Biology subjects

Stephan-Otto Attolini, C.

Publications and source records attributed to Stephan-Otto Attolini, C..

12 recordsLinked to original sources

bioRxiv2025

BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis

Ageing is characterised by persistent low-grade inflammation that is linked to impaired tissue homeostasis and functionality. However, the molecular mechanisms driving age-associated inflammation remain poorly understood. The mammalian skin is a clinically relevant target of age-driven inflammation associated with compromised barrier function, inefficient wound healing, elevated oxidative stress, and DNA damage accumulation. Here, we show that upon ageing a previously uncharacterised BMAL1-YAP transcriptional complex is hijacked from chromatin regions associated with homeostatic genes in adult epidermis and redirected to inflammation-related enhancers, amplifying the transcription of their target genes. Independently of its known role as a core circadian clock component, BMAL1 partners with the mechanosensitive transcriptional cofactor YAP at enhancer regions to regulate epidermal identity genes. In contrast, in aged skin, BMAL1-YAP complexes bind to enhancers of inflammation-related genes, co-regulated by NF-KB. Interestingly, aged pro-inflammatory signals from the IL-17 pathway activate YAP in a Hippo-independent manner. These findings unveil a transcriptional mechanism underlying epidermal ageing, linking chromatin dynamics to inflammatory transcriptional programs through BMAL1-YAP-bound enhancer rewiring. By elucidating how ageing reprograms transcriptional networks, our work highlights potential strategies to counteract chronic inflammation and restore tissue homeostasis across age-related loss of functionality.

molecular biology↗

bioRxiv2024

Targeted KRAS(G12V) degradation elicits efficient and durable lung adenocarcinoma regression in vivo

Recent drug discovery breakthroughs led to the approval of KRASG12C inhibitors in lung adenocarcinoma (LUAD). Unfortunately, clinical responses remain limited due to rapid resistance onset. Proteolysis-targeting chimeras (PROTACs) have emerged as promising alternatives to traditional inhibition. However, there is limited mechanistic understanding of KRAS degradation in vivo. Here, we developed a preclinical LUAD mouse model and demonstrated that targeted oncogenic KRAS degradation induces rapid tumor regression. Transcriptional, histological, and immunophenotypic analyses revealed a substantial remodeling of the tumor microenvironment. Notably, disease relapse observed during long-term degrader treatment stems from proteolysis machinery dysregulation, indicating resistance mechanisms distinct from those reported upon KRAS inhibition. Our findings highlight the therapeutic potential of KRAS degradation in LUAD, offering insights into cell-intrinsic and extrinsic mechanisms driving durable antitumor responses and supporting further clinical exploration. SIGNIFICANCEGiven the short duration of the clinical responses to KRAS inhibitors, complementary therapies are a dire medical need. Our preclinical findings endorse KRAS degradation as a therapeutic alternative in LUAD, where cell-intrinsic and extrinsic mechanisms drive tumor regression and durable therapeutic responses.

cancer biology↗

bioRxiv2024

Perturbation-driven transcriptional heterogeneity impacts cell fitness

Heterogeneity is inherent to living organisms and it determines cell fate and phenotypic variability1-3. Indeed, even isogenic cell populations vary in quantifiable phenotypes. Here we generated a high-resolution single-cell yeast transcriptome atlas using genotype and clone RNA barcoded deletions to profile 3500 mutants under control and stress conditions in a genome-scale genetic and environmental perturbation screen. We uncovered a myriad of cell states within a population with specific transcriptional architectures that are both intrinsically and extrinsically regulated, thereby suggesting a continuum of cell states. Cell state occupancy and transition can be genetically modulated with specific mutants that act as state attractors, resulting in differential fitness. By exploiting the power of intra-genetic variability, we identified regulators of transcriptional heterogeneity that are functionally diverse and influenced by the environment. One-Sentence SummaryThe yeast single cell-transcriptome atlas based on RNA-traceable genetic perturbations served to map cellular states and define their underlying genetic basis.

