99901
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Identification of the Complete Chloroplast Genome of Malus zhaojiaoensis Jiang and Its Comparison and Evolutionary Analysis with Other Malus Species. Genes (Basel) 2022; 13:genes13040560. [PMID: 35456366 PMCID: PMC9028542 DOI: 10.3390/genes13040560] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/19/2022] [Accepted: 03/19/2022] [Indexed: 12/02/2022] Open
Abstract
The genus Malus is rich in species and many of its plastid genomes have been released. However, limited resources and few markers are not conducive to the comparison of differences among species and resource identification and evaluation. In this study, the complete chloroplast genome of Malus zhaojiaoensis was studied by NGS sequencing, with a total length of 159998 bp. It consists of four regions, LSC (88,070 bp), IRB (26,359 bp), SSC (19,210 bp) and IRA (26,359 bp). M. zhaojiaoensis cp genome contained a total of 111 genes made up of three classes: 78 coding sequences, 29 tRNA genes, and four rRNA genes. In addition, a total of 91 SSRs and 43 INEs were found in the M. zhaojiaoensis cp genome, which was slightly different from M. baccata and M. hupehensis in number. The analysis of codon usage and RNA editing showed that high-frequency codons tended to end at A/U bases and RNA editing mainly occurred at the second codon. Comparative genome analysis suggested that the cp genomes of eight Malus species had higher overall similarity, but there were more variation hotspots (rps16_trnK-UUU, trnG-UCC_atpA, atpH_atpF, trnT-GGU_psbD, etc.) in the LSC region. By building evolutionary trees, it can be clearly observed that M. zhaojiaoensis formed a large group with eight species of Malus, but was relatively independent in differentiation. In conclusion, this study provides high-quality chloroplast genome resources of M. zhaojiaoensis and discusses the genetic variation characteristics of Malus genus. The findings of this study will provide a good reference for plastid genome assembly and interspecific comparison in the future.
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99902
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Dufour CR, Scholtes C, Yan M, Chen Y, Han L, Li T, Xia H, Deng Q, Vernier M, Giguère V. The mTOR chromatin-bound interactome in prostate cancer. Cell Rep 2022; 38:110534. [PMID: 35320709 DOI: 10.1016/j.celrep.2022.110534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/07/2021] [Accepted: 02/24/2022] [Indexed: 11/03/2022] Open
Abstract
A growing number of studies support a direct role for nuclear mTOR in gene regulation and chromatin structure. Still, the scarcity of known chromatin-bound mTOR partners limits our understanding of how nuclear mTOR controls transcription. Herein, comprehensive mapping of the mTOR chromatin-bound interactome in both androgen-dependent and -independent cellular models of prostate cancer (PCa) identifies a conserved 67-protein interaction network enriched for chromatin modifiers, transcription factors, and SUMOylation machinery. SUMO2/3 and nuclear pore protein NUP210 are among the strongest interactors, while the androgen receptor (AR) is the dominant androgen-inducible mTOR partner. Further investigation reveals that NUP210 facilitates mTOR nuclear trafficking, that mTOR and AR form a functional transcriptional module with the nucleosome remodeling and deacetylase (NuRD) complex, and that androgens specify mTOR-SUMO2/3 promoter-enhancer association. This work identifies a vast network of mTOR-associated nuclear complexes advocating innovative molecular strategies to modulate mTOR-dependent gene regulation with conceivable implications for PCa and other diseases.
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Affiliation(s)
- Catherine R Dufour
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada
| | - Charlotte Scholtes
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada
| | - Ming Yan
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada
| | - Yonghong Chen
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, Faculty of Medicine, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Lingwei Han
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, Faculty of Medicine, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Ting Li
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada
| | - Hui Xia
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, Faculty of Medicine, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Qiyun Deng
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, Faculty of Medicine, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Mathieu Vernier
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada
| | - Vincent Giguère
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, Faculty of Medicine, McGill University, Montréal, QC H3G 1Y6, Canada.
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99903
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IP-Se-06, a Selenylated Imidazo[1,2-a]pyridine, Modulates Intracellular Redox State and Causes Akt/mTOR/HIF-1α and MAPK Signaling Inhibition, Promoting Antiproliferative Effect and Apoptosis in Glioblastoma Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3710449. [PMID: 35360199 PMCID: PMC8964227 DOI: 10.1155/2022/3710449] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 12/11/2022]
Abstract
Glioblastoma multiforme (GBM) is a notably lethal brain tumor associated with high proliferation rate and therapeutic resistance, while currently effective treatment options are still lacking. Imidazo[1,2-a]pyridine derivatives and organoselenium compounds are largely used in medicinal chemistry and drug development. This study is aimed at further investigating the antitumor mechanism of IP-Se-06 (3-((2-methoxyphenyl)selanyl)-7-methyl-2-phenylimidazol[1,2-a]pyridine), a selenylated imidazo[1,2-a]pyridine derivative in glioblastoma cells. IP-Se-06 exhibited high cytotoxicity against A172 cells (IC50 = 1.8 μM) and selectivity for this glioblastoma cell. The IP-Se-06 compound has pharmacological properties verified in its ADMET profile, especially related to blood-brain barrier (BBB) permeability. At low concentration (1 μM), IP-Se-06 induced intracellular redox state modulation with depletion of TrxR and GSH levels as well as inhibition of NRF2 protein. IP-Se-06 also decreased mitochondrial membrane potential, induced cytochrome c release, and chromatin condensation. Furthermore, IP-Se-06 induced apoptosis by decreasing levels of Bcl-xL while increasing levels of γ-H2AX and p53 proteins. Treatment with IP-Se-06 induced cell cycle arrest and showed antiproliferative effect by inhibition of Akt/mTOR/HIF-1α and ERK 1/2 signaling pathways. In addition, IP-Se-06 displayed significant inhibition of p38 MAPK and p-p38, leading to inhibition of inflammasome complex proteins (NLRP3 and caspase-1) in glioblastoma cells. These collective findings demonstrated that IP-Se-06 is a bioactive molecule that can be considered a candidate for the development of a novel drug for glioblastoma treatment.
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99904
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South-to-north migration preceded the advent of intensive farming in the Maya region. Nat Commun 2022; 13:1530. [PMID: 35318319 PMCID: PMC8940966 DOI: 10.1038/s41467-022-29158-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/25/2022] [Indexed: 11/16/2022] Open
Abstract
The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region. The genetic prehistory of central America has not been well explored. Here, the authors find evidence from ancient DNA from twenty individuals who lived in Belize 9,600 to 3,700 years ago of a migration from the south that coincided with the first evidence for forest clearing and the spread of maize horticulture.
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99905
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Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids. Nat Commun 2022; 13:1545. [PMID: 35318330 PMCID: PMC8941075 DOI: 10.1038/s41467-022-29264-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/07/2022] [Indexed: 01/08/2023] Open
Abstract
Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are archaeal monolayer membrane lipids that can provide a competitive advantage in extreme environments. Here, we identify a radical SAM protein, tetraether synthase (Tes), that participates in the synthesis of GDGTs. Attempts to generate a tes-deleted mutant in Sulfolobus acidocaldarius were unsuccessful, suggesting that the gene is essential in this organism. Heterologous expression of tes homologues leads to production of GDGT and structurally related lipids in the methanogen Methanococcus maripaludis (which otherwise does not synthesize GDGTs and lacks a tes homolog, but produces a putative GDGT precursor, archaeol). Tes homologues are encoded in the genomes of many archaea, as well as in some bacteria, in which they might be involved in the synthesis of bacterial branched glycerol dialkyl glycerol tetraethers.
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99906
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Brain-wide projection reconstruction of single functionally defined neurons. Nat Commun 2022; 13:1531. [PMID: 35318336 PMCID: PMC8940919 DOI: 10.1038/s41467-022-29229-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/04/2022] [Indexed: 12/23/2022] Open
Abstract
Reconstructing axonal projections of single neurons at the whole-brain level is currently a converging goal of the neuroscience community that is fundamental for understanding the logic of information flow in the brain. Thousands of single neurons from different brain regions have recently been morphologically reconstructed, but the corresponding physiological functional features of these reconstructed neurons are unclear. By combining two-photon Ca2+ imaging with targeted single-cell plasmid electroporation, we reconstruct the brain-wide morphologies of single neurons that are defined by a sound-evoked response map in the auditory cortices (AUDs) of awake mice. Long-range interhemispheric projections can be reliably labelled via co-injection with an adeno-associated virus, which enables enhanced expression of indicator protein in the targeted neurons. Here we show that this method avoids the randomness and ambiguity of conventional methods of neuronal morphological reconstruction, offering an avenue for developing a precise one-to-one map of neuronal projection patterns and physiological functional features. Brain-wide axonal projections of single neurons have been extensively reconstructed without any functional characterization. The authors present a method that allows for developing a precise one-to-one map of both projection patterns and functional features of single neurons in mice.
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99907
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Zhang L, Liu G, Xia T, Yang X, Sun G, Zhao C, Xu C, Zhang H. Evolution of toll-like receptor gene family in amphibians. Int J Biol Macromol 2022; 208:463-474. [PMID: 35337917 DOI: 10.1016/j.ijbiomac.2022.03.112] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 02/09/2022] [Accepted: 03/17/2022] [Indexed: 12/24/2022]
Abstract
The evolutionary position and lifestyle of amphibians highlights the important roles of the immune system in adaptive radiation and their adaptation to a complex pathogenic environment. Toll-like receptors (TLRs) are membrane-like sensors that recognize and bind conserved molecular motifs in pathogens to initiate downstream immune responses. To understand the evolutionary patterns of TLRs in amphibians, we analyzed TLR genes from the genomes and transcriptomes of 102 amphibian species. Phylogenetic results showed that 578 intact amphibian TLR sequences belonged to 16 TLR genes and were divided into seven subfamilies. The TLR4 subfamily was only identified in the Anura. Purification selection plays a leading role in amphibian TLR evolution and mean ω (dN/dS) values ranged from 0.252 for TLR7 to 0.381 for TLR19. Furthermore, the ω values of different domains were significantly different. We found positive selection patterns for 141 of 12,690 codons (1.1%) in all amphibian TLRs, most of which were located in leucine-rich repeats (LRRs). We also observed low to moderate levels of single-nucleotide polymorphisms (SNPs) in Pelophylax nigromaculatus and Bombina orientalis. This study provided critical primers, meaningful information regarding TLR gene family evolution in amphibians, and insights into the complex evolutionary patterns and implications of TLR polymorphisms.
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Affiliation(s)
- Lei Zhang
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Guangshuai Liu
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Tian Xia
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Xiufeng Yang
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Guolei Sun
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Chunzhu Xu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China.
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99908
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Chen W, Yang H, Hou C, Sun Y, Shang Y, Zeng Y, Hu Y, Qu Y, Zhu J, Fang F, Lu D, Song H. The influence of childhood asthma on adult height: evidence from the UK Biobank. BMC Med 2022; 20:94. [PMID: 35313867 PMCID: PMC8939112 DOI: 10.1186/s12916-022-02289-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/08/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND To elucidate the influence of childhood asthma on adult height after consideration of genetic heterogeneity in height. METHODS Based on the UK Biobank, we conducted a matched cohort study, including 13,602 European individuals with asthma diagnosed before 18 years old and 136,008 matched unexposed individuals without such an experience. Ascertainment of asthma was based on self-reported data (97.6%) or clinical diagnosis in healthcare registers (2.4%). We studied three height outcomes, including (1) the attained adult height (in centimeters), (2) the height deviation measured as the difference between a person's rank of genetically determined height (based on generated polygenetic risk score) and their rank of attained adult height in the study population (deviation in % of height order after standardization), and (3) the presence of height deficit comparing genetically determined and attained height (yes or no). We applied linear mixed-effect models to assess the associations of asthma diagnosed at different ages with attained adult height and height deviation, and conditional logistic regression models to estimate the associations of asthma with the risk of height deficit. RESULTS 40.07% (59,944/149,610) of the study participants were born before 1950, and most of them were men (57.65%). After controlling for multiple covariates, childhood asthma was associated with shorter attained adult height, irrespective of age at asthma diagnosis. However, in the analysis of height deviation (deviation in %), we observed the greatest height deviation among individuals with asthma diagnosed before 4 years of age (- 2.57 [95% CI - 4.14 to - 1.00] and - 2.80 [95% CI - 4.06 to - 1.54] for the age of ≤ 2 and 3-4 years, respectively). The magnitude of height deviation in relation to asthma declined thereafter and became null after age 6. Similarly, there was a statistically significant height deficit in relation to an asthma diagnosis at ages ≤ 2 and 3-4 (odds ratios = 1.21, 95% CI 1.04 to 1.40, and 1.15, 95% CI 1.02 to 1.29) but not thereafter. The result pattern was similar when separately analyzing asthma with or without inhaled glucocorticoid (ICS) use, despite that the estimates were consistently stronger among asthma individuals who used ICS. CONCLUSIONS Our results suggest a notable association of childhood asthma, primarily asthma diagnosed at an early age, with adult height, after consideration of genetic heterogeneity in height and use of ICS. This finding highlights the need for surveillance on the growth problems among children with asthma.
