bluuebunny/crossref_metadata_2025 huggingface dataset:
Advances in preclinical assessment of therapeutic targets for bladder cancer precision medicine
Authors: Nössing Christoph , Herek Paula , Shariat Shahrokh F. , Berger Walter , Englinger Bernhard
Published: April 2024

Purpose of review

Bladder cancer incidence is on the rise, and until recently, there has been little to no change in treatment regimens over the last 40 years. Hence, it is imperative to work on strategies and approaches to untangle the complexity of intra- and inter-tumour heterogeneity of bladder cancer with the aim of improving patient-specific care and treatment outcomes. The focus of this review is therefore to highlight novel targets, advances, and therapy approaches for bladder cancer patients.

Recent findings

The success of combining an antibody-drug conjugate (ADC) with immunotherapy has been recently hailed as a game changer in treating bladder cancer patients. Hence, interest in other ADCs as a treatment option is also rife. Furthermore, strategies to overcome chemoresistance to standard therapy have been described recently. In addition, other studies showed that targeting genomic alterations (e.g. mutations in FGFR3, DNA damage repair genes and loss of the Y chromosome) could also be helpful as prognostic and treatment stratification biomarkers. The use of single-cell RNA sequencing approaches has allowed better characterisation of the tumour microenvironment and subsequent identification of novel targets. Functional precision medicine could be another avenue to improve and guide personalized treatment options.

Several novel preclinical targets and treatment options have been described recently. The validation of these advances will lead to the development and implementation of robust personalized treatment regimens for bladder cancer patients.
Chest Compression Depth Targets in Critically Ill Infants and Children Measured With a Laser Distance Meter: Single-Center Retrospective Study From Japan, 2019–2022*
Authors: Ikeyama Takanari , Hozumi Takunori , Kikuyama Kazuki , Niles Dana , Nadkarni Vinay , Ito Komei
Published: April 2024

OBJECTIVES:

Current resuscitation guidelines recommend target chest compression depth (CCd) of approximately 4cm for infants and 5cm for children. Previous reports based on chest CT suggest these recommended CCd targets might be too deep for younger children. Our aim was to examine measurements of anterior-posterior chest diameter (APd) with a laser distance meter and calculate CCd targets in critically ill infants and children.

DESIGN:

A retrospective descriptive study.

SETTING:

Single-center PICU, using data from May 2019 to May 2022.

PATIENTS:

All critically ill children admitted to PICU and under 8 years old were eligible to be included in the retrospective cohort.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

The chest APd measurements using a laser distance meter are part of our usual practice on the PICU. Target CCd and the over-compression threshold CCd for each age group was calculated as 1/3 and 1/2 of APd, respectively. In 555 patients, the median (interquartile range) of the calculated target CCd for each age group was: 2.7 cm (2.5–2.9 cm), 2.9 cm (2.7–3.2 cm), 3.2 cm (3–3.5 cm), 3.4 cm (3.2–3.6 cm), 3.4 cm (3.2–3.6 cm), 3.6 cm (3.4–3.8 cm), 3.6 cm (3.4–4 cm), and 4 cm (3.5–4.2 cm), for 0, 2, 3–5, 6–8, 9–11, 12–17, 18–23, 24 to less than 60, and 60 to less than 96 months, respectively. Using guideline-recommended absolute CCd targets, 4 cm for infants and 5 cm for children, 49% of infants between 0 and 2 months, and 45.5% of children between 12 and 17 months would be over-compressed during cardiopulmonary resuscitation.

CONCLUSIONS:

In our cohort, the 1/3 CCd targets calculated from APd measured by laser meter were shallower than the guideline-recommended CCd. Further studies including evaluating hemodynamics during cardiopulmonary resuscitation with these shallower CCd targets are needed.
Strengthening Protocols for Rapid Response to Disruptions in Access to Prescription Opioids: Considerations for State and Territorial Health Agencies
Authors: Pough Jessica L. , Swanson Stephanie , Ranade Richa
Published: April 2024

Prescription opioid disruptions pose a danger and lead to adverse health outcomes for patients taking prescription opioids for pain or medication for opioid use disorder. State and territorial health agencies are uniquely positioned to respond to disruptions and potentially prevent risks associated with service disruptions. Responding to disruptions in access to prescription opioids necessitates a multifaceted, collaborative approach that prioritizes care continuity and patient well-being. State and territorial health agencies may benefit from developing and exercising a formal response protocol that outlines roles and activities during these types of events, strengthening capacity to rapidly respond and serve patient needs.
Design and Modification of COVID-19 Case Investigation and Contact Tracing Interview Scripts Used by Health Departments Throughout the COVID-19 Pandemic
Authors: Orfield Cara , Loosier Penny S. , Wagner Sarah , Sabin E. Rain , Fiscus Michelle , Matulewicz Holly , Vohra Divya , Staatz Colleen , Taylor Melanie M. , Caruso Elise C. , DeLuca Nickolas , Moonan Patrick K. , Oeltmann John E. , Thorpe Phoebe
Published: April 2024

Objectives:

We sought to (1) document how health departments (HDs) developed COVID-19 case investigation and contact tracing (CI/CT) interview scripts and the topics covered, and (2) understand how and why HDs modified those scripts.

