bluuebunny/crossref_metadata_2025 huggingface dataset:
Psilocybin reduces heroin seeking behavior and modulates inflammatory gene expression in the nucleus accumbens and prefrontal cortex of male rats
Authors: Floris Gabriele , Dabrowski Konrad R. , Zanda Mary Tresa , Daws Stephanie E.
Published: June 2024

Preclinical and human studies indicate psilocybin may reduce perseverant maladaptive behaviors, including nicotine and alcohol seeking. Such studies in the opioid field are lacking, though opioids are involved in more >50% of overdose deaths. Psilocybin is an agonist at the serotonin 2A receptor (5-HT2AR), a well-documented target for modulation of drug seeking, and evidence suggests 5-HT2AR agonists may dampen motivation for opioids. We sought to investigate the therapeutic efficacy of psilocybin in mediating cessation of opioid use and maintenance of long-lasting abstinence from opioid seeking behavior in a rat model of heroin self-administration (SA). Psilocybin or 5-HT2AR antagonists ketanserin and volinanserin were administered systemically to rats prior to SA of 0.075 mg/kg/infusion of heroin, or relapse following forced abstinence. Psilocybin did not alter heroin taking, but a single exposure to 3.0 mg/kg psilocybin 4-24 hours prior to a relapse test blunted cue-induced heroin seeking. Conversely, 5-HT2AR antagonists exacerbated heroin relapse. To begin to elucidate mechanisms of psilocybin, drug-naïve rats received psilocybin and/or ketanserin, and tissue was collected from the prefrontal cortex (PFC), a region critical for drug seeking and responsive to psilocybin, 24 hours later for RNA-sequencing. 3.0 mg/kg psilocybin regulated ∼2-fold more genes in the PFC than 1.0 mg/kg, including genes involved in the cytoskeleton and cytokine signaling. Ketanserin blocked >90% of psilocybin-regulated genes, including the IL-17a cytokine receptor,Il17ra. Psychedelic compounds have reported anti-inflammatory properties, and therefore we performed a gene expression array to measure chemokine/cytokine molecules in the PFC of animals that displayed psilocybin-mediated inhibition of heroin seeking. Psilocybin regulated 4 genes, includingIl17a, and a subset of genes correlated with relapse behavior. Selective inhibition of PFC IL-17a was sufficient to reduce heroin relapse. We conclude that psilocybin reduces heroin relapse and highlight IL-17a signaling as a potential downstream pathway of psilocybin that also reduces heroin seeking.
A hemoperfusion column selectively adsorbs LAP+lymphocytes to improve anti-tumor immunity and survival of tumor-bearing rats
Authors: Teramoto Kazuo , Ueda Yuji , Murai Ryosuke , Ogasawara Kazumasa , Nakayama Misako , Ishigaki Hirohito , Itoh Yasushi
Published: June 2024

A decrease of immune suppressive cells in blood is thought to be one of the means to activate anti-tumor immunity that works as a treatment for cancers. We have developed an adsorbent that selectively adsorbs lymphocytes expressing latency-associated peptide (LAP), which include regulatory T cells (Tregs). The adsorbent, diethylenetriamine-conjugated polysulfone coated on polyethylene terephthalate fibers, was packed in a column for direct hemoperfusion (DHP). The therapeutic efficacy of DHP with the column was examined in rats carrying KDH-V liver cancer cells, in which LAP+cells were increased in blood. After DHP, LAP+T cells were decreased in peripheral blood, and a cytotoxic T-lymphocyte response against KDH-V cells was increased in tumor-bearing rats that had been immunized with X ray-irradiated KDH-V cells. Furthermore, the survival time of the rats was longer than that of rats without DHP. Thus, the removal of LAP+T cells can potentially be applied to the treatment of cancer regardless of the origin since an increase in the number of LAP+cells has been observed in the peripheral blood of various cancer patients.
Inference of heterogeneous effects in single-cell genetic perturbation screens
Authors: Fu Zichu , Hou Lin
Published: June 2024

Recent single-cell CRISPR screening experiments have combined the advances of genetic editing and single-cell technologies, leading to transcriptome-scale readouts of responses to perturbations at single-cell resolution. An outstanding question is how to efficiently identify heterogeneous causal effects of perturbations using these technologies. Here we present scCAPE, a tool designed to facilitate causal analysis of heterogeneous perturbation effects at the single-cell level. scCAPE disentangles perturbation effects from the inherent cell-state variations and provides nonparametric inferences of perturbation effects at single-cell resolution, permitting a range of downstream tasks including perturbation effect analysis, genetic interaction analysis, perturbation clustering and prioritizing. We benchmarked scCAPE through simulation studies and real datasets to evaluate its performance in characterizing latent confounding factors and accuracy in estimating heterogeneous perturbation effects. The application of scCAPE identified novel heterogeneous genetic interactions among erythroid differentiation drivers. For example, our analysis pinpointed the role of the synergistic interaction between CBL and CNN1 in the S phase.
Decoding the hidden variabilities in mPFC descending pathways across emotional states
Authors: Lai Chien-Hsien , Park Gyeongah , Xu Pan , Sun Xiaoqian , Ge Qian , Jin Zhen , Betts Sarah , Liu Xiaojie , Liu Qingsong , Simha Rahul , Zeng Chen , Lu Hui , Du Jianyang
Published: June 2024

