bluuebunny/crossref_metadata_2025 huggingface dataset:
Boosting biodiversity monitoring using smartphone-driven, rapidly accumulating community-sourced data
Authors: Atsumi Keisuke , Nishida Yuusuke , Ushio Masayuki , Nishi Hirotaka , Genroku Takanori , Fujiki Shogoro
Published: September 2023

Comprehensive biodiversity data is crucial for ecosystem protection. The ‘Biome’ mobile app, launched in Japan, efficiently gathers species observations from the public using species identification algorithms and gamification elements. The app has amassed >6M observations since 2019. Nonetheless, community-sourced data may exhibit spatial and taxonomic biases. Species distribution models (SDMs) estimate species distribution while accommodating such bias. Here, we investigated the quality ofBiomedata and its impact on SDM performance. Species identification accuracy exceeds 95% for birds, reptiles, mammals, and amphibians, but seed plants, mollusks, and fishes scored below 90%. Our SDMs for 132 terrestrial plants and animals across Japan revealed that incorporatingBiomedata into traditional survey data improved accuracy. For endangered species, traditional survey data required >2,000 records for accurate models (Boyce index ≥ 0.9), while blending the two data sources reduced this to around 300. The uniform coverage of urban-natural gradients byBiomedata, compared to traditional data biased towards natural areas, may explain this improvement. Combining multiple data sources better estimates species distributions, aiding in protected area designation and ecosystem service assessment. Establishing a platform for accumulating community-sourced distribution data will contribute to conserving and monitoring natural ecosystems.
Direct and indirect effects of the increase in atmospheric CO2and temperature on groundwater organisms
Authors: Schmidt Susanne I. , Svátková Miroslava , Kodeš Vít , Shabarova Tanja
Published: September 2023

Atmospherically rising temperature and CO2impact all freshwater systems, including groundwater. Increasing CO2leads to more intense weathering of silicate rocks. Here, we tested whether the increased levels, the weathering, or rather the increasing temperature, impacted on fauna and prokaryotes in the groundwater ecosystem. We conducted the analyses separately for deep, i.e. secluded, and shallow, quaternary aquifers which exchange with the surface more intensely. Organism abundances and relative composition did not correlate with temperature or CO2levels. While many organisms rely on silica, in contrast, we found negative correlations between silica and fauna. The increases in silica over time, i.e. temporal trends, also partly correlated negatively with organisms. We hypothesize that the unexpected negative correlations are not direct effects, but indirectly indicate that groundwater communities do not adapt rapidly enough to changes. This jeopardizes future drinking water production which relies on the self-cleaning ecosystem services in groundwater.
Description ofPhylloneura rupestrissp. nov. (Odonata, Platycnemididae) from the Western Ghats, India with notes on its reproductive behavior
Authors: Chandran Ayikkara Vivek , Chandran Reji , Suraj S R , Jose Subin K. , Koparde Pankaj
Published: September 2023

PhylloneuraFraser, 1922 is a genus of damselflies which was till date regarded monotypic. It is represented by the nominate species,Phylloneura westermanni(Hagen in Selys, 1860) which is endemic to the Western Ghats in India. In our study, we came across a population ofPhylloneuranear Ponmudi hills, Thiruvananthapuram, which displayed morphological and behavioral differences fromP. westermanni. We describe it as a species new to science with detailed photographs and illustrations. We also provide notes on its reproductive behavior.
DEVIL peptides control cell growth and differentiation in different developmental processes
Authors: Alarcia Ana , Primo-Capella Amparo , Perpiñán Elena , Rossetto Priscilla , Ferrándiz Cristina
Published: September 2023

The DEVIL/ROTUNDIFOLIA-LIKE (DVL/RTFL) family of plant peptides is present in all land plants, but their biological role and mode of action remains largely unknown, in part due to the lack of reported phenotypes associated to DVL/RTFL loss of function. In this work we have generated high order mutants and characterized their phenotypes in reproductive development. Our results indicate thatdvlmutants are affected in cell elongation processes, mainly related to pollen tube growth, and they appear to provide robustness to these processes. We also show that DVL peptides may act in different domains to those where the corresponding genes are transcribed, suggesting a putative role in the coordination of organ growth by participating in cell-to-cell communication.
Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer
Authors: Alexander Katherine A. , Yu Ruofan , Skuli Nicolas , Coffey Nathan J. , Nguyen Son , Faunce Christine , Huang Hua , Dardani Ian P. , Good Austin L. , Lim Joan , Li Catherine , Biddle Nicholas , Joyce Eric F. , Raj Arjun , Lee Daniel , Keith Brian , Simon M. Celeste , Berger Shelley L.
Published: September 2023

