bluuebunny/crossref_metadata_2025 huggingface dataset:
Fear memory in humans is consolidated over time independent of sleep
Authors: Pavlov Yuri G. , Pavlova Nadezhda V. , Diekelmann Susanne , Kotchoubey Boris
Published: April 2022

Fear memories can be altered after acquisition by processes such as fear memory consolidation or fear extinction, even without further exposure to the fear-eliciting stimuli, but factors contributing to these processes are not well understood. Sleep is known to consolidate, strengthen and change newly acquired declarative and procedural memories. However, evidence on the role of time and sleep in the consolidation of fear memories is inconclusive. Here, we used highly sensitive electrophysiological measures to examine the development of fear-conditioned responses over time and sleep in humans. We assessed event-related brain potentials (ERP) in 18 healthy young individuals during fear conditioning before and after a 2-hour afternoon nap or a corresponding wake interval in a counterbalanced within-subject design. The procedure involved pairing a neutral tone (CS+) with a highly unpleasant sound (US). As a control, another neutral tone (CS-) was paired with a neutral sound. Fear responses were examined before the interval during a habituation phase and an acquisition phase as well as after the interval during an extinction phase and a re-acquisition phase. Differential fear conditioning during acquisition was evidenced by a more negative slow ERP component (stimulus-preceding negativity) developing before the unconditioned stimulus (loud noise). This differential fear response was even stronger after the interval during re-acquisition compared to initial acquisition, but this effect was similarly pronounced after sleep and wakefulness. These findings suggest that fear memories are consolidated over time, with this effect being independent of intervening sleep.
Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory
Authors: Abdulla Amith Z. , Vaillant Cédric , Jost Daniel
Published: April 2022

In eukaryotes, many stable and heritable phenotypes arise from the same DNA sequence, owing to epigenetic regulatory mechanisms relying on the molecular cooperativity of “reader-writer” enzymes. In this work, we focus on the fundamental, generic mechanisms behind the epigenome memory encoded by post-translational modifications of histone tails. Based on experimental knowledge, we introduce a unified modeling framework, the painter model, describing the mechanistic interplay between sequence-specific recruitment of chromatin regulators, chromatin-state-specific reader-writer processes and long-range spreading mechanisms. A systematic analysis of the model building blocks highlights the crucial impact of tridimensional chromatin organization and state-specific recruitment of enzymes on the stability of epigenomic domains and on gene expression. In particular, we show that enhanced 3D compaction of the genome and enzyme limitation facilitate the formation of ultra-stable, confined chromatin domains. The model also captures how chromatin state dynamics impact the intrinsic transcriptional properties of the region, slower kinetics leading to noisier expression. We finally apply our framework to analyze experimental data, from the propagation of γH2AX around DNA breaks in human cells to the maintenance of heterochromatin in fission yeast, illustrating how the painter model can be used to extract quantitative information on epigenomic molecular processes.
Plant-invertebrate interactions across a forested retrogressive chronosequence
Authors: Kempel Anne , Allan Eric , Gossner Martin M. , Jochum Malte , Wardle David A.
Published: April 2022

In the long-term absence of disturbance, ecosystems often enter a decline or retrogressive phase which leads to reductions in primary productivity, plant biomass, nutrient cycling and foliar quality. However, the consequences of ecosystem retrogression for higher trophic levels such as herbivores and predators, are less clear. Using a post-fire forested island-chronosequence across which retrogression occurs, we show that nutrient availability strongly controls invertebrate herbivore biomass when predators are few, but that there is a switch from bottom-up to top-down control when predators are common. This trophic flip in herbivore control probably arises because invertebrate predators respond to alternative energy channels from the adjacent aquatic matrix, which were independent of plant biomass. Our results suggest that effects of nutrient limitation, following ecosystem retrogression, on trophic cascades are modified by independent variation in predator abundance, which requires a more holistic approach to trophic ecology to better understand herbivore effects on plant communities.
Cross-neutralization of Omicron BA.1 against BA.2 and BA.3 SARS-CoV-2
Authors: Zou Jing , Kurhade Chaitanya , Xia Hongjie , Liu Mingru , Xie Xuping , Ren Ping , Shi Pei-Yong
Published: April 2022

The Omicron SARS-CoV-2 has three distinct sublineages, among which sublineage BA.1 is responsible for the initial Omicron surge and is now being replaced by BA.2 world-wide, whereas BA.3 is currently at a low frequency. The ongoing BA.1-to-BA.2 replacement underscores the importance to understand the cross-neutralization among the three Omicron sublineages. Here we tested the neutralization of BA.1-infected human sera against BA.2, BA.3, and USA/WA1-2020 (a strain isolated in late January 2020). The BA.1-infected sera neutralized BA.1, BA.2, BA.3, and USA/WA1-2020 SARS-CoV-2s with geometric mean titers (GMTs) of 445, 107, 102, and 16, respectively. Thus, the neutralizing GMTs against heterologous BA.2, BA.3, and USA/WA1-2020 were 4.2-, 4.4-, and 28.4-fold lower than the GMT against homologous BA.1, respectively. These findings have implications in COVID-19 vaccine strategy.
The dynamical Matryoshka model: 3. Diffusive nature of the atomic motions contained in a new dynamical model for deciphering local lipid dynamics
Authors: Matsuo Tatsuhito , Cisse Aline , Plazanet Marie , Natali Francesca , Koza Michael Marek , Ollivier Jacques , Bicout Dominique J. , Peters Judith
Published: April 2022

