bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative analysis of cold-stored apheresis platelet units in additive solution with or without pathogen reduction: Implications of cytochrome c supplementation
Authors: Ekaney Michael L. , Bartl Neal E. , McKillop Iain H. , Evans Susan L.
Published: December 2024

BACKGROUND

Platelets are limited in supply, and the preservation of platelet function during storage remains challenging. Novel storage approaches are being explored to improve platelet quality, extend shelf life, and reduce risk of infection. This study sought to elucidate platelet function in cold-stored apheresis units in additive solution (platelet additive solution [PAS]) and subjected to pathogen reduction (PR) as well as the impact of cytochrome c (cyt c) supplementation. We hypothesized that the PR would decrease stored platelet function, regardless of cyt c supplementation.

METHODS

Platelet apheresis units (PAS) were collected (N = 5 volunteers) and divided into PR or no PR (PAS) and supplemented with vehicle or cyt c (100 μM). Units were stored at 4°C for 15 days, sequential aliquots were removed, and platelet/mitochondrial respiratory function and biochemical parameters were analyzed.

RESULTS

There was no difference in platelet aggregation in response to adenosine diphosphate between PAS and PR platelets. Aggregation function in response to arachidonic acid was higher in PR versus PAS platelets. Maximum clot strength was not different between PAS and PR from Day 0 to Day 5 but declined in PR platelets on Days 10 and 15. Oxygen consumption declined at the same rate in PAS and PR platelets, while rate of lactate and TCO2 decrease was greater in PR platelets than in PAS platelets. Supplementation with cyt c did not alter platelet function or biochemical parameters in PAS or PR platelets.

CONCLUSION

Platelet additive solution and PR platelets show similar declines in respiratory capacity, and biochemical parameters during cold storage, but PR platelets demonstrated significantly increased arachidonic acid–induced aggregation across all time points. Further understanding this mechanism may provide a means to prolong platelet shelf life.
Penalizing underage alcohol use is associated with lower mortality for young drivers: Use/lose laws and their association with motor vehicle collision mortality
Authors: Shin Gi Jung , Zogg Cheryl K. , Rice William , Xu Ruidi , Castillo-Angeles Manuel , Swain Sonal , Agarwal Suresh K. , Haines Krista L.
Published: December 2024

BACKGROUND

Motor vehicle collisions (MVC) continue to be a leading cause of mortality for youth in the United States. Since 2010, seven states have revoked mandatory laws that suspended licenses for underage alcohol use, also known as use/lose laws. This study analyzed whether each state’s policy change was associated with increased youth MVC mortality.

METHODS

State mortality data for youth ages 15 years to 20 years in MVCs involving a young driver (i.e., ages 15–20 years) were obtained from the Fatality Analysis Reporting System. Population data was retrieved from the Centers for Disease Control and Prevention’s Wide-ranging ONline Data for Epidemiologic Research. Motor vehicle collisions mortality rates were calculated for each state with a law change per 1,000,000 persons. For difference-in-difference analysis, each state’s youth MVC mortality rates from 3 years prior to the law change were compared with rates from 3 years post-law changes, relative to a national average compiled of states with no law changes.

RESULTS

From 2010 to 2020, seven states revoked one or more of their mandatory use/lose laws. For all states, young driver MVC mortality rates significantly increased after removal of use/lose legislation (South Dakota: 5.4 excess deaths per million (EDPM), Indiana: 5.6 EDPM, Georgia 28.0 EDPM, Oregon: +41.9 EDPM, Pennsylvania: +10.4 EDPM, Delaware: +45.4 EDPM, Illinois +29.2 EDPM, all p < 0.001).

CONCLUSION

Examining mortality rates at the state reveals a significant negative association between penalizing underage alcohol use and young driver MVC deaths. Future legislation and health outcomes analysis should consider state-level differences to retain and develop effective policies that reduce injury-related mortality.

LEVEL OF EVIDENCE

Prognostic and Epidemiological; Level IV.
Assessment and Prediction of Clinical Outcomes for ICU-Admitted Patients Diagnosed with Hepatitis: Integrating Sociodemographic and Comorbidity Data
Authors: Alluri Dimple Sushma , Pabon-Rodriguez Felix M.
Published: December 2024

Hepatitis, a leading global health challenge, contributes to over 1.3 million deaths annually, with hepatitis B and C accounting for the majority of these fatalities. Intensive care unit (ICU) management of patients is particularly challenging due to the complex clinical care and resource demands. This study focuses on predicting Length of Stay (LoS) and discharge outcomes for ICU-admitted hepatitis patients using machine learning models. Despite advancements in ICU predictive analytics, limited research has specifically addressed hepatitis patients, creating a gap in optimizing care for this population. Leveraging data from the MIMIC-IV database, which includes around 94,500 ICU patient records, this study uses sociodemographic details, clinical characteristics, and resource utilization metrics to develop predictive models. Using Random Forest, Logistic Regression, Gradient Boosting Machines, and Generalized Additive Model with Negative Binomial Regression, these models identified medications, procedures, comorbidities, age, and race as key predictors. Total LoS emerged as a pivotal factor in predicting discharge outcomes and location. These findings provide actionable insights to improve resource allocation, enhance clinical decision-making, and inform future ICU management strategies for hepatitis patients.
Multi-Step Pathway Engineering in ProbioticSaccharomyces boulardiifor Abscisic Acid Production in the Gut
Authors: Van Gaever Femke , Vandecruys Paul , Driege Yasmine , Kim Seo Woo , Thevelein Johan M. , Beyaert Rudi , Staal Jens
Published: December 2024

