt;A (2%)), two in PIK3CA (c.1173A&gt;G (16%) & c.3140A&gt;G (2%)) and one in PIK3R1 (c.978G&gt;A (23%)). The two variants PIK3CA (c.1173A&gt;G) & PIK3R1 (c.978G&gt;A)) were found to be more related to the African ethnicity (0.21 & 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.

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

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 & CHEK2 genes harbored 19 and 4 variants, respectively. The most frequently detected pathogenic mutations in the ATM were COSM1350741 (29%), COSM1351020 (26%) & COSM41596 (17%) while those pathogenic mutations detected in the CHEK2 were rs772683219 (2%) & rs587780181 (2%). As per MMR genes, it has been shown that MLH1, MLH3, MSH2, MSH3, MSH6, PMS1 & PMS2 harbored 6, 6, 8, 6, 7, 3 & 4 variants, respectively. The identified pathogenic mutations in the MLH1 were COSM1131469 (32%) & 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, & 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 & 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.

Genomic characterization of SARS-CoV-2 in Egypt

Introduction

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 115,000 individuals were infected so far.

Objective

In the present study, the objective is to perform a complete genome sequence of SAR-CoV2 isolated from Egyptian coronavirus disease (COVID-19) patients.

Methods

Nasopharyngeal swabs were collected from 61 COVID-19 patients who attended at National Cancer Institute, Kasr Al-Aini Hospital and the army hospital. Viral RNA was extracted and whole genomic sequencing was conducted using Next Generation Sequencing.

Results

In all cases, the sequenced virus has at least 99% identity to the reference Wuhan 1. The sequence analysis showed 204 distinct genome variations including 114 missense mutations, 72 synonymous mutations, 1 disruptive in-frame deletion, 7 downstream gene mutations, 6 upstream gene mutations, 3 frame-shift deletions, and 1 in-frame deletion. The most dominant clades were G/GH/GR/O and the dominant type is B.

Conclusion

The whole genomic sequence of SARS-CoV2 showed 204 variations in the genomes of the Egyptian isolates, where the Asp614Gly (D614G) substitution is the most common among the samples (60/61). So far, there were no strikingly variations specific to the Egyptian population, at least for this set of samples.

The role of circulating tumor cells and K-ras mutations in patients with locally advanced rectal cancer: a prospective study

Rectal cancer is a common malignancy with a relatively poor prognosis. We assessed the possible prognostic and predictive role(s) of circulating tumor cells (CTCs) and K-ras mutations in locally advanced rectal carcinoma (LARC) patients. CTCs number and K-ras mutation status were assessed in the Peripheral blood and tumor tissue samples of 60 patients with LARC compared to control group (normal rectal mucosa). Data were correlated to relevant clinico-pathological features, response to treatment, disease free (DFS) and overall survival (OS) rates. K-ras mutations were present in 24/60 (40%) patients. Baseline CTCs (< 5 cells/7 ml blood) were detected in 23/60 (38.3%) patients, and 37 (61.7%) had baseline CTCs (≥ 5 cells/7 ml) blood (P = 0.071). Serial sampling showed a decrease in CTCs levels in 40 (66.7%) patients and increase in 20 (33.3%) patients (P = 0.01). Patients with K-ras mutations had a significantly poor response to treatment, with reduced DFS and OS rates (P = 0.001, 0.004, and 0.001; respectively). Similarly, decreased CTCs levels during treatment associated significantly with better pathological responses (P = 0.003). Multivariate analysis demonstrated that K-ras mutation and baseline CTCs are independent prognostic factors for DFS (P = 0.014 and 0.045; respectively) and OS (P = 0.002 and 0.045; respectively). The presence of mutant K-ras and baseline CTCs ≥ 5 cells associated significantly with poor pathological response, shorter DFS and OS rates compared to those with either K-ras mutation or CTCs ≥ 5 cells only (P = 0.014, 0.005 and 0.001, respectively). K-ras mutations, baseline and serial CTCs changes represent good prognostic and predictive factors for LARC patients.

Impact of nano-conjugate on Drosophila for early diagnosis of Alzheimer's disease

Alzheimer's disease (AD) is an irreversible neurodegenerative disease. Recent identification of AD biomarkers has led to the diagnosis of AD before the onset of dementia. It has been shown that Drosophila melanogaster is a valuable model for studying human neurodegeneration, including AD. According to its properties, curcumin shows promising potential for the diagnosis of AD. In order to improve its use, new formulations, including nanotechnology-based delivery systems, have been applied. The current study aims to diagnose AD by detecting the accumulation of amyloid beta-peptide via carbon-dot-curcumin nanoparticle conjugation in Drosophila. The accumulation of amyloid beta-peptide has been detected via the conjugate using the fluorescence imaging technique. These results suggest that carbon-dot-curcumin nanoparticle conjugation could be used as a diagnostic tool for AD.

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

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&gt;C (10%)), AXIN2 (c.1975C&gt;T (5%)), FLCN (c.1285dupC (8%)), KRAS (c.35G&gt;T (8%)), MSH6 (c.3261dupC (5%)), SLC9A9 (c.1765A&gt;G (10%)), TP53 (c.1024C&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&gt;A), BRCA1 (c.3548A&gt;G, c.2612C&gt;T), BRCA2 (c.1114A&gt;C), IGF2 (c.677delG), KIT (c.1621A&gt;C), MLH1 (c.655A&gt;G), MLK4 (c.2223G&gt;T, c.2182G&gt;A), PIK3CA (c.1173A&gt;G), PTPN12 (c.964G&gt;A), RET (c.2071G&gt;A), TP53 (c.121delG, c.215C&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.

Abstract 2491: Targeted next generation sequencing identifies somatic variants in Egyptian breast cancer patients

Breast cancer (BC) is the leading cause of cancer-related death in women worldwide and its incidence is progressively increasing in Egypt. Recent advances in next generation sequencing have been used to detect the acquired somatic mutations driving BC. However, there is insufficient knowledge of the acquired somatic mutations in Egyptian BC patients which limit our understanding of disease progression. Up to our knowledge, this is the first Egyptian cohort to sequence a multiple-gene panel of cancer related genes on BC patients.

