Biology subjects

Jakalski, M.

Publications and source records attributed to Jakalski, M..

5 recordsLinked to original sources

bioRxiv2026

Spatial Transcriptomics of TNBC tumours and corresponding lymph node metastasis reveals immune hubs driven by TNF/NF-κB signalling of TMSB4X and CD74 expressing cells.

PurposeLymph node metastasis is a critical prognostic factor in triple-negative breast cancer (TNBC), but the spatial organization of signalling networks driving metastatic colonization and persistence remains poorly defined. Understanding these networks may reveal therapeutic vulnerabilities in metastatic TNBC. MethodsWe applied Visium spatial transcriptomics to paired primary tumours and lymph node metastases from four TNBC patients. Spatial gene expression profiles were analysed using trajectory inference, cell-type deconvolution, and cell-cell communication mapping. Results were validated in independent single-cell RNA sequencing datasets from TNBC tumours and lymph node metastases. ResultsTMSB4X and CD74 emerged as key drivers of metastasis-associated transcriptional programs, defining spatially distinct immune communication hubs enriched in myeloid, stromal, and endothelial cells. These hubs preferentially activated NF-{kappa}B/TNF signalling alongside PI3K-Akt and Rap1 pathways. In primary tumours, NF-{kappa}B/TNF signalling was confined to localized immune hubs, whereas lymph node metastases exhibited widespread signalling across cellular compartments with additional IL-1 pathway activation. This spatial rewiring coincided with endothelial cells assuming central coordinating roles in metastatic lesions. Independent validation confirmed myeloid-endothelial crosstalk as a conserved feature of TNBC, with TMSB4X-CD74 programs enriched in clinically relevant immune and vascular subpopulations. ConclusionTNBC lymph node metastases display spatially expanded inflammatory networks centred on TMSB4X-CD74 immune hubs. Metastatic progression involves coordinated myeloid-endothelial signalling, suggesting these pathways as potential biomarkers and therapeutic targets. Disrupting inflammatory and vascular communication networks may offer a strategy to prevent metastatic persistence and overcome therapy resistance in TNBC.

molecular biology↗

bioRxiv2025

The effect of cold ischemia time on hypoxia, EMT, and apoptosis pathways in normal colon mucosa

Cold ischemia time (CIT), the interval between tissue excision and preservation, is a critical preanalytical variable that profoundly impacts gene expression profiles. Variability in CIT can lead to inconsistent transcriptomic results, making study interpretation challenging and undermining reproducibility in biomedical research. Our study aimed to evaluate the impact of CIT on the expression of cancer-related genes, particularly these involved in hypoxia, apoptosis, and epithelial-to-mesenchymal transition (EMT). We performed RNA sequencing on 54 normal colon mucosa samples from nine patients undergoing colorectal cancer surgeries, freezing samples at predefined intervals ranging from 0 to 60 minutes. A total of 44 differentially expressed genes (DEGs) (p < 0.05) were identified when comparing samples frozen immediately (T0) with those frozen after 60 minutes (T5). These DEGs were further analyzed through functional and pathway enrichment analyses and weighted gene coexpression network analysis (WGCNA). The enrichment analysis revealed significant alterations in pathways associated with apoptosis, hypoxia, EMT, and cancer progression, including p53 and HIF-1 signaling. WGCNA highlighted two co-expressed gene modules: ME2, which showed downregulation of apoptosis-related genes, and ME4, linked to apoptosis and cellular metabolism. Our findings highlight CIT as a critical preanalytical variable, showing that prolonged ischemia can induce transcriptomic changes that may mimic malignancy, and potentially confound research outcomes. To minimize such effects, we recommend keeping CIT under 45-60 minutes.

cancer biology↗

bioRxiv2024

Prelude to Malignancy: A Gene Expression Signature in Normal Mammary Gland from Breast Cancer Patients Suggests Pre-tumorous Alterations and Is Associated with Adverse Outcomes

Despite advances in early detection and treatment strategies, breast cancer recurrence and mortality remain a significant health issue. Recent insights suggest the prognostic potential of microscopically healthy mammary gland, in the vicinity of the breast lesion. Nonetheless, a comprehensive understanding of the gene expression profiles in these tissues and their relationship to patient outcomes is still missing. Furthermore, the increasing trend towards breast-conserving surgery may inadvertently lead to the retention of existing cancer-predisposing mutations within the normal mammary gland. This study assessed the transcriptomic profiles of 242 samples from 83 breast cancer patients with unfavorable outcomes, including paired uninvolved mammary gland samples collected at varying distances from primary lesions. As a reference, control samples from 53 mammoplasty individuals without cancer history were studied. A custom panel of 634 genes linked to breast cancer progression and metastasis was employed for expression profiling, followed by whole-transcriptome verification experiments and statistical analyses to discern molecular signatures and their clinical relevance. A distinct gene expression signature was identified in uninvolved mammary gland samples, featuring key cellular components encoding keratins, CDH1, CDH3, EPCAM cell adhesion proteins, matrix metallopeptidases, oncogenes, tumor suppressors, along with crucial genes (FOXA1, RAB25, NRG1, SPDEF, TRIM29, and GABRP) having dual roles in cancer. Enrichment analyses revealed disruptions in epithelial integrity, cell adhesion, and estrogen signaling. This signature, named KAOS for Keratin-Adhesion-Oncogenes-Suppressors, was significantly associated with reduced tumor size but increased mortality rates. Integrating molecular assessment of non-malignant mammary tissue into disease management could enhance survival prediction and facilitate personalized patient care.

genomics↗

bioRxiv2022

Size matters - the impact of nucleus size on results from spatial transcriptomics

Visium Spatial Gene Expression (ST) is a method combining histological spatial information with transcriptomics profiles directly from tissue sections. The use of spatial information has made it possible to discover novel modes of gene expression regulations. However, in the ST experiment, the nucleus size of cells may exceed the thickness of a tissue slice. This may, in turn, negatively affect comprehensive capturing the transcriptomics profile in a single slice, especially for tissues having large differences in the size of nuclei. Here, we defined the effect of Consecutive Slices Data Integration (CSDI) on results from spatial transcriptomic study of human postmortem brains. CSDI can be applied to investigate consecutive sections studied with ST in the human cerebral cortex, avoiding misinterpretation of spot clustering and annotation, increasing accuracy of cell recognition as well as improvement in uncovering the layers of grey matter in the human brain.

bioinformatics↗

bioRxiv2020

The genomic impact of mycoheterotrophy: targeted gene losses but extensive expression reprogramming.

ABSTRACTMycoheterotrophic plants have lost the ability to photosynthesize and they parasitize their associated fungus to get the mineral and organic nutrients they need. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy occurred independently in almost all major lineages of land plants, but most often in Orchidaceae. Yet the molecular mechanisms underlying this shift are still poorly understood. The comparison of the transcriptomes of Epipogium aphyllum and Neottia nidus-avis, two mycoheterotrophic orchids, to other autotrophic and mycoheterotrophic orchids showed massive molecular function losses restricted to photosynthetic activities. In addition to these targeted losses, the analysis of their expression profiles showed that many orthologs had inverted root/shoot ratios compared to autotrophic species. Fatty acid and amino acid biosynthesis as well as primary cell wall metabolism were among the pathways most impacted by this expression reprogramming. Our study suggests that, while associated with function losses rather than metabolic innovations, the shift in nutritional mode from autotrophy to mycoheterotrophy remodeled the architecture of the plant metabolism.View Full Text

plant biology↗