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Affiliation(s)
- Wenwen Chen
- Division of Nephrology, Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.,West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China.,Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Huazhen Yang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China.,Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Can Hou
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China.,Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Yajing Sun
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China.,Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Yanan Shang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China.,Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Yu Zeng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China.,Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Yao Hu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China.,Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Yuanyuan Qu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China.,Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Jianwei Zhu
- Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Fang Fang
- Institute of Environmental Medicine, Karolinska Institute, 17177, Stockholm, Sweden
| | - Donghao Lu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China.,Institute of Environmental Medicine, Karolinska Institute, 17177, Stockholm, Sweden.,Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA, 02215, USA
| | - Huan Song
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Guo Xue Lane 37, Chengdu, 610041, China. .,Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China. .,Center of Public Health Sciences, Faculty of Medicine, University of Iceland, 101, Reykjavík, Iceland.
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99909
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Tamošiūnė I, Andriūnaitė E, Vinskienė J, Stanys V, Rugienius R, Baniulis D. Enduring Effect of Antibiotic Timentin Treatment on Tobacco In Vitro Shoot Growth and Microbiome Diversity. PLANTS (BASEL, SWITZERLAND) 2022; 11:832. [PMID: 35336713 PMCID: PMC8954828 DOI: 10.3390/plants11060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Plant in vitro cultures initiated from surface-sterilized explants often harbor complex microbial communities. Antibiotics are commonly used to decontaminate plant tissue culture or during genetic transformation; however, the effect of antibiotic treatment on the diversity of indigenous microbial populations and the consequences on the performance of tissue culture is not completely understood. Therefore, the aim of this study was to assess the effect of antibiotic treatment on the growth and stress level of tobacco (Nicotiana tabacum L.) shoots in vitro as well as the composition of the plant-associated microbiome. The study revealed that shoot cultivation on a medium supplemented with 250 mg L-1 timentin resulted in 29 ± 4% reduced biomass accumulation and a 1.2-1.6-fold higher level of oxidative stress injury compared to the control samples. Moreover, the growth properties of shoots were only partially restored after transfer to a medium without the antibiotic. Microbiome analysis of the shoot samples using multivariable region-based 16S rRNA gene sequencing revealed a diverse microbial community in the control tobacco shoots, including 59 bacterial families; however, it was largely dominated by Mycobacteriaceae. Antibiotic treatment resulted in a decline in microbial diversity (the number of families was reduced 4.5-fold) and increased domination by the Mycobacteriaceae family. These results imply that the diversity of the plant-associated microbiome might represent a significant factor contributing to the efficient propagation of in vitro tissue culture.
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99910
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2, 3, 5, 4'-tetrahydroxystilbene-2-O-beta-D-glucoside protects against neuronal cell death and traumatic brain injury-induced pathophysiology. Aging (Albany NY) 2022; 14:2607-2627. [PMID: 35314517 PMCID: PMC9004580 DOI: 10.18632/aging.203958] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/01/2022] [Indexed: 11/25/2022]
Abstract
Traumatic brain injury (TBI) is a global health issue that affects at least 10 million people per year. Neuronal cell death and brain injury after TBI, including apoptosis, inflammation, and excitotoxicity, have led to detrimental effects in TBI. 2, 3, 5, 4’-tetrahydroxystilbene-2-O-beta-D-glucoside (THSG), a water-soluble compound extracted from the Chinese herb Polygonum multiflorum, has been shown to exert various biological functions. However, the effects of THSG on TBI is still poorly understood. THSG reduced L-glutamate-induced DNA fragmentation and protected glial and neuronal cell death after L-glutamate stimulation. Our results also showed that TBI caused significant behavioral deficits in the performance of beam walking, mNSS, and Morris water maze tasks in a mouse model. Importantly, daily administration of THSG (60 mg/kg/day) after TBI for 21 days attenuated the injury severity score, promoted motor coordination, and improved cognitive performance post-TBI. Moreover, administration of THSG also dramatically decreased the brain lesion volume. THSG reduced TBI-induced neuronal apoptosis in the brain cortex 24 h after TBI. Furthermore, THSG increased the number of immature neurons in the subgranular zone (SGZ) of the dentate gyrus (DG) of the hippocampus. Our results demonstrate that THSG exerts neuroprotective effects on glutamate-induced excitotoxicity and glial and neuronal cell death. The present study also demonstrated that THSG effectively protects against TBI-associated motor and cognitive impairment, at least in part, by inhibiting TBI-induced apoptosis and promoting neurogenesis.
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99911
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Eroglu B, Jin X, Deane S, Öztürk B, Ross OA, Moskophidis D, Mivechi NF. Dusp26 phosphatase regulates mitochondrial respiration and oxidative stress and protects neuronal cell death. Cell Mol Life Sci 2022; 79:198. [PMID: 35313355 PMCID: PMC10601927 DOI: 10.1007/s00018-022-04162-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/04/2022] [Accepted: 01/21/2022] [Indexed: 11/29/2022]
Abstract
The dual specificity protein phosphatases (Dusps) control dephosphorylation of mitogen-activated protein kinases (MAPKs) as well as other substrates. Here, we report that Dusp26, which is highly expressed in neuroblastoma cells and primary neurons is targeted to the mitochondrial outer membrane via its NH2-terminal mitochondrial targeting sequence. Loss of Dusp26 has a significant impact on mitochondrial function that is associated with increased levels of reactive oxygen species (ROS), reduction in ATP generation, reduction in mitochondria motility and release of mitochondrial HtrA2 protease into the cytoplasm. The mitochondrial dysregulation in dusp26-deficient neuroblastoma cells leads to the inhibition of cell proliferation and cell death. In vivo, Dusp26 is highly expressed in neurons in different brain regions, including cortex and midbrain (MB). Ablation of Dusp26 in mouse model leads to dopaminergic (DA) neuronal cell loss in the substantia nigra par compacta (SNpc), inflammatory response in MB and striatum, and phenotypes that are normally associated with Neurodegenerative diseases. Consistent with the data from our mouse model, Dusp26 expressing cells are significantly reduced in the SNpc of Parkinson's Disease patients. The underlying mechanism of DA neuronal death is that loss of Dusp26 in neurons increases mitochondrial ROS and concurrent activation of MAPK/p38 signaling pathway and inflammatory response. Our results suggest that regulation of mitochondrial-associated protein phosphorylation is essential for the maintenance of mitochondrial homeostasis and dysregulation of this process may contribute to the initiation and development of neurodegenerative diseases.
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Affiliation(s)
- Binnur Eroglu
- Molecular Chaperone Biology, Georgia Cancer Center, Medical College of Georgia at Augusta University, 1120 15th St., CN3153, Augusta, GA, 30912, USA
| | - Xiongjie Jin
- Molecular Chaperone Biology, Georgia Cancer Center, Medical College of Georgia at Augusta University, 1120 15th St., CN3153, Augusta, GA, 30912, USA
| | - Sadiki Deane
- Molecular Chaperone Biology, Georgia Cancer Center, Medical College of Georgia at Augusta University, 1120 15th St., CN3153, Augusta, GA, 30912, USA
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Bahadır Öztürk
- Molecular Chaperone Biology, Georgia Cancer Center, Medical College of Georgia at Augusta University, 1120 15th St., CN3153, Augusta, GA, 30912, USA
- Medical Biochemistry Department, Selcuk University Medical Faculty, Konya, Turkey
| | - Owen A Ross
- Mayo Clinic, 4500 San Pablo Rd., Jacksonville, FL, 32224, USA
| | - Demetrius Moskophidis
- Molecular Chaperone Biology, Georgia Cancer Center, Medical College of Georgia at Augusta University, 1120 15th St., CN3153, Augusta, GA, 30912, USA.
- Department of Medicine, Medical College of Georgia at Augusta University, 1120 15th St., CN3153, Augusta, GA, 30912, USA.
| | - Nahid F Mivechi
- Molecular Chaperone Biology, Georgia Cancer Center, Medical College of Georgia at Augusta University, 1120 15th St., CN3153, Augusta, GA, 30912, USA.
- Departments of Radiation Oncology, Medical College of Georgia at Augusta University, 1120 15th St., CN3153, Augusta, GA, 30912, USA.
- Charlie Norwood VAMC, One Freedom Way, Augusta, GA, 30904, USA.
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99912
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Lau M, Wigmann C, Kress S, Schikowski T, Schwender H. Evaluation of tree-based statistical learning methods for constructing genetic risk scores. BMC Bioinformatics 2022; 23:97. [PMID: 35313824 PMCID: PMC8935722 DOI: 10.1186/s12859-022-04634-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/14/2022] [Indexed: 04/11/2024] Open
Abstract
Background Genetic risk scores (GRS) summarize genetic features such as single nucleotide polymorphisms (SNPs) in a single statistic with respect to a given trait. So far, GRS are typically built using generalized linear models or regularized extensions. However, these linear methods are usually not able to incorporate gene-gene interactions or non-linear SNP-response relationships. Tree-based statistical learning methods such as random forests and logic regression may be an alternative to such regularized-regression-based methods and are investigated in this article. Moreover, we consider modifications of random forests and logic regression for the construction of GRS. Results In an extensive simulation study and an application to a real data set from a German cohort study, we show that both tree-based approaches can outperform elastic net when constructing GRS for binary traits. Especially a modification of logic regression called logic bagging could induce comparatively high predictive power as measured by the area under the curve and the statistical power. Even when considering no epistatic interaction effects but only marginal genetic effects, the regularized regression method lead in most cases to inferior results. Conclusions When constructing GRS, we recommend taking random forests and logic bagging into account, in particular, if it can be assumed that possibly unknown epistasis between SNPs is present. To develop the best possible prediction models, extensive joint hyperparameter optimizations should be conducted. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04634-w.
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Affiliation(s)
- Michael Lau
- Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany. .,IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany.
| | - Claudia Wigmann
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Sara Kress
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Tamara Schikowski
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany
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99913
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Fukuda N, Takeuchi M. Complete dominant inheritance of intracellular leucine accumulation traits in polyploid yeasts. Yeast 2022; 39:272-282. [PMID: 35315123 DOI: 10.1002/yea.3700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 02/04/2022] [Accepted: 02/22/2022] [Indexed: 11/11/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is widely used for ethanol production. In the production of alcoholic beverages, flavours are affected mainly by yeast metabolism in the fermentation process. To increase the contents of initial scented fruity flavours, such as isoamyl alcohol and isoamyl acetate, leucine accumulation in yeast cells is induced by a decrease of leucine feedback inhibition in the l-leucine synthetic pathway using conventional mutagenesis. Diploid strains are commonly used in sake brewing because of better fermentation performance, such as vitality and endurance, compared with those of haploid strains. Heterozygous mutations are mostly detected in target genes of brewing yeasts generated through mutation breeding. Here we describe that an allele of the LEU4 gene, LEU4G516S , dominantly induced leucine accumulation even in triploid and tetraploid yeasts as with in diploid yeasts. Importantly, we demonstrated that there is no difference in the intracellular amount of branched-chain amino acids between LEU4G516S /LEU4 heterozygous diploids and LEU4G516S /LEU4G516S homozygous diploids. The approach to increase isoamyl alcohol and isoamyl acetate by intracellular leucine accumulation can potentially be applied to a variety of yeast strains, including aneuploid and polyploid yeasts.
