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1,917 results on '"Ragon Institute of MGH, MIT and Harvard"'

1. Point-of-Care HIV Testing and Early Dolutegravir Use for Infants (Moso)

Author

Botswana Harvard AIDS Institute Partnership, Ragon Institute of MGH, MIT and Harvard, Botswana Ministry of Health, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), and Roger Shapiro, Associate Professor of Immunology and Infectious Diseases

Published
2024

2. Vaginal lIve Biotherapeutic RANdomized Trial (VIBRANT)

Author

Bill and Melinda Gates Foundation, Ragon Institute of MGH, MIT and Harvard, Centre for the AIDS Programme of Research in South Africa, and Caroline Mitchell, Associate Professor of Obstetrics, Gynecology & Reproductive Biology

Published
2023

3. Early Infant HIV Treatment in Botswana (EIT)

Author

Ragon Institute of MGH, MIT and Harvard, Brigham and Women's Hospital, University of California, San Diego, and Roger Shapiro, Principal Investigator

Published
2023

9. Ugandan Non-Communicable Diseases and Aging Cohort (UGANDAC)

Author

Mbarara University of Science and Technology, University of California, San Francisco, Ragon Institute of MGH, MIT and Harvard, National Institutes of Health (NIH), Harvard University, and Mark Siedner, Assistant in Medicine

Published
2019

11. Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation

Author

Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Kummerlowe, Conner, Mwakamui, Simutanyi, Hughes, Travis K, Mulugeta, Nolawit, Mudenda, Victor, Besa, Ellen, Zyambo, Kanekwa, Shay, Jessica ES, Fleming, Ira, Vukovic, Marko, Doran, Ben A, Aicher, Toby P, Wadsworth, Marc H, Bramante, Juliet Tongue, Uchida, Amiko M, Fardoos, Rabiah, Asowata, Osaretin E, Herbert, Nicholas, Yilmaz, Ömer H, Kløverpris, Henrik N, Garber, John J, Ordovas-Montañes, José, Gartner, Zev J, Wallach, Thomas, Shalek, Alex K, Kelly, Paul, Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Kummerlowe, Conner, Mwakamui, Simutanyi, Hughes, Travis K, Mulugeta, Nolawit, Mudenda, Victor, Besa, Ellen, Zyambo, Kanekwa, Shay, Jessica ES, Fleming, Ira, Vukovic, Marko, Doran, Ben A, Aicher, Toby P, Wadsworth, Marc H, Bramante, Juliet Tongue, Uchida, Amiko M, Fardoos, Rabiah, Asowata, Osaretin E, Herbert, Nicholas, Yilmaz, Ömer H, Kløverpris, Henrik N, Garber, John J, Ordovas-Montañes, José, Gartner, Zev J, Wallach, Thomas, Shalek, Alex K, and Kelly, Paul

Abstract

Environmental enteropathy (EE) is a subclinical condition of the small intestine that is highly prevalent in low- and middle-income countries. It is thought to be a key contributing factor to childhood malnutrition, growth stunting, and diminished oral vaccine responses. Although EE has been shown to be the by-product of a recurrent enteric infection, its full pathophysiology remains unclear. Here, we mapped the cellular and molecular correlates of EE by performing high-throughput, single-cell RNA-sequencing on 33 small intestinal biopsies from 11 adults with EE in Lusaka, Zambia (eight HIV-negative and three HIV-positive), six adults without EE in Boston, United States, and two adults in Durban, South Africa, which we complemented with published data from three additional individuals from the same clinical site. We analyzed previously defined bulk-transcriptomic signatures of reduced villus height and decreased microbial translocation in EE and showed that these signatures may be driven by an increased abundance of surface mucosal cells—a gastric-like subset previously implicated in epithelial repair in the gastrointestinal tract. In addition, we determined cell subsets whose fractional abundances associate with EE severity, small intestinal region, and HIV infection. Furthermore, by comparing duodenal EE samples with those from three control cohorts, we identified dysregulated WNT and MAPK signaling in the EE epithelium and increased proinflammatory cytokine gene expression in a T cell subset highly expressing a transcriptional signature of tissue-resident memory cells in the EE cohort. Together, our work elucidates epithelial and immune correlates of EE and nominates cellular and molecular targets for intervention.

Published
2023

12. HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity

Author

Ragon Institute of MGH, MIT and Harvard, Naicker, Delon, Sonela, Nelson, Jin, Steven W., Mulaudzi, Takalani, Ojwach, Doty, Reddy, Tarylee, Brockman, Mark A., Brumme, Zabrina L., Ndung’u, Thumbi, Mann, Jaclyn K., Ragon Institute of MGH, MIT and Harvard, Naicker, Delon, Sonela, Nelson, Jin, Steven W., Mulaudzi, Takalani, Ojwach, Doty, Reddy, Tarylee, Brockman, Mark A., Brumme, Zabrina L., Ndung’u, Thumbi, and Mann, Jaclyn K.

Abstract

Background Nef performs multiple cellular activities that enhance HIV-1 pathogenesis. The role of Nef-mediated down-regulation of the host restriction factor SERINC5 in HIV-1 pathogenesis is not well-defined. We aimed to investigate if SERINC5 down-regulation activity contributes to HIV-1 subtype C disease progression, to assess the relative contribution of this activity to overall Nef function, and to identify amino acids required for optimal activity. We measured the SERINC5 down-regulation activity of 106 subtype C Nef clones, isolated from individuals in early infection, for which the Nef activities of CD4 and HLA-I down-regulation as well as alteration of TCR signalling were previously measured. The relationship between SERINC5 down-regulation and markers of disease progression, and the relative contribution of SERINC5 down-regulation to a Nef fitness model-derived E value (a proxy for overall Nef fitness in vivo), were assessed. Results No overall relationship was found between SERINC5 down-regulation and viral load set point (p = 0.28) or rate of CD4+ T cell decline (p = 0.45). CD4 down-regulation (p = 0.02) and SERINC5 down-regulation (p = 0.003) were significant determinants of E values in univariate analyses, with the greatest relative contribution for SERINC5 down-regulation, and only SERINC5 down-regulation remained significant in the multivariate analysis (p = 0.003). Using a codon-by-codon analysis, several amino acids were significantly associated with increased (10I, 11V, 38D, 51T, 65D, 101V, 188H and, 191H) or decreased (10K, 38E, 65E, 135F, 173T, 176T and, 191R) SERINC5 down-regulation activity. Site-directed mutagenesis experiments of selected mutants confirmed a substantial reduction in SERINC5 down-regulation activity associated with the mutation 173T, while mutations 10K, 135F, and 176T were associated with more modest reductions in activity that were not statistically significant. Conclusions These results suggest that SERINC5 down-re

Published
2023

13. An adjuvant strategy enabled by modulation of the physical properties of microbial ligands expands antigen immunogenicity

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Howard Hughes Medical Institute, Irvine, Darrell, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Howard Hughes Medical Institute, and Irvine, Darrell

Abstract

Activation of the innate immune system via pattern recognition receptors (PRRs) is key to generate lasting adaptive immunity. PRRs detect unique chemical patterns associated with invading microorganisms, but whether and how the physical properties of PRR ligands influence the development of the immune response remains unknown. Through the study of fungal mannans, we show that the physical form of PRR ligands dictates the immune response. Soluble mannans are immunosilent in the periphery but elicit a potent pro-inflammatory response in the draining lymph node (dLN). By modulating the physical form of mannans, we developed a formulation that targets both the periphery and the dLN. When combined with viral glycoprotein antigens, this mannan formulation broadens epitope recognition, elicits potent antigen-specific neutralizing antibodies, and confers protection against viral infections of the lung. Thus, the physical properties of microbial ligands determine the outcome of the immune response and can be harnessed for vaccine development.