Design:

Qualitative analysis of CI/CT interview scripts and in-depth key informant interviews with public health officials in 14 HDs. Collected scripts represent 3 distinct points (initial, the majority of which were time stamped May 2020; interim, spanning from September 2020 to August 2021; and current, as of April 2022).

Setting:

Fourteen state, local, and tribal health jurisdictions and Centers for Disease Control and Prevention (CDC).

Participants:

Thirty-six public health officials involved in leading CI/CT from 14 state, local, and tribal health jurisdictions (6 states, 3 cities, 4 counties, and 1 tribal area).

Main Outcome Measure:

Interview script elements included in CI/CT interview scripts over time.

Results:

Many COVID-19 CI/CT scripts were developed by modifying questions from scripts used for other communicable diseases. Early in the pandemic, scripts included guidance on isolation/quarantine and discussed symptoms of COVID-19. As the pandemic evolved, the length of scripts increased substantially, with significant additions on contact elicitation, vaccinations, isolation/quarantine recommendations, and testing. Drivers of script changes included changes in our understanding of how the virus spreads, risk factors and symptoms, new treatments, new variants, vaccine development, and adjustments to CDC's official isolation and quarantine guidance.

Conclusions:

Our findings offer suggestions about components to include in future CI/CT efforts, including educating members of the public about the disease and its symptoms, offering mitigation guidance, and providing sufficient support and resources to help people act on that guidance. Assessing the correlation between script length and number of completed interviews or other quality and performance measures could be an area for future study.
Few Prison Systems Release Individual Death Data: Death in Custody Reporting Act Completeness, Speed, and Compliance
Authors: Fliss Mike Dolan , Lao Jennifer , Behne Forrest , Brinkley-Rubinstein Lauren
Published: April 2024

The United States has one of the largest incarcerated populations per capita. Prisons are dangerous environments, with high in-prison and postrelease mortality. The Death in Custody Reporting Acts (DCRAs) of 2000 and 2013 require deaths of people in correctional custody or caused by law enforcement to be reported to the Bureau of Justice Assistance. These deaths must be reported within 3 months of the death and include 10 required fields (eg, age, cause of death). There is no public reporting requirement. Our Third City Mortality project tracks near-real-time data about individual deaths released publicly and prison system metadata, including data completeness and release speed, across (N = 54) US state, federal (N = 2; Bureau of Prisons, Immigration and Customs Enforcement), Washington, District of Columbia, and Puerto Rico prison systems. Twenty-one (38%) systems release no individual death data; 13 systems release incomplete data slower than 1 year; 19 release timely, but incomplete, death data; and only one system (Iowa) releases complete and timely data. Incomplete, untimely, public prison mortality data limit protective community responses and epidemiology.
National Trends in Utilization of Normothermic Machine Perfusion in DCD Liver Transplantation
Authors: Abu-Gazala Samir , Tang Helen , Abt Peter , Mahmud Nadim
Published: April 2024

Background.

In liver transplantation, advances in ex situ normothermic machine perfusion (NMP) have improved outcomes compared with traditional static cold storage (SCS) in donation after circulatory death (DCD) organs. We aimed to characterize trends in the utilization of NMP versus SCS in DCD liver transplantation in the United States.

Methods.

This retrospective cohort study used data from the United Network for Organ Sharing database to identify recipient–donor adult liver transplant pairs from DCD donors from January 2016 to June 2022. Utilization of NMP and changes in donor risk index (DRI) and components between NMP and SCS were assessed across transplant year eras (2016–2018, 2019–2020, and 2021–2022). Statistical comparisons were made using the Kruskal-Wallis test or the chi-square test.

Results.

A total of 3937 SCS and 127 NMP DCD donor transplants were included. Utilization of NMP ranged from ~0.4% to 3.5% from 2016 to 2021 and rose significantly to 11.2% in early 2022. Across transplant eras, median DRI increased significantly for SCS and NMP, but the magnitude of the increase was larger for NMP. With NMP DCDs, there were significant increases in median donor age, national share proportion, and “cold ischemic time” over time. Finally, there was a shift toward including higher DRI donors and higher model for end-stage liver disease score transplant recipients with NMP in later transplant eras.

Conclusions.

In recent years, NMP utilization has increased and expanded to donors with higher DRI and recipients with higher model for end-stage liver disease score at transplant, suggesting increasing familiarity and risk tolerance with NMP technology. As NMP remains a relatively new technique, ongoing study of patient outcomes, organ allocation practices, and utilization patterns is critical.
Gut Microbiome Changes in Patients With Idiopathic Normal Pressure Hydrocephalus
Authors: Brandt Emilia , Koivisto Anne , Pereira Pedro , Mustanoja Ella , Auvinen Petri , Saari Toni , Lehtola Juha-Matti , Hannonen Sanna , Rusanen Minna , Leinonen Ville , Scheperjans Filip , Kärkkäinen Virve
Published: April 2024

Background:

The gut microbiome is a complex system within the human gastrointestinal tract. The bacteria play a significant role in human health, and some can promote inflammation and pathologic processes through chemical interactions or metabolites. Gut microbiome dysbiosis has been linked to some neurological and other diseases. Here we aimed to examine microbiome differences between patients with a progressive neurological disorder, idiopathic normal pressure hydrocephalus (iNPH), compared with healthy controls (CO).

