bluuebunny/crossref_metadata_2025 huggingface dataset:
Gene Set-Based Analysis of the Endosomal Sorting Processes Cargo Selection and Membrane Tubulation with Human Reward System Reactivity
Authors: Treutlein Jens , Krämer Bernd , Rex-Haffner Monika , Awasthi Swapnil , Ripke Stephan , Binder Elisabeth B. , Gruber Oliver
Published: July 2023

Dysfunction of the dopaminergic reward system has been implicated in the pathophysiology of several neuropsychiatric disorders. The endosomal network encompasses important processes related to neurotransmission in dopamine neurons, e.g, endocytosis, sorting, recycling and degradation of receptors. In the present study, we investigated whether genetic variation influencing the endosomal sorting machinery, in particular cargo selection and membrane tubulation, may impact on the activation strength in key regions of the mesolimbic reward system, i.e. the ventral tegmental area (VTA) and the nucleus accumbens (NAc).

To test our hypothesis, the VTA and NAc responses to conditioned reward stimuli were investigated using the ‘desire-reason dilemma’ (DRD) paradigm during functional magnetic resonance imaging (fMRI). Association of these neural responses with a set of genetic variants related to endosomal sorting processes were tested in two independent samples (N = 182; N = 214).

In the first sample, the gene set was associated with both VTA and NAc responses to conditioned reward stimuli [empirical P -values: R-VTA 0.0036; R-NAc 0.0016; L-NAc 0.0094], while the effect in the R-VTA could be replicated in the second sample [empirical P -value: R-VTA 0.0443] at the level of the gene set. For the NAc, an additional exploratory analysis of a patient-only subsample of the first sample (N = 64) suggested that the gene set may express its effect in this brain region predominantly in patients.

These findings provide first evidence that the endosomal sorting processes cargo selection and membrane tubulation influence neural responses of the reward system to conditioned stimuli. Further studies are required to clarify the role of endosomal sorting processes in the pathophysiology of neuropsychiatric disorders.
Physiological and metabolic insights into the first cultured anaerobic representative of deep-seaPlanctomycetesbacteria
Authors: Zheng Rikuan , Wang Chong , Liu Rui , Cai Ruining , Sun Chaomin
Published: July 2023

Planctomycetesbacteria are ubiquitously distributed across various biospheres and play key roles in global element cycles. However, few deep-seaPlanctomycetesmembers have been cultivated, limiting our understanding ofPlanctomycetesin the deep biosphere. Here, we have successfully cultured a novel strain ofPlanctomycetes(strain ZRK32) from a cold seep sediment, by using an enriched medium supplemented with rifampicin and different nitrogen sources. Our genomic, physiological and phylogenetic analyses indicate that strain ZRK32 is a novel species, which we propose be named:Poriferisphaera heterotrophicis. We show that strain ZRK32 replicates using a budding mode of division. Based on the combined results from growth assays and transcriptomic analyses, we found that rich nutrients, or supplementation with NO3-or NH4+promoted the growth of strain ZRK32 by facilitating energy production through the tricarboxylic acid (TCA) cycle and the Embden–Meyerhof–Parnas (EMP) glycolysis pathway. Moreover, supplementation with NO3-or NH4+induced strain ZRK32 to release a bacteriophage in a chronic manner, without host cell lysis. This bacteriophage then enabled strain ZRK32, and another marine bacterium that we studied, to metabolize nitrogen through the function of auxiliary metabolic genes (AMGs). Overall, these findings expand our understanding of deep-seaPlanctomycetesbacteria, while highlighting their ability to metabolize nitrogen when reprogrammed by chronic viruses.
Spinal neural tube formation and tail development in human embryos
Authors: Santos Chloe , Marshall Abigail R. , Murray Ailish , Metcalfe Kate , Narayan Priyanka , de Castro Sandra C. P. , Maniou Eirini , Greene Nicholas D. E. , Galea Gabriel L. , Copp Andrew J.
Published: July 2023

