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Biology subjects

Piga, I.

Publications and source records attributed to Piga, I..

5 recordsLinked to original sources

Acute IFN-γ elicits long-term proteomic IFN-γ signature in melanoma cells

Interferon-{gamma} (IFN-{gamma}) is a central mediator of antitumor immunity, and its downstream effects are widely assumed to require continuous cytokine exposure. Here, we applied state-of-the-art mass spectrometry (MS)-based proteomics to patient-derived melanoma cells exposed either continuously to IFN-{gamma} or to a 3-hour pulse followed by cytokine removal. A transient IFN-{gamma} exposure was sufficient to establish a stable proteomic state indistinguishable from continuous stimulation, demonstrating that IFN-{gamma}-induced remodeling is rapidly triggered and durably maintained independently of ligand persistence. Proximal JAK-STAT signaling was rapid, saturable at low cytokine concentrations, and fully reversible upon washout, yet downstream proteomic programs remained durably imprinted. In contrast, functional consequences such as cytostasis remained dose-dependent, revealing a disconnect between signaling activation and phenotypic sensitivity. Together, these findings challenge long-standing assumptions about IFN-{gamma} signaling, redefine the temporal requirements for cytokine-driven tumor cell programming, and provide a mechanistic framework for improving immunotherapies primarily working via IFN-{gamma}-signaling and physiologically relevant in vitro models of tumor-immune interactions.

biochemistry↗

The Human Cell Line Phosphoproteome Atlas: A Deep Empirical Resource Revealing Kinase Activity Landscapes

Protein phosphorylation orchestrates cellular signaling and controls diverse biological processes, with its dysregulation driving diseases, notably cancer. Comprehensive, high-throughput phosphoproteomics remains limited by detection sensitivity, data completeness, and computational bottlenecks, especially in low-input settings. We present the deepest empirical human phosphoproteome resource to date, regrouping over 200,000 class I phosphosites across 33 diverse human cell lines, and demonstrate that this spectral library dramatically improves single-shot phosphoproteomics with 30-fold faster data processing compared to library-free approaches and enhanced confidence in phosphosite localization even from minimal sample input. Integrating proteome and phosphoproteome data, we developed a combined kinase activity score, revealing cell line- and cancer-specific signaling vulnerabilities, many correlating with drug sensitivity. This resource accelerates deep, reproducible phosphoproteomics, enabling systematic functional mapping of cellular signaling networks, and empowers precision oncology by highlighting actionable kinase targets in diverse cell states.

biochemistry↗

The proteomics and phosphoproteomics landscape of melanoma under T cell attack

Understanding how tumor cells interact with tumor-infiltrating lymphocytes (TILs) in the tumor microenvironment (TME) is crucial for identifying targetable immune checkpoints and predictive biomarkers for immunotherapy. While transcriptional responses have been characterized, protein-level changes remain largely unexplored. Here, we used a system reproducing the interaction of TILs with cancer cells occurring in the TME, by co-culturing patient-derived cancer cells with matched autologous TILs at sub-lethal ratios. Using this system, we profiled the early response that cancer (melanoma) cells and TILs activate following autologous T cell attack. To distinguish melanoma from TIL proteomes, we applied stable isotope labeling by amino acids in cell culture (SILAC) combined with Orbitrap Astral-based data-independent acquisition (DIA) mass spectrometry, enabling cell type-specific profiling of protein and phosphorylation dynamics without FACS sorting. This approach also captured the global newly synthesized proteome of the mixed cultures. Our analyses resolved interferon-{gamma}-dependent proteome changes occurring in melanoma cells, identified the cytotoxic and regulatory T-cell molecule (CRTAM) as a selective marker of reactive cytotoxic T lymphocytes, and revealed tumor-intrinsic kinase activation signatures. Among these, multiple DNA damage response-associated kinases were activated during immune attack, suggesting potential therapeutic vulnerabilities. Overall, this framework enables proteomic dissection of tumor-immune interactions and provides a resource for guiding biomarker discovery and therapeutic strategies to improve immunotherapy outcomes.

cancer biology↗

Organoid-based modeling of platinum resistance identifies KRT17 as both a response mediator and biomarker for targeted therapy in ovarian cancer

Variable platinum responses drive high mortality in high-grade serous ovarian cancer (HGSOC), but to date, there is no molecular approach to define resistance levels for clinical decision-making. Here, we developed the organoid drug resistance assay (ODR-test) with patient-derived organoids from our ovarian cancer biobank and found that all HGSOC patients develop molecular resistance under exposure to carboplatin, although with varying clinical implications. Sustained phenotypic reprogramming and cellular plasticity under carboplatin pressure emerged as a conserved mechanism irrespective of the basal resistance level. Transcriptional and proteomic analyses revealed changes in cell adhesion and differentiation in post-platinum lines as adaptive responses that drive the increase in resistance. We identified Keratin 17 (KRT17) as a mediator of developing platinum resistance and validated its function by CRISPR/Cas9 and overexpression. Additionally, we found that KRT17 expression status (K-score) is a significant negative prognostic histopathological biomarker in a large cohort (N=384) of advanced HGSOC patients. In organoids, increased KRT17 levels enhanced sensitivity to PI3K/Akt inhibitors Alpelisib and Afuresertib, highlighting the potential of KRT17 as a stratification biomarker for targeted therapies.

cancer biology↗

Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics

Improving coverage, robustness and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography tandem mass spectrometry (LC-MS/MS) runs from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-beads phosphoproteomics sample preparation with focus on low input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample and loading buffer volumes, allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 {micro}g of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA). Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=159 HEIGHT=200 SRC="FIGDIR/small/568418v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@f455d9org.highwire.dtl.DTLVardef@130537eorg.highwire.dtl.DTLVardef@1b99287org.highwire.dtl.DTLVardef@42e72e_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