Nuclear speckles are membrane-less bodies within the cell nucleus enriched in RNA biogenesis, processing, and export factors. In this study we investigated speckle phenotype variation in human cancer, finding a reproducible speckle signature, based on RNA expression of speckle-resident proteins, across >20 cancer types. Of these, clear cell renal cell carcinoma (ccRCC) exhibited a clear correlation between the presence of this speckle expression signature, imaging-based speckle phenotype, and clinical outcomes. ccRCC is typified by hyperactivation of the HIF-2α transcription factor, and we demonstrate here that HIF-2α drives physical association of a select subset of its target genes with nuclear speckles. Disruption of HIF-2α-driven speckle association via deletion of itsspeckle targetingmotifs (STMs)—defined in this study—led to defective induction of speckle-associating HIF-2α target genes without impacting non-speckle-associating HIF-2α target genes. We further identify the RNA export complex, TREX, as being specifically altered in speckle signature, and knockdown of key TREX component, ALYREF, also compromises speckle-associated gene expression. By integrating tissue culture functional studies with tumor genomic and imaging analysis, we show that HIF-2α gene regulatory programs are impacted by specific manipulation of speckle phenotype and by abrogation of speckle targeting abilities of HIF-2α. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of a specific subset of HIF-2α-regulated target genes that, in turn, influence patient outcomes. We also identify STMs in other transcription factors, suggesting that DNA-speckle targeting may be a general mechanism of gene regulation.

HIGHLIGHTS

– Nuclear speckles shown to reproducibly vary in cancer, predicting patient survival in ccRCC

– HIF-2α drives DNA/gene-speckle contacts dependent on identified speckle targeting motifs within HIF-2α

– Putative speckle targeting motifs are highly enriched among regulators of gene expression

– Partitioning of transcription factor functional programs may be a major biological function of nuclear speckles
γδ T cells impair airway macrophage differentiation in lung adenocarcinoma
Authors: Raffo-Iraolagoitia Ximena L. , McFarlane Amanda J. , Kruspig Bjorn , Fercoq Frédéric , Secklehner Judith , De Donatis Marco , Mackey John B. G. , Wiesheu Robert , Laing Sarah , Hsieh Ya-Ching , Shaw Robin , Corbyn Ryan , Nixon Colin , Miller Crispin , Kirschner Kristina , Bain Calum C. , Murphy Daniel J. , Coffelt Seth B. , Carlin Leo M.
Published: September 2023

Protecting mucosal barriers, γδ T cells hold promise for the development of new cancer immunotherapies. In mice, γδ T cells can largely be segregated into CD27+and CD27−cells, and their functions are modulated by interactions with surrounding cells. However, which cells communicate directly with γδ T cells in lung adenocarcinoma remains unknown. To address this, we combined flow cytometry, confocal microscopy, and scRNA-seq, using an autochthonous genetically engineered mouse model and different γδ T cell-deficient settings. We found that γδ T cells were increased in tumour-bearing lungs, with an altered phenotype. CD27−and CD27+γδ T cells differed in their localisation and interactions including their tropism for macrophages. Overall, we propose a model where CD27+γδ T cells undermine the differentiation of tumour-associated macrophages into airway macrophages, fostering a negative outcome in lung adenocarcinoma. Determining its translatability to human health may offer new avenues for immunotherapeutic strategies.

Guardians of pulmonary homeostasis, γδ T cells remain enigmatic regarding their role in lung adenocarcinoma. Raffo-Iraolagoitia et al. report that a subset of γδ T cells impairs the differentiation of tumour-associated macrophages into airway macrophages, relevant for the outcome of lung adenocarcinoma.

Graphical Abstract
Cell competition promotes metastatic intestinal cancer through a multistage process
Authors: García Ana Krotenberg , Ledesma-Terrón Mario , Vriend Joyce , van Luyk Merel E , Suijkerbuijk Saskia JE
Published: September 2023

Cell competition plays an instrumental role in quality control during tissue development and homeostasis. Nevertheless, cancer cells can exploit this process for their own proliferative advantage. In our study, we generated mixed murine organoids and microtissues to explore the impact of cell competition on liver metastasis. Unlike competition at the primary site, the initial effect on liver progenitor cells does not involve the induction of apoptosis. Instead, metastatic competition manifests as a multistage process. Initially, liver progenitors undergo compaction, which is followed by cell cycle arrest, ultimately forcing differentiation. Subsequently, the newly differentiated liver cells exhibit reduced cellular fitness, rendering them more susceptible to outcompetion by intestinal cancer cells. Notably, cancer cells leverage different interactions with different epithelial populations in the liver, using them as scaffolds to facilitate their growth. Consequently, tissue-specific mechanisms of cell competition are fundamental in driving metastatic intestinal cancer.
An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia
Authors: Torres-Diz Manuel , Reglero Clara , Falkenstein Catherine D , Castro Annette , Hayer Katharina E. , Radens Caleb M. , Quesnel-Vallières Mathieu , Ang Zhiwei , Sehgal Priyanka , Li Marilyn M. , Barash Yoseph , Tasian Sarah K. , Ferrando Adolfo , Thomas-Tikhonenko Andrei
Published: September 2023

Relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) is a major cause of pediatric cancer-related deaths. Relapse-specific mutations do not account for all chemotherapy failures in B- ALL patients, suggesting additional mechanisms of resistance. By mining RNA-seq datasets of paired diagnostic/relapse pediatric B-ALL samples, we discovered pervasive alternative splicing (AS) patterns linked to relapse and affecting drivers of resistance to glucocorticoids, anti-folates, and thiopurines. Most splicing variations represented cassette exon skipping, “poison” exon inclusion, and intron retention, phenocopying well-documented loss-of-function mutations. In contrast, relapse-associated AS of NT5C2 mRNA yielded an isoform with the functionally uncharacterized in-frame exon 6a. Incorporation of the 8-amino acid sequence SQVAVQKR into this enzyme created a putative phosphorylation site and resulted in elevated nucleosidase activity, which is a known consequence of gain-of-function mutations in NT5C2 and a common determinant of 6-mercaptopurine (6-MP) resistance. Consistent with this finding, NT5C2ex6a and the R238W hotspot variant conferred comparable levels of resistance to 6-MP in B-ALL cells both in vitro and in vivo. Furthermore, both the NT5C2ex6a and R238W variants induced collateral sensitivity to the inosine monophosphate dehydrogenase (IMPDH) inhibitor mizoribine. These results ascribe an important role for splicing perturbations in chemotherapy resistance in relapsed B-ALL and suggest that IMPDH inhibitors, including the commonly used immunosuppressive agent mycophenolate mofetil, could be a valuable therapeutic option for treating thiopurine-resistant leukemias.
Deposited footprints let cells switch between confined, oscillatory, and exploratory migration
Authors: Ipiña Emiliano Perez , d’Alessandro Joseph , Ladoux Benoît , Camley Brian A.
Published: September 2023

For eukaryotic cells to heal wounds, respond to immune signals, or metastasize, they must migrate, often by adhering to extracellular matrix. Cells may also deposit extracellular matrix components, leaving behind a footprint that influences their crawling. Recent experiments showed that some epithelial cells on micropatterned adhesive stripes move persistently in regions they have previously crawled over, where footprints have been formed, but barely advance into unexplored regions, creating an oscillatory migration of increasing amplitude. Here, we explore through mathematical modeling how footprint deposition and cell responses to footprint combine to allow cells to develop oscillation and other complex migratory motions. We simulate cell crawling with a phase field model coupled to a biochemical model of cell polarity, assuming local contact with the deposited footprint activates Rac1, a protein that establishes the cell’s front. Depending on footprint deposition rate and response to the footprint, cells on micropatterned lines can display many types of motility, including confined, oscillatory, and persistent motion. On two-dimensional substrates, we predict a transition between cells undergoing circular motion and cells developing an exploratory phenotype. Small quantitative changes in a cell’s interaction with its footprint can completely alter exploration, allowing cells to tightly regulate their motion, leading to different motility phenotypes (confined vs exploratory) in different cells when deposition or sensing is variable from cell to cell. Consistent with our computational predictions, we find in earlier experimental data evidence of cells undergoing both circular and exploratory motion.

Significance Statement

Recent experiments showed that epithelial cells modify and sense their local environment, creating a footprint that guides their own motion. Here, we explore how these deposited footprints regulate cell motility. We can recapitulate earlier experimental results with a model that assumes the footprint activates proteins that establish the cell front. We find that cells can use their footprints to change how they explore their surroundings, and that small changes in sensing or depositing footprint can switch the cell from being trapped to being able to explore new environments easily. We find both behaviors in experimental data, suggesting that cells can exhibit multiple crawling behaviors depending on how they deposit and respond to their foot-print.
The impact of gestational diabetes on functional capacity of the infant gut microbiome is modest and transient
Authors: Chieu Ryan V. , Hamilton Katharine , Ryan Paul M. , Copeland Julia , Wang Pauline W. , Retnakaran Ravi , Guttman David S. , Parkinson John , Hamilton Jill
Published: September 2023

Gestational diabetes mellitus (GDM) is a metabolic complication that manifests as hyperglycemia during the later stages of pregnancy. In high resource settings, careful management of GDM limits risk to the pregnancy, and hyperglycemia typically resolves after birth. At the same time, previous studies have revealed that the gut microbiome of infants born to mothers who experienced GDM exhibit reduced diversity and reduction in the abundance of several key taxa, includingLactobacillus. What is not known is what the functional consequences of these changes might be. In this case control study, we applied 16S rRNA sequence surveys and metatranscriptomics to profile the gut microbiome of 30 twelve-month old infants to examine the impact of GDM during pregnancy. Relative to mode of delivery and sex of the infant, maternal GDM status had only a limited impact on the structure and function of the developing microbiome. While GDM samples were associated with a decrease in alpha diversity, we observed no effect on beta diversity and no differentially abundant taxa. Further, while mode of delivery and sex of infant affected the expression of multiple bacterial pathways, most of the impact of GDM status on the function of the infant microbiome appears to be lost by twelve months of age. These data serve to reassure parents and paediatricians that, at least in high resource settings, while mode of delivery appears to impact function and diversity for longer than anticipated, GDM may not have persistent effects on the function nor composition of the infant gut microbiome.
Pharmacological control of CAR T cells through CRISPR-driven rapamycin resistance
Authors: Levesque Sébastien , Carleton Gillian , Duque Victoria , Goupil Claudia , Fiset Jean-Philippe , Villeneuve Sarah , Normandeau Eric , Morin Geneviève , Dumont Nellie , Nelson Brad H. , Laganière Josée , Boyle Brian , Lum Julian J. , Doyon Yannick
Published: September 2023