Formation of the nervous system in the spinal region of higher vertebrates involves primary and secondary neurulation, in which the neural tube forms by closure and canalisation respectively. These processes are incompletely understood in humans, in part due to the challenge of accessing neurulation-stage embryos (3-7 weeks post-conception). Here we present findings on completion of primary neurulation and formation of the ‘secondary body’ (including secondary neurulation) in 108 human embryos that span Carnegie Stages (CS) 10 to 18. Several outstanding questions on low spinal development in humans are addressed: we show that primary neurulation is completed at the human posterior neuropore with a pattern of neural plate bending similar to that in the mouse. There is no evidence of a ‘transition zone’ to secondary neurulation, which proceeds from CS13 with formation of a single lumen as in mouse, not coalescence of multiple lumens as has been claimed based on chick neurulation. Secondary neural tube ‘splitting’ is seen in the more proximal tail regions of 60% of human embryos. A somite is formed every 7 h in human, compared with 2 h in mice and a 5 h ‘segmentation clock’ in human organoids. Termination of axial elongation occurs after downregulation ofWNT3AandFGF8in the CS15 embryonic tailbud, with a ‘burst’ of apoptosis that may remove the neuro-mesodermal progenitors. We conclude that low spinal neurulation and secondary body formation follow a similar pattern in humans as in mammalian model systems such as mouse and rat. Investigators are now attempting to recapitulate events of neurulation in organoids derived from human stem cells, and our findings provide ‘normative data’ for interpretation of such in vitro results.
Heme oxygenase-1 expressing omental macrophages as a therapeutic target in ovarian high grade serous carcinoma
Authors: Spear Sarah , Le Saux Olivia , Mirza Hasan B. , Tyson Katie , Bickel Jasmine , Freile Fabio Grundland , Siskos Alexandros P. , Balcells Cristina , Walton Josephine B. , Woodman Chloé , Ennis Darren P. , Iyer Nayana , Hernandez Carmen Aguirre , Xu Yuewei , Spiliopoulou Pavlina , Brenton James D. , Costa-Pereira Ana P. , Keun Hector C. , Triantafyllou Evangelos , Arnold James N. , McNeish Iain A.
Published: July 2023

Ovarian high grade serous carcinoma (HGSC) remains a disease of poor prognosis that is unresponsive to current immune checkpoint inhibitors. Although PI3K pathway alterations are common in HGSC, attempts to target this pathway have been unsuccessful. We hypothesised aberrant PI3K pathway activation may alter the HGSC immune microenvironment and present a novel targeting strategy. We used both murine models and HGSC patient samples to study the impact of loss ofPten, a negative regulator of PI3K pathway signalling. We identified populations of resident macrophages specifically inPtennull omental tumours. These macrophages derive from peritoneal fluid macrophages and have a unique gene expression programme, marked by high levels ofHMOX1expression, the gene for the enzyme heme oxygenase-1. Targeting resident peritoneal macrophages prevents appearance of HMOX1himacrophages and in doing so reduces tumour growth. Furthermore, direct inhibition of HMOX1 extends survivalin vivo. HMOX1himacrophages with corresponding gene expression programmes are also identified in human HGSC tumours and their presence correlates with activated tumoural PI3K pathway/mTOR signalling and poor overall survival in HGSC patients. In contrast, tumours with low number of HMOX1himacrophages are marked by increased adaptive immune response gene expression. Our data suggest that HMOX1himacrophages represent a potential therapeutic target and biomarker for poor prognosis HGSC.
Identification of full-sibling families from natural single-tree ash progenies based on SSR markers and genome-wide SNPs
Authors: Krautwurst Melina , Past Franziska , Kersten Birgit , Bubner Ben , Müller Niels A.
Published: July 2023

Common ash,Fraxinus excelsior, is threatened by the invasive pathogenHymenoscyphus fraxineus, which causes ash dieback. The pathogen is rapidly spreading throughout Europe with severe ecological and economic consequences. Multiple studies have presented evidence for the existence of a small fraction of genotypes with low susceptibility. Such genotypes can be targets for natural and artificial selection to conserveF. excelsiorand associated ecosystems. To resolve the genetic architecture of variation in susceptibility it is necessary to analyze segregating populations. Here we employed about 1,000 individuals of each of four single-tree progenies from potentially tolerant mother trees to identify full-sibling (full-sib) families. To this end, we first genotyped all 4,000 individuals and the four mothers with eight SSR markers. We then used the program Colony to predict full-sibs without knowledge of the paternal genotypes. For each single-tree progeny, Colony predicted dozens of full-sib families, ranging from 3-165 individuals. In a next step, 910 individuals assigned to full-sib families with more than 30 individuals were subjected to high-resolution genotyping using over one million genome-wide SNPs which were identified with Illumina low-coverage resequencing. Using these SNP genotyping data in principal component analyses we were able to assign individuals to full-sib families with high confidence. Together the analyses revealed five large families with 80-212 individuals. These can be used to generate genetic linkage maps and to perform quantitative trait locus analyses for ash dieback susceptibility or other traits toH. fraxineusor other traits. The elucidation of the genetic basis of natural variation in ash may support breeding and conservation efforts and may contribute to more robust forest ecosystems.
Drosophilaaxis extension is robust to an orthogonal pull by invaginating mesoderm
Authors: Lye Claire M , Blanchard Guy B. , Evans Jenny , Nestor-Bergmann Alexander , Sanson Bénédicte
Published: July 2023