Effective emotional regulation, crucial for adaptive behavior, is mediated by the medial prefrontal cortex (mPFC) via connections to the basolateral amygdala (BLA) and nucleus accumbens (NAc), traditionally considered functionally similar in modulating reward and aversion responses. However, how the mPFC balances these descending pathways to control behavioral outcomes remains unclear. We found that while overall firing patterns appeared consistent across emotional states, deeper analysis revealed distinct variabilities. Specifically, mPFC→BLA neurons, especially “center-ON” neurons, exhibited heightened activity during anxiety-related behaviors, highlighting their role in anxiety encoding. Conversely, mPFC→NAc neurons were more active during exploratory behaviors, implicating them in processing positive emotional states. Notably, mPFC→NAc neurons showed significant pattern decorrelation during social interactions, suggesting a pivotal role in encoding social preference. Additionally, chronic emotional states affected these pathways differently: positive states enhanced mPFC→NAc activity, while negative states boosted mPFC→BLA activity. These findings challenge the assumed functional similarity and highlight distinct contributions to emotional regulation, suggesting new avenues for therapeutic interventions.
Exposure to the pesticide tefluthrin causes developmental neurotoxicity in zebrafish
Authors: Mesmar Fahmi , Muhsen Maram , Farooq Ibraheem , Maxey Grant , Tourigny Jason P. , Tennessen Jason , Bondesson Maria
Published: June 2024

BACKGROUND

The insecticide tefluthrin is widely used in agriculture, resulting in widespread pollution. Tefluthrin is a type I pyrethroid characterized by its high persistence in the environment. Understanding the mechanisms of toxicity of tefluthrin will improve its risk assessment.

OBJECTIVES

We aimed to decipher the molecular modes of action of tefluthrin.

METHODS

Phenotypic developmental toxicity was assessed by exposing zebrafish embryos and larvae to increasing concentrations of tefluthrin.Tg(mnx:mGFP)line was used to assess neurotoxicity. Multi-omics approaches including transcriptomics and lipidomics were applied to analyze RNA and lipid contents, respectively. Finally, anin-silicoligand–protein docking computational method was used to study a possible interaction between tefluthrin and a protein target.

RESULTS

Tefluthrin exposure caused severe morphological malformations in zebrafish larvae, including motor neuron abnormalities. The differentially expressed genes were associated with neurotoxicity and metabolic disruption. Lipidomics analysis revealed a disruption in fatty acid, phospholipid, and lysophospholipid recycling. Protein docking modeling suggested that the LPCAT3 enzyme, which recycles lysophospholipids in the Land’s cycle, directly interacts with tefluthrin.

CONCLUSIONS

Tefluthrin exposure causes morphological and neuronal malformations in zebrafish larvae at nanomolar concentrations. Multi-omics results revealed a potential molecular initiating event i.e., inhibition of LPCAT3, and key events i.e., an altered lysophospholipid to phospholipid ratio, leading to the adverse outcomes of neurotoxicity and metabolic disruption.
Capillary interactions drive the self-organization of bacterial colonies
Authors: Black Matthew E. , Fei Chenyi , Alert Ricard , Wingreen Ned S. , Shaevitz Joshua W.
Published: June 2024

Many bacteria inhabit thin layers of water on solid surfaces both naturally in soils or on hosts or textiles and in the lab on agar hydrogels. In these environments, cells experience capillary forces, yet an understanding of how these forces shape bacterial collective behaviors remains elusive. Here, we show that the water menisci formed around bacteria lead to capillary attraction between cells while still allowing them to slide past one another. We develop an experimental apparatus that allows us to control bacterial collective behaviors by varying the strength and range of capillary forces. Combining 3D imaging and cell tracking with agent-based modeling, we demonstrate that capillary attraction organizes rod-shaped bacteria into densely packed, nematic groups, and profoundly influences their collective dynamics and morphologies. Our results suggest that capillary forces may be a ubiquitous physical ingredient in shaping microbial communities in partially hydrated environments.
The intestinal microbiota contributes to the development of immune-mediated cardiovascular inflammation and vasculitis in mice
Authors: Jena Prasant K. , Wakita Daiko , Gomez Angela C. , Carvalho Thacyana T. , Atici Asli E. , Narayanan Meena , Lee Youngho , Fishbein Michael C. , Cani Patrice D. , de Vos Willem M. , Underhill David M. , Devkota Suzanne , Chen Shuang , Shimada Kenichi , Crother Timothy R. , Arditi Moshe , Rivas Magali Noval
Published: June 2024

Alterations in the intestinal microbiota contribute to the pathogenesis of various cardiovascular disorders, but how they affect the development of Kawasaki disease (KD), an acute pediatric vasculitis, remains unclear. We report that depleting the gut microbiota reduces the development of cardiovascular inflammation in a murine model mimicking KD vasculitis. The development of cardiovascular lesions was associated with alterations in the intestinal microbiota composition and, notably, a decreased abundance ofAkkermansia muciniphilaandFaecalibacterium prausnitzii.Oral supplementation with either of these live or pasteurized individual bacteria, or with short-chain fatty acids (SCFAs) produced by them, attenuated cardiovascular inflammation. Treatment with Amuc_1100, the TLR-2 signaling outer membrane protein fromA. muciniphila, also decreased the severity of vascular inflammation. This study reveals an underappreciated gut microbiota-cardiovascular inflammation axis in KD vasculitis pathogenesis and identifies specific intestinal commensals that regulate vasculitis in mice by producing metabolites or via extracellular proteins acting on gut barrier function.