Methods:

We recruited 37 neurologically healthy CO and 10 patients with shunted iNPH. We evaluated these participants’ cognition using the CERAD-NB test battery and CDR test, and collected a variety of information, including about dietary habits and health. We also collected fecal samples, which were subjected to 16S amplicon sequencing to analyze differences in gut microbiome composition.

Results:

We found that the iNPH group exhibited significantly different abundances of 10 bacterial genera compared with the CO group. The Escherichia/Shigella and Anaeromassilibacillus genera were most remarkably increased. Other increased genera were Butyrivibrio, Duncaniella, and an unidentified genus. The decreased genera were Agathobaculum, Paramuribaculum, Catenibacterium, and 2 unidentified genera.

Conclusions:

Here we report the first identified microbiome differences in iNPH patients compared with healthy controls.
The mechanical properties of different cross-veins in the hind wing of locust
Locusta migratoria
under uniaxial tensile and stress relaxation tests
Authors: Zhou Yizun , Bai Linxin , Wan Chao
Published: April 2024

Locust
Locusta migratoria
exhibits remarkable aerial performances, relying predominantly on its hind wings that generate most of lift and thrust for flight. The mechanical properties of the cross-veins determine the deformation of the hind wing, which greatly affect the aerodynamic performance of flapping flight. However, whether the mechanical behaviours of the locust cross-veins change with loading rate is still unknown. In this study, cross-veins in four physiological regions (anterior–medial, anterior–lateral, posterior–medial and posterior–lateral) of the hind wing from adult locusts were investigated using uniaxial tensile test, stress relaxation test and fluorescence microscopy. It was found that the cross-veins were a type of viscoelastic material (including rate-independent elastic modulus and obvious stress relaxation). The cross-veins in the two anterior regions of the hind wing had significantly higher elastic moduli and higher ultimate tensile stress than those of its two posterior regions. This difference might be attributed to different resilin distribution patterns in the cross-veins. These findings furnish new insights into the mechanical characteristics of the locust cross-veins, which might deepen our understanding of the aerodynamic mechanisms of locust flapping flight.
Desert locusts (
Schistocerca gregaria
) feed with self-sharpening, scissor-like mandibles
Authors: Wegst Ulrike G. K. , Cloetens Peter , Betz Oliver
Published: April 2024

The mandibles of the desert locust
Schistocerca gregaria
(Forsskål, 1775) are digger-shovel-shaped mouthparts that are part of the locust's exoskeleton formed by the insect cuticle. The cuticle is a polymer–fibre composite, which supports, encases and protects the entire body. Mandibles experience heavy loading and wear due to direct contact with hard and abrasive food, just like teeth, their mineralized analogues in vertebrates. With dual-energy X-ray tomography, we image well-defined regions of zinc (Zn)-enriched cuticle at the mandible cutting edges and quantify the Zn concentrations in these regions. Zn is known to increase stiffness, hardness and wear resistance of the otherwise purely polymeric insect cuticle. In
S. gregaria,
the position of the Zn-enriched cutting-edge regions relative to one another suggests that the mandibles form a scissor-like cutting tool, which sharpens itself as the mouthparts shear past one another during feeding. Comparing the architecture of these purely polymeric mandibles with the mineralized incisors of rodents, we find fundamental design differences in cutting-tool structure and performance. Locusts' scissors and rodents’ carving knives perform different functions, because they act on food that differs significantly in properties and shape: softer, sheet-like material in the case of locusts and harder bulk material in the case of rodents.
Tanning of the tarsal and mandibular cuticle in adult
Anax imperator
(Insecta: Odonata) during the emergence sequence
Authors: Preuss Anika , Appel Esther , Gorb Stanislav N. , Büsse Sebastian
Published: April 2024

The arthropod cuticle offers strength, protection, and lightweight. Due to its limit in expandability, arthropods have to moult periodically to grow. While moulting is beneficial in terms of parasite or toxin control, growth and adaptation to environmental conditions, it costs energy and leaves the soft animal's body vulnerable to injuries and desiccation directly after ecdysis. To investigate the temporal change in sclerotization and pigmentation during and after ecdysis, we combined macrophotography, confocal laser scanning microscopy, scanning electron microscopy and histological sectioning. We analysed the tarsal and mandibular cuticle of the blue emperor dragonfly to compare the progress of tanning for structures that are functionally involved during emergence (tarsus/tarsal claws) with structures whose functionality is required much later (mandibles). Our results show that: (i) the tanning of the tarsal and mandibular cuticle increases during emergence; (ii) the tarsal cuticle tans faster than the mandibular cuticle; (iii) the mandibles tan faster on the aboral than on the oral side; and (iv) both the exo- and the endocuticle are tanned. The change in the cuticle composition of the tarsal and mandibular cuticle reflects the demand for higher mechanical stability of these body parts when holding on to the substrate during emergence and during first walking or hunting attempts.
Decrease in Purifying Selection Pressures on Wheat Homoeologous Genes: TetraploidizationvsHexaploidization
Authors: Ezoe Akihiro , Todaka Daisuke , Utsumi Yoshinori , Takahashi Satoshi , Kawaura Kanako , Seki Motoaki
Published: April 2024

