bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRAIL-induced cytokine production via NFKB2 pathway promotes neutrophil chemotaxis and immune suppression in triple negative breast cancers
Authors: Kundu Manjari , Greer Yoshimi E. , Lobanov Alexei , Ridnour Lisa , Donahue Renee N. , Ng Yeap , Ratnayake Shashi , Voeller Donna , Weltz Sarah , Chen Qingrong , Lockett Stephen J. , Cam Maggie , Meerzaman Daoud , Wink David A. , Weigert Roberto , Lipkowitz Stanley 
Published: July 2024

AbstractTumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potential cancer therapeutic that induces apoptosis in cancer cells while sparing the non-malignant cells in preclinical models. However, its efficacy in clinical trials has been limited, suggesting unknown modulatory mechanisms responsible for the lack of TRAIL activity in patients. Here, we hypothesized that TRAIL treatment elicits transcriptional changes in triple negative breast cancer (TNBC) cells that alter the immune milieu. To test this, we performed an RNAseq analysis of MDA-MB-231 cells treated with TRAIL, followed by validation in additional TNBC cell lines. TRAIL significantly induces expression of multiple cytokines such as CXCLs 1, 2, 3, 8,11 and IL-6, which are known to modify neutrophil function. Mechanistically, the induction of these cytokines was predominantly mediated by death receptor 5, caspase 8 (but not caspase 8 enzymatic activity), and the non-canonical NFKB2 pathway. The cytokines produced by the TRAIL-treated TNBC cells enhanced chemotaxis of healthy human donor isolated neutrophils.In vivo, TRAIL treated TNBC murine xenograft tumors showed activation of the NFKB2 pathway, elevated production of CXCLs and IL-6, and increased neutrophil recruitment into the tumors. Moreover, donor isolated neutrophils preincubated in supernatants from TRAIL-treated TNBC cells exhibited impaired cytotoxic effect against TNBC cells. Transcriptomic analysis of neutrophils incubated with either TRAIL alone or supernatant of TRAIL-treated TNBC cells revealed increased expression of inflammatory cytokines, immune modulatory genes, immune checkpoint genes, and genes implicated in delayed neutrophil apoptosis. Functional studies with these neutrophils confirmed their suppressive effect on T cell proliferation and an increase in Treg suppressive phenotype. Collectively, our study demonstrates a novel role of TRAIL-induced NFKB2-dependent cytokine production that promotes neutrophil chemotaxis and immune suppression.
TheLYCOPENE EPSILON CYCLASEuntranslated mRNA leader modulates carotenoid feedback and post-transcriptional regulation
Authors: Alagoz Yagiz , Nayak Jwalit J. , Aryal Rishi , Watkins Jacinta L. , Holland Sophie , Tissue David T. , Pogson Barry J. , Cazzonelli Christopher I. 
Published: July 2024

ABSTRACTMetabolic feedback is proposed to modulate nuclear gene expression and carotenoid biosynthesis in plastids, however few mechanisms have been identified so far in plants. Utilising mutants, overexpression lines, and chemical inhibitors, we demonstrate that ArabidopsisLYCOPENE EPSILON CYCLASE(εLCY) mRNA levels correlate with changes in β-carotenoid accumulation. Transgenic seedlings harbouring theεLCY5’ leader sequence fused toFIREFLY LUCIFERASE(FiLUC) showed reporter responsiveness to metabolic feedback triggered by norflurazon or loss-of-function in the CAROTENOID ISOMERASE (CRTISO). TheεLCY5’UTR harboured three alternative transcription start sites (TSS). The most abundant -133bp sequence generated in dark and light grown seedlings harboured a 5’ conserved domain (CD) with otherBrassicaceaespecies and a viral internal ribosome entry site (IRES) proximal to the start codon.In silicomodelling predicted the 5’UTR formed two energetically separated RNA structural probabilities having a minimal free energy consistent with metabolite-binding RNA riboswitches that was distinguished by hairpin structures within the CD. Site-specific mutations were used to stabilize the 5’UTR into a single RNA shape definition having negligible separation between the mountain plot structure prediction curves and a distal terminator-like hairpin structure. Stabilizing the 5’UTR shape triggered the posttranscriptional repression of FiLUC activity enabled by the CaMV35S promoter in tobacco transient assays and stable transgenic Arabidopsis lines. The stabilised shape fragment became responsive to metabolic feedback induced by norflurazon and incrtisomutant etiolated and de-etiolated seedlings. TheεLCY5’UTR resembles a conformational RNA regulatory switch harbouring a posttranscriptional expression platform and aptamer domain responsive to carotenoid-mediated feedback signalling.
CGPA: multi-context insights from the cancer gene prognosis atlas
Authors: Cao Biwei , Yu Xiaoqing , Gonzalez Gullermo , Murthy Amith R , Li Tingyi , Shen Yuanyuan , Yao Sijie , Conejo-Garcia Jose R. , Jiang Peng , Wang Xuefeng 
Published: July 2024

