MGH Center for Systems Biology

Ferraro B, Leoni G, Hinkel R, Ormanns S, Paulin N, Ortega-Gomez A, Viola JR, de Jong R, Bongiovanni D, Bozoglu T, Maas SL, D'Amico M, Kessler T, Zeller T, Hristov M, Reutelingsperger C, Sager HB, Döring Y, Nahrendorf M, Kupatt C, Soehnlein O

Pro-Angiogenic Macrophage Phenotype to Promote Myocardial Repair.

J Am Coll Cardiol. 2019;73(23):2990-3002 - PMID: 31196457 - DOI: 10.1016/j.jacc.2019.03.503

Tawakol A, Osborne MT, Wang Y, Hammed B, Tung B, Patrich T, Oberfeld B, Ishai A, Shin LM, Nahrendorf M, Warner ET, Wasfy J, Fayad ZA, Koenen K, Ridker PM, Pitman RK, Armstrong KA

Stress-Associated Neurobiological Pathway Linking Socioeconomic Disparities to Cardiovascular Disease.

J Am Coll Cardiol. 2019;73(25):3243-3255 - PMID: 31248544 - PMCID: PMC6767929 - DOI: 10.1016/j.jacc.2019.04.042

Libby P, Swirski FK, Nahrendorf M

The Myocardium: More Than Myocytes.

J Am Coll Cardiol. 2019;74(25):3136-3138 - PMID: 31856970 - DOI: 10.1016/j.jacc.2019.10.031

Cremer S, Schloss MJ, Vinegoni C, Foy BH, Zhang S, Rohde D, Hulsmans M, Fumene Feruglio P, Schmidt S, Wojtkiewicz G, Higgins JM, Weissleder R, Swirski FK, Nahrendorf M

Diminished Reactive Hematopoiesis and Cardiac Inflammation in a Mouse Model of Recurrent Myocardial Infarction.

J Am Coll Cardiol. 2020;75(8):901-915 - PMID: 32130926 - PMCID: PMC7254576 - DOI: 10.1016/j.jacc.2019.12.056

Nahrendorf M

Innate Lymphoid Cells Participate in Myocardial Inflammation After Ischemia.

J Am Coll Cardiol. 2021;78(11):1143-1144 - PMID: 34503683 - DOI: 10.1016/j.jacc.2021.07.013

Aguirre AD, Arbab-Zadeh A, Soeda T, Fuster V, Jang IK

Optical Coherence Tomography of Plaque Vulnerability and Rupture: JACC Focus Seminar Part 1/3.

J Am Coll Cardiol. 2021;78(12):1257-1265 - PMID: 34531027 - PMCID: PMC9851427 - DOI: 10.1016/j.jacc.2021.06.050

Atri M, Zhang Z, Marques H, Gorelick J, Harisinghani M, Sohaib A, Koh D, Raman S, Gee MS, Choi H, Landrum LM, Mannel RS, Chuang LT, Yu JQ, McCourt CK, Gold M,

Utility of preoperative ferumoxtran-10 enhanced MRI to evaluate retroperitoneal lymph node metastasis in advanced cervical cancer: Results of ACRIN 6671/GOG 0233.

J Clin Oncol. 2011;29(15_suppl):5035 - PMID: 28023716

Gold M, Zhang Z, Marques H, Gorelick J, Landrum LM, Mannel RS, Chuang LT, Yu JQ, McCourt CK, Harisinghani M, Sohaib A, Koh D, Raman S, Gee MS, Choi H, Atri M

MRI prior to systematic lymphadenectomy in patients with locally advanced cervical cancer.

J Clin Oncol. 2011;29(15_suppl):5042 - PMID: 28023697

Santo L, Hideshima T, Kung AL, Yang M, Tamang D, Jarpe M, van Duzer JH, Mazitschek R, Cirstea D, Patel K, Tseng J, Rodig S, Pozzi S, Bradner J, Anderson KC, Jones SS, Raje NS

The effect of selective inhibition of HDAC6 with ACY1215 on bortezomib activity in multiple myeloma (MM).

J Clin Oncol. 2011;29(15_suppl):e18569 - PMID: 28023028

D'Souza G, Gross ND, Pai SI, Haddad R, Anderson KS, Rajan S, Gerber J, Gillison ML, Posner MR

Oral human papillomavirus (HPV) infection in HPV-positive patients with oropharyngeal cancer and their partners.

