Biology subjects

Schittenhelm, R.

Publications and source records attributed to Schittenhelm, R..

3 recordsLinked to original sources

bioRxiv2026

Simultaneous single-cell profiling of the transcriptome and proteome

Transcriptomic and proteomic measurements from the same single cell provide complementary information that cannot be inferred from either modality alone, yet methods for the parallel recovery of both analyte classes from a single-cell lysate remain limited. Here, we describe a workflow in which individual cells are isolated by automated dispensing into a minimal, MS-compatible lysis volume, followed by sequential mRNA capture and protein supernatant recovery, prior to independent downstream processing. The method is compatible with standard library preparation and data-independent acquisition proteomics pipelines and requires no dedicated instrumentation beyond a single-cell dispensing platform. We evaluated workflow performance on 67 single cells across 3 iBlastoids. Transcriptomic sequencing detected a median of 5375 genes per cell, and proteomic analysis identified a median of 2123 protein groups per cell across two mass spectrometry platforms. Compared with a standalone single-cell proteomics protocol, incorporating the mRNA extraction step reduced median proteomic depth by approximately 11% (median 1,965 vs. 2,204 protein groups per cell), while mean per-cell identification remained comparable across workflows (1,790 vs. 1,775 protein groups per cell). Direct comparison of paired transcript and protein abundance yielded a median Spearman correlation of {rho} {approx} 0.38; after correction for detection depth, the partial correlation was 0.067.

systems biology↗

bioRxiv2024

Molecular Landscape of Modality-Specific Exercise Adaptation in Human Skeletal Muscle through Large-Scale Multi-OMICs Integration

We conducted a large-scale, statistically powered, meta-analysis of exercise adaptations in human skeletal muscles, integrating epigenetic, transcriptomic, transcription factors, and proteomic data across 12 independent cohorts comprising over 1000 participants and 2340 human muscle samples. Our study identified distinctive signatures associated with maximal oxygen consumption (VO2max), and identified five genes robustly intersecting multi-OMIC layers. Notably, transcription factors predominantly functioned as activators across these layers, regulating expression of target genes irrespective of whether DNA methylation levels were low or high, indicating a synergistic effect between TFs and the methylome. Analysis of distinct exercise modalities (aerobic and resistance exercise) revealed unique gene pathways, contrasting with patterns observed in inactivity (muscle disuse) studies. These findings offer a comprehensive understanding of exercise and modality-specific adaptations, shedding light on muscle health and the molecular mechanisms associated with cardiorespiratory fitness, aging, and disease prevention.

molecular biology↗

bioRxiv2020

A DNA vaccine strategy to activate natural killer cells for therapeutic targeting of XPO1-positive tumors

Natural killer (NK) cells are key components of the immune response to viral infections and cancer. Their functions are controlled by activating and inhibitory killer-cell immunoglobulin-like receptors (KIR) which have MHC class I ligands. KIR2DS2 is an activating KIR, that binds conserved viral peptides in the context of HLA-C and has been associated with protective responses to both cancer and viral infections. We sought to investigate whether NK cells can be specifically activated in a peptide:MHC dependent manner to generate functional immune responses as a potential immunotherapeutic strategy. We developed a peptide-based KIR targeting DNA vaccine. Immunizing KIR-Tg mice with the vaccine construct generated in vivo peptide-specific activation of KIR2DS2-positive NK cells leading to canonical and cross-reactive peptide specific immune responses in vitro, and also in vivo inhibition of tumor growth. Using immunopeptidomics we identified that the nuclear export protein XPO1, which has been associated with a poor prognosis in many different human cancers, furnishes an HLA-C restricted cancer-associated peptide ligand for KIR2DS2-positive NK cells. We thus define a novel strategy to activate KIR in a peptide-specific manner and identify a rationale for its use in cancer immunotherapy. Significance statementNatural killer (NK) cells are known to have important roles in determining the outcomes of viral infections and cancer. The killer cell immunoglobulin-like receptors (KIR), and in particular the activating receptor KIR2DS2, have been associated with the outcome of a number of different human cancers. Specific activation of NK cells through KIR2DS2 is challenging because it shares high (>98%) sequence homology with related inhibitory KIR. We have used a peptide:MHC targeting strategy to activate NK cells through KIR2DS2 and identified a novel cancer-associated ligand for this receptor. The work provides a proof-of-concept for targeting NK cells through activating KIR as a cancer immunotherapy strategy.

immunology↗