Published
2023

14. STING agonist delivery by tumour-penetrating PEG-lipid nanodiscs primes robust anticancer immunity

Author

Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Ragon Institute of MGH, MIT and Harvard, Dane, Eric L, Belessiotis-Richards, Alexis, Backlund, Coralie, Wang, Jianing, Hidaka, Kousuke, Milling, Lauren E, Bhagchandani, Sachin, Melo, Mariane B, Wu, Shengwei, Li, Na, Donahue, Nathan, Ni, Kaiyuan, Ma, Leyuan, Okaniwa, Masanori, Stevens, Molly M, Alexander-Katz, Alfredo, Irvine, Darrell J, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Ragon Institute of MGH, MIT and Harvard, Dane, Eric L, Belessiotis-Richards, Alexis, Backlund, Coralie, Wang, Jianing, Hidaka, Kousuke, Milling, Lauren E, Bhagchandani, Sachin, Melo, Mariane B, Wu, Shengwei, Li, Na, Donahue, Nathan, Ni, Kaiyuan, Ma, Leyuan, Okaniwa, Masanori, Stevens, Molly M, Alexander-Katz, Alfredo, and Irvine, Darrell J

Abstract

AbstractActivation of the innate immune STimulator of INterferon Genes (STING) pathway potentiates antitumour immunity, but systemic delivery of STING agonists to tumours is challenging. We conjugated STING-activating cyclic dinucleotides (CDNs) to PEGylated lipids (CDN-PEG-lipids; PEG, polyethylene glycol) via a cleavable linker and incorporated them into lipid nanodiscs (LNDs), which are discoid nanoparticles formed by self-assembly. Compared to state-of-the-art liposomes, intravenously administered LNDs carrying CDN-PEG-lipid (LND-CDNs) exhibited more efficient penetration of tumours, exposing the majority of tumour cells to STING agonist. A single dose of LND-CDNs induced rejection of established tumours, coincident with immune memory against tumour rechallenge. Although CDNs were not directly tumoricidal, LND-CDN uptake by cancer cells correlated with robust T-cell activation by promoting CDN and tumour antigen co-localization in dendritic cells. LNDs thus appear promising as a vehicle for robust delivery of compounds throughout solid tumours, which can be exploited for enhanced immunotherapy.

Published
2023

15. Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Ragon Institute of MGH, MIT and Harvard, Wamhoff, Eike-Christian, Romanov, Anna, Huang, Hellen, Read, Benjamin J, Ginsburg, Eric, Knappe, Grant A, Kim, Hyun Min, Farrell, Nicholas P, Irvine, Darrell J, Bathe, Mark, Massachusetts Institute of Technology. Department of Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Ragon Institute of MGH, MIT and Harvard, Wamhoff, Eike-Christian, Romanov, Anna, Huang, Hellen, Read, Benjamin J, Ginsburg, Eric, Knappe, Grant A, Kim, Hyun Min, Farrell, Nicholas P, Irvine, Darrell J, and Bathe, Mark

Abstract

Viruslike particles (VLPs) fabricated using wireframe DNA origami are emerging as promising vaccine and gene therapeutic delivery platforms due to their programmable nature that offers independent control over their size and shape, as well as their site-specific functionalization. As materials that biodegrade in the presence of endonucleases, specifically DNase I and II, their utility for the targeting of cells, tissues, and organs depends on their stability in vivo. Here, we explore minor groove binders (MGBs) as specific endonuclease inhibitors to control the degradation half-life of wireframe DNA origami. Bare, unprotected DNA-VLPs composed of two-helix edges were found to be stable in fetal bovine serum under typical cell culture conditions and in human serum for 24 h but degraded within 3 h in mouse serum, suggesting species-specific endonuclease activity. Inhibiting endonucleases by incubating DNA-VLPs with diamidine-class MGBs increased their half-lives in mouse serum by more than 12 h, corroborated by protection against isolated DNase I and II. Our stabilization strategy was compatible with the functionalization of DNA-VLPs with HIV antigens, did not interfere with B-cell signaling activity of DNA-VLPs in vitro, and was nontoxic to B-cell lines. It was further found to be compatible with multiple wireframe DNA origami geometries and edge architectures. MGB protection is complementary to existing methods such as PEGylation and chemical cross-linking, offering a facile protocol to control DNase-mediated degradation rates for in vitro and possibly in vivo therapeutic and vaccine applications.

Published
2023

16. Dendritic cell-mediated cross presentation of tumor-derived peptides is biased against plasma membrane proteins

Author

Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Biology, Ragon Institute of MGH, MIT and Harvard, Fessenden, Tim B, Stopfer, Lauren E, Chatterjee, Fiona, Zulueta, Julian, Mesfin, Josh, Cordero Dumit, Therese, Reijers, Irene, Hoefsmit, Esmee P, Blank, Christian, White, Forest, Spranger, Stefani, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Biology, Ragon Institute of MGH, MIT and Harvard, Fessenden, Tim B, Stopfer, Lauren E, Chatterjee, Fiona, Zulueta, Julian, Mesfin, Josh, Cordero Dumit, Therese, Reijers, Irene, Hoefsmit, Esmee P, Blank, Christian, White, Forest, and Spranger, Stefani

Published
2023

17. Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Biology, Genshaft, Alex S, Ziegler, Carly GK, Tzouanas, Constantine N, Mead, Benjamin E, Jaeger, Alex M, Navia, Andrew W, King, Ryan P, Mana, Miyeko D, Huang, Siyi, Mitsialis, Vanessa, Snapper, Scott B, Yilmaz, Ömer H, Jacks, Tyler, Van Humbeck, Jeffrey F, Shalek, Alex K, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Biology, Genshaft, Alex S, Ziegler, Carly GK, Tzouanas, Constantine N, Mead, Benjamin E, Jaeger, Alex M, Navia, Andrew W, King, Ryan P, Mana, Miyeko D, Huang, Siyi, Mitsialis, Vanessa, Snapper, Scott B, Yilmaz, Ömer H, Jacks, Tyler, Van Humbeck, Jeffrey F, and Shalek, Alex K

Abstract

AbstractA cell’s phenotype and function are influenced by dynamic interactions with its microenvironment. To examine cellular spatiotemporal activity, we developed SPACECAT—Spatially PhotoActivatable Color Encoded Cell Address Tags—to annotate, track, and isolate cells while preserving viability. In SPACECAT, samples are stained with photocaged fluorescent molecules, and cells are labeled by uncaging those molecules with user-patterned near-UV light. SPACECAT offers single-cell precision and temporal stability across diverse cell and tissue types. Illustratively, we target crypt-like regions in patient-derived intestinal organoids to enrich for stem-like and actively mitotic cells, matching literature expectations. Moreover, we apply SPACECAT to ex vivo tissue sections from four healthy organs and an autochthonous lung tumor model. Lastly, we provide a computational framework to identify spatially-biased transcriptome patterns and enriched phenotypes. This minimally perturbative and broadly applicable method links cellular spatiotemporal and/or behavioral phenotypes with diverse downstream assays, enabling insights into the connections between tissue microenvironments and (dys)function.

