Biology subjects

Wagner, G.

Publications and source records attributed to Wagner, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecular Data From Herbarium Specimens Reveal A Potential Extirpation of Azolla microphylla From California

Previous studies have shown that there may be more species of Azolla in California than currently recognized, including a recent introduction of the non-native Azolla caroliniana. To better assess the status and species diversity of Azolla in California, we sequenced four historical herbarium specimens, some over 100 years old, and increased our sampling of extant populations across seven counties in California. We found that many specimens from California thought to be Azolla microphylla are actually Azolla filiculoides or members of one of two non-native "Azolla caroliniana" clades. We also found that some specimens collected from California from the 1960s through the 1980s fall within an Azolla microphylla-mexicana clade. However, there is no evidence of this species from any recent collections even from counties where it was previously found, which points to a potential extirpation of this species from California.

ecology↗

bioRxiv2026

Conceptus attachment coincides with initiation of an anti-inflammatory cytokine profile in the pig endometrium

In eutherian mammals, blastocyst implantation is often associated with a quasi-inflammatory reaction in the endometrium, which is resolved with the establishment of the definitive placenta. This is understandable in the case of invasive placentation, since implantation entails a nidatory injury to the maternal tissue due to the invading blastocyst. Quasi-inflammatory processes have also been documented in pregnant pigs, even though the blastocyst only attaches to, rather than invades into, the endometrium of the uterus. In this study, we asked what processes in early porcine pregnancy lead to the resolution of attachment-associated inflammation. In generic wound healing the transition from a pro- to an anti-inflammatory state is caused by a corresponding transition from M1 to M2 polarized macrophages following efferocytosis by macrophages of apoptotic neutrophils. In order to determine whether this scenario applies to the pregnancy-related resolution of inflammation in the porcine uterus, we produced a series of bulk transcriptome samples spanning days (D) 13 to 25 of gestation. This time span corresponds to the transition from pre- to post-attachment stages of pregnancy. We found slower changes in the transcriptome between D20 and D25 than prior to D20, suggesting a turning point in pregnancy-related reprogramming. The turning point at D20 corresponds to the time of firm attachment of trophectoderm to uterine luminal epithelium and the cessation of IFNG signaling from the blastocyst. This transition coincides with increased expression of RNAs of genes implicated in resolution of inflammation and M2 polarization such as ARG1, MRC1/CD206, CD86, TGFb1 and IL10, as well as a significant increase in expression of HGPD, the enzyme that metabolizes prostaglandins. While immunoreactivity for ARG1 was found in putative macrophages in the sub-epithelial stratum compactum, other markers of M2 polarized macrophages were localized to non-immune cells: MRC1 was found on fibroblast-like stromal cells, CD86 on trophoblast cells, and IL10 in luminal and glandular epithelia. These results suggest that intrauterine immune regulation is decoupled from that of the rest of the body by engaging non-immune cell types as anti-inflammatory mediators during the peri-attachment period of pregnancy.

developmental biology↗

bioRxiv2026

Comprehensive genomic analysis of Trypanosoma rangeli reveals key insights into the biology and evolution of this non-virulent American mammalian trypanosome

BackgroundTrypanosoma rangeli is a non-virulent hemoflagellate protozoan parasite that infects mammals, including humans, in Central and South America. It is primarily transmitted through the bites of triatomine bugs and shares an overlapping geographical distribution with T. cruzi, as well as triatomine vectors and mammalian hosts, and various shared surface antigens. The life cycle of T. rangeli differs from those of other human-infecting trypanosomes, such as T. cruzi and T. brucei, and the molecular mechanisms underlying host-parasite and host-vector interactions are not well understood, demanding improved molecular and genomic resources. ResultsThe use of a hybrid approach to sequence and assemble the T. rangeli genome, complemented by transcriptomics and proteomics for functional gene annotation, led to the generation of the near-complete genome sequence of the parasite. Detailed intra- and inter-specific comparative genomics allowed analysis of polymorphisms, genome structure and improved resolution of genes coding for important surface molecules such as Mucins, TASV and GP63. ConclusionsThe improved T. rangeli genome assembly, combined with comparative genomics has yielded novel biological insights. These included the first description of a metalloprotease activity, attributed to specific GP63 genes that are absent in Leishmania species. In addition, a TASV gene family that is absent in T. cruzi was identified, which indicates a possible role in the T. rangeli infection process.