A series of polyploidizations in higher-order polyploids is the main event affecting the gene contents in a genome, and this is frequently observed in domesticated plants. Each polyploidization event is expected to lead to functional divergence because of the associated decrease in the selection pressures on the duplicated genes, but it is unclear whether the initial tetraploidization or the subsequent higher-order polyploidization has a greater evolutionary impact on the duplicated genes. To address this uncertainty, we focused on theTriticum–Aegilopscomplex lineage and compared the selection pressures before and after the tetraploidization and hexaploidization events. The results indicated that while both events decreased the selection pressures on homoeologous gene pairs (compared with the selection pressures on their ancestral diploid and tetraploid orthologous genes), the initial tetraploidization had a greater impact on the selection pressures on homoeologous gene pairs than the subsequent hexaploidization. This was supported by the analyzed expression patterns. Surprisingly, the decreases in the selection pressures on these homoeologous genes were independent of the existence of in-paralogs within the same subgenome. This result suggests that unique functions are maintained in the homoeologous genes, including the functions that are unlikely to be preserved in duplicate gene pairs derived from other duplication mechanisms. We also revealed their unique functions were different between the tetra- and hexaploidization (e.g., Reproductive system and chromosome segregation processes). The findings of this study imply that the substantial number of gene pairs resulting from multiple allopolyploidization events, especially the initial tetraploidization, may have been a unique source of functional divergence.
Machine Learned Classification of Ligand Intrinsic Activities at Humanµ-Opioid Receptor
Authors: Oh Myongin , Shen Maximilian , Liu Ruibin , Stavitskaya Lidiya , Shen Jana
Published: April 2024

Opioids are small-molecule agonists ofµ-opioid receptor (µOR), while reversal agents such as naloxone are antagonists ofµOR. Here we developed machine learning (ML) models to classify the intrinsic activities of ligands at the humanµOR based on the SMILE strings and two-dimensional molecular descriptors. We first manually curated a database of 983 small molecules with measuredEmaxvalues at the humanµOR. Analysis of the chemical space allowed identification of dominant scaffolds and structurally similar agonists and antagonists. Decision tree models and directed message passing neural networks (MPNNs) were then trained to classify agonistic and antagonistic ligands. The hold-out test AUCs (areas under the receiver operator curves) of the extra-tree (ET) and MPNN models are 91.5 ± 3.9% and 91.8 ± 4.4%, respectively. To overcome the challenge of small dataset, a student-teacher learning method called tri-training with disagreement was tested using an unlabeled dataset comprised of 15,816 ligands of human, mouse, or ratµOR,κOR, orδOR. We found that the tri-training scheme was able to increase the hold-out AUC of MPNN to as high as 95.7%. Our work demonstrates the feasibility of developing ML models to accurately predict the intrinsic activities ofµOR ligands, even with limited data. We envisage potential applications of these models in evaluating uncharacterized substances for public safety risks and discovering new therapeutic agents to counteract opioid overdoses.

TOC Graphic
Sox9 marks limbal stem cells and is required for asymmetric cell fate switch in the corneal epithelium
Authors: Rice Gabriella , Farrelly Olivia , Huang Sixia , Kuri Paola , Curtis Ezra , Ohman Lisa , Li Ning , Lengner Christopher , Lee Vivian , Rompolas Panteleimon
Published: April 2024

Adult tissues with high cellular turnover require a balance between stem cell renewal and differentiation, yet the mechanisms underlying this equilibrium are unclear. The cornea exhibits a polarized lateral flow of progenitors from the peripheral stem cell niche to the center; attributed to differences in cellular fate. To identify genes that are critical for regulating the asymmetric fates of limbal stem cells and their transient amplified progeny in the central cornea, we utilized an in vivo cell cycle reporter to isolate proliferating basal cells across the anterior ocular surface epithelium and performed single-cell transcriptional analysis. This strategy greatly increased the resolution and revealed distinct basal cell identities with unique expression profiles of structural genes and transcription factors. We focused on Sox9; a transcription factor implicated in stem cell regulation across various organs. Sox9 was found to be differentially expressed between limbal stem cells and their progeny in the central corneal. Lineage tracing analysis confirmed that Sox9 marks long-lived limbal stem cells and conditional deletion led to abnormal differentiation and squamous metaplasia in the central cornea. These data suggest a requirement for Sox9 for the switch to asymmetric fate and commitment toward differentiation, as transient cells exit the limbal niche. By inhibiting terminal differentiation of corneal progenitors and forcing them into perpetual symmetric divisions, we replicated the Sox9 loss-of-function phenotype. Our findings reveal an essential role for Sox9 for the spatial regulation of asymmetric fate in the corneal epithelium that is required to sustain tissue homeostasis.
Glycolytic enzymes form membrane-less condensates in the malaria parasitePlasmodium falciparumby sensing glucose levels
Authors: Ishii Ryuta , Sakura Takaya , Inaoka Daniel Ken , Tokumasu Fuyuki
Published: April 2024

Recent studies have shown that liquid-liquid phase separation (LLPS) in cells can regulate essential cellular events, including metabolic processes. Glycolytic bodies (G-bodies) are biomolecular condensates formed through the LLPS of glycolytic enzymes, and they accelerate glycolysis to overcome hypoxic stress in several organisms. Although the asexual blood stage (ABS) of the human malaria parasitePlasmodium falciparumhighly depends on glycolysis for energy production, there have been no reports of the formation of such G-bodies throughout the parasite’s lifecycle. Using fluorescence tagging and live imaging, we found that G-body-like condensates containing phosphofructokinase 9 (PFK9) and phosphoglycerate kinase (PGK) were formed in the parasite cells after long-term culture under conditions of low glucose. These G-body-like structures appeared stable, but membrane staining and osmotic stress experiments suggested that the observed condensates were not associated with lipid membrane. Further microscopic observations and mathematical analyses of high signal-to-noise ratio images indicated that small condensates were formed transiently first, and these then gradually grew and stabilized in the cytosol. These results suggested that the formation of glycolytic enzyme condensates may be an important cellular response for adapting to blood sugar level oscillations in the host and maintaining the parasite’s multiplication in the ABS.

