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Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer's disease 期刊论文
NATURE, 2020, 577 (7790) : 399-+
作者:  Gate, David;  Saligrama, Naresha;  Leventhal, Olivia;  Yang, Andrew C.;  Unger, Michael S.;  Middeldorp, Jinte;  Chen, Kelly;  Lehallier, Benoit;  Channappa, Divya;  De Los Santos, Mark B.;  McBride, Alisha;  Pluvinage, John;  Elahi, Fanny;  Tam, Grace Kyin-Ye;  Kim, Yongha;  Greicius, Michael;  Wagner, Anthony D.;  Aigner, Ludwig;  Galasko, Douglas R.;  Davis, Mark M.;  Wyss-Coray, Tony
收藏  |  浏览/下载:6/0  |  提交时间:2020/07/03

Alzheimer'  s disease is an incurable neurodegenerative disorder in which neuroinflammation has a critical function(1). However, little is known about the contribution of the adaptive immune response in Alzheimer'  s disease(2). Here, using integrated analyses of multiple cohorts, we identify peripheral and central adaptive immune changes in Alzheimer'  s disease. First, we performed mass cytometry of peripheral blood mononuclear cells and discovered an immune signature of Alzheimer'  s disease that consists of increased numbers of CD8(+) T effector memory CD45RA(+) (T-EMRA) cells. In a second cohort, we found that CD8(+) T-EMRA cells were negatively associated with cognition. Furthermore, single-cell RNA sequencing revealed that T cell receptor (TCR) signalling was enhanced in these cells. Notably, by using several strategies of single-cell TCR sequencing in a third cohort, we discovered clonally expanded CD8(+) T-EMRA cells in the cerebrospinal fluid of patients with Alzheimer'  s disease. Finally, we used machine learning, cloning and peptide screens to demonstrate the specificity of clonally expanded TCRs in the cerebrospinal fluid of patients with Alzheimer'  s disease to two separate Epstein-Barr virus antigens. These results reveal an adaptive immune response in the blood and cerebrospinal fluid in Alzheimer'  s disease and provide evidence of clonal, antigen-experienced T cells patrolling the intrathecal space of brains affected by age-related neurodegeneration.


  
Is there a link between air pollution and impaired memory? Evidence on 34, 000 english citizens 期刊论文
ECOLOGICAL ECONOMICS, 2020, 169
作者:  Powdthavee, Nattavudh;  Oswald, Andrew J.
收藏  |  浏览/下载:5/0  |  提交时间:2020/07/02
Memory  NO2  PM10  Air  Pollution  Particulates  
Experimental demonstration of memory-enhanced quantum communication 期刊论文
NATURE, 2020
作者:  Quinn, Robert A.;  Melnik, Alexey, V;  Vrbanac, Alison;  Fu, Ting;  Patras, Kathryn A.;  Christy, Mitchell P.;  Bodai, Zsolt;  Belda-Ferre, Pedro;  Tripathi, Anupriya;  Chung, Lawton K.;  Downes, Michael;  Welch, Ryan D.;  Quinn, Melissa;  Humphrey, Greg;  Panitchpakdi, Morgan;  Weldon, Kelly C.;  Aksenov, Alexander;  da Silva, Ricardo;  Avila-Pacheco, Julian;  Clish, Clary;  Bae, Sena;  Mallick, Himel;  Franzosa, Eric A.;  Lloyd-Price, Jason;  Bussell, Robert;  Thron, Taren;  Nelson, Andrew T.;  Wang, Mingxun;  Leszczynski, Eric;  Vargas, Fernando;  Gauglitz, Julia M.;  Meehan, Michael J.;  Gentry, Emily;  Arthur, Timothy D.;  Komor, Alexis C.;  Poulsen, Orit;  Boland, Brigid S.;  Chang, John T.;  Sandborn, William J.;  Lim, Meerana;  Garg, Neha;  Lumeng, Julie C.;  Xavier, Ramnik J.;  Kazmierczak, Barbara, I;  Jain, Ruchi;  Egan, Marie;  Rhee, Kyung E.;  Ferguson, David;  Raffatellu, Manuela;  Vlamakis, Hera;  Haddad, Gabriel G.;  Siegel, Dionicio;  Huttenhower, Curtis;  Mazmanian, Sarkis K.;  Evans, Ronald M.;  Nizet, Victor;  Knight, Rob;  Dorrestein, Pieter C.
收藏  |  浏览/下载:36/0  |  提交时间:2020/07/03

