Showing papers by "University of Texas Health Science Center at San Antonio published in 2022"

Spatial transcriptomics of dorsal root ganglia identifies molecular signatures of human nociceptors

Abstract: Nociceptors are specialized sensory neurons that detect damaging or potentially damaging stimuli and are found in the dorsal root ganglia (DRG) and trigeminal ganglia. These neurons are critical for the generation of neuronal signals that ultimately create the perception of pain. Nociceptors are also primary targets for treating acute and chronic pain. Single-cell transcriptomics on mouse nociceptors has transformed our understanding of pain mechanisms. We sought to generate equivalent information for human nociceptors with the goal of identifying transcriptomic signatures of nociceptors, identifying species differences and potential drug targets. We used spatial transcriptomics to molecularly characterize transcriptomes of single DRG neurons from eight organ donors. We identified 12 clusters of human sensory neurons, 5 of which are C nociceptors, as well as 1 C low-threshold mechanoreceptors (LTMRs), 1 Aβ nociceptor, 2 Aδ, 2 Aβ, and 1 proprioceptor subtypes. By focusing on expression profiles for ion channels, G protein-coupled receptors (GPCRs), and other pharmacological targets, we provided a rich map of potential drug targets in the human DRG with direct comparison to mouse sensory neuron transcriptomes. We also compared human DRG neuronal subtypes to nonhuman primates showing conserved patterns of gene expression among many cell types but divergence among specific nociceptor subsets. Last, we identified sex differences in human DRG subpopulation transcriptomes, including a marked increase in calcitonin-related polypeptide alpha (CALCA) expression in female pruritogen receptor-enriched nociceptors. This comprehensive spatial characterization of human nociceptors might open the door to development of better treatments for acute and chronic pain disorders.

Targeting LIF/LIFR signaling in cancer

Abstract: Leukemia inhibitory factor (LIF), and its receptor (LIFR), are commonly over-expressed in many solid cancers and recent studies have implicated LIF/LIFR axis as a promising clinical target for cancer therapy. LIF/LIFR activate oncogenic signaling pathways including JAK/STAT3 as immediate effectors and MAPK, AKT, mTOR further downstream. LIF/LIFR signaling plays a key role in tumor growth, progression, metastasis, stemness and therapy resistance. Many solid cancers show overexpression of LIF and autocrine stimulation of the LIF/LIFR axis; these are associated with a poorer relapse-free survival. LIF/LIFR signaling also plays a role in modulating multiple immune cell types present in tumor micro environment (TME). Recently, two targeted agents that target LIF (humanized anti-LIF antibody, MSC-1) and LIFR inhibitor (EC359) were under development. Both agents showed effectivity in preclinical models and clinical trials using MSC-1 antibody are in progress. This article reviews the significance of LIF/LIFR pathways and inhibitors that disrupt this process for the treatment of cancer.

An Immunogenic Model of KRAS-Mutant Lung Cancer Enables Evaluation of Targeted Therapy and Immunotherapy Combinations

Abstract: Abstract Mutations in oncogenes such as KRAS and EGFR cause a high proportion of lung cancers. Drugs targeting these proteins cause tumor regression but ultimately fail to elicit cures. As a result, there is an intense interest in how to best combine targeted therapies with other treatments, such as immunotherapies. However, preclinical systems for studying the interaction of lung tumors with the host immune system are inadequate, in part due to the low tumor mutational burden in genetically engineered mouse models. Here we set out to develop mouse models of mutant KRAS–driven lung cancer with an elevated tumor mutational burden by expressing the human DNA cytosine deaminase, APOBEC3B, to mimic the mutational signature seen in human lung cancer. This failed to substantially increase clonal tumor mutational burden and autochthonous tumors remained refractory to immunotherapy. However, establishing clonal cell lines from these tumors enabled the generation of an immunogenic syngeneic transplantation model of KRAS-mutant lung adenocarcinoma that was sensitive to immunotherapy. Unexpectedly, antitumor immune responses were not directed against neoantigens but instead targeted derepressed endogenous retroviral antigens. The ability of KRASG12C inhibitors to cause regression of KRASG12C -expressing tumors was markedly potentiated by the adaptive immune system, highlighting the importance of using immunocompetent models for evaluating targeted therapies. Overall, this model provides a unique opportunity for the study of combinations of targeted and immunotherapies in immune-hot lung cancer. Significance: This study develops a mouse model of immunogenic KRAS-mutant lung cancer to facilitate the investigation of optimal combinations of targeted therapies with immunotherapies.

Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer’s disease

Abstract: Abstract Dysregulation of sphingomyelin and ceramide metabolism have been implicated in Alzheimer’s disease. Genome-wide and transcriptome-wide association studies have identified various genes and genetic variants in lipid metabolism that are associated with Alzheimer’s disease. However, the molecular mechanisms of sphingomyelin and ceramide disruption remain to be determined. We focus on the sphingolipid pathway and carry out multi-omics analyses to identify central and peripheral metabolic changes in Alzheimer’s patients, correlating them to imaging features. Our multi-omics approach is based on (a) 2114 human post-mortem brain transcriptomics to identify differentially expressed genes; (b) in silico metabolic flux analysis on context-specific metabolic networks identified differential reaction fluxes; (c) multimodal neuroimaging analysis on 1576 participants to associate genetic variants in sphingomyelin pathway with Alzheimer’s disease pathogenesis; (d) plasma metabolomic and lipidomic analysis to identify associations of lipid species with dysregulation in Alzheimer’s; and (e) metabolite genome-wide association studies to define receptors within the pathway as a potential drug target. We validate our hypothesis in amyloidogenic APP/PS1 mice and show prolonged exposure to fingolimod alleviated synaptic plasticity and cognitive impairment in mice. Our integrative multi-omics approach identifies potential targets in the sphingomyelin pathway and suggests modulators of S1P metabolism as possible candidates for Alzheimer’s disease treatment.

Mechanisms of Electrochemical N₂ Splitting by a Molybdenum Pincer Complex

Abstract: Molybdenum complexes supported by tridentate pincer ligands are exceptional catalysts for dinitrogen fixation using chemical reductants, but little is known about their prospects for electrochemical reduction of dinitrogen. The viability of electrochemical N2 binding and splitting by a molybdenum(III) pincer complex, (pyPNP)MoBr3 (pyPNP = 2,6-bis(tBu2PCH2)-C5H3N)), is established in this work, providing a foundation for a detailed mechanistic study of electrode-driven formation of the nitride complex (pyPNP)Mo(N)Br. Electrochemical kinetic analysis, optical and vibrational spectroelectrochemical monitoring, and computational studies point to two concurrent reaction pathways: In the reaction-diffusion layer near the electrode surface, the molybdenum(III) precursor is reduced by 2e- and generates a bimetallic molybdenum(I) Mo2(μ-N2) species capable of N-N bond scission; and in the bulk solution away from the electrode surface, over-reduced molybdenum(0) species undergo chemical redox reactions via comproportionation to generate the same bimetallic molybdenum(I) species capable of N2 cleavage. The comproportionation reactions reveal the surprising intermediacy of dimolybdenum(0) complex trans,trans-[(pyPNP)Mo(N2)2](μ-N2) in N2 splitting pathways. The same "over-reduced" molybdenum(0) species was also found to cleave N2 upon addition of lutidinium, an acid frequently used in catalytic reduction of dinitrogen.

Domesticating Rewilding: Interpreting Rewilding in England's Green and Pleasant Land

Abstract: There are many different forms and interpretations of rewilding: the concept and its practice vary from country to country, with distinct interpretations according to its geographical location. Despite the term rewilding having been present in the lexicon for three decades, the concept of rewilding in England has experienced a prolonged developmental stage. This paper argues that a unique form of English rewilding is now emerging, which is distinct from rewilding in other parts of the world. Compared to other locations rewilding in England operates at smaller spatial scales; its ambitions to increase biodiversity, restore ecosystem functioning and increase natural autonomy are somewhat curtailed; it involves higher levels of human intervention; and, perhaps most tellingly of all, it goes by another name - 'wilding', 'wild' or 'wilder' with little mention of the much-maligned prefix 're'. This conclusion has been developed following a comparative case study of two English 'rewilding' sites (the Avalon Marshes and Wild Ennerdale) involving 49 semi-structured interviews: twelve expert interviews and nineteen and eighteen stakeholder/practitioner interviews at the Avalon Mashes and Wild Ennerdale respectively.

Vertical Inhibition of the RAF–MEK–ERK Cascade Induces Myogenic Differentiation, Apoptosis, and Tumor Regression in<i>H/NRASQ61X</i>Mutant Rhabdomyosarcoma

