bluuebunny/crossref_metadata_2025_split huggingface dataset:
The energy landscape reshaped by strain-specific mutations underlies the long-range epistasis in NS1 evolution of influenza A virus
Authors: Kim Iktae , Dubrow Alyssa , Zuniga Bryan , Zhao Baoyu , Sherer Noah , Bastiray Abhishek , Li Pingwei , Cho Jae-Hyun 
Published: May 2022

AbstractThe mechanisms underlying how individual mutations affect the protein energy landscape are crucial for understanding how proteins evolve. However, predicting mutational effects remains challenging because of epistasis—the nonadditive interactions between mutations. Here, we investigate the biophysical mechanism of strain-specific epistasis in the nonstructural protein 1 (NS1) of the influenza A virus (IAV). To understand the molecular basis of epistasis, we conducted comprehensive analyses of four NS1s of IAV strains that emerged between 1918 and 2004. We find that strain-specific mutations of NS1s are near-neutral with respect to the association with the p85β subunit of PI3K. However, the individual residues on the p85β-binding interface show long-range epistatic interactions with strain-specific mutations. We reveal that strain-specific mutations reshaped the energy landscape of NS1, leading to long-range epistasis. Our findings offer a high-resolution mechanism of how near-neutral mutations silently alter the biophysical energy landscapes, resulting in diverse background effects during molecular evolution.
Free meals during breeding: increased resource access does not benefit Arcic-nesting shorebirds
Authors: Montagano Laurent , Lecomte Nicolas 
Published: May 2022

AbstractArctic ecosystems are facing intensifying impacts of climate change, notably an increase in air temperature that can boost local productivity. Yet whether such resource surge can benefit declining migratory birds is unclear. Here we experimentally increased prey abundance and measure its effect on the body condition, nesting patterns, and nesting success of the white-rumped sandpiper (Calidris fuscicollis). We captured females at the beginning and at the end of their incubation to assess body condition and we installed small temperature probes inside their nests to measure their incubation recess. To estimate nest survival, we regularly monitored experimental and control nests during two consecutive summers (2016–2017). For both experimental years with contrasting nest success (73% vs. 21%), we found no evidence of an effect of our supplementation experiment mimicking an increased abundance of arthropods in the Canadian Arctic. This suggests that in situ resources are not limiting during incubation. Breeding strategies and success in shorebirds seem to be driven by inter-individual traits related to body condition upon the initiation of incubation.
CAR-T Engager Proteins Optimize Anti-CD19 CAR-T Cell Therapies for Lymphoma
Authors: Su Lihe , Wu Lan , Lobb Roy R. , Rennert Paul D. , Ambrose Christine 
Published: May 2022

AbstractB cell lymphoma therapy has been transformed by CD19-targeting cellular therapeutics that induce high clinical response rates and impressive remissions in relapsed and refractory patients. However, approximately half of all patients who respond to CD19-directed cell therapy relapse, the majority within six months. One characteristic of relapse is loss or reduction of CD19 expression on malignant B cells. We designed a unique therapeutic to prevent and reverse relapses due to lost or reduced CD19 expression. This novel biologic, a CAR T Engager, binds CD20 and displays the CD19 extracellular domain. This approach increases the apparent CD19 antigen density on CD19-positive/CD20-positive lymphoma cells, and prevents CD19 antigen-oss induced relapse, as CD19 bound to CD20 remains present on the cell surface. We demonstrate that this novel therapeutic prevents and reverses lymphoma relapse in vitro and prevents CD19-negative lymphoma growth and relapse in vivo.
Reticular Adhesion Formation is Mediated by Flat Clathrin Lattices and Opposed by Fibrillar Adhesions
Authors: Hakanpää Laura , Abouelezz Amr , Lenaerts An-Sofie , Culfa Seyda , Algie Michael , Bärlund Jenny , Katajisto Pekka , McMahon Harvey T. , Almeida-Souza Leonardo 
Published: May 2022

