bluuebunny/crossref_metadata_2025 huggingface dataset:
Loss of PARP7 increases type I interferon signalling and prevents pancreatic tumour growth by enhancing immune cell infiltration
Authors: Kannen Vinicius , Rasmussen Marit , Das Siddhartha , Giuliana Paolo , Izzati Fauzia N. , Choksi Hani , Erlingsson Linnea A. M. , Olafsen Ninni E. , Cappello Paola , Teino Indrek , Maimets Toivo , Jaudzems Kristaps , Gulbinas Antanas , Dambrauskas Zilvinas , Edgar Landon , Grant Denis M. , Matthews Jason
Published: September 2024

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal forms of cancer, and despite low incidence rates, it remains the sixth leading cause of cancer related deaths worldwide. Immunotherapy, which aims to enhance the immune system’s ability to recognize and eliminate cancer cells, has emerged as a promising approach in the battle against PDAC. PARP7, a mono-ADP-ribosyltransferase, is a negative regulator of the type I interferon (IFN-I) pathway and has been reported to reduce anti-tumour immunity. Using murine pancreatic cancer cells, we found that loss ofParp7elevated the levels of interferon stimulated gene factor 3 (ISGF3) and its downstream target genes, even in the absence of STING. Cancer cells deficient inParp7produced smaller tumours when injected into immunocompetent mice. Transcriptomic analyses revealed that tumours knocked out forParp7(Parp7KO) had increased expression of genes involved in immunoregulatory interactions and interferon signalling pathways. Characterization of tumour infiltrating leukocyte (TIL) populations showed that Parp7KOtumours had higher proportions of natural killer cells, CD8 T cells and a lower proportion of anti-inflammatory macrophages (M2). The overall TIL profile of Parp7KOtumours was suggestive of a less suppressive microenvironment. Our data show that loss ofParp7reduces PDAC tumour growth by increasing the infiltration of immune cells and enhancing anti-tumour immunity. These findings provide support to pursue PARP7 as a therapeutic target for PDAC.
BioPAX-Explorer: a Python Object-Oriented framework for overcoming the complexity of querying biological networks
Authors: Moreews François , Bougaud Jean-Baptiste , Becker Emmanuelle , Gondret Florence , Dameron Olivier
Published: September 2024

Motivation

Biological Pathway Exchange (BioPAX) is a standard language, represented in OWL, that aims to enable the integration, exchange, visualization and analysis of biological pathway data. While public databanks increasingly provide datasets in BioPAX format, their use remains below potential. Users may encounter challenges in harnessing the data due to the BioPAX intricately detailed underlying model. Moreover, extracting data demands specific technical skills, posing a barrier for many potential users.

Results

To address these obstacles, we developped BioPAX-Explorer. This toolis designed to facilitate the adoption and usage of BioPAX for extracting data or build algorithms and models, within the Python community. BioPAX-Explorer is a Python package that provides an object-oriented data model automatically generated from the BioPAX OWL specification. Moreover, it offers expressive query capabilities that shield users from BioPAX inner complexity. BioPAX-Explorer supports dataset building features, validation facilities and pre-build queries. It simplifies the extraction and processing of data from BioPAX sources by automatically generating SPARQL queries. BioPAX-Explorer also offers a user-friendly interface for Python users, allowing exhaustive exploration of large datasets through features such as memory-efficient query execution, entity-oriented queries without the need for SPARQL knowledge. It also allows to learn and reuse complex SPARQL queries for biological network analysis. Additionally, BioPAX-Explorer can accelerate the development of Python-based network analysis software, since it generates graph data structures from BioPAX queries and facilitates the creation of transparent, reproducible workflows based on the BioPAX OWL standard.

Availability and implementation

BioPAX-Explorer is freely available. We provide the source code, documentation, installation instructions and a Jupyter notebook with tutorial athttps://fjrmoreews.github.io/biopax-explorer/
A CYCLIC PEPTIDE TARGETS GLIOBLASTOMA BY BINDING TO ABERRANTLY EXPOSED SNAP25
Authors: Arias Alberto G , Tovar-Martinez Laura , Asciutto Eliana K , Mann Aman , Posnograjeva Kristina , Simon Gracia Lorena , Royo Miriam , Haugas Maarja , Teesalu Tambet , Smulski Cristian , Ruoslahti Erkki , Scodeller Pablo
Published: September 2024

Disease-specific changes in tumors and other diseased tissues are an important target of research because they provide clues on the pathophysiology of the disease as well as uncovering potentially useful markers for diagnosis and treatment. Here, we report a new cyclic peptide, CESPLLSEC (CES), that specifically accumulated (homed) in intracranial U87MG and the WT-GBM model of glioblastoma from intravenous (IV) injection, associating with the vasculature. Affinity chromatography of U87MG tumor extracts on insolubilized CES peptide identified Synaptosomal Associated Protein 25 (SNAP25) as a candidate target molecule (receptor) for CES. Several results supported the identification of SNAP25 as the CES receptor. IV-injected FAM-CES colocalized with SNAP25 in the tumors, and direct binding studies showed specific CES peptide binding to recombinant human SNAP25. A CES peptide-drug conjugate designed for photodynamic therapy showed selective cytotoxicity to SNAP25+ glioblastoma cell lines. Specific accumulation of systemically injected anti-SNAP25 antibody in U87MG glioblastoma, and labeling of intact U87MG cells with anti-SNAP in flow cytometry showed that SNAP25 is available from the circulation but not in normal tissues and that it is present at the cell surface. Using an array of ECM proteins and surface plasmon resonance revealed that SNAP25 binds moderately to collagen V and strongly to collagen VI. Modeling studies suggested that CES and collagen VI compete for the same binding site on SNAP25. Our results introduce CES as a valuable targeting peptide for drug delivery, and its receptor SNAP25 as a possible molecular marker of interest for glioblastoma.
Independent derivations of the axis of arrhythmia for predicting drug-induced torsades de pointes
Authors: Heitmann Stewart , Vandenberg Jamie I , Hill Adam P
Published: September 2024

