Biology subjects

Ahmed, E.

Publications and source records attributed to Ahmed, E..

9 recordsLinked to original sources

bioRxiv2026

Inflammation-driven reprogramming of goblet cells underlies the onset of serrated adenomas in colon cancer

In the context of inflammation, fully committed and post-mitotic cell lineages can initiate intestinal tumorigenesis in the mouse through dedifferentiation and acquisition of revival stem cell (RSC) features1,2. Likewise, by means of machine-learning analysis of whole-genome mutation spectra, the secretory goblet cell was predicted as the most frequent cell-of-origin (COO) of colon cancer in inflammatory bowel disease (IBD) patients2. Of note, even among sporadic (non-IBD) colon cancer patients, goblet cells were predicted as the most common differentiated COO of cancer in the colonic epithelium2, suggestive of the main role played by diet-induced inflammation in the onset of a large proportion of malignancies of the large bowel. However, how goblet cells respond to inflammation and reprogram their identity to become potential tumor-initiating cells remains unclear. Here, by taking advantage of publicly available single-cell RNAseq data from colonic tissues of ulcerative colitis (UC) patients3, we have characterized the inflammation-driven reprogramming of goblet cells. By means of an RNA velocity-based computational approach, we show that the mucus-producing goblet cells acquire an aberrant proliferative state earmarked by MUC5AC+ expression. Trajectory analysis of serrated adenoma cells4 reveal aberrant goblet cells as an intermediate state in the transition to revival stem cells, notably more common in BRAF-mutant cases. In support of these findings, COO predictions using whole-genome mutation spectra from a cohort of sporadic colon cancers5 connect tumors with a predicted goblet origin to BRAF mutations and reveal transcriptional remnants of the aberrant goblet cell state.

Cancer Biology↗

bioRxiv2025

Tracking breast cancer progression using Methylscape

Cancer progression is intricately driven by epigenetic reprogramming, where aberrant DNA methylation patterns reshape gene regulation and cellular phenotypes. These alterations include promoter hypermethylation of tumour suppressor genes and global hypomethylation, collectively fuelling oncogenesis and disease advancement. We previously introduced the Methylscape--a distinct cancer-specific DNA methylation landscape characterized by clustered promoter hypermethylation and gene body hypomethylation--that enhances DNAs physical affinity for gold surfaces. In this study, we demonstrate that Methylscape can be leveraged to monitor cancer progression. Using a breast cancer epithelial-mesenchymal transition (EMT) model, we observe an increase in Methylscape enrichment of mesenchymal-state DNA during EMT, suggesting that this method can sensitively detect subtle epigenetic remodelling linked to tumour progression. Using a gold-based DNA desorption enrichment strategy coupled with methylation sequencing and qPCR, we show that hypermethylated regions are preferentially enriched. Finally, we developed a low-cost, disposable screen-printed electrode platform for stage-specific breast cancer monitoring. Together, these findings establish Methylscape as a promising biophysical biomarker for non-invasive and real-time monitoring of cancer progression, advancing its potential for clinical translation.

bioengineering↗

bioRxiv2023

Human airway ex vivo models: new tools to study the airway epithelial cell response to SARS-CoV-2 infection

Airway-liquid interface cultures of primary epithelial cells and of induced pluripotent stem cell-derived airway epithelial cells (ALI and iALI, respectively) are physiologically relevant models for respiratory virus infection studies because they can mimic the in vivo human bronchial epithelium. Here, we investigated gene expression profiles in human airway cultures (ALI and iALI models) infected or not with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using publicly available and our own bulk and single-cell transcriptome datasets. SARS-CoV-2 infection significantly increased the expression of interferon-stimulated genes (IFI44, IFIT1, IFIT3, IFI35, IRF9, MX1, OAS1, OAS3 and ISG15) and inflammatory genes (NFKBIA, CSF1, FOSL1, IL32 and CXCL10) at day 4 post-infection, indicating activation of the interferon and immune responses to the virus. Extracellular matrix genes (ITGB6, ITGB1 and GJA1) also were altered in infected cells. Single-cell RNA sequencing data revealed that SARS-CoV-2 infection damaged the respiratory epithelium, particularly mature ciliated cells. The expression of genes encoding intercellular communication and adhesion proteins also was deregulated, suggesting a mechanism to promote shedding of infected epithelial cells. These data demonstrate that ALI/iALI models help to understand the airway epithelium response to SARS-CoV-2 infection and are a key tool for developing COVID-19 treatments.

cell biology↗

bioRxiv2021

The Immune landscape of solid pediatric tumors.