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Affiliation(s)
- Nobuo Fukuda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Osaka, Japan
| | - Mio Takeuchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Osaka, Japan
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99914
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Chen H, Yang Q, Fu H, Chen K, Zhao S, Zhang C, Cai T, Wang L, Lu W, Dang H, Gao M, Li H, Yuan X, Varshney RK, Zhuang W. Identification of Key Gene Networks and Deciphering Transcriptional Regulators Associated With Peanut Embryo Abortion Mediated by Calcium Deficiency. FRONTIERS IN PLANT SCIENCE 2022; 13:814015. [PMID: 35386666 PMCID: PMC8978587 DOI: 10.3389/fpls.2022.814015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Peanut embryo development is easily affected by a variety of nutrient elements in the soil, especially the calcium level. Peanut produces abortive embryos in calcium-deficient soil, but underlying mechanism remains unclear. Thus, identifying key transcriptional regulators and their associated regulatory networks promises to contribute to a better understanding of this process. In this study, cellular biology and gene expression analyses were performed to investigate peanut embryo development with the aim to discern the global architecture of gene regulatory networks underlying peanut embryo abortion under calcium deficiency conditions. The endomembrane systems tended to disintegrate, impairing cell growth and starch, protein and lipid body accumulation, resulting in aborted seeds. RNA-seq analysis showed that the gene expression profile in peanut embryos was significantly changed under calcium deficiency. Further analysis indicated that multiple signal pathways were involved in the peanut embryo abortion. Differential expressed genes (DEGs) related to cytoplasmic free Ca2+ were significantly altered. DEGs in plant hormone signaling pathways tended to be associated with increased IAA and ethylene but with decreased ABA, gibberellin, cytokinin, and brassinosteroid levels. Certain vital genes, including apoptosis-inducing factor, WRKYs and ethylene-responsive transcription factors, were up-regulated, while key regulators of embryo development, such as TCP4, WRI1, FUS3, ABI3, and GLK1 were down-regulated. Weighted gene co-expression network analysis (WGCNA) identified 16 significant modules associated with the plant hormone signaling, MAPK signaling, ubiquitin mediated proteolysis, reserve substance biosynthesis and metabolism pathways to decipher regulatory network. The most significant module was darkolivegreen2 and FUS3 (AH06G23930) had the highest connectivity among this module. Importantly, key transcription factors involved in embryogenesis or ovule development including TCP4, GLK1, ABI3, bHLH115, MYC2, etc., were also present in this module and down regulated under calcium deficiency. This study presents the first global view of the gene regulatory network involved in peanut embryo abortion under calcium deficiency conditions and lays foundation for improving peanut tolerances to calcium deficiency by a targeted manipulation of molecular breeding.
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Affiliation(s)
- Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiwen Fu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kun Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shanshan Zhao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lihui Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenzhi Lu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hao Dang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meijia Gao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Agricultural Biotechnology Center, Center for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Huaqi Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Agricultural Biotechnology Center, Center for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Xinyi Yuan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Agricultural Biotechnology Center, Center for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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99915
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Ramautar R. Capillary electrophoresis mass spectrometry for metabolomics: reflecting on the next steps. Bioanalysis 2022; 14:393-396. [PMID: 35311379 DOI: 10.4155/bio-2022-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
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99916
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Tsurumoto T, Fujikawa Y, Onoda Y, Kamimori M, Hiramatsu K, Tanimoto H, Ohta D, Okazawa A. Effect of high-dose 290 nm UV-B on resveratrol content in grape skins. Biosci Biotechnol Biochem 2022; 86:502-508. [PMID: 35092419 DOI: 10.1093/bbb/zbac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022]
Abstract
UV-C irradiation increases resveratrol content in grape skins, but it reaches a maximum at a certain UV-C dose. In contrast, UV-B has a weak resveratrol-enhancing effect at low doses, but it has not been investigated at high doses. In this study, we investigated the effect of high-dose UV-B on resveratrol contents in grape skins. Irradiation of Muscat Bailey A with 290 nm UV-B LED at 22 500 and 225 000 µmol m-2 increased the resveratrol contents in the grape skins by 2.1- and 9.0-fold, respectively, without significant increases in other phenolic compounds. The effect was also confirmed for 2 other cultivars: Shine Muscat and Delaware. Transcriptome analysis of the grape skins of Muscat Bailey A immediately after irradiation with UV-B at 225 000 µmol m-2 showed that genes related to biotic and abiotic stresses were upregulated. Hence, it was suggested that high-dose UV-B irradiation induces a stress response and specifically activates resveratrol biosynthesis.
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Affiliation(s)
- Tomohiro Tsurumoto
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan.,Yokohama Research Center, Nichia Corporation, Yokohama, Japan
| | - Yasuo Fujikawa
- Yokohama Research Center, Nichia Corporation, Yokohama, Japan
| | - Yushi Onoda
- Yokohama Research Center, Nichia Corporation, Yokohama, Japan
| | - Masahiro Kamimori
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, Habikino, Japan
| | - Kazuya Hiramatsu
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, Habikino, Japan
| | - Hideo Tanimoto
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, Habikino, Japan
| | - Daisaku Ohta
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Atsushi Okazawa
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
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99917
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Morgan T, Falkoski DL, Tavares MP, Oliveira MB, Guimarães VM, de Oliveira Mendes TA. Penicillium Ochrochloron RLS11 Secretome Containing Carbohydrate-Active Enzymes Improves Commercial Enzyme Mixtures During Sugarcane Straw Saccharification. Appl Biochem Biotechnol 2022; 194:2946-2967. [PMID: 35312974 DOI: 10.1007/s12010-022-03898-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/14/2022] [Indexed: 11/29/2022]
Abstract
Filamentous fungi are prolific producers of carbohydrate-active enzymes (CAZymes) and important agents that carry out plant cell wall degradation in natural environments. The number of fungal species is frequently reported in the millions range, with a huge diversity and genetic variability, reflecting on a vast repertoire of CAZymes that these organisms can produce. In this study, we evaluated the ability of previously selected ascomycete and basidiomycete fungi to produce plant cell wall-degrading enzyme (PCWDE) activities and the potential of the culture supernatants to increase the efficiency of the Cellic® CTec2/HTec2 for steam-exploded sugarcane straw saccharification. The culture supernatant of Penicillium ochrochloron RLS11 showed a promising supplementation effect on Cellic® CTec2/HTec2, and we conducted the whole-genome sequencing and proteomic analysis for this fungus. The size of the assembled genome was 38.06 Mbp, and a total of 12,015 protein-coding genes were identified. The repertoire of PCWDE-coding genes was comparatively high among Penicillium spp. and showed an expansion in important cellulases and xylanases families, such as GH3, GH6, GH7, and GH11. The proteomic analysis indicated cellulases that probably enhanced the biomass saccharification performance of the Cellic® CTec2/HTec2, which included enzymes from GH3, GH6, and GH7 families.
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Affiliation(s)
- Túlio Morgan
- Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Av. Presidente Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil. .,Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil.
| | - Daniel Luciano Falkoski
- Novozymes Latin America - R. Prof. Francisco Ribeiro, 683 - Barigui, Araucária, PR, 83707-660, Brazil
| | - Murillo Peterlini Tavares
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Mariana Bicalho Oliveira
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Valéria Monteze Guimarães
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Tiago Antônio de Oliveira Mendes
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil.
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99918
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Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. mSystems 2022; 7:e0151821. [PMID: 35311563 PMCID: PMC9040814 DOI: 10.1128/msystems.01518-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Shewanella spp. play important ecological and biogeochemical roles, due in part to their versatile metabolism and swift integration of stimuli. While Shewanella spp. are primarily considered environmental microbes, Shewanella algae is increasingly recognized as an occasional human pathogen. S. algae shares the broad metabolic and respiratory repertoire of Shewanella spp. and thrives in similar ecological niches. In S. algae, nitrate and dimethyl sulfoxide (DMSO) respiration promote biofilm formation strain specifically, with potential implication of taxis and cyclic diguanosine monophosphate (c-di-GMP) signaling. Signal transduction systems in S. algae have not been investigated. To fill these knowledge gaps, we provide here an inventory of the c-di-GMP turnover proteome and chemosensory networks of the type strain S. algae CECT 5071 and compare them with those of 41 whole-genome-sequenced clinical and environmental S. algae isolates. Besides comparative analysis of genetic content and identification of laterally transferred genes, the occurrence and topology of c-di-GMP turnover proteins and chemoreceptors were analyzed. We found S. algae strains to encode 61 to 67 c-di-GMP turnover proteins and 28 to 31 chemoreceptors, placing S. algae near the top in terms of these signaling capacities per Mbp of genome. Most c-di-GMP turnover proteins were predicted to be catalytically active; we describe in them six novel N-terminal sensory domains that appear to control their catalytic activity. Overall, our work defines the c-di-GMP and chemosensory signal transduction pathways in S. algae, contributing to a better understanding of its ecophysiology and establishing S. algae as an auspicious model for the analysis of metabolic and signaling pathways within the genus Shewanella. IMPORTANCEShewanella spp. are widespread aquatic bacteria that include the well-studied freshwater model strain Shewanella oneidensis MR-1. In contrast, the physiology of the marine and occasionally pathogenic species Shewanella algae is poorly understood. Chemosensory and c-di-GMP signal transduction systems integrate environmental stimuli to modulate gene expression, including the switch from a planktonic to sessile lifestyle and pathogenicity. Here, we systematically dissect the c-di-GMP proteome and chemosensory pathways of the type strain S. algae CECT 5071 and 41 additional S. algae isolates. We provide insights into the activity and function of these proteins, including a description of six novel sensory domains. Our work will enable future analyses of the complex, intertwined c-di-GMP metabolism and chemotaxis networks of S. algae and their ecophysiological role.
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99919
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Kreimer A, Ashuach T, Inoue F, Khodaverdian A, Deng C, Yosef N, Ahituv N. Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation. Nat Commun 2022; 13:1504. [PMID: 35315433 PMCID: PMC8938438 DOI: 10.1038/s41467-022-28659-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 02/04/2022] [Indexed: 02/08/2023] Open
Abstract
Gene regulatory elements play a key role in orchestrating gene expression during cellular differentiation, but what determines their function over time remains largely unknown. Here, we perform perturbation-based massively parallel reporter assays at seven early time points of neural differentiation to systematically characterize how regulatory elements and motifs within them guide cellular differentiation. By perturbing over 2,000 putative DNA binding motifs in active regulatory regions, we delineate four categories of functional elements, and observe that activity direction is mostly determined by the sequence itself, while the magnitude of effect depends on the cellular environment. We also find that fine-tuning transcription rates is often achieved by a combined activity of adjacent activating and repressing elements. Our work provides a blueprint for the sequence components needed to induce different transcriptional patterns in general and specifically during neural differentiation. How gene regulatory elements regulate gene expression during cellular differentiation remains largely unknown. Here the authors use perturbation-based massively parallel reporter assays at early time points of neural differentiation to systematically characterize how regulatory elements and motifs within them guide different transcriptional patterns.
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99920
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Chau JFT, Yu MHC, Chui MMC, Yeung CCW, Kwok AWC, Zhuang X, Lee R, Fung JLF, Lee M, Mak CCY, Ng NYT, Chung CCY, Chan MCY, Tsang MHY, Chan JCK, Chan KYK, Kan ASY, Chung PHY, Yang W, Lee SL, Chan GCF, Tam PKH, Lau YL, Yeung KS, Chung BHY, Tang CSM. Comprehensive analysis of recessive carrier status using exome and genome sequencing data in 1543 Southern Chinese. NPJ Genom Med 2022; 7:23. [PMID: 35314707 PMCID: PMC8938515 DOI: 10.1038/s41525-022-00287-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Traditional carrier screening has been utilized for the detection of carriers of genetic disorders. Since a comprehensive assessment of the carrier frequencies of recessive conditions in the Southern Chinese population is not yet available, we performed a secondary analysis on the spectrum and carrier status for 315 genes causing autosomal recessive disorders in 1543 Southern Chinese individuals with next-generation sequencing data, 1116 with exome sequencing and 427 with genome sequencing data. Our data revealed that 1 in 2 people (47.8% of the population) was a carrier for one or more recessive conditions, and 1 in 12 individuals (8.30% of the population) was a carrier for treatable inherited conditions. In alignment with current American College of Obstetricians and Gynecologists (ACOG) pan-ethnic carrier recommendations, 1 in 26 individuals were identified as carriers of cystic fibrosis, thalassemia, and spinal muscular atrophy in the Southern Chinese population. When the >1% expanded carrier screening rate recommendation by ACOG was used, 11 diseases were found to meet the criteria in the Southern Chinese population. Approximately 1 in 3 individuals (35.5% of the population) were carriers of these 11 conditions. If the 1 in 200 carrier frequency threshold is used, and additional seven genes would meet the criteria, and 2 in 5 individuals (38.7% of the population) would be detected as a carrier. This study provides a comprehensive catalogue of the carrier spectrum and frequency in the Southern Chinese population and can serve as a reference for careful evaluation of the conditions to be included in expanded carrier screening for Southern Chinese people.