microbiology↗

bioRxiv2025

Fetal inflammatory signals regulate maternal investment in a pregnant marsupial

Marsupial pregnancy is strikingly short: placental attachment in the gray short-tailed opossum Monodelphis domestica lasts only two days. This brevity has been attributed to a maternal immune response to fetal contact which only eutherian mammals have evolved mechanisms to tolerate. The attachment period is characterized by a spike in inflammatory signaling, development of an expanded uterine capillary network, and exponential fetal growth. Several inflammatory cytokines, including interleukin-1A (IL-1A) and interleukin-6 (IL-6), are produced primarily by fetal cells. We hypothesized that placental cytokines function as solicitation signals that increase maternal investment. To test this, we treated pregnant opossums with inhibitors of IL-1 and IL-6 during the rapid growth phase. Inhibition of IL-1 and IL-6 signaling significantly increased average biomass per fetus (+12% and +10%), and as such these signals impose costs, rather than direct benefits, to intrauterine growth. However, uninhibited controls showed greater surviving litter sizes than IL-1-inhibited animals, suggesting that IL-1A promotes offspring survival. Single-cell transcriptomes reveal that maternal vascular endothelial cells, perivascular cells, and fibroblasts are the primary targets of fetal IL-1A, and maternal cells simultaneously upregulate antagonists IL1R2 and IL1RN, suggesting resistance to fetal signaling. Placental transcriptomics reveals that the cytokine surge is restricted to the final day of pregnancy when placental cells fuse to form syncytial knots, and that these cells produce additional vasomodulatory signals including a truncated isoform of VEGFA. Maternal cells, in contrast, increase production of functional antagonists IL1R2 and IL1RN, suggesting resistance to fetal signals. We propose that marsupials co-opted inflammatory signals to perform a novel function promoting fetal survival through maternal vascular remodeling.

evolutionary biology↗

bioRxiv2025

Mechanistic Insights into the Plasmodium Phosphatase UIS2 in eIF2α Dephosphorylation via Integrated Structure-Based Modeling

The development of novel antimalarial drugs requires the identification of parasite-specific vulnerabilities. Translation control, regulated by eIF2 dephosphorylation, is essential for Plasmodium development during infection. The parasite phosphatase UIS2 regulates this modification. However, the structural basis for UIS2 substrate recognition remains unknown. Here, we show that UIS2 is crucial for parasite development in both liver and blood stages. Its N-terminal and phosphatase domains each independently bind the eIF2 phosphoserine-59 loop through electrostatic interactions. Integrated structural modeling, using AlphaFold and molecular dynamics simulations, reveals a defined binding pocket within the phosphatase domain, with a geometry distinct from human PP1. This pocket contains six cooperative binding patches that use an electrostatic network to stabilize the phosphopeptide near the active site and contribute to substrate specificity. Metadynamics simulations show that the inhibitor Salubrinal competes with the phosphopeptide for binding to this pocket. Molecular docking and free energy perturbation analyses show that Salubrinal targets three of these binding patches through hydrophobic and hydrogen-bonding interactions, blocking substrate binding. These findings show the structural and energetic basis of eIF2 dephosphorylation by UIS2. They provide an integrated modeling approach for phosphatase-substrate interactions and a mechanistic rationale for selective inhibition of a parasite-specific translation regulator.

biophysics↗

bioRxiv2025

Identifying genes underlying parallel evolution of stromal resistance to placental and cancer invasion

Stromal regulation of cancer dissemination is now well recognized, however causal stromal genes and factors have yet not been identified. Placental invasion into endometrial stroma phenotypically is similar to cancer dissemination. There are also vast differences in the extent of placental invasion across mammals, with human pregnancies at the higher extreme end of invasiveness. We have previously demonstrated that epitheliochorial species, characterized by non-invasive placentation, have acquired stromal resistance to placental invasion, correlating with low cancer malignancy rates. Similarly, decidualization of human endometrial fibroblasts confers resistance to placental invasion. We hypothesized that both trajectories may convergently use similar pathways, using endometrial fibroblasts from 9 species to identify putative ELI-D1 genes underlying stromal vulnerability to invasion. ELI-D1 were negatively enriched in T1-T2 stage transition in many human cancers, typically preceding dissemination, bioinformatically validating their contribution to dissemination-preceding fibroblast activation in cancers. Finally, we have identified candidate transcriptional regulators underlying variation in ELI-D1 genes across eutherians, functionally showing that a key transcriptional regulator of ELI-D1 genes across species, Nr2f6, can regulate stromal resistance to invasion in human fibroblasts. Our comparative approach provides us with a putative, limited, gene-set linked to stromal vulnerability in human cancers, providing therapeutic opportunities to target cancer dissemination.