The ability to communicate quantum information over long distances is of central importance in quantum science and engineering(1). Although some applications of quantum communication such as secure quantum key distribution(2,3) are already being successfully deployed(4-7), their range is currently limited by photon losses and cannot be extended using straightforward measure-and-repeat strategies without compromising unconditional security(8). Alternatively, quantum repeaters(9), which utilize intermediate quantum memory nodes and error correction techniques, can extend the range of quantum channels. However, their implementation remains an outstanding challenge(10-16), requiring a combination of efficient and high-fidelity quantum memories, gate operations, and measurements. Here we use a single solid-state spin memory integrated in a nanophotonic diamond resonator(17-19) to implement asynchronous photonic Bell-state measurements, which are a key component of quantum repeaters. In a proof-of-principle experiment, we demonstrate high-fidelity operation that effectively enables quantum communication at a rate that surpasses the ideal loss-equivalent direct-transmission method while operating at megahertz clock speeds. These results represent a crucial step towards practical quantum repeaters and large-scale quantum networks(20,21).


A solid-state spin memory is used to demonstrate quantum repeater functionality, which has the potential to overcome photon losses involved in long-distance transmission of quantum information.


  
Current-driven magnetic domain-wall logic 期刊论文
NATURE, 2020, 579 (7798) : 214-+
作者:  Culp, Elizabeth J.;  Waglechner, Nicholas;  Wang, Wenliang;  Fiebig-Comyn, Aline A.;  Hsu, Yen-Pang;  Koteva, Kalinka;  Sychantha, David;  Coombes, Brian K.;  Van Nieuwenhze, Michael S.;  Brun, Yves, V;  Wright, Gerard D.
收藏  |  浏览/下载:31/0  |  提交时间:2020/07/03

Spin-based logic architectures provide nonvolatile data retention, near-zero leakage, and scalability, extending the technology roadmap beyond complementary metal-oxide-semiconductor logic(1-13). Architectures based on magnetic domain walls take advantage of the fast motion, high density, non-volatility and flexible design of domain walls to process and store information(1,3,14-16). Such schemes, however, rely on domain-wall manipulation and clocking using an external magnetic field, which limits their implementation in dense, large-scale chips. Here we demonstrate a method for performing all-electric logic operations and cascading using domain-wall racetracks. We exploit the chiral coupling between neighbouring magnetic domains induced by the interfacial Dzyaloshinskii-Moriya interaction(17-20), which promotes non-collinear spin alignment, to realize a domain-wall inverter, the essential basic building block in all implementations of Boolean logic. We then fabricate reconfigurable NAND and NOR logic gates, and perform operations with current-induced domain-wall motion. Finally, we cascade several NAND gates to build XOR and full adder gates, demonstrating electrical control of magnetic data and device interconnection in logic circuits. Our work provides a viable platform for scalable all-electric magnetic logic, paving the way for memory-in-logic applications.


  
Selective loading and processing of prespacers for precise CRISPR adaptation 期刊论文
NATURE, 2020
作者:  Liu, Guoxia;  Papa, Arianne;  Katchman, Alexander N.;  Zakharov, Sergey I.;  Roybal, Daniel;  Hennessey, Jessica A.;  Kushner, Jared;  Yang, Lin;  Chen, Bi-Xing;  Kushnir, Alexander;  Dangas, Katerina;  Gygi, Steven P.;  Pitt, Geoffrey S.;  Colecraft, Henry M.;  Ben-Johny, Manu;  Kalocsay, Marian;  Marx, Steven O.
收藏  |  浏览/下载:5/0  |  提交时间:2020/07/03