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Affiliation(s)
- Jeffrey Fong Ting Chau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mullin Ho Chung Yu
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Martin Man Chun Chui
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Cyrus Chun Wing Yeung
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Aaron Wing Cheung Kwok
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xuehan Zhuang
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ryan Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jasmine Lee Fong Fung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mianne Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Christopher Chun Yu Mak
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Nicole Ying Ting Ng
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Claudia Ching Yan Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Marcus Chun Yin Chan
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mandy Ho Yin Tsang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Joshua Chun Ki Chan
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kelvin Yuen Kwong Chan
- Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Hong Kong SAR, China
| | - Anita Sik Yau Kan
- Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Hong Kong SAR, China
| | - Patrick Ho Yu Chung
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - So Lun Lee
- Department of Paediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, Hong Kong SAR, China
| | - Godfrey Chi Fung Chan
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Paul Kwong Hang Tam
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Li Dak-Sum Research Centre, The University of Hong Kong-Karolinska Institute Collaboration in Regenerative Medicine, Hong Kong SAR, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kit San Yeung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Brian Hon Yin Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Clara Sze Man Tang
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Li Dak-Sum Research Centre, The University of Hong Kong-Karolinska Institute Collaboration in Regenerative Medicine, Hong Kong SAR, China.
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99921
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Abstract
The distortions in the high-order structure of therapeutic monoclonal antibodies (mAbs) under different environmental conditions acutely affect mAb stability, resulting in altered safety, efficacy, and shelf-life profiles. The overall stability of mAbs depends on many factors, and it requires complementary techniques for an in-depth analysis. The stability of mAbs can be characterized by differential centrifugal sedimentation (DCS), differential scanning calorimetry (DSC), differential scanning fluorimetry (DSF), and size exclusion chromatography (SEC) techniques. In this report, temperature-ramped dynamic light scattering (DLS), and circular dichroism (CD) spectroscopy were employed as complementary tools to show how temperature and pH affect the aggregation of a model mAb, trastuzumab, in solution. The results showed that the aggregation onset temperature of trastuzumab defined by DLS was 75 °C, which decreases the amount of β-sheets and causes a slight increase in helix structures. Moreover, the melting temperature of trastuzumab was determined to be between 80–83 °C by temperature-ramped CD spectrophotometry, which is in line with the Tm of trastuzumab’s Fab region tested with DSC. Thus, unfolding and aggregation of trastuzumab start simultaneously at 75 °C, and unfolding triggers the aggregation. The temperature-ramped CD and DLS methods are robust tools to determine the thermal behavior of biosimilars in various solution conditions. Their complementary usage provides solid scientific background for regulatory applications and a better understanding of mAb instability and its relationship with structural changes.
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99922
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Kreisel T, Mendel M, Queen AE, Deckers K, Hupperich D, Riegger J, Fricke C, Schoenebeck F. Modular Generation of (Iodinated) Polyarenes Using Triethylgermane as Orthogonal Masking Group. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tatjana Kreisel
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Marvin Mendel
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Adele E. Queen
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Kristina Deckers
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Daniel Hupperich
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Julian Riegger
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Christoph Fricke
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Franziska Schoenebeck
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Germany
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99923
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Qiao Z, Pan DN, Hoid D, van Winkel R, Li X. When the approaching threat is uncertain: Dynamics of defensive motivation and attention in trait anxiety. Psychophysiology 2022; 59:e14049. [PMID: 35307851 DOI: 10.1111/psyp.14049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 11/26/2022]
Abstract
Uncertainty of threat has been linked to anxiety, but little is known about how neurophysiological responses change as uncertain threats approach and whether trait anxiety modulates these changes. The current study was designed to explore aspects of the dynamics of defensive motivation (startle reflex elicited by acoustic startle probes), attention (probe N100 component of event-related potentials elicited by acoustic startle probes), and autonomic nervous system activity (heart rate) when the approaching threat was certain or uncertain in a variant of the threat probability task. Behavioral results showed that high-trait anxious individuals reported higher levels of anxiety than low-trait anxious individuals only under the uncertain threat condition. Electromyographic data showed that high-trait anxious individuals tended to produce a more pronounced startle reflex, especially when the uncertain threat was proximal. This pattern was not observed in low-trait anxious individuals. By examining early attention engagement through probe N100, we observed a similar pattern in relation to defensive motivation. Moreover, under the uncertain threat condition, high-trait anxious individuals yielded a greater deceleration of heart rate than low-trait anxious individuals. These results indicate a distinct modulation effect of trait anxiety in the dynamics of defensive motivation, attention, and the autonomic nervous system during the anticipation of uncertain threats.
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Affiliation(s)
- Zhiling Qiao
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, China.,KU Leuven, Department of Neuroscience, Research Group Psychiatry, Center for Clinical Psychiatry, Leuven, Belgium
| | - Dong-Ni Pan
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Delhii Hoid
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Ruud van Winkel
- KU Leuven, Department of Neuroscience, Research Group Psychiatry, Center for Clinical Psychiatry, Leuven, Belgium.,UPC KU Leuven, Leuven, Belgium.,Department of Psychiatry and Psychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Xuebing Li
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
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99924
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Nanopore sequencing approach for variation detection of a live attenuated Newcastle disease virus vaccine. Biotechniques 2022; 72:201-206. [PMID: 35311385 DOI: 10.2144/btn-2022-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Live attenuated Newcastle disease virus (NDV) vaccines have been used widely to protect chickens against Newcastle disease. However, the vaccine issues caused by genome mutations can seriously affect poultry health. In this study, the authors demonstrate the use of nanopore sequencing technology for rapid genome determination and variation analysis from a live attenuated NDV vaccine. NDV-specific reads were detected immediately after sequencing, and 24× genome coverage was obtained within 10 min. Variation analysis revealed 19 variant sites across the vaccine genome compared to the NDV clone 30 reference sequence . The sequencing and data analysis workflow employed enables all basic molecular biology laboratories to perform detailed genome sequencing in live attenuated vaccine, providing an effective means of quality control for vaccine production.
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99925
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Tang X, Zhang Y, Yuan HM, Zhai J, Huang X. Reprogramming of the Hevea brasiliensis Epigenome and Transcriptome in Response to Cold Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:831839. [PMID: 35386670 PMCID: PMC8979024 DOI: 10.3389/fpls.2022.831839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Low temperature is a key factor limiting the rubber plantation extending to high latitude area. Previous work has shown that cold-induced DNA demethylation was coordinated with the expression of cold-responsive (COR) genes in Hevea brasiliensis. In this work, reduced representation bisulphite sequencing analysis of H. brasiliensis showed that cold treatment induced global genomic DNA demethylation and altered the sequence contexts of methylated cytosines, but the levels of mCG methylation in transposable elements were slightly enhanced by cold treatment. Integrated analysis of the DNA methylome and transcriptome revealed 400 genes whose expression correlated with altered DNA methylation. DNA demethylation in the upstream region of gene seems to correlate with higher gene expression, whereas demethylation in the gene body has less association. Our results suggest that cold treatment globally change the genomic DNA methylation status of the rubber tree, which might coordinate reprogramming of the transcriptome.
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Affiliation(s)
- Xiao Tang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yonglei Zhang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
| | - Hong-Mei Yuan
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
| | - Jinling Zhai
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
| | - Xi Huang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
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99926
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Krause S, Debon S, Pälchen K, Jakobi R, Rega B, Bonazzi C, Grauwet T. In vitro digestion of protein and starch in sponge cakes formulated with pea ( Pisum sativum L.) ingredients. Food Funct 2022; 13:3206-3219. [PMID: 35212347 DOI: 10.1039/d1fo03601g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study investigated the in vitro digestion of purified pea fractions (protein isolate and starch) in sponge cakes when compared to unrefined pea flour and to the whole wheat flour and purified maize starch commonly used in the food industry. Proteins in the wheat cake were hydrolysed more rapidly than those in cakes made with either pea flour or a combination of pea proteins and purified starch. In absolute terms, however, more readily bioaccessible protein was released from these pea cakes (by around 40%). By contrast, cakes containing wheat flour or maize starch were more susceptible to amylolysis compared to those based on pea starch in the form of the purified ingredient or whole flour. This could be attributed to a higher proportion of amylose and resistant starch in the pea cakes as well as structural characteristics that might have decelerated enzyme-substrate interactions. Interestingly, similar digestion patterns were observed regarding the purified pea ingredients and unrefined whole pea flour. It was therefore concluded that pea ingredients, and particularly the less purified and thus more sustainable whole pea flour, are promising plant-based alternatives for use in gluten-free baked products.
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Affiliation(s)
- Svenja Krause
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91300, Massy, France
| | - Stéphane Debon
- Cargill R&D Centre Europe, Havenstraat 84, 1800 Vilvoorde, Belgium
| | - Katharina Pälchen
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Center (LFoRCe), Laboratory of Food Technology, Kasteelpark Arenberg 22, PB 2457, 3001 Leuven, Belgium.
| | - Ralf Jakobi
- Cargill R&D Centre Europe, Havenstraat 84, 1800 Vilvoorde, Belgium
| | - Barbara Rega
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91300, Massy, France
| | - Catherine Bonazzi
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91300, Massy, France
| | - Tara Grauwet
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Center (LFoRCe), Laboratory of Food Technology, Kasteelpark Arenberg 22, PB 2457, 3001 Leuven, Belgium.
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99927
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Hasenleithner SO, Speicher MR. A clinician’s handbook for using ctDNA throughout the patient journey. Mol Cancer 2022; 21:81. [PMID: 35307037 PMCID: PMC8935823 DOI: 10.1186/s12943-022-01551-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/24/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
The promise of precision cancer medicine presently centers around the genomic sequence of a patient’s tumor being translated into timely, actionable information to inform clinical care. The analysis of cell-free DNA from liquid biopsy, which contains circulating tumor DNA (ctDNA) in patients with cancer, has proven to be amenable to various settings in oncology. However, open questions surrounding the clinical validity and utility of plasma-based analyses have hindered widespread clinical adoption.
Main body
Owing to the rapid evolution of the field, studies supporting the use of ctDNA as a biomarker throughout a patient’s journey with cancer have accumulated in the last few years, warranting a review of the latest status for clinicians who may employ ctDNA in their precision oncology programs. In this work, we take a step back from the intricate coverage of detection approaches described extensively elsewhere and cover basic concepts around the practical implementation of next generation sequencing (NGS)-guided liquid biopsy. We compare relevant targeted and untargeted approaches to plasma DNA analysis, describe the latest evidence for clinical validity and utility, and highlight the value of genome-wide ctDNA analysis, particularly as it relates to early detection strategies and discovery applications harnessing the non-coding genome.
Conclusions
The maturation of liquid biopsy for clinical application will require interdisciplinary efforts to address current challenges. However, patients and clinicians alike may greatly benefit in the future from its incorporation into routine oncology care.
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99928
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Bockwoldt JA, Meng C, Ludwig C, Kupetz M, Ehrmann MA. Proteomic Analysis Reveals Enzymes for β-D-Glucan Formation and Degradation in Levilactobacillus brevis TMW 1.2112. Int J Mol Sci 2022; 23:ijms23063393. [PMID: 35328813 PMCID: PMC8951740 DOI: 10.3390/ijms23063393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/01/2023] Open
Abstract
Bacterial exopolysaccharide (EPS) formation is crucial for biofilm formation, for protection against environmental factors, or as storage compounds. EPSs produced by lactic acid bacteria (LAB) are appropriate for applications in food fermentation or the pharmaceutical industry, yet the dynamics of formation and degradation thereof are poorly described. This study focuses on carbohydrate active enzymes, including glycosyl transferases (GT) and glycoside hydrolases (GH), and their roles in the formation and potential degradation of O2-substituted (1,3)-β-D-glucan of Levilactobacillus (L.) brevis TMW 1.2112. The fermentation broth of L. brevis TMW 1.2112 was analyzed for changes in viscosity, β-glucan, and D-glucose concentrations during the exponential, stationary, and early death phases. While the viscosity reached its maximum during the stationary phase and subsequently decreased, the β-glucan concentration only increased to a plateau. Results were correlated with secretome and proteome data to identify involved enzymes and pathways. The suggested pathway for β-glucan biosynthesis involved a β-1,3 glucan synthase (GT2) and enzymes from maltose phosphorylase (MP) operons. The decreased viscosity appeared to be associated with cell lysis as the β-glucan concentration did not decrease, most likely due to missing extracellular carbohydrate active enzymes. In addition, an operon was discovered containing known moonlighting genes, all of which were detected in both proteome and secretome samples.
