A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

Therapy Induced Senescence (TIS) leads to sustained growth arrest of cancer cells. The associated cytostasis has been shown to be reversible and cells escaping senescence further enhance the aggressiveness of cancers. Chemicals specifically targeting senescent cells, so-called senolytics, constitute a promising avenue for improved cancer treatment in combination with targeted therapies. Understanding how cancer cells evade senescence is needed to optimise the clinical benefits of this therapeutic approach. Here we characterised the response of three different NRAS mutant melanoma cell lines to a combination of CDK4/6 and MEK inhibitors over 33 days. Transcriptomic data show that all cell lines trigger a senescence programme coupled with strong induction of interferons. Kinome profiling revealed the activation of Receptor Tyrosine Kinases (RTKs) and enriched downstream signaling of neurotrophin, ErbB and insulin pathways. Characterisation of the miRNA interactome associates miR-211-5p with resistant phenotypes. Finally, iCell-based integration of bulk and single-cell RNA-seq data identifies biological processes perturbed during senescence and predicts 90 new genes involved in its escape. Overall, our data associate insulin signaling with persistence of a senescent phenotype and suggest a new role for interferon gamma in senescence escape through the induction of EMT and the activation of ERK5 signaling.VG is supported by the Luxembourg National Research Fond (FNR) PRIDE DTU CanBIO [grant reference: 21/16763386]. TR is supported by the FNR PRIDE DTU CriTiCS [grant reference: 10907093]. Project-related work performed by VG, HH, CM, DP, MTN, MB, AG, FT and SK were also supported by the University of Luxembourg and the Fondation Cancer, Luxembourg (grant “SecMelPro”). KM and NP are supported by funding from the European Union’s EU Framework Programme for Research and Innovation Horizon 2020, Innovative Training Networks (MSCA-ITN-2019), funded under EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions, Grant Agreement No 860895. KM, NMD, GC and NP are supported by funding from the European Research Council (ERC) Consolidator Grant 770827. NP is also supported by funding from the Spanish State Research Agency AEI 10.13039/501100011033 grant number PID2019-105500GB-I00.Peer Reviewed"Article signat per 22 autors/es: Vincent Gureghian, Hailee Herbst, Ines Kozar, Katarina Mihajlovic, Noël Malod-Dognin, Gaia Ceddia, Cristian Angeli, Christiane Margue, Tijana Randic, Demetra Philippidou, Milène Tetsi Nomigni, Ahmed Hemedan, Leon-Charles Tranchevent, Joseph Longworth, Mark Bauer, Apurva Badkas, Anthoula Gaigneaux, Arnaud Muller, Marek Ostaszewski, Fabrice Tolle, Nataša Pržulj & Stephanie Kreis"Postprint (published version

