bluuebunny/crossref_metadata_2025_split huggingface dataset:
CST1 inhibits ferroptosis and promotes gastric cancer metastasis by regulating GPX4 protein stability via OTUB1
Authors: Li Dongbao , Wang Yuhong , Dong Chao , Chen Tao , Dong Anqi , Ren Jiayu , Li Weikang , Shu Gege , Yang Jiaoyang , Shen Wenhao , Qin Lei , Hu Lin , Zhou Jin 
Published: November 2022

AbstractMetastasis is an important factor contributing to poor prognosis in patients with gastric cancer; yet, the molecular mechanism leading to this cell behavior is still not well understood. In this study, we explored the role of cysteine protease inhibitor SN (Cystatin SN, CST1) in promoting gastric cancer metastasis. We hypothesized that CST1 could regulate gastric cancer progression by regulating GPX4 and ferroptosis. Whole transcriptome sequencing suggested that the expression of CST1 was significantly increased in metastatic cancer, and high CST1 expression was correlated with a worse prognosis. Our data further confirmed that the overexpression of CST1 may significantly promote the migration and invasion of gastric cancer cells in vitro and enhance liver, lung, and peritoneal metastasis of gastric cancer in nude mice. Meanwhile, high expression of CST1 promoted the epithelial-mesenchymal transition (EMT) of gastric cancer cells. Mechanistically, a co-immunoprecipitation experiment combined with mass spectrometry analysis confirmed that CST1 could interact with GPX4, a key protein regulating ferroptosis. CST1 relieves GPX4 ubiquitination modification by recruiting OTUB1, improving GPX4 protein stability and reducing intracellular reactive oxygen species (ROS), thereby inhibiting ferroptosis and, in turn, promoting gastric cancer metastasis. Moreover, clinical data suggested that CST1 is significantly increased in peripheral blood and ascites of gastric cancer patients with metastasis; multivariate Cox regression model analysis showed that CST1 was an independent risk factor for the prognosis of gastric cancer patients. Overall, our results elucidated a critical pathway through which high CST1 expression protects gastric cancer cells from undergoing ferroptosis, thus promoting its progression and metastasis. CST1 may be used as a new oncological marker and potential therapeutic target for gastric cancer metastasis.
Genome-wide transcriptomics of the amygdala reveals similar oligodendrocyte-related responses to acute and chronic alcohol drinking in female mice
Authors: Narendra Sharvari , Klengel Claudia , Hamzeh Bilal , Patel Drasti , Otten Joy , Lardenoije Roy , Newman Emily L. , Miczek Klaus A. , Klengel Torsten , Ressler Kerry J. , Suh Junghyup 
Published: November 2022

AbstractRepeated excessive alcohol consumption is a risk factor for alcohol use disorder (AUD). Although AUD has been more common in men than women, women develop more severe behavioral and physical impairments. However, relatively few new therapeutics targeting development of AUD, particularly in women, have been validated. To gain a better understanding of molecular mechanisms underlying alcohol intake, we conducted a genome-wide RNA-sequencing analysis in female mice exposed to different modes (acute vs chronic) of ethanol drinking. We focused on transcriptional profiles in the amygdala including the central and basolateral subnuclei, brain areas previously implicated in alcohol drinking and seeking. Surprisingly, we found that both drinking modes triggered similar changes in gene expression and canonical pathways, including upregulation of ribosome-related/translational pathways and myelination pathways, and downregulation of chromatin binding and histone modification. In addition, analyses of hub genes and upstream regulatory pathways revealed that voluntary ethanol consumption affects epigenetic changes via histone deacetylation pathways, oligodendrocyte and myelin function, and the oligodendrocyte-related transcription factor, Sox17. Furthermore, a viral vector-assisted knockdown of Sox17 gene expression in the amygdala prevented a gradual increase in alcohol consumption during repeated accesses. Overall, these results suggest that the expression of oligodendrocyte-related genes in the amygdala is sensitive to voluntary alcohol drinking in female mice. These findings suggest potential molecular targets for future therapeutic approaches to prevent the development of AUD, due to repeated excessive alcohol consumption, particularly in women.
Nck1 activity in lateral amygdala regulates long-term fear memory formation
Authors: Ilovich Or , Dines Monica , Paul Blesson K. , Barkai Edi , Lamprecht Raphael 
Published: November 2022

