bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hematopoietic stem cell division is governed by distinct RUNX1 binding partners
Authors: Robertson Anne L. , Yue Lu , Choudhuri Avik , Kubaczka Caroline , Wattrus Samuel J. , Mandelbaum Joseph , Avagyan Serine , Yang Song , Freeman Rebecca J. , Chan Victoria , Blair Megan C. , Daley George Q. , Zon Leonard I. 
Published: June 2024

AbstractA defined number of hematopoietic stem cell (HSC) clones are born during development and expand to form the pool of adult stem cells. An intricate balance between self-renewal and differentiation of these HSCs supports hematopoiesis for life. HSC fate is determined by complex transcription factor networks that drive cell-type specific gene programs. The transcription factor RUNX1 is required for definitive hematopoiesis, and mutations in Runx1 have been shown to reduce clonal diversity. The RUNX1 cofactor, CBFý, stabilizes RUNX1 binding to DNA, and disruption of their interaction alters downstream gene expression. Chemical screening for modulators of Runx1 and HSC expansion in zebrafish led us to identify a new mechanism for the RUNX1 inhibitor, Ro5-3335. We found that Ro5-3335 increased HSC divisions in zebrafish, and animals transplanted with Ro5-3335 treated cells had enhanced chimerism compared to untreated cells. Using human CD34+ cells, we show that Ro5-3335 remodels the RUNX1 transcription complex by binding to ELF1, independent of CBFý. This allows specific expression of cell cycle and hematopoietic genes that enhance HSC self-renewal and prevent differentiation. Furthermore, we provide the first evidence to show that it is possible to pharmacologically increase the number of stem cell clonesin vivo, revealing a previously unknown mechanism for enhancing clonal diversity. Our studies have revealed a mechanism by which binding partners of RUNX1 determine cell fate, with ELF transcription factors guiding cell division. This information could lead to treatments that enhance clonal diversity for blood diseases.
A first-in-Plasmodiumstudy on tRNA intron splicing endonuclease ‘PfTSEN1’ and its substrate expression in clinical stage malaria
Authors: Maurya Mukesh Kumar , Behl Ankita , Kahlon Amandeep Kaur , Leon Fernando De , Middha Palak , Nirban Reena , Joshi Prerna , Singhal Jhalak , Kumari Geeta , Munjal Akshay , Shoaib Rumaisha , Jha Neha , Pandey Jagriti , Dutta Tanmay , Arenz Christoph , Ranganathan Anand , Singh Shailja 
Published: June 2024

AbstractMature tRNAs play critical role in several cellular processes including protein translation, post-translational-modifications and programmed-cell-death. Maturation of pre-tRNAs require removal of 5’-leaders, 3’-trailers, splicing of introns and addition of conserved 3’-terminal CCA sequence. The tRNA splicing mechanism, an essential step in tRNA maturation govern by a tRNA splicing endonuclease. While the existence of functional tRNA splicing endonuclease(s) inPlasmodium falciparumhas not been identified, its significance in other eukaryotes suggests a potential role in tRNA splicing event. Our study identified total tRNAs inPlasmodiumand characterize aPftRNA splicing endonuclease (annotated asPfTSEN1) recognised recently as a component of ribonucleoprotein (RNP) complex, and synthesized a naphthoquinone derivative as a novel anti-malarial compound (‘TSENi’) targeting the functional activity of this protein. Enzyme activity assays elucidated thatPfTSEN1 catalyses splicing ofin vitrotranscribed pre-tRNAleu, the expression of which was confirmed during the clinical stages of malaria parasite by RT-PCR. Interestingly, TSENibinds to and inhibits enzymatic activity ofPfTSEN1, and showed potent anti-malarial activity against chloroquine-sensitive 3D7 and resistant strains Dd2 ofP. falciparum. Overall, our study deliver key knowledge towards the functional role ofPftRNA splicing endonuclease, and its inhibitor TSENias potent anti-malarial.
Structural Basis for Polθ-Helicase DNA Binding and Microhomology-Mediated End-Joining
Authors: Ito Fumiaki , Li Ziyuan , Minakhin Leonid , Khant Htet A. , Pomerantz Richard T. , Chen Xiaojiang S. 
Published: June 2024

