bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Contribution of Cancer-Associated Fibroblasts in Glioblastoma
Authors: Galbo Phillip M. , Liu Yang , Peng Mou , Wei Yao , Madsen Anne Tranberg , Graff Sarah , Montagna Cristina , Segall Jeffrey E. , Sidoli Simone , Zang Xingxing , Zheng Deyou 
Published: April 2022

AbstractThe abundance and biological contribution of cancer associated fibroblasts (CAFs) in glioblastoma are poorly understood. Here, we applied single-cell RNA sequencing and spatial transcriptomics analyses to identify and characterize CAFs in human glioblastoma tumors and then performed functional enrichment analysis and in vitro assays to investigate their interactions with malignant glioblastoma cells. We found that CAF abundance was significantly correlated with tumor grade, poor clinical outcome, and activation of extracellular matrix remodeling, using three large databases containing bulk RNA-sequencing data and clinical information. Proteomic analysis of the CAFs and their secretome revealed fibronectin (FN1) as a strong candidate mediating CAF functions. This was validated using in vitro cellular models, which demonstrated that CAF conditioned media and recombinant FN1 could facilitate the migration and invasion of glioblastoma cells. In addition, we showed that CAFs were more abundant in the mesenchymal-like state (or subtype) than in other states of glioblastomas, while cell lines resembling the proneural-state responded to the CAF signaling better in terms of the migratory and invasive phenotypes. Investigating the in-situ expression of gene markers specifically associated with CAFs and mesenchymal malignant cells further indicated that CAFs were enriched in the perinecrotic and pseudopalisading zones of human tumors, where mesenchymal-like glioblastoma cells co-resided and thus likely interacted. Overall, this study characterized the molecular features and functional impacts of CAFs in glioblastoma, alluding to a novel cell-to-cell interaction axis mediated by CAFs in the glioblastoma microenvironment.
Discovery of a novel human antibody VH domain with potent activity against mesothelin expressing cancer cells in both CAR T-cell and antibody drug conjugate formats
Authors: Sun Zehua , Chu Xiaojie , Adams Cynthia , Ilina Tatiana V. , Guerrero Michel , Lin Guowu , Chen Chuan , Jelev Dontcho , Ishima Rieko , Li Wei , Mellors John W , Calero Guillermo , Dimitrov Dimiter S 
Published: April 2022

AbstractAntibody based therapeutics targeting mesothelin (MSLN) have shown limited anticancer activity in clinical trials. Novel antibodies with high affinity and better therapeutic properties are needed. In the current study, we have isolated and characterized a novel VH domain 3C9 from a large size human immunoglobulin heavy chain variable (VH) domain library. 3C9 exhibited high affinity [KD (dissociation constant) < 3 nM] and binding specificity in a membrane proteome array (MPA). In a mouse xenograft model, 3C9 fused to human Fc became visible at tumor sites as early as 8 hours post infusion and persisted at the tumor site for more than 10 days. Both CAR-T cells and antibody domain drug conjugations (DDCs) generated with 3C9 were highly effective at killing MSLN positive cells in vitro without off-target effects. The X-ray crystal structure of full-length MSLN in complex with 3C9 reveals interaction of the 3C9 domains with two distinctive residues patches on the MSLN surface. 3C9 fused to human Fc domain drug conjugate was efficacious to inhibit tumor growth in a mouse xenograft model. This newly discovered VH antibody domain holds promise as a therapeutic candidate for MSLN-expressing cancers.
Structural insights into the mechanism of the sodium/iodide symporter (NIS)
Authors: Ravera Silvia , Nicola Juan Pablo , de Simone Glicella Salazar , Sigworth Fred J. , Karakas Erkan , Amzel L. Mario , Bianchet Mario A. , Carrasco Nancy 
Published: April 2022

