bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of 3D MINFLUX data for quantitative structural biology in cells revisited
Authors: Gwosch Klaus C. , Balzarotti Francisco , Pape Jasmin K. , Hoess Philipp , Ellenberg Jan , Ries Jonas , Matti Ulf , Schmidt Roman , Sahl Steffen J. , Hell Stefan W.
Published: May 2022

Prakash and Curd provide a re-analysis1 of individual datasets taken from our report2 demonstrating MINFLUX 3D imaging in cells. Their evaluation confirms the unique localization precision provided by MINFLUX2,3 featuring a standard deviation of σ = 1-3 nm. We appreciate their confirmation and also welcome the opportunity to clarify their remaining points. The hitherto almost unconceivable 3D localization precision attained by MINFLUX is likely to hold the key to an all-optical dynamical structural biology.
CvkR, a novel MerR-type transcriptional regulator, is a repressor of class 2 type V-K CRISPR-associated transposase systems
Authors: Ziemann Marcus , Reimann Viktoria , Liang Yajing , Shi Yue , Xie Yuman , Li Hui , Zhu Tao , Lu Xuefeng , Hess Wolfgang R.
Published: May 2022

CRISPR-associated transposons (CASTs) exist in different groups of bacteria, including certain cyanobacteria, which contain type V-K CAST systems. These systems contain genes encoding Tn7-like transposase subunits and a divergent number of cargo genes. How the activity of these systems is controlled in situ has remained largely unknown but possibly regulatory genes within these elements are prime candidates. Deletion of the respective regulator gene alr3614 in the cyanobacterium Anabaena (Nostoc) sp. PCC 7120 led to the overexpression of CRISPR tracrRNA, precursor crRNAs and mRNAs encoding the Cas12k effector protein (all3613) and Tn7-like transposase subunits. Upon complementation, these same genes were repressed again. DNase I footprinting and electrophoretic mobility shift assays verified the direct interaction between Alr3614 and the promoter of cas12k and identified a widely conserved binding motif. Structural analysis of Alr3614 at 1.5 Å resolution revealed that it belongs to the MerR-type transcription factor family but with distinct dimerization and effector-binding domains. This protein assembles into a homodimer interacting with DNA through its N-terminal winged helix-turn-helix (wHTH) domain and binds an effector molecule through a C-terminal α-helical domain lacking a conserved cysteine. These results identify Alr3614 as a transcriptional repressor of the CAST system in Anabaena sp. PCC 7120. We suggest naming this family of repressors CvkR for Cas V-K repressors, which are at the core of a widely conserved regulatory mechanism that controls type V-K CAST systems.
Vitamin K-dependent γ-carboxylation regulates calcium flux and adaptation to metabolic stress in β-cells
Authors: Lacombe Julie , Guo Kevin , Bonneau Jessica , Faubert Denis , Gioanni Florian , Vivoli Alexis , Muir Sarah M. , Hezzaz Soraya , Poitout Vincent , Ferron Mathieu
Published: May 2022

Vitamin K is a micronutrient necessary for the γ-carboxylation of glutamic acids. This post-translational modification occurs in the endoplasmic reticulum (ER) and affects secreted proteins. Clinical studies have recently implicated vitamin K in the pathophysiology of diabetes, but the underlying molecular mechanism remains unknown. Here, we show that mouse β-cells lacking γ-carboxylation fail to adapt their insulin secretion in the context of age-related insulin resistance or diet-induced β-cell stress. In human islets, γ-carboxylase expression positively correlates with improved insulin secretion in response to glucose. We identified Endoplasmic Reticulum Gla Protein (ERGP) as a novel γ-carboxylated ER-resident calcium-binding protein expressed in β-cells. Mechanistically, γ-carboxylation of ERGP protects cells against calcium overfilling by diminishing STIM1 and Orai1 interaction and restraining store-operated calcium entry. These results reveal a critical role for vitamin K-dependent γ-carboxylation in the regulation of calcium flux in β-cells and in their capacity to adapt to metabolic stress.
Porous marine snow differentially benefits chemotactic, motile, and non-motile bacteria
Authors: Borer Benedict , Zhang Irene , Baker Amy E. , O’Toole George A. , Babbin Andrew R.
Published: May 2022

Particulate organic carbon settling through the marine water column is a key process that regulates global climate by sequestering atmospheric carbon. The initial colonization of marine particles by heterotrophic bacteria represents the first step in recycling this carbon back to inorganic constituents – setting the magnitude of vertical carbon transport to the abyss. Here, we demonstrate experimentally that bacterial motility is required for particle colonization and chemotaxis specifically benefits at higher settling velocities. We further explore the role of particle microstructure on the colonization efficiency of bacteria with different motility traits. We highlight that non-motile cells benefit disproportionally from the porous microstructure and are relatively enriched in the particle wake due to the efficient particle colonization of chemotactic and motile cells. Our results imply that although the chemotactic and motile bacteria benefit from the high nutrient availability when colonizing the particles, scavenging of these cells benefits the often oligotrophic, non-motile cells common among the planktonic community.