Torsades de pointes is a potentially lethal ventricular arrhythmia that may be caused by many classes of drugs. The likelihood of arrhythmia depends upon the particular combination of cardiac ion-channels that the drug targets. The risk for a given drug can be measured against the axis of arrhythmia, which is a conceptual line in the parameter space of ventricular cardiomyocyte electrophysiology. The axis describes the most potent combination of ion-channel blocks that is theoretically possible. It thus serves as a convenient yardstick for quantifying the pro-arrhythmic risk of novel drugs from their channel-blocking profiles. To date, the axis of arrhythmia has only been derived from biophysical computer simulations. Here, we derive the axis directly from the response profiles of selected ion-channels to known drugs (n=109). The new method provides an independent line of evidence for estimating the axis of arrhythmia. Using step-wise reduction, the two methods were found to converge to identical estimates of the axis in two ion-currents(ICaLandIKr). The resulting axis predicted the pro-arrhythmic risk of the test drugs with 89.9% to 91.7% accuracy, depending on the dose at which the drug was assessed. The axis of arrhythmia offers a practical method for predicting the pro-arrhythmic risk of novel drugs without the need for drug-specific computer simulations. It is the only metric of pro-arrhythmic risk that has been derived from both a biophysical model and a purely statistical model. It thus combines the benefits of biophysical interpretation and computational efficiency in assessing the torsadogenic risk of new drugs prior to clinical trials.

Significance Statement

Many classes of drugs can cause lethal cardiac arrhythmias by blocking ion-channels that are needed by heart cells for normal rhythm. International safety guidelines thus require all new drugs be tested in animal hearts or cell cultures prior to undertaking clinical trials in humans. Computer models offer an ethical alternative for drug testing that is gaining acceptance in the safety pharmacology community. However, the current corpus of models are usually too complex to apply outside of specialist computing laboratories. We recently proposed a new approach that eliminates the need for drug-specific computer simulations by using a large one-off computer simulation to identify the most pro-arrhythmic drug that is theoretically possible. Thereafter, that hypothetical drug can be used to assess the pro-arrhythmic risk of real drugs using only pen-and-paper calculations. In that study, the hypothetical drug was described by theaxis of arrhythmiain the cardiac cell model. In the present study, we propose an alternative method for deriving the axis of arrhythmia directly from drug datasets. The two derivations are independent, yet they arrive at the same result. Together, they provide converging lines of evidence in support of this new approach to drug testing in safety pharmacology.
UnifiedGreatMod: A New Holistic Modeling Paradigm for Studying Biological Systems on a Complete and Harmonious Scale
Authors: Aucello Riccardo , Pernice Simone , Tortarolo Dora , Calogero Raffaele A. , Herrera-Rincon Celia , Ronchi Giulia , Geuna Stefano , Cordero Francesca , Lió Pietro , Beccuti Marco
Published: September 2024

Motivation

Computational models are crucial for addressing critical questions about systems evolution and deciphering system connections. The pivotal feature of making this concept recognisable from the biological and clinical community is the possibility of quickly inspecting the whole system, bearing in mind the different granularity levels of its components. This holistic view of system behaviour expands the evolution study by identifying the heterogeneous behaviours applicable, for example, to the cancer evolution study.

Results

To address this aspect, we propose a new modelling paradigm, UnifiedGreatMod, which allows modellers to integrate fine-grained and coarse-grained biological information into a unique model. It allows for functional studies, in which the understanding of the system’s multi-level stable condition and the system’s fluctuating condition are combined to investigate the functional dependencies among the biological entities in the system under study. This is achieved thanks to the hybridisation of two analysis approaches that capture a system’s different granularity levels. The proposed paradigm was then implemented into the open-source, general modelling framework GreatMod, in which a graphical meta-formalism is exploited to simplify the model creation phase and R languages to define user-defined analysis workflows. The proposal’s effectiveness was demonstrated by mechanistically simulating the metabolic output ofEcherichia coliunder environmental nutrient perturbations and integrating a gene expression dataset. Additionally, the UnifiedGreatMod was used to examine the responses of luminal epithelial cells toClostridium difficileinfection.
Nucleus Pulposus Cell Network Modelling in the Intervertebral Disc
Authors: Tseranidou Sofia , Segarra-Queralt Maria , Chemorion Francis Kiptengwer , Le Maitre Christine , Piñero Janet , Noailly Jérôme
Published: September 2024

