Biology subjects

Schaefer, M. H.

Publications and source records attributed to Schaefer, M. H..

11 recordsLinked to original sources

bioRxiv2026

Towards reconstruction of the human interactome from positive and negative experimental evidence

Protein-protein interactions (PPIs) have been detected and reported in the millions, but while they are used in many different contexts for better understanding cellular processes in health and disease, the knowledge of the human PPI network is far from complete, containing many false positive measurements and being highly biased. Both to chart the extent of those problems and to solve them requires not just a knowledge of high-confidence positive interactions, but also likely non-interacting protein pairs. However, this information is typically not reported in PPI studies. We developed a methodology to reconstruct this knowledge from existing PPI data. We reconstruct the experimental search space in which PPI screens have been performed and then create a model that informs how likely a PPI is real given its testing and observation frequency. We argue that negative protein pairs allow us to estimate the error rates of experimental and computational screens. We show how this knowledge could be incorporated for calibration. Finally, we evaluate a simple machine learning approach to PPI prediction and propose how such negative data can be used for training instead of random protein pairs. Together, our results show that reconstructing the experimental search space recovers a largely overlooked layer of information from existing PPI data that can help guide a more accurate and complete mapping of the human interactome.

bioinformatics↗

bioRxiv2025

Systematic identification of regions where DNA methylation is correlated with transcription refines regulatory logic in normal and tumour tissues

DNA methylation at gene promoters is generally considered to be associated with transcriptional repression. However, lack of a clear picture of where promoter methylation is most important for transcriptional regulation has hindered our understanding of this relationship and resulted in the use of a wide variety of arbitrary promoter definitions. We demonstrate here that the use of different promoter definitions can lead to contradictory results between studies of promoter methylation. In response, we have developed Methodical, a computational method that combines RNA-seq and whole genome bisulfite sequencing (WGBS) data to identify genomic regions where DNA methylation is highly correlated with transcriptional activity. We refer to these regions as transcript-proximal methylation-associated regulatory sites (TMRs). We applied Methodical to one normal prostate tissue data set, one prostate tumour dataset and one prostate metastases dataset and characterized the identified TMRs. We show that the region just downstream of the TSS, particularly within the first exon and intron, is the most common location for TMRs and that TMRs are enriched for particular genomic features, chromatin states and transcription factor binding sites. Finally, we demonstrate that the methylation of TMRs is generally strongly correlated with transcription in diverse cancer types and that TMRs are highly subject to altered DNA methylation in cancer.

cancer biology↗

bioRxiv2025

Palmitate-induced mitochondrial damage restricts histone acetylation in CD8+ T cells to impair anti-tumor immunity.

Accumulation of lipids in the tumor microenvironment (TME) is a feature of several solid tumors and increased palmitate (PA) availability fosters tumor progression and metastases. The intrinsic effects of PA on cancer cells are well understood, but its role in modulating CD8+ T cells (CTL) functional performances remains elusive. Here, we found that PA alters the mitochondrial metabolism of CTL and prevents their effector functions in an irreversible manner, resulting in impaired antitumoral immunity. Mechanistically, PA-induced mitochondrial block demotes histone acetylation and chromatin accessibility and decrease transcription of genes promoting DNA replication and production of effector molecules. We identified the metabolic enzyme Sphingosine Kinase 2 (SPHK2) as a molecular target of PA in establishing CTL dysfunction. Consistently, pharmacological inhibition of SPHK2 restored CTL mitochondrial fitness, effector functions and anti-tumor potential. Thus, we reveal a critical function of PA in tumor progression by undermining CTL antitumor immunity and highlight the therapeutic potential of inhibiting SPHK2 activity to optimize T cell functionality.

immunology↗

bioRxiv2023

Emergence of power-law distributions in protein-protein interaction networks through study bias

Protein-protein interaction (PPI) networks are power-law-distributed. However, the experimental procedures for detecting PPIs are affected by technical and study bias. For instance, cancer-associated proteins have received disproportional attention. Moreover, bait proteins in large-scale experiments tend to have many false-positive interaction partners. This raises the question of whether PL distributions in observed PPI networks could be explained by these biases alone. To assess this question, we studied the degree distribution of thousands of PPI networks of controlled provenance. Our findings are supported by mathematical models and extensive simulations and indicate that study bias and technical bias suffice to produce the observed PL distribution. It is, hence, problematic to derive hypotheses about the degree distribution and the true biological interactome from the PL distributions in observed PPI networks. Our study casts doubt on the use of the PL property of biological networks as a modeling assumption or quality criterion in network biology.