The plant hormone abscisic acid (ABA) has gained attention for its role in animals and humans, particularly due to its protective effects in various immune and inflammatory disorders. Given its high concentrations in fruits like figs, bilberries and apricots, ABA shows promise as a nutraceutical. However scalability, short half-life and cost limit the use of ABA-enriched fruit extracts and synthetic supplements. In this study, we propose an alternative ABA administration method to overcome these challenges. We genetically engineered a strain of the probioticSaccharomyces boulardiito produce and deliver ABA directly to the gut of mice. Using the biosynthesis pathway fromBotrytis cinerea, four genes (bcaba1-4) were integrated intoS. boulardii, enabling ABA production at 30°C, as previously described inSaccharomyces cerevisiae. Introducing an additional cytochrome P450 reductase gene resulted in a 7-fold increase in ABA titers, surpassing previous ABA-producingS. cerevisiaestrains. Supplementation of the ABA-producingS. boulardiiin the diet of mice (at a concentration of 5 x 108CFU/g) led to effective gut colonization but resulted in low serum ABA levels (approximately 1.8 ng/mL). The absence of detectable serum ABA after administration of the ABA-producing probiotic through oral gavage, prompted further investigation to determine the underlying cause. The physiological body temperature (37°C) was identified as a major bottleneck for ABA production. Modifications to enhance the mevalonate pathway flux improved ABA levels at 37°C. However, additional modifications are needed to optimize ABA production before testing this probiotic in disease contexts in mice.
Most Autophagic Cell Death Studies Lack Evidence of Causality
Authors: Ghaseminejad Yasmin , Özkaya Ali Burak
Published: December 2024

Autophagy plays a critical role in maintaining cellular homeostasis and is implicated in various physiological and pathological processes, including cancer, neurodegeneration, and metabolic disorders. Although typically associated with cell survival, autophagy has also been proposed to contribute to cell death, referred to as autophagic cell death (ACD). Despite its importance, the identification of ACD remains contentious due to inconsistencies in experimental methodologies and terminological misuse. In this study, we evaluated 104 research articles published in 2022 that claimed to demonstrate ACD. Articles were assessed based on established criteria, including evidence for autophagy, evidence for cell death, exclusion of apoptosis, and experimental designs demonstrating causality. Our findings reveal that only 12.5% of the articles fulfilled all the criteria for ACD, while 37.5% provided only correlation-level evidence. Additionally, 32.7% of the articles relied on viability loss rather than direct evidence of cell death, and 45.0% of studies utilizing autophagy inhibition to prove causality failed to demonstrate actual inhibition of autophagy. Inconsistent terminology was also prevalent, with cases of ‘autophagy-mediated cell death’ being incorrectly classified as ACD and instances where the term ACD was misused as an umbrella term to describe the coexistence of autophagy and cell death, which should have been labeled ‘autophagy-associated cell death.’ These issues highlight a lack of rigor in current practices, with reliance on correlation-level evidence and inappropriate experimental designs undermining the robustness of many studies. This analysis underscores the need for greater rigor in experimental approaches and article revision processes.
The CD4 T cell-independent IgG response during persistent virus infection favors emergence of neutralization-escape variants
Authors: Ayers Katelyn N , Lauver Matthew D , Alexander Kalynn M , Jin Ge , Paraiso Kitt , Ochetto Alyssa , Garg Sonal , Goetschius Daniel J , Hafenstein Susan L , Wang Joseph Che-Yen , Lukacher Aron E
Published: December 2024

How changes in the quality of anti-viral antibody (Ab) responses due to pre-existing or acquired CD4 T cell insufficiency affect virus evolution during persistent infection are unknown. Using mouse polyomavirus (MuPyV), we found that CD4 T cell depletion before infection results in short-lived plasma cells secreting low-avidity antiviral IgG with limited BCR diversity and weak virus-neutralizing ability. CD4 T cell deficiency during persistent infection incurs a shift from a T-dependent (TD) to T-independent (TI) Ab response, resembling the pre-existing TI Ab response. CD4 T cell loss before infection or during persistent infection is conducive for emergence of Ab-escape variants. Cryo-EM reconstruction of complexes of MuPyV virions with polyclonal IgG directly from infected mice with pre-existing or acquired CD4 T cell deficiency enabled visualization of shortfalls in TI IgG binding. By debilitating the antiviral IgG response, CD4 T cell deficiency sets the stage for outgrowth of variant viruses resistant to neutralization.

ONE SENTENCE SUMMARY

Pre-existing and acquired CD4 T cell deficiency facilitates outgrowth of Ab-escape viral variants during persistent infection.
Per vaginal bleeding-an important but ignored feature of dengue
Authors: Wijewickrama Ananda , Kuruppu Heshan , Idampitiya Damayanthi , Wickramanayake Rivindu , Kottahachchi Anagi Shakya , Jayamali Jeewantha , Chathurangika Padukkage Harshani , Senatilleke Nushara , Warnakulasuriya Navanjana , Jeewandara Chandima , Malavige Gathsaurie Neelika
Published: December 2024

