bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new class of penicillin-binding protein inhibitors to address drug-resistantNeisseria gonorrhoeae
Authors: Uehara Tsuyoshi , Zulli Allison L. , Miller Brittany , Avery Lindsay M. , Boyd Steven A. , Chatwin Cassandra L. , Chu Guo-Hua , Drager Anthony S. , Edwards Mitchell , Emeigh Hart Susan G. , Myers Cullen L. , Rongala Gopinath , Stevenson Annie , Uehara Kyoko , Yi Fan , Wang Bibo , Liu Zhenwu , Wang Mingyue , Zhao Zhichao , Zhou Xinming , Zhao Haiyan , Stratton Caleb M. , Bala Sandeepchowdary , Davies Christopher , Tkavc Rok , Jerse Ann E. , Pevear Daniel C. , Burns Christopher J. , Daigle Denis M. , Condon Stephen M. 
Published: December 2024

ABSTRACTβ-Lactams are the most widely used antibiotics for the treatment of bacterial infections because of their proven track record of safety and efficacy. However, susceptibility to β-lactam antibiotics is continually eroded by resistance mechanisms. Emerging multidrug-resistant (MDR)Neisseria gonorrhoeaestrains possessing alteredpenAalleles (encoding PBP2) pose a global health emergency as they threaten the utility of ceftriaxone, the last remaining outpatient antibiotic. Here we disclose a novel benzoxaborinine-based penicillin-binding protein inhibitor series (boro-PBPi) that is envisioned to addresspenA-mediated resistance while offering protection against evolution and expansion of β-lactamases. Optimization of boro-PBPi led to the identification of compound21(VNRX-14079) that exhibits potent antibacterial activity against MDRN. gonorrhoeaeachieved by high affinity binding to the PBP2 target. Boro-PBPi/PBP2 complex structures confirmed covalent interaction of the boron atom with Ser310 and the importance of the β3-β4loop for improved affinity.21elicits bactericidal activity, a low frequency of resistance, a good safety profile, suitable pharmacokinetic properties, and in vivo efficacy in a murine infection model against ceftriaxone-resistantN. gonorrhoeae.21is a promising anti-gonorrhea agent poised for further advancement.
Human precentral gyrus neurons link speech sequences from listening to speaking
Authors: Xu Duo , Chung Jason E. , Silva Alexander B. , Metzger Sean L. , Greicius Quinn R. , Zhang Yizhen , Leonard Matthew K. , Aghi Manish K. , Hervey-Jumper Shawn L. , Chang Edward F. 
Published: December 2024

SummarySpeech perception and production are interconnected processes, but the underlying neural mechanisms remain unclear. We investigated this relationship by recording large-scale single-neuron activity in the human brain during a delayed sentence repetition task. Contrary to the traditional view that the precentral gyrus is solely responsible for motor execution, we found that neurons there encoded activity across all task phases of listening, delay, initiation, and speaking. Notably, we discovered “mirror” neurons that activated transiently after hearing and before producing specific speech sounds, and “bridge” neurons that maintained activity between the same speech elements during listening and speaking. Population analysis revealed distinct latent components for each task phase and persistent dynamics for specific sentences. Overall, this study provides novel insights into the neuronal basis of speech processing, emphasizing the intricate interplay between perception, production, and verbal working memory.
Inhibition of the extracellular matrix protein fibulin-3 reduces immunosuppressive signaling in tumor stem cells and increases macrophage activation against glioblastoma
Authors: Kundu Somanath , Mitra Soham , Roshini Arivazhagan , Longo John A. , Longo Sharon L. , Venskus Abigail , Babu Harish , Viapiano Mariano S. 
Published: December 2024

