Almoatazbellah Youssef

Malignant pleural mesothelioma (MPM) is an aggressive asbestos-linked cancer with limited therapeutic options and a dismal 5-year survival rate of ~5%. While aberrant production of reactive oxygen and nitrogen species (ROS/RNS) is a hallmark of MPM, targeted approaches to exploit these redox vulnerabilities remain scarce. Here, using the MOSAIC multimodal cancer patient atlas, we identify Peroxiredoxin 5 (PRDX5) as being significantly upregulated in the epithelioid subtype of MPM. We show that MPM cells exhibit enhanced resistance to nitrosative and oxidative stress compared to healthy mesothelial cells, a phenotype correlated with basal PRDX5 expression. Next, utilising a machine learning guided discovery pipeline, we identified three putative allosteric pockets in PRDX5 and conducted a virtual screen of 3.6 million compounds. High-throughput biochemical validation of 452 candidates yielded 36 non-covalent hits, including sub-micromolar inhibitors. These findings establish PRDX5 as a novel, subtype specific therapeutic target in MPM and provide a chemical framework for the development of next-generation redox-modulating oncology treatments.

Emerging high-throughput sequencing technologies promise lower costs and higher scalability, yet their performance on archival clinical samples remains poorly characterized. Here, we benchmarked Ultima Genomics UG100 against Illumina Novaseq platforms across single-nuclei RNA-seq (snRNA-seq), whole-transcriptome (WTS), whole-exome (WES), and whole-genome sequencing (WGS) using FFPE tissues from oncologic and immune-mediated diseases. Across matched samples, we systematically assessed data quality, coverage profiles, error spectra, variant concordance and transcriptomic reproducibility. UG100 produced highly comparable results to Illumina, capturing key oncogenic and immune-related transcripts, accurately resolving cellular composition in snRNA-seq, and maintaining sensitivity for lowly expressed genes, despite characteristic insertion-biased indels and modest differences in multi-mapping reads. Discrepancies were subtle, largely limited to pseudogene and non-coding transcripts, and did not affect pathway-level conclusions. Ultima UG100 platform prioritized high precision and reduced low-frequency artifacts, offering a cleaner but more conservative variant-calling profile compared to the more sensitive, yet noisier, Illumina/DRAGEN workflow. This multimodal, clinically oriented assessment provides the first comprehensive evaluation of UG100, demonstrating its translational utility in population-scale genomics, and highlighting the potential for emerging sequencing technologies to lower the cost of biomedical research and clinical diagnostics.

Background: Glioblastoma (GBM), the most aggressive primary brain tumor, has a median survival of approximately 15 months. Twenty percent of patients survive beyond three years, but known clinical factors like age, performance status, resection extent, and MGMT promoter methylation status do not fully explain the observed outcomes. Objective: Our objective was to identify novel histology derived biomarkers associated with end-of-spectrum overall survival (OS) to provide novel biological insight with a translational potential. Methods: We analyzed a total of 748 GBM patients from 3 different cohorts, uniquely enriched in long survivors (n=98 with overall survival (OS) > 5y including n=196 with OS≥3y), with clinical data and H&E slides obtained from the primary tumor at baseline. We propose an interpretable machine learning (ML) methodology for the discovery of histological biomarkers. Our method learned to segment each H&E slide into three distinct regions associated with long-term survival, short-term survival, and non-informative tissue. We characterized these regions by integrating unsupervised learning, nuclei segmentation, blood vessels detection, pathologist annotations, and multimodal data including spatial transcriptomics from n=31 patients of the GBM MOSAIC dataset to discover fully interpretable biomarkers. Results: Our OS prediction model using histology and clinical data as input achieved an area under the curve (AUC) of 0.85 for the classification of patients between OSPLIN2 expression and lipid accumulation- is consistently enriched in histological areas predictive of poor prognosis. Conclusion: Our interpretable ML methodology identified a novel prognostic impact of biological processes and cell types according to distinct tumor regions of GBM. These results pave the way for spatially-informed biomarkers to improve risk stratification and for personalized spatially-targeted therapeutic strategies. Key highlights: Our ML model identified histological biomarkers predicting prognosis independently from known clinical factors The region of lowly infiltrated white matter enriched in malignant cells including a mesenchymal-like phenotype is predictive of poor prognosis Angiogenesis is increased in areas predictive of long survival in main non-necrotic tumor regions. The subtype of macrophages expressing PLIN2 and associated with increased lipid metabolism was associated with poor prognosis in all GBM regions. Highlights:

