bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arresting microbiome development limits immune system maturation and resistance to infection
Authors: Lubin Jean-Bernard , Green Jamal , Maddux Sarah , Denu Lidiya , Duranova Tereza , Lanza Matthew , Wynosky-Dolfi Meghan , Brodsky Igor E. , Planet Paul J. , Silverman Michael A. 
Published: January 2022

AbstractDisruptions to the intestinal microbiome during weaning lead to long-term negative effects on host immune function. However, the critical host-microbe interactions occurring during weaning required for healthy immune system development remain poorly understood. We find that restricting microbiome maturation during weaning leads to stunted immune system development and increased susceptibility to enteric infection. We developed a gnotobiotic mouse model of the early-life microbiome designated as Pediatric Community (PedsCom). This nine-member consortium of microbes derived from intestinal microbiomes of preweaning mice stably colonized germfree adult mice and was efficiently transmitted to offspring for multiple generations. Unexpectedly, the relative abundance of PedsCom microbes were largely unaffected by the transition from a milk-based to a fiber rich solid food diet. PedsCom mice developed less peripheral regulatory T cells and Immunoglobulin A, hallmarks of microbiota-driven immune system development. Consistent with defects in maturation, adult PedsCom mice retain high susceptibility to salmonella infection characteristic of young mice and humans. Altogether, our work illustrates how the post-weaning transition in intestinal microbiome composition contributes to normal immune maturation and protection from enteric infection. Accurate modelling of the pre-weaning microbiome provides a window into the microbial requirements of healthy immune development and suggests an opportunity to design microbial interventions at weaning to improve immune system development in human infants.One Sentence SummaryArresting microbiome development stunts immune ontogeny
Structural basis for Nirmatrelvir in vitro efficacy against SARS-CoV-2 variants
Authors: Greasley Samantha E , Noell Stephen , Plotnikova Olga , Ferre Rose Ann , Liu Wei , Bolanos Ben , Fennell Kimberly , Nicki Jennifer , Craig Tim , Zhu Yuao , Stewart Al E , Steppan Claire M 
Published: January 2022

AbstractThe COVID-19 pandemic continues to be a public health threat with emerging variants of SARS-CoV-2. Nirmatrelvir (PF-07321332) is a reversible, covalent inhibitor targeting the main protease (Mpro) of SARS-CoV-2 and the active protease inhibitor in PAXLOVID™ (nirmatrelvir tablets and ritonavir tablets). We evaluated the in vitro catalytic activity and in vitro potency of nirmatrelvir against the main protease (Mpro) of prevalent variants of concern (VOC) or variants of interest (VOI): Alpha (α, B.1.1.7), Beta (β, B.1.351), Delta (δ, B1.617.2), Gamma (γ, P.1), Lambda (λ, B.1.1.1.37/C37), Omicron (o, B.1.1.529) as well as the original Washington or wildtype strain. These VOC/VOI carry prevalent mutations at varying frequencies in the Mpro specifically for: α, β, γ (K90R), λ (G15S) and o (P132H). In vitro biochemical enzymatic assay characterization of the enzyme kinetics of the mutant Mpros demonstrate that they are catalytically comparable to wildtype. Nirmatrelvir has similar potency against each mutant Mpro including P132H that is observed in the Omicron variant with a Ki of 0.635 nM as compared to a Ki of 0.933nM for wildtype. The molecular basis for these observations were provided by solution-phase structural dynamics and structural determination of nirmatrelvir bound to the o, λ and β Mpro at 1.63 - 2.09 Å resolution. These in vitro data suggest that PAXLOVID has the potential to maintain plasma concentrations of nirmatrelvir many-fold times higher than the amount required to stop the SARS-CoV-2 VOC/VOI, including Omicron, from replicating in cells (1).
Super-silencers regulated by chromatin interactions control apoptotic genes
Authors: Zhang Ying , Chen Kaijing , Cai Yichao , Nambu Akiko , See Yi Xiang , Fu Chaoyu , Raju Anandhkumar , Lakshmanan Manikandan , Osato Motomi , Tergaonkar Vinay , Fullwood Melissa Jane 
Published: January 2022