Significance statement

Bacteria in the ocean rely on ephemeral nutrient patches from sinking marine particles, but attaching to these structures is challenging as particle settling rates often exceed bacterial swimming velocities and the numerically dominant marine bacteria are non-motile – posing an interesting paradox about the prominence of particle foraging. Here, we quantify the importance of chemotaxis and motility for the efficient colonization of marine particles and find that although chemotaxis provides a clear advantage, motility is the basic requirement for particle colonization. We expand this analysis to consider highly heterogeneous particle structures and find a disproportionate benefit for non-motile cells by facilitating a direct encounter with the particle surface and enriching non-motile microbes in the nutrient-rich particle plume.
Aberrant association of chromatin with nuclear periphery induced by Rif1 leads to mitotic defect and cell death
Authors: Kanoh Yutaka , Matsumoto Seiji , Ueno Masaru , Hayano Motoshi , Kudo Satomi , Masai Hisao
Published: May 2022

Chromatin is compartmentalized in nuclei and its architecture and nuclear location may have impacts on chromatin events. Rif1, identified as a potent suppressor of hsk1-null mutation (defective in initiation of DNA replication) in fission yeast, recognizes G-quadruplex structures and inhibits origin firing in their 50∼100-kb vicinity, leading us to postulate that Rif1 may generate chromatin higher-order structures inhibitory for initiation. However, effects of Rif1 on chromatin localization in nuclei have not been known. We show here that overexpression of Rif1 causes growth inhibition and eventually cell death in fission yeast. Chromatin binding activities of Rif1, but not recruitment of phosphatase PP1, are required for growth inhibitory effect. Overexpression of a PP1 binding site mutant of Rif1 does not delay S-phase, but still causes cell death, indicating that cell death is caused not by S-phase problems but by issues in other phases of cell cycle, most likely M-phase. Indeed, Rif1 overexpression generates cells with unequally segregated chromosomes. Rif1 overexpression relocates chromatin near nuclear periphery in a manner dependent on its chromatin-binding ability, and this correlates with growth inhibition and cell death induction. Thus, regulated Rif1-mediated chromatin association with nuclear periphery is important for coordinated progression of S- and M-phases.
Status epilepticus induces chronic silencing of burster and dominance of regular firing neurons during sharp wave-ripples in the mouse subiculum
Authors: Lippmann Kristina , Klaft Zin-Juan , Salar Seda , Hollnagel Jan-Oliver , Maslarova Anna
Published: May 2022

Sharp wave-ripples (SWRs) are hippocampal oscillations associated with memory consolidation. The subiculum, as the hippocampal output structure, ensures that hippocampal memory representations are transferred correctly to the consolidating neocortical regions. Because patients with temporal lobe epilepsy often develop memory deficits, we hypothesized that epileptic networks may disrupt subicular SWRs. We therefore investigated the impact of experimentally induced status epilepticus (SE) on subicular SWRs and contributing pyramidal neurons using electrophysiological recordings in mouse hippocampal slices. Subicular SWRs expressed hyperexcitable features post-SE, including increased ripple and unit activity. While regular firing neurons normally remain silent during SWRs, selective disinhibition recruited more regular firing neurons for action potential generation during SWRs post-SE. By contrast, burster neurons generated fewer action potential bursts during SWRs post-SE. Furthermore, altered timing of postsynaptic and action potentials suggested distorted neuronal recruitment during SWRs. Distorted subicular SWRs may therefore impair information processing and memory consolidation in epilepsy.
Three-doses of BNT162b2 COVID-19 mRNA vaccine establishes long-lasting CD8+ T cell immunity in CLL and MDS patients
Authors: Amaya Hernandez Susana Patricia , Hersby Ditte Stampe , Munk Kamilla Kjærgaard , Tamhane Tripti , Trubach Darya , Tagliamonte Maria , Buonaguro Luigi , Gang Anne Ortved , Hadrup Sine Reker , Saini Sunil Kumar
Published: May 2022

Patients with hematological malignancies are prioritized for COVID-19 vaccine due to their high risk for severe SARS-CoV-2 infection related disease and mortality. To understand T cell immunity, its long-term persistence, and correlation with antibody response, we evaluated the BNT162b2 COVID-19 mRNA vaccine-specific immune response in chronic lymphocytic leukemia (CLL) and myeloid dysplastic syndrome (MDS) patients. Longitudinal analysis of CD8+ T cells using DNA-barcoded peptide-MHC multimers covering the full SARS-CoV-2 Spike-protein (415 peptides) showed vaccine-specific T cell activation and persistence of memory T cells up to six months post-vaccination. Surprisingly, a higher frequency of vaccine-induced antigen-specific CD8+ T cell was observed in the patient group compared to a healthy donor group. Furthermore, and importantly, immunization with the second booster dose significantly increased the frequency of antigen-specific CD8+ T cells as well as the total number of T cell specificities. Altogether 59 BNT162b2 vaccine-derived immunogenic epitopes were identified, of which 23 established long-term CD8+ T cell memory response with a strong immunodominance for NYNYLYRLF (HLA-A24:02) and YLQPRTFLL (HLA-A02:01) epitopes. In summary, we mapped the vaccine-induced antigen-specific CD8+ T cells and showed a booster-specific activation and enrichment of memory T cells that could be important for long-term disease protection in this patient group.

Key Points

COVID-19 mRNA vaccine induced an early and persistent activation of antigen-specific CD8+ T cells in this patient group.