409 cancer related genes were sequenced in 46 fresh breast tumors of Egyptian BC patients to identify somatic mutations and their frequencies, using the Ion Ampliseq Comprehensive Cancer Panel based on the Ion torrent DNA sequencing technology. The identified sequences were mapped to the human reference genome (hg19) and the detected genetic variants were annotated against different reference databases. The average depth of coverage is 668X and the average of the aligned reads which cover the target regions is 99.6%.

Our results showed that TP53 and PIK3CA were the most top two frequently mutated genes. We detected 15 different somatic mutations in TP53 and 8 different ones in PIK3CA, each in 27 samples (58.7%). Most of the detected somatic mutations in TP53 and PIK3CA are pathogenic and well established in known hotspot regions. According to Clinvar database; we found 19 pathogenic somatic mutations: 7 in p53, 5 in PIK3CA, and single variants of VHL, STK11, AKT1, KRAS, IDH2, PTEN and ERBB2. We also identified 5 variants with uncertain significance (4 in TP53 and 1 in CEBPA) and 4 variants with conflicting interpretations of pathogenicity (2 in TP53 and 1 in each of APC and JAK3). Moreover, 4 novel variants were identified in JAK2, MTOR, KIT and EPHB.

In this cohort, we shed the light on the most frequently detected somatic mutations in Egyptian BC patients which allows for more knowledge about BC progression.

Citation Format: Auhood Nassar, Mohamed abouelhoda, Abeer Bahnassy, Amira Salah El-Din Youssef, Mai M. Lotfy, ola S. Ahmed, Hoda Ismail, Abdel-Rahman N. Zekri. Targeted next generation sequencing identifies somatic variants in Egyptian breast cancer patients [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 2491.

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

Aim: This study aimed to sequence BRCA1 & 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%) & c.3214delC (16%). Moreover, 3 common begnin SNP variants were found to be related to ethnicity (c.3548A&gt;G (58%), c.2612C&gt;T (60%), c.4900A&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%) & c.36delT (34%).

Conclusion: Our data showed that BRCA1 & 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 & 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.

Targeted next generation sequencing identifies somatic mutations in a cohort of Egyptian breast cancer patients

Breast cancer (BC) incidence is progressively increasing in Egypt. However, there is insufficient knowledge of the acquired somatic mutations in Egyptian BC patients which limit our understanding of its progression. To the best of our knowledge, this is the first Egyptian cohort to sequence a multiple-gene panel of cancer related genes on BC patients. Four hundred and nine cancer related genes were sequenced in 46 fresh breast tumors of Egyptian BC patients to identify somatic mutations and their frequencies. TP53 and PIK3CA were the most top two frequently mutated genes. We detected 15 different somatic mutations in TP53 and 8 different ones in PIK3CA, each in 27 samples (58.7%). According to Clinvar database; we found 19 pathogenic somatic mutations: 7 in Tp53, 5 in PIK3CA, and single variants of VHL, STK11, AKT1, KRAS, IDH2, PTEN and ERBB2. We also identified 5 variants with uncertain significance (4 in TP53 and 1 in CEBPA) and 4 variants with conflicting interpretations of pathogenicity (2 in TP53 and 1 in each of APC and JAK3). Moreover, one drug response variant (p.P72R) in TP53 was detected in 8 samples. Furthermore, four novel variants were identified in JAK2, MTOR, KIT and EPHB. Further analysis, by Ingenuity Variant Analysis software (IVA), showed that PI3K/AKT signaling is altered in greater than 50% of Egyptian BC patients which implicates PI3K/AKT signaling as a therapeutic target. In this cohort, we shed the light on the most frequently detected somatic mutations and the most altered pathway in Egyptian BC patients.

Clinicopathological Characteristics and Clinical Outcome in Egyptian Female Breast Cancer Patients With and Without BRCA1/2 Mutations

Introduction:

Germline mutations in BRCA1 and BRCA2 genes confer high risk of developing breast cancer. We sought to examine whether the clinicopathological characteristics and the clinical outcome differ in patients with and without BRCA mutations.

Patients and Methods:

A series of 103 Egyptian female patients were recruited from Breast Cancer Unit, Clinical Oncology Department, Ain Shams University, Egypt. The enrolled patients, unselected for age of onset or family history, were tested for BRCA1/2 mutations using HRM analysis and direct sequencing. The clinical and pathological features of the patients were retrospectively assessed and comparisons were made using Chi-square. Disease free survival (DFS) was estimated by Kaplan–Meier method and compared in the two groups with log-rank.

Results:

The overall rate of BRCA1/2 mutations was 44%. Novel deleterious mutations were detected and submitted to NCBI Clinvar database. Deleterious mutations were identified in 29 cases and unclassified variants in 32 cases, 15 of which had a co-occuring deleterious mutation. Patients with BRCA mutations tended to have early onset breast cancer compared to non-carriers ( P=0.002), more often premenopausal ( P=0.006), with a familial history of breast cancer as well as other cancers ( P=0.005). BRCA-related breast cancers were more likely to have T3-T4 stage than wild type (41% versus 28%, P=0.02), positive lymph node involvement (78 versus 53%, P=0.007) and develop bilateral breast cancers (24% versus 9%, P =0.007). The incidence of ER negative and PR negative tumors was higher in BRCA carriers, but not statistically significant ( P=0.17 and 0.15, respectively). No difference in HER-2/ neu status was observed ( P=0.25). Early age at onset, positive lymph node involvement, family history of any cancer were independent predictive factors for occurrence of BRCA1/2 mutations. The median follow-up time for the cohort was 5.53 years. Patients with BRCA mutations had poorer 5-year DFS compared to non-carriers (47.7% versus 67.4%, P=0.041); but Cox regression analysis failed to demonstrate a significant independent influence of BRCA mutation status on DFS.