SummaryHuman silencers have been shown to exist and regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated such as the working mechanism and whether they can form “super-silencers”. Here, through interrogating two putative silencer components of FGF18 gene, we found that two silencers can cooperate via compensated chromatin interactions to form a “super-silencer”. Furthermore, double knock-out of two silencers exhibited synergistic upregulation of FGF18 expression and changes of cell identity. To disturb the “super-silencers”, we applied combinational treatment of an EZH2 inhibitor GSK343, and a REST inhibitor, X5050 (“GR”). We found that GR led to severe loss of TADs and loops, while the use of just one inhibitor by itself only showed mild changes. Such changes of TADs and loops may due to reduced CTCF protein level observed upon GR treatment. Moreover, GSK343 and X5050 worked together synergistically to upregulate the apoptotic genes controlled by super-silencers, and thus gave rise to antitumor effects including apoptosis, cell cycle arrest and tumor growth inhibition. Overall, our data demonstrated the first example of a “super-silencer” and showed that combinational usage of GSK343 and X5050 could potentially lead to cancer ablation through disruption of “super-silencers”.
Activation of the Integrated Stress Response overcomes multidrug resistance in FBXW7-deficient cells
Authors: Sanchez-Burgos Laura , Navarro-González Belén , García-Martín Santiago , Tejero Héctor , Antón Marta Elena , Al-Shahrour Fátima , Fernandez-Capetillo Oscar 
Published: January 2022

SUMMARYFBXW7 is one of the most frequently mutated tumor suppressors, the deficiency of which has been associated with resistance to some anticancer therapies. Through bioinformatic analyses and genome-wide CRISPR screens, we here reveal that FBXW7 deficiency leads to multidrug resistance (MDR), to a bigger extent than well-established MDR-drivers such as overexpression of the drug-efflux pump ABCB1. Proteomic data from FBXW7-deficient cancer cells identify the upregulation of mitochondrial function as a hallmark of FBXW7 deficiency, which has been previously linked to an increased resistance to chemotherapy. Accordingly, genetic or chemical targeting of mitochondria is preferentially toxic for FBXW7-deficient cells in vitro and in vivo. Mechanistically, we show that the toxicity associated with therapies that target mitochondrial translation such as the antibiotic tigecycline relates to the activation of the Integrated Stress Response (ISR). Furthermore, while searching for additional drugs that could overcome the MDR of FBXW7-deficient cells, we found that all of them unexpectedly also activated the ISR regardless of their currently accepted mechanism of action. Together, our study reveals that one of the most frequent mutations in cancer reduces the sensitivity to the vast majority of available therapies, and identifies a general principle to overcome such resistance.
Single cell profiling of γδ hepatosplenic T-cell lymphoma unravels tumor cell heterogeneity associated with disease progression
Authors: Song Wei , Zhang Haixi , Yang Fan , Nakahira Kiichi , Wang Cheng , Shi Keqian , Zhang Ruoyu 
Published: January 2022

AbstractHepatosplenic T-cell lymphoma (HSTCL), mostly derived from γδ T cells, is a rare but very aggressive lymphoma with poor outcomes. The molecular pathogenesis driving HSTCL is largely unknown while only limited treatment options are available. In this study, by performing paired single cell RNA-seq and T cell receptor (TCR) sequencing on biopsies from a HSTCL patient pre- and post-chemotherapy treatments, we characterized unique gene expressing signatures of malignant γδ T cells, with a set of marker genes were newly identified in HSTCL (AREG, PLEKHA5, VCAM1 etc.). Although the malignant γδ T cells were expanded from a single TCR clonotype according to their TCR identities, they evolved into two transcriptional distinct tumor subtypes during the disease progression. The Tumor_1 subtype was dominant in pre-treatment samples with highly aggressive phenotypes. While the Tumor_2 had relative mild cancer hallmark signatures but expressed genes associated with tumor survival signal and drug resistance (IL32, TOX2, AIF1, AKAP12 etc.), and finally became the main tumor subtype post-treatment. We further dissected the tumor microenvironment of the HSTCL and noticed that CD8 memory T cells were clonal expanded post-treatment. In addition, we discovered dynamically rewiring cell-cell interaction networks during the treatment. The tumor cells had reduced communications with the microenvironment post-treatment. Our study reveals heterogenous and dynamic tumor and microenvironment underlying pathogenesis of HSTCL and may contribute to identify novel targets for diagnosis and cure of HSTCL in the future.
xia2.multiplex: a multi-crystal data analysis pipeline
Authors: Gildea Richard J. , Beilsten-Edmands James , Axford Danny , Horrell Sam , Aller Pierre , Sandy James , Sanchez-Weatherby Juan , Owen C. David , Lukacik Petra , Strain-Damerell Claire , Owen Robin L. , Walsh Martin A. , Winter Graeme 
Published: January 2022