AbstractReticular adhesions (RAs) consist of integrin αvβ5 and harbor flat clathrin lattices (FCLs), long-lasting structures with similar molecular composition to clathrin mediated endocytosis (CME) carriers. Why FCLs and RAs colocalize is not known. Here, we show that FCLs assemble RAs in a process controlled by fibronectin (FN) and its receptor, integrin αvβ5. We observed that cells on FN-rich matrices displayed fewer FCLs and RAs. CME machinery inhibition abolished RAs and live-cell imaging showed that RA establishment requires FCL co-assembly. The inhibitory activity of FN was mediated by the activation of integrin α5β1 at Tensin1-positive fibrillar adhesions. Conventionally, endocytosis disassembles cellular adhesions by internalization of their components. Our results present a novel paradigm in the relationship between these two processes by showing that endocytic proteins can actively function in the assembly of cell adhesions. Furthermore, we show this novel adhesion assembly mechanism is coupled to cell migration via a unique crosstalk between cell matrix adhesions.
Spatially Resolved Metabolites in Stable and Vulnerable Human Atherosclerotic Plaques Identified by Mass Spectrometry Imaging
Authors: Seeley Erin H. , Liu Zhipeng , Yuan Shuai , Stroope Chad , Cockerham Elizabeth , Rashdan Nabil , Finney Alexandra C , Kumar Dhananjay , Das Sandeep , Razani Babak , Liu Wanqing , Traylor James , Rom Oren , Pattillo Christopher , Yurdagul Arif 
Published: May 2022

ABSTRACTImpairments in carbohydrate, lipid, and amino acid metabolism drive features of plaque instability. However, where these impairments occur within the atheroma remains largely unknown. Therefore, we sought to characterize the spatial distribution of metabolites within stable and unstable atherosclerosis in both the fibrous cap and necrotic core. Atherosclerotic tissue specimens were scored based on the Stary classification scale and subdivided into stable and unstable atheromas. After performing mass spectrometry imaging (MSI) on these samples, we identified over 850 metabolite-related peaks. Using MetaboScape, METASPACE, and HMDB, we confidently annotated 170 of these metabolites and found over 60 of these were different between stable and unstable atheroma. We then integrated these results with an RNA-sequencing dataset comparing stable and unstable human atherosclerosis. Upon integrating our MSI results with the RNA-seq dataset, we discovered that pathways related to lipid metabolism and long-chain fatty acids were enriched in stable plaques, whereas reactive oxygen species, aromatic amino acid, and tryptophan metabolism were increased in unstable plaques. Acylcarnitines and acylglycines were increased in stable plaques whereas tryptophan metabolites were enriched in unstable plaques. Evaluating spatial differences in stable plaques revealed lactic acid in the necrotic core, whereas pyruvic acid was elevated in the fibrous cap. In unstable plaques, 5-hydroxyindole-acetic acid was enriched in the fibrous cap. Our work herein represents the first step to defining an atlas of metabolic pathways involved in plaque destabilization in human atherosclerosis. We anticipate this will be a valuable resource and open new avenues of research in cardiovascular disease.GRAPHICAL ABSTRACT
Thymus Antibody-Secreting Cells Represent a Tissue Specific Population That Possess an Activated Cellular Phenotype
Authors: Pioli KimAnh T. , Lau Kin H. , Pioli Peter D. 
Published: May 2022

SummaryAntibody-secreting cells (ASCs) are key contributors to humoral immunity through immunoglobulin production and the potential to be long-lived. ASCs have been recently identified in the thymus (THY) which is of interest as autoreactive THY B cells regulate T cell tolerance. Here, we showed that the young female THY was skewed towards higher production of ASCs relative to males. However, these differences disappeared with age. Intravenous labeling combined with blockade of CD154(CD40L) suggested that THY ASCs were generatedin situin a T cell dependent fashion. Single cell RNA-sequencing revealed that THY ASCs possessed a transcriptional signature indicative of interferon signaling and activation. Flow cytometry confirmed that THY ASCs had increased levels of Toll-like receptor 7 as well as the activation markers CD69 and major histocompatibility class II. Overall, THY ASCs are a unique population that require further investigation to fully appreciate their biological significance.
Diminished motor neuron activity driven by abnormal astrocytic GLAST glutamate transporter activity in spinal muscular atrophy is not fully restored after lentiviral SMN delivery
Authors: Welby Emily , Ebert Allison D. 
Published: May 2022

