bluuebunny/crossref_metadata_2025 huggingface dataset:
Treatment Patterns for End-Stage Kidney Failure in Patients With Systemic Lupus Erythematous
Authors: Lao Chunhuan , Van Dantzig Philippa , Rabindranath Kannaiyan , White Douglas , Lawrenson Ross
Published: May 2024

Background

This study aims to examine the treatment patterns of end-stage kidney disease (ESKD) among SLE patients and to compare the outcome of hemodialysis (HD) and peritoneal dialysis (PD).

Methods

SLE patients identified from the national administration dataset in 2005–2021 were linked to the Australia and New Zealand Dialysis and Transplant Registry to identify ESKD cases. The adjusted odds ratio of having PD instead of HD as the first treatment for ESKD for Asian, Māori, and Pacific compared with European/others was estimated with the logistic regression model. The adjusted hazards ratio of all-cause mortality for patients having PD first compared with HD first was calculated.

Results

Two hundred ten ESKD patients with SLE were identified. Two thirds (137/210) of the ESKD patients had HD as the first treatment, and one third (68, 32.4%) had PD first. Around 60% of Asian patients had PD as the first treatment, compared with 30% in other ethnic groups. The adjusted odds ratio of having PD as the first treatment for Asian patients compared with European/others was 3.00 (95% confidence interval, 1.16–7.73). The adjusted hazards ratio of all-cause mortality for patients in the PD group compared with the HD group was 0.60 (95% confidence interval, 0.37–0.97).

Conclusions

Asian patients with ESKD were more likely to have PD as the first treatment. The optimal dialysis type for ESKD patients with SLE might be different from ESKD patients caused by other diseases. ESKD patients with SLE receiving PD first had superior outcomes than patients receiving HD first.
TEMPORAL CHANGES IN INNATE AND ADAPTIVE IMMUNITY DURING SEPSIS AS DETERMINED BY ELISPOT
Authors: Unsinger Jacqueline , Osborne Dale , Walton Andrew H. , Han Ethan , Sheets Lauren , Mazer Monty B. , Remy Kenneth E. , Griffith Thomas S. , Rao Mahil , Badovinac Vladimir P. , Brakenridge Scott C. , Turnbull Isaiah , Efron Philip A. , Moldawer Lyle L. , Caldwell Charles C. , Hotchkiss Richard S.
Published: May 2024

Background: The inability to evaluate host immunity in a rapid quantitative manner in patients with sepsis has severely hampered development of novel immune therapies. The enzyme-linked immunospot (ELISpot) assay is a functional bioassay that measures the number of cytokine-secreting cells and the relative amount of cytokine produced at the single-cell level. A key advantage of ELISpot is its excellent dynamic range enabling a more precise quantifiable assessment of host immunity. Herein, we tested the hypothesis that the ELISpot assay can detect dynamic changes in both innate and adaptive immunity as they often occur during sepsis. We also tested whether ELISpot could detect the effect of immune drug therapies to modulate innate and adaptive immunity. Methods: Mice were made septic using sublethal cecal ligation and puncture. Blood and spleens were harvested serially, and ex vivo interferon γ and TNF-α production were compared by ELISpot and enzyme-linked immunosorbent assay. The capability of ELISpot to detect changes in innate and adaptive immunity due to in vivo immune therapy with dexamethasone, IL-7, and arginine was also evaluated. Results: ELISpot confirmed a decreased innate and adaptive immunity responsiveness during sepsis progression. More importantly, ELISpot was also able to detect changes in adaptive and innate immunity in response to immune-modulatory reagents, for example, dexamethasone, arginine, and IL-7, in a readily quantifiable manner, as predicted by the reagents known mechanisms of action. ELISpot and enzyme-linked immunosorbent assay results tended to parallel one another although some differences were noted. Conclusion: ELISpot offers a unique capability to assess the functional status of both adaptive and innate immunity over time. The results presented herein demonstrate that ELISpot can also be used to detect and follow the in vivo effects of drugs to ameliorate sepsis-induced immune dysfunction. This capability would be a major advance in guiding new immune therapies in sepsis.
SIRTUIN 5 ALLEVIATES EXCESSIVE MITOCHONDRIAL FISSION VIA DESUCCINYLATION OF ATPASE INHIBITORY FACTOR 1 IN SEPSIS-INDUCED ACUTE KIDNEY INJURY
Authors: Li Jiaxin , Yao Yi , Lei Xiaobao , Bao Jingna , An Sheng , Hu Hongbin , Sha Tong , Huang Qiaobing , Li Tao , Zeng Zhenhua , Wang Xiang , Cai Shumin
Published: May 2024