Intervertebral disc degeneration (IDD) arises from an intricate imbalance between the anabolic and catabolic processes governing the extracellular matrix (ECM) within the disc. Biochemical processes are complex, redundant and feedback-looped, thus improved integration of knowledge is needed. To address this, a literature-based regulatory network model (RNM) for nucleus pulposus cells (NPC) is proposed, representing the normal state of the intervertebral disc (IVD) cells, in which proteins are represented by nodes that interact with each other through activation and/or inhibition edges. This model includes 32 different proteins and 150 edges by incorporating critical biochemical interactions in IVD regulation, testedin vivoorin vitroin human and animal NPC, alongside non-tissue-specific protein-protein interactions. We used the network to calculate the dynamic regulation of each node through a semi-quantitative method. The basal steady state successfully represented the activity of a normal NPC, and the model was assessed through the published literature, by replicating two independent experimental studies in human normal NPC. Pro-catabolic or pro-anabolic shifts of the network activated by nodal perturbations could be predicted. Sensitivity analysis underscored the significant influence of transforming growth factor beta (TGF-β) and interleukin-1 receptor antagonist (IL-1Ra) on the regulation of structural proteins and degrading enzymes within the system. Given the ongoing challenge of elucidating the mechanisms that drive ECM degradation in IDD, this unique IVD RNM holds promise as a tool for exploring and predicting IDD progression, shedding light on IVD phenotypes and guiding experimental research efforts.
A Single-Cell Network Approach to Decode Metabolic Regulation in Gynecologic and Breast Cancers
Authors: Srivastava Akansha , Vinod P K
Published: September 2024

Cancer metabolism is characterized by significant heterogeneity, presenting challenges for treatment efficacy and patient outcomes. Understanding this heterogeneity and its regulatory mechanisms at single-cell resolution is crucial for developing personalized therapeutic strategies. In this study, we employed a single-cell network approach to characterize malignant heterogeneity in gynecologic and breast cancers, focusing on the transcriptional regulatory mechanisms driving metabolic alterations. By leveraging single-cell RNA sequencing (scRNA-seq) data, we assessed the metabolic pathway activities and inferred cancer-specific protein-protein interactomes (PPI) and gene regulatory networks (GRNs). We explored the crosstalk between these networks to identify key alterations in metabolic regulation. Clustering cells by metabolic pathways revealed tumor heterogeneity across cancers, highlighting variations in oxidative phosphorylation, glycolysis, cholesterol, fatty acid, hormone, amino acid, and redox metabolism. Our analysis identified metabolic modules associated with these pathways, along with their key transcriptional regulators. Notably, transcription factors related to ER stress, immune response, and cell proliferation, along with hypoxia-inducible factor and sterol regulatory element-binding proteins were found to drive metabolic reprogramming. These findings provide new insights into the complex interplay between metabolic rewiring and transcriptional regulation in gynecologic and breast cancers, offering potential avenues for targeted therapeutic strategies in precision oncology. Furthermore, this pipeline for dissecting coregulatory metabolic networks can be broadly applied to decipher metabolic regulation in any disease at single-cell resolution.
Phytochromes Enable Social Behavior in Marine Diatoms
Authors: Font-Muñoz Joan S. , Jaubert Marianne , Sourisseau Marc , Tuval Idan , Bailleul Benjamin , Duchêne Carole , Basterretxea Gotzon , Falciatore Angela
Published: September 2024

The phytochrome superfamily, a group of proteins that enable some organisms to detect changes in light intensity and quality, is widespread in terrestrial and marine microbes, fungi, algae, and plants. In terrestrial plants, these photosensory receptors monitor variations in the light environment by sensing red (R) and far-red (FR) regions of the spectrum and trigger important developmental, metabolic, and physiological responses. However, the role of these photosensors in marine microbes, living in environments where, due to absorption of water moleculesRandFRradiation does not penetrate beyond the upper few meters, remains controversial. Here, we investigate the role of phytochromes in light perception of the marine diatomPhaeodactylum tricornutumand their involvement in light-driven collective behavior. We perform experiments comparing the social conduct of wild-type and phytochrome knock-out strains to different light wavelengths. Our results show that cell movements become synchronized in a coordinated wobbling dance upon activation of their phytochromes by blue or far-red light, therefore, demonstrating the key role of phytochrome in light-mediated diatom collective behaviour. Furthermore, our experiments suggest that the observed phytochrome-mediated concerted dance implies a form of intercell communication, proposedly mediated by variable R/FR autofluorescence emission in the frequency range of diatom wobbling movements. Our findings provide new insights into communication pathways in aquatic microorganisms and emphasize the importance of social conduct in the sea at all ecological levels.
Natural killer cell function is regulated by TGF-β signaling in pregnancy and tumor progression
Authors: Yalin Adam , Wang Shuang-Yin , Landsberger Tomer , Gamliel Moriya , Elefant Naama , Kotzur Rebecca , Goldman-Wohl Debra , David Eyal , Molgora Martina , Bhattarai Bishan , Cella Marina , Meir-Salame Tomer , Gilad Ronit , Abdelkader Rana , Shveiky David , Yagel Simcha , Zuk Or , Colonna Marco , Mandelboim Ofer , Amit Ido
Published: September 2024

