Biology subjects

Gil, J.

Publications and source records attributed to Gil, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Soil nitrogen dynamics in riparian zones of two Arctic rivers

Riparian zones act as protective buffers, filtering land-to-river nutrient inputs through retention and nitrogen (N) gas losses. While rapid Arctic warming and permafrost thaw may enhance terrestrial nutrient inputs to aquatic systems, comprehensive assessments of N cycling in Arctic riparian soils are lacking. Conventionally, these zones are considered inactive due to N limitation of Arctic soils and low temperatures, leaving their N cycling unexplored. To address this, we investigated N pools and turnover processes in riparian zones of two Arctic rivers in Finland and Greenland. We combined measurements of the extractable N pool and in-situ nitrous oxide (N2O) flux with 15N-labeling techniques to quantify gross mineralization, nitrification, potential denitrification, and potential dissimilatory nitrate reduction to ammonium (DNRA). Our findings reveal that mineral N cycling in high-latitude riparian zones is more active than previously assumed. Despite low temperatures and low to intermediate soil organic carbon content, we found high gross N mineralization rates, alongside detectable rates of gross nitrification and potential DNRA. We attribute the unexpectedly high N activity in C-poor soils to low C/N ratios, which create a stoichiometric imbalance, thereby enhancing N mineralization. The presence or absence of vegetation largely determined the dominance and magnitude of these pathways. While dense vascular plant cover was associated with higher extractable N pools and gross mineralization rate, low nitrification rates and elevated DNRA potential indicated a tight N cycle. Conversely, sparsely vegetated patches with cryptogamic biocrusts acted as N2O hotspots. In bare sandy soils adjacent to the river, we found high gross nitrification rate and detectable N2O losses, possibly driven by riverine organic N inputs. Taken together, this research shows that Arctic riparian zones may play an important role in reducing terrestrial N inputs to the rivers, which should be considered when studying the fate of N in the rapidly changing Arctic.

ecology↗

bioRxiv2026

From Routine Pathology to Precision Oncology: Automated FFPE Tissue Processing for Large-Scale Molecular Studies

Melanoma incidence continues to rise globally, with formalin-fixed paraffin-embedded (FFPE) tissue archives representing an invaluable resource for large-scale retrospective proteomic studies. However, inconsistent deparaffinization remains a critical pre-analytical bottleneck limiting protein yield, reproducibility, and downstream data quality. In this study, we developed and validated a fully automated FFPE deparaffinization workflow using the Fluent(R) 780 liquid handling workstation (Tecan (C)) and evaluated its performance against a conventional manual protocol in a cohort of 54 patients with primary cutaneous melanoma, predominantly at early AJCC 8th edition stage I-II. The automated workflow achieved superior protein identification (6,146 {+/-} 860 vs. 4,941 {+/-} 1,091 proteins; p < 0.0001) with lower technical variability, while maintaining highly comparable global proteomic profiles as confirmed by principal component analysis and hierarchical clustering. A total of 8,305 proteins (96.1%) were identified by both methods, supporting the reproducibility and equivalence of the automated approach. Patients were stratified by the presence (N=21) or absence (N=33) of histological regression in the primary tumor. Proteomic comparison revealed 97 upregulated and 226 downregulated proteins in regressing melanomas, with pathway enrichment analysis demonstrating elevated mitochondrial and translational activity alongside reduced innate immune and complement pathway activation in the regression group. No statistically significant differences in overall, disease-free, or progression-free survival were observed between groups, consistent with the early-stage composition of the cohort. Digital pathology validated tissue morphology preservation across processing conditions. These findings support the integration of automated FFPE processing with proteomic and digital pathology workflows as a scalable platform for precision melanoma research. TOC Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/744404v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1a3ea5dorg.highwire.dtl.DTLVardef@6fb8edorg.highwire.dtl.DTLVardef@d60a4dorg.highwire.dtl.DTLVardef@3e47b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

Proteomics-Enhanced AI-Digital Pathology in Metastatic Mucinous Colorectal Carcinoma: A Case Report