As tissues grow and change shape during animal development, they physically pull and push on each other and these mechanical interactions can be important for morphogenesis. DuringDrosophilagastrulation, mesoderm invagination temporally overlaps with the extension of the ectodermal germband; the latter is caused primarily by Myosin II-driven polarised cell intercalation. Here we investigate the impact of mesoderm invagination on ectoderm extension, examining possible mechanical and mechanotransductive effects on Myosin II recruitment and polarised cell intercalation. We find that the germband ectoderm is deformed by the mesoderm pulling in the orthogonal direction, showing mechanical coupling between these tissues. However, we do not find a significant change in Myosin II planar polarisation in response to mesoderm invagination, nor an effect on the rate of junction shrinkage leading to cell intercalation events. We find some impact on the orientation of neighbour exchange events, and an increased rate of growth of new cell junctions, but this makes little difference to the rate of cell intercalation. We conclude that the cellular mechanisms of axis extension are robust to the mechanical pull of mesoderm invagination.
Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization
Authors: Salari Hossein , Fourel Geneviève , Jost Daniel
Published: July 2023

Although our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription
Authors: LaMarca Elizabeth A. , Saito Atsushi , Plaza-Jennings Amara , Espeso-Gil Sergio , Hellmich Allyse , Fernando Michael B. , Javidfar Behnam , Liao Will , Estill Molly , Townsley Kayla , Florio Anna , Ethridge James E. , Do Catherine , Tycko Benjamin , Shen Li , Kamiya Atsushi , Tsankova Nadejda M. , Brennand Kristen J. , Akbarian Schahram
Published: July 2023

Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivityin vivoandin vitro. Therefore, R- loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth
Authors: Coleman Daniel J.L. , Keane Peter , Luque-Martin Rosario , Chin Paulynn S , Blair Helen , Ames Luke , Kellaway Sophie G. , Griffin James , Holmes Elizabeth , Potluri Sandeep , Assi Salam A. , Bushweller John , Heidenreich Olaf , Cockerill Peter N. , Bonifer Constanze
Published: July 2023

AML is a heterogenous disease caused by different mutations. We have previously shown that each mutational sub-type develops its specific gene regulatory network (GRN) with transcription factors interacting with multiple gene modules, many of which are transcription factor genes themselves. Here we hypothesized that highly connected nodes within such networks comprise crucial regulators of AML maintenance. We tested this hypothesis using FLT3-ITD mutated AML as a model and conducted an shRNA drop-out screen informed by this analysis. We show that AML-specific GRNs predict identifying crucial regulatory modules required for AML but not normal cellular growth. Furthermore, our work shows that all modules are highly connected and regulate each other. The careful multi-omic analysis of the role of one (RUNX1) module by shRNA and chemical inhibition shows that this transcription factor and its target genes stabilize the GRN of FLT3-ITD AML and that its removal leads to GRN collapse and cell death.
Into the deep: The subthalamic and para-subthalamic nuclei in behavioral avoidance
Authors: Serra Gian Pietro , Guillaumin Adriane , Vlcek Bianca , Delgado-Zabalza Lorena , Ricci Alessia , Rubino Eleonora , Dumas Sylvie , Baufreton Jérôme , Georges François , Wallén-Mackenzie Åsa
Published: July 2023

The subthalamic nucleus (STN) is a key component of the brain network for movement control. However, the STN is strikingly heterogeneous and also intricately engaged in limbic and cognitive functions. The STN shows aberrant firing activity in several neurological and neuropsychiatric disorders, including Parkinsońs disease (PD). Deep brain stimulation (DBS) in the STN alleviates motor impairment in PD, but patients have reported altered mood as adverse side-effect. Recent observations suggest that optogenetic STN activation in mice induces flight behavior. We hypothesized that STN activation stand at risk of causing an aversive response with behavioral avoidance as consequence. The STN is directly adjoined with the para-STN (pSTN), a hypothalamic area correlated with appetitive and aversive behavior. STN-DBS aiming to correct STN might thereby also modulate pSTN. To dissociate the impact of STN and pSTN, we took advantage of selective promoters in mice, identified in our recent RNA- sequencing of the subthalamic area, to selectively direct optogenetic excitation. Acute photostimulation resulted in aversion via both the STN and pSTN, but only STN- stimulation-paired cues resulted in conditioned avoidance. Viral-genetic tracing coupled with electrophysiological recordings identified a polysynaptic pathway from the STN to the lateral habenula, a critical hub for aversion and associated with clinical depression. This study demonstrates that STN activation is directly correlated with aversion, and thereby contributes neurobiological underpinnings to emotional affect upon STN manipulation with implications for STN-targeted treatment outcome.
Tailoring TfhProfiles Enhances Antibody Persistence to a Clade C HIV-1 Vaccine in Rhesus Macaques
Authors: Verma Anil , Hawes Chase E , Elizaldi Sonny R , Smith Justin C. , Rajasundaram Dhivyaa , Pedersen Gabriel Kristian , Shen Xiaoying , Williams LaTonya D , Tomaras Georgia D. , Kozlowski Pamela A. , Amara Rama R. , Iyer Smita S.
Published: July 2023

