bluuebunny/crossref_metadata_2025 huggingface dataset:
Single Cell Transcriptomics of Fibrotic Lungs Unveils Aging-associated Alterations in Endothelial and Epithelial Cell Regeneration
Authors: Raslan Ahmed A. , Pham Tho X. , Lee Jisu , Hong Jeongmin , Schmottlach Jillian , Nicolas Kristina , Dinc Taha , Bujor Andreea M. , Caporarello Nunzia , Thiriot Aude , von Andrian Ulrich H. , Huang Steven K. , Nicosia Roberto F. , Trojanowska Maria , Varelas Xaralabos , Ligresti Giovanni
Published: January 2023

Lung regeneration deteriorates with aging leading to increased susceptibility to pathologic conditions, including fibrosis. Here, we investigated bleomycin-induced lung injury responses in young and aged mice at single-cell resolution to gain insights into the cellular and molecular contributions of aging to fibrosis. Analysis of 52,542 cells in young (8 weeks) and aged (72 weeks) mice identified 15 cellular clusters, many of which exhibited distinct injury responses that associated with age. We identifiedPdgfra+alveolar fibroblasts as a major source of collagen expression following bleomycin challenge, with those from aged lungs exhibiting a more persistent activation compared to young ones. We also observed age-associated transcriptional abnormalities affecting lung progenitor cells, including ATII pneumocytes and general capillary (gCap) endothelial cells (ECs). Transcriptional analysis combined with lineage tracing identified a sub-population of gCap ECs marked by the expression of Tropomyosin Receptor Kinase B (TrkB) that appeared in bleomycin-injured lungs and accumulated with aging. This newly emerged TrkB+EC population expressed common gCap EC markers but also exhibited a distinct gene expression signature associated with aberrant YAP/TAZ signaling, mitochondrial dysfunction, and hypoxia. Finally, we defined ACKR1+venous ECs that exclusively emerged in injured lungs of aged animals and were closely associated with areas of collagen deposition and inflammation. Immunostaining and FACS analysis of human IPF lungs demonstrated that ACKR1+venous ECs were dominant cells within the fibrotic regions and accumulated in areas of myofibroblast aggregation. Together, these data provide high-resolution insights into the impact of aging on lung cell adaptability to injury responses.
Breakdown in seasonal dynamics of subtropical ant communities with land-cover change
Authors: Kass Jamie M. , Yoshimura Masashi , Ogasawara Masako , Suwabe Mayuko , Garcia Francisco Hita , Fischer Georg , Dudley Kenneth L. , Donohue Ian , Economo Evan P.
Published: January 2023

Concerns about widespread human-induced declines in insect populations are mounting, yet little is known about how land-use change modifies the dynamics of insect communities, particularly in understudied biomes. Here, we examine how the seasonal patterns of ant activity—key drivers of terrestrial ecosystem functioning—vary with human-induced land cover change on a subtropical island landscape. Using trap captures sampled biweekly from a biodiversity monitoring network covering Okinawa Island, Japan, we processed 1.2 million individuals and reconstructed activity patterns within and across habitat types. Forest communities exhibited greater variability than those in more developed areas. Using time-series decomposition to deconstruct this pattern, we found that ant communities at sites with greater human development exhibited diminished seasonality, reduced synchrony, and higher stochasticity compared to those at sites with greater forest cover. Our results cannot be explained by variation in either regional orin situtemperature patterns, or by differences in species richness or composition among sites. We conclude that the breakdown of natural seasonal patterns of functionally key insect communities may comprise an important and underappreciated consequence of global environmental change that must be better understood across Earth’s biomes.
Comparison of wholemount dissection methods for neuronal subtype marker expression in the mouse myenteric plexus
Authors: Gomez-Frittelli Julieta , Hamnett Ryan , Kaltschmidt Julia A.
Published: January 2023

Background

Accurately reporting the identity and representation of enteric nervous system (ENS) neuronal subtypes along the length of the gastrointestinal (GI) tract is critical to advancing our understanding of ENS control of GI tract function. Reports of varying proportions of subtype marker expression have employed different dissection techniques to achieve wholemount muscularis preparations of myenteric plexus. In this study we asked whether differences in GI dissection methods could introduce variability into the quantification of marker expression.

Methods

We compared three commonly used methods of ENS wholemount dissection: two flat-sheet preparations that differed in the order of microdissection and fixation as well as a rod-mounted peeling technique. We assessed marker expression using immunohistochemistry, genetic reporter lines, confocal microscopy, and automated image analysis.

