bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-molecule characterisation of soluble beta-amyloid aggregate binding by Aducanumab, Lecanemab, Gantenerumab, and Donanemab
Authors: Fertan Emre , Lam Jeff Y. L. , Albertini Giulia , Dewilde Maarten , Wu Yunzhao , Akingbade Oluwatomi E. S. , Böken Dorothea , English Elizabeth A. , De Strooper Bart , Klenerman David 
Published: October 2024

AbstractMonoclonal antibodies Aducanumab, Lecanemab, Gantenerumab, and Donanemab have been developed for treatment of Alzheimer’s disease. Here, we have used single-molecule detection techniques and super-resolution imaging to characterise the binding of these antibodies to beta-amyloid aggregates including human post-mortem brain samples. Lecanemab is the best antibody in terms of binding to the small-soluble beta-amyloid aggregates, affinity, aggregate coating, and the ability to bind to post-translationally modified species, explaining its therapeutic success.
Amino acid-level differences in alpha tubulin sequences are uniquely required for meiosis
Authors: Chen Li , Chen Xi , Kashina Anna 
Published: October 2024

SUMMARYTubulin is the major structural constituent of the microtubule cytoskeleton. YeastSchizosaccharomyces pombecontain two α- tubulins genes,nda2andatb2, that are highly functionally distinct:nda2deletion is lethal, while lack ofatb2does not interfere with cell viability. The functional determinants underlying this distinction are unknown. Here we used CRISPR-Cas9 gene editing to generate a yeast strain expressing Atb2 amino acid sequence utilizing Nda2 codon usage in the native Nda2 locus. Such Nda2-coded Atb2 (NCA) yeast, unlike Nda2 knockout, were viable and displayed no visible abnormalities in cell morphology or vegetative life cycle. However, these NCA yeast showed strong impairments in sporulation and meiosis, including major meiotic delays and high rates of abnormal chromosome segregation. Our data indicate that the amino acid sequence of Nda2 is uniquely required for normal meiosis, and identify a novel determinant that underlies functional distinction between closely related tubulin isoforms.
Cocaine taking and craving produce distinct transcriptional profiles in dopamine neurons
Authors: Pollock Tate A. , Margetts Alexander V. , Vilca Samara J. , Tuesta Luis M. 
Published: October 2024

ABSTRACTDopamine (DA) signaling plays an essential role in reward valence attribution and in encoding the reinforcing properties of natural and artificial rewards. The adaptive responses from midbrain dopamine neurons to artificial rewards such as drugs of abuse are therefore important for understanding the development of substance use disorders. Drug-induced changes in gene expression are one such adaptation that can determine the activity of dopamine signaling in projection regions of the brain reward system. One of the major challenges to obtaining this understanding involves the complex cellular makeup of the brain, where each neuron population can be defined by a distinct transcriptional profile. To bridge this gap, we have adapted a virus-based method for labeling and capture of dopamine nuclei, coupled with nuclear RNA-sequencing, to study the transcriptional adaptations, specifically, of dopamine neurons in the ventral tegmental area (VTA) during cocaine taking and cocaine craving, using a mouse model of cocaine intravenous self-administration (IVSA). Our results show significant changes in gene expression across non-drug operant training, cocaine taking, and cocaine craving, highlighted by an enrichment of repressive epigenetic modifying enzyme gene expression during cocaine craving. Immunohistochemical validation further revealed an increase of H3K9me3 deposition in DA neurons during cocaine craving. These results demonstrate that cocaine-induced transcriptional adaptations in dopamine neurons vary by phase of self-administration and underscore the utility of this approach for identifying relevant phase-specific molecular targets to study the behavioral course of substance use disorders.
When Rivals Are Absent: Male Aggression Towards Females in Bluefin Killifish
Authors: Karatgi Ratna , Fuller Rebecca C. 
Published: October 2024

