bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human alveolar Type 2 epithelium transdifferentiates into metaplastic KRT5+ basal cells during alveolar repair
Authors: Kathiriya Jaymin J. , Wang Chaoqun , Brumwell Alexis , Cassandras Monica , Le Saux Claude , Wolters Paul , Matthay Michael , Chapman Harold A , Peng Tien 
Published: June 2020

SUMMARYUnderstanding differential lineage potential of orthologous stem cells across species can shed light on human disease. Here, utilizing 3D organoids, single cell RNAseq, and xenotransplants, we demonstrate that human alveolar type 2 cells (hAEC2s), unlike murine AEC2s, are multipotent and able to transdifferentiate into KRT5+ basal cells when co-cultured with primary fibroblasts in 3D organoids. Trajectory analyses and immunophenotyping of epithelial progenitors in idiopathic pulmonary fibrosis (IPF) indicate that hAEC2s transdifferentiate into metaplastic basal cells through alveolar-basal intermediate (ABI) cells that we also identify in hAEC2-derived organoids. Modulating hAEC2-intrinsic and niche factors dysregulated in IPF can attenuate metaplastic basal cell transdifferentiation and preserve hAEC2 identity. Finally, hAEC2s transplanted into fibrotic immune-deficient murine lungs engraft as either hAEC2s or differentiated KRT5+ basal cells. Our study indicates that hAEC2s-loss and expansion of alveolar metaplastic basal cells in IPF are causally connected, which would not have been revealed utilizing murine AEC2s as a model.HighlightsHuman AEC2s transdifferentiate into KRT5+ basal cells when accompanied by primary adult human lung mesenchyme in 3D organoid culture.Alterations of hAEC2-intrinsic and niche factors dysregulated in IPF can modify metaplastic hAEC2 transdifferentiation.hAEC2s engraft into fibrotic lungs of immune-deficient mice and transdifferentiate into metaplastic basal cells.Transcriptional trajectory analysis suggests that hAEC2s in IPF gives rise to metaplastic basal cells via alveolar-basal intermediate cells.
Chromatin and transcriptional response to loss of TBX1 in early differentiation of mouse cells
Authors: Cirino Andrea , Aurigemma Ilaria , Franzese Monica , Lania Gabriella , Righelli Dario , Ferrentino Rosa , Illingworth Elizabeth , Angelini Claudia , Baldini Antonio 
Published: June 2020

ABSTRACTThe T-box transcription factor TBX1 has critical roles in the cardiopharyngeal lineage and the gene is haploinsufficient in DiGeorge syndrome, a typical developmental anomaly of the pharyngeal apparatus. Despite almost two decades of research, if and how TBX1 function triggers chromatin remodeling is not known.Here, we explored genome-wide gene expression and chromatin remodeling in two independent cellular models of Tbx1 loss of function, mouse embryonic carcinoma cells P19Cl6, and mouse embryonic stem cells (mESCs). The results of our study revealed that the loss or knockdown of TBX1 caused extensive transcriptional changes, some of which were cell type-specific, some were in common between the two models. However, unexpectedly we observed only limited chromatin changes in both systems. In P19Cl6 cells, differentially accessible regions (DARs) were not enriched in T-BOX binding motifs; in contrast, in mESCs, 34% (n=47) of all DARs included a T-BOX binding motif and almost all of them gained accessibility in Tbx1-/- cells.In conclusion, despite a clear transcriptional response of our cell models to loss of TBX1 in early cell differentiation, chromatin changes were relatively modest.
Whole-exome analysis in Parkinson’s disease reveals a high burden of ultra rare variants in early onset cases
Authors: Bustos Bernabe I. , Krainc Dimitri , Lubbe Steven J. ,   for The International Parkinson’s Disease Genomics Consortium (IPDGC)
Published: June 2020