CD4 T follicular helper cells (Tfh) are essential for establishing serological memory and have distinct helper attributes that impact both the quantity and quality of the antibody response. Insights into Tfhsubsets that promote antibody persistence and functional capacity can critically inform vaccine design. Based on the Tfhprofiles evoked by the live attenuated measles virus vaccine, renowned for its ability to establish durable humoral immunity, we investigated the potential of a Tfh1/17 recall response during the boost phase to enhance persistence of HIV-1 Envelope (Env) antibodies in rhesus macaques. Using a DNA-prime encoding gp160 antigen and Tfhpolarizing cytokines (interferon protein-10 (IP-10) and interleukin-6 (IL-6)), followed by a gp140 protein boost formulated in a cationic liposome-based adjuvant (CAF01), we successfully generated germinal center (GC) Tfh1/17 cells. In contrast, a similar DNA-prime (including IP-10) followed by gp140 formulated with monophosphoryl lipid A (MPLA)+QS-21 adjuvant predominantly induced GC Tfh1 cells. While the generation of GC Tfh1/17 cells with CAF01 and GC Tfh1 cells with MPLA+QS-21 induced comparable peak Env antibodies, the latter group demonstrated significantly greater antibody concentrations at week 8 after final immunization which persisted up to 30 weeks (gp140 IgG ng/ml-MPLA; 5500; CAF01, 2155; p <0.05). Notably, interferon γ+ Env-specific Tfhresponses were consistently higher with gp140 in MPLA+QS-21 and positively correlated with Env antibody persistence. These findings suggest that vaccine platforms maximizing GC Tfh1 induction promote persistent Env antibodies, important for protective immunity against HIV.
Discovery of post-translationally modified self-peptides that promote hypertension
Authors: Bloodworth Nathaniel , Chen Wei , Patrick David , Palubinsky Amy , Phillips Elizabeth , Roeth Daniel , Kalkum Markus , Mallal Simon , Davies Sean , Ao Mingfang , Moretti Rocco , Meiler Jens , Harrison David G
Published: July 2023

Post translational modifications can enhance immunogenicity of self-proteins. In several conditions including hypertension, systemic lupus, and heart failure, isolevuglandins (IsoLGs) are formed by lipid peroxidation and covalently bond with protein lysine residues. Here we show that the murine class-I major histocompatibility complex (MHC-I) variant H-2Dbuniquely presents isoLG modified peptides and developed a computational pipeline that identifies structural features for MHC-I accommodation of such peptides. We identified isoLG-adducted peptides from renal proteins including the sodium glucose transporter 2, Cadherin 16, Kelch Domain containing protein 7A and solute carrier family 23, that are recognized by CD8+T cells in tissues of hypertensive mice, induce T cell proliferationin vitro, and prime hypertension after adoptive transfer. Finally, we find similar patterns of isoLG-adducted antigen restriction in class-I human leukocyte antigens as in murine analogues. Thus, we have used a combined computational and experimental approach to define likely antigenic peptides in hypertension.
scRNA-seq reveals novel genetic pathways and sex chromosome regulation inTriboliumspermatogenesis
Authors: Robben Michael , Ramesh Balan , Pau Shana , Meletis Demetra , Luber Jacob , Demuth Jeffery
Published: July 2023

Insights into single cell expression data are generally collected through well conserved biological markers that separate cells into known and unknown populations. Unfortunately for non-model organisms that lack known markers, it is often impossible to partition cells into biologically relevant clusters which hinders analysis into the species.Tribolium castaneum, the red flour beetle, lacks known markers for spermatogenesis found in insect species likeDrosophila melanogaster. Using single cell sequencing data collected from adult beetle testes, we implement a strategy for elucidating biologically meaningful cell populations by using transient expression stage identification markers, weighted principal component leiden clustering. We identify populations that correspond to observable points in sperm differentiation and find species specific markers for each stage. We also develop an innovative method to differentiate diploid from haploid cells based on scRNA-Seq reads and use it to corroborate our predicted demarcation of meiotic cell stages. Our results demonstrate that molecular pathways underlying spermatogenesis in Coleoptera are highly diverged from those in Diptera, relying on several genes with female meiotic pathway annotations. We find that the X chromosome is almost completely silenced throughout pre-meiotic and meiotic cells. Further evidence suggests that machinery homologous to the Drosophila dosage compensation complex (DCC) may mediate escape from meiotic sex chromosome inactivation and postmeiotic reactivation of the X chromosome.
Solution-state NMR Assignment and Secondary Structure Analysis of the MonomericPseudomonasBiofilm-Forming Functional Amyloid Accessory Protein FapA
Authors: Byeon Chang-Hyeock , Akbey Ümit
Published: July 2023