Significance statement

Glycolytic bodies (G-bodies), which are biomolecular condensates formed through the liquid-liquid phase separation of glycolytic enzymes, can accelerate glycolysis to produce energy and overcome hypoxic stress. The parasites that cause malaria depend on glycolysis for energy production, but there have been no reports that these parasites form G-bodies. We demonstrated that membrane-less G-body-like structures formed in media containing low levels of glucose. Small condensates appeared first and over time, the condensates became larger and more stable. The formation of glycolytic enzyme condensates may be important for the malaria parasite to adapt to fluctuating blood sugar levels in the host. These results further our understanding of the cellular mechanisms for the survival of malaria parasites.
Physiological and transcriptional changes associated with obligate aestivation in the cabbage stem flea beetle (Psylliodes chrysocephala)
Authors: Guney Gozde , Cedden Doga , Koernig Johannes , Ulber Bernd , Beran Franziska , Scholten Stefan , Rostas Michael
Published: April 2024

Aestivation is a form of seasonal dormancy observed in various insect species, usually coinciding with the summer season. Psylliodes chrysocephala (Coleoptera: Chrysomelidae), the cabbage stem flea beetle, is a key pest of oilseed rape and obligatorily aestivates as adult in late summer. At present, our understanding of the physiological and transcriptional changes linked to aestivation in P. chrysocephala is still limited. In this study, physiological parameters and RNA-seq analyses were performed with laboratory-reared beetles at pre-aestivation, aestivation, and post-aestivation stages. Measurements of CO2 production supported the notion that aestivating beetles dramatically reduce their metabolic rate and, together with assessments of reproductive maturation, allowed precise discrimination between the three adult stages. Aestivating beetles showed a reduction in carbohydrate reserves and an increase in lipid reserves compared to pre-aestivating beetles, indicating that aestivation is associated with drastic changes in energy metabolism. In agreement with these findings, we found that genes involved in carbohydrate and lipid metabolism, digestion, and mitochondrial activity are differentially expressed between the three stages. Furthermore, RNA-seq analysis suggested the regulation of transcription factors associated with aestivation maintenance and the involvement of cytochrome P450s in conferring a summer-resistant phenotype during the aestivation period. In conclusion, this study represents the first exploration of the transcriptomic and physiological aspects of the aestivation response in P. chrysocephala.
Humanizedin vivobone marrow models orchestrate multi-lineage human hematopoietic cell development
Authors: Renou Laurent , Sun Wenjie , Friedrich Chloe , Galant Klaudia , Conrad Cecile , Plantier Evelia , Schallmoser Katharina , Krisch Linda , Barroca Vilma , Devanand Saryami , Déchamp Nathalie , Reinisch Andreas , Martinovic Jelena , Magnani Alessandra , Faivre Lionel , Calvo Julien , Perie Leila , Kosmider Olivier , Pflumio Françoise
Published: April 2024

Hematopoiesis develops in the bone marrow (BM) where multiple interactions regulate differentiation and preservation of hematopoietic stem/progenitor cells (HSPCs). Although murine BM has been extensively analyzed, the human BM microenvironment remains less understood. Immune-deficient murine models have enabled the analysis of molecular and cellular regulation of human HSPCs, which remains limited as human hematopoietic cells develop in xenogenic microenvironments. In this study, we thoroughly characterized a humanized (h)in vivoBM model, based on mesenchymal stromal cell (MSC) differentiation (called hOssicles (hOss)), and hematopoietic cell compartments generated 3 months post-transplant of CD34+cells using single-cell RNA sequencing and cellular barcoding. Serial isolation of MSCs and HSPCs from hOss and transplant experiments revealed the dynamic nature of these hBM niches. hOss altered human hematopoietic development by modulating myeloid/lymphoid cell production and HSPC levels. Clonal tracking highlighted hematopoietic cell cross-talks between the murine BM and hOss, indicating the multipotent or more restricted lineage origin of human hematopoiesis shared in the BM sites.
Activity-dependent COX-2 proteolysis generates a catalytically inactive fragment that affects aerobic respiration and proliferation
Authors: Benishay Liat Hartal , Tal Sharon , Elkader Amal Abd , Ehsainieh Omar , Srouji-Eid Ranin , Mikl Martin , Barki-Harrington Liza
Published: April 2024

Cyclooxygenase-2 (COX-2) catalyzes arachidonic acid (AA) into PGH2, the single source of all prostaglandins (PGs), ligands that activate multiple inflammatory pathways. AA catalysis quickly results in suicide inactivation, rendering the enzyme catalytically inactive. We show that the catalytic activity also leads to controlled cleavage of COX-2, an event that is differentially regulated by fatty acids, and blocked by COX inhibitors. We also observe COX-2 cleavage in human colon tumors. Using mass spectrometry, we identify two adjacent cleavage points within the catalytic domain, which give rise to COX-2 fragments that are catalytically inactive and localize to different cellular compartments. One of these fragments significantly alters the expression of mitochondrial electron transport genes and functional assays show that it leads to reduced mitochondrial function, increased lactate production, and enhanced proliferation. We propose that in addition to its role in generating PGs, COX-2 has subsequent PG-independent cellular functions that may account for the complex role of COX-2 in proliferative diseases and chronic inflammation.