Key Results and Conclusions

We found no significant differences between the two flat-sheet preparation methods in the expression of calretinin, neuronal nitric oxide synthase (nNOS), or somatostatin (SST) in ileum myenteric plexus. However, the rod-mounted peeling method resulted in decreased marker labeling for both calretinin and nNOS. This method also resulted in decreased transgenic reporter fluorescent protein (tdTomato) for substance P in ileum and choline acetyltransferase (ChAT) in both ileum and distal colon. These results suggest that labeling among some markers, both native protein and transgenic fluorescent reporters, is decreased by the rod-mounted mechanical method of peeling, demonstrating a critical variability in wholemount muscularis dissection methods.
Adaptations to water stress and pastoralism in the Turkana of northwest Kenya
Authors: Lea AJ , Caldas IV , Garske KM , Echwa J , Gurven M , Handley C , Kahumbu J , Kamau  , Kinyua P , Lotukoi F , Lopurudoi A , Lowasa S , Mallarino R , Martins D , Messer PW , Miano C , Muhoya B , Peng J , Phung T , Rabinowitz JD , Roichman A , Siford R , Stone A , Oill AM Taravella , Mathew S , Wilson MA , Ayroles JF
Published: January 2023

The Turkana people inhabit arid regions of east Africa—where temperatures are high and water is scarce—and they practice subsistence pastoralism, such that their diet is primarily composed of animal products. Working with Turkana communities, we sequenced 367 genomes and identified 8 regions putatively involved in adaptation to water stress and pastoralism. One of these regions includes a putative enhancer for STC1—a kidney-expressed gene involved in the response to dehydration and the metabolism of purine-rich foods such as red meat. We show that STC1 is induced by antidiuretic hormone in humans, is associated with urea levels in the Turkana themselves, and is under strong selection in this population (s∼0.041). This work highlights that partnerships with subsistence-level groups can lead to new models of human physiology with biomedical relevance.
Predictive Motor Control Based on a Generative Adversarial Network
Authors: Lenninger Movitz , Choi Whan-Hyuk , Choi Hansol
Published: January 2023

Predictive processing models suggest that a brain decides actions through inference using its internal generative model over the world’s states and their transitions. Most of the predictive processing models have been formalized using explicit representations of the probability distributions, with explicit structures and parameters. They are difficult to learn in general and needs explanation about representation of structure and parameters of distributions, and the method for statistical arithmetic on them, each of which are questions not easy to answer. In this study, we explore an alternative representation for predictive processing which is based on an implicit model known as generative adversarial networks, which has been widely explored recently in machine learning studies as they can learn a distribution directly from data. We demonstrate how a generative adversarial network can be trained to learn an implicit generative model of motor dynamics. And then, we show that such a model can perform approximate inference using the trained model, providing the necessary computations for both the forward and inverse model of motor control. Our framework may provide another formalization for brain’s inference model, especially for learning process. Additionally, we suggest that the functional architecture of the cortical-basal ganglia circuit may modeled as the generator and discriminator in the generative adversarial network model.
Bromodomain-containing Protein 4 Regulates Innate Inflammation in Airway Epithelial Cells via Modulation of Alternative Splicing
Authors: Mann Morgan , Fu Yao , Xu Xiaofang , Roberts David S. , Li Yi , Zhou Jia , Ge Ying , Brasier Allan R.
Published: January 2023

Bromodomain-containing Protein 4 (BRD4) is a transcriptional regulator which coordinates gene expression programs controlling cancer biology, inflammation, and fibrosis. In airway viral infection, non-toxic BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory cytokines and prevent downstream remodeling. Although the chromatin modifying functions of BRD4 in inducible gene expression have been extensively investigated, its roles in post-transcriptional regulation are not as well understood. Based on its interaction with the transcriptional elongation complex and spliceosome, we hypothesize that BRD4 is a functional regulator of mRNA processing. To address this question, we combine data-independent analysis - parallel accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to achieve deep and integrated coverage of the proteomic and transcriptomic landscapes of human small airway epithelial cells exposed to viral challenge and treated with BRD4i. The transcript-level data was further interrogated for alternative splicing analysis, and the resulting data sets were correlated to identify pathways subject to post-transcriptional regulation. We discover that BRD4 regulates alternative splicing of key genes, including Interferon-related Developmental Regulator 1 (IFRD1) and X-Box Binding Protein 1 (XBP1), related to the innate immune response and the unfolded protein response, respectively. These findings extend the transcriptional elongation-facilitating actions of BRD4 in control of post-transcriptional RNA processing in innate signaling.
Lateral membrane organization as target of an antimicrobial peptidomimetic compound
Authors: Melcrová Adéla , Maity Sourav , Melcr Josef , de Kok Niels A. W. , Gabler Mariella , van der Eyden Jonne , Stensen Wenche , Svendsen John S. M. , Driessen Arnold J. M. , Marrink Siewert J. , Roos Wouter H.
Published: January 2023

Antimicrobial resistance is one of the leading concerns in medical care. Here we resolve the functional mechanism of the antimicrobial action of the cationic tripeptide AMC-109 by combining high speed-atomic force microscopy, molecular dynamics, fluorescence assays, and lipidomic analysis. We show that AMC-109 activity on the negatively charged plasma membrane ofStaphylococcus aureusconsists of two crucial steps. First, AMC-109 self-assembles into stable aggregates with specificity for negatively charged membranes. Second, by incorporation into theS. aureusmembrane the lateral membrane organization is affected, dissolving membrane nanodomains. Domain dissolution affects membrane functions such as protein sorting and cell wall synthesis, and is suggested to cause a loss of resistance of methicillin-resistantS. aureus(MRSA) to methicillin. As the AMC-109 mode of action is similar to the activity of the disinfectant benzalkonium chloride (BAK), a broad applicability, but with low cytotoxicity to human cells, is expected.
The prevalence of dementia in humans could be the result of a functional adaptation
Authors: Holt Alan G , Davies Adrian M
Published: January 2023

In this paper we propose that high copy number of the mitochondrial genome in neurons is a functional adaptation. We simulated the proliferation of deletion mutants of the human mitochondrial genome in a virtual mitochondrion and recorded the cell loss rates due to deletions overwhelming the wild-type.

