bluuebunny/crossref_metadata_2025 huggingface dataset:
Data Driven Approach to Characterize Rapid Decline in Autosomal Dominant Polycystic Kidney Disease
Authors: Sim John J. , Shu Yu-Hsiang , Bhandari Simran K. , Chen Qiaoling , Harrison Teresa N. , Lee Min Young , Munis Mercedes A. , Morrissette Kerresa , Sundar Shirin , Pareja Kristin , Nourbakhsh Ali , Willey Cynthia J.
Published: January 2024

Background

Autosomal dominant polycystic kidney disease (ADPKD) is a genetic kidney disease with high phenotypic variability. Insights into ADPKD progression could lead to earlier detection and management prior to end stage kidney disease (ESKD). We sought to identify patients with rapid decline (RD) in kidney function and to determine clinical factors associated with RD using a data-driven approach.

Methods

A retrospective cohort study was performed among patients with incident ADPKD (1/1/2002-12/31/2018). Latent class mixed models were used to identify RD patients using rapidly declining eGFR trajectories over time. Predictors of RD were selected based on agreements among feature selection methods, including logistic, regularized, and random forest modeling. The final model was built on the selected predictors and clinically relevant covariates.

Results

Among 1,744 patients with incident ADPKD, 125 (7%) were identified as RD. Feature selection included 42 clinical measurements for adaptation with multiple imputations; mean (SD) eGFR was 85.2 (47.3) and 72.9 (34.4) in the RD and non-RD groups, respectively. Multiple imputed datasets identified variables as important features to distinguish RD and non-RD groups with the final prediction model determined as a balance between area under the curve (AUC) and clinical relevance which included 6 predictors: age, sex, hypertension, cerebrovascular disease, hemoglobin, and proteinuria. Results showed 72%-sensitivity, 70%-specificity, 70%-accuracy, and 0.77-AUC in identifying RD. 5-year ESKD rates were 38% and 7% among RD and non-RD groups, respectively.

Conclusion

Using real-world routine clinical data among patients with incident ADPKD, we observed that six variables highly predicted RD in kidney function.
Analysis of Repeated Measurements of HIV Viral Load as a Continuous Variable while Accounting for Missing Values
Authors: Sendege Susan Habert , Omala Saint Kizito , Wandiembe Symon Peter , Dumba Isaac
Published: January 2024

Recent HIV research predominantly uses Single Measure Frameworks (SMF), focusing solely on the latest viral load data and overlooking missing values. This study explored repeated measures frameworks to assess factors affecting viral load copies while accounting for missing data. The analysis involved 1670 records of HIV patients,using the generalized linear mixed models (GLMM). All variables, except for treatment regimen changes and adherence rating, were recorded at patients’ treatment enrollment. A GLMM was applied to data before and after imputation accounting for the repeated nature of the HIV viral load copies over time. The best-fitting model, selected for discussion, was the GLMM fitted to multiply imputed data. Gender and adherence rating did not significantly affect viral load copies. The analysis included other variables such as patient age, marital status, treatment duration, WHO clinical stages, and facility ownership. Results show that viral load copies were higher among currently or formerly married individuals (β= 0.49, 0.30;SE= 0.042, 0.052;p= 0.0000). In contrast, viral load copies were lower for patients with longer treatment durations (β= −0.01;SE= 0.001;p= 0.0000) and those receiving treatment at a private facility (β= −0.196;SE= 0.077;p= 0.0000). The study highlights the significance of recognizing repeated data patterns in longitudinal settings and addressing missing values in health research. It proposes a similar investigation in controlled environments to evaluate SMF and RMF in presence of missing values.

Author summary

This work was conceptualized by, Susan Habert Sendege. The author was responsible for the initial drafting of the paper, including the analysis, discussion, conclusions, and recommendations. Saint Kizito and Symon Peter played a pivotal role in shaping the study and all provided numerous hours of time for proofreading and editing.
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofSF3B1mutations
Authors: Pacholewska Alicja , Lienhard Matthias , Brüggemann Mirko , Hänel Heike , Bilalli Lorina , Königs Anja , Becker Kerstin , Köhrer Karl , Kaiser Jesko , Gohlke Holger , Gattermann Norbert , Hallek Michael , Herling Carmen D. , König Julian , Grimm Christina , Herwig Ralf , Zarnack Kathi , Schweiger Michal R.
Published: January 2024

Background

Mutations in splicing factor 3B subunit 1 (SF3B1) frequently occur in patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDS). These mutations have a different effect on the disease prognosis with beneficial effect in MDS and worse prognosis in CLL patients. A full-length transcriptome approach can expand our knowledge onSF3B1mutation effects on RNA splicing and its contribution to patient survival and treatment options.

Results

We applied long-read transcriptome sequencing to 44 MDS and CLL patients with and withoutSF3B1mutations and found > 60% of novel isoforms. Splicing alterations were largely shared between cancer types and specifically affected the usage of introns and 3’ splice sites. Our data highlighted a constrained window at canonical 3’ splice sites in which dynamic splice site switches occurred inSF3B1-mutated patients. Using transcriptome-wide RNA binding maps and molecular dynamics simulations, we showed multimodal SF3B1 binding at 3’ splice sites and predicted reduced RNA binding at the second binding pocket of SF3B1K700E.

Conclusions

Our work presents the hitherto most complete long-read transcriptome sequencing study in CLL and MDS and provides a resource to study aberrant splicing in cancer. Moreover, we showed that different disease prognosis results most likely from the different cell types expanded during cancerogenesis rather than different mechanism of action of the mutatedSF3B1. These results have important implications for understanding the role ofSF3B1mutations in hematological malignancies and other related diseases.