J Clin Oncol. 2014;32(23):2408-15 - PMID: 24778397 - PMCID: PMC4263818 - DOI: 10.1200/JCO.2014.55.1341

Ashida N, Senbanerjee S, Kodama S, Foo SY, Coggins M, Spencer JA, Zamiri P, Shen D, Li L, Sciuto T, Dvorak A, Gerszten RE, Lin CP, Karin M, Rosenzweig A

IKKb regulates essential functions of the vascular endothelium through kinase-dependent and -independent pathways.

Nat Commun. 2011;2:318 - PMID: 21587235 - PMCID: PMC3113230 - DOI: 10.1038/ncomms1317

Shi P, Scott MA, Ghosh B, Wan D, Wissner-Gross Z, Mazitschek R, Haggarty SJ, Yanik MF

Synapse microarray identification of small molecules that enhance synaptogenesis.

Nat Commun. 2011;2:510 - PMID: 22027590 - PMCID: PMC3544154 - DOI: 10.1038/ncomms1518

Lee S, Vinegoni C, Feruglio PF, Fexon L, Gorbatov R, Pivovarov M, Sbarbati A, Nahrendorf M, Weissleder R

Real-time in vivo imaging of the beating mouse heart at microscopic resolution

Nat Commun. 2012;3:1054 - PMID: 22968700 - PMCID: PMC3622400 - DOI: 10.1038/ncomms2060

Thurber GM, Yang KS, Reiner T, Kohler RH, Sorger P, Mitchison T, Weissleder R

Single-cell and subcellular pharmacokinetic imaging allows insight into drug action in vivo.

Nat Commun. 2013;4:1504 - PMID: 23422672 - PMCID: PMC3579506 - DOI: 10.1038/ncomms2506

Liong M, Hoang AN, Chung J, Gural N, Ford CB, Min C, Shah RR, Ahmad R, Fernandez-Suarez M, Fortune SM, Toner M, Lee H*, Weissleder R*

Magnetic barcode assay for genetic detection of pathogens

Nat Commun. 2013;4:1752 - PMID: 23612293 - PMCID: PMC3635151 - DOI: 10.1038/ncomms2745

Gurkar AU, Chu K, Raj L, Bouley R, Lee SH, Kim YB, Dunn SE, Mandinova A, Lee SW

Identification of ROCK1 kinase as a critical regulator of Beclin1-mediated autophagy during metabolic stress.

Nat Commun. 2013;4:2189 - PMID: 23877263 - PMCID: PMC3740589 - DOI: 10.1038/ncomms3189

Ageta-Ishihara N, Miyata T, Ohshima C, Watanabe M, Sato Y, Hamamura Y, Higashiyama T, Mazitschek R, Bito H, Kinoshita M

Septins promote dendrite and axon development by negatively regulating microtubule stability via HDAC6-mediated deacetylation.

Nat Commun. 2013;4:2532 - PMID: 24113571 - PMCID: PMC3826633 - DOI: 10.1038/ncomms3532

Duivenvoorden R, Tang J, Cormode DP, Mieszawska AJ, Izquierdo-Garcia D, Ozcan C, Otten MJ, Zaidi N, Lobatto ME, van Rijs SM, Priem B, Kuan EL, Martel C, Hewing B, Sager H, Nahrendorf M, Randolph GJ, Stroes ES, Fuster V, Fisher EA, Fayad ZA, Mulder WJ

A statin-loaded reconstituted high-density lipoprotein nanoparticle inhibits atherosclerotic plaque inflammation.

Nat Commun. 2014;5:3065 - PMID: 24445279 - PMCID: PMC4001802 - DOI: 10.1038/ncomms4065

Dubach JM, Vinegoni C, Mazitschek R, Fumene Feruglio P, Cameron LA, Weissleder R

In vivo imaging of specific drug-target binding at subcellular resolution.

Nat Commun. 2014;5:3946 - PMID: 24867710 - PMCID: PMC4362617 - DOI: 10.1038/ncomms4946

Lee SK, Mortensen LJ, Lin CP, Tung CH

An authentic imaging probe to track cell fate from beginning to end.

Nat Commun. 2014;5:5216 - PMID: 25323442 - PMCID: PMC4852472 - DOI: 10.1038/ncomms6216

Shen K, Luk S, Hicks DF, Elman JS, Bohr S, Iwamoto Y, Murray R, Pena K, Wang F, Seker E, Weissleder R, Yarmush ML, Toner M, Sgroi D, Parekkadan B

Resolving cancer-stroma interfacial signalling and interventions with micropatterned tumour-stromal assays.