Sepsis-induced acute kidney injury (SAKI) poses a significant clinical challenge with high morbidity and mortality. Excessive mitochondrial fission has been identified as the central pathogenesis of sepsis-associated organ damage, which is also implicated in the early stages of SAKI. Sirtuin 5 (SIRT5) has emerged as a central regulator of cellular mitochondrial function; however, its role in the regulation of sepsis-induced excessive mitochondrial fission in kidney and the underlying mechanism remains unclear. In this study, SAKI was modeled in mice through cecal ligation and puncture, and in human renal tubular epithelial (HK-2) cells stimulated with lipopolysaccharide (LPS), to mimic the cell SAKI model. Our findings revealed that septic mice with a SIRT5 knockout exhibited shortened survival times and elevated levels of renal injury compared to wild-type mice, suggesting the significant involvement of SIRT5 in SAKI pathophysiology. Additionally, we observed that SIRT5 depletion led to increased renal mitochondrial fission, while the use of a mitochondrial fission inhibitor (Mdivi-1) reversed the detrimental effects caused by SIRT5 depletion, emphasizing the pivotal role of SIRT5 in preventing excessive mitochondrial fission. In vitro experiments demonstrated that the overexpression of SIRT5 effectively mitigated the adverse effects of LPS on HK-2 cells viability and mitochondrial fission. Conversely, downregulation of SIRT5 decreased HK-2 cells viability and exacerbated LPS-induced mitochondrial fission. Mechanistically, the protective function of SIRT5 may be in part, ascribed to its desuccinylating action on ATPase inhibitory factor 1. In conclusion, this study provides novel insights into the underlying mechanisms of SAKI, suggesting the possibility of identifying future drug targets in terms of improved mitochondrial dynamics by SIRT5.
Central neural mechanisms of cancer cachexia
Authors: Yule Michael S. , Brown Leo R. , Skipworth Richard J. E. , Laird Barry J. A.
Published: May 2024

Purpose of review

Cachexia is a devasting syndrome which impacts a large number of patients with cancer. This review aims to provide a comprehensive overview of the central mechanisms of cancer cachexia. In particular, it focuses on the role of the central nervous system (CNS), the melanocortin system, circulating hormones and molecules which are produced by and act on the CNS and the psychological symptoms of cancer cachexia.

Recent findings

A growing body of evidence suggests that a central mechanism of action underpins this multi-system disorder. Recent research has focused on the role of neuroinflammation that drives the sickness behaviour seen in cancer cachexia, with emphasis on the role of the hypothalamus. Melanocortin receptor antagonists are showing promise in preclinical studies. There are also new pharmacological developments to overcome the short half-life of ghrelin. GDF-15 has been identified as a core target and trials of compounds that interfere with its signalling or its central receptor are underway.

Understanding the central mechanisms of cancer cachexia is pivotal for enhancing treatment outcomes in patients. While emerging pharmacological interventions targeting these pathways have shown promise, further research is essential.
Transcript profiling ofplastid ferrochelatase twomutants reveals that chloroplast singlet oxygen signals lead to global changes in RNA profiles and are mediated by Plant U-Box 4
Authors: Rai Snigdha , Lemke Matthew D. , Arias Anika M. , Mendez Maria F. Gomez , Dehesh Katayoon , Woodson Jesse D.
Published: May 2024

Background

In response to environmental stresses, chloroplasts generate reactive oxygen species, including singlet oxygen (1O2), an excited state of oxygen that regulates chloroplast-to-nucleus (retrograde) signaling, chloroplast turnover, and programmed cell death (PCD). Yet, the central signaling mechanisms and downstream responses remain poorly understood. TheArabidopsis thaliana plastid ferrochelatase two(fc2) mutant conditionally accumulates1O2and Plant U-Box 4 (PUB4), a cytoplasmic E3 ubiquitin ligase, is involved in propagating1O2signals for chloroplast turnover and cellular degradation. Thus, thefc2andfc2 pub4mutants are useful genetic tools to elucidate these signaling pathways. Previous studies have focused on the role of1O2in promoting cellular degradation infc2mutants, but its impact on retrograde signaling from mature chloroplasts (the major site of1O2production) is poorly understood.

Results

To gain mechanistic insights into1O2signaling pathways, we compared transcriptomes of adult wt,fc2, andfc2 pub4plants. The accumulation of1O2infc2plants broadly repressed genes involved in chloroplast function and photosynthesis, while inducing genes and transcription factors involved in abiotic and biotic stress, the biosynthesis of jasmonic acid (JA) and salicylic acid (SA), microautophagy, and senescence. Elevated JA and SA levels were observed in1O2-stressedfc2plants.pub4reversed most of this1O2-induced gene expression and reduced the JA content infc2plants. Thepub4mutation also blocked JA-induced senescence pathways in the dark. However, fc2 pub4 plantsmaintained constitutively elevated levels of SA even in the absence of bulk1O2accumulation.

Conclusions

Together, this work demonstrates that infc2plants,1O2leads to a robust retrograde signal that may protect cells by downregulating photosynthesis and ROS production while simultaneously mounting a stress response involving SA and JA. The induction of microautophagy and senescence pathways indicate that1O2-induced cellular degradation is a genetic response to this stress, and the bulk of this transcriptional response is modulated by the PUB4 protein. However, the effect ofpub4on hormone synthesis and signaling is complex and indicates that an intricate interplay of SA and JA are involved in promoting stress responses and programmed cell death during photo-oxidative damage.
Deep phenotyping of the prostate tumor microenvironment reveals molecular stratifiers of relapse linked to inflammatory chemokine expression and aberrant metabolism
Authors: Krossa Sebastian , Andersen Maria K. , Midtbust Elise , Wess Maximilian , Kiviaho Antti , Sharma Abhibhav , Viset Trond , Størkersen Øystein , Giskeødegård Guro F. , Nykter Matti , Urbanucci Alfonso , Rye Morten B. , Tessem May-Britt
Published: May 2024

