Publications related to From gut homeostasis to cancer

Related publications (39)

Abstract IA02: Cancer-specific foundation models: Friend or foe in healthcare AI?

Foundation models have become a powerful tool in single-cell transcriptomics, enabling broad generalization across tasks such as cell type annotation, data integration, and drug response prediction. Yet, most current models are trained predominantly on hea ...

American Association for Cancer Research (AACR)2025

HPV16-Expressing Tumors Release Multiple IL-1 Ligands to Orchestrate Systemic Immunosuppression Whose Disruption Enables Efficacy of a Therapeutic Vaccine

Marjorie Gabrielle Marie Cayatte, Dilara Selin Ozdoganlar, Douglas Hanahan, Krisztian Homicsko, Morgane Marie Lecointre, Jeremy Gilles Louis Guillot

It is well-established that symptomatic cancers evade immune destruction by coalescing tumor microenvironments to suppress adaptive immunity. Additionally, mouse models of cervical and other cancers have revealed a capability of tumors to systemically indu ...

American Association for Cancer Research (AACR)2025

A comparative analysis of gene expression profiling by statistical and machine learning approaches

Anaïs Betsabeh Haget, Maria Boulougouri

Motivation Many machine learning (ML) models developed to classify phenotype from gene expression data provide interpretations for their decisions, with the aim of understanding biological processes. For many models, including neural networks, interpretati ...

OXFORD UNIV PRESS2025

Explaining the Relationships Between Age, Endocrine Therapy Persistence, and Risk of Recurrence in Hormone Receptor–Positive Early Breast Cancer: A Nationwide Cohort Study

Mats Julius Stensrud, Elise Hélène Dumas

Young age is associated with increased risk of recurrence in hormone receptor (HR)–positive early-stage breast cancer (eBC). Lack of adherence to endocrine therapy (ET) is a potential reason for the lower survival proportions observed in younger patients, ...

American Society of Clinical Oncology (ASCO)2025

Computational design of complex protein folds and soluble analogs of membrane proteins

Casper Alexander Goverde

Proteins are the molecular machines of life, driving essential biological processes such as enzymatic catalysis, cellular signaling, and immune responses. The ability to design entirely new proteins with desired structures and functions has immense implica ...

EPFL2025

Bioengineering functional organoid models across scales

Tania Hübscher

The last two decades have seen the development of organoid models for many different tissues and organs. Organoids are three-dimensional organ-mimetics derived from stem or progenitor cells comprising various specialized cell types, resembling the architec ...

EPFL2024

Accessible and highly observable gastrointestinal organoid model systems for studying host-pathogen interactions

Moritz Hofer

Traditional cell cultures have long been fundamental to biological research, offering an alternative to animal models burdened by ethical constraints and procedural intricacies, often lacking relevance to human physiology and disease. Moreover, their inabi ...

EPFL2024

Cytokine-armed dendritic cell progenitors for antigen-agnostic cancer immunotherapy

Ali Ghasemi

Dendritic cells (DCs) are specialized myeloid cells with the ability to uptake, process, and present antigens to T lymphocytes. They also generate cytokine and chemokine gradients that regulate immune cell trafficking, activation, and function. Monocyte-de ...

EPFL2024

Characterization of the gut-bone marrow axis through bile acid signaling

Alejandro Alonso Calleja

Communication between the intestine and other organs such as the lungs, brain or bones is mediated by several metabolites, like short-chain fatty acids or bile acids, that relay information about nutritional and microbiota status. Bile acids are endogenous ...

EPFL2024

Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) methods for the therapeutic drug monitoring of cytotoxic anticancer drugs: An update

Sandro Carrara, Myriam Briki

In the era of precision medicine, there is increasing evidence that conventional cytotoxic agents may be suitable candidates for therapeutic drug monitoring (TDM)- guided drug dosage adjustments and patient's tailored personalization of non-selective chemo ...

Elsevier2024

The conceptual foundations of innate immunity: Taking stock 30 years later

Bruno Lemaitre

While largely neglected over decades during which adaptive immunity captured most of the attention, innate immune mechanisms have now become central to our understanding of immunology. Innate immunity provides the first barrier to infection in vertebrates, ...

2024

Tumor-educated Gr1+CD11b+cells drive breast cancer metastasis via OSM/IL-6/JAK-induced cancer cell plasticity

Nadine Fournier, Annamaria Kauzlaric, Manon Bulliard, Rachel Marcone

Cancer cell plasticity contributes to therapy resistance and metastasis, which represent the main causes of cancer-related death, including in breast cancer. The tumor microenvironment drives cancer cell plasticity and metastasis, and unraveling the underl ...

Amer Soc Clinical Investigation Inc2024

Development of patient-derived lymphomoids with preserved tumor architecture for lymphoma therapy screening

Justine Epiney, Divyanshu Srivastava, Elisa Oricchio, Daniele Tavernari, Albert Santamaria Martinez

The efficacy of anti-cancer therapies depends on the genomic composition of the tumor, its microenvironment, spatial organization, and intra-tumor heterogeneity. B-cell lymphomas are a heterogeneous group of tumors emerging from B-cells at different stages ...

Nature Portfolio2024

Next-Generation Modeling of Cancer Using Organoids

Wouter Richard Karthaus, Jillian Rose Love

In the last decade, organoid technology has become a cornerstone in cancer research. Organoids are long-term primary cell cultures, usually of epithelial origin, grown in a three-dimensional (3D) protein matrix and a fully defined medium. Organoids can be ...

Cold Spring Harbor Lab Press, Publications Dept2024

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Alex Russell Lederer

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

EPFL2024

Clinically compliant cryopreservation of differentiated retinal pigment epithelial cells

Cheng Zhao, Gioele La Manno, Alex Russell Lederer

Background aims: Age-related macular degeneration (AMD) is the most common cause of blindness in elderly patients within developed countries, affecting more than 190 million worldwide. In AMD, the retinal pigment epithelial (RPE) cell layer progressively d ...

Elsevier Sci Ltd2024

NMR and MS reveal characteristic metabolome atlas and optimize esophageal squamous cell carcinoma early detection

Lijing Xin

Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. Here, we conduct NMR- and MS-based metabo ...

Nature Portfolio2024

Engineering hydrogel microenvironments for epithelial organoid culture

Antonius Chrisnandy

Organoids, miniature tissues generated from self-organizing stem cells within three-dimensional (3D) extracellular matrices (ECM), have opened up exciting possibilities for in vitro studies of complex physiological processes. A key factor in the success of ...

EPFL2024

A chemical biology approach to decipher chromatin ubiquitylation by RNF168

Pauline Franz

DNA damage signaling following DNA double-strand breaks (DSBs) involves numerous regulating proteins, which dynamically recognize ('read') and alter ('write' or 'erase') histone post-translational modifications (PTMs). Among these PTMs, the ubiquitin syste ...

EPFL2024

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Fides Zenk

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Nature Portfolio2024