Biology subjects

Reuter, C.

Publications and source records attributed to Reuter, C..

8 recordsLinked to original sources

bioRxiv2026

Label-free identification and classification of leukocyte subpopulations in peripheral blood smears by optical photothermal infrared spectroscopy

The differential count of leukocyte subpopulations from peripheral blood smears remains a cornerstone of clinical hematology but relies on staining protocols or flow cytometry, that introduce variability and obscure native biochemistry. This study presents label-free workflows that distinguish leukocytes from erythrocytes in full blood smears and classifies the leukocyte subtypes as granulocytes, lymphocytes and monocytes using their single cell optical photothermal infrared (OPTIR) spectra. The first approach uses discrete wavenumber images using two key bands at 1546 and 2922 cm-1 to screen leukocytes. The second approach using intrinsic fluorescence imaging of leukocytes offers approximately 1000 times faster screening. Multiple OPTIR spectra are acquired per leukocyte followed by post-acquisition Giemsa staining for cytological cell verification. Full blood smears were prepared on calcium fluoride and standard glass slides to compare substrate effects, and OPTIR spectra were collected with 532 and 785 nm probe lasers to assess probe wavelengths effects. Principal component-linear discriminant analysis separated granulocytes from mononuclear subtypes under all substrate-probe laser combinations tested on the basis of lipid, nucleic-acid and protein bands in OPTIR spectra. Lymphocytes and monocytes were better distinguished on calcium fluoride than on glass. The OPTIR spectra stayed stable over 14 days of storage on both substrates, whereas the intrinsic fluorescence used for cell localization was weak in fresh smears and increased with storage. The non-destructive, fixation-free measurement preserves native protein and lipid composition and allows subsequent cytological staining, supporting OPTIR on routine glass slides for future label-free hematological screening.

biophysics↗

bioRxiv2026

Damaging RBM20 E-rich domain variants are not rescued by gene replacement

The promise of precision therapeutics in genetic cardiomyopathies relies on linking specific therapies to variant mechanisms. Missense variants in the cardiac splice regulator RBM20 cause a highly penetrant and arrhythmogenic dilated cardiomyopathy. Disease-causing variants in RBM20s arginine-serine rich (RS) domain act via formation of toxic gain of function cytoplasmic granules, but this is not true for a small number of clinically adjudicated pathogenic variants in its glutamate(E)-rich domain. To better define the effects of E-rich domain variants, we developed a scalable screen based on induced pluripotent stem cell (iPSC) cardiomyocyte differentiation that identified several additional damaging variants. Several of these reduced RBM20 protein abundance and stability. We therefore hypothesized that, unlike RS domain variants, these E-rich variants might be rescued by RBM20 overexpression. To test this hypothesis, we generated induced pluripotent stem cells (iPSCs) from a patient with a pathogenic E-rich domain variant (p.E913K), and confirmed reduced RBM20 protein expression in these RBM20+/p.E913K cells after differentiation to iPSC-derived cardiomyocytes (iPSC-CM, vs. engineered isogenic RBM20+/+). These iPSC-CMs also displayed aberrant transcriptional splicing, reduced contractility, increased calcium-induced calcium release, and nuclear localization of RBM20 protein, often with more than the two expected RBM20-centric splice factories. AAV-based overexpression of RBM20 reversed some, but not all of the mis-splicing events identified in RBM20+/p.E913K iPSC-CMs, and did not improve their abnormal contractility, calcium handling or supernumerary RBM20 nuclear granules. In summary, our data indicate that pathogenic E-rich domain variants reduce RBM20 protein abundance, but that their mechanism is unlikely to be explained by haploinsufficiency alone.

genetics↗

bioRxiv2025

Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity

Short tandem repeat (STR) instability is a major cause of disease association, yet their full length-distributions and sequence content have been difficult to resolve with short-read sequencing. By analyzing long-read sequencing genomes from 2,645 participants of the All of Us Research Program, we establish a comprehensive STR resource of 23 billion alleles covering a catalog of 4.4 million loci. We find that known disease-associated STR loci exhibit markedly elevated allelic variability relative to genome-wide distributions, which is most pronounced when based on the length of uninterrupted, pure repeat motifs (Odds Ratio: 244, p=1.62e-29). We establish the Pure Length Variability Index (PLVI) as a measure of this instability, which is robust across ancestries and replicated in 500 samples from the 1000 Genomes Project (Odds Ratio: 84, p=2.72e-28). To illustrate, we identify 55 unstable coding CAG and 5-UTR CGG STR loci with this metric, 60% of which have not been associated with disease. From this set, we document potential pathogenic repeat expansions for FAM193B and EP400 by integrating PLVI with single-genome length outlier analysis. These data establish a population-scale framework for STR discovery in rare and common diseases using long-read sequencing cohorts.