Our results showed that cell loss increased with mtDNA copy number. Given that neuron loss equates to cognitive dysfunction, it would seem counter-intuitive that there would be a selective pressure for high copy number over low. However, for a low copy number, the onset of cognitive decline, while mild, started early in life. Whereas, for high copy number, it did not start until middle age but progressed rapidly. There could have been an advantage to high copy number in the brain if it delayed the onset of cognitive decline until after reproductive age. The prevalence of dementia in our aged population is a consequence of this functional adaptation.
MOXD1 is a gate-keeper of organ homeostasis and functions as a tumor-suppressor in neuroblastoma
Authors: Fredlund Elina , Andersson Stina , Hilgert Elien , Álvarez-Hernán Guadalupe , Monferrer Ezequiel , Karakaya Sinan , Gregor Tomas , Loontiens Siebe , Bek Jan Willem , Lecomte Estelle , Magnusson Emma , Miltenyte Enrika , Cabirol Marie , Kyknas Michail , Engström Niklas , Henriksson Marie Arsenian , Hammarlund Emma , Noguera Rosa , Speleman Frank , van Nes Johan , Mohlin Sofie
Published: January 2023

Neuroblastoma is a childhood cancer believed to result from dysfunctional development. Its origin during embryogenesis remains poorly understood. The lack of appropriate models has hindered in-depth mapping of tumor-driving events. Here, we identify a novel tumor-suppressor gene that predicts poor survival in high-risk disease, by applying bulk and single cell RNA sequencing data of neuroblastoma and human fetal adrenal glands. Trunk neural crest-specific MOXD1 discriminates cell populations during normal and tumor development, with implications for deciphering neuroblastoma cell origin. We created an embryonic conditional knockout model and show that cell type-specific loss ofMOXD1leads to disrupted organ homeostasis and failed adrenal gland formation, home for neuroblastoma. We show that MOXD1 is a tumor suppressor gene in zebrafish, chick, and micein vivomodels.

One-Sentence Summary

Neural crest-specific MOXD1 is ade novotumor-suppressor gene in childhood cancers arising during embryogenesis.
Low level of antioxidant capacity biomarkers but not target overexpression predicts vulnerability to ROS-inducing drugs
Authors: Samarin Jana , Fabrowski Piotr , Kurilov Roman , Nuskova Hana , Hummel-Eisenbeiss Johanna , Pink Hannelore , Li Nan , Weru Vivienn , Alborzinia Hamed , Yildiz Umut , Grob Laura , Taubert Minerva , Czech Marie , Morgen Michael , Brandstädter Christina , Becker Katja , Mao Lianghao , Jayavelu Ashok Kumar , Goncalves Angela , Uhrig Ulrike , Seiler Jeanette , Lyu Yanhong , Diederichs Sven , Klingmüller Ursula , Muckenthaler Martina , Kopp-Schneider Annette , Teleman Aurelio , Miller Aubry K , Gunkel Nikolas
Published: January 2023

Despite a strong rationale for why cancer cells are susceptible to redox-targeting drugs, such drugs often face tumor resistance or dose-limiting toxicity in preclinical and clinical studies. An important reason is the lack of specific biomarkers to better select susceptible cancer entities and stratify patients. Using a large panel of lung cancer cell lines, we identified a set of “antioxidant-capacity” biomarkers (ACB), which were tightly repressed, partly by STAT3 and STAT5A/B in sensitive cells, rendering them susceptible to multiple redox-targeting and ferroptosis-inducing drugs. Contrary to expectation, constitutively low ACB expression was not associated with an increased steady state level of reactive oxygen species (ROS) but a high level of nitric oxide, which is required to sustain high replication rates. Using ACBs, we identified cancer entities with a high percentage of patients with favorable ACB expression pattern, making it likely that more responders to ROS-inducing drugs could be stratified for clinical trials.
Motor cortex retains and reorients neural dynamics during motor imagery
Authors: Dekleva Brian M. , Chowdhury Raeed H. , Batista Aaron P. , Chase Steven M. , Yu Byron M. , Boninger Michael L. , Collinger Jennifer L.
Published: January 2023

The most prominent role of motor cortex is generating patterns of neural activity that lead to movement, but it is also active when we simply imagine movements in the absence of actual motor output. Despite decades of behavioral and imaging studies, it is unknown how the specific activity patterns and temporal dynamics within motor cortex during covert motor imagery relate to those during motor execution. Here we recorded intracortical activity from the motor cortex of two people with residual wrist function following incomplete spinal cord injury as they performed both actual and imagined isometric wrist extensions. We found that we could decompose the population-level activity into orthogonal subspaces such that one set of components was similarly active during both action and imagery, and others were only active during a single task type—action or imagery. Although they inhabited orthogonal neural dimensions, the action-unique and imagery-unique subspaces contained a strikingly similar set of dynamical features. Our results suggest that during motor imagery, motor cortex maintains the same overall population dynamics as during execution by recreating the missing components related to motor output and/or feedback within a unique imagery-only subspace.
Size tuning of neural response variability in laminar circuits of macaque primary visual cortex
Authors: Nurminen Lauri , Bijanzadeh Maryam , Angelucci Alessandra
Published: January 2023