Understanding the molecular characteristics and changes of the tumor microenvironment (TME) associated with aggressive prostate cancer (PCa) is essential for precise diagnosis and treatment. We interrogated spatially resolved integrated transcriptomics and metabolomics data to build molecular strafiers discriminating patients with aggressive, potentially relapsing, and metastasizing PCa. We report a relapse associated (RA) gene expression signature characterized by upregulated immune response related gene expression scoring high in cancer, stroma, and glandular tissue of relapsing patients. Further, we identified a signature specific to a distinct sub-group of morphologically non-cancerous glands in prostate tissue from patients with relapsing cancer. This signature, named chemokine-enriched-gland (CEG) signature, was characterized by upregulated gene expression of pro-inflammatory chemokines. Glands with a high CEG score were enriched for club-like cells and surrounding stroma was infiltrated by immune cells. Tissue regions scoring high for both CEG and RA signatures were associated with reduced levels of citrate and zinc and loss of normal prostate secretory gland functions via reduced expression of genes necessary for citrate secretion. In summary we report that aggressive PCa is associated with an increased inflammatory status linked to chemokine production and club-like cell enrichment in potentially pre-cancerous prostate glands displaying an aberrant metabolism.
Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells
Authors: van Bentum Mirjam , Klinger Bertram , Sieber Anja , Lehmann Nadine , Naghiloo Sheyda , Haji Mohamed , Niquet Sylvia , Mertins Philipp , Blüthgen Nils , Selbach Matthias
Published: May 2024

Targeted kinase inhibitors are a cornerstone of cancer therapy, but their success is often hindered by the complexity of cellular signaling networks that can lead to resistance. Overcoming this challenge necessitates a deep understanding of cellular signaling responses. While standard global phosphoproteomics offers extensive insights, lengthy processing times, the complexity of data interpretation, and frequent omission of crucial phosphorylation sites limit its utility. Here, we combine data-independent acquisition (DIA) with spike-in of synthetic heavy stable isotope-labeled phosphopeptides to facilitate the targeted detection of particularly informative phosphorylation sites. Our spike-in enhanced detection in DIA (SPIED-DIA) approach integrates the improved sensitivity of spike-in-based targeted detection with the discovery potential of global phosphoproteomics into a simple workflow. We employed this method to investigate synergistic signaling responses in colorectal cancer cell lines following MEK inhibition. Our findings highlight that combining MEK inhibition with growth factor stimulation synergistically activates JNK signaling in HCT116 cells. This synergy emphasizes the therapeutic potential of concurrently targeting MEK and JNK pathways, as evidenced by the significantly impaired growth of HCT116 cells when treated with both inhibitors. Our results demonstrate that SPIED-DIA effectively identifies synergistic signaling responses in colorectal cancer cells, presenting a valuable tool for uncovering new therapeutic targets and strategies in cancer treatment.
Fundamental transport mechanism of mucin-2 ER-to-Golgi trafficking identifies source of ER stress in inflammatory bowel disease
Authors: Morsink Margaretha A.J. , Koch Lena S. , Hu Shixian , Weersma Rinse K. , van Goor Harry , Bourgonje Arno R. , Broersen Kerensa
Published: May 2024

The intestinal mucous layer relies on mucin-2 secretion. While the mucin-2 secretory pathway has been studied, endoplasmic reticulum (ER) to Golgi apparatus (Golgi) trafficking remains poorly understood. The size of mucin-2 exceeds the capacity of regular coat protein complex II (COPII) vesicles, responsible for ER-to-Golgi transport. After confirming conventional secretion of mucin-2, we showed that COPII vesicle enlargement is facilitated by TANGO1 and cTAGE5, and promoted by KLHL12. Inflammatory bowel disease (IBD) is characterized by a compromised mucous layer, altered activity of Transforming Growth Factor β (TGF-β), and increased ER stress. Using a cell culture, we showed that TGF-β inhibition induces TANGO1-mediated ER stress. Mucosal gene expression analysis in IBD patients confirmed elevated ER stress and validated concomitantly altered mRNA levels of TGF-β with mucin-2 and transport proteins TANGO1 and cTAGE5. In conclusion, we propose that the unsuccessful formation of enlarged COPII vesicles could be a source of ER stress in IBD, because of lowered TANGO1 protein expression, subsequently leading to decreased mucin-2 secretion.
CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis
Authors: Xiao Yihang , Liu Jinyi , Zheng Yan , Xie Xiaohan , Hao Jianye , Li Mingzhi , Wang Ruitao , Ni Fei , Li Yuxiao , Luo Jintian , Jiao Shaoqing , Peng Jiajie
Published: May 2024