BackgroundImmunotherapy is quickly coming to the forefront of cancer treatment; however, the implementation of immunotherapy in solid pediatric cancers, which classically display a low mutational load, is hindered by insufficient understanding of the determinants of cancer immune responsiveness in children. In order to better understand tumor-host interplay, we sought to characterize solid pediatric cancers based on immunological parameters using analytes extracted from gene expression data. MethodsWe used RNAseq data from the publicly available TARGET studies for five pediatric solid tumor types (408 patients): Wilms tumor (WT), neuroblastoma (NBL), osteosarcoma (OS), clear cell sarcoma of the kidney (CCSK) and rhabdoid tumor of the kidney (RT). We assessed the performance of previously identified immune signatures like the Immunologic Constant of Rejection (ICR), which captures an active Th1/cytotoxic response associated with favorable prognosis and responsiveness to immunotherapy. We also performed gene set enrichment analysis (ssGSEA) and clustering, using more than 100 immune signatures to define immune subtypes in pediatric tumors and compared the overall survival across subtypes. The expression of immune checkpoints and enrichment of oncogenic pathways were also assessed across the immune subtypes. ResultsThe five tumor types showed distinct ICR score distributions. A higher ICR score was associated with better survival in OS and NBL-HR-MYCN_NA, but with poorer survival in WT. The clustering of immune signatures revealed the same five principal modules observed in adult solid tumors: Wound Healing, TGF-B signaling, IFN-G signaling, Macrophages, and Lymphocytes. These modules clustered pediatric patients into six immune subtypes (S1-S6) with distinct survival outcomes. The S2 cluster showed the best overall survival and was characterized by low enrichment of the wound healing signature, high Th1, low Th2. Conversely, cluster S4 showed the worst survival and highest enrichment of wound healing signature, low Th1, and high Th2. Furthermore, the upregulation of the WNT/Beta-catenin pathway is associated with unfavorable outcomes and lack of T-cell infiltration in OS. ConclusionsWe demonstrated that extracranial solid pediatric tumors could be classified according to their immune disposition, unveiling similarity with adults tumors. Immunological parameters might be explored to refine diagnostic and prognostic biomarkers and to identify potential immune-responsive tumors.

cancer biology↗

bioRxiv2020

Differentiation of human induced pluripotent stem cells into functional airway epithelium

RationaleHighly reproducible in vitro generation of human bronchial epithelium from pluripotent stem cells is an unmet key goal for drug screening to treat lung diseases. The possibility of using induced pluripotent stem cells (hiPSC) to model normal and diseased tissue in vitro from a simple blood sample will reshape drug discovery for chronic lung, monogenic and infectious diseases. MethodsWe devised a simple and reliable method that drives a blood sample reprogrammed into hiPSC subsequently differentiated within 45 days into air-liquid interface bronchial epithelium (iALI), through key developmental stages, definitive-endoderm (DE) and Ventralized-Anterior-Foregut-Endoderm (vAFE) cells. ResultsReprogramming blood cells from one healthy and 3 COPD patients, and from skin-derived fibroblasts obtained in one PCD patient, succeeded in 100% of samples using Sendai viruses. Mean cell purity at DE and vAFE stages was greater than 80%, assessed by expression of CXCR4 and NKX2.1, avoiding the need of cell sorting. When transferred to ALI conditions, vAFE cells reliably differentiated within 4 weeks into bronchial epithelium with large zones covered by beating ciliated, basal, goblets, club cells and neuroendocrine cells as found in vivo. Benchmarking all culture conditions including hiPSCs adaptation to single-cell passaging, cell density and differentiation induction timing allowed for consistently producing iALI bronchial epithelium from the five hiPSC lines. ConclusionsReliable reprogramming and differentiation of blood-derived hiPSCs into mature and functional iALI bronchial epithelium is ready for wider use and this will allow better understanding lung disease pathogenesis and accelerating the development of novel gene therapies and drug discovery.

bioengineering↗

bioRxiv2019

Recurrent genetic abnormalities in human pluripotent stem cells: definition and routine detection in culture supernatant by targeted droplet digital PCR

Genomic integrity of human pluripotent stem cells (hPSCs) is essential for research and clinical applications. However, genetic abnormalities can accumulate during hPSC generation and routine culture and following gene editing. Their occurrence should be routinely monitored, but the current assays to assess hPSC genomic integrity are not fully suitable for suchregular screening. To address this issue, we first carried out a large meta-analysis of all hPSC genetic abnormalities reported in more than 100 publications and identified 738 recurrent genetic abnormalities (i.e., overlapping abnormalities found in at least five distinct scientific publications). We then developed a test based on the droplet digital PCR technology that can potentially detect 94.3% of these hPSC recurrent genetic abnormalities in DNA extracted from culture supernatant samples. This test can be used to routinely screen genomic integrity in hPSCs.