Salivary gland tumors (SGTs) are a relevant, highly diverse subgroup of head and neck tumors whose entity determination can be difficult. Confocal Raman imaging in combination with multivariate data analysis may possibly support their correct classification. For the analysis of the translational potential of Raman imaging in SGT determination, a multi-stage evaluation process is necessary. By measuring a sample set of Warthin tumor, pleomorphic adenoma and non-tumor salivary gland tissue, Raman data were obtained and a thorough Raman band analysis was performed. This evaluation revealed highly overlapping Raman patterns with only minor spectral differences. Consequently, a principal component analysis (PCA) was calculated and further combined with a discriminant analysis (DA) to enable the best possible distinction. The PCA-DA model was characterized by accuracy, sensitivity, selectivity and precision values above 90% and validated by predicting model-unknown Raman spectra, of which 93% were classified correctly. Thus, we state our PCA-DA to be suitable for parotid tumor and non-salivary salivary gland tissue discrimination and prediction. For evaluation of the translational potential, further validation steps are necessary.

Telepathology facilitates histological diagnoses through sharing expertise between pathologists. However, the associated costs are high and frequently prohibitive, especially in low-resource settings, where telepathology would paradoxically be of paramount importance due to a paucity of pathologists.We have constructed a telepathology system (TelePi) with a budget of < €120 using the small, single-board computer Raspberry Pi Zero and its High-Quality Camera Module in conjunction with a standard microscope and open-source software. The system requires no maintenance costs or service contracts, has a small footprint, can be moved and shared across several microscopes, and is independent from other computer operating systems. TelePi uses a responsive and high-resolution web-based live stream which allows remote consultation between two or more locations. TelePi can serve as a telepathology system for remote diagnostics of frozen sections. Additionally, it can be used as a standard microscope camera for teaching of medical students and for basic research. The quality of the TelePi system compared favorable to a commercially available telepathology system that exceed its cost by more than 125-fold. Additionally, still images are of publication quality equal to that of a whole slide scanner that costs 800 times more.In summary, TelePi is an affordable, versatile, and inexpensive camera system that potentially enables telepathology in low-resource settings without sacrificing image quality.

Telepathology facilitates histological diagnoses through sharing expertise between pathologists, with added benefits in terms of teaching and potential research collaborations. However, the associated costs are high and frequently prohibitive, especially in low-resource settings, where telepathology would paradoxically be of paramount importance due to a paucity of pathologists. We have constructed a telepathology system (TelePi) with a budget of < 120 € using the small, single-board computer Raspberry Pi Zero and its High-Quality Camera Module in conjunction with a standard microscope and open-source software on a Linux operating system. The system requires no additional hardware parts, maintenance costs or service contracts, has a small footprint, can be moved and shared across several microscopes, and is independent from other computer operating systems. TelePi uses a responsive and high-resolution web-based live stream which allows remote consultation between two or more locations. TelePi has several potential usage scenarios. It can serve as a telepathology system for remote diagnostics of frozen sections. Additionally, it can be used as a standard microscope camera for teaching of medical students and for basic research. When paired with the open-source image analysis package Fiji, it allows for stitching of multiple images taken at high resolution into one large image that exceeds the field of view of the chosen objective. The quality of the TelePi system compared favorable to a commercially available telepathology system that exceed its cost by more than 125-fold. Additionally, still images are of publication quality equal to that of a whole slide scanner that costs 800 times more. In summary, TelePi is an affordable, versatile, and inexpensive camera system that potentially enables telepathology in low-resource settings without sacrificing image quality.

Due to the wide variety of benign and malignant salivary gland tumors, classification and malignant behavior determination based on histomorphological criteria can be difficult and sometimes impossible. Spectroscopical procedures can acquire molecular biological information without destroying the tissue within the measurement processes. Since several tissue preparation procedures exist, our study investigated the impact of these preparations on the chemical composition of healthy and tumorous salivary gland tissue by Fourier-transform infrared (FTIR) microspectroscopy. Sequential tissue cross-sections were prepared from native, formalin-fixed and formalin-fixed paraffin-embedded (FFPE) tissue and analyzed. The FFPE cross-sections were dewaxed and remeasured. By using principal component analysis (PCA) combined with a discriminant analysis (DA), robust models for the distinction of sample preparations were built individually for each parotid tissue type. As a result, the PCA-DA model evaluation showed a high similarity between native and formalin-fixed tissues based on their chemical composition. Thus, formalin-fixed tissues are highly representative of the native samples and facilitate a transfer from scientific laboratory analysis into the clinical routine due to their robust nature. Furthermore, the dewaxing of the cross-sections entails the loss of molecular information. Our study successfully demonstrated how FTIR microspectroscopy can be used as a powerful tool within existing clinical workflows.