genetics↗

bioRxiv2024

Persister cancer cells are characterized by H4K20me3 heterochromatin that defines a low inflammatory profile

Anti-cancer therapies may induce proliferative arrest in cancer cells in the form of senescence or drug-tolerant persistency, the latter being a reversible arrest with similarities to embryonic diapause. Here, we use mTOR/PI3K inhibition to develop and characterize a model of persistency/diapause-like arrest in human cancer cells of various origins. We show that persister and senescent cancer cells share an expanded lysosomal compartment and hypersensitivity to BCL-XL inhibition. However, persister cells do not exhibit other features of senescence, such as the loss of Lamin B1, senescence-associated b-galactosidase activity, and an inflammatory phenotype. Compared to senescent cells, persister cells have a profoundly diminished senescence-associated secretory phenotype (SASP), low activation of interferon signaling pathways and lack upregulation of MHC-I presentation. Based on a genome-wide CRISPR/Cas9 screen performed in diapause mouse embryonic stem cells (mESC), we discover that persister human cancer cells are hypersensitive to the inhibition of one-carbon metabolism. This finding led us to uncover that the repressive heterochromatic mark H4K20me3 is enriched at promoters of SASP and interferon response genes in persister cells, but not in senescent cells. Collectively, we define novel features and vulnerabilities of persister cancer cells and we provide insight into the epigenetic mechanisms underlying their low inflammatory and immunogenic activity.

cancer biology↗

bioRxiv2022

Induction of senescence renders cancer cells highly immunogenic

Cellular senescence is a stress response that activates innate immunity. However, the interplay between senescent cells and the adaptive immune system remains largely unexplored. Here, we show that senescent cells display enhanced MHC class I (MHC-I) antigen processing and presentation. Immunization of mice with senescent syngeneic fibroblasts generates CD8 T cells reactive against both normal and senescent fibroblasts, some of them targeting senescence-associated MHC-I-peptides. In the context of cancer, we demonstrate that senescent cancer cells trigger strong anti-tumor protection mediated by antigen-presenting cells and CD8 T cells. This response is superior to the protection elicited by cells undergoing immunogenic cell death. Finally, induction of senescence in patient-derived cancer cells exacerbates the activation of autologous tumor-reactive CD8 tumor-infiltrating lymphocytes (TILs) with no effect on non-reactive TILs. Our study indicates that immunization with senescent cancer cells strongly activates anti-tumor immunity, and this can be exploited for cancer therapy. STATEMENT OF SIGNIFICANCEOur study shows that senescent cells are endowed with a high immunogenic potential, superior to the gold standard of immunogenic cell death. The induction of senescence in cancer cells can be exploited to develop efficient and protective CD8-dependent anti-tumor immune responses.

cancer biology↗

bioRxiv2022

Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming

The expression of the pluripotency factors OCT4, SOX2, KLF4 and MYC (OSKM) can convert somatic differentiated cells into pluripotent stem cells in a process known as reprogramming. Notably, cycles of brief OSKM expression do not change cell identity but can reverse markers of aging in cells and extend longevity in progeroid mice. However, little is known about the mechanisms involved. Here, we have studied changes in the DNA methylome, transcriptome and metabolome in naturally aged mice subject to a single period of transient OSKM expression. We found that this is sufficient to reverse DNA methylation changes that occur upon aging in the pancreas, liver, spleen and blood. Similarly, we observed reversion of transcriptional changes, especially regarding biological processes known to change during aging. Finally, some serum metabolites altered with aging were also restored to young levels upon transient reprogramming. These observations indicate that a single period of OSKM expression can drive epigenetic, transcriptomic and metabolomic changes towards a younger configuration in multiple tissues and in the serum.