Mucinous colorectal carcinoma (CRC) is a distinct histomorphological subtype characterized by abundant extracellular mucin that may promote immune evasion and chemoresistance. We describe a metastatic mucinous CRC case integrating digital pathology and proteomics to investigate disease progression and therapy resistance. Formalin-fixed paraffin-embedded samples from the primary tumor, peritoneal metastasis, and hepatoduodenal ligament metastasis of a 56-year-old patient were analyzed. Whole-slide imaging with QuPath-based AI enabled detailed histological annotation, while data-independent acquisition mass spectrometry identified over 6,000 proteins. Digital pathology revealed extensive mucin pools, architectural evolution from heterogeneous glandular patterns in the primary tumor to cribriform morphology in advanced metastases, and immune cell exclusion from mucin-rich regions. Proteomics revealed metabolic reprogramming, suppressed antigen presentation, and stage-specific activation of inflammatory, angiogenic, EMT, and PI3K/AKT/mTOR-MYC signaling pathways, consistent with proliferative and therapy-resistant phenotypes.Integration of AI-assisted histopathology with spatial proteomics highlighted the mucin barrier as a key mediator of immune evasion and chemoresistance. These findings support a personalized therapeutic framework targeting mucin-associated mechanisms alongside pathway-directed inhibitors, suggesting that spatial multi-omics may guide precision management strategies for aggressive mucinous colorectal cancer.

pathology↗

bioRxiv2026

How to build dense cities without jeopardizing biodiversity? Insights from bird observations in Gothenburg, Sweden

A central challenge for sustainable urban development is balancing the trade-offs of high urban densities. We examined how biodiversity can be supported within dense or compact urban areas by analyzing bird species richness and composition across 30 sites representing three dense and compact urban form types and species-rich reference areas in Gothenburg, Sweden. Species richness and composition differed significantly between dense-compact urban forms and reference areas, but not between the urban form types themselves. Within dense-compact urban forms, however, sites with higher local natural habitat area and/or better connectivity to surrounding natural habitats supported higher species richness, whereas variation in species composition was associated primarily with local habitat area. Rarely recorded species in dense or compact urban areas were also observed where suitable habitat conditions existed. These results suggest that biodiversity can be supported within dense or compact cities through both site-level interventions and broader-scale planning for habitat connectivity.

ecology↗

bioRxiv2026

Standard treatment against paediatric BRAF-V600E glioma promotes senescence and sensitizes tumours to BCL-xL inhibition

BackgroundChemo-, radio-, and targeted therapies can induce senescence in tumour cells, a process called therapy-induced senescence (TIS), which can be exploited therapeutically using compounds that kill senescent cells (senolytics). Children with BRAF-V600E activated brain tumours are commonly treated with Dabrafenib, Trametinib or Vinblastine (alone or in combination) with good responses. However, a subset of patients experiences tumour regrowth upon treatment withdrawal. Here, we explore the role of TIS and senolytic therapies in preclinical models of paediatric BRAF-V600E driven brain tumours. MethodsHuman BT-40 tumour cells derived from pleomorphic xanthoastrocytoma are used in vitro or in vivo orthotopically transplanted into mice and treated with either Dabrafenib, Trametinib or Vinblastine. Senescence is assessed by immunostaining and RNA sequencing. Sensitivity to senolytics is determined in vitro in dose response assays and in vivo. ResultsTrametinib treatment induces a senescent phenotype in BT-40 cells in vivo with activation of a senescence-associated secretory phenotype (SASP) and expansion of IBA-1 microglia. Senescence is induced in BT-40 cells in vitro when treated not only with Trametinib, but also with Dabrafenib and Vinblastine. In vitro testing identifies Navitoclax as a potent senolytic against BT-40 senescent cells, mostly through inhibition of the anti-apoptotic protein BCL-xL. In BT-40 tumour bearing mice, combination of Trametinib and Navitoclax causes the ablation of senescent BT-40 cells with significant reduction in tumour regrowth after treatment withdrawal and increased mouse survival. ConclusionsThis study shows that Navitoclax enhances the anti-tumour efficacy of Trametinib and limits tumour regrowth following treatment withdrawal. Key PointsO_LITrametinib, Dabrafenib and Vinblastine induce senescence in BT-40 cells in vitro C_LIO_LISenescent BT-40 cells are sensitive to BCL-xL inhibition C_LIO_LICombination of Trametinib and Navitoclax reduces rebound tumour growth in vivo C_LI Importance of the StudyChildren with BRAF-V600E activated glioma are frequently treated with Dabrafenib, Trametinib or Vinblastine with good responses. However, a subset of patients shows tumour regrowth when the treatment is stopped. To prevent this rebound growth, patients must continue treatment with potential aggravation in quality of life and risk of malignant progression. Our research demonstrates that these therapies induce BT-40 tumour cells to enter a non-proliferative state that shows features of cellular senescence. We identify that senescent tumour cells can be killed using Navitoclax, and potent inhibitor of the anti-apoptotic protein BCL-xL and a well-studied senolytic. We demonstrate that the combination of Trametinib and Navitoclax reduces tumour regrowth after treatment withdrawal. Our research provides a strong rationale supporting the combined use of senolytics with current conventional and targeted therapies against BRAF-V600E mutated brain tumours.