Graphical Abstract
Coping with Cannabis During Pregnancy: Trajectories of Depression, Stress, and Cannabis Use across the Prenatal Period
Authors: Constantino-Pettit Anna , Tillman Rebecca , Wilson Jillian , Lashley-Simms Nicole , Vatan Naazanene , Atkinson Azaria , Leverett Shelby , Lenze Shannon , Smyser Christopher , Bogdan Ryan , Rogers Cynthia , Agrawal Arpana
Published: April 2024

Objective

We examined trajectories of stress, depression, and cannabis use across the prenatal period. We also investigated whether individuals who reported using cannabis to alleviate stress and depressive symptoms experienced symptom relief across the prenatal period.

Methods

Pregnant individuals (n=436) with a history of lifetime cannabis use were recruited and identified either as prenatal cannabis users (PCU; continued cannabis use following knowledge of pregnancy in the first trimester) or non-prenatal cannabis users (NPCU; no cannabis use following knowledge of pregnancy in the first trimester). PCU individuals additionally reported on reasons for continued cannabis use during pregnancy. We employed longitudinal multivariate modeling to examine trajectories of depression (maternal self-report; Edinburgh Postnatal Depression Scale), stress (maternal self-report; Perceived Stress Scale), and cannabis use (maternal self-report and urinalysis) over time, stratified by motives for use during the perinatal period.

Results

Stress, depression, and cannabis use decreased from the first to the third trimester (slopeB=-0.21, -0.35, and -0.31, respectively). While cannabis use and depression at the first trimester were correlated with one another, they did not affect the other’s rate of change. Cannabis use similarly did not affect the rate of change in stress. Finally, while individuals using cannabis to cope with mental health symptoms experienced a decrease in overall depression symptoms, this slope was roughly equivalent to individuals who were not using cannabis prenatally (slopeB=- 0.43 and -0.51, respectively).

Conclusion

Our sample experienced a collective decrease in depression, stress, and cannabis use prenatally. This decline in cannabis use – even among those who reported using to cope with mental health conditions – was not attributable to the decrease in depressive symptoms. This study lends valuable insight into the reasons why individuals continue to use cannabis during pregnancy, which providers can use to help tailor recommendations for other sources of coping and support to childbearing individuals.
Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment
Authors: Snabel Rebecca R. , Cofiño-Fabrés Carla , Baltissen Marijke , Schwach Verena , Passier Robert , Veenstra Gert Jan C.
Published: April 2024

Stem cell-based models of human heart tissue and cardiac differentiation employ monolayer and 3D organoid cultures with different properties, cell type composition, and maturity. Here we show how cardiac monolayer, embryoid body, and engineered heart tissue trajectories compare in a single-cell roadmap of atrial and ventricular differentiation conditions. Using a multiomic approach and gene-regulatory network inference, we identified regulators of the epicardial, atrial and ventricular cardiomyocyte lineages. We identifiedZNF711as a regulatory switch and safeguard for cardiomyocyte commitment. We show thatZNF711ablation prevents cardiomyocyte differentiation in the absence of retinoic acid, causing progenitors to be diverted more prominently to epicardial and other lineages. Retinoic acid rescues this shift in lineage commitment and promotes atrial cardiomyocyte differentiation by regulation of shared and complementary target genes, showing an interplay betweenZNF711and retinoic acid in cardiac lineage commitment.

GRAPHICAL ABSTRACT

HIGHLIGHTS

We present an atlas of cardiac differentiation under different culture conditions, showing progenitor trajectories and cell states reminiscent of the fetal heart.

Multiome and chromatin accessibility analysis identified candidate regulators of cardiomyocyte and non-cardiomyocyte lineages.

Distinct trajectories of lineage commitment and differentiation under different culture conditions shows plasticity of first and second heart field progenitors and different ratios of cardiomyocyte and non-myocyte lineages.

ZNF711 is required for balanced commitment to epicardial and ventricular cardiomyocyte lineages. Retinoic acid rescues a requirement for ZNF711 in cardiomyocyte differentiation, promoting both atrial cardiomyocyte and epicardial differentiation.
Active state structures of a bistable visual opsin bound to G proteins
Authors: Tejero Oliver , Pamula Filip , Koyanagi Mitsumasa , Nagata Takashi , Afanasyev Pavel , Das Ishita , Deupi Xavier , Sheves Mordechai , Terakita Akihisa , Schertler Gebhard F.X. , Rodrigues Matthew J. , Tsai Ching-Ju
Published: April 2024