The immune compartment of the maternal-fetal interface must balance between supporting maternal-fetal interactions and maintaining maternal tolerance. Despite recent advances, the cellular and molecular regulators that drive maternal immune cell remodeling remain largely unknown. Using index and transcriptional single-cell sorting, we comprehensively characterized the immune compartment dynamics in the maternal-fetal interface of both human and mouse and charted the markers and functional pathways associated with these cells. Comparing immune signatures in decidua and tumors of human and mice, we identify conserved gene modules that are activated in natural killer (NK) cells of both compartments, including TFG-β signaling. Genetic ablation and antibody blockade of the TGF-β pathway in NK cells resulted in enhanced anti-tumor immunity.
Bimodal Specificity of TF-DNA Recognition in Embryonic Stem Cells
Authors: Povolotskii Michael , Yehezkehely Maor , Ram Oren , Lukatsky David B.
Published: September 2024

Transcription factors (TFs) bind genomic DNA regulating gene expression and developmental programs in embryonic stem cells (ESCs). Even though comprehensive genome-wide molecular maps for TF-DNA binding are experimentally available for key pluripotency-associated TFs, the understanding of molecular design principles responsible for TF-DNA recognition remains incomplete. Here, we show that binding preferences of key pluripotency TFs, such as Pou5f1 (Oct4), Smad1, Otx2, Srf, and Nanog, exhibit bimodality in the local GC-content distribution. Sequence-dependent binding specificity of these TFs is distributed across three major contributions. First, local GC-content is dominant in high-GC-content regions. Second, recognition of specifick-mers is predominant in low-GC-content regions. Third, short tandem repeats (STRs) are highly predictive in both low- and high-GC-content regions. In sharp contrast, the binding preferences of c-Myc are exclusively dominated by local GC-content and STRs in high-GC-content genomic regions. We demonstrate that the transition in the TF-DNA binding landscape upon ESC differentiation is solely regulated by the concentration of c-Myc, which forms a bivalent c-Myc-Max heterotetramer upon promoter binding, competing with key pluripotency factors such as Smad1. Finally, a direct interaction between c-Myc and key pluripotency factors is not required to achieve this transition.

Graphical abstract
TSTA: Thread and SIMD-Based Trapezoidal Pairwise/Multiple Sequence Alignment Method
Authors: Zong Peiyu , Deng Wenpeng , Liu Jian , Ruan Jue
Published: September 2024

Abstracts

The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method is known to be highly time-consuming. The proposed TSTA algorithm leverages both vector-level and thread-level parallelism to accelerate pairwise and multiple sequence alignments.

Availability & Implementation

Source code are available athttps://github.com/bxskdh/TSTA.
Quantitative analysis of non-histone lysine methylation sites and lysine demethylases in breast cancer cell lines
Authors: Berryhill Christine A. , Evans Taylor N. , Doud Emma H. , Smith-Kinnaman Whitney R. , Hanquier Jocelyne N. , Mosley Amber L. , Cornett Evan M.
Published: September 2024

Growing evidence shows that lysine methylation is a widespread protein post-translational modification that regulates protein function on histone and non-histone proteins. Numerous studies have demonstrated that dysregulation of lysine methylation mediators contributes to cancer growth and chemotherapeutic resistance. While changes in histone methylation are well documented with extensive analytical techniques available, there is a lack of high-throughput methods to reproducibly quantify changes in the abundances of the mediators of lysine methylation and non-histone lysine methylation (Kme) simultaneously across multiple samples. Recent studies by our group and others have demonstrated that antibody enrichment is not required to detect lysine methylation, prompting us to investigate the use of Tandem Mass Tag (TMT) labeling for global Kme quantification sans antibody enrichment in four different breast cancer cell lines (MCF-7, MDA-MB-231, HCC1806, and MCF10A). To improve the quantification of KDMs, we incorporated a lysine demethylase (KDM) isobaric trigger channel, which enabled 96% of all KDMs to be quantified while simultaneously quantifying 326 Kme sites. Overall, 142 differentially abundant Kme sites and eight differentially abundant KDMs were identified between the four cell lines, revealing cell line-specific patterning.
Polymeric Lysosomal-Targeting Chimeras: Extracellular Targeted Protein Degradation Without Co-opting Lysosome-Targeting Receptors
Authors: Lu Ryan Hung-Hsun , Krishna Jithu , Alp Yasin , Thayumanavan S.
Published: September 2024

Extracellular targeted protein degradation (eTPD) is an emerging modality to regulate protein levels without genomic interruption. Current strategies co-opt lysosome-targeting receptors (LTRs) that are ubiquitously present in most cells, offering a high success rate of eTPD across cell types and tissues. Opening up the binding complementarity requirement from LTRs to any overexpressed cell surface receptor offers to endow eTPD platforms with new cellular targeting capabilities. Here, we report polymeric lysosome-targeting chimeras (PolyTACs), a polymer-antibody conjugate based platform for the targeted degradation of membrane-bound and soluble proteins without the need for involving LTRs. Mechanistic investigations suggest a non-classical uptake pathway that is attributed to the membrane tension caused by the multivalent interaction between the PolyTACs and the overexpressed functionalities on the cell surface. The utility of PolyTACs in eTPD has been demonstrated with three therapeutically relevant membrane proteins. Additionally, the same design principle has also been leveraged to bind and drag soluble extracellular proteins into the lysosome. The design and fabrication simplicity, non-reliance on LTRs, and tissue-targeting capabilities open up new avenues for eTPD in many disease-specific applications.
MutLγ enforces meiotic crossovers inArabidopsis thaliana
Authors: Durand Stéphanie , Lian Qichao , Solier Victor , Fernandes Joiselle Blanche , Mercier Raphael
Published: September 2024