AbstractGlioblastoma tumors remain a formidable challenge for immune-based treatments because of their molecular heterogeneity, poor immunogenicity, and growth in the largely isolated and immunosuppressive neural environment. As the tumor grows, GBM cells change the composition and architecture of the neural extracellular matrix (ECM), affecting the mobility, survival, and function of immune cells such as tumor-associated microglia and infiltrated macrophages (TAMs). We have previously described the unique expression of the ECM protein EFEMP1/fibulin-3 in GBM compared to normal brain and demonstrated that this secreted protein promotes the growth of the GBM stem cell (GSC) population. Here, we describe a novel immunomodulatory role of fibulin-3 and the immuno-boosting effects of targeting this ECM protein. Mice carrying fibulin-3-deficient intracranial tumors showed increased myeloid infiltration and reduced expression of TAM pro-tumoral markers (Arginase, CD206) compared to controls. The opposite was observed in orthotopic tumors overexpressing fibulin-3.In silicodataset analysis of clinical datasets revealed positive correlation of fibulin-3 with an immunosuppressive signature, which was validated in GSCs andin vivo. We further demonstrated that fibulin-3 regulates the expression of immunosuppressive signals (CSF-1, TGFβ) and the innate immune checkpoint CD47 in GSCs via autocrine activation of NF-κB signaling. Accordingly, immunosuppressive signals were downregulated in GSCs by knockdown of fibulin-3 or inhibition of this protein with an anti-fibulin-3 antibody. Co-culture of GBM cells with syngeneic macrophage lines or primary macrophages in presence of anti-fibulin-3 antibody increased macrophage phagocytosis and antibody-dependent killing of the tumor cells, Furthermore, locoregional delivery of anti-fibulin-3 antibody in mice carrying intracranial GBM increased the infiltration of TAMs expressing pro-inflammatory markers, reducing tumor viability. Our findings show that anti-fibulin-3 approaches, which impact the pericellular ECM surrounding tumor cells and TAMs, can diminish immunosuppression in GBM and boost innate immune responses against the tumor.
Expandable, Functional Hepatocytes Derived from Primary Cells Enable Liver Therapeutics
Authors: Mallanna Sunil K. , Karanth Soujanya S. , Marturano Joseph E. , Kudva Abhijith K. , Lehmann Marcus , Morse Julie K. , Jamiel Morgan , Norman Timothy , Wilson Christopher , Munarin Fabiola , Broderick David , Buskirk Maxwell Van , Uddin Esha , Ret Michael , Steele Christopher , Cheema Mehar , Black Justin , Vanderploeg Eric , Chen Christopher , Bhatia Sangeeta , Rezania Alireza , Lowery Thomas J. , Cazanave Sophie , Chhabra Arnav 
Published: December 2024

AbstractLiver disease affects millions annually in the United States, with orthotopic transplantation as the only curative option for many patients. However, the scarcity of donor organs highlights a need for alternative cell-based therapies. Hepatocyte-based approaches are promising due to the cells’ inherent synthetic, metabolic, and detoxifying functions, but they face critical barriers, including the lack of a scalable source of functional hepatocytes and poor engraftment. In this study, we developed a scalable process for expanding primary human hepatocytes (PHHs) while preserving their identity and function. By leveraging heterocellular aggregation with stromal cells, we generated cryopreserved “seed” constructs that maintained viability and function post-thaw. Seeds demonstrated enhanced metabolic and detoxification functions and robust engraftment across multiple anatomic sites outside of the liver. Our approach addresses key limitations of hepatocyte-based therapies, offering a stable, scalable, and clinically viable platform for liver cell therapy applications.
Biofilm formation on glycated collagen modulatesStreptococcus mutansbacterial extracellular vesicle production and cargo
Authors: Leiva-Sabadini Camila , Berríos Pablo , Saavedra Paula , Carrasco-Rojas Javiera , González-Aramundiz José Vicente , Vera Mario , Tarifeño-Saldivia Estefanía , Schuh Christina MAP , Aguayo Sebastian 
Published: December 2024

AbstractStreptococcus mutansis the major microbial etiological agent of dental caries and can adhere to surfaces such as type-I collagen, present in dentin and periodontal tissues. Recent studies have characterized planktonicS. mutansbacterial extracellular vesicles (bEVs) and demonstrated environmental-induced changes due to sugar presence or pH alterations. However, to date there are no studies exploring if surface-derived changes - such as tissue glycation - can modulate bEV production in the context of oral biofilm formation in the elderly. Therefore, the aim of this work was to determine the role of biofilm formation and collagen glycation on the morphology and composition ofS. mutansbEVs. For this, bEVs fromS. mutansbiofilms on native and glycated collagen surfaces were isolated, characterized, and compared to bEVs from planktonic cells. Nanoparticle tracking analysis and microscopy confirmed bEV production and showed that bEVs from biofilms are smaller in size and less abundant than those from planktonic cells. Furthermore, proteome analysis revealed thatS. mutansbiofilm formation on native and glycated collagen led to the enrichment of several key virulence proteins such as Eno, LuxS, Tpx, and ScrB. Also, a shift towards proteins involved in metabolic processes was found in bEVs following biofilm formation on collagen surfaces, whereas glucan metabolism proteins were overexpressed in vesicles from the planktonic state. These results demonstrate that biofilm formation, as well as the glycation of collagen associated with aging and hyperglycemia, can modulate bEV characteristics and cargo and could play a central role inS. mutansvirulence and the development of diseases such as dental caries and periodontal disease.
The KDM6 histone demethylase inhibitor GSK-J4 induces metal and stress responses in multiple myeloma cells
Authors: Cribbs Adam P , Hookway Edward S , Yapp Clarence , Che Ka-Hing , Dunford James E , Gutheridge Karina , Lari Federica , Wells Graham , Philpott Martin , Cain Peter , Brotherton Deborah , Palmer Charlotte , Maret Wolfgang , Fitzgibbons Jude , Christianson John C. , Oppermann Udo 
Published: December 2024

