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. 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.

El-Sherbiny, G. M., M. H. Kalaba, A. M. Foda, S. M E, A. S. E. - D. Youssef, I. A Elsehemy, E. E. Farghal, and E. M. El-Fakharany, "Nanoemulsion of cinnamon oil to combat colistin-resistant Klebsiella pneumoniae and cancer cells.", Microbial pathogenesis, vol. 192, pp. 106705, 2024. Abstract

This study aimed to investigate the potential of cinnamon oil nanoemulsion (CONE) as an antibacterial agent against clinical strains of colistin-resistant Klebsiella pneumoniae and its anticancer activity. The prepared and characterized CONE was found to have a spherical shape with an average size of 70.6 ± 28.3 nm under TEM and a PDI value of 0.076 and zeta potential value of 6.9 mV using DLS analysis. The antibacterial activity of CONE against Klebsiella pneumoniae strains was investigated, and it was found to have higher inhibitory activity (18.3 ± 1.2-30.3 ± 0.8 mm) against the tested bacteria compared to bulk cinnamon oil (14.6 ± 0.88-20.6 ± 1.2) with MIC values ranging from 0.077 to 0.31 % v/v which equivalent to 0.2-0.82 ng/ml of CONE. CONE inhibited the growth of bacteria in a dose and time-dependent manner based on the time-kill assay in which Klebsiella pneumoniae B-9 was used as a model among the bacterial strains under investigation. The study also investigated the expression of the mcr-1 gene in the Klebsiella pneumoniae strains and found that all strains were positive for the gene expression and subsequently its presence. The level of mcr-1 gene expression among the B-2, B-4, B-9, and B-11 control strains and that treated with colistin was similar, but it was different in both B-5 and B-2. However, all strains exhibited a significant downregulation in gene expression (ranging from 3.97 to 8.7-fold) after their treatment with CONE. Additionally, the CONE-treated bacterial cells appeared with a great deformation compared with control cells under TEM. Finally, CONE exhibited selective toxicity against different cancer cell lines depending on comparison with the normal cell lines.

Abdullah, N. H., N. A. Elbialy, M. A. Amer, M. K. Gabr, A. S. E. - D. Youssef, M. H. Sharaf, M. E. Shehata, M. H. Kalaba, and E. R. S. Soliman, "Iron/Copper/Phosphate nanocomposite as antimicrobial, antisnail, and wheat growth-promoting agent.", BMC biotechnology, vol. 24, issue 1, pp. 11, 2024. Abstract

BACKGROUND: One of the current challenges is to secure wheat crop production to meet the increasing global food demand and to face the increase in its purchasing power. Therefore, the current study aimed to exploit a new synthesized nanocomposite to enhance wheat growth under both normal and drought regime. The effectiveness of this nanocomposite in improving the microbiological quality of irrigation water and inhibiting the snail's growth was also assessed.

RESULTS: Upon the employed one-step synthesis process, a spherical Fe/Cu/P nanocomposite was obtained with a mean particle size of 4.35 ± 1.524 nm. Cu, Fe, and P were detected in the dried nanocomposite at 14.533 ± 0.176, 5.200 ± 0.208, and 34.167 ± 0.203 mg/ml concentration, respectively. This nanocomposite was found to exert antibacterial activity against Escherichia coli and Salmonella typhi. It caused good inhibition percent against Fusarium oxysporum (43.5 ± 1.47%) and reduced both its germination rate and germination efficiency. The lethal concentration 50 (LC of this nanocomposite against Lanistes carinatus snails was 76 ppm. The treated snails showed disturbance in their feeding habit and reached the prevention state. Significant histological changes were observed in snail digestive tract and male and female gonads. Drought stress on wheat's growth was mitigated in response to 100 and 300 ppm treatments. An increase in all assessed growth parameters was reported, mainly in the case of 100 ppm treatment under both standard and drought regimes. Compared to control plants, this stimulative effect was accompanied by a 2.12-fold rise in mitotic index and a 3.2-fold increase in total chromosomal abnormalities.

CONCLUSION: The finding of the current study could be employed to mitigate the effect of drought stress on wheat growth and to enhance the microbiological quality of irrigation water. This is due to the increased efficacy of the newly synthesized Fe/Cu/P nanocomposite against bacteria, fungi, and snails. This methodology exhibits potential for promoting sustainable wheat growth and water resource conservation.

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.