AbstractFear conditioning leads to long-term fear memory formation and is a model for studying fear-related psychopathological conditions such as phobias and post-traumatic stress disorder. Long-term fear memory formation is believed to involve alterations of synaptic efficacy mediated by changes in synaptic transmission and morphology in lateral amygdala (LA). Nck1 is a key neuronal adaptor protein involved in the regulation of the actin cytoskeleton and the neuronal processes believed to be involved in memory formation. However, the role of Nck1 in memory formation is not known. Here we explored the role of Nck1 in fear memory formation in lateral amygdala (LA). Reduction of Nck1 in excitatory neurons in LA enhanced long-term, but not short-term, auditory fear conditioning memory. Activation of Nck1, by using a photoactivatable Nck1 (PA-Nck1), during auditory fear conditioning in excitatory neurons in LA impaired long-term, but not short-term, fear memory. Activation of Nck1 immediately or a day after fear conditioning did not affect fear memory. The hippocampal-mediated contextual fear memory was not affected by the reduction or activation of Nck1 in LA. We show that Nck1 is localized to the presynapses in LA. Nck1 activation in LA excitatory neurons decreased the frequency of AMPA receptors-mediated miniature excitatory synaptic currents (mEPSCs). Nck1 activation did not affect GABA receptor-mediated inhibitory synaptic currents (mIPSCs). These results show that Nck1 activity in excitatory neurons in LA regulates glutamate release and sets the threshold for fear memory formation. Moreover, our research shows that Nck1 may serve as a target for pharmacological treatment of fear and anxiety disorders.
SETD2 transcriptional control of ATG14L/S isoforms regulates autophagosome–lysosome fusion
Authors: González-Rodríguez Patricia , Delorme-Axford Elizabeth , Bernard Amélie , Keane Lily , Stratoulias Vassilis , Grabert Kathleen , Engskog-Vlachos Pinelopi , Füllgrabe Jens , Klionsky Daniel J. , Joseph Bertrand 
Published: November 2022

AbstractMacroautophagy/autophagy is an evolutionarily conserved and tightly regulated catabolic process involved in the maintenance of cellular homeostasis whose dysregulation is implicated in several pathological processes. Autophagy begins with the formation of phagophores that engulf cytoplasmic cargo and mature into double-membrane autophagosomes; the latter fuse with lysosomes/vacuoles for cargo degradation and recycling. Here, we report that yeast Set2, a histone lysine methyltransferase, and its mammalian homolog, SETD2, both act as positive transcriptional regulators of autophagy. However, whereas Set2 regulates the expression of several autophagy-related (Atg) genes upon nitrogen starvation, SETD2 effects in mammals were found to be more restricted. In fact, SETD2 appears to primarily regulate the differential expression of protein isoforms encoded by the ATG14 gene. SETD2 promotes the expression of a long ATG14 isoform, ATG14L, that contains an N-terminal cysteine repeats domain, essential for the efficient fusion of the autophagosome with the lysosome, that is absent in the short ATG14 isoform, ATG14S. Accordingly, SETD2 loss of function decreases autophagic flux, as well as the turnover of aggregation-prone proteins such as mutant HTT (huntingtin) leading to increased cellular toxicity. Hence, our findings bring evidence to the emerging concept that the production of autophagy-related protein isoforms can differentially affect core autophagy machinery bringing an additional level of complexity to the regulation of this biological process in more complex organisms.
ADCK1 is a potential therapeutic target of osteosarcoma
Authors: Zhuo Bao-biao , Zhu Lun-qing , Yao Chen , Wang Xi-hua , Li Shi-xian , Wang Rong , Li Yuan , Ling Zhuo-yan 
Published: November 2022

