Discovery Institute

A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.

AUTORES: Daniel J Klionsky1745,1749*, Kotb Abdelmohsen840, Akihisa Abe1237, Md Joynal Abedin1762, Hagai Abeliovich425,
\nAbraham Acevedo Arozena789, Hiroaki Adachi1800, Christopher M Adams1669, Peter D Adams57, Khosrow Adeli1981,
\nPeter J Adhihetty1625, Sharon G Adler700, Galila Agam67, Rajesh Agarwal1587, Manish K Aghi1537, Maria Agnello1826,
\nPatrizia Agostinis664, Patricia V Aguilar1960, Julio Aguirre-Ghiso784,786, Edoardo M Airoldi89,422, Slimane Ait-Si-Ali1376,
\nTakahiko Akematsu2010, Emmanuel T Akporiaye1097, Mohamed Al-Rubeai1394, Guillermo M Albaiceta1294,
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\nIraide Alloza642,888, Alexandru Almasan206, Maylin Almonte-Beceril524, Emad S Alnemri1212, Covadonga Alonso544,
\nNihal Altan-Bonnet848, Dario C Altieri1205, Silvia Alvarez1497, Lydia Alvarez-Erviti1395, Sandro Alves107,
\nGiuseppina Amadoro860, Atsuo Amano930, Consuelo Amantini1554, Santiago Ambrosio1458, Ivano Amelio756,
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\nAgnieszka Bagniewska-Zadworna2, Hua Bai90, Jie Bai667, Xue-Yuan Bai1133, Yannick Bailly884,
\nKithiganahalli Narayanaswamy Balaji473, Walter Balduini2002, Andrea Ballabio316, Rena Balzan1711, Rajkumar Banerjee239,
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\nMaria Teresa Batista1578, Henri Batoko1336, Maurizio Battino970, Kyle Bauckman2085, Bradley L Baumgarner1909,
\nK Ulrich Bayer1594, Rupert Beale1553, Jean-Fran¸cois Beaulieu1360, George R. Beck Jr48,294, Christoph Becker336,
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\nIvana Bjedov1258, Craig Blackstone843, Lionel Blanc1183, Guillermo A Blanco1496, Heidi Kiil Blomhoff1812,
\nEmilio Boada-Romero1297, Stefan B€ockler1464, Marianne Boes1423, Kathleen Boesze-Battaglia1835, Lawrence H Boise286,287,
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\nLisa A Brennan322, Emery H Bresnick2022, Patrick Brest490, Dave Bridges1939, Marie-Agn es Bringer124, Marisa Brini1822,
\nGlauber C Brito1311, Bertha Brodin631, Paul S Brookes1872, Eric J Brown352, Karen Brown1690, Hal E Broxmeyer480,
\nAlain Bruhat486,1339, Patricia Chakur Brum1893, John H Brumell446, Nicola Brunetti-Pierri315,1171,
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\nScott J Bultman1792, Geert Bultynck665, Vladimir Bumbasirevic1470, Yan Burelle1356, Robert E Burke216,217,
\nMargit Burmeister1750, Peter B€utikofer1473, Laura Caberlotto1987, Ken Cadwell896, Monika Cahova112, Dongsheng Cai24,
\nJingjing Cai2099, Qian Cai1018, Sara Calatayud2007, Nadine Camougrand1343, Michelangelo Campanella1700,
\nGrant R Campbell1525, Matthew Campbell1249, Silvia Campello556,1876, Robin Candau1769, Isabella Caniggia1983,
\nLavinia Cantoni560, Lizhi Cao116, Allan B Caplan1656, Michele Caraglia1051, Claudio Cardinali1043, Sandra Morais Cardoso1579, Jennifer S Carew208, Laura A Carleton874, Cathleen R Carlin101, Silvia Carloni2002,
\nSven R Carlsson1267, Didac Carmona-Gutierrez1643, Leticia AM Carneiro312, Oliana Carnevali971, Serena Carra1318,
\nAlice Carrier120, Bernadette Carroll900, Caty Casas1324, Josefina Casas1116, Giuliana Cassinelli324, Perrine Castets1462,
\nSusana Castro-Obregon214, Gabriella Cavallini1841, Isabella Ceccherini568, Francesco Cecconi253,555,1884,
\nArthur I Cederbaum459, Valent ın Ce~na199,1281, Simone Cenci1323,2064, Claudia Cerella444, Davide Cervia1996,
\nSilvia Cetrullo1478, Hassan Chaachouay2028, Han-Jung Chae187, Andrei S Chagin634, Chee-Yin Chai626,628,
\nGopal Chakrabarti1502, Georgios Chamilos1601, Edmond YW Chan1142, Matthew TV Chan181, Dhyan Chandra1003,
\nPallavi Chandra548, Chih-Peng Chang818, Raymond Chuen-Chung Chang1653, Ta Yuan Chang345, John C Chatham1434,
\nSaurabh Chatterjee1910, Santosh Chauhan527, Yongsheng Che62, Michael E Cheetham1263, Rajkumar Cheluvappa1783,
\nChun-Jung Chen1153, Gang Chen598,1676, Guang-Chao Chen9, Guoqiang Chen1078, Hongzhuan Chen1077, Jeff W Chen1514,
\nJian-Kang Chen370,371, Min Chen249, Mingzhou Chen2104, Peiwen Chen1823, Qi Chen1674, Quan Chen172,
\nShang-Der Chen138, Si Chen325, Steve S-L Chen10, Wei Chen2125, Wei-Jung Chen829, Wen Qiang Chen979, Wenli Chen1113,
\nXiangmei Chen1133, Yau-Hung Chen1157, Ye-Guang Chen1250, Yin Chen1447, Yingyu Chen953,955, Yongshun Chen2135,
\nYu-Jen Chen712, Yue-Qin Chen1145, Yujie Chen1208, Zhen Chen339, Zhong Chen2123, Alan Cheng1702,
\nChristopher HK Cheng184, Hua Cheng1728, Heesun Cheong814, Sara Cherry1836, Jason Chesney1703,
\nChun Hei Antonio Cheung817, Eric Chevet1359, Hsiang Cheng Chi140, Sung-Gil Chi656, Fulvio Chiacchiera308,
\nHui-Ling Chiang958, Roberto Chiarelli1826, Mario Chiariello235,567,577, Marcello Chieppa835, Lih-Shen Chin290,
\nMario Chiong1285, Gigi NC Chiu878, Dong-Hyung Cho676, Ssang-Goo Cho650, William C Cho982, Yong-Yeon Cho105,
\nYoung-Seok Cho1064, Augustine MK Choi2095, Eui-Ju Choi656, Eun-Kyoung Choi387,400,685, Jayoung Choi1563,
\nMary E Choi2093, Seung-Il Choi2116, Tsui-Fen Chou412, Salem Chouaib395, Divaker Choubey1574, Vinay Choubey1936,
\nKuan-Chih Chow822, Kamal Chowdhury730, Charleen T Chu1856, Tsung-Hsien Chuang827, Taehoon Chun657,
\nHyewon Chung652, Taijoon Chung978, Yuen-Li Chung1194, Yong-Joon Chwae18, Valentina Cianfanelli254,
\nRoberto Ciarcia1775, Iwona A Ciechomska886, Maria Rosa Ciriolo1876, Mara Cirone1042, Sofie Claerhout1694,
\nMichael J Clague1698, Joan Cl aria1457, Peter GH Clarke1687, Robert Clarke361, Emilio Clementi1045,1398, C edric Cleyrat1781,
\nMiriam Cnop1366, Eliana M Coccia574, Tiziana Cocco1459, Patrice Codogno1375, J€orn Coers271, Ezra EW Cohen1533,
\nDavid Colecchia235,567,577, Luisa Coletto25, N uria S Coll123, Emma Colucci-Guyon516, Sergio Comincini1829,
\nMaria Condello578, Katherine L Cook2073, Graham H Coombs1929, Cynthia D Cooper2076, J Mark Cooper1395,
\nIsabelle Coppens601, Maria Tiziana Corasaniti1387, Marco Corazzari485,1884, Ramon Corbalan1566,
\nElisabeth Corcelle-Termeau251, Mario D Cordero1899, Cristina Corral-Ramos1289, Olga Corti507,1109, Andrea Cossarizza1767,
\nPaola Costelli1993, Safia Costes1518, Susan L Cotman721, Ana Coto-Montes946, Sandra Cottet566,1688, Eduardo Couve1301,
\nLori R Covey1015, L Ashley Cowart762, Jeffery S Cox1536, Fraser P Coxon1427, Carolyn B Coyne1846, Mark S Cragg1919,
\nRolf J Craven1679, Tiziana Crepaldi1995, Jose L Crespo1300, Alfredo Criollo1285, Valeria Crippa558, Maria Teresa Cruz1576,
\nAna Maria Cuervo26, Jose M Cuezva1277, Taixing Cui1907, Pedro R Cutillas987, Mark J Czaja27, Maria F Czyzyk-Krzeska1572,
\nRuben K Dagda2068, Uta Dahmen1404, Chunsun Dai800, Wenjie Dai1187, Yun Dai2059, Kevin N Dalby1940,
\nLuisa Dalla Valle1822, Guillaume Dalmasso1340, Marcello D’Amelio557, Markus Damme188, Arlette Darfeuille-Michaud1340,
\nCatherine Dargemont950, Victor M Darley-Usmar1433, Srinivasan Dasarathy205, Biplab Dasgupta202, Srikanta Dash1254,
\nCrispin R Dass242, Hazel Marie Davey8, Lester M Davids1560, David D avila227, Roger J Davis1731, Ted M Dawson604,
\nValina L Dawson606, Paula Daza1898, Jackie de Belleroche470, Paul de Figueiredo1180,1182,
\nRegina Celia Bressan Queiroz de Figueiredo135, Jos e de la Fuente1023, Luisa De Martino1775,
\nAntonella De Matteis1171, Guido RY De Meyer1443, Angelo De Milito631, Mauro De Santi2002,