Single-cell RNA sequencing (scRNA-seq) data analysis is crucial for biological research, as it enables the precise characterization of cellular heterogeneity. However, manual manipulation of various tools to achieve desired outcomes can be labor-intensive for researchers. To address this, we introduce CellAgent (http://cell.agent4science.cn/), an LLM-driven multi-agent framework, specifically designed for the automatic processing and execution of scRNA-seq data analysis tasks, providing high-quality results with no human intervention. Firstly, to adapt general LLMs to the biological field, CellAgent constructs LLM-driven biological expert roles—planner, executor, and evaluator—each with specific responsibilities. Then, CellAgent introduces a hierarchical decision-making mechanism to coordinate these biological experts, effectively driving the planning and step-by-step execution of complex data analysis tasks. Furthermore, we propose a self-iterative optimization mechanism, enabling CellAgent to autonomously evaluate and optimize solutions, thereby guaranteeing output quality. We evaluate CellAgent on a comprehensive benchmark dataset encompassing dozens of tissues and hundreds of distinct cell types. Evaluation results consistently show that CellAgent effectively identifies the most suitable tools and hyperparameters for single-cell analysis tasks, achieving optimal performance. This automated framework dramatically reduces the workload for science data analyses, bringing us into the “Agent for Science” era.
Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells
Authors: Haberman Nejc , Cheung Rebecca , Pizza Grazia , Cvetesic Nevena , Nagy Dorka , Maude Hannah , Blazquez Lorea , Lenhard Boris , Cebola Inês , Rutter Guy A. , Martinez-Sanchez Aida
Published: May 2024

Liver kinase B1 (LKB1/STK11) is an important regulator of pancreatic β-cell identity and function. Elimination ofLkb1from the β-cell results in improved glucose-stimulated insulin secretion and is accompanied by profound changes in gene expression, including the upregulation of several neuronal genes. The mechanisms through which LKB1 controls gene expression are, at present, poorly understood. Here, we explore the impact of β cell- selective deletion ofLkb1on chromatin accessibility in mouse pancreatic islets. To characterize the role of LKB1 in the regulation of gene expression at the transcriptional level, we combine these data with a map of islet active transcription start sites and histone marks. We demonstrate that LKB1 elimination from β-cells results in widespread changes in chromatin accessibility, correlating with changes in transcript levels. Changes occurred in hundreds of promoter and enhancer regions, many of which were close to neuronal genes. We reveal that dysregulated enhancers are enriched in binding motifs for transcription factors important for β-cell identity, such as FOXA, MAFA or RFX6 and we identify microRNAs (miRNAs) that are regulated by LKB1 at the transcriptional level. Overall, our study provides important new insights into the epigenetic mechanisms by which LKB1 regulates β-cell identity and function.
A Novel Mutation in LXRα Uncovers a Role for Cholesterol Sensing in Limiting Metabolic Dysfunction-Associated Steatohepatitis (MASH)
Authors: Clark Alexis T. , Russo-Savage Lillian , Ashton Luke A. , Haghshenas Niki , Schulman Ira G.
Published: May 2024

Liver x receptor alpha (LXRα, Nr1h3) functions as an important intracellular cholesterol sensor that regulates fat and cholesterol metabolism at the transcriptional level in response to the direct binding of cholesterol derivatives. We have generated mice with a mutation in LXRα that reduces activity in response to endogenous cholesterol derived LXR ligands while still allowing transcriptional activation by synthetic agonists. The mutant LXRα functions as a dominant negative that shuts down cholesterol sensing. When fed a high fat, high cholesterol diet LXRα mutant mice rapidly develop pathologies associated with Metabolic Dysfunction-Associated Steatohepatitis (MASH) including ballooning hepatocytes, liver inflammation, and fibrosis. Strikingly LXRα mutant mice have decreased liver triglycerides but increased liver cholesterol. Therefore, MASH-like phenotypes can arise in the absence of large increases in triglycerides. Reengaging LXR signaling by treatment with synthetic agonist reverses MASH suggesting that LXRα normally functions to impede the development of liver disease.
Unveiling Conserved Allosteric Hot Spots in Protein Domains from Sequences
Authors: Hacisuleyman Aysima , Fasshauer Dirk
Published: May 2024

The amino acid sequence determines the structure, function, and dynamics of a protein. In recent years, enormous progress has been made in translating sequence information into 3D structural information using artificial intelligence. However, because of the underlying methodology, it is an immense computational challenge to extract this information from the ever-increasing number of sequences. In the present study, we show that it is possible to create 2D contact maps from sequences, for which only a few exemplary structures are available on a laptop without the need for GPUs. This is achieved by using a pattern-matching approach. The resulting contact maps largely reflect the interactions in the 3D structures and contain information about its function and dynamics. This approach was used to explore the evolutionarily conserved allosteric mechanisms and identify the source– sink (driver-driven) relationships by using an established method that combines Schreiber’s concept of entropy transfer with a simple Gaussian network model. The validity of our method was tested on the DHFR, PDZ, SH3, and S100 domains, with our predictions consistently aligning with the experimental findings.
Brain-specificGata4downregulation inGreywickfemale mice models the metabolic subtype of polycystic ovary syndrome
Authors: Nawaito Sherin A. , Esmael Mostafa , Souchkova Ouliana , Cardinal Tatiana , Bernas Guillaume , Bergeron Karl-F. , Gayda Fanny , Bergeron Francis , Bouchard Marie-France , Zhou Xiang , Ongaro Luisina , Bernard Daniel J. , Short Jacob , Wray Susan , Viger Robert S. , Mounier Catherine , Pilon Nicolas
Published: May 2024