Published
2022

18. The Human Cell Atlas & Equity: Lessons Learned

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Broad Institute of MIT and Harvard, Majumder, Partha P, Mhlanga, Musa M, Shalek, Alexander K, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Broad Institute of MIT and Harvard, Majumder, Partha P, Mhlanga, Musa M, and Shalek, Alexander K

Published
2022

19. Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Mathematics, Dwyer, Daniel F, Ordovas-Montanes, Jose, Allon, Samuel J, Buchheit, Kathleen M, Vukovic, Marko, Derakhshan, Tahereh, Feng, Chunli, Lai, Juying, Hughes, Travis K, Nyquist, Sarah K, Giannetti, Matthew P, Berger, Bonnie, Bhattacharyya, Neil, Roditi, Rachel E, Katz, Howard R, Nawijn, Martijn C, Berg, Marijn, van den Berge, Maarten, Laidlaw, Tanya M, Shalek, Alex K, Barrett, Nora A, Boyce, Joshua A, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Mathematics, Dwyer, Daniel F, Ordovas-Montanes, Jose, Allon, Samuel J, Buchheit, Kathleen M, Vukovic, Marko, Derakhshan, Tahereh, Feng, Chunli, Lai, Juying, Hughes, Travis K, Nyquist, Sarah K, Giannetti, Matthew P, Berger, Bonnie, Bhattacharyya, Neil, Roditi, Rachel E, Katz, Howard R, Nawijn, Martijn C, Berg, Marijn, van den Berge, Maarten, Laidlaw, Tanya M, Shalek, Alex K, Barrett, Nora A, and Boyce, Joshua A

Abstract

Mast cells (MCs) play a pathobiologic role in type 2 (T2) allergic inflammatory diseases of the airway, including asthma and chronic rhinosinusitis with nasal polyposis (CRSwNP). Distinct MC subsets infiltrate the airway mucosa in T2 disease, including subepithelial MCs expressing the proteases tryptase and chymase (MCTC) and epithelial MCs expressing tryptase without chymase (MCT). However, mechanisms underlying MC expansion and the transcriptional programs underlying their heterogeneity are poorly understood. Here, we use flow cytometry and single-cell RNA-sequencing (scRNA-seq) to conduct a comprehensive analysis of human MC hyperplasia in CRSwNP, a T2 cytokine-mediated inflammatory disease. We link discrete cell surface phenotypes to the distinct transcriptomes of CRSwNP MCT and MCTC, which represent polarized ends of a transcriptional gradient of nasal polyp MCs. We find a subepithelial population of CD38highCD117high MCs that is markedly expanded during T2 inflammation. These CD38highCD117high MCs exhibit an intermediate phenotype relative to the expanded MCT and MCTC subsets. CD38highCD117high MCs are distinct from circulating MC progenitors and are enriched for proliferation, which is markedly increased in CRSwNP patients with aspirin-exacerbated respiratory disease, a severe disease subset characterized by increased MC burden and elevated MC activation. We observe that MCs expressing a polyp MCT-like effector program are also found within the lung during fibrotic diseases and asthma, and further identify marked differences between MCTC in nasal polyps and skin. These results indicate that MCs display distinct inflammation-associated effector programs and suggest that in situ MC proliferation is a major component of MC hyperplasia in human T2 inflammation.

Published
2022

20. A single-cell liver atlas of Plasmodium vivax infection

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Chemistry, Ragon Institute of MGH, MIT and Harvard, Mancio-Silva, Liliana, Gural, Nil, Real, Eliana, Wadsworth, Marc H, Butty, Vincent L, March, Sandra, Nerurkar, Niketa, Hughes, Travis K, Roobsoong, Wanlapa, Fleming, Heather E, Whittaker, Charlie A, Levine, Stuart S, Sattabongkot, Jetsumon, Shalek, Alex K, Bhatia, Sangeeta N, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Chemistry, Ragon Institute of MGH, MIT and Harvard, Mancio-Silva, Liliana, Gural, Nil, Real, Eliana, Wadsworth, Marc H, Butty, Vincent L, March, Sandra, Nerurkar, Niketa, Hughes, Travis K, Roobsoong, Wanlapa, Fleming, Heather E, Whittaker, Charlie A, Levine, Stuart S, Sattabongkot, Jetsumon, Shalek, Alex K, and Bhatia, Sangeeta N

Abstract

Malaria-causing Plasmodium vivax parasites can linger in the human liver for weeks to years and reactivate to cause recurrent blood-stage infection. Although they are an important target for malaria eradication, little is known about the molecular features of replicative and non-replicative intracellular liver-stage parasites and their host cell dependence. Here, we leverage a bioengineered human microliver platform to culture patient-derived P. vivax parasites for transcriptional profiling. Coupling enrichment strategies with bulk and single-cell analyses, we capture both parasite and host transcripts in individual hepatocytes throughout the course of infection. We define host- and state-dependent transcriptional signatures and identify unappreciated populations of replicative and non-replicative parasites that share features with sexual transmissive forms. We find that infection suppresses the transcription of key hepatocyte function genes and elicits an anti-parasite innate immune response. Our work provides a foundation for understanding host-parasite interactions and reveals insights into the biology of P. vivax dormancy and transmission.

Published
2022

21. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Biology, Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Chemistry, Bui, Linh T., Winters, Nichelle I., Chung, Mei-I, Joseph, Chitra, Gutierrez, Austin J., Habermann, Arun C., Adams, Taylor S., Schupp, Jonas C., Poli, Sergio, Peter, Lance M., Taylor, Chase J., Blackburn, Jessica B., Richmond, Bradley W., Nicholson, Andrew G., Rassl, Doris, Wallace, William A., Rosas, Ivan O., Jenkins, R. Gisli, Kaminski, Naftali, Kropski, Jonathan A., Banovich, Nicholas E., Misharin, Alexander V., Tsankov, Alexander M., Spira, Avrum, Barbry, Pascal, Brazma, Alvis, Samakovlis, Christos, Shepherd, Douglas P., Rawlins, Emma L., Theis, Fabian J., Griffonnet, Jennifer, Lee, Haeock, Schiller, Herbert B., Hofman, Paul, Powell, Joseph E., Schultze, Joachim L., Whitsett, Jeffrey, Choi, Jiyeon, Lundeberg, Joakim, Ordovas-Montanes, Jose, Rajagopal, Jayaraj, Meyer, Kerstin B., Krasnow, Mark A., Saeb‐Parsy, Kourosh, Zhang, Kun, Lafyatis, Robert, Leroy, Sylvie, Haniffa, Muzlifah, Nawijn, Martijn C., Nikolić, Marko Z., van den Berge, Maarten, Kuhnemund, Malte, Marquette, Charles-Hugo, Von Papen, Michael, Eickelberg, Oliver, Rosenblatt-Rosen, Orit, Reyfman, Paul A., Pe’er, Dana, Horvath, Peter, Tata, Purushothama Rao, Regev, Aviv, Rojas, Mauricio, Seibold, Max A., Shalek, Alex K., Spence, Jason R., Teichmann, Sarah A., Quake, Stephen, Duong, Thu Elizabeth, Biancalani, Tommaso, Desai, Tushar, Sun, Xin, Zaragosi, Laure Emmanuelle, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Biology, Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Chemistry, Bui, Linh T., Winters, Nichelle I., Chung, Mei-I, Joseph, Chitra, Gutierrez, Austin J., Habermann, Arun C., Adams, Taylor S., Schupp, Jonas C., Poli, Sergio, Peter, Lance M., Taylor, Chase J., Blackburn, Jessica B., Richmond, Bradley W., Nicholson, Andrew G., Rassl, Doris, Wallace, William A., Rosas, Ivan O., Jenkins, R. Gisli, Kaminski, Naftali, Kropski, Jonathan A., Banovich, Nicholas E., Misharin, Alexander V., Tsankov, Alexander M., Spira, Avrum, Barbry, Pascal, Brazma, Alvis, Samakovlis, Christos, Shepherd, Douglas P., Rawlins, Emma L., Theis, Fabian J., Griffonnet, Jennifer, Lee, Haeock, Schiller, Herbert B., Hofman, Paul, Powell, Joseph E., Schultze, Joachim L., Whitsett, Jeffrey, Choi, Jiyeon, Lundeberg, Joakim, Ordovas-Montanes, Jose, Rajagopal, Jayaraj, Meyer, Kerstin B., Krasnow, Mark A., Saeb‐Parsy, Kourosh, Zhang, Kun, Lafyatis, Robert, Leroy, Sylvie, Haniffa, Muzlifah, Nawijn, Martijn C., Nikolić, Marko Z., van den Berge, Maarten, Kuhnemund, Malte, Marquette, Charles-Hugo, Von Papen, Michael, Eickelberg, Oliver, Rosenblatt-Rosen, Orit, Reyfman, Paul A., Pe’er, Dana, Horvath, Peter, Tata, Purushothama Rao, Regev, Aviv, Rojas, Mauricio, Seibold, Max A., Shalek, Alex K., Spence, Jason R., Teichmann, Sarah A., Quake, Stephen, Duong, Thu Elizabeth, Biancalani, Tommaso, Desai, Tushar, Sun, Xin, and Zaragosi, Laure Emmanuelle