During meiosis, each chromosome pair experiences at least one crossover (CO), which directs their balanced segregation in addition to shuffling genetic information. COs tend to be away from each other, a phenomenon known as CO interference. The main biochemical pathway for CO formation, which is conserved in distant eukaryotes, involves the ZMM proteins together with the MLH1-MLH3 complex (MutLγ). Here, we aim to clarify the role of MutLγ in CO formation inArabidopsis thaliana. We show that AtMutLγ is partially dispensable for ZMM-dependant CO formation. HEI10 large foci - that mark CO sites in wild-type-form at a normal level inmlh1andmlh3mutants, but are inefficiently maturated into COs. Mutating theMUS81nuclease in eithermlh1ormlh3leads to chromosome fragmentation, which is suppressed by further mutating thezmm msh5. This suggests that in the absence of MutLγ, recombination intermediates produced by ZMMs are resolved by MUS81, which does not ensure CO formation. Finally, CO interference is not affected inmlh1, which is compatible with a random sub-sampling of normally patterned CO sites. We conclude that AtMutLγ imposes designated recombination intermediates to be resolved exclusively as COs, supporting the view that MutLγ asymmetrically resolves double-Holliday junctions, yielding COs.
Reversal of elevatedGli3in Autosomal Recessive Polycystic Kidney Disease does not alter cystogenesis
Authors: Russell Lauren G , Kolatsi-Joannou Maria , Wilson Laura , Chandler Jennifer C , Tejedor Nuria Perretta , Stagg Georgie , Price Karen L , Rowan Christopher J , Crompton Tessa , Rosenblum Norman D , Winyard Paul JD , Long David A
Published: September 2024

Polycystic kidney diseases (PKD) are genetic disorders characterised by the formation of fluid-filled cysts, which disrupt kidney architecture and function. Autosomal recessive PKD (ARPKD) is a rare form of PKD, caused by mutations inPKHD1,and clinically more severe than the more common autosomal dominant PKD (ADPKD). Prior studies have implicated the ciliary-located Hedgehog (Hh) pathway in ADPKD, with increased levels of Hh components in experimental ADPKD models, and reduced cystogenesis following pharmacological Hh inhibition. In contrast, the role of the Hh pathway in ARPKD is poorly understood. We hypothesised that Hh pathway activity would be elevated during ARPKD pathogenesis, and its modulation may inhibit cystogenesis, akin to prior findings in ADPKD. To test this, we utilisedCpkmice, a model which replicates the pathophysiology of ARPKD, and generated a human cellular ARPKD 3-dimensional cystogenesis model by mutatingPKHD1in human collecting duct cells through CRISPR-Cas9 technology. We found significantly elevated levels of the Hh transcriptional effectorGli3in theCpkmouse, a finding replicated in our human cellular ARPKD model. In theCpkmouse, we also observed an increase in total GLI3 and GLI3 repressor protein levels. However, reduction of increasedGli3levels via genetic deletion in theCpkmouse did not affect cyst formation. Similarly, loweringGLI3transcript to wildtype levels, did not influence cyst size in our human cellular ARPKD model. Collectively, these data show that elevated Gli3 does not modulate cyst progression in the context of ARPKD, highlighting the complexity of the Hh pathway in PKD.

New and Noteworthy

The role of the Hedgehog pathway in autosomal recessive polycystic kidney disease (ARPKD) is poorly understood. Here, we describe elevated levels ofGli3,the Hedgehog transcriptional effector, in murine and human ARPKD models. However, reversal of the increase inGli3did not significantly affect cystogenesis in a human cell model of ARPKD or disease progression in a mouse model which replicates ARPKD pathophysiology. Collectively, our data indicates that Gli3 does not modulate ARPKD progression.
Pharmacological SOS1 inhibitor BI-3406 demonstratesin vivoanti-tumor activity comparable to SOS1 genetic ablation in KRAS mutant tumors
Authors: Baltanas Fernando C. , Kramer-Drauberg Maximilian , Garcia-Navas Rósula , Patrucco Enrico , Petrini Ettore , Arnhof Heribert , Juan Andrea Olarte-San , Rodríguez-Ramos Pablo , Borrajo Javier , Calzada Nuria , Castellano Esther , Mair Barbara , Kostyrko Kaja , Hofmann Marco H. , Ambrogio Chiara , Santos Eugenio
Published: September 2024

Resistance to KRASmutinhibitors frequently arises, warranting further searches for anti-RAS cancer therapies. We evaluated the tolerability and efficacy of SOS1 pharmacological inhibition in comparison to genetic ablation in different KRAS-dependent tumor settings. Contrary to the rapid lethality caused by SOS1 genetic ablation in SOS2KO mice, SOS1 pharmacological inhibition by its specific inhibitor BI-3406 did not significantly affect animal weight/viability nor cause noteworthy systemic toxicity. In BI-3406-treated KRASmutMEFs, we observed significantly reduced RAS-GTP levels and RAS downstream signaling, as well as decreased tumor burden and slower disease progression resulting from tumor-intrinsic and extrinsic therapeutic drug effects. In vivo analyses of KRASG12Dallografts in immunocompromised mice and KRASG12D-driven lung adenocarcinomas in immunocompetent mice showed that systemic BI-3406 treatment impaired tumor growth and downmodulated components of the tumor microenvironment comparably to the KRASG12Dinhibitor MRTX1133. Markedly stronger synergistic antitumor effects were observed upon concomitant BI-3406+MRTX113 treatment, confirming SOS1 as an actionable therapy target in RAS-dependent cancers.
IL15/IL15Rα complex induces an anti-tumor immune response following radiation therapy only in the absence of Tregs and fails to induce expansion of progenitor TCF1+ CD8 T cells
Authors: Piper Miles , Gadwa Jacob , Hodgson Chloe , Knitz Michael , Yee Elliott , Zhu Yuwen , Larson Keira Y. , Klein Christian , Amann Maria , Saviola Anthony , Karam Sana D
Published: September 2024