AbstractThe process of obtaining mates, mating, and (potentially) caring for offspring is costly. While there are inherent costs to reproduction, behavioral interactions among individuals are often the primary drivers of reproductive costs. Males frequently compete for territories and females; females may compete for food or males; males often harass females. Here, we sought to determine whether reproductive costs were primarily due to male/male competition, female/female competition, or male/female interactions in the bluefin killifish. In this species, males guard small spawning territories where females visit them daily to spawn. To manipulate the potential for male and female competition and male/female interactions, we altered the sex ratio and density of each sex across four treatments (1 male: 1 female, 1 male : 3 females, 3 males: 1 female, 3 males: 3 females). Female mortality was higher than male mortality. Surprisingly, female mortality and male aggressive behaviors towards females (i.e., chases) were highest in treatments with a single male. Male-male aggression was present, but males often resolved these disputes via signaling by flaring their fins. There was little evidence for overt aggression among females. When males lack rivals, they turn their territorial defense towards females. These costs help explain why, in nature, females promptly leave male territories following spawning and join loose shoals with conspecific females and minnows.
miR126-mediated impaired vascular integrity in Rett syndrome
Authors: Osaki Tatsuya , Wan Zhengpeng , Haratani Koji , Jin Ylliah , Campisi Marco , Barbie David A. , Kamm Roger , Sur Mriganka 
Published: October 2024

AbstractRett syndrome (RTT) is a neurodevelopmental disorder that is caused by mutations in melty-CpG binding protein 2 (MeCP2). MeCP2 is a non-cell type-specific DNA binding protein, and its mutation influences not only neural cells but also non-neural cells in the brain, including vasculature associated with endothelial cells. Vascular integrity is crucial for maintaining brain homeostasis, and its alteration may be linked to the pathology of neurodegenerative disease, but a non-neurogenic effect, especially the relationship between vascular alternation and Rett syndrome pathogenesis, has not been shown. Here, we recapitulate a microvascular network using Rett syndrome patient-derived induced pluripotent stem (iPS) cells that carry MeCP2[R306C] mutation to investigate early developmental vascular impact. To expedite endothelial cell differentiation, doxycycline (DOX)-inducible ETV2 expression vectors were inserted into the AAVS1 locus of Rett syndrome patient-derived iPS cells and its isogenic control by CRISPR/Cas9. With these endothelial cells, we established a disease microvascular network (Rett-dMVNs) and observed higher permeability in the Rett-dMVNs compared to isogenic controls, indicating altered barrier function by MeCP2 mutation. Furthermore, we unveiled that hyperpermeability is involved in the upregulation of miR126-3p in Rett syndrome patient-derived endothelial cells by microRNA profiling and RNAseq, and rescue of miR126-3p level can recover their phenotype. We discover miR126-3p-mediated vascular impairment in Rett syndrome patients and suggest the potential application of these findings for translational medicine.
Striatal lateral inhibition regulates action selection in a mouse model of levodopa-induced dyskinesia
Authors: Twedell Emily L. , Bair-Marshall Chloe J. , Girasole Allison E. , Scaria Lara K. , Sridhar Sadhana , Nelson Alexandra B. 
Published: October 2024

SUMMARYStriatal medium spiny neurons (MSNs) integrate multiple external inputs to shape motor output. In addition, MSNs form local inhibitory synaptic connections with one another. The function of striatal lateral inhibition is unknown, but one possibility is in selecting an intended action while suppressing alternatives. Action selection is disrupted in several movement disorders, including levodopa-induced dyskinesia (LID), a complication of Parkinson’s disease (PD) therapy characterized by involuntary movements. Here, we identify chronic changes in the strength of striatal lateral inhibitory synapses in a mouse model of PD/LID. These synapses are also modulated by acute dopamine signaling. Chemogenetic suppression of lateral inhibition originating from dopamine D2 receptor-expressing MSNs lowers the threshold to develop involuntary movementsin vivo, supporting a role in motor control. By examining the role of lateral inhibition in basal ganglia function and dysfunction, we expand the framework surrounding the role of striatal microcircuitry in action selection.
Species-specific satellite DNA composition dictatesde novoformation of PRC1-mediated pericentric heterochromatin
Authors: Lamelza Piero , Parrado Malena , Hamlin Emma , Lampson Michael A. 
Published: October 2024

