[HTML][HTML] Single-cell transcriptomics in cancer immunobiology: the future of precision oncology

F Valdes-Mora, K Handler, AMK Law… - Frontiers in …, 2018 - frontiersin.org
Cancer is a heterogeneous and complex disease. Tumors are formed by cancer cells and a
myriad of non-cancerous cell types that together with the extracellular matrix form the tumor …

[HTML][HTML] Active eosinophils regulate host defence and immune responses in colitis

…, K Bach, IE Acar, NG Núñez, D Crepaz, K Handler… - Nature, 2023 - nature.com
In the past decade, single-cell transcriptomics has helped to uncover new cell types and
states and led to the construction of a cellular compendium of health and disease. Despite this …

[HTML][HTML] Fragment-sequencing unveils local tissue microenvironments at single-cell resolution

K Handler, K Bach, C Borrelli, S Piscuoglio… - Nature …, 2023 - nature.com
Cells collectively determine biological functions by communicating with each other—both
through direct physical contact and secreted factors. Consequently, the local microenvironment …

A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons

…, F Mhamedi, O David, SB Sain, K Handler… - Nucleic Acids …, 2022 - academic.oup.com
Asymmetric subcellular mRNA localization allows spatial regulation of gene expression and
functional compartmentalization. In neurons, localization of specific mRNAs to neurites is …

[HTML][HTML] Differential regulation of β-catenin-mediated transcription via N-and C-terminal co-factors governs identity of murine intestinal epithelial stem cells

C Borrelli, T Valenta, K Handler, K Vélez… - Nature …, 2021 - nature.com
The homeostasis of the gut epithelium relies upon continuous renewal and proliferation of
crypt-resident intestinal epithelial stem cells (IESCs). Wnt/β-catenin signaling is required for …

Single-cell RNA sequencing unveils intestinal eosinophil development and specialization

…, NG Núñez, I Gonzalez-Perez, D Crepaz, K Handler… - bioRxiv, 2021 - biorxiv.org
Eosinophils are an integral part of the gastrointestinal (GI) immune system that contribute to
homeostatic and inflammatory processes. Here, we investigated the existence of functional …

TiO2 nanoparticles abrogate the protective effect of the Crohn's disease-associated variation within the PTPN22 gene locus

M Schwarzfischer, A Niechcial, K Handler, Y Morsy… - Gut, 2023 - gut.bmj.com
Objective Inflammatory bowel disease (IBD) is a multifactorial condition driven by genetic
and environmental risk factors. A genetic variation in the protein tyrosine phosphatase non-…

Sphere-sequencing unveils local tissue microenvironments at single cell resolution

K Handler, K Bach, C Borrelli, X Ficht, IE Acar, AE Moor - bioRxiv, 2022 - biorxiv.org
The spatial organization of cells within tissues is tightly linked to their biological function. Yet,
methods to probe the entire transcriptome of multiple native tissue microenvironments at …

Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)

…, K Bach, JA Kretz, K Handler… - Molecular Systems …, 2024 - embopress.org
Sequencing-based spatial transcriptomics (ST) methods allow unbiased capturing of RNA
molecules at barcoded spots, charting the distribution and localization of cell types and …

Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues

…, LR de la Fuente, B Gloss, AMK Law, K Handler… - bioRxiv, 2023 - biorxiv.org
Single-cell transcriptomics has emerged as the preferred tool to define cell identity through
the analysis of gene expression signatures. However, there are limited studies that have …