AbstractThe sodium/iodide symporter (NIS) is the essential plasma membrane protein that mediates active iodide (I-) transport into the thyroid gland, the first step in the biosynthesis of the thyroid hormones—the master regulators of intermediary metabolism. NIS couples the inward translocation of I- against its electrochemical gradient to the inward transport of Na+ down its electrochemical gradient. For nearly 50 years before its molecular identification, NIS was already the molecule at the center of the single most effective internal radiation cancer therapy ever devised: radioiodide (131I-) treatment for thyroid cancer. Mutations in NIS cause congenital hypothyroidism, which must be treated immediately after birth to prevent stunted growth and cognitive deficiency. To date, the structure of NIS has been unknown. Here, we report three structures of rat NIS, determined by single-particle cryo-electron microscopy (cryo-EM): one with no substrates bound, one with 2 Na+ and 1 I- bound, and one with 1 Na+ and the oxyanion perrhenate bound. Structural analyses, functional characterization, and computational studies reveal the substrate binding sites and residues key for transport activity. Our results yield insights into how NIS selects, couples, and translocates anions—thereby establishing a framework for understanding NIS function—and into how it transports different substrates with different stoichiometries and releases substrates from its substrate-binding cavity into the cytosol.
Impairments in SHMT2 expression or cellular folate availability reduce oxidative phosphorylation and pyruvate kinase activity
Authors: Fiddler Joanna L. , Blum Jamie E. , Castillo Luisa F. , Thalacker-Mercer Anna E. , Field Martha S. 
Published: April 2022

ABSTRACTBackgroundSerine hydroxymethyltransferase 2 (SHMT2) catalyzes the reversible conversion of tetrahydrofolate (THF) and serine producing THF-conjugated one-carbon units and glycine in the mitochondria. Biallelic SHMT2 variants were identified in humans and suggested to alter the protein’s active site, potentially disrupting enzymatic function. SHMT2 expression has also been shown to decrease with aging in human fibroblasts. Immortalized cells models of total SHMT2 loss or folate deficiency exhibit decreased oxidative capacity and impaired mitochondrial complex I assembly and protein levels, suggesting folate-mediated one-carbon metabolism (FOCM) and the oxidative phosphorylation system are functionally coordinated. This study examined the role of SHMT2 and folate availability in regulating mitochondrial function, energy metabolism, and cellular proliferative capacity in both heterozygous and homozygous cell models of reduced SHMT2 expression.MethodsPrimary mouse embryonic fibroblasts (MEF) were isolated from a C57Bl/6 dam crossed with a heterozygous Shmt2+/- male to generate Shmt2+/+ (wild-type) or Shmt2+/- (HET) MEF cells. In addition, haploid chronic myeloid leukemia cells (HAP1, wild-type) or HAP1 cells lacking SHMT2 expression (ΔSHMT2) were cultured for 4 doublings in either low-folate or folate-sufficient culture media. Cells were examined for proliferation, total folate levels, mtDNA content, protein levels of pyruvate kinase and PGC1α, pyruvate kinase enzyme activity, mitochondrial membrane potential, and mitochondrial function.ResultsHomozygous loss of SHMT2 in HAP1 cells impaired cellular folate accumulation and altered mitochondrial DNA content, membrane potential, and basal respiration. Formate rescued proliferation in HAP1, but not ΔSHMT2, cells cultured in low-folate medium. Pyruvate kinase activity and protein levels were impaired in ΔSHMT2 cells and in MEF cells exposed to low-folate medium. Mitochondrial biogenesis protein levels were elevated in Shmt2+/- MEF cells, while mitochondrial mass was increased in both homozygous and heterozygous models of SHMT2 loss.ConclusionsThe results from this study indicate disrupted mitochondrial FOCM impairs mitochondrial folate accumulation and respiration, glycolytic activity, and cellular proliferation. These changes persist even after a potentially compensatory increase in mitochondrial biogenesis as a result of decreased SHMT2 levels.
The impact of AlphaFold on experimental structure solution
Authors: Edich Maximilian , Briggs David C. , Kippes Oliver , Gao Yunyun , Thorn Andrea 
Published: April 2022

AbstractAlphaFold2 is a machine-learning based program that predicts a protein structure based on the amino acid sequence. In this article, we report on the current usages of this new tool and give examples from our work in the Coronavirus Structural Task Force. With its unprecedented accuracy, it can be utilized for the design of expression constructs, de novo protein design and the interpretation of Cryo-EM data with an atomic model. However, these methods are limited by their training data and are of limited use to predict conformational variability and fold flexibility; they also lack co-factors, posttranslational modifications and multimeric complexes with oligonucleotides. They also are not always perfect in terms of chemical geometry. Nevertheless, machine learning based fold prediction are a game changer for structural bioinformatics and experimentalists alike, with exciting developments ahead.
The Gene Knockout of Angiotensin II Type 1a Receptor Improves High-fat Diet-Induced Obesity in rat via Promoting Adipose Lipolysis
Authors: Li Aiyun , Shi Wenjuan , Wang Jin , Wang Xuejiao , Zhang Yan , Lei Zhandong , Jiao Xiang-Ying 
Published: April 2022

