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美科研人员呼吁采用区域和具体情况的方法来研究海洋热浪 快报文章
资源环境快报,2025年第5期
作者:  魏艳红
Microsoft Word(20Kb)  |  收藏  |  浏览/下载:427/0  |  提交时间:2025/03/14
Marine Heatwaves  Extreme Events  Regional and Context-specific Approaches  
The single-cell pathology landscape of breast cancer 期刊论文
NATURE, 2020, 578 (7796) : 615-+
作者:  Fouda, Abdelrahman Y.
收藏  |  浏览/下载:34/0  |  提交时间:2020/07/03

Single-cell analyses have revealed extensive heterogeneity between and within human tumours(1-4), but complex single-cell phenotypes and their spatial context are not at present reflected in the histological stratification that is the foundation of many clinical decisions. Here we use imaging mass cytometry(5) to simultaneously quantify 35 biomarkers, resulting in 720 high-dimensional pathology images of tumour tissue from 352 patients with breast cancer, with long-term survival data available for 281 patients. Spatially resolved, single-cell analysis identified the phenotypes of tumour and stromal single cells, their organization and their heterogeneity, and enabled the cellular architecture of breast cancer tissue to be characterized on the basis of cellular composition and tissue organization. Our analysis reveals multicellular features of the tumour microenvironment and novel subgroups of breast cancer that are associated with distinct clinical outcomes. Thus, spatially resolved, single-cell analysis can characterize intratumour phenotypic heterogeneity in a disease-relevant manner, with the potential to inform patient-specific diagnosis.


A single-cell, spatially resolved analysis of breast cancer demonstrates the heterogeneity of tumour and stroma tissue and provides a more-detailed method of patient classification than the current histology-based system.


  
The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K 期刊论文
NATURE, 2020
作者:  Chen, Guorui;  Sharpe, Aaron L.;  Fox, Eli J.;  Zhang, Ya-Hui;  Wang, Shaoxin;  Jiang, Lili;  Lyu, Bosai;  Li, Hongyuan;  Watanabe, Kenji;  Taniguchi, Takashi;  Shi, Zhiwen;  Senthil, T.;  Goldhaber-Gordon, David;  Zhang, Yuanbo;  Wang, Feng
收藏  |  浏览/下载:65/0  |  提交时间:2020/07/03

The cyclin-dependent kinase inhibitor CR8 acts as a molecular glue compound by inducing the formation of a complex between CDK12-cyclin K and DDB1, which results in the ubiquitination and degradation of cyclin K.


Molecular glue compounds induce protein-protein interactions that, in the context of a ubiquitin ligase, lead to protein degradation(1). Unlike traditional enzyme inhibitors, these molecular glue degraders act substoichiometrically to catalyse the rapid depletion of previously inaccessible targets(2). They are clinically effective and highly sought-after, but have thus far only been discovered serendipitously. Here, through systematically mining databases for correlations between the cytotoxicity of 4,518 clinical and preclinical small molecules and the expression levels of E3 ligase components across hundreds of human cancer cell lines(3-5), we identify CR8-a cyclin-dependent kinase (CDK) inhibitor(6)-as a compound that acts as a molecular glue degrader. The CDK-bound form of CR8 has a solvent-exposed pyridyl moiety that induces the formation of a complex between CDK12-cyclin K and the CUL4 adaptor protein DDB1, bypassing the requirement for a substrate receptor and presenting cyclin K for ubiquitination and degradation. Our studies demonstrate that chemical alteration of surface-exposed moieties can confer gain-of-function glue properties to an inhibitor, and we propose this as a broader strategy through which target-binding molecules could be converted into molecular glues.


  
poly(UG)-tailed RNAs in genome protection and epigenetic inheritance 期刊论文
NATURE, 2020, 582 (7811) : 283-+
作者:  Raj, Dipak K.;  Das Mohapatra, Alok;  Jnawali, Anup;  Zuromski, Jenna;  Jha, Ambrish;  Cham-Kpu, Gerald;  Sherman, Brett;  Rudlaff, Rachel M.;  Nixon, Christina E.;  Hilton, Nicholas;  Oleinikov, Andrew V.;  Chesnokov, Olga;  Merritt, Jordan;  Pond-Tor, Sunthorn
收藏  |  浏览/下载:26/0  |  提交时间:2020/07/03

Mobile genetic elements threaten genome integrity in all organisms. RDE-3 (also known as MUT-2) is a ribonucleotidyltransferase that is required for transposon silencing and RNA interference in Caenorhabditis elegans(1-4). When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3 '  termini of these RNAs (designated poly(UG) or pUG tails)(5). Here we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNA interference, as well as to transposon RNAs. RNA fragments attached to pUG tails with more than 16 perfectly alternating 3 '  U and G nucleotides become gene-silencing agents. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases, which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA-templated siRNA synthesis and siRNA-directed pUG RNA biogenesis underlie double-stranded-RNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA-siRNA silencing loop enables parents to inoculate progeny against the expression of unwanted or parasitic genetic elements.