Background Elderly individuals, those with comorbidities and pregnant women are at a higher risk of developing severe dengue and succumbing to their illness. However, an increased incidence of severe dengue and fatalities are seen in females of the reproductive age. As per vaginal (PV) bleeding is an important complication that has not been well characterized, we sought to determine the frequency, complications and disease outcomes in women who develop PV bleeding. Methodology/Principal findings 288 adult female patients were recruited from the National Institute of Infectious Diseases Sri Lanka. All clinical features and laboratory investigations were recorded throughout the duration of hospital admission along with treatment received. 28/288 (9.72%) reported PV bleeding, with 12/28 (42.85%) developing dengue haemorrhagic fever (DHF) compared to 65/260 (25%) of those who did not have bleeding. Women who developed PV bleeding were more likely to have developed DHF (OR 2.2, 95% CI 0.98 to 5.1, p=0.06), abdominal pain (OR=2.17, 95% CI = 0.99 to 4.69, p = 0.06), vomiting (OR= 2.0, 95% CI= 0.89 to 4.44, p= 0.10), diarhoea (OR= 4.35, 95% CI = 1.908 to 9.610, p= 0.0004) or evidence of any fluid leakage (OR= 1.98, 95% CI = 0.91 to 4.5, p = 0.11). Although not significant, those who had PV bleeding were more likely to have been given intravenous fluids, blood transfusions and colloids. Conclusions PV bleeding appears to associate with worse disease outcomes. The possible contribution of PV bleeding to higher incidence of severe dengue and fatality rates observed in many countries, should be further investigated.
The 1001G+ project: A curated collection ofArabidopsis thalianalong-read genome assemblies to advance plant research
Authors:   The 1001 Genomes Plus Consortium, Alonso-Blanco Carlos C. , Ashkenazy Haim , Baduel Pierre , Bao Zhigui , Becker Claude , Caillieux Erwann , Colot Vincent , Crosbie Duncan , De Oliveira Louna , Fitz Joffrey , Fritschi Katrin , Grigoreva Elizaveta , Guo Yalong , Habring Anette , Henderson Ian , Hou Xing-Hui , Hu Yiheng , Igolkina Anna , Kang Minghui , Kemen Eric , Kersey Paul J. , Kornienko Aleksandra , Lian Qichao , Liu Haijun , Liu Jianquan , Lucke Miriam , Mayjonade Baptiste , Mercier Raphaël , Mollá Morales Almudena , Movilli Andrea , Murray Kevin D. , Naish Matthew , Nordborg Magnus , Rabanal Fernando A. , Roux Fabrice , Schandry Niklas , Schneeberger Korbinian , Schwab Rebecca , Shirsekar Gautam , Sushko Svitlana , Tao Yueqi , Teasdale Luisa , Vorbrugg Sebastian , Weigel Detlef , Xian Wenfei
Published: December 2024

Arabidopsis thalianawas the first plant for which a high-quality genome sequence became available. The publication of the first reference genome sequence almost 25 years ago was already accompanied by genome-wide data on sequence polymorphisms in another accession, or naturally occurring strain. Since then, inventories of genome-wide diversity have been generated at increasingly precise levels. High-density genotype data forA. thaliana, including those from the 1001 Genomes Project, were key to demonstrating the enormous power of GWAS in inbred populations of wild plants, and the comparison of intraspecific polymorphism with interspecific divergence has illuminated many aspects of plant genome evolution. Over the past decade, an increasing number of nearly complete genome sequences have been published for many more accessions. Here, we highlight the diversity of a curated collection of previously published and so far unpublished genome sequences assembled using different types of long reads, including PacBio Continuous Long Reads (CLR), PacBio High Fidelity (HiFi) reads, and Oxford Nanopore Technologies (ONT) reads. This 1001 Genomes Plus (1001G+) resource is being made available athttp://1001genomes.org. We invite colleagues with yet unpublished genome assemblies fromA. thalianaaccessions to contribute to this effort.
POLO kinase inhibits Protein Phosphatase 1 to promote the Spindle Assembly Checkpoint and prevent aneuploidy
Authors: Moura Margarida , Barbosa João , Pinto Inês , Leça Nelson , Cunha-Silva Sofia , Verza Arianna Esposito , Pedroso Paulo D. , Lemaire Sarah , Duro Joana , Silva Miguel , Oliveira André , Reis Ricardo , Nilsson Jakob , Sunkel Claudio , Musacchio Andrea , Bollen Mathieu , Conde Carlos
Published: December 2024

Protein phosphatase 1 (PP1) is essential for spindle assembly checkpoint (SAC) silencing and mitotic exit, but its regulation during mitosis remains ill-defined. Here, we demonstratein vitroand inDrosophilacells that the mitotic kinase POLO phosphorylates PP1α87B at a conserved residue (T286) within a pocket implicated in the recognition of RVxF-containing target proteins. Phosphorylation of T286 inhibits PP1α87B binding to the RVxF motif of the SAC kinase MPS1, dampening the dephosphorylation of MPS1 T-loop. Phosphorylation of T286 is dynamically regulated during mitosis. It occurs at unattached/tensionless kinetochores and decreases as chromosomes congress. Expression of phosphomimetic PP1α87BT286Dprevents MPS1 inactivation in metaphase and causes a SAC-dependent delay of anaphase onset. Conversely, an unphosphorylatable PP1α87BT286Amutant impairs MPS1 activation at unattached kinetochores and weakens the SAC.In vivo, larval neuroblasts expressing PP1α87BT286phosphomutants exhibit frequent chromosome mis-segregation and aneuploidy. Thus, our findings identify POLO-mediated phosphorylation of PP1α87B as a critical regulatory strategy that fine-tunes phosphatase activity to ensure a robust and timely SAC and prevent genome instability.
APR-246 & COTI-2 increase chemoradiotherapy sensitivity via ROS-induced DNA damage and ferroptosis in p53 mutant HPV negative head and neck squamous cell carcinoma
Authors: de Bakker Tycho , Cogels Morgane , Iliadi Chrysanthi , Penninckx Sebastien , Martinive Philippe , Gestel Dirk Van
Published: December 2024

About 80% of patients with HPV negative head and neck squamous cell carcinoma are diagnosed at stage III or IV. In these cases, Surgical resection followed by (chemo-)radiotherapy is the standard treatment for most cases. However, many patients present with unresectable and/or resistant disease and even metastases, limiting therapeutic options. A common molecular defect in these tumours is the deactivation of the tumour suppressor gene TP53, frequently through inactivating mutations. Restoring TP53 function, combined with the standard chemoradiotherapy may enhance the therapeutic outcomes.