cancer biology↗

bioRxiv2025

Nanoprotrusion enlargement conducts cytocapsular tube elongation along the path of least resistance

Cancer metastasis is a major source of cancer lethality. Recently, we reported that the ATP-dependent calcium pump PMCA2 is enriched in cytocapsular membranes as biomarker of native malignant tumors. Cytocapsular tubes (CCTs) provide membrane-enclosed freeways for protected and bi-directional cancer metastasis in cytocapsular tumor network systems (CTNSs). It is obscure how CCTs initiate and elongate in heterogeneous human tissues and organs against diverse blocks of resistance. Here, we report that thin CCT nanoprotrusions (NPs) enlarge in directions of least resistance to grow into enlarged NPs. Subsequently, enlarged NPs develop into initial CCTs (ICCTs) followed by development into full CCTs. The full CCTs elongate in paths of least resistance over long distances, as observed in 34 kinds of human tissues and organs. Sideways CCT branching proceeds via a NP bifid format, which increases CCT numbers and expands 3D CCT networks in tissues. CCT regeneration additionally drives repeated cancer metastasis. CCT superstructures facilitate full cancer metastasis. This study demonstrated nanoprotrusion-conducted CCT elongation along the path of least resistance and branching morphogenesis in bifid branching style. The cytocapsular membrane system expansion mechanics of CCTs and CCT networks described here may open new avenues for native cancer research and CTNS-targeted effective cancer cure. (200 words) Significance statementThe recent identification of PMCA2 as a biomarker for malignant tumors, allows imaging very early native cancer growths on culture plates in vitro and in human bodies as revealed from snapshot images of numerous cancer biopsies in vivo. Aggressive cancer metastasis, cancer progression, repeated cancer relapse, limited cancer therapy outcomes, pan-cancer drug resistance, immune cell attack escape, and immunotherapy non-responsive "cold" tumors are unmet challenges in clinical cancer therapy. However, the cytocapsular tube (CCT) elongation mechanisms in human tissues/organs with heterogeneous resistances are still unclear. Here, we report that CCT nanoprotrusions (NPs) extend into enlarged NPs apparently towards tissue of least resistance and subsequently develop into initial CCTs. Intracytocapsular oncocells released cytocapsulasomes to fuse into the membranes of initial CCTs and increase cytocapsular membrane areas. This enables oncocells to push and deform initial CCT membranes and to generate new CCTs with new nanoprotrusion layers. Furthermore, CCT branching morphogenesis develops in a bifid format, significantly increasing CCT numbers and expanding 3D CCT networks in all kinds of human tissues. CCT superstructures promote complete cancer metastasis in AMCC complexes. Repeated CCT regeneration drives repeated cancer relapses. This study reveals the CCT elongation laws, and elucidates that CCT elongation and branching morphogenesis drives cytocapsular membrane protected cancer metastasis, and that repeated CCT regeneration promotes repeated tumor relapses in vivo.

cancer biology↗

bioRxiv2024

Genetic Characterization of the Cell Types of in Developing Feathers, and the Evolution of Feather Complexity

Feathers are the most complex and diverse epidermal appendages found in vertebrates. Their unique hierarchical organization and development is based on a diversity of cell types and morphologies. Despite being well characterized morphologically and extensive molecular developmental research focusing on candidate genes, little is known about the gene regulatory identities of these presumptive feather cell types. Here, we use single cell and single nuclear RNA sequencing with in situ hybridization to identify and characterize cells types in embryonic chicken feathers. We show that the distinct cell morphologies correspond to feather cell types with distinct gene expression profiles. We also describe a previously unidentified cell type, the basal barb ridge epithelium, which appears to play a role in signaling necessary for barb ridge differentiation and pulp cap production. We also analyze RNA velocity trajectories of developing feather cells, and find distinct developmental trajectories for epidermal cells that constitute the mature feather and those that function only in feather development. Finally, we produce an evolutionary tree of feather cell types based on transcription factor expression in order to test prior developmental hypotheses about feather evolution. Our tree is consistent with the developmental model of feather evolution, and sheds light on the influence of ancestral epidermal stratification on feather cell evolution. This transcriptomic approach to study feather cell types helps lay the ground work for understanding the developmental evolutionary complexity and diversity of feathers.

