Publications
Read below the 20 most recent publications from iCAN.
- by Nolan K NewmanMOTIVATION: Reconstructing and analyzing single-sample regulatory networks has proven useful for understanding mechanisms of regulatory biology and its disruption in disease, but traditionally required a fair amount of programming experience and work from the user.
- by Suitiala RoosaCONCLUSIONS: Most of the diabetic PC-patients have been diagnosed with DM within a close proximity of cancer diagnosis. The progression from diabetes to clinically detectable cancer seems to be rapid-less than 6 months. Given the aggressive nature of PC and the fact that NOD can be an early sign, screening may need to begin at […]
- by Joona PohjonenFoundation models are trained on massive amounts of data to capture complex patterns in images. Subsequently, a wide range of downstream tasks can be adopted with minimal computational resources. We have developed HistoEncoder, a foundation model for prostate cancer digital pathology by pre-training on 48 million prostate tissue tile images. HistoEncoder allows automated extraction of […]
- by D A PalmerRUNX1 is a critical regulator of hematopoiesis. In CML, somatic RUNX1 mutations and RUNX1::MECOM/EVI1, are associated with TKI resistance and progression to BP-CML. To examine post-transcriptional dysregulation downstream of RUNX1 aberrations, we used orthogonal organic phase separation to characterise the RNA-binding proteome of RUNX1 deficient BP-CML cells. RUNX1 depleted BP-CML cells exhibited significant alterations to […]
- by Lilianny Querino Rocha de OliveiraCONCLUSION: High SLC7A3 protein levels were associated with OSCC cell migration and invasion and improved disease-specific survival, suggesting its potential as an indicator of tumor aggressiveness and a promising prognostic potential.
- by Olegs BorodinsEpigenetic regulation and gene transcription are dynamically modulated by extracellular signals, including focal adhesions; however, the role of integrins in these processes remains poorly understood. In this study in HPV-negative head and neck squamous cell carcinoma, (HNSCC), we combined investigations in physiological three-dimensional, matrix-embedded cell models and patient-derived organoids with multi-omics analyses, bioinformatics and artificial […]
- by Naroa BarrenaAberrant metabolism, a hallmark of cancer, reveals vulnerabilities across human tumors. Here, we demonstrate that transcriptomic alterations of metabolism-related genes (metabolic transcriptome) in multiple myeloma (MM), classify patients into six metabolic-transcriptional groups characterized by specific metabolic pathways and cytogenetic alterations, independent of currently described myeloma risk groups. Interestingly, hyperdiploid patients clustered into 2 groups (MM5 […]
- by Luca ManninoCONCLUSIONS: Overall, EGG links epitope prioritization to tumor systems biology and evolutionary rationale, prioritizing biologically contextualized cancer vaccine candidates from SNVs, indels, fusions, and splicing-derived epitopes while streamlining dataset analysis. EGG is available from GitHub at https://github.com/fhaive/epitope_generation_gateway.
- by Alberto LópezMulti-modal learning, in which diverse data types are integrated and analyzed together, has become a central area of research in artificial intelligence, driving major advances in a wide range of domains. However, in many practical situations, certain modalities or variables may be missing for part of the samples, leading to a limited performance or failure […]
- by Emma W ViitalaCancer-associated fibroblasts (CAFs) promote tumorigenesis and represent potential therapeutic targets, highlighting the need for precise understanding of CAF heterogeneity. In colorectal cancer (CRC), CAF subsets and nomenclature vary widely, and many studies overlook the diversity of normal colon fibroblasts that shapes tumor mesenchyme. Here, we combine large-scale single-cell RNA-sequencing analysis with spatial validation and functional […]
- by Sara C DegerholmCONCLUSIONS: Immunohistochemical markers routinely applied in cutaneous melanoma (SOX-10 and PRAME) are also expressed in head and neck mucosal melanoma. Tumour-infiltrating immune cells showed trend toward better survival, as has been previously found out in cutaneous melanoma. Strong p16 positivity may be an independent predictor of favorable prognosis in head and neck mucosal melanoma, irrespective […]
- by Krista JuurikkaMMPs are essential for the physiological tissue turnover within the oral cavity and maxillofacial structures but their dysregulation may lead to pathogenic, tissue-destructive oral diseases. Within oral tissues, matrix metalloproteinases (MMPs) are produced by a variety of cells, including fibroblasts, keratinocytes, epithelial cells, immune cells, osteoclasts, osteoblasts, and odontoblasts. Activation of MMPs in periodontal tissues […]
- by Piia PeltoniemiNo abstract
- by Micaela A MacchioneMagnetic nanodiscs (MNDs) act as nanoscale heaters under high magnetic fields. Here, MNDs were coated with the positively charged thermoresponsive polymer poly(N-isopropylacrylamide-co-2-(dimethylamino)ethyl methacrylate) (P(NIPAM-co-DMAEMA) and evaluated for adenovirus complexation and magnetothermal release, enabling viral delivery by remote regulation of transfection through thermal modulation of electrostatic interactions.
- by Diego GilioliChemotherapy resistance and disease relapse are major determinants of treatment failure in acute myeloid leukemia (AML). Therapy-induced senescence (TIS) is one outcome of chemotherapy, but its immunological consequences in AML remain unclear. Here we show that ex vivo chemotherapy induces senescence in a subset of therapy-naïve AML samples. TIS is marked by elevated interferon signaling, […]
- by Ana PopovićCancer cells utilize filopodia to explore, adhere to and invade their surrounding microenvironment, yet the protein networks that organize these protrusions remain incompletely defined. To uncover the molecular machinery underlying MYO10-positive filopodia, we targeted the fast biotin ligase TurboID to the motor protein MYO10. Proximity biotinylation in two cell types revealed hundreds of potential MYO10 […]
- by Michaela FeodoroffINTRODUCTION: Clear cell renal cell carcinoma (ccRCC) remains a significant therapeutic challenge due to its biological heterogeneity, variable clinical behavior, and limited efficacy of single-agent systemic therapies. Combination strategies targeting multiple tumor-promoting pathways may improve therapeutic outcomes.
- by Linh LinLung cancer, a leading cause of cancer-related mortality, is often driven by mutations in the key oncogenes epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma virus (KRAS). Despite advancements of targeted therapies such as tyrosine kinase inhibitors, resistance remains a significant hurdle. Overexpression of HER3, associated with poor prognosis in non-small cell lung cancer […]
- by Dimitrios TsallosTP53 abnormalities contribute to treatment resistance and poor prognosis in multiple myeloma (MM), yet their functional consequences remain unclear. Here, we integrate ex vivo drug sensitivity profiling, genomics, transcriptomics, and proteomics across 167 CD138^(+) bone marrow patient samples to characterize TP53-associated vulnerabilities. Genome-wide CRISPR-Cas9 and RNAi screening identify vulnerabilities in TP53-mutated MM, with or without […]
- by Jani HuuhtanenOccasional complete responses (CR) to immune checkpoint inhibitor therapy demonstrate that acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) can be immunosensitive when appropriately targeted. In this study, we analyzed patients with AML/MDS (n = 14) who were treated with the anti-TIM3 sabatolimab and the hypomethylating agent decitabine in a phase Ib clinical trial (NCT03066648) […]