Chimeric antigen receptors (CARs) reprogram T cells to recognize and target cancer cells. Despite remarkable responses observed with CAR-T cell therapy in patients with hematological malignancies, CAR-T cell engineering still relies mostly on randomly integrating vectors, limiting the possibilities of fine-tuning T cell function. Here, we designed a CRISPR-based marker-free selection strategy to simultaneously target a therapeutic transgene and a gain-of-function mutation to theMTORlocus to enrich cells resistant to rapamycin, a clinically used immunosuppressant. We readily engineered rapamycin-resistant (RapaR) CAR-T cells by targeting CAR expression cassettes to theMTORlocus. Usingin vitrocytotoxicity assays, and a humanized mouse model of acute lymphoblastic leukemia, we show that RapaR-CAR-T cells can efficiently target CD19+leukemia cells in presence of immunosuppressing doses of rapamycin. Furthermore, our strategy allows multiplexed targeting of rapamycin-regulated immunoreceptors complexes (DARICs) to theMTORandTRACloci to pharmacologically control CAR-T cells’ activity. We foresee that our approach could both facilitate the enrichment of CRISPR-engineered CAR-T cellsex vivoandin vivowhile improving tumor eradication.
Multiomic single-cell analysis identifies von Willebrand factor and TIM3-expressingBCR-ABL1+CML stem cells
Authors: Nilsson Malin S. , Komic Hana , Gustafsson Johan , Sheybani Zahra , Paul Sanchari , Rolfson Ola , Hellstrand Kristoffer , Wennström Lovisa , Martner Anna , Thorén Fredrik B.
Published: September 2023

Tyrosine kinase inhibitors (TKI) only rarely eradicate leukemic stem cells (LSC) in chronic myeloid leukemia (CML) which commonly necessitates life-long therapy and monitoring of patients. Understanding details of leukemic hematopoiesis in CML may identify targetable pathways for sustained LSC elimination. This study utilized multiomic single-cell characterization of the CD14-CD34+hematopoietic stem and progenitor cell (HSPC) compartment in CML. Combined proteo-transcriptomic profiling of 597 genes and 51 proteins (CITE-seq) was performed along with parallel detection ofBCR-ABL1transcripts in 70,000 HSPC from 16 chronic phase patients and five healthy controls. CD14-CD34+HSPC from diagnosis samples displayed distinct myeloid cell bias with cells mainly annotated as LSC, lympho-myeloid progenitors (LMP)-II, erythrocyte and megakaryocyte progenitors, while few hematopoietic stem cells (HSC), LMP-I, dendritic cell or B cell progenitors were detected. In-depth analysis of the immature CD14-CD34+CD38-/lowcompartment revealed two distinct populations ofBCR-ABL1-expressing CML LSC (denoted LSC-I and LSC-II), where LSC-I showed features of quiescence and CD45RA-cKIT-CD26+TKI therapy-resistant phenotype. These subtypes of immature LSC showed high surface expression of TIM3 and transcription of the von Willebrand factor gene (VWF). Our findings imply that expression ofVWFand TIM3 distinguish LSC from HSC and may be linked to aberrant myeloid-biased hematopoiesis in CML. Additionally, the results identify TIM3 as a conceivable target for sustained elimination of immature LSC in CML.

Key points

We present a method to detectBCR-ABL1expression at the single-cell level that is compatible with high-throughput CITE-seq

The most immatureBCR-ABL1-expressing LSC population in primary CML shows enhanced expression of von Willebrand factor and TIM3
OmicsPharLeuDB: an integrative database for mining pharmacogenomic data in acute lymphoblastic leukemia
Authors: Peng Yu Zhong
Published: September 2023

Leukemia is one of the most common hematological malignancies in children. Recent cancer pharmacogenomic studies profiled large panels of cell lines against hundreds of approved drugs and experimental chemical compounds. However, until now, no comprehensive databases have been specifically designed for leukemia. Therefore, we have developed OmicsPharLeuDB (mugpeng.shinyapps.io/leu_web_english_peng_v2/), a database that includes the largest published studies investigating the viability response of human leukemia cell lines to chemical compound treatment, and the association between drug sensitivity and multi-omics, and also provides a user-friendly interactive website allowing the user to assess drug sensitivity data from a different platform and find the potential relationship between drugs and omics.
Multimodal profiling of chordoma immunity reveals distinct immune contextures
Authors: van Oost S. , Meijer D.M. , IJsselsteijn M.E. , Roelands J. , van den Akker B. , van der Breggen R. , Briaire-de Bruijn I.H. , van der Ploeg M. , Wijers-Koster P.M. , Polak S.B. , Peul W.C. , van der Wal R.J.P. , de Miranda N.F.C.C. , Bovee J.V.M.G.
Published: September 2023