ABSTRACTCancer transcriptomic data are used extensively to interrogate the prognostic value of targeted genes, yet basic scientists and clinicians have predominantly relied on univariable survival analysis for this purpose. This method often fails to capture the full prognostic potential and contextual relevance of the genes under study, inadvertently omitting a group of genes we term univariable missed-opportunity prognostic (UMOP) genes. Recognizing the complexity of revealing multifaceted prognostic implications, especially when extending the analysis to include various covariates and thresholds, we present the Cancer Gene Prognosis Atlas (CGPA). This platform greatly enhances gene-centric biomarker research across cancer types by offering an interactive and user-friendly interface for highly customized, in-depth prognostic analysis. CGPA notably supports data-driven exploration of gene pairs and gene-hallmark relationships, elucidating key composite biological mechanisms like synthetic lethality and immunosuppression. It further expands its capabilities to assess multi-gene panels using both public and user-provided data, facilitating a seamless mechanism-to-machine analysis. Additionally, CGPA features a designated portal for discovering prognostic gene modules using curated cancer immunotherapy data. Ultimately, CGPA’s comprehensive, accessible tools allow cancer researchers, including those without statistical expertise, to precisely investigate the prognostic landscape of genes, customizing the model to fit specific research hypotheses and enhancing biomarker discovery and validation through a synergy of mechanistic and data-driven strategies.SignificanceCGPA is a streamlined, interactive platform for multi-context gene-centric prognostic analysis, simplifying biomarker discovery and validation in oncology for clinicians and basic scientists, and bridging a critical gap in translational cancer research.
A tethering mechanism underlies Pin1-catalyzed prolinecis-transisomerization at a noncanonical site
Authors: Williams Christopher C. , Chuck Jonathan , Munoz-Tello Paola , Kojetin Douglas J. 
Published: July 2024

ABSTRACTThe prolyl isomerase Pin1 catalyzes thecis-transisomerization of proline peptide bonds, a non-covalent post-translational modification that influences cellular and molecular processes, including protein-protein interactions. Pin1 is a two-domain enzyme containing a WW domain that recognizes phosphorylated serine/threonine-proline (pS/pT-P) canonical motifs and an enzymatic PPIase domain that catalyzes prolinecis-transisomerization of pS/pT-P motifs. Here, we show that Pin1 uses a tethering mechanism to bind and catalyze prolinecis-transisomerization of a noncanonical motif in the disordered N-terminal activation function-1 (AF-1) domain of the human nuclear receptor PPARγ. NMR reveals multiple Pin1 binding regions within the PPARγ AF-1, including a canonical motif that when phosphorylated by the kinase ERK2 (pS112-P113) binds the Pin1 WW domain with high affinity. NMR methods reveal that Pin1 also binds and acceleratescis-transisomerization of a noncanonical motif containing a tryptophan-proline motif (W39-P40) previously shown to be involved in an interdomain interaction with the C-terminal ligand-binding domain (LBD). Cellular transcription studies combined with mutagenesis and Pin1 inhibitor treatment reveal a functional role for Pin1-mediated acceleration ofcis-transisomerization of the W39-P40 motif. Our data inform a refined model of the Pin1 catalytic mechanism where the WW domain binds a canonical pS/T-P motif and tethers Pin1 to the target, which enables the PPIase domain to exert catalyticcis-transisomerization at a distal noncanonical site.SIGNIFICANCEProline peptide bonds naturally occur incisconformations and isomerize totransconformations on exchange regimes on the order of seconds to minutes. Pin1, a prolyl isomerase, catalyzes the isomerization of proline peptide bonds that contain a specific phospho-motif—a phosphorylated serine or threonine followed by a proline (pS/pT-P)—allowing for switch-like effects on target protein structure and function. One protein substrate of Pin1 is the nuclear receptor peroxisome proliferator activated receptor gamma (PPARγ), which is shown here to undergo Pin1-catalyzed isomerization at a noncanonical proline distal to a canonical pS/pT-P binding site. These studies lay the foundation for understanding the role of Pin1 in mediating PPARγ-regulated transcription and expand understanding of Pin1-catalyzed enzymatic activities and functions.
Proteome-wide 4-hydroxy-2-nonenal signature of oxidative stress in the marine invasive tunicateBotryllus schlosseri
Authors: Kültz Dietmar , Gardell Alison M. , DeTomaso Anthony , Stoney Greg , Rinkevich Baruch , Qarri Andy , Hamar Jens 
Published: July 2024