Highlights

Long-read transcriptome sequencing data enables the identification of > 60% of novel isoforms in the transcriptomes of CLL and MDS patients and isogenic cell lines.

SF3B1mutations trigger common splicing alterations uponSF3B1mutations across patient cohorts, most frequently decreased intron retention and increased alternative 3’ splice site usage.

Mutation effect depends on alternative 3’ splice site and branch point positioning that coincide with bimodal SF3B1 binding at these sites

Molecular dynamics simulations predict reduced binding of SF3B1K700Eto mRNA at the second binding pocket harboring the polypyrimidine tract.
The nunatak andtabula rasahypotheses may be compatible: the European phylogeography of a riparian earthworm
Authors: de Sosa Irene , Marchán Daniel F , Erséus Christer , Lapied Emmanuel , Jelic Misel , Jabłońska Aleksandra , Szederjesi Timea , Almodóvar Ana , Novo Marta , Cosín Darío Díaz
Published: January 2024

Thetabula rasahypothesis of postglacial immigration supports the notion that species now found in northern European areas must have been recently recolonized from historical refugia. Until the 1960s, however, there was almost complete consensus that disjunctions and endemism in the North Atlantic region of Europe could not be explained without in situ survival during glacial periods (the nunatak hypothesis). Although some earthworms can survive in permafrost and tolerate cold conditions, it is generally believed that most earthworms were eradicated from northern latitudes during the Last Glacial Maximum. To test which hypothesis explains the phylogeography of the riparian and parthenogenetic earthwormEiseniella tetraedra, we collected 1,640 specimens from 19 different countries in Europe. We examined three molecular markers (COI, 16S and 28S) and their morphology. Eleven lineages were found, nested in five clades. Clade I was more prevalent in cold biogeographical regions such as the continental, the Atlantic or even the Arctic, while clade II was prevalent in Mediterranean regions. We investigated their potential niches through Species Distribution Models, which agreed with the distribution trends. The presence of restricted clades in the Iberian and Scandinavian peninsulas, as well as in Eastern Europe, suggests that these three regions served as refugia during the Last Glacial Maximum. Thus, both hypotheses were necessary to explain the actual distribution of this shore-dwelling earthworm.
PTBP2 promotes cell survival and autophagy in Chronic Myeloid Leukemia by stabilizing BNIP3
Authors: Barik Bibhudev , Lama Shristi , Sajitha IS , Chanda Sayantan , Mohapatra Sonali , Biswas Sutapa , Biswas Ghanashyam , Chakraborty Soumen
Published: January 2024

Polypyrimidine tract binding protein 2 (PTBP2) regulates alternative splicing in neuronal, muscle, and Sertoli cells. PTBP2 and its paralog, PTBP1, which plays a role in B-cell development, was found to be expressed aberrantly in myeloid leukemia. Genetic ablation of Ptbp2 in the cells resulted in decreased cellular proliferation and repopulating ability, decreased reactive oxygen species (ROS), and altered mitochondrial morphology. The sensitivity of CML cells to imatinib increased after the knockout of Ptbp2. RNA immunoprecipitation followed by sequencing (RIP-seq) and functional assays confirmed that PTBP2 binds to Bcl-2 Interacting Protein 3 (Bnip3)-3’UTR and stabilizes its expression. Our study also suggests that PTBP2 promotes autophagy, as evidenced by the low levels of LC3-II expression in Ptbp2-knockout cells treated with Bafilomycin A1. This effect was restored upon overexpression of Bnip3 in the knockout cells. Notably, when KCL22-NTC cells were subcutaneously injected into the flanks of mice, they gave rise to malignant tumors, unlike Ptbp2-KO-KCL22 cells. This underscores the role of PTBP2 in promoting cell proliferation and tumor formation while enhancing autophagy through Bnip3, thereby supporting the role of PTBP2 as an oncogene in CML.
The integrated stress response/eIF2a pathway controls cytokine production in tissue-resident memory CD4+T cells
Authors: Asada Nariaki , Ginsberg Pauline , Paust Hans-Joachim , Song Ning , Riedel Jan-Hendrik , Turner Jan-Eric , Peters Anett , Kaffke Anna , Engeßer Jonas , Wang Huiying , Zhao Yu , Gild Philipp , Dahlem Roland , Das Sarada , Ignatova Zoya , Huber Tobias B. , Prinz Immo , Gagliani Nicola , Mittrücker Hans-Willi , Krebs Christian F. , Panzer Ulf
Published: January 2024

Tissue-resident memory T (Trm) cells are a specialized T cell population that resides in tissues and can play both a protective and pathogenic role. The mechanism that enables Trm cells to provide a rapid protective response while restricting their function in homeostasis remains unclear. Here, we show that human and mouse CD4+Trm cells exist in apoisedstate, characterized by storage of proinflammatory type-1 and type-3 cytokine mRNAs without protein production. In steady-state conditions, cytokine mRNA translation in Trm cells is suppressed by the integrated stress response (ISR)/eIF2α pathway, whereas Trm-cell activation under inflammatory conditions results in eIF2α dephosphorylation, leading to derepression and rapid translation of the cytokine mRNAs stored in stress granules. Pharmacological inhibition of eIF2α dephosphorylation resulted in reduced cytokine production from Trm cells, and ameliorated autoimmune kidney disease in mice. Consistent with these results, the ISR pathway in Trm cells was downregulated in patients with immune-mediated diseases of the kidney and the intestine. Our results identify ISR/eIF2α-mediated control of cytokine mRNA translation as an underlying mechanism that restricts Trm cell activity in homeostasis but also promotes rapid response upon local infection or autoimmune reaction.
Super-resolved protein imaging using bifunctional light-up aptamers
Authors: Grün Franziska , van den Bergh Niklas , Klevanski Maja , Verma Mrigank S. , Bühler Bastian , Nienhaus G. Ulrich , Kuner Thomas , Jäschke Andres , Sunbul Murat
Published: January 2024