Polycystic ovary syndrome (PCOS) is a heterogenous disorder characterized by reproductive and metabolic abnormalities. PCOS etiology remains poorly understood, although the hypothalamus is suspected to play a central role in many cases. Human genetic studies have also shown an association with the transcription factor-coding geneGATA4, but without providing a functional link. Here, we show that adultGreywickfemale mice may bridge this gap. These mice phenocopy PCOS with partial penetrance, due to serendipitous insertion of aGata4promoter-driven transgene in a strong enhancer region. Resulting robust transgene expression in subsets of hypothalamic neurons and glia impairs endogenousGata4expression, resulting in misexpression of genes linked to the control of fertility and food intake. We also show that this previously overlooked role of GATA4 in the hypothalamus can be replicated by conditional knockout approaches. Overall, this study sheds light not only on PCOS etiology but also on the role played by GATA4 in the central control of reproduction.
The role of mu-opioid receptors in pancreatic islet alpha cells
Authors: Kong Chen , Castro Daniel C. , Lee Jeongmin , Piston David W.
Published: May 2024

30% of people in the United States have diabetes or pre-diabetes. Many of these individuals will develop diabetic neuropathy as a comorbidity, which is often treated with exogenous opioids like morphine, oxycodone, or tramadol. Although these opioids are effective analgesics, growing evidence indicates that they may directly impact the endocrine pancreas function in human and preclinical models. One common feature of these exogenous opioid ligands is their preference for the mu opioid receptor (MOPR), so we aimed to determine if endogenous MOPRs directly regulate pancreatic islet metabolism and hormone secretion. We show that pharmacological antagonism of MOPRs enhances glucagon secretion, but not insulin secretion, from human islets under high glucose conditions. This increased secretion is accompanied by increased cAMP signaling. mRNA expression of MOPRs is enriched in human islet α-cells, but downregulated in T2D islet donors, suggesting a link between metabolism and MOPR expression. Conditional genetic knockout of MOPRs in murine α-cells increases glucagon secretion in high glucose conditions without increasing glucagon content. Consistent with downregulation of MOPRs during metabolic disease, conditional MOPR knockout mice treated with a high fat diet show impaired glucose tolerance, increased glucagon secretion, increased insulin content, and increased islet size. Finally, we show that MOPR-mediated changes in glucagon secretion are driven, in part, by KATPchannel activity. Together, these results demonstrate a direct mechanism of action for endogenous opioid regulation of endocrine pancreas.
Rab7 deficiency induces lysosome formation from recycling endosomes leading to an increased degradation of cell surface proteins
Authors: Wang Guan M , Xu Peng , Yu Kaikai , Guo Shiny Shengzhen , Faessler Reinhard
Published: May 2024

Cell surface receptors such as integrins are repeatedly internalized from and recycled back to the plasma membrane before routed to lysosomes for degradation. In search for modulators of β1 integrin surface stability, we identified the Rab7 small GTPase, believed to be required for lysosome biogenesis, as integrin stabilizer. We show that Rab7 deficiency produces late endosomes and lysosomes with acidic pH, lysosome-specific proteins and membrane architectures that are functional in protein degradation and organelle fusion. Furthermore, Rab7-deficient lysosomes form from Rab4- and transferrin receptor-positive recycling endosomes, resulting in the degradation of proteins designated for recycling. Finally, we also found that overexpression of Rab4 can direct lysosome formation from recycling endosomes in absence as well as presence of Rab7, however, the latter to a much lesser extent. Our findings reveal a lysosome biogenesis and lysosomal protein degradation pathway that becomes dominant in absence of Rab7 or when Rab4 is highly abundant.
Multi-omics phenotyping characterizes molecular divergence underlying different clinical scenarios of inflammatory bowel disease
Authors: Tien Nguyen Tran Nam , Choi Eun Jeong , Thu Nguyen Quang , Yu Seung Jung , Nguyen Duc Ninh , Kim Dong Hyun , Long Nguyen Phuoc , Lee Hong Sub
Published: May 2024

Clinically heterogeneous spectrum and molecular phenotypes of inflammatory bowel disease (IBD) remain to be comprehensively elucidated. This study set out to explore the serum molecular profiles (I) of IBD subtypes; in association with (II) elevated fecal calprotectin and (III) disease activity states; (IV) upon treatment escalation; and (V) in patients who needed treatment escalation. The serum proteome, metabolome, and lipidome of 75 treated IBD patients were profiled. Single- and multi-omic data analysis was performed to determine differential analytes and integrative biosignatures. (I) Chronic inflammation, and phosphatidylcholine and bile acid homeostasis disturbances underlined the differences between Crohn’s disease (CD) and ulcerative colitis. (II) Elevated calprotectin was associated with higher levels of inflammatory proteins and sphingomyelins (SM) and lower levels of bile acids, amino acids, and triacylglycerols (TG). Relative to patient remission, active disease state (III) was characterized by decreased SMs and increased inflammatory proteins and TGs. (IV) Treatment escalation was associated with augmented levels of inflammatory response-related proteins and reduced levels of amino acids. Most TG species increased in the post-treatment escalation. Moreover, needed-treatment-escalation patients had significantly lower levels of TGs (V). They also showed increased SMs and decreased signaling receptor binding proteins. Multi-omics analysis revealed biosignatures that captured the differences between groups of each scenario. Eight analytes, including NFASC, ANGPTL4, and chenodeoxycholate, were found in at least three biosignatures. Collectively, disturbances in immune response, bile acid homeostasis, amino acids, and lipids alteration potentially underlie the clinically heterogeneous spectrum of IBD.
A Postdoctoral Training Program in Bioimage Analysis
Authors: Cimini Beth A , Tromans-Coia Callum , Stirling David , Sivagurunathan Suganya , Senft Rebecca , Ryder Pearl , Miglietta Esteban , Llanos Paula , Jamali Nasim , Diaz-Rohrer Barbara , Dasgupta Shatavisha , Cruz Mario , Weisbart Erin , Carpenter Anne E
Published: May 2024