AbstractDNA double-strand breaks (DSBs) present a critical threat to genomic integrity, often precipitating genomic instability and oncogenesis. Repair of DSBs predominantly occurs through homologous recombination (HR) and non-homologous end joining (NHEJ). In HR-deficient cells, DNA polymerase theta (Polθ) becomes critical for DSB repair via microhomology-mediated end joining (MMEJ), also termed theta-mediated end joining (TMEJ). Thus, Polθ is synthetically lethal with BRCA1/2 and other HR factors, underscoring its potential as a therapeutic target in HR-deficient cancers. However, the molecular mechanisms governing Polθ-mediated MMEJ remain poorly understood. Here we present a series of cryo-electron microscopy structures of the Polθ helicase domain (Polθ-hel) in complex with DNA containing 3′-overhang. The structures reveal the sequential conformations adopted by Polθ-hel during the critical phases of DNA binding, microhomology searching, and microhomology annealing. The stepwise conformational changes within the Polθ-hel subdomains and its functional dimeric state are pivotal for aligning the 3′-overhangs, facilitating the microhomology search and subsequent annealing necessary for DSB repair via MMEJ. Our findings illustrate the essential molecular switches within Polθ-hel that orchestrate the MMEJ process in DSB repair, laying the groundwork for the development of targeted therapies against the Polθ-hel.
A VLP vaccine platform comprising the core protein of hepatitis B virus with N-terminal antigen capture
Authors: Fatema Kaniz , Snowden Joseph S. , Watson Alexander , Sherry Lee , Ranson Neil A. , Stonehouse Nicola J. , Rowlands David J. 
Published: June 2024

AbstractNanoparticle presentation systems offer the potential to develop new vaccines rapidly in response to emerging diseases, a public health need that has become increasingly evident in the wake of the COVID-19 pandemic. Previously, we reported a nanoparticle scaffold system termed VelcroVax. This was constructed by insertion of a high affinity SUMO binding protein (Affimer), able to recognise a SUMO peptide tag, into the major immunodominant region of VLPs assembled from a tandem (fused dimer) form of hepatitis B virus (HBV) core protein (HBc). Here we describe a modified form of VelcroVax, comprising monomeric HBc with the Affimer inserted at the N-terminus (termed N-VelcroVax). In contrast to the tandem form of VelcroVax, N-VelcroVax VLPs were expressed well inE. coli.The VLPs effectively bound SUMO-tagged Junín virus glycoprotein, gp1 as assessed by structural and serological analyses. Cryo-EM characterisation of N-VelcroVax complexed with a SUMO-Junín gp1 showed continuous density attributable to the fused Affimer, in addition to evidence of target antigen capture. Collectively, these data suggest that N-VelcroVax has potential as a versatile next generation vaccine scaffold.
Neural basis of cognitive control signals in anterior cingulate cortex during delay discounting
Authors: Seamans Jeremy K. , White Shelby , Morningstar Mitchell , Emberly Eldon , Linsenbardt David , Ma Baofeng , Czachowski Cristine L. , Lapish Christopher C. 
Published: June 2024

SummaryCognitive control involves allocating cognitive effort according to internal needs and task demands and the Anterior Cingulate Cortex (ACC) is hypothesized to play a central role in this process. We investigated the neural basis of cognitive control in the ACC of rats performing an adjusting-amount delay discounting task. Decision-making in this this task can be guided by using either a lever-value tracking strategy, requiring a ‘resource-based’ form of cognitive effort or a lever-biased strategy requiring a ‘resistance-based’ form of cognitive effort. We found that ACC ensembles always tightly tracked lever value on each trial, indicative of a resource-based control signal. These signals were prevalent in the neural recordings and were influenced by the delay. A shorter delay was associated with devaluing of the immediate option and a longer delay was associated with overvaluing of the immediate option. In addition, ACC theta (6-12Hz) oscillations were observed at the choice point of rats exhibiting a resistance-based strategy. These data provide candidates of neural activity patterns in the ACC that underlie the use of ‘resource-based’ and ‘resistance-based’ cognitive effort. Furthermore, these data illustrate how strategies can be engaged under different conditions in individual subjects.
Mechanisms of gene regulation by SRCAP and H2A.Z
Authors: Tollenaere Armelle , Ugur Enes , Dalla-Longa Susanna , Deluz Cédric , Assenheimer Devin , Gebhardt J Christof M , Leonhardt Heinrich , Suter David M 
Published: June 2024