Vaccination with a booster dose is required to maintain vaccine-specific CD8+ T cells.
Reversal of splicing infidelity is a pre-activation step in B cell differentiation
Authors: O’Grady Tina M. , Baddoo Melody , Flemington Samuel A. , Ungerleider Nate A. , Flemington Erik K.
Published: May 2022

B cell activation and differentiation is central to the adaptive immune response. Changes in exon usage can have major impacts on cellular signaling and differentiation but have not been systematically explored in differentiating B cells. We analyzed exon usage and intron retention in RNA-Seq data from subsets of human B cells at various stages of differentiation, and in anin vitrolaboratory model of B cell activation and differentiation (Epstein Barr virus infection). Blood naïve B cells were found to have an unusual splicing profile, with unannotated splicing events in over 30% of expressed genes. Splicing changed substantially upon naïve B cell entry into secondary lymphoid tissue and before activation, involving significant increases in exon commitment and reductions in intron retention. These changes preferentially involved short introns with weak splice sites and were likely mediated by an overall increase in splicing efficiency induced by the lymphoid environment. The majority of transcripts affected by splicing changes showed restoration of encoded conserved protein domains and/or reduced targeting to the nonsense-mediated decay pathway. Affected genes were enriched in functionally important immune cell activation pathways such as antigen-mediated signaling, cell cycle control and mRNA processing and splicing. Functional observations from donor B cell subsets in progressive states of differentiation and from timecourse experiments using thein vitromodel suggest that these widespread changes in mRNA splicing play a role in preparing naïve B cells for the decisive step of antigen-mediated activation and differentiation.
Predictive and robust gene selection for spatial transcriptomics
Authors: Covert Ian , Gala Rohan , Wang Tim , Svoboda Karel , Sümbül Uygar , Lee Su-In
Published: May 2022

A prominent trend in single-cell transcriptomics is providing spatial context alongside a characterization of each cell’s molecular state. This typically requires targeting ana prioriselection of genes, often covering less than 1% of the genome, and a key question is how to optimally determine the small gene panel. Reference data from these methods covering the whole genome is unavailable, and using single-cell RNA sequencing (scRNA-seq) datasets as a surrogate can result in suboptimal gene panels due to the fundamentally different data distributions across technologies. We address these challenges by introducing a flexible deep learning framework, PERSIST, to identify informative gene targets for spatial transcriptomics studies by leveraging existing scRNA-seq data. Using datasets spanning different brain regions, species, and scRNA-seq technologies, we show that PERSIST reliably identifies gene panels that provide more accurate prediction of the genome-wide expression profile, thereby capturing more information with fewer genes. Furthermore, PERSIST can be adapted to meet specific biological goals, such as classifying cell types or discerning neuronal electrical properties. Finally, via a simulation study based on a recentin situhybridization-based dataset, we demonstrate that PERSIST’s binarization of gene expression levels enables models trained on scRNA-seq data to generalize with input data obtained using spatial transcriptomics, despite the complex domain shift between these technologies.
High- and Low-Frequency Deep Brain Stimulation in the Subthalamic Nucleus differentially modulate Response Inhibition and Action Selection in Parkinson’s Disease
Authors: Waldthaler Josefine , Sperlich Alexander , König Aylin , Stüssel Charlotte , Bremmer Frank , Timmermann Lars , Pedrosa David
Published: May 2022

Background

While deep brain stimulation (DBS) in the subthalamic nucleus (STN) improves motor functions in Parkinson’s disease (PD), it has also been associated with increased impulsivity.

Methods

A combined approach of eye-tracking and high-density EEG was used to investigate how high- and low-frequency DBS impact impulsive actions in the antisaccade task in a cohort of ten persons with PD. Computational modelling of the behavioral outcomes allowed a nuanced insight into the effect of DBS on response inhibition and action selection processes. Results: Against our expectations, both 130 Hz- and 60 Hz-DBS improved response inhibition as both resulted in a reduced rate of early reflexive errors. Correspondingly, DBS with both frequencies led to increased desynchronization of beta power during the preparatory period which may be a correlate of anticipatory activation in the oculomotor network.

Low-frequency DBS additionally was associated with increased midfrontal theta power, an established marker of cognitive control. While higher midfrontal theta power predicted longer antisaccade latencies in off-DBS state on a trial-by-trial basis, 130 Hz-DBS reversed this relationship. As informed by the computational model, 130 Hz-DBS further led to a shift in the speed-accuracy trade-off causing an acceleration and error-proneness of actions later in the trial.

Conclusions

Our results disentangle the impact of DBS on early and late impulsive actions. Only 130 Hz-DBS may disrupt theta-mediated cognitive control mechanisms via medial frontal – STN pathways that are involved in delaying action selection. 60 Hz-DBS may provide beneficial effects on response inhibition without the detrimental effect on action selection seen with 130 Hz-DBS.

Funding

This study was supported by the SUCCESS program of Philipps-University Marburg (JW), the Hessian Ministry of Sciences and the Arts, clusterproject: The Adaptive Mind – TAM (FB / AK) and the German Research Foundation (DFG). International Research Training Group 1901 (FB / AK)
The intrinsically disordered cytoplasmic tail of a dendrite branching receptor uses two distinct mechanisms to regulate the actin cytoskeleton
Authors: Kramer Daniel A. , Narvaez-Ortiz Heidy Y. , Patel Urval , Shi Rebecca , Shen Kang , Nolen Brad J. , Roche Julien , Chen Baoyu
Published: May 2022