FapA is an accessory protein within the biofilm forming functional bacterial amyloid related fap-operon inPseudomonas. We present a complete sequential assignment of1Hamide,13Cα,13Cβ, and15N NMR resonances for the functional form of the monomeric soluble FapA protein, comprising amino acids between 29-152. From these observed chemical shifts, the secondary structure propensities (SSPs) were determined. FapA predominantly adopts a random coil conformation, however, we also identified small propensities for α-helical and β-sheet conformations. Notably, these observed SSPs are smaller compared to the ones we recently observed for the monomeric soluble FapC protein. These NMR results will provide valuable insights into the activity of FapA in functional amyloid formation and regulation, that will also aid developing strategies targeting amyloid formation within biofilms and addressing chronic infections.
Single cell RNA analysis uncovers the cell differentiation trajectories and functionalization for air breathing of frog lung
Authors: Chang Liming , Chen Qiheng , Wang Bin , Liu Jiongyu , Zhang Meihua , Zhu Wei , Jiang Jianping
Published: July 2023

The evolution and development of vertebrate lungs have received extensive concerns for the significance in terrestrial adaptation. Amphibians possess the most primitive lungs among tetrapods, underscoring the evolutionary importance of lungs in bridging the transition from aquatic to terrestrial life. However, the intricate process of cell differentiation during amphibian lung development is still lacking. Using single cell RNA-seq, we identified 21 cell types in the developing lung of a land-dwelling frog (Microhyla fissipes). We elucidated that single type of alveolar epithelial cells (AECs) existed in amphibian and the diversity of AECs may correspond to the capacity for terrestrial adaptation in tetrapods. Based on pseudotime trajectories analysis, we revealed previously unrecognized developmental-specific transition cell states of epithelial and endothelial cells supporting the rapid morphogenesis of lung during metamorphic climax. We illustrated the cellular and molecular processes during lung functionalization. These findings uncover the cell differentiation trajectories and functionalization for air breathing of frog lungs and highlight the evolutionary peculiarity of the primitive lungs.

Graphical abstract
Random,de novoand conserved proteins: How structure and disorder predictors perform differently
Authors: Middendorf Lasse , Eicholt Lars A.
Published: July 2023

Understanding the emergence and structural characteristics ofde novoand random proteins is crucial for unraveling protein evolution and designing novel enzymes. However, experimental determination of their structures remains challenging. Recent advancements in protein structure prediction, particularly with AlphaFold2 (AF2), have expanded our knowledge of protein structures, but their applicability tode novoand random proteins is unclear. In this study, we investigate the structural predictions and confidence scores of AF2 and protein language model (pLM)-based predictor ESMFold forde novo, random, and conserved proteins. We find that the structural predictions forde novoand random proteins differ significantly from conserved proteins. Interestingly, a positive correlation between disorder and confidence scores (pLDDT) is observed forde novoand random proteins, in contrast to the negative correlation observed for conserved proteins. Furthermore, the performance of structure predictors forde novoand random proteins is hampered by the lack of sequence identity. We also observe varying predicted disorder among different sequence length quartiles for random proteins, suggesting an influence of sequence length on disorder predictions. In conclusion, while structure predictors provide initial insights into the structural composition ofde novoand random proteins, their accuracy and applicability to such proteins remain limited. Experimental determination of their structures is necessary for a comprehensive understanding. The positive correlation between disorder and pLDDT could imply a potential for conditional folding and transient binding interactions ofde novoand random proteins.
NSD2 maintains lineage plasticity and castration-resistance in neuroendocrine prostate cancer
Authors: Li Jia J. , Vasciaveo Alessandro , Karagiannis Dimitrios , Sun Zhen , Chen Xiao , Socciarelli Fabio , Frankenstein Ziv , Zou Min , Pannellini Tania , Chen Yu , Gardner Kevin , Robinson Brian D. , de Bono Johann , Abate-Shen Cory , Rubin Mark A. , Loda Massimo , Sawyers Charles L. , Califano Andrea , Lu Chao , Shen Michael M.
Published: July 2023