Abstract

AbstractPatients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 (COVID-19) and poor outcomes. Here, we analyze the transcriptomes of 611,398 single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in patients with chronic lung diseases. We observe a similar cellular distribution and relative expression of SARS-CoV-2 entry factors in control and CLD lungs. CLD AT2 cells express higher levels of genes linked directly to the efficiency of viral replication and the innate immune response. Additionally, we identify basal differences in inflammatory gene expression programs that highlight how CLD alters the inflammatory microenvironment encountered upon viral exposure to the peripheral lung. Our study indicates that CLD is accompanied by changes in cell-type-specific gene expression programs that prime the lung epithelium for and influence the innate and adaptive immune responses to SARS-CoV-2 infection.

Published
2022

22. High-Throughput CRISPR Screens To Dissect Macrophage- Shigella Interactions

Author

Singapore-MIT Alliance in Research and Technology (SMART), Massachusetts Institute of Technology. Synthetic Biology Center, Massachusetts Institute of Technology. Research Laboratory of Electronics, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Biological Engineering, Lai, Yong, Cui, Liang, Babunovic, Gregory H, Fortune, Sarah M, Doench, John G, Lu, Timothy K, Singapore-MIT Alliance in Research and Technology (SMART), Massachusetts Institute of Technology. Synthetic Biology Center, Massachusetts Institute of Technology. Research Laboratory of Electronics, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Biological Engineering, Lai, Yong, Cui, Liang, Babunovic, Gregory H, Fortune, Sarah M, Doench, John G, and Lu, Timothy K

Abstract

Treatment for shigellosis is becoming increasingly difficult as resistance to antibiotics becomes more prevalent. One way to prevent this significant public health problem from developing into a full-blown crisis is to approach shigellosis intervention from the point of view of the host.

Published
2022

23. Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Chemical Engineering, Shalek, Alexander, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Chemical Engineering, and Shalek, Alexander

Abstract

RNA sequencing of cerebral hematoma myeloid cells reveals a two-stage functional and metabolic program associated with recovery.

Published
2022

24. Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip

Author

Harvard University--MIT Division of Health Sciences and Technology, Ragon Institute of MGH, MIT and Harvard, Bein, Amir, Kim, Seongmin, Goyal, Girija, Cao, Wuji, Fadel, Cicely, Naziripour, Arash, Sharma, Sanjay, Swenor, Ben, LoGrande, Nina, Nurani, Atiq, Miao, Vincent N, Navia, Andrew W, Ziegler, Carly GK, Montañes, José Ordovas, Prabhala, Pranav, Kim, Min Sun, Prantil-Baun, Rachelle, Rodas, Melissa, Jiang, Amanda, O’Sullivan, Lucy, Tillya, Gladness, Shalek, Alex K, Ingber, Donald E, Harvard University--MIT Division of Health Sciences and Technology, Ragon Institute of MGH, MIT and Harvard, Bein, Amir, Kim, Seongmin, Goyal, Girija, Cao, Wuji, Fadel, Cicely, Naziripour, Arash, Sharma, Sanjay, Swenor, Ben, LoGrande, Nina, Nurani, Atiq, Miao, Vincent N, Navia, Andrew W, Ziegler, Carly GK, Montañes, José Ordovas, Prabhala, Pranav, Kim, Min Sun, Prantil-Baun, Rachelle, Rodas, Melissa, Jiang, Amanda, O’Sullivan, Lucy, Tillya, Gladness, Shalek, Alex K, and Ingber, Donald E

Abstract

Many patients infected with coronaviruses, such as SARS-CoV-2 and NL63 that use ACE2 receptors to infect cells, exhibit gastrointestinal symptoms and viral proteins are found in the human gastrointestinal tract, yet little is known about the inflammatory and pathological effects of coronavirus infection on the human intestine. Here, we used a human intestine-on-a-chip (Intestine Chip) microfluidic culture device lined by patient organoid-derived intestinal epithelium interfaced with human vascular endothelium to study host cellular and inflammatory responses to infection with NL63 coronavirus. These organoid-derived intestinal epithelial cells dramatically increased their ACE2 protein levels when cultured under flow in the presence of peristalsis-like mechanical deformations in the Intestine Chips compared to when cultured statically as organoids or in Transwell inserts. Infection of the intestinal epithelium with NL63 on-chip led to inflammation of the endothelium as demonstrated by loss of barrier function, increased cytokine production, and recruitment of circulating peripheral blood mononuclear cells (PBMCs). Treatment of NL63 infected chips with the approved protease inhibitor drug, nafamostat, inhibited viral entry and resulted in a reduction in both viral load and cytokine secretion, whereas remdesivir, one of the few drugs approved for COVID19 patients, was not found to be effective and it also was toxic to the endothelium. This model of intestinal infection was also used to test the effects of other drugs that have been proposed for potential repurposing against SARS-CoV-2. Taken together, these data suggest that the human Intestine Chip might be useful as a human preclinical model for studying coronavirus related pathology as well as for testing of potential anti-viral or anti-inflammatory therapeutics.