ABSTRACTThe colonial ascidianBoytryllus schlosseriis an invasive marine chordate that thrives under conditions of anthropogenic climate change. We show that the B. schlosseri expressed proteome contains unusually high levels of proteins that are adducted with 4-hydroxy-2-nonenal (HNE). HNE represents a prominent posttranslational modification resulting from oxidative stress. Although numerous studies have assessed oxidative stress in marine organisms HNE protein modification has not previously been determined in any marine species. LC/MS proteomics was used to identify 1052 HNE adducted proteins in B. schlosseri field and laboratory populations. Adducted amino acid residues were ascertained for 1849 modified sites, of which 1195 had a maximum amino acid localization score. Most HNE modifications were at less reactive lysines (rather than more reactive cysteines). HNE prevelance on most sites was high. These observations suggest that B. schlosseri experiences and tolerates high intracellular reactive oxygen species levels, resulting in substantial lipid peroxidation. HNE adducted B. schlosseri proteins show enrichment in mitochondrial, proteostasis, and cytoskeletal functions. Based on these results we propose that redox signaling contributes to regulating energy metabolism, the blastogenic cycle, oxidative burst defenses, and cytoskeleton dynamics during B. schlosseri development and physiology. A DIA assay library was constructed to quantify HNE adduction at 72 sites across 60 proteins that represent a holistic network of functionally discernable oxidative stress bioindicators. We conclude that the vast amount of HNE protein adduction in this circumpolar tunicate is indicative of high oxidative stress tolerance contributing to its range expansion into diverse environments.NEW & NOTEWORTHYOxidative stress results from environmental challenges that increase in frequency and severity during the Anthropocene. Oxygen radical attack causes lipid peroxidation leading to HNE production. Proteome-wide HNE adduction is highly prevalent inBotryllus schlosseri, a widely distributed, highly invasive, and economically important biofouling ascidian and the first marine species to be analyzed for proteome HNE modification. HNE adduction of specific proteins physiologically sequesters reactive oxygen species, which enhances fitness and resilience during environmental change.
AI-driven Discovery of Morphomolecular Signatures in Toxicology
Authors: Jaume Guillaume , Peeters Thomas , Song Andrew H. , Pettit Rowland , Williamson Drew F. K. , Oldenburg Lukas , Vaidya Anurag , de Brot Simone , Chen Richard J. , Thiran Jean-Philippe , Le Long Phi , Gerber Georg , Mahmood Faisal 
Published: July 2024