developmental biology↗

bioRxiv2024

Medial prefrontal cortical neurotransmitters reactive to relapse-promoting and relapse-suppressing cues in rats trained to self-administer cocaine or alcohol

Environmental cues conditioned to signal drug availability (S+) or omission (S-) activate specific neurons (neuronal ensembles/engram cells) within the medial prefrontal cortex (mPFC) to promote and suppress drug relapse in rats. However, the neurochemical source of such cue-specific activation remains unknown. In this study, we determined extracellular neurotransmitter fluctuations reactive to S+ vs. S- in the infralimbic (IL) and prelimbic (PL) cortices of male rats trained to lever-press for cocaine or alcohol self-administration. In cocaine- or alcohol-trained rats exposed to S+, no significant neurotransmitter fluctuations were observed in IL or PL. In cocaine-trained rats exposed to S-, glutamate, serotonin, taurine and adenosine were increased in PL but not in IL. In alcohol-trained rats exposed to S-, glutamate was increased, while dopamine and GABA were decreased, in IL but not in PL. Although S+ reactive neurotransmitters driving neuronal activation in mPFC remains to be elucidated, glutamate is likely the source of such activation by S- in rats trained to self-administer cocaine or alcohol. While drugs used for self-administration and cue-conditioning appear to dictate the type and anatomical specificity of S- evoked neurotransmission within mPFC, glutamate may serve as a common therapeutic target to mimic relapse-suppression by S- across cocaine and alcohol use disorders (CUD and AUD). In contrast, serotonin, taurine and adenosine may serve as the targets in CUD, while dopamine and GABA may serve as the targets in AUD.

neuroscience↗

bioRxiv2024

Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation

Protein language models trained on the masked language modeling objective learn to predict the identity of hidden amino acid residues within a sequence using the remaining observable sequence as context. They do so by embedding the residues into a high dimensional space that encapsulates the relevant contextual cues. These embedding vectors serve as an informative context-sensitive representation that not only aids with the defined training objective, but can also be used for other tasks by downstream models. We propose a scheme to use the embeddings of an unmasked sequence to estimate the corresponding masked probability vectors for all the positions in a single forward pass through the language model. This One Fell Swoop (OFS) approach allows us to efficiently estimate the pseudo-perplexity of the sequence, a measure of the models uncertainty in its predictions, that can also serve as a fitness estimate. We find that ESM2 OFS pseudo-perplexity performs nearly as well as the true pseudo-perplexity at fitness estimation, and more notably it defines a new state of the art on the ProteinGym Indels benchmark. The strong performance of the fitness measure prompted us to investigate if it could be used to detect the elevated stability reported in reconstructed ancestral sequences. We find that this measure ranks ancestral reconstructions as more fit than extant sequences. Finally, we show that the computational efficiency of the technique allows for the use of Monte Carlo methods that can rapidly explore functional sequence space.

bioinformatics↗

bioRxiv2024

Structural and mechanistic insights into Plasmodium eIF2alpha dephosphorylation by UIS2 during the erythrocytic stage