Background

This work seeks to understand whether IL15-incorporating treatments improve response to radiotherapy and uncover mechanistic rationale for overcoming resistance to IL15 agonism using novel therapeutic combinations.

Experimental Design

Orthotopic tumor models of PDAC were used to determine response to treatment. IL15-/- and Rag1-/- mouse models were employed to determine dependence on IL15 and CTLs, respectively. Flow cytometry was used to assess immune cell frequency and activation state. Phospho-proteomic analyses were used to characterize intracellular signaling pathways.

Results

We show that the combination of radiation therapy (RT) and an IL15/IL15Ra fusion complex (denoted IL15c) fails to confer anti-tumor efficacy; however, a CD8-driven anti-tumor immune response is elicited with the concurrent administration of an aCD25 Treg-depleting antibody. Using IL15-/- and Rag1-/- mice, we demonstrate that response to RT + IL15c + aCD25 is dependent on both IL15 and CTLs. Furthermore, despite an equivalent survival benefit following treatment with RT + IL15c + aCD25 and combination RT + PD1-IL2v, a novel immunocytokine with PD-1 and IL2Rβγ binding domains, CTL immunophenotyping and phospho-proteomic analysis of intracellular metabolites showed significant upregulation of activation and functionality in CD8 T cells treated with RT + PD1-IL2v. Finally, we show the immunostimulatory response to RT + PD1-IL2v is significantly diminished with a concurrent lack of TCF+ CD8 T cell generation in the absence of functional IL15 signaling.

Conclusions

Our results are illustrative of a mechanism wherein unimpeded effector T cell activation through IL2Rβ signaling and Treg inhibition are necessary in mediating an anti-tumor immune response.
Human Mesofluidic Intestinal Model for Studying Transport of Drug Carriers and Bacteria Through a Live Mucosal Barrier
Authors: Wang Chia-Ming , Oberoi Hardeep S. , Law Devalina , Li Yuan , Kassis Timothy , Griffith Linda G. , Breault David T. , Carrier Rebecca L.
Published: September 2024

The intestinal mucosal barrier forms a critical interface between lumen contents such as bacteria, drugs, and drug carriers and the underlying tissue. Currentin vitrointestinal models, while recapitulating certain aspects of this barrier, generally present challenges with respect to imaging transport across mucus and uptake into enterocytes. A human mesofluidic small intestinal chip was designed to enable facile visualization of a mucosal interface created by growing primary human intestinal cells on a vertical hydrogel wall separating channels representing the intestinal lumen and circulatory flow. Type I collagen, fortified via cross-linking to prevent deformation and leaking during culture, was identified as a suitable gel wall material for supporting primary organoid-derived human duodenal epithelial cell attachment and monolayer formation. Addition of DAPT and PGE2 to culture medium paired with air-liquid interface culture increased the thickness of the mucus layer on epithelium grown within the device for 5 days from approximately 5 mm to 50 μm, making the model suitable for revealing intriguing features of interactions between luminal contents and the mucus barrier using live cell imaging. Time-lapse imaging of nanoparticle diffusion within mucus revealed a zone adjacent to the epithelium largely devoid of nanoparticles up to 4.5 hr after introduction to the lumen channel, as well as pockets of dimly lectin-stained mucus within which particles freely diffused, and apparent clumping of particles by mucus components. Multiple particle tracking conducted on the intact mucus layer in the chip revealed significant size-dependent differences in measured diffusion coefficients. E. coli introduced to the lumen channel were freely mobile within the mucus layer and appeared to intermittently contact the epithelial surface over 30 minute periods of culture. Mucus shedding into the lumen and turnover of mucus components within cells were visualized. Taken together, this system represents a powerful tool for visualization of interactions between luminal contents and an intact live mucosal barrier.
Loss ofSMARCB1evokes targetable epigenetic vulnerabilities in Epithelioid Sarcoma
Authors: Jin Jia Xiang , Fuchslocher Fabia , Carreno-Gonzalez Martha , Zahnow Felina , Ceranski A. Katharina , Will Rainer , Helm Dominic , Bestvater Felix , Banito Ana , Imle Roland , Ohmura Shunya , Cidre-Aranaz Florencia , Grünewald Thomas G. P.
Published: September 2024

Dysfunction of epigenetic modulators, such as the SWI/SNF complex, is a wide-spread but relatively ill-defined feature of a broad spectrum of cancer entities. Among SWI/SNF-mutant entities,SMARCB1-deficient cancers, such as the highly aggressive Epithelioid Sarcoma (EpS), are characterized by this genetic event in an otherwise rather silent mutational landscape. This renders EpS an ideal model to study how epigenetic reprogramming by a single mutation can contribute to tumorigenesis.