We herein describe a postdoctoral training program designed to train biologists with microscopy experience in bioimage analysis. We detail the rationale behind the program, the various components of the training program, and outcomes in terms of works produced and the career effects on past participants. We analyze the results of an anonymous survey distributed to past and present participants, indicating overall high value of all 12 rated aspects of the program, but significant heterogeneity in which aspects were most important to each participant. Finally, we propose this model as a template for other programs which may want to train experts in professional skill sets, and discuss the important considerations when running such a program. We believe that such programs can have extremely positive impact for both the trainees themselves and the broader scientific community.
Magnetically Steered Cell Therapy For Functional Restoration Of Intraocular Pressure Control In Open-Angle Glaucoma
Authors: Fard M. Reza Bahrani , Chan Jessica , Read A. Thomas , Li Guorong , Cheng Lin , Safa Babak N. , Siadat Seyed Mohammad , Jhunjhunwala Anamik , Grossniklaus Hans E. , Emelianov Stanislav Y. , Stamer W. Daniel , Kuehn Markus H. , Ethier C. Ross
Published: May 2024

Trabecular meshwork (TM) cell therapy has been proposed as a next-generation treatment for elevated intraocular pressure (IOP) in glaucoma, the most common cause of irreversible blindness. Using a magnetic cell steering technique with excellent efficiency and tissue-specific targeting, we delivered two types of cells into a mouse model of glaucoma: either human adipose-derived mesenchymal stem cells (hAMSCs) or induced pluripotent cell derivatives (iPSC-TM cells). We observed a 4.5 [3.1, 6.0] mmHg or 27% reduction in intraocular pressure (IOP) for nine months after a single dose of only 1500 magnetically-steered hAMSCs, associated with restoration of function to the conventional outflow pathway, as judged by increased outflow facility and TM cellularity. iPSC-TM cells were also effective, but less so, showing only a 1.9 [0.4, 3.3] mmHg or 13% IOP reduction and increased risk of tumorigenicity. In both cases, injected cells remained detectable in the iridocorneal angle three weeks post-transplantation. Based on the locations of the delivered cells, the mechanism of IOP lowering is most likely paracrine signaling. We conclude that magnetically-steered hAMSC cell therapy has potential for long-term treatment of ocular hypertension in glaucoma.

One Sentence Summary

A novel magnetic cell therapy provided effective intraocular pressure control in a mouse model of glaucoma, motivating future translational studies.
Sodium/Potassium ATPase Alpha 1 Subunit Fine-tunes Platelet GPCR Signaling Function and is Essential for Thrombosis
Authors: Li Oliver Q. , Yue Hong , DeHart Autumn R. , Roytenberg Renat , Aguilar Rodrigo , Olanipekun Olalekan , Bai Fang , Liu Jiang , Fedorova Olga , Kennedy David , Thompson Ellen , Pierre Sandrine V. , Li Wei
Published: May 2024

Background

Thrombosis is a major cause of myocardial infarction and ischemic stroke. The sodium/potassium ATPase (NKA), comprising α and β subunits, is crucial in maintaining intracellular sodium and potassium gradients. However, the role of NKA in platelet function and thrombosis remains unclear.

Methods

We utilized wild-type (WT, α1+/+) and NKA α1 heterozygous (α1+/-) mice, aged 8 to 16 weeks, of both sexes. An intravital microscopy-based, FeCl3-induced carotid artery injury thrombosis model was employed for in vivo thrombosis assessment. Platelet transfusion assays were used to evaluate platelet NKA α1 function on thrombosis. Human platelets isolated from healthy donors and heart failure patients treated with/without digoxin were used for platelet function and signaling assay. Complementary molecular approaches were used for mechanistic studies.

Results

NKA α1 haplodeficiency significantly reduced its expression on platelets without affecting sodium homeostasis. It significantly inhibited 7.5% FeCl3-induced thrombosis in male but not female mice without disturbing hemostasis. Transfusion of α1+/-, but not α1+/+, platelets to thrombocytopenic WT mice substantially prolonged thrombosis. Treating WT mice with low-dose ouabain or marinobufagenin, both binding NKA α1 and inhibiting its ion-transporting function, markedly inhibited thrombosis in vivo. NKA α1 formed complexes with leucine-glycine-leucine (LGL)-containing platelet receptors, including P2Y12, PAR4, and thromboxane A2 receptor. This binding was significantly attenuated by LGL>SFT mutation or LGL peptide. Haplodeficiency of NKA α1 in mice or ouabain treatment of human platelets notably inhibited ADP-induced platelet aggregation. While not affecting 10% FeCl3-induced thrombosis, NKA α1 haplodeficiency significantly prolonged thrombosis time in mice treated with an ineffective dose of clopidogrel.