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Affiliation(s)
- Julia A. Bockwoldt
- Lehrstuhl für Mikrobiologie, Technische Universität München, 85354 Freising, Germany;
| | - Chen Meng
- Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS), Technische Universität München, 85354 Freising, Germany; (C.M.); (C.L.)
| | - Christina Ludwig
- Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS), Technische Universität München, 85354 Freising, Germany; (C.M.); (C.L.)
| | - Michael Kupetz
- Lehrstuhl für Brau- und Getränketechnologie, Technische Universität München, 85354 Freising, Germany;
| | - Matthias A. Ehrmann
- Lehrstuhl für Mikrobiologie, Technische Universität München, 85354 Freising, Germany;
- Correspondence:
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99929
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He W, Zhang X, Lv P, Wang W, Wang J, He Y, Song Z, Cai D. Full-length transcriptome reconstruction reveals genetic differences in hybrids of Oryza sativa and Oryza punctata with different ploidy and genome compositions. BMC PLANT BIOLOGY 2022; 22:131. [PMID: 35313821 PMCID: PMC8935693 DOI: 10.1186/s12870-022-03502-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/01/2022] [Indexed: 07/07/2023]
Abstract
BACKGROUND Allopolyploid breeding is an efficient technique for improving the low seed setting rate of autotetraploids in plant breeding and one of the most promising breeding methods. However, there have been few comprehensive studies of the posttranscriptional mechanism in allopolyploids. RESULTS By crossing cultivated rice (Oryza sativa, genome AA) with wild rice (Oryza punctata, genome BB), we created hybrid rice lines with different ploidy and genome compositions [diploid hybrid F01 (AB), allotetraploid hybrid F02 (AABB) and F03 (AAAB)]. The genetic differences of the hybrids and the mechanism of allopolyploid breeding dominance were revealed through morphological and cytological observations and single molecule real-time sequencing techniques. The tissues and organs of allotetraploid hybrid F02 exhibited "gigantism" and the highest levels of fertility. The numbers of non-redundant transcripts, gene loci and new isoforms in the polyploid rice lines were higher and the isoform lengths greater than those of the diploid line. Moreover, alternative splicing (AS) events occurred twice as often in the polyploid rice lines than the diploid line. During these events, intron retention dominated. Furthermore, a large number of new genes and isoforms specific to the lines of different ploidy were discovered. CONCLUSIONS The results indicated that alternative polyadenylation (APA) and AS events contributed to the complexity and superiority of polyploids in the activity of translation regulators, nucleic acid binding transcription factor activities and the regulation of molecular function. Therefore, these APA and AS events in allopolyploid rice were found to play a role in regulation. Our study provides new germplasm for polyploid rice breeding and reveals complex regulatory mechanisms that may be related to heterosis and fertility.
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Affiliation(s)
- Wenting He
- School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Xianhua Zhang
- School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Pincang Lv
- School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Wei Wang
- School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Jie Wang
- School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Yuchi He
- School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Zhaojian Song
- School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China.
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China.
| | - Detian Cai
- School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China.
- Wuhan Polyploid Biotechnology Co., Ltd., Wuhan, 430345, People's Republic of China.
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99930
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Bell-Glenn S, Thompson JA, Salas LA, Koestler DC. A Novel Framework for the Identification of Reference DNA Methylation Libraries for Reference-Based Deconvolution of Cellular Mixtures. FRONTIERS IN BIOINFORMATICS 2022; 2. [PMID: 35419567 PMCID: PMC9004796 DOI: 10.3389/fbinf.2022.835591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Reference-based deconvolution methods use reference libraries of cell-specific DNA methylation (DNAm) measurements as a means toward deconvoluting cell proportions in heterogeneous biospecimens (e.g., whole-blood). As the accuracy of such methods depends highly on the CpG loci comprising the reference library, recent research efforts have focused on the selection of libraries to optimize deconvolution accuracy. While existing approaches for library selection work extremely well, the best performing approaches require a training data set consisting of both DNAm profiles over a heterogeneous cell population and gold-standard measurements of cell composition (e.g., flow cytometry) in the same samples. Here, we present a framework for reference library selection without a training dataset (RESET) and benchmark it against the Legacy method (minfi:pickCompProbes), where libraries are constructed based on a pre-specified number of cell-specific differentially methylated loci (DML). RESET uses a modified version of the Dispersion Separability Criteria (DSC) for comparing different libraries and has four main steps: 1) identify a candidate set of cell-specific DMLs, 2) randomly sample DMLs from the candidate set, 3) compute the Modified DSC of the selected DMLs, and 4) update the selection probabilities of DMLs based on their contribution to the Modified DSC. Steps 2–4 are repeated many times and the library with the largest Modified DSC is selected for subsequent reference-based deconvolution. We evaluated RESET using several publicly available datasets consisting of whole-blood DNAm measurements with corresponding measurements of cell composition. We computed the RMSE and R2 between the predicted cell proportions and their measured values. RESET outperformed the Legacy approach in selecting libraries that improve the accuracy of deconvolution estimates. Additionally, reference libraries constructed using RESET resulted in cellular composition estimates that explained more variation in DNAm as compared to the Legacy approach when evaluated in the context of epigenome-wide association studies (EWAS) of several publicly available data sets. This finding has implications for the statistical power of EWAS. RESET combats potential challenges associated with existing approaches for reference library assembly and thus, may serve as a viable strategy for library construction in the absence of a training data set.
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Affiliation(s)
- Shelby Bell-Glenn
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
| | - Jeffrey A. Thompson
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
| | - Lucas A. Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, United States
| | - Devin C. Koestler
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- *Correspondence: Devin C. Koestler,
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99931
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Dhanwani R, Lima-Junior JR, Sethi A, Pham J, Williams G, Frazier A, Xu Y, Amara AW, Standaert DG, Goldman JG, Litvan I, Alcalay RN, Peters B, Sulzer D, Arlehamn CSL, Sette A. Transcriptional analysis of peripheral memory T cells reveals Parkinson's disease-specific gene signatures. NPJ Parkinsons Dis 2022; 8:30. [PMID: 35314697 PMCID: PMC8938520 DOI: 10.1038/s41531-022-00282-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease (PD) is a multi-stage neurodegenerative disorder with largely unknown etiology. Recent findings have identified PD-associated autoimmune features including roles for T cells. To further characterize the role of T cells in PD, we performed RNA sequencing on PBMC and peripheral CD4 and CD8 memory T cell subsets derived from PD patients and age-matched healthy controls. When the groups were stratified by their T cell responsiveness to alpha-synuclein (α-syn) as a proxy for an ongoing inflammatory autoimmune response, the study revealed a broad differential gene expression profile in memory T cell subsets and a specific PD associated gene signature. We identified significant enrichment of transcriptomic signatures previously associated with PD, including for oxidative stress, phosphorylation, autophagy of mitochondria, cholesterol metabolism and inflammation, and the chemokine signaling proteins CX3CR1, CCR5, and CCR1. In addition, we identified genes in these peripheral cells that have previously been shown to be involved in PD pathogenesis and expressed in neurons, such as LRRK2, LAMP3, and aquaporin. Together, these findings suggest that features of circulating T cells with α-syn-specific responses in PD patients provide insights into the interactive processes that occur during PD pathogenesis and suggest potential intervention targets.
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Affiliation(s)
- Rekha Dhanwani
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - João Rodrigues Lima-Junior
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ashu Sethi
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - John Pham
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Gregory Williams
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Yaqian Xu
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.,Department of Neurology, Columbia University, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Amy W Amara
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.,Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - David G Standaert
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.,Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Jennifer G Goldman
- Shirley Ryan AbilityLab, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Irene Litvan
- Department of Neuroscience, University of California San Diego, La Jolla, CA, 92093, USA
| | - Roy N Alcalay
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - David Sulzer
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.,Department of Neurology, Columbia University, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, 10032, USA.,Departments of Psychiatry and Pharmacology, Columbia University, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Cecilia S Lindestam Arlehamn
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA. .,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA. .,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA. .,Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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99932
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Choi JM, Park HS, He MT, Kim YS, Kim HY, Lee AY, Cho EJ. Membrane-Free Stem Cells and Pyridoxal 5'-Phosphate Synergistically Enhance Cognitive Function in Alzheimer's Disease Mouse Model. Antioxidants (Basel) 2022; 11:antiox11030601. [PMID: 35326251 PMCID: PMC8945526 DOI: 10.3390/antiox11030601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 01/27/2023] Open
Abstract
Accumulation of amyloid beta (Aβ) is a major pathological hallmark of Alzheimer’s disease (AD). In this study, we evaluated the protective effect of membrane-free stem cell extract (MFSCE), which is a component of adipose-tissue-derived stem cells, on cognitive impairment in Aβ25–35-injected AD mice. The ICR mice were i.c.v. injected with Aβ25–35 and then treated with MFSCE for 14 days (i.p.). The Aβ25–35-injected mice showed deficits in spatial and object perception abilities, whereas treatment with MFSCE inhibited Aβ25–35-induced learning and memory impairment in the T-maze, novel object recognition, and Morris water maze tests. Moreover, Aβ25–35-induced lipid peroxidation and nitric oxide overproduction were attenuated by treatment with MFSCE. These antioxidant effects of MFSCE were related to the inhibition of the apoptotic signaling pathway. In particular, the combination treatment of MFSCE and pyridoxal 5′-phosphate (PLP) showed greater suppression of Bax and cleaved caspase-3 protein expression compared to the MFSCE- or PLP-only treatment. Furthermore, the MFSCE and PLP combination significantly downregulated the amyloidogenic-pathway-related protein expressions, such as amyloid precursor protein, presenilin 1, and presenilin 2. Therefore, the MFSCE and PLP combination may synergistically prevent Aβ25–35-induced neuronal apoptosis and amyloidogenesis, which contributes to cognitive improvement and has potential therapeutic implications for AD patients.
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Affiliation(s)
- Ji Myung Choi
- Department of Food Science and Nutrition, Pusan National University, Busan 46241, Korea; (J.M.C.); (H.S.P.); (M.T.H.)
- Department of Food Science and Biotechnology, Kyungsung University, Busan 48434, Korea
| | - Hye Sook Park
- Department of Food Science and Nutrition, Pusan National University, Busan 46241, Korea; (J.M.C.); (H.S.P.); (M.T.H.)
- T-Stem Co., Ltd., Changwon 51573, Korea;
| | - Mei Tong He
- Department of Food Science and Nutrition, Pusan National University, Busan 46241, Korea; (J.M.C.); (H.S.P.); (M.T.H.)
| | | | - Hyun Young Kim
- Department of Food Science and Nutrition, Gyeongsang National University, Jinju 52828, Korea;
| | - Ah Young Lee
- Department of Food Science and Nutrition, Gyeongsang National University, Jinju 52828, Korea;
- Correspondence: (A.Y.L.); (E.J.C.)
| | - Eun Ju Cho
- Department of Food Science and Nutrition, Pusan National University, Busan 46241, Korea; (J.M.C.); (H.S.P.); (M.T.H.)
- Correspondence: (A.Y.L.); (E.J.C.)
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99933
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Guo SK, Sodt AJ, Johnson ME. Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins. PLoS Comput Biol 2022; 18:e1009969. [PMID: 35312692 PMCID: PMC8979592 DOI: 10.1371/journal.pcbi.1009969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 03/31/2022] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Clathrin-coated structures must assemble on cell membranes to internalize receptors, with the clathrin protein only linked to the membrane via adaptor proteins. These structures can grow surprisingly large, containing over 20 clathrin, yet they often fail to form productive vesicles, instead aborting and disassembling. We show that clathrin structures of this size can both form and disassemble spontaneously when adaptor protein availability is low, despite high abundance of clathrin. Here, we combine recent in vitro kinetic measurements with microscopic reaction-diffusion simulations and theory to differentiate mechanisms of stable vs unstable clathrin assembly on membranes. While in vitro conditions drive assembly of robust, stable lattices, we show that concentrations, geometry, and dimensional reduction in physiologic-like conditions do not support nucleation if only the key adaptor AP-2 is included, due to its insufficient abundance. Nucleation requires a stoichiometry of adaptor to clathrin that exceeds 1:1, meaning additional adaptor types are necessary to form lattices successfully and efficiently. We show that the critical nucleus contains ~25 clathrin, remarkably similar to sizes of the transient and abortive structures observed in vivo. Lastly, we quantify the cost of bending the membrane under our curved clathrin lattices using a continuum membrane model. We find that the cost of bending the membrane could be largely offset by the energetic benefit of forming curved rather than flat structures, with numbers comparable to experiments. Our model predicts how adaptor density can tune clathrin-coated structures from the transient to the stable, showing that active energy consumption is therefore not required for lattice disassembly or remodeling during growth, which is a critical advance towards predicting productive vesicle formation.