AbstractWe here showed that ADCK1 (AarF domain-containing kinase 1), a mitochondrial protein, is upregulated in human osteosarcoma (OS) tissues and OS cells. In primary and established OS cells, ADCK1 shRNA or CRISPR/Cas9-induced ADCK1 knockout (KO) remarkably inhibited cell viability, proliferation and migration, and provoked apoptosis activation. Conversely, ectopic ADCK1 overexpression exerted pro-cancerous activity by promoting OS cell proliferation and migration. ADCK1 depletion disrupted mitochondrial functions in OS cells and induced mitochondrial membrane potential reduction, ATP depletion, reactive oxygen species production. Significantly, ADCK1 silencing augmented doxorubicin-induced apoptosis in primary OS cells. mTOR activation is important for ADCK1 expression in OS cells. The mTOR inhibitors, rapamycin and AZD2014, as well as mTOR shRNA, potently decreased ADCK1 expression in primary OS cells. In nude mice, the growth of subcutaneous pOS-1 xenografts was largely inhibited when bearing ADCK1 shRNA or ADCK1 KO construct. Moreover, ADCK1 KO largely inhibited pOS-1 xenograft in situ growth in proximal tibia of nude mice. ADCK1 depletion, apoptosis activation and ATP reduction were detected in pOS-1 xenografts bearing ADCK1 shRNA or ADCK1 KO construct. Together, the mitochondrial protein ADCK1 is required for OS cell growth and is a novel therapeutic target of OS.
LINC00472 inhibits cell migration by enhancing intercellular adhesion and regulates H3K27ac level via interacting with P300 in renal clear cell carcinoma
Authors: Wang Songmao , Luo Cheng , Li Bing , Zhang Shikuan , Liao Weijie , Xin Qilei , Xu Naihan , Xie Weidong , Zhu Yuanchang , Zhang Yaou 
Published: November 2022

AbstractRenal clear cell carcinoma (RCCC) is the most common type of renal cell carcinoma, which is also difficult to diagnose and easy to metastasize. Currently, there is still a lack of effective clinical diagnostic indicators and treatment targets. This study aims to find effective diagnostic markers and therapeutic targets from the perspective of noncoding RNA. In this study, we found that the expression of Long noncoding RNA LINC00472 was significantly decreased in RCCC and showed a downward trend with the progression of cancer stage. Patients with low LINC00472 expression have poor prognosis. Inhibition of LINC00472 significantly increased cell proliferation and migration, while overexpression of LINC00472 obviously inhibited cell proliferation and enhanced intercellular adhesion. Transcriptome sequencing analysis demonstrated that LINC00472 was highly correlated with extracellular matrix and cell metastasis-related pathways, and the consistent results were obtained by The Cancer Genome Atlas (TCGA) data analysis. Additionally, we discovered that the integrin family protein ITGB8 is a potential target gene of LINC00472. Mechanistically, we found that the change of LINC00472 affected the acetylation level of H3K27 site in cells, and we speculate that this effect is likely to be generated through the interaction with acetyltransferase P300. In conclusion, LINC00472 has an important impact on the proliferation and metastasis of renal clear cells, and probably participate in the regulation of histone modification, and it may be used as a potential diagnostic marker of RCCC.
CLIMB: High-dimensional association detection in large scale genomic data
Authors: Koch Hillary , Keller Cheryl A. , Xiang Guanjue , Giardine Belinda , Zhang Feipeng , Wang Yicheng , Hardison Ross C. , Li Qunhua 
Published: November 2022

AbstractJoint analyses of genomic datasets obtained in multiple different conditions are essential for understanding the biological mechanism that drives tissue-specificity and cell differentiation, but they still remain computationally challenging. To address this we introduce CLIMB (Composite LIkelihood eMpirical Bayes), a statistical methodology that learns patterns of condition-specificity present in genomic data. CLIMB provides a generic framework facilitating a host of analyses, such as clustering genomic features sharing similar condition-specific patterns and identifying which of these features are involved in cell fate commitment. We apply CLIMB to three sets of hematopoietic data, which examine CTCF ChIP-seq measured in 17 different cell populations, RNA-seq measured across constituent cell populations in three committed lineages, and DNase-seq in 38 cell populations. Our results show that CLIMB improves upon existing alternatives in statistical precision, while capturing interpretable and biologically relevant clusters in the data.
Distinct immunological and molecular signatures underpinning influenza vaccine responsiveness in the elderly
Authors: Riese Peggy , Trittel Stephanie , Akmatov Manas K. , May Marcus , Prokein Jana , Illig Thomas , Schindler Christoph , Sawitzki Birgit , Elfaki Yassin , Floess Stefan , Huehn Jochen , Błażejewski Adrian J. , Strowig Till , Hernandez-Vargas Esteban A. , Geffers Robert , Zhang Bowen , Li Yang , Pessler Frank , Guzmán Carlos A. 
Published: November 2022