Published
2022

25. Efficient blockade of locally reciprocated tumor-macrophage signaling using a TAM-avid nanotherapy

Author

Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Biological Engineering, Wang, Stephanie J, Li, Ran, Ng, Thomas SC, Luthria, Gaurav, Oudin, Madeleine J, Prytyskach, Mark, Kohler, Rainer H, Weissleder, Ralph, Lauffenburger, Douglas A, Miller, Miles A, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Biological Engineering, Wang, Stephanie J, Li, Ran, Ng, Thomas SC, Luthria, Gaurav, Oudin, Madeleine J, Prytyskach, Mark, Kohler, Rainer H, Weissleder, Ralph, Lauffenburger, Douglas A, and Miller, Miles A

Abstract

© 2020 American Association for the Advancement of Science. All rights reserved. Interpreting how multicellular interactions in the tumor affect resistance pathways to BRAF and MEK1/2 MAPK inhibitors (MAPKi) remains a challenge. To investigate this, we profiled global ligand-receptor interactions among tumor and stromal/immune cells from biopsies of MAPK-driven disease. MAPKi increased tumor-associated macrophages (TAMs) in some patients, which correlated with poor clinical response, and MAPKi coamplified bidirectional tumor-TAM signaling via receptor tyrosine kinases (RTKs) including AXL, MERTK, and their ligand GAS6. In xenograft tumors, intravital microscopy simultaneously monitored in situ single-cell activities of multiple kinases downstream of RTKs, revealing MAPKi increased TAMs and enhanced bypass signaling in TAM-proximal tumor cells. As a proof-of-principle strategy to block this signaling, we developed a multi-RTK kinase inhibitor nanoformulation that accumulated in TAMs and delayed disease progression. Thus, bypass signaling can reciprocally amplify across nearby cell types, offering new opportunities for therapeutic design.

Published
2022

26. RNA-Mediated Feedback Control of Transcriptional Condensates

Author

Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Henninger, Jonathan E, Oksuz, Ozgur, Shrinivas, Krishna, Sagi, Ido, LeRoy, Gary, Zheng, Ming M, Andrews, J Owen, Zamudio, Alicia V, Lazaris, Charalampos, Hannett, Nancy M, Lee, Tong Ihn, Sharp, Phillip A, Cissé, Ibrahim I, Chakraborty, Arup K, Young, Richard A, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Henninger, Jonathan E, Oksuz, Ozgur, Shrinivas, Krishna, Sagi, Ido, LeRoy, Gary, Zheng, Ming M, Andrews, J Owen, Zamudio, Alicia V, Lazaris, Charalampos, Hannett, Nancy M, Lee, Tong Ihn, Sharp, Phillip A, Cissé, Ibrahim I, Chakraborty, Arup K, and Young, Richard A

Abstract

© 2020 Elsevier Inc. During the early steps of transcription initiation, nascent RNAs stimulate transcriptional condensate formation, whereas the burst of RNAs produced during elongation stimulates condensate dissolution.

Published
2022

27. Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Pae, Juhee, Ersching, Jonatan, Castro, Tiago BR, Schips, Marta, Mesin, Luka, Allon, Samuel J, Ordovas-Montanes, Jose, Mlynarczyk, Coraline, Melnick, Ari, Efeyan, Alejo, Shalek, Alex K, Meyer-Hermann, Michael, Victora, Gabriel D, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Pae, Juhee, Ersching, Jonatan, Castro, Tiago BR, Schips, Marta, Mesin, Luka, Allon, Samuel J, Ordovas-Montanes, Jose, Mlynarczyk, Coraline, Melnick, Ari, Efeyan, Alejo, Shalek, Alex K, Meyer-Hermann, Michael, and Victora, Gabriel D

Abstract

© 2020 Pae et al. During affinity maturation, germinal center (GC) B cells alternate between proliferation and somatic hypermutation in the dark zone (DZ) and affinity-dependent selection in the light zone (LZ). This anatomical segregation imposes that the vigorous proliferation that allows clonal expansion of positively selected GC B cells takes place ostensibly in the absence of the signals that triggered selection in the LZ, as if by "inertia."We find that such inertial cycles specifically require the cell cycle regulator cyclin D3. Cyclin D3 dose-dependently controls the extent to which B cells proliferate in the DZ and is essential for effective clonal expansion of GC B cells in response to strong T follicular helper (Tfh) cell help. Introduction into the Ccnd3 gene of a Burkitt lymphoma-associated gain-of-function mutation (T283A) leads to larger GCs with increased DZ proliferation and, in older mice, clonal B cell lymphoproliferation, suggesting that the DZ inertial cell cycle program can be coopted by B cells undergoing malignant transformation.

Published
2022

28. Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice

Author

Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Koch Institute for Integrative Cancer Research at MIT, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Mechanical Engineering, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Biological Engineering, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology. Department of Chemistry, Ragon Institute of MGH, MIT and Harvard, Ludwig Center for Molecular Oncology (Massachusetts Institute of Technology), Hamza, Bashar, Miller, Alex B., Meier, Lara, Stockslager, Max, Ng, Sheng Rong, King, Emily M., Lin, Lin, DeGouveia, Kelsey L., Mulugeta, Nolawit, Calistri, Nicholas L., Strouf, Haley, Bray, Christina, Rodriguez, Felicia, Freed-Pastor, William A., Chin, Christopher R., Jaramillo, Grissel C., Burger, Megan L., Weinberg, Robert A., Shalek, Alex K., Jacks, Tyler, Manalis, Scott R., Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Koch Institute for Integrative Cancer Research at MIT, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Mechanical Engineering, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Biological Engineering, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology. Department of Chemistry, Ragon Institute of MGH, MIT and Harvard, Ludwig Center for Molecular Oncology (Massachusetts Institute of Technology), Hamza, Bashar, Miller, Alex B., Meier, Lara, Stockslager, Max, Ng, Sheng Rong, King, Emily M., Lin, Lin, DeGouveia, Kelsey L., Mulugeta, Nolawit, Calistri, Nicholas L., Strouf, Haley, Bray, Christina, Rodriguez, Felicia, Freed-Pastor, William A., Chin, Christopher R., Jaramillo, Grissel C., Burger, Megan L., Weinberg, Robert A., Shalek, Alex K., Jacks, Tyler, and Manalis, Scott R.

Abstract

AbstractExisting preclinical methods for acquiring dissemination kinetics of rare circulating tumor cells (CTCs) en route to forming metastases have not been capable of providing a direct measure of CTC intravasation rate and subsequent half-life in the circulation. Here, we demonstrate an approach for measuring endogenous CTC kinetics by continuously exchanging CTC-containing blood over several hours between un-anesthetized, tumor-bearing mice and healthy, tumor-free counterparts. By tracking CTC transfer rates, we extrapolated half-life times in the circulation of between 40 and 260 s and intravasation rates between 60 and 107,000 CTCs/hour in mouse models of small-cell lung cancer (SCLC), pancreatic ductal adenocarcinoma (PDAC), and non-small cell lung cancer (NSCLC). Additionally, direct transfer of only 1−2% of daily-shed CTCs using our blood-exchange technique from late-stage, SCLC-bearing mice generated macrometastases in healthy recipient mice. We envision that our technique will help further elucidate the role of CTCs and the rate-limiting steps in metastasis.