AbstractDiscriminating regulatory functions of chromatin composition from those of chromatin-modifying complexes is a central problem in gene regulation. This question remains unexplored in the context of histone variants and their dedicated chromatin remodelers. Here we dissect the distinct and cell cycle-dependent functions of Snf2 Related CREBBP Activator Protein (SRCAP) and H2A.Z in gene regulation of pluripotent stem cells. We uncover dynamic changes of H2A.Z occupancy and continuous requirement of SRCAP over the cell cycle. We discover that SRCAP exhibits essential H2A.Z-independent functions in inhibiting DNA binding of dozens of pioneer transcription factors at enhancers by steric hindrance. In contrast, H2A.Z acts mainly as a transcriptional repressor gatekeeping the expression of lineage-specific genes. Our study establishes the catalytic-independent role of a chromatin remodeler in broadly regulating transcription factor binding, and demonstrates how a chromatin remodeler-histone variant pair orchestrates transcription to maintain self-renewal and plasticity of pluripotent stem cells.
Bursts boost nonlinear encoding in electroreceptor afferents
Authors: Barayeu Alexandra , Schlungbaum Maria , Lindner Benjamin , Grewe Jan , Benda Jan 
Published: June 2024

AbstractNonlinear mechanisms are at the heart of neuronal information processing, for example to fire an action potential, the membrane voltage must exceed a threshold nonlinearity. Even though, linear encoding schemes are commonly used and often successfully describe large parts of sensory encoding nonlinear mechanisms such as thresholds and saturations are well known to be crucial to encode behaviorally relevant features in the stimulus space not captured by linear methods. Here we analyze the role of bursts in p-type electroreceptor afferents (P-units) in the weakly electric fishApteronotus leptorhynchus. It is long known that subpopulations of these cells fire bursts of action potentials while others do not. Previous research suggests, that the non-bursting cells are better at encoding the stimulus time-course while bursting neurons are better suited to encode special features in the stimulus. We here show, based on the analysis of experimental data and modeling, that bursts affect the linear as well as the nonlinear encoding. Theoretical work predicts that in simple leaky-integrate-and-fire model neurons, two periodic stimuli interact nonlinearly when the sum of the two frequencies matches the neuron’s baseline firing rate as quantified by the second-order susceptibility. Indeed, such nonlinear responses have been found in non-bursting P-units when stimulated by two beats simultaneously but only in those cells, that exhibit very low levels of intrinsic noise. In this study, we found that bursts strongly enhance these nonlinear responses which may play a critical role in the detection of weak intruder signals in the presence of a strong female signal, i.e. an electrosensory cocktail party.
Enhancing oncolytic virotherapy by exosome-mediated microRNA reprograming of the tumour microenvironment
Authors: Jennings Victoria A. , Rumbold-Hall Reah , Migneco Gemma , Barr Tyler , Reilly Katarina , Ingram Nicola , Hilare Isabelle St , Heaton Samuel , Alzamel Noura , Jackson David , Ralph Christy , McNeish Iain , Bell John C. , Melcher Alan A. , Ilkow Carolina , Cook Graham , Errington-Mais Fiona 
Published: June 2024

