Anne Bertolini
A5059488186- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Immune cells in cancer
- Cell Image Analysis Techniques
- Extracellular vesicles in disease
- Bioinformatics and Genomic Networks
- Enzyme Structure and Function
- Gene expression and cancer classification
- Advanced Biosensing Techniques and Applications
- Immunotherapy and Immune Responses
- Cervical Cancer and HPV Research
- ATP Synthase and ATPases Research
- Prostate Cancer Treatment and Research
- Endometrial and Cervical Cancer Treatments
- Photosynthetic Processes and Mechanisms
- Biomedical Text Mining and Ontologies
- Cancer therapeutics and mechanisms
- Cancer Immunotherapy and Biomarkers
- CAR-T cell therapy research
- Cell death mechanisms and regulation
- Microbial Metabolic Engineering and Bioproduction
- Cancer, Hypoxia, and Metabolism
- Tissue Engineering and Regenerative Medicine
- Bladder and Urothelial Cancer Treatments
- Phagocytosis and Immune Regulation
ETH Zurich
2020-2024
SIB Swiss Institute of Bioinformatics
2020-2024
University of Freiburg
2024
Recent technological advances have led to an increase in the production and availability of single-cell data. The ability integrate a set multi-technology measurements would allow identification biologically or clinically meaningful observations through unification perspectives afforded by each technology. In most cases, however, profiling technologies consume used cells thus pairwise correspondences between datasets are lost. Due sheer size can acquire, scalable algorithms that able...
Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read RNA sequencing (scRNA-seq) on clinical samples from three ovarian patients presenting with omental metastasis and increase PacBio depth to 12,000 reads per cell. Our approach captures 152,000 isoforms, which over 52,000 were not previously reported. Isoform-level analysis accounting for non-coding isoforms reveals 20% overestimation protein-coding gene...
CD8+ tumor-infiltrating T cells can be regarded as one of the most relevant predictive biomarkers in immune-oncology. Highly infiltrated tumors, referred to inflamed (clinically "hot"), show favorable response immune checkpoint inhibitors contrast tumors with a scarce infiltrate called desert or excluded "cold"). Nevertheless, quantitative and reproducible methods examining their prevalence within are lacking. We therefore established computational diagnostic algorithm quantitatively measure...
Hydroxylation of prolines to 4-trans-hydroxyproline (Hyp) is mediated by prolyl-4 hydroxylases (P4Hs). In plants, Hyps occur in Hydroxyproline-rich glycoproteins (HRGPs), and are frequently O-glycosylated. While both modifications important, e.g. for cell wall stability, they undesired plant-made pharmaceuticals. Sequence motifs prolyl-hydroxylation were proposed but did not include data from mosses, such as Physcomitrella. We identified six moss P4Hs phylogenetic reconstruction. Our...
Deep single-cell multi-omic profiling offers a promising approach to understand and overcome drug resistance in relapsed or refractory (rr) acute myeloid leukemia (AML). Here, we combine ex vivo (pharmacoscopy) with bulk DNA, RNA, protein analyses, alongside clinical data from 21 rrAML patients. Unsupervised integration reveals reduced response the Bcl-2 inhibitor venetoclax (VEN) patients treated both hypomethylating agent (HMA) VEN, compared those pre-exposed chemotherapy HMA alone....
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique to decipher tissue composition at the single-cell level and inform on disease mechanisms, tumor heterogeneity, state of immune microenvironment. Although multiple methods for computational analysis scRNA-seq data exist, their application in clinical setting demands standardized reproducible workflows, targeted extract, condense, display clinically relevant information. To this end, we designed scAmpi ( S ingle C ell A...
Abstract Identifying cell types based on expression profiles is a pillar of single analysis. Existing machine-learning methods identify predictive features from annotated training data, which are often not available in early-stage studies. This can lead to overfitting and inferior performance when applied new data. To address these challenges we present scROSHI, utilizes previously obtained type-specific gene lists does require or the existence By respecting hierarchical nature type...