Dendrite morphogenesis is essential for neural circuit formation, yet the molecular mechanisms underlying complex dendrite branching remain elusive. Previous studies on the highly branchedC. elegansPVD sensory neuron identified a membrane co-receptor complex that links extracellular signals to intracellular actin remodeling machinery, promoting high-order dendrite branching. In this complex, the claudin-like transmembrane protein HPO-30 recruits the WAVE regulatory complex (WRC) to dendrite branching sites, stimulating the Arp2/3 complex to polymerize actin. We report here our biochemical and structural analysis of this interaction, revealing that the intracellular domain (ICD) of HPO-30 is intrinsically disordered and employs two distinct mechanisms to regulate the actin cytoskeleton. First, HPO-30 ICD binding to the WRC requires dimerization and involves the entire ICD sequence, rather than a short linear peptide motif. This interaction enhances WRC activation by the GTPase Rac1. Second, HPO-30 ICD directly binds to the sides and barbed end of actin filaments. Binding to the barbed end requires ICD dimerization and inhibits both actin polymerization and depolymerization, resembling the actin capping protein CapZ. These dual functions provide an intriguing model of how membrane proteins can integrate distinct mechanisms to fine-tune local actin dynamics.
Polycomb proteins translate histone methylation to chromatin folding
Authors: Lizana Ludvig , Nahali Negar , Schwartz Yuri B.
Published: May 2022

Epigenetic repression often involves covalent histone modifications. Yet, how the presence of a histone mark translates into changes in chromatin structure that ultimately benefit the repression is largely unclear. Polycomb group proteins comprise a family of evolutionarily conserved epigenetic repressors. They act as multi-subunit complexes one of which trimethylates histone H3 at Lysine 27 (H3K27). Here we describe a novel Monte Carlo – Molecular Dynamics simulation framework, which we employed to discover that stochastic interaction of the Polycomb Repressive Complex 1 (PRC1) with tri-methylated H3K27 is sufficient to fold the methylated chromatin. Unexpectedly, such chromatin folding leads to spatial clustering of the DNA elements bound by PRC1.
Mouse primary T cell phosphotyrosine proteomics enabled by BOOST
Authors: Chua Xien Yu , Callahan Kenneth P. , Griffith Alijah A. , Hildebrandt Tobias , Fu Guoping , Hu Mengzhou , Wen Renren , Salomon Arthur R.
Published: May 2022

The Broad Spectrum Optimization of Selective Triggering (BOOST) approach was recently developed to increase the quantitative depth of the tyrosine phosphoproteome by mass spectrometry-based proteomics. While BOOST has been demonstrated in the Jurkat T cell line, it has not been demonstrated in scarce mice primary T cells. Here, we show the first phosphotyrosine proteomics experiment performed in mice primary T cells using BOOST. We identify and precisely quantify more than 2,000 unique pTyr sites from more than 3,000 unique pTyr peptide PSMs using only 1 mg of protein from T cell receptor-stimulated primary T cells from mice. We further reveal the importance of the phase-constrained spectrum deconvolution method (ΦSDM) parameter on Orbitrap instruments that, when disabled, enhances quantitation depth, accuracy, and precision in low-abundance samples. Using samples with contrived ratios, we find that disabling ΦSDM allows for up to a two-fold increase in the number of statistically significant intensity ratios detected while enabling ΦSDM degrades quantitation, especially in low-abundance samples.

TOC Graphic
The development of 3D bovine intestinal organoid derived models to investigate Mycobacterium avium ssp paratuberculosis pathogenesis
Authors: Blake Rosemary , Jensen Kirsty , Mabbott Neil , Hope Jayne , Stevens Jo
Published: May 2022

Mycobacterium avium subspecies paratuberculosis (MAP) is the etiologic agent of Johne’s Disease, a chronic enteritis of ruminants prevalent across the world. It is estimated that approximately 50% of UK dairy herds are infected with MAP, but this is likely an underestimate of the true prevalence. Infection can result in reduced milk yield, infertility and premature culling of the animal, leading to significant losses to the farming economy and negatively affecting animal welfare. Understanding the initial interaction between MAP and the host is critical to develop improved diagnostic tools and novel vaccines. Here we describe the characterisation of three different multicellular in vitro models derived from bovine intestinal tissue, and their use for the study of cellular interactions with MAP. In addition to the previously described basal-out 3D bovine enteroids, we have established viable 2D monolayers and 3D apical-out organoids. The apical-out enteroids differ from previously described bovine enteroids as the apical surface is exposed on the exterior surface of the 3D structure, enabling study of host-pathogen interactions at the epithelial surface without the need for microinjection. We have characterised the cell types present in each model system using RT-qPCR to detect predicted cell type-specific gene expression and confocal microscopy for cell type-specific protein expression. Each model contained the cells present in the bovine ileum and were therefore representative of the bovine gut. Exposure of the three model systems to the reference strain MAP K10, and a recent Scottish isolate referred to as C49, led to the observation of intracellular bacteria by confocal microscopy. Enumeration of the bacteria by genome copy number quantification, indicated that K10 was less invasive than C49 at early time points in infection in all model systems. This study shows that bovine enteroid-based models are permissive to infection with MAP and that these models may be useful in investigating early stages of MAP pathogenesis in a physiologically relevant in vitro system, whilst reducing the use of animals in scientific research.
The targeted deletion of genes responsible for expression of the Mth60 fimbriae leads to loss of cell-cell connections in M. thermautotrophicus ΔH
Authors: Fink Christian , Martinez-Cano Gines , Shuster Jeremiah , Panzera Aurora , Angenent Largus T. , Molitor Bastian
Published: May 2022

This study was continued by the Environmental Biotechnology Group of the University of Tübingen in memoriam to Reinhard Wirth, who initiated the work on Mth60 fimbriae at the University of Regensburg.