UIS2 is a promising therapeutic target for malaria due to its essential role in the transmission and infectivity of Plasmodium to the host hepatocytes. In Plasmodium, UIS2 acts as a phosphatase toward phosphorylated eIF2alpha at Ser59, regulating translation initiation. However, its role during the erythrocytic stage, which causes clinical symptoms, remains unclear, and its protein structure for elucidating the dephosphorylation mechanism is unavailable. In this study, we analyzed the Plasmodium phenotype screening database and found that UIS2-deficient Plasmodium fails to proliferate during the erythrocytic stages. Single-cell transcriptomic data from the Malaria Cell Atlas revealed UIS2 expression during both hepatic and erythrocytic stages, with significant upregulation in trophozoites and late schizonts, suggesting UIS2s essential role in erythrocytic stage development. Structural analyses using AlphaFold modeling demonstrated that the UIS2 phosphatase domain (UIS2-PD) shares homology with human purple acid phosphatase, featuring conserved catalytic site residues. We observed that the N-terminal domain of UIS2 interacts with the S1 domain loop of a phospho-mimic mutant (Ser59Asp) eIF2alpha via electrostatic interactions. This protein interaction is distal to the phosphatase domain, indicating a unique substrate recruitment mechanism distinct from mammalian serine/threonine phosphatase PP1. Additionally, we identified a negatively charged cavity in UIS2-PD capable of binding the Ser59-containing loop in eIF2alpha for substrate recognition. Molecular docking studies showed that the phosphatase inhibitor salubrinal binds to this negatively charged cavity, potentially obstructing enzyme-substrate interactions. These structural insights into UIS2 and its interaction with eIF2alpha provide promising avenues for developing novel antimalarial drugs. Significance StatementMalaria poses a significant global health challenge, particularly with rising resistance to artemisinin therapies. This study reveals the critical role of UIS2 in Plasmodium proliferation during the symptomatic blood stage through phenotype screening and single-cell transcriptomics. We characterized the catalytic site within UIS2-PD and discovered a surface cavity for recognizing phosphorylated eIF2alpha by UIS2-PD, which can be inhibited by small molecules. Our findings identify UIS2 as a promising target for new antimalarial drugs, addressing both blood-stage parasites to alleviate clinical symptoms and liver-stage parasites for prophylactic treatment. This dual targeting strategy could prevent malaria onset post-exposure and reduce the overall parasite burden. The protein interaction between UIS2 and eIF2alpha is chemically targetable, facilitating the development of effective UIS2 inhibitors.

biochemistry↗

bioRxiv2024

lncRNA ADEPTR loss-of-function elicits sex-specific behavioral and spine deficits

Activity-dependent changes in neuronal connections are fundamental to learning and long-term memory storage. However, the precise contribution of long noncoding RNAs (lncRNAs) to these modifications remains unclear. In this study, we assessed the role of the lncRNA ADEPTR, a cAMP-modulated lncRNA localized in dendrites, which is crucial for synapse morphology. By generating two different mouse models--one with a deletion of ADEPTR (L-ADEPTR) and one with a deletion of its protein interaction region (S-ADEPTR)--we investigated the sex-specific impacts of ADEPTR loss of function on learning, memory, dendritic arborization, and synapse morphology. Our behavioral analyses revealed a reduction in anxiety in adult male mice, while learning and memory remained unaffected in both models. Systematic evaluations of neuronal morphology across various developmental stages ([~]3-day-old postnatal neuronal cultures and postnatal 14- and 42-day-old male and female mice) uncovered substantial deficits in neuronal architecture in both S- and L-ADEPTR male and female neuronal cultures. At postnatal day 42, in contrast to their male counterparts, L-ADEPTR female mice exhibited a significant deficiency in thin spines. Additionally, we found that the expression of plasticity-related gene BDNF, and immediate early gene cFOS were enhanced in both the cortex and hippocampus of adult male and female S- and L-ADEPTR mice, suggesting the activation of a compensatory mechanism protecting against learning and memory deficits. Collectively, these observations underscore the sex-specific role of lncRNA ADEPTR in shaping neuronal morphology and anxiety behavior.

neuroscience↗

bioRxiv2024

Differences in polygenic associations with educational attainment between West and East Germany before and after reunification

Here we examine geographical and historical differences in polygenic associations with educational attainment in East and West Germany around reunification. We test this in n = 1902 25-85-year-olds from the German SOEP-G[ene] cohort. We leverage a DNA-based measure of genetic influence, a polygenic index calculated based on a previous genome-wide association study of educational attainment in individuals living in democratic countries. We find that polygenic associations with educational attainment were significantly stronger among East, but not West, Germans after but not before reunification. Negative control analyses of a polygenic index of height with educational attainment and height indicate that this gene-by-environemt interaction is specific to the educational domain. These findings suggest that the shift from an East German state-socialist to a free-market West German system increased the importance of genetic variants previously identified as important for education. One Sentence SummaryWe find that polygenic associations with educational attainment were significantly stronger among East, but not West, Germans after but not before reunification.