A defining feature of the cortex is its laminar organization, which is likely critical for cortical information processing. For example, visual stimuli of different size evoke distinct patterns of laminar activity. Visual information processing is also influenced by the response variability of individual neurons and the degree to which this variability is correlated among neurons. To elucidate laminar processing, we studied how neural response variability across the layers of macaque primary visual cortex is modulated by visual stimulus size. Our laminar recordings revealed that single neuron response variability and the shared variability among neurons are tuned for stimulus size, and this size-tuning is layer-dependent. In all layers, stimulation of the receptive field (RF) reduced single neuron variability, and the shared variability among neurons, relative to their pre-stimulus values. As the stimulus was enlarged beyond the RF, both single neuron and shared variability increased in supragranular layers, but either did not change or decreased in other layers. Surprisingly, we also found that small visual stimuli could increase variability relative to baseline values. Our results suggest multiple circuits and mechanisms as the source of variability in different layers and call for the development of new models of neural response variability.
PEGylated recombinantAplysia punctataink toxin depletes arginine and lysine and inhibits growth of tumor xenografts
Authors: Wolkersdorfer Alena M. , Bergmann Birgit , Adelmann Juliane , Ebbinghaus Matthias , Günther Eckhard , Gutmann Marcus , Hahn Lukas , Hurwitz Robert , Krähmer Ralf , Leenders Frank , Lühmann Tessa , Schueler Julia , Schmidt Luisa , Teifel Michael , Meinel Lorenz , Rudel Thomas
Published: January 2023

In recent years, a novel treatment method for cancer emerged, which is based on the starvation of tumors of amino acids like arginine. The deprivation of arginine in serum is based on enzymatic degradation and can be realized by arginine deaminases like the L-amino acid oxidase found in the ink toxin of the sea hareAplysia punctata. Previously isolated from the ink, the L-amino acids oxidase was described to oxidate the essential amino acid L-lysine and L-arginine to their corresponding deaminated alpha-keto acids. Here, we present the recombinant production and functionalization of amino acid oxidaseAplysia Punctataink toxin (APIT). PEGylated APIT (APIT-PEG) increased the blood circulation time. APIT-PEG treatment of patient-derived xenografted mice shows a significant dose dependent reduction of tumor growth over time mediated by amino acid starvation of the tumor. Treatment of mice with APIT-PEG which lead to deprivation of arginine was well tolerated.
Dynamic Effects of Ventral Hippocampal NRG3/ERBB4 Signaling on Nicotine Withdrawal-Induced Responses
Authors: Fisher Miranda L. , Prantzalos Emily R. , O’Donovan Bernadette , Anderson Tanner , Sahoo Pabitra K. , Twiss Jeffery L. , Ortinski Pavel I. , Turner Jill R.
Published: January 2023

Tobacco smoking remains a leading cause of preventable death in the United States, with a less than 5% success rate for smokers attempting to quit. High relapse rates have been linked to several genetic factors, indicating that the mechanistic relationship between genes and drugs of abuse is a valuable avenue for the development of novel smoking cessation therapies. For example, various single nucleotide polymorphisms (SNPs) in the gene for neuregulin 3 (NRG3) and its cognate receptor, the receptor tyrosine-protein kinase erbB-4 (ERBB4), have been linked to nicotine addiction. Our lab has previously shown that ERBB4 plays a role in anxiety-like behavior during nicotine withdrawal (WD); however, the neuronal mechanisms and circuit-specific effects of NRG3-ERBB4 signaling during nicotine and WD are unknown. The present study utilizes genetic, biochemical, and functional approaches to examine the anxiety-related behavioral and functional role of NRG3-ERBB4 signaling, specifically in the ventral hippocampus (VH). We report that 24hWD from nicotine is associated with altered synaptic expression of VH NRG3 and ERBB4, and genetic disruption of VHErbB4leads to an elimination of anxiety-like behaviors induced during 24hWD. Moreover, we observed attenuation of GABAergic transmission as well as alterations in Ca2+-dependent network activity in the ventral CA1 area of VHErbB4knock-down mice during 24hWD. Our findings further highlight contributions of the NRG3-ERBB4 signaling pathway to anxiety-related behaviors seen during nicotine WD.
Caffeine-tolerant mutations selected through an at-home yeast experimental evolution teaching lab
Authors: Moresi Naomi G. , Geck Renee C. , Skophammer Ryan , Godin Dennis ,   yEvo Students, Taylor M. Bryce , Dunham Maitreya J.
Published: January 2023

yEvo is a curriculum for high school students centered around evolution experiments inS. cerevisiae. To adapt the curriculum for remote instruction, we created a new protocol to evolve non-GMO yeast in the presence of caffeine. Evolved strains had increased caffeine tolerance and distinct colony morphologies. Many possessed copy number variations, transposon insertions, and mutations affecting genes with known relationships to caffeine and TOR signaling - which is inhibited by caffeine - and in other genes not previously connected with caffeine. This demonstrates that our accessible, at-home protocol is sufficient to permit novel insights into caffeine tolerance.
Defining T cell receptor repertoires using nanovial-based affinity and functional screening
Authors: Koo Doyeon , Mao Zhiyuan , Dimatteo Robert , Tsubamoto Natalie , Noguchi Miyako , McLaughlin Jami , Tran Wendy , Lee Sohyung , Cheng Donghui , de Rutte Joseph , Sojo Giselle Burton , Witte Owen N. , Carlo Dino Di
Published: January 2023

The ability to selectively bind to antigenic peptides and secrete cytokines can define populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with millions of peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs and secrete cytokines on nanovials, allowing sorting based on both affinity and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes we could link TCR sequence to targets with 100% accuracy. We identified with high specificity an expanded repertoire of functional TCRs targeting viral antigens compared to standard techniques.