Chordomas are cancers from the axial skeleton presenting immunological hallmarks of unknown significance. In recent years, some clinical trials demonstrated that chordomas can respond to immunotherapy. We present a comprehensive characterisation of immunological features of 76 chordomas through application of a multimodal approach comprising transcriptional profiling, multidimensional immunophenotyping and TCR profiling. Chordomas generally presented an immune “hot” microenvironment in comparison to other sarcomas, as indicated by the immunologic constant of rejection transcriptional signature. We identified two distinct groups of chordomas based on T cell infiltration. The highly infiltrated group was further characterised by high dendritic cell infiltration and the presence of multicellular immune aggregates in tumours, whereas low T cell infiltration was associated with lower overall cell densities of immune and stromal cells. Interestingly, patients with higher T cell infiltration displayed a more pronounced clonal enrichment of the T cell receptor repertoire compared to those with low T cell counts. Furthermore, we observed that the majority of chordomas maintained HLA class I expression. Our findings shed light on the natural immunity against chordomas. Understanding their immune landscape could guide the development and application of immunotherapies in a tailored manner, ultimately leading to an improved clinical outcome for chordoma patients.
BET inhibition rescues ciliogenesis and ameliorates pancreatitis-driven phenotypic changes in mice with Par3 loss
Authors: Shields Mario A. , Metropulos Anastasia E. , Spaulding Christina , Hirose Tomonori , Ohno Shigeo , Pham Thao N.D. , Munshi Hidayatullah G.
Published: September 2023

The apical-basal polarity of pancreatic acinar cells is essential for maintaining tissue architecture. However, the mechanisms by which polarity proteins regulate acinar pancreas tissue homeostasis are poorly understood. Here, we evaluate the role of Par3 in acinar pancreas injury and homeostasis. While Par3 loss in the mouse pancreas disrupts tight junctions, Par3 loss is dispensable for pancreatogenesis. However, with aging, Par3 loss results in low-grade inflammation, acinar degeneration, and pancreatic lipomatosis. Par3 loss also exacerbates pancreatitis-induced acinar cell loss, resulting in pronounced pancreatic lipomatosis and failure to regenerate. Moreover, Par3 loss in mice harboring mutant Kras causes extensive pancreatic intraepithelial neoplastic (PanIN) lesions and large pancreatic cysts. We also show that Par3 loss restricts injury-induced primary ciliogenesis. Significantly, targeting BET proteins enhances primary ciliogenesis during pancreatitis-induced injury and, in mice with Par3 loss, limits pancreatitis-induced acinar loss and facilitates acinar cell regeneration. Combined, this study demonstrates how Par3 restrains pancreatitis- and Kras-induced changes in the pancreas and identifies a potential role for BET inhibitors to attenuate pancreas injury and facilitate pancreas tissue regeneration.
Loss of EIF4G2 Mediates Aggressiveness in Distinct Human Endometrial Cancer Subpopulations with Poorer Survival Outcome in Patients
Authors: Meril Sara , Avni Maya Muhlbauer , Lior Chen , Bahlsen Marcela , Olender Tsviya , Savidor Alon , Krausz Judit , Peled Hila Belhanes , Birisi Hila , David Nofar , Bialik Shani , Scherz-Shouval Ruth , David Yehuda Ben , Kimchi Adi
Published: September 2023

The non-canonical translation initiation factor EIF4G2 plays essential roles in embryonic development and differentiation, and contributes to the cellular stress response via translation of selective mRNA cohorts. Currently there is limited and conflicting information regarding the potential involvement of EIF4G2 in cancer development and progression. Endometrial cancer (EC) is the most pervasive gynecological cancer in the developed world, with increasing incidence every year. High grade ECs are largely refractory to conventional treatments, presenting poor survival rates and lacking suitable prognostic markers. Here we assayed a cohort of 280 EC patients across different types, grades, and stages, and found that low EIF4G2 expression highly correlated with poor overall and recurrence free survival in Grade 2 EC patients, monitored over a period of up to 12 years. To establish a causative connection between low EIF4G2 expression and cancer progression, we analyzed in parallel two independent human EC cell lines and demonstrated that stable EIF4G2 knock-down resulted in increased resistance to conventional therapies. Depletion of EIF4G2 also increased the prevalence of molecular markers for aggressive cell subsets, and altered their transcriptional and proteomic landscapes. Prominent among the proteins with decreased abundance were Kinesin-1 motor proteins KIF5B and KLC1, 2, 3. Multiplexed imaging of the tumors from this EC patient cohort showed a correlation between decreased protein expression of either KIF5B or KLC1, and poor survival in patients of certain grades and stages. The findings herein reveal potential novel biomarkers for Grade 2 EC with potential ramifications for patient stratification and therapeutic interventions.

Significance

Decreased EIF4G2 protein results in increased drug resistance of aggressive sub-populations of endometrial cancer cells, is associated with poor patient survival, and may serve as a novel prognosis marker for endometrial cancer.
Biased Signaling in Mutated Variants ofβ2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations
Authors: Madhu Midhun K. , Shewani Kunal , Murarka Rajesh K.
Published: September 2023