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Affiliation(s)
- Si-Kao Guo
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Alexander J. Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Margaret E. Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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99934
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Krüppel-like Transcription Factor 7 Is a Causal Gene in Autism Development. Int J Mol Sci 2022; 23:ijms23063376. [PMID: 35328799 PMCID: PMC8949233 DOI: 10.3390/ijms23063376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 01/27/2023] Open
Abstract
Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disease. To date, more than 1000 genes have been shown to be associated with ASD, and only a few of these genes account for more than 1% of autism cases. Klf7 is an important transcription factor of cell proliferation and differentiation in the nervous system, but whether klf7 is involved in autism is unclear. Methods: We first performed ChIP-seq analysis of klf7 in N2A cells, then performed behavioral tests and RNA-seq in klf7+/− mice, and finally restored mice with adeno-associated virus (AAV)-mediated overexpression of klf7 in klf7+/− mice. Results: Klf7 targeted genes are enriched with ASD genes, and 631 ASD risk genes are also differentially expressed in klf7+/− mice which exhibited the core symptoms of ASD. When klf7 levels were increased in the central nervous system (CNS) in klf7+/− adult mice, deficits in social interaction, repetitive behavior and majority of dysregulated ASD genes were rescued in the adults, suggesting transcriptional regulation. Moreover, knockdown of klf7 in human brain organoids caused dysregulation of 517 ASD risk genes, 344 of which were shared with klf7+/− mice, including some high-confidence ASD genes. Conclusions: Our findings highlight a klf7 regulation of ASD genes and provide new insights into the pathogenesis of ASD and promising targets for further research on mechanisms and treatments.
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99935
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Merabet O, Pietrosemoli N, Perthame E, Armengaud J, Gaillard JC, Borges-Cardoso V, Daniau M, Legras-Lachuer C, Carnec X, Baize S. Infection of Human Endothelial Cells with Lassa Virus Induces Early but Transient Activation and Low Type I IFN Response Compared to the Closely-Related Nonpathogenic Mopeia Virus. Viruses 2022; 14:v14030652. [PMID: 35337059 PMCID: PMC8953476 DOI: 10.3390/v14030652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023] Open
Abstract
Lassa virus (LASV), an Old World arenavirus, is responsible for hemorrhagic fevers in western Africa. The privileged tropism of LASV for endothelial cells combined with a dysregulated inflammatory response are the main cause of the increase in vascular permeability observed during the disease. Mopeia virus (MOPV) is another arenavirus closely related to LASV but nonpathogenic for non-human primates (NHPs) and has never been described in humans. MOPV is more immunogenic than LASV in NHPs and in vitro in human immune cell models, with more intense type I IFN and adaptive cellular responses. Here, we compared the transcriptomic and proteomic responses of human umbilical vein endothelial cells (HUVECs) to infection with the two viruses to further decipher the mechanisms involved in their differences in immunogenicity and pathogenicity. Both viruses replicated durably and efficiently in HUVECs, but the responses they induced were strikingly different. Modest activation was observed at an early stage of LASV infection and then rapidly shut down. By contrast, MOPV induced a late but more intense response, characterized by the expression of genes and proteins mainly associated with the type I IFN response and antigen processing/presentation. Such a response is consistent with the higher immunogenicity of MOPV relative to LASV, whereas the lack of an innate response induced in HUVECs by LASV is consistent with its uncontrolled systemic dissemination through the vascular endothelium.
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Affiliation(s)
- Othmann Merabet
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, 75015 Paris, France; (N.P.); (E.P.)
| | - Emeline Perthame
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, 75015 Paris, France; (N.P.); (E.P.)
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (LI2D), Service de Pharmacologie et Immunoanalyse (SPI), Commissariat à l’Energie Atomique, 30200 Bagnols-sur-Cèze, France; (J.A.); (J.-C.G.)
| | - Jean-Charles Gaillard
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (LI2D), Service de Pharmacologie et Immunoanalyse (SPI), Commissariat à l’Energie Atomique, 30200 Bagnols-sur-Cèze, France; (J.A.); (J.-C.G.)
| | - Virginie Borges-Cardoso
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
| | - Maïlys Daniau
- ViroScan3D SAS, 01600 Trévoux, France; (M.D.); (C.L.-L.)
| | | | - Xavier Carnec
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
- Correspondence: ; Tel.: +33-4-3728-2440
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99936
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Sacco SA, Tuckowski AM, Trenary I, Kraft L, Betenbaugh MJ, Young JD, Smith KD. Attenuation of glutamine synthetase selection marker improves product titer and reduces glutamine overflow in Chinese hamster ovary cells. Biotechnol Bioeng 2022; 119:1712-1727. [PMID: 35312045 DOI: 10.1002/bit.28084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 11/10/2022]
Abstract
The glutamine synthetase (GS) expression system is commonly used to ensure stable transgene integration and amplification in CHO host lines. Transfected cell populations are typically grown in the presence of the GS inhibitor, methionine sulfoximine (MSX), to further select for increased transgene copy number. However, high levels of GS activity produce excess glutamine. We hypothesized that attenuating the GS promoter while keeping the strong IgG promoter on the GS-IgG expression vector would result in a more efficient cellular metabolic phenotype. Herein, we characterized CHO cell lines expressing GS from either an attenuated promoter or an SV40 promoter and selected with/without MSX. CHO cells with the attenuated GS promoter had higher IgG specific productivity and lower glutamine production compared to cells with SV40-driven GS expression. Selection with MSX increased both specific productivity and glutamine production, regardless of GS promoter strength. 13 C metabolic flux analysis (MFA) was performed to further assess metabolic differences between these cell lines. Interestingly, central carbon metabolism was unaltered by the attenuated GS promoter while the fate of glutamate and glutamine varied depending on promoter strength and selection conditions. This study highlights the ability to optimize the GS expression system to improve IgG production and reduce wasteful glutamine overflow, without significantly altering central metabolism. Additionally, a detailed supplementary analysis of two "lactate runaway" reactors provides insight into the poorly understood phenomenon of excess lactate production by some CHO cell cultures. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sarah A Sacco
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Angela M Tuckowski
- Biotherapeutics Development, Janssen Research and Development, Spring House, PA, USA.,Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Lauren Kraft
- Biotherapeutics Development, Janssen Research and Development, Spring House, PA, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Kevin D Smith
- Biotherapeutics Development, Janssen Research and Development, Spring House, PA, USA.,Asimov, 1325 Boylston St, Boston, MA, 02215
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99937
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Chen H, Peng T, Shang H, Shang X, Zhao X, Qu M, Song X. RNA-Seq Analysis Reveals the Potential Molecular Mechanisms of Puerarin on Intramuscular Fat Deposition in Heat-Stressed Beef Cattle. Front Nutr 2022; 9:817557. [PMID: 35387191 PMCID: PMC8978796 DOI: 10.3389/fnut.2022.817557] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
To investigate the effect of Puerarin on intramuscular fat deposition in heat-stressed beef cattle and its underlying mechanism. Thirty-two healthy Jinjiang bulls were randomly divided into four groups and dietary with 0 (Control), 200 (Pue200), 400 (Pue400), and 800 (Pue800) mg/kg Puerarin in the feed concentrate. The results showed that Puerarin treatment enhanced the concentration of crude fat, fatty acid (C14:1 and C17:1), and the activity of fatty acid synthase in Longissimus thoracis (LT), but decreased the levels of blood leptin (P < 0.05). High-throughput sequencing of mRNA technology (RNA-Seq) was used and the analysis showed that 492 genes were down-regulated and 341 genes were up-regulated in LT, and these genes were significantly enriched to the pathways related to lipid metabolism. These results indicated that dietary supplemental with Puerarin enhanced intramuscular fat deposition by regulating lipid metabolism of heat-stressed beef cattle.
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99938
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Yum JH, Sugiyama H, Park S. Harnessing DNA as a Designable Scaffold for Asymmetric Catalysis: Recent Advances and Future Perspectives. CHEM REC 2022; 22:e202100333. [PMID: 35312235 DOI: 10.1002/tcr.202100333] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Since the first report of DNAzyme by in vitro selection in 1994, catalytic DNA has investigated extensively, and their application has expanded continually in virtue of rapid advances in molecular biology and biotechnology. Nowadays, DNA is in the second prime time by way of DNA-based hybrid catalysts and DNA metalloenzymes in which helical chirality of DNA serves to asymmetric catalysis. DNA-based hybrid catalysts are attractive system to respond the demand of the times to pursuit green and sustainable society beyond traditional catalytic systems that value reaction efficiency. Herein, we highlight the recent advances and perspective of DNA-based hybrid catalysts with various aspects of DNA as a versatile scaffold for asymmetric synthesis. We hope that scientists in a variety of fields will be encouraged to join and promote remarkable evolution of this interesting research.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center (iFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan.,Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan
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99939
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Cardinale A, Cantalupo S, Lasorsa VA, Montella A, Cimmino F, Succoio M, Vermeulen M, Baltissen MP, Esposito M, Avitabile M, Formicola D, Testori A, Bonfiglio F, Ghiorzo P, Scalvenzi M, Ayala F, Zambrano N, Iles MM, Xu M, Law MH, Brown KM, Iolascon A, Capasso M. Functional annotation and investigation of the 10q24.33 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1. Hum Mol Genet 2022; 31:863-874. [PMID: 34605909 PMCID: PMC9077268 DOI: 10.1093/hmg/ddab293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/07/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022] Open
Abstract
The 10q24.33 locus is known to be associated with susceptibility to cutaneous malignant melanoma (CMM), but the mechanisms underlying this association have been not extensively investigated. We carried out an integrative genomic analysis of 10q24.33 using epigenomic annotations and in vitro reporter gene assays to identify regulatory variants. We found two putative functional single nucleotide polymorphisms (SNPs) in an enhancer and in the promoter of OBFC1, respectively, in neural crest and CMM cells, one, rs2995264, altering enhancer activity. The minor allele G of rs2995264 correlated with lower OBFC1 expression in 470 CMM tumors and was confirmed to increase the CMM risk in a cohort of 484 CMM cases and 1801 controls of Italian origin. Hi-C and chromosome conformation capture (3C) experiments showed the interaction between the enhancer-SNP region and the promoter of OBFC1 and an isogenic model characterized by CRISPR-Cas9 deletion of the enhancer-SNP region confirmed the potential regulatory effect of rs2995264 on OBFC1 transcription. Moreover, the presence of G-rs2995264 risk allele reduced the binding affinity of the transcription factor MEOX2. Biologic investigations showed significant cell viability upon depletion of OBFC1, specifically in CMM cells that were homozygous for the protective allele. Clinically, high levels of OBFC1 expression associated with histologically favorable CMM tumors. Finally, preliminary results suggested the potential effect of decreased OBFC1 expression on telomerase activity in tumorigenic conditions. Our results support the hypothesis that reduced expression of OBFC1 gene through functional heritable DNA variation can contribute to malignant transformation of normal melanocytes.
