Biology subjects

Rehrauer, H.

Publications and source records attributed to Rehrauer, H..

11 recordsLinked to original sources

bioRxiv2024

Heterogeneous and Novel Transcript Expression in Single Cells of Patient-Derived ccRCC Organoids

Splicing is often dysregulated in cancer, leading to alterations in the expression of canonical and alternative splice isoforms. This complex phenomenon can be revealed by an in-depth understanding of cellular heterogeneity at the single-cell level. Recent advances in single-cell long- read sequencing technologies enable comprehensive transcriptome sequencing at the single-cell level. In this study, we have generated single-cell long-read sequencing of Patient-Derived Organoid (PDO) cells of clear-cell Renal Cell Carcinoma (ccRCC), an aggressive and lethal form of cancer that arises in kidney tubules. We have used the Multiplexed Arrays Sequencing (MAS-ISO-Seq) protocol of PacBio to sequence full-length transcripts exceptionally deep across 2,599 single cells to obtain the most comprehensive view of the alternative landscape of ccRCC to date. On average, we uncovered 86,182 transcripts across PDOs, of which 31,531 (36.6%) were previously uncharacterized. In contrast to known transcripts, many of these novel isoforms appear to exhibit cell-specific expression. Nonetheless, >50% of these novel transcripts were predicted to possess a complete protein-coding open reading frame. This finding suggests a biological role for these transcripts within kidney cells. Moreover, an analysis of the most dominant transcript switching events between ccRCC and non-ccRCC cells revealed that many switching events were cell and sample-specific, underscoring the heterogeneity of alternative splicing events in ccRCC. Overall, our research elucidates the intricate transcriptomic architecture of ccRCC, potentially exposing the mechanisms underlying its aggressive phenotype and resistance to conventional cancer therapies.

cancer biology↗

bioRxiv2024

Comparison of Single-cell Long-read and Short-read Transcriptome Sequencing of Patient-derived Organoid Cells of ccRCC: Quality Evaluation of the MAS-ISO-seq Approach

Single-cell RNA sequencing is used in profiling gene expression differences between cells. Short-read sequencing platforms provide high throughput and high-quality information at the gene-level, but the technique is hindered by limited read length, failing in providing an understanding of the cell heterogeneity at the isoform level. This gap has recently been addressed by the long-read sequencing platforms that provide the opportunity to preserve full-length transcript information during sequencing. To objectively evaluate the information obtained from both methods, we sequenced four samples of patient-derived organoid cells of clear cell renal cell carcinoma and one healthy sample of kidney organoid cells on Illumina Novaseq 6000 and PacBio Sequel IIe. For both methods, for each sample, the cDNA was derived from the same 10x Genomics 3 single-cell gene expression cDNA library. Here we present the technical characteristics of both datasets and compare cell metrics and gene-level information. We show that the two methods largely overlap in the results but we also identify sources of variability which present a set of advantages and disadvantages to both methods.

genomics↗

bioRxiv2023

The impact of PCR duplication on RNA-seq data generated using NovaSeq 6000, NovaSeq X, AVITI and G4 sequencers.

RNA sequencing (RNA-seq) is a powerful technology for gene expression and functional genomics profiling. Expression profiles generated using this approach can be impacted by the methods utilised for cDNA library generation. Selection of the optimal parameters for each step during the protocol are crucial for acquisition of high-quality data. Polymerase chain reaction (PCR) amplification of transcripts is a common step in many RNA-seq protocols and, if not optimised, high PCR duplicate proportions can be generated, resulting in the inflation of transcript counts and introduction of bias. In this study, we investigate the impact of input amount and PCR cycle number on the PCR duplication rate and on the RNA-seq data quality using a broad range of inputs (1 ng -1,000 ng) for RNA-seq library preparation with unique molecular identifiers (UMIs) and sequencing the data on four different short-read sequencing platforms: Illumina NovaSeq 6000, Illumina NovaSeq X, Element Biosciences AVITI, and Singular Genomics G4. Across all platforms, samples of input amounts greater than 125 ng had a negligible PCR duplication rate and the number of PCR cycles did not have a significant effect on data quality. However, for input amounts lower than 125ng we observed a strong negative correlation between input amount and the proportion of PCR duplicates; between 34% and 96% of reads were discarded via deduplication. Fortunately, UMIs were effective for removing in silico PCR duplicates without removing valuable biological information. Removal of PCR duplicates resulted in more comparable gene expression obtained from the different PCR cycles. Data generated with each of the four sequencing platforms presented similar associations between starting material amount and the number of PCR cycles on PCR duplicates, a similar number of genes detected, and comparable gene expression profiles. However, the sequencers using conversion kits for Illumina libraries (AVITI, G4) exhibited lower adapter dimer abundance across all input amounts, but also a higher PCR duplication rate in very low input amounts (<15ng). Overall, this study showed that the choice of input amount and number of PCR cycles are important parameters for obtaining high-quality RNA-seq data across all sequencing platforms. UMI deduplication is an effective way to remove PCR duplicates, improving the data quality and removing any variation caused by the conversion kits.