Abstract: Oncogenic RAS signaling is an attractive target for fusion-negative rhabdomyosarcoma (FN-RMS). Our study validates the role of the ERK MAPK effector pathway in mediating RAS dependency in a panel of H/NRASQ61X mutant RMS cells and correlates in vivo efficacy of the MEK inhibitor trametinib with pharmacodynamics of ERK activity. A screen is used to identify trametinib-sensitizing targets, and combinations are evaluated in cells and tumor xenografts. We find that the ERK MAPK pathway is central to H/NRASQ61X dependency in RMS cells; however, there is poor in vivo response to clinically relevant exposures with trametinib, which correlates with inefficient suppression of ERK activity. CRISPR screening points to vertical inhibition of the RAF-MEK-ERK cascade by cosuppression of MEK and either CRAF or ERK. CRAF is central to rebound pathway activation following MEK or ERK inhibition. Concurrent CRAF suppression and MEK or ERK inhibition, or concurrent pan-RAF and MEK/ERK inhibition (pan-RAFi + MEKi/ERKi), or concurrent MEK and ERK inhibition (MEKi + ERKi) all synergistically block ERK activity and induce myogenic differentiation and apoptosis. In vivo assessment of pan-RAFi + ERKi or MEKi + ERKi potently suppress growth of H/NRASQ61X RMS tumor xenografts, with pan-RAFi + ERKi being more effective and better tolerated. We conclude that CRAF reactivation limits the activity of single-agent MEK/ERK inhibitors in FN-RMS. Vertical targeting of the RAF-MEK-ERK cascade and particularly cotargeting of CRAF and MEK or ERK, or the combination of pan-RAF inhibitors with MEK or ERK inhibitors, have synergistic activity and potently suppress H/NRASQ61X mutant RMS tumor growth.

A Review of Extracorporeal Blood Purification Techniques for the Treatment of Critically Ill Coronavirus Disease 2019 Patients

Abstract: In late 2019, a novel betacoronavirus, later termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was discovered in patients with an unknown respiratory illness in Wuhan, China. SARS-CoV-2 and the disease caused by the novel coronavirus, coronavirus disease 2019 (COVID-19), spread rapidly and resulted in the World Health Organization declaring a pandemic in March 2020. In a minority of patients infected with SARS-CoV-2, severe illness develops characterized by a dysregulated immune response, acute respiratory distress syndrome, and multisystem organ failure. Despite the development of antiviral and multiple immunomodulatory therapies, outcomes of severe illness remain poor. In response, the Food and Drug Administration in the United States authorized the emergency use of several extracorporeal blood purification (EBP) devices for critically ill patients with COVID-19. Extracorporeal blood purification devices target various aspects of the host response to infection to reduce immune dysregulation. This review highlights the underlying technology, currently available literature on use in critically ill COVID-19 patients, and future studies involving four EBP platforms: 1) oXiris filter, 2) CytoSorb filter, 3) Seraph 100 Microbind blood affinity filter, and 4) the Spectra Optia Apheresis System with the Depuro D2000 Adsorption Cartridge.

A comparison of the post-fusion outcome of patients with early-onset scoliosis treated with traditional and magnetically controlled growing rods

Abstract: The aim of this study was to compare the clinical and radiological outcomes of patients with early-onset scoliosis (EOS), who had undergone spinal fusion after distraction-based spinal growth modulation using either traditional growing rods (TGRs) or magnetically controlled growing rods (MCGRs).We undertook a retrospective review of skeletally mature patients who had undergone fusion for an EOS, which had been previously treated using either TGRs or MCGRs. Measured outcomes included sequential coronal T1 to S1 height and major curve (Cobb) angle on plain radiographs and any complications requiring unplanned surgery before final fusion.We reviewed 43 patients (63% female) with a mean age of 6.4 years (SD 2.6) at the index procedure, and 12.2 years (SD 2.2) at final fusion. Their mean follow-up was 8.1 years (SD 3.4). A total of 16 patients were treated with MCGRs and 27 with TGRs. The mean number of distractions was 7.5 in the MCGR group and ten in the TGR group (p = 0.471). The mean interval between distractions was 3.4 months in the MCGR group and 8.6 months in the TGR group (p < 0.001). The mean Cobb angle had improved by 25.1° in the MCGR group and 23.2° in TGR group (p = 0.664) at final follow-up. The mean coronal T1 to S1 height had increased by 16% in the MCGR group and 32.9% in TGR group (p = 0.001), although the mean T1 to S1 height achieved at final follow-up was similar in both. Unplanned operations were needed in 43.8% of the MCGR group and 51.2% of TGR group (p = 0.422).In this retrospective, single-centre review, there were no significant differences in major curve correction or gain in spinal height at fusion. Although the number of planned procedures were fewer in patients with MCGRs, the rates of implant-related complications needing unplanned revision surgery were similar in the two groups. Cite this article: Bone Joint J 2022;104-B(2):257-264.