Conclusion:

This study shows that BRCA-related breast cancers in the Egyptian population have distinctive clinical and tumor features as well as outcome. This data has important health implications for guiding cancer control policies.

The Role of Breast Cancer Stem Cells and Some Related Molecular Biomarkers in Metastatic and Nonmetastatic Breast Cancer

BACKGROUND

Breast cancer stem cells (BCSCs) play important role(s) in the development and progression of invasive duct carcinoma (IDC). We assessed the role of BCSC marker expression and the number of mammospheres in cultures of breast cancer (BC) tissues and correlated these data to relevant clinicopathologic features of the patients and overall survival (OS).

METHODS

Fresh tumor tissue samples were collected from 44 Egyptian female patients with IDC of the breast and 25 healthy women undergoing reduction mammoplasty as a control. The mammosphere number and the RNA expression levels of some cancer stem cell-related genes (PTEN, PI3K, AKT, Wnt, and β-catenin) were assessed by reverse-transcriptase polymerase chain reaction at different stages of BCSC differentiation compared with control samples.

RESULTS

The number of CD44⁺CD24^-/low cells associated significantly at the end of culture with the expression level of Wnt, β-catenin, and distant metastasis (P < .001, P = .015 and P = .003, respectively). There was significant association between the mammosphere number and CD44⁺CD24^-/low cells as well as AKT expression (P = .040 and .021, respectively). PTEN messenger RNA expressed significantly in BC (P < .05). Wnt-RNA expression associated significantly with high tumor stage, positive lymph node status, Her2-neu overexpression, and metastasis (P = .009, .012, .026, and .001, respectively), whereas OS associated significantly with distant metastasis, Wnt, and PTEN expressions (P < .001, P = .001, P = .014, respectively).

CONCLUSION

BCSCs and their related genes (PTEN, PI3K, AKT, Wnt, and β-catenin) play important roles in the development and progression of BC and they can be used as potential prognostic and predictive biomarkers for patients with BC or as target therapy.

Whole-genome sequencing of human Pegivirus variant from an Egyptian patient co-infected with hepatitis C virus: a case report

Background

Human pegivirus (HPgV) is structurally similar to hepatitis C virus (HCV) and was discovered 20 years ago. Its distribution, natural history and exact rule of this viral group in human hosts remain unclear. Our aim was to determine, by deep next-generation sequencing (NGS), the entire genome sequence of HPgV that was discovered in an Egyptian patient while analyzing HCV sequence from the same patient. We also inspected whether the co-infection of HCV and HPgV will affect the patient response to HCV viral treatment. To the best of our knowledge, this is the first report for a newly isolated HPgV in an Egyptian patient who is co-infected with HCV.

Case presentation

The deep Next Generation Sequencing (NGS) technique was used to detect HCV sequence in hepatitis C patient’s plasma. The results revealed the presence of HPgV with HCV. This co-infection was confirmed using conventional PCR of the HPgV 5′ untranslated region. The patient was then subjected to direct-acting-antiviral treatment (DAA). At the end of the treatment, the patient showed a good response to the HCV treatment (i.e., no HCV-RNA was detected in the plasma), while the HPgV-RNA was still detected. Sequence alignment and phylogenetic analyses demonstrated that the detected HPgV was a novel isolate and was not previously published.

Conclusion

We report a new variant of HPgV in a patient suffering from hepatitis C viral infection.

Abstract 1777: Correlation between different C-KIT exon mutation and clinical outcome to Imatinib Mesylate treatment in patients with gastro-intestinal stromal tumors (GIST)

Aim: C-KIT exon mutations were assessed in patients with gastrointestinal stromal tumor (GIST) in relation to patients’ characteristics, response to treatment and survival rates.

Methods: C-KIT mutations were assessed in the representative formalin fixed paraffinembedded tissues (FFPETs) of 89 patients with GIST compared to 35 normal control (NC) subjects using the Real Time PCR (Rt-PCR) and immunohistochemistry (IHC).

Results: C-KIT mutations were detected in 61/89 (68.5%) patients, compared to none of the NC subjects (P=&lt;0.001). Most mutations were detected in exon 11 (50.8%), followed by exon 9 (24.5%), exon 13 (19.6%), exon 7 (4.1%), and exon 12 (only 1%). C-KIT protein expression was detected in 69 (77.5%) patients compared to none of the NC subjects (p=&lt;0.001). Significant measure of agreement was detected between C-KIT expression by IHC and and RT-PCR (K=0.774, p=0.0001).

The presence of C-KIT mutations associated significantly with large tumor size (P=0.01), High mitotic rate, lymph nodes metastasis and high tumor risk (p=0.001, for all). Patients with exon 11 mutations 26/31 (83.9%) had a better response to treatment compared to those with exon nine 7 (46.7%) and exon 13 mutation 1/12 (8.3%; P=0.001). Exon 11 mutations associated significantly with better PFS and OS compared to those with exon 9 and 13 mutations (P= 0.001, P= 0.0001; respectively). On univariate analysis, Exon 13 mutations was the most significantly associated with reduced PFS (P=0.0001), whereas advanced disease stage, absence of adequate safety margins and the site of exon mutation associated significantly with reduced OS. (P=0.012, P=0.05 and P=0.005; respectively.

Conclusion: GIST patients with C-KIT exon 11 mutations have a better response to imatinib treatment (predictive value), better OS and lower risk of disease progression than those with exon 9 and 13 mutations. Our specified mutations in exons 9& 13 mutations could be used as an independent prognostic factor for GIST patients.

Citation Format: Abeer A. Bahnnasy, Ola Khorshid, Mona S. Abdellateif, Ghada Y. Zakaria, Nasr M. Allahloubi, Auhood Nassar, Abdel-Rahman N. Zekri. Correlation between different C-KIT exon mutation and clinical outcome to Imatinib Mesylate treatment in patients with gastro-intestinal stromal tumors (GIST) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1777.