ABSTRACTParkinson’s disease (PD) is a complex neurodegenerative disorder with a strong genetic component. We performed a “hypothesis-free” exome-wide burden-based analysis of different variant frequencies, predicted functional impact and age of onset classes, in order to expand the understanding of rare variants in PD. Analyzing whole-exome data from a total of 1,425 PD cases and 596 controls, we found a significantly increased burden of ultra-rare (URV= private variants absent from gnomAD) protein altering variants (PAV) in early-onset PD cases (EOPD, <40 years old; P=3.95×10−26, beta=0.16, SE=0.02), compared to LOPD cases (>60 years old, late-onset), where more common PAVs (allele frequencies <0.001) showed the highest significance and effect (P=0.026, beta=0.15, SE=0.07). Gene-set burden analysis of URVs in EOPD highlighted significant disease- and tissue-relevant genes, pathways and protein-protein interaction networks that were different to that observed in non-EOPD cases. Heritability estimates revealed that URVs account for 15.9% of the genetic component in EOPD individuals. Our results suggest that URVs play a significant role in EOPD and that distinct etiological bases may exist for EOPD and sporadic PD. By providing new insights into the genetic architecture of PD, our study may inform approaches aimed at novel gene discovery and provide new directions for genetic risk assessment based on disease age of onset.
Cross-neutralization antibodies against SARS-CoV-2 and RBD mutations from convalescent patient antibody libraries
Authors: Lou Yan , Zhao Wenxiang , Wei Haitao , Chu Min , Chao Ruihua , Yao Hangping , Su Junwei , Li Yanan , Li Xiulan , Cao Yu , Feng Yanyan , Wang Ping , Xia Yongyang , Shang Yushuan , Li Fengping , Ge Pingju , Zhang Xinglin , Gao Wenjing , Du Bing , Liang Tingbo , Qiu Yunqing , Liu Mingyao 
Published: June 2020

AbstractThe emergence of coronavirus disease 2019 (COVID-19) pandemic led to an urgent need to develop therapeutic interventions. Among them, neutralizing antibodies play crucial roles for preventing viral infections and contribute to resolution of infection. Here, we describe the generation of antibody libraries from 17 different COVID-19 recovered patients and screening of neutralizing antibodies to SARS-CoV-2. After 3 rounds of panning, 456 positive phage clones were obtained with high affinity to RBD (receptor binding domain). Then the positive clones were sequenced and reconstituted into whole human IgG for epitope binning assays. After that, all 19 IgG were classified into 6 different epitope groups or Bins. Although all these antibodies were shown to have ability to bind RBD, the antibodies in Bin2 have more superiority to inhibit the interaction between spike protein and angiotensin converting enzyme 2 receptor (ACE2). Most importantly, the antibodies from Bin2 can also strongly bind with mutant RBDs (W463R, R408I, N354D, V367F and N354D/D364Y) derived from SARS-CoV-2 strain with increased infectivity, suggesting the great potential of these antibodies in preventing infection of SARS-CoV-2 and its mutations. Furthermore, these neutralizing antibodies strongly restrict the binding of RBD to hACE2 overexpressed 293T cells. Consistently, these antibodies effectively neutralized pseudovirus entry into hACE2 overexpressed 293T cells. In Vero-E6 cells, these antibodies can even block the entry of live SARS-CoV-2 into cells at only 12.5 nM. These results suggest that these neutralizing human antibodies from the patient-derived antibody libraries have the potential to become therapeutic agents against SARS-CoV-2 and its mutants in this global pandemic.
Quantitative nascent proteome profiling by dual pulse labeling withO-propargyl-puromycin and stable isotope labeled amino acids
Authors: Uchiyama Junki , Ishihama Yasushi , Imami Koshi 
Published: June 2020

SummaryMonitoring translational regulation in response to environmental signals is crucial for understanding cellular proteostasis. However, only limited approaches are currently available for quantifying acute changes in protein synthesis induced by stimuli. Recently, a clickable puromycin analog,O-propargyl-puromycin (OPP), was developed and applied to label the C-termini of nascent polypeptide chains (NPCs). Following affinity purification via a click reaction, OPP allows for a proteomic analysis of NPCs. Despite its advantage, the affinity purification of NPCs using magnetic beads or resins inherently suffers from significant non-specific protein binding, which hinders accurate quantification of the nascent proteins. To address this issue, we employed dual pulse labeling of NPCs with both OPP and stable isotope labeled amino acids to distinguishbona fideNPCs from non-specific proteins, thereby enabling the accurate quantitative profiling of NPCs. We applied this method to dissecting the transcription-coupled translation responses and quantified ~3,000 nascent proteins. We found that the translation of a subset of ribosomal proteins (e.g., RPSA, RPLP0) as well as signaling proteins (e.g., BCAR3, EFNA1, DUSP1) was significantly repressed by transcription inhibition. Together, the present method provides an accurate and broadly applicable nascent proteome profiling for many biological applications at the level of translation.
Proinflammatory S100A9 Regulate Differentiation and Aggregation of Neural Stem Cells
Authors: Tian Yin , Cao Rui , Che Bingchen , Tang Yong , Jiang Lin , Qiao Bai , Liu Yonggang , Morozovaroche Ludmilla A , Zhang Ce 
Published: June 2020

