Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution

Mimpen, J. Y.; Baldwin, M. J.; Paul, C.; Ramos-Mucci, L.; Kurjan, A.; Cohen, C. J.; Sharma, S.; Chevalier Florquin, M. S. N.; Hulley, P. A.; McMaster, J.; Titchener, A.; Martin, A.; Costa, M. L.; Gwilym, S. E.; Cribbs, A. P.; Snelling, S. J. B.

doi:10.1101/2024.09.06.611599

bioRxiv · 10.1101/2024.09.06.611599

Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution

Mimpen, J. Y.·Baldwin, M. J.·Paul, C.·Ramos-Mucci, L.·Kurjan, A.·Cohen, C. J.·Sharma, S.·Chevalier Florquin, M. S. N.·Hulley, P. A.·McMaster, J.·Titchener, A.·Martin, A.·Costa, M. L.·Gwilym, S. E.·Cribbs, A. P.·Snelling, S. J. B.

View original source ↗Export metadata ↓

Abstract

Tendon ruptures in humans have regularly been studied during the chronic phase of injury. However, the early response to injury remains less investigated. Quadriceps tendons, which require prompt surgical treatment, offer a model to investigate this early response. Therefore, this study aimed to explore the early cellular changes in ruptured compared to healthy human quadriceps tendons. Quadriceps tendon samples were collected from patients undergoing tibial shaft fracture repair (healthy) or tendon repair surgery for complete rupture (collected 7-8 days post-injury). Nuclei were isolated for single-nucleus RNA sequencing, and comprehensive transcriptomic analysis was conducted to profile cellular changes. The transcriptomes of 12,808 nuclei were profiled, including 7,268 nuclei from healthy and 5,540 nuclei from ruptured quadriceps tendons, revealing 12 major cell types and several cell subtypes and states. Rupture samples showed increased expression of genes related to extracellular matrix organisation and cell cycle signalling, and a decrease in expression of genes in lipid metabolism pathways. These changes were driven predominantly by gene expression changes in the fibroblast, vascular endothelial cells (VECs), mural cell, and macrophage populations: fibroblasts shift to an activated phenotype upon rupture and there is an increase in proportion of capillary and dividing VECs, suggesting an angiogenic response. A diverse immune environment was observed, with a shift from homeostatic to activated macrophages following rupture. Cell-cell interactions increased in rupture, both in their number and diversity, and primarily involving fibroblast and endothelial cell populations. Collectively, this transcriptomic analysis suggests that fibroblasts and endothelial cells are key orchestrators of the early injury response within ruptured quadriceps tendon.

Source connections

Published article ↗

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Mimpen, J. Y., Baldwin, M. J., Paul, C., Ramos-Mucci, L., Kurjan, A., Cohen, C. J., Sharma, S., Chevalier Florquin, M. S. N., Hulley, P. A., McMaster, J., Titchener, A., Martin, A., Costa, M. L., Gwilym, S. E., Cribbs, A. P., Snelling, S. J. B.. 2024-09-08. Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution. https://doi.org/10.1101/2024.09.06.611599

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗

bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗

bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