In this study, the efficacy of two TP53 reactivating compound, APR-246 and COTI-2, was evaluated in combination with chemoradiotherapy on two different human HNSCC cell lines. Results highlight a synergistic effect of the combination treatment, significantly reducing clonogenic survival, spheroid growth and subcutaneous tumour growth in a preclinical murine model. Mechanistic investigation suggests that this effect is linked to redox imbalance caused by the generation of reactive oxygen species. This appears to play a key role in the Fenton reaction, further facilitated by an increase in DMT1 or decrease in FTH1 expression, leading to elevated cytosolic iron and lipid peroxide levels. Additionally, the reactive oxygen species may contribute towards the increase in both single and double strands breaks observed in several western blots. Overall, these results suggest that combining TP53 reactivation with chemoradiotherapy could trigger ferroptosis, improving tumour control in HNSCC.
Expression of Intron-containing HIV-1 RNA Induces NLRP1 Inflammasome Activation in Myeloid Cells
Authors: Jalloh Sallieu , Hughes Ivy K , Akiyama Hisashi , Gojanovich Aldana , Quiñones Andres , Yang Mengwei , Henderson Andrew J. , Mostoslavsky Gustavo , Gummuluru Suryaram
Published: December 2024

Despite the success of antiretroviral therapy (ART) in suppressing plasma viremia in people living with human immunodeficiency virus type-1 (HIV-1), persistent viral RNA expression in tissue reservoirs is observed and can contribute to HIV-1-induced immunopathology and comorbidities. Infection of long-lived innate immune cells, such as tissue-resident macrophages and microglia may contribute to persistent viral RNA production and chronic inflammation. We recently reported thatde-novocytoplasmic expression of HIV-1 intron-containing RNA (icRNA) in macrophages and microglia leads to MDA5 and MAVS-dependent innate immune sensing and induction of type I IFN responses, demonstrating that HIV icRNA is a pathogen-associated molecular pattern (PAMP). In this report, we show that cytoplasmic expression of HIV-1 icRNA also induces NLRP1 inflammasome activation and IL-1β secretion in macrophages and microglia in a RLR- and endosomal TLR-independent manner. Infection of both macrophages and microglia with either replication-competent or single-cycle HIV-1 induced IL-1β secretion, which was attenuated when cytoplasmic expression of viral icRNA was prevented. While IL-1β secretion was blocked by treatment with caspase-1 inhibitors or knockdown of NLRP1 or caspase-1 expression in HIV- infected macrophages, overexpression of NLRP1 significantly enhanced IL-1β secretion in an HIV-icRNA-dependent manner. Immunoprecipitation analysis revealed interaction of HIV-1 icRNA, but not multiply-spliced HIV-1 RNA, with NLRP1, suggesting that HIV-1 icRNA sensing by NLRP1 is sufficient to trigger inflammasome activation. Together, these findings reveal a pathway of NLRP1 inflammasome activation induced byde novoexpressed HIV icRNA in HIV- infected myeloid cells.
Comparative sensitivity ofin vitroacute and chronic apical and transcriptomic points of departure for perfluorooctanoic acid in human vascular endothelial cells
Authors: Opacic Marija , Stanic Bojana , Andric Nebojsa
Published: December 2024

In vitrohuman cell models and new approach methodologies offer valuable alternatives to animal testing, providing human-relevant data for chemical risk assessment. However, the impact of exposure duration and biological levels on the sensitivity of responses in human cellsin vitroremains underexplored. In this study, we employed benchmark concentration modeling to derive and compare points of departure (PODs) for apical (A-POD) and transcriptomic (T-POD) changes in human vascular endothelial cells EA.hy926 following short-term (48 h) and long-term (6 and 12 weeks) exposure to 1, 10, and 100 µM and 1, 10, and 100 nM perfluorooctanoic acid (PFOA), respectively. We found that A-POD could not be calculated for short-term exposure; however, A-PODs after 6 and 12 weeks were determined to be 3.7 nM and 5.4 nM, respectively. mRNA sequencing revealed a significant number of differentially expressed genes in PFOA-exposed EA.hy926 cells across all time points. T-POD values after 6 and 12 weeks (4.1 nM and 22.1 nM, respectively) demonstrated greater sensitivity than the acute T-POD (6.3 µM) and were comparable to the chronic A-POD. Functional gene analysis revealed that transcription was a sensitive, yet general molecular pathway affected by acute exposure, while the IL-17 pathway and extracellular matrix and cytokine-cytokine interactions were implicated after 6 and 12 weeks of exposure to PFOA, respectively. In conclusion, chronic PODs proved to be more informative than acute PODs for chemical risk assessment in PFOA-exposed human endothelial cells. Furthermore, transcriptomics data from long-term exposure can elucidate early molecular pathways associated with chemical exposure, highlighting their potential to connect toxicity effects across different biological levels.
Cell-specific delivery of GJB2 restores auditory function in mouse models of DFNB1 deafness and mediates appropriate expression in NHP cochlea
Authors: Ivanchenko Maryna V. , Booth Kevin T.A. , Karavitaki K. Domenica , Antonellis Larisa M. , Nagy M. Aurel , Peters Cole W. , Price Spencer , Li Yaqiao , Lytvyn Anton , Ward Andrew , Griffith Eric C. , Hrvatin Sinisa , Greenberg Michael E. , Corey David P.
Published: December 2024