AbstractAimsThe renin-angiotensin system (RAS) is over-activated and the serum angiotensin II (Ang II) level increased in obese patients, while their correlations were incompletely understood. This study aims to explore the role of Ang II in diet-induced obesity by focusing on adipose lipolysis.MethodsRat model of AT1aR gene knockout were established to investigate the special role of Ang II. Wild-type (WT) and AT1aR gene knockout (AT1aR-/-) SD rats were fed with normal diet or high-fat diet for 12 weeks. Adipose morphology and adipose lipolysis were examined.ResultsAT1aR deficiency activated lipolysis-related enzymes and increased the levels of NEFAs and glycerol released from adipose tissue in high-fat diet rats, while did not affect triglycerides synthesis. Besides, AT1aR knockout promoted energy expenditure and fatty acids oxidation in adipose tissue. cAMP levels and PKA phosphorylation in the adipose tissue were significantly increased in AT1aR-/- rats fed with high-fat. Activated PKA could promote adipose lipolysis and thus improved adipose histomorphology and insulin sensitivity in high-fat diet rats.ConclusionsAT1aR deficiency alleviated adipocyte hypertrophy in high-fat diet rats by promoting adipose lipolysis via cAMP/PKA pathway, and thereby delayed the onset of obesity and related metabolic diseases.
Biogeography and taxonomy of theHemileuca maia-nevadensisStretch species complex (Lepidoptera: Saturniidae): insights to the midcontinental populations
Authors: Schmidt Christian 
Published: April 2022

AbstractAn integrated assessment of geographic distribution, genetic variation and interpopulation reproductive barriers of the Great Plains and Great Lakes populations of theHemileuca maia-nevadensisspecies complex is presented. The taxonomic circumscription ofHemileuca nevadensisStretch, key to understanding the complex evolutionary history of the group, has previously been misinterpreted. Detailed distribution maps based on historic, literature, and contemporary occurrence records, combined with analysis of genetic variation using mtDNA-COI barcode sequences and pheromone compatibility trials, indicate that Great PlainsH. “nevadensis” are disjunct and genetically divergent from nominateH. nevadensis, instead being more closely related to Great Lakes populations. Despite the genomic differentiation of the bog buckmoth established in recent studies, similar or identical mtDNA-COI haplotypes indicate past genetic linkages among now-isolated populations across the northern range periphery of themaia-complex. Based on the current evidence, northern Great PlainsHemileuca latifasciaBarnes & McDunnoughstat. nov. and eastern Great Lakes (bog buckmoth)Hemileuca menyanthevoraPavulaanstat. nov. (=Hemileuca iroquoisDirig & Cryansyn. nov.) should be considered as species distinct from others in themaia-group. Post-glacial dispersal hypotheses are evaluated in light of molecular variation and ecology, and key knowledge gaps are identified to guide future research.
Modeling protected species distributions and habitats to inform siting and management of pioneering ocean industries: A case study for Gulf of Mexico aquaculture
Authors: Farmer Nicholas A. , Powell Jessica R. , Morris James A. , Soldevilla Melissa S. , Wickliffe Lisa C. , Jossart Jonathan A. , MacKay Jonathan K. , Randall Alyssa L. , Bath Gretchen E. , Ruvelas Penny , Gray Laura , Lee Jennifer , Piniak Wendy , Garrison Lance , Hardy Robert , Hart Kristen M. , Sasso Chris , Stokes Lesley , Riley Kenneth L. 
Published: April 2022