Hence, to characterize and compare the function of theSMARCB1-deficient, residual and the physiological SWI/SNF complex in cancer, we generated a panel ofSMARCB1re-expressing EpS cell lines and employed a functional multi-omics approach. Here, we show that SWI/SNF holds canonical characteristics of both tumor-suppressors and proto-oncogenes due to its multi-faceted role in the regulation of the epigenome. Our data indicates that the loss ofSMARCB1causes an overall loss of SWI/SNF chromatin affinity atcis-regulatory enhancer elements, inducing a preference for uncontrolled proliferation and cell cycle progression as opposed to development and differentiation. We further demonstrate that EpS cell lines depend on residual SWI/SNF action to maintain clonogenicity and proliferation. Consequently, EpS cell lines exhibit markedly increased sensitivity to pharmacological inhibition of the residual SWI/SNF when compared with SWI/SNF-proficient cancer entities.

Collectively, our results from the EpS model shed new light on how a single mutation can rewire the pleiotropic effects of an epigenetic master regulator and provide inroads for therapeutic intervention.
Seasonality of the estrus cycle in laboratory mice under constant conditions
Authors: Reichard Tess M. , Miller Caitlin H. , Yang Jay , Sheehan Michael J.
Published: September 2024

Seasonality governs every aspect of life in the natural environment. Controlled laboratory settings are intended to keep animals under a constant set of environmental cues with no seasonality. However, prior research suggests that seasonal variation may exist despite aseasonal lab environments. Here, we examined if seasonal reproductive variation was present in a laboratory mouse strain (C57BL/6J) under standard laboratory housing conditions. We found that female C57BL/6J mice exhibited reproductive seasonality mirroring the outside environment, in a controlled “simulated summer” environment. In the winter and spring, females have longer ovulating phases (proestrus and estrus), compared to the fall. Females similarly experience lengthier complete cycles in the spring, with the most rapid cycling occurring in the fall. Additionally, females spent more time in ovulating phases across seasons than previously reported. Laboratory mice are sensitive to external seasonal changes, despite their local environment being light, temperature, and humidity controlled. This may be due to the detection of an unidentified external cue providing information about external seasonal changes. These findings represent just one example of how seasonality may impact mouse physiology in laboratory settings, emphasizing the need to account for such influences in biomedical research.
Protrusion force and cell-cell adhesion play a critical role in collective tumor cluster migration
Authors: Wang Huijing , Ardila Catalina , Jindal Ajita , Aggarwal Vaishali , Wang Weikang , Vande Geest Jonathan , Jiang Yi , Xing Jianhua , Sant Shilpa
Published: September 2024

While collective migration is shown to enhance invasive and metastatic potential in cancer, the mechanisms driving this behavior and regulating tumor migration plasticity remain poorly understood. This study provides a mechanistic framework explaining the emergence of different modes of collective migration under hypoxia-induced secretome. We focus on the interplay between cellular protrusion force and cell-cell adhesion using collectively migrating three-dimensional microtumors as models with well-defined microenvironment. Large microtumors show directional migration due to intrinsic hypoxia, while small microtumors exhibit radial migration in response to hypoxic secretome. Here, we developed the minimal multi-scale microtumor model (MSMM) to elucidate underlying mechanisms. We identified distinct migration modes within specific regions of protrusion force and cell-cell adhesion parameter space. We show that sufficient cellular protrusion force is crucial for both, radial and directional collective microtumor migration. Radial migration emerges when sufficient cellular protrusion force is generated, driving neighboring cells to move collectively in diverse directions. Within migrating tumors, strong cell-cell adhesion enhances the alignment of cell polarity, breaking the symmetric angular distribution of protrusion forces, and leading to directional microtumor migration. The integrated results from the experimental and computational models provide fundamental insights into collective migration in response to different microenvironment stimuli.
Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome
Authors: Rajczewski Andrew T. , Alfredo Blakeley-Ruiz J. , Meyer Annaliese , Vintila Simina , McIlvin Matthew R. , Van Den Bossche Tim , Searle Brian C. , Griffin Timothy J. , Saito Mak A. , Kleiner Manuel , Jagtap Pratik D.
Published: September 2024

Mass spectrometry (MS)-based metaproteomics is used to identify and quantify proteins in microbiome samples, with the frequently used methodology being Data-Dependent Acquisition mass spectrometry (DDA-MS). However, DDA-MS is limited in its ability to reproducibly identify and quantify lower abundant peptides and proteins. To address DDA-MS deficiencies, proteomics researchers have started using Data-Independent Acquisition Mass Spectrometry (DIA-MS) for reproducible detection and quantification of peptides and proteins. We sought to evaluate the reproducibility and accuracy of DIA-MS metaproteomic measurements relative to DDA-MS using a mock community of known taxonomic composition. Artificial microbial communities of known composition were analyzed independently in three laboratories using DDA- and DIA-MS acquisition methods. DIA-MS yielded more protein and peptide identifications than DDA-MS in each laboratory. In addition, the protein and peptide identifications were more reproducible in all laboratories and provided an accurate quantification of proteins and taxonomic groups in the samples. We also identified some limitations of current DIA tools when applied to metaproteomic data, highlighting specific needs to improve DIA tools enabling analysis of metaproteomic datasets from complex microbiomes. Ultimately, DIA-MS represents a promising strategy for MS-based metaproteomics due to its large number of detected proteins and peptides, reproducibility, deep sequencing capabilities, and accurate quantitation.
Estimation of demography and mutation rates from one million haploid genomes
Authors: Schraiber Joshua G. , Spence Jeffrey P. , Edge Michael D.
Published: September 2024