Efficient labeling methods for protein visualization with minimal tag size and appropriate photophysical properties are required for single-molecule localization microscopy (SMLM), providing insights into the organization and interactions of biomolecules in cells at the molecular level. Among the fluorescent light-up aptamers (FLAPs) originally developed for RNA imaging, RhoBAST stands out due to its remarkable brightness, photostability, fluorogenicity, and rapid exchange kinetics, enabling super-resolved imaging with high localization precision. Here, we expand the applicability of RhoBAST to protein imaging by fusing it to protein-binding aptamers. The versatility of such bifunctional aptamers is demonstrated by employing a variety of protein-binding DNA or RNA aptamers and different FLAPs. Moreover, fusing RhoBAST with the GFP-binding aptamer AP3 facilitates high- and super-resolution imaging of GFP-tagged proteins, which is particularly valuable in view of the widespread availability of plasmids and stable cell lines expressing proteins fused to GFP. The bifunctional aptamers compare favorably with standard antibody-based immunofluorescence protocols, as they are 7-fold smaller than antibody conjugates and exhibit higher bleaching-resistance. We demonstrate the effectiveness of our approach in super-resolution microscopy in secondary mammalian cell lines and primary neurons by RhoBAST-PAINT, an SMLM protein imaging technique that leverages the transient binding of the fluorogenic rhodamine dye SpyRho to RhoBAST.
Uncovering functional lncRNAs by scRNA-seq with ELATUS
Authors: Goñi Enrique , Mas Aina Maria , Abad Amaya , Santisteban Marta , Fortes Puri , Huarte Maite , Hernaez Mikel
Published: January 2024

Long non-coding RNAs (lncRNAs) play fundamental roles in cellular processes and pathologies, regulating gene expression at multiple levels. Despite being highly cell type-specific, their study at single-cell (sc) level has been challenging due to their less accurate annotation and low expression compared to protein-coding genes. To identify the important, albeit widely overlooked, specific lncRNAs from scRNA-seq data, here, we develop a computational framework, ELATUS, based on the pseudoaligner Kallisto that enhances the detection of functional lncRNAs previously undetected and exhibits higher concordance with the ATAC-seq profiles in single-cell multiome data. Importantly, we then independently confirmed the expression patterns of cell type-specific lncRNAs exclusively detected with ELATUS and unveiled biologically important lncRNAs, such asAL121895.1, a previously undocumented cis-repressor lncRNA, whose role in breast cancer progression was unnoticed by traditional methodologies. Our results emphasize the necessity for an alternative scRNA-seq workflow tailored to lncRNAs that sheds light on the multifaceted roles of lncRNAs.
Planar, Spiral, and Concentric Traveling Waves Distinguish Cognitive States in Human Memory
Authors: Das Anup , Zabeh Erfan , Ermentrout Bard , Jacobs Joshua
Published: January 2024

A fundamental challenge in neuroscience is explaining how widespread brain regions flexibly interact to support behaviors. We hypothesize that traveling waves of oscillations are a key mechanism of neural coordination, such that they propagate across the cortex in distinctive patterns that control how different regions interact. To test this hypothesis, we used direct brain recordings from humans performing multiple memory experiments and an analytical framework that flexibly measures the propagation patterns of traveling waves. We found that traveling waves propagated along the cortex in not only plane waves, but also spirals, sources and sinks, and more complex patterns. The propagation patterns of traveling waves correlated with novel aspects of behavior, with specific wave shapes reflecting particular cognitive processes and even individual remembered items. Our findings suggest that large-scale cortical patterns of traveling waves reveal the spatial organization of cognitive processes in the brain and may be relevant for neural decoding.
Highly specific intracellular ubiquitination of a small molecule
Authors: Li Weicheng , Garcia-Rivera Enrique M. , Mitchell Dylan C. , Chick Joel M. , Maetani Micah , Knapp John M. , Matthews Geoffrey M. , Shirasaki Ryosuke , de Matos Simoes Ricardo , Viswanathan Vasanthi , Pulice John L. , Rees Matthew G. , Roth Jennifer A. , Gygi Steven P. , Mitsiades Constantine S. , Kadoch Cigall , Schreiber Stuart L. , Ostrem Jonathan M.L.
Published: January 2024

Ubiquitin is a small, highly conserved protein that acts as a posttranslational modification in eukaryotes. Ubiquitination of proteins frequently serves as a degradation signal, marking them for disposal by the proteasome. Here, we report a novel small molecule from a diversity-oriented synthesis library, BRD1732, that is directly ubiquitinated in cells, resulting in dramatic accumulation of inactive ubiquitin monomers and polyubiquitin chains causing broad inhibition of the ubiquitin-proteasome system. Ubiquitination of BRD1732 and its associated cytotoxicity are stereospecific and dependent upon two homologous E3 ubiquitin ligases, RNF19A and RNF19B. Our finding opens the possibility for indirect ubiquitination of a target through a ubiquitinated bifunctional small molecule, and more broadly raises the potential for posttranslational modificationin trans.
Global MEG Resting State Functional Connectivity in Children with Autism and Sensory Processing Dysfunction
Authors: Demopoulos Carly , Jesson Xuan , Gerdes Molly Rae , Jurigova Barbora G. , Hinkley Leighton B. , Ranasinghe Kamalini G. , Desai Shivani , Honma Susanne , Mizuiri Danielle , Findlay Anne , Nagarajan Srikantan S. , Marco Elysa J.
Published: January 2024