cancer biology↗

bioRxiv2025

Targeted metagenomic sequencing with spiked primers for enrichment of viruses in wastewater for pathogen surveillance

BackgroundWastewater surveillance offers an underutilized opportunity to identify high-risk viral pathogens that pose public health risks. Although metagenomic approaches have been increasingly adopted for human wastewater surveillance, little attention has been given to its application in rural agricultural settings. Untargeted metagenomic sequencing of wastewater poses considerable technical challenges for viral detection due to fragmented genomes and low viral abundance. While existing enrichment methods partially address these challenges, high costs and proprietary protocols limit adoption in resource-constrained settings. ObjectiveWe developed a fully open-source primer design algorithm (Open MSSPE Design) and evaluated Metagenomic Sequencing with Spiked Primer Enrichment (MSSPE)1, as a practical strategy for metagenomic surveillance of swine slurry and farm wastewater samples collected from rural agricultural settings. This non-invasive MSSPE strategy addresses the challenge of detecting extremely low-abundance viral targets amid samples dominated by a background of bacterial and eukaryotic nucleic acids. MethodologyWe generated fifteen primer sets targeting high-priority DNA and RNA viral pathogens affecting human and animal health in Southeast Asia using our open-source primer design algorithm. Twenty-five wastewater and swine slurry samples from smallholder farms in northern Thailand underwent parallel library preparation--untargeted mNGS and MSSPE--for direct comparison. Libraries were sequenced on Illumina platforms and analyzed using Chan Zuckerberg ID (CZ ID)2. Rarefaction analysis assessed performance at sequencing depths of 100,000-1.5 million reads per sample. ResultsWe detected multiple high-risk DNA and RNA viruses in wastewater samples from smallholder farm operations. MSSPE achieved substantial viral enrichment across nine pathogenic DNA and RNA viruses, with a median two-fold enrichment of reads per million, with variability across targets (IQR: 1.01-3.44x) and a nearly 10% median increase in breadth of genome coverage (IQR: 4.54-11.84%), while retaining sensitivity for untargeted pathogens. MSSPE also increased the odds of detecting targeted viruses (OR 1.35, CI 1.14-1.60), with the greatest advantage at shallow sequencing depths where MSSPE required fewer reads to identify targeted viral taxa relative to mNGS. ConclusionsMSSPE demonstrated the ability to enrich shallow-depth sequencing (<2M reads per sample) sufficiently to detect priority viruses without substantially increasing library preparation time or cost. This open-source workflow supports cost-effective metagenomic viral surveillance for resource-constrained settings, providing a non-invasive method for detecting low-abundance viral targets in high-background sample types at rural agricultural interfaces with elevated risk of zoonotic spillover.

genomics↗

bioRxiv2025

Non-canonical TERT function mitigates adipose tissue inflammation in obesity by modulating stem cell-macrophage communication and macrophage states