The clinical use of potent androgen receptor (AR) inhibitors has promoted the emergence of novel subtypes of metastatic castration-resistant prostate cancer (mCRPC), including neuroendocrine prostate cancer (CRPC-NE), which is highly aggressive and lethal1. These mCRPC subtypes display increased lineage plasticity and often lack AR expression2–5. Here we show that neuroendocrine differentiation and castration-resistance in CRPC-NE are maintained by the activity of Nuclear Receptor Binding SET Domain Protein 2 (NSD2)6, which catalyzes histone H3 lysine 36 dimethylation (H3K36me2). We find that organoid lines established from genetically-engineered mice7recapitulate key features of human CRPC-NE, and can display transdifferentiation to neuroendocrine states in culture. CRPC-NE organoids express elevated levels of NSD2 and H3K36me2 marks, but relatively low levels of H3K27me3, consistent with antagonism of EZH2 activity by H3K36me2. Human CRPC-NE but not primary NEPC tumors expresses high levels of NSD2, consistent with a key role for NSD2 in lineage plasticity, and high NSD2 expression in mCRPC correlates with poor survival outcomes. Notably, CRISPR/Cas9 targeting ofNSD2or expression of a dominant-negative oncohistone H3.3K36M mutant results in loss of neuroendocrine phenotypes and restores responsiveness to the AR inhibitor enzalutamide in mouse and human CRPC-NE organoids and grafts. Our findings indicate that NSD2 inhibition can reverse lineage plasticity and castration-resistance, and provide a potential new therapeutic target for CRPC-NE.
Resolving evolutionary relationships in the groundsels: phylogenomics, divergence time estimates, and biogeography ofPackera(Asteraceae: Senecioneae)
Authors: Moore-Pollard Erika R. , Mandel Jennifer R.
Published: July 2023

The genusPackerabelongs to the sunflower family and contains an estimated 64 species and varieties endemic to North America. SomePackeraare known to hybridize or exhibit polyploidy, making it difficult to reconstruct evolutionary relationships within the group. Previous molecular phylogenetic studies ofPackeraemploying ITS data recovered low resolution trees, providing little information on the evolutionary relationships within this complex genus. Therefore, we used next-generation sequencing data to infer nuclear and plastid phylogenies ofPackeraand related Senecioneae taxa. The nuclear phylogeny was calibrated to produce a timetree, then used to reconstruct the macroevolutionary history ofPackera,including its historical biogeography. We then compared the reconstructed evolutionary history to previously published scenarios based on phylogenetic and geohistorical data. We found that the nuclear and plastid phylogenies were highly incongruent, with the nuclear tree presenting higher resolution than the plastid tree which had an apparent lack of plastid diversity. The nuclear tree indicated that geography may have played a major role in the evolution and taxonomic diversification ofPackera. The estimated origin ofPackeraat approximately 19.2MY – 25.9MY (late Oligocene to early Miocene) is older than in most other studies. Nonetheless, it aligns well with previous geohistorical predictions, which suggest that speciation and diversification events inPackerawere driven by changes in geography and climate in North America. Moreover,Packeralikely originated in the western United States or Mexico, and subsequently diversified north and east into the rest of North America and Russia, in agreement with other studies.
Elucidation of the essentiality of lumazine synthase (RibH) forMycobacterium tuberculosissurvival and discovery of potent inhibitors for enhanced antimycobacterial therapy
Authors: Singh Monica , Dhanwal Anannya , Verma Arpita , Augustin Linus , Kumari Niti , Chakraborti Soumyananda , Agarwal Nisheeth , Sriram Dharmarajan , Dey Ruchi Jain
Published: July 2023

Tuberculosis (TB) continues to be a global health crisis, necessitating urgent interventions to address drug resistance and improve treatment efficacy. In this study, we validate the indispensable role of lumazine synthase (RibH), a vital enzyme in the riboflavin biosynthetic pathway, in the survival ofMycobacterium tuberculosis (M. tb)using a CRISPRi-based conditional gene knockdown strategy. We show that genetic and functional ablation of RibH inM. tbcannot be compensated by exogenous supply of Riboflavin, or co-factors Flavin Adenine Dinucleotide (FAD) or Flavin Mononucleotide (FMN). Capitalizing on the essentiality of RibH, we employ a high-throughput molecular docking approach to screen ∼600,000 compounds and identify inhibitors of RibH. Throughin vitroscreening of 55 shortlisted compounds, we discover 3 inhibitors that exhibit potent antimycobacterial activity. These compounds effectively also eradicate intracellularM. tbduring macrophage infection and prevent the resuscitation of the nutrient-starved persister bacteria. Moreover, these 3 compounds synergistically enhance the bactericidal effect of first-line anti-TB drugs, Isoniazid and Rifampicin. Corroborating with thein silicopredicted high docking scores along with favorable ADME and toxicity profiles, all 3 compounds demonstrate exceptional binding affinity towards purified lumazine synthase enzymein vitro, and display an acceptable safety profile in mammalian cells, with a high selective index. By providing mechanistic evidence for the essentiality of RibH inM. tbsurvival, and discovering potent RibH inhibitors with outstanding antimycobacterial activity, our study contributes to the development of superior TB treatment strategies and advances the global fight against this devastating disease.
Shared structure facilitates working memory of multiple sequences
Authors: Huang Qiaoli , Luo Huan
Published: July 2023