Sensory processing dysfunction not only affects most individuals with autism spectrum disorder (ASD), but at least 5% of children without ASD also experience dysfunctional sensory processing. Our understanding of the relationship between sensory dysfunction and resting state brain activity is still emerging. This study compared long-range resting state functional connectivity of neural oscillatory behavior in children aged 8-12 years with autism spectrum disorder (ASD; N=18), those with sensory processing dysfunction (SPD; N=18) who do not meet ASD criteria, and typically developing control participants (TDC; N=24) using magnetoencephalography (MEG). Functional connectivity analyses were performed in the alpha and beta frequency bands, which are known to be implicated in sensory information processing. Group differences in functional connectivity and associations between sensory abilities and functional connectivity were examined. Distinct patterns of functional connectivity differences between ASD and SPD groups were found only in the beta band, but not in the alpha band. In both alpha and beta bands, ASD and SPD cohorts differed from the TDC cohort. Somatosensory cortical beta-band functional connectivity was associated with tactile processing abilities, while higher-order auditory cortical alpha-band functional connectivity was associated with auditory processing abilities. These findings demonstrate distinct long-range neural synchrony alterations in SPD and ASD that are associated with sensory processing abilities. Neural synchrony measures could serve as potential sensitive biomarkers for ASD and SPD.
Evaluation of cancer incidence among Marines and Navy personnel and civilian workers exposed to contaminated drinking water at USMC Base Camp Lejeune: a cohort study
Authors: Bove Frank J.
Published: January 2024

Background

Drinking water at U.S. Marine Corps Base Camp Lejeune, North Carolina was contaminated with trichloroethylene and other industrial solvents from 1953 to 1985.

Methods

A cohort cancer incidence study was conducted of Marines/Navy personnel who, between 1975 and 1985, began service and were stationed at Camp Lejeune, North Carolina (N=154,821) or Camp Pendleton, California (N=163,484), and civilian workers employed at Camp Lejeune (N=6,494) or Camp Pendleton (N=5,797) between October 1972 and December 1985. Camp Pendleton’s drinking water was not known to be contaminated between 1972 and 1985. Individual-level information on all primary invasive cancers and in-situ bladder cancer diagnosed from 1996 to 2017 was obtained from data linkages with 54 cancer registries in the U.S. Survival methods were used to calculate hazard ratios (HRs) comparing cancer incidence between the Camp Lejeune and Camp Pendleton cohorts. Precision of effect estimates were evaluated using the 95% confidence interval (CI) ratio.

Results

Cancers among Camp Lejeune Marines/Navy personnel and civilian workers totaled 12,083 (354/100,000) and 1,563 (1,301/100,000), respectively. Cancers among Camp Pendleton Marines/Navy personnel and civilian workers totaled 12,144 (335/100,000) and 1,416 (1,372/100,000), respectively.

Compared to Camp Pendleton, Camp Lejeune Marines/Navy personnel had adjusted HRs ≥1.20 with 95% CI ratios (CIRs) ≤3 for acute myeloid leukemia (HR=1.38, 95% CI: 1.03, 1.85), all myeloid cancers including polycythemia vera (HR=1.24, 95% CI:1.03, 1.49), myelodysplastic and myeloproliferative syndromes (HR=1.68, 95% CI: 1.07, 2.62), polycythemia vera alone (HR=1.41, 95% CI: 0.94, 2.11), cancers of the esophagus (HR=1.27, 95% CI: 1.03, 1.56), larynx (HR=1.21, 95% CI: 0.98, 1.50), soft tissue (HR=1.21, 95% CI: 0.92, 1.59) and thyroid (HR=1.22, 95% CI: 1.03, 1.45). Compared to Camp Pendleton, Camp Lejeune civilian workers had adjusted HRs ≥1.20 with 95% CIRs ≤3 for all myeloid cancers including polycythemia vera (HR=1.40, 95% CI: 0.83, 2.36), squamous cell lung cancer (HR=1.63, 95% CI: 1.10, 2.41) and female ductal breast cancer (HR=1.32, 95% CI:1.02, 1.71). Sensitivity analyses indicated that confounding bias due to unmeasured risk factors (e.g., smoking and alcohol consumption) is unlikely to significantly impact the findings.

Conclusion

Increased risks of several cancers were observed among Marines/Navy personnel and civilian workers likely exposed to contaminated drinking water at Camp Lejeune compared to personnel at Camp Pendleton.
Evaluation of Autophagy in conjunctival fibroblasts
Authors: Mehrbod Parvaneh , Brun Paola , Rosani Umberto , Leonardi Andrea , Ghavami Saeid
Published: January 2024