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%-85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors.

Although several clinical trials are now underway to test possible therapies, the worldwide response to the COVID-19 outbreak has been largely limited to monitoring/containment. We report here that Ivermectin, an FDA-approved anti-parasitic previously shown to have broad-spectrum anti-viral activity in vitro, is an inhibitor of the causative virus (SARS-CoV-2), with a single addition to Vero-hSLAM cells 2 h post infection with SARS-CoV-2 able to effect ~5000-fold reduction in viral RNA at 48 h. Ivermectin therefore warrants further investigation for possible benefits in humans.

The p53 tumor suppressor gene product can induce apoptotic cell death through an unknown mechanism. Here we demonstrate that a temperature-sensitive p53 induces temperature-dependent decreases in the expression of the apoptosis-suppressing gene bcl-2 in the murine leukemia cell M1, while simultaneously stimulating increases in the expression of bax, a gene which encodes a dominant-inhibitor of the Bcl-2 protein. Mice deficient in p53 exhibit increases in Bcl-2 and decreases in Bax protein levels in several tissues as determined by immunohistochemical and immunoblot methods. The findings suggest a potential mechanism by which p53 regulates apoptosis, as well as responses to radiation and chemotherapeutic drugs in cancer.

Another host factor for SARS-CoV-2 Virus-host interactions determine cellular entry and spreading in tissues. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the earlier SARS-CoV use angiotensin-converting enzyme 2 (ACE2) as a receptor; however, their tissue tropism differs, raising the possibility that additional host factors are involved. The spike protein of SARS-CoV-2 contains a cleavage site for the protease furin that is absent from SARS-CoV (see the Perspective by Kielian). Cantuti-Castelvetri et al. now show that neuropilin-1 (NRP1), which is known to bind furin-cleaved substrates, potentiates SARS-CoV-2 infectivity. NRP1 is abundantly expressed in the respiratory and olfactory epithelium, with highest expression in endothelial and epithelial cells. Daly et al. found that the furin-cleaved S1 fragment of the spike protein binds directly to cell surface NRP1 and blocking this interaction with a small-molecule inhibitor or monoclonal antibodies reduced viral infection in cell culture. Understanding the role of NRP1 in SARS-CoV-2 infection may suggest potential targets for future antiviral therapeutics. Science , this issue p. 856 , p. 861 ; see also p. 765

Like most organisms, plants have endogenous biological clocks that coordinate internal events with the external environment. We used high-density oligonucleotide microarrays to examine gene expression in Arabidopsis and found that 6% of the more than 8000 genes on the array exhibited circadian changes in steady-state messenger RNA levels. Clusters of circadian-regulated genes were found in pathways involved in plant responses to light and other key metabolic pathways. Computational analysis of cycling genes allowed the identification of a highly conserved promoter motif that we found to be required for circadian control of gene expression. Our study presents a comprehensive view of the temporal compartmentalization of physiological pathways by the circadian clock in a eukaryote.

Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discuss preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.