The molecular basis of receptor bias in G protein-coupled receptors (GPCRs) caused by mutations that preferentially activate specific intracellular transducers over others remains poorly understood. Two experimentally identified biased variants ofβ2-adrenergic receptors (β2AR), a prototypical GPCR, are a triple mutant (T68F, Y132A, and Y219A) and a single mutant (Y219A); the former bias the receptor towards theβ-arrestin pathway by disfavoring G protein engagement, while the latter induces G protein signaling explicitly due to selection against GPCR kinases (GRKs) that phosphorylate the receptor as a prerequisite ofβ-arrestin binding. Though rigorous characterizations have revealed functional implications of these mutations, the atomistic origin of the observed transducer selectivity is not clear. In this study, we investigate the allosteric mechanism of receptor bias inβ2AR using microseconds of all-atom Gaussian accelerated molecular dynamics (GaMD) simulations. Our observations reveal distinct rearrangements in transmembrane helices, intracellular loop 3, and critical residues R1313.50and Y3267.53in the conserved motifs D(E)RY and NPxxY for the mutant receptors, leading to their specific transducer interactions. The reorganization of allosteric communications from the extracellular agonist BI-167107 to the intracellular receptor-transducer interfaces drives the conformational rearrangements responsible for receptor bias in the single and triple mutants. The molecular insights into receptor bias ofβ2AR presented here could improve the understanding of biased signaling in GPCRs, potentially opening new avenues for designing novel therapeutics with fewer side effects and superior efficacy.
When paleontology meets genomics: complete mitochondrial genomes of two saber-toothed cats’ species (Felidae: Machairodontinae)
Authors: Rodrigues-Oliveira Igor Henrique , da Silva Iuri Batista , Rocha Renan Rodrigues , Silva Soares Rafael Augusto , Menegídio Fabiano Bezerra , Garcia Caroline , Pasa Rubens , Kavalco Karine Frehner
Published: September 2023

Within the Machairodontinae subfamily, commonly referred as saber-toothed cats, it is worth noting that only two species, namelyHomotherium latidens, recognized as the scimitar-toothed cat, andSmilodon populator, renowned as the saber-toothed tiger, possess partial mitochondrial genomes accessible in the NCBI database. These sequences, however, do not include the mitogenome control region (D-loop) and have several gaps in their genes, including protein-coding genes (PCGs) that are widely used in phylogenetic analysis. In this study, we aimed to obtain a complete assembly of the mitogenomes of these two species from next-generation sequencing data available at NCBI’s SRA. Thede novoassemblies showed complete mitogenomes with 17,323bp (H. latidens) and 16,769 bp (S. populator), both with 13 PCGs, 22tRNAs, two rRNAs and the D-loop (Control region), with all genes following the standard order and position of most vertebrate mitogenomes. Our phylogeny and molecular dating, despite being generally very similar to previous studies, reveals an earliest divergence between North American and North SeaH. latidensspecimens which may be related to an Early Pleistocene migration across Beringia.
A HEV ORF2 protein-mediated mechanism of hepatitis E-associated kidney disease
Authors: Helmchen Birgit , Leblond Anne-Laure , Lenggenhager Daniela , Jetzer Jasna , Ankavay Maliki , Helmchen Fritjof , Yurtsever Hueseyin , Parrotta Rossella , Healy Marc E. , Pöschel Amiskwia , Markkanen Enni , Semmo Nasser , Ferrié Martin , Cocquerel Laurence , Seeger Harald , Hopfer Helmut , Müllhaupt Beat , Gouttenoire Jérôme , Moradpour Darius , Gaspert Ariana , Weber Achim
Published: September 2023

Hepatitis E virus (HEV) infection, one of the most common forms of hepatitis worldwide, is often associated with extrahepatic, particularly renal, manifestations. However, the underlying mechanisms are incompletely understood. Here, we report the development of ade novoimmune complex-mediated glomerulonephritis (GN) in a kidney transplant recipient with chronic hepatitis E. Applying immunostaining, electron microscopy, and mass spectrometry after laser-capture microdissection, we show that GN developed in parallel with increasing glomerular deposition of a noninfectious form of HEV open reading frame 2 (ORF2, capsid) protein secreted in excess. HEV particles or RNA, however, were not detectable. Patients with acute hepatitis E displayed similar but less pronounced deposits. Our results elucidate an immunologic mechanism by which this hepatotropic virus causes variable renal manifestations and establish a link between the HEV ORF2 protein and hepatitis E-associated GN. They directly provide a tool for etiology-based diagnosis of HEV-associated GN as a distinct entity and suggest therapeutic implications.
Generating Novel Leads for Drug Discovery using LLMs with Logical Feedback
Authors: Brahmavar Shreyas Bhat , Srinivasan Ashwin , Dash Tirtharaj , Krishnan Sowmya R , Vig Lovekesh , Roy Arijit , Aduri Raviprasad
Published: September 2023

Large Language Models (LLMs) can be used as repositories of biological and chemical information to generate pharmacological lead compounds. However, for LLMs to focus on specific drug targets typically require experimentation with progressively more refined prompts. Results thus become dependent not just on what is known about the target, but also on what is known about the prompt-engineering. In this paper, we separate the prompt into domain-constraints that can be written in a standard logical form, and a simple text-based query. We investigate whether LLMs can be guided, not by refining prompts manually, but by refining the the logical component automatically, keeping the query unchanged. We describe an iterative procedure LMLF (“Language Models with Logical Feedback”) in which the constraints are progressively refined using a logical notion of generalisation. On any iteration, newly generated instances are verified against the constraint, providing “logical-feedback” for the next iteration’s refinement of the constraints. We evaluate LMLF using two well-known targets (inhibition of the Janus Kinase 2; and Dopamine Receptor D2); and two different LLMs (GPT-3 and PaLM). We show that LMLF, starting with the same logical constraints and query text, can guide both LLMs to generate potential leads. We find: (a) Binding affinities of LMLF-generated molecules are skewed towards higher binding affinities than those from existing baselines; LMLF results in generating molecules that are skewed towards higher binding affinities than without logical feedback; (c) Assessment by a computational chemist suggests that LMLF generated compounds may be novel inhibitors. These findings suggest that LLMs with logical feedback may provide a mechanism for generating new leads without requiring the domain-specialist to acquire sophisticated skills in prompt-engineering.
Joint modelling of whole genome sequence data for human height via approximate message passing
Authors: Depope Al , Bajzik Jakub , Mondelli Marco , Robinson Matthew R.
Published: September 2023