Development of a tRNA-derived small RNA diagnostic and prognostic signature in liver cancer

Abstract: Liver cancer presents divergent clinical behaviors. There remain opportunities for molecular markers to improve liver cancer diagnosis and prognosis, especially since tRNA-derived small RNAs (tsRNA) have rarely been studied. In this study, a random forests (RF) diagnostic model was built based upon tsRNA profiling of paired tumor and adjacent normal samples and validated by independent validation (IV). A LASSO model was used to developed a seven-tsRNA-based risk score signature for liver cancer prognosis. Model performance was evaluated by a receiver operating characteristic curve (ROC curve) and Precision-Recall curve (PR curve). The five-tsRNA-based RF diagnosis model had area under the receiver operating characteristic curve (AUROC) 88% and area under the precision-recall curve (AUPR) 87% in the discovery cohort and 87% and 86% in IV-AUROC and IV-AUPR, respectively. The seven-tsRNA-based prognostic model predicts the overall survival of liver cancer patients (Hazard Ratio 2.02, 95% CI 1.36-3.00, P < 0.001), independent of standard clinicopathological prognostic factors. Moreover, the model successfully categorizes patients into high-low risk groups. Diagnostic and prognostic modeling can be reliably utilized in the diagnosis of liver cancer and high-low risk classification of patients based upon tsRNA characterization.

MYC, mitochondrial metabolism and O-GlcNAcylation converge to modulate the activity and subcellular localization of DNA and RNA demethylases

Abstract: Mitochondria can function as signaling organelles, and part of this output leads to epigenetic remodeling. The full extent of this far-reaching interplay remains undefined. Here, we show that MYC transcriptionally activates IDH2 and increases alpha-ketoglutarate (αKG) levels. This regulatory step induces the activity of αKG-dependent DNA hydroxylases and RNA demethylases, thus reducing global DNA and RNA methylation. MYC, in a IDH2-dependent manner, also promotes the nuclear accumulation of TET1-TET2-TET3, FTO and ALKBH5. Notably, this subcellular movement correlated with the ability of MYC, in an IDH2-dependent manner, and, unexpectedly, of αKG to directly induce O-GlcNAcylation. Concordantly, modulation of the activity of OGT and OGA, enzymes that control the cycling of this non-canonical mono-glycosylation, largely recapitulated the effects of the MYC-IDH2-αKG axis on the subcellular movement of DNA and RNA demethylases. Together, we uncovered a hitherto unsuspected crosstalk between MYC, αKG and O-GlcNAcylation which could influence the epigenome and epitranscriptome homeostasis.

Trigeminal neurons control immune-bone cell interaction and metabolism in apical periodontitis

Abstract: Abstract Apical periodontitis (AP) is an inflammatory disease occurring following tooth infection with distinct osteolytic activity. Despite increasing evidence that sensory neurons participate in regulation of non-neuronal cells, their role in the development of AP is largely unknown. We hypothesized that trigeminal ganglia (TG) Nav1.8 + nociceptors regulate bone metabolism changes in response to AP. A selective ablation of nociceptive neurons in Nav1.8 Cre /Diphtheria toxin A (DTA) Lox mouse line was used to evaluate the development and progression of AP using murine model of infection-induced AP. Ablation of Nav1.8 + nociceptors had earlier progression of AP with larger osteolytic lesions. Immunohistochemical and RNAscope analyses demonstrated greater number of macrophages, T-cells, osteoclast and osteoblast precursors and an increased RANKL:OPG ratio at earlier time points among Nav1.8 Cre / DTA Lox mice. There was an increased expression of IL-1α and IL-6 within lesions of nociceptor-ablated mice. Further, co-culture experiments demonstrated that TG neurons promoted osteoblast mineralization and inhibited osteoclastic function. The findings suggest that TG Nav1.8 + neurons contribute to modulation of the AP development by delaying the influx of immune cells, promoting osteoblastic differentiation, and decreasing osteoclastic activities. This newly uncovered mechanism could become a therapeutic strategy for the treatment of AP and minimize the persistence of osteolytic lesions in refractory cases. Graphical abstract