Vernal keratoconjunctivitis (VKC) is a serious eye allergy characterized by poorly understood pathogenic mechanisms and a lack of effective treatments. Autophagy, a process involved in both triggering and suppressing immune and inflammatory responses, plays a role in VKC’s pathophysiology. Understanding autophagy’s involvement in VKC could lead to new treatment possibilities, such as utilizing specific topical substances to induce or inhibit autophagy and prevent severe complications of this eye condition. In our current protocol, we present a robust methodology established in our laboratory for studying autophagy in primary conjunctival fibroblasts. We assess autophagy through techniques like immunocytochemistry, immunoblotting, and qPCR.
Host-associated genetic differentiation in the face of ongoing gene flow: ecological speciation in a pathogenic parasite of freshwater fish
Authors: Nazarizadeh Masoud , Nováková Milena , Vlček Jakub , Štefka Jan
Published: January 2024

Adaptation to varying environments, leading to population divergence, is one of the key processes of natural selection. However, its effectiveness amidst ongoing gene flow remains controversial. Our study explores this phenomenon by focusing on a tapeworm parasite (Ligula intestinalis), which is capable of parasitising a wide spectrum of fish species, overcoming their immunological defence and having a highly pathogenic impact. We analysed the population genetic structure, the degree of gene flow, and the level of genomic divergence between sympatrically occurring parasites from different cyprinid fish hosts. Utilising genome-wide Single Nucleotide Polymorphisms (SNPs) and transcriptome data, we investigated whether individual host species impose selection pressures on the parasite populations. Genetic clustering analyses indicated a divergence between the parasites infecting breams and those in roaches, bleaks and rudds. Historical demography modelling suggested that the most plausible scenario for this divergence is isolation with continuous gene flow. Selection analysis identified 896 SNPs under selection, exhibiting higher nucleotide diversity and genetic divergence compared to neutral loci. Transcriptome profiling corroborated these results, revealing distinct gene expression profiles for the two parasite populations. An in-depth examination of the selected SNPs and differentially expressed genes revealed specific genes and their physiological functions, as candidates for the molecular mechanisms of immune evasion and, thus, for driving ecological speciation in the parasite. This study showcases the interplay between host specificity, population demography and disruptive selection in ecological speciation. By dissecting the genomic factors at play, we gain a better understanding of the mechanisms facilitating population divergence in the presence of gene flow.
Oncogenic RAS signaling suppresses ferroptosis via transcriptional upregulation of GCH1
Authors: Lim Jonathan K. M. , Stölting Frauke , Levy Tal , Thewes Leonie , Picard Daniel , Tishina Sofya , Zhang Hai-Feng , Lewandowska Oksana , Reiff Tobias , Remke Marc , Brägelmann Johannes , Beleggia Filippo , Berndt Carsten , von Karstedt Silvia , Reifenberger Guido , Rotblat Barak , Leprivier Gabriel
Published: January 2024

Ferroptosis is an iron-dependent form of regulated cell death arising from excessive lipid peroxidation. While seminal work described that oncogenic RAS transformation drives synthetic lethal vulnerability to archetypal ferroptosis inducers including erastin (eradicator of RAS and ST-expressing cells) and RSL3 (Ras selective lethal 3), more recent work suggest that oncogenic RAS signaling may confer ferroptosis resistance. Thus, the impact of oncogenic RAS on the cellular response to ferroptosis is still unclear. Here, we provide unifying evidence across multiple cellular models that oncogenic RAS signaling suppresses ferroptosis. Using integrated proteo- and transcriptomic analyses, we uncovered that oncogenic RAS signaling upregulates the ferroptosis suppressor GTP cyclohydrolase I (GCH1) via transcriptional induction by the transcription factor ETS1 downstream of the RAS-MAPK signaling cascade. Targeted repression of Gch1 or of the tetrahydrobiopterin (BH4) synthesis pathway, which is mediated by GCH1, was sufficient to sensitize oncogenic RAS transformed cells to ferroptosis in 2D and 3D cell models, highlighting a mechanism through which RAS promotes resistance to ferroptosis induction. Furthermore, we found that GCH1 expression is clinically relevant and correlates with RAS signaling activation in human cancers. Overall, this study redefines oncogenic RAS signaling to be a ferroptosis suppressor, and identifies GCH1 as a mediator of this effect and a potential vulnerability for targeting RAS driven cancers.
Telencephalic eversion in embryos and early larvae of four teleost species
Authors: Folgueira Mónica , Clarke Jonathan D. W.
Published: January 2024

1.

The telencephalon of ray-finned fishes undergoes eversion, which is very different to the evagination that occurs in most other vertebrates. Ventricle morphogenesis is key in order to build an everted telencephalon. Thus, here we use the apical markerzona occludens 1(ZO1) to understand ventricle morphology, extension of thetela choroideaand the eversion process during early telencephalon development of four teleost species: giant danio (Devario aequipinnatus),blind cavefish(Astyanax mexicanus),medaka(Oryzias latipes)and paradise fish (Macroposus opercularis).In addition, by using immunohistochemistry against tubulin and calcium binding proteins, we analyse the general morphology of the telencephalon, showing changes in the location and extension of the olfactory bulb and other telencephalic regions from 2 to 5 days of development. We also analyse the impact of abnormal eye and telencephalon morphogenesis on eversion, showing thatcyclopsmutants do undergo eversion despite very dramatic abnormal eye morphology. We discuss how the formation of the telencephalic ventricle in teleost fish, with its characteristic shape, is crucial event during eversion.
ACKR3 Proximity Labeling Identifies Novel G protein- and β-arrestin-independent GPCR Interacting Proteins
Authors: Hicks Chloe , Gardner Julia , Eiger Dylan Scott , Camarda Nicholas D. , Pham Uyen , Dhar Saisha , Rodriguez Hailey , Chundi Anand , Rajagopal Sudarshan
Published: January 2024

The canonical paradigm of GPCR signaling recognizes G proteins and β-arrestins as the two primary transducers that promote GPCR signaling. Recent evidence suggests the atypical chemokine receptor 3 (ACKR3) does not couple to G proteins, and β-arrestins are dispensable for some of its functions. Here, we employed proximity labeling to identify proteins that interact with ACKR3 in cells devoid of β-arrestin. We identified proteins involved in the endocytic machinery and evaluated a subset of proteins conserved across several GPCR-based proximity labeling experiments. We discovered that the bone morphogenic protein 2-inducible kinase (BMP2K) interacts with many different GPCRs with varying dependency on β-arrestin. Together, our work highlights the existence of modulators that can act independently of G proteins and β-arrestins to regulate GPCR signaling and provides important evidence for other targets that may regulate GPCR signaling.