Human height is a model for the genetic analysis of complex traits, and recent studies suggest the presence of thousands of common genetic variant associations and hundreds of low-frequency/rare variants. Here, we show that existing variable selection methods may fail to either select the correct genomic regions, or the appropriate genetic variants due to the complex and potentially long-distance correlation structure of whole genome sequence (WGS) data. To address this, we develop a new algorithmic paradigm based on approximate message passing, gVAMP, which we show accurately localizes associations to variants with the correct frequency and position in the DNA. We apply gVAMP to jointly model the relationship of tens of millions of WGS variants with human height in hundred of thousands of UK Biobank individuals. We find a power relationship of effect size and frequency of −1.1 ± 0.2, identify 59 rare variants and gene burden scores alongside many hundreds of DNA regions containing common variant associations, and show that understanding the genetic basis of complex traits will require the joint analysis of hundreds of millions of variables measured on millions of people. The polygenic risk scores obtained from gVAMP have high accuracy (including a prediction accuracy of ∼ 46% for human height) and outperform current methods for downstream tasks such as mixed linear model association testing across 13 UK Biobank traits. In conclusion, gVAMP offers a scalable foundation towards a wider range of analyses in WGS data.
Reduced glutamate decarboxylase 1 underlies morphine-promoted lung metastasis of triple-negative breast cancer in mice
Authors: Chen Shih-Hong , Shih Chien-Hung , Ke Ting-Ling , Hsiung Chia-Ni , Chen Kuo-Chin , Huang Zi-Xuan , Chuang Tsung-Hsien , Chen Li-Kuei , Chen Linyi
Published: September 2023

Introduction

Morphine is commonly used for cancer-related pain management. Long-term morphine use is not only addictive but also has been associated with risk factor for cancer.

Methods

We intraperitoneally administered morphine to mice for 14 days and then implanted EO771 cells, triple negative breast cancer cells, into their mammary fat pad. After primary tumors were removed on 38th day, a subset of mice were continuously giving saline or morphine until the 68th day. Tumor size, organ metastasis, and tumor RNA expression were analyzed.

Results

Our results revealed that long-term morphine treatment increased lung metastasis in the triple-negative breast cancer mouse model. To determine cellular pathways responsible for morphine-mediated metastasis, we performed RNA sequencing analysis to compare transcriptional profiles during metastasis. Transcriptional analysis revealed a significant number of genes down-regulated by morphine treatment. Based on pathway analysis, we focused on the novel effect of morphine on down-regulating taurine/hypotaurine biosynthesis. Considering that morphine, droperidol (dopamine receptor antagonist), and naloxone (opioid receptor antagonist) may act through opioid receptor or dopamine receptor, we further demonstrated that taurine reduced EO771 cell invasion caused by morphine, but not by droperidol, or naloxone treatment. In addition, morphine treatment significantly reduced the expression ofGAD1, one of the enzymes required for biosynthesis of taurine, whereas droperidol and naloxone did not.

Conclusion

These novel findings of morphine reducesGAD1level and taurine reverses invasion suggest that taurine could potentially be employed as a supplement for triple negative breast cancer patients using morphine as pain management.

Key Messages

Morphine usage has been implicated in modulating immune system and affecting cancer progression.

Long-term usage of morphine promotes metastasis of triple negative breast cancer through reducing taurine biosynthesis.

These novel findings of morphine reduces GAD1 level and taurine reverses invasion suggest that taurine could potentially be employed as a supplement for triple negative breast cancer patients using morphine as pain management.
Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state
Authors: D’Amore Vincenzo Maria , Conflitti Paolo , Marinelli Luciana , Limongelli Vittorio
Published: September 2023

G protein coupled receptors (GPCRs) are membrane proteins of greatest pharmacological relevance, targeted by over one third of marketed drugs. These receptors are activated by orthosteric ligands and undergo large conformational changes that lead to coupling diverse effector proteins. To achieve a fine regulation of the drug pharmacological response, it is imperative to shed light on the yet poorly understood aspects of GPCRs activation. In this work, we elucidate the entire activation mechanism of the adenosine A2A receptor (A2AR), a class A GPCR, performing minute timescale molecular dynamics and free energy calculations. We have explored the entire conformational landscape of A2AR in its basal apo form and in differently ligated conditions, elucidating the ligand intrinsic activity and the receptor’s lowest energy functional states. Among these is a novel pseudo-active state (pAs) of the A2AR apo form stabilised by specific “microswitch” residues interactions, including the salt bridge between the class A conserved residues R5.66and E6.30. In the pAs state, A2AR is able to couple β-arrestin 1 over G proteins, providing unprecedented structural basis for receptor desensitization and G protein-alternative cellular pathways. Our simulation protocol is generalisable and can be applied to study the activation of any GPCR, resulting a precious tool for drug design and biased signaling studies.
Proteomic adaptations in the kidney reveal orchestration of local and secreted antimicrobial peptides in human pyelonephritis
Authors: Borgards Lars , Siebels Bente , Voss Hannah , Krisp Christoph , Schmitz Jessica , Schwarz Lisa , Siemes Devon , Spangenberg Philippa , Bräsen Jan H , von Vietinghoff Sibylle , Schlüter Hartmut , Wagenlehner Florian , Engel Daniel R. , Shevchuk Olga
Published: September 2023