Growth in biofilms or biofilm-like structures is the prevailing lifestyle for most microbes in nature. The first step to initiate biofilms is the adherence of microbes to biotic and abiotic surfaces. Therefore, it is important to elucidate the initial step of biofilm formation, which is generally established through cell-surface structures (i.e., cell appendages), such as fimbriae or pili, that adhere to surfaces. The Mth60 fimbriae of Methanothermobacter thermautotrophicus ΔH are one of only few known archaeal cell appendages that do not assemble via the type-IV assembly mechanism. Here, we report the constitutive expression of Mth60 fimbriae-encoding genes from a shuttle-vector construct, as well as the deletion of the Mth60 fimbriae-encoding genes from the genomic DNA of M. thermautotrophicus ΔH. We expanded our system for genetic modification of M. thermautotrophicus ΔH by an allelic-exchange method. While overexpression of the respective genes resulted in an increase of the Mth60 fimbriae, deletion of the Mth60 fimbriae-encoding genes led to a loss of Mth60 fimbriae in planktonic cells of M. thermautotrophicus ΔH. This either increased or decreased number of Mth60 fimbriae correlated with a significant increase or decrease of biotic cell-cell connections in the respective M. thermautotrophicus ΔH strains compared to the wild-type strain.

Originality-Significance Statement

Methanothermobacter spp. have been studied for the biochemistry of hydrogenotrophic methanogenesis for many years. However, due to the lack of genetic tools, the detailed investigation of certain aspects, such as regulatory processes, was not possible. Here, we amend our genetic toolbox for M. thermautotrophicus ΔH with an allelic exchange method. We report the deletion of genes that encode for the Mth60 fimbriae. Our findings provide a first insight into the regulation of the expression of these genes and reveal a role of the Mth60 fimbriae in the formation of cell-cell connections of M. thermautotrophicus ΔH.
The Influences of Stomatal Size and Density on Rice Drought, Salinity and VPD Resilience
Authors: Caine Robert S. , Harrison Emily L. , Sloan Jennifer M. , Flis Paulina M. , Fischer Sina , Phuoc Nguyen Trong , Lang Nguyen Thi , Gray Julie E. , Croft Holly L.
Published: May 2022

A warming climate coupled with reductions in water availability and rising salinity are increasingly affecting rice yields (Oryza sativa L.). Elevated temperatures are causing vapour pressure deficit (VPD) rises, leading to stomata closure, further reducing plant productivity and cooling. It is unclear which conformation of stomatal size (SS) and stomatal density (SD) will best suit these future environmental extremes.

To understand the influence of stomatal characteristics on rice abiotic stress tolerance, we screened the stomatal characteristics of 72 traditionally-bred varieties. We found significant variation in SS, SD and maximal stomatal conductance (gsmax) but did not identify any varieties with SD and gsmax as low as the genetically manipulated stomatal development mutant OsEPF1oe.

Traditionally-bred varieties with high SD and small SS (resulting in high gsmax) typically had lower biomasses, and these plants were more resilient to drought than low SD and large SS plants, which were physically larger. None of the varieties tested were as resilient to drought or salinity as low SD OsEPF1oe mutants. High SD and small SS rice displayed faster stomatal closure during rising VPD, but photosynthesis and plant cooling were reduced.

Compromises will be required when choosing rice SS and SD to tackle multiple future environmental stresses.
MYC Overexpression Drives Immune Evasion in Human Cancer that is Reversible Through Restoration of Pro-Inflammatory Macrophages
Authors: Dhanasekaran Renumathy , Hansen Aida S. , Park Jangho , Lai Ian , Adeniji Nia , Kuruvilla Sibu , Suresh Akanksha , Swamy Varsha , Felsher Dean W.
Published: May 2022

Cancers evade immune surveillance that in some, but not in many, cases can be reversed through immune checkpoint therapy. Here we report that the MYC oncogene suppresses immune surveillance, activates immune checkpoint expression, and predicts responsiveness to immune checkpoint inhibition. First, when MYC is genomically amplified and overexpressed in 33 different human cancers, this increases immune checkpoint expression, drives immune checkpoint therapeutic resistance, and is associated with both Th2-like immune profile, and reduced CD8 T cell infiltration. Second, experimentally, MYC-driven tumors suppress pro-inflammatory antigen-presenting macrophages with increased CD40 and MHCII expression, which in turn impedes T cell response. This MYC-driven suppression of macrophages can be reversed by combined but not individual blockade of PDL1 and CTLA4. Third, the depletion of macrophages abrogated the anti-neoplastic effects of PDL1 and CTLA4 blockade. Hence, MYC is a predictor of immune checkpoint responsiveness and a key driver of immune evasion through the suppression of pro-inflammatory macrophages. The immune evasion by MYC can be overcome by combined PDL1 and CTLA4 blockade.

Statement of Significance

MYC is the most commonly activated oncogene in human cancers. In this study, we identify macrophage-mediated immune evasion as a major therapeutic vulnerability of MYC-driven cancers. Our results have implications for developing effective immunotherapies for MYC-driven human cancers and also for prioritizing patients with MYC-driven tumors for combination immunotherapy.
iPSC-derived models of PACS1 syndrome reveal transcriptional and functional deficits in neuron activity
Authors: Rylaarsdam Lauren , Rakotomamonjy Jennifer , Pope Eleanor , Guemez-Gamboa Alicia
Published: May 2022