Abstract 1828: Genetic profiling of breast cancer confirms a pivotal role of EGFR pathway in the development of acquired resistance to tamoxifen

Background: Metastatic breast cancer (MBC) represents a major health problem in Egypt and worldwide. Prognostic and predictive factors for patients with MBC are highly needed, for better management and improved survival. The aim of this study was to assess the prognostic and predictive value(s) of CYP2D6 polymorphisms in MBC patients on Tamoxifen and to determine the genetic profile(s) of Tamoxifen responders and non-responders. Methods: We assessed 157 females with hormone receptor positive, locally recurrent inoperable and/or metastatic breast cancer (MBC) patients from Egypt for 1) CYP2D6 polymorphisms and 2) genetic aberrations in the EGFR pathway (92 genes). All patients received Tamoxifen and according to their response they were divided into Tamoxifen-responders and refractory. RNA was extracted from tumor and normal tissue samples and used to assess the genetic profiles of the patients using the SABioscience array (Qiagen) with four house-keeping genes. Results: 92(58.6%) patients were ER and PR positive, 51 (32.5%) were ER positive and 14 (8.9%) were PR positive. CYP2D6 *3/*4 was significantly prevalent in the refractory group (86.6%).Variants *10/*10 and *10/*3 were more common in the responders (85.5%) compared to refractory (P=0.027). CYP2D6 polymorphism associated significantly with Her-2 amplification (P&lt;0.001), and reduced overall survival rate of patients in both refractory and responder groups (P&lt; 0.001). Fifty-six genes were differentially over-expressed in the refractory group compared to responders, of which only JAK1, COL1A1, GAB1, FN1and MKNK1 showed a significant difference. In the refractory group 34 genes were differentially reduced compared to responders; none of them showed significant difference. Response to Tamoxifen associated significantly with disease site since patients with bone only disease showed better response than those with visceral metastases (P&lt;0.005). Conclusion: A panel of 5 genes in EGFR pathway (MJAK1, COL1A1, GAB1, FN1 and MKNK1) together with CYP2D6 polymorphism scan predict response to Tamoxifen in metastatic BC patients though this has to be verified in an extended study including larger sample.

Citation Format: Abeer A. Bahnnasy, Ibrahim Malash, Nasr Al-Lahlouby, Osman Mansour, Sabry Shaarawy, Mona S. Abdellateif, Hend Yousef, Mai M. Lotfy, Rabab Gaafar, Mohamed. elsesy, Abdel-Rahman N. Zekri. Genetic profiling of breast cancer confirms a pivotal role of EGFR pathway in the development of acquired resistance to tamoxifen [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1828.

Abstract 4243: Genetic variants frequently detected in Egyptian breast cancer tumors: Comprehensive cancer panel by ion torrent DNA sequencing technology

Breast cancer is the leading cause of cancer-related death in women worldwide. In Egypt, it is the most common cancer among females and its incidence is progressively increasing with a great tendency to occur with advanced stages in younger ages. Due to the heterogeneity of breast cancer, it was classified into different subtypes, each exhibits a unique gene mutation profile, based on biological characteristics and on gene expression pattern. Therefore, further research is needed to investigate the unknown genetic mutations involved in the progression of that disease. This study aimed to sequence 409 exons of tumor suppressor genes and oncogenes to identify the frequency of the detected genetic mutations in breast cancer using Ion Comprehensive Cancer Panel. Forty-eight tissue samples of various breast cancer subtypes were collected from National Cancer Institute (NCI) outpatient clinic, Cairo University. Analysis revealed 191 exonic and splicing variants. In this paper, we will address the most frequently detected Egyptian genetic variants (in 31.25 % of cases or more) as well as other deleterious variants commonly associated with breast cancer. Most of the detected genetic variants were checked in 1000g, dbSNP and Exac All databases. Other variants were found at known hotspot sites. We reported fifty-one somatic and germline mutations in thirty-two genes; AKAP9, BUB1B, RPS6KA2, AURKB, FANCA, RNF213, FGFR4, KAT6B, NLRP1, KAT6A, PER1, ERBB4, IL6ST, PIK3CA, P53, AURKA, WRN, PALB2, PTEN, GATA3, AKT1, ERBB2 and KRAS. Only KAT6B incurred non-frameshift deletion and only GATA3 had frameshift insertion while KAT6A, ERBB4 and PTEN had frameshift deletion. All the identified variants were detected with different frequencies in each breast cancer subtype. Each sample harbored at least four mutations and the maximum number of mutations per sample was twelve. The current data showed that gene panels analyzed

by Next-Generation Sequencing (NGS) identifies large number of germline and somatic mutations that is crucial for understanding cancer predisposition and developing personalized or combination therapies that efficiently target the individual breast cancer-specific mutations.

Key words: Breast cancer, Somatic mutations, Germline mutations, Ion torrent sequencing, Targeted sequencing.

Note: This abstract was not presented at the meeting.

Citation Format: Abdel-Rahman N. Zekri, Osman Mansour, Samah A. Loutfy, Mohamed M. Hafez, M. Gomaa, Abeer Bahnassy, Mai M. Lotfy, Amira S. Youssef, Ola S. Ahmed, Mohammed Abouelhouda, Auhood Nassar. Genetic variants frequently detected in Egyptian breast cancer tumors: Comprehensive cancer panel by ion torrent DNA sequencing technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4243.