AbstractBackgroundThere has been limited success of cancer immunotherapies in the treatment of ovarian cancer (OvCa) to date, largely due to the immunosuppressive tumour microenvironment (TME). Tumour-associated macrophages (TAMs) are a major component of both the primary tumour and malignant ascites, promoting tumour growth, angiogenesis, metastasis, chemotherapy resistance and immunosuppression. Differential microRNA (miRNA) profiles have been implicated in the plasticity of TAMs. Therefore, delivering miRNA to TAMs to promote an anti-tumour phenotype is a novel approach to reverse their pro-tumour activity and enhance the efficacy of cancer immunotherapies. Oncolytic viruses (OVs) preferentially replicate in tumour cells making them ideal vehicles to deliver miRNA mimetics to the TME. Importantly, miRNA expressed by OVs get packaged within tumour-derived extracellular vesicles (TDEVs), and release of TDEV is augmented by OV infection, thus enhancing the dissemination of miRNA throughout the TME.MethodSmall RNAseq was used to identify differentially expressed miRNA during TAM generation and following LPS/IFNγ stimulation to induce an anti-tumour phenotype. Two differentially expressed miRNA identified, miR-155 and miR-19a, were cloned into oncolytic rhabdovirus (ORV), and anti-tumour efficacy was investigated using bothin vitroandin vivomodels of OvCa.ResultsThis study demonstrates that ORV infection enhances TDEV production in OvCa cell lines bothin vitroandin vivoand that TDEV are preferentially taken up by myeloid cells, including TAMs. Small RNAseq identified 23 miRNAs that were significantly upregulated in anti-tumour TAMs, including miR-155-5p. While 101 miRNAs were downregulated during pro-tumour TAM differentiation, including miR-19a-3p. Culturing TDEV expressing miR-155 or miR-19a with TAMs reversed their immunosuppressive activity, as measured by T cell proliferation. While ORV-miR-155 enhanced the generation of anti-tumour T cells, only ORV-miR19a significantly improved survival of mice bearing ovarian tumours.ConclusionThis study demonstrates (i) that arming ORVs with immunomodulatory miRNA is an effective approach to deliver miRNA to myeloid cells within the TME and (ii) that miRNA have the capacity to reverse the tumour promoting properties of TAMs and improve the efficacy of cancer immunotherapies, such as OV.
PLA2G15 is a Lysosomal BMP Hydrolase and its Targeting Ameliorates Lysosomal Disease
Authors: Nyame Kwamina , Xiong Jian , Alsohybe Hisham N. , de Jong Arthur PH , Peña Isabelle V. , de Miguel Ricardo , Brummelkamp Thijn R. , Hartmann Guido , Nijman Sebastian M.B. , Raaben Matthijs , Simcox Judith A. , Blomen Vincent A. , Abu-Remaileh Monther 
Published: June 2024

AbstractLysosomes catabolize lipids and other biological molecules, a function essential for cellular and organismal homeostasis. Key to lipid catabolism in the lysosome is bis(monoacylglycero)phosphate (BMP), a major lipid constituent of intralysosomal vesicles and a stimulator of lipid-degrading enzymes. BMP levels are altered in a broad spectrum of human conditions, including neurodegenerative diseases. While a lysosomal BMP synthase was recently discovered, the enzymes that mediate BMP turnover has remained elusive. Here we show that the lysosomal phospholipase PLA2G15 is a physiological BMP hydrolase. We further demonstrate that BMP’s resistance to hydrolysis in the lysosome is conferred by the combination of its uniquesn2, sn2’esterification position and stereochemistry, as neither feature alone is sufficient to provide this resistance. Purified PLA2G15 catabolizes most BMP species derived from cell and tissue lysosomes under acidic conditions. Furthermore, PLA2G15 catalytic activity against synthesized BMP stereoisomers with primary esters was comparable to its canonical substrates challenging the long-held thought that BMP’s unique stereochemistry is sufficient to confer resistance to acid phospholipases. Conversely, BMP with secondary esters andS,Sstereoconfiguration is intrinsically stable in vitro and requires acyl migration for hydrolysis in lysosomes. Consistent with our biochemical data, PLA2G15-deficient cells and tissues accumulate multiple BMP species, a phenotype reversible by supplementing wildtype PLA2G15 but not its catalytically dead mutant. In addition, targeting PLA2G15 to increase BMP reverses the cholesterol phenotype in Niemann Pick Disease Type C (NPC1) patient fibroblasts and significantly ameliorates disease pathologies in NPC1-deficient mice leading to extended lifespan. Our findings establish the rules that govern the stability of BMP in the lysosome and identify PLA2G15 as a lysosomal BMP hydrolase and a potential target for therapeutic intervention in neurodegenerative diseases.
Determinants of raffinose family oligosaccharide use inBacteroidesspecies
Authors: Basu Anubhav , Adams Amanda N.D. , Degnan Patrick H. , Vanderpool Carin K. 
Published: June 2024