In accompanying papers [Bicout et al., BBA – Biomembr. Submitted; Cissé et al., BBA – Biomembr. Submitted], a new model called Matryoshka model has been proposed to describe the geometry of atomic motions in phospholipid molecules in bilayers and multilamellar vesicles based on their quasielastic neutron scattering (QENS) spectra. Here, in order to characterize the relaxational aspects of this model, the energy widths of the QENS spectra of the samples were analyzed first in a model-free way. The spectra were decomposed into three Lorentzian functions, which are classified as slow, intermediate, and fast motions depending on their widths. The analysis provides the diffusion coefficients, residence times, and geometrical parameters for the three classes of motions. The results corroborate the parameter values such as the amplitudes and the mobile fractions of atomic motions obtained by the application of the Matryoshka model to the same samples. Since the current analysis was carried out independently of the development of the Matryoshka model, the present results enhance the validity of the model. The model will serve as a powerful tool to decipher the dynamics of lipid molecules not only in model systems, but also in more complex systems such as mixtures of different kinds of lipids or natural cell membranes.
Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis
Authors: Jefferson RE , Oggier A , Füglistaler A , Camviel N , Hijazi M , Rico Villarreal A , Arber C , Barth P
Published: April 2022

Engineering protein biosensors that sensitively respond to specific biomolecules by triggering precise cellular responses is a major goal of diagnostics and synthetic cell biology. Previous biosensor designs have largely relied on binding structurally well-defined molecules. In contrast, approaches that couple the sensing of flexible compounds to intended cellular responses would greatly expand potential biosensor applications. Here, to address these challenges, we develop a computational strategy for designing signaling complexes between conformationally dynamic proteins and peptides. To demonstrate the power of the approach, we create ultrasensitive chemotactic receptor—peptide pairs capable of eliciting potent signaling responses and strong chemotaxis in primary human T cells. Unlike traditional approaches that engineer static binding complexes, our dynamic structure design strategy optimizes contacts with multiple binding and allosteric sites accessible through dynamic conformational ensembles to achieve unprecedented signaling efficacy and potency. Our study suggests that a conformationally adaptable binding interface coupled to a robust allosteric transmission region is a key evolutionary determinant of peptidergic GPCR signaling systems. The approach lays a foundation for designing peptide-sensing receptors and signaling peptide ligands for basic and therapeutic applications.
Mathematical modeling to guide experimental design: T cell clustering as a case study
Authors: Rajakaruna Harshana , Ganusov Vitaly V.
Published: April 2022

Mathematical modeling provides a rigorous way to quantify immunological processes and to discriminate between alternative mechanisms driving specific biological phenomena. It is typical that mathematical models of immunological phenomena are developed by modellers to explain specific sets of experimental data after the data have been collected by experimental collaborators. Whether the available data are sufficient to accurately estimate model parameters or to discriminate between alternative models is not typically investigated. While previously collected data may be sufficient to guide development of alternative models and help estimating model parameters, such data often do not allow to discriminate between alternative models. As a case study we develop a series of power analyses to determine optimal sample sizes that allow for accurate estimation of model parameters and for discrimination between alternative models describing clustering of T cells around Plasmodium liver stages. In our typical experiments, mice are infected intravenously with Plasmodium sporozoites that invade hepatocytes (liver cells), and then activated CD8 T cells are transferred into the infected mice. The number of T cells found in the vicinity of individual infected hepatocytes at different times after T cell transfer is counted using intravital microscopy. We previously developed a series of mathematical models aimed to explain highly variable number of T cells per parasite; one of such model, the density-dependent recruitment (DDR) model, fitted the data from preliminary experiments better than the alternative models, such as the density-independent exit (DIE) model. Here we show that the ability to discriminate between these alternative models depends on the number of parasites imaged in the analysis; analysis of about n = 50 parasites at 2, 4, and 8 hours after T cell transfer will allow for over 95% probability to select the correct model. The type of data collected also has an impact; following T cell clustering around individual parasites over time (called as longitudinal (LT) data) allows for a more precise and less biased estimates of the parameters of the DDR model than that generated from a more traditional way of imaging individual parasites in different liver areas/mice (cross-sectional (CS) data). However, LT imaging comes at a cost of a need to keep the mice alive under the microscope for hours which may be ethically unacceptable. We finally show that the number of time points at which the measurements are taken also impacts the precision of estimation of DDR model parameters; in particular, measuring T cell clustering at one time point does not allow accurately estimating all parameters of the DDR model. Using our case study, we propose a general framework on how mathematical modeling can be used to guide experimental designs and power analyses of complex biological processes.
Improved Centromere Assemblies for RefGen_v4
Authors: Laspisa Daniel J. , Schneider Kevin L. , Presting Gernot G.
Published: April 2022