IN BRIEF

It remains unclear whether changes in the intestinal microbiota composition are involved in the development of cardiovascular lesions associated with Kawasaki disease (KD), an immune-mediated vasculitis. Jenaet al.observe alterations in the intestinal microbiota composition of mice developing vasculitis, characterized by reducedA. muciniphilaandF. prausnitzii. Oral supplementation with either of these bacteria, live or pasteurized, or with bacteria-produced short-chain fatty acids (SCFAs) or Amuc_1100, the TLR-2 signaling outer membrane protein ofA. muciniphila, was sufficient to alleviate the development of cardiovascular lesions in mice by promoting intestinal barrier function.

HIGHLIGHTS

Absence or depletion of the microbiota decreases the severity of vasculitis in a murine model mimicking KD vasculitis.

Supplementation ofB. wadsworthiaandB. fragilispromotes murine KD vasculitis.

Decreased abundances ofF. prausnitziiandA. muciniphilaare associated with the development of cardiovascular lesions in mice.

Supplementation with either live or pasteurizedA. muciniphilaandF. prausnitzii,or the TLR-2 signaling Amuc_1100, reduces the severity of vasculitis by promoting gut barrier function.
ApoE ε4-dependent alteration of CXCR3+CD127+CD4+T cells is associated with elevated plasma neurofilament light chain in Alzheimer’s disease
Authors: Hu Dan , Chen Mei , Li Xuyang , Morin Peter , Daley Sarah , Han Yuyang , Hemberg Martin , Weiner Howard L. , Xia Weiming
Published: June 2024

Recent findings indicate a correlation between the peripheral adaptive immune system and neuroinflammation in Alzheimer’s disease (AD). To characterize the composition of adaptive immune cells in the peripheral blood of AD patients, we utilized single-cell mass cytometry (CyTOF) to profile peripheral blood mononuclear cells (PBMCs). Concurrently, we assessed the concentration of proteins associated with AD and neuroinflammation in the plasma of the same subjects. We found that the abundance of proinflammatory CXCR3+CD127+Type 1 T helper (Th1) cells in AD patients was negatively correlated with the abundance of neurofilament light chain (NfL) protein. This correlation is apolipoprotein E (ApoE) ε4-dependent. Analyzing public single-cell RNA-sequencing (scRNA-seq) data, we found that, contrary to the scenario in the peripheral blood, the cell frequency of CXCR3+CD127+Th1 cells in the cerebrospinal fluid (CSF) of AD patients was increased compared to healthy controls (HCs). Moreover, the proinflammatory capacity of CXCR3+CD127+Th1 cells in the CSF of AD patients was further increased compared to HCs. These results reveal an association of a peripheral T-cell change with neuroinflammation in AD and suggest that dysregulation of peripheral adaptive immune responses, particularly involving CXCR3+CD127+Th1 cells, may potentially be mediated by factors such as ApoE ε4 genotype.

One sentence summary

An apolipoprotein E (ApoE) ε4-dependent alteration of CD4 T cell subpopulation in peripheral blood is associated with neuroinflammation in patients with Alzheimer’s disease.
Walking with increased step length variability increases the metabolic cost of walking
Authors: Grimmitt Adam B. , Whelan Maeve E. , Martini Douglas N. , Hoogkamer Wouter
Published: June 2024

Older adults and neurological populations tend to walk with slower speeds, more gait variability, and a higher metabolic cost. This higher metabolic cost could be related to their increased gait variability, but this relationship is still unclear. The purpose of this study was to determine how increased step length variability affects the metabolic cost of waking. Eighteen healthy young adults completed a set of 5-minute trials of treadmill walking at 1.20 m/s while we manipulated their step length variability. Illuminated rectangles were projected onto the surface of a treadmill to cue step length variabilities of 0, 5 and 10% (coefficient of variation). Actual step lengths and their variability were tracked with reflective markers on the feet, while metabolic cost was measured using indirect calorimetry. Changes in metabolic cost across habitual walking (no projections) and the three variability conditions were analyzed using a linear mixed effects model. Metabolic power was largest in the 10% condition (4.30 ± 0.23 W/kg) compared to 0% (4.16 ± 0.18 W/kg) and habitual (3.98 ± 0.25 W/kg). The participant’s actual step length variability did not match projected conditions for 0% (3.10%) and 10% (7.03%). For every 1% increase in step length variability, there is an 0.7% increase in metabolic cost. Our results demonstrate an association between the metabolic cost of walking and gait step length variability. This suggests that increased gait variability contributes to a portion of the increased cost of walking seen in older adults and neurological populations.

Summary Statement

For every 1% increase in step length variability, there is an 0.7% increase in the metabolic cost of walking.
Altered liver metabolism post-wean abolishes efficacy of vitamin D for breast cancer prevention in a mouse model
Authors: Bernhardt Sarah M , Ozaki Michelle K , Betts Courtney , Bleyle Lisa A , DeBarber Andrea E , Fornetti Jaime , Liberty Abigail L , De Wilde Elise , Zhang Yi , Xia Zheng , Schedin Pepper
Published: June 2024

Young women have increased risk of vitamin D deficiency, which may increase breast cancer incidence. Here, we assessed the anti-cancer efficacy of vitamin D in mouse models of young-onset breast cancer. In never-pregnant mice, vitamin D supplementation increased serum 25(OH)D and hepatic 1,25(OH)2D3, reduced tumor size, and associated with anti-tumor immunity. These anti-tumor effects were not replicated in a mouse model of postpartum breast cancer, where hepatic metabolism of vitamin D was suppressed post-wean, which resulted in deficient serum 25(OH)D and reduced hepatic 1,25(OH)2D3. Treatment with active 1,25(OH)2D3induced hypercalcemia exclusively in post-wean mice, highlighting metabolic imbalance post-wean. RNAseq revealed suppressed CYP450 expression postpartum. In sum, we provide evidence that vitamin D anti-tumor activity is mediated through immunomodulatory mechanisms and is ineffective in the post-wean window due to altered hepatic metabolism. These findings have implications for suppressed xenobiotic metabolism in postpartum women beyond vitamin D.