AbstractBacteroidesspecies are successful colonizers of the human gut and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in Polysaccharide Utilization Loci (PULs). While recent work has uncovered the PULs required for use of some polysaccharides, howBacteroidesutilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by ⍺-1,6 bonds to a sucrose (glucose ⍺-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization inBacteroides thetaiotaomicron. Here, we identify two different types of mutations that increaseBT1871mRNA levels and improveB. thetaiotaomicrongrowth on RFOs. First, a novel spontaneous duplication ofBT1872andBT1871places these genes under control of a ribosomal promoter, driving highBT1871transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increaseBT1871transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization inB. thetaiotaomicron. Examining the genomes of otherBacteroidesspecies, we found homologs of BT1871 in subset and show that representative strains of species containing a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide.ImportanceThe gut microbiome is important in health and disease. The diverse and densely populated environment of the gut makes competition for resources fierce. Hence, it is important to study the strategies employed by microbes for resource usage. Raffinose family oligosaccharides are abundant in plants and are a major source of nutrition for the gut microbiota since they remain undigested by the host. Here, we study how the model gut commensal,Bacteroides thetaiotaomicronutilizes raffinose family oligosaccharides. This work highlights how an important member of the microbiota uses an abundant dietary resource.
The combination of three CD4-induced antibodies targeting highly conserved Env regions with a small CD4-mimetic achieves potent ADCC activity
Authors: Marchitto Lorie , Richard Jonathan , Prévost Jérémie , Tauzin Alexandra , Yang Derek , Chiu Ta-Jung , Chen Hung-Ching , Díaz-Salinas Marco A. , Nayrac Manon , Benlarbi Mehdi , Beaudoin-Bussières Guillaume , Anand Sai Priya , Dionne Katrina , Bélanger Étienne , Chatterjee Debashree , Medjahed Halima , Bourassa Catherine , Tolbert William D. , Hahn Beatrice H. , Munro James B. , Pazgier Marzena , Smith Amos B. , Finzi Andrés 
Published: June 2024

ABSTRACTThe majority of naturally-elicited antibodies against the HIV-1 envelope glycoproteins (Env) are non-neutralizing (nnAbs), because they are unable to recognize the Env timer in its native “closed” conformation. Nevertheless, it has been shown that nnAbs have the potential to eliminate HIV-1-infected cells by Antibody-Dependent Cellular Cytotoxicity (ADCC) provided that Env is present on the cell surface in its “open” conformation. This is because most nnAbs recognize epitopes that become accessible only after Env interaction with CD4 and the exposure of epitopes that are normally occluded in the closed trimer. HIV-1 limits this vulnerability by downregulating CD4 from the surface of infected cells, thus preventing a premature encounter of Env with CD4. Small CD4-mimetics (CD4mc) sensitize HIV-1-infected cells to ADCC by opening the Env glycoprotein and exposing CD4-induced (CD4i) epitopes. There are two families of CD4i nnAbs, termed anti-cluster A and anti-CoRBS Abs, which are known to mediate ADCC in the presence of CD4mc. Here, we performed Fab competition experiments and found that anti-gp41 cluster I antibodies comprise a major fraction of the plasma ADCC activity in people living with HIV (PLWH). Moreover, addition of gp41 cluster I antibodies to cluster A and CoRBS antibodies greatly enhanced ADCC mediated cell killing in the presence of a potent indoline CD4mc, CJF-III-288. This cocktail outperformed broadly-neutralizing antibodies and even showed activity against HIV-1 infected monocyte-derived macrophages. Thus, combining CD4i antibodies with different specificities achieves maximal ADCC activity, which may be of utility in HIV cure strategies.IMPORTANCEThe elimination of HIV-1-infected cells remains an important medical goal. While current antiretroviral therapy decreases viral loads below detection levels, it does not eliminate latently infected cells which form the viral reservoir. Here, we developed a cocktail of non-neutralizing antibodies targeting highly conserved Env regions and combined it with a potent indoline CD4mc. This combination exhibited very potent ADCC activity against HIV-1-infected primary CD4+ T cells as well as monocyte-derived macrophages, suggesting its potential utility in decreasing the size of the viral reservoir.