Background and aimsObesity drives adipose tissue (AT) expansion and chronic inflammation, leading to metabolic dysfunction through adipocyte hypertrophy, impaired ASPC differentiation, immune infiltration, and fibrosis. Stromal vascular remodeling prominently features expansion of Gdf15- and Trem2-expressing lipid-associated macrophages (LAMs), which respond to adipocyte stress and act as lipid scavengers to buffer excess lipids released by adipocytes. Here, we examined macrophage reprogramming in p21+/Tert and p21+/TertCi mice, which express active TERT or its catalytically inactive TERTCi mutant from the endogenous Cdkn1a promoter. ResultsFollowing HFD exposure, conditional expression of TERT or TERTCi resulted in a pronounced downregulation of p21 in macrophage subsets, accompanied by a reduction in AT inflammation. Notably, TERT and TERTCi expression reshaped the adipose-tissue macrophage (ATM) landscape depleting Trem2+ and Gdf15+ LAMs while preserving resident macrophages. This shift was accompanied by marked suppression of the Trem2 transcriptional program and down-regulation of PPAR-{gamma} and NR1H3 in LAMs and by impaired ASPC-LAM signaling pathways that normally drive LAM recruitment and activation. Proteomic profiling further showed that p21+/Tert ASPCs secreted markedly higher levels of proteins associated with non-conventional secretion, while extracellular matrix-associated factors and cytokines/chemokines including key mediators of ASPC-LAM communication such as Ccl2, C3, and Csf1 were substantially reduced. However, only p21+/Tert mice, and not p21+/TertCi mice, exhibited significant metabolic improvements, indicating that macrophage remodeling alone is insufficient to restore systemic metabolic function. Consistent with this, enhanced ASPC expansion and differentiation, supporting improved adipose-tissue remodeling, was observed exclusively in p21+/Tert obese mice. ConclusionsTERT remodels adipose tissue immunity independently of its enzymatic activity, and TERT-driven reprogramming of the ASPC secretome may emerge as a promising strategy to combat obesity-related metabolic dysfunction. HighlightsO_LIConditional expression of TERT or catalytically inactive TERTCi results in the depletion Trem2+ and Gdf15+ LAMs while preserving resident macrophages C_LIO_LITERT and TERTCi expression impairs ASPC-adipocyte/LAM communication pathways that normally drive LAM recruitment and activation. C_LIO_LIIn vitro, TERT conditional expression in ASPCs promotes non-conventional protein secretion and reduces the secretion of key mediators of ASPC-LAM communication C_LIO_LIOnly p21+/Tert mice, and not p21+/TertCi mice, exhibited enhanced ASPC expansion, improved adipose-tissue remodeling, and systemic metabolic benefits, demonstrating that macrophage remodeling alone is insufficient to restore metabolic function. C_LI

physiology↗

bioRxiv2025

Phosphoproteomic profiling reveals post-translational dysregulation in Huntington's disease patient-derived neurons

Huntingtons disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion in the Huntingtin (HTT) gene. Although transcriptomic and proteomic changes have been characterized in patient-derived neurons, the contribution of post-translational modifications (PTMs), such as phosphorylation, remains poorly understood. Here, we present the first phosphoproteomic analysis by mass spectrometry (P-MS) of human induced neurons (iNs) directly reprogrammed from HD patient fibroblasts. We identified 177 phosphopeptides with significantly altered abundance in HD-iNs, mapping to phosphoproteins associated with key signaling pathways known to be affected in HD, such as splicing and autophagy. By integrating P-MS data with previously published proteomic and transcriptomic data from the same donors, we identified distinct subsets of ON-OFF phosphopeptides that exhibited a complete loss of phosphorylation in either HD- or Ctrl-iNs, without corresponding changes at the RNA or protein level. An exception was MXRA8, previously described in glial cells as a mediator of blood-brain barrier integrity and astrocyte-mediated neuroinflammation. This protein showed increased protein abundance despite the absence of phosphorylation in HD- iNs, suggesting a compensatory mechanism - a pattern also observed in human post mortem cortical HD tissue. Additionally, MXRA8 showed altered protein-protein interactions with lysosomal and metabolic regulators in HD-iNs, highlighting its potential role in autophagy impairment as well as in neurovascular dysfunction. These findings uncover a distinct layer of post-translational dysregulation in HD, suggesting that phospho-switch proteins such as MXRA8 may be candidate effectors of pathology and thus site-specific phosphorylation loss may contribute to impaired signaling and proteostasis in human HD neurons.