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

Therapy Induced Senescence (TIS) leads to sustained growth arrest of cancer cells. The associated cytostasis has been shown to be reversible and cells escaping senescence further enhance the aggressiveness of cancers. Chemicals specifically targeting senescent cells, so-called senolytics, constitute a promising avenue for improved cancer treatment in combination with targeted therapies. Understanding how cancer cells evade senescence is needed to optimise the clinical benefits of this therapeutic approach. Here we characterised the response of three different NRAS mutant melanoma cell lines to a combination of CDK4/6 and MEK inhibitors over 33 days. Transcriptomic data show that all cell lines trigger a senescence programme coupled with strong induction of interferons. Kinome profiling revealed the activation of Receptor Tyrosine Kinases (RTKs) and enriched downstream signaling of neurotrophin, ErbB and insulin pathways. Characterisation of the miRNA interactome associates miR-211-5p with resistant phenotypes. Finally, iCell-based integration of bulk and single-cell RNA-seq data identifies biological processes perturbed during senescence and predicts 90 new genes involved in its escape. Overall, our data associate insulin signaling with persistence of a senescent phenotype and suggest a new role for interferon gamma in senescence escape through the induction of EMT and the activation of ERK5 signaling.VG is supported by the Luxembourg National Research Fond (FNR) PRIDE DTU CanBIO [grant reference: 21/16763386]. TR is supported by the FNR PRIDE DTU CriTiCS [grant reference: 10907093]. Project-related work performed by VG, HH, CM, DP, MTN, MB, AG, FT and SK were also supported by the University of Luxembourg and the Fondation Cancer, Luxembourg (grant “SecMelPro”). KM and NP are supported by funding from the European Union’s EU Framework Programme for Research and Innovation Horizon 2020, Innovative Training Networks (MSCA-ITN-2019), funded under EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions, Grant Agreement No 860895. KM, NMD, GC and NP are supported by funding from the European Research Council (ERC) Consolidator Grant 770827. NP is also supported by funding from the Spanish State Research Agency AEI 10.13039/501100011033 grant number PID2019-105500GB-I00.Peer ReviewedArticle signat per 22 autors/es: Vincent Gureghian 1, Hailee Herbst 1, Ines Kozar 2, Katarina Mihajlovic 3, Noël Malod-Dognin 3, Gaia Ceddia 3, Cristian Angeli 1, Christiane Margue 1, Tijana Randic 1, Demetra Philippidou 1, Milène Tetsi Nomigni 1, Ahmed Hemedan 4, Leon-Charles Tranchevent 4, Joseph Longworth 5, Mark Bauer 1, Apurva Badkas 1, Anthoula Gaigneaux 1, Arnaud Muller 6, Marek Ostaszewski 4, Fabrice Tolle 1, Nataša Pržulj 3, 7, 8 and Stephanie Kreis 1 // 1 Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; 2 Laboratoire National de Santé, Dudelange, Luxembourg; 3 Barcelona Supercomputing Center, 08034 Barcelona, Spain; 4 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; 5 Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg; 6 LuxGen, TMOH and Bioinformatics platform, Data Integration and Analysis unit, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg; 7 Department of Computer Science, University College London, London WC1E 6BT, UK; 8 ICREA, Pg. Lluís Companys 23, 08010 Barcelona, SpainPostprint (published version

GABA-Producing Natural Dairy Isolate From Artisanal Zlatar Cheese Attenuates Gut Inflammation and Strengthens Gut Epithelial Barrier in vitro

Probiotic bacteria are recognized for their health-promoting properties, including maintenance of gut epithelial integrity and host immune system homeostasis. Taking into account the beneficial health-promoting effects of GABA, the presence of the gadB gene, encoding glutamate decarboxylase that converts L-glutamate to GABA, was analyzed in Lactic Acid Bacteria (LAB) natural isolates from Zlatar cheese. The results revealed that 52% of tested Lactobacillus spp. and 8% of Lactococcus spp. isolates harbor the gadB gene. Qualitative and quantitative analysis of GABA production performed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) revealed the highest GABA production by Lactobacillus brevis BGZLS10-17. Since high GABA-producing LAB natural isolates are the most valuable source of naturally produced GABA, the probiotic properties of BGZLS10-17 were characterized. This study demonstrated high adhesion of BGZLS10-17 strain to Caco-2 cells and the ability to decrease the adhesion of Escherichia coli ATCC25922 and Salmonella enterica C29039. Treatment of differentiated Caco-2 cells monolayer with BGZLS10-17 supernatant containing GABA alleviated inflammation (production of IL-8) caused by IL-1β and significantly stimulated the expression of tight junction proteins (zonulin, occludin, and claudin 4), as well as the expression of TGF-β cytokine leading to the conclusion that immunosuppression and strengthening the tight junctions can have significant role in the maintenance of intestinal epithelial barrier integrity. Taken together the results obtained in this study support the idea that using of GABA producing BGZLS10-17 probiotic strain could be a good strategy to modulate immunological response in various inflammatory diseases, and at the same time, it could be a good candidate for adjunct starter culture for production of GABA-enriched dairy foods and beverages offering new perspectives in designing the novel functional foods

Cardiovascular Properties of the Androgen-Induced PCOS Model in Rats: The Role of Oxidative Stress