Graphical Abstract
Inhibition of ADAM17 increases cytotoxic effect of cisplatin in cervical spheroids and organoids
Authors: Holthaus David , Rogmans Christoph , Gursinski Ina , Quevedo-Olmos Alvaro , Ehsani Marzieh , Mangler Mandy , Flörkemeier Inken , Weimer Jörg P. , Meyer Thomas F. , Maass Nicolai , Bauerschlag Dirk O. , Hedemann Nina
Published: January 2024

Background

Cervical cancer represents one of the main causes of female, cancer-related mortality worldwide. The majority of cancers are caused by human papillomaviruses such as HPV16 and HPV18. As chemotherapeutic resistance to first-line platinum treatment is still a predominant clinical challenge in advanced cervical cancer, novel treatment options including combinatorial therapies are urgently required to overcome chemotherapeutic resistance. Inhibition ofA Disintegrin And Metalloproteinase (ADAM)-family members, heavily involved in tumour progression of a vast range of solid tumours, strongly improved response to chemotherapeutic treatment in other tumour entities including ovarian cancer.

Methods

We established two- and three-dimensional models derived from three traditional cervical cancer cell lines and ectocervical cancer-derived organoids. Following characterisation, these models were used to investigate their response to cisplatin treatment in the absence and presence of ADAM inhibitors using viability assays and automated live cell imaging.

Results

The pivotal role of the metalloprotease ADAM17 driving chemotherapy resistance was detectable in all ectocervical cultures irrespective of the model system used, whereas ADAM10 inhibition was predominantly effective only in loosely aggregated spheroids. We showed prominent differences regarding treatment responses between 2D monolayers compared to 3D spheroid and 3D organoid model systems. Particularly, the organoid system, regarded as the closest representation of primary tumours, exhibited reliably the combinatorial effect of ADAM17 inhibition and cisplatin in all three individual donors.

Conclusions

As two- and three-dimensional models of the same cell lines differ in their responses to chemotherapy it is essential to validate treatment strategies in more advanced model systems representing the patient situation more realistically. Ectocervical organoids showed reliable results regarding treatment responses closely mimicking the primary tumours and could therefore serve as an important tool for personalized medicine in cervical cancer. These findings strengthen the role of ADAM17 as a potential novel target for combinatorial treatments to overcome chemoresistance in cervical cancer.
Neural stem cells isolated from activated brain neurogenic niches after traumatic injury demonstrate distinct behaviorsin vitro
Authors: Schiro Lars Erik , Bauer Ulrich Stefan , Bjorkli Christiana , Sandvig Axel , Sandvig Ioanna
Published: January 2024

The subventricular zone (SVZ) of the lateral ventricle and subgranular zone (SGZ) of the dentate gyrus (DG) in the hippocampus represents neurogenic niches within the brain housing distinct populations of neural stem cells (NSCs), known for their exclusive capacity to sustain neurogenesis in the adult mammalian CNS. These niches respond to traumatic brain injury (TBI) by becoming activated, leading to NSC proliferation, a small number of which subsequently migrate towards the injury site, and differentiate predominantly into astrocytes. Although the capacity of activated NSCs to differentiate into neurons appears to be limited, it is intrinsically interesting to determine whether these cells may represent a potential source of new neurons that may replenish and replace damaged and lost neuronal tissue.

To address this question, it is necessary to understand the intrinsic behavior of NSCs derived from the activated SVZ and SGZ neurogenic niches after TBI, in terms of cell maturation, and differentiation capacity.

In this study, we induced a focal TBI lesion specifically targeting the SVZ or SGZ neurogenic niche in adult rats, harvested NSCs three days post-lesioning, and subsequently expanded them in culture. We found that the isolated NSCs displayed distinct proliferation, differentiation, and spontaneous organizationin vitro, dependent on the activated niche of origin. Furthermore, these behaviors differed from NSCs derived from the SVZ or SGZ niche of uninjured control animals.
KSHV promotes oncogenic FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation
Authors: Majerciak Vladimir , Alvarado-Hernandez Beatriz , Ma Yanping , Duduskar Shivalee , Lobanov Alexei , Cam Maggie , Zheng Zhi-Ming
Published: January 2024