AbstractIn macromolecular crystallography radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals, for example small-wedge data collections on micro-crystals, in situ room-temperature data collections, and collection from membrane proteins in lipidic mesophase. Whilst indexing and integration of individual data sets may be relatively straightforward with existing software, merging multiple data sets from small wedges presents new challenges. Identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. Furthermore, the presence of non-isomorphous or poor-quality data sets may reduce the overall quality of the final merged data set.To facilitate and help optimise the scaling and merging of multiple data sets, we developed a new program, xia2.multiplex, which takes data sets individually integrated with DIALS and performs symmetry analysis, scaling and merging of multicrystal data sets. xia2.multiplex also performs analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferential orientation. After describing a number of use cases, we demonstrate the benefit of xia2.multiplex within a wider autoprocessing framework in facilitating a multi-crystal experiment collected as part of in situ room-temperature fragment screening experiments on the SARS-CoV-2 main protease.
AXL-TBK1 driven nuclear AKT3 promotes metastasis
Authors: Arner Emily N. , Westcott Jill M. , Hinz Stefan , Tiron Crina Elena , Blø Magnus , Mai Anja , Virtakoivu Reetta , Phinney Natalie , Nord Silje , Aguilera Kristina Y. , Rizvi Ali , Toombs Jason E. , Reese Tanner , Fey Vidal , Micklem David , Gausdal Gro , Ivaska Johanna , Lorens James B. , Brekken Rolf A. 
Published: January 2022

AbstractEpithelial-to-mesenchymal transition (EMT) contributes to tumor cell survival, immune evasion, migration, invasion, and therapy resistance. Across human cancer, tumors that are high grade, poorly differentiated, and have undergone EMT carry a worse prognosis with a higher likelihood of metastasis. AXL, a receptor tyrosine kinase, drives EMT and is implicated in tumor progression, metastasis, and therapy resistance in multiple cancer types including pancreatic cancer and breast cancer. TANK-binding kinase 1 (TBK1) is central to AXL-driven EMT yet, the mechanism of how TBK1 induces EMT remains unclear. Here, we report that AXL activation stimulates TBK1 binding and phosphorylation of AKT3. TBK1 activation of AKT3 drives binding and phosphorylation of slug/snail resulting in protection from proteasomal degradation and translocation of the complex into the nucleus. We show that nuclear translocation of AKT3 is required for AXL-driven EMT and metastasis. Congruently, nuclear AKT3 expression correlates with worse outcome in aggressive breast cancer. To advance AKT3 as a therapeutic target, an AKT3-isoform selective allosteric small molecule inhibitor, BGB214, was developed. BGB214 inhibits AKT3 nuclear translocation, EMT-TF stability, AKT3-mediated invasion of breast cancer cells and reduces tumor initiation in vivo. Our results suggest that AKT3 nuclear activity is an important feature of AXL-driven epithelial plasticity and that selective AKT3 inhibition represents a novel therapeutic avenue for treating aggressive cancer.SignificanceNuclear AKT3 activity is an important feature of AXL-TBK1 driven EMT and metastasis, thus selective AKT3 targeting represents a novel approach to treat aggressive cancer.
Mapping the developing human immune system across organs
Authors: Suo Chenqu , Dann Emma , Goh Issac , Jardine Laura , Kleshchevnikov Vitalii , Park Jong-Eun , Botting Rachel A. , Stephenson Emily , Engelbert Justin , Tuong Zewen Kelvin , Polanski Krzysztof , Yayon Nadav , Xu Chuan , Suchanek Ondrej , Elmentaite Rasa , Conde Cecilia Domínguez , He Peng , Pritchard Sophie , Miah Mohi , Moldovan Corina , Steemers Alexander S. , Prete Martin , Marioni John C. , Clatworthy Menna R. , Haniffa Muzlifah , Teichmann Sarah A. 
Published: January 2022

AbstractRecent advances in single cell genomics technologies have facilitated studies on the developing immune system at unprecedented scale and resolution. However, these studies have focused on one or a few organs and were thus limited in understanding the developing immune system as a distributed network across tissues. Here, we profiled prenatal haematopoietic organs, lymphoid organs and non-lymphoid tissues using a combination of single-cell RNA sequencing, paired antigen-receptor sequencing and spatial transcriptomics to reconstruct the developing human immune system. Our analysis revealed the acquisition of immune effector transcriptome profiles in macrophages, mast cells and NK cells from the second trimester, and the transcriptomic changes accompanying the late-stage maturation of developing monocytes and T cells that extended from their organ of origin to peripheral tissues. We uncovered system-wide blood and immune cell development beyond the conventional primary haematopoietic organs. We further identified, extensively characterised and functionally validated the human prenatal B1 cells. Finally, we provide evidence for thymocyte-thymocyte selection origin for αβTCR- expressing unconventional T cells based on TCR gene usage and anin vitroartificial thymic organoid culture model. Our comprehensive atlas of the developing human immune system provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine and disease understanding.One-Sentence SummaryBy performing a comprehensive single-cell RNA sequencing atlas of human developing immune system together with antigen-receptor sequencing and spatial transcriptomics, we explored the cross-gestation and cross-organ variability in immune cells, discovered system-wide blood and immune cell development, identified, characterised and functionally validated the properties of human prenatal B1 cells and the origin of unconventional T cells.
Ultra high diversity factorizable libraries for efficient therapeutic discovery
Authors: Dai Zheng , Saksena Sachit D. , Horny Geraldine , Banholzer Christine , Ewert Stefan , Gifford David K. 
Published: January 2022

AbstractThe successful discovery of novel biological therapeutics by selection requires highly diverse libraries of candidate sequences that contain a high proportion of desirable candidates. Here we propose the use of computationally designed factorizable libraries made of concatenated segment libraries as a method of creating large libraries that meet an objective function at low cost. We show that factorizable libraries can be designed efficiently by representing objective functions that describe sequence optimality as an inner product of feature vectors, which we use to design an optimization method we call Stochastically Annealed Product Spaces (SAPS). We then use this approach to design diverse and efficient libraries of antibody CDR-H3 sequences with various optimized characteristics.
A genome-wide screen identifies SCAI as a modulator of the UV-induced replicative stress response in human cells
Authors: Lemay Jean-François , St-Hilaire Edlie , Gezzar-Dandashi Sari , McQuaid Mary , Ronato Daryl A. , Gao Yuandi , Bélanger François , Sawchyn Christina , Ishimwe Aimé Boris Kimenyi , Mallette Frédérick A. , Masson Jean-Yves , Drobetsky Elliot A. , Wurtele Hugo 
Published: January 2022

ABSTRACTHelix-destabilizing DNA lesions induced by environmental mutagens such as UV light cause genomic instability by strongly blocking the progression of DNA replication forks (RF). At blocked RF, single-stranded DNA (ssDNA) accumulates and is rapidly bound by Replication Protein A (RPA) complexes. Such stretches of RPA-ssDNA constitute platforms for recruitment/activation of critical factors that promote DNA synthesis restart. However, during periods of severe replicative stress, RPA availability may become limiting due to inordinate sequestration of this multifunctional complex on ssDNA, thereby negatively impacting multiple vital RPA-dependent processes. Here, we performed a genome-wide screen to identify factors which restrict the accumulation of RPA-ssDNA during UV-induced replicative stress. While this approach revealed some expected “hits” acting in pathways such as nucleotide excision repair, translesion DNA synthesis, and the intra-S phase checkpoint, it also identifed SCAI, whose role in the replicative stress response was previously unappreciated. Upon UV exposure, SCAI knock-down caused elevated accumulation of RPA-ssDNA during S phase, accompanied by reduced cell survival and compromised RF progression. These effects were independent of the previously reported role of SCAI in 53BP1-dependent DNA double-strand break repair. We also found that SCAI colocalized with stalled RF, and that its depletion promoted nascent DNA degradation. Finally, we (i) provide evidence that EXO1 is the major nuclease underlying ssDNA formation and consequent DNA replication defects in SCAI knockout cells and, consistent with this, (ii) demonstrate that SCAI inhibits EXO1 activity on a ssDNA gap in vitro. Taken together, our data establish SCAI as a novel regulator of the replicative stress response in human cells.
SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients
Authors: Charvet Benjamin , Brunel Joanna , Pierquin Justine , Iampietro Mathieu , Decimo Didier , Queruel Nelly , Lucas Alexandre , del Mar Encabo-Berzosa María , Arenaz Izaskun , Marmolejo Tania Perez , Morales Francina Valezka Bolaños , Gonzalez Arturo Ivan Gonzalez , Maldonado Armando Castorena , Rivero César Luna , Mathieu Cyrille , Küry Patrick , Flores-Rivera Jose , Rios Santiago Avila , de Oca Gonzalo Salgado Montes , Schoorlemmer Jon , Horvat Branka , Perron Hervé 
Published: January 2022

AbstractPatients with COVID-19 may develop abnormal inflammatory response and lymphopenia, followed in some cases by delayed-onset syndromes, often long-lasting after the initial SARS-CoV-2 infection. As viral infections may activate human endogenous retroviral elements (HERV), we studied the effect of SARS-CoV-2 on HERV-W and HERV-K envelope (ENV) expression, known to be involved in immunological and neurological pathogenesis of human diseases. Our results have showed that the exposure to SARS-CoV-2 virus activates early HERV-W and K transcription but only HERV-W ENV protein expression, in an infection- and ACE2-independent way within peripheral blood mononuclear cell cultures from one-third of healthy donors. Moreover, HERV-W ENV protein was significantly increased in serum and plasma of COVID-19 patients, correlating with its expression in CD3+ lymphocytes and with disease severity. Finally, HERV-W ENV was found expressed in post-mortem tissues of lungs, heart, brain olfactory bulb and nasal mucosa from acute COVID-19 patients in cell-types relevant for COVID-19-associated pathogenesis within affected organs, but different from those expressing of SARS-CoV-2 antigens. Altogether, the present study revealed that SARS-CoV-2 can induce HERV-W ENV expression in cells from individuals with symptomatic and severe COVID-19. Our data suggest that HERV-W ENV is likely to be involved in pathogenic features underlying symptoms of acute and post-acute COVID. It highlights the importance to further understand patients’ genetic susceptibility to HERV-W activation and the relevance of this pathogenic element as a prognostic marker and a therapeutic target in COVID-19 associated syndromes.Graphical abstract
Genomic surveillance of Bacillus cereus sensu lato strains isolated from meat and poultry products in South Africa enables inter- and intra-national surveillance and source tracking
Authors: Carroll Laura M. , Pierneef Rian , Mathole Aletta , Atanda Abimbola , Matle Itumeleng 
Published: January 2022

AbstractMembers of the Bacillus cereus sensu lato (s.l.) species complex, also known as the B. cereus group, vary in their ability to cause illness, but are frequently isolated from foods, including meat products; however, food safety surveillance efforts that employ whole-genome sequencing (WGS) often neglect these potential pathogens. Here, WGS was used to characterize B. cereus s.l. strains (n = 25) isolated during surveillance of meat products in South Africa. Strains were collected from beef, poultry, and mixed meat products obtained from (i) retail outlets, processing plants, and butcheries across six South African provinces (n = 15, 7, and 1, respectively), and (ii) imports in cold stores (n = 2). Strains were assigned to panC Groups IV, III, II, and V (n = 18, 5, 1, and 1, respectively) and spanned multiple genomospecies, regardless of the taxonomy used. All strains possessed diarrheal toxin-encoding genes, while one sequence type 26 (ST26) strain possessed cereulide (emetic toxin) synthetase-encoding genes. No strains harbored anthrax toxin- or capsule-encoding genes. The 25 strains were partitioned into 15 lineages via in silico seven-gene multi-locus sequence typing (MLST), six of which contained multiple strains sequenced in this study, which were identical or nearly identical at the whole-genome scale. Five MLST lineages contained (nearly) identical genomes collected from two or three South African provinces; one MLST lineage contained nearly identical genomes from two countries (South Africa and the Netherlands), indicating that B. cereus s.l. can spread intra- and inter-nationally via foodstuffs.ImportanceNation-wide foodborne pathogen surveillance programs that employ high-resolution genomic methods have been shown to provide vast public health and economic benefits. However, B. cereus s.l. are often overlooked during large-scale, routine WGS efforts. Thus, to our knowledge, no studies to date have evaluated the potential utility of WGS for B. cereus s.l. surveillance and source tracking in foodstuffs. In this proof-of-concept study, we applied WGS to B. cereus s.l. strains collected via South Africa’s national surveillance program of domestic and imported meat products, and we provide strong evidence that B. cereus s.l. can be disseminated intra- and inter-nationally via the agro-food supply chain. Our results showcase that WGS can be used for source tracking of B. cereus s.l. in foods, although future WGS and isolate metadata collection efforts are needed to ensure that B. cereus s.l. surveillance initiatives are on par with those of other foodborne pathogens.