Polycystic ovary syndrome (PCOS) is a multifaced reproductive endocrinopathy affecting 6-20% of women of childbearing age. It was previously shown that women with PCOS have an increased risk of cardiovascular (CV) diseases. The aim of this study was to evaluate the cardiodynamic parameters of isolated rats' hearts, blood pressure levels, and histomorphological changes in the heart tissue following the androgen-induced PCOS model in rats and the role of oxidative stress in the development of these CV properties of PCOS. 21-day-old female rats (n=12) were divided into control and PCOS groups. PCOS was induced by administration of testosterone enanthate (1 mg/kg BW, daily) during 35 days. During the autoregulation protocol (40-120 mmHg) on the Langendorff apparatus, ex vivo cardiodynamic parameters of retrogradely perfused hearts showed enhanced contractile function and increased lusitropic effects in the left ventricle (LV) in PCOS rats. Systolic and diastolic pressures in LV were elevated at all perfusion pressure values. Systemic arterial systolic blood pressure showed borderline elevation, while mean arterial blood pressure was significantly higher in PCOS rats. Histological evaluation of heart tissue depicted hypertrophic (8.3%) alterations in LV cardiomyocytes and increase (7.3%) in LV wall thickness. Oxidative stress parameters were altered in systemic circulation, coronary venous effluent (CVE), and heart tissue. Levels of superoxide dismutase and reduced glutathione were decreased in blood and heart tissue, while catalase activity was not altered. Degree of lipid peroxidation was increased in circulation as well as heart tissue. Increased levels of O2- in CVE indicated the cardiotoxic effects in the rat PCOS model. The mentioned alterations of oxidative stress parameters in the blood, CVE, and heart could be recommended as potential contributors underlying the development of CV risk in PCOS women

Comparison of 2D proteomic maps revealed properties of Ambrosia artemisiifolia sub-pollen particles accounting for more severe asthma symptoms than its whole pollen grains

Aims and scopes: It is known that sub-pollen particles (SPP) cause more severe symptoms of asthma than its whole pollen grain counterparts, due to its smaller size and ability to penetrate deeper into the lungs. To reveal other possible causes of such more severe asthma symptoms induced by Ambrosia artemisiifolia SPP, its sub-pollen particle and pollen grain proteomes were characterized and compared. Experimental description: Protein extract of short ragweed (Ambrosia artemisiifolia) pollen and its SPP were prepared and subjected to denaturing 2-D electrophoresis. Pollen proteome spots were excised a er colloidal coomassie blue brillinat (cCBB) staining and in gel digested for liquid chromatography coupled with high resolution LTQ Orbitrap XL hybrid mass spectrometry. Parallel to that, cCBB stained gels were analyzed and quanti ed with laser scanner Typhoon 7000 series and Image 2D Master Platinum 7.0 soware (GE Healthcare, USA). Results: ere is statistically signi cant di erence between the contents of major allergen Amb a 1.05 subgroup in the ragweed whole pollen grains and SPP, the latter being richer in Amb a 1.05 (2 times), in major allergen Amb a 11 (5 times), in minor allergens Amb a 4 (7 times) and Amb a 6 (4 times). e 30 kDa basic antigen group in SPP (8 times more abundant) needs further investigation. sia artemisiifolia allergens, Amb a 1.05 and Amb a 11, minor allergens Amb a 4 and Amb a 6 which could contribute to more severe asthma symptoms caused by SPP

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

Therapy Induced Senescence (TIS) leads to sustained growth arrest of cancer cells. The associated cytostasis has been shown to be reversible and cells escaping senescence further enhance the aggressiveness of cancers. Chemicals specifically targeting senescent cells, so-called senolytics, constitute a promising avenue for improved cancer treatment in combination with targeted therapies. Understanding how cancer cells evade senescence is needed to optimise the clinical benefits of this therapeutic approach. Here we characterised the response of three different NRAS mutant melanoma cell lines to a combination of CDK4/6 and MEK inhibitors over 33 days. Transcriptomic data show that all cell lines trigger a senescence programme coupled with strong induction of interferons. Kinome profiling revealed the activation of Receptor Tyrosine Kinases (RTKs) and enriched downstream signaling of neurotrophin, ErbB and insulin pathways. Characterisation of the miRNA interactome associates miR-211-5p with resistant phenotypes. Finally, iCell-based integration of bulk and single-cell RNA-seq data identifies biological processes perturbed during senescence and predicts 90 new genes involved in its escape. Overall, our data associate insulin signaling with persistence of a senescent phenotype and suggest a new role for interferon gamma in senescence escape through the induction of EMT and the activation of ERK5 signaling

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma.