Daily experiences often involve the processing of multiple sequences, yet storing them challenges the limited capacity of working memory (WM). To achieve efficient memory storage, relational structures shared by sequences would be leveraged to reorganize and compress information. Here, participants memorized a sequence of items with different colors and spatial locations and later reproduced the full color and location sequences one after another. Crucially, we manipulated the consistency between location and color sequence trajectories. First, sequences with consistent trajectories demonstrate improved memory performance and a trajectory correlation between reproduced color and location sequences. Second, sequences with consistent trajectories show neural reactivation of common trajectories, and display spontaneous replay of color sequences when recalling locations. Finally, neural reactivation correlates with WM behavior. Our findings suggest that shared common structure is leveraged for storage of multiple sequences through compressed encoding and neural replay, together facilitating efficient information organization in WM.
An allele-sharing, moment-based estimator of global, population specific and population pairsFSTunder a general model of population structure
Authors: Goudet Jérôme , Weir Bruce S.
Published: July 2023

Being able to properly quantify genetic differentiation is key to understanding the evolutionary potential of a species. One central parameter in this context isFST, the mean coancestry within populations relative to the mean coancestry between populations. Researchers have been estimatingFSTglobally or between pairs of populations for a long time. More recently, it has been proposed to estimate population specificFSTvalues, and between population-pair mean relative coancestry. Here, we review the several definitions and estimation methods ofFST, and stress that they provide values relative to a reference population. We show the good statistical properties of an allele sharing, method of moments based estimator ofFST(global, population specific and population pairs) under a very general model of population structure. We point to the limitation of existing likelihood and Bayesian estimators when the populations are not independent. Last, we show that recent attempts to estimate absolute, rather than relative, mean coancestry fail to do so.

Author summary
Using random forests to uncover the predictive power of distance–varying cell interactions in tumor microenvironments
Authors: VanderDoes Jeremy , Marceaux Claire , Yokote Kenta , Asselin-Labat Marie-Liesse , Rice Gregory , Hywood Jack D.
Published: July 2023

Tumor microenvironments (TMEs) contain vast amounts of information on patient’s cancer through their cellular composition and the spatial distribution of tumor cells and immune cell populations. Exploring variations in TMEs among patients and cancer types, as well as determining the extent to which this information can predict variables such as patient survival or treatment success with emerging immunotherapies, is of great interest. Moreover, in the face of a large number of potential spatial cell interactions to consider, we often wish to identify specific interactions that are useful in making such predictions. We present an approach to achieve these goals based on summarizing spatial relationships in the TME using spatialKfunctions, and then applying functional data analysis and random forest models to both predict outcomes of interest and identify important spatial relationships. This approach is shown to be effective in simulation experiments. We further used the proposed approach to interrogate two real data sets of Multiplexed Ion Beam Images of TMEs in triple negative breast cancer and lung cancer patients. The methods proposed are publicly available in a companionRpackagefunkycells.

Author summary

Spatial data on the tumor microenvironment (TME) are becoming more prevalent. Existing methods to interrogate such data often have several deficiencies: (1) they rely on estimating the spatial relationships among cells by examining simple counts of cells within asingleradius, (2) they do not come with ways to evaluate the statistical significance of any findings, or (3) they consider multiple individual interactions resulting in overly optimistic estimates of interaction importances. Our approach, which leverages techniques in spatial statistics and uses a benchmark ensemble machine learning method addresses (1), since theKfunctions used encode the relative densities of cells over all radii up to a user-selected maximum radius, and (2) we have developed a custom approach based on permutation and cross-validation to evaluate the statistical significance of any findings of significant spatial interactions in the TME, (3) over potentially multiple interactions. Our approach is also freely available with anRimplementation calledfunkycells. In the analysis of two real data sets, we have seen that the method performs well, and gives the expected results. We think this will be a robust tool to add to the toolbox for researchers looking to interrogate, what can be sometimes unwieldy, TME data.
Microglia at Sites of Atrophy Restrict the Progression of Retinal Degeneration via Galectin-3 and Trem2 Interactions
Authors: Yu Chen , Lad Eleonora M , Mathew Rose , Littleton Sejiro , Chen Yun , Schlepckow Kai , Degan Simone , Chew Lindsey , Amason Joshua , Kalnitsky Joan , Rickman Catherine Bowes , Proia Alan D , Colonna Marco , Haass Christian , Saban Daniel R
Published: July 2023

Degenerative diseases of the outer retina, including age-related macular degeneration (AMD), are characterized by atrophy of photoreceptors and retinal pigment epithelium (RPE). In these blinding diseases, macrophages are known to accumulate ectopically at sites of atrophy, but their ontogeny and functional specialization within this atrophic niche remain poorly understood, especially in the human context. Here, we uncovered a transcriptionally unique profile of microglia, marked by galectin-3 upregulation, at atrophic sites in mouse models of retinal degeneration and in human AMD. Using disease models, we found that conditional deletion of galectin-3 in microglia led to defects in phagocytosis and consequent augmented photoreceptor death, RPE damage and vision loss, suggestive of a protective role.