Published
2022

29. Inferring the intrinsic mutational fitness landscape of influenzalike evolving antigens from temporally ordered sequence data

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Chemistry, Ragon Institute of MGH, MIT and Harvard, Doelger, Julia, Kardar, Mehran, Chakraborty, Arup K, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Chemistry, Ragon Institute of MGH, MIT and Harvard, Doelger, Julia, Kardar, Mehran, and Chakraborty, Arup K

Abstract

There still are no effective long-term protective vaccines against viruses that continuously evolve under immune pressure such as seasonal influenza, which has caused, and can cause, devastating epidemics in the human population. To find such a broadly protective immunization strategy, it is useful to know how easily the virus can escape via mutation from specific antibody responses. This information is encoded in the fitness landscape of the viral proteins (i.e., knowledge of the viral fitness as a function of sequence). Here we present a computational method to infer the intrinsic mutational fitness landscape of influenzalike evolving antigens from yearly sequence data. We test inference performance with computer-generated sequence data that are based on stochastic simulations mimicking basic features of immune-driven viral evolution. Although the numerically simulated model does create a phylogeny based on the allowed mutations, the inference scheme does not use this information. This provides a contrast to other methods that rely on reconstruction of phylogenetic trees. Our method just needs a sufficient number of samples over multiple years. With our method, we are able to infer single as well as pairwise mutational fitness effects from the simulated sequence time series for short antigenic proteins. Our fitness inference approach may have potential future use for the design of immunization protocols by identifying intrinsically vulnerable immune target combinations on antigens that evolve under immune-driven selection. In the future, this approach may be applied to influenza and other novel viruses such as SARS-CoV-2, which evolves and, like influenza, might continue to escape the natural and vaccine-mediated immune pressures.

Published
2022

30. PI3K activation allows immune evasion by promoting an inhibitory myeloid tumor microenvironment

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Collins, Natalie B, Al Abosy, Rose, Miller, Brian C, Bi, Kevin, Zhao, Qihong, Quigley, Michael, Ishizuka, Jeffrey J, Yates, Kathleen B, Pope, Hans W, Manguso, Robert T, Shrestha, Yashaswi, Wadsworth, Marc, Hughes, Travis, Shalek, Alex K, Boehm, Jesse S, Hahn, William C, Doench, John G, Haining, W Nicholas, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Collins, Natalie B, Al Abosy, Rose, Miller, Brian C, Bi, Kevin, Zhao, Qihong, Quigley, Michael, Ishizuka, Jeffrey J, Yates, Kathleen B, Pope, Hans W, Manguso, Robert T, Shrestha, Yashaswi, Wadsworth, Marc, Hughes, Travis, Shalek, Alex K, Boehm, Jesse S, Hahn, William C, Doench, John G, and Haining, W Nicholas

Abstract

BackgroundOncogenes act in a cell-intrinsic way to promote tumorigenesis. Whether oncogenes also have a cell-extrinsic effect on suppressing the immune response to cancer is less well understood.MethodsWe use an in vivo expression screen of known cancer-associated somatic mutations in mouse syngeneic tumor models treated with checkpoint blockade to identify oncogenes that promote immune evasion. We then validated candidates from this screen in vivo and analyzed the tumor immune microenvironment of tumors expressing mutant protein to identify mechanisms of immune evasion.ResultsWe found that expression of a catalytically active mutation in phospho-inositol 3 kinase (PI3K), PIK3CA c.3140A>G (H1047R) confers a selective growth advantage to tumors treated with immunotherapy that is reversed by pharmacological PI3K inhibition. PIK3CA H1047R-expression in tumors decreased the number of CD8+ T cells but increased the number of inhibitory myeloid cells following immunotherapy. Inhibition of myeloid infiltration by pharmacological or genetic modulation of Ccl2 in PIK3CA H1047R tumors restored sensitivity to programmed cell death protein 1 (PD-1) checkpoint blockade.ConclusionsPI3K activation enables tumor immune evasion by promoting an inhibitory myeloid microenvironment. Activating mutations in PI3K may be useful as a biomarker of poor response to immunotherapy. Our data suggest that some oncogenes promote tumorigenesis by enabling tumor cells to avoid clearance by the immune system. Identification of those mechanisms can advance rational combination strategies to increase the efficacy of immunotherapy.

Published
2022

31. Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform

Author

Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Gerdemann, Ulrike, Fleming, Ryan A, Kaminski, James, McGuckin, Connor, Rui, Xianliang, Lane, Jennifer F, Keskula, Paula, Cagnin, Lorenzo, Shalek, Alex K, Tkachev, Victor, Kean, Leslie S, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Gerdemann, Ulrike, Fleming, Ryan A, Kaminski, James, McGuckin, Connor, Rui, Xianliang, Lane, Jennifer F, Keskula, Paula, Cagnin, Lorenzo, Shalek, Alex K, Tkachev, Victor, and Kean, Leslie S

Abstract

T cell receptor (TCR) clonotype tracking is a powerful tool for interrogating T cell mediated immune processes. New methods to pair a single cell’s transcriptional program with its TCR identity allow monitoring of T cell clonotype-specific transcriptional dynamics. While these technologies have been available for human and mouse T cells studies, they have not been developed for Rhesus Macaques (RM), a critical translational organism for autoimmune diseases, vaccine development and transplantation. We describe a new pipeline, ‘RM-scTCR-Seq’, which, for the first time, enables RM specific single cell TCR amplification, reconstruction and pairing of RM TCR’s with their transcriptional profiles. We apply this method to a RM model of GVHD, and identify and track in vitro detected alloreactive clonotypes in GVHD target organs and explore their GVHD driven cytotoxic T cell signature. This novel, state-of-the-art platform fundamentally advances the utility of RM to study protective and pathogenic T cell responses.

Published
2022

32. Antibody Subclass and Glycosylation Shift Following Effective TB Treatment

Author

Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Biological Engineering, Grace, Patricia S, Dolatshahi, Sepideh, Lu, Lenette L, Cain, Adam, Palmieri, Fabrizio, Petrone, Linda, Fortune, Sarah M, Ottenhoff, Tom HM, Lauffenburger, Douglas A, Goletti, Delia, Joosten, Simone A, Alter, Galit, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Biological Engineering, Grace, Patricia S, Dolatshahi, Sepideh, Lu, Lenette L, Cain, Adam, Palmieri, Fabrizio, Petrone, Linda, Fortune, Sarah M, Ottenhoff, Tom HM, Lauffenburger, Douglas A, Goletti, Delia, Joosten, Simone A, and Alter, Galit

Abstract

With an estimated 25% of the global population infected with Mycobacterium tuberculosis (Mtb), tuberculosis (TB) remains a leading cause of death by infectious diseases. Humoral immunity following TB treatment is largely uncharacterized, and antibody profiling could provide insights into disease resolution. Here we focused on the distinctive TB-specific serum antibody features in active TB disease (ATB) and compared them with latent TB infection (LTBI) or treated ATB (txATB). As expected, di-galactosylated glycan structures (lacking sialic acid) found on IgG-Fc differentiated LTBI from ATB, but also discriminated txATB from ATB. Moreover, TB-specific IgG4 emerged as a novel antibody feature that correlated with active disease, elevated in ATB, but significantly diminished after therapy. These findings highlight 2 novel TB-specific antibody changes that track with the resolution of TB and may provide key insights to guide TB therapy.