AbstractInflammation is the primary pathological feature of neurodegenerative diseases such as Alzheimer’s (AD) and Parkinson’s disease. Proinflammatory molecules (e.g. S100A9) play important roles during progression of the diseases by regulating behavior and fate of multiple cell types in the nervous system (1). Our earlier studies reveal that S100A9 is toxic to neurons, and its interaction with Aβpeptides leads to the formation of large non-toxic amyloidogenic aggregates, suggesting a protective role of Aβamyloids (2). We herein, demonstrate that S100A9 interacts with neural stem cells (NSCs) and causes NSC differentiation. In the brain of transgenic AD mouse models, we found large quantities of proinflammatory S100A9, which colocalizes with the differentiated NSCs. NSC sphere formation, which is a representative character of NSC stemness, is also substantially inhibited by S100A9. These results suggest that S100A9 is a representative marker for the inflammatory conditions in AD, and it promotes NSC differentiation. Intriguingly, in contrast to the death of both stem and differentiated NSCs caused by high S100A9 doses, S100A9 at a moderate concentration is toxic only to the early differentiated NSCs (i.e. progenitor cells and immature neurons), but not the stem cells. We therefore postulate that at the early stage of AD, expression of S100A9 leads to NSC differentiation, which remedies the neuron damages. The application drugs, which help maintain NSC stemness (e.g. PDGF), may help overcome the acute inflammatory conditions and improve the efficacy of NSC transplantation therapy.
Site-Specific Incorporation of Citrulline into Proteins in Mammalian Cells
Authors: Mondal Santanu , Wang Shu , Zheng Yunan , Sen Sudeshna , Chatterjee Abhishek , Thompson Paul R. 
Published: June 2020

AbstractCitrullination is a post-translational modification (PTM) of arginine that is crucial for several physiological processes, including gene regulation and neutrophil extracellular trap formation. Despite recent advances, studies of protein citrullination remain challenging due to the difficulty of accessing proteins homogeneously citrullinated at a specific site. Herein, we report a novel technology that enables the site-specific incorporation of citrulline (Cit) into proteins in mammalian cells. This approach exploits anE. coli-derived engineered leucyl tRNA synthetase-tRNA pair that incorporates a photocaged-citrulline (SM60) into proteins in response to a nonsense codon. Subsequently,SM60is readily converted to Cit with lightin vitroand in living cells. To demonstrate the utility of the method, we biochemically characterized the effect of incorporating Cit at two known autocitrullination sites in Protein Arginine Deiminase 4 (PAD4, R372 and R374) and showed that the R372Cit and R374Cit mutants are 181- and 9-fold less active than the wild-type enzyme. This powerful technology possesses immense potential to decipher the biology of citrullination.
An In situ Collagen-HA Hydrogel System Promotes Survival and Preserves the Proangiogenic Secretion of hiPSC-derived Vascular Smooth Muscle Cells
Authors: Dash Biraja C. , Duan Kaiti , Xing Hao , Kyriakides Themis R. , Hsia Henry C. 
Published: June 2020

AbstractHuman induced pluripotent stem cell-derived vascular smooth muscle cells (hiPSC-VSMCs) with proangiogenic properties have huge therapeutic potential. While hiPSC-VSMCs have already been utilized for wound healing using a biomimetic collagen scaffold, an in situ forming hydrogel mimicking the native environment of skin offers the promise of hiPSC-VSMC mediated repair and regeneration. Herein, the impact of a collagen type-I-hyaluronic acid (HA) in situ hydrogel cross-linked using a PEG-based cross-linker on hiPSC-VSMCs viability and proangiogenic paracrine secretion was investigated. Our study demonstrated increases in cell viability, maintenance of phenotype and proangiogenic growth factor secretion, and proangiogenic activity in response to the conditioned medium. The optimally cross-linked and functionalized collagen type-I/HA hydrogel system developed in this study shows promise as an in situ hiPSC-VSMC carrier system for wound regeneration.
Single nucleus multi-omics regulatory atlas of the murine pituitary
Authors: Ruf-Zamojski Frederique , Zhang Zidong , Zamojski Michel , Smith Gregory R. , Mendelev Natalia , Liu Hanqing , Nudelman German , Moriwaki Mika , Pincas Hanna , Gomez Castanon Rosa , Nair Venugopalan D. , Seenarine Nitish , Amper Mary Anne S. , Zhou Xiang , Ongaro Luisina , Toufaily Chirine , Schang Gauthier , Nery Joseph R. , Bartlett Anna , Aldridge Andrew , Jain Nimisha , Childs Gwen V. , Troyanskaya Olga G. , Ecker Joseph R. , Turgeon Judith L. , Welt Corrine K. , Bernard Daniel J. , Sealfon Stuart C. 
Published: June 2020