Mutations in theGJB2gene cause the most common form of human hereditary hearing loss, known as DFNB1.GJB2is expressed in two cell groups of the cochlea—epithelial cells of the organ of Corti and fibrocytes of the inner sulcus and lateral wall—but not by sensory hair cells or neurons. Attempts to treat mouse models of DFNB1 with AAV vectors mediating nonspecificGjb2expression have not substantially restored function, perhaps because inappropriate expression in hair cells and neurons could compromise their electrical activity. Here, we used genomic chromatin accessibility profiling to identify candidate gene regulatory elements (GREs) that could drive cell-type-specific expression ofGjb2in the cochlea. HA-tagged GJB2, delivered to a conditional knockout model in an AAV vector with GRE control of expression, was localized to the appropriate cell types, prevented the cochlear degeneration observed in untreated knockout mice, and partially rescued hearing sensitivity. In aGjb2partial knockdown mouse model, such exogenous GJB2 prevented degeneration and completely restored hearing sensitivity. We tested control of expression by these GREs in nonhuman primate cochleas and found that vector-delivered human GJB2.HA was located in the appropriate cell types and caused little or no reduction in hearing sensitivity. Together, these findings suggest that GRE-mediated expression ofGJB2could prevent hearing loss in DFNB1 patients.
Elucidation of gene clusters underlying withanolide biosynthesis in ashwagandha through yeast metabolic engineering
Authors: Reynolds Erin , Trauger Marena , Li Fu-Shuang , Huang Jonathan , Moss Trevor , Christ Bastien , Xu Menglong , Knoch Eva , Weng Jing-Ke
Published: December 2024

Withanolides are medicinally relevant steroidal lactones produced byWithania somnifera(ashwagandha) amongst other Solanaceae family plants. However, the biosynthetic pathway to withanolides is largely unknown, preventing scale-up and hindering pharmaceutical applications. We sequenced the genome ofW. somniferaand identified two biosynthetic gene clusters exhibiting a segmented tissue-specific expression pattern. We characterized the cluster enzymes through stepwise pathway reconstitution in yeast and transient expression inNicotiana benthamiana, leading to the identification of three cytochrome P450s (CYP87G1, CYP88C7, and CYP749B2) and a short-chain dehydrogenase that produce a lactone ring- containing intermediate when co-expressed. A fourth cytochrome P450 (CYP88C10) and a sulfotransferase convert this into an intermediate with the characteristic withanolide A-ring structure, featuring a C1ketone and C2-C3unsaturation. The discovery of the sulfotransferase as a core pathway enzyme challenges the conventional paradigm of sulfotransferases as tailoring enzymes. These insights pave the way for an efficient biomanufacturing process for withanolides and future development of withanolide-derived drugs.
Multi-omics analysis of long-term cultured human islets
Authors: Sun Guihua , Qi Meirigeng , Sun Olivia , Lizhar Elizabeth M. , Hussey Deborah , Shi Yanhong , Riggs Arthur D.
Published: December 2024

β-cell dysfunction in pancreatic islets, characterized as either the loss of β-cell mass or the resistance of β-cell to glucose, is the leading cause of progression to diabetes. Islet transplantation became a promising approach to replenish functional β-cell mass. However, not much known about changes in islets used for transplantation after isolation. We have subjected human islets into long-termin vitroculture (LTC) and characterized those survived islets. While most of the dysregulated genes were downregulated during LTC, specific groups of mRNA or miRNA were upregulated, and they are involved in specific pathways. In general, α-cells and β-cells of LTC-islets have elevated expressions ofMAFBandMAFAgenes, respectively. We also found that exocrine cells were eliminated faster than endocrine cells, and β-cells were lost at a higher rate than α-cells. Interestingly, one specific group of cells that have characteristics of immature α-cells or β-cells, were enriched in LTC-islets, revealing the possibility of transdifferentiation of α-cells to β-cells, or dedifferentiation of β-cells to α -cells, underin vitroculture. Our results suggest that there are intrinsic cellular and molecular mechanisms in pancreatic cells that are associated with their maturity and correlated with their survival ability under unfavorable living conditions.
Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoates-producing mixed microbial cultures via meta-omics study
Authors: Yao Jian , Zeng Yan , Hong Xia , Wang Meng , Zhang Quan , Chen Yating , Gou Min , Xia Zi-Yuan , Tang Yue-Qin
Published: December 2024

The dynamics of the structure of polyhydroxyalkanoates-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, we enriched five PHA-MMCs and sampled temporally to study the interactions between phage and prokaryotic members by combining metagenomics and metatranscriptomics. 963 metagenome-assemble genomes and 4294 phage operational taxonomic units were assembled from bulk metagenomic data. There were complex interactions between the phages in Casadabanvirus and Unclassified Hendrixvirinae and the dominant species inAzomonas,Paracoccus,ThaueraandBreundimonas. The dynamic change of the structure of phage and prokaryotic communities were remarkably consistent. Further structural equation modeling analysis showed that phage communities could significantly affect the activity and community structure of prokaryotic microorganisms. In addition, seven key auxiliary metabolic genes (phaC, fadJ, acs, ackA, phbB, acdAB and fadD) in the PHA synthesis pathway were identified from phage sequences. Importantly, these auxiliary metabolic genes were expressed at the transcriptional level, indicating that they were in an active functional state. This meta-analysis provides the first catalog of phages in PHA-MMCs and the auxiliary metabolic genes they carry, as well as how they play a role in the dynamic changes of prokaryotic communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of artificial open microbial systems.