Conclusion

NKA α1 plays an essential role in enhancing platelet activation through binding to LGL-containing platelet GPCRs. NKA α1 haplodeficiency or inhibition with low-dose ouabain and marinobufagenin significantly inhibited thrombosis and sensitized clopidogrel’s anti-thrombotic effect. Targeting NKA α1 emerges as a promising antiplatelet and antithrombotic therapeutic strategy.
Gill ionocyte remodeling mediates blood pH regulation in rockfish (Sebastes diploproa) exposed to environmentally relevant hypercapnia
Authors: Kwan Garfield T. , Clifford Alexander M. , Prime Kaelan J. , Harter Till S. , Tresguerres Martin
Published: May 2024

Marine fishes excrete excess H+using basolateral Na+/K+-ATPase (NKA) and apical Na+/H+-exchanger 3 (NHE3) in gill ionocytes. However, the mechanisms that regulate H+excretion during exposure to environmentally relevant hypercapnia (ERH) remain poorly understood. Here, we explored transcriptomic, proteomic, and cellular responses in gills of juvenile splitnose rockfish (Sebastes diploproa) exposed to three days of ERH conditions (pH ∼7.5; ∼1,600 μatmpCO2). Blood pH was fully regulated at ∼7.75 despite a lack of significant changes in gill (1) mRNAs coding for proteins involved in blood acid-base regulation, (2) total NKA and NHE3 protein abundance, and (3) ionocyte density. However, ERH-exposed rockfish demonstrated increased NKA and NHE3 abundance on the ionocyte plasma membrane coupled with wider apical membranes and greater extension of apical microvilli. The observed gill ionocyte remodeling is consistent with enhanced H+excretion that maintains blood pH homeostasis during exposure to ERH and does not necessitate changes at the expression or translation levels. These mechanisms of phenotypic plasticity may allow fishes to regulate blood pH during environmentally relevant acid-base challenges, and thus have important implications for both understanding how organisms respond to climate change and for selecting appropriate metrics to evaluate its impact on marine ecosystems.
Plastic microfibers found in high numbers around Kantamanto, the world’s largest secondhand textile market in Accra, Ghana
Authors: Deheyn Dimitri D. , Ayesu Joe ,   The Or Foundation, Skinner Branson
Published: May 2024

Located in Accra (Ghana), Kantamanto is the world’s largest secondhand textile market where tons of garments are exported every week by Global North countries, including the USA, Canada, the UK, the EU27, China and South Korea. We looked at the abundance of microfibers from textiles in this very dynamic environment. Continuous monitoring of air quality using PurpleAir sensors showed large numbers of airborne particles around the market, which were shown to drop with rain events. Rainwater was collected and shown to contain dozens to hundreds of microfibers and microplastics, depending on the intensity of the rain and on whether dry weather preceded the rain. The first hour of rain seemed to bring down the larger numbers of airborne microfibers, especially if it had not rained for 3-4 days. Microfiber and microplastics counts from airborne samples showed numbers about >20x to >100x greater than those reported from other mega-cities, respectively. Comparison of these counts from water of the adjacent Korle Lagoon was similarly striking, with about >100x more microfibers and >200x more microplastics than reported for coastal waters around the world. The impacts of garments were also demonstrated beyond the microscale, with a strong similarity of global brand assemblages in the textile waste found in the market and on the nearby beaches.
Engineered Cardiac Microtissue Biomanufacturing Using Human Induced Pluripotent Stem Cell Derived Epicardial Cells
Authors: Butler Kirk , Ahmed Saif , Jablonski Justin , Hookway Tracy A.
Published: May 2024

Epicardial cells are a crucial component in constructingin vitro3D tissue models of the human heart, contributing to the ECM environment and the resident mesenchymal cell population. Studying the human epicardium and its development from the proepicardial organ is difficult, but induced pluripotent stem cells can provide a source of human epicardial cells for developmental modeling and for biomanufacturing heterotypic cardiac tissues. This study shows that a robust population of epicardial cells (approx. 87.7% WT1+) can be obtained by small molecule modulation of the Wnt signaling pathway. The population maintains WT1 expression and characteristic epithelial morphology over successive passaging, but increases in size and decreases in cell number, suggesting a limit to their expandability in vitro. Further, low passage number epicardial cells formed into more robust 3D microtissues compared to their higher passage counterparts, suggesting that the ideal time frame for use of these epicardial cells for tissue engineering and modeling purposes is early on in their differentiated state. Additionally, the differentiated epicardial cells displayed two distinct morphologic sub populations with a subset of larger, more migratory cells which led expansion of the epicardial cells across various extracellular matrix environments. When incorporated into a mixed 3D co-culture with cardiomyocytes, epicardial cells promoted greater remodeling and migration without impairing cardiomyocyte function. This study provides an important characterization of stem cell-derived epicardial cells, identifying key characteristics that influence their ability to fabricate consistent engineered cardiac tissues.
A microscopy reporter for cGAMP reveals rare cGAS activation following DNA damage, and a lack of correlation with micronuclear cGAS enrichment
Authors: Lebrec Vivianne , Afshar Negar , Davies Lauren R. , Kujirai Tomoya , Kanellou Alexandra , Tidu Federico , Zierhut Christian
Published: May 2024