AbstractEarly identification of drug toxicity is essential yet challenging in drug development. At the preclinical stage, toxicity is assessed with histopathological examination of tissue sections from animal models to detect morphological lesions. To complement this analysis, toxicogenomics is increasingly employed to understand the mechanism of action of the compound and ultimately identify lesion-specific safety biomarkers for whichin vitroassays can be designed. However, existing works that aim to identify morphological correlates of expression changes rely on qualitative or semi-quantitative morphological characterization and remain limited in scale or morphological diversity. Artificial intelligence (AI) offers a promising approach for quantitatively modeling this relationship at an unprecedented scale. Here, we introduce GEESE, an AI model designed to impute morphomolecular signatures in toxicology data. Our model was trained to predict 1,536 gene targets on a cohort of 8,231 hematoxylin and eosin-stained liver sections fromRattus norvegicusacross 127 preclinical toxicity studies. The model, evaluated on 2,002 tissue sections from 29 held-out studies, can yield pseudo-spatially resolved gene expression maps, which we correlate with six key drug-induced liver injuries (DILI). From the resulting 25 million lesion-expression pairs, we established quantitative relations between up and downregulated genes and lesions. Validation of these signatures against toxicogenomic databases, pathway enrichment analyses, and human hepatocyte cell lines asserted their relevance. Overall, our study introduces new methods for characterizing toxicity at an unprecedented scale and granularity, paving the way for AI-driven discovery of toxicity biomarkers.Live demo:https://mahmoodlab.github.io/tox-discovery-ui/
A transposable element insertion inIAA16disrupts splicing and causes dicamba resistance inBassia scoparia
Authors: Montgomery Jacob S. , Soni Neeta , Marques Hill Sofia , Morran Sarah , Patterson Eric L. , Edwards Seth A. , Ratnayake Sandaruwan , Hung Yu-Hung , Pandesha Pratheek H. , Slotkin R. Keith , Napier Richard , Dayan Franck , Gaines Todd A. 
Published: July 2024

AbstractA dicamba-resistant population of kochia (Bassia scoparia) identified in Colorado, USA in 2012 was used to generate a synthetic mapping population that segregated for dicamba resistance. Linkage mapping associating dicamba injury with genotype derived from restriction-site-associated DNA sequencing identified a single locus in the kochia genome associated with resistance on chromosome 4. A mutant version ofAuxin/Indole-3-Acetic Acid 16(AUX/IAA16; a gene previously implicated in dicamba resistance in kochia) was found near the middle of this locus in resistant plants. Long read sequencing of dicamba-resistant plants identified a recently inserted Ty1/Copia retrotransposon near the beginning of the second exon ofAUX/IAA16, leading to disruption of normal splicing. A molecular marker for this insertion allows for rapid detection of resistance. Stable transgenic lines ofArabidopsis thalianaectopically expressing the mutant and wildtype alleles ofAUX/IAA16were developed.Arabidopsis thalianaplants expressing the mutantAUX/IAA16allele grew shorter roots on control media. However, transgenic root growth was less inhibited on media containing either dicamba (5 μM) or IAA (0.5 μM) when compared to non-transgenic plants or those expressing the wildtype allele ofAUX/IAA16.In vitro assays indicate reduced binding affinity and more rapid dissociation of the mutant AUX/IAA with TIR1 in the presence of several auxins, and protein modeling suggests the substitution of the glycine residue in the degron domain of AUX/IAA16 is especially important for resistance. A fitness cost associated with the mutant allele ofAUX/IAA16has implications for resistance evolution and management of kochia populations with this resistance mechanism.SignificanceAuxin mimics are amongst the most important herbicides in modern agriculture. Evolution of weeds that are resistant to these herbicides threatens sustainable crop production. Understanding the basis of auxin herbicide resistance informs the development of improved weed control technologies. Additionally, auxin-resistant mutations and their pleotropic effects help us understand auxin perception and signalling. We describe a transposable element insertion within an herbicide target site gene that alters splicing and reduces synthetic and natural auxin perception.
Modelling alcohol consumption in rodents using two-bottle choice home cage drinking and optional lickometry-based microstructural analysis
Authors: Hou Shikun , Arce Soto Nathaly M , Glover Elizabeth J 
Published: July 2024

