El Leithy, A. A., A. S. E. - D. Youssef, A. Nassar, R. K. Aziz, N. M. Khaled, M. T. Mahrous, G. N. Farahat, A. H. Mohamed, and Y. M. Bakr, "Long-read 16S rRNA amplicon sequencing reveals microbial characteristics in patients with colorectal adenomas and carcinoma lesions in Egypt.", Gut pathogens, vol. 17, issue 1, pp. 8, 2025 Feb 02. Abstract

BACKGROUND: Colorectal cancer (CRC) is among the five leading causes of cancer incidence and mortality. During the past decade, the role of the gut microbiota and its dysbiosis in colorectal tumorigenesis has been emphasized. Metagenomics and amplicon-based microbiome profiling provided insights into the potential role of microbial dysbiosis in the development of CRC.

AIM: To address the scarcity of information on differential microbiome composition of tumor tissue in comparison to adenomas and the lack of such data from Egyptian patients with CRC.

MATERIALS AND METHODS: Long-read nanopore sequencing of 16S rRNA amplicons was used to profile the colonic microbiota from fresh colonoscopic biopsy samples of Egyptian patients with CRC and patients with colonic polyps.

RESULTS: Species richness of CRC lesions was significantly higher than that in colonic polyps (p-value = 0.0078), while evenness of the CRC group was significantly lower than the colonic polyps group (p-value = 0.0055). Both species richness and Shannon diversity index of the late onset CRC samples were significantly higher than those of the early onset ones. The Firmicutes-to-Bacteroidetes (F/B) ratio was significantly higher in the CRC group than in the colonic polyps group (p-value = 0.0054), and significantly higher in samples from early-onset CRC. The Enterococcus spp. were significantly overabundant in patients with rectal cancer and early-onset CRC, while Staphylococcus spp. were significantly higher in patients with sigmoid cancer and late-onset CRC. In addition, the relative abundance of Fusobacterium nucleatum was significantly higher in CRC patients.

CONCLUSION: Differentiating trends were identified at phylum, genus, and species levels, despite the inter-individual differences. In summary, this study addressed the microbial dysbiosis associated with CRC and colonic polyps groups, paving the way for a better understanding of the pathogenesis of early and late-onset CRC in Egyptian patients.

Ramadan, N., O. A. Rabiee, M. M. Hafez, N. A. F. Fattah, E. N. Khorshed, khaled khalafalla, and A. Nassar, "Molecular detection of HPV, EBV, and polyomaviruses in thyroid tumors and their clinicopathological relevance.", Journal of cancer research and clinical oncology, vol. 151, issue 12, pp. 298, 2025 Oct 20. Abstract

OBJECTIVE: Oncogenic viruses have been implicated in thyroid carcinogenesis, yet their prevalence and clinicopathological associations remain incompletely understood. Thus, it is crucial to investigate the prevalence of human papillomavirus (HPV), Epstein-Barr virus (EBV), and polyomaviruses (JCV and BKV) in thyroid tumors and assess their association with clinic-pathological characteristics.

METHODS: This study included 70 fresh biopsy samples collected from 45 TC patients and 25 patients with benign thyroid tumors, along with 10 normal thyroid tissues. Viral DNA was extracted and screened for HPV, EBV, and polyomaviruses using SYBR Green-based real-time PCR.

RESULTS: HPV, EBV, and polyomaviruses, particularly JCV, were detected at significantly lower frequencies in the normal group when compared to malignant and benign groups (p-value = 0.030, p-value = 0.030, and p-value = 0.001, respectively). In TC patients, HPV common, HPV-16, HPV-6, and HPV-11 positivity was correlated with obesity (p-value < 0.05), polyomaviruses, particularly JCV, with older age (p-value = 0.041 and p-value = 0.011), BKV with larger tumor size (p-value = 0.030), and EBV with family cancer history (p-value = 0.020). In benign tumors, polyomavirus was absent in Hashimoto thyroiditis (p-value = 0.020), BKV was linked to older age (p-value = 0.030), and absence of BKV was associated with COVID-19 vaccination (p-value = 0.046).

CONCLUSION: The current study is the first of its kind in Egypt to investigate the prevalence of HPV, EBV, and polyomaviruses in thyroid tumors and to examine their associations with certain clinicopathological characteristics. The findings underline the importance of viral profiling in understanding thyroid tumor behavior and influencing cancer risk as well.