PACS1 syndrome is a neurodevelopmental disorder characterized by intellectual disability and distinct craniofacial abnormalities resulting from ade novop.R203W variant in phosphofurin acidic cluster sorting protein 1 (PACS1). PACS1 is known to play roles in the endosomal pathway and nucleus, but how the p.R203W variant affects developing neurons is not understood, leaving patients with few therapeutic options. Here we differentiated stem cells towards various neuronal models to investigate the impact of the PACS1 syndrome-causing variant on cortical development. While few deleterious effects were detected in PACS1(+/R203W)neural precursors, mature PACS1(+/R203W)glutamatergic neurons exhibited impaired expression of genes strongly enriched for synaptic signaling processes. Subsequent characterization of neural activity using calcium imaging and multielectrode arrays revealed the p.R203W PACS1 variant leads to a strikingly prolonged neuronal network burst duration mediated by an increased inter-spike interval. This work is the first to investigate the impact of the PACS1 p.R203W variant on developing human neural tissue and uncovers putative electrophysiological underpinnings of disease along with candidate targets for pharmacological intervention.
Site pleiotropy of a stickleback tooth and fin enhancer
Authors: Rowley Alyssa J. , Square Tyler A. , Miller Craig T.
Published: May 2022

Development and regeneration are orchestrated by gene regulatory networks that operate in part through transcriptional enhancers. Although many enhancers are pleiotropic and are active in multiple tissues, little is known about whether enhancer pleiotropy is due to 1) site pleiotropy, in which individual transcription factor binding sites (TFBS) are required for activity in multiple tissues, or 2) multiple distinct sites that regulate expression in different tissues. Here, we investigated the pleiotropy of an intronic enhancer of the stickleback Bone morphogenetic protein 6 (Bmp6) gene. This enhancer was previously shown to regulate evolved changes in tooth number and tooth regeneration, and is highly pleiotropic, with robust activity in both fins and teeth throughout embryonic, larval, and adult life. We tested the hypothesis that the pleiotropy of this enhancer is due to site pleiotropy of an evolutionarily conserved predicted Foxc1 TFBS. Transgenic analysis and site-directed mutagenesis experiments both deleting and scrambling this predicted Foxc1 TFBS revealed that the binding site is required for enhancer activity in both teeth and fins throughout embryonic, larval, and adult development. Collectively these data support a model where the pleiotropy of this Bmp6 enhancer is due to site pleiotropy and this putative binding site is required for enhancer activity in multiple anatomical sites from the embryo to the adult.
Kidney collecting duct cells make vasopressin in response to NaCl induced hypertonicity
Authors: Arroyo Juan Pablo , Terker Andrew S. , Zuchowski Yvonne , Watts Jason A. , Bock Fabian , Meyer Cameron , Luo Wentian , Kapp Meghan , Gould Edward R. , Miranda Adam X. , Carty Joshua , Jiang Ming , Vanacore Roberto , Hammock Elizabeth , Wilson Matthew H. , Zent Roy , Zhang Mingzhi , Bhave Gautam , Harris Raymond C.
Published: May 2022

Vasopressin has traditionally been thought to be produced by the neurohypophyseal system and then released into the circulation where it regulates water homeostasis. The syndrome of inappropriate secretion of anti-diuretic hormone (vasopressin) raised the question if vasopressin could be produced outside of the brain and whether the kidney could be a source of vasopressin. We found that mouse and human kidneys expressed vasopressin mRNA. Using an antibody that detects the pre-pro-vasopressin, we found that immunoreactive pre-pro-vasopressin protein is found in mouse and human kidneys. Moreover, we found that murine collecting duct cells make biologically active vasopressin which increases in response to NaCl mediated hypertonicity, and that water restriction increases the abundance of kidney-derived vasopressin mRNA and protein expression in mouse kidneys. Thus, we provide evidence of biologically active production of kidney-derived vasopressin in kidney tubular epithelial cells.
Structural basis of Yta7 ATPase-mediated nucleosome disassembly
Authors: Wang Feng , Feng Xiang , He Qing , Li Hua , Li Huilin
Published: May 2022

Yta7 is a novel chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes and unfolds histone H3 to promote nucleosome disassembly for DNA replication. By cryo-EM analysis, we here show that Yta7 assembles a three-tiered hexamer ring with a top spiral, a middle AAA1-tier, and a bottom AAA2-tier. Unexpectedly, the Yta7 BRD stabilizes a four-stranded β-helix termed BRD- interacting motif (BIM) of the largely disordered N-terminal region, and they together assemble the spiral structure on top of the hexamer to engage the nucleosome. We found that the Yta7 BRD lacks key residues involved in acetylated peptide recognition, and as such, it is a noncanonical BRD that does not distinguish the H3 acetylation state, consistent with its role in general DNA replication. Upon nucleosome binding, the BRD/BIM spiral transitions into a flat ring to allow threading of the histone H3 tail into the AAA+ chamber. The H3 peptide is stabilized by the AAA1 pore loops 1 and 2 that spiral around the peptide. Therefore, Yta7 unfolds the nucleosome by pulling on the H3 peptide in a rotary staircase mechanism. Our study sheds light on the nucleosome recognition and unfolding mechanism of Yta7.
Regulation of Chlamydia RsbU phosphatase activity by the enolase product, phosphoenolpyruvate
Authors: Rosario Christopher , Tan Ming
Published: May 2022

The intracellular pathogen Chlamydia temporally regulates the expression of its genes but the upstream signals that control transcription are not known. The best studied regulatory pathway is a partner switching mechanism that involves an anti-sigma factor RsbW, which inhibits transcription by binding and sequestering the sigma subunit of RNA polymerase. RsbW is itself regulated by an anti-anti-sigma factor RsbV whose phosyphorylation state is controlled by the phosphatase RsbU. In this study, we showed that Chlamydia trachomatis RsbU requires manganese or magnesium as a cofactor and dephosphorylates RsbV1 and RsbV2, which are the two chlamydial paralogs of RsbV. The gene for RsbU is adjacent to the enolase gene in a number of Chlamydia genomes, and we showed that eno and rsbU are co-transcribed from the same operon. In other bacteria, there is no known functional connection between the Rsb pathway and enolase, which is an enzyme in the glycolytic pathway. We found, however, that Chlamydia RsbU phosphatase activity was inhibited by phosphoenolpyruvate (PEP), the product of the enolase reaction, but not by 2-phosphoglycerate (2PGA), which is the substrate. These findings suggest that the enolase reaction, and more generally glucose metabolism, may provide an upstream signal that regulates transcription in Chlamydia through the RsbW pathway.