cell biology↗

bioRxiv2021

A comparison of rotation-based scores for gene set analysis

Gene-wise differential expression is usually the first major step in the statistical analysis of high-throughput data obtained from tech-niques such as microarrays or RNA-sequencing. The analysis at gene level is often complemented by the screening of the data in a broader biological context that considers as unit of analysis meaningful groups of genes that may have functions in certain biological processes. Among the vast number of publications about gene set analysis, the rotation test for gene set analysis, also referred by roast, is a general sample randomization approach that maintains the integrity of the intra-gene set correlation structure in defining the null distribution of the test. In this work we compare the performance of several enrichment score functions using such rotational approach for hypothesis testing. We find that computationally intensive measures based on Kolmogorov-Smirnov statistics fail to improve the rates of simpler measures of GSA like mean and maxmean scores. We also show the importance of ac-counting for the gene linear dependence structure of the testing set, which it is linked to the loss of effective signature size. In this regard, weighted statistics are introduced with the aim of maximizing the ef-fective signature size. These are found to out-power other usual scores in some simulations scenarios. The average of absolute values is found to be the most powerful score using both simulated and benchmarking data. All tools are available in the roastgsa R package.

bioinformatics↗

bioRxiv2021

Identification and drug-induced reversion of molecular signatures of Alzheimers disease onset and progression in AppNL-G-F, AppNL-F and 3xTg-AD mouse models

Alzheimers disease (AD) is the most common form of dementia. Over fifty years of intense research have revealed many key elements of the biology of this neurodegenerative disorder. However, our understanding of the molecular bases of the disease is still incomplete, and the medical treatments available for AD are mainly symptomatic and hardly effective. Indeed, the robustness of biological systems has revealed that the modulation of a single target is unlikely to yield the desired outcome and we should therefore move from gene-centric to systemic therapeutic strategies. Here we present the complete characterization of three murine models of AD at different stages of the disease (i.e. onset, progression and advanced). To identify genotype-to-phenotype relationships, we combine the cognitive assessment of these mice with histological analyses and full transcriptional and protein quantification profiling of the hippocampus. Comparison of the gene and protein expression trends observed in AD progression and physiological aging revealed certain commonalities, such as the upregulation of microglial and inflammation markers. However, although AD models show accelerated aging, other factors specifically associated with A{beta} pathology are involved. Despite the clear correlation between mRNA and protein levels of the dysregulated genes, we discovered a few proteins whose abundance increases with AD progression, while the corresponding transcript levels remain stable. Indeed, we show that at least two of these proteins, namely lfit3 and Syt11, co-localize with A{beta} plaques in the brain. Finally, we derived specific A{beta}-related molecular AD signatures and looked for drugs able to globally revert them. We found two NSAIDs (dexketoprofen and etodolac) and two anti-hypertensives (penbutolol and bendroflumethiazide) that overturn the cognitive impairment in AD mice while reducing A{beta} plaques in the hippocampus and partially restoring the physiological levels of AD signature genes to wild-type levels. TeaserThe comprehensive characterization of three AD mouse models reveals disease signatures that we used to identify approved drugs able to modify the etiology of the pathology and overturn cognitive impairment.

neuroscience↗

bioRxiv2018

chroGPS 2.0: differential analysis of epigenome maps in R.

1In the last years, after systematic mapping of epigenomics data from multiple organisms, tissues and cell lines, the ability to efficiently integrate, visualize and compare such information remains a challenge. Here we present chroGPS version 2, a major update of our previously developed software chroGPS, for visualization and differential analysis of epigenomes. Methods are provided for efficient integration and comparison of data from different conditions or biological backgrounds, accounting and adjusting for systematic biases in order to provide an efficient and statistically robust base for differential analysis. We also include functionalities for general data assessment and quality control prior to comparing maps, such as functions to study chromatin domain conservation between epigenomic backgrounds, to detect gross technical outliers and also to help in the selection of candidate marks for de-novo epigenome mapping.\n\nAvailabilityhttps://www.bioconductor.org/packages/release/bioc/html/chroGPS.html - Contact: oscar.reina@irbbarcelona.org

bioinformatics↗

bioRxiv2018

Adjusting for systematic technical biases in risk assessment of gene signatures in transcriptomic cancer cohorts