systems biology↗

bioRxiv2022

Using protein-per-mRNA differences among human tissues in codon optimization

Codon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized that different tissues have distinct tRNA profiles and codon usages in their transcriptomes, the effect of tissue-specific codon optimality on protein synthesis remains elusive. Here, we leverage existing state-of-the-art transcriptomics and proteomics datasets from the GTEx project and the Human Protein Atlas to compute the protein-to-mRNA ratios of 36 human tissues. Using this as a proxy of translational efficiency, we build a machine learning model that identifies codons enriched or depleted in specific tissues. In particular, we detect two clusters of tissues with an opposite pattern of codon preferences. We then use the identified patterns for the development of CUSTOM, a codon optimizer algorithm which suggests a synonymous codon design in order to optimize protein production in a tissue-specific manner. In a human cell model, we provide evidence that codon optimization should indeed take into account particularities of the translational machinery of the tissues in which the target proteins are expressed and that our approach can design genes with tissue-optimized expression profiles. Altogether, CUSTOM could benefit biological and biotechnological research, such as the design of tissue-targeted therapies and vaccines.

systems biology↗

bioRxiv2022

Evolutionary conservation of A/T-ending codons reflects co-regulation of expression and complex formation.

BackgroundIn a wide variety of organisms, synonymous codons are used with different frequencies, a phenomenon known as codon bias that plays an important role in determining expression levels. However, the importance of codon bias to facilitate the simultaneous turnover of thousands of protein-coding transcripts to bring about phenotypic changes in cellular programs such as development, has not yet been investigated in detail. ResultsHere, we discover that genes with A/T-ending codon preferences are expressed coordinately and display a high codon conservation in mammals. This feature is not observed in genes enriched in G/C-ending codons. A paradigmatic case of this phenomenon is KRAS, from the RAS family, an A/T-rich gene with a high codon conservation (95%) in comparison to HRAS (76%). Also, we find that genes with similar codon composition are more likely to be part of the same protein complex, and that genes with A/T-ending codons are more prone to form protein complexes than those rich in G/C. The codon preferences of genes with A/T-ending codons are conserved among vertebrates. We propose that codon conservation, a feature of expression-coordinated transcripts, is linked to the high expression variation and coordination of tRNA isoacceptors reading A/T-ending codons. ConclusionsOur data indicate that cells exploit A/T-ending codons to generate coordinated, fine-tuned changes of protein-coding transcripts. We suggest that this orchestration contributes to tissue-specific and ontogenetic-specific expression, which can facilitate, for instance, timely protein complex formation.

evolutionary biology↗

bioRxiv2021

GZMKhigh CD8+ T effector memory cells are associated with CD15high neutrophil abundance in early-stage colorectal tumors and predict poor clinical outcome.

Tumor contexture has emerged as a major prognostic determinant and tumor infiltrating CD8+ T cells have been associated with a better prognosis in several solid tumors, including early-stage colorectal cancer (CRC). However, the tumor immune infiltrate is highly heterogeneous and understanding how the interplay between different immune cell compartments impacts on the clinical outcome is still in its infancy. Here, we describe in a prospective cohort a novel CD8+ T effector memory population, which is characterized by high levels of Granzyme K (GZMKhigh CD8+ TEM) and is correlated with CD15high tumor infiltrating neutrophils. We provide both in vitro and in vivo evidence of the role of stromal cell-derived factor 1 (CXCL12/SDF-1) in driving functional changes on neutrophils at the tumor site, promoting their retention and increasing the crosstalk with CD8+ T cells. Mechanistically, as a consequence of the interaction with neutrophils, CD8+ T cells are skewed towards a CD8+ TEM phenotype and produce high levels of GZMK, which in turn decreases E-cadherin pathway. The correlations of GZMKhigh CD8+ TEM and neutrophils with both tumor progression in mice and early relapse in CRC patients demonstrate the role of GZMKhigh CD8+ TEM in promoting malignancy. Indeed, a gene signature defining GZMKhigh CD8+ TEM was associated with worse prognosis on a larger independent cohort of CRC patients and a similar analysis was extended to lung cancer (TCGA). Overall, our results highlight the emergence of GZMKhigh CD8+ TEM in early-stage CRC tumors as a hallmark driven by the interaction with neutrophils, which could implement current patient stratification and be targeted by novel therapeutics.

immunology↗

bioRxiv2021

Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors

Aneuploidy, a state of chromosome imbalance, is a hallmark of human tumors, but its role in cancer still remains to be fully elucidated. To understand the consequences of whole chromosome-level aneuploidies on the proteome, we integrated aneuploidy, transcriptomic and proteomic data from hundreds of TCGA/CPTAC tumor samples. We found a surprisingly large number of expression changes happened on other, non-aneuploid chromosomes. Moreover, we identified an association between those changes and co-complex members of proteins from aneuploid chromosomes. This co-abundance association is tightly regulated for aggregation-prone aneuploid proteins and those involved in a smaller number of complexes. On the other hand, we observe that complexes of the cellular core machinery are under functional selection to maintain their stoichiometric balance in aneuploid tumors. Ultimately, we provide evidence that those compensatory and functional maintenance mechanisms are established through post-transcriptional control and that the degree of success of a tumor to deal with aneuploidy-induced stoichiometric imbalance impacts the activation of cellular protein degradation programs and patient survival.