Kaposi’s sarcoma-associated herpesvirus (KSHV) ORF57 is a lytic RNA-binding protein. We applied BCBL-1 cells in lytic KSHV infection and performed UV cross-linking immunoprecipitation (CLIP) followed by RNA-seq of the CLIPed RNA fragments (CLIP-seq). We identified ORF57-bound transcripts from 544 host protein-coding genes. By comparing with the RNA-seq profiles from BCBL-1 cells with latent and lytic KSHV infection and from HEK293T cells with and without ORF57 expression, we identified FOS and CITED2 RNAs being two common ORF57-specific RNA targets. FOS dimerizes with JUN as a transcription factor AP-1 involved in cell proliferation, differentiation, and transformation. Knockout of the ORF57 gene from the KSHV genome led BAC16-iSLK cells incapable of FOS expression in KSHV lytic infection. The dysfunctional KSHV genome in FOS expression could be rescued by Lenti-ORF57 virus infection. ORF57 protein does not regulate FOS translation but binds to the 13-nt RNA motif near the FOS RNA 5ʹ end and prolongs FOS mRNA half-life 7.7 times longer than it is in the absence of ORF57. This binding of ORF57 to FOS RNA is competitive to the binding of a host nuclease AEN (also referred to as ISG20L1). KSHV infection inhibits the expression of AEN, but not exosomal RNA helicase MTR4. FOS expression mediated by ORF57 inhibitsAENtranscription, but transactivatesRGS2,a regulator of G-protein coupled receptors. FOS binds a conserved AP-1 site in theRGS2promoter and enhances RGS2 expression to phosphorylate AKT. Altogether, we have discovered that KSHV ORF57 specifically binds and stabilizes FOS RNA to increase FOS expression, thereby disturbing host gene expression and inducing pathogenesis during KSHV lytic infection.

Significance

We discovered that FOS, a heterodimer component of oncogenic transcription factor AP- 1, is highly elevated in KSHV infected cells by expression of a viral lytic RNA-binding protein, ORF57, which binds a 13-nt RNA motif near the FOS RNA 5ʹ end to prolong FOS RNA half-life. This binding of ORF57 to FOS RNA is competitive to the binding of host RNA destabilizer(s). KSHV infection inhibits expression of host nuclease AEN (or ISG20L1), but not MTR4. FOS inhibitsAENtranscription, but transactivatesRGS2by binding to a conserved AP-1 site in theRGS2promoter, thereby enhancing RGS2 expression and phosphorylation of AKT. Our data conclude that viral RNA-binding protein ORF57 controls the expression of a subset of genes for signaling, cell cycle progression, and proliferation to contribute viral pathogenesis.
Tooth Loss, Patient Characteristics, and Coronary Artery Calcification
Authors: Pham Tuan D. , Zou Lifong , Patel Mangala , Holmes Simon B. , Coulthard Barts Paul ,   The London Faculty of Medicine and Dentistry
Published: January 2024

This study, for the first time, explores the integration of data science and machine learning for the classification and prediction of coronary artery calcium (CAC) scores, investigating both tooth loss and patient characteristics as key input features. By employing these advanced analytical techniques, we aim to enhance the accuracy of classifying CAC scores into tertiles and predicting their values. Our findings reveal that patient characteristics are particularly effective for tertile classification, while tooth loss provides more accurate predicted CAC scores. Moreover, the combination of patient characteristics and tooth loss demonstrates improved accuracy in identifying individuals at higher risk of cardiovascular issues related to CAC. This research contributes valuable insights into the relationship between oral health indicators, such as tooth loss, patient characteristics, and cardiovascular health, shedding light on their potential roles in predictive modeling and classification tasks for CAC scores.
High impact AMPAkines induce a Gq-protein coupled endoplasmic calcium release in cortical neurons: a possible mechanism for explaining the toxicity of high impact AMPAkines
Authors: Radin DP , Zhong S , Cerne Rok , Witkin Jeffrey , Lippa A
Published: January 2024

Positive allosteric modulators of the AMPA receptor (AMPAkines) have a multitude of promising therapeutic properties. The pharmaceutical development of high impact AMPAkines has however been limited by the appearance of calcium-dependent neuronal toxicity and convulsions in vivo. Such toxicity is not observed at exceptionally high concentrations of low impact ampakines. Since most AMPAR are somewhat impermeable to calcium, the current study sought to examine the extent to which different mechanisms contribute to the rise in intracellular calcium in the presence of high impact ampakines. In the presence of AMPA alone, cytosolic calcium elevation is shown to be sodium-dependent. In the presence of high impact AMPAkines such as cyclothiazide (CTZ) or CX614, however, AMPAR potentiation also activates an additional mechanism that induces calcium release from endoplasmic reticular (ER) stores. The pathway that connects AMPAR to the ER system involves a Gq-protein, phospholipase Cβ–mediated inositol triphosphate (InsP3) formation and ultimately stimulation of InsP3-receptors located on the ER. The same linkage was not observed using high concentrations of the low impact AMPAkines, CX516 (Ampalex) and CX717. We also demonstrate that CX614 produces neuronal hyper-excitability at therapeutic doses while the newer generation low impact AMPAkine CX1739 is safe at exceedingly high doses. While earlier studies have demonstrated a functional linkage between AMPAR and G-proteins, this report demonstrates that in the presence of high impact AMPAkines, AMPAR also couple to a Gq-protein, which triggers a secondary calcium release from the ER and provides insight into the disparate actions of high and low impact AMPAkines.
Cerebrovascular pathology mediates associations between hypoxemia during rapid eye movement sleep and medial temporal lobe structure and function in older adults
Authors: Berisha Destiny E. , Rizvi Batool , Chappel-Farley Miranda G. , Tustison Nicholas , Taylor Lisa , Dave Abhishek , Sattari Negin S. , Chen Ivy Y. , Lui Kitty K. , Janecek John C. , Keator David , Neikrug Ariel B. , Benca Ruth M. , Yassa Michael A. , Mander Bryce A.
Published: January 2024