Alsaeed, S. A., A. M. Lymona, A. Atef, A. M. Moawad, H. Morsi, M. Alkaffas, A. Nassar, and H. M. Aboubakr, "Bisphenol A exposure modulates ovarian cancer gene expression and oxidative stress markers: a case-control study.", Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, pp. 115810, 2025 Oct 16. Abstract

In this case‒control study conducted at Cairo's National Cancer Institute, the associations between bisphenol A (BPA), an endocrine-disrupting chemical (EDC), and ovarian cancer were investigated. BPA levels in the urine, oxidative stress markers (reactive oxygen species (ROS) and superoxide dismutase (SOD) activity), and KRT4 gene expression were analyzed in 30 patients and 30 controls. Significant risk factors for BPA exposure included consuming microwave meals, consuming canned beverages, using PVC food storage, eating fast food, handling thermal paper, exposure to dust, and recurrent hospitalizations (all p < 0.001). Compared with normal controls, ovarian cancer patients presented increased BPA levels, ROS, and KRT4 expression, along with reduced SOD activity (p < 0.001). A strong positive correlation was found between BPA and KRT4, suggesting that KRT4 is a potential biomarker. The cutoff values for urinary BPA and KRT4 achieved 100% sensitivity and specificity in distinguishing patients from controls. These findings suggest that BPA plays a role in ovarian cancer pathogenesis, likely through oxidative stress and gene dysregulation. This study emphasizes the importance of minimizing BPA exposure (e.g., by reducing the use of canned or packaged foods) and calls for larger studies to further investigate the role of EDCs in hormone-dependent cancers.

Nourhan E. Mohamed, Noha A. Mahana, A. M. Badr, Ola S. Ahmed, Ahmed M. Lymona, S. S. Nasr, and A. Nassar, " Impact of IL-12 and IL-18 Combined Stimulation on INF-γ and TNF-α Production by PBMCs Derived from Egyptian Ovarian Cancer Patients", International Journal of Biomedicine, vol. 14, issue 3, pp. 435-440, 2024 Sep 06.
Mohamed, N. E., N. F. Abdel Fattah, M. G. Seadawy, A. M. Lymona, S. S. Nasr, A. A. El Leithy, F. M. Abdelwahed, and A. Nassar, "The clinical importance of IFN-γ and human epididymis protein 4 in Egyptian patients with epithelial ovarian cancer combined with HPV infection.", Human immunology, vol. 85, issue 5, pp. 111089, 2024 Sep. Abstract

BACKGROUND: High-grade Epithelial Ovarian Cancer (HGEOC) is an aggressive disease that usually presents at an advanced stage. Thus, detecting the circulating cytokines (IFNγ and TNF-α) may serve as a biomarker to identify malignancy and manage therapeutic decisions.

OBJECTIVES: Assessing the clinical importance of inflammatory mediators and tumor markers in EOC Egyptian patients compared with benign cases. Moreover, identifying the distinct inflammatory mediators in EOC patients combined with HPV infection.

METHODS: This study was conducted on 61 Egyptian patients, divided into 25 patients with HGEOC, 22 patients with LGEOC, and 14 benign ovarian tumor cases. Measurements of serum HE4, CA125, CEA, and CA19-9 were determined by Roche Elecsys immunoassays. Serum levels of TNF-α and IFN-γ were measured using quantitative sandwich ELISA. Quantitative genotyping of HPV DNA types 16, 18, and 45 was assessed for the HPV DNA-positive samples.

RESULTS: HPV DNA was detected in 25.53 % of malignant cases, HPV 16 was detected in 50 % of HPV-positive cases, and only 1 case of HPV 18 was detected out of 12 positive cases. The Human Epididymis protein 4 (HE4) was statistically different between patients with EOC and benign cases (p-value = 0.007) and between HPV DNA positive and HPV DNA negative cases (p-value = 0.008). The serum levels of IFN- γ were statistically different between HGEOC and LGEOC (p-value < 0.001), while the serum levels of TNF-α didn't differ statistically between the two groups.

CONCLUSION: IFN-γ could be used as a biomarker to discriminate HGEOC and LGEOC. Initial evidence for the possible association between HE4 and the progression of HPV-associated EOC was speculated.