Importance

The synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (MMCs), with extremely low cost, has the potential for expanded production. However, there is a gap of understanding of the dynamics of dominant species in MMCs to better control community structure. Our results demonstrate for the first time the impact of phages on the structure of prokaryotic communities in the MMCs. There are complex interactions between the PHA producers (Azomonas,Paracoccus,Thauera) and phages (Casadabanvirus and Unclassified Hendrixvirinae). Phage communities can negatively regulate the activity and structure of prokaryotic communities. In addition, the auxiliary metabolic genes in the PHA synthesis pathways carried by phages may promote the PHA synthesis ability of prokaryotic members. This study highlights the impact of phages on prokaryotic community structure, suggesting that phages have the potential to become a tool for better controlling the microbial community structure of PHA-MMCs.
Global and genetic regulation of gene expression in human endothelial and vascular smooth muscle cells
Authors: Liu Pengyuan , Ray Atrayee , Liu Yong , Mishra Manoj K. , Qiu Qiongzi , Pandey Rajan , Therani Bhavika , Huang Jing , Ren Jiayi , Stelloh Cary , Bai Xiaowen , Greene Andrew S. , Cowley Allen W. , Geurts Aron M. , Rao Sridhar , Liang Mingyu
Published: December 2024

Background

The understanding of genetic and epigenetic regulation of gene expression in endothelial and vascular smooth muscle cells remains fragmented with limited experimental validation.

Methods

Chromatin conformation (Micro-C), DNA methylation (RRBS), chromatin accessibility (ATAC-seq), and transcriptome profiles (RNA-seq) were mapped in human induced pluripotent stem cell (hiPSC)-derived, isogenic endothelial and vascular smooth muscle cells (iECs and iVSMCs). CTCF and RAD21 were depleted to assess the functional relevance of chromatin architecture, and genome editing was used to evaluate the allelic effect of a blood pressure-associated single nucleotide polymorphism (SNP).

Results

Significant correlations were identified between gene expression levels and chromatin interactions, chromatin accessibility, and DNA methylation in iECs and iVSMCs, with chromatin interactions showing the strongest association. Chromatin contact regions displayed distinct epigenetic landscapes depending on the types of regulatory element interactions involved. Perturbation of CTCF and RAD21 revealed their differential regulatory effects, particularly on the expression of genes overlapping chromatin contacts, with RAD21 exhibiting a broader regulatory impact. SNPs associated with several vascular traits were enriched in chromatin loops or accessible regions in iECs or iVSMCs. Precise genome editing demonstrated allele-dependent effects of SNP rs9833313 on the expression ofSHOX2located 247.4 kbp away but within the same chromatin loops as the SNP.

Conclusion

This study provides an extensive epigenetic landscape of vascular cells that may drive novel research on the role of genetic and epigenetic mechanisms of vascular function and disease as demonstrated by our targeted experiments.
A vestibulospinal pathway for context-dependent motor control of the mouse tail
Authors: Lacava Salvatore Andrea , Isilak Necmettin , Ranawat Nishtha , Katzke Julian , Hugo Hoedemaker Johannes Frederik , Yoshida Yutaka , Uusisaari Marylka Yoe
Published: December 2024

The tail movement is critical for maintaining balance during locomotion in many animal species, yet its underlying neuro-muscular control remains poorly understood. In this study we investigated what are the neuronal substrates responsible for tail control in mice. Using high-resolution microCT scans and retrograde labeling, we lay out the neuro-muscular organization of the tail and identified distinct pools of motoneurons in the spinal cord that innervate proximal and distal muscles. We further show that the spinal vestibular nucleus (SpVN) in the brainstem sends direct projections to the same spinal cord segments where tail motoneurons are located. The activation of these vestibulospinal neurons using optogenetics results in more accurate tail movements during challenging balance tasks. Our results reveal that the vestibular system’s influence on tail control is context-dependent, enhancing balance performance under uncertain sensory conditions. These findings provide novel insights into the neural circuits responsible for maintaining balance, highlighting the role of the vestibulospinal pathway in context-dependent modulation of tail movement to maintain stability during complex locomotor tasks.
A single-cell map of hypertension
Authors: Qiu Qiongzi , Liu Yong , Xue Hong , Pandey Rajan , He Lishu , Liu Jing , Liu Pengyuan , Therani Bhavika , Kumar Vinod , Huang Jing , Guenther Maya , Usa Kristie , Grzybowski Michael , Vanden Avond Mark A. , Greene Andrew S. , Cowley Allen W. , Rao Sridhar , Geurts Aron M. , Liang Mingyu
Published: December 2024