peer reviewedTherapy Induced Senescence (TIS) leads to sustained growth arrest of cancer cells. The associated cytostasis has been shown to be reversible and cells escaping senescence further enhance the aggressiveness of cancers. Chemicals specifically targeting senescent cells, so-called senolytics, constitute a promising avenue for improved cancer treatment in combination with targeted therapies. Understanding how cancer cells evade senescence is needed to optimise the clinical benefits of this therapeutic approach. Here we characterised the response of three different NRAS mutant melanoma cell lines to a combination of CDK4/6 and MEK inhibitors over 33 days. Transcriptomic data show that all cell lines trigger a senescence programme coupled with strong induction of interferons. Kinome profiling revealed the activation of Receptor Tyrosine Kinases (RTKs) and enriched downstream signaling of neurotrophin, ErbB and insulin pathways. Characterisation of the miRNA interactome associates miR-211-5p with resistant phenotypes. Finally, iCell-based integration of bulk and single-cell RNA-seq data identifies biological processes perturbed during senescence and predicts 90 new genes involved in its escape. Overall, our data associate insulin signaling with persistence of a senescent phenotype and suggest a new role for interferon gamma in senescence escape through the induction of EMT and the activation of ERK5 signaling

Bridging the gap in precision medicine: TranSYS training programme for next-generation scientists

IntroductionIn the evolving healthcare landscape, precision medicine's rise necessitates adaptable doctoral training. The European Union has recognized this and promotes the development of international, training-focused programmes called Innovative Training Networks (ITNs). In this article, we introduce TranSYS, an ITN focused on educating the next generation of precision medicine researchers. In an ambition to go beyond describing the consortium goals, our article explores two key aspects of ITNs: the training and collaboration.MethodsUsing self-report questionnaires, we evaluate the scientific, professional, and personal growth of ESRs over the duration of the ITN and investigate whether this can be linked to network activities.ResultsOur quantitative analysis approach reveals substantial improvements in scientific, professional, and social skills among young researchers facilitated by the engagement in this interdisciplinary network. We provide case studies underlining the advantages of collaborative environments, featuring innovative scientific exchange within TranSYS.DiscussionWhile challenging, ITNs foster positive growth in young researchers, yet exhibit weaknesses such as balancing stakeholder interests and partner commitment. We believe this study may benefit a variety of stakeholders, from prospective ITN creators to industry partners, to design better sustainable training networks going forward

Sex difference and intra-operative tidal volume: Insights from the LAS VEGAS study

BACKGROUND: One key element of lung-protective ventilation is the use of a low tidal volume (VT). A sex difference in use of low tidal volume ventilation (LTVV) has been described in critically ill ICU patients.OBJECTIVES: The aim of this study was to determine whether a sex difference in use of LTVV also exists in operating room patients, and if present what factors drive this difference.DESIGN, PATIENTS AND SETTING: This is a posthoc analysis of LAS VEGAS, a 1-week worldwide observational study in adults requiring intra-operative ventilation during general anaesthesia for surgery in 146 hospitals in 29 countries.MAIN OUTCOME MEASURES: Women and men were compared with respect to use of LTVV, defined as VT of 8 ml kg-1 or less predicted bodyweight (PBW). A VT was deemed 'default' if the set VT was a round number. A mediation analysis assessed which factors may explain the sex difference in use of LTVV during intra-operative ventilation.RESULTS: This analysis includes 9864 patients, of whom 5425 (55%) were women. A default VT was often set, both in women and men; mode VT was 500 ml. Median [IQR] VT was higher in women than in men (8.6 [7.7 to 9.6] vs. 7.6 [6.8 to 8.4] ml kg-1 PBW, P < 0.001). Compared with men, women were twice as likely not to receive LTVV [68.8 vs. 36.0%; relative risk ratio 2.1 (95% CI 1.9 to 2.1), P < 0.001]. In the mediation analysis, patients' height and actual body weight (ABW) explained 81 and 18% of the sex difference in use of LTVV, respectively; it was not explained by the use of a default VT.CONCLUSION: In this worldwide cohort of patients receiving intra-operative ventilation during general anaesthesia for surgery, women received a higher VT than men during intra-operative ventilation. The risk for a female not to receive LTVV during surgery was double that of males. Height and ABW were the two mediators of the sex difference in use of LTVV.TRIAL REGISTRATION: The study was registered at Clinicaltrials.gov, NCT01601223