Abstract The hydroxylation of proline residues to 4-trans-hydroxyproline (Hyp) is a common post-translational protein modification in plants, mediated by prolyl 4-hydroxylases (P4Hs). Hyps predominantly occur group cell wall proteins, the Hydroxyproline-rich glycoproteins (HRGPs), where they are frequently O -glycosylated. While prolyl-hydroxylation and -glycosylation important, e.g. for stability, undesired on plant-made pharmaceuticals. Sequence motifs recognized derived from vascular...
Abstract Identifying cell types based on expression profiles is a pillar of single analysis. Existing machine-learning methods identify predictive features from annotated training data, which are often not available in early-stage studies. This can lead to overfitting and inferior performance when applied new data. To address these challenges we present scROSHI, utilizes previously obtained type-specific gene sets does require or the existence By respecting hierarchical nature type...
Abstract Summary Recently, CITE-seq emerged as a multimodal single-cell technology capturing gene expression and surface protein information from the same single cells, which allows unprecedented insights into disease mechanisms heterogeneity, well immune cell profiling. Multiple profiling methods exist, but they are typically focused on either or antibody analysis, not their combination. Moreover, existing software suites easily scalable to multitude of samples. To this end, we designed...
Abstract Resistance to chemotherapy and PARPi inhibitors remains a critical challenge in the treatment of epithelial ovarian cancer, mainly due disabled apoptotic responses tumor cells. Given mesothelin’s pivotal role cancer its restricted expression healthy tissues, we conducted drug-screening discovery analysis across range genetically modified cells unveil therapeutic impact. We observed enhanced cell death with low mesothelin when exposed second mitochondria-derived activator caspases...
Multimodal profiling strategies promise to produce more informative insights into biomedical cohorts via the integration of information each modality contributes. To perform this integration, however, development novel analytical is needed. often come at expense lower sample numbers, which can challenge methods uncover shared signals across a cohort. Thus, factor analysis approaches are commonly used for high-dimensional data in molecular biology, they typically do not yield representations...
Abstract Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique to decipher tissue composition at the single-cell level and inform on disease mechanisms, tumor heterogeneity, state of immune microenvironment. Although multiple methods for computational analysis scRNA-seq data exist, their application in clinical setting demands standardized reproducible workflows, targeted extract, condense, display clinically relevant information. To this end, we designed scAmpi ( S...
<h3>Introduction/Background</h3> Vulvar cancer responds poorly to systemic treatment and in contrast other gynecological cancers, targeted therapies remain at an early stage. Interactions of clinical, immune, molecular biomarkers understood for this rare type. Here, we characterized the proteogenome vulvar squamous cell carcinoma (vSCC) provide a computational workflow integrate publicly available data study aggressive <h3>Methodology</h3> Whole exome sequencing, bulk RNA-sequencing,...
You have accessJournal of UrologyCME1 May 2022MP06-08 SINGLE-CELL SEQUENCING OF PARENTAL BLADDER CANCER AND SUBSEQUENT ORGANOIDS REVEALS DIFFERENTIAL CELL PRESERVATION Roland Seiler, Martina Minoli, Franziaks Singer, Anne Bertolini, Ulrike Menzel, Christian Beisel, and Marianna Kruithof-de Julio SeilerRoland Seiler More articles by this author , MinoliMartina Minoli SingerFranziaks Singer BertoliniAnne Bertolini MenzelUlrike Menzel BeiselChristian Beisel JulioMarianna View All Author...
Abstract Summary Single-cell RNA sequencing (scRNA-seq) based gene expression analysis is now an established powerful technique to decipher tissues at a single-cell level. Recently, CITE-seq emerged as multimodal technology capturing and surface protein information from the same single-cells, which allows unprecedented insights into disease mechanisms heterogeneity, well immune cell profiling. Multiple profiling methods exist, but they are typically focussed on either or antibody analysis,...