IMPORTANCE

The RsbW pathway is a phosphorelay that regulates gene expression in Chlamydia but its upsteam signal has not been identified. We showed that RsbU, a phosphatase in this pathway is inhibited by phosphoenolpyruvate, which is the product of the enolase reaction. As enolase is an enzyme in the glycolytic pathway, these results reveal an unrecognized link between glucose metabolism and gene regulation in chlamydiae. Moreover, as these intracellular bacteria acquire gluose from the infected host cell, our findings suggest that glucose availability may be an external signal that controls chlamydial gene expression.
Surface-Induced cAMP Signaling Requires Multiple Features of the Pseudomonas aeruginosa Type IV Pili
Authors: Kuchma S.L. , O’Toole G.A.
Published: May 2022

Pseudomonas aeruginosa type IV pili (TFP) are important for twitching motility and biofilm formation. TFP have been implicated in surface sensing, a process whereby surface-engaged cells up-regulate synthesis of the second messenger cAMP to propagate a signaling cascade leading to biofilm initiation and repression of motility. Here we show that mutations in PilA impairing proteolytic processing of the prepilin into mature pilin as well as the disruption of essential TFP components, including the PilC platform protein and PilB assembly motor protein, fail to induce surface-dependent cAMP signaling. We show that TFP retraction by surface-engaged cells is required to induce signaling, and that the retractile motor PilT is both necessary and sufficient to power surface-specific induction of cAMP. The PilU retraction motor, in contrast, is unable to support full signaling in the absence of PilT. Finally, while we have confirmed that PilA and PilJ interact by bacterial two-hybrid analysis, our data do not support the current model that PilJ-PilA interaction drives cAMP signaling.

Importance

Surface sensing by P. aeruginosa requires TFP. TFP play a critical role in the induction of the second messenger cAMP upon surface contact; this second messenger is part of a larger cascade involved in the transition from a planktonic to biofilm lifestyle. Here we show that TFP must be deployed and actively retracted by the PilT motor for the full induction of cAMP signaling. Furthermore, the mechanism whereby TFP retraction triggers cAMP induction is not well understood, and our data argues against one of the current models in the field proposed to address this knowledge gap.
A SCID mouse model to evaluate the efficacy of antivirals against SARS-CoV-2 infection
Authors: Abdelnabi Rana , Foo Caroline S. , Kaptein Suzanne J. F. , Boudewijns Robbert , Vangeel Laura , De Jonghe Steven , Jochamns Dirk , Weynand Birgit , Neyts Johan
Published: May 2022

Ancestral SARS-CoV-2 lacks the intrinsic ability to bind to the mouse ACE2 receptor and therefore establishment of SARS-CoV-2 mouse models has been limited to the use of mouse-adapted viruses or genetically modified mice. Interestingly, some of the variants of concern, such as the beta B.1.351 variant, show an improved binding to the mouse receptor and hence better replication in different Wild type (WT) mice species. Here, we desribe the establishment of SARS-CoV-2 beta B.1.351 variant infection model in male SCID mice as a tool to assess the antiviral efficacy of potential SARS-CoV-2 small molecule inhibitors. Intranasal infection of male SCID mice with 105 TCID50 of the beta B.1.351 variant resulted in high viral loads in the lungs and moderate signs of lung pathology on day 3 post-infection (pi). Treatment of infected mice with the antiviral drugs Molnupiravir (200 mg/kg, BID) or Nirmatrelvir (300 mg/kg, BID) for 3 consecutive days significantly reduced the infectious virus titers in the lungs by 1.9 and 3.8 log10 TCID50/mg tissue, respectively and significantly improved lung pathology. Together, these data demonstrate the validity of this SCID mice/beta B.1.351 variant infection model as a convenient preclinical model for assessment of potential activity of antivirals against SARS-CoV-2.

Importance

Unlike the ancestral SARS-CoV-2 strain, the beta (B.1.351) VoC has been reported to replicate to some extent in WT mice (species C57BL/6 and BALB/c). We here demonstrate that infection of SCID mice with SARS-CoV-2 beta variant results in high viral loads in the lungs on day 3 post-infection (pi). Treatment of infected mice with the antiviral drugs Molnupiravir or Nirmatrelvir for 3 consecutive days markedly reduced the infectious virus titers in the lungs and improved lung pathology. The advantages of using this mouse model over the standard hamster infection models to assess the in vivo efficacy of small molecule antiviral drugs are (i) the use of a clinical isolate without the need to use mouse-adapted strains or genetically modified animals (ii) lower amount of the test drug is needed and (ii) more convenient housing conditions compared to bigger rodents such as hamsters.
Hydroxylation site-specific and production-dependent roles of endogenous oxysterols in cellular cholesterol homeostasis
Authors: Saito Hodaka , Sato Ryuichiro , Shimizu Makoto , Yamauchi Yoshio
Published: May 2022