genomics↗

bioRxiv2023

Multiomic ALS signatures highlight sex differences and molecular subclusters and identify the MAPK pathway as therapeutic target

Amyotrophic lateral sclerosis (ALS) is the most common motor neuron disease and lacks effective disease-modifying treatments. Here, we performed a multiomic analysis of the prefrontal cortex of 51 patients with sporadic ALS and 50 control subjects, as well as four transgenic mouse models of C9orf72-, SOD1-, TDP-43-, and FUS-ALS to characterize early and sex-specific disease mechanisms in ALS. Integrated analyses of transcriptomes, (phospho)proteomes, and miRNAomes revealed more pronounced changes in males. We identified transcriptome-based human ALS subclusters driven by the immune response, ECM, mitochondrial respiration, and RNA metabolism. The molecular signatures of human subclusters were reflected in specific mouse models. Individual and integrative multiomics analysis highlighted the mitogen-activated protein kinase pathway as an early disease-relevant mechanism. Its modulation by trametinib in vitro and in vivo validated that mitogen-activated protein kinase kinase 2 is a promising therapeutic target with beneficial effects in females.

neuroscience↗

bioRxiv2023

Human pluripotent stem cells-derived Inner ear organoids recapitulate otic development in vitro.

Our molecular understanding of the early stages of human inner ear development has been limited by the difficulty in accessing fetal samples at early gestational stages. As an alternative, previous studies have shown that inner ear morphogenesis can be partially recapitulated using induced pluripotent stem cells (iPSCs) directed to differentiate into Inner Ear Organoids (IEOs). Once validated and benchmarked, these systems could represent unique tools to complement and refine our understanding of human otic differentiation and model developmental defects. Here, we provide the first direct comparisons of the early human embryonic otocyst and human iPSC-derived IEOs. We use multiplexed immunostaining, and single-cell RNA sequencing to characterize IEOs at three key developmental steps, providing a new and unique signature of in vitro derived otic -placode, -epithelium, -neuroblasts, and -sensory epithelia. In parallel, we evaluate the expression and localization of critical markers at these equivalent stages in human embryos. We show that the placode derived in vitro (days 8-12) has similar marker expression to the developing otic placode of Carnegie Stage (CS) 11 embryos and subsequently (days 20-40) this gives rise to otic epithelia and neuroblasts comparable to the CS13 embryonic stage. Differentiation of sensory epithelia, including supporting cells and hair cells starts in vitro at days 50-60 of culture. The maturity of these cells is equivalent to vestibular sensory epithelia at week 10 or cochlear tissue at week 12 of development, before functional onset. Together, our data indicate that the current state-of-the-art protocol enables the specification of bona fide otic tissue, supporting the further application of IEOs to inform inner ear biology and disease.

developmental biology↗

bioRxiv2023

Single-cell transcriptomics analysis reveals extracellular matrix remodelling in carious human dental pulp

The carious lesion is a bacteria caused destruction of tooth mineralized matrices marked by concurrent tissue reparative and immune responses in the dental pulp. While major molecular players in tooth pulp decay have been uncovered, a detailed map of the molecular and cellular landscape of the diseased pulp is still missing. Here we used single-cell RNA sequencing analysis, to generate a comprehensive single-cell atlas of the carious human dental pulp tissue. Our data demonstrated modifications in various cell clusters of the carious pulp, such as immune cells, mesenchymal stem cells (MSC) and fibroblasts, when compared to the healthy dental pulp. These changes include upregulation of genes encoding extracellular matrix (ECM) components and the enrichment of the fibroblast cluster with myofibroblasts. Assessment of the Fibronectin fibres mechanical strain showed a significant tension reduction in the carious human pulp, compared to the healthy one. Collectively, the present data demonstrate molecular, cellular and biomechanical alterations in the carious pulp tissue, indicative of extensive ECM remodelling and reminiscent of fibrosis observed in other organs.

cell biology↗

bioRxiv2022

Heterogeneity of RNA editing in mesothelioma and how RNA editing enzyme ADAR2 affects mesothelioma cell growth, response to chemotherapy and tumor microenvironment

We previously observed increased levels of adenosine-deaminase-acting-on-dsRNA (Adar)-dependent RNA editing during mesothelioma development in mice exposed to asbestos. The aim of this study was to characterize and assess the role of ADAR-dependent RNA editing in mesothelioma. Tumors and mesothelioma primary cultures have higher ADAR-mediated RNA editing compared to mesothelial cells. Unsupervised clustering of editing in different genomic regions revealed heterogeneity between tumor samples as well as mesothelioma primary cultures. ADAR2 expression levels are higher in BRCA1-associated protein 1 wild-type tumors, with corresponding changes in RNA editing in transcripts and 3UTR. ADAR2 knockdown and rescue models indicated a role in cell proliferation, altered cell cycle, increased sensitivity to antifolate treatment and type-1 interferon signaling upregulation, leading to changes in the microenvironment in vivo. Our data indicate that RNA editing contributes to mesothelioma heterogeneity and highlights an important role of ADAR2 not only in growth regulation in mesothelioma but also chemotherapy response, in addition to regulating inflammatory response downstream of sensing nucleic acid structures.