AbstractPericentromeres are heterochromatic regions adjacent to centromeres that ensure accurate chromosome segregation. Despite their conserved function, they are composed of rapidly evolving A/T-rich satellite DNA. This paradoxical observation is partially resolved by epigenetic mechanisms that maintain heterochromatin, independent of specific DNA sequences. However, it is unclear how satellite DNA sequence variation impactsde novoformation of pericentric heterochromatin, which is initially absent from paternal chromosomes in the zygote. Here we show that satellite variation has functional consequences for zygotic heterochromatin formation, recruitment of the Chromosome Passenger Complex (CPC), and interactions with spindle microtubules. InM. musculuszygotes, Polycomb Repressive Complex 1 (PRC1) is recruited to pericentric satellites by its AT-hook domain, which binds runs of A/T nucleotides, to generate H2AK119ub1 (H2Aub) heterochromatin. By fertilizingM. musculuseggs with sperm from other mouse species, we show that species-specific satellite sequences differ in their ability to recruit PRC1 and form H2Aub. This satellite-DNA mediated increase in PRC1 heterochromatin leads to reduced CPC recruitment and increased microtubule forces on kinetochores. Our results provide a direct link between satellite DNA composition and pericentromere function in the zygote, when epigenetic pathways maintaining pericentromere heterochromatin are absent.
Active RNA synthesis patterns nuclear condensates
Authors: Banani Salman F. , Goychuk Andriy , Natarajan Pradeep , Zheng Ming M. , Dall’Agnese Giuseppe , Henninger Jonathan E. , Kardar Mehran , Young Richard A. , Chakraborty Arup K. 
Published: October 2024

AbstractBiomolecular condensates are membraneless compartments that organize biochemical processes in cells. In contrast to well-understood mechanisms describing how condensates form and dissolve, the principles underlying condensate patterning – including their size, number and spacing in the cell – remain largely unknown. We hypothesized that RNA, a key regulator of condensate formation and dissolution, influences condensate patterning. Using nucleolar fibrillar centers (FCs) as a model condensate, we found that inhibiting ribosomal RNA synthesis significantly alters the patterning of FCs. Physical theory and experimental observations support a model whereby active RNA synthesis generates a non-equilibrium state that arrests condensate coarsening and thus contributes to condensate patterning. Altering FC condensate patterning by expression of the FC component TCOF1 impairs ribosomal RNA processing, linking condensate patterning to biological function. These results reveal how non-equilibrium states driven by active chemical processes regulate condensate patterning, which is important for cellular biochemistry and function.
Brain Pretargeted PET – New Horizons to Image CNS Targets with Monoclonal Antibodies
Authors: Gustavsson Tobias , Kustermann Thomas , Hvass Lars , Shalgunov Vladimir , Clausen Anne Skovsbo , Stotz Sophie , Wünsche Thomas Erik , Knudsen Gitte M. , Aldana Blanca I. , Niewoehner Jens , Gobbi Luca , Honer Michael , Battisti Umberto , Kjaer Andreas , Herth Matthias M. 
Published: October 2024

AbstractAntibodies are excellent targeting vectors for molecular imaging. Slow pharmacokinetics and low blood-brain barrier penetration hinder their widespread application for molecular imaging within CNS. Improved brain uptake can be achieved via transferrin-mediated transcytosis. Pretargeted imaging can increase imaging contrast and reduce radiation exposure to the patient. Here, we report for the first time that pretargeted imaging of CNS targets using intravenously administered target vectors is feasible. Specific binding to Aβ-bound antibody was achieved. We believe that this proof-of-concept study will facilitate molecular imaging of currently ‘undruggable’ targets with antibodies where small molecule PET tracer discovery has been challenging.
Chromatin Environment-Dependent Effects of DOT1L on Gene Expression in Male Germ Cells
Authors: Coulée Manon , de la Iglesia Alberto , Blanco Mélina , Gobé Clara , Lapoujade Clémentine , Ialy-Radio Côme , Alvarez-Gonzalez Lucia , Meurice Guillaume , Ruiz-Herrera Aurora , Fouchet Pierre , Cocquet Julie , El Khattabi Laïla 
Published: October 2024