One-sentence Summary

Affinity and secretion-based screening of antigen-specific T cells using nanovials defines a functional TCR repertoire
The evolution of the gliotoxin biosynthetic gene cluster inPenicilliumfungi
Authors: Balamurugan Charu , Steenwyk Jacob L. , Goldman Gustavo H. , Rokas Antonis
Published: January 2023

Fungi biosynthesize a diversity of secondary metabolites, small organic bioactive molecules that play diverse roles in fungal ecology. Fungal secondary metabolites are often encoded by physically clustered sets of genes known as biosynthetic gene clusters (BGCs). Fungi in the genusPenicilliumproduce diverse secondary metabolites that have been both useful (e.g., the antibiotic penicillin and the cholesterol-lowering drug mevastatin) and harmful (e.g., the mycotoxin patulin and the immunosuppressant gliotoxin) to human affairs. BGCs often also encode resistance genes that confer self-protection to the secondary metabolite-producing fungus. SomePenicilliumspecies, such asPenicillium lilacinoechinulatumandPenicillium decumbens, are known to produce gliotoxin, a secondary metabolite with known immunosuppressant activity; however, an evolutionary characterization of the BGC responsible for gliotoxin biosynthesis amongPenicilliumspecies is lacking. Here, we examine the conservation of genes involved in gliotoxin biosynthesis and resistance in 35Penicilliumgenomes from 23 species. We found homologous, less fragmented gliotoxin BGCs in 12 genomes, mostly fragmented remnants of the gliotoxin BGC in 21 genomes, whereas the remaining twoPenicilliumgenomes lacked the gliotoxin BGC altogether. In contrast, we observed broad conservation of homologs of resistance genes that reside outside the BGC acrossPenicilliumgenomes. Evolutionary rate analysis revealed that BGCs with higher numbers of genes evolve slower than BGCs with few genes. Even though the gliotoxin BGC is fragmented to varying degrees in nearly all genomes examined, ancestral state reconstruction suggests that the ancestor ofPenicilliumspecies possessed the gliotoxin BGC. Our analyses suggest that genes that are part of BGCs can be retained in genomes long after the loss of secondary metabolite biosynthesis.
Impact of carbon monoxide on neural activation during a reaction time task
Authors: Wilson Lucy Anne , Herigstad Mari
Published: January 2023

Individuals are routinely exposed to low-level carbon monoxide (CO), by factors such as ambient pollution and tobacco smoking. It is known that inhalation of high levels of CO have a detrimental impact on cognitive function. This study sought to investigate the impact of low-level CO exposure on central nervous system cognitive processing speed, using Blood Oxygen Level Dependant (BOLD) functional Magnetic Resonance Imaging (fMRI). The effects of low-level CO (raised up to 6ppm in exhaled air) on reaction times and fMRI activation maps were measured in healthy non-smoking participants. Participants received BOLD fMRI scans on two separate occasions (air and CO intervention days) and were scanned during the performance of a simple reaction time task. Results showed mean activation in cerebellum and motor cortex for all conditions. A significant reduction in BOLD response in the right temporal gyrus was found following CO inhalation, compared to the air control. Reaction times were significantly slower after CO exposure on the CO experimental day, but did not significantly change on the air control experimental day. This suggest that even low-level CO may impact both behavioural and BOLD fMRI outcomes.
Predicting tumor immune microenvironment and checkpoint therapy response of head & neck cancer patients from blood immune single-cell transcriptomics
Authors: Cao Yingying , Chang Tiangen , Schischlik Fiorella , Wang Kun , Sinha Sanju , Hannenhalli Sridhar , Jiang Peng , Ruppin Eytan
Published: January 2023

The immune state of tumor microenvironment is crucial for determining immunotherapy response but is not readily accessible. Here we investigate if we can infer the tumor immune state from the blood and further predict immunotherapy response. First, we analyze a dataset of head and neck squamous cell carcinoma (HNSCC) patients with matched scRNA-Seq of peripheral blood mononuclear cells (PBMCs) and tumor tissues. We find that the tumor immune cell fractions of different immune cell types and many of the genes they express can be inferred from the matched PBMC scRNA-Seq. Second, analyzing another HNSCC dataset with PBMC scRNA-Seq and immunotherapy response, we find that the inferred ratio between tumor memory B and regulatory T cell fractions is predictive of immunotherapy response and is superior to the well-established cytolytic and exhausted T-cell signatures. Overall, these results showcase the potential of scRNA-Seq liquid biopsies in cancer immunotherapy, calling for their larger-scale testing.