Statement of Significance

In a rodent model of postpartum breast cancer, weaning suppresses hepatic CYP450 activity and renders vitamin D supplementation ineffective, with implications for xenobiotic drug efficacy and safety. A tailored approach to therapy based on reproductive history is crucial for young breast cancer patients, and for healthcare strategies for postpartum women.
Working memory performance predicts, but does not reduce, cocaine- and cannabinoid-seeking in adult male rats
Authors: Stringfield Sierra J. , Kirschmann Erin K. , Torregrossa Mary M.
Published: June 2024

Background

Cognitive deficits reflecting impaired executive function are commonly associated with psychiatric disorders, including substance use. Cognitive training is proposed to improve treatment outcomes for these disorders by promoting neuroplasticity within the prefrontal cortex, enhancing executive control, and mitigating cognitive decline due to drug use. Additionally, brain derived neurotrophic factor (BDNF) can facilitate plasticity in the prefrontal cortex and reduce drug-seeking behaviors. We investigated whether working memory training could elevate BDNF levels in the prefrontal cortex and if this training would predict or protect against cocaine or cannabinoid seeking.

Methods

Adult male rats were trained to perform a ‘simple’ or ‘complex’ version of a delayed- match-to-sample working memory task. Rats then self-administered cocaine or the synthetic cannabinoid WIN55,212-2 and were tested for cued drug-seeking during abstinence. Tissue from the prefrontal cortex and dorsal hippocampus was analyzed for BDNF protein expression.

Results

Training on the working memory task enhanced endogenous BDNF protein levels in the prelimbic prefrontal cortex but not the dorsal hippocampus. Working memory training did not impact self-administration of either drug but predicted the extent of WIN self-administration and cocaine seeking during abstinence.

Conclusions

These results suggest that working memory training promotes endogenous BDNF but does not alter drug-seeking or drug-taking behavior. However, individual differences in cognitive performance prior to drug exposure may predict vulnerability to future drug use.
Pharmacodynamic modeling of colistin and imipenem againstin vitro Pseudomonas aeruginosabiofilms
Authors: Guo Yuchen , Yin Jinqiu , Aulin Linda B.S. , Ciofu Oana , Moser Claus , Upadhyay Parth J. , Høiby Niels , Wang Hengzhuang , Guo Tingjie , van Hasselt J. G. Coen
Published: June 2024

Introduction

Antibiotic treatment of chronic biofilm-associated infections can be challenging. Characterization of pharmacokinetic-pharmacodynamic (PK-PD) relationships for biofilm-associated infections may be relevant to inform the design of antibiotic treatment regimens for biofilm-associated infections. To this end, we aim to develop a mathematical PK-PD model for planktonic and biofilm bacterial infections and demonstrate how PK-PD simulations can be used to design optimized dosing schedules, using imipenem and colistin as proof-of-concept examples.

Methods

Pharmacodynamic models were developed using time-kill assay data from planktonic and alginate-bead biofilm cultures ofPseudomonas aeruginosaexposed to imipenem or colistin. The PD models were coupled to population PK models for plasma and epithelial lining fluid (ELF) to translate PD relationships for clinical dosing schedules and PK-PD indices.

Results

The developed models incorporated sensitive and resistant bacterial subpopulations and were able to adequately capture the observed time-kill data. Simulation studies identified differences in suppression of bacterial growth dynamics for multiple clinical intravenous and inhalation-based treatment regimens and were used to infer biofilm-specific PK-PD indices associated with ELF target site concentrations.

Conclusion

In conclusion, we demonstrate the utility of mathematical modeling for the characterization of PK-PD relationships underlying time-kill kinetic profiles in biofilm-associated infections and their utility in translating experimental findings to inform the optimization of clinical dosing schedules.
Caldas meets Janzen: Thermal regimes of montane plants and implications for global patterns of speciation
Authors: Sanchez Adriana , Quintero Ignacio , Pedraza Sara , Bonilla Diana , Lohmann Lúcia G. , Cadena Carlos Daniel , Zapata Felipe
Published: June 2024

The seasonality hypothesis posits that limited seasonal temperature variability in tropical mountains leads to greater climatic zonation along elevation gradients compared to temperate regions. This is predicted to result in narrow thermal tolerances and restricted dispersal for organisms, which may reduce gene flow and increase opportunities for climate-associated parapatric or allopatric speciation in tropical mountains relative to temperate-zone mountains. This hypothesis has been tested in various animal groups but not in plants. We examine the elevational and thermal ranges of pairs of sister species of angiosperms from mountains worldwide. Our findings indicate no significant difference in the breadth and overlap of elevational ranges between tropical and temperate species. However, tropical species have narrower thermal ranges and show greater similarity in these ranges between sister species compared to temperate ones. Such narrow thermal specialization in tropical plants facilitates population divergence and allopatric speciation within thermal zones more than in temperate species.
The curses of performing differential expression analysis using single-cell data
Authors: Wu Chih-Hsuan , Zhou Xiang , Chen Mengjie
Published: June 2024