neuroscience↗

bioRxiv2025

A proteomic study of the dual oncogenic and tumor- suppressive roles of SIRT3 in lung and breast cancer cell lines

Mitochondria play a crucial role in metabolism and energy production by generating adenosine triphosphate (ATP) through oxidative phosphorylation. They also help maintain intracellular calcium levels, facilitate communication between the nucleus and cytoplasm, detoxify reactive oxygen species (ROS), and regulate apoptosis (programmed cell death). Reversible acetylation of mitochondrial proteins is a key post-translational modification influencing these processes, with the NAD+-dependent deacetylase SIRT3 being a major regulator. While SIRT3 has been described as a tumor suppressor in some contexts and as a tumor promoter in others, its role appears to be tissue- and metabolism-specific. Here, we compared the proteomic and acetylomic responses of lung adenocarcinoma (A549) and breast adenocarcinoma (MCF7) cell lines to SIRT3 inhibition by 3-(1H-1,2,3-triazol-4-yl)pyridine (3-TYP). The two lines were selected based on distinct metabolic phenotypes and reported differences in basal SIRT3 abundance. Total proteome and mitochondrial-enriched fractions were analyzed separately for each cell line to avoid cross-line normalization bias. We identified 6,457 proteins and 4,199 acetylated peptides, revealing divergent pathway enrichments and acetylation patterns following SIRT3 inhibition. A549 cells showed enrichment of oxidative metabolism pathways, whereas MCF7 cells exhibited features consistent with metabolic reprogramming. These findings suggest that the cellular context determines the proteomic consequences of SIRT3 modulation and highlight the importance of metabolism in shaping SIRT3-associated phenotypes. All raw mass spectrometry data are publicly available in [repository accession number]. SignificanceSIRT3s impact on cancer metabolism is context-dependent. By separately profiling lung (A549) and breast (MCF7) cancer cells, we demonstrate that SIRT3 inhibition leads to distinct proteomic and acetylomic outcomes in each cell type. Our findings underscore the need for cell-type-specific strategies when targeting SIRT3 in cancer therapy and provide an open-access proteomic resource for further mechanistic studies.

cancer biology↗

bioRxiv2025

Inhibition of cytosolic DNA sensing and transposon activity safeguards pluripotency

Transposable elements (TEs) are mobile DNA sequences that make up a sizeable fraction of mammalian genomes yet are often tightly repressed by transcriptional and epigenetic mechanisms. During early development, epigenetic reprogramming selectively loosens TE repression, and TE transcription actively contributes to embryogenesis. This raises the question: how can embryos and embryonic stem cells (ESCs) tolerate TE expression without incurring widespread inflammation or DNA damage? Here, we reveal multiple mechanisms that prevent innate immune activation by TE-derived cytosolic DNA, including reduced cGAS/STING expression and signalling, dampening of Type I interferon responses by pluripotency factors, and post-transcriptional restriction of retrotransposition. These layers of protection are essential, as experimental perturbation triggers loss of ESC self-renewal and pluripotency. Our data explain how early development can be permissive to TE expression while safeguarding against harmful effects of TE activity.

developmental biology↗

bioRxiv2025

TERT prevents obesity-induced metabolic disorders by promoting adipose stem cell expansion and differentiation