AbstractSpinal muscular atrophy (SMA) is a pediatric neuromuscular disease characterized by the loss of the lower spinal motor neurons due to survival motor neuron (SMN) deficiency. Motor neuron dysfunction at the glutamatergic afferent synapse is observed during early stages of SMA disease progression, which could be targeted therapeutically prior to cell death. However, the motor neuron cell autonomous and non-cell autonomous disease mechanisms driving this phenotype remain unclear. Our study reveals a non-cell autonomous SMN-associated disease mechanism affecting glutamate transporter (GLAST) activity in astrocytes that contributes to human motor neuron dysfunction in SMA. Transcriptomic analysis of SMA patient human induced pluripotent stem cell (iPSC)-derived astrocytes identified a significant downregulation of genes associated with astrocytic regulation of the synapse, including glutamate neurotransmission. This finding was substantiated by our microelectrode array analysis of motor neuron activity, which was severely diminished specifically in the presence of patient-derived astrocytes. Co-culturing patient-derived motor neurons with healthy-derived astrocytes showed comparable firing rates and bursting activity to healthy-derived motor neurons, suggesting diminished neural activity is an astrocyte-mediated phenotype in this system. Towards defining astrocyte-intrinsic defects that could induce motor neuron dysfunction, we identified abnormally low levels of excitatory amino acid transporter (EAAT1/GLAST) in patient-derived astrocytes, which when selectively inhibited in healthy co-cultures could phenocopy the diminished neural activity previously observed in patient-derived co-cultures. Caveolin-1, an SMN-interacting lipid raft protein associated with glutamate transporter regulation, showed increased protein levels and accumulation in patient astrocytes. Both GLAST and caveolin-1 phenotypes could be partially rescued via lentiviral-mediated SMN re-expression in patient astrocytes. Together, our work defines a novel SMN-associated disease mechanism involving abnormal glutamate transporter activity and regulation in astrocytes that can directly diminish motor neuron function in SMA.
Ultra high-throughput whole-genome methylation sequencing reveals trajectories in precancerous polyps to early colorectal adenocarcinoma
Authors: Lee Hayan , Krieger Gat , Clark Tyson , Khan Aziz , Hanson Casey Ryan , Zhu Yizhou , Bararpour Nasim , Horning Aaron M. , Esplin Edward D. , Nevins Stephanie , Weimer Annika K. , Meiri Eti , Gilad Shlomit , Benjamin Sima , Lebanony Danit , Iremadze Nika , Oberstrass Florian , Jaimovich Ariel , Greenleaf William , Ford James M. , Lipson Doron , Shipony Zohar , Snyder Michael P. 
Published: May 2022

AbstractAberrant shifts in DNA methylation have long been regarded as an early marker for cancer onset and progression. To chart DNA methylation changes that occur during the transformation from normal healthy colon tissue to malignant colorectal cancer (CRC), we collected over 50 samples from 15 familial adenomatous polyposis (FAP) and non-FAP colorectal cancer patients, and generated 30-70x whole-genome methylation sequencing (WGMS) runs via the novel Ultima Genomics ultra high-throughput sequencing platform. We observed changes in DNA methylation that occur early in the malignant transformation process, in gene promoters and in distal regulatory elements. Among these changes are events of hyper-methylation which are associated with a bivalent “poised” chromatin state at promoters and are CRC-specific. Distal enhancers show nonlinear dynamics, lose methylation in the progression from normal mucosa to dysplastic polyps but regain methylation in the adenocarcinoma state. Enhancers that gain chromatin accessibility in the adenocarcinoma state and are enriched with HOX transcription factor binding sites, a marker of developmental genes. This work demonstrates the feasibility of generating large high quality WGMS data using the Ultima Genomics platform and provides the first detailed view of methylation dynamics during CRC formation and progression in a model case.
The Network Zoo: a multilingual package for the inference and analysis of biological networks
Authors: Guebila Marouen Ben , Wang Tian , Lopes-Ramos Camila M. , Fanfani Viola , Weighill Deborah , Burkholz Rebekka , Schlauch Daniel , Paulson Joseph N. , Altenbuchinger Michael , Sonanwane Abhijeet , Lim James , Calderer Genis , van Ijzendoorn David , Morgan Daniel , Marin Alessandro , Chen Cho-Yi , Song Alex , Shutta Kate , DeMeo Dawn , Padi Megha , Platig John , Kuijjer Marieke L. , Glass Kimberly , Quackenbush John 
Published: May 2022

