A5051109523- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Renal and related cancers
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Genetic and Kidney Cyst Diseases
- Plant Molecular Biology Research
- Protist diversity and phylogeny
- Pancreatic and Hepatic Oncology Research
- Gene expression and cancer classification
- MicroRNA in disease regulation
- Single-cell and spatial transcriptomics
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Metabolism and Genetic Disorders
- Pediatric Urology and Nephrology Studies
- Ion channel regulation and function
- Flood Risk Assessment and Management
- Neuroscience and Neuropharmacology Research
- PI3K/AKT/mTOR signaling in cancer
- Cancer Genomics and Diagnostics
- Advanced Image and Video Retrieval Techniques
- Colorectal Cancer Screening and Detection
- Protein Degradation and Inhibitors
- Biomedical Research and Pathophysiology
IRCCS Ospedale San Raffaele
2022-2024
Vita-Salute San Raffaele University
2023-2024
Istituti di Ricovero e Cura a Carattere Scientifico
2023-2024
École Polytechnique Fédérale de Lausanne
2015-2022
University of Zurich
2015-2022
Life Science Zurich
2015-2022
ETH Zurich
2021
FZI Research Center for Information Technology
2017
Research Institute of Molecular Pathology
2014
Vienna Biocenter
2014
RNA sequencing (RNA-seq) has become a standard procedure to investigate transcriptional changes between conditions and is routinely used in research clinics. While differential expression (DE) analysis two been extensively studied, improved over the past decades, RNA-seq time course (TC) DE algorithms are still their early stages. In this study, we compare, for first time, existing TC tools on an extensive simulation data set validated best performing published data. Surprisingly, were...
Abstract Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here, we use Nanopore long-read sequencing cap analysis expression (CAGE-seq) document the landscape 5′ 3′ untranslated region (UTR) isoforms transcription start sites epidermal stem cells, wild-type keratinocytes squamous cell carcinomas. Focusing on carcinomas, show that a small cohort genes with...
Polycystic kidney disease (PKD) is a genetic disorder characterized by bilateral cyst formation. We showed that PKD cells and kidneys display metabolic alterations, including the Warburg effect glutaminolysis, sustained in vitro enzyme asparagine synthetase (ASNS). Here, we used antisense oligonucleotides (ASO) against Asns orthologous slowly progressive murine models show treatment leads to drastic reduction of total volume (measured MRI) prominent rescue renal function mouse....
The dark proteome includes a rapidly expanding catalog of microproteins with unknown functions that have been historically ignored in genome annotations. Here, we exploit an vivo single-cell CRISPR screening strategy the mouse epidermis to systematically investigate tissue-wide function microproteins. We document global and cell-type-specific roles during epidermal development homeostasis at transcriptomic resolution. Focusing on select candidates, identify novel microprotein Gm10076,...
Abstract Low flows can impact water use and instream ecology. Therefore, reliable predictions of low‐flow metrics are crucial. In this study, we assess which catchment characteristics (climate, topography, geology landcover) explain the spatial variability at two different scales: regional scale small headwater scale. For regional‐scale analysis, calculated mean 7‐day annual minimum flow ( q min ), that is exceeded 95% year 95 master recession constant C ) for 280 independent gauging...
Abstract MicroRNA (miRNA) loaded Argonaute (AGO) complexes regulate gene expression via direct base pairing with their mRNA targets. Previous works suggest that up to 60% of mammalian transcripts might be subject miRNA‐mediated regulation, but it remains largely unknown which fraction these interactions are functional in a specific cellular context. Here, we integrate transcriptome data from set miRNA‐depleted mouse embryonic stem cell (mESC) lines published miRNA interaction predictions and...
Neuronal L-type voltage-gated calcium channels (LTCCs) are involved in several physiological functions, but increased activity of LTCCs has been linked to pathology. Due the coupling LTCC-mediated Ca(2+) influx Ca(2+)-dependent conductances, such as KCa or non-specific cation channels, act important regulators neuronal excitability. Augmentation after-hyperpolarizations may be one mechanism that shows how elevated LTCC can lead neurological malfunctions. However, little is known about other...
Stratification of patients with pancreatic ductal adenocarcinoma (PDAC) remains a key challenge in the field clinical oncology. No predictive biomarkers have yet been found for any available treatment options. Previously, we identified SERPINB7 as putative biomarker PDAC and thus, herein, aimed to validate our previous findings assessed value SERPINB7. Patients who underwent surgery received gemcitabine (gem) or plus nab-paclitaxel (gem/nab) adjuvant therapy, between 2011 2017, were included...
Pancreatic cancer is a dismal disease with mortality rate almost similar to its incidence rate. To date, there are neither validated predictive nor prognostic biomarkers for this lethal disease. Thus, the aim of present study was retrospectively investigate capability biochemical parameters and molecular profiles predict survival patients metastatic pancreatic ductal adenocarcinoma (mPDAC) who participated in phase II clinical trial test safety efficacy combination treatment capecitabine...
SUMMARY MicroRNA (miRNA) loaded Argonaute (AGO) complexes regulate gene expression via direct base pairing with their mRNA targets. Current prediction approaches identified that between 20 to 60% of mammalian transcriptomes are regulated by miRNAs, but it remains largely unknown which fraction these interactions functional in a specific cellular context. Here, we integrated transcriptome data from set miRNA-depleted mouse embryonic stem cell (mESC) lines published miRNA interaction...
The Argonaute proteins (AGOs) are well known for their role in post-transcriptional gene silencing the microRNA (miRNA) pathway. Here we show that mouse embryonic stem cells, AGO1&2 serve additional functions go beyond miRNA Through combined deletion of both Agos, identified a specific set genes uniquely regulated by AGOs but not other biogenesis factors. Deletion Ago2&1 caused global reduction repressive histone mark H3K27me3 due to downregulation at protein levels Polycomb complex 2...
The fibroblast growth factor (FGF) and the transforming factor-β (TGF-β) pathways are both involved in maintenance of human embryonic stem cells (hESCs) regulate onset their differentiation. Their converging functions have suggested that these might share a wide range overlapping targets. Published studies focused on long-term effects (24–48 h) FGF TGF-β inhibition hESCs, identifying direct indirect target genes. In this study, we earliest transcriptome changes occurring between 3 9 h after...
ABSTRACT The Argonaute proteins (AGO) are well-known for their essential role in post-transcriptional gene silencing the microRNA (miRNA) biogenesis pathway. Only two AGOs (AGO1 and AGO2) expressed mouse embryonic stem cells (mESCs). transcriptome of Ago mutant mESCs revealed a large specific set misregulated genes, compared to other miRNA factor cells, suggesting additional functions cells. In this study, we endeavored understand miRNA-independent roles expression regulation through...
Abstract Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here we use long-read sequencing document the 5’and 3’untranslated region (UTR) isoform landscape epidermal stem cells, wild-type keratinocytes squamous cell carcinomas. Focusing on carcinomas, show that a small cohort genes with alternative 5’UTR isoforms exhibit overall increased efficiencies...
Abstract Polycystic Kidney Disease (PKD) is a genetic disorder characterized by bilateral cyst formation. We showed that PKD cells and kidneys display metabolic alterations, including the Warburg effect glutaminolysis, sustained in vitro enzyme asparagine synthetase (ASNS). Here, we used antisense oligonucleotides (ASO) against Asns orthologous slowly progressive murine models show treatment leads to drastic reduction of total kidney volume (measured MRI) prominent rescue renal function...
Journal of the American Society Nephrology 34(11S):p 203, November 2023. | DOI: 10.1681/ASN.20233411S1203b