hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing.

RNA splicing is pivotal in post-transcriptional gene regulation, yet the exponential expansion of intron length in humans poses a challenge for accurate splicing. Here, we identify hnRNPM as an essential RNA-binding protein that suppresses cryptic splicing through binding to deep introns, maintaining human transcriptome integrity. Long interspersed nuclear elements (LINEs) in introns harbor numerous pseudo splice sites. hnRNPM preferentially binds at intronic LINEs to repress pseudo splice site usage for cryptic splicing. Remarkably, cryptic exons can generate long dsRNAs through base-pairing of inverted ALU transposable elements interspersed among LINEs and consequently trigger an interferon response, a well-known antiviral defense mechanism. Significantly, hnRNPM-deficient tumors show upregulated interferon-associated pathways and elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity by repressing cryptic splicing and suggest that targeting hnRNPM in tumors may be used to trigger an inflammatory immune response, thereby boosting cancer surveillance.

Enabling food system innovation: accelerators for change.

It is widely accepted that current food systems are not on a trajectory for achieving the Sustainable Development Goals by the end of the decade. Technological innovation will have a considerable role to play in different parts of the food system; many promising options exist or are in the pipeline, some of which may be highly disruptive to existing value chains. Scaling up the innovations required, at the same time as protecting those who may lose out in the short term, will require a strong enabling environment. Here we apply an existing framework of eight change accelerators to six case studies of historical agricultural innovation. We estimated the degree to which each accelerator had been addressed at some stage in the innovation process, as a measure of the gap between what was needed and what was achieved. For the innovations that are being taken to scale and widely utilized, these accelerator gaps are small. Uptake of other innovations is stalled, and for these we found large gaps for one or more of the eight accelerators. Impactful innovation processes address all eight change accelerators at some point, with different phasing of the accelerators depending on the nature of the technology and on the impact pathway being pursued. This simple framework, when used in combination with narratives of uptake based on theories of change and impact pathways, may provide an effective means of screening future innovation processes to help prioritize and guide investment that can lead to more resilient, sustainable and equitable food systems.

APOE loss of function: A genetic shield against Alzheimer's disease.

In this issue of Neuron, Chemparathy et al.1 provide human genetics data suggesting that APOE loss-of-function mutations may confer resistance to Alzheimer's disease (AD) without compromising longevity. These data strongly support the APOE toxic gain-of-function hypothesis for AD.

Molecular Testing for Bethesda III Thyroid Nodules: Trends in Implementation, Cytopathology Call Rates, Surgery Rates, and Malignancy Yield at a Single Institution.

Background: Molecular testing (MT) has become standard practice to more accurately rule out malignancy in indeterminate Bethesda III (BIII) thyroid lesions. We sought to assess the adoption of this technology and its impact on cytology reporting, malignancy yield, and rates of surgery across community and academic sites affiliated with a tertiary medical center. Methods: We performed a retrospective cross-sectional study including all fine-needle aspirations (FNAs) analyzed at our institution from 2017 to 2021. We analyzed trends in MT utilization by platform and by community or academic site. We compared BIII call rates, MT utilization rates, rates of subsequent surgery, and malignancy yield on final pathology before and after MT became readily available using chi-square analysis and linear regression. Results: A total of 8960 FNAs were analyzed at our institution from 2017 to 2021. There was broad adoption of MT across both community and academic sites. There was a significant increase in both the BIII rate and the utilization of MT between the pre- and post-MT periods (p < 0.001 and p < 0.001). There was no significant change in the the malignancy yield on final pathology (57.1% vs. 50.0%, p = 0.347), while the positive predictive value of MT decreased from 85% to 50% (p = 0.008 [confidence interval 9.5-52.5% decrease]). Conclusions: The use of MT increased across the institution over the study period, with the largest increase seen after a dedicated pass for MT was routinely collected. This increased availability of MT may have led to an unintended increase in the rates of BIII lesions, MT utilization, and surgery for benign nodules. Physicians who use MT should be aware of potential consequences of its adoption to appropriately counsel patients.

Comparative and integrative single cell analysis reveals new insights into the transcriptional immaturity of stem cell-derived ß cells.

Diabetes cell replacement therapy has the potential to be transformed by human pluripotent stem cell-derived ß cells (SC-ß cells). However, the precise identity of SC-ß cells in relationship to primary fetal and adult ß-cells remains unclear. Here, we used single-cell sequencing datasets to characterize the transcriptional identity of islets from in vitro differentiation, fetal islets, and adult islets. Our analysis revealed that SC-ß cells share a core ß-cell transcriptional identity with human adult and fetal ß-cells, however SC-ß cells possess a unique transcriptional profile characterized by the persistent expression and activation of progenitor and neural-biased gene networks. These networks are present in SC-ß cells, irrespective of the derivation protocol used. Notably, fetal ß-cells also exhibit this neural signature at the transcriptional level. Our findings offer insights into the transcriptional identity of SC-ß cells and underscore the need for further investigation of the role of neural transcriptional networks in their development.

Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis in C. elegans.

Caenorhabditis elegans males undergo sex-specific tail tip morphogenesis (TTM) under the control of the transcription factor DMD-3. To find genes regulated by DMD-3, We performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males vs. dmd-3(-) males and hermaphrodites. The transcription profile of dmd-3(-) tail tips is similar to that in hermaphrodites. For validation, we analyzed transcriptional reporters for 49 genes and found male-specific or male-biased expression for 26 genes. Only 11 DE genes overlapped with genes found in a previous RNAi screen for defective TTM. GO enrichment analysis of DE genes finds upregulation of genes within the UPR (unfolded protein response) pathway and downregulation of genes involved in cuticle maintenance. Of the DE genes, 40 are transcription factors, indicating that the gene network downstream of DMD-3 is complex and potentially modular. We propose modules of genes that act together in TTM and are coregulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response.

Wildlife ecological risk assessment in the 21st century: Promising technologies to assess toxicological effects.

Despite advances in toxicity testing and the development of new approach methodologies (NAMs) for hazard assessment, the ecological risk assessment (ERA) framework for terrestrial wildlife (i.e., air-breathing amphibians, reptiles, birds, and mammals) has remained unchanged for decades. While survival, growth, and reproductive endpoints derived from whole-animal toxicity tests are central to hazard assessment, nonstandard measures of biological effects at multiple levels of biological organization (e.g., molecular, cellular, tissue, organ, organism, population, community, ecosystem) have the potential to enhance the relevance of prospective and retrospective wildlife ERAs. Other factors (e.g., indirect effects of contaminants on food supplies and infectious disease processes) are influenced by toxicants at individual, population, and community levels, and need to be factored into chemically based risk assessments to enhance the "eco" component of ERAs. Regulatory and logistical challenges often relegate such nonstandard endpoints and indirect effects to postregistration evaluations of pesticides and industrial chemicals and contaminated site evaluations. While NAMs are being developed, to date, their applications in ERAs focused on wildlife have been limited. No single magic tool or model will address all uncertainties in hazard assessment. Modernizing wildlife ERAs will likely entail combinations of laboratory- and field-derived data at multiple levels of biological organization, knowledge collection solutions (e.g., systematic review, adverse outcome pathway frameworks), and inferential methods that facilitate integrations and risk estimations focused on species, populations, interspecific extrapolations, and ecosystem services modeling, with less dependence on whole-animal data and simple hazard ratios. Integr Environ Assess Manag 2024;20:725-748. © 2023 His Majesty the King in Right of Canada and The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). Reproduced with the permission of the Minister of Environment and Climate Change Canada. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Toxicological effects assessment for wildlife in the 21st century: Review of current methods and recommendations for a path forward.

Model species (e.g., granivorous gamebirds, waterfowl, passerines, domesticated rodents) have been used for decades in guideline laboratory tests to generate survival, growth, and reproductive data for prospective ecological risk assessments (ERAs) for birds and mammals, while officially adopted risk assessment schemes for amphibians and reptiles do not exist. There are recognized shortcomings of current in vivo methods as well as uncertainty around the extent to which species with different life histories (e.g., terrestrial amphibians, reptiles, bats) than these commonly used models are protected by existing ERA frameworks. Approaches other than validating additional animal models for testing are being developed, but the incorporation of such new approach methodologies (NAMs) into risk assessment frameworks will require robust validations against in vivo responses. This takes time, and the ability to extrapolate findings from nonanimal studies to organism- and population-level effects in terrestrial wildlife remains weak. Failure to adequately anticipate and predict hazards could have economic and potentially even legal consequences for regulators and product registrants. In order to be able to use fewer animals or replace them altogether in the long term, vertebrate use and whole organism data will be needed to provide data for NAM validation in the short term. Therefore, it is worth investing resources for potential updates to existing standard test guidelines used in the laboratory as well as addressing the need for clear guidance on the conduct of field studies. Herein, we review the potential for improving standard in vivo test methods and for advancing the use of field studies in wildlife risk assessment, as these tools will be needed in the foreseeable future. Integr Environ Assess Manag 2024;20:699-724. © 2023 His Majesty the King in Right of Canada and The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). Reproduced with the permission of the Minister of Environment and Climate Change Canada. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Bipolar radiofrequency ablation lesion areas and confluence: An ex vivo study and technical report.