Nassar, A., A. R. N. Zekri, M. H. Elberry, A. M. Lymona, M. M. Lotfy, M. Abouelhoda, and A. S. E. - D. Youssef, "Somatic Mutations Alter Interleukin Signaling Pathways in Grade II Invasive Breast Cancer Patients: An Egyptian Experience.", Current issues in molecular biology, vol. 44, issue 12, pp. 5890-5901, 2022. Abstract

This study aimed to investigate the impact of somatic mutations on various interleukin signaling pathways associated with grade II invasive breast cancer (BC) in Egyptian patients to broaden our understanding of their role in promoting carcinogenesis. Fifty-five grade II invasive BC patients were included in this study. Data for somatic mutations in 45 BC patients were already available from a previous study. Data for somatic mutations of 10 new BC patients were included in the current study. Somatic mutations were identified using targeted next-generation sequencing (NGS) to study their involvement in interleukin signaling pathways. For pathway analysis, we used ingenuity variant analysis (IVA) to identify the most significantly altered pathways. We identified somatic mutations in components of the interleukin-2, interleukin-6, and inter-leukin-7 signaling pathways, including mutations in , and genes. Interestingly, six mutations which were likely to be novel deleterious were identified: two in the gene, two in the gene, and one in each of the and genes. According to IVA analysis, interleukin 2, interleukin 6, and interleukin 7 signaling pathways were the most altered in 34.5%, 29%, and 23.6% of our BC group, respectively. Our multigene panel sequencing analysis reveals that our BC patients have altered interleukin signaling pathways. So, these results highlight the prominent role of interleukins in the carcinogenesis process and suggest its potential role as promising candidates for personalized therapy in Egyptian 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.

Youssef, A. S. E. - D., M. A. Abdel-Fattah, M. M. Lotfy, A. Nassar, M. Abouelhoda, A. O. Touny, Z. K. Hassan, M. M. Eldin, A. A. Bahnassy, H. Khaled, et al., "Multigene Panel Sequencing Reveals Cancer-Specific and Common Somatic Mutations in Colorectal Cancer Patients: An Egyptian Experience.", Current issues in molecular biology, vol. 44, issue 3, pp. 1332-1352, 2022. Abstract

This study aims at identifying common pathogenic somatic mutations at different stages of colorectal carcinogenesis in Egyptian patients. Our cohort included colonoscopic biopsies collected from 120 patients: 20 biopsies from patients with inflammatory bowel disease, 38 from colonic polyp patients, and 62 from patients with colorectal cancer. On top of this, the cohort included 20 biopsies from patients with non-specific mild to moderated colitis. Targeted DNA sequencing using a customized gene panel of 96 colorectal related genes running on the Ion Torrent NGS technology was used to process the samples. Our results revealed that 69% of all cases harbored at least one somatic mutation. Fifty-seven genes were found to carry 232 somatic non-synonymous variants. The most frequently pathogenic somatic mutations were localized in , , , and In total, 16 somatic mutations were detected in the CRC group and in either the IBD or CP group. In addition, our data showed that 51% of total somatic variants were CRC-specific variants. The average number of CRC-specific variants per sample is 2.4. The top genes carrying CRC-specific mutations are , , , , , and It seems obvious that and genes were the most affected genes with somatic mutations in all groups. Of interest, 85% and 28% of the and deleterious somatic mutations were located in Exon 14 and Exon 3, respectively. Besides, 37% and 28% of the total somatic mutations identified in and were CRC-specific variants, respectively. Moreover, we identified that, in 29 somatic mutations in 21 genes, their association with CRC patients was unprecedented. Ten detected variants were likely to be novel: six in and four variants in . The detected P53, Wnt/βcatenin, Angiogenesis, EGFR, TGF-β and Interleukin signaling pathways were the most altered pathways in 22%, 16%, 12%, 10%, 9% and 9% of the CRC patients, respectively. These results would contribute to a better understanding of the colorectal cancer and in introducing personalized therapies for Egyptian CRC patients.

ARN Zekri, World journal of gastroenterology 22(16), 4168, A. S. Youssef, Y. M. Bakr, R. M. Gabr, O. S. Ahmed, and M. H. Elberry, "Early detection of hepatocellular carcinoma co-occurring with hepatitis C virus infection: A mathematical model", World journal of gastroenterology, vol. 22, issue 16, pp. 4168, 2016. mathematical_paper_wjg.pdf
Zekri, A. R., A. S. Youssef, Y. M. Bakr, and R. M. Gabr, "Serum Biomarkers for Early Detection of Hepatocellular Carcinoma Associated with HCV Infection in Egyptian Patients", Asian Pac J Cancer Prev, vol. 16, issue 3, pp. 1281-1287, 2015.
Zekri, A. R., A. A. Nassar, M. N. El-Rouby, H. I. Shousha, A. B. Barakat, E. D. El-Desouky, N. A. Zayed, O. S. Ahmed, and A. S. Youssef, "Disease Progression from Chronic Hepatitis C to Cirrhosis and Hepatocellular Carcinoma is Associated with Increasing DNA Promoter Methylation", Asian Pac J Cancer Prev, vol. 14, issue 11, pp. 6721-6726., 2014.