Nat Commun. 2014;5:5662 - PMID: 25489927 - PMCID: PMC4261930 - DOI: 10.1038/ncomms6662

Shao H, Chung J, Lee K, Balaj L, Min C, Carter BS, Hochberg FH, Breakefield XO, Lee H*, Weissleder R*

Chip-based analysis of exosomal mRNA mediating drug resistance in glioblastoma

Nat Commun. 2015;6:6999 - PMID: 25959588 - PMCID: PMC4430127 - DOI: 10.1038/ncomms7999

Lai CP, Kim EY, Badr CE, Weissleder R, Mempel TR, Tannous BA, Breakefield XO

Visualization and tracking of tumour extracellular vesicle delivery and RNA translation using multiplexed reporters.

Nat Commun. 2015;6:7029 - PMID: 25967391 - PMCID: PMC4435621 - DOI: 10.1038/ncomms8029

Miller MA, Zheng YR, Gadde S, Pfirschke C, Zope H, Engblom C, Kohler RH, Iwamoto Y, Yang KS, Askevold B, Kolishetti N, Pittet M, Lippard SJ, Farokhzad OC, Weissleder R

Tumour-associated macrophages act as a slow-release reservoir of nano-therapeutic Pt(IV) pro-drug.

Nat Commun. 2015;6:8692 - PMID: 26503691 - PMCID: PMC4711745 - DOI: 10.1038/ncomms9692

Signore S, Sorrentino A, Borghetti G, Cannata A, Meo M, Zhou Y, Kannappan R, Pasqualini F, O'Malley H, Sundman M, Tsigkas N, Zhang E, Arranto C, Mangiaracina C, Isobe K, Sena BF, Kim J, Goichberg P, Nahrendorf M, Isom LL, Leri A, Anversa P, Rota M

Late Na(+) current and protracted electrical recovery are critical determinants of the aging myopathy.

Nat Commun. 2015;6:8803 - PMID: 26541940 - PMCID: PMC4638135 - DOI: 10.1038/ncomms9803

Roy J*, Kim B*, Hill E, Visconti P, Krapf D, Vinegoni C, Weissleder R, Brown D, Breton S

Tyrosine kinase-mediated axial motility of basal cells revealed by intravital imaging.

Nat Commun. 2016;7:10666 - PMID: 26868824 - PMCID: PMC4754344 - DOI: 10.1038/ncomms10666

Vinegoni C, Leon Swisher C, Fumene Feruglio P, Giedt RJ, Rousso DL, Stapleton S, Weissleder R

Real-time high dynamic range laser scanning microscopy.

Nat Commun. 2016;7:11077 - PMID: 27032979 - PMCID: PMC4821995 - DOI: 10.1038/ncomms11077

Aryal B, Rotllan N, Araldi E, Ramírez CM, He S, Chousterman BG, Fenn AM, Wanschel A, Madrigal-Matute J, Warrier N, Martín-Ventura JL, Swirski FK, Suárez Y, Fernández-Hernando C

ANGPTL4 deficiency in haematopoietic cells promotes monocyte expansion and atherosclerosis progression.

Nat Commun. 2016;7:12313 - PMID: 27460411 - PMCID: PMC4974469 - DOI: 10.1038/ncomms12313

Keliher EJ, Ye YX, Wojtkiewicz GR, Aguirre AD, Tricot B, Senders ML, Groenen H, Fay F, Perez-Medina C, Calcagno C, Carlucci G, Reiner T, Sun Y, Courties G, Iwamoto Y, Kim HY, Wang C, Chen JW, Swirski FK, Wey HY, Hooker J, Fayad ZA, Mulder WJ, Weissleder R, Nahrendorf M

Polyglucose nanoparticles with renal elimination and macrophage avidity facilitate PET imaging in ischaemic heart disease.

Nat Commun. 2017;8:14064 - PMID: 28091604 - PMCID: PMC5241815 - DOI: 10.1038/ncomms14064

Cuccarese MF, Dubach JM, Pfirschke C, Engblom C, Garris C, Miller MA, Pittet MJ, Weissleder R

Heterogeneity of macrophage infiltration and therapeutic response in lung carcinoma revealed by 3D organ imaging.

Nat Commun. 2017;8:14293 - PMID: 28176769 - PMCID: PMC5309815 - DOI: 10.1038/ncomms14293

Schlomann U, Koller G, Conrad C, Ferdous T, Golfi P, Garcia AM, Höfling S, Parsons M, Costa P, Soper R, Bossard M, Hagemann T, Roshani R, Sewald N, Ketchem RR, Moss ML, Rasmussen FH, Miller MA, Lauffenburger DA, Tuveson DA, Nimsky C, Bartsch JW

ADAM8 as a drug target in pancreatic cancer.