genomics↗

bioRxiv2023

RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci

Tandem repeats (TRs) are polymorphic sequences of DNA that are composed of repeating units of motifs, whose lengths can vary depending on the type of TR. Expansions of TRs are responsible for approximately 50 monogenic diseases, compared to over 4,300 disease causing genes disrupted by single nucleotide variants and small indels. It appears thus reasonable to expect the discovery of additional pathogenic repeat expansions, which has the potential of significantly narrowing the current diagnostic gap in many diseases. Recently, short and long-read whole genome sequencing with the use of advanced bioinformatics tools, have identified a growing number of TR expansions in the human population. The majority of these loci are expanded in <1% of genomes. Categorizing and prioritizing such TR loci is a growing challenge to human genomic studies. We present a first-in-class machine learning tool, RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), which is designed to distinguish pathogenic from benign TR expansions. Leave-one-out cross validation results demonstrated that an ensemble approach comprised of support vector machines (SVM) and extreme gradient boosted decision tree (XGB) classify TRs with a precision of 92% and a recall of 90%. Further validation of RExPRT on unseen test data demonstrate a similar precision of 86%, and a recall of 60%. RExPRTs high precision in particular, will be of significant value to large-scale discovery studies, which require the prioritization of promising candidate loci for time-consuming and costly functional follow-up studies. Application of RExPRT to ~800,000 TRs in the reference genome identified ~30,000 TRs that would be likely pathogenic upon expansion. Thus, RExPRT establishes a foundation for the application of machine learning approaches to categorize the pathogenicity of tandem repeat loci.

bioinformatics↗

bioRxiv2021

Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms

Transmission of Trypanosoma brucei by tsetse flies involves the deposition of the cell cycle-arrested metacyclic life cycle stage into mammalian skin at the site of the flys bite. In the skin, the metacyclic parasites reactivate and differentiate into proliferative trypanosomes before colonizing the hosts blood and tissues. We generated an advanced human skin equivalent and used tsetse flies to naturally infect the artificial skin with trypanosomes. We detailed the chronological order of the parasites development in the skin, and found a rapid activation of metacyclic trypanosomes and differentiation to proliferative parasites. Single-cell parasite transcriptomics were used to document the biological events during differentiation and host invasion at five different timepoints. After the establishment of a proliferative trypanosome population in the skin, the parasites entered a reversible quiescent state characterized by slow replication and a strongly reduced metabolism. We termed these quiescent trypanosomes skin tissue forms (STF), a parasite population that may play an important role in maintaining the infection over long time periods and in asymptomatic infected individuals.

microbiology↗

bioRxiv2021

VisVariant: A java program to visualise genetic variants in next-generation sequencing data

SummaryExtremely large datasets are impossible or very difficult for humans to comprehend by standard mental approaches. Intuitive visualization of genetic variants in genomic sequencing data could help in the review and confirmation process of variants called by automated variant calling programs. To help facilitate interpretation of genetic variant next-generation sequencing (NGS) data we developed VisVariant, a customizable visualization tool that creates a figure showing the overlapping sequence information of thousands of individual reads including the variant and flanking regions. Availability and implementationDetailed information on how to download, install and run VisVariant together with an example is available on our github website [https://github.com/hugging-biorxiv/visvariant].

bioinformatics↗

bioRxiv2020

Meaningful Effects in the Adolescent Brain Cognitive Development Study

The Adolescent Brain Cognitive Development (ABCD) Study is the largest single-cohort prospective longitudinal study of neurodevelopment and childrens health in the United States. A cohort of n= 11,880 children aged 9-10 years (and their parents/guardians) were recruited across 22 sites and are being followed with in-person visits on an annual basis for at least 10 years. The study approximates the US population on several key sociodemographic variables, including sex, race, ethnicity, household income, and parental education. Data collected include assessments of health, mental health, substance use, culture and environment and neurocognition, as well as geocoded exposures, structural and functional magnetic resonance imaging (MRI), and whole-genome genotyping. Here, we describe the ABCD Study aims and design, as well as issues surrounding estimation of meaningful associations using its data, including population inferences, hypothesis testing, power and precision, control of covariates, interpretation of associations, and recommended best practices for reproducible research, analytical procedures and reporting of results.

neuroscience↗

bioRxiv2019

A modification to the life cycle of the parasite Trypanosoma brucei

African trypanosomes cause sleeping sickness in humans and nagana in cattle. These unicellular parasites are transmitted by the bloodsucking tsetse fly. In the mammalian hosts circulation, tissues, and interstitium, at least two main life cycle stages exist: slender and stumpy bloodstream stages. Proliferating slender stage cells differentiate into cell cycle-arrested stumpy stage cells at high population densities. This developmental stage transition occurs in response to the quorum sensing factor SIF (stumpy induction factor), and is thought to fulfil two main functions. First, it auto-regulates the parasite load in the host. Second, the stumpy stage is regarded as pre-adapted for tsetse fly infection and the only stage capable of successful vector transmission. Here, we show that proliferating slender stage trypanosomes are able to complete the complex life cycle in the fly as successfully as the stumpy stage, and that a single parasite is sufficient for productive infection. Our findings not only propose a revision to the traditional rigid view of the trypanosome life cycle, but also suggest a solution to a long-acknowledged paradox in the transmission event: parasitaemia in chronic infections is characteristically low, and so the probability of a tsetse ingesting a stumpy cell during a bloodmeal is also low. The finding that proliferating slender parasites are infective to tsetse flies helps shed light on this enigma.

microbiology↗