Differential expression analysis is pivotal in single-cell transcriptomics for unraveling cell-type– specific responses to stimuli. While numerous methods are available to identify differentially expressed genes in single-cell data, recent evaluations of both single-cell–specific methods and methods adapted from bulk studies have revealed significant shortcomings in performance. In this paper, we dissect the four major challenges in single-cell DE analysis: normalization, excessive zeros, donor effects, and cumulative biases. These “curses” underscore the limitations and conceptual pitfalls in existing workflows. In response, we introduce a novel paradigm addressing several of these issues.
vClassifier: a toolkit for species-level classification of prokaryotic viruses
Authors: Zhou Kun , Kosmopoulos James C. , Anantharaman Karthik
Published: June 2024

As the most abundant and diverse biological entities, prokaryotic viruses play pivotal roles in ecological systems. Their taxonomic classification has been instrumental in elucidating their diversity and ecological functions. However, determination of viral taxonomy remains a considerable challenge. Recently developed approaches succeed in assignment of viral taxonomy at higher ranks, such as at the family level and above, but struggle at the subfamily level and below to the genus and species resolutions. Here, we describe the vClassifier toolkit, a phylogeny-informed methodology to provide species-level taxonomic assignments of viruses. We used single-copy marker genes relevant to specific taxa and reference phylogenetic trees for these groups which facilitates direct comparisons with the taxonomic framework of the International Committee on Taxonomy of Viruses (ICTV). Our method demonstrated significant congruence with the ICTV taxonomy, showing 84−91% alignment at the subfamily and genus levels. For species-level classification, our strategy was integrated with average nucleotide identity, yielding a high congruence rate of over 92% with the taxonomic data from the NCBI Virus database. Benchmarking comparisons revealed that vClassifier matches or surpasses other available tools regarding precision and classification success rates. By achieving objectivity and high levels of consistency, vClassifier streamlines the taxonomic categorization of prokaryotic viral genomes. Accurate assignments at the subfamily, genus, and species levels will significantly refine the taxonomic resolution of viruses, fostering a deeper understanding of viral diversity in microbiomes and ecosystems.
A Patient-Specific Morphoelastic Growth Model of Aortic Dissection Evolution
Authors: Khabaz Kameel , Kim Junsung , Milner Ross , Nguyen Nhung , Pocivavsek Luka
Published: June 2024

The human aorta undergoes complex morphologic changes that indicate the evolution of disease. Finite element analysis enables the prediction of aortic pathologic states, but the absence of a biomechanical understanding hinders the applicability of this computational tool. We incorporate geometric information from computed tomography angiography (CTA) imaging scans into finite element analysis (FEA) to predict a trajectory of future geometries for four aortic disease patients. Through defining a geometric correspondence between two patient scans separated in time, a patient-specific FEA model can recreate the deformation of the aorta between the two time points, showing pathologic growth drives morphologic heterogeneity. A shape-size geometric feature space plotting the variance of the shape index versus the inverse square root of aortic surface area (δ𝒮 vs.) quantitatively demonstrates the simulated breakdown in aortic shape. An increase in δ𝒮 closely parallels the true geometric progression of aortic disease patients.
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations
Authors: Gardner Andrea L. , Jost Tyler A. , Brock Amy
Published: June 2024

Intratumor heterogeneity reduces treatment efficacy and complicates our understanding of tumor progression. There is a pressing need to understand the functions of heterogeneous tumor cell subpopulations within a tumor, yet biological systems to study these processesin vitroare limited. With the advent of single-cell RNA sequencing (scRNA-seq), it has become clear that some cancer cell line models include distinct subpopulations. Heterogeneous cell lines offer a unique opportunity to study the dynamics and evolution of genetically similar cancer cell subpopulations in controlled experimental settings. Here, we present clusterCleaver, a computational package that uses metrics of statistical distance to identify candidate surface markers maximally unique to transcriptomic subpopulations in scRNA-seq which may be used for FACS isolation. clusterCleaver was experimentally validated using the MDA-MB-231 and MDA-MB-436 breast cancer cell lines. ESAM and BST2/tetherin were experimentally confirmed as surface markers which identify and separate major transcriptomic subpopulations within MDA-MB-231 and MDA-MB-436 cells, respectively. clusterCleaver is a computationally efficient and experimentally validated workflow for identification and enrichment of distinct subpopulations within cell lines which paves the way for studies on the coexistence of cancer cell subpopulations in well-definedin vitrosystems.
RESPIRATION DEFECTS LIMIT SERINE SYNTHESIS REQUIRED FOR LUNG CANCER GROWTH AND SURVIVAL
Authors: Lopes Eduardo Cararo , Shi Fuqian , Sawant Akshada , Ibrahim Maria , Gomez-Jenkins Maria , Hu Zhixian , Manchiraju Pranav , Bhatt Vrushank , Wang Wenping , Hinrichs Christian S. , Wallace Douglas C. , Su Xiaoyang , Rabinowitz Joshua D. , Chan Chang S. , Guo Jessie Yanxiang , Ganesan Shridar , Lattime Edmund C. , White Eileen
Published: June 2024