cancer biology↗

bioRxiv2020

Hypersilencing of SRRM4 suppresses basal microexon inclusion and promotes tumor growth across cancers

RNA splicing is widely dysregulated in cancer, frequently due to altered expression or activity of splicing factors. Microexons are extremely small exons (3-27 nucleotides long) that are highly evolutionarily conserved and play critical roles in promoting neuronal differentiation and development. Inclusion of microexons in mRNA transcripts is mediated by the splicing factor SRRM4, whose expression is largely restricted to neural tissues. However, microexons have been largely overlooked in prior analyses of splicing in cancer, as their small size necessitates specialized computational approaches for their detection. Here we demonstrate that despite having low expression in normal non-neural tissues, SRRM4 is hypersilenced in tumors, resulting in the suppression of basal microexon inclusion. Remarkably, SRRM4 is the most consistently silenced splicing factor across all tumor types analyzed, implying a general advantage of microexon downregulation in cancer independent of its tissue of origin. We show that this silencing is favorable for tumor growth, as decreased SRRM4 expression in tumors is correlated with an increase in mitotic gene expression, and upregulation of SRRM4 in cancer cell lines dose-dependently inhibits proliferation in vitro and in a mouse xenograft model. Further, this proliferation inhibition is accompanied by induction of neural-like expression and splicing patterns in cancer cells, suggesting that SRRM4 expression shifts the cell state away from proliferation and towards differentiation. We therefore conclude that SRRM4 acts as a proliferation brake, and tumors gain a selective advantage by cutting off this brake. SignificanceMicroexons are extremely small exons enriched in the brain that play important roles in neural development. Their inclusion is mediated by the splicing factor SRRM4, also predominantly expressed in the brain. Surprisingly, we find that low expression of SRRM4 outside of the brain is further decreased in tumors, and in fact SRRM4 is the most consistently silenced splicing factor in tumors across tissue types. We demonstrate that SRRM4 inhibits cancer cell proliferation in vitro and in vivo by inducing a neuronal differentiation program. Our findings add a new element to the overall picture of splicing dysregulation in cancer, reveal an antiproliferative function for SRRM4 and microexons outside of the brain, and may present a common therapeutic intervention point across cancer types.

cancer biology↗

bioRxiv2019

Translational efficiency across healthy and tumor tissues is proliferation-related

BackgroundDifferent tissues express genes with particular codon usage and anticodon tRNA repertoires. However, the codon-anticodon co-adaptation in humans is not completely understood, as well as its effect on tissue-specific protein levels.\n\nResultsWe first validated the accuracy of small RNA-seq for tRNA quantification across five human cell lines. We then analyzed tRNA expression in more than 8000 tumor samples from TCGA, together with their paired mRNA-seq and proteomics data, to determine the Relative Translation Efficiency. We thereby elucidate that the dynamic adaptation of the tRNA pool is largely related to the proliferative state across tissues, which determines tissue-specific translation efficiency. Furthermore, the aberrant translational efficiency of ProCCA and GlyGGT in cancer, among other codons, which is partly regulated by the tRNA gene copy numbers and their promoter DNA methylation, is associated with poor patient survival.\n\nConclusionsThe distribution of tissue-specific tRNA pools over the whole cellular translatome affects the subsequent translational efficiency, which functionally determines a condition-specific expression program in tissues both in healthy and tumor states.

systems biology↗

bioRxiv2019

Proliferation specific codon usage facilitates oncogene translation

Tumors evolve under selection for gene mutations that give a growth advantage to the cancer cell. Intriguingly, some cancer genes are more often found mutated in tumors than their closely related family members. For example, KRAS mutations are more frequently observed in cancer in comparison to HRAS and NRAS. Here, we find that for RAS and six oncogene families, the most prevalent mutated members in cancer have a codon usage characteristic of genes involved in proliferation. The codon usage of KRAS is more adapted to be efficiently translated in proliferative cells than the codon usage of HRAS. We also show that the translation efficiency of KRAS varies between cell lines in a manner related to their tRNA expression. Altogether, our study demonstrates that a dynamic translation program contributes to shaping the expression profiles of oncogenes. We propose that codon bias related to cell proliferation contributes to the prevalence of mutations in certain members of oncogene families.

cancer biology↗