Genome assemblies based on long read sequencing technology have revolutionized the assembly of repeat-rich centromere regions. However, because maize centromeres are highly enriched for the tandem repeat CentC and centromeric retrotransposons (CR), automated genome assembly left gaps even in the excellent B73 RefGen_v4 reference genome constructed from long-read data. Manual editing of >140 Mb spanning the ten centromeres of maize inbred B73 resulted in the closure of 127 sequence gaps and the addition of >8.4 Mb of previously unanchored sequence (unitigs and reads) containing 24 genes, 2 Mb of CR repeat and 887 kb of CentC without including any additional sequence data. The functional centromeres of five maize chromosomes were closed completely, including a 7 Mb region spanning the extremely CR2-rich CEN2. This improved assembly, B73 RefGen_v4CEN, was completed in February 2019 and has been available at https://doi.org/10.25739/7y1p-5169, both as pseudomolecules and as centromere assemblies alone. Thus, the manual editing of existing sequence data significantly improved the centromere regions of the B73 RefGen_v4 reference genome. These data were used for centromere analyses until the release of RefGen_v5.
Hand–foot coordination is significantly influenced by motion direction in individuals with autism spectrum disorder
Authors: Umesawa Yumi , Matsushima Kanae , Fukatsu Reiko , Terao Yasuo , Ide Masakazu
Published: April 2022

Abstract and keywords

Generally, when individuals attempt to move two limbs rhythmically in the opposite direction (e.g., flex the left hand and extend the left foot along the sagittal plane), the movements tend to be instead performed in the same direction. This phenomenon, known as directional constraint, can be harnessed to examine the difficulties in movement coordination exhibited by most individuals with autism spectrum disorder (ASD). While such difficulties have already been investigated through standardized clinical assessments, they have not been examined through kinematic methods. Thus, we employed a clinical assessment scale in an experimentally controlled environment to investigate whether stronger directional constraint during the rhythmic movement of two limbs is more pronounced and associated with decreased movement coordination in individuals with ASD. ASD and typically developing (TD) participants were asked to rhythmically move two limbs either in the same or opposite directions. In addition, the coordination skills of participants were assessed using the Bruininks-Oseretsky Test of Motor Proficiency Second Edition (BOT-2). Subjects with ASD showed significantly stronger directional constraint than TD participants during the contralateral and ipsilateral movement of the hand and foot. According to the pooled data from both groups, participants who showed stronger directional constraint during these two movement conditions also exhibited poorer coordinated movement skills in the BOT-2. Furthermore, stronger directional constraint was associated with severe autistic traits. These results suggest that people with ASD may have difficulties in inhibiting the neural signals that synchronize the direction of inter-limb movements, thus resulting in coordination disabilities.

Lay Summary

Individuals with autism spectrum disorder (ASD) often exhibit difficulties in coordinated movements. We asked those with ASD and healthy participants to move two limbs (e.g., left hand and left foot) either in the same or the opposite direction. Results demonstrated that participants with ASD had more difficulties in counteracting the tendency of their hand and foot to synchronously move in the same direction. Our findings suggested that difficulties to suppress synchronized movements of the hand and foot result in coordination disabilities.
Rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing
Authors: Peng Kerui , Nowicki Theodore Scott , Campbell Katie , Peng Dandan , Nagareddy Anish , Huang Yu-Ning , Karlsberg Aaron , Miller Zachary , Brito Jaqueline , Pak Victoria M. , Abedalthagafi Malak S. , Burkhardt Amanda M. , Alachkar Houda , Ribas Antoni , Mangul Serghei
Published: April 2022

The ability to identify and track T cell receptor (TCR) sequences from patient samples is becoming central to the field of cancer research and immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumor antigens is important to determine the persistence of these cells and quantify tumor responses. The available high-throughput method to profile T cell receptor repertoires is generally referred to as TCR sequencing (TCR-Seq). However, the available TCR-Seq data is limited compared to RNA sequencing (RNA-Seq). In this paper, we have benchmarked the ability of RNA-Seq-based methods to profile TCR repertoires by examining 19 bulk RNA-Seq samples across four cancer cohorts including both T cell rich and poor tissue types. We have performed a comprehensive evaluation of the existing RNA-Seq-based repertoire profiling methods using targeted TCR-Seq as the gold standard. We also highlighted scenarios under which the RNA-Seq approach is suitable and can provide comparable accuracy to the TCR-Seq approach. Our results show that RNA-Seq-based methods are able to effectively capture the clonotypes and estimate the diversity of TCR repertoires, as well as to provide relative frequencies of clonotypes in T cell rich tissues and monoclonal repertoires. However, RNA-Seq-based TCR profiling methods have limited power in T cell poor tissues, especially in polyclonal repertoires of T cell poor tissues. The results of our benchmarking provide an additional appealing argument to incorporate the RNA-Seq into immune repertoire screening of cancer patients as it offers broader knowledge into the transcriptomic changes that exceed the limited information provided by TCR-Seq.
Chemokine Receptor 1 and its associated immune pathway are downregulated in SF3B1MT blood and non-blood cancers
Authors: Dastpak Mahtab , Kim Hyunmin , Paraggio Christina L. , Leonard Claudia E. , Yin Shanye , Chi Binkai , Nassar Kelsey W. , Rowe R. Grant , Hou Zhonggang , Zhang Jiuchun , Cohn Erin F. , Yang Na , Marion William , Zhang Yosra , Daley George Q. , Reed Robin
Published: April 2022