ABSTRACTThioneins are cysteine-rich apoproteins that regulate divalent metal homeostasis by virtue of their metal-chelation properties resulting in the ligand-bound metallothionein state. Previous studies show transient upregulation of the metallothionein (MT) gene cluster as part of a complex transcriptional response to a class of histone demethylase tool compounds targeting human Fe2+dependent ketoglutarate oxygenases KDM6A (UTX) and KDM6B (JmjD3). The prototypic bioactive KDM6 inhibitor GSK-J4 induces apoptotic cell death in multiple myeloma cells and corresponding transcriptomic profiles are dominated by metal and metabolic stress response signatures, also observed in primary human myeloma cells. Here we investigate the hypothesis that metal-chelation by GSK-J4 provides the means for transport and intracellular release of Zn2+leading to a metallothionein transcriptomic response signature. Live cell imaging of myeloma cells shows transient increases in intracellular free Zn2+concentrations when exposed to GSK-J4, consistent with a model of inhibitor-mediated metal transport. Comparisons of GSK-J4 and ZnSO4treatments in the presence or absence of metal chelators show that both treatment conditions induce different transcription factor repertoires with an overlapping MTF1 transcriptional regulation responsible for metallothionein and metal ion transport regulation. The data provide a possible explanation for the observed metal response upon GSK-J4 inhibition however the relationship with the pro-apoptotic mechanism in myeloma cells requires further investigation.
Eliminating Aggressive Cancers via PROTAC-like Inducers of Ferroptosis
Authors: Oknin-Vaisman Avital , Panda Deepanjan , Novak Rostislav , Bitman-Lotan Eliya , Pahor Nikolett , Ahmed Yamen Abu , Kamnesky Guy , Diefenbacher Markus E. , Brik Ashraf , Orian Amir 
Published: December 2024

AbstractAggressive and therapy-resistant cancers present a significant challenge to treatment and are associated with poor patients’ survival. Identifying molecular pathways and compounds that target these pathways is critical for improving patient outcomes. RNF4, an E3-ubiquitin ligase, is pivotal in oncoprotein stabilization and DNA repair, enhancing cancer cell survival driving tumorigenesis. Elevated RNF4 levels are associated with poor prognosis in cancer patients. Here, we describe the development of R4VPs, proteolysis-targeted chimeras-like (PROTACs-like). R4VPs promote RNF4 degradation and reduce the levels of its stabilized oncoproteins. Notably, R4VPs induce ferroptotic cell death selectively in cancer cells, sparing non-tumorigenic and primary cells. Surprisingly, R4VPs-induced ferroptosis is independent of RNF4 but preferentially targets tumor-driving mutations, particularly those in the EGFR pathway, while not affecting PI3K-transformed cells. R4VPs effectively induce cell death in therapy-resistant melanoma and sarcomas including patient-derived sarcoma tumor cells. Our findings highlight the potential of ferroptosis inducers such as R4VPs as a therapeutic strategy for therapy resistance, aggressive, and hard-to-treat cancers.TeaserR4VPs induce ferroptotic death of melanoma and sarcoma cells including patient-derived tumor cells sparing non-transomed cells.
Base edited “universal” donor CAR T cell strategies for acute myeloid leukaemia
Authors: Kadirkamanathan Renuka , Georgiadis Christos , Kloos Arnold , Etuk Annie , Preece Roland , Gough Oliver , Schambach Axel , Sauer Martin , Heuser Michael , Qasim Waseem 
Published: December 2024