INTRODUCTION: Radiofrequency ablation (RFA) has been used for nearly 100 years, treating an array of medical conditions including chronic pain. Radiofrequency (RF) energy depolarizes and repolarizes tissues adjacent to a probe producing heat and causing direct thermal injury. When positioned adjacent to neural structures, it leads to neural tissue injury and cell death interrupting pain signaling with the ultimate goal of providing lasting pain relief. Today, RFA is commonly used to treat cervical, thoracic, and lumbar zygapophyseal joints, sacroiliac joint, and more recently large peripheral joint-mediated pain. There are several applications of RFA systems, including bipolar, conventional thermal, cooled, protruding, and pulsed. As yet, no study has determined the best technical practice for bipolar RFA. OBJECTIVE: This ex vivo study examines RFA lesion midpoint (LMP) area and lesion confluence comparing three different commonly used gauge (g) probes (18-g, 20-g, and 22-g) with 10-mm active tips at various interprobe distances (IPD) to guide best technical practices for its clinical application. METHODS: Bipolar RFA lesions were generated in preservative-free chicken breast specimens using three different gauge probes (18-g, 20-g, and 22-g) with 10-mm active tips at various IPD (6, 8, 10, 12, 14, 16, and 18 mm). RF was applied for 105 s (15-s ramp time) at 80°C for each lesion at both room and human physiological temperature. The specimen tissues were dissected through the lesion to obtain a length, width, and depth, which were used to calculate the LMP area (mm2 ). The LMP areas of each thermal ablation were investigated using visualization and descriptive analysis. The Kruskal-Wallis test was performed to compare LMP areas between the two temperature groups and the three different gauge probe subgroups at the various IPDs. RESULTS: Of the 36 RF lesions (14: 18-g, 12: 20-g, and 10: 22-g) performed, 24 demonstrated lesion confluence. The average time to reach 80°C was 16-17 s; therefore, the average time of RF-energy delivery (at goal temperature) was 88-89 s despite varying needle size or IPD. Comparing the 25 and 37°C groups, 18-g probes produced mean LMP areas of 73.7 and 79.2 mm2 , respectively; 20-g probes produced mean LMP areas of 66 and 66.8 mm2 , respectively; 22-g probes produced mean LMP areas of 56.6 and 59.7 mm2 , respectively. There was no statistical evidence to state a difference regarding LMP area between temperature groups; however, the 18-g probes produced consistently larger LMP areas in the 37°C compared to 25°C specimen groups at each IPD. Lesion confluence was lost for 18-g, 20-g, and 22-g probes at IPD of 14, 12, and 10 mm, respectively, in both 25 and 37°C groups. LMP area was similar between 6 and 8 mm IPD in all of the three-gauge groups; however, there was a significant drop in LMP area from 8 mm IPD to 10 mm and greater. The 18-g, 20-g, and 22-g probes all demonstrated a sharp decline in LMP area when increasing the IPD from 8 to 10 mm. CONCLUSION: This ex vivo technical study evaluated bipolar RFA LMP areas and lesion confluence, and determined the recommended IPD of 18-g, 20-g, and 22-g probes to be less than 12, 10, and 8 mm, respectively, for best clinical practice. Placing bipolar probes at an IPD greater than 14, 12, and 10 mm, respectively, risks the loss of lesion confluence and failure to produce a clinically significant treatment response due to lack of nerve capture. In clinical practice, the use of injectate may produce larger lesions than demonstrated in this study. Additionally, in vivo factors may impact ablation zone size and ablation patterns. As there are a paucity of studies comparing various RFA applications and conventional RFA needles are least expensive, it is possible that bipolar conventional RFA is more cost-effective than other techniques.

The novel gene, mtre-1 , is expressed downstream of MAB-3 and DMD-3 in the male tail tip at the termination of male tail tip retraction.