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Affiliation(s)
- Antonella Cardinale
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
- Department of Pediatric Hematology and Oncology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sueva Cantalupo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
| | - Vito Alessandro Lasorsa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
| | - Annalaura Montella
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
| | | | | | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
| | - Matteo Esposito
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
| | - Marianna Avitabile
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
| | - Daniela Formicola
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
- SOC Genetica Medica, Azienda Ospedaliera Universitaria Meyer, Firenze 50139, Italy
| | - Alessandro Testori
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
| | - Ferdinando Bonfiglio
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
- Dipartimento di Ingegneria chimica, dei Materiali e della Produzione industriale, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Paola Ghiorzo
- Genetica dei Rumori Rari, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Dipartimento di Medicina Interna e Specialità Mediche, Università degli Studi di Genova, Genova, Italy
| | - Massimiliano Scalvenzi
- Dipartimento di Medicina clinica e Chirurgia, Università degli Studi di Napoli Federico II, Naples 80136, Italy
| | - Fabrizio Ayala
- Department of Melanoma and Cancer Immunotherapy, Istituto Nazionale Tumori IRCCS Fondazione Pascale, Napoli, Italy
| | - Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
| | - Mark M Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Mai Xu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute Brisbane, Queensland 4006, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples 80136, Italy
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
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99940
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Abdisalaam S, Mukherjee S, Bhattacharya S, Kumari S, Sinha D, Ortega J, Li GM, Sadek H, Krishnan S, Asaithamby A. NBS1-CtIP-mediated DNA end resection suppresses cGAS binding to micronuclei. Nucleic Acids Res 2022; 50:2681-2699. [PMID: 35189637 PMCID: PMC8934670 DOI: 10.1093/nar/gkac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 01/12/2022] [Accepted: 01/25/2022] [Indexed: 01/07/2023] Open
Abstract
Cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) is activated in cells with defective DNA damage repair and signaling (DDR) factors, but a direct role for DDR factors in regulating cGAS activation in response to micronuclear DNA is still poorly understood. Here, we provide novel evidence that Nijmegen breakage syndrome 1 (NBS1) protein, a well-studied DNA double-strand break (DSB) sensor-in coordination with Ataxia Telangiectasia Mutated (ATM), a protein kinase, and Carboxy-terminal binding protein 1 interacting protein (CtIP), a DNA end resection factor-functions as an upstream regulator that prevents cGAS from binding micronuclear DNA. When NBS1 binds to micronuclear DNA via its fork-head-associated domain, it recruits CtIP and ATM via its N- and C-terminal domains, respectively. Subsequently, ATM stabilizes NBS1's interaction with micronuclear DNA, and CtIP converts DSB ends into single-strand DNA ends; these two key events prevent cGAS from binding micronuclear DNA. Additionally, by using a cGAS tripartite system, we show that cells lacking NBS1 not only recruit cGAS to a major fraction of micronuclear DNA but also activate cGAS in response to these micronuclear DNA. Collectively, our results underscore how NBS1 and its binding partners prevent cGAS from binding micronuclear DNA, in addition to their classical functions in DDR signaling.
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Affiliation(s)
- Salim Abdisalaam
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shibani Mukherjee
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Souparno Bhattacharya
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sharda Kumari
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Debapriya Sinha
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Janice Ortega
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hesham A Sadek
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sunil Krishnan
- Department of Radiation Oncology, Mayo Clinic Florida, Jacksonville, FL 32082, USA
| | - Aroumougame Asaithamby
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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99941
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IPA-3: An Inhibitor of Diadenylate Cyclase of Streptococcus suis with Potent Antimicrobial Activity. Antibiotics (Basel) 2022; 11:antibiotics11030418. [PMID: 35326881 PMCID: PMC8944544 DOI: 10.3390/antibiotics11030418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/13/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
Antimicrobial resistance (AMR) poses a huge threat to public health. The development of novel antibiotics is an effective strategy to tackle AMR. Cyclic diadenylate monophosphate (c-di-AMP) has recently been identified as an essential signal molecule for some important bacterial pathogens involved in various bacterial physiological processes, leading to its synthase diadenylate cyclase becoming an attractive antimicrobial drug target. In this study, based on the enzymatic activity of diadenylate cyclase of Streptococcus suis (ssDacA), we established a high-throughput method of screening for ssDacA inhibitors. Primary screening with a compound library containing 1133 compounds identified IPA-3 (2,2′-dihydroxy-1,1′-dinapthyldisulfide) as an ssDacA inhibitor. High-performance liquid chromatography (HPLC) analysis further indicated that IPA-3 could inhibit the production of c-di-AMP by ssDacA in vitro in a dose-dependent manner. Notably, it was demonstrated that IPA-3 could significantly inhibit the growth of several Gram-positive bacteria which harbor an essential diadenylate cyclase but not E. coli, which is devoid of the enzyme, or Streptococcus mutans, in which the diadenylate cyclase is not essential. Additionally, the binding site in ssDacA for IPA-3 was predicted by molecular docking, and contains residues that are relatively conserved in diadenylate cyclase of Gram-positive bacteria. Collectively, our results illustrate the feasibility of ssDacA as an antimicrobial target and consider IPA-3 as a promising starting point for the development of a novel antibacterial.
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99942
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Rütsche D, Michalak-Micka K, Zielinska D, Moll H, Moehrlen U, Biedermann T, Klar AS. The Role of CD200-CD200 Receptor in Human Blood and Lymphatic Endothelial Cells in the Regulation of Skin Tissue Inflammation. Cells 2022; 11:cells11061055. [PMID: 35326506 PMCID: PMC8947338 DOI: 10.3390/cells11061055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
CD200 is a cell membrane glycoprotein that interacts with its structurally related receptor (CD200R) expressed on immune cells. We characterized CD200–CD200R interactions in human adult/juvenile (j/a) and fetal (f) skin and in in vivo prevascularized skin substitutes (vascDESS) prepared by co-culturing human dermal microvascular endothelial cells (HDMEC), containing both blood (BEC) and lymphatic (LEC) EC. We detected the highest expression of CD200 on lymphatic capillaries in j/a and f skin as well as in vascDESS in vivo, whereas it was only weakly expressed on blood capillaries. Notably, the highest CD200 levels were detected on LEC with enhanced Podoplanin expression, while reduced expression was observed on Podoplanin-low LEC. Further, qRT-PCR analysis revealed upregulated expression of some chemokines, including CC-chemokine ligand 21 (CCL21) in j/aCD200+ LEC, as compared to j/aCD200− LEC. The expression of CD200R was mainly detected on myeloid cells such as granulocytes, monocytes/macrophages, T cells in human peripheral blood, and human and rat skin. Functional immunoassays demonstrated specific binding of skin-derived CD200+ HDMEC to myeloid CD200R+ cells in vitro. Importantly, we confirmed enhanced CD200–CD200R interaction in vascDESS in vivo. We concluded that the CD200–CD200R axis plays a crucial role in regulating tissue inflammation during skin wound healing.
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Affiliation(s)
- Dominic Rütsche
- Tissue Biology Research Unit, Department of Surgery, University Children’s Hospital Zurich, 8032 Zurich, Switzerland; (D.R.); (K.M.-M.); (D.Z.); (H.M.); (U.M.); (T.B.)
- Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland
| | - Katarzyna Michalak-Micka
- Tissue Biology Research Unit, Department of Surgery, University Children’s Hospital Zurich, 8032 Zurich, Switzerland; (D.R.); (K.M.-M.); (D.Z.); (H.M.); (U.M.); (T.B.)
- Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland
| | - Dominika Zielinska
- Tissue Biology Research Unit, Department of Surgery, University Children’s Hospital Zurich, 8032 Zurich, Switzerland; (D.R.); (K.M.-M.); (D.Z.); (H.M.); (U.M.); (T.B.)
- Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland
| | - Hannah Moll
- Tissue Biology Research Unit, Department of Surgery, University Children’s Hospital Zurich, 8032 Zurich, Switzerland; (D.R.); (K.M.-M.); (D.Z.); (H.M.); (U.M.); (T.B.)
- Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland
| | - Ueli Moehrlen
- Tissue Biology Research Unit, Department of Surgery, University Children’s Hospital Zurich, 8032 Zurich, Switzerland; (D.R.); (K.M.-M.); (D.Z.); (H.M.); (U.M.); (T.B.)
- Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland
- Department of Pediatric Surgery, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
| | - Thomas Biedermann
- Tissue Biology Research Unit, Department of Surgery, University Children’s Hospital Zurich, 8032 Zurich, Switzerland; (D.R.); (K.M.-M.); (D.Z.); (H.M.); (U.M.); (T.B.)
- Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland
| | - Agnes S. Klar
- Tissue Biology Research Unit, Department of Surgery, University Children’s Hospital Zurich, 8032 Zurich, Switzerland; (D.R.); (K.M.-M.); (D.Z.); (H.M.); (U.M.); (T.B.)
- Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland
- Correspondence: ; Tel.: +41-446348819
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99943
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Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220. Sci Rep 2022; 12:4805. [PMID: 35314715 PMCID: PMC8938411 DOI: 10.1038/s41598-022-08459-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
Paradigms of metabolic strategies employed by photoautotrophic marine picocyanobacteria have been challenged in recent years. Based on genomic annotations, picocyanobacteria are predicted to assimilate organic nutrients via ATP-binding cassette importers, a process mediated by substrate-binding proteins. We report the functional characterisation of a modified sugar-binding protein, MsBP, from a marine Synechococcus strain, MITS9220. Ligand screening of MsBP shows a specific affinity for zinc (KD ~ 1.3 μM) and a preference for phosphate-modified sugars, such as fructose-1,6-biphosphate, in the presence of zinc (KD ~ 5.8 μM). Our crystal structures of apo MsBP (no zinc or substrate-bound) and Zn-MsBP (with zinc-bound) show that the presence of zinc induces structural differences, leading to a partially-closed substrate-binding cavity. The Zn-MsBP structure also sequesters several sulphate ions from the crystallisation condition, including two in the binding cleft, appropriately placed to mimic the orientation of adducts of a biphosphate hexose. Combined with a previously unseen positively charged binding cleft in our two structures and our binding affinity data, these observations highlight novel molecular variations on the sugar-binding SBP scaffold. Our findings lend further evidence to a proposed sugar acquisition mechanism in picocyanobacteria alluding to a mixotrophic strategy within these ubiquitous photosynthetic bacteria.
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99944
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Büllmann SM, Kolmar T, Zorn NF, Zaumseil J, Jäschke A. A DNA‐Based Two‐Component Excitonic Switch Utilizing High‐Performance Diarylethenes. Angew Chem Int Ed Engl 2022; 61:e202117735. [PMID: 35076154 PMCID: PMC9305942 DOI: 10.1002/anie.202117735] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Indexed: 11/13/2022]
Abstract
Nucleosidic diarylethenes (DAEs) are an emerging class of photochromes but have rarely been used in materials science. Here, we have developed doubly methylated DAEs derived from 2′‐deoxyuridine with high thermal stability and fatigue resistance. These new photoswitches not only outperform their predecessors but also rival classical non‐nucleosidic DAEs. To demonstrate the utility of these new DAEs, we have designed an all‐optical excitonic switch consisting of two oligonucleotides: one strand containing a fluorogenic double‐methylated 2′‐deoxyuridine as a fluorescence donor and the other a tricyclic cytidine (tC) as acceptor, which together form a highly efficient conditional Förster‐Resonance‐Energy‐Transfer (FRET) pair. The system was operated in liquid and solid phases and showed both strong distance‐ and orientation‐dependent photochromic FRET. The superior ON/OFF contrast was maintained over up to 100 switching cycles, with no detectable fatigue.
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Affiliation(s)
- Simon M. Büllmann
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Theresa Kolmar
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Nicolas F. Zorn
- Institute for Physical Chemistry Heidelberg University Im Neuenheimer Feld 253 69120 Heidelberg Germany
| | - Jana Zaumseil
- Institute for Physical Chemistry Heidelberg University Im Neuenheimer Feld 253 69120 Heidelberg Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
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99945
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Keren-Kaplan T, Sarić A, Ghosh S, Williamson CD, Jia R, Li Y, Bonifacino JS. RUFY3 and RUFY4 are ARL8 effectors that promote coupling of endolysosomes to dynein-dynactin. Nat Commun 2022; 13:1506. [PMID: 35314674 PMCID: PMC8938451 DOI: 10.1038/s41467-022-28952-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
The small GTPase ARL8 associates with endolysosomes, leading to the recruitment of several effectors that couple endolysosomes to kinesins for anterograde transport along microtubules, and to tethering factors for eventual fusion with other organelles. Herein we report the identification of the RUN- and FYVE-domain-containing proteins RUFY3 and RUFY4 as ARL8 effectors that promote coupling of endolysosomes to dynein-dynactin for retrograde transport along microtubules. Using various methodologies, we find that RUFY3 and RUFY4 interact with both GTP-bound ARL8 and dynein-dynactin. In addition, we show that RUFY3 and RUFY4 promote concentration of endolysosomes in the juxtanuclear area of non-neuronal cells, and drive redistribution of endolysosomes from the axon to the soma in hippocampal neurons. The function of RUFY3 in retrograde transport contributes to the juxtanuclear redistribution of endolysosomes upon cytosol alkalinization. These studies thus identify RUFY3 and RUFY4 as ARL8-dependent, dynein-dynactin adaptors or regulators, and highlight the role of ARL8 in the control of both anterograde and retrograde endolysosome transport.