Microsatellite instability profiling in Egyptian bladder cancer patients: A pilot study

Microsatellite alterations have been implicated in the pathogenesis of many cancers; however, they are still not well addressed in the bladder cancer (BC) of Egyptian population. We assessed microsatellite instability (MSI) profile and loss of heterozygosity (LOH) using 13 microsatellite markers in tumor tissue samples and urine sediments obtained from 30 Egyptian patients with BC. The concordance between MSI in tumor tissue and urine samples was determined, and correlated to relevant clinicopathologic features. We found that MSI was more frequent than LOH (100% and 46.7%, respectively). D16S310, MBP, and IFN-α showed the highest MSI frequency in urine samples (70%, 70%, and 66.67%, respectively), while MBP, ACTBP2, and D9S171 (66.67%, 63.33%, and 60%, respectively) were the most frequently detected in tumor tissues. All assessed MSI markers correlated significantly with pathologic subtype (being more frequent in TCC) and with hematuria. The concordance between tissue and urine samples was statistically significant for D16S476, D9S171, FGA, and ACTBP2 (P = 0.04, 0.015, 0.02, and 0.007, respectively). When we combined D16S476 and D9S171, the sensitivity, specificity, positive predictive value, and negative predictive value for the diagnosis of BC were 80.0%, 75.0%, 82.8%, and 71.4%, respectively. Accordingly, we concluded that MSI in urine sediments could be a potential tool for the diagnosis of BC.

Prognostic significance of circulating tumor cells (CTCs) in Egyptian non-metastatic colorectal cancer patients: A comparative study for four different techniques of detection (Flowcytometry, CellSearch, Quantitative Real-time PCR and Cytomorphology)

PURPOSE

We assessed CTCs counts in NMCRC patients using four different techniques.

METHODS

CTCs were detected in 63 NMCRC patients, 40 benign bowel diseases (BBD) and 40 normal controls (NC) using, flow-cytometry (FCM), CellSearch (CS), cytomorphology and quantitative real time (qPCR) for CK19, MUC1, CD44, CD133, ALDH1 expression. Results were correlated to progression free (PFS) and overall (OS).

RESULTS

Positive CTCs (≥4 cells /7.5 mL blood) were detected in 50.8% (32/63) NMCRC by FCM and 7.5% (3/40) BBD (p < .001). CTCs were detected in 34/63 (54%) NMCRC, 4/40 (10%) BBD (p < .001) by CS. CK19, MUC1, CD44, CD133 and ALDH1 were expressed in 35 (55.6%), 29 (46.0%), 28 (44.4%), 26 (41.3%) and 25 (41.3%) cases of NMCRC. In BBD 4/40 (10%) cases expressed CK19, MUC1 and CD44, while 2/40 (5%) expressed CD133. Cytomorphology showed the lowest sensitivity (47.6%) and specificity (90%) for CTCs detection. The combined use of FCM or CS with CTCs-mRNA markers improved the sensitivity and specificity to 68.3%, and 95.0%; respectively. Positive CTCs and mRNA markers expression were significantly associated with shorter 5-yr PFS and OS. In multivariate analysis, CTCs mRNA markers were independent prognostic factors for PFS and OS.

CONCLUSIONS

Enumeration of CTCs by FCM and RNA expression for specific colon cancer markers are comparable to CS regarding sensitivity and specificity. CTCs also represent novel therapeutic targets for NMCRC cases.

The role of E-cadherin and Runx3 in Helicobacter Pylori - Associated gastric carcinoma is achieved through regulating P21waf and P27 expression

BACKGROUND

We assessed the role of E-cadherin (CDH1), runt-related transcription factor 3, p21waf and p27 promoter methylation (PM) and protein expression in Helicobacter pylori (HP)-associated gastric carcinomas (GCs) and adjacent non-neoplastic tissues (ANNTs).

PATIENTS AND METHODS

192 cases were assessed for PM and protein expression of CDH1, RUNX3, p21waf and p27 by methylation-specific PCR (MSP) and immunohistochemistry. The CagA gene was also assessed.

RESULTS

In GCs, 66 (34.4%) and 84 (43.8%) cases showed CDH1-PM and reduced expression. It is significantly affected in GCs rather than in non-neoplastic groups (p < 0.001). In ANNTs, 108 (56.3%) cases showed CDH1-PM and all cases revealed preserved protein expression. RUNX3-PM was detected in 78 GCs (40.6%) and 69 ANNTs (35.9%), whereas reduced protein expression was detected in 99 (51.65%) GC compared to ANNTs 90 (46.9%). p21WAF and p27 showed PM in (48.4% and 45.3%) GCs and ANNTs; respectively. p21waf protein was reduced in 90 (46.9%) cases and 91 ANNTs (47.4%). p27 was reduced in 86 (44.8%) cases and 87 ANNTs (45.3%). CDH1 aberrations correlated with HP in tumors and ANNTs and with diffuse/intestinal tumors (p = 0.014, p = 0.014 and p = 0.02). RUNX3 aberrations associated with HP (p = 0.04), high grade (p = 0.04), and advanced stage (p = 032). Tumor grade associated with RUNX3-PM, CDH, p21 and p27 protein (p < 0.05 for all). Tumor stage associated significantly with PM and reduced protein expression of all markers. Positive lymph nodes associated significantly with p27PM (p < 0.001).

CONCLUSIONS

HP plays an important role in the development and progression of GC through silencing of CDH1, RUNX3, p21WAF and p27 expression.

Polymorphisms of base-excision repair genes and the hepatocarcinogenesis

AIM

To determine the possible association between polymorphisms of DNA repair genes, including XRCC1 Arg194Tryp, Arg280His, and Arg399Glu, APE1 Asp148Glu, and NEIL2 Arg257Leu, and the risk of developing hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC).

METHODS

A total of 264 subjects were recruited in this retrospective case-control study and were categorized into four groups: 88 control subjects (CR), 53 chronic hepatitis C patients (CHC), 36 liver cirrhotic patients (LC), and 87 HCC patients. The XRCC1 Arg194Tryp, Arg280His, and Arg399Glu polymorphisms were detected using PCR-RFLP, while real-time PCR was used to genotype APE1 Asp148Glu and NEIL2 Arg257Leu.