CRISPR-Cas immunity protects prokaryotes against invading genetic elements(1). It uses the highly conserved Cas1-Cas2 complex to establish inheritable memory (spacers)(2-5). How Cas1-Cas2 acquires spacers from foreign DNA fragments (prespacers) and integrates them into the CRISPR locus in the correct orientation is unclear(6,7). Here, using the high spatiotemporal resolution of single-molecule fluorescence, we show that Cas1-Cas2 selects precursors of prespacers from DNA in various forms-including single-stranded DNA and partial duplexes-in a manner that depends on both the length of the DNA strand and the presence of a protospacer adjacent motif (PAM) sequence. We also identify DnaQ exonucleases as enzymes that process the Cas1-Cas2-loaded prespacer precursors into mature prespacers of a suitable size for integration. Cas1-Cas2 protects the PAM sequence from maturation, which results in the production of asymmetrically trimmed prespacers and the subsequent integration of spacers in the correct orientation. Our results demonstrate the kinetic coordination of prespacer precursor selection and PAM trimming, providing insight into the mechanisms that underlie the integration of functional spacers in the CRISPR loci.


Cas1-Cas2 selects precursor prespacers from DNA fragments in a length- and PAM-sequence-dependent manner, and these precursors are trimmed by DnaQ exonucleases to enable integration into the CRISPR locus in the correct orientation.


  
Tertiary lymphoid structures improve immunotherapy and survival in melanoma 期刊论文
NATURE, 2020, 577 (7791) : 561-+
作者:  Cabrita, Rita;  Lauss, Martin;  Sanna, Adriana;  Donia, Marco;  Larsen, Mathilde Skaarup;  Mitra, Shamik;  Johansson, Iva;  Phung, Bengt;  Harbst, Katja;  Vallon-Christersson, Johan;  van Schoiack, Alison;  Loevgren, Kristina;  Warren, Sarah;  Jirstroem, Karin;  Olsson, Hakan;  Pietras, Kristian;  Ingvar, Christian;  Isaksson, Karolin;  Schadendorf, Dirk;  Schmidt, Henrik;  Bastholt, Lars;  Carneiro, Ana;  Wargo, Jennifer A.;  Svane, Inge Marie;  Jonsson, Goran
收藏  |  浏览/下载:44/0  |  提交时间:2020/07/03

Checkpoint blockade therapies that reactivate tumour-associated T cells can induce durable tumour control and result in the long-term survival of patients with advanced cancers(1). Current predictive biomarkers for therapy response include high levels of intratumour immunological activity, a high tumour mutational burden and specific characteristics of the gut microbiota(2,3). Although the role of T cells in antitumour responses has thoroughly been studied, other immune cells remain insufficiently explored. Here we use clinical samples of metastatic melanomas to investigate the role of B cells in antitumour responses, and find that the co-occurrence of tumour-associated CD8(+) T cells and CD20(+) B cells is associated with improved survival, independently of other clinical variables. Immunofluorescence staining of CXCR5 and CXCL13 in combination with CD20 reveals the formation of tertiary lymphoid structures in these CD8(+)CD20(+) tumours. We derived a gene signature associated with tertiary lymphoid structures, which predicted clinical outcomes in cohorts of patients treated with immune checkpoint blockade. Furthermore, B-cell-rich tumours were accompanied by increased levels of TCF7(+) naive and/or memory T cells. This was corroborated by digital spatial-profiling data, in which T cells in tumours without tertiary lymphoid structures had a dysfunctional molecular phenotype. Our results indicate that tertiary lymphoid structures have a key role in the immune microenvironment in melanoma, by conferring distinct T cell phenotypes. Therapeutic strategies to induce the formation of tertiary lymphoid structures should be explored to improve responses to cancer immunotherapy.


The co-occurrence of tumour-associated CD8(+) T cells and CD20(+) B cells, and the formation of tertiary lymphoid structures, are linked with improved survival in cohorts of patients with metastatic melanoma.