AbstractThe pituitary regulates growth, reproduction and other endocrine systems. To investigate transcriptional network epigenetic mechanisms, we generated paired single nucleus (sn) transcriptome and chromatin accessibility profiles in single mouse pituitaries and genome-wide sn methylation datasets. Our analysis provided insight into cell type epigenetics, regulatory circuit and gene control mechanisms. Latent variable pathway analysis detected corresponding transcriptome and chromatin accessibility programs showing both inter-sexual and inter-individual variation. Multi-omics analysis of gene regulatory networks identified cell type-specific regulons whose composition and function were shaped by the promoter accessibility state of target genes. Co-accessibility analysis comprehensively identified putative cis-regulatory regions, including a domain 17kb upstream ofFshbthat overlapped the fertility-linked rs11031006 human polymorphism.In vitroCRISPR-deletion at this locus increasedFshblevels, supporting this domain’s inferred regulatory role. The sn pituitary multi-omics atlas (snpituitaryatlas.princeton.edu) is a public resource for elucidating cell type-specific gene regulatory mechanisms and principles of transcription circuit control.
Heterozygous, polyploid, giant bacterium,Achromatium, possesses an identical functional inventory worldwide across drastically different ecosystems
Authors: Ionescu Danny , Zoccarato Luca , Zaduryan Artur , Schorn Sina , Bižić Mina , Pinnow Solvig , Cypionka Heribert , Grossart Hans-Peter 
Published: June 2020

AbstractAchromatiumis large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain ca. 300 different chromosomes with allelic diversity typical of entire bacterial communities. Surveying all publicly available sediment sequence archives, we showAchromatiaare common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Nevertheless,Achromatiadisplay no ecotypic phylogenetic signal and contain a, globally identical, complete functional inventory.Achromatiacells from differing ecosystems (e.g. freshwater vs. saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility ofAchromatium, and its genomic features, reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.
TMIGD1, a putative tumor suppressor, induces G2-M cell cycle checkpoint arrest in colon cancer cells
Authors: De La Cena Kyle Oliver Corcino , Ho Rachel Xi-Yeen , Amraei Razie , Woolf Nick , Tashjian Joseph Y. , Zhao Qing , Richards Sean , Walker Josh , Huang Juanni , Chitalia Vipul , Rahimi Nader 
Published: June 2020

ABSTRACTColorectal cancer (CRC) is a leading non-familial cause of cancer mortality among men and women. Although various genetic and epigenetic mechanisms have been identified, the full molecular mechanisms deriving CRC tumorigenesis remains incompletely understood. In this study, we demonstrate that cell adhesion molecule transmembrane and immunoglobulin domain containing1 (TMIGD1) is highly expressed in mouse and human normal intestinal epithelial cells. We have developed TMIGD1 knockout mice and show that the loss of TMIGD1 in mice results in the development of adenomas in small intestine and colon. Additionally, the loss of TMIGD1 in mouse impaired intestinal epithelium brush border formation, junctional polarity and maturation. Mechanistically, TMIGD1 inhibits tumor cell proliferation, cell migration, arrests cell cycle at G2/M phase and induces expression of p21CIP1(cyclin-dependent kinase inhibitor 1), and p27KIP1(cyclin-dependent kinase inhibitor 1B) expression, key cell cycle inhibitor proteins involved in the regulation of the cell cycle. Moreover, we demonstrate that TMIGD1 is progressively downregulated in sporadic human CRC and correlates with poor overall survival. Our findings identify TMIGD1 as a novel tumor suppressor gene and provide insights into the pathogenesis of colorectal cancer and possibilities as a potential therapeutic target.
The histone methyltransferase SETD2 couples transcription and splicing by engaging pre-mRNA processing factors through its SHI domain
Authors: Bhattacharya Saikat , Levy Michaella J. , Zhang Ning , Li Hua , Florens Laurence , Washburn Michael P. , Workman Jerry L. 
Published: June 2020