Pyelonephritis (PN) is a frequent bacterial infection of the kidney and is often associated with severe diseases, organ loss and sepsis. Antibiotics are the cornerstone of therapy, however, increasing antibiotic resistance threatens therapy success and necessitates novel treatment strategies. Various proteins, such as antimicrobial peptides (AMPs), are key molecules of the innate immune response and insights into their regulation may help overcome multi-drug resistance and severe diseases. Using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS), several cellular, biological, and metabolic processes important for the antimicrobial response were identified, including a significant increase in previously undescribed proteins in human PN with antimicrobial function. Among others, we observed elevation of AMPs, such as calprotectin, azurocidin-1, and cathepsin G in the kidney, which we validated in the urine. Additionally, we observed a negative correlation of azurocidin-1 with plasma levels of C-reactive protein suggesting that the presence in the kidney may protect from severe diseases and systemic inflammation. This study represents the first renal proteomic dataset of human PN, enabling novel insights into the expression of AMPs in the context of PN.

Lay Summary

Growing antimicrobial resistance necessitates a better understanding of the expression of proteins that are critical for the immune response. Using mass spectrometry we identified AMPs in the kidney and urine of PN patients. Elevated levels of the AMP azurocidin-1 was associated with reduced systemic inflammation, indicated by lower C-reactive protein. Overall, this study identified expression of previously undescribed AMPs in the context of human PN. These proteins may play a pivotal role in protection from severe diseases and systemic inflammation.
Acute and sub-chronic toxicity of aqueous stem-bark extract ofAnnickia polycarpa
Authors: Lartey Nathaniel Lartey , Nyarko Eric Nana Yaw , Asare-Anane Henry , Antwi Stephen , Okine Laud Kenneth
Published: September 2023

Background and aim

The lack of standardization and scientific validation of the use of most plant extracts leads to toxicity problems. The stem bark extract ofAnnickia polycarpahas been shown to possess antioxidant, antidiabetic, analgesic, and anti-colitis effects. However, nothing is known about the effects of the prolonged use of the extract. Thus, we investigated the acute and sub-chronic toxicity of the aqueous stem bark extract of (APE) in Sprague-Dawley rats.

Experimental procedure

The LD50 and sub-chronic toxicity of APE (20 mg/kg, 100 mg/kg, and 500 mg/kg) was studied over 3 months in Sprague-Dawley rats. Serum alkaline phosphatase (ALP), alanine transaminase (ALT), direct bilirubin and creatinine were measured after 3 months of treatment. Hematological analysis and urinalysis were also performed. Also, the effect of APE on blood clotting time and pentobarbital-induced sleeping time were determined at the termination of treatment. Finally, histological analysis was done on liver, kidney, lung, and heart after hematoxylin-eosin staining of tissue cross-sections at the termination of treatment.

Results and conclusion

The LD50 of APE in rats was higher than 5000 mg/kg with no observable signs of toxicity. APE also showed no hematotoxic effect when used consistently for 3 months. Additionally, APE had no adverse effect on the liver and kidney evidenced by a lack of effect on serum biochemical parameters (ALP, ALT, direct bilirubin, and creatinine), urinalysis as well as the tissue morphology of these organs. No adverse morphological effects were also observed with the heart muscle cells. However, APE showed mild selective toxicity to the lung characterized by alveolar space closing and interstitial fibrosis and alveolar septa thickening. These results indicate that APE is generally non-toxic at the tested doses but shows mild selective pneumotoxicity when used over a long period of time.
EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks
Authors: Roche Rahmatullah , Moussad Bernard , Shuvo Md Hossain , Tarafder Sumit , Bhattacharya Debswapna
Published: September 2023

Protein language models (pLMs) trained on a large corpus of protein sequences have shown unprecedented scalability and broad generalizability in a wide range of predictive modeling tasks, but their power has not yet been harnessed for predicting protein-nucleic acid binding sites, critical for characterizing the interactions between proteins and nucleic acids. Here we present EquiPNAS, a new pLM-informed E(3) equivariant deep graph neural network framework for improved protein-nucleic acid binding site prediction. By combining the strengths of pLM and symmetry-aware deep graph learning, EquiPNAS consistently outperforms the state-of-the-art methods for both protein-DNA and protein-RNA binding site prediction on multiple datasets across a diverse set of predictive modeling scenarios ranging from using experimental input to AlphaFold2 predictions. Our ablation study reveals that the pLM embeddings used in EquiPNAS are sufficiently powerful to dramatically reduce the dependence on the availability of evolutionary information without compromising on accuracy, and that the symmetry-aware nature of the E(3) equivariant graph-based neural architecture offers remarkable robustness and performance resilience. EquiPNAS is freely available athttps://github.com/Bhattacharya-Lab/EquiPNAS.