In Caenorhabditis elegans, the ribonucleotidyltransferase RDE-3 adds alternating uridine and guanosine ribonucleotides to the 3 '  termini of RNAs, a key step in RNA interference and thus epigenetic inheritance in the C. elegans germline.


  
Feedback generates a second receptive field in neurons of the visual cortex 期刊论文
NATURE, 2020
作者:  Shi, Enzheng;  Yuan, Biao;  Shiring, Stephen B.;  Gao, Yao;  Akriti;  Guo, Yunfan;  Su, Cong;  Lai, Minliang;  Yang, Peidong;  Kong, Jing;  Savoie, Brett M.;  Yu, Yi;  Dou, Letian
收藏  |  浏览/下载:53/0  |  提交时间:2020/07/03

Animals sense the environment through pathways that link sensory organs to the brain. In the visual system, these feedforward pathways define the classical feedforward receptive field (ffRF), the area in space in which visual stimuli excite a neuron(1). The visual system also uses visual context-the visual scene surrounding a stimulus-to predict the content of the stimulus(2), and accordingly, neurons have been identified that are excited by stimuli outside their ffRF(3-8). However, the mechanisms that generate excitation to stimuli outside the ffRF are unclear. Here we show that feedback projections onto excitatory neurons in the mouse primary visual cortex generate a second receptive field that is driven by stimuli outside the ffRF. The stimulation of this feedback receptive field (fbRF) elicits responses that are slower and are delayed in comparison with those resulting from the stimulation of the ffRF. These responses are preferentially reduced by anaesthesia and by silencing higher visual areas. Feedback inputs from higher visual areas have scattered receptive fields relative to their putative targets in the primary visual cortex, which enables the generation of the fbRF. Neurons with fbRFs are located in cortical layers that receive strong feedback projections and are absent in the main input layer, which is consistent with a laminar processing hierarchy. The observation that large, uniform stimuli-which cover both the fbRF and the ffRF-suppress these responses indicates that the fbRF and the ffRF are mutually antagonistic. Whereas somatostatin-expressing inhibitory neurons are driven by these large stimuli, inhibitory neurons that express parvalbumin and vasoactive intestinal peptide have mutually antagonistic fbRF and ffRF, similar to excitatory neurons. Feedback projections may therefore enable neurons to use context to estimate information that is missing from the ffRF and to report differences in stimulus features across visual space, regardless of whether excitation occurs inside or outside the ffRF. By complementing the ffRF, the fbRF that we identify here could contribute to predictive processing.


Feedback projections onto neurons of the mouse primary visual cortex generate a second excitatory receptive field that is driven by stimuli outside of the classical feedforward receptive field, with responses mediated by higher visual areas.


  
A reference map of the human binary protein interactome 期刊论文
NATURE, 2020, 580 (7803) : 402-+
作者:  Fan, Chen;  Sukomon, Nattakan;  Flood, Emelie;  Rheinberger, Jan;  Allen, Toby W.;  Nimigean, Crina M.
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships(1,2). Here we present a human '  all-by-all'  reference interactome map of human binary protein interactions, or '  HuRI'  . With approximately 53,000 protein-protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome(3), transcriptome(4) and proteome(5) data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein-protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes.


  
A genomic and epigenomic atlas of prostate cancer in Asian populations 期刊论文
NATURE, 2020: 93-+
作者:  Perry, Rachel J.;  Zhang, Dongyan;  Guerra, Mateus T.;  Brill, Allison L.;  Goedeke, Leigh;  Nasiri, Ali R.;  Rabin-Court, Aviva;  Wang, Yongliang;  Peng, Liang;  Dufour, Sylvie;  Zhang, Ye;  Zhang, Xian-Man;  Butrico, Gina M.;  Toussaint, Keshia;  Nozaki, Yuichi;  Cline, Gary W.;  Petersen, Kitt Falk;  Nathanson, Michael H.;  Ehrlich, Barbara E.;  Shulman, Gerald I.
收藏  |  浏览/下载:46/0  |  提交时间:2020/07/03

Prostate cancer is the second most common cancer in men worldwide(1). Over the past decade, large-scale integrative genomics efforts have enhanced our understanding of this disease by characterizing its genetic and epigenetic landscape in thousands of patients(2,3). However, most tumours profiled in these studies were obtained from patients from Western populations. Here we produced and analysed whole-genome, whole-transcriptome and DNA methylation data for 208 pairs of tumour tissue samples and matched healthy control tissue from Chinese patients with primary prostate cancer. Systematic comparison with published data from 2,554 prostate tumours revealed that the genomic alteration signatures in Chinese patients were markedly distinct from those of Western cohorts: specifically, 41% of tumours contained mutations in FOXA1 and 18% each had deletions in ZNF292 and CHD1. Alterations of the genome and epigenome were correlated and were predictive of disease phenotype and progression. Coding and noncoding mutations, as well as epimutations, converged on pathways that are important for prostate cancer, providing insights into this devastating disease. These discoveries underscore the importance of including population context in constructing comprehensive genomic maps for disease.