Obesity is linked to limited adipose tissue (AT) remodeling capacity, leading to hypertrophic adipocytes, senescence, and inflammation. We used a mouse model expressing mTert (p21+/Tert) from the Cdkn1a locus to investigate the role of mTERT in obesity-induced metabolic disorders. Conditional expression of mTERT reduces metabolic disorders associated with obesity. In AT, this is accompanied by a decrease in the number of senescent p21-positive cells, very short telomeres, and oxidative DNA damage. Single nucleus RNA-seq data reveal TERT expression attenuates senescence induced by HFD in particular in adipose stem and progenitor cells (ASPC). We show that ASPC expansion and differentiation are promoted in p21+/Tert obese mice, thereby reducing metabolic disorders. We further report that mTERT remodels the landscape of macrophages in AT of obese mice. Strikingly, inactivation of mTERT catalytic activity in p21+/Tert (p21+/TertCi) mice suppresses the promotion of adipocyte formation, but neither affects attenuation of senescence nor macrophage remodeling. These results highlight mTERTs canonical and non-canonical functions in reducing obesity-associated metabolic disorders. Conditional expression of TERT thus appears as a potential therapeutic option for obesity.

physiology↗

bioRxiv2024

Targeted inhibition of Bcl-xL following radiation reduces tumourigenesis in preclinical models of H3K27M-altered diffuse midline glioma

BackgroundDiffuse midline gliomas (DMGs) with histone H3K27M mutations represent a devastating paediatric brain cancer characterized by abysmal prognosis and limited treatment options. The only approved treatment is radiotherapy (RT), but most of the tumours relapse with fatal consequences. In this study, we sought to investigate whether irradiation leads to senescence induction and explore the efficacy of senolytics against DMG. MethodsWe have characterised the senescent phenotype of five genetically heterogeneous H3K27M-altered human DMG cell lines, combining cellular and/or molecular approaches. The sensitivity of senescent cells to Bcl-xL inhibition has been demonstrated in dose/response curves in vitro and in a PDX model of DMG. ResultsHere, we show that ionizing radiation induces senescence and SASP responses in both TP53 mutant and wild-type H3K27M-altered human DMG cell lines. We identify Navitoclax as a potent senolytic agent that selectively targets senescent DMG cells into apoptosis by inhibiting Bcl-xL. Related compounds, such as a proteolysis-targeting chimera (PROTAC)-mediated Bcl-xL degradation and a galacto-conjugated form of Navitoclax also show an effective senolytic activity in senescent cancer cells. Finally, we show that a combination therapy of irradiation and Navitoclax results in reduced tumor burden and increased mouse survival in an orthotopic xenograft DMG model. ConclusionThese results offer a rationale for further clinical development of senolytic therapies as part of multimodal treatment approaches for DMG patients/ Key PointsO_LIIonising irradiation induces senescence in human DMG cells independently of the p53 status. C_LIO_LIBcl-xL inhibition results in apoptosis of human DMG senescent cells in synergy with irradiation. C_LIO_LICombination of irradiation and BcL-xL inhibition reduces tumourigenesis in a PDX model of DMG. C_LI Importance of the StudyH3K27M-altered DMG are devastating paediatric tumours with an abysmal prognosis. The only approved treatment is radiotherapy but this is palliative and tumours almost always relapse with fatal consequences for the patients. In this study, we show that radiotherapy results in senescence induction in five genomically heterogeneous human DMG cell lines. We identify that drugs targeting the anti-apoptotic protein Bcl-xL show a strong senolytic activity in conjunction with radiotherapy both in vitro in DMG cells and in vivo in a PDX model of H3K27M-altered DMG. Treatment with Bcl-xL inhibitor Navitoclax, or related compounds targeting Bcl-xL protein degradation or containing a galactose conjugated form of Navitoclax results in DMG cancer cell apoptosis. As several of these inhibitors are currently being tested in ongoing clinical trials against other diseases, our data support the use of Bcl-xL inhibition mediated senolytics as an adjuvant therapy to radiotherapy to potentially improve outcomes in this challenging disease setting.

cancer biology↗

bioRxiv2024

Predicting immune checkpoint therapy response in three independent metastatic melanoma cohorts