In recent years, many efforts in clinical and basic research have focused on finding molecular features of tumor samples with prognostic or classification potential. Among these, the association of the expression of gene signatures with survival probability is of special interest given its relatively direct applicability in the clinic and its power to shed insights into the molecular basis of cancer.\n\nAlthough great efforts have been invested in data processing to control for unknown sources of variability in a gene-wise manner, little is known about the behaviour of gene signatures with respect to the effect of technical variables.\n\nHere we show that the association of signatures with survival may be biased due to technical reasons and propose a simple and low intensive methodology based on correction by expectation under gene randomization. The resulting estimates are centred around zero and ensure correct asymptotic inference. Moreover, our methodology is robust against spurious correlations between global dataset tendencies and clinical outcome.\n\nAll tools (will be soon) available in the \"HRunbiased\" R package as well as processed datasets for colorectal and breast cancer.

bioinformatics↗

bioRxiv2018

Blimp-1 mediates the temporal control of embryonic tube maturation

The specification of tissue identity during embryonic development requires precise spatiotemporal coordination of gene expression. Many transcription factors required for the development of organs have been identified and their expression patterns are known; however, the mechanisms through which they coordinate gene expression in time remain poorly understood. Here we show that hormone-induced transcription factor Blimp-1 participates in the temporal coordination of tubulogenesis in Drosophila melanogaster by regulating the expression of many genes involved in tube maturation. In particular, we demonstrate that Blimp-1 regulates the expression of genes involved in chitin deposition and F-actin organization. We show that Blimp-1 is involved in the temporal control of lumen maturation by regulating the beginning of chitin deposition. We also report that Blimp-1 represses a variety of genes involved in tracheal maturation. Finally, we reveal that the kinase Btk29A serves as a link between Blimp-1 transcriptional repression and apical extra-cellular matrix organization.

developmental biology↗

bioRxiv2017

Drosophila larval brain neoplasms present tumour-type dependent genome instability

Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) are found at different rates in human cancer. To determine if these genetic lesions appear in Drosophila tumours we have sequenced the genomes of 17 malignant neoplasms caused by mutations in l(3)mbt, brat, aurA, or lgl. We have found CNVs and SNPs in all the tumours. Tumour-linked CNVs range between 11 and 80 per sample, affecting between 92 and 1546 coding sequences. CNVs are in average less frequent in l(3)mbt than in brat lines. Nearly half of the CNVs fall within the 10 to 100Kb range, all tumour samples contain CNVs larger that 100 Kb and some have CNVs larger than 1Mb. The rates of tumour-linked SNPs change more than 20-fold depending on the tumour type: late stage brat, l(3)mbt, and aurA and lgl lines present median values of SNPs/Mb of exome of 0.16, 0.48, and 3.6, respectively. Higher SNP rates are mostly accounted for by C>A transversions, which likely reflect enhanced oxidative stress conditions in the affected tumours. Both CNVs and SNPs turn over rapidly. We found no evidence for selection of a gene signature affected by CNVs or SNPs in the cohort. Altogether, our results show that the rates of CNVs and SNPs, as well as the distribution of CNV sizes in this cohort of Drosophila tumours are well within the range of those reported for human cancer. Genome instability is therefore inherent to Drosophila malignant neoplastic growth at a variable extent that is tumour type dependent.\n\nAUTHOR SUMMARYDrosophila models of malignant growth can help to understand the molecular mechanisms of malignancy. These models are known to exhibit some of the hallmarks of cancer like sustained growth, immortality, metabolic reprogramming, and others. However, it is currently unclear if these fly models are affected by genome instability, which is another hallmark of many human malignant tumours. To address this issue we have sequenced and analysed the genomes of a cohort of seventeen fly tumour samples. We have found that genome instability is a common trait of Drosophila malignant tumours, which occurs at an extent that is tumour-type dependent, at rates that are similar to those of different human cancers.

cancer biology↗