Publications by Giovanna Ambrosini

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

biogrowleR: Enhancing Longitudinal Data Analysis

Cathrin Brisken, Giovanna Ambrosini, Andrea Agnoletto, Carlos Henrique Venturi Ronchi, Hazel Margaret Quinn

Time course measurements are used for many applications in biomedical research, ranging from growth curves to drug efficacy testing and high-throughput screening. Statistical methods used to analyze the resulting longitudinal data, such as t-tests or repea ...

Springer Science and Business Media LLC2025

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

Structural and molecular characterization of astrocyte and vasculature connectivity in the mouse hippocampus and cortex

Henry Markram, Giovanna Ambrosini, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Romain Guiet, Nicolas René Chiaruttini, Elvis Boci

The relation of astrocytic endfeet to the vasculature plays a key functional role in the neuro‐glia‐vasculature unit. We characterize the spatial organization of astrocytes and the structural aspects that facilitate their involvement in molecular exchanges ...

Wiley2024

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

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

MarrowQuant 2.0: A Digital Pathology Workflow Assisting Bone Marrow Evaluation in Experimental and Clinical Hematology

Olivier Burri, Giovanna Ambrosini, Bart Deplancke, Arne Seitz, Olaia Maria Naveiras Torres-Quiroga, Frédérica Schyrr, Rita Sarkis, Mariangela Costanza, Martin Weigert

2023

Integrating distribution kinetics and toxicodynamics to assess repeat dose neurotoxicity in vitro using human BrainSpheres: a case study on amiodarone

Giovanna Ambrosini

For ethical, economical, and scientific reasons, animal experimentation, used to evaluate the potential neurotoxicity of chemicals before their release in the market, needs to be replaced by new approach methodologies. To illustrate the use of new approach ...

FRONTIERS MEDIA SA2023

Estrogen receptor positive breast cancers have patient specific hormone sensitivities and rely on progesterone receptor

Cathrin Brisken, Giovanna Ambrosini, Ayyakkannu Ayyanan, Laura Battista, Valentina Scabia, Csaba Ferenc László, Fabio De Martino, Andrea Agnoletto

Estrogen and progesterone receptor (ER, PR) signaling control breast development and impinge on breast carcinogenesis. ER is an established driver of ER + disease but the role of the PR, itself an ER target gene, is debated. We assess the issue in clinical ...

Nature Portfolio2022

Epithelial-mesenchymal plasticity determines estrogen receptor positive breast cancer dormancy and epithelial reconversion drives recurrence

Cathrin Brisken, Giovanna Ambrosini, Georgios Sflomos, Patrik Aouad, Fabio De Martino, Yueyun Zhang, Céline Marie Victoria Stibolt, Kelly Spry Maggs, Hazel Margaret Quinn

More than 70% of human breast cancers (BCs) are estrogen receptor α-positive (ER+). A clinical challenge of ER+ BC is that they can recur decades after initial treatments. Mechanisms governing latent disease remain elusive due to lack of adequate in vivo m ...

Nature Research2022

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1

Philipp Bucher, Cathrin Brisken, Giovanna Ambrosini, Ayyakkannu Ayyanan, Laura Battista, Georgios Sflomos, Valentina Scabia, Maryse Fiche, Patrik Aouad, Fabio De Martino

Invasive lobular carcinoma (ILC) is the most frequent special histological subtype of breast cancer, typically characterized by loss of E‐cadherin. It has clinical features distinct from other estrogen receptor‐positive (ER+) breast cancers but the molecul ...

2021

Contraceptive progestins with androgenic properties stimulate breast epithelial cell proliferation

Philipp Bucher, Cathrin Brisken, Giovanna Ambrosini, Laura Battista, Céline Berthe Constantin, Valentina Scabia, Marie Shamseddin, Csaba Ferenc László, Fabio De Martino

Hormonal contraception exposes women to synthetic progesterone receptor (PR) agonists, progestins, and transiently increases breast cancer risk. How progesterone and progestins affect the breast epithelium is poorly understood because we lack adequate mode ...

2021

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux

BackgroundPositional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological application ...

2020

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux, René Dreos, Patrick Meylan

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

2020

The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche

Philipp Bucher, Cathrin Brisken, Renuga Devi Rajaram, Giovanna Ambrosini, Marian Caikovski, Rachel Marcone, Céline Berthe Constantin, Dalya Ataca, Marie Shamseddin, Patrik Aouad, Csaba Ferenc László

Estrogens and progesterone control breast development and carcinogenesis via their cognate receptors expressed in a subset of luminal cells in the mammary epithelium. How they control the extracellular matrix, important to breast physiology and tumorigenes ...

Nature Research2020

Chromatin three-dimensional interactions mediate genetic effects on gene expression

Philipp Bucher, David Hacker, Giovanna Ambrosini, Sanjeev Kumar

Studying the genetic basis of gene expression and chromatin organization is key to characterizing the effect of genetic variability on the function and structure of the human genome. Here we unravel how genetic variation perturbs gene regulation using a da ...

American Association for the Advancement of Science2019

Common genetic variants associated with Parkinson's disease display widespread signature of epigenetic plasticity

Philipp Bucher, Giovanna Ambrosini, Amit Sharma, Tikam Chand Dakal

Parkinson disease (PD) is characterized by a pivotal progressive loss of substantia nigra dopaminergic neurons and aggregation of alpha-synuclein protein encoded by the SNCA gene. Genome-wide association studies identified almost 100 sequence variants link ...

Springer Nature2019

Chromatin 3D interactions mediate genetic effects on gene expression

Philipp Bucher, David Hacker, Giovanna Ambrosini

NATURE PUBLISHING GROUP2019

SNP2TFBS-a database of regulatory SNPs affecting predicted transcription factor binding site affinity

Philipp Bucher, Giovanna Ambrosini, Sanjeev Kumar

NATURE PUBLISHING GROUP2018

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-r ...

2018