Mutation of the essential splicing factor SF3B1 is primarily associated with hematological cancers but also occurs in solid tumors. We edited the most common mutation, K700E, into human embryonic stem (ES) cells to determine the effects of this mutation alone in an undifferentiated/non-cancer background. Unexpectedly, >20% of the significantly upregulated genes in the SF3B1K700E ES lines have immune functions. Thus, SF3B1 may have an additional role in proper expression of immune genes in appropriate cell types. In striking contrast, we found that published RNA-seq data from SF3B1 blood (MDS, CLL, AML) and non-blood (BRCA, UVM) cancers exhibited the opposite, downregulation of a multitude of immune pathways with 7 of the pathways shared among all 5 of the SF3B1 cancers. One of these pathways, “leukocyte migration”, is the 1st reported pathway shared among all splicing factor cancers, including the 5 SF3B1 cancers and MDS associated with U2AF1, SRSF2 and ZRSR2. Importantly, we identified CCR1, which is in the leukocyte migration pathway as the only shared downregulated gene in the 5 SF3B1 cancers and in U2AF1MT MDS. We conclude that downregulation of CCR1 and its associated immune pathway may play a key role in pathogenesis of these splicing factor cancers and are thus potential therapeutic targets.
PanGu Drug Model: Learn a Molecule Like a Human
Authors: Lin Xinyuan , Xu Chi , Xiong Zhaoping , Zhang Xinfeng , Ni Ningxi , Ni Bolin , Chang Jianlong , Pan Ruiqing , Wang Zidong , Yu Fan , Tian Qi , Jiang Hualiang , Zheng Mingyue , Qiao Nan
Published: April 2022

Recent achievements in large-scale pre-trained models like GPT-3 and PanGu-α showed amazing performances in many downstream tasks, which makes AI friendlier toward industrial users. Deep learning has been recognized as the most promising technology for pharmaceuticals, a powerful molecule pre-trained model could save researchers tons of time. In chemistry classes, the students learn two molecule representations, the molecular formula and the structure formula, and learn to translate them from one way to the other. Inspired by this, we developed a novel deep learning architecture using a graph-to-sequence asymmetric conditional variational autoencoders, called PanGu Drug Model, which can appropriately characterize the molecule from both representations and improve the performance of downstream drug discovery tasks. After pretrained with 1.7 billion small molecules, our proposed model achieved the state-of-the-art results in 20 drug discovery tasks, such as molecule property prediction (predict ADMET properties, compound-target interactions, drug-drug interactions and chemical reaction productivity), molecule generation and molecule optimization. A new drug screening library of 100 million drug-like small molecules with 99.68% novelty was generated by PanGu molecule generator, which could efficiently produce novel compounds with similar physiochemical properties to given distribution, this library could be used to supplement existing compound databases. In addition, PanGu molecule optimizer could optimize the chemical structures of starting molecule with improved molecular property of interest. An automatic multi-objective optimization web application implemented by PanGu Drug Model is available at http://www.pangu-drug.com/.
Quantitative crosslinking and mass spectrometry determine binding interfaces and affinities mediating kinetochore stabilization
Authors: Hagemann Goetz , Solis-Mezarino Victor , Singh Sylvia , Potocnjak Mia , Kumar Chandni , Herzog Franz
Published: April 2022

Crosslinking and mass spectrometry (XLMS) are used in integrative structural biology to acquire spatial restraints. We found a dependency between crosslink distances and intensities and developed a quantitative workflow to simultaneously estimate apparent dissociation constants (KD) of contacts within multi-subunit complexes and to aid interface prediction. Quantitative XLMS was applied to study the assembly of the macromolecular kinetochore complex, which is built on centromeric chromatin and establishes a stable link to spindle microtubules in order to segregate chromosomes during cell division. Inter-protein crosslink intensities facilitated determination of phosphorylation-induced binding interfaces and affinity changes. Phosphorylation of outer and inner kinetochore proteins mediated cooperative kinetochore stabilization and decreased the KD values of its interactions to the centromeric nucleosome by ~200-fold, which was essential for cell viability. This work demonstrates the potential of quantitative XLMS for characterizing mechanistic effects on protein assemblies upon post-translational modifications or cofactor interaction and for biological modeling.
A chromosome-length assembly of the Hawaiian Monk seal (Neomonarchus schauinslandi) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging”
Authors: Mohr David W. , Gaughran Stephen J. , Paschall Justin , Naguib Ahmed , Chun Pang Andy Wing , Dudchenko Olga , Aiden Erez Lieberman , Church Deanna M. , Scott Alan F.
Published: April 2022

The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here we report a chromosomal reference assembly for a male animal produced using a variety of methods including linked-read sequencing, Hi-C contiguity mapping, optical genome mapping, and nanopore long read sequencing. The final assembly consisted of 16 autosomes, an X and portions of the Y chromosomes. We compared variants in the reference animals to nine other HMS and to the human reference NA12878 confirming a low level of variation within the species and one-eighth that of the human reference. A lack of variation in several MHC genes was documented suggesting that this species may be at risk for infectious disease. Lastly, the HMS chromosomal assembly confirmed significant synteny with other pinnipeds. This reference should be a useful tool for long-term management of HMS and evolutionary studies of other carnivorans.
Frontal Cortex Gates Distractor Stimulus Encoding in Sensory Cortex
Authors: Zhang Zhaoran , Zagha Edward
Published: April 2022