cancer biology↗

bioRxiv2021

Molecular atlas of the human brain vasculature at the single-cell level

A broad range of brain pathologies critically relies on the vasculature, and cerebrovascular disease is a leading cause of death worldwide. However, the cellular and molecular architecture of the human brain vasculature remains poorly understood. Here, we performed single-cell RNA sequencing of 599,215 freshly isolated endothelial, perivascular and other tissue-derived cells from 47 fetuses and adult patients to construct a molecular atlas of the developing fetal, adult control and diseased human brain vasculature. We uncover extensive molecular heterogeneity of healthy fetal and adult human brains and across eight vascular-dependent CNS pathologies including brain tumors and brain vascular malformations. We identify alteration of arteriovenous differentiation and reactivated fetal as well as conserved dysregulated pathways in the diseased vasculature. Pathological endothelial cells display a loss of CNS-specific properties and reveal an upregulation of MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell-cell interaction analyses predict numerous endothelial-to-perivascular cell ligand-receptor crosstalk including immune-related and angiogenic pathways, thereby unraveling a central role for the endothelium within brain neurovascular unit signaling networks. Our single-cell brain atlas provides insight into the molecular architecture and heterogeneity of the developing, adult/control and diseased human brain vasculature and serves as a powerful reference for future studies.

neuroscience↗

bioRxiv2020

Comparative analysis of single-cell RNA Sequencing Platforms and Methods

Single-cell RNA sequencing (scRNA-seq) offers great new opportunities for increasing our understanding of complex biological processes. In particular, development of an accurate Human Cell Atlas is largely dependent on the rapidly advancing technologies and molecular chemistries employed in scRNA-seq. These advances have already allowed an increase in throughput for scRNA-seq from 96 to 80,000 cells on a single instrument run by capturing cells within nano-liter droplets. While this increase in throughput is critical for many experimental questions, a thorough comparison between microfluidic-, plate-, and droplet-based technologies or between multiple available platforms utilizing these technologies is largely lacking. Here, we report scRNA-seq data from SUM149PT cells treated with the histone deacetylase inhibitor TSA vs. untreated controls across several scRNA-seq platforms (Fluidigm C1, WaferGen iCell8, 10X Genomics Chromium Controller, and Illumina/BioRad ddSEQ). The primary goal of this project was to demonstrate RNA sequencing (RNA-seq) methods for profiling the ultra-low amounts of RNA present in individual cells, and this report discusses the results of the study as well as technical challenges/lesson learned and present general guidelines for best practices in sample preparation and analysis.

genomics↗

bioRxiv2018

Long fragments achieve lower base quality in Illumina paired-end sequencing

Illuminas technology provides high quality reads of DNA fragments with error rates below 1/1000 per base. Runs typically generate a millions of reads where the vast majority of the reads has also an average error rate below 1/1000. However, some paired-end sequencing data show the presence of a subpopulation of reads where the second read has lower average qualities. We show that the fragment length is a major driver of increased error rates in the R2 reads. Fragments above 500 nt tend to yield lower base qualities and higher error rates than shorter fragments. We demonstrate the fragment length dependency of the R2 read qualities using publicly available Illumina data generated by various library protocols, in different labs and using different sequencer models. Our finding extends the understanding of the Illumina read quality and has implications on error models for Illumina reads. It also sheds a light on the importance of the fragmentation during library preparation and the resulting fragment length distribution.

bioinformatics↗

bioRxiv2017

How asbestos drives the tissue towards tumors: YAP activation, macrophage and mesothelial precursor recruitment, RNA editing and somatic mutations

Chronic exposure to intraperitoneal asbestos triggered a marked response in the mesothelium well before tumor development. Macrophages, mesothelial precursor cells, cytokines and growth factors accumulated in the peritoneal lavage. Transcriptome profiling revealed YAP/TAZ activation in inflamed mesothelium with further activation in tumors, paralleled by increased levels of cells with nuclear YAP/TAZ. Arg1 was one of the highest upregulated genes in inflamed tissue and tumor. Inflamed tissue showed increased levels of single nucleotide variations, with an RNA-editing signature, which were even higher in the tumor samples. Subcutaneous injection of asbestos-treated, but tumor-free mice with syngeneic mesothelioma tumor cells resulted in a significantly higher incidence of tumor growth when compared to naive mice supporting the role of the environment in tumor progression.\n\nHighlightsO_LIAsbestos increases levels of cytokines and growth factors in mesothelium environment\nC_LIO_LIRecruitment of macrophages and mesothelial precursor cells prior to tumor development\nC_LIO_LIYAP/TAZ signaling upregulated in pre-neoplastic tissues and cancer\nC_LIO_LIIncreased RNA-editing and somatic mutations as early steps in tumor development\nC_LI

cancer biology↗