RESULTS

Our data revealed that, compared with the healthy controls, for those subjects with the XRCC1 Arg194Trp genotype, the risk of developing CHC, LC, and HCC was increased by 6.66- (odds ratio (OR) = 6.667; 95% confidence interval (CI) = 3.244-13.701; P > 0.01), 3.85- (OR = 3.852; 95% CI = 1.797-8.256; P > 0.01), and 2.14-fold (OR = 2.14; 95% CI = 1.13-4.06; P > 0.05), respectively. There was no association between the risk of HCC development and the XRCC1 Arg280His or XRCC1 Arg399Gln genotypes. Moreover, the analysis showed a lack of association between APE1 Asp148Glu and the risk of HCC development. The analysis of clinicopathological parameters showed that the HCC patients with the XRCC1 Arg280His polymorphism were 2.9 fold more likely to have hepatic lesions in both hepatic lobes (OR: 2.9; 95% CI: 1.15-7.29). Notably, in the HCC patients, the prevalence of the APE1 polymorphism in the males was four times higher than that in the females (OR = 4; 95% CI = 1.129-14.175; P > 0.05).

CONCLUSION

Our results indicate that the XRCC1 Arg194Trp polymorphism could be a risk factor for HCV-related HCC development in Egypt.

Role of relevant immune-modulators and cytokines in hepatocellular carcinoma and premalignant hepatic lesions

AIM

To assess the levels of different immune modulators in patients with hepatocellular carcinoma (HCC), in relation to other hepatic diseases.

METHODS

Eighty-eight patients were included in the current study and represented patients with HCC (20), liver cirrhosis (28) and chronic hepatitis (CH; 25), and normal controls (NC; 15). Peripheral blood was isolated for immunophenotyping of active myeloid dendritic cells (mDCs; CD1c and CD40), mature inactive myeloid cells (CD1c and HLA), active plasmacytoid cells (pDCs; CD303 and CD40), mature inactive pDCs (CD30 and HLA), active natural killer (NK) cells (CD56 and CD161), active NK cells (CD56 and CD314) and inactive NK cells (CD56 and CD158) was done by flow cytometry. Serum levels of interleukin (IL)-2, IL-10, IL-12, IL-1β, interferon (IFN)-α, IFN-γ and tumor necrosis factor (TNF)-αR2 were assessed by ELISA.

RESULTS

Active mDCs (CD1C+/CD40+) and inactive mDCs (CD1c+/HLA+) were significantly decreased in HCC patients in relation to NC (P < 0.001). CD40+ expression on active pDCs was decreased in HCC patients (P < 0.001), and its level was not significantly changed among other groups. Inactive pDCs (CD303+/HLA+), inactive NKs (CD56+/CD158+) and active NKs (CD56+/CD161+) were not statistically changed among the four groups studied; however, the latter was increased in CH (P < 0.05). NKG2D was statistically decreased in HCC, CH and cirrhosis (P < 0.001), and it was not expressed in 63% (12/20) of HCC patients. There was significant decrease of IL-2, IFN-α and IFN-γ (P < 0.001), and a significant increase in IL-10, IL-1β, and TNF-αR2 (P <0.01, P < 0.001 and P < 0.001; respectively) in HCC patients. There was inverted correlation between IL-12 and IL-1β in HCC (r = -0.565, P < 0.01), with a strong correlation between pDCs (CD303+/CD40+) and NKs (CD56+/CD161+; r = 0.512, P < 0.05) as well as inactive mDCs (CD1c+/HLA+) and inactive NK cells (CD56+/CD158+; r = 0.945, P < 0.001).

CONCLUSION

NKG2D, CD40, IL-2 and IL-10 are important modulators in the development and progression of HCC.

MicroRNA Signatures for circulating CD133-positive cells in hepatocellular carcinoma with HCV infection

AIM

Molecular characterization of the CD133+ stem cells associated with hepatocarinogensis through identifying the expression patterns of specific microRNAs (miRNAs).

METHODS

We investigated the expression pattern of 13 miRNAs in purified CD133+ cells separated from the peripheral blood of healthy volunteers, chronic hepatitis C (CHC), liver cirrhosis (LC) and hepatocellular carcinoma (HCC) patients a long with bone marrow samples from the healthy volunteers and the LC patients using custom miScript miRNA PCR array.

RESULTS

The differential expression of the 13 studied miRNAs in CD133+ cells separated from the HCC patients' peripheral blood compared to the controls revealed that miR-602, miR-181b, miR-101, miR-122, miR-192, miR-125a-5p, and miR-221 were significantly up regulated (fold change = 1.8, 1.7, 2, 5.4, 1.6, 2.9 & 1.5 P value = 0.039, 0.0019, 0.0013, 0.0370, 00024, 0.000044 &0.000007 respectively). As for the HCC group compared to the CHC group; miR-602, miR-122, miR-181b, miR-125a-5p, and miR-192 were significantly up regulated (fold change = 13, 3.1, 2.8, 1.6 & 1.56, P value = 0.01, 0.001, 0.000004, 0.002 & 0.007 respectively). Upon comparing the HCC group to the LC group; miR-199a-3p, miR-192, miR-122, miR-181b, miR-224, miR-125a-5p, and miR-885-5p were significantly up regulated (fold change = 5, 6.7, 2.3, 3, 2.5, 4.2 & 39.5 P value = 0.001025, 0.000024, 0.000472, 0.000278, 0.000004, 0.000075 & 0.0000001 respectively) whereas miR-22 was significantly down regulated (fold change = 0.57 P value = 0.00002). Only, miR-192, miR-122, miR-181b and miR-125a-5p were significant common miRNAs in CD133+ cells of the HCC group compared to the other non-malignant groups.

CONCLUSION

We identified a miRNA panel comprised of four miRNAs (miR-192, miR-122, miR-181b and miR-125a-5p) that may serve as a molecular tool for characterization of the CD133+ cells associated with different stages of hepatocarinogensis. This panel may aid in developing a new target therapy specific for those CD133+ cells.

Gene expression profiling of circulating CD133+ cells of hepatocellular carcinoma patients associated with HCV infection

AIM

Identifying the genetic expression profile of CD133⁺ cells from HCC patients compared to CD133⁺ cells from healthy volunteers that may contribute in hepatocarcinogenesis process.