Mitochondrial function is important for both energetic and anabolic metabolism. Pathogenic mitochondrial DNA (mtDNA) mutations directly impact these functions, resulting in the detrimental consequences seen in human mitochondrial diseases. The role of pathogenic mtDNA mutations in human cancers is less clear; while pathogenic mtDNA mutations are observed in some cancer types, they are almost absent in others. We report here that the proofreading mutant DNA polymerase gamma (PolGD256A) induced a high mtDNA mutation burden in non-small-cell lung cancer (NSCLC), and promoted the accumulation of defective mitochondria, which is responsible for decreased tumor cell proliferation and viability and increased cancer survival. In NSCLC cells, pathogenic mtDNA mutations increased glycolysis and caused dependence on glucose. The glucose dependency sustained mitochondrial energetics but at the cost of a decreased NAD+/NADH ratio that inhibitedde novoserine synthesis. Insufficient serine synthesis, in turn, impaired the downstream synthesis of GSH and nucleotides, leading to impaired tumor growth that increased cancer survival. Unlike tumors with intact mitochondrial function, NSCLC with pathogenic mtDNA mutations were sensitive to dietary serine and glycine deprivation. Thus, mitochondrial function in NSCLC is required specifically to sustain sufficient serine synthesis for nucleotide production and redox homeostasis to support tumor growth, explaining why these cancers preserve functional mtDNA.

In brief

High mtDNA mutation burden in non-small-cell lung cancer (NSCLC) leads to the accumulation of respiration-defective mitochondria and dependency on glucose and glycolytic metabolism. Defective respiratory metabolism causes a massive accumulation of cytosolic nicotinamide adenine dinucleotide + hydrogen (NADH), which impedes serine synthesis and, thereby, glutathione (GSH) and nucleotide synthesis, leading to impaired tumor growth and increased survival.

Highlights

Proofreading mutations in Polymerase gamma led to a high burden of mitochondrial DNA mutations, promoting the accumulation of mitochondria with respiratory defects in NSCLC.

Defective respiration led to reduced proliferation and viability of NSCLC cells increasing survival to cancer.

Defective respiration caused glucose dependency to fuel elevated glycolysis.

Altered glucose metabolism is associated with high NADH that limits serine synthesis, leading to impaired GSH and nucleotide production.

Mitochondrial respiration defects sensitize NSCLC to dietary serine/glycine starvation, further increasing survival.

Abstract Figure
Efficient small fragment sequencing of human, cow, and bison miRNA, small RNA or csRNA-seq libraries using AVITI
Authors: McDonald Anna L. , Boddicker Andrew M. , Savenkova Marina I. , Brabb Ian M. , Qi Xiaodong , Moré Daniela D. , Cunha Cristina W. , Zhao Junhua , Duttke Sascha H.
Published: June 2024

Next-Generation Sequencing (NGS) catalyzed breakthroughs across various scientific domains. Illumina’s sequencing by synthesis method has long been essential for NGS but emerging technologies like Element Biosciences’ sequencing by avidity (AVITI) represent a novel approach. It has been reported that AVITI offers improved signal-to-noise ratios and cost reductions. However, the method relies on rolling circle amplification which can be impacted by polymer size, raising questions about its efficacy sequencing small RNAs (sRNA) molecules including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and others that are crucial regulators of gene expression and involved in various biological processes. In addition, capturing capped small RNAs (csRNA-seq) has emerged as a powerful method to map active or “nascent” RNA polymerase II transcription initiation in tissues and clinical samples. Here, we report a new protocol for seamlessly sequencing short DNA fragments on the AVITI and demonstrate that AVITI and Illumina sequencing technologies equivalently capture human, cattle (Bos taurus) and the bison (Bison bison) sRNA or csRNA sequencing libraries, augmenting the confidence in both approaches. Additionally, analysis of generated nascent transcription start sites (TSSs) data for cattle and bison revealed inaccuracies in their current genome annotations and highlighted the possibility and need to translate small RNA sequencing methodologies to livestock. Our accelerated and optimized protocol therefore bridges the advantages of AVITI sequencing and critical methods that rely on sequencing short DNA fragments.
Avian Atlas: Unveiling the Diversity Divide in Desert Realms between Tropics
Authors: Mukherjee Manasi , Mukerji Mitali
Published: June 2024

Understanding diversity gradients across global deserts remains a significant challenge. The unique characteristics of deserts complicate conservation efforts for these biomes, which are highly affected by climate change. Here, we conduct a comprehensive study of ecological traits to determine the behavior and uniqueness of avian communities in ten major tropical deserts, using crowd-sourced avian diversity data fromGBIF.orgas a key analytical tool. Our results reveal significant variations in bird diversity among tropical deserts, with heightened diversity in deserts near the Tropic of Cancer (TCan) compared to those near the Tropic of Capricorn (TCap).

The analysis of ecological traits indicates that, unlike TCap deserts, TCan deserts have a higher prevalence of migratory species. This is facilitated by a broader niche breadth among sedentary bird species, which reduces niche competition and allows the influx of migratory invertivores. This study is the first to identify a differential avian diversity gradient within tropical deserts, demonstrating that avian species richness in deserts is more closely linked to tropical locations than to realm classifications.