The development of the adult C. elegans male tail involves an extensive remodeling during the last larval stage where the pointed tail of the L4 male is converted into the blunt-ended adult tail with its collection of mechano-sensitive rays. The first step in this remodeling is the retraction of the four hypodermal cells of the tail tip to generate the blunt-ended tail. Male tail tip retraction is an excellent model for characterizing how upstream regulatory networks interact with the downstream cell biological effectors that drive morphogenetic changes in all animals. Previously, we've shown that two DM-domain transcription factors, MAB-3 and DMD-3 , are central regulators of male tail tip retraction. Using a microarray-based approach we have identified ~400 genes that are more highly expressed in the L4 male tail tip relative to the hermaphrodite L4 tail tip. The uncharacterized gene T05H10.3 , which we've named mtre-1 , was highly over-represented in the male tail tip vs. the hermaphrodite tail tip and was under-represented in mab-3 ; dmd-3 mutant male tail tips vs. wild-type male tail tips. A transcriptional reporter for mtre-1 shows clear expression in the male tail tip cells for a short period (~3 hours) at the end of retraction. This expression is dependent on the activity of MAB-3 and DMD-3 , since expression is reduced in dmd-3 single mutant males and absent in mab-3 ; dmd-3 mutant males. Finally, males homozygous for a putative null allele of mtre-1 display a phenotypically wild-type adult male tail, indicating that mtre-1 is not essential for male tail morphogenesis.

Ethanol Ablation of a Thyroglossal Duct Cyst and Review of the Literature.

Ultrasound-guided ethanol ablation (EA) is a less invasive alternative to surgical resection for the management of thyroglossal duct cysts (TGDCs). However, to date, EA is rarely used in the United States to treat TGDCs. We present a case of TGDC successfully treated with EA in the United States. A 66-year-old man presented with a mobile anterior neck mass. Neck ultrasonography revealed a complex cystic mass in the midline directly anterior to the trachea, measuring 52 × 41 × 50 mm. Fine needle aspiration revealed no malignant cells, and pathology was consistent with TGDC. The patient had no contraindications to surgical resection. The patient's pretreatment symptom score was 7 and cosmetic score was 3. One month after EA, volume reduction ratio was 40%, symptom score was 1, and cosmetic score was 3. Four months after EA, the TGDC was resolved without need for an additional procedure. The volume reduction ratio was 96.8%, and symptom score and cosmetic score were both 1. In summary, EA is a viable alternative to surgical resection, even in patients who are surgical candidates. EA is attractive due to its simplicity, cost effectiveness, and tolerable side effect profile. Further studies are needed to evaluate long-term safety and efficacy, particularly in United States patients.

Medicine and the Law.

Problems arise when a lawfully appointed surrogate decision-maker wishes to decide on a course of action on behalf of a mentally incompetent patient that is against the patient's best interests. This may arise: (i) where there is no advance directive, and the decision is made by the surrogate decision-maker on religious grounds; (ii) where the medical practitioners are of the opinion that the surrogate decision-maker's decision is not in the best interests of the patient; (iii) where the close relatives of the patient do not agree with the decision by the surrogate decision-maker; and (iv) where the surrogate decision-maker asks the medical practitioners to undertake treatment or a procedure on the patient that is unlawful or unethical. Suggestions are made regarding what doctors should do when faced with each of these situations.

Loss of succinyl-CoA synthetase in mouse forebrain results in hypersuccinylation with perturbed neuronal transcription and metabolism.

Lysine succinylation is a subtype of protein acylation associated with metabolic regulation of succinyl-CoA in the tricarboxylic acid cycle. Deficiency of succinyl-CoA synthetase (SCS), the tricarboxylic acid cycle enzyme catalyzing the interconversion of succinyl-CoA to succinate, results in mitochondrial encephalomyopathy in humans. This report presents a conditional forebrain-specific knockout (KO) mouse model of Sucla2, the gene encoding the ATP-specific beta isoform of SCS, resulting in postnatal deficiency of the entire SCS complex. Results demonstrate that accumulation of succinyl-CoA in the absence of SCS leads to hypersuccinylation within the murine cerebral cortex. Specifically, increased succinylation is associated with functionally significant reduced activity of respiratory chain complex I and widescale alterations in chromatin landscape and gene expression. Integrative analysis of the transcriptomic data also reveals perturbations in regulatory networks of neuronal transcription in the KO forebrain. Together, these findings provide evidence that protein succinylation plays a significant role in the pathogenesis of SCS deficiency.

Contaminant biomonitoring augmented with a qPCR array indicates hepatic mRNA gene expression effects in wild-collected seabird embryos.

Birds can bioaccumulate persistent contaminants, and maternal transfer to eggs may expose embryos to concentrations sufficient to cause adverse effects during sensitive early-life stages. However, using tissue residue concentrations alone to infer whether contaminant effects are occurring suffers from uncertainty, and efficient, sensitive biomarkers remain limited in wildlife. We studied relationships between whole embryo contaminant concentrations (total mercury, organochlorine pesticides, perfluoroalkyl substances, polychlorinated biphenyls, and halogenated flame retardants) together with mRNA expression in embryonic liver tissue from a Pacific Ocean seabird, the rhinoceros auklet (Cerorhinca monocerata). Fresh eggs were collected, incubated under controlled conditions, and from the pre-hatch embryo, hepatic RNA was extracted for qPCR array analysis to measure gene expression (2-∆Cq), while the remaining embryo was analyzed for contaminant residues. Contaminant and gene expression data were assessed with a combination of multivariate approaches and linear models. Results indicated correlations between embryonic total mercury and several genes such as sepp1, which encodes selenoprotein P. Correlation between the biotransformation gene cyp1a4 and the C7 perfluoroalkyl carboxylic acid PFHpA was also evident. This study demonstrates that egg collection from free-living populations for contaminant biomonitoring programs can relate chemical residues to in ovo mRNA gene expression effects in embryo hepatic tissue.