Hypertension is a leading risk factor for disease burden and death worldwide. Several organ systems are involved in the development of hypertension, which contributes to stroke, heart disease, and kidney disease. Despite the broad health relevance, our understanding of the molecular landscape in hypertension is limited and lags other major diseases. Here we report an extensive analysis of the molecular landscape in hypertension and its end-organ damage and uncover novel mechanisms linking human genetic variants to the development of these diseases. We obtained single-nucleus RNA-seq (612,984 nuclei), single-nucleus ATAC-seq (179,637 nuclei), or spatial transcriptome data from five organs (hypothalamus, kidney, heart, 3rdorder mesenteric artery, middle cerebral artery) in three mouse and rat models under twelve experimental conditions. More than one third of all hypertension research in animal models involves these three models. We identified both model-specific and convergent responses in cell types, genes, and pathways. By integrating our data with human genomic data, we partitioned the blood pressure and end-organ damage traits into cell type-specific transcriptional contributions and cell types common across multiple traits. Using genomic editing in animal models and human induced pluripotent stem cells, we extended key findings and identified new mechanisms linking human genetic variants to the development of hypertension and related renal injury. We anticipate that our rich data sets and findings will broadly drive forward the research of hypertension and hypertensive end-organ damage. Our approach of integrating multi-model and multi-tissue single-cell analysis with human genetic data and in vivo and in vitro genome editing can be applied to investigate other complex traits.
Candida albicansinduce hypoxia response via activating EGFR to promote colorectal cancer progression
Authors: Wang Wanqiu , Li Haihuang , Gong FangLei , Zhang Zhenyu , Ma Yanping , Zhao Yu , Du Changzheng , Li Ningning , He Guiwei , Sun Kun
Published: December 2024

Colorectal cancer (CRC) is one of the leading causes of cancer-related mortality worldwide. Gut microbiota, including fungi, are considered to associate with CRC progression, while their functions and underlying mechanisms remain largely elusive. Here, we assessed the engagement ofCandida albicans(C. albicans), a common fungus, in CRC progression. Using a cell-fungi co-culture system, we found thatC. albicanscould activate critical pro-metastatic genes and pathways, including MAPK and NF-κB, to up-regulate the expression of transcription factor, c-Jun, and c-Myc. Subsequently, c-Jun and c-Myc provoked hypoxia inducible factor 1α (HIF-1α) stabilization at normoxia, which further promote angiogenesis and tumor progression. Loss-of-function investigation showed that during this procedure, the virulence factor candidalysin secreted byC. albicanswas essential for eliciting cancer cell responses through inducing the phosphorylation of epidermal growth factor receptor (EGFR) and Toll-like Receptors (TLRs) in the tumor cell, preferably in a species and cancer cell-dependent manner. The activation of hypoxia pathway byC. albicanswas reinforced in colon organoids derived from CRC specimens. Hence, our results demonstrated thatC. albicansactivated the EGFR/TLR2 – ERK/NF-κB – HIF-1α signaling pathway and induced a hypoxia response to promote cancer progression, thereby presenting a potential therapeutic target for CRC treatment.
Universality of representation in biological and artificial neural networks
Authors: Hosseini Eghbal , Casto Colton , Zaslavsky Noga , Conwell Colin , Richardson Mark , Fedorenko Evelina
Published: December 2024

Many artificial neural networks (ANNs) trained with ecologically plausible objectives on naturalistic data align with behavior and neural representations in biological systems. Here, we show that this alignment is a consequence of convergence onto the same representations by high-performing ANNs and by brains. We developed a method to identify stimuli that systematically vary the degree of inter-model representation agreement. Across language and vision, we then showed that stimuli from high-and low-agreement sets predictably modulated model-to-brain alignment. We also examined which stimulus features distinguish high-from low-agreement sentences and images. Our results establish representation universality as a core component in the model-to-brain alignment and provide a new approach for using ANNs to uncover the structure of biological representations and computations.
Structure-based mechanistic principles for the paradoxical effects of pathological RET mutations
Authors: Fassler Bakhman Anna , Cohen Michal , Kolodny Rachel , Kosloff Mickey
Published: December 2024

The RET receptor is a transmembrane protein that belongs to the receptor tyrosine kinase family. RET activates signaling pathways regulating cell growth, differentiation and survival in diverse tissues that include the thyroid and enteric nervous system. Mutations that reduce RET levels or function can cause Hirschsprung’s (HSCR) disease, characterized by abnormal distal colon innervation in the developing embryo. In contrast, mutations that constitutively activate RET can lead to tumorigenesis, most notably in multiple endocrine neoplasia type 2 (MEN2) syndromes usually identified in the thyroid. Paradoxically, some RET mutations can both reduce RET activity in enteric ganglia, and increase signaling in other tissues, resulting in co-occurrence of both HSCR and MEN2A. Although extensive research has been conducted on RET mutations, the structural and mechanistic bases underlying these paradoxical effects remain unclear. Here, we assimilated data on 70 positions in RET extracellular domains where point-mutations were associated with HSCR, MEN2A, or both. Using 3D structure-based approaches, we predict the potential structural effects of mutations in these positions. Our analysis suggests that approximately 90% of positions associated with HSCR disease can, upon mutation, disrupt intramolecular interactions that stabilize RET tertiary structure: residues buried in the protein core, calcium-binding sites, or residues participating in stabilizing intramolecular electrostatic/covalent bonds. A smaller subset of mutations involves substitutions to/from glycines or prolines in key positions. Only a small minority of HSCR-associated positions affect protein-protein interactions needed for signal activation. On the other hand, our analysis showed that ∼75% of mutations in positions that cause MEN2A lead to an unpaired cysteine that can form an intermolecular disulfide bond between two RET monomers. Other mutations that cause MEN2A are also predicted to enhance RET homodimerization via extracellular domains that are proximal to the membrane. Importantly, a substitution leading to an unpaired cysteine that concurrently destabilizes RET tertiary structure is predicted to cause the paradoxical co-occurrence of MEN2A and HSCR. Our findings suggest a mechanistic basis for almost all identified pathological mutations in RET and that therapeutic strategies for targeting RET activity in HSCR and MEN2A may need to be orthogonal.
Ectopic gene conversion causing quantitative trait variation
Authors: Pfalz Marina , Naadja Seïf-Eddine , Shykoff Jacqui Anne , Kroymann Juergen
Published: December 2024