ligand competent metal ion-dependent adhesion site monoclonal antibody intracellular adhesion molecule vascular cell adhesion molecule mucosal addressin cell adhesion molecule The “integrin” terminology was applied in a 1987 review article (1.Hynes R.O. Cell. 1987; 48: 549-550Abstract Full Text PDF PubMed Scopus (3579) Google Scholar) to describe a family of structurally, immunochemically, and functionally related cell-surface heterodimeric receptors, which integrated the extracellular matrix with the intracellular cytoskeleton to mediate cell migration and adhesion. The three original β subunits (β1, β2, and β3) identified have now expanded to eight, and the number of α subunits stands at 17. These subunits interact noncovalently in a restricted manner to form more than 20 family members. The diversity of integrins is expanded further by alternative splicing, post-translational modifications, and interactions with other cell-surface and intracellular molecules (2.Green L.J. Mould A.P. Humphries M.J. Int. J. Biochem. Cell Biol. 1998; 30: 179-184Crossref PubMed Scopus (48) Google Scholar, 3.Porter J.C. Hogg N. Trends Cell Biol. 1998; 8: 390-396Abstract Full Text Full Text PDF PubMed Scopus (208) Google Scholar, 4.De Melker A.A. Sonnenberg A. Bioessays. 1999; 21: 499-509Crossref PubMed Scopus (109) Google Scholar). The number of integrins and the remarkable breadth of their cellular distribution support the statement that the phenotype of virtually every cell is uniquely influenced by its display of integrins. Over the past 13 years, more than 14,000 scientific articles have dealt with various aspects of integrin biology and almost 1,000 have appeared in theJournal of Biological Chemistry. This article examines a central aspect of integrin biology: ligand recognition and the structural basis for this function. A hallmark of the integrins is the ability of individual family members to recognize multiple ligands. Indeed, the extent of the integrin family pales in comparison with the number of their ligands. Table Isummarizes the major extracellular ligands of integrins; the listing is undoubtedly incomplete. The list includes a large number of extracellular matrix proteins (bone matrix proteins, collagens, fibronectins, fibrinogen, laminins, thrombospondins, vitronectin, and von Willebrand factor), reflecting the primary function of integrins in cell adhesion to extracellular matrices. Many “counter-receptors” are ligands, reflecting the role of integrins in mediating cell-cell interactions. Included are numerous microorganisms, which utilize integrins to gain entry into cells. There are direct and multiple linkages between integrins and host defense systems, created by their recognition of hemostatic and complement factors. The preference of any given integrin among its ligands is determined by relative affinity, availability within a specific microenvironment, and the conformational state of the ligand, which controls exposure of its integrin recognition sequence.Table IIntegrin extracellular ligandsLigandIntegrinAdenovirus penton base proteinαvβ3, αvβ5Bone sialoproteinαvβ3, αvβ5Borrelia burgdorferiαIIbβ3Candida albicansαMβ2Collagensα1β1, α2β1, α11β1, αIbβ3Denatured collagenα5β1, αvβ3, αIIbβ3Cytotactin/tenascin-Cα8β1, α9β1, αvβ3, αvβ6DecorsinαIIbβ3Disintegrinsαvβ3, αIIbβ3E cadherinαEβ7Echovirus 1α2β1Epiligrinα3β1Factor XαMβ2Fibronectinα2β1, α3β1, α4β1, α4β7, α5β1, α8β1, αvβ1, αvβ3, αvβ5, αvβ6, αvβ8, αIIbβ3Fibrinogenα5β1, αMβ2, αvβ3, αxβ2, αIIbβ3HIV Tat proteinαvβ3, αvβ5iC3bαMβ2, αxβ2ICAM-1αLβ2, αMβ2ICAM-2,3,4,5αLβ2Invasinα3β1, α4β1, α5β1, α6β1Lamininα1β1, α2β1, α6β1, α7β1, α6β4, αvβ3MAdCAM-1α4β7Matrix metalloproteinase-2αvβ3Neutrophil inhibitory factorαMβ2Osteopontinαvβ3PlasminogenαIIbβ3Prothrombinαvβ3, αIIbβ3Sperm fertilinα6β1Thrombospondinα3β1, αvβ3, αIIbβ3VCAM-1α4β1, α4β7Vitronectinαvβ1, αvβ3, αvβ5, αIIbβ3von Willebrand factorαvβ3, αIIbβ3 Open table in a new tab A primary goal of many structure-function analyses in the integrin field has been the reduction of macromolecular ligands to minimal recognition sequences. This endeavor has been highly successful, and many bioactive amino acid sequences have been teased out of large extracellular matrix proteins (5.Ruoslahti E. Annu. Rev. Cell Biol. 1996; 12: 697-715Crossref Scopus (2633) Google Scholar). The prototypic example is the RGD sequence. RGD was originally identified as the sequence in fibronectin that engages the fibronectin receptor, integrin α5β1, but now is known to serve as a recognition motif in multiple ligands for several different integrins (see Table II). Although RGD peptides inhibit ligand binding to integrins with an RGD recognition specificity (Table II), these receptors can discriminate among RGD-containing ligands. The context of the RGD sequence (flanking residues, three-dimensional presentation, and individual features of the integrin binding pockets) determine whether productive interactions occur (6.Haas T.A. Plow E.F. Curr. Opin. Cell Biol. 1994; 6: 656-662Crossref PubMed Scopus (273) Google Scholar). As an illustrative example of the nuances of the RGD recognition specificity, whereas both of the β3 integrins, αIIbβ3 and αVβ3, recognize fibrinogen, which contains multiple RGD sequences, and RGD peptides inhibit the binding of fibrinogen to these integrins, both integrins can recognize other sequences in fibrinogen (7.Yokoyama K. Zhang X.-P. Medved L. Takada Y. Biochemistry. 1999; 38: 5872-5877Crossref PubMed Scopus (75) Google Scholar, 8.Farrell D.H. Thiagarajan P. Chung D.W. Davie E.W. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 10729-10732Crossref PubMed Scopus (307) Google Scholar). Thus, recognition of this seemingly simple tripeptide sequence is complex. A second set of fibronectin sequences also has received considerable attention: those recognized by α4β1. Originally, the CS-1 sequence, which resides in an alternatively spliced segment of fibronectin, was determined to be a recognition site, but now several additional fibronectin sequences have been identified that interact with α4β1 (9.Wayner E.A. Garcia-Pardo A. Humphries M.J. McDonald J.A. Carter W.G. J. Cell Biol. 1989; 109: 1321-1330Crossref PubMed Scopus (773) Google Scholar, 10.Mould A.P. Komoriya A. Yamada K.M. Humphries M.J. J. Biol. Chem. 1991; 266: 3579-3585Abstract Full Text PDF PubMed Google Scholar, 11.Domı́nguez-Jiménez C. Sánchez-Aparicio P. Albar J.P. Garcı́a-Pardo A. Cell Adhes. Commun. 