Zekri, A. - R. N., E. R. El-Sisi, A. S. E. - D. Youssef, M. M. Kamel, A. Nassar, O. S. Ahmed, M. El Kassas, A. B. Barakat, A. I. Abd El-Motaleb, and A. A. Bahnassy, "MicroRNA Signatures for circulating CD133-positive cells in hepatocellular carcinoma with HCV infection.", PloS one, vol. 13, issue 3, pp. e0193709, 2018. Abstract

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.

Zekri, A. - R. N., A. S. E. - D. Youssef, M. M. Lotfy, R. Gabr, O. S. Ahmed, A. Nassar, N. Hussein, D. Omran, E. medhat, S. Eid, et al., "Circulating Serum miRNAs as Diagnostic Markers for Colorectal Cancer.", PloS one, vol. 11, issue 5, pp. e0154130, 2016. Abstract

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.

Zekri, A. - R. N., A. S. E. - D. Youssef, E. D. El-Desouky, O. S. Ahmed, M. M. Lotfy, A. A. - M. Nassar, and A. A. Bahnassey, "Serum microRNA panels as potential biomarkers for early detection of hepatocellular carcinoma on top of HCV infection.", Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine, vol. 37, issue 9, pp. 12273-12286, 2016. Abstract

The identification of new high-sensitivity and high-specificity markers for hepatocellular carcinoma (HCC) is essential. We aimed at identifying serum microRNAs (miRNAs) as potential biomarkers for early detection of HCC on top hepatitis C virus (HCV) infection. We investigated serum expression of 13 miRNAs in 384 patients with HCV-related chronic liver disease (192 with HCC, 96 with liver cirrhosis (LC), and 96 with chronic hepatitis C (CHC)) in addition to 96 healthy participants enrolled as a control group. The miRNA expression was performed using real-time quantitative PCR-based SYBR Green custom miRNA arrays. The area under the receiver operating characteristic curve (AUC) was used to evaluate the diagnostic performance of miRNA panels for early detection of HCC. Using miRNA panel of miR-122, miR-885-5p, and miR-29b with alpha fetoprotein (AFP) provided high diagnostic accuracy (AUC = 1) for early detection of HCC in normal population while using miRNA panel of miR-122, miR-885-5p, miR-221, and miR-22 with AFP provided high diagnostic accuracy (AUC = 0.982) for early detection of HCC in LC patients. However, using miRNA panel of miR-22 and miR-199a-3p with AFP provided high diagnostic accuracy (AUC = 0.988) for early detection of HCC in CHC patients. We identified serum miRNA panels that could have a considerable clinical use in early detection of HCC in both normal population and high-risk patients.

Youssef, A. S. E. - D., A. R. N. Zekri, M. Mohanad, S. A. Loutfy, N. F. Abdel Fattah, M. H. Elberry, A. A. El Leithy, A. El-Touny, A. S. Rabie, M. Shalaby, et al., "Deleterious and ethnic-related BRCA1/2 mutations in tissue and blood of Egyptian colorectal cancer patients and its correlation with human papillomavirus.", Clinical and experimental medicine, vol. 23, issue 8, pp. 5063-5088, 2023. Abstract

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.

Nassar, A., A. - R. N. Zekri, M. M. Kamel, M. H. Elberry, M. M. Lotfy, M. G. Seadawy, Z. K. Hassan, H. K. Soliman, A. M. Lymona, and A. S. E. - D. Youssef, "Frequency of Pathogenic Germline Mutations in Early and Late Onset Familial Breast Cancer Patients Using Multi-Gene Panel Sequencing: An Egyptian Study.", Genes, vol. 14, issue 1, 2022. Abstract

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: , , , , , , , , , , and . Thirty-one patients (30.6%) had mutations and twenty (19.8%) had mutations. Our results showed that exon 10 and exon 11 harbored 3 and 5 mutations, respectively, in and genes. Our analysis also revealed that the gene significantly co-occurred with each of the gene ( = 0.003, event ratio 11/21), the gene ( = 0.01, 4/10), the gene ( = 0.02, 4/11), and the gene ( = 0.04, 4/12). In addition, the gene significantly co-occurred with the gene ( = 0.01, 3/7). Furthermore, there was a significant mutually exclusive event between the gene and the gene ( = 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 , , and 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.

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