Frontal cortex suppresses behavioral responses to distractor stimuli. One possible mechanism by which this occurs is by modulating sensory responses in sensory cortex. However, it is currently unknown how frontal cortex modulations of sensory cortex contribute to distractor response suppression. We trained mice to respond to target stimuli in one whisker field and ignore distractor stimuli in the opposite whisker field. During expert task performance, optogenetic inhibition of frontal cortex increased behavioral responses to distractor stimuli. During expert task performance, within sensory cortex we observed expanded propagation of target stimulus responses and contracted propagation of distractor stimulus responses. In contrast to current models of frontal cortex function, frontal cortex did not substantially modulate the response amplitude of preferred stimuli. Rather, frontal cortex specifically suppressed the propagation of distractor stimulus responses, thereby preventing target-preferring neurons from being activated by distractor stimuli. Single unit analyses revealed that wMC decorrelates target and distractor stimulus encoding in target-preferring S1 neurons, which likely improves selective target stimulus detection by downstream readers. Moreover, we observed proactive top-down modulation from frontal to sensory cortex, through the preferential activation of GABAergic neurons. Overall, our study provides important mechanistic details about how frontal cortex gates sensory propagation in sensory cortex to prevent behavioral responses to distractor stimuli.

Highlights

Pairing of frontal cortex optogenetic inhibition with sensory cortex recordings during a target-distractor Go/NoGo task.

During expert task performance, we observed target stimulus response expansion and distractor stimulus response contraction.

Optogenetic inhibition of frontal cortex increased false alarm rates and selectively increased the propagation of distractor evoked responses into target-aligned sensory cortex.

Even before stimulus onset, frontal cortex preferentially drives GABAergic neurons in distractor-aligned sensory cortex.
The genome sequence of the scarce swallowtail, Iphiclides podalirius
Authors: Mackintosh Alexander , Laetsch Dominik R. , Baril Tobias , Ebdon Sam , Jay Paul , Vila Roger , Hayward Alex , Lohse Konrad
Published: April 2022

The scarce swallowtail, Iphiclides podalirius (Linnaeus, 1758), is a species of butterfly in the family Papilionidae. Here we present a chromosome-level genome assembly for I. podalirius as well as gene and transposable element annotations. We estimate heterozygosity within different partitions of the genome and find a negative correlation between chromosome length and heterozygosity at fourfold-degenerate sites. This high quality genome assembly, the first for any species in the tribe Leptocircini, will be a valuable resource for population genomics in the genus Iphiclides and comparative genomics more generally.
CIS calibrates GM-CSF signalling strength to regulate macrophage polarization via a STAT5-IRF8 axis
Authors: Zhang Shengbo , Rautela Jai , Bediaga Naiara G , Kolesnik Tatiana B , You Yue , Dagley Laura F , Bedo Justin , Wang Hanqing , Sun Li , Sutherland Robyn , Surgenor Elliot , Iannarella Nadia , Allan Rhys , Souza-Fonseca-Guimaraes Fernando , Xie Yi , Wang Qike , Zhang Yuxia , Xu Yuekang , Nutt Stephen L , Lew Andrew M , Huntington Nicholas D , Nicholson Sandra E , Chopin Michaël , Zhan Yifan
Published: April 2022

The cytokine granulocyte-macrophage-colony stimulating factor (GM-CSF) possesses the ability to differentiate macrophages (MØs) with opposing functions, namely proinflammatory M1-like and immunosuppressive M2-like. Despite the importance and opposing functional outcomes of these processes, the intrinsic mechanism that regulates the functional polarization of MØs under GM-CSF signaling remains elusive. Here we show that GM-CSF induced MØs polarisation resulted in the expression of the Cytokine-inducible SH2-containing protein (CIS), and that CIS deficiency diverted differentiation of monocytes into immunosuppressive M2-like MØs expression. CIS deficiency resulted in the hyperactivation of the JAK-STAT5 signaling pathway, consequently promoting the downregulation of the transcription factor Interferon Regulatory Factor 8 (IRF8). Loss and gain of function approaches highlighted IRF8 as a critical instructor of the M1-like polarisation program. In vivo, CIS deficiency led to skewing to M2-like macrophages, which induced strong Th2 immune responses characterised by the development of severe experimental asthma. Collectively, we reveal a CIS-censored mechanism interpreting the opposing actions of GM-CSF in MØ differentiation and uncovering its role in controlling allergic inflammation.
Integrated single-cell (phospho-)protein and RNA detection uncovers phenotypic characteristics of human antibody secreting cells
Authors: van Buijtenen Erik , Janssen Wout , Vink Paul , Habraken Maurice J.M. , Wingens Laura J. A. , van Elsas Andrea , Huck Wilhelm T.S. , van Buggenum Jessie A.G.L. , van Eenennaam Hans
Published: April 2022

Antibody-secreting cells (ASCs) secrete IgM, IgA, or IgG antibodies and are key components of humoral immunity; however, little is known about unique characteristics of the Ig-classes due to limited availability of material and challenges to quantify many intracellular molecular modalities at a single-cell resolution. We combined a method to in vitro differentiate peripheral B-cells into ASCs with integrated multi-omic single-cell sequencing technologies to quantify subclass-specific hallmark surface markers, transcriptional profiles and signaling transduction pathway components. Our approach detected differential expression of plasmablast and plasma cell markers, homing receptors and IL-2, IL-6, JAK/STAT and mTOR signaling activity across Ig-subclasses. Taken together, our integrated multi-omics approach allowed high-resolution phenotypic characterization of single cells in a complex sample of in vitro differentiated human ASCs. Our strategy is expected to further our understanding of human ASCs in healthy and diseased samples and provide a valuable tool to identify novel biomarkers and potential drug targets.