genetics↗

bioRxiv2023

FastProtein: An automated software for in silico proteomic analysis

BackgroundAlthough various tools provide proteomic information, each has its limitations regarding execution platforms, libraries, versions, and data output format. Therefore, integrating data analyses generated using different software programs is a manual process that can prolong the analysis time. ResultsThis paper presents FastProtein, a protein analysis pipeline tool developed in Java. This tool is user-friendly, easily installable, and provides important information regarding the subcellular location, transmembrane domains, signal peptide, molecular weight, isoelectric point, hydropathy, aromaticity, gene ontology, endoplasmic reticulum retention domains, and N- glycosylation domains of a protein. Furthermore, it helps determine the presence of glycosylphosphatidylinositol and obtain annotation information using InterProScan, PANTHER, PFam, and alignment-based annotation searches. Additionally, the software outputs a protein dataset with evidence of membrane localization. ConclusionsThe proposed tool provides the scientific community with an easy and user-friendly computational tool for proteomics data analysis. The tool is applicable to both small datasets and proteome-wide studies. It can be used in either the command line interface mode or through a web interface installed on a local server or via the BioLib web interface (http://biolib.com/UFSC/FastProtein). FastProtein also accelerates proteomics analysis routines by generating multiple results in a one-step run. The software is open-source and freely available. Installation and execution instructions, as well as the source code and test files generated for tool validation, are provided at https://github.com/bioinformatics-ufsc/FastProtein.

bioinformatics↗

bioRxiv2023

Computational inference of eIF4F complex function and structure in human cancers

The canonical eukaryotic initiation factor 4F (eIF4F) complex, composed of eIF4G1, eIF4A1, and the cap-binding protein eIF4E, plays a crucial role in cap-dependent translation initiation in eukaryotic cells (1). However, cap-independent initiation can occur through internal ribosomal entry sites (IRESs), involving only eIF4G1 and eIF4A1 present, which is considered to be a complementary process to cap-dependent initiation in tumors under stress conditions (2). The selection and molecular mechanism of specific translation initiation in human cancers remains poorly understood. Thus, we analyzed gene copy number variations (CNVs) in TCGA tumor samples and found frequent amplification of genes involved in translation initiation. Copy number gains in EIF4G1 and EIF3E frequently co-occur across human cancers. Additionally, EIF4G1 expression strongly correlates with genes from cancer cell survival pathways including cell cycle and lipogenesis, in tumors with EIF4G1 amplification or duplication. Furthermore, we revealed that eIF4G1 and eIF4A1 protein levels strongly co-regulate with ribosomal subunits, eIF2, and eIF3 complexes, while eIF4E co-regulates with 4E-BP1, ubiquitination, and ESCRT proteins. Using Alphafold predictions, we modeled the eIF4F structure with and without eIF4G1-eIF4E binding. The modeling for cap-dependent initiation suggests that eIF4G1 interacts with eIF4E through its N-terminal eIF4E-binding domain, bringing eIF4E near the eIF4A1 mRNA binding cavity and closing the cavity with both eIF4G1 HEAT-2 domain and eIF4E. In the cap-independent mechanism, -helix5 of eIF4G1 HEAT-2 domain instead directly interacts with the eIF4A1 N-terminal domain to close the mRNA binding cavity without eIF4E involvement, resulting in a stronger interaction between eIF4G1 and eIF4A1. Significance StatementTranslation initiation is primarily governed by eIF4F, employing a "cap-dependent" mechanism, but eIF4F dysregulation may lead to a "cap-independent" mechanism in stressed cancer cells. We found frequent amplification of translation initiation genes, and co-occurring copy number gains of EIF4G1 and EIF3E genes in human cancers. EIF4G1 amplification or duplication may be positively selected for its beneficial impact on the overexpression of cancer survival genes. The co-regulation of eIF4G1 and eIF4A1, distinctly from eIF4E, reveals eIF4F dysregulation favoring cap-independent initiation. Alphafold predicts changes in the eIF4F complex assembly to accommodate both initiation mechanisms. These findings have significant implications for evaluating cancer cell vulnerability to eIF4F inhibition and developing treatments that target cancer cells with dependency on the translation initiation mechanism.

