Publications de Nicolas Jean Philippe Guex

Melanin and Neurotransmitter Signalling Genes Are Differentially Co-Expressed in Growing Feathers of White and Rufous Barn Owls

Christian Iseli, Nicolas Jean Philippe Guex

Regulation of melanin-based pigmentation is complex, involving multiple genes. Because different genes can contribute to the same pigmentation phenotype, the genes identified in model organisms may not necessarily apply to wild species. In the barn owl (Ty ...

WILEY2025

Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing

Christian Iseli, Nicolas Jean Philippe Guex, Giovanna Ambrosini

Crop genomes accumulate deleterious mutations—a phenomenon known as the cost of domestication. Precision genome editing has been proposed to eliminate such potentially harmful mutations; however, experimental demonstration is lacking. Here we identified a ...

2025

DNA methylation by CcrM contributes to genome maintenance in the Agrobacterium tumefaciens plant pathogen

Christian Iseli, Nicolas Jean Philippe Guex, Giovanna Ambrosini

The cell cycle-regulated DNA methyltransferase CcrM is conserved in most Alphaproteobacteria, but its role in bacteria with complex or multicentric genomes remains unexplored. Here, we compare the methylome, the transcriptome and the phenotypes of wild-typ ...

OXFORD UNIV PRESS2024

Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING

Christian Iseli, Nicolas Jean Philippe Guex, Daniel Constam, Giovanna Ambrosini, Katarina Pinjusic

The transforming growth factor-beta (TGF-beta) family member activin A (hereafter Activin-A) is overexpressed in many cancer types, often correlating with cancer-associated cachexia and poor prognosis. Activin-A secretion by melanoma cells indirectly imped ...

Frontiers Media Sa2024

Comparative assessment of cytometry by time-of-flight and full spectral flow cytometry based on a 33-color antibody panel

Nicolas Jean Philippe Guex, Julien Dorier, Miguel Garcia

Mass cytometry and full spectrum flow cytometry have recently emerged as new promising single cell proteomic analysis tools that can be exploited to decipher the extensive diversity of immune cell repertoires and their implication in human diseases. In thi ...

Elsevier2024

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Christian Iseli, Nicolas Jean Philippe Guex, Giovanna Ambrosini

Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpre ...

BMC2024

tRNA-derived fragments in T lymphocyte-beta cell crosstalk and in type 1 diabetes pathogenesis in NOD mice

Christian Iseli, Nicolas Jean Philippe Guex

Aims/hypothesistRNAs play a central role in protein synthesis. Besides this canonical function, they were recently found to generate non-coding RNA fragments (tRFs) regulating different cellular activities. The aim of this study was to assess the involveme ...

SPRINGER2024

Mechanopathology of biofilm-like Mycobacterium tuberculosis cords

Nicolas Jean Philippe Guex, Graham Knott, John McKinney, Neeraj Dhar, Jessica Sordet, Maxime Jan, Kunal Sharma, Mélanie Thérèse Marie Hannebelle, Vivek Vijay Thacker, Richa Mishra

Mycobacterium tuberculosis (Mtb) cultured axenically without detergent forms biofilm-like cords, a clinical identifier of virulence. In lung-on-chip (LoC) and mouse models, cords in alveolar cells contribute to suppression of innate immune signaling via nu ...

Cell Press2023

A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy

Nicolas Jean Philippe Guex

GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, i ...

2023

DNA modifications impact natural transformation of Acinetobacter baumannii

Christian Iseli, Nicolas Jean Philippe Guex, Melanie Blokesch, Nina Vesel, Alexandre Lemopoulos

Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes o ...

2023

Chromosome-level organization of the regulatory genome in the Drosophila nervous system

Christian Iseli, Nicolas Jean Philippe Guex, Julien Dorier, Marion Leleu, Brian Donal McCabe, Rebecca Carolyn Smith

Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta-domains ...

2023

Molecular insights into sex-specific metabolic alterations in Alzheimer’s mouse brain using multi-omics approach

Nicolas Jean Philippe Guex, Jean-Yves Chatton, Maxime Jan

2023

SPICA: Swiss portal for immune cell analysis

Christian Iseli, Nicolas Jean Philippe Guex

Single-cell transcriptomics allows the study of immune cell heterogeneity at an unprecedented level of resolution. The Swiss portal for immune cell analysis (SPICA) is a web resource dedicated to the exploration and analysis of single-cell RNA-seq data of ...

OXFORD UNIV PRESS2022

Essential role of Cp190 in physical and regulatory boundary formation

Christian Iseli, Nicolas Jean Philippe Guex, Julien Dorier

Boundaries in animal genomes delimit contact domains with enhanced internal contact frequencies and have debated functions in limiting regulatory cross-talk between domains and guiding enhancers to target promoters. Most mammalian boundaries form by stalli ...

2022

Unexpected post‐glacial colonisation route explains the white colour of barn owls ( Tyto alba ) from the British Isles

Christian Iseli, Nicolas Jean Philippe Guex

The climate fluctuations of the Quaternary shaped the movement of species in and out of glacial refugia. In Europe, the majority of species followed one of the described traditional postglacial recolonization routes from the southern peninsulas towards the ...

2022

Revisiting the specificity and ability of phospho-S129 antibodies to capture alpha-synuclein biochemical and pathological diversity

Christian Iseli, Nicolas Jean Philippe Guex, Hilal Lashuel, Anass Chiki, Ramanath Narayana Hegde, Anne-Laure Mahul Mellier, Ritwik Burai, Sean Michael Deguire, Melek Firat Altay, Sonia Donzelli, Jonathan Jean-Pierre Ricci, Salvatore Novello, Pedro José Santana Ribeiro Magalhães, Yllza Jasiqi

Antibodies against phosphorylated alpha-synuclein (aSyn) at 5129 have emerged as the primary tools to investigate, monitor, and quantify aSyn pathology in the brain and peripheral tissues of patients with Parkinson's disease and other neurodegenerative dis ...

NATURE PORTFOLIO2022

Soil protist function varies with elevation in the Swiss Alps

Nicolas Jean Philippe Guex, Enrique Lara, Edward Mitchell, Aline Buri

Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, u ...

2022

Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean

Nicolas Jean Philippe Guex, Eléonore Lavanchy

The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. A ...

2022

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

Christian Iseli, Nicolas Jean Philippe Guex, Julien Dorier, Flavia Marzetta

Vertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding ...

Nature Research2021

DBnorm as an R package for the comparison and selection of appropriate statistical methods for batch effect correction in metabolomic studies

Nicolas Jean Philippe Guex, Cristian Carmeli, Aurélien Thomas, Tiziana Caputo, Murielle Bochud

As a powerful phenotyping technology, metabolomics provides new opportunities in biomarker discovery through metabolome-wide association studies (MWAS) and the identification of metabolites having a regulatory effect in various biological processes. While ...

Nature Research2021