Recognizing the vulnerability of TCap deserts and the diverse trophic roles played by avian species, our analysis underscores the need for targeted conservation strategies. Protecting the unique avian diversity in TCan deserts and mitigating extinction risks in TCap deserts are essential steps to ensure the resilience and sustainability of these critical ecosystems.
Brachiopod genome unveils the evolution of the BMP–Chordin network in bilaterian body patterning
Authors: Lewin Thomas D. , Shimizu Keisuke , Liao Isabel Jiah-Yih , Chen Mu-En , Endo Kazuyoshi , Satoh Noriyuki , Holland Peter W. H. , Wong Yue Him , Luo Yi-Jyun
Published: June 2024

Bone morphogenetic protein (BMP) signalling is crucial in regulating dorsal–ventral patterning and cell fate determination during early development in bilaterians. Interactions between BMP ligands and their main antagonist, Chordin, establish BMP gradients, subdivide embryos into distinct territories and organise body plans. However, the molecular control and evolutionary origins of dorsal–ventral patterning within spiralians, one of the three major bilaterian groups, have been obscured by their unique embryonic development. Here we present the chromosome-level genome of a spiralian with deuterostome-like development, the brachiopodLingula anatina, and apply functional transcriptomics to study dorsal–ventral patterning under the control of BMP signalling. We uncover the presence of a dorsal–ventral BMP signalling gradient in theL. anatinagastrula withbmp2/4andchordinexpressed at its dorsal and ventral sides, respectively. Using small-molecule drugs, exogenous recombinant BMP proteins and RNA sequencing, we show that a high level of BMP pathway activation inhibits the expression of neural genes during gastrula and larval stages. We also show that BMP signalling splits the developing larval shell field into two valves. The discovery of a BMP-mediated dorsal–ventral patterning system in a spiralian, similar to those observed in deuterostomes and non-spiralian protostomes, suggests deep conservation of this mechanism across all three major bilaterian clades. This is further supported by striking similarities in the gene sets regulated by BMP signalling in brachiopods and the vertebrate modelXenopus. We argue that the spiralian ancestor retained the basal bilaterian mechanism of dorsal–ventral patterning, although downstream components of the BMP–Chordin network have undergone dynamic evolutionary changes.
Pencil Beam Based X-ray Luminescence Computed Tomography Imaging of Deep Targets Three-dimensionally and Quantitatively
Authors: Fang Yile , Zhang Yibing , Li Changqing
Published: June 2024

X-ray luminescence computed tomography (XLCT), especially pencil beam based XLCT, has been emerged for more than 15 years because it can image deep targets in tissue with high spatial resolution and high measurement sensitivity. However, its application is limited by long scanning time and the tedious efforts of finite element mesh generation for model based reconstruction. Our previous study has addressed the imaging speed issue. In this study, we propose to reconstruct XLCT with weighted filtered back projection (wFBP) which makes it possible to perform XLCT imaging three dimensionally for complex objects at a high spatial resolution. We have also proposed measurements with multiple detectors to obtain quantitative XLCT images. To evaluate the proposed methods, we have performed numerical simulations and different sets of phantom experiments including phantom experiments with a control contrast target, different concentrations, and different target sizes. We have also successfully reconstructed deep targets with a diameter of approximately 0.15 mm. For the phantom experiments with targets of different concentrations, using a 4-channel XLCT system and the wFBP, we achieved the ratio of 3.8:1.79:1, closely resembling the ground truth ratio of 4:2:1. Lastly, we have, for the first time, reconstructed different 3D targets at high spatial resolution, successfully, including a printed M target, a triangular hollow bar, and a hot background cuboid with “UCM Li Lab” slots. Our results indicate that the proposed wFBP advances the promising XLCT technology and makes it ready for in vivo studies in the future.
Transplantation of a kidney with a ureter and part of the bladder as a single block: an experimental study
Authors: Kuttymuratov Gani , Ainakulov Ardak , Ayaganov Askar , Oshakbayev Kuat , Mirmanov Arman , Zharasov Daulet , Imanberdiev Zhandos , Taszhurekov Askar , Abdimazhitov Bakhytzhan , Asanova Aruzhan , Abdurakhman Tleuzhan , Uderbayev Nurlybek , Kalieva Arnagul
Published: June 2024

Objective

To evaluate the effectiveness of en bloc transplantation of a donor kidney, ureters and part of the bladder to a recipient with simulated microcystis in an experimental trial.

Methods

Study Design: a 29-day, open, pilot prospective experimental trial: 14 days constituted an adaptation period, 5 days for the interventions, and 10 days constituted an observation period. The study totally included ten White Landras sibling pigs, which were divided into 12 donors and 12 recipients. The pigs were 3-4 months old and weighing 35-45 kg of both sexes from the same sow to avoid transplant rejection. The pigs lived 7-9 days after transplantation before they were euthanized, and then there were performed macrovisual and histological investigations. Descriptive, inferential statistics, and calculation of percentages were used. The Local Ethics Committee of West Kazakhstan Medical University approved the study.

Results

Eleven pigs survived the operation, but one pig died 10 hours after the operation. The cause of death was pulmonary embolism according to the pathological autopsy. In the eleven animals the kidney, ureters and part of the bladder transplanted as en block visually were filled with urine, full of blood, and tissue turgor was good. Visual inspection of the kidney and ureters was satisfactory, bright red. The implanted bladder had a red-burgundy color in all eleven cases. No anastomotic leakage was observed. A histological examination of the graft tissue on the 7-9 after-surgery days showed the preservation of blood flow in the tissues of the bladder and ureters. No total tissue necrosis was detected.

Conclusions

In our experimental model, transplantation of a donor kidney, ureters and part of the bladder to a recipient with a simulated microcyst is effectively feasible. Pigs are a relevant animal model for genitourinary organ transplantation.

Trial Registration

AnimalStudyRegistry.orgDOI10.17590/asr.0000336. Registered 25 January 2024.
Urinary acetaminophen metabolites and clinical outcomes in premature infants
Authors: Guardado Miguel , Torgerson Dara , Chapin Cheryl , Atum Azuka , Hernandez Ryan D. , Ronald B , Simmons Rebecca , Parry Samuel , Ballard Philip L.
Published: June 2024

BACKGROUND

Extremely premature infants are treated with acetaminophen (APAP) for discomfort and patent ductus arteriosus. A recent study found an association between APAP metabolite levels in mothers’ breast milk and the diagnoses of both bronchopulmonary dysplasia (BPD) and retinopathy of prematurity (ROP) in their infants.