1996; 4: 251-267Crossref PubMed Scopus (18) Google Scholar). Multiple recognition sites also exist in fibrinogen for αMβ2 (12.Ugarova T.P. Solovjov D.A. Zhang L. Loukinov D.I. Yee V.C. Medved L.V. Plow E.F. J. Biol. Chem. 1998; 273: 22519-22527Abstract Full Text Full Text PDF PubMed Scopus (138) Google Scholar). Two generalizations can be derived from these examples: 1) integrin recognition specificities can often be reduced to small peptide sequences; and 2) peptide inhibition studies need to be complemented with other approaches to assess the role of specific sequences in ligand recognition by integrins.Table IIIntegrin recognition sequencesRecognition sequenceLigandIntegrinRGDAdenovirus penton base protein, bone sialoprotein, collagen, decorsin, disintegrins, fibrinogen, fibronectin, prothrombin, tenascin, thrombospondin, vitronectin, von Willebrand factorα3β1, α5β1, α8β1, αvβ1, αvβ3, αvβ5, αvβ6, αIIbβ3HHLGGAKQAGDVγ-Chain of fibrinogenαIIbβ3GPRα-Chain of fibrinogenαxβ2P1 peptideγ-Chain of fibrinogenαMβ2P2 peptideγ-Chain of fibrinogenαMβ2AEIDGIELTenascinα9β1QIDSVCAM-1α4β1LDTMAdCAM-1α4β7CS-1 peptideFibronectinα4β1, α4β7CS-5 peptideFibronectinα4β1IDAPSFibronectinα4β1ICAM peptidesICAM-1, -2, -3αLβ2, αMβ2DLXXLTenascinαvβ6GFOGER aO, hydroxyproline.Collagenα1β1, α2β1a O, hydroxyproline. Open table in a new tab Each integrin heterodimer contains 3–5 divalent cation binding sites of relatively low affinity (μm−1 to mm−1), and the bound cations exert profound effects on integrin function. Collectively, these bound divalent ions can act as effectors, promoting ligand binding; as antagonists, inhibiting ligand binding; and as selectors, changing the ligand binding specificity. One proposal to explain the influential role of cations on integrin function is that ligand and divalent cation share a common binding pocket on the integrin. This hypothesis was supported by data showing that RGD ligands could displace two receptor-bound metal ions and that divalent ion and RGD peptide could bind, in a mutually exclusive manner, a peptide from the β3 subunit (13.D'Souza S.E. Haas T.A. Piotrowicz R.S. Byers-Ward V. McGrath D.E. Soule H.R. Cierniewski C.S. Plow E.F. Smith J.W. Cell. 1994; 79: 659-667Abstract Full Text PDF PubMed Scopus (214) Google Scholar). Thus, a “displacement model” was proposed, in which RGD ligands initially form a ternary complex with receptor-bound divalent ion; then, as contacts between RGD and integrin stabilize, the divalent ion may be displaced. Recently, this model was extended to other integrins (14.Dickeson S.K. Bhattacharyya-Pakrasei M. Mathis N.L. Schlesinger P.H. Santoro S.A. Biochemistry. 1998; 37: 11280-11288Crossref PubMed Scopus (33) Google Scholar); collagen displaced Tb3+bound to the I domain of the α2 subunit. Dissection of the ligand binding reaction into ligand association and dissociation steps provided further insights into the roles of divalent ions in integrin function (15.Hu D.D. Barbas III, C.F. Smith J.W. J. Biol. Chem. 1996; 271: 21745-21751Abstract Full Text Full Text PDF PubMed Scopus (82) Google Scholar). Using surface plasmon resonance, the β3 integrins were shown to contain two classes of ion binding sites. One class must be occupied for ligand to bind, ligand-competent (LC)1 sites; and the second class has an inhibitory effect on ligand binding, I sites. The I site(s) display specificity for Ca2+ and increase the rate of ligand dissociation. Because the I sites are allosteric to the ligand binding pocket, they can bind Ca2+even when ligand is prebound to integrin, providing a potential mechanism for the release of pre-existing cell-matrix contacts. Thus, it is the coordination between the LC and I cation binding sites that regulates the ligand binding event. There are at least two structurally distinct classes of ion binding motifs within integrins. A series of EF-hand-like domains are present in each of the integrin α subunits (16.Tuckwell D.S. Brass A. Humphries M.J. Biochem. J. 1992; 285: 325-331Crossref PubMed Scopus (101) Google Scholar). The integrin EF-hand loops lack a glutamate that is found at the 12th position in virtually all other EF-hand loops and is one of the ligands for Ca2+. The absence of this residue in integrins is likely to explain their lower affinity and selectivity for divalent ions. Two studies have examined the ion and ligand binding function of recombinant fragments containing the integrin EF-hands. Gulino et al. (17.Gulino D. Boudignon C. Zhang L.Y. Concord E. Rabiet M.J. Marguerie G. J. Biol. Chem. 1992; 267: 1001-1007Abstract Full Text PDF PubMed Google Scholar) produced a fragment composed of the four EF-hand sites within the αIIbsubunit and found that it contained two affinity classes for Ca2+, which could also bind Mg2+ and Mn2+ and fibrinogen, a physiologic ligand for this integrin. These observations are generally consistent with results obtained from Ca2+ binding studies on the purified integrin (18.Rivas G.A. Gonzalez-Rodriguez J. Biochem. J. 1991; 276: 35-40Crossref PubMed Scopus (55) Google Scholar) and synthetic peptides corresponding to the individual loops of each EF-hand (19.Cierniewski C.S. Haas T.A. Smith J.W. Plow E.F. Biochemistry. 1994; 33: 12238-12246Crossref PubMed Scopus (37) Google Scholar). The EF-hand domains of the α5 integrin also contain two affinity classes of ion binding sites and can bind fibronectin and RGD peptides (20.Baneres J.L. Roquet F. Green M. LeCalvez H. Parello J. J. Biol. Chem. 1998; 273: 24744-24753Abstract Full Text Full Text PDF PubMed Scopus (36) Google Scholar). All four EF-hands were required for ligand binding, even though each pair of EF-hands was able to bind divalent ion. The second type of cation binding site in integrins is a metal ion-dependent adhesion site (MIDAS) motif. The first evidence for a unique cation binding motif came from mutagenesis studies of the I domain of the αM subunit (21.Michishita M. Videm V. Arnaout M.A. Cell. 1993; 72: 857-867Abstract Full Text PDF PubMed Scopus (346) Google Scholar). Soon thereafter, the I domain of the αM subunit and other integrin α subunits were crystallized (22.Lee J.-O. Rieu P. Arnaout M.A. Liddington R. Cell. 1995; 80: 631-638Abstract Full Text PDF PubMed Scopus (816) Google Scholar, 23.Qu A. Leahy D.J. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 10277-10281Crossref PubMed Scopus (291) Google Scholar, 24.Emsley J. King S.L. Bergelson J.M. Liddington R.C. J. Biol. Chem. 1997; 272: 28512-28517Abstract Full Text Full Text PDF PubMed Scopus (262) Google Scholar). In Fig.1, the crystal structures of two I domains are displayed with the MIDAS motif at their upper surface. Within the MIDAS motif, five separate residues coordinate the divalent ion. The first three are closely spaced within a DXSXS motif; the fourth is a threonine separated from the DXSXS in the primary structure by ∼70 residues; and the fifth coordinating ligand is an aspartate about 100 residues downstream of the DXSXS. In the crystal structure, two of the αMI domains were linked via a Mg2+ ion in the MIDAS motif, and a glutamate from one I domain donated a sixth coordinating ligand to the Mg2+bound in an adjacent I domain. This quirk in the crystal structure provided evidence that metal ion bound to the MIDAS can ligand with carboxylates donated from another protein, consistent with the cation displacement model. Indeed, this finding has prompted the hypothesis that such a structure is a snapshot of I domain bound with “ligand” and led to the prevailing notion that integrins bind to their ligands by “grabbing an Asp” (25.Bergelson J.M. Hemler M.E. Curr. Biol. 1995; 5: 615-617Abstract Full Text Full Text PDF PubMed Scopus (53) Google Scholar). All integrin β subunits may contain an ion binding site homologous to a MIDAS motif. This proposition stems from early work showing that a naturally occurring mutation of Y119D in integrin αIIbβ3 led to a receptor with abnormal ligand and cation binding functions (26.Loftus J.C. O'Toole T.E. Plow E.F. Glass A. Frelinger A.L. Ginsberg M.H. Science. 1990; 249: 915-918Crossref PubMed Scopus (390) Google Scholar), and it was proposed that this residue was part of an EF-hand. In retrospect, this ion binding site is more likely to be a MIDAS motif with Asp-119 being the first residue of the DXSXS motif. of any of these residues within the β2, subunits ligand binding to integrins McDonald S. Smith J.W. J. Biol. Chem. 1997; 272: Full Text Full Text PDF PubMed Scopus Google and Takada Y. J. Biol. Chem. 1996; 271: Full Text Full Text PDF PubMed Scopus Google Scholar). Although the DXSXS motif to ligand with the residues that the fourth and fifth coordinating ligands in the β subunit MIDAS and McDonald S. Smith J.W. J. Biol. Chem. 1997; 272: Full Text Full Text PDF PubMed Scopus Google Scholar, Takada Y. J. Biol. Chem. 1996; 271: Full Text Full Text PDF PubMed Scopus Google Scholar, Liddington R.C. M.J. J.C. J. Biol. Chem. 1996; 271: Full Text Full Text PDF PubMed Scopus Google Scholar). The three-dimensional structure of a β subunit may be for is structural to the I Ca2+ binding site that is found on integrins. All of the ion binding sites that have been the EF-hand sites in the α subunits and the MIDAS motifs in the β to ion binding, are LC sites (15.Hu D.D. Barbas III, C.F. Smith J.W. J. Biol. Chem. 1996; 271: 21745-21751Abstract Full Text Full Text PDF PubMed Scopus (82) Google Scholar, McDonald S. Smith J.W. J. Biol. Chem. 1997; 272: Full Text Full Text PDF PubMed Scopus Google Scholar, D.D. S. N. Smith J.W. J. Biol. Chem. 1999; Full Text Full Text PDF PubMed Scopus Google Scholar). One of the more the of this I site is that the ion binding site within the integrin β subunits can into an EF-hand a MIDAS domain. may act as a MIDAS when Mn2+ but Ca2+ could an EF-hand the of divalent ions on cell adhesion and ligand binding to integrins, on the physiologic role of the ion binding sites is One is physiologic is the adhesion of The to the bone surface J. D. S.L. D.A. J. Biol. Chem. 1993; Full Text PDF PubMed Google Scholar). to the bone surface must be to as bone is the of Ca2+ the and and of This effect may be by the allosteric I Ca2+ binding site on the of Ca2+ and Mg2+ is in the of J. 1995; PubMed Scopus Google Scholar). the the of Mg2+ and the of from the of to Because Mg2+ generally cell adhesion and Ca2+ is generally this increase in may be the ion binding sites also may a role in integrin Mn2+ the of multiple integrins for their ligands. Mn2+ to MIDAS and two of the MIDAS can be by the manner in which the bound metal is J.-O. Arnaout M.A. Liddington R.C. 1995; Full Text Full Text PDF PubMed Scopus Google Scholar, R. Rieu P. D. Arnaout M.A. J. Cell Biol. 1998; PubMed Scopus Google Scholar). Thus, Mn2+ could structural in the I which in hypothesis that is by the binding of Ca2+ to the allosteric I of this site by Ca2+ the integrin in a The of four different integrin receptors, αMβ2 and These integrins are in virtually every aspect of the adhesion to and the of and The of the integrins is by the of these integrins to (see G.A. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar, and of and to and Recently, it has to the function of individual integrin receptors in in αMβ2 and The integrins are the of a separate review in this The on their I domains and their role in ligand The α subunits of all integrins contain of amino the I A domain. I domains are found in several other integrin α subunits and other proteins, such as and complement I domains mediate and in integrins, they are in the binding of ligands (14.Dickeson S.K. Bhattacharyya-Pakrasei M. Mathis N.L. Schlesinger P.H. Santoro S.A. Biochemistry. 1998; 37: 11280-11288Crossref PubMed Scopus (33) Google Scholar, J.-O. Rieu P. Arnaout M.A. Liddington R. Cell. 1995; 80: 631-638Abstract Full Text PDF PubMed Scopus (816) Google Scholar, Hogg N. J. Biol. Chem. 1994; Full Text PDF PubMed Google Scholar). I those in integrin α can be as recombinant and can bind ligands. though I domains are highly homologous to each they are highly for of ligands. the a I domain can recognize multiple and structurally ligands (see ligand of αMβ2 in Table Thus, it is the individual amino acid within the highly structural of the I domains that ligand specificity. The crystal structures of several integrin and I domains have now been J.-O. Rieu P. Arnaout M.A. Liddington R. Cell. 1995; 80: 631-638Abstract Full Text PDF PubMed Scopus (816) Google Scholar, 23.Qu A. Leahy D.J. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 10277-10281Crossref PubMed Scopus (291) Google Scholar, 24.Emsley J. King S.L. Bergelson J.M. Liddington R.C. J. Biol. Chem. 1997; 272: 28512-28517Abstract Full Text Full Text PDF PubMed Scopus (262) Google Scholar). Each of five β by α which are by loops (see The I domains of the integrins contain the cation binding MIDAS motif. In the I domains of αMβ2 and the binding for several ligands has been to the upper in to the bound cation R. Rieu P. D. Arnaout M.A. J. Cell Biol. 1998; PubMed Scopus Google Scholar, L. Plow E.F. J. Biol. Chem. 1997; 272: Full Text Full Text PDF PubMed Scopus Google Scholar). in other of the I domains the I domains can exert allosteric on ligand binding R. Rieu P. D. Arnaout M.A. J. Cell Biol. 1998; PubMed Scopus Google Scholar, L. Plow E.F. J. Biol. Chem. 1996; 271: Full Text Full Text PDF PubMed Scopus (48) Google Scholar, C. C. T.A. Proc. Natl. Acad. Sci. U. S. A. 1999; PubMed Scopus Google Scholar). Although the I domains the ligand binding functions of their integrins, other of the α subunits ligand As in αMβ2 a an the I domain but in the αM