Genomic, transcriptomic and DNA methylation data from tissue samples from 208 Chinese patients with prostate cancer define the landscape of alterations in this population, and comparison with data from Western cohorts suggests that the disease may stratify into different molecular subtypes.


  
A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol 期刊论文
NATURE, 2020
作者:  Suskiewicz, Marcin J.;  Zobel, Florian;  Ogden, Tom E. H.;  Fontana, Pietro;  Ariza, Antonio;  Yang, Ji-Chun;  Zhu, Kang;  Bracken, Lily;  Hawthorne, William J.;  Ahel, Dragana;  Neuhaus, David;  Ahel, Ivan
收藏  |  浏览/下载:57/0  |  提交时间:2020/07/03

Haploid genetic screening of cells under different types of mitochondrial perturbation shows that a pathway involving OMA1, DELE1 and the eIF2 alpha kinase HRI communicates mitochondrial stress to the cytosol to trigger the integrated stress response.


Mitochondrial fidelity is tightly linked to overall cellular homeostasis and is compromised in ageing and various pathologies(1-3). Mitochondrial malfunction needs to be relayed to the cytosol, where an integrated stress response is triggered by the phosphorylation of eukaryotic translation initiation factor 2 alpha (eIF2 alpha) in mammalian cells(4,5). eIF2 alpha phosphorylation is mediated by the four eIF2 alpha kinases GCN2, HRI, PERK and PKR, which are activated by diverse types of cellular stress(6). However, the machinery that communicates mitochondrial perturbation to the cytosol to trigger the integrated stress response remains unknown(1,2,7). Here we combine genome engineering and haploid genetics to unbiasedly identify genes that affect the induction of C/EBP homologous protein (CHOP), a key factor in the integrated stress response. We show that the mitochondrial protease OMA1 and the poorly characterized protein DELE1, together with HRI, constitute the missing pathway that is triggered by mitochondrial stress. Mechanistically, stress-induced activation of OMA1 causes DELE1 to be cleaved into a short form that accumulates in the cytosol, where it binds to and activates HRI via its C-terminal portion. Obstruction of this pathway can be beneficial or adverse depending on the type of mitochondrial perturbation. In addition to the core pathway components, our comparative genetic screening strategy identifies a suite of additional regulators. Together, these findings could be used to inform future strategies to modulate the cellular response to mitochondrial dysfunction in the context of human disease.


  
Pathway paradigms revealed from the genetics of inflammatory bowel disease 期刊论文
NATURE, 2020, 578 (7796) : 527-539
作者:  Yu, Kwanha;  Lin, Chia-Ching John;  Hatcher, Asante;  Lozzi, Brittney;  Kong, Kathleen;  Huang-Hobbs, Emmet;  Cheng, Yi-Ting;  Beechar, Vivek B.;  Zhu, Wenyi;  Zhang, Yiqun;  Chen, Fengju;  Mills, Gordon B.;  Mohila, Carrie A.;  Creighton, Chad J.;  Noebels, Jeffrey L.;  Scott, Kenneth L.;  Deneen, Benjamin
收藏  |  浏览/下载:19/0  |  提交时间:2020/07/03

Inflammatory bowel disease (IBD) is a complex genetic disease that is instigated and amplified by the confluence of multiple genetic and environmental variables that perturb the immune-microbiome axis. The challenge of dissecting pathological mechanisms underlying IBD has led to the development of transformative approaches in human genetics and functional genomics. Here we describe IBD as a model disease in the context of leveraging human genetics to dissect interactions in cellular and molecular pathways that regulate homeostasis of the mucosal immune system. Finally, we synthesize emerging insights from multiple experimental approaches into pathway paradigms and discuss future prospects for disease-subtype classification and therapeutic intervention.


This Review examines inflammatory bowel disease in the context of human genetics studies that help to identify pathways that regulate homeostasis of the mucosal immune system and discusses future prospects for disease-subtype classification and therapeutic intervention.


  
Genomic basis for RNA alterations in cancer 期刊论文
NATURE, 2020, 578 (7793) : 129-+
作者:  Petitprez, Florent;  39;han
收藏  |  浏览/下载:27/0  |  提交时间:2020/07/03

Transcript alterations often result from somatic changes in cancer genomes(1). Various forms of RNA alterations have been described in cancer, including overexpression(2), altered splicing(3) and gene fusions(4)  however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)(5). Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed '  bridged'  fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.