  
VEGF-C-driven lymphatic drainage enables immunosurveillance of brain tumours 期刊论文
NATURE, 2020, 577 (7792) : 689-+
作者:  Toll, Velle;  Christensen, Matthew;  Quaas, Johannes;  Bellouin, Nicolas
收藏  |  浏览/下载:9/0  |  提交时间:2020/07/03

In a mouse model of glioblastoma, treatment with VEGF-C increases lymphatic drainage in the central nervous system and improves the immune response, suggesting that modulating meningeal lymphatics could enhance checkpoint inhibitor therapy.


Immune surveillance against pathogens and tumours in the central nervous system is thought to be limited owing to the lack of lymphatic drainage. However, the characterization of the meningeal lymphatic network has shed light on previously unappreciated ways that an immune response can be elicited to antigens that are expressed in the brain(1-3). Despite progress in our understanding of the development and structure of the meningeal lymphatic system, the contribution of this network in evoking a protective antigen-specific immune response in the brain remains unclear. Here, using a mouse model of glioblastoma, we show that the meningeal lymphatic vasculature can be manipulated to mount better immune responses against brain tumours. The immunity that is mediated by CD8 T cells to the glioblastoma antigen is very limited when the tumour is confined to the central nervous system, resulting in uncontrolled tumour growth. However, ectopic expression of vascular endothelial growth factor C (VEGF-C) promotes enhanced priming of CD8 T cells in the draining deep cervical lymph nodes, migration of CD8 T cells into the tumour, rapid clearance of the glioblastoma and a long-lasting antitumour memory response. Furthermore, transfection of an mRNA construct that expresses VEGF-C works synergistically with checkpoint blockade therapy to eradicate existing glioblastoma. These results reveal the capacity of VEGF-C to promote immune surveillance of tumours, and suggest a new therapeutic approach to treat brain tumours.


  
Negative supercoil at gene boundaries modulates gene topology 期刊论文
NATURE, 2020, 577 (7792) : 701-+
作者:  Yuan, Guowen;  Lin, Dongjing;  Wang, Yong;  Huang, Xianlei;  Chen, Wang;  Xie, Xuedong;  Zong, Junyu;  Yuan, Qian-Qian;  Zheng, Hang;  Wang, Di;  Xu, Jie;  Li, Shao-Chun;  Zhang, Yi;  Sun, Jian;  Xi, Xiaoxiang;  Gao, Libo
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/03

Transcription challenges the integrity of replicating chromosomes by generating topological stress and conflicts with forks(1,2). The DNA topoisomerases Top1 and Top2 and the HMGB family protein Hmo1 assist DNA replication and transcription(3-6). Here we describe the topological architecture of genes in Saccharomyces cerevisiae during the G1 and S phases of the cell cycle. We found under-wound DNA at gene boundaries and over-wound DNA within coding regions. This arrangement does not depend on Pol II or S phase. Top2 and Hmo1 preserve negative supercoil at gene boundaries, while Top1 acts at coding regions. Transcription generates RNA-DNA hybrids within coding regions, independently of fork orientation. During S phase, Hmo1 protects under-wound DNA from Top2, while Top2 confines Pol II and Top1 at coding units, counteracting transcription leakage and aberrant hybrids at gene boundaries. Negative supercoil at gene boundaries prevents supercoil diffusion and nucleosome repositioning at coding regions. DNA looping occurs at Top2 clusters. We propose that Hmo1 locks gene boundaries in a cruciform conformation and, with Top2, modulates the architecture of genes that retain the memory of the topological arrangements even when transcription is repressed.


  
Decoding the development of the human hippocampus 期刊论文
NATURE, 2020, 577 (7791) : 531-+
作者:  Zhong, Suijuan;  Ding, Wenyu;  Sun, Le;  Lu, Yufeng;  Dong, Hao;  Fan, Xiaoying;  Liu, Zeyuan;  Chen, Ruiguo;  Zhang, Shu;  Ma, Qiang;  Tang, Fuchou;  Wu, Qian;  Wang, Xiaoqun
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/03