Why is there so much non-neutral genetic variation segregating in natural populations? We dissect function and evolution of a near-cryptic quantitative trait locus (QTL) for defense metabolites in Arabidopsis using the CRISPR/Cas9 system and nucleotide polymorphism patterns. The QTL is explained by genetic variation in a family of four tightly linked indole-glucosinolateO-methyltransferase genes. Some of this variation appears to be maintained by balancing selection, some appears to be generated by non-reciprocal transfer of sequence, also known as ectopic gene conversion (EGC), between functionally diverged gene copies. Here we elucidate how EGC, as an inevitable consequence of gene duplication, could be a general mechanism for generating genetic variation for fitness traits.
McsB regulates CtsR thermosensing through periphery arginine phosphorylation
Authors: Cai Huahuan , Hua Boyang , Guo Yeting , Xia Xing-Hua , Zhao Yufen
Published: December 2024

Post-translational protein modifications (PTMs) are a ubiquitous phenomenon that exists in all domains of life. The bacterial transcription repressor CtsR becomes phosphorylated by the arginine kinase McsB when cells sense an elevated temperature in the environment. Here, we perform single-molecule experiments based on the protein-induced fluorescence enhancement (PIFE) effect to monitor the DNA-CtsR-McsB interaction. Our single-molecule analysis reveals that CtsR binds rapidly and stably to the cognate DNA, and that McsB transiently interacts with the DNA-bound CtsR. We determined the binding kinetics between McsB and the DNA-bound CtsR by single-molecule real-time binding assays, withkonandkoffof 0.80 μM-1s-1and 0.14 s-1, respectively. Through this interaction, McsB does not remove CtsR from the DNA, but instead alters its thermosensing behavior, lowering the temperature threshold for CtsR dissociation. Phosphorylation of several periphery arginine residues on CtsR underlies a plausible molecular mechanism for this effect. Taken together, these results provide insights into how CtsR might integrate inputs from different environment stresses and regulate the initiation of the heat-shock response when cells are faced with complex environment conditions.
MethylQUEEN: A Methylation Encoded DNA Foundation Model
Authors: Li Mingyang , Gu Ruichu , Fan Shiyu , Fan Yu , He Bo , Yang Jinmin , Chen Yuting , Xin Mengling , Wen Han , Yi Chengqi
Published: December 2024

DNA 5-methylcytosine (5mC) modification plays a pivotal role in many biological processes, yet 5mC information and pattern hidden behind remains to be explored. Here, we developMethylation Language Model based onQuintupleBidirectional Transformer (MethylQUEEN), a novel pre-trained DNA methylation foundation model capable of sensing methylation states and covering the genome-wide methylation landscape. Through tailored methylation-prone pre-training, MethylQUEEN effectively captured epigenetics information hidden within the DNA sequences: it accurately traces DNA’s tissue-of-origin, and successfully recovers the expression profile through methylation states. Integrative analysis on MethylQUEEN’s attention scores also enables us to reveal the unique methylation status of a tissue for precise disease detection, and identifying key regulatory 5mC sites for disease intervention. As a result, MethylQUEEN signifies a new paradigm in methylation analysis for various biological problems. Besides, our study demonstrates the effectiveness of directly integrating methylation information into pre-training, offering new perspectives and methodologies for a range of methylation-related biological processes. It serves as an initial exploration for the development of more comprehensive epigenomic models.
FAM162A is Crucial for Mitochondrial Structure, Dynamics, and Bioenergetics, Driving Cellular Protection and Longevity
Authors: Matamoros Andrea , Soffia Juan Pablo , Muñoz Marcelo , Maturana Michael , Gonzalez-Ibañez Alvaro , Gomez-Lillo Gabriela , Astorga Cesar , Ruiz Lina M. , Jorquera Ramón , Elorza Alvaro A.
Published: December 2024

Introduction

FAM162A is a mitochondrial protein evolutionarily conserved across taxa and ubiquitously expressed in various tissues. It is known for its role in hypoxia-induced apoptosis. However, paradoxically, FAM162A is overexpressed in cancer, where its pro-apoptotic function seems overridden, suggesting an alternative role associated with mitochondrial function and cell survival. Additionally, its precise localization and topology remain controversial.

Objectives

To assess the role of FAM162A in mitochondrial structure, dynamics, and bioenergetics and its impact on cell viability, while establishing its precise localization, orientation, and topology. Additionally, to generate a transgenic Drosophila model overexpressing human FAM162A to evaluate its effects on organismal survival under normal and stress conditions.

Methods

Localization, orientation, and topology were determined by protease protection assays in COS7 cells. Loss-and gain-of-function experiments were performed to assess mitochondrial function and turnover by confocal microscopy, immunoblots and Seahorse technology. A transgenic Drosophila model overexpressing human FAM162A was generated to evaluate organismal survival under normal and stress conditions.

Results

FAM162A is essential for maintaining mitochondrial ultrastructure and bioenergetics, thereby influencing cell viability and stress resistance. Localization studies revealed that FAM162A resides predominantly in the inner mitochondrial membrane, particularly within the cristae, where it modulates the fusion protein OPA1. Transgenic Drosophila overexpressing human FAM162A exhibited increased lifespan and locomotor activity under both normal and heat stress conditions.

Conclusion

FAM162A emerges as a crucial player in maintaining mitochondrial integrity and bioenergetics. Its functional role, potentially mediated through interaction with OPA1, impacts mitochondrial health, stress resistance, cellular viability, and organismal longevity.