While Immune checkpoint inhibition (ICI) therapy shows significant efficacy in metastatic melanoma, only about 50% respond, lacking reliable predictive methods. We introduce a panel of six proteins aimed at predicting response to ICI therapy. Evaluating previously reported proteins in two untreated melanoma cohorts, we used a published predictive model (EaSIeR score) to identify potential proteins distinguishing responders and non-responders. Six proteins initially identified in the ICI cohort correlated with predicted response in the untreated cohort. Additionally, three proteins correlated with patient survival, both at the protein, and at the transcript levels, in an independent immunotherapy treated cohort. Our study identifies predictive biomarkers across three melanoma cohorts, suggesting their use in therapeutic decision-making. O_FIG O_LINKSMALLFIG WIDTH=164 HEIGHT=200 SRC="FIGDIR/small/592032v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@754668org.highwire.dtl.DTLVardef@1616263org.highwire.dtl.DTLVardef@827009org.highwire.dtl.DTLVardef@1899ba7_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Identifying Ferroptosis Inducers, HDAC, and RTK Inhibitor Sensitivity in Melanoma Subtypes through Unbiased Drug Target Prediction

The utilization of PD1 and CTLA4 inhibitors has revolutionized the treatment of malignant melanoma (MM). However, resistance to targeted and immune-checkpoint-based therapies still poses a significant problem. Here we mine large scale MM proteogenomic data integrating it with MM cell line dependency screen, and drug sensitivity data to identify druggable targets and forecast treatment efficacy and resistance. Leveraging protein profiles from established MM subtypes and molecular structures of 82 cancer treatment drugs, we identified nine candidate hub proteins, mTOR, FYN, PIK3CB, EGFR, MAPK3, MAP4K1, MAP2K1, SRC and AKT1, across five distinct MM subtypes. These proteins serve as potential drug targets applicable to one or multiple MM subtypes. By analyzing transcriptomic data from 48 publicly accessible melanoma cell lines sourced from Achilles and CRISPR dependency screens, we forecasted 162 potentially targetable genes. We also identified genetic resistance in 260 genes across at least one melanoma subtype. In addition, we employed publicly available compound sensitivity data (Cancer Therapeutics Response Portal, CTRPv2) on the cell lines to assess the correlation of compound effectiveness within each subtype. We have identified 20 compounds exhibiting potential drug impact in at least one melanoma subtype. Remarkably, employing this unbiased approach, we have uncovered compounds targeting ferroptosis, that demonstrate a striking 30x fold difference in sensitivity among different subtypes. This implies that the proteogenomic classification of melanoma has the potential to predict sensitivity to ferroptosis compounds. Our results suggest innovative and novel therapeutic strategies by stratifying melanoma samples through proteomic profiling, offering a spectrum of novel therapeutic interventions and prospects for combination therapy. Highlights(1) Proteogenomic subtype classification can define the landscape of genetic dependencies in melanoma (2) Nine proteins from molecular subtypes were identified as potential drug targets for specified MM patients (3) 20 compounds identified that show potential effectiveness in at least one melanoma subtype (4) Proteogenomics can predict specific ferroptosis inducers, HDAC, and RTK Inhibitor sensitivity in melanoma subtypes O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/579424v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@73dd77org.highwire.dtl.DTLVardef@d0cb8eorg.highwire.dtl.DTLVardef@1e4117forg.highwire.dtl.DTLVardef@38b727_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