ABSTRACTTwo-bottle choice home cage drinking is one of the most widely used paradigms to study ethanol consumption in rodents. In its simplest form, animals are provided with access to two drinking bottles, one of which contains regular tap water and the other ethanol, for 24 hr/day with daily intake measured via change in bottle weight over the 24 hr period. Consequently, this approach requires no specialized laboratory equipment. While such ease of implementation is likely the greatest contributor to its widespread adoption by preclinical alcohol researchers, the resolution of drinking data acquired using this approach is limited by the number of times the researcher measures bottle weight (e.g., once daily). However, the desire to examine drinking patterns in the context of overall intake, pharmacological interventions, and neuronal manipulations has prompted the development of home cage lickometer systems that can acquire data at the level of individual licks. Although a number of these systems have been developed recently, the open-source system, LIQ HD, has garnered significant attention in the field for its affordability and user friendliness. Although exciting, this system was designed for use in mice. Here, we review appropriate procedures for standard and lickometer-equipped two-bottle choice home cage drinking. We also introduce methods for adapting the LIQ HD system to rats including hardware modifications to accommodate larger cage size and a redesigned 3D printed bottle holder compatible with standard off-the-shelf drinking bottles. Using this approach, researchers can examine daily drinking patterns in addition to levels of intake in many rats in parallel thereby increasing the resolution of acquired data with minimal investment in additional resources. These methods provide researchers with the flexibility to use either standard bottles or a lickometer-equipped apparatus to interrogate the neurobiological mechanisms underlying alcohol drinking depending on their precise experimental needs.SUMMARYThis protocol describes a standard intermittent-access two-bottle choice home cage drinking paradigm to model alcohol consumption in rats. In addition, it provides step-by-step instructions to augment the standard protocol with a DIY lickometer system that enables microstructural analysis of drinking behavior.
Hydrophilic/ Omniphobic droplet arrays for high-throughput and quantitative enzymology
Authors: Lee Byungjin , Sunden Fanny , Miller Michael , Pak Bumshik , Krebber Anker , Lutz Stefan , Fordyce Polly Morrell 
Published: July 2024

AbstractEngineered enzymes with enhanced or novel functions are specific catalysts with wide-ranging applications in industry and medicine. Here, we introduce Droplet Array Microfluidic Enzyme Kinetics (DA-MEK), a high-throughput enzyme screening platform that combines water-in-air droplet microarrays formed on patterned superhydrophilic/omniphobic surfaces with cell-free protein synthesis to enable cost-effective expression and quantitative kinetic characterization of enzyme variants. By printing DNA templates encoding enzyme variants onto hydrophilic spots, stamping slides to add cell-free expression mix, and imaging the resulting arrays, we demonstrate reproducible expression of hundreds of enzyme variants per slide. Subsequent stamping of fluorogenic substrates and time-lapse imaging allows determination of Michaelis-Menten parameters for each variant, with measured catalytic efficiencies spanning 5 orders of magnitude and agreeing well with values obtained via traditional microtiter plate assays. DA-MEK consumes orders of magnitude less reagents than plate-based assays while providing accurate and detailed kinetic information for both beneficial and deleterious mutations. In future work, we anticipate DA-MEK will provide a powerful and versatile platform to accelerate enzyme engineering and enable screening of large variant libraries under diverse conditions.
High microsatellite but no mitochondrial DNA variation in an invasive Japanese mainland population of the parasitoid waspMelittobia sosui
Authors: Abe Jun , Takahashi Jun-ichi , Tsuchida Koji 
Published: July 2024

AbstractTheory predicts that bottleneck events reduce genetic diversity in invasive populations. The parasitoid waspMelittobia sosuiwas only identified in the subtropical area of Japanese south islands and Taiwan, but recently found also in the temperate area of the Japanese mainland. The species may expand their distribution northward due to factors such as recent global warming. We investigated population genetics in both the native and invasive areas using mitochondrial and nuclear microsatellite DNA. As expected, there was mitochondrial variation in the native area, but not in the invasive area, which only had one haplotype. However, the two areas had a similar level of microsatellite variation, with averagely 43% and 38% alleles uniquely found in the native and invasive populations, respectively. The difference of genetic variation between mitochondrial and microsatellite DNA in the invasive populations may be explained by the faster mutation rate of microsatellites, as well as the population structure ofMelittobia, in which subdivided small inbreeding lineages may facilitate the accumulation of mutations. The high proportion of private alleles suggests that the mainland population diverged from the native populations at least 100 years ago, ruling out the possibility that the mainland population was established recently. Instead, the present study suggests thatM. sosuimight have already existed in the mainland but with a low frequency, or the mainland population was derived from a third population which diverged from the native populations over 100 years ago.