AbstractInference and analysis of cellular biological networks requires software tools that integrate multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is an open-source software suite to model biological networks, including context-specific gene regulatory networks and multi-omics partial correlation networks, to conduct differential analyses, estimate community structure, and model the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages (R, Python, MATLAB, and C) and between methods to allow a better integration of these tools into analytical pipelines. To demonstrate the value of this integrated toolkit, we analyzed the multi-omic data from the Cancer Cell Line Encyclopedia (CCLE) by inferring gene regulatory networks for each cancer cell line and associating network features with other phenotypic attributes such as drug sensitivity. This allowed us to identify transcription factors that play a critical role in both drug resistance and cancer development in melanoma. We also used netZoo to build a pan-cancer, multi-tiered CCLE map and used it to identify known metabolic hallmarks of cancer and to estimate novel context-specific elements that mediate post-transcriptional regulation. Because the netZoo tools are open-source and there is a growing community of both users and developers, we built an ecosystem to support community contributions, share use cases, and visualize networks online. As additional data types become available and our suite of methods grows, we will expand “the zoo” to incorporate an increasingly sophisticated collection of tools for network inference and analysis.
A Chloroplast Protein Atlas Reveals Novel Structures and Spatial Organization of Biosynthetic Pathways
Authors: Wang Lianyong , Patena Weronika , Van Baalen Kelly A. , Xie Yihua , Singer Emily R. , Gavrilenko Sophia , Warren-Williams Michelle , Han Linqu , Harrigan Henry R. , Chen Vivian , Ton Vinh T.N.P. , Kyin Saw , Shwe Henry H. , Cahn Matthew H. , Wilson Alexandra T. , Hu Jianping , Schnell Danny J. , McWhite Claire D. , Jonikas Martin 
Published: May 2022

SummaryChloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,032 candidate chloroplast proteins by using fluorescent protein tagging in the model algaChlamydomonas reinhardtii. The localizations provide insights into the functions of hundreds of poorly-characterized proteins, including identifying novel components of nucleoids, plastoglobules, and the pyrenoid. We discovered and further characterized novel organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and diverse unexpected spatial distributions of enzymes within the chloroplast. We observed widespread protein targeting to multiple organelles, identifying proteins that likely function in multiple compartments. We also used machine learning to predict the localizations of allChlamydomonasproteins. The strains and localization atlas developed here will serve as a resource to enable studies of chloroplast architecture and functions.Graphical AbstractHighlights1,032 candidate chloroplast proteins localized by fluorescent tagging.This protein atlas reveals novel chloroplast structures, functional regions, and components.Prevalent dual-organelle localization suggests extensive cross-compartment coordination.Atlas-trained machine learning predicts localizations of allC. reinhardtiiproteins.
The IFT81-IFT74 complex enhances GTP hydrolysis to inactivate RabL2 during early steps of intraflagellar transport
Authors: Boegholm Niels , Petriman Narcis A. , Lopez Marta Loureiro , Kanie Tomoharu , Jackson Peter K. , Andersen Jens S. , Lorentzen Esben 
Published: May 2022

AbstractCilia are important organelles for signaling and motility and are constructed via intraflagellar transport (IFT). RabL2 is a small Rab-like GTPase that localizes to the basal body of cilia via an interaction with the centriolar protein CEP19 before downstream association with the IFT machinery to regulate the initiation of IFT. We have mapped the interaction with RabL2 to residues 107-195 of CEP19, purified the RabL2-CEP19 complex to show that CEP19 is not a GTPase activator protein for RabL2. In contrast, a reconstituted pentameric IFT complex containing IFT81/74 enhances the GTP hydrolysis in RabL2 by 20-fold. The binding site on IFT81/74 that promotes GTP hydrolysis in RabL2 is mapped to a 70 amino acid long coiled-coil region of IFT81/74. We present structural models for minimal IFT81/74-RabL2 complexes and demonstrate that the Chlamydomonas IFT81/74 complex enhances GTP hydrolysis of human RabL2 suggesting an ancient evolutionarily conserved function. Our results provide a mechanistic understanding of RabL2 function in the initiation step of IFT and a molecular rationale for why RabL2 dissociates from anterograde IFT trains soon after departure from the ciliary base.
The ERK5/NF-κB signaling pathway targets endometrial cancer proliferation and survival
Authors: Diéguez-Martínez Nora , Espinosa-Gil Sergio , Yoldi Guillermo , Megías-Roda Elisabet , Bolinaga-Ayala Idoia , Viñas-Casas Maria , Domingo-Ortí Inés , Pérez-Montoyo Héctor , Bayascas Jose R , Colas Eva , Dolcet Xavier , Lizcano Jose M 
Published: May 2022