cell biology↗

bioRxiv2019

S. cerevisiae Srs2 helicase ensures normal recombination intermediate metabolism during meiosis and prevents accumulation of Rad51 aggregates

We investigated the meiotic role of Srs2, a multi-functional DNA helicase/translocase that destabilizes Rad51-DNA filaments, and is thought to regulate strand invasion and prevent hyper-recombination during the mitotic cell cycle. We find that Srs2 activity is required for normal meiotic progression and spore viability. A significant fraction of srs2 mutant cells progress through both meiotic divisions without separating the bulk of their chromatin, although sister centromeres often separate. Undivided nuclei contain aggregates of Rad51 colocalized with the ssDNA-binding protein RPA, suggesting the presence of persistent single-strand DNA. Rad51 aggregate formation requires Spo11-induced DSBs, Rad51 strand-invasion activity, and progression past the pachytene stage of meiosis, but not the DSB end-resection or the bias towards inter-homologue strand invasion characteristic of normal meiosis. srs2 mutants also display altered meiotic recombination intermediate metabolism, revealed by defects in the formation of stable joint molecules. We suggest that Srs2, by limiting Rad51 accumulation on DNA, prevents the formation of aberrant recombination intermediates that otherwise would persist and interfere with normal chromosome segregation and nuclear division.

genetics↗

bioRxiv2018

Immunoinformatics Prediction of Epitope Based Peptide Vaccine Against Madurella mycetomatis Translationally Controlled Tumor Protein

BackgroundMadurella. mycetomatis is most common causative agent of mycetoma in Sudan and worldwide. No vaccines are available till now so design of effective vaccine is essential as protection tool. Peptide vaccine can overcome the common side effects of the conventional vaccines. The aim of this study was to design peptide based vaccine for M.Mycetomatis Translationally Controlled Tumor Protein (TCTP) using immunoinformatics tools.\n\nMaterials and methodsTCTP sequences were retrieved from NCBI and then processed using BioEdit program to determine conserved regions and different immunoinformatics tools from IEDB. Population coverage analysis was performed for the most promising epitopes. Homology modelling was performed to show their structural positions in TCTP. Protein analysis was done using Expasy (ProtParamsotware).\n\nResults and conclusionFour epitopes passed the Bepipred, Emini, Kolaskar and Tongaonkar tools. 111 epitopes were predicted to interact with MHCI alleles with IC50 < 500 nM, three of them were most promising. 274 predicted epitopes were interacted with MHCII alleles with IC50 < 100 nM, four of them were most promising. The epitope (YMKSVKKAL) was the most promising one concerning its binding with MHCI alleles, while (FRLQSTSFD) was the most promising for MHC II. The epitope (YLKAYMKSV) is shared betweenMHC I and II. For the population coverage of M. Mycetomatis TCTP vaccine Sudan (90.39%) had the highest percentage for MHC I. This is the first computational vaccinology study conducted in mycetoma caused by M. Mycetomatis using TCTP.

bioinformatics↗

bioRxiv2018

Household Transmission Study of Cryptosporidiosis in Bangladesh

BackgroundCryptosporidium, an apicomplexan protozoa, is a leading contributor to diarrheal morbidity and mortality in children under five years old worldwide. As there is no vaccine and no approved drug for Cryptosporidium spp. in young children, preventing parasite transmission is crucial. We undertook a pilot case-control study to define the extent of person-to-person transmission of cryptosporidiosis within families in an urban and rural community in Bangladesh.\n\nMethodsWe enrolled 48 case families with a Cryptosporidium-infected child aged 6-18 months. Controls were age-sex matched Cryptosporidium-negative children (n=12). Once children were identified, we enrolled all household members. We then followed these individuals for 8 weeks, with weekly surveillance stools and testing with qPCR for Cryptosporidium spp.\n\nFindingsIn the 48 case families, the rate of secondary infections with Cryptosporidium was 18.6% (22/118) compared to 0 new infections (0/35) in the 12 control families. In the 22 urban Mirpur households, the secondary attack rate was 30% (18/60) in cases compared to 0% (0/14) in controls (chi-square p = 0.018). In contrast, in the 21 rural Mirzapur households, the secondary attack rate was 6.9% (4/58) in case households compared to 0% (0/21) in controls (chi-square p = 0.22). Genotyping by gp60 demonstrated infection with the same subspecies in five of six families. Serologic response to Cryptosporidium infection was associated with younger age, longer duration of infection, and C hominis gp60_IbA9G3R2 infection.\n\nInterpretationThe high rate of secondary infection in Mirpur suggests that person-to-person transmission is likely a major source of Cryptosporidium infection for young children living in this region. GP 60 genotyping demonstrated direction of infection in 2 households, and concurrent infection in five households. Further work is needed to understand the differences in parasite transmissibility and immunity to different genotypes.

microbiology↗