Opsins are G protein-coupled receptors (GPCRs) that have evolved to detect light stimuli and initiate intracellular signaling cascades. Their role as signal transducers is critical to light perception across the animal kingdom. Opsins covalently bind to the chromophore 11-cis retinal, which isomerizes to the all-trans isomer upon photon absorption, causing conformational changes that result in receptor activation. Monostable opsins, responsible for vision in vertebrates, release the chromophore after activation and must bind another retinal molecule to remain functional. In contrast, bistable opsins, responsible for non-visual light perception in vertebrates and for vision in invertebrates, absorb a second photon in the active state to return the chromophore and protein to the inactive state. Structures of bistable opsins in the activated state have proven elusive, limiting our understanding of how they function as bidirectional photoswitches. Here we present active state structures of a bistable opsin, jumping spider rhodopsin isoform-1 (JSR1), in complex with its downstream signaling partners, the Gi and Gq heterotrimers. These structures elucidate key differences in the activation mechanisms between monostable and bistable opsins, offering essential insights for the rational engineering of bistable opsins into diverse optogenetic tools to control G protein signaling pathways.
Transdifferentiation is uncoupled from progenitor pool expansion during hair cell regeneration in the zebrafish inner ear
Authors: Beaulieu Marielle O. , Thomas Eric D. , Raible David W.
Published: April 2024

Death of mechanosensory hair cells in the inner ear is a common cause of auditory and vestibular impairment in mammals, which have a limited ability to regrow these cells after damage. In contrast, non-mammalian vertebrates including zebrafish can robustly regenerate hair cells following severe organ damage. The zebrafish inner ear provides an understudied model system for understanding hair cell regeneration in organs that are highly conserved with their mammalian counterparts. Here we quantitatively examine hair cell addition during growth and regeneration of the larval zebrafish inner ear. We used a genetically encoded ablation method to induce hair cell death and observed gradual regeneration with correct spatial patterning over two weeks following ablation. Supporting cells, which surround and are a source of new hair cells, divide in response to hair cell ablation, expanding the possible progenitor pool. In parallel, nascent hair cells arise from direct transdifferentiation of progenitor pool cells uncoupled from progenitor division. These findings reveal a previously unrecognized mechanism of hair cell regeneration with implications for how hair cells may be encouraged to regenerate in the mammalian ear.

SUMMARY STATEMENT

Hair cell regeneration in the zebrafish inner ear occurs through transdifferentiation after a transient wave of supporting cell proliferation that expands the precursor pool.
Intracellular binding pocket revealed in the human bitter taste receptor TAS2R14
Authors: Peri Lior , Matzov Donna , Huxley Dominic R. , Rainish Alon , Fierro Fabrizio , Sapir Liel , Pfeiffer Tara , Waterloo Lukas , Hübner Harald , Weikert Dorothee , Peleg Yoav , Gmeiner Peter , McCormick Peter J. , Niv Masha Y. , Shalev-Benami Moran
Published: April 2024

Bitter taste receptors (TAS2Rs), a subfamily of G-protein coupled receptors (GPCRs) expressed orally and extraorally, elicit signaling in response to a large set of ligands. Among the 25 functional TAS2Rs encoded in the human genome, TAS2R14 is the most promiscuous, and responds to hundreds of chemically diverse agonists. Here, we present the cryo–electron microscopy (cryo-EM) structure of the human TAS2R14 (hTAS2R14) in complex with its cognate signaling partner gustducin, and bound to flufenamic acid (FFA), a clinically approved nonsteroidal anti-inflammatory drug. The structure reveals an unusual binding mode for FFA, where two copies are bound at distinct binding pockets: one at the canonical GPCR site within the trans-membrane bundle, and the other in the intracellular facet, bridging the receptor with gustducin. Combined with site-directed mutagenesis and the design of a fluorescent FFA derivative for pocket-specific ligand binding BRET assays, our studies support a dual binding mode for FFA in TAS2R14. These results fill a gap in the understanding of bitter taste signaling and provide tools for guided design of TAS2R-targeted compounds.
Ovoselenol, a Selenium-containing Antioxidant Derived from Convergent Evolution
Authors: Kayrouz Chase M. , Ireland Kendra A. , Ying Vanessa , Davis Katherine M. , Seyedsayamdost Mohammad R.
Published: April 2024

Selenium is an essential micronutrient, but its presence in biology has been limited to protein and nucleic acid biopolymers. The recent identification of the first biosynthetic pathway for selenium-containing small molecules suggests that there is a larger family of selenometabolites that remains to be discovered. Using a bioinformatic search strategy that relies on mapping of composite active site motifs, we identify a recently evolved branch of abundant and uncharacterized metalloenzymes that we predict are involved in selenometabolite biosynthesis. Biochemical studies confirm this prediction and show that these enzymes form an unusual C–Se bond onto histidine, thus giving rise to a novel selenometabolite and potent antioxidant that we have termed ovoselenol. Aside from providing insights into the evolution of this enzyme class and the structural basis of C–Se bond formation, our work offers a blueprint for charting the microbial selenometabolome in the future.
Multiple pathways for licensing human replication origins
Authors: Yang Ran , Hunker Olivia , Wise Marleigh , Bleichert Franziska
Published: April 2024