Published
2022

33. Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states

Author

Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Song, Hanbing, Weinstein, Hannah NW, Allegakoen, Paul, Wadsworth, Marc H, Xie, Jamie, Yang, Heiko, Castro, Ethan A, Lu, Kevin L, Stohr, Bradley A, Feng, Felix Y, Carroll, Peter R, Wang, Bruce, Cooperberg, Matthew R, Shalek, Alex K, Huang, Franklin W, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Song, Hanbing, Weinstein, Hannah NW, Allegakoen, Paul, Wadsworth, Marc H, Xie, Jamie, Yang, Heiko, Castro, Ethan A, Lu, Kevin L, Stohr, Bradley A, Feng, Felix Y, Carroll, Peter R, Wang, Bruce, Cooperberg, Matthew R, Shalek, Alex K, and Huang, Franklin W

Abstract

AbstractProstate cancer is the second most common malignancy in men worldwide and consists of a mixture of tumor and non-tumor cell types. To characterize the prostate cancer tumor microenvironment, we perform single-cell RNA-sequencing on prostate biopsies, prostatectomy specimens, and patient-derived organoids from localized prostate cancer patients. We uncover heterogeneous cellular states in prostate epithelial cells marked by high androgen signaling states that are enriched in prostate cancer and identify a population of tumor-associated club cells that may be associated with prostate carcinogenesis. ERG-negative tumor cells, compared to ERG-positive cells, demonstrate shared heterogeneity with surrounding luminal epithelial cells and appear to give rise to common tumor microenvironment responses. Finally, we show that prostate epithelial organoids harbor tumor-associated epithelial cell states and are enriched with distinct cell types and states from their parent tissues. Our results provide diagnostically relevant insights and advance our understanding of the cellular states associated with prostate carcinogenesis.

Published
2022

34. Cancer Cell Coating Nanoparticles for Optimal Tumor-Specific Cytokine Delivery

Author

Massachusetts Institute of Technology. Department of Chemical Engineering, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Institute for Soldier Nanotechnologies, Barberio, Antonio E, Smith, Sean G, Correa, Santiago, Nguyen, Cathy, Nhan, Bang, Melo, Mariane, Tokatlian, Talar, Suh, Heikyung, Irvine, Darrell J, Hammond, Paula T, Massachusetts Institute of Technology. Department of Chemical Engineering, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Institute for Soldier Nanotechnologies, Barberio, Antonio E, Smith, Sean G, Correa, Santiago, Nguyen, Cathy, Nhan, Bang, Melo, Mariane, Tokatlian, Talar, Suh, Heikyung, Irvine, Darrell J, and Hammond, Paula T

Abstract

© 2020 American Chemical Society. Although cytokine therapy is an attractive strategy to build a more robust immune response in tumors, cytokines have faced clinical failures due to toxicity. In particular, interleukin-12 has shown great clinical promise but was limited in translation because of systemic toxicity. In this study, we demonstrate an enhanced ability to reduce toxicity without affecting the efficacy of IL-12 therapy. We engineer the material properties of a NP to meet the enhanced demands for optimal cytokine delivery by using the layer-by-layer (LbL) approach. Importantly, using LbL, we demonstrate cell-level trafficking of NPs to preferentially localize to the cell's outer surface and act as a drug depot, which is required for optimal payload activity on neighboring cytokine membrane receptors. LbL-NPs showed efficacy against a tumor challenge in both colorectal and ovarian tumors at doses that were not tolerated when administered carrier-free.

Published
2022

35. IgG-Engineered Protective Antigen for Cytosolic Delivery of Proteins into Cancer Cells

Author

Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Center for Environmental Health Sciences, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Biological Engineering, Lu, Zeyu, Truex, Nicholas L, Melo, Mariane B, Cheng, Yiran, Li, Na, Irvine, Darrell J, Pentelute, Bradley L, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Center for Environmental Health Sciences, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Biological Engineering, Lu, Zeyu, Truex, Nicholas L, Melo, Mariane B, Cheng, Yiran, Li, Na, Irvine, Darrell J, and Pentelute, Bradley L

Abstract

© 2020 American Chemical Society. All rights reserved. Therapeutic immunotoxins composed of antibodies and bacterial toxins provide potent activity against malignant cells, but joining them with a defined covalent bond while maintaining the desired function is challenging. Here, we develop novel immunotoxins by dovetailing full-length immunoglobulin G (IgG) antibodies and nontoxic anthrax proteins, in which the C terminus of the IgG heavy chain is connected to the side chain of anthrax toxin protective antigen. This strategy enabled efficient conjugation of protective antigen variants to trastuzumab (Tmab) and cetuximab (Cmab) antibodies. The conjugates effectively perform intracellular delivery of edema factor and N terminus of lethal factor (LFN) fused with diphtheria toxin and Ras/Rap1-specific endopeptidase. Each conjugate shows high specificity for cells expressing human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR), respectively, and potent activity across six Tmab- and Cmab-resistant cell lines. The conjugates also exhibit increased pharmacokinetics and pronounced in vivo safety, which shows promise for further therapeutic development.

Published
2022

36. A simple model for how the risk of pandemics from different virus families depends on viral and human traits

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Chemistry, Ragon Institute of MGH, MIT and Harvard, Doelger, Julia, Chakraborty, Arup K, Kardar, Mehran, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Department of Chemistry, Ragon Institute of MGH, MIT and Harvard, Doelger, Julia, Chakraborty, Arup K, and Kardar, Mehran

Abstract

Different virus families, like influenza or corona viruses, exhibit characteristic traits such as typical modes of transmission and replication as well as specific animal reservoirs in which each family of viruses circulate. These traits of genetically related groups of viruses influence how easily an animal virus can adapt to infect humans, how well novel human variants can spread in the population, and the risk of causing a global pandemic. Relating the traits of virus families to their risk of causing future pandemics, and identification of the key time scales within which public health interventions can control the spread of a new virus that could cause a pandemic, are obviously significant. We address these issues using a minimal model whose parameters are related to characteristic traits of different virus families. A key trait of viruses that "spillover" from animal reservoirs to infect humans is their ability to propagate infection through the human population (fitness). We find that the risk of pandemics emerging from virus families characterized by a wide distribution of the fitness of spillover strains is much higher than if such strains were characterized by narrow fitness distributions around the same mean. The dependences of the risk of a pandemic on various model parameters exhibit inflection points. We find that these inflection points define informative thresholds. For example, the inflection point in variation of pandemic risk with time after the spillover represents a threshold time beyond which global interventions would likely be too late to prevent a pandemic.

Published
2022

37. Mining for humoral correlates of HIV control and latent reservoir size

Author

Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Biological Engineering, Das, Jishnu, Devadhasan, Anush, Linde, Caitlyn, Broge, Tom, Sassic, Jessica, Mangano, Max, O'Keefe, Sean, Suscovich, Todd, Streeck, Hendrik, Irrinki, Alivelu, Pohlmeyer, Chris, Min-Oo, Gundula, Lin, Shu, Weiner, Joshua A, Cihlar, Thomas, Ackerman, Margaret E, Julg, Boris, Deeks, Steven, Lauffenburger, Douglas A, Alter, Galit, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Biological Engineering, Das, Jishnu, Devadhasan, Anush, Linde, Caitlyn, Broge, Tom, Sassic, Jessica, Mangano, Max, O'Keefe, Sean, Suscovich, Todd, Streeck, Hendrik, Irrinki, Alivelu, Pohlmeyer, Chris, Min-Oo, Gundula, Lin, Shu, Weiner, Joshua A, Cihlar, Thomas, Ackerman, Margaret E, Julg, Boris, Deeks, Steven, Lauffenburger, Douglas A, and Alter, Galit

Abstract

© 2020 Das et al. While antiretroviral therapy (ART) has effectively revolutionized HIV care, the virus is never fully eliminated. Instead, immune dysfunction, driven by persistent non-specific immune activation, ensues and progressively leads to premature immunologic aging. Current biomarkers monitoring immunologic changes encompass generic inflammatory biomarkers, that may also change with other infections or disease states, precluding the antigen-specific monitoring of HIV-infection associated changes in disease. Given our growing appreciation of the significant changes in qualitative and quantitative properties of disease-specific antibodies in HIV infection, we used a systems approach to explore humoral profiles associated with HIV control. We found that HIV-specific antibody profiles diverge by spontaneous control of HIV, treatment status, viral load and reservoir size. Specifically, HIV-specific antibody profiles representative of changes in viral load were largely quantitative, reflected by differential HIV-specific antibody levels and Fc-receptor binding. Conversely, HIV-specific antibody features that tracked with reservoir size exhibited a combination of quantitative and qualitative changes marked by more distinct subclass selection profiles and unique HIVspecific Fc-glycans. Our analyses suggest that HIV-specific antibody Fc-profiles provide antigen-specific resolution on both cell free and cell-associated viral loads, pointing to potentially novel biomarkers to monitor reservoir activity.