Mechanistically, Trem2 signaling orchestrated the migration of microglial cells to sites of atrophy, and there, induced galectin-3 expression. Moreover, pharmacologic Trem2 agonization led to heightened protection, but only in a galectin-3-dependent manner, further signifying the functional interdependence of these two molecules. Likewise in elderly human subjects, we identified a highly conserved population of microglia at the transcriptomic, protein and spatial levels, and this population was enriched in the macular region of postmortem AMD subjects. Collectively, our findings reveal an atrophy-associated specialization of microglia that restricts the progression of retinal degeneration in mice and further suggest that these protective microglia are conserved in AMD.

One Sentence Summary

A common neuroprotective response of microglia at the site of retinal atrophy is identified in mice and humans.
Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery
Authors: Hanssen Friederike , Garcia Maxime U. , Folkersen Lasse , Pedersen Anders Sune , Lescai Francesco , Jodoin Susanne , Miller Edmund , Seybold Matthias , Wacker Oskar , Smith Nicholas ,   nf-core community, Gabernet Gisela , Nahnsen Sven
Published: July 2023

DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2emissions low. The code is available athttps://nf-co.re/sarek.
Genomic analyses capture the human-induced demographic collapse and recovery in a wide-ranging cervid
Authors: Kessler Camille , Shafer Aaron B.A.
Published: July 2023

The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonisation. Here, we analysed 73 re-sequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found a strong signal of glacial-induced vicariance and demographic decline; notably, there is a severe decline in white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Nein all analysed populations. Historical census size and restocking data show a clear parallel to historical Neestimates, and temporal Ne/Ncratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune-genes that we surmise reflect the changing land-use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity, and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.
Adaptive evolution ofP. aeruginosain human airways shows phenotypic convergence despite diverse patterns of genomic changes
Authors: Espaillat Akbar , Colque Claudia Antonella , Rago Daniela , La Rosa Ruggero , Molin Søren , Johansen Helle Krogh
Published: July 2023

Selective forces in the environment drive bacterial adaptation to novel niches, choosing the fitter variants in the population. However, in dynamic and changing environments, the evolutionary processes controlling bacterial adaptation are difficult to monitor. Here, we follow 9 cystic fibrosis patients chronically infected withPseudomonas aeruginosa, as a proxy for bacterial adaptation. We identify and describe the bacterial changes and evolution occurring between 15 and 35 years of within host evolution. We combine whole genome sequencing, RNAseq and metabolomics, and compare the evolutionary trajectories directed by the adaptation of four differentP. aeruginosalineages to the lung. Our data suggest divergent evolution at the genomic level for most of the genes, with signs of convergent evolution with respect to acquisition of mutations in regulatory genes, which drive the transcriptional and metabolomic program at late time of evolution. Metabolomics further confirmed convergent adaptive phenotypic evolution as documented by reduction of the quorum sensing molecules acyl-homoserine lactone, phenazines and rhamnolipids (except for quinolones). The modulation of the quorum sensing repertoire suggests that similar selective forces characterize at late times of evolution independent of the patient. Collectively, our data suggest that similar environments and similarP. aeruginosapopulations in the patients at prolonged time of infection are associated with an overall reduction of virulence-associated features and phenotypic convergence.

Selective forces in the human environment drive bacterial adaptation to novel niches, choosing the fitter variants in the population. We have investigated the evolutionary processes in 9 CF patients infected withPseudomonas aeruginosain the airways for several decades. To describe the within host evolution and trajectories of four differentP. aeruginosalineages to the lung environment we have combined whole genome sequencing, RNAseq and metabolomics. In this patient cohorte with persistent bacterial infections our data suggest that similar environments and similarP. aeruginosapopulations in the patients at prolonged time of infection are associated with an overall reduction of virulence-associated features and phenotypic convergence
Separation of evolutionary timescales in coevolving species
Authors: Buckingham Lydia J. , Ashby Ben
Published: July 2023

Abstract

Many coevolutionary processes, including host-parasite and host-symbiont interactions, involve one species or trait which evolves much faster than the other. Whether or not a coevolutionary trajectory converges depends on the relative rates of evolutionary change in the two species, and so current adaptive dynamics approaches generally either determine convergence stability by considering arbitrary (often comparable) rates of evolutionary change or else rely on necessary or sufficient conditions for convergence stability. We propose a method for determining convergence stability in the case where one species is expected to evolve much faster than the other. This requires a second separation of timescales, which assumes that the faster evolving species will reach its evolutionary equilibrium (if one exists) before a new mutation arises in the more slowly evolving species. This method, which is likely to be a reasonable approximation for many coevolving species, both provides straightforward conditions for convergence stability and is less computationally expensive than traditional analysis of coevolution models, as it reduces the trait space from a two-dimensional plane to a one-dimensional manifold. In this paper, we present the theory underlying this new separation of timescales and provide examples of how it could be used to determine coevolutionary outcomes from models.