Nat Commun. 2015;6:6175 - PMID: 25629724 - PMCID: PMC5014123 - DOI: 10.1038/ncomms7175

Walsh RM, Shen EY, Bagot RC, Anselmo A, Jiang Y, Javidfar B, Wojtkiewicz GJ, Cloutier J, Chen JW, Sadreyev R, Nestler EJ, Akbarian S, Hochedlinger K

Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice.

Nat Commun. 2017;8:15142 - PMID: 28485378 - PMCID: PMC5436068 - DOI: 10.1038/ncomms15142

Chen X, Park HR, Pelton M, Piao X, Lindquist NC, Im H, Kim YJ, Ahn JS, Ahn KJ, Park N, Kim DS, Oh SH

Atomic layer lithography of wafer-scale nanogap arrays for extreme confinement of electromagnetic waves.

Nat Commun. 2013;4:2361 - PMID: 23999053 - DOI: 10.1038/ncomms3361

Miller MA, Askevold B, Mikula H, Kohler RH, Pirovich D, Weissleder R

Nano-palladium is a cellular catalyst for in vivo chemistry

Nat Commun. 2017;8:15906 - PMID: 28699627 - PMCID: PMC5510178 - DOI: 10.1038/ncomms15906

Ingram JR, Dougan M, Rashidian M, Knoll M, Keliher EJ, Garrett S, Garforth S, Blomberg OS, Espinosa C, Bhan A, Almo SC, Weissleder R, Lodish H, Dougan SK, Ploegh HL

PD-L1 is an activation-independent marker of brown adipocytes.

Nat Commun. 2017;8(1):647 - PMID: 28935898 - PMCID: PMC5608754 - DOI: 10.1038/s41467-017-00799-8

Kitano K, Schwartz DM, Zhou H, Gilpin SE, Wojtkiewicz GR, Ren X, Sommer CA, Capilla AV, Mathisen DJ, Goldstein AM, Mostoslavsky G, Ott HC

Bioengineering of functional human induced pluripotent stem cell-derived intestinal grafts.

Nat Commun. 2017;8(1):765 - PMID: 29018244 - PMCID: PMC5635127 - DOI: 10.1038/s41467-017-00779-y

Shao L, Chang J, Feng W, Wang X, Williamson EA, Li Y, Schajnovitz A, Scadden D, Mortensen LJ, Lin CP, Li L, Paulson A, Downing J, Zhou D, Hromas RA

The Wave2 scaffold Hem-1 is required for transition of fetal liver hematopoiesis to bone marrow.

Nat Commun. 2018;9(1):2377 - PMID: 29915352 - PMCID: PMC6006146 - DOI: 10.1038/s41467-018-04716-5

Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW

Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq.

Nat Commun. 2018;9(1):3588 - PMID: 30181541 - PMCID: PMC6123496 - DOI: 10.1038/s41467-018-06052-0

Giedt RJ, Pathania D, Carlson JCT, McFarland PJ, Del Castillo AF, Juric D, Weissleder R

Single-cell barcode analysis provides a rapid readout of cellular signaling pathways in clinical specimens

Nat Commun. 2018;9(1):4550 - PMID: 30382095 - PMCID: PMC6208406 - DOI: 10.1038/s41467-018-07002-6

Liu P, Zhao L, Pol J, Levesque S, Petrazzuolo A, Pfirschke C, Engblom C, Rickelt S, Yamazaki T, Iribarren K, Senovilla L, Bezu L, Vacchelli E, Sica V, Melis A, Martin T, Xia L, Yang H, Li Q, Chen J, Durand S, Aprahamian F, Lefevre D, Broutin S, Paci A, Bongers A, Minard-Colin V, Tartour E, Zitvogel L, Apetoh L, Ma Y, Pittet MJ, Kepp O, Kroemer G

Crizotinib-induced immunogenic cell death in non-small cell lung cancer.

Nat Commun. 2019;10(1):1486 - PMID: 30940805 - PMCID: PMC6445096 - DOI: 10.1038/s41467-019-09415-3

Pastore A, Gaiti F, Lu SX, Brand RM, Kulm S, Chaligne R, Gu H, Huang KY, Stamenova EK, Béguelin W, Jiang Y, Schulman RC, Kim KT, Alonso A, Allan JN, Furman RR, Gnirke A, Wu CJ, Melnick AM, Meissner A, Bernstein BE, Abdel-Wahab O, Landau DA

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL.