AbstractSeasonal influenza outbreaks, especially in high-risk groups such as the elderly, represent an important public health problem. Prevailing inadequate efficacy of seasonal vaccines is a crucial bottleneck. Understanding the immunological and molecular mechanisms underpinning differential influenza vaccine responsiveness is essential to improve vaccination strategies. Here we show comprehensive characterization of the immune response of randomly selected elderly participants (≥ 65 years), immunized with the adjuvanted influenza vaccine Fluad. In-depth analyses by serology, multi-parametric flow cytometry, multiplex and transcriptome analysis, coupled to bioinformatics and mathematical modelling, reveal distinguishing immunological and molecular features between responders and non-responders defined by vaccine-induced seroconversion. Non-responders are specifically characterized by multiple suppressive immune mechanisms. The generated comprehensive high dimensional dataset enables the identification of putative mechanisms and nodes responsible for vaccine non-responsiveness independently of confounding age-related effects, with the potential to facilitate development of tailored vaccination strategies for the elderly.
Long-range GABAergic projections contribute to cortical feedback control of sensory processing
Authors: Mazo Camille , Nissant Antoine , Saha Soham , Peroni Enzo , Lledo Pierre-Marie , Lepousez Gabriel 
Published: November 2022

AbstractIn the olfactory system, the olfactory cortex sends glutamatergic projections back to the first stage of olfactory processing, the olfactory bulb (OB). Such corticofugal excitatory circuits — a canonical circuit motif described in all sensory systems— dynamically adjust early sensory processing. Here, we uncover a corticofugal inhibitory feedback to OB, originating from a subpopulation of GABAergic neurons in the anterior olfactory cortex and innervating both local and output OB neurons. In vivo imaging and network modeling showed that optogenetic activation of cortical GABAergic projections drives a net subtractive inhibition of both spontaneous and odor-evoked activity in local as well as output neurons. In output neurons, stimulation of cortical GABAergic feedback enhances separation of population odor responses in tufted cells, but not mitral cells. Targeted pharmacogenetic silencing of cortical GABAergic axon terminals impaired discrimination of similar odor mixtures. Thus, corticofugal GABAergic projections represent an additional circuit motif in cortical feedback control of sensory processing.
Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine
Authors: Dowman Luke J. , Kulkarni Sameer S. , Alegre-Requena Juan V. , Giltrap Andrew M. , Norman Alexander R. , Sharma Ashish , Gallegos Liliana C. , Mackay Angus S. , Welegedara Adarshi P. , Watson Emma E. , van Raad Damian , Niederacher Gerhard , Huhmann Susanne , Proschogo Nicholas , Patel Karishma , Larance Mark , Becker Christian F. W. , Mackay Joel P. , Lakhwani Girish , Huber Thomas , Paton Robert S. , Payne Richard J. 
Published: November 2022

AbstractThe importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21stamino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.
DOPAnization of tyrosine in α-synuclein by tyrosine hydroxylase leads to the formation of oligomers
Authors: Jin Mingyue , Matsumoto Sakiko , Ayaki Takashi , Yamakado Hodaka , Taguchi Tomoyuki , Togawa Natsuko , Konno Ayumu , Hirai Hirokazu , Nakajima Hiroshi , Komai Shoji , Ishida Ryuichi , Chiba Syuhei , Takahashi Ryosuke , Takao Toshifumi , Hirotsune Shinji 
Published: November 2022

AbstractParkinson’s disease is a progressive neurodegenerative disorder characterized by the preferential loss of tyrosine hydroxylase (TH)-expressing dopaminergic neurons in the substantia nigra. Although the abnormal accumulation and aggregation of α-synuclein have been implicated in the pathogenesis of Parkinson’s disease, the underlying mechanisms remain largely elusive. Here, we found that TH converts Tyr136 in α-synuclein into dihydroxyphenylalanine (DOPA; Y136DOPA) through mass spectrometric analysis. Y136DOPA modification was clearly detected by a specific antibody in the dopaminergic neurons of α-synuclein-overexpressing mice as well as human α-synucleinopathies. Furthermore, dopanized α-synuclein tended to form oligomers rather than large fibril aggregates and significantly enhanced neurotoxicity. Our findings suggest that the dopanization of α-synuclein by TH may contribute to oligomer and/or seed formation causing neurodegeneration with the potential to shed light on the pathogenesis of Parkinson’s disease.
Ultra-fast triplet-triplet-annihilation-mediated high-lying reverse intersystem crossing triggered by participation of nπ*-featured excited states
Authors: Luo Yanju , Zhang Kai , Ding Zhenming , Chen Ping , Peng Xiaomei , Zhao Yihuan , Chen Kuan , Li Chuan , Zheng Xujun , Huang Yan , Pu Xuemei , Liu Yu , Su Shi-Jian , Hou Xiandeng , Lu Zhiyun 
Published: November 2022