AbstractEndometrial cancer (EC) is the most common type of gynaecologic cancer in women of developed countries. Despite surgery combined with chemo-/radiotherapy regimens, overall survival of patients with high-risk EC tumors is poor, indicating a need for novel molecular therapies. The MEK5-ERK5 pathway is activated in response to growth factors and to different forms of stress, including oxidative stress and cytokines. Previous evidence support a role for the MEK5-ERK5 pathway in the pathology of several cancers. We have investigated the role of ERK5 in EC. In silico analysis of the PanCancer Atlas dataset showed alterations in components of the MEK5-ERK5 pathway in 48% of EC patients. Here, we show that ERK5 inhibition decreased EGF-induced EC cell proliferation, and that depletion of MEK5 resulted in EC impaired proliferation and reduced tumor growth capacity in nude mice. Pharmacologic or genetic silencing of ERK5 impaired NF-kB pathway in EC cells and xenografts. Furthermore, we found a positive correlation between ERK5 and p65/RELA protein levels in human EC tumor samples. Mechanistically, impairment of ERK5 resulted in downregulation of NEMO/IKKγ expression, leading to impaired p65/RELA activity and to apoptosis in EC cells and xenografts, which was rescued by NEMO/IKKγ overexpression. Notably, ERK5 inhibition, MEK5 depletion or NF-kB inhibition sensitized EC cells to standard EC chemotherapy (paclitaxel/carboplatin) toxicity, whereas ERK5 inhibition synergized with paclitaxel to reduce tumor xenograft growth in mice. Together, our results suggest that the ERK5-NEMO-NF-κB pathway mediates EC cell proliferation and survival. We propose the ERK5/NF-κB axis as new target for EC treatment.
SAM-dependent viral MTase inhibitors: herbacetin and caffeic acid phenethyl ester, structural insights into dengue MTase
Authors: Bhutkar Mandar , Kumar Amith , Rani Ruchi , Singh Vishakha , Pathak Akashjyoti , Kothiala Aditi , Mahajan Supreeti , Waghmode Bhairavnath , Kumar Ravi , Mudgal Rajat , Sircar Debabrata , Kumar Pravindra , Tomar Shailly 
Published: May 2022

AbstractChikungunya (CHIKV) and dengue (DENV) viruses pose a public health risk and lack antiviral treatment. Structure-based virtual screening of natural MTase substrates library identified herbacetin (HC) and caffeic acid phenethyl ester (CAPE) as potential CHIKV nsP1 and DENV NS5 MTase inhibitors. Binding affinities and MTase inhibition were confirmed using purified proteins. Crystal structure of DENV3 NS5 MTase and CAPE complex revealed CAPE binding at GTP and cap 0 RNA sites. Interestingly, HC and CAPE depleted polyamines, which are crucial for RNA virus replication, and effectively diminished replication with IC50values of ∼13.44 µM and ∼0.57 µM against CHIKV, and ∼7.24 µM and ∼1.01 µM against DENV, respectively. Polyamine addition did not reverse the antiviral effects, suggesting a dual inhibition mechanism.Graphical abstract
Persistent Inflammatory Lipotoxicity Impedes Pancreatic β-cell Function in Diet-Induced Obese Mice Despite Correction of Glucotoxicity
Authors: Valdez Ivan A. , Palavicini Juan Pablo , Bakewell Terry M. , Fourcaudot Marcel , Ayala Iriscilla , Xu Ziying , Khattab Ahmed , Han Xianlin , Shannon Chris E. , Norton Luke 
Published: May 2022

ABSTRACTInsulin resistance is a hallmark feature of Type 2 Diabetes (T2D), but the progression of the disease is closely linked to a deterioration in β-cell mass and function. While the precise mechanisms of β-cell failure are unclear, chronic hyperglycemia (glucotoxicity) and dyslipidemia (lipotoxicity) are considered contributing factors; however, the relative importance of these insults on β-cell function remains controversial. To examine this, we dissociated glucotoxicity from lipotoxicity using a high-fat diet (HFD)-fed mouse model of T2D and the glucose-lowering SGLT2 inhibitor, canagliflozin (CANA). As expected, HFD-feeding impaired glucose tolerance and isolated islet function. However, despite improvements in glucose tolerance and indices of β-cell insulin secretory function in vivo, CANA failed to restore isolated β-cell function. Shotgun lipidomics analysis of isolated islets revealed that HFD-feeding induced glycerophospholipid remodeling with a persistent increase in arachidonic acid (20:4)-enriched molecular species. Further analysis revealed that lysophosphatidylcholine (LPC) was the predominant lipid class elevated in HFD islets following correction of glucotoxicity with CANA. In follow-up experiments, LPC stimulations acutely and dose-dependently impaired glucose-stimulated insulin secretion (GSIS) in isolated wild-type islets, mechanistically linking this lipid class to β-cell dysfunction. Our findings indicate that persistent inflammatory lipotoxicity impedes β-cell function in diet-induced obese (DIO) rodents even after normalization of hyperglycemia. If replicated in humans, these data suggest that interventions targeting lipotoxicity may be beneficial for the long-term protection of pancreatic β-cell function in T2D.