AbstractMarine Spatial Planning (MSP) provides a process that uses spatial data and models to evaluate environmental, social, economic, cultural, and management trade-offs when siting ocean industries. Aquaculture is the fastest-growing food sector in the world. The U.S. has substantial opportunity for offshore aquaculture development given the size of its exclusive economic zone, habitat diversity, and variety of candidate species for cultivation. However, many protected species rely upon habitats that overlap with promising aquaculture areas. Siting surveys, farm construction, operations, and decommissioning can alter the habitat and behavior of animals in the vicinity of these activities. Vessel activity, underwater noise, and physical interactions between protected species and farms can potentially increase the risk of injury or cause direct mortality. In 2020, the U.S. Gulf of Mexico was identified as one of the first regions to be evaluated for offshore aquaculture opportunities as directed by a Presidential Executive Order. We developed a generalized scoring model for protected species data layers that captures vulnerability using species conservation status and demographic information. We applied this approach to data layers for eight species listed under the Endangered Species Act, including five species of sea turtles, Rice’s Whale, Smalltooth Sawfish, and Giant Manta Ray. We evaluated several methods for scoring (e.g., arithmetic mean, geometric mean, product, lowest scoring layer) and created a combined protected species data layer that was used within a multi-criteria decision-making modeling framework for MSP. The product approach for scoring provided the most logical ordering of and the greatest contrast in site suitability scores. This approach provides a transparent and repeatable method to identify aquaculture site alternatives with the least conflict with protected species. These modeling methods are transferable to other regions, to other sensitive or protected species, and for spatial planning for other ocean-uses.
Trypanosoma cruzi PARP is enriched in the nucleolus and is present in a thread connecting nuclei during mitosis
Authors: Kevorkian María Laura , Vilchez Larrea Salomé C. , Fernández Villamil Silvia H. 
Published: April 2022

AbstractPoly (ADP-ribose) polymerase (PARP) is responsible for the synthesis of ADP-ribose polymers, which are involved in a wide range of cellular processes such as preservation of genome integrity, DNA damage signaling and repair, molecular switch between distinct cell death pathways and cell cycle progression. Previously, we demonstrated that the only PARP present in T. cruzi migrates to the nucleus upon genotoxic stimulus. In this work, we identify the N-terminal domain as being sufficient for TcPARP nuclear localization and describe for the first time that TcPARP is enriched in the parasite nucleolus. We also describe that TcPARP is present in a thread that connects two dividing nuclei and co-localizes with nucleolar material and microtubules. Furthermore, ADP-ribose polymers could also be detected in this wire during mitosis. These findings represent a first approach to new potential TcPARP functions inside the nucleus and will help understand its role well beyond the largely described DNA damage response protein in trypanosomatids.
The Streptococcus pyogenes hyaluronic acid capsule promotes experimental nasal and skin infection by preventing neutrophil-mediated clearance
Authors: Hurst Jacklyn R. , Shannon Blake A. , Craig Heather C. , Tuffs Stephen W. , McCormick John K. 
Published: April 2022

ABSTRACTStreptococcus pyogenes is a globally prominent human-specific pathogen responsible for an enormous burden of human illnesses, including >600 million pharyngeal and >100 million skin infections each year. Despite intensive efforts that focus on invasive indications, much remains unknown about this bacterium in its natural state during colonization of the nasopharynx and skin. Using acute experimental infection models in HLA-transgenic mice, we evaluated how the hyaluronic acid (HA) capsule contributes to S. pyogenes MGAS8232 infection within these limited biological niches. Herein, we demonstrate that HA capsule expression promotes bacterial burden in murine nasal turbinates and skin lesions by resisting neutrophil-mediated killing. HA capsule production is encoded by the hasABC operon and compared to wildtype S. pyogenes infections, mice infected with a ΔhasA mutant exhibited over a 1000-fold CFU reduction at 48-hours post­nasal challenge, and a 10,000-fold CFU reduction from skin lesions 72-hours post-skin challenge. HA capsule expression contributed substantially to skin lesion size development following subdermal inoculations. In the absence of capsule expression, S. pyogenes revealed drastically impeded growth in whole human blood and increased susceptibility to killing by isolated neutrophils ex vivo, highlighting its important role in resisting phagocytosis. Furthermore, we establish that neutrophil depletion in mice, but not macrophage depletion, recovered the reduced burden by the ΔhasA mutant in both the nasopharynx and skin. Together, this work confirms that the HA capsule is a key virulence determinant during acute infections by S. pyogenes and demonstrates that its predominant function is to protect S. pyogenes against neutrophil-mediated killing.AUTHOR SUMMARYStreptococcus pyogenes is a globally disseminated and human-adapted bacterial pathogen that has evolved an arsenal of evasion strategies to overcome and escape host immune clearing mechanisms. Many strains of S. pyogenes are covered by a polysaccharide capsule composed of hyaluronic acid (HA) that is widely recognized to promote severe infections. In this study, we demonstrate using the encapsulated S. pyogenes MGAS8232 strain that the HA capsule is a key virulence factor that facilitates non-invasive infections of the nasopharynx and skin. Although bacterial adhesion and entry into host cells was impeded by HA capsule expression, we show that the key function for both nasal and skin infections is to protect S. pyogenes from neutrophil-mediated killing. Depletion of neutrophils, but not macrophages, recovered the low bacterial burden by unencapsulated S. pyogenes at both sites of infection. Our findings outline an important interaction between the HA capsule and neutrophils in the establishment of acute upper respiratory and skin infections by S. pyogenes.
Restricting α-Synuclein Transport into Mitochondria by Inhibition of α-Synuclein-VDAC Complexation as a Potential Therapeutic Target for Parkinson’s Disease Treatment
Authors: Rajendran Megha , Queralt-Martín María , Gurnev Philip A. , Rosencrans William M. , Rovini Amandine , Jacobs Daniel , Abrantes Kaitlin , Hoogerheide David P. , Bezrukov Sergey M. , Rostovtseva Tatiana K. 
Published: April 2022