Teaser

Integrated single-cell analysis allows tri-modal phenotypic analysis of in-vitro generated human antibody-secreting cells.
Predicting catchment suitability for biodiversity at national scales
Authors: Dobson Barnaby , Barry Saoirse , Maes-Prior Robin , Mijic Ana , Woodward Guy , Pearse William D.
Published: April 2022

Biomonitoring of water quality and catchment management are often disconnected, due to mismatching scales. Great effort and money is spent each year on routine reach-scale surveying across many sites, particularly in the UK, and typically with a focus on pre-defined indicators of organic pollution to compare observed vs expected subsets of common macroinvertebrate indicator species. Threatened species are often ignored due to their rarity as are many invasive species, which are seen as undesirable even though they are increasingly common in freshwaters, especially in urban ecosystems. However, these taxa are monitored separately for reasons related to biodiversity concerns rather than for gauging water quality. Repurposing such monitoring data could therefore provide important new biomonitoring tools that can help catchment managers to directly link the water quality that they aim to control with the biodiversity that they are trying to protect. Here we used the England Non-Native and Rare/Protected species records that track these two groups of species as a proof-of-concept for linking catchment scale management of freshwater ecosystems and biodiversity to a range of potential drivers across England. We used national land use (Centre for Ecology and Hydrology land cover map) and water quality indicator (Environment Agency water quality data archive) datasets to predict the presence or absence of 48 focal threatened or invasive species of concern routinely sampled by the English Environment Agency at catchment scale, with a median accuracy of 0.81 area under the receiver operating characteristic curve. A variety of water quality indicators and land-use types were useful in predictions, highlighting that future biomonitoring schemes could use such complementary measures to capture a wider spectrum of drivers and responses. In particular, the percentage of a catchment covered by freshwater was the single most important metric, reinforcing the need for space/habitat to support biodiversity. We show how our method could inform new catchment management approaches, by highlighting how key relationships can be identified and how to understand, visualise and prioritise catchments that are most suitable for restorations or water quality interventions. The scale of this work, in terms of number of species, drivers and locations, represents a step towards a new approach to catchment management that enables managers to link drivers they can control (water quality and land use) to the biota they are trying to protect (biodiversity).
Bladder cancer organoids as a functional system to model different disease stages and therapy response
Authors: Minoli Martina , Cantore Thomas , Kiener Mirjam , Fedrizzi Tarcisio , Manna Federico La , Karkampouna Sofia , Genitisch Vera , Rodriguez Antonio , Klima Irena , Gasperini Paola , Kiss Bernhard , Seiler-Blarer Roland , Demichelis Francesca , Thalmann George N. , Julio Marianna Kruithof-de
Published: April 2022

Bladder Cancer (BLCa) inter-patient heterogeneity is considered the primary cause of tumor reoccurrence and treatment failure, suggesting that BLCa patients could benefit from a more personalized treatment approach. Patient-derived organoids (PDOs) have been successfully used as a functional model for predicting drug response in different cancer types. In our study, we established BLCa PDO cultures from different BLCa stages. BLCa PDOs preserve the histological and molecular heterogeneity of the parental tumors, including their multiclonal genetic landscapes. BLCa PDOs consistently share key genetic alterations detected in parental tumors, mirroring tumor evolution in longitudinal sampling. Our drug screening pipeline was implemented using BLCa PDOs, testing both standard-of-care and additional FDA-approved compounds for other solid tumors. Integrative analysis of drug response profiles with matched PDO genomic analysis was used to determine enrichment thresholds for candidate markers of therapy resistance and sensitivity. By assessing the clinical history of longitudinally sampled cases, the clonal evolution of the disease could be determined and matched with drug response profiles. In conclusion, we have developed a clinically relevant pipeline for drug response profile assessment and discovery of candidate markers of therapy resistance.
Sialophorin is an essential host element for vaccine immunity against pulmonary fungal infections
Authors: Mudalagiriyappa Srinivasu , Deepe George S , Nanjappa Som Gowda
Published: April 2022

The global burden of fungal infections is alarming, primarily due to the increasing immune-compromised population. The immuno-preventive/therapeutic measures, including vaccines, are necessary to prevent or control fungal diseases. Identifying a protective host element as a functional phenotypic marker is immensely valuable. We identified a host element, sialophorin, preferentially associated with antifungal memory T cells. We investigated its role in vaccine immunity using a mouse model of pulmonary fungal infection. We found that sialophorin was essential to bolster CD8+T-cell responses to the vaccine by enhancing their differentiation and expanding cytokine-producing cells required for immunity. Using a gain-of-function approach, activating sialophorin using mAb augmented the CD8+T cell responses, and sialophorin-sufficient CD8+T cells were competitively superior in differentiation and expansion to the deficient cells. Sialophorin-mediated vaccine immunity was independent of the T cell trafficking effect. Finally, we show that sialophorin is a potential functional phenotypic marker of fungal vaccine-potency and immunity. Our study revealed that sialophorin is an essential host-target element to bolster vaccine responses and serves as apotential biomarkerof fungal immunity.

