Faculty Bibliography

The science of metabolic profiling exploits chemical compound byproducts of metabolism called metabolites¹ that explain internal biological functions, physiological health and disease, and provide evidence of external influences specific to an organism's habitat. Here we assess palaeometabolomes from fossilized mammalian hard tissues as a molecular ecological strategy to provide evidence of an ancient organism's relationship with its environment. From eastern, central and southern African Plio-Pleistocene localities of palaeoanthropological significance, we study six fossils from Olduvai Gorge, Tanzania, one from the Chiwondo Beds, Malawi, and one from Makapansgat, South Africa. We perform endogeneity assessments by analysing palaeometabolomes of palaeosols and the effects of owl digestion on rodent bones to enable prudent ecological inferences. Diagenesis is indicated by metabolites of collagenase-producing bacteria², whereas the preservation of peptides including those of collagen are identified by proteomics. Endogenous metabolites document biological functions and exogenous metabolites render environmental details including soil characteristics and woody cover, and enable annual minimum and maximum rainfall and temperature reconstructions at Olduvai Gorge, supporting the freshwater woodland and grasslands of Olduvai Gorge Bed I^3-5, and the dry woodlands and marsh of Olduvai Gorge Upper Bed II⁶. All sites denote wetter and/or warmer conditions than today. We infer that metabolites preserved in hard tissues derive from an extravasated vasculature serum filtrate that becomes entombed within developing mineralized matrices, and most probably survive palaeontological timeframes in the nanoscopic 'pool' of structural-bound water that occurs in hard tissue niches⁷.

Cells adapt to proteostatic and metabolic stresses, in part, through stress activated eIF2α kinases that stimulate the translation of ATF4. Stress-induced ATF4 translation is regulated through elements at ATF4 mRNA's 5' leader. In addition to eIF2α kinases, ATF4 induction requires other regulators that remain poorly understood. Here, we report an ATF4 regulatory network consisting of eIF4E-Homologous Protein (4EHP), NELF-E, the 40S ribosome, and eIF3 subunits. Specifically, we found that the mRNA cap-binding protein, 4EHP, was required for ATF4 signaling in the Drosophila larval fat body and in disease models associated with abnormal ATF4 signaling. NELF-E mRNA, encoding a regulator of pol II-mediated transcription, was identified as a top interactor of 4EHP in a TRIBE (Targets of RNA Binding through Editing) screen. Quantitative proteomics analysis revealed that the knockdown of NELF-E or 4EHP commonly reduced several subunits of the 40S ribosome (RpS) and the eIF3 translation initiation factor. Moreover, reduction of NELF-E, 4EHP, RpS12, eIF3l, or eIF3h suppressed the expression of ATF4 and its target genes. These results uncover a previously unrecognized ATF4 regulatory network consisting of 4EHP and NELF-E that impacts proteostasis during normal development and in disease models.

Homeostasis of the nervous system is maintained by a population of resident neural stem cells (NSCs) retained in a state of reversible cell-cycle arrest called quiescence. Quiescent NSCs can resume proliferation in response to different physiological stimuli. Reactivation requires changes in gene expression, much of which is regulated at the epigenomic level. We mapped epigenomic changes in NSC chromatin during stem cell quiescence and reactivation in Drosophila in vivo. Contrary to expectations, chromatin accessibility is increased in quiescent NSCs. Surprisingly, genes crucial for cell-cycle progression are repressed while remaining within permissive H3K36me3-bound euchromatin. At the same time, genes necessary for cell-cell communication are derepressed by eviction of histone H1 and transition to an SWI/SNF-enriched active state. Our results reveal global expansion of accessible chromatin in quiescent NSCs without concomitant transcriptional activation. Strikingly, this process reverses upon reactivation, indicating that opening of chromatin is a quiescence-specific event.

Understanding the molecular mechanisms driving lineage decisions and differentiation during development is challenging in complex systems with a diverse progenitor pool, such as the mammalian cerebellum. Importantly, how different transcription factors cooperate to generate neural diversity and the gene regulatory mechanisms that drive neuron production, especially during the late stages of cerebellum development, are poorly understood. We used single cell RNA-sequencing (scRNA-seq) to investigate the developmental trajectories of Nestin-expressing progenitors (NEPs) in the neonatal mouse cerebellum. We identified FOXO1 as a key regulator of NEP-to-inhibitory neuron differentiation, acting directly downstream of ASCL1. Genome occupancy and functional experiments using primary NEP cultures showed that both ASCL1 and FOXO1 regulate neurogenesis genes during differentiation while independently regulating proliferation and survival, respectively. Furthermore, we demonstrated that WNT signalling promotes the transition from an ASCL1+ to a FOXO1+ cellular state. Finally, the role of WNT signalling in promoting neuron production via FOXO1 is conserved in primary human NEP cultures. By resolving how cerebellar inhibitory neurons differentiate, our findings could have implications for cerebellar disorders such as spinocerebellar ataxia, where these cells are overproduced.

Signaling interactions between the dermal papilla (DP) and neighboring stem cells in the hair germ (HGSCs) and bulge (BuSCs) regulate new follicle growth in the hair cycle. To study these interactions, the three populations had been profiled together by now-outdated microarrays or separately by bulk RNA-sequencing. Recent single-cell transcriptomics established signatures of DP, BuSCs and HGSCs, but low detection sensitivity limited the depth of gene expression discovery. Here, we define the transcriptomes of DP, BuSCs, HGSCs, epidermal, follicle and dermal fibroblast cells-after flow-sorting each population from four neighboring mouse back skin regions-to gain deeper insights into the unique gene expression programs of SCs and their instructive niche. With cross-comparisons of 56 whole-transcriptome measurements, we classify cell type-specific molecular signatures of enriched genes with unprecedented sensitivity. Joint analysis with signatures from 15 leading studies published in the last 20 years revealed many previously undescribed DP, BuSC and HGSC genes in mouse and human counterparts. With ligand-receptor mapping and CellChat analyses we then uncover comprehensive cell-cell communication insights. Finally, we provide a new installment of our Hair-Gel repository along with numerous signature and other gene tables for easy exploration of gene expression in hair follicle SCs and their niche.