The hippocampus is an important part of the limbic system in the human brain that has essential roles in spatial navigation and the consolidation of information from short-term memory to long-term memory(1,2). Here we use single-cell RNA sequencing and assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis to illustrate the cell types, cell linage, molecular features and transcriptional regulation of the developing human hippocampus. Using the transcriptomes of 30,416 cells from the human hippocampus at gestational weeks 16-27, we identify 47 cell subtypes and their developmental trajectories. We also identify the migrating paths and cell lineages of PAX6(+) and HOPX+ hippocampal progenitors, and regional markers of CA1, CA3 and dentate gyrus neurons. Multiomic data have uncovered transcriptional regulatory networks of the dentate gyrus marker PROX1. We also illustrate spatially specific gene expression in the developing human prefrontal cortex and hippocampus. The molecular features of the human hippocampus at gestational weeks 16-20 are similar to those of the mouse at postnatal days 0-5 and reveal gene expression differences between the two species. Transient expression of the primate-specific gene NBPF1 leads to a marked increase in PROX1(+) cells in the mouse hippocampus. These data provides a blueprint for understanding human hippocampal development and a tool for investigating related diseases.


Single-cell RNA sequencing is used to catalogue and explore the developmental trajectories of more than 30,000 cells in the developing human hippocampus.


  
B cells and tertiary lymphoid structures promote immunotherapy response 期刊论文
NATURE, 2020, 577 (7791) : 549-+
作者:  Zhang, Liangsheng;  Chen, Fei;  Zhang, Xingtan;  Li, Zhen;  Zhao, Yiyong;  Lohaus, Rolf;  Chang, Xiaojun;  Dong, Wei;  Ho, Simon Y. W.;  Liu, Xing;  Song, Aixia;  Chen, Junhao;  Guo, Wenlei;  Wang, Zhengjia;  Zhuang, Yingyu;  Wang, Haifeng;  Chen, Xuequn;  Hu, Juan;  Liu, Yanhui;  Qin, Yuan;  Wang, Kai;  Dong, Shanshan;  Liu, Yang;  Zhang, Shouzhou;  Yu, Xianxian;  Wu, Qian;  Wang, Liangsheng;  Yan, Xueqing;  Jiao, Yuannian;  Kong, Hongzhi;  Zhou, Xiaofan;  Yu, Cuiwei;  Chen, Yuchu;  Li, Fan;  Wang, Jihua;  Chen, Wei;  Chen, Xinlu;  Jia, Qidong;  Zhang, Chi;  Jiang, Yifan;  Zhang, Wanbo;  Liu, Guanhua;  Fu, Jianyu;  Chen, Feng;  Ma, Hong;  Van de Peer, Yves;  Tang, Haibao
收藏  |  浏览/下载:43/0  |  提交时间:2020/07/03

Multiomic profiling of several cohorts of patients treated with immune checkpoint blockade highlights the presence and potential role of B cells and tertiary lymphoid structures in promoting therapy response.


Treatment with immune checkpoint blockade (ICB) has revolutionized cancer therapy. Until now, predictive biomarkers(1-10) and strategies to augment clinical response have largely focused on the T cell compartment. However, other immune subsets may also contribute to anti-tumour immunity(11-15), although these have been less well-studied in ICB treatment(16). A previously conducted neoadjuvant ICB trial in patients with melanoma showed via targeted expression profiling(17) that B cell signatures were enriched in the tumours of patients who respond to treatment versus non-responding patients. To build on this, here we performed bulk RNA sequencing and found that B cell markers were the most differentially expressed genes in the tumours of responders versus non-responders. Our findings were corroborated using a computational method (MCP-counter(18)) to estimate the immune and stromal composition in this and two other ICB-treated cohorts (patients with melanoma and renal cell carcinoma). Histological evaluation highlighted the localization of B cells within tertiary lymphoid structures. We assessed the potential functional contributions of B cells via bulk and single-cell RNA sequencing, which demonstrate clonal expansion and unique functional states of B cells in responders. Mass cytometry showed that switched memory B cells were enriched in the tumours of responders. Together, these data provide insights into the potential role of B cells and tertiary lymphoid structures in the response to ICB treatment, with implications for the development of biomarkers and therapeutic targets.