Author Summary

Fungal infections have been rising in recent years due to increased immunocompromised individuals. Vaccination ofat-riskindividuals helps counter the infections. Thus, suitable vaccine platforms are needed with apt adjuvants, and a phenotypic marker of vaccine immunity will bolster the efforts. We identified a phenotypic marker, sialophorin, associated with T cell vaccine immunity to fungal infection. Our findings show an essential role of sialophorin for fungal immunity, as a target of adjuvanticity, and as a potential biomarker of vaccine immunity against many fungal infections.
GPR183 mediates the capacity of the novel CD47-CD19 bispecific antibody TG-1801 to heighten ublituximab-umbralisib (U2) anti-lymphoma activity
Authors: Ribeiro Marcelo Lima , Profitós-Pelejà Núria , Santos Juliana Carvalho , Blecua Pedro , Garau Diana Reyes , Armengol Marc , Fernández-Serrano Miranda , Miskin Hari P. , Bosch Francesc , Esteller Manel , Normant Emmanuel , Roué Gael
Published: April 2022

Targeted therapies have considerably improved the survival rate of B-cell non-Hodgkin lymphoma (B-NHL) patients in the last decade; however, most subtypes remain incurable. TG-1801, a bispecific antibody that targets CD47 selectively on CD19+ B-cells, is under clinical evaluation in relapsed/refractory B-NHL patients either as a single-agent or in combination with ublituximab, a CD20 antibody, which is also being combined with the PI3Kδ/CK1e inhibitor, umbralisib (“U2”-regimen). In this study, we demonstrated that TG-1801 potentiates ublituximab-mediated antibody-dependent cell death (ADCC) and antibody-dependent cell phagocytosis (ADCP), leading to an additive anti-tumour effect of the TG-1801/U2 combination in B-NHL co-cultures. Accordingly, in a B-NHL xenotransplant model, the triplet achieved a 93% tumour growth inhibition, with 40% of the animals remaining tumour-free 35 days after the last dosing. Transcriptomic analysis further uncovered the upregulation of the G protein-coupled receptor, GPR183, as a crucial event associated with TG-1801/U2 synergism, while pharmacological blockade or genetic depletion of this factor impaired ADCP initiation, as well as cytoskeleton remodelling and cell migration, in B-NHL cultures exposed to the drug combination. Thus, our results set the preclinical rationale and support a combination strategy of TG-1801 with PI3Kδ- and CD20-targeting agents in patients with B-NHL.
Spatially resolved transcriptomics reveals innervation-responsive functional clusters in skeletal muscle
Authors: D’Ercole Chiara , D’Angelo Paolo , Ruggieri Veronica , Proietti Daisy , Riera Carles Sanchez , Macone Alberto , Bonvissuto Davide , Sette Claudio , Giordani Lorenzo , Madaro Luca
Published: April 2022

Striated muscle is a highly organized structure composed by well-defined anatomical domains with integrated but distinct assignments. So far, the lack of a direct correlation between tissue architecture and gene expression has limited our understanding of how each unit responds to physio-pathologic contexts.

Here, we show how the combined use of spatially resolved transcriptomics and immunofluorescence can bridge this gap by enabling the unbiased identification of such domains and the characterization of their response to external perturbations. Using a spatiotemporal analysis, we followed the changes in the transcriptomics profile of specific domains in muscle in a model of denervation. Furthermore, our approach allowed us to identify the spatial distribution and nerve dependence of atrophic signalling pathway and polyamine metabolism to glycolytic fibers. Indeed, we demonstrate a pronounced alteration of polyamine homeostasis upon denervation. Our dataset will serve as a resource for future studies of the mechanisms underlying skeletal muscle homeostasis and innervation.

Graphical Abstract
mEos4b photoconversion efficiency depends on laser illumination conditions used in PALM
Authors: Wulffele Jip , Thedié Daniel , Glushonkov Oleksandr , Bourgeois Dominique
Published: April 2022

Green-to-red photoconvertible fluorescent proteins (PCFPs) are widely employed as markers in photoactivated localization microscopy (PALM). However, their highly complex photophysical behavior complicates their usage. The fact that only a limited fraction of a PCFP ensemble can form the photoconverted state upon near-UV light illumination, termed photoconversion efficiency (PCE), lowers the achievable spatial resolution in PALM and creates undercounting errors in quantitative counting applications. Here, we show that the PCE of mEos4b is not a fixed property of this PCFP, but strongly depends on illumination conditions. Attempts to reduce long-lived blinking in red mEos4b by application of 488 nm light leads to a reduction of the PCE. Furthermore, the PCE of mEos4b strongly depends on the applied 405-nm power density. A refined photophysical model of mEos4b accounts for the observed effects, involving nonlinear green-state photobleaching upon violet light illumination favored by photon absorption by a putative radical dark state.