AbstractThe harvesting of ‘hot’ triplet excitons through high-lying reverse intersystem crossing mechanism has emerged as a hot research issue in the field of organic light-emitting diodes. However, if high-lying reverse intersystem crossing materials lack the capability to convert ‘cold’ T1 excitons into singlet ones, the actual maximum exciton utilization efficiency would generally deviate from 100%. Herein, through comparative studies on two naphthalimide-based compounds CzNI and TPANI, we revealed that the ‘cold’ T1 excitons in high-lying reverse intersystem crossing materials can be utilized effectively through the triplet-triplet annihilation-mediated high-lying reverse intersystem crossing process if they possess certain triplet-triplet upconversion capability. Especially, quite effective triplet-triplet annihilation-mediated high-lying reverse intersystem crossing can be triggered by endowing the high-lying reverse intersystem crossing process with a 3ππ*→1nπ* character. By taking advantage of the permanent orthogonal orbital transition effect of 3ππ*→1nπ*, spin–orbit coupling matrix elements of ca. 10 cm−1 can be acquired, and hence ultra-fast mediated high-lying reverse intersystem crossing process with rate constant over 109 s−1 can be realized.
Identification of visual cortex cell types and species differences using single-cell RNA sequencing
Authors: Wei Jia-Ru , Hao Zhao-Zhe , Xu Chuan , Huang Mengyao , Tang Lei , Xu Nana , Liu Ruifeng , Shen Yuhui , Teichmann Sarah A. , Miao Zhichao , Liu Sheng 
Published: November 2022

AbstractThe primate neocortex exerts high cognitive ability and strong information processing capacity. Here, we establish a single-cell RNA sequencing dataset of 133,454 macaque visual cortical cells. It covers major cortical cell classes including 25 excitatory neuron types, 37 inhibitory neuron types and all glial cell types. We identified layer-specific markers includingHPCAL1andNXPH4, and also identified two cell types, anNPY-expressing excitatory neuron type that expresses the dopamine receptor D3 gene; and a primate specific activity-dependentOSTN + sensory neuron type. Comparisons of our dataset with humans and mice show that the gene expression profiles differ between species in relation to genes that are implicated in the synaptic plasticity and neuromodulation of excitatory neurons. The comparisons also revealed that glutamatergic neurons may be more diverse across species than GABAergic neurons and non-neuronal cells. These findings pave the way for understanding how the primary cortex fulfills the high-cognitive functions.
TLR3 forms a highly organized cluster when bound to a poly(I:C) RNA ligand
Authors: Lim Chan Seok , Jang Yoon Ha , Lee Ga Young , Han Gu Min , Jeong Hye Jin , Kim Ji Won , Lee Jie-Oh 
Published: November 2022

AbstractToll-like Receptor 3 (TLR3) initiates a potent anti-viral immune response by binding to double-stranded RNA ligands. Previous crystallographic studies showed that TLR3 forms a homodimer when bound to a 46-base pair RNA ligand. However, this short RNA fails to initiate a robust immune response. To obtain structural insights into the length dependency of TLR3 ligands, we determine the cryo-electron microscopy structure of full-length TLR3 in a complex with a synthetic RNA ligand with an average length of ~400 base pairs. In the structure, the dimeric TLR3 units are clustered along the double-stranded RNA helix in a highly organized and cooperative fashion with a uniform inter-dimer spacing of 103 angstroms. The intracellular and transmembrane domains are dispensable for the clustering because their deletion does not interfere with the cluster formation. Our structural observation suggests that ligand-induced clustering of TLR3 dimers triggers the ordered assembly of intracellular signaling adaptors and initiates a robust innate immune response.