The cholesterol metabolites oxysterols play central roles in cholesterol feedback control. They modulate the activity of two master transcription factors that control cholesterol homeostatic responses, sterol regulatory element-binding protein-2 (SREBP-2) and liver X receptor (LXR). Although the role of exogenous oxysterols has been well-established, whether endogenously synthesized oxysterols similarly control both SREBP-2 and LXR to those added exogenously remains poorly explored. Here, we carefully validate the role of oxysterols enzymatically synthesized within cells in cholesterol homeostatic responses. We first show that SREBP-2 responds more sensitively to exogenous oxysterols than LXR. We then show that endogenous 25-hydroxycholesterol (25-HC), 27-HC, and 24S-HC synthesized by CH25H, CYP27A1, and CYP46A1, respectively, suppress SREBP-2 activity at different degrees by stabilizing Insig proteins whereas 7a-HC has little impact on SREBP-2. The results explain the hydroxylation site-specific role of endogenous oxysterols. On the other hand, the expression of CH25H, CYP46A1, CYP27A1, or CYP7A1 fails to induce LXR target gene expression. We also show the 25-HC production-dependent suppression of SREBP-2 using a tetracycline-inducible CH25H expression system. Moreover, we quantitatively determine the specificity of the four cholesterol hydroxylases in living cells. Based on these results, we propose that endogenous side-chain oxysterols primarily regulate the activity of SREBP-2, not LXR.
Nanoparticle-induced augmentation of neutrophils’ phagocytosis of bacteria
Authors: Rubey Kathryn M. , Mukhitov Alexander R. , Nong Jia , Wu Jichuan , Krymskaya Vera P. , Myerson Jacob W. , Worthen G. Scott , Brenner Jacob S.
Published: May 2022

Despite the power of antibiotics, bacterial infections remain a major killer, due to antibiotic resistance and hosts with dysregulated immune systems. We and others have been developing drug-loaded nanoparticles that home to the sites of infection and inflammation via engineered tropism for neutrophils, the first-responder leukocytes in bacterial infections. Here, we examined how a member of a broad class of neutrophil-tropic nanoparticles affects neutrophil behavior, specifically questioning whether the nanoparticles attenuate an important function, bacterial phagocytosis. We found these nanoparticles actually augment phagocytosis of non-opsonized bacteria, increasing it by ~50%. We showed this augmentation of phagocytosis is likely co-opting an evolved response, as opsonized bacteria also augment phagocytosis of non-opsonized bacteria. Enhancing phagocytosis of non-opsonized bacteria may prove particularly beneficial in two clinical situations: in hypocomplementemic patients (meaning low levels of the main bacterial opsonins, complement proteins, seen in conditions such as neonatal sepsis and liver failure) or for bacteria that are largely resistant to complement opsonization (e.g., Neisseria). Additionally, we observe that; a) prior treatment with bacteria augments neutrophil uptake of neutrophil-tropic nanoparticles; b) neutrophil-tropic nanoparticles colocalize with bacteria inside of neutrophils. The observation that neutrophil-tropic nanoparticles enhance neutrophil phagocytosis and localize with bacteria inside neutrophils suggests that these nanoparticles will serve as useful carriers for drugs to ameliorate bacterial diseases.
The Scar/WAVE complex drives normal actin protrusions without the Arp2/3 complex, but proline-rich domains are required
Authors: Buracco Simona , Singh Shashi , Claydon Sophie , Paschke Peggy , Tweedy Luke , Whitelaw Jamie , McGarry Lynn , Thomason Peter A. , Insall Robert H.
Published: May 2022

Cell migration requires the constant modification of cellular shape by reorganization of the actin cytoskeleton. The pentameric Scar/WAVE regulatory complex (WRC) is the main catalyst of pseudopod and lamellipodium formation. Its actin nucleation activity has been attributed to its ability to combine monomeric actin and Arp2/3 complex through the VCA domain of Scar/WAVE, while other regions of the complex are typically thought to mediate spatial and temporal regulation and have no direct role in actin polymerization.

Here we show that the Scar/WAVE with its VCA domain deleted can still induce the formation of morphologically normal actin protrusions. Equivalent results are seen in B16-F1 mouse melanoma cells and Dictyostelium discoideum cells. This actin polymerization occurs independently of the Arp2/3 complex, whose recruitment to the leading edge is greatly reduced by the loss of the VCA domain. We also expressed Scar/WAVE with VCA and polyproline domains both deleted. In Dictyostelium cells, these were only active if WASP (which contains its own proline-rich domain) was available. Similarly, in B16-F1 cells both Abi and WAVE proline-rich domains needed to be deleted before the function of the WRC was lost. Thus we conclude that proline-rich domains play a central role in actin nucleation.

Our data demonstrate a new actin nucleation mechanism of the WRC that is independent of its VCA domain and the Arp2/3 complex. We also show that proline-rich domains are more fundamental than has been thought. Together, these findings suggest a new mechanism for WRC action.
Detecting apoptosis via DODO
Authors: Zhang Ziheng , Sun Zhe , Liu Ji-Long
Published: May 2022

The real-time detection of intracellular biological processes by coded sensors has broad application prospects. Here we develop a degron based modular reporting system: the Device of Death Operation (DODO), which can be used to detect a series of biological processes. The DODO system consists of “reporter”, “sensor” and degron. After protease activation and cleavage, the degron will be released from the fluorescent protein and eventually lead to the stabilization of the fluorescent protein. By replacing different “sensors” and “reporters”, a series of biological processes can be reported through different signals. The system can effectively report the existence of TEV. To prove this concept, we successfully apply the DODO system to report apoptosis. In addition, the reporter based on degron will help to design protease reporters other than caspase.