The loading of replicative helicases constitutes an obligatory step in the assembly of DNA replication machineries. In eukaryotes, the MCM2-7 replicative helicase motor is deposited onto DNA by the origin recognition complex (ORC) and co-loader proteins as a head-to-head MCM double hexamer to license replication origins. Although extensively studied in the budding yeast model system, the mechanisms of origin licensing in higher eukaryotes remain poorly defined. Here, we use biochemical reconstitution and electron microscopy (EM) to reconstruct the human MCM loading pathway. Unexpectedly, we find that, unlike in yeast, ORC’s Orc6 subunit is not essential for human MCM loading but can enhance loading efficiency. EM analyses identify several intermediatesen routeto MCM double hexamer formation in the presence and absence of Orc6, including an abundant DNA-loaded, closed-ring single MCM hexamer intermediate that can mature into a head-to-head double hexamer through different pathways. In an Orc6-facilitated pathway, ORC and a second MCM2-7 hexamer are recruited to the dimerization interface of the first hexamer through an MCM-ORC intermediate that is architecturally distinct from an analogous intermediate in yeast. In an alternative, Orc6-independent pathway, MCM double hexamer formation proceeds through dimerization of two independently loaded single MCM2-7 hexamers, promoted by a propensity of human MCM2-7 hexamers to dimerize without the help of other loading factors. This redundancy in human MCM loading pathways likely provides resilience against replication stress under cellular conditions by ensuring that enough origins are licensed for efficient DNA replication. Additionally, the biochemical reconstitution of human origin licensing paves the way to address many outstanding questions regarding DNA replication initiation and replication-coupled events in higher eukaryotes in the future.
Phage-Encoded Bismuth Bicycles: Instant Access to Targeted Bioactive Peptides
Authors: Ullrich Sven , Somathilake Upamali , Shang Minghao , Nitsche Christoph
Published: April 2024

Genetically encoded libraries play a crucial role in discovering structurally rigid, high-affinity macrocyclic peptide ligands for therapeutic applications. This study represents the first genetic encoding of peptide-bismuth and peptide-arsenic bicyclic peptides in phage display. We introduce bismuth tripotassium dicitrate (gastrodenol) as a water-soluble Bi(III) reagent for phage library modification andin situbicyclic peptide preparation, eliminating the need for organic co-solvents. Additionally, we explore As(III) as an alternative thiophilic element used analogously to our previously introduced class of peptide-bismuth bicycles. The modification of phage libraries and peptides with these elements is instantaneous and entirely biocompatible, offering an advantage over conventional alkylation-based methods. In a pilot display screening campaign aimed at identifying ligands for the biotin-binding protein streptavidin, we demonstrate the enrichment of bicyclic peptides with dissociation constants two orders of magnitude lower than those of their linear counterparts, underscoring the impact of structural constraint on binding affinity.
Tissue-level integration overrides gradations of differentiating cell identity in beetle extraembryonic tissue
Authors: Mann Katie E. , Panfilio Kristen A.
Published: April 2024

During animal embryogenesis, one of the earliest specification events distinguishes extraembryonic (EE) from embryonic tissue fates: the serosa in the case of the insects. While it is well established that the homeodomain transcription factor Zen1 is the critical determinant of the serosa, subsequent realization of the tissue’s identity has not been investigated. Here, we examine serosal differentiation in the beetleTribolium castaneumbased on quantification of morphological and morphogenetic features, comparing embryos from aTc-zen1RNAi dilution series, where complete knockdown results in amnion-only EE tissue identity. We assess features including cell density, tissue boundary morphology, and nuclear size as dynamic readouts for progressive tissue maturation. While some features exhibit an all-or-nothing outcome, other key features show dose-dependent phenotypic responses with trait-specific thresholds. Collectively, these findings provide nuance beyond the known status of Tc-Zen1 as a selector gene for serosal tissue patterning. Overall, our approach illustrates how analysis of tissue maturation dynamics from live imaging extends but also challenges interpretations based on gene expression data, refining our understanding of tissue identity and when it is achieved.
Multiplexed Assays of Human Disease-relevant Mutations Reveal UTR Dinucleotide Composition as a Major Determinant of RNA Stability
Authors: Su Jia-Ying , Wang Yun-Lin , Hsieh Yu-Tung , Chang Yu-Chi , Yang Cheng-Han , Kang YoonSoon , Huang Yen-Tsung , Lin Chien-Ling
Published: April 2024

UTRs contain crucial regulatory elements for RNA stability, translation and localization, so their integrity is indispensable for gene expression. Approximately 3.7% of genetic variants associated with diseases occur in UTRs, yet a comprehensive understanding of UTR variant functions remains limited due to inefficient experimental and computational assessment methods. To systematically evaluate the effects of UTR variants on RNA stability, we established a massively parallel reporter assay on 6,555 UTR variants reported in human disease databases. We examined the RNA degradation patterns mediated by the UTR library in two cell lines, and then applied LASSO regression to model the influential regulators of RNA stability. We found that UA dinucleotides and UA-rich motifs are the most prominent destabilizing element. Gain of UA dinucleotide outlined mutant UTRs with reduced stability. Studies on endogenous transcripts indicate that high UA-dinucleotide ratios in UTRs promote RNA degradation. Conversely, elevated GC content and protein binding on UA dinucleotides protect high-UA RNA from degradation. Further analysis reveals polarized roles of UA- dinucleotide-binding proteins in RNA protection and degradation. Furthermore, the UA- dinucleotide ratio of both UTRs is a common characteristic of genes in innate immune response pathways, implying a coordinated stability regulation through UTRs at the transcriptomic level. We also demonstrate that stability-altering UTRs are associated with changes in biobank-based health indices, underscoring the importance of precise UTR regulation for wellness. Our study highlights the importance of RNA stability regulation through UTR primary sequences, paving the way for further exploration of their implications in gene networks and precision medicine.