Cyclic GMP-AMP (cGAMP) synthase (cGAS) is the primary intracellular responder to pathogen DNA. Upon DNA-binding, cGAS generates cGAMP, which binds to STING, ultimately driving inflammatory signalling. Although normally silenced on self-DNA, cGAS can be activated during genotoxic stress. A universal by-product of these conditions are micronuclei, which accumulate cGAS, and which are therefore thought to be major cGAS activators. However, due to the inability to visualise cGAS activation in single cells, this hypothesis remains largely untested. Here we solve this question with an improved intracellular cGAMP reporter, which is compatible with microscopy, flow-cytometry and plate reader setups. Surprisingly, cGAS activation in response to multiple types of genotoxic stress is limited to a subfraction of cells and does not correlate with cGAS enrichment in micronuclei. Overall, our findings suggest a revised model of innate immune signalling in response to genotoxic stress, and introduce a novel and flexible tool with which to examine this model in future.
Differential effects of aging and epilepsy in discriminating and reactivating memories
Authors: Tai Xin You , Sen Arjune , Husain Masud , Manohar Sanjay
Published: May 2024

Pattern separation and pattern completion are distinct neurocognitive processes involved in encoding and retrieval of memories. However, there is currently no robust behavioural task in humans to measure both processes within the same paradigm. We describe the Memory Pinhole task, a novel paradigm which offers a distinct measure of each process, applied to healthy young, healthy older and people with epilepsy. Both pattern separation and pattern completion are observed in healthy younger individuals. A pattern completion deficit is seen in people with epilepsy, while the healthy older cohort show a deficit in pattern separation. To understand the neural mechanisms, we simulated human performance using an auto-associative neural network. Modelling indicated that disruption in different neuronal populations could explain the distinct memory profiles observed in ageing and epilepsy. These results demonstrate that pattern separation and pattern completion are distinct processes that can be measured from a single behavioural task and are differentially affected by ageing and epilepsy.
Epigenetic control of CD8+T cell tissue homing and tissue resident memory T cell precursors by the histone methyltransferase SUV39H1
Authors: Suarez Guadalupe , Heurtebise-Chrétien Sandrine , Bonté Pierre-Emmanuel , Beuchet Héloïse , Fuentealba Jaime , Goudot Christel , Lantz Olivier , Amigorena Sebastian
Published: May 2024

Activation of CD8+ T cells leads to the differentiation of short-lived terminal effectors and memory precursors. Some of these memory precursors remain in lymphoid organs and become long-lived central memory T cells (TCM), while others home to non-lymphoid peripheral tissues early after antigen recognition and differentiate into tissue resident memory T cells (TRM). The early stages of memory precursor tissue homing and TRMdifferentiation remain poorly understood. We show here that at steady state, during space-induced “homeostatic” expansion, and after flu infection, deletion of the histone 3-lysine 9 methyltransferase SUV39H1 in CD8+T cells, increases the homing to non-lymphoid tissues (including liver, lungs, gut and skin). SUV39H1-defective cells in tissues express CD49d and differentiate into CD69+/CD103-TRMafter adoptive transfer or Flu infection. SUV39H1-defective T cells that accumulate in lungs are fully functional in both Flu re-infection and lung tumor models. We conclude that SUV39H1 restrains CD8+T cell tissue homing and TRMdifferentiation in WT mice. These results should encourage the use of SUV39H1-depletion in the context of adoptive T cell therapies to enhance tissue homing, thereby optimizing the efficiency of target cell eradication and long-term protection in the context of infection and cancer.
GenAI Exceeds Clinical Experts in Predicting Acute Kidney Injury following Paediatric Cardiopulmonary Bypass2
Authors: Sharabiani Mansour , Mahani Alireza , Bottle Alex , Srinivasan Yadav , Issitt Richard , Stoica Serban
Published: May 2024

The emergence of large language models (LLMs) offers new opportunities to leverage, often unused, information in clinical text. This study examines the utility of text embeddings generated by LLMs in predicting postoperative acute kidney injury (AKI) in paediatric cardiopulmonary bypass (CPB) patients using electronic health record (EHR) text, and to explore methods for explaining their output. AKI is a significant complication in paediatric CPB and its prediction can significantly improve patient outcomes by enabling timely interventions. We evaluate various text embedding algorithms such as Doc2Vec, top-performing sentence transformers on Hugging Face, and commercial LLMs from Google and OpenAI. We benchmark the out-of-sample predictive performance of these ‘AI models’ against a ‘baseline model’ as well as an established clinically-defined ‘expert model’. The baseline model includes patient gender, age, height, body mass index and length of operation. The majority of AI models surpass, not only the baseline model, but also the expert model. An ensemble of AI and clinical-expert models improves discriminative performance by nearly 23% compared to the baseline model. Consistency of patient clusters formed from AI-generated embeddings with clinical-expert clusters - measured via the adjusted rand index and adjusted mutual information metrics - illustrates their medical validity. We use text-generating LLMs to explain the output of embedding LLMs, e.g., by summarising the differences between AI and expert clusters, and/or by providing descriptive labels for the AI clusters. Such ‘explainability’ can increase medical practitioners’ trust in the AI applications, and help generate new hypotheses, e.g., by correlating cluster memberships with outcomes of interest.

Highlights

LLMs outperform clinical experts in predicting risk of AKI after paediatric CPB.

LLMs generate clinically plausible explanations and hypotheses using embeddings.

Successful application of LLMs in paediatric CPB suggests potential in other specialised fields.

Fine-tuning LLMs on domain data and forming ensembles of AI and clinical experts may boost accuracy.