METHOD

Circulating CD133⁺ cells were sorted from the peripheral blood of HCC patients as well as from healthy volunteers using magnetic activated cell sorting. The differential expression profile of stem cell related genes was performed using the Stem Cell PCR profiling assay.

RESULTS

Data analysis of stem cells related genes in CD133⁺ cells of the HCC group compared to the control group showed that; CCND2, COL1A1, CTNNA1, DLL3, JAG1, KRT15, MYC, NOTCH2, T and TERT were up-regulated (fold change=80, 68.6, 6.67, 7.22, 3.8, 15.2, 14.5, 105.6, 26.6 and 99 respectively while only CD3D was down-regulated (fold change=0.055) in HCC patients. However, after application of Beferroni correction to adjust P-value; KRT15 was the only gene that was significantly over expressed in CD133⁺ cells of HCC compared to control group (P-value=0.012).

CONCLUSION

KRT15 can be used to differentiate between circulating CD133⁺ cells from HCC group and control group. However, further study may be needed to confirm on the protein level.

BRCA1-IRIS overexpression promotes and maintains the tumor initiating phenotype: implications for triple negative breast cancer early lesions

Tumor-initiating cells (TICs) are cancer cells endowed with self-renewal, multi-lineage differentiation, increased chemo-resistance, and in breast cancers the CD44+/CD24-/ALDH1+ phenotype. Triple negative breast cancers show lack of BRCA1 expression in addition to enhanced basal, epithelial-to-mesenchymal transition (EMT), and TIC phenotypes. BRCA1-IRIS (hereafter IRIS) is an oncogene produced by the alternative usage of the BRCA1 locus. IRIS is involved in induction of replication, transcription of selected oncogenes, and promoting breast cancer cells aggressiveness. Here, we demonstrate that IRIS overexpression (IRISOE) promotes TNBCs through suppressing BRCA1 expression, enhancing basal-biomarkers, EMT-inducers, and stemness-enforcers expression. IRISOE also activates the TIC phenotype in TNBC cells through elevating CD44 and ALDH1 expression/activity and preventing CD24 surface presentation by activating the internalization pathway EGFR→c-Src→cortactin. We show that the intrinsic sensitivity to an anti-CD24 cross-linking antibody-induced cell death in membranous CD24 expressing/luminal A cells could be acquired in cytoplasmic CD24 expressing IRISOE TNBC/TIC cells through IRIS silencing or inactivation. We show that fewer IRISOE TNBC/TICs cells form large tumors composed of TICs, resembling TNBCs early lesions in patients that contain metastatic precursors capable of disseminating and metastasizing at an early stage of the disease. IRIS-inhibitory peptide killed these IRISOE TNBC/TICs, in vivo and prevented their dissemination and metastasis. We propose IRIS inactivation could be pursued to prevent dissemination and metastasis from early TNBC tumor lesions in patients.

Arabinoxylan rice bran (Biobran) suppresses the viremia level in patients with chronic HCV infection: A randomized trial

Current treatments for Hepatitis C virus (HCV) have severe side effects and are very expensive. There is a need to explore effective natural therapies against HCV that are less toxic and more cost-effective. In the current study, 37 chronic HCV patients were randomized into two groups and treated with either pegylated interferon (PEG IFN) plus ribavirin (n = 21) or Biobran, an arabinoxylan from rice bran (1 g/day) (n = 16). We examined viremia, liver enzymes, interferon-γ (IFN-γ) levels in serum, and toxicity before and three months after treatment. Both groups showed a significant and similar reduction in viral load after three months of treatment relative to the baseline viral load (P <0.05). In addition, treatment with Biobran resulted in a significant increase in the level of IFN-γ (P <0.001). Patients in the PEG IFN plus ribavirin group showed fever, anemia, thrombocytopenia, and easy fatigue. Patients in the Biobran group showed no side effects and reported good health. We conclude that Biobran is a potential novel therapeutic regimen that has a similar effect to PEG IFN plus ribavirin and is safe and cost-effective in the treatment of chronic HCV. Our finding of Biobran's efficacy against HCV infection warrants further investigation in multiple clinical trials (Clinical Trials Registration: NCT02690103).

Differential expression of viral agents in lymphoma tissues of patients with ABC diffuse large B-cell lymphoma from high and low endemic infectious disease regions

Diffuse large B-cell lymphoma (DLBCL), the most common type of non-Hodgkin's lymphoma (NHL) in adults, accounts for approximately 30-40% of newly diagnosed lymphomas worldwide. Environmental factors, such as viruses and bacteria, may contribute to cancer development through chronic inflammation and the integration of oncogenes, and have previously been indicated in cervical cancer, hepatocellular carcinoma, gastric cancer and lymphoproliferative disorders. In the present study, the presence of microbial agents was analyzed in the lymphoma tissue of patients with activated B-cell like (ABC) DLBCL. The present study compared two groups of patients from geographically varied regions that possess a difference in the prevalence of viral and other microbial agents. The patient populations were from Sweden (a low endemic infectious disease region) and Egypt (a high endemic infectious disease region). A differential expression of several viruses in lymphoma tissues was noted when comparing Swedish and Egyptian patients. JC polyomavirus (JCV) was detected in Swedish and Egyptian patients and, uniquely, the complete hepatitis B virus (HBV) genome was detected only in Egyptian lymphoma patients. None of these viruses were detected in control lymph tissues from Sweden or Egypt. In total, 38% of the Egyptian patients were found to have HBV surface antigens (HBsAgs) in their serum; however, HBsAgs were not found in any of the Swedish patients. The percentage of serum HBsAgs in Egyptian patients with ABC DLBCL was significantly increased compared with the general Egyptian population (P<0.05). The present study may support a notion that viral agents, including JCV and HBV, may be involved in the tumorigenesis of DLBCL in regions of high infectious disease.