Significance

This head and neck cancer study demonstrates the potential of using blood single-cell transcriptomics to (1) infer the tumor immune status and (2) predict immunotherapy response from the tumor immune status inferred from blood. These results showcase the potential of single-cell transcriptomics liquid biopsies for further advancing personalized cancer immunotherapy.
Specific and non-linear effects of glaucoma on optic radiation tissue properties
Authors: Kruper John , Richie-Halford Adam , Benson Noah C. , Caffarra Sendy , Owen Julia , Wu Yue , Lee Aaron Y. , Lee Cecilia S. , Yeatman Jason D. , Rokem Ariel
Published: January 2023

Changes in sensory input with aging and disease affect brain tissue properties. To establish the link between glaucoma, the most prevalent cause of irreversible blindness, and changes in major brain connections, we characterized white matter tissue properties in diffusion MRI measurements in a large sample of subjects with glaucoma (N=905; age 49-80) and healthy controls (N=5,292; age 45-80) from the UK Biobank. Confounds due to group differences were mitigated by matching a sub-sample of controls to glaucoma subjects. A convolutional neural network (CNN) accurately classified whether a subject has glaucoma using information from the primary visual connection to cortex (the optic radiations, OR), but not from non-visual brain connections. On the other hand, regularized linear regression could not classify glaucoma, and the CNN did not generalize to classification of age-group or of age-related macular degeneration. This suggests a unique non-linear signature of glaucoma in OR tissue properties.
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function
Authors: Boadu Frimpong , Cao Hongyuan , Cheng Jianlin
Published: January 2023

Motivation

Millions of protein sequences have been generated by numerous genome and transcriptome sequencing projects. However, experimentally determining the function of the proteins is still a time consuming, low-throughput, and expensive process, leading to a large protein sequence-function gap. Therefore, it is important to develop computational methods to accurately predict protein function to fill the gap. Even though many methods have been developed to use protein sequences as input to predict function, much fewer methods leverage protein structures in protein function prediction because there was lack of accurate protein structures for most proteins until recently.

Results

We developed TransFun - a method using a transformer-based protein language model and 3D-equivariant graph neural networks to distill information from both protein sequences and structures to predict protein function. It extracts feature embeddings from protein sequences using a pre-trained protein language model (ESM) via transfer learning and combines them with 3D structures of proteins predicted by AlphaFold2 through equivariant graph neural networks. Benchmarked on the CAFA3 test dataset and a new test dataset, TransFun outperforms several state-of-the-art methods, indicating the language model and 3D-equivariant graph neural networks are effective methods to leverage protein sequences and structures to improve protein function prediction. Combining TransFun predictions and sequence similarity-based predictions can further increase prediction accuracy.

Availability

The source code of TransFun is available athttps://github.com/jianlin-cheng/TransFun

Contact

chengji@missouri.edu
Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates
Authors: Kovacs Toby G. L. , Walker James , Hellemans Simon , Bourguignon Thomas , Tatarnic Nikolai J. , Mcrae Jane M. , Ho Simon Y. W. , Lo Nathan
Published: January 2023

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analysed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by phylogenetic analyses of mitochondrial genomes and UCE loci. Furthermore, Bayesian dating analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all ten major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ∼115 million years ago despite both containing representatives of the genusNocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.
Implantable flexible multielectrode arrays for multi-site sensing of serotonin tonic levels
Authors: Castagnola Elisa , Robbins Elaine M. , Krahe Daniela , Wu Bingchen , Pwint May Yoon , Cao Qun , Cui Xinyan Tracy
Published: January 2023

Real-time multi-channel measurements of tonic serotonin (5-hydroxytryptamine, 5-HT) concentrations across different brain regions are of utmost importance to the understanding of 5-HT’s role in anxiety, depression, and impulse control disorders, which will improve the diagnosis and treatment of these neuropsychiatric illnesses. Chronic sampling of 5-HT is critical in tracking disease development as well as the time course of pharmacological treatments. Despite their value,in vivochronic multi-site measurements of 5-HT have not been reported.

To fill this technological gap, we batch fabricated implantable glassy carbon (GC) microelectrode arrays (MEAs) on a flexible SU-8 substrate to provide an electrochemically stable and biocompatible device/tissue interface. Then, to achieve multi-site detection of tonic 5-HT concentrations, we incorporated the poly(3,4-ethylenedioxythiophene)/functionalized carbon nanotube (PEDOT/CNT) coating on the GC microelectrodes in combination with a new square wave voltammetry (SWV) approach, optimized for selective 5-HT measurement.In vitro, the PEDOT/CNT coated GC microelectrodes achieved high sensitivity towards 5-HT, good fouling resistance in the presence of 5-HT, and excellent selectivity towards the most common neurochemical interferents.In vivo, our PEDOT/CNT-coated GC MEAs were able to successfully detect basal 5-HT concentrations at different locations of the CA2 hippocampal region of mice in both anesthetized and awake head-fixed conditions. Furthermore, the implanted PEDOT/CNT-coated MEA achieved stable detection of tonic 5-HT concentrations for one week. Finally, histology data in the hippocampus shows reduced tissue damage and inflammatory responses compared to stiff silicon probes. To the best of our knowledge, this PEDOT/CNT-coated GC MEA is the first implantable flexible multisite sensor capable of chronicin vivomulti-site sensing of tonic 5-HT. This implantable MEA can be custom-designed according to specific brain region of interests and research questions, with the potential to combine electrophysiology recording and multiple analyte sensing to maximize our understanding of neurochemistry.