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Affiliation(s)
- Tal Keren-Kaplan
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Amra Sarić
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Saikat Ghosh
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Rui Jia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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99946
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Zheng H, Xie J, Song K, Yang J, Xiao H, Zhang J, Li K, Yuan R, Zhao Y, Gu Y, Zhao W. StemSC: a cross-dataset human stemness index for single-cell samples. Stem Cell Res Ther 2022; 13:115. [PMID: 35313979 PMCID: PMC8935746 DOI: 10.1186/s13287-022-02803-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 03/07/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Stemness is defined as the potential of cells for self-renewal and differentiation. Many transcriptome-based methods for stemness evaluation have been proposed. However, all these methods showed low negative correlations with differentiation time and can't leverage the existing experimentally validated stem cells to recognize the stem-like cells. METHODS Here, we constructed a stemness index for single-cell samples (StemSC) based on relative expression orderings (REO) of gene pairs. Firstly, we identified the stemness-related genes by selecting the genes significantly related to differentiation time. Then, we used 13 RNA-seq datasets from both the bulk and single-cell embryonic stem cell (ESC) samples to construct the reference REOs. Finally, the StemSC value of a given sample was calculated as the percentage of gene pairs with the same REOs as the ESC samples. RESULTS We validated the StemSC by its higher negative correlations with differentiation time in eight normal datasets and its higher positive correlations with tumor dedifferentiation in three colorectal cancer datasets and four glioma datasets. Besides, the robust of StemSC to batch effect enabled us to leverage the existing experimentally validated cancer stem cells to recognize the stem-like cells in other independent tumor datasets. And the recognized stem-like tumor cells had fewer interactions with anti-tumor immune cells. Further survival analysis showed the immunotherapy-treated patients with high stemness had worse survival than those with low stemness. CONCLUSIONS StemSC is a better stemness index to calculate the stemness across datasets, which can help researchers explore the effect of stemness on other biological processes.
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Affiliation(s)
- Hailong Zheng
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jiajing Xie
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China
| | - Kai Song
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Jing Yang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Huiting Xiao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Jiashuai Zhang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Keru Li
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Rongqiang Yuan
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Yuting Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
| | - Wenyuan Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
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99947
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Xolalpa-Cueva L, García-Carlos CA, Villaseñor-Zepeda R, Orta-Salazar E, Díaz-Cintra S, Peña-Ortega F, Perry G, Mondragón-Rodríguez S. Hyperphosphorylated Tau Relates to Improved Cognitive Performance and Reduced Hippocampal Excitability in the Young rTg4510 Mouse Model of Tauopathy. J Alzheimers Dis 2022; 87:529-543. [PMID: 35342085 DOI: 10.3233/jad-215186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Tau hyperphosphorylation at several sites, including those close to its microtubule domain (MD), is considered a key pathogenic event in the development of tauopathies. Nevertheless, we recently demonstrated that at the very early disease stage, tau phosphorylation (pTau) at MD sites promotes neuroprotection by preventing seizure-like activity. OBJECTIVE To further support the notion that very early pTau is not detrimental, the present work evaluated the young rTg4510 mouse model of tauopathy as a case study. Thus, in mice at one month of age (PN30-35), we studied the increase of pTau within the hippocampal area as well as hippocampal and locomotor function. METHODS We used immunohistochemistry, T-maze, nesting test, novel object recognition test, open field arena, and electrophysiology. RESULTS Our results showed that the very young rTg4510 mouse model has no detectable changes in hippocampal dependent tasks, such as spontaneous alternation and nesting, or in locomotor activity. However, at this very early stage the hippocampal neurons from PN30-35 rTg4510 mice accumulate pTau protein and exhibit changes in hippocampal oscillatory activity. Moreover, we found a significant reduction in the somatic area of pTau positive pyramidal and granule neurons in the young rTg4510 mice. Despite this, improved memory and increased number of dendrites per cell in granule neurons was found. CONCLUSION Altogether, this study provides new insights into the early pathogenesis of tauopathies and provides further evidence that pTau remodels hippocampal function and morphology.
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Affiliation(s)
- Lorena Xolalpa-Cueva
- UNAM Developmental Neurobiology and Neurophysiology, Institute of Neurobiology, National Autonomous University of México, Querétaro, México
| | - Carlos Antonio García-Carlos
- UNAM Developmental Neurobiology and Neurophysiology, Institute of Neurobiology, National Autonomous University of México, Querétaro, México
| | - Rocío Villaseñor-Zepeda
- UNAM Developmental Neurobiology and Neurophysiology, Institute of Neurobiology, National Autonomous University of México, Querétaro, México
| | - Erika Orta-Salazar
- UNAM Developmental Neurobiology and Neurophysiology, Institute of Neurobiology, National Autonomous University of México, Querétaro, México
| | - Sofia Díaz-Cintra
- UNAM Developmental Neurobiology and Neurophysiology, Institute of Neurobiology, National Autonomous University of México, Querétaro, México
| | - Fernando Peña-Ortega
- UNAM Developmental Neurobiology and Neurophysiology, Institute of Neurobiology, National Autonomous University of México, Querétaro, México
| | - George Perry
- UTSA Neuroscience Institute and Department of Biology, College of Sciences, University of Texas at San Antonio, San Antonio, TX, USA
| | - Siddhartha Mondragón-Rodríguez
- UNAM Developmental Neurobiology and Neurophysiology, Institute of Neurobiology, National Autonomous University of México, Querétaro, México.,CONACYT National Council for Science and Technology, México, México
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99948
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Dong J, Duchesne A, Bayne AN, Mohamed NV, Yi W, Mathur M, Chen CXQ, You Z, Abdian N, Taylor L, Fon EA, Durcan TM, Trempe JF. An Approach to Measuring Protein Turnover in Human Induced Pluripotent Stem Cell Organoids by Mass Spectrometry. Methods 2022; 203:17-27. [PMID: 35331912 DOI: 10.1016/j.ymeth.2022.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/15/2022] [Accepted: 03/19/2022] [Indexed: 02/06/2023] Open
Abstract
Patient-derived organoids from induced pluripotent stem cells have emerged as a model for studying human diseases beyond conventional two-dimensional (2D) cell culture. Briefly, these three-dimensional organoids are highly complex, capable of self-organizing, recapitulate cellular architecture, and have the potential to model diseases in complex organs, such as the brain. For example, the hallmark of Parkinson's disease (PD) - proteostatic dysfunction leading to the selective death of neurons in the substantia nigra - present a subtle distinction in cell type specificity that is lost in 2D cell culture models. As such, the development of robust methods to study global proteostasis and protein turnover in organoids will remain essential as organoid models evolve. To solve this problem, we have designed a workflow to reproducibly extract proteins from brain organoids, measure global turnover using mass spectrometry, and statistically investigate turnover differences between genotypes. We also provide robust methodology for data filtering and statistical treatment of turnover data. Using human midbrain organoids (hMO) as a model system, our method accurately characterized the half-lives of 773 midbrain proteins. We compared these half-lives both to Parkin knockout hMOs and to previously reported data from primary cell cultures and in vivo models. Overall, this method will facilitate the study of proteostasis in organoid models of human disease and will provide an analytical and statistical framework to measure protein turnover in organoids of all cell types.
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Affiliation(s)
- Jing Dong
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada
| | - Anthony Duchesne
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada
| | - Andrew N Bayne
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada
| | - Nguyen-Vi Mohamed
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, Quebec, H3A 2B4, Canada
| | - Wei Yi
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, Quebec, H3A 2B4, Canada
| | - Meghna Mathur
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, Quebec, H3A 2B4, Canada
| | - Carol X Q Chen
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, Quebec, H3A 2B4, Canada
| | - Zhipeng You
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, Quebec, H3A 2B4, Canada
| | - Narges Abdian
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, Quebec, H3A 2B4, Canada
| | - Lorne Taylor
- Proteomics Platform, Centre for Translational Biology, Research Institute of the McGill University Health Centre, 1001 Bd Décarie, Montréal, Quebec, H4A 3J1, Canada
| | - Edward A Fon
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, Quebec, H3A 2B4, Canada
| | - Thomas M Durcan
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, Quebec, H3A 2B4, Canada
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada; Proteomics Platform, Centre for Translational Biology, Research Institute of the McGill University Health Centre, 1001 Bd Décarie, Montréal, Quebec, H4A 3J1, Canada; Brain Repair and Integrative Neuroscience (BRaIN) Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, 1001 Bd Décarie, Montréal, Quebec, H4A 3J1, Canada.
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99949
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Omar A, Wali A, Arken A, Gao Y, Aisa HA, Yili A. Covalent binding of flavonoids with silk sericin hydrolysate: Anti‐inflammatory, antioxidant, and physicochemical properties of flavonoid–sericin hydrolysate conjugates. J Food Biochem 2022; 46:e14125. [DOI: 10.1111/jfbc.14125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/18/2022] [Accepted: 02/16/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Adil Omar
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
- University of the Chinese Academy of Sciences Beijing China
| | - Ahmidin Wali
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
| | - Amina Arken
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
- University of the Chinese Academy of Sciences Beijing China
| | - Yanhua Gao
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
| | - Haji Akber Aisa
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
| | - Abulimiti Yili
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
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99950
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Tzouras NV, Scattolin T, Gobbo A, Bhandary S, Rizzolio F, Cavarzerani E, Canzonieri V, Van Hecke K, Vougioukalakis GC, Cazin CSJ, Nolan SP. A Green Synthesis of Carbene-Metal-Amides (CMAs) and Carboline-Derived CMAs with Potent in vitro and ex vivo Anticancer Activity. ChemMedChem 2022; 17:e202200135. [PMID: 35312174 DOI: 10.1002/cmdc.202200135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Indexed: 11/06/2022]
Abstract
The modularity and ease of synthesis of carbene-metal-amide (CMA) complexes based on the coinage metals (Au, Ag, Cu) and N-heterocyclic carbenes (NHCs) as ancillary ligands pave the way for the expansion of their applications beyond photochemistry and catalysis. Herein, we further improve the synthesis of such compounds by circumventing the use of toxic organic solvents which were previously required for their purification, and we expand their scope to include complexes incorporating carbolines as the amido fragments. The novel complexes are screened both in vitro and ex vivo, against several cancer cell lines and high-grade serous ovarian cancer (HGSOC) tumoroids, respectively. Excellent cytotoxicity values are obtained for most complexes, while the structural variety of the CMA library screened thus far, provides promising leads for future developments. Variations of all three components (NHC, metal, amido ligand), enable the establishment of trends regarding cytotoxicity and selectivity towards cancerous over normal cells.
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Affiliation(s)
- Nikolaos V Tzouras
- Department of Chemistry and Centre for Sustainable Chemistry, Ghent University, Krijgslaan 281,S-3, 9000, Ghent, Belgium.,Department of Chemistry, Laboratory of Organic Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece
| | - Thomas Scattolin
- Department of Molecular Sciences and Nanosystems, Università Ca' Foscari, Campus Scientifico Via Torino 155, 30174, Venezia-Mestre, Italy.,Pathology Unit, Centro di Riferimento Oncologico di Aviano (C.R.O.) IRCCS, via Franco Gallini 2, 33081, Aviano, Italy
| | - Alberto Gobbo
- Department of Chemistry and Centre for Sustainable Chemistry, Ghent University, Krijgslaan 281,S-3, 9000, Ghent, Belgium
| | - Subhrajyoti Bhandary
- Department of Chemistry and Centre for Sustainable Chemistry, Ghent University, Krijgslaan 281,S-3, 9000, Ghent, Belgium
| | - Flavio Rizzolio
- Department of Molecular Sciences and Nanosystems, Università Ca' Foscari, Campus Scientifico Via Torino 155, 30174, Venezia-Mestre, Italy.,Pathology Unit, Centro di Riferimento Oncologico di Aviano (C.R.O.) IRCCS, via Franco Gallini 2, 33081, Aviano, Italy
| | - Enrico Cavarzerani
- Department of Molecular Sciences and Nanosystems, Università Ca' Foscari, Campus Scientifico Via Torino 155, 30174, Venezia-Mestre, Italy
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (C.R.O.) IRCCS, via Franco Gallini 2, 33081, Aviano, Italy.,Department of Medical, Surgical and Health Sciences, Università degli Studi di Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | - Kristof Van Hecke
- Department of Chemistry and Centre for Sustainable Chemistry, Ghent University, Krijgslaan 281,S-3, 9000, Ghent, Belgium
| | - Georgios C Vougioukalakis
- Department of Chemistry, Laboratory of Organic Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece
| | - Catherine S J Cazin
- Department of Chemistry and Centre for Sustainable Chemistry, Ghent University, Krijgslaan 281,S-3, 9000, Ghent, Belgium
| | - Steven P Nolan
- Department of Chemistry and Centre for Sustainable Chemistry, Ghent University, Krijgslaan 281,S-3, 9000, Ghent, Belgium
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