Published
2022

38. Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Singh, Alveera, Kazer, Samuel W, Roider, Julia, Krista, Kami C, Millar, Jane, Asowata, Osaretin E, Ngoepe, Abigail, Ramsuran, Duran, Fardoos, Rabiah, Ardain, Amanda, Muenchhoff, Maximilian, Kuhn, Warren, Karim, Farina, Ndung’u, Thumbi, Shalek, Alex K, Goulder, Philip, Leslie, Alasdair, Kløverpris, Henrik N, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Singh, Alveera, Kazer, Samuel W, Roider, Julia, Krista, Kami C, Millar, Jane, Asowata, Osaretin E, Ngoepe, Abigail, Ramsuran, Duran, Fardoos, Rabiah, Ardain, Amanda, Muenchhoff, Maximilian, Kuhn, Warren, Karim, Farina, Ndung’u, Thumbi, Shalek, Alex K, Goulder, Philip, Leslie, Alasdair, and Kløverpris, Henrik N

Abstract

© 2020 The Author(s) Innate lymphoid cells (ILCs) are important for response to infection and for immune development in early life. HIV infection in adults depletes circulating ILCs, but the impact on children infected from birth remains unknown. We study vertically HIV-infected children from birth to adulthood and find severe and persistent depletion of all circulating ILCs that, unlike CD4+ T cells, are not restored by long-term antiretroviral therapy unless initiated at birth. Remaining ILCs upregulate genes associated with cellular activation and metabolic perturbation. Unlike HIV-infected adults, ILCs are also profoundly depleted in tonsils of vertically infected children. Transcriptional profiling of remaining ILCs reveals ongoing cell-type-specific activity despite antiretroviral therapy. Collectively, these data suggest an important and ongoing role for ILCs in lymphoid tissue of HIV-infected children from birth, where persistent depletion and sustained transcriptional activity are likely to have long-term immune consequences that merit further investigation.

Published
2022

39. An in vivo selection-derived d-peptide for engineering erythrocyte-binding antigens that promote immune tolerance

Author

Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Howard Hughes Medical Institute, Massachusetts Institute of Technology. Center for Environmental Health Sciences, Loftis, Alexander R, Zhang, Genwei, Backlund, Coralie, Quartararo, Anthony J, Pishesha, Novalia, Hanna, Cameron C, Schissel, Carly K, Garafola, Daniel, Loas, Andrei, Collier, R John, Ploegh, Hidde, Irvine, Darrell J, Pentelute, Bradley L, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Howard Hughes Medical Institute, Massachusetts Institute of Technology. Center for Environmental Health Sciences, Loftis, Alexander R, Zhang, Genwei, Backlund, Coralie, Quartararo, Anthony J, Pishesha, Novalia, Hanna, Cameron C, Schissel, Carly K, Garafola, Daniel, Loas, Andrei, Collier, R John, Ploegh, Hidde, Irvine, Darrell J, and Pentelute, Bradley L

Abstract

When displayed on erythrocytes, peptides and proteins can drive antigen-specific immune tolerance. Here, we investigated a straightforward approach based on erythrocyte binding to promote antigen-specific tolerance to both peptides and proteins. We first identified a robust erythrocyte-binding ligand. A pool of one million fully d-chiral peptides was injected into mice, blood cells were isolated, and ligands enriched on these cells were identified using nano-liquid chromatography–tandem mass spectrometry. One round of selection yielded a murine erythrocyte-binding ligand with an 80 nM apparent dissociation constant, Kd. We modified an 83-kDa bacterial protein and a peptide antigen derived from ovalbumin (OVA) with the identified erythrocyte-binding ligand. An administration of the engineered bacterial protein led to decreased protein-specific antibodies in mice. Similarly, mice given the engineered OVA-derived peptide had decreased inflammatory anti-OVA CD8+ T cell responses. These findings suggest that our tolerance-induction strategy is applicable to both peptide and protein antigens and that our in vivo selection strategy can be used for de novo discovery of robust erythrocyte-binding ligands.

Published
2022

40. Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells

Author

Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Jiang, Ruoyi, Meng, Hailong, Raddassi, Khadir, Fleming, Ira, Hoehn, Kenneth B, Dardick, Kenneth R, Belperron, Alexia A, Montgomery, Ruth R, Shalek, Alex K, Hafler, David A, Kleinstein, Steven H, Bockenstedt, Linda K, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Jiang, Ruoyi, Meng, Hailong, Raddassi, Khadir, Fleming, Ira, Hoehn, Kenneth B, Dardick, Kenneth R, Belperron, Alexia A, Montgomery, Ruth R, Shalek, Alex K, Hafler, David A, Kleinstein, Steven H, and Bockenstedt, Linda K

Abstract

The skin lesion erythema migrans (EM) is an initial sign of the Ixodes tick-transmitted Borreliella spirochetal infection known as Lyme disease. T cells and innate immune cells have previously been shown to predominate the EM lesion and promote the reaction. Despite the established importance of B cells and antibodies in preventing infection, the role of B cells in the skin immune response to Borreliella is unknown. Here, we used single-cell RNA-Seq in conjunction with B cell receptor (BCR) sequencing to immunophenotype EM lesions and their associated B cells and BCR repertoires. We found that B cells were more abundant in EM in comparison with autologous uninvolved skin; many were clonally expanded and had circulating relatives. EM-associated B cells upregulated the expression of MHC class II genes and exhibited preferential IgM isotype usage. A subset also exhibited low levels of somatic hypermutation despite a gene expression profile consistent with memory B cells. Our study demonstrates that single-cell gene expression with paired BCR sequencing can be used to interrogate the sparse B cell populations in human skin and reveals that B cells in the skin infection site in early Lyme disease expressed a phenotype consistent with local antigen presentation and antibody production.

Published
2022

41. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

Author

Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Kotliar, Dylan, Lin, Aaron E, Logue, James, Hughes, Travis K, Khoury, Nadine M, Raju, Siddharth S, Wadsworth, Marc H, Chen, Han, Kurtz, Jonathan R, Dighero-Kemp, Bonnie, Bjornson, Zach B, Mukherjee, Nilanjan, Sellers, Brian A, Tran, Nancy, Bauer, Matthew R, Adams, Gordon C, Adams, Ricky, Rinn, John L, Melé, Marta, Schaffner, Stephen F, Nolan, Garry P, Barnes, Kayla G, Hensley, Lisa E, McIlwain, David R, Shalek, Alex K, Sabeti, Pardis C, Bennett, Richard S, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Kotliar, Dylan, Lin, Aaron E, Logue, James, Hughes, Travis K, Khoury, Nadine M, Raju, Siddharth S, Wadsworth, Marc H, Chen, Han, Kurtz, Jonathan R, Dighero-Kemp, Bonnie, Bjