bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systems biological assessment of the temporal dynamics of immunity to a viral infection in the first weeks and months of life
Authors: Wimmers Florian , Burrell Allison R. , Feng Yupeng , Zheng Hong , Arunachalam Prabhu S. , Hu Mengyun , Spranger Sara , Nyhoff Lindsay , Joshi Devyani , Trisal Meera , Awasthi Mayanka , Bellusci Lorenza , Ashraf Usama , Kowli Sangeeta , Konvinse Katherine C. , Yang Emily , Blanco Michael , Pellegrini Kathryn , Tharp Gregory , Hagan Thomas , Chinthrajah R. Sharon , Grifoni Alba , Sette Alessandro , Nadeau Kari C. , Haslam David B. , Bosinger Steven E. , Wrammert Jens , Maecker Holden T. , Utz Paul J. , Wang Taia T. , Khurana Surender , Khatri Purvesh , Staat Mary A. , Pulendran Bali 
Published: January 2023

AbstractThe dynamics of innate and adaptive immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to SARS-CoV-2 infection in infants and young children in the first weeks and months of life by analyzing blood samples collected before, during, and after infection with Omicron and Non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, were stably maintained for >300 days. Antigen-specific memory B cell (MCB) responses were durable for 150 days but waned thereafter. Somatic hypermutation of V-genes in MCB accumulated progressively over 9 months. The innate response was characterized by upregulation of activation markers on blood innate cells, and a plasma cytokine profile distinct from that seen in adults, with no inflammatory cytokines, but an early and transient accumulation of chemokines (CXCL10, IL8, IL-18R1, CSF-1, CX3CL1), and type I IFN. The latter was strongly correlated with viral load, and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell transcriptomics. Consistent with this, single-cell ATAC-seq revealed enhanced accessibility of chromatic loci targeted by interferon regulatory factors (IRFs) and reduced accessibility of AP-1 targeted loci, as well as traces of epigenetic imprinting in monocytes, during convalescence. Together, these data provide the first snapshot of immunity to infection during the initial weeks and months of life.
Loss of WNT5 Proteins Reprograms Neutrophils in the Spleen to Provide Protection for DSS-Induced Colitis
Authors: Luan Yi , Hu Jiajia , Wang Qijun , Li Wenxue , Wang Xujun , Qu Rihao , Rajendran Barani Kumar , Zhou Hongyue , Liu Peng , Shi Yu , Liu Yansheng , Lu Jun , Tang Wenwen , Wu Dianqing 
Published: January 2023

AbstractWNT5A and WNT5B are two close homologs, both of which are implicated in the pathogenesis of inflammatory bowel diseases. However, the roles these two proteins play in the disease remain largely uncharacterized. Here, we report that double knockout ofWnt5aandWnt5b(Wnt5DKO) protects mice from Dextran Sodium Sulfate (DSS)-induced colitis in mice, accompanied with greater splenomegaly, stronger expansion of peripheral myeloid cells, and less colonic CD8+T cell granzyme B expression than those of the control mice. Depletion of neutrophils or splenectomy abrogates the phenotypic differences betweenWnt5DKO and control mice largely by exacerbating colitis phenotypes and increasing colonic CD8+T cell GZMB expression in theWnt5DKO mice. In addition, neutrophils from theWnt5DKO colitic mice exert stronger suppression of CD8+T cells than those from the control mice in culture. Single-cell RNA sequencing and proteomic analyses indicate that neutrophils from DSS-treatedWnt5DKO mice are of hyper-immunosuppressive and hypo-inflammatory characteristics and are distinct from those of DSS-treated control mice as well as myeloid-derived suppressor cells in tumor-bearing mice. Thus, our study reveals that the lack of WNT5 reprograms neutrophils in spleens to limit colonic injury during DSS-induced colitis.
Kinetic modelling of sterol transport between plasma membrane and endo-lysosomes based on quantitative fluorescence and X-ray imaging data
Authors: Wüstner Daniel , Juhl Alice Dupont , Egebjerg Jacob Marcus , Werner Stephan , McNally James , Schneider Gerd 
Published: January 2023

AbstractNiemann Pick type C1 and C2 (NPC1 and NPC2) are two sterol-binding proteins which, together, orchestrate cholesterol transport through late endosomes and lysosomes (LE/LYSs). NPC2 can facilitate sterol exchange between model membranes severalfold, but how this is connected to its function in cells is poorly understood. Using fluorescent analogs of cholesterol and quantitative fluorescence microscopy, we have recently measured the transport kinetics of sterol between plasma membrane (PM), recycling endosomes (REs) and LE/LYSs in control and NPC2 deficient fibroblasts. Here, we employ kinetic modeling of this data to determine rate constants for sterol transport between intracellular compartments. Our model predicts that sterol is trapped in intraluminal vesicles (ILVs) of LE/LYSs in the absence of NPC2, causing delayed sterol export from LE/LYSs in NPC2 deficient fibroblasts. Using soft X-ray tomography, we confirm, that LE/LYSs of NPC2 deficient cells but not of control cells contain enlarged, carbon-rich intraluminal vesicular structures, supporting our model prediction of lipid accumulation in ILVs. By including sterol export via exocytosis of ILVs as exosomes and by release of vesicles – ectosomes – from the PM, we can reconcile measured sterol efflux kinetics and show that both pathways can be reciprocally regulated by the intraluminal sterol transfer activity of NPC2 inside LE/LYSs. Our results thereby connect the in vitro function of NPC2 as sterol transfer protein between membranes with its in vivo function.
Programmable RNA detection with CRISPR-Cas12a
Authors: Rananaware Santosh R. , Vesco Emma K. , Shoemaker Grace M. , Anekar Swapnil S. , Sandoval Luke Samuel W. , Meister Katelyn S. , Macaluso Nicolas C. , Nguyen Long T. , Jain Piyush K. 
Published: January 2023

AbstractCRISPR is a prominent bioengineering tool and the type V CRISPR-associated protein complex, Cas12a, is widely used in diagnostic platforms due to its innate ability to cleave DNA substrates. Here we demonstrate that Cas12a can also be programmed to directly detect RNA substrates without the need for reverse transcription or strand displacement. We discovered that while the PAM-proximal “seed” region of the crRNA exclusively recognizes DNA for initiatingtrans-cleavage, the PAM-distal region or 3’-end of the crRNA can tolerate both RNA and DNA substrates. Utilizing this property, we developed a method named Split Activators for Highly Accessible RNA Analysis or ‘SAHARA’ to detect RNA sequences at the PAM-distal region of the crRNA by merely supplying a short ssDNA or a PAM containing dsDNA to the seed region. Notably, SAHARA is Mg2+concentration- and pH-dependent, and it was observed to work robustly at room temperature with multiple orthologs of Cas12a. SAHARA also displayed a significant improvement in the specificity for target recognition as compared to the wild-type CRISPR-Cas12a, at certain positions along the crRNA. By employing SAHARA we achieved amplification-free detection of picomolar concentrations of miRNA-155 and hepatitis C virus RNA. Finally, SAHARA can use a PAM-proximal DNA as a switch to control the trans-cleavage activity of Cas12a for the detection of both DNA and RNA targets. With this, multicomplex arrays can be made to detect distinct DNA and RNA targets with pooled crRNA/Cas12a complexes. In conclusion, SAHARA is a simple, yet powerful nucleic acid detection platform based on Cas12a that can be applied in a multiplexed fashion and potentially be expanded to other CRISPR-Cas enzymes.Abstract Figure
A Systematic Approach to the Discovery of Protein-Protein Interaction Stabilizers
Authors: Kenanova Dyana N. , Visser Emira J. , Virta Johanna M. , Sijbesma Eline , Centorrino Federica , Vickery Holly R. , Zhong Mengqi , Neitz R. Jeffrey , Brunsveld Luc , Ottmann Christian , Arkin Michelle R. 
Published: January 2023

ABSTRACTProtein-protein interactions (PPIs) are responsible for the proper function of biological processes and, when dysregulated, commonly lead to disease. PPI stabilization has only recently been systematically explored for drug discovery despite being a powerful approach to selectively target intrinsically disordered proteins and hub proteins, like 14-3-3, with multiple interaction partners. Disulfide tethering is a site-directed fragment-based drug discovery (FBDD) methodology for screening small molecules in a quantitative, high-throughput manner. We explore the scope of the disulfide tethering technology for the discovery of selective fragments as starting points for the development of potent small molecule PPI stabilizers and molecular glues using the hub protein 14-3-3σ. The complexes with 5 biologically and structurally diverse phospho-peptides, derived from the 14-3-3 client proteins ERα, FOXO1, C-RAF, USP8, and SOS1, were screened for hit identification. Stabilizing fragments could be found for 4/5 client complexes with a diversified hit-rate and stabilizing efficacy for the different 14-3-3/client phospho-peptides. Extensive structural elucidation revealed the ability and adaptivity of the peptide to make productive interactions with the tethered fragments as key criterion for cooperative complex formation. We validated eight fragment stabilizers, six of which showed selectivity for one phospho-peptide client, and structurally characterized two nonselective hits and four fragments that selectively stabilized C-RAF or FOXO1. The most efficacious of these fragments increased 14-3-3σ/C-RAF phospho-peptide affinity by 430-fold. Disulfide tethering to the wildtype C38 in 14-3-3σ provided diverse structures for future optimization of 14-3-3/client stabilizers and highlighted a systematic method to discover molecular glues.
Overexpression of ADAR1 in mice does not initiate or accelerate cancer formationin vivo
Authors: Ruiz Shannon Mendez , Chalk Alistair M , Goradia Ankita , Heraud-Farlow Jacki , Walkley Carl R 
Published: January 2023

ABSTRACTAdenosine to inosine editing (A-to-I) in regions of double stranded RNA (dsRNA) is mediated by adenosine deaminase acting on RNA 1 (ADAR1) or ADAR2. ADAR1 and A-to-I editing levels are increased in many human cancers. It is not established if elevated ADAR1 represents a driver or passenger during cancer formation. We established a series of murine alleles to allowin vivooverexpression of ADAR1, its individual isoforms or mutant forms of ADAR1 to understand how it contributes to cancer pathogenesis. The widespread overexpression of ADAR1 or either the p110 or p150 isoforms as sole lesions was well tolerated and did not result in cancer formation. Therefore, ADAR1 overexpression alone is not sufficient to initiate cancer. We demonstrate that endogenous ADAR1 and A-to-I editing levels increased upon immortalization by loss of p53 in murine cells, consistent with the observations from human cancers. We tested if ADAR1 overexpression could co- operate with cancer initiated by loss of tumour suppressors using a model of osteosarcoma. We did not see a disease potentiating or modifying effect of overexpressing ADAR1 or its isoforms. We conclude that the increase in ADAR1 expression and A-to-I editing in cancers is a passenger, rather than a driver, of tumor formation.
Heterozygous Nonsense Variants in the Ferritin Heavy Chain GeneFTH1Cause a Novel Pediatric Neuroferritinopathy
Authors: Shieh Joseph T , Tintos-Hernández Jesus A , Murali Chaya N. , Penon-Portmann Monica , Flores-Mendez Marco , Santana Adrian , Bulos Joshua A. , Du Kang , Dupuis Lucie , Damseh Nadirah , Mendoza-Londoño Roberto , Berera Camilla , Lee Julieann C , Phillips Joanna J , Alves César A P F , Dmochowski Ivan J , Ortiz-González Xilma R 
Published: January 2023

AbstractFerritin, the iron storage protein, is composed of light and heavy chain subunits, encoded byFTLandFTH1, respectively. Heterozygous variants inFTLcause hereditary neuroferritinopathy, a type of neurodegeneration with brain iron accumulation (NBIA). Variants inFTH1have not been previously associated with neurologic disease. We describe the clinical, neuroimaging, and neuropathology findings of five unrelated pediatric patients withde novoheterozygousFTH1variants. Children presented with developmental delay, epilepsy, and progressive neurologic decline. NonsenseFTH1variants were identified using whole exome sequencing, with a recurrentde novovariant (p.F171*) identified in three unrelated individuals. Neuroimaging revealed diffuse volume loss, features of pontocerebellar hypoplasia and iron accumulation in the basal ganglia. Neuropathology demonstrated widespread ferritin inclusions in the brain. Patient-derived fibroblasts were assayed for ferritin expression, susceptibility to iron accumulation, and oxidative stress. VariantFTH1mRNA transcripts escape nonsense-mediated decay (NMD), and fibroblasts show elevated ferritin protein levels, markers of oxidative stress, and increased susceptibility to iron accumulation. C-terminus variants inFTH1truncate ferritin’s E-helix, altering the four-fold symmetric pores of the heteropolymer and likely diminish iron-storage capacity.FTH1pathogenic variants appear to act by a dominant, toxic gain-of-function mechanism. The data support the conclusion that truncating variants in the last exon ofFTH1cause a novel disorder in the spectrum of NBIA. Targeted knock-down of mutantFTH1transcript with antisense oligonucleotides rescues cellular phenotypes and suggests a potential therapeutic strategy for this novel pediatric neurodegenerative disorder.
Real-time evaluation and adaptation to facilitate rapid recruitment in a large cohort
Authors: Honushefsky Ashley , Wagner Eric S. , Sheridan Kathleen , Spickard Kathleen M. , LeMasters William R. , Walter Carroll N. , Beaver Taryn , Rahm Alanna Kulchak , Buchanan Adam H. 
Published: January 2023

ABSTRACTObjectivesRecruiting large, diverse cohorts efficiently can speed the translation of findings into care across a range of scientific disciplines and medical specialties. Yet, efficient recruitment can be hampered by factors such as financial barriers, logistical concerns, and lack of resources for patients and clinicians. Here we use a case study of a large, prospective trial of a multi-cancer early detection test to describe how the study team tracked enrollment, protocol fidelity, and participant experience and iteratively adapted procedures.MethodsWhile conducting a large, prospective trial of a multi-cancer early detection blood test at Geisinger, an integrated health system in central Pennsylvania, we monitored recruitment progress, fidelity to protocol procedures, and participants’ satisfaction. Tracking mechanisms such as paper records, electronic health records, research databases, dashboards, and electronic files were utilized to measure each outcome. We then reviewed study procedures and timelines to list the implementation strategies that were used to address barriers to recruitment, protocol fidelity and participant satisfaction.ResultsWe enrolled 10,006 women ages 65-75 over 22 months. Adaptations to recruitment and enrollment methods that contributed to achieving the enrollment goal included adopting group consenting, improving visit convenience, increasing electronic capture and tracking of data and source documents, staffing optimization via leveraging resources external to the study team when appropriate, and integrating the disclosure of study results into routine clinical care without adding unfunded work for physicians. We maintained high protocol fidelity and positive participant experience as exhibited by a very low protocol deviation rate and a low number of participant complaints.ConclusionRecruiting rapidly for large studies – and thereby facilitating clinical translation – requires a nimble, creative approach that marshals available resources and changes course according to data. Planning a rigorous assessment of a study’s implementation outcomes prior to study recruitment can further ground study adaptations and facilitate translation into practice. This can be accomplished by proactively and continuously assessing and revising implementation strategies.Strengths and limitations of this studySynthesis and tracking of various dataReal-time identification of necessary adaptationsMapping of adaptations to problems and consequencesAnalysis of results post-hocInability to analyze the value or impact of a single adaptation
Effect of Pathway-specific Polygenic Risk Scores for Alzheimer’s Disease (AD) on Rate of Change in Cognitive Function and AD-related Biomarkers among Asymptomatic Individuals
Authors: Xu Yuexuan , Vasiljevic Eva , Deming Yuetiva K. , Jonaitis Erin M. , Koscik Rebecca L. , Van Hulle Carol A. , Lu Qiongshi , Carboni Margherita , Kollmorgen Gwendlyn , Wild Norbert , Carlsson Cynthia M. , Johnson Sterling C. , Zetterberg Henrik , Blennow Kaj , Engelman Corinne D. 
Published: February 2023

AbstractBackgroundGenetic scores for late-onset Alzheimer’s disease (LOAD) have been associated with preclinical cognitive decline and biomarker variations. Compared with an overall polygenic risk score (PRS), a pathway-specific PRS (p-PRS) may be more appropriate in predicting a specific biomarker or cognitive component underlying LOAD pathology earlier in the lifespan.ObjectiveIn this study, we leveraged 10 years of longitudinal data from initially cognitively unimpaired individuals in the Wisconsin Registry for Alzheimer’s Prevention and explored changing patterns in cognition and biomarkers at various age points along six biological pathways.MethodsPRS and p-PRSs with and without apolipoprotein E (APOE) were constructed separately based on the significant SNPs associated with LOAD in a recent genome-wide association study meta-analysis and compared toAPOEalone. We used a linear mixed-effects model to assess the association between PRS/p-PRSs and global/domain-specific cognitive trajectories among 1,175 individuals. We also applied the model to the outcomes of cerebrospinal fluid biomarkers for beta-amyloid 42 (Aβ42), Aβ42/40 ratio, total tau, and phosphorylated tau in a subset. Replication analyses were performed in an independent sample.ResultsWe found p-PRSs and the overall PRS can predict preclinical changes in cognition and biomarkers. The effects of p-PRSs/PRS on rate of change in cognition, beta-amyloid, and tau outcomes are dependent on age and appear earlier in the lifespan whenAPOEis included in these risk scores compared to whenAPOEis excluded.ConclusionIn addition toAPOE, the p-PRSs can predict age-dependent changes in beta-amyloid, tau, and cognition. Once validated, they could be used to identify individuals with an elevated genetic risk of accumulating beta-amyloid and tau, long before the onset of clinical symptoms.
Evaluation of a Commercially Available Rapid RT-PCR Assay’s Detection of SARS-CoV-2 Novel Variants
Authors: Back Lewis , Logue Jennifer K. , Wolf Caitlin R. , Han Peter D. , Starita Lea M. , Chu Helen Y. 
Published: February 2023

AbstractRapid molecular diagnostic tests have been critical in the response to the COVID-19 pandemic. It is important to evaluate the ability of these assays to identify variants of concern, particularly across varying collection and storage conditions. Nasal swabs positive for Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.167.2), Gamma (P.1), or Omicron (B.1.1.529) variants of concern (VOCs) were stored in TE buffer and viral transport media (VTM). We evaluated the sensitivity of the Cepheid Xpert® Xpress SARS-CoV-2 assay in detecting VOC samples and validated TE buffer for use with the assay. Testing of known VOC positives revealed no substantial reduction of PCR sensitivity. Comparison of TE and VTM samples also revealed no reduction in performance when using TE buffer, validating the use of TE buffer to store SARS-CoV-2 samples. SARS-CoV-2 VOCs collected and stored across various conditions can be detected by the Cepheid Xpert® Xpress SARS-CoV-2 assay.
Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022
Authors: Sisay Abay , Tshiabuila Derek , Tesfaye Abraham , Mboowa Gerald , Oyola Samuel O. , Tesema Sofonias Kifle , Baxter Cheryl , Martin Darren , Lessells Richard , Tegally Houriiyah , van Wyk Stephanie , Moir Monika , Giandhari Jennifer , Pillay Sureshnee , Singh Lavanya , Ramphal Yajna , Maharaj Arisha , Pillay Yusasha , Maharaj Akhil , Naidoo Yeshnee , Ramphal Upasana , Chabuka Lucious , Wilkinson Eduan , de Oliveira Tulio , Desta Adey Feleke , San James E. 
Published: January 2023

AbstractEthiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499 000 cases, and ∼7 500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was out-competed by the Delta variant. Notably, Ethiopia’s lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia’s role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.