As genetic sequencing costs have plummeted, datasets with sizes previously un-thinkable have begun to appear. Such datasets present new opportunities to learn about evolutionary history, particularly via rare alleles that record the very recent past. However, beyond the computational challenges inherent in the analysis of many large-scale datasets, large population-genetic datasets present theoretical problems. In particular, the majority of population-genetic tools require the assumption that each mutant allele in the sample is the result of a single mutation (the “infinite sites” assumption), which is violated in large samples. Here, we present DR EVIL, a method for estimating mutation rates and recent demographic history from very large samples. DR EVIL avoids the infinite-sites assumption by using a diffusion approximation to a branching-process model with recurrent mutation. The branching-process approach limits the method to rare alleles, but, along with recent results, renders tractable likelihoods with recurrent mutation. We show that DR EVIL performs well in simulations and apply it to rare-variant data from a million haploid samples, identifying a signal of mutation-rate heterogeneity within commonly analyzed classes and predicting that in modern sample sizes, most rare variants at sites with high mutation rates represent the descendants of multiple mutation events.
Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells
Authors: Adams Nicholas M. , Galitsyna Aleksandra , Tiniakou Ioanna , Esteva Eduardo , Lau Colleen M. , Reyes Jojo , Abdennur Nezar , Shkolikov Alexey , Yap George S. , Khodadadi-Jamayran Alireza , Mirny Leonid A. , Reizis Boris
Published: September 2024

The cohesin protein complex extrudes chromatin loops, stopping at CTCF-bound sites, to organize chromosomes into topologically associated domains, yet the biological implications of this process are poorly understood. We show that cohesin is required for the post-mitotic differentiation and function of antigen-presenting dendritic cells (DCs), particularly for antigen cross-presentation and IL-12 secretion by type 1 conventional DCs (cDC1s)in vivo. The chromatin organization of DCs was shaped by cohesin and the DC-specifying transcription factor IRF8, which controlled chromatin looping and chromosome compartmentalization, respectively. Notably, optimal expression of IRF8 itself required CTCF/cohesin-binding sites demarcating theIrf8gene. During DC activation, cohesin was required for the induction of a subset of genes with distal enhancers. Accordingly, the deletion of CTCF sites flanking theIl12bgene reduced IL-12 production by cDC1s. Our data reveal an essential role of cohesin-mediated chromatin regulation in cell differentiation and functionin vivo, and its bi-directional crosstalk with lineage-specifying transcription factors.
Isolating the Direct Effects of Growth Hormone on Lifespan and Metabolism
Authors: Lasher Alexander Tate , Liu Kaimao , Fitch Michael , Sun Liou Y.
Published: September 2024

Prior studies show that disrupting somatotropic axis components extends laboratory mouse lifespan, but confounding effects of additional genes and hormones obscure the specific impact of growth hormone (GH) on longevity. We address this issue by using mice with a specific knockout of the GH gene, revealing that disrupting GH alone substantially increases lifespan. The longevity effects are accompanied by altered metabolic fuel utilization, directly linking GH action to aging mechanisms.
Chromosome-level assemblies ofAmaranthus palmeri,Amaranthus retroflexus, andAmaranthus hybridusallow for genomic comparisons and identification of a sex-determining region
Authors: Raiyemo Damilola A. , Montgomery Jacob S. , Cutti Luan , Abdollahi Fatemeh , Llaca Victor , Fengler Kevin , Lopez Alexander J. , Morran Sarah , Saski Christopher A , Nelson David R. , Patterson Eric , Gaines Todd A. , Tranel Patrick J.
Published: September 2024

Amaranthus palmeri (Palmer amaranth), A. retroflexus (redroot pigweed), and A. hybridus (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as 'pigweeds', these species are incredibly adaptive and have become successful competitors in diverse agricultural settings. Development of genomic resources for these species promises to facilitate the elucidation of the genetic basis of traits such as biotic and abiotic stress tolerance (e.g., herbicide resistance) and sex determination. Here, we sequenced and assembled chromosome-level genomes of these three pigweed weed species. By combining the haplotype-resolved assembly of A. palmeri with existing restriction site-associated DNA sequencing data, we identified a ~2.84 Mb region on chromosome 3 of Hap1 that is male-specific and contains 37 genes. Transcriptomic analysis revealed two genes within the male-specific region, RESTORER OF FERTILITY 1 (Rf1) and TLC DOMAIN-CONTAINING PROTEIN (TLC), were upregulated in male individuals across the shoot apical meristem, the floral meristem, and mature flowers, indicating their potential involvement in sex determination in A. palmeri. In addition, we rigorously classified cytochrome P450 genes in all three pigweeds due to their involvement in non-target site herbicide resistance. Finally, we identified contiguous extrachromosomal circular DNA (eccDNA) in A. palmeri, a critical component of glyphosate resistance in this species. The findings of this study advance our understanding of sex determination in A. palmeri and provide genomic resources for elucidating the genetic basis and evolutionary origins of adaptive traits within the genus.