Abstract 504: Circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) are superior to CA 15-3 in predicting tumor burden, patients response to treatment and overall survival (OS) rates in metastatic breast cancer patients from Egypt

Background: Monitoring of tumor burden in patients with metastatic breast cancer (mBC) is crucial to determine response to treatment. In addition to radiological procedures and serological biomarkers, circulating, tumor cells (CTCs) are now used to assess the tumor burden and patients’ response to treatment. The circulating cell-free tumor DNA (ctDNA) harboring tumor-specific aberrations has not been properly assessed yet.

Methods: 100 Egyptian patients with locally mBC were assessed for CA 15-3 levels, CTCs number by flowcytometry (FCM) confirmed by RT-PCR (CK and mammaglobin expression), and for ctDNA. The results of the three techniques were compared to the radiographic imaging of tumors, patients response to treatment and overall survival (OS) rates. Paraffin blocks for 40 tumor samples, obtained from the studied patients (20 non-responders and 20 responders) were used to detect p53 gene mutations exons 5-9. CA 15-3 levels and CTC numbers were measured at the same time intervals.

Results: Somatic mutations of p53 were detected in 23/40 (57.5%) sequenced tumors. ctDNA showing the identified mutations in tumor samples, was detected in 78 cases (78%) with high dynamic range. CTCs&gt;4/7.5ml blood were present in 57 out of the 78 (73.1%) ctDNA positive cases, and CA 15-3 was detected in 30 (38.5%) cases. Changes in ctDNA levels and CTCs&gt;4 correlated significantly with the tumor burden (p = 0.034), patients response to treatment (p&lt;0.01), and lower OS rates (p = 0.034&p = 0.01; respectively). CTCs number and ctDNA levels showed higher correlation with changes in tumor burden, compared to CA 15-3 (p&lt;0.001 versus p = 0.046). However, ctDNA provided the earliest measure of treatment response in most of the patients (53%).

Conclusions: ctDNA is an informative, highly sensitive and specific biomarker that could be used to monitor tumor burden in mBC. Together with enumeration of CTCs they can predict tumor response and OS in mBC patients with high accuracy.

Citation Format: Abdel-Rahman N. Zekri, Abeer A. Bahnassy. Circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) are superior to CA 15-3 in predicting tumor burden, patients response to treatment and overall survival (OS) rates in metastatic breast cancer patients from Egypt. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 504.

Circulating Serum miRNAs as Diagnostic Markers for Colorectal Cancer

AIM

The study was designed to assess the possibility of using circulating miRNAs (serum miRNAs) as diagnostic biomarkers in colorectal cancer (CRC) and to identify their possibility as candidates for targeted therapy.

METHODS

The study involved two sample sets: 1- a training set which included 90 patients with colorectal related disease (30 with CRC, 18 with inflammatory bowel disease (IBD), 18 with colonic polyps (CP) and 24 with different colonic symptoms but without any colonoscopic abnormality who were enrolled as control group) and 2- a validation set which included 100 CRC patients. Serum miRNAs were extracted from all subjects to assess the expression profiles for the following miRNAs (miR-17, miR-18a, miR-19a, miR-19b, miR-20a, miR-21, miR-146a, miR-223, miR-24, miR-454, miR-183, miR-135a, miR- 135b and miR- 92a) using the custom miScript miRNA PCR-based sybergreen array. The area under the receiver operating characteristic curve (AUC) was used to evaluate the diagnostic performance of the studied miRNAs for colorectal cancer diagnosis.

RESULTS

Data analysis of miRNA from the training set showed that; compared to control group, only miR-19b was significantly up-regulated in patients with IBD group (fold change = 5.24, p = 0.016), whereas in patients with colonic polyps, miR-18a was significantly up-regulated (fold change = 3.49, p-value = 0.018). On the other hand, miR-17, miR-19a, miR-20a and miR-223 were significantly up-regulated (fold change = 2.35, 3.07, 2.38 and 10.35; respectively and p-value = 0.02, 0.015, 0.017 and 0.016; respectively in CRC patients. However, the validation set showed that only miR-223 was significantly up-regulated in CRC patients (fold change = 4.06, p-value = 0.04).

CONCLUSION

Aberrant miRNA expressions are highly involved in the cascade of colorectal carcinogenesis. We have found that (miR-17, miR-19a, miR-20a and miR-223) could be used as diagnostic biomarkers for CRC. On the other hand, miR-19b and miR-18a could be used as diagnostic biomarkers for CP and IBD respectively.

Differentially expressed genes in metastatic advanced Egyptian bladder cancer

BACKGROUND

Bladder cancer is one of the most common cancers worldwide. Gene expression profiling using microarray technologies improves the understanding of cancer biology. The aim of this study was to determine the gene expression profile in Egyptian bladder cancer patients.

MATERIALS AND METHODS

Samples from 29 human bladder cancers and adjacent non-neoplastic tissues were analyzed by cDNA microarray, with hierarchical clustering and multidimensional analysis.

RESULTS

Five hundred and sixteen genes were differentially expressed of which SOS1, HDAC2, PLXNC1, GTSE1, ULK2, IRS2, ABCA12, TOP3A, HES1, and SRP68 genes were involved in 33 different pathways. The most frequently detected genes were: SOS1 in 20 different pathways; HDAC2 in 5 different pathways; IRS2 in 3 different pathways. There were 388 down-regulated genes. PLCB2 was involved in 11 different pathways, MDM2 in 9 pathways, FZD4 in 5 pathways, p15 and FGF12 in 4 pathways, POLE2 in 3 pathways, and MCM4 and POLR2E in 2 pathways. Thirty genes showed significant differences between transitional cell cancer (TCC) and squamous cell cancer (SCC) samples. Unsupervised cluster analysis of DNA microarray data revealed a clear distinction between low and high grade tumors. In addition 26 genes showed significant differences between low and high tumor stages, including fragile histidine triad, Ras and sialyltransferase 8 (alpha) and 16 showed significant differences between low and high tumor grades, like methionine adenosyl transferase II, beta.

CONCLUSIONS

The present study identified some genes, that can be used as molecular biomarkers or target genes in Egyptian bladder cancer patients.