Obstructive sleep apnea (OSA) is common in older adults and is associated with medial temporal lobe (MTL) degeneration and memory decline in aging and Alzheimer’s disease (AD). However, the underlying mechanisms linking OSA to MTL degeneration and impaired memory remains unclear. By combining magnetic resonance imaging (MRI) assessments of cerebrovascular pathology and MTL structure with clinical polysomnography and assessment of overnight emotional memory retention in older adults at risk for AD, cerebrovascular pathology in fronto-parietal brain regions was shown to statistically mediate the relationship between OSA-related hypoxemia, particularly during rapid eye movement (REM) sleep, and entorhinal cortical thickness. Reduced entorhinal cortical thickness was, in turn, associated with impaired overnight retention in mnemonic discrimination ability across emotional valences for high similarity lures. These findings identify cerebrovascular pathology as a contributing mechanism linking hypoxemia to MTL degeneration and impaired sleep-dependent memory in older adults.
In vivoCRISPR screens identify novel virulence genes among proteins of unassigned subcellular localization inToxoplasma
Authors: Tachibana Yuta , Sasai Miwa , Yamamoto Masahiro
Published: January 2024

The research field to identify and characterize virulence genes inToxoplasma gondiihas been dramatically advanced by a series ofin vivoCRISPR screens. Although subcellular localizations of thousands of proteins were predicted by the spatial proteomic method called hyperLOPIT, those of more than 1000 proteins remained unassigned and their essentiality in virulence was also unknown. In this study, we generated two small-scale gRNA libraries targeting approximately 600 hyperLOPIT-unassigned proteins and performedin vivoCRISPR screens. As a result, we identified severalin vivofitness-conferring genes that were previously unreported. We further characterized two candidates, TgGTPase and TgRimM, which are localized in the cytoplasm and the apicoplast, respectively. Both genes are essential for parasite virulence and widely conserved in the phylum Apicomplexa. Collectively, our current study provides a resource for estimating thein vivoessentiality ofToxoplasmaproteins with previously unknown localizations.

IMPORTANCE

Toxoplasma gondiiis a protozoan parasite that causes severe infection in immunocompromised patients or newborns.Toxoplasmapossesses more than 8000 genes; however, the genes that determine parasite virulence were not fully identified. The apicomplexan parasites, includingToxoplasma, developed unique organelles that do not exist in other model organisms; thus, determining the subcellular location of parasite proteins is important for understanding their functions. Here, we usedin vivoCRISPR genetic screens that enabled us to investigate hundreds of genes inToxoplasmaduring mouse infection. We screened approximately 600 parasite proteins with previously unknown subcellular localizations. We identified many novel genes that confer parasite fitness in mice. Among the top hits, we characterized two essential virulence genes, TgGTPase and TgRimM, which are widely conserved in the phylum Apicomplexa. Our findings will contribute to understanding how apicomplexans adapt to the host environment and cause disease.
Degradome analysis to identify direct protein substrates of small-molecule degraders
Authors: Jochem Marco , Schrempf Anna , Wagner Lina-Marie , Cisneros Jose , Ng Amanda , Winter Georg E. , Krijgsveld Jeroen
Published: January 2024

Targeted protein degradation (TPD) has emerged as a powerful strategy to selectively eliminate cellular proteins using small-molecule degraders, offering therapeutic promise for targeting proteins that are otherwise undruggable. However, a remaining challenge is to unambiguously identify primary TPD targets that are distinct from secondary downstream effects in the proteome. Here we introduce an approach that combines stable isotope labeling and click-chemistry for selective quantification of protein degradation by mass spectrometry, excluding confounding effects of altered transcription and translation induced by target depletion. We show that the approach efficiently operates at the time scale of TPD (hours) and we demonstrate its utility by analyzing the Cyclin K degraders dCeMM2 and dCeMM4, which induce widespread transcriptional downregulation, and the GSPT1 degrader CC-885, an inhibitor of protein translation. Additionally, we apply it to characterize compound 1, a previously uncharacterized degrader, and identify the zinc-finger protein FIZ1 as a degraded target.
Limited variation in microbial communities across populations ofMacrostelesleafhoppers (Hemiptera: Cicadellidae)
Authors: Mulio Sandra Åhlén , Zwolińska Agnieszka , Klejdysz Tomasz , Prus-Frankowska Monika , Michalik Anna , Kolasa Michał , Łukasik Piotr
Published: January 2024

Microbial symbionts play important roles in insect biology, but their diversity, distribution, and dynamics over time across host populations are poorly understood. We surveyed the spatio-temporal distribution of bacterial symbionts in the broadly distributed and economically significant leafhopper genusMacrosteles, with emphasis onMacrosteles laevis, using host and symbiont marker gene amplicon sequencing. The cytochrome oxidase I (COI) gene data revealed no strong genetic differentiation acrossM. laevispopulations, significant levels of heteroplasmy, and multiple cases of parasitoid infections. 16S rRNA data confirmed the universal presence of the ancient nutritional endosymbiontsSulciaandNasuiaand a high prevalence ofArsenophonus. Interestingly, in contrast to most previously surveyed species, inM. laeviswe found only occasional cases of infection with facultative endosymbionts and other bacteria. There was no significant variation in symbiont prevalence across populations, or among sampling years for the same population. Facultative endosymbionts includingRickettsia,Wolbachia,Cardinium, andLariskella, were more common in other Macrosteles species. Combined, our data demonstrate that not all species show clear spatial and temporal variation in genetic structure and microbial prevalence. However, simultaneous characterization of host and symbiont marker gene amplicons in large insect collections can help understand the dynamics of host-microbe interactions.