ABSTRACTInvolvement of alpha-synuclein (αSyn) in Parkinson’s disease (PD) is complicated and difficult to trace on cellular and molecular levels. Recently we established that αSyn can regulate mitochondrial function by voltage-activated complexation with the Voltage-Dependent Anion Channel (VDAC) of the outer mitochondrial membrane. When complexed with αSyn, the VDAC pore is partially blocked, reducing the transport of ATP/ADP and other metabolites. Further, αSyn can translocate into the mitochondria through VDAC, where it interferes with mitochondrial respiration. Recruitment of αSyn to the VDAC-containing lipid membrane appears to be a crucial prerequisite for both the blockage and translocation processes. Here we report an inhibitory effect of HK2p, a small membrane-binding peptide from the mitochondria-targeting N-terminus of hexokinase 2, on the αSyn membrane binding, and hence on αSyn complex formation with VDAC and translocation through it. In electrophysiology experiments, addition of HK2p at micromolar concentrations to the same side of the membrane as αSyn results in dramatic reduction of the frequency of blockage events in a concentration-dependent manner, reporting on complexation inhibition. Using two complementary methods of measuring protein-membrane binding, bilayer overtone analysis and fluorescence correlation spectroscopy, we found that HK2p induces detachment of αSyn from lipid membranes. Experiments with live HeLa cells using proximity ligation assay confirmed that HK2p impedes αSyn entry into mitochondria. Our results demonstrate that it is possible to regulate αSyn-VDAC complexation by a rationally designed peptide, thus suggesting new avenues in the search for peptide therapeutics to alleviate αSyn mitochondrial toxicity in PD and other synucleinopathies.
Visualizing Molecular Interactions that Determine Assembly of a Bullet-Shaped Vesicular Stomatitis Virus Particle
Authors: Jenni Simon , Horwitz Joshua A. , Bloyet Louis-Marie , Whelan Sean P.J. , Harrison Stephen C. 
Published: April 2022

SUMMARYVesicular stomatitis virus (VSV) is a negative-strand RNA virus with a non-segmented genome, closely related to rabies virus. Both have characteristic bullet-like shapes. We report the structure of intact, infectious VSV particles determined by cryogenic electron microscopy. By compensating for polymorphism among viral particles with computational classification, we obtained a reconstruction of the shaft (“trunk”) at 3.5 Å resolution, with lower resolution for the rounded tip. The ribonucleoprotein (RNP), genomic RNA complexed with nucleoprotein (N), curls into a dome-like structure with about eight gradually expanding turns before transitioning into the regular helical trunk. Two layers of matrix (M) protein link the RNP with the membrane. Radial inter-layer subunit contacts are fixed within single RNA-N-M1-M2 modules, but flexible lateral and axial interactions allow assembly of polymorphic virions. Together with published structures of recombinant N in various states, our results suggest a mechanism for membrane- coupled self-assembly of VSV and its relatives.