Despite bone's robust regenerative capacity, complications such as delayed union and nonunion affect 5-10% of fractures, with significant clinical and economic burdens. The rising incidence of fractures, particularly in an aging population, highlights the importance of optimizing fracture healing strategies. This review explores current therapies aimed at enhancing bone regeneration, focusing on 2 main categories: local biologic therapies and mechanical therapies. Local biologic treatments, including concentrated bone marrow aspirate, platelet-rich plasma, bone morphogenetic proteins, and platelet-derived growth factor, aim to stimulate osteogenesis at the fracture site. Therapies, such as electrical stimulation, low-intensity pulsed ultrasound, and extracorporeal shockwave therapy, are theorized to modify the mechanical environment to promote healing. Although these therapies show promise, variability in clinical outcomes emphasizes the need for further research to standardize protocols and refine treatment strategies. Overall, advancing our understanding of bone healing mechanisms will continue to drive innovation in fracture management, improving patient outcomes and reducing health care costs.

BACKGROUND/UNASSIGNED:This study compares outcomes and complications of patients with Bado II Monteggia fracture-dislocations that required radial head fixation or replacement based upon approach to the radial head. METHODS/UNASSIGNED:A retrospective review was performed of 159 consecutive patients with proximal ulna fractures and a radial head dislocation or fracture (Monteggia Variant). Injuries were classified by Bado type. Forty-one patients with Bado II Monteggia injuries treated with either a radial head replacement or fixation with complete follow up were included. Demographics, injury information, surgical details, and follow up information including elbow range of motion (ROM) and complications were collected. A trans-osseous posterior (TOP) approach working through the ulna fracture to address the radial head first was used in 19 patients, while 22 patients had their radial head treated via a separate lateral (Kocher) interval after ulnar fixation. Ulnar plate fixation was performed for all patients. Comparisons were made using independent t-tests. RESULTS/UNASSIGNED:Forty-one Monteggia lesions treated through TOP (19, 46 %) or Kocher (22, 64 %) approaches underwent a radial head replacement (33, 80.5 %) or fracture repair (8, 19.5 %) with a mean final follow-up of 15.3 months. At all post-operative visits, groups displayed similar rates of functional elbow ROM. At latest follow-up rates of patient-reported pain, ultimate elbow ROM, time to radiographic healing were equivalent. No significant differences were observed in ulna non-union, joint malalignment, post-operative nerve injury, post-operative infection, heterotopic ossification, incidence of hardware failure, patient-reported pain, and rate of removal of symptomatic hardware. Sub-analysis of radial head replacement versus fixation revealed equivalent percentage of patients with full ROM at each post-operative time point. CONCLUSION/UNASSIGNED:For Bado II Monteggia fracture-dislocations, the surgical approach to the radial head-TOP versus Kocher-does not influence ultimate patient outcomes or complication rates. Radial head replacement and fixation provide comparable results. LEVEL OF EVIDENCE/UNASSIGNED:III.

BACKGROUND & AIM/UNASSIGNED:Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing health issue. Identifying factors that prevent hepatic lipid accumulation could inform new MASLD prevention or treatment strategies. We previously demonstrated that adipocyte microsomal triglyceride transfer protein (MTP) regulates intracellular lipolysis by inhibiting adipose triglyceride lipase activity. The aim of this study was to investigate the impact of adipose MTP deficiency on MASLD. METHODS/UNASSIGNED: RESULTS/UNASSIGNED: CONCLUSION/UNASSIGNED:These findings highlight the importance of regulated FA flux from adipose tissue to the liver and the liver's adaptive capacity to utilize adipose-derived FAs in maintaining hepatic health. Modulation of adipocyte FA release may represent a therapeutic strategy to reduce hepatic steatosis. IMPACT AND IMPLICATIONS/UNASSIGNED:This study provides significant insights into the role of adipose-specific microsomal triglyceride transfer protein in regulating hepatic lipid metabolism and its potential implications for treating metabolic dysfunction-associated steatotic liver disease. By demonstrating that microsomal triglyceride transfer protein deficiency in adipose tissue leads to increased fatty acid oxidation and reduced hepatic steatosis through enhanced PPARα activation, the research underscores the importance of adipose-liver crosstalk in maintaining liver health. These findings suggest that targeting adipocyte fatty acid release could be a promising therapeutic strategy to mitigate hepatic lipid accumulation and combat metabolic dysfunction-associated steatotic liver disease, offering a novel approach to addressing this growing health issue.

Phosphorylation of hundreds of protein extracellular domains is mediated by two kinase families but the functional role of these kinases is underexplored. We find that the presynaptic release of the tyrosine-directed ectokinase, vertebrate lonesome kinase (VLK/Pkdcc), is necessary and sufficient for the direct extracellular interaction between EphB2 and GluN1 at synapses for phosphorylation of the ectodomain of EphB2 and mediation of injury-induced pain. Pkdcc is an essential gene in the nervous system, and VLK is enriched at synapses and released from neurons in an activity- and soluble N-ethylmaleimide-sensitive factor activating protein receptor (SNARE)-dependent manner to drive extracellular interactions. Our results show that presynaptic sensory neuron-specific VLK knockout attenuates postsurgical pain in mice without changing sensorimotor performance, suggesting that VLK critically regulates synaptic protein-protein interactions and acute pain in response to injury.