Highlights

PEDOT/CNT-coated GC microelectrodes enabled sensitive and selective tonic detection of serotonin (5-HT) using a new square wave voltammetry (SWV) approach

PEDOT/CNT-coated GC MEAs achieved multi-sitein vivo5-HT tonic detection for one week.

Flexible MEAs lead to reduced tissue damage and inflammation compared to stiff silicon probes.
Long COVID brain fog and muscle pain are associated with longer time to clearance of SARS-CoV-2 RNA from the upper respiratory tract during acute infection
Authors: Antar Annukka A. R. , Yu Tong , Demko Zoe O , Hu Chen , Tornheim Jeffrey A. , Blair Paul W. , Thomas David L. , Manabe Yukari C. ,   OutSMART Study Group
Published: January 2023

The incidence of long COVID is substantial, even in people who did not require hospitalization for acute COVID-19. The pathobiological mechanisms of long COVID and the role of early viral kinetics in its development are largely unknown. Seventy-three non-hospitalized adult participants were enrolled within approximately 48 hours of their first positive SARS-CoV-2 RT-PCR test, and mid-turbinate nasal and saliva samples were collected up to 9 times within the first 45 days after enrollment. Samples were assayed for SARS-CoV-2 using RT-PCR and additional test results were abstracted from the clinical record. Each participant indicated the presence and severity of 49 long- COVID symptoms at 1-, 3-, 6-, 12-, and 18-months post-COVID-19 diagnosis. Time from acute COVID-19 illness onset to SARS-CoV-2 RNA clearance greater or less than 28 days was tested for association with the presence or absence of each of 49 long COVID symptoms at 90+ days from acute COVID-19 symptom onset. Brain fog and muscle pain at 90+ days after acute COVID-19 onset were negatively associated with viral RNA clearance within 28 days of acute COVID-19 onset with adjustment for age, sex, BMI ≥ 25, and COVID vaccination status prior to COVID-19 (brain fog: aRR 0.46, 95% CI 0.22-0.95; muscle pain: aRR 0.28, 95% CI 0.08-0.94). This work indicates that at least two long COVID symptoms - brain fog and muscle pain – at 90+ days from acute COVID-19 onset are specifically associated with longer time to clearance of SARS-CoV-2 RNA from the upper respiratory tract.
The effectiveness of malaria camps as part of the malaria control program in Odisha, India
Authors: Ompad Danielle C. , Padhan Timir K. , Kessler Anne , Mohanty Stuti , Tozan Yesim , Jones Abbey M. , van Eijk Anna Maria , Sullivan Steven A. , Haque Mohammed A. , Pradhan Madan Mohan , Mohanty Sanjib , Carlton Jane M. , Sahu Praveen K.
Published: January 2023

Durgama Anchalare Malaria Nirakaran (DAMaN) is a multi-component malaria intervention for hard-to-reach villages in Odisha, India. The main component, Malaria Camps (MCs), consists of mass screening, treatment, education, and intensified vector control. We evaluated MC effectiveness using a quasi-experimental cluster-assigned stepped-wedge study with a pretest-posttest control group in 15 villages: six immediate (Arm A), six delayed (Arm B), and three previous interventions (Arm C). The primary outcome was PCR+Plasmodiuminfection prevalence. Across all arms, the odds of PCR+ malaria were 54% lower at the third follow-up compared to baseline. A time (i.e., visit) x study arm interaction revealed significantly lower odds of PCR+ malaria in Arm A versus B at the third follow-up. The cost per person ranged between US$3-8, the cost per tested US$4-7, and the cost per treated US$82-1,614, per camp round. These results suggest that the DAMaN intervention is a promising, financially feasible approach for malaria control.
Effect of soilless media on small-scale propagation ofPinguicula gigantea
Authors: Tarner Kevin , Jones Hakon , Ingwers Mile , Gaya Heather , McNair Mason
Published: January 2023

Because of their large size, colorful flowers, and insectivorous habit, butterworts (genusPinguicula)are desirable ornamental plants among hobbyists and botanical conservatories. Propagation via leaves is a popular propagation method for the genus, especially for tropical species.P. gigantea, a species found approximately 700m above sea level in Oaxaca, Mexico, was selected to evaluate its preference for various blends of soilless media. This study found that number of leaves produced by plantlets is significantly impacted by soil type. However, there was no significant difference in biomass, plantlet diameter or average number of plantlets produced between soil treatments. These results suggest that soils with high nitrogen content may promote increased leaf number, but do not significantly affect plant biomass.
Proteomics of the astrocyte secretome reveals changes in their response to soluble oligomeric Aß
Authors: Matafora Vittoria , Gorb Alena , Noble Wendy , Bachi Angela , Perez-Nievas Beatriz Gomez , Jimenez-Sanchez Maria
Published: January 2023