AbstractAcute myeloid leukaemia (AML) is often aggressive and life-threatening with limited curative options. Immunotherapies including chimeric antigen receptor (CAR) T cell approaches are under investigation, but high levels of disease heterogeneity remain a major hurdle to achieving durable responses. Targeting of multiple surface antigens may ensure complete immunological coverage of leukemic blast populations, but such antigens are often also present on healthy haematopoietic populations. To address likely aplasia, strategies can be designed to bridge CAR T cell therapies to allogeneic stem cell transplantation (allo-SCT), as demonstrated in recent anti-CD7 CAR T cell studies. Here we report that monotherapy using base edited (BE) ‘universal’ donor CAR T cells against CD33, CLL-1, or CD7 delivered inhibition of AML in immunodeficient mice when antigen expression was homogenous, but combined use of BE-CAR33 and BE-CARCLL-1 T cells was required to address heterogenous CLL-1-/+CD33-/+disease. We also demonstrate that removal of shared CD7 antigens enabled compatibility of BE-CAR33 with BE-CAR7 T cells, including in a patient-derived xenograft (PDX) model of AML. Therapeutic strategies envisage ‘pick and mix’ applications of base edited universal CAR T cells in combinations determined by patient-specific antigen profiles. Such approaches also offer the possibility of deep, cell-based, de-bulking and preparative conditioning ahead of allo-SCT followed by donor-derived reconstitution.
Dynamic Coupling and Entropy Changes in KRAS G12D Mutation: Insights into Molecular Flexibility, Allostery and Function
Authors: Hacisuleyman Aysima , Yuret Deniz , Erman Burak 
Published: December 2024

AbstractThe oncogenic G12D mutation in KRAS is a major driver of cancer progression, yet the complete mechanism by which this mutation alters protein dynamics and function remains incompletely understood. Here, we investigate how the G12D mutation alters KRAS’s conformational landscape and residue-residue interactions using molecular dynamics simulations coupled with entropy calculations and mutual information (MI) analysis. We demonstrate that the mutation increases local entropy at key functional residues (D12, Y32, G60, and Q61), and introduces new peaks to the Ramachandran angles, disrupting the precise structural alignment necessary for GTP hydrolysis. Notably, while individual residue entropy increases, joint entropy analysis shows a complex reorganization pattern. MI analysis identifies enhanced dynamic coupling between distant residues, suggesting that the mutation establishes new long-range interactions that stabilize the active state. These findings show how G12D mutation redefines KRAS’s dynamic network, leading to persistent activation through enhanced residue coupling rather than mere local disruption. Our results suggest novel therapeutic strategies focused on modulating protein dynamics rather than targeting specific binding sites, potentially offering new approaches to combat KRAS-driven cancers.HighlightsThe G12D mutation increases entropy and mutual information between residue pairs, resulting in more correlated motions due to enhanced flexibility.Characteristic features of local and long-range allostery in wild-type (WT) and G12D KRAS are determined using structural proximity and mutual information analysis.The dynamics of KRAS interactions with its natural ligand atoms and the coordination of bridging water molecules provide insights into the changes induced by the G12D mutation.
Molecular determinants underlying differential recruitment of p115RhoGEF and PDZRhoGEF to activated Gα13
Authors: Fassler Bakhman Anna , Lukasheva Viktoriya , Le Gouill Christian , Kosloff Mickey , Bouvier Michel 
Published: December 2024

ABSTRACTHeterotrimeric G proteins, particularly Gα12and Gα13, are pivotal regulators of cellular signaling pathways. Their direct downstream effectors, which include p115RhoGEF and PDZRhoGEF, engage downstream signaling via Rho activation. Yet the molecular determinants that dictate their differential recruitment by Gα12/13are not fully understood. Here, we combined quantitative computational residue-level analysis with site-directed mutagenesis and bioluminescence resonance energy transfer (BRET)-based assays to dissect Gα13interactions with these RhoGEFs. We mapped the contributions of individual residues to binding and identified specific Gα13residues in its helical domain, switch regions, and effector-binding site as key yet differential contributors to p115RhoGEF and PDZRhoGEF recruitment. Experimental validation with BRET confirmed that changes in many Gα13residues impact p115RhoGEF more substantially than PDZRhoGEF, underscoring the specificity of Gα13interactions with p115RhoGEF. Investigation of the p115RhoGEFs identified critical residues that contribute to interactions with Gα13and Gα12. Our findings highlight residue-level differences in the molecular interactions of Gα13with p115RhoGEF and PDZRhoGEF, providing insights into the specificity and regulation of Gα13-mediated signaling pathways. The resulting residue-level maps lay the groundwork for development of selective therapeutic strategies targeting Gα13-RhoGEF interactions.
Multifaceted B-cell response to transient HIV viraemia in elite controllers
Authors: Muir Luke , Suchanek Ondrej , Thomas Peter , Griffith Sarah A. , Touizer Emma , Rees-Spear Chloe , Yoshida Masahiro , Pinder Christopher L. , Nikolic Marko Z. , Doores Katie J. , Van Gils Marit J. , Gupta Ravindra K. , Clatworthy Menna R. , McCoy Laura E. 
Published: December 2024