cancer biology↗

bioRxiv2023

Ribosomal S6 kinase 1 regulates inflammaging via the senescence secretome

Inhibition of the nutrient-responsive mTOR (mammalian target of rapamycin) signalling pathway including the key downstream effector S6 kinase 1 (S6K1) extends lifespan and improves healthspan in mice. However, the underlying mechanisms contributing to the broad range of age-related benefits observed with loss of S6K1 signalling are unclear. Cellular senescence is a stable growth arrest accompanied by an inflammatory phenotype (termed the senescence-associated secretory phenotype, or SASP). While both cellular senescence and SASP-mediated chronic inflammation contribute to age-related pathology, the specific role of S6K1 signalling in these processes has not been determined. Here, focussing on mouse liver, a key target tissue for the beneficial metabolic effects of loss of S6K1 signalling, we show that S6K1 deletion does not reduce senescence but ameliorates inflammation and immune cell infiltration in aged livers. Using human and mouse models of senescence, we demonstrated that reduced inflammation is a liver-intrinsic effect associated with S6K deletion. Furthermore, gene expression analysis suggested that downregulated cGAS/STING and IRF3 activation might mediate the impaired SASP observed upon S6K deletion. Using a hepatic oncogene induced senescence model, we showed in vivo that S6K1 deletion results in reduced IRF3 activation, impaired production of cytokines such as IL1y and reduced immune infiltration. Overall, deletion of S6K reduces inflammation in the liver suggesting that suppression of the inflammatory SASP by loss of S6K could contribute to explain the beneficial effects of inhibiting this pathway on healthspan and lifespan.

physiology↗

bioRxiv2023

Histopathology-assisted proteogenomics provides foundations for stratification of melanoma metastases

Here we describe the histopathology-driven proteogenomic landscape of 142 treatment-naive metastatic melanoma samples. We identified five proteomic subtypes that integrate the immune and stroma microenvironment components, and associate with clinical and histopathological parameters, providing foundations for an in-depth molecular classification of melanoma. Our study shows that BRAF V600 mutated melanomas display heterogeneous biology, where the presence of an oncogene-induced senescence-like phenotype improves patient survival. Therefore, we propose a mortality-risk-based stratification, which may contribute to a more personalized approach to patient treatment. We also found a strong association between tumor microenvironment composition, disease progression, and patient outcome supported by single-cell omic signatures that point to straightforward histopathological connective tissue-to-tumor ratio assessment for better informed medical decisions. A melanoma-associated signature of single amino acid variants (SAAV) responsible for remodeling the extracellular matrix was uncovered together with SAAV-derived neoantigen candidates as targets of anti-tumor immune responses. Overall, this study offers comprehensive stratifications of melanoma metastases that may help develop tailored strategies for diagnosing and treating the disease.

cancer biology↗

bioRxiv2023

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori

Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these are mainly observed in model organisms, and most eukaryotes remain unexplored. Using Hi-C in the silkworm Bombyx mori we discover a novel chromatin folding structure, compartment S, which is "secluded" from the rest of the chromosome. This compartment exhibits loop extrusion features and a unique genetic and epigenetic landscape, and it localizes towards the periphery of chromosome territories. While euchromatin and heterochromatin display preferential compartmental contacts, S domains are remarkably devoid of contacts with other regions, including with other S domains. Polymer simulations show that this contact pattern can only be explained by high loop-extrusion activity within compartment S, combined with low extrusion elsewhere through the genome. This unique, targeted extrusion represents a novel phenomenon and underscores how evolutionarily conserved mechanisms--compartmentalization and loop extrusion--can be repurposed to create new 3D genome architectures.

genomics↗

bioRxiv2023

Inhibition of an immunometabolic axis of mTORC1 activation extends mammalian healthspan

Human ageing is associated with metabolic dysfunction, sarcopenia and frailty that taken together reduce healthspan. For age-associated diseases and lifespan, ERK, AMPK and mTORC1 represent critical pathways, across species1-7. Here we examined the hypothesis that IL11, recently shown to regulate ERK/mTORC1, is an inflammaging factor important for healthspan. As mice age, IL11 is progressively upregulated in liver, skeletal muscle, and fat to stimulate an ERK/AMPK/mTORC1 axis of cellular, tissue- and organismal-level ageing pathologies. In old mice, deletion of Il11 or Il11ra1 protects against metabolic multi-morbidity, sarcopenia, and frailty. Administration of anti-IL11 therapy to elderly mice for six months reactivates an age-repressed program of white fat beiging, reverses metabolic dysfunction, restores muscle function, and reduces frailty. Across studies, inhibition of IL11 lowers epigenetic age, reduces telomere attrition, and preserves mitochondrial function. Towards clinical translation, we generated, humanised, and engineered a neutralising, high-affinity IL11 antibody. These studies identify IL11 as a key inflammaging factor and therapeutic target for mammalian healthspan.

molecular biology↗