Astrocytes associate with amyloid plaques in Alzheimer’s disease (AD). Astrocytes react to changes in the brain environment, including to increasing concentrations of amyloid-ß (Aß). However, the precise response of astrocytes to soluble small Aß oligomers at concentrations similar to those present in the human brain has not been addressed. In this study, we exposed astrocytes to neuronal media containing soluble human Aß oligomers and used proteomics to investigate changes in the astrocyte secretome. Our data shows dysregulated secretion of astrocytic proteins involved in the extracellular matrix and cytoskeletal organization and increase secretion of proteins involved in oxidative stress responses and those with chaperone activity. Several of these proteins have been identified in previous transcriptomic and proteomic studies using brain tissue from human AD and cerebrospinal fluid (CSF). Our work highlights the relevance of studying astrocyte secretion to understand the brain response to AD pathology and the potential use of these proteins as biomarkers for the disease.
Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics
Authors: Unterweger Iris. A. , Klepstad Julie , Hannezo Edouard , Lundegaard Pia R. , Trusina Ala , Ober Elke A.
Published: January 2023

To meet the physiological demands of the body, organs need to establish a functional tissue architecture and adequate size as the embryo develops to adulthood. In the liver, uni- and bipotent progenitor differentiation into hepatocytes and biliary epithelial cells (BECs), and their relative proportions comprise the functional architecture. Yet, the contribution of individual liver progenitors at the organ level to both fates, and their specific proportion is unresolved. Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage tracing in zebrafish, we demonstrate that a precise BEC to hepatocyte ratio is established (i) fast, (ii) solely by heterogeneous lineage decisions from uni- and bipotent progenitors, and (iii) independent of subsequent cell type-specific proliferation. Extending lineage tracing to adulthood determined that embryonic cells undergo spatially heterogeneous three-dimensional growth associated with distinct environments. Strikingly, giant clusters comprising almost half a ventral lobe suggest lobe-specific dominant-like growth behaviours. We show substantial hepatocyte polyploidy in juveniles representing another hallmark of postembryonic liver growth. Our findings uncover heterogeneous progenitor contributions to tissue architecture-defining cell type proportions and postembryonic organ growth as key mechanisms forming the adult liver.
Mll1 pioneers histone H3K4me3 deposition and promotes formation of CD8+T stem cell memory
Authors: Getzler Adam J. , Frederick Megan A. , Milner Justin J. , Venables Thomas , Diao Huitian , Toma Clara , Nagaraja Shashank D. , Albao Dominic S. , Bélanger Simon , Tsuda Shanel M. , Kim Jihye , Crotty Shane , Goldrath Ananda W. , Pipkin Matthew E.
Published: January 2023

CD8+T cells with stem cell-like properties (TSCM) sustain adaptive immunity to intracellular pathogens and tumors. However, the developmental origins and chromatin regulatory factors (CRFs) that establish their differentiation are unclear. Using an RNA interference screen of all CRFs we discovered the histone methylase Mll1 was required during T cell receptor (TCR) stimulation for development of a TSCMprecursor state and mature memory (TMEM) cells, but not short-lived or transitory effector cell-like states, in response to viral infections and tumors. Mll1 was essential for widespreadde novodeposition of histone H3 lysine 4 trimethylation (H3K4me3) upon TCR stimulation, which accounted for 70% of all activation-induced sites in mature TMEMcells. Mll1 promoted both H3K4me3 deposition and reduced TCR-induced Pol II pausing at genes whose single-cell transcriptional dynamics explained trajectories into nascent TSCMprecursor states during viral infection. Our results suggest Mll1-dependent control of Pol II elongation and H3K4me3 establishes and maintains differentiation of CD8+TSCMcell states.
Immune-mediated tumor control in the 5TGM1 transfer model of multiple myeloma
Authors: Kellermayer Zoltán , Tahri Sabrin , de Jong Madelon M. E. , Papazian Natalie , Fokkema Cathelijne , Hoogenboezem Remco , Sanders Mathijs A. , Boon Louis , Hollander Chelsea Den , Broijl Annemiek , Sonneveld Pieter , Cupedo Tom
Published: January 2023

Multiple myeloma is a disease of malignant plasma cells residing in the bone marrow, where interactions with local immune cells are thought to contribute to disease pathobiology. However, since a multiple myeloma diagnosis is virtually always preceded by an asymptomatic precursor phase, identifying early alterations in the bone marrow micro-environment following occupation by multiple myeloma cells remains challenging. Here we used the 5TGM1 transfer model of murine myeloma in combination with myeloma-permissive KaLwRij mice and myeloma-resistant C57Bl/6 mice and hypothesized that differential sensitivity to myeloma in these HLA-identical mouse strains has an immunological basis and might allow for dissection of early immune responses to myeloma cells.

Using flow cytometry and single-cell RNA sequencing we show that C57Bl/6 mice can restrain tumor growth for prolonged periods, associated with activation of cytotoxic immune responses that were absent from KaLwRij mice. Transcriptional analysis of immune cells and stromal cells identified a central role for IFN-signaling in tumor containment, and antibody-mediated neutralization of IFNγ increased both incidence and outgrowth of multiple myeloma in C57Bl/6 mice. Together these findings highlight the ability of a fully functional immune system to control multiple myeloma progression in an IFNγ−dependent manner and suggest that transfer of 5TGM1 cells into parental C57Bl/6 mice can serve as a faithful model to track anti-myeloma immune responses in immune competent and genetically modifiable mice.