METHODS

Urine samples from 314 infants <29 weeks gestation in the TOLSURF and PROP studies were analyzed by untargeted UHPLC:MS/MS. We performed multivariate logistic regression and meta-analysis to examine associations between APAP metabolite levels and clinical outcomes.

RESULTS

4-APAP sulfate was the highest detected and most abundant metabolite of 8 detected and was present in 98% of urines. In longitudinal studies (day 6-56), periods of elevated urinary 4-APAP-sulfate occurred in 24 of 28 infants and were of longer duration (10.1 vs 4.2 days, p=0.004) and higher levels (13.3 vs 5.6, p=0.013) in infants on enteral vs total parenteral nutrition. At both day 10 and 28 there were no significant associations between levels of APAP metabolites and BPD or ROP in all infants or only those on TPN or enteral feeds.

CONCLUSION

In two cohorts of premature infants, APAP metabolites were detected uniformly and levels were not associated with increased risk for two adverse clinical outcomes.

Impact Statement

Premature infants are treated with acetaminophen (APAP) for analgesia and closure of patent ductus arteriosus, however an association has been reported between APAP levels in maternal milk and infant bronchopulmonary dysplasia (BPD) and retinopathy of prematurity (ROP).

In an untargeted metabolomic study of 2 cohorts of premature infants, the major urinary APAP metabolite was detected in most urine samples of all infants, and there were intervals of elevated levels.

Using both longitudinal and cross-sectional analyses, we found no association between APAP levels and either BPD or ROP.

Although APAP is known to have toxic effects at high doses, our findings suggest that APAP exposure, at doses experienced by infants in these cohorts, does not increase the risk for two adverse outcomes in the neonatal period.
Are rare heterozygousSYNJ1variants associated with Parkinson’s disease?
Authors: Senkevich Konstantin , Parlar Sitki Cem , Chantereault Cloe , Yu Eric , Ahmad Jamil , Ruskey Jennifer A. , Asayesh Farnaz , Spiegelman Dan , Waters Cheryl , Monchi Oury , Dauvilliers Yves , Dupré Nicolas , Miliukhina Irina , Timofeeva Alla , Emelyanov Anton , Pchelina Sofya , Greenbaum Lior , Hassin-Baer Sharon , Alcalay Roy N. , Gan-Or Ziv
Published: June 2024

Previous studies have suggested that rare biallelicSYNJ1mutations may cause autosomal recessive parkinsonism and Parkinson’s disease (PD). Our study explored the impact of rareSYNJ1variants in non-familial settings, including 8,165 PD cases, 818 early-onset PD (EOPD, <50 years) and 70,363 controls. Burden meta-analysis using optimized sequence Kernel association test (SKAT-O) revealed an association between rare nonsynonymous variants in the Sac1 SYNJ1 domain and PD (Pfdr=0.040). Additionally, a meta-analysis focusing on patients with EOPD demonstrated an association between all rareSYNJ1variants and PD (Pfdr=0.029). RareSYNJ1variants may be associated with sporadic PD, and more specifically with EOPD.
Scalable Differentiable Folding for mRNA Design
Authors: Krueger Ryan , Ward Max
Published: June 2024

mRNA is an emerging therapeutic platform with applications ranging from vaccines to genome editing. However, there are an exponential number of mRNA sequences to deliver a given payload and the choice in nucleotide sequence largely determines stability and translation efficiency. There exist several computational approaches for optimizing mRNA sequences but these algorithms are limited in performance or the choice of optimization metric. In this work we describe a new mRNA design algorithm that overcomes both of these limitations and is based on differentiable folding, a recently developed paradigm for RNA design in which a probabilistic sequence representation is optimized via gradient-based methods. First, we present major improvements to the original differentiable folding algorithm that drastically reduce the memory overhead of the gradient calculation. Second, we formulate the mRNA design problem in the context of continuous sequences, requiring the generalization of existing metrics and careful treatment of constraints. Given this scaled algorithm and our mRNA design formalism, we then developed a generative deep learning approach that treats our differentiable folding algorithm as a module in a larger optimization pipeline to learn a network that samples optimized sequences. As a demonstration of our method, we optimize mRNA sequences via complex, therapeutically relevant objective functions.
First chromosome-level genome assembly of the colonial tunicateBotryllus schlosseri
Authors: De Thier Olivier , M.Tawfeeq Mohammed , Faure Roland , Lebel Marie , Dru Philippe , Blanchoud Simon , Alié Alexandre , Brown Federico D. , Flot Jean-François , Tiozzo Stefano
Published: June 2024

Botryllus schlosseri(Tunicata) is a colonial chordate that has long been studied for its multiple developmental pathways and regenerative abilities and its genetically determined allorecognition system based on a polymorphic locus that controls chimerism and cell parasitism. We present the first chromosome-level genome assembly from an isogenic colony ofB. schlossericlade A1 using a mix of long and short reads scaf-folded using Hi-C. This haploid assembly spans 533 Mb, of which 96% are found in 16 chromosome-scale scaffolds. With a BUSCO completeness of 91.2%, this complete and contiguousB. schlosserigenome assembly provides a valuable genomic resource for the scientific community and lays the foundation for future investigations into the molecular mechanisms underlying coloniality, regeneration, histocompatibility, and the immune system in tunicates.