Transcriptomic Landscape and Immune Microenvironment AroundWound Bed Define Regenerative versus Non-regenerative Outcomesin Mouse Digit Amputation

Prabahar, A.; Chamberlain, C.; Vanderby, R.; Murphy, W.; Dangelo, W.; Mangesh, K.; Brown, B.; Mazumder, B.; Badylak, S.; Jiang, P.

doi:10.1101/2024.12.04.626910

bioRxiv · 10.1101/2024.12.04.626910

Transcriptomic Landscape and Immune Microenvironment AroundWound Bed Define Regenerative versus Non-regenerative Outcomesin Mouse Digit Amputation

Prabahar, A.·Chamberlain, C.·Vanderby, R.·Murphy, W.·Dangelo, W.·Mangesh, K.·Brown, B.·Mazumder, B.·Badylak, S.·Jiang, P.

View original source ↗Export metadata ↓

Abstract

In the mouse distal terminal phalanx (P3), it remains unclear why amputation at less than 33% of the digit results in regeneration, while amputation exceeding 67% leads to non-regeneration. Unraveling the molecular mechanisms underlying this disparity could provide crucial insights for regenerative medicine. In this study, we aim to investigate the tissues within the wound bed to understand the tissue microenvironment associated with regenerative versus non-regenerative outcomes. We employed a P3-specific amputation model in mice, integrated with time-series RNA-seq and a macrophage assay challenged with pro- and anti-inflammatory cytokines, to explore these mechanisms. Our findings revealed that non-regenerative digits exhibit a greater intense early transcriptional response in the wound bed compared to regenerative ones. Furthermore, early macrophage phenotypes differ distinctly between regenerative and non-regenerative outcomes. Regenerative digits also display unique co-expression modules related to Bone Morphogenetic Protein 2 (BMP2). The differentially expressed genes (DEGs) between regenerative and non-regenerative digits are enriched in targets of several transcription factors, such as HOXA11 and HOXD11 from the HOX gene family, showing a time-dependent pattern of enrichment. These transcription factors, known for their roles in bone regeneration, skeletal patterning, osteoblast activity, fracture healing, angiogenesis, and key signaling pathways, may act as master regulators of the regenerative gene signatures. Additionally, we developed a deep learning AI model capable of predicting post-amputation time and level from RNA-seq data, with potential applications in personalized treatment strategies and assessing the impact of interventions on regenerative outcomes.

Explore related subjects

developmental biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Prabahar, A., Chamberlain, C., Vanderby, R., Murphy, W., Dangelo, W., Mangesh, K., Brown, B., Mazumder, B., Badylak, S., Jiang, P.. 2024-12-09. Transcriptomic Landscape and Immune Microenvironment AroundWound Bed Define Regenerative versus Non-regenerative Outcomesin Mouse Digit Amputation. https://doi.org/10.1101/2024.12.04.626910

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

KEEP EXPLORING

Related preprints

bioRxiv2026

Neural regulation of hatching in amphibians

Many animal embryos hatch in response to threats or opportunities, yet how cue sensing activates hatching is unknown. We screened red-eyed treefrog (Agalychnis callidryas) eggs in the field with small molecules to discover that the neurotransmitter acetylcholine is a key mediator of hatching enzyme release. Using behavioral pharmacology, microscopy, and transcriptional profiling we identify direct cholinergic input on hatching gland cells that triggers enzyme release for egg rupture, and serotonergic transduction of embryonic hypoxia sensing. Independent hypoxia-sensing and mechanosensory predation-detection pathways converge on a hatching decision that elicits acetylcholine-dependent enzyme release and coordinated hatching-specific behavior. Cholinergic regulation of hatching enzyme release is conserved in a distantly related frog and salamander, suggesting a shared ancestral hatching mechanism. These results provide a neural basis for hatching plasticity which may have contributed to the evolution of diverse hatching modes in amphibians.

developmental biology↗

bioRxiv2026

Towards Understanding the Microenvironmental Control of Reindeer Antler Regeneration

Deer antlers are the only mammalian appendages capable of complete periodic regeneration and therefore provide a natural model for investigating mechanisms of skeletal regeneration. However, current knowledge of the structural and molecular characteristics of the regenerative antler microenvironment remains incomplete. Here, we compared antler tip and antler base tissues from Rangifer tarandus (reindeer) with mature metacarpal cortical bone using structural, compositional, histological, and proteomic analyses. Antler tissues exhibited smaller and less crystalline apatite structures, elevated carbonate substitution, and higher organic matrix content compared with metacarpal bone, indicating an immature mineral phase. Antlers also exhibited lower bone mineral density, greater porosity, reduced bone volume fraction, and greater trabecular separation, particularly in central regions, consistent with a dynamic remodeling microenvironment. Histological examination revealed abundant active osteons and extensive osteoid seams in antler tissues, whereas metacarpal bone predominantly comprised mature lamellar bone with limited remodeling activity. Proteomic profiling identified distinct extracellular matrix signatures between antler and metacarpal tissues. Metacarpal bone was enriched in proteins associated with skeletal homeostasis, mechanotransduction, and bone remodeling, whereas antler tissues were enriched in proteins involved in extracellular matrix reorganization, metabolic adaptation, and regeneration. Collectively, these findings indicate that reindeer antlers possess a specialized regenerative skeletal microenvironment characterized by immature mineral organization, active remodeling, and distinct molecular signatures associated with rapid tissue growth. These results provide new insights into the biological basis of mammalian appendage regeneration and may facilitate the development of regenerative strategies for bone repair and skeletal tissue engineering.

developmental biology↗

bioRxiv2026

Endogenous expression of mutant RagC in mice results in early-onset dilated cardiomyopathy with features of the Long-Olsen-Distelmaier syndrome

Dilated cardiomyopathy (DCM) is a severe heart condition often linked to arrhythmias, clots, and heart failure, for which treatments are not yet curative. Recently, de novo mutations in genes encoding components of the Rag GTPase nutrient signaling pathway, particularly in RRAGC, have been found in unrelated patients with a severe, early-onset DCM syndrome called Long-Olsen-Distelmaier. Cancer cell lines, hiPSC-derived cardiomyocytes and zebrafish have been used to study this Ragopathy, but a mammalian model to investigate this syndrome has not been generated. Here, we show that mice engineered to endogenously express mutations in Serine 74 (orthologous to the Serine 75 mutated in patients), exhibit early-onset features of DCM with decreased heart size, fibrosis, diastolic dysfunction and aortic insufficiency, characteristics reminiscent of the human syndrome. Moreover, Rragc-mutant hearts display decreased left ventricular mass and interventricular septum. Endogenous heterozygous expression of Rragc mutant variants result in a milder, sublethal defective physiological cardiac growth with increased systolic and diastolic blood pressure. Mechanistically, active RagC does not cause abnormal increase in cardiomyocyte size, but leads to suppressed transcriptional activity of Tfeb and alterations in cardiomyocyte metabolism. Transcriptional profiling of neonatal mutant hearts reveals multiple signatures of impaired mitochondrial activity. Ex vivo and in vitro analyses of murine cardiomyocyte mitochondria from Rragc-mutant mice show suppressed mitochondrial respiration, disturbed complex IV multimerization and super-complex organization. These data point to abnormal early postnatal heart metabolism by deregulated nutrient - Rag GTPase signaling with a potential molecular explanation to the early onset of DCM in patients with de novo missense mutations in RRAGC, and suggests the relevance of early metabolic interventions in conditions with altered nutrient signaling

developmental biology↗