AbstractThe H3K79 methyltransferase DOT1L is essential for multiple aspects of mammalian development where it has been shown to regulate gene expression. Here, by producing and integrating epigenomic and spike-in RNA-seq data, we deciphered the molecular role of DOT1L during mouse spermatogenesis and show that it has opposite effects on gene expression depending on chromatin environment. On the one hand, DOT1L represses autosomal genes that are devoid of H3K79me2 at their bodies and located in H3K27me3-rich/H3K27ac-poor environments. On the other hand, it activates the expression of genes enriched in H3K79me2 and located in H3K27me3-poor/H3K27ac-rich environments, predominantly X chromosome-linked genes, after meiosis I. This coincides with a significant increase in DOT1L expression at this stage and a genome-wide acquisition of H3K79me2, particularly on the sex chromosomes. Taken together, our results show that H3K79me2 positively correlates with male germ cell genetic program throughout spermatogenesis, with DOT1L predominantly inhibiting rather than activating gene expression. Interestingly, while DOT1L appears to directly regulate the (re)activation of X genes following meiotic sex chromosome inactivation, it also controls the timely expression of (autosomal) differentiation genes during spermatogenesis.
Improved optogenetic modification of the spiral ganglion neurons for future optical cochlear implants
Authors: Thirumalai Anupriya , Henseler Jana , Enayati Marzieh , Kusch Kathrin , Hessler Roland , Moser Tobias , Huet Antoine Tarquin 
Published: October 2024

AbstractOptogenetic stimulation has become a promising approach for restoring lost body function. For example, partial restoration of vision has been achieved in a blind patient and proof-of-concept has been demonstrated for optogenetic hearing restoration in rodents. In order to prepare clinical translation of hearing restoration, efficient and safe optogenetic modification of spiral ganglion neurons (SGNs) in the mature cochlea remains to be developed. Here, we established microcatheter-based administration adeno-associated virus (AAV) to scala tympani of the cochlea of Mongolian gerbils and compared it to the previously developed AAV-injection into the spiral ganglion. We probed the potential AAV-PHP.S capsid to express channelrhodopsins (ChRs) under the control of the human synapsin promotor in mature SGNs in hearing and deafened gerbils. Using the microcatheter approach, but not with the AAV-modiolus injection, we achieved reliable ChR expression in SGN enabling optogenetic stimulation of the auditory pathway in 80% of the treated animals. Yet, the efficiency of SGN transduction was modest with only ∼30% ChR-expressing SGNs. Moreover, we encountered off-target expression in hair cells in hearing gerbils in both approaches, but not ChR expression in the central nervous system using microcatheter administration. Comparing optogenetic auditory brainstem responses of gerbils with and without hair cell transduction confirmed that SGNs were the primary site of optogenetic stimulation of the pathway.
Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes
Authors: Deka Ranjit K. , Tso Shih-Chia , Liu Wei Z. , Brautigam Chad A. 
Published: October 2024

AbstractUnraveling the metabolism ofTreponema pallidumis a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway inT. pallidumand related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogenTreponema vincentii, TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzyme activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme’s substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, buttressing the existence of the acetogenic pathway in pathogenic treponemes.
High yield purification of an Isoleucine zipper modified CD95 Ligand with either biotin or DNA-oligomer binding domain for efficient Cell Apoptosis Induction
Authors: Shang Xiaoyue , Bartels Nina , Weck Johann Moritz , Suppmann Sabine , Basquin Jérôme , Heuer-Jungemann Amelie , Monzel Cornelia 
Published: October 2024