subunit ligand binding V. M. R.C. J. 1996; Google Scholar); and the EF-hand in and α2β1, integrins with I domains in their α to ligand recognition P. J. Hogg N. J. 1994; PubMed Scopus Google Scholar, S.K. Santoro S.A. J. Biol. Chem. 1997; 272: Full Text Full Text PDF PubMed Scopus Google Scholar). The αM and other α contains a which is in of ligands, and may the function of the I domain V. J. 1996; PubMed Scopus Google Scholar). The role of the β subunit in ligand binding to the integrins is the of the β subunit in ligand recognition has been and mutagenesis S.L. J. Biol. Chem. 1995; Full Text Full Text PDF PubMed Scopus Google Scholar), its direct in ligand has to be in the which ligand binding, may exert effect on ligand binding Plow E.F. Zhang L. J. 1998; Google Scholar). The central role that in has on αIIbβ3 recognition sequences within its ligands and the ligand within the Many of the insights from these studies to the several of the and both β3 integrins share a RGD recognition specificity. A second recognition specificity of to the function of αIIbβ3 is the of the fibrinogen M. S. J. Biochem. Commun. PubMed Scopus Google Scholar). Each sequence contains an acid that is for an with receptor-bound cation (26.Loftus J.C. O'Toole T.E. Plow E.F. Glass A. Frelinger A.L. Ginsberg M.H. Science. 1990; 249: 915-918Crossref PubMed Scopus (390) Google Scholar). The two recognition peptides inhibit the binding of each other to αIIbβ3 but may bind to separate but linked sites D.D. S. N. Smith J.W. J. Biol. Chem. 1999; Full Text Full Text PDF PubMed Scopus Google Scholar, C.S. M. Haas T.A. J. Zhang L. M. Plow E.F. J. Biol. Chem. 1999; Full Text Full Text PDF PubMed Scopus Google Scholar). data have the of potential ligand sites within the of inhibitory of and the of recombinant of αIIbβ3 have that the minimal ligand binding fragment contains the of each subunit J.C. Smith J.W. Ginsberg M.H. J. Biol. Chem. 1994; Full Text PDF PubMed Google Scholar). The specificity of αIIbβ3 for ligands was to the residues of J.C. Ginsberg M.H. J.A. Smith J.W. J. Biol. Chem. 1996; 271: Full Text Full Text PDF PubMed Scopus Google Scholar). studies have the of ligand in the of S.E. Ginsberg M.H. T.A. Plow E.F. J. Biol. Chem. 1990; Full Text PDF PubMed Google Scholar) and S.A. Cell. 1987; 48: Full Text PDF PubMed Scopus Google Scholar, S.E. Ginsberg M.H. Plow E.F. J. Biol. Chem. Full Text PDF PubMed Google Scholar), and it is likely that binding of macromolecular ligands to αIIbβ3 multiple contacts in each subunit. residues identified to can be into two major 1) the highly residues of the amino in and 2) the of Two within β3 to the ligand binding function of the RGD peptides to a of β3 by to S.E. Ginsberg M.H. Plow E.F. J. Biol. Chem. Full Text PDF PubMed Google Scholar). of β3 to was identified by of RGD peptides to J.W. D.A. J. Biol. Chem. Full Text PDF PubMed Google Scholar). As a naturally occurring mutation in this results in of ligand binding function (26.Loftus J.C. O'Toole T.E. Plow E.F. Glass A. Frelinger A.L. Ginsberg M.H. Science. 1990; 249: 915-918Crossref PubMed Scopus (390) Google Scholar), as at residues in this G. M. 1997; PubMed Google Scholar). The second potential ligand site in β3 is by residues to corresponding to this sequence and these peptides inhibit fibrinogen binding L. M.A. J. Biol. Chem. 1991; 266: Full Text PDF PubMed Google Scholar) as at β3 Ginsberg M.H. Frelinger III, A.L. J.C. J. Biol. Chem. 1992; 267: Full Text PDF PubMed Google Scholar, F. A. D. M. G. J. 1992; 89: PubMed Google Scholar). The of these two of β3 is likely of their in the of a MIDAS motif (21.Michishita M. Videm V. Arnaout M.A. Cell. 1993; 72: 857-867Abstract Full Text PDF PubMed Scopus (346) Google Scholar, J.-O. Rieu P. Arnaout M.A. Liddington R. Cell. 1995; 80: 631-638Abstract Full Text PDF PubMed Scopus (816) Google Scholar) as it as to whether this of β3 an I domain McDonald S. Smith J.W. J. Biol. Chem. 1997; 272: Full Text Full Text PDF PubMed Scopus Google Scholar, Liddington R.C. M.J. J.C. J. Biol. Chem. 1996; 271: Full Text Full Text PDF PubMed Scopus Google Scholar). the two of β3 are in cation binding, they also may direct sites for and recombinant fragments of β3 bind fibrinogen and and RGD peptides C.S. M. Haas T.A. J. Zhang L. M. Plow E.F. J. Biol. Chem. 1999; Full Text Full Text PDF PubMed Scopus Google Scholar, M. Concord E. J. M. A. Marguerie G. Gulino D. 1996; PubMed Google Scholar). of the ligand contacts in have a role for its As a recombinant fragment of containing the four EF-hand-like sequences fibrinogen in a and manner (17.Gulino D. Boudignon C. Zhang L.Y. Concord E. Rabiet M.J. Marguerie G. J. Biol. Chem. 1992; 267: 1001-1007Abstract Full Text PDF PubMed Google Scholar). This of has been further in ligand binding ligand peptides within the second cation binding S.E. Ginsberg M.H. T.A. Plow E.F. J. Biol. Chem. 1990; Full Text PDF PubMed Google Scholar). from this inhibit fibrinogen binding to αIIbβ3 and bind fibrinogen in a manner S.E. Ginsberg M.H. Plow E.F. 1991; PubMed Scopus Google Scholar, J. Biol. Chem. 1992; 267: Full Text PDF PubMed Google Scholar). these data a of the cation binding domains in ligand interactions. a form of to which contain any of the divalent cation with β3 and recognized ligand D.S. S. D. J. Biol. Chem. 1996; 271: Full Text Full Text PDF PubMed Scopus Google Scholar). have been at a structural model of integrin α A model that the the of a domain T.A. Proc. Natl. Acad. Sci. U. S. A. 1997; PubMed Scopus Google Scholar). These domains contain in a a with known have their sites at the of the adjacent loops in with this the to in one and in a second both to be at the of the have been in ligand binding by mutagenesis A. M. Takada Y. J. Biol. Chem. 1996; 271: Full Text Full Text PDF PubMed Scopus Google Scholar, Ginsberg M.H. J.C. 1999; PubMed Google Scholar). The of residues for ligand binding to α4β1 and the model Takada Y. Biochem. J. 1995; PubMed Scopus Google Scholar, A.P. L. Humphries M.J. J. Biol. Chem. 1998; 273: Full Text Full Text PDF PubMed Scopus Google Scholar). this model to the data the direct of the and α5 cation binding motifs in ligand The model these motifs on the lower surface of the from the ligand on the upper surface of the The data that the ligand binding pocket of of both the and β3 subunits and is consistent with the that binding of macromolecular ligands multiple in the model 2) is that αIIbβ3 has at least two distinct ligand binding domains that are linked and αIIbβ3 conformational and ligand it be to these the individual ligand binding domains as as these the manner in which the and each other to a structural basis for ligand binding to