SUMMARYHeterogeneous ribonucleoproteins (hnRNPs) are RNA binding molecules that are involved in key processes such as RNA splicing and transcription. One such hnRNP protein, hnRNP L, regulates alternative splicing (AS) by binding to pre-mRNA transcripts. However, it is unclear what factors contribute to hnRNP L-regulated AS events. Using proteomic approaches, we identified several key factors that co-purify with hnRNP L. We demonstrate that one such factor, the histone methyltransferase SETD2, specifically interacts with hnRNP Lin vitroandin vivo. This interaction occurs through a previously uncharacterized domain in SETD2, the SETD2-hnRNP L Interaction (SHI) domain, the deletion of which, leads to a reduced H3K36me3 deposition. Functionally, SETD2 regulates a subset of hnRNP L-targeted AS events. Our findings demonstrate that SETD2 by interacting with Pol II as well as hnRNP L, can mediate the crosstalk between the transcription and the splicing machinery.
Cell adhesion molecule IGPR-1 activates AMPK connecting cell adhesion to energy sensing and autophagy
Authors: Amraei Razie , Alwani Tooba , Ho Rachel Xi-Yeen , Aryan Zahra , Wang Shawn , Rahimi Nader 
Published: June 2020

ABSTRACTImmunoglobulin (Ig) and proline-rich receptor-1 (IGPR-1) is a cell adhesion molecule that regulates angiogenesis and endothelial barrier function. IGPR-1 is activated by shear stress and mediates endothelial cell’s response to shear stress. Autophagy plays critical roles in the maintenance of endothelial cells in response to cellular stress caused by blood flow. However, whether IGPR-1 is activated in response to, and mediates autophagy remains unknown. In this study, we demonstrate that IGPR-1 is activated by autophagy inducing stimuli, such as amino acid starvation, nutrient deprivation, rapamycin and lipopolysaccharide (LPS). We have identified IκB kinaseβ (IKKβ) as a key serine/threonine kinase activated by autophagy stimuli and mediates phosphorylation of IGPR-1 at Ser220. Activation of IGPR-1, in turn, stimulates phosphorylation of AMP-activated protein kinase (AMPK), which leads to phosphorylation of key pro-autophagy proteins, ULK1 and Beclin-1 (BECN1), increased LC3-II levels and accumulation of LC3 punctum. This study demonstrates that IGPR-1 is activated by and regulates autophagy, connecting cell adhesion to autophagy, a finding that has important significance for autophagy-driven pathologies such cardiovascular diseases and cancer.
A chromosome-level genome assembly for the Eastern Fence Lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology
Authors: Westfall Aundrea K. , Telemeco Rory S. , Grizante Mariana B. , Waits Damien S. , Clark Amanda D. , Simpson Dasia Y. , Klabacka Randy L. , Sullivan Alexis P. , Perry George H. , Sears Michael W. , Cox Christian L. , Cox Robert M. , Gifford Matthew E. , John-Alder Henry B. , Langkilde Tracy , Angilletta Michael J. , Leaché Adam D. , Tollis Marc , Kusumi Kenro , Schwartz Tonia S. 
Published: June 2020

AbstractHigh-quality genomic resources facilitate population-level and species-level comparisons to answer questions about behavioral ecology, morphological and physiological adaptations, as well as the evolution of genomic architecture. Squamate reptiles (lizards and snakes) are particularly diverse in characteristics that have intrigued evolutionary biologists, but high-quality genomic resources for squamates are relatively sparse. Lizards in the genusSceloporushave a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. We present a high-quality chromosome-level reference genome assembly, SceUnd1.0, (utilizing 10X Genomics Chromium, HiC, and PacBio data) and tissue/developmental stage transcriptomes for the Eastern Fence Lizard,Sceloporus undulatus. We performed synteny analysis with other available squamate chromosome-level assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes inS. undulatus. Using this newS. undulatusgenome assembly we conducted reference-based assemblies for 34 otherSceloporusspecies to improve draft nuclear genomes assemblies from 1% coverage to 43% coverage on average. Across these species, typically >90% of reads mapped for species within 20 million years divergence fromS. undulatus, this dropped to 75% reads mapped for species at 35 million years divergence. Finally we use RNAseq and whole genome resequencing data to compare the three assemblies as references, each representing an increased level of sequencing, cost and assembly efforts: Supernova Assembly with data from10X Genomics Chromium library; HiRise Assembly that added data from HiC library; and PBJelly Assembly that added data from PacBio sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq, but the chromosome-level scaffolds provided by the addition of the HiC data allowed the reference to be used for other whole genome analysis, including synteny and whole genome association mapping analyses. The addition of PacBio data provided negligible gains. Overall, these new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.