Network analysis identifies strain-dependent response to tau and tau seeding-associated genes.

Previous research demonstrated that genetic heterogeneity is a critical factor in modeling amyloid accumulation and other Alzheimer's disease phenotypes. However, it is unknown what mechanisms underlie these effects of genetic background on modeling tau aggregate-driven pathogenicity. In this study, we induced tau aggregation in wild-derived mice by expressing MAPT. To investigate the effect of genetic background on the action of tau aggregates, we performed RNA sequencing with brains of C57BL/6J, CAST/EiJ, PWK/PhJ, and WSB/EiJ mice (n = 64) and determined core transcriptional signature conserved in all genetic backgrounds and signature unique to wild-derived backgrounds. By measuring tau seeding activity using the cortex, we identified 19 key genes associated with tau seeding and amyloid response. Interestingly, microglial pathways were strongly associated with tau seeding activity in CAST/EiJ and PWK/PhJ backgrounds. Collectively, our study demonstrates that mouse genetic context affects tau-mediated alteration of transcriptome and tau seeding. The gene modules associated with tau seeding provide an important resource to better model tauopathy.

Beyond the Food Systems Summit: Linking Recommendations to Action-The True Cost of Food.

A transformation of food systems is needed to achieve the 17 Sustainable Development Goals specified in the 2030 Agenda for Sustainable Development. Recognizing the true costs and benefits of food production and consumption can help guide public policy decisions to effectively transform food systems in support of sustainable healthy diets. A new, expanded framework is presented that allows the quantification of costs and benefits in three domains: health, environmental, and social. The implications for policy makers are discussed. Curr Dev Nutr 2023;x:xx.

Single-nucleus multi-omics of human stem cell-derived islets identifies deficiencies in lineage specification.

Insulin-producing ß cells created from human pluripotent stem cells have potential as a therapy for insulin-dependent diabetes, but human pluripotent stem cell-derived islets (SC-islets) still differ from their in vivo counterparts. To better understand the state of cell types within SC-islets and identify lineage specification deficiencies, we used single-nucleus multi-omic sequencing to analyse chromatin accessibility and transcriptional profiles of SC-islets and primary human islets. Here we provide an analysis that enabled the derivation of gene lists and activity for identifying each SC-islet cell type compared with primary islets. Within SC-islets, we found that the difference between ß cells and awry enterochromaffin-like cells is a gradient of cell states rather than a stark difference in identity. Furthermore, transplantation of SC-islets in vivo improved cellular identities overtime, while long-term in vitro culture did not. Collectively, our results highlight the importance of chromatin and transcriptional landscapes during islet cell specification and maturation.

Network analysis reveals strain-dependent response to misfolded tau aggregates.

Mouse genetic backgrounds have been shown to modulate amyloid accumulation and propagation of tau aggregates. Previous research into these effects has highlighted the importance of studying the impact of genetic heterogeneity on modeling Alzheimer's disease. However, it is unknown what mechanisms underly these effects of genetic background on modeling Alzheimer's disease, specifically tau aggregate-driven pathogenicity. In this study, we induced tau aggregation in wild-derived mice by expressing MAPT (P301L). To investigate the effect of genetic background on the action of tau aggregates, we performed RNA sequencing with brains of 6-month-old C57BL/6J, CAST/EiJ, PWK/PhJ, and WSB/EiJ mice (n=64). We also measured tau seeding activity in the cortex of these mice. We identified three gene signatures: core transcriptional signature, unique signature for each wild-derived genetic background, and tau seeding-associated signature. Our data suggest that microglial response to tau seeds is elevated in CAST/EiJ and PWK/PhJ mice. Together, our study provides the first evidence that mouse genetic context influences the seeding of tau. SUMMARY: Seeding of tau predates the phosphorylation and spreading of tau aggregates. Acri and colleagues report transcriptomic responses to tau and elevated tau seeds in wild-derived mice. This paper creates a rich resource by combining genetics, tau biosensor assays, and transcriptomics.