biochemistry↗

bioRxiv2023

Cytocapsular oncocells drive membrane-sheltered cancer progression

Cancer is a leading source of human lethality but current therapies have had limited efficacy in many cancers, which highlights an unmet need to assess the underlying mechanisms that govern cancer progression in vivo. Here we show that, upon malignant transformation, aggressive oncocells generate extracellular membranous compartments, cytocapsulas or cytocapsular tubes (CCTs), to enclose oncocells and engender cytocapsular oncocells in vivo. Cytocapsular oncocells are universally present in solid cancers and appear in hematologic cancers in the immune organs. Networks of cytocapsular tubes provide membrane-enclosed freeways for protected cancer metastasis. CCT networks interconnect cytocapsular tumors creating cytocapsular tumor network systems. Our findings suggest that cytocapsular oncocells drive membrane-encompassed cancer progression. Thus, interconnected cytocapsular oncocells, CCT networks and cytocapsular tumor network systems coordinate cancer progression in the integrated cytocapsular membrane systems.

cancer biology↗

bioRxiv2023

Evolutionary innovations in germline biology of placental mammals revealed by transcriptomics of first wave spermatogenesis in opossum

Mammalian spermatogenesis is a deeply conserved developmental program that is essential for fitness. Paradoxically, spermatogenic development also allows rapid divergence in gene expression and is thought to be a source of evolutionary novelty and gene birth. How mammalian spermatogenic cells protect a conserved developmental program while enabling exceptionally rapid divergence in gene expression and function is unknown. Here, we comprehensively profile the spermatogenic gene expression program in grey short-tailed opossum (Monodelphis domestica, a model marsupial) and compare it to equivalent data from the mouse (Mus musculus, a model placental mammal) to discover contrasting forces underlying the unique evolutionary dynamics of gene expression during mammalian spermatogenesis. For the first time, we describe the timing of the first wave of opossum spermatogenesis, and we combine bulk transcriptomic data from first-wave juvenile testes with single-cell transcriptomic data from adult testes to define conserved and divergent gene expression programs across the placental-marsupial split. We substantiate and extend our findings using genome-wide chromatin and multi-species transcriptome data and identify three classes of genes with different evolutionary trajectories: a deeply conserved central gene regulatory program governing spermatogenic progression; a separate class of spermatogenic genes exhibiting dynamic expression across placental mammals; and a third set of genes with evidence for directional selection in the placental mammal ancestor and constraint on expression levels within the placental mammalian lineage, representing placental innovations in germline gene expression and including biologically critical modules such as the DNA recombination and repair machinery.

genomics↗

bioRxiv2023

VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules

Identifying potent lead molecules for specific targets remains a major bottleneck in drug discovery. As structural information about proteins becomes increasingly available, ultra-large virtual screenings (ULVSs) which computationally evaluate billions of molecules offer a powerful way to accelerate early-stage drug discovery. Here, we introduce AdaptiveFlow, an open-source platform designed to make ULVSs more accessible, scalable, and efficient. AdaptiveFlow provides free access to a screening-ready version of the Enamine REAL Space (1), the largest library of ready-to-dock, drug-like molecules, containing 69 billion compounds that we prepared using the ligand preparation module of the platform. A key innovation of the platform is its use of a multi-dimensional grid of molecular properties, which helps researchers explore and prioritize chemical space more effectively and reduce the computational costs by a factor of approximately 1000. This grid forms the basis of a new method for identifying promising regions of chemical space, enabling systematic exploration and prioritization of compound libraries. An optional active learning component can further accelerate this process by adaptively steering the search toward molecules most likely to bind a given target. To support a broad range of applications, AdaptiveFlow is compatible with over 1,500 docking protocols. The platform achieves near-linear scaling on up to 5.6 million CPUs in the AWS Cloud, setting a new benchmark for large-scale cloud computing in drug discovery. Using this approach, we identified nanomolar inhibitors of two disease-relevant targets: ferroptosis suppressor protein 1 (FSP1) and poly(ADP-ribose) polymerase 1 (PARP-1) (2, 3). By leveraging newly solved crystal structures of FSP1 in complex with NAD+, FAD, and coenzyme Q1, we validated these hits experimentally and determined the co-crystal structures of FSP1 bound to small-molecule inhibitors, enabling insights into inhibitor binding mechanisms previously unknown. With its high scalability, flexibility, and open accessibility, AdaptiveFlow offers a powerful new resource for discovering and optimizing drug candidates at an unprecedented scale and speed.

bioinformatics↗