A new connective tissue protein, which we call fibrillin, has been isolated from the medium of human fibroblast cell cultures. Electrophoresis of the disulfide bond-reduced protein gave a single band with an estimated molecular mass of 350,000 D. This 350-kD protein appeared to possess intrachain disulfide bonds. It could be stained with periodic acid-Schiff reagent, and after metabolic labeling, it contained [3H]glucosamine. It could not be labeled with [35S]sulfate. It was resistant to digestion by bacterial collagenase. Using mAbs specific for fibrillin, we demonstrated its widespread distribution in the connective tissue matrices of skin, lung, kidney, vasculature, cartilage, tendon, muscle, cornea, and ciliary zonule. Electron microscopic immunolocalization with colloidal gold conjugates specified its location to a class of extracellular structural elements described as microfibrils. These microfibrils possessed a characteristic appearance and averaged 10 nm in diameter. Microfibrils around the amorphous cores of the elastic fiber system as well as bundles of microfibrils without elastin cores were labeled equally well with antibody. Immunolocalization suggested that fibrillin is arrayed periodically along the individual microfibril and that individual microfibrils may be aligned within bundles. The periodicity of the epitope appeared to match the interstitial collagen band periodicity. In contrast, type VI collagen, which has been proposed as a possible microfibrillar component, was immunolocalized with a specific mAb to small diameter microfilaments that interweave among the large, banded collagen fibers; it was not associated with the system of microfibrils identified by the presence of fibrillin.

Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.

ISSN:0959-6658

Alzheimer's disease (AD) is the most common neurodegenerative disorder seen in age-dependent dementia. There is currently no effective treatment for AD, which may be attributed in part to lack of a clear underlying mechanism. Studies within the last few decades provide growing evidence for a central role of amyloid β (Aβ) and tau, as well as glial contributions to various molecular and cellular pathways in AD pathogenesis. Herein, we review recent progress with respect to Aβ- and tau-associated mechanisms, and discuss glial dysfunction in AD with emphasis on neuronal and glial receptors that mediate Aβ-induced toxicity. We also discuss other critical factors that may affect AD pathogenesis, including genetics, aging, variables related to environment, lifestyle habits, and describe the potential role of apolipoprotein E (APOE), viral and bacterial infection, sleep, and microbiota. Although we have gained much towards understanding various aspects underlying this devastating neurodegenerative disorder, greater commitment towards research in molecular mechanism, diagnostics and treatment will be needed in future AD research.

Mitochondrial apoptosis is mediated by BAK and BAX, two proteins that induce mitochondrial outer membrane permeabilization, leading to cytochrome c release and activation of apoptotic caspases. In the absence of active caspases, mitochondrial DNA (mtDNA) triggers the innate immune cGAS/STING pathway, causing dying cells to secrete type I interferon. How cGAS gains access to mtDNA remains unclear. We used live-cell lattice light-sheet microscopy to examine the mitochondrial network in mouse embryonic fibroblasts. We found that after BAK/BAX activation and cytochrome c loss, the mitochondrial network broke down and large BAK/BAX pores appeared in the outer membrane. These BAK/BAX macropores allowed the inner mitochondrial membrane to herniate into the cytosol, carrying with it mitochondrial matrix components, including the mitochondrial genome. Apoptotic caspases did not prevent herniation but dismantled the dying cell to suppress mtDNA-induced innate immune signaling.

These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.

and the cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825 and ONO 5334. Notably, MDL-28170, ONO 5334 and apilimod were found to antagonize viral replication in human pneumocyte-like cells derived from induced pluripotent stem cells, and apilimod also demonstrated antiviral efficacy in a primary human lung explant model. Since most of the molecules identified in this study have already advanced into the clinic, their known pharmacological and human safety profiles will enable accelerated preclinical and clinical evaluation of these drugs for the treatment of COVID-19.

One mechanism contributing to immunologic unresponsiveness toward tumors may be presentation of tumor antigens by tolerogenic host APCs. We show that mouse tumor-draining LNs (TDLNs) contained a subset of plasmacytoid DCs (pDCs) that constitutively expressed immunosuppressive levels of the enzyme indoleamine 2,3-dioxygenase (IDO). Despite comprising only 0.5% of LN cells, these pDCs in vitro potently suppressed T cell responses to antigens presented by the pDCs themselves and also, in a dominant fashion, suppressed T cell responses to third-party antigens presented by nonsuppressive APCs. Adoptive transfer of DCs from TDLNs into naive hosts created profound local T cell anergy, specifically toward antigens expressed by the transferred DCs. Anergy was prevented by targeted disruption of the IDO gene in the DCs or by administration of the IDO inhibitor drug 1-methyl-D-tryptophan to recipient mice. Within the population of pDCs, the majority of the functional IDO-mediated suppressor activity segregated with a novel subset of pDCs coexpressing the B-lineage marker CD19. We hypothesize that IDO-mediated suppression by pDCs in TDLNs creates a local microenvironment that is potently suppressive of host antitumor T cell responses.

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae , that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type–related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.