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Fundamental trade-off between speed of switching and robustness of genetic switches limits dynamic control of metabolism
Authors: Raj Kaushik , Wong William T. Z. , Zhang Beini , Mahadevan Radhakrishnan
Published: April 2022

1

Bi-stable gene regulatory motifs are found in a wide variety of natural gene regulatory networks and effect transcriptional switching between stable phenotypic states in cells. In synthetic gene regulatory circuits, these architectures can be leveraged to dynamically switch between distinct metabolic states for metabolic engineering and therapeutic applications. However, the lack of modularity and predictability of these motifs in varying environments has limited widespread application, especially since the factors that affect switching characteristics are still unclear. In this work, we use a mathematical model along with a newly developed dynamical modeling and continuity analysis framework to analyze the dynamics and robustness of bi-stable switches over a range of biologically relevant model parameter values. We identify a hitherto undiscovered fundamental trade-off between the robustness of the motif - the parameter ranges over which it retains bi-stable function, and the speed at which it effects a phenotypic change. Further, usingE. colias a model host, we constructed a large library (100) of transcriptional switches that show a wide range of switching speeds, to experimentally demonstrate the presence of this trade-off. The presence of this trade-off has significant implications on the design of transcriptional switches for diverse applications and explains the circuit architecture of naturally occurring transcriptional switches as well. Additionally, we anticipate that our diverse library of experimentally validated robust bi-stable switches will be valuable to effect phenotypic changes with differing switching speed requirements for metabolic engineering applications.

2

Significance statement

The ability to switch genes on and off in response to spatio-temporal stimuli is critical to the survival of all organisms. At the cellular level, such switching is effected by regulatory motifs such as the bi-stable genetic toggle switch. Bi-stable motifs also serve as a primitive mode of cellular memory - “remembering” the last environment to which the cells have been exposed. In this work, we uncover a fundamental trade-off between the robust functioning of these switches and the speed at which they can effect a change in the gene expression landscape. These findings have a broad impact on the design and use of such synthetic gene regulatory devices across several fields such as industrial biotechnology, healthcare, etc.
Aberrant MYCN expression drives oncogenic hijacking of EZH2 as a transcriptional activator in peripheral T cell lymphoma
Authors: Vanden Bempt Marlies , Debackere Koen , Demeyer Sofie , Van Thillo Quentin , Meeuws Nienke , Provost Sarah , Mentens Nicole , Jacobs Kris , Gielen Olga , Nittner David , Ogawa Seishi , Kataoka Keisuke , Graux Carlos , Tousseyn Thomas , Cools Jan , Dierickx Daan
Published: April 2022

Peripheral T cell lymphoma (PTCL) is a heterogeneous group of hematological cancers arising from the malignant transformation of mature T cells. In a cohort of 28 PTCL cases, we identified recurrent overexpression of MYCN, a member of the MYC family of oncogenic transcription factors. Approximately half of all PTCL cases was characterized by a MYC expression signature. Inducible expression of MYCN in lymphoid cells in a mouse model caused T cell lymphoma that recapitulated human PTCL with a MYC expression signature. Integration of mouse and human expression data identified EZH2 as a key downstream target of MYCN. Remarkably, EZH2 was found to be an essential co-factor for the transcriptional activation of the MYCN-driven gene expression program, which was independent of methyltransferase activity, but dependent on phosphorylation by CDK1. MYCN-driven T cell lymphoma was sensitive to EZH2 degradation or CDK1 inhibition, which displayed synergy with FDA-approved HDAC inhibitors.

Key points

- Transcriptomic analysis of PTCL tumors reveals recurrent MYCN overexpression and the presence of a MYC signature in 50% of PTCL cases

- EZH2 is a transcriptional cofactor for the MYCN-driven gene expression program, which confers sensitivity to HDAC inhibition
Small molecules from Bacopa monneiri as potent inhibitors against Neurodegenerative disorders
Authors: Sangeet Satyam , Khan Arshad
Published: April 2022

Alzheimer’s is characterized by the formation of senile plaques and fibril tangles. Several methodologies have been employed to treat the disease. Albeit engineered medications which are accessible for the treatment of Alzheimer’s, due to their numerous side-effects, it becomes imperative to formulate and synthesize novel drug candidates. Plants could be utilized as an alternative for these manufactured medications because of their low incidental effects in contrast with the engineered drugs. Bacopa monneiri (BM) is a therapeutic plant which is accounted for to be utilized to treat NDs. Therefore, in current study an in-silico approach was carried out to evaluate the pharmacological effect of BM. Molecular Docking was carried out to screen the active phytochemicals of BM which can act as potential drug candidates against amyloid-β plaques. A total of 8 biologically active phytochemicals from BM were docked against p75NTR receptor. Based on molecular docking study it was observed that the phytocompounds Bacopasaponin D and Bacopasaponin G of BM significantly fits to the active site of p75NTR. Further Molecular Dynamics simulation study was performed to examine the stability of the binding of these phytochemicals with the selected targets. Our findings suggested that the phytocompounds Bacopasaponin D and Bacopasaponin G significantly binds with p75NTR and thus might have a potential to inhibit the natural binding activity of amyloid-b plaques and act as a potential anti-neurodegenerative drug.