AbstractBackgroundCluster of differentiation 95 (CD95/Fas/Apo1) as part of the Tumor-necrosis factor (TNF) receptor family is a prototypic trigger of the ‘extrinsic’ apoptotic pathway and its activation by the trimeric ligand CD95L is of high interest for anticancer therapy. However, CD95L, when presented in solution, exhibits a low efficiency to induce apoptosis signaling in human cells.ResultsHere, we design a recombinant CD95L exhibiting an isoleucine zipper (IZ) motif at the N-terminus for stabilization of the trimerized CD95L and demonstrate its high apoptosis induction efficiency. A cysteine amino acid fused behind the IZ is further used as a versatile coupling site for bionanotechnological applications or for the development of biomedical assays. A fast, cheap, and high-yield production of CD95Lviathe HEK293T secretory expression system is presented, along with CD95L affinity purification and functionalization. We verified the biological activity of the purified protein and identified a stabilized trimeric CD95L structure as the most potent inducer of apoptosis signaling.ConclusionsThe workflow and the findings reported here will streamline a wide array of future low- or high-throughput TNF-ligand screens, and their modification towards improving apoptosis induction efficiency and anticancer therapy.
Nerve-associated macrophages control adipose homeostasis across lifespan and restrain age-related inflammation
Authors: Gonzalez-Hurtado Elsie , Leveau Claire , Li Keyi , Qu Rihao , Mishra Manish , Goldberg Emily L. , Sidorov Sviatoslav , Yeung Stephen T. , Khairallah Camille , Gonzalez David , Shepard Taverlyn M. , Camell Christina , Artyomov Maxim N. , Kluger Yuval , Khanna Kamal M. , Dixit Vishwa Deep 
Published: October 2024

AbstractAge-related inflammation or ‘inflammaging’ is a key mechanism that increases disease burden and may control lifespan. How adipose tissue macrophages (ATMs) control inflammaging is not well understood in part because the molecular identities of niche-specific ATMs are incompletely known. Using intravascular labeling to exclude circulating myeloid cells and subsequent single-cell sequencing with orthogonal validation, we define the diversity and alterations in niche resident ATMs through lifespan. Aging led to depletion of vessel-associated macrophages (VAMs), expansion of lipid-associated macrophages (LAMs), and emergence of a unique subset of CD38+age-associated macrophages (AAMs) in visceral white adipose tissue (VAT). Interestingly, CD169+CD11c−ATMs are enriched in a subpopulation of nerve-associated macrophages (NAMs) that declines with age. Depletion of CD169+NAMs in aged mice increases inflammaging and impairs lipolysis suggesting that they are necessary for preventing catecholamine resistance in VAT. These findings reveal specialized ATMs control adipose homeostasis and link inflammation to tissue dysfunction during aging.
Muti-omics characterization reveals brain-wide disruption of synapses and region- and age-specific changes in neurons and glia inSp4mutant mice, a genetic model of schizophrenia and bipolar disorder
Authors: Kwon Min Jee , Perzel Mandell Kira A. , Aryal Sameer , Geng Chuhan , Nicolella Ally A. , Valle-Tojeiro Antia , Natarajan Sahana , Misri Deeksha , Hall Alyssa , Song Bryan J. , Farsi Zohreh , Keshishian Hasmik , Carr Steven A. , Sheng Morgan 
Published: October 2024

AbstractSchizophrenia and bipolar disorder are highly heritable mental illnesses with unclear pathophysiology. Heterozygous loss-of-function mutations ofSp4, a zinc-finger transcription factor, greatly increase risk of schizophrenia and bipolar disorder. To investigate the molecular functions ofSp4in an unbiased mannerin vivo, we performed multi-omics analyses ofSp4mutant mice. Bulk and single nucleus RNA-seq data showed prominent gene expression changes in all brain regions and most cell types, including neuronal and non-neuronal cells. Gene set enrichment analysis of transcriptomic changes revealed alterations in many molecular pathways, including synapse, oxidative phosphorylation, and ribosome. Synapse proteomics ofSp4mutants pointed to impaired glutamatergic signaling and altered presynaptic function. InSp4heterozygous mutant mice, prefrontal cortex and striatum exhibited downregulation of synapse pathways and neuronal hypoactivity at 1 month, associated with reduced sterol biosynthesis in astrocytes, whereas at 3 months, there was a shift to neuronal hyperactivity, concurrent with suppressed immune pathways in the striatal microglia. Furthermore, our study found that much of the transcriptomic changes might be accounted for by a set of transcription regulators (Nr3c1,Creb1, andKdm5b) under the control ofSp4. Overall, this study provides cellular and molecular features resulting fromSp4LoF that may explain the pathophysiology of SCZ-BD psychotic disorder spectrum.