A First-in-Class Inhibitor of ER Coregulator PELP1 Targets ER+ Breast Cancer

Abstract: Most patients with estrogen receptor alpha-positive (ER+) breast cancers initially respond to treatment but eventually develop therapy resistance with disease progression. Overexpression of oncogenic ER coregulators, including proline, glutamic acid, and leucine-rich protein 1 (PELP1), are implicated in breast cancer progression. The lack of small molecules that inhibits PELP1 represents a major knowledge gap. Here, using a yeast-two-hybrid screen, we identified novel peptide inhibitors of PELP1 (PIP). Biochemical assays demonstrated that one of these peptides, PIP1, directly interacted with PELP1 to block PELP1 oncogenic functions. Computational modeling of PIP1 revealed key residues contributing to its activity and facilitated the development of a small-molecule inhibitor of PELP1, SMIP34, and further analyses confirmed that SMIP34 directly bound to PELP1. In breast cancer cells, SMIP34 reduced cell growth in a dose-dependent manner. SMIP34 inhibited proliferation of not only wild-type (WT) but also mutant (MT) ER+ and therapy-resistant breast cancer cells, in part by inducing PELP1 degradation via the proteasome pathway. RNA sequencing analyses showed that SMIP34 treatment altered the expression of genes associated with estrogen response, cell cycle, and apoptosis pathways. In cell line-derived and patient-derived xenografts of both WT and MT ER+ breast cancer models, SMIP34 reduced proliferation and significantly suppressed tumor progression. Collectively, these results demonstrate SMIP34 as a first-in-class inhibitor of oncogenic PELP1 signaling in advanced breast cancer.Development of a novel inhibitor of oncogenic PELP1 provides potential therapeutic avenues for treating therapy-resistant, advanced ER+ breast cancer.

American Academy of Periodontology best evidence consensus statement on the use of biologics in clinical practice

Abstract: A biologic is a therapeutic agent with biological activity that is administered to achieve an enhanced regenerative or reparative effect. The use of biologics has progressively become a core component of contemporary periodontal practice. However, some questions remain about their safety, indications, and effectiveness in specific clinical scenarios. Given their availability for routine clinical use and the existing amount of related evidence, the goal of this American Academy of Periodontology (AAP) best evidence consensus (BEC) was to provide a state-of-the-art, evidence-based perspective on the therapeutic application of autologous blood-derived products (ABPs), enamel matrix derivative (EMD), recombinant human platelet-derived growth factor BB (rhPDGF-BB), and recombinant human bone morphogenetic protein 2 (rhBMP-2). A panel of experts with extensive knowledge on the science and clinical application of biologics was convened. Three systematic reviews covering the areas of periodontal plastic surgery, treatment of infrabony defects, and alveolar ridge preservation/reconstruction and implant site development were conducted a priori and provided the foundation for the deliberations. The expert panel debated the merits of published data and exchanged experiential information to formulate evidence-based consensus statements and recommendations for clinical practice and future research. Based on an analysis of the current evidence and expert opinion, the panel concluded that the appropriate use of biologics in periodontal practice is generally safe and provides added benefits to conventional treatment approaches. However, therapeutic benefits and risks range based on the specific biologics used as well as patient-related local and systemic factors. Given the limited evidence available for some indications (e.g., gingival augmentation therapy, alveolar ridge preservation/reconstruction, and implant site development), future clinical studies that can expand the knowledge base on the clinical use of biologics in periodontal practice are warranted.

GNE-064: A Potent, Selective, and Orally Bioavailable Chemical Probe for the Bromodomains of SMARCA2 and SMARCA4 and the Fifth Bromodomain of PBRM1

Abstract: Bromodomains are acetyllysine recognition domains present in a variety of human proteins. Bromodomains also bind small molecules that compete with acetyllysine, and therefore bromodomains have been targets for drug discovery efforts. Highly potent and selective ligands with good cellular permeability have been proposed as chemical probes for use in exploring the functions of many of the bromodomain proteins. We report here the discovery of a class of such inhibitors targeting the family VIII bromodomains of SMARCA2 (BRM) and SMARCA4 (BRG1), and PBRM1 (polybromo-1) bromodomain 5. We propose one example from this series, GNE-064, as a chemical probe for the bromodomains SMARCA2, SMARCA4, and PBRM1(5) with the potential for in vivo use.

Information Model to Advance Explainable AI-Based Decision Support Systems in Manufacturing System Design

Abstract: Artificial intelligence is currently being used in more and more areas of production. Be it in the field of industrial robotics, automated quality inspection or cognitive support for employees in production, artificial intelligence contributes to creating smart as well as sustainable manufacturing systems. In the area of manufacturing system design, decision support models are increasingly used to facilitate the work of system designers. In this paper, we address how information models can be used to design explainable artificial intelligence decision support systems. The paper will survey and describe the information that is necessary to communicate manufacturing system design requirements to meet customer needs and use cases. The objective is to propose an information model to express system design requirements with the goal to provide a transparent representation of decisions as well as alternatives of decisions to improve the description of artificial intelligence-based decision support systems during the manufacturing system (re)design phase. The purpose of the information model is to explore the requirements and technical solutions necessary to advance manufacturing systems without losing track of alternatives, and to be able to dynamically adapt them to changing conditions in the market or the production environment.