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Oral inflammatory diseases affect nearly half of the global population. Among them, newly defined peri-implantitis and high-grade periodontitis represent rapidly advancing inflammatory disease types, marked by relatively rapid tissue destruction. Despite their prevalence, the cell mechanisms and spatial architecture driving this severity remain poorly understood. Focusing first on peri-implantitis versus low- and moderate-grade periodontitis, we applied microbial profiling, single-cell RNA sequencing (scRNA-seq), and spatial proteomics (sp-proteomics) to uncover shared pathogenic programs linked to accelerated niche breakdown. Furthermore, to preserve spatial fidelity, each tissue was anatomically orientated along the tooth- or implant-epithelial interface, analogous sites of disease origination. Laser capture microdissection followed by microbiome analysis of unique tissue compartments revealed reduced bacterial load and diversity in peri-implantitis stroma. We then expanded our version-1 Human Periodontal Atlas by integrating newly generated peri-implantitis scRNAseq data (36-total samples; 121395-cells), revealing widespread transcriptional alterations, including oxidative stress, hypoxic, and NAD metabolism-associated signatures, primarily in a subpopulation of / post-capillary venules. We then performed high-resolution sp-proteomics (15-total samples; 337260-cells) and analyzed VEC states and associated neighborhoods via using newly developed tri-wise spatial analysis. This revealed CD34-VEC loss and CD38-VEC expansion almost exclusively in peri-implantitis. We extended this analysis to high-grade periodontitis. Mucosal biopsies from four lesion-affected and four unaffected sites within the same individuals (1:1 matched; 8-samples; 225137-cells) again demonstrated spatially restricted CD38-VEC remodeling exclusively in affected tissues, with similar vasculopathy front patterning. The findings nominate spatially distinct vasculopathy patterning as a hallmark of rapidly advancing oral inflammation and a targetable therapeutic axis.
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http://dx.doi.org/10.1101/2025.07.29.667333 | DOI Listing |
Theor Appl Genet
September 2025
Institute for Breeding Research on Agricultural Crops, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Sanitz, 18190, Germany.
Low-cost and high-throughput RNA sequencing data for barley RILs achieved GP performance comparable to or better than traditional SNP array datasets when combined with parental whole-genome sequencing SNP data. The field of genomic selection (GS) is advancing rapidly on many fronts including the utilization of multi-omics datasets with the goal of increasing prediction ability and becoming an integral part of an increasing number of breeding programs ensuring future food security. In this study, we used RNA sequencing (RNA-Seq) data to perform genomic prediction (GP) on three related barley RIL populations.
View Article and Find Full Text PDFGenes Dev
September 2025
RU Adipocytes and Metabolism, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany;
Adipose tissue is rapidly expanding early in life. Elucidating the queues facilitating this process will advance our understanding of metabolically healthy obesity. Using single-cell RNA sequencing, we identified compositional differences of prewean and adult murine subcutaneous adipose tissue.
View Article and Find Full Text PDFJ Immunother Cancer
September 2025
CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
Neoadjuvant immunochemotherapy (nICT) has demonstrated significant potential in improving pathological response rates and survival outcomes for patients with locally advanced esophageal squamous cell carcinoma (ESCC). However, substantial interindividual variability in therapeutic outcomes highlights the urgent need for more precise predictive tools to guide clinical decision-making. Traditional biomarkers remain limited in both predictive performance and clinical feasibility.
View Article and Find Full Text PDFBiotechnol Adv
September 2025
Key Laboratory of Microbiological Metrology, Measurement & Bio-product Quality Security, State Administration for Market Regulation, China Jiliang University, Hangzhou 310018, China. Electronic address:
Nanopore direct RNA sequencing (DRS) is a transformative technology that enables full-length, single-molecule sequencing of native RNA, capturing transcript isoforms and preserving epitranscriptomic modifications without cDNA conversion. This review outlines key advances in DRS, including optimized protocols for mRNA, rRNA, tRNA, circRNA, and viral RNA, as well as analytical tools for isoform quantification, poly(A) tail measurement, fusion transcript identification, and base modification profiling. We highlight how DRS has redefined transcriptomic studies across diverse systems-from uncovering novel transcripts and alternative splicing events in cancer, plants, and parasites to enabling the direct detection of m6A, m5C, pseudouridine, and RNA editing events.
View Article and Find Full Text PDFAngiogenesis
September 2025
Division of Plastic Surgery, Department of Surgery, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, 17033, USA.
Vascularization of implanted biomaterials is critical to reconstructive surgery and tissue engineering. Ultimately, the goal is to promote a rapidly perfusable hierarchical microvasculature that persists with time and can meet underlying tissue needs. We have previously shown that using a microsurgical technique, termed micropuncture (MP), in combination with porous granular hydrogel scaffolds (GHS) fabricated via interlinking hydrogel microparticles (microgels) results in a rapidly perfusable patterned microvasculature.
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