Nat Commun. 2019;10(1):1874 - PMID: 31015400 - PMCID: PMC6478836 - DOI: 10.1038/s41467-019-09645-5

Liu CL, Zhang X, Liu J, Wang Y, Sukhova GK, Wojtkiewicz GR, Liu T, Tang R, Achilefu S, Nahrendorf M, Libby P, Guo J, Zhang JY, Shi GP

Na+ - H+ exchanger 1 determines atherosclerotic lesion acidification and promotes atherogenesis.

Nat Commun. 2019;10(1):3978 - PMID: 31484936 - PMCID: PMC6726618 - DOI: 10.1038/s41467-019-11983-3

Tarjan DR, Flavahan WA, Bernstein BE

Epigenome editing strategies for the functional annotation of CTCF insulators.

Nat Commun. 2019;10(1):4258 - PMID: 31534142 - PMCID: PMC6751197 - DOI: 10.1038/s41467-019-12166-w

Cabal-Hierro L, van Galen P, Prado MA, Higby KJ, Togami K, Mowery CT, Paulo JA, Xie Y, Cejas P, Furusawa T, Bustin M, Long HW, Sykes DB, Gygi SP, Finley D, Bernstein BE, Lane AA

Chromatin accessibility promotes hematopoietic and leukemia stem cell activity.

Nat Commun. 2020;11(1):1406 - PMID: 32179749 - PMCID: PMC7076002 - DOI: 10.1038/s41467-020-15221-z

Boivin G, Faget J, Ancey PB, Gkasti A, Mussard J, Engblom C, Pfirschke C, Contat C, Pascual J, Vazquez J, Bendriss-Vermare N, Caux C, Vozenin MC, Pittet MJ, Gunzer M, Meylan E

Durable and controlled depletion of neutrophils in mice.

Nat Commun. 2020;11(1):2762 - PMID: 32488020 - PMCID: PMC7265525 - DOI: 10.1038/s41467-020-16596-9

Luthria G, Li R, Wang S, Prytyskach M, Kohler RH, Lauffenburger DA, Mitchison TJ, Weissleder R, Miller MA

In vivo microscopy reveals macrophage polarization locally promotes coherent microtubule dynamics in migrating cancer cells

Nat Commun. 2020;11:3521 - PMID: 32665556 - PMCID: PMC7360550 - DOI: 10.1038/s41467-020-17147-y

Javed N, Farjoun Y, Fennell TJ, Epstein CB, Bernstein BE, Shoresh N

Detecting sample swaps in diverse NGS data types using linkage disequilibrium.

Nat Commun. 2020;11(1):3697 - PMID: 32728101 - PMCID: PMC7391710 - DOI: 10.1038/s41467-020-17453-5

Oki T, Mercier F, Kato H, Jung Y, McDonald TO, Spencer JA, Mazzola MC, van Gastel N, Lin CP, Michor F, Kitamura T, Scadden DT

Imaging dynamic mTORC1 pathway activity in vivo reveals marked shifts that support time-specific inhibitor therapy in AML.

Nat Commun. 2021;12(1):245 - PMID: 33431855 - PMCID: PMC7801403 - DOI: 10.1038/s41467-020-20491-8

Stewart-Ornstein J, Iwamoto Y, Miller MA, Prytyskach MA, Ferretti S, Holzer P, Kallen J, Furet P, Jambhekar A, Forrester WC, Weissleder R, Lahav G

p53 dynamics vary between tissues and are linked with radiation sensitivity

Nat Commun. 2021;12(1):898 - PMID: 33563973 - PMCID: PMC7873198 - DOI: 10.1038/s41467-021-21145-z

Bénard A, Jacobsen A, Brunner M, Krautz C, Klösch B, Swierzy I, Naschberger E, Podolska MJ, Kouhestani D, David P, Birkholz T, Castellanos I, Trufa D, Sirbu H, Vetter M, Kremer AE, Hildner K, Hecker A, Edinger F, Tenbusch M, Mühl-Zürbes P, Steinkasserer A, Richter E, Streeck H, Berger MM, Brenner T, Weigand MA, Swirski FK, Schett G, Grützmann R, Weber GF

Interleukin-3 is a predictive marker for severity and outcome during SARS-CoV-2 infections.

Nat Commun. 2021;12(1):1112 - PMID: 33602937 - PMCID: PMC7893044 - DOI: 10.1038/s41467-021-21310-4