ABSTRACTChronic HIV infection drives B-cell dysfunction associated with the accumulation of tissue-like memory (TLMs) and activated memory B cells (MBCs) but decline in resting memory B cells. TLMs express multiple inhibitory receptors and lack response to soluble antigens. However, their origin and the mechanisms driving their expansion in HIV infection remain unclear. By using bulk BCR sequencing of memory B cell subsets from elite HIV controllers and an ART-controlled cohort, we revealed that TLMs (CD21-CD27-B cells) were significantly less mutated but also less diverse than other MBCs, suggesting an enrichment for innate-like B cells or that they belong to a less mature subset. Subsequent detailed multi-omics study of an immune response in an elite controller to a transient HIV viraemia demonstrated a functional increase in Env-reactive IgG and MBCs with non-TLM phenotype. Single-cell RNA/BCR sequencing of PMBCs enriched for B cells revealed an orchestrated TNF-alpha response followed by interferon alpha and gamma response across all B cells subsets. We noted an emergence of innate-like extrafollicular PLD4+ plasmablasts and previously undepreciated heterogeneity of a stable TLM population. We identified two distinct TLM subsets: TLM1 (T-betlow) and TLM2 (T-bethi) that differed in their differentiation stage, isotype use and mutational burden. Surprisingly, both subsets (TLM1 more than TLM2) were enriched for IGHV4-34 segment use (associated with self-reactivity) and displayed a persistent activation and BCR signalling signature, indicating (with other BCR indices) a strong presence of innate-like B cells. However, pseudotime analyses revealed that TLMs contained not only innate-like B cells but also cells from the conventional memory B cell lineages, further highlighting the complexity of the whole TLM compartment. This study provides a new insight into multifaceted functional B-cell response to transient HIV viraemia as likely happens during the early phase of anti-retroviral therapy cessation, highlighting the TLM heterogeneity and the contribution of innate-like B cells which might have important clinical implications for anti-HIV vaccine and therapy design.
Volitional stopping is preceded by a transient beta oscillation
Authors: Doutel Figueira Joana F. , Ojala Reetta A. , Vasilev Dmitrii , De Miguel Alejandro , Jeay-Bizot Lucas , Iwai Ryo , Raposo Isabel , Safaei Negar , de Sardenberg Schmid Lilian , Maoz Uri , Watanabe Masataka , Totah Nelson K. 
Published: December 2024

AbstractHuman motor cortex EEG beta (15-30 Hz) oscillations undergo transient power modulations (bursts) during volitional control of movements. They are a potential control signal for brain-machine interfaces and are a therapeutic target in Parkinson’s disease. The prevailing view is that EEG beta bursts increase during stopping and immobility, but do not precede stopping. In contrast to prior work in humans and animals that used a latent and unobservable stopping time in the stop-signal task, we developed a translational animal model to align EEG with overt action stopping. We recorded 32-electrode EEG along with the angular velocity of a treadmill while head-fixed rats stopped in-progress running on a freely-rotating, non-motorized treadmill. Contrasting prior work, motor cortex beta bursts increased before stopping and not during stopping or immobility. Using information theoretic measures, we show that beta power was informative about treadmill velocity 200 msec in the future, but only during planning to stop. By introducing artificial temporal jitter to mimic the estimation of stopping time used in prior work, we show that this predictive brain-action relationship fails with even small jitter. Finally, we use a variety of machine learning methods to show that, despite EEG beta oscillations being a clear neural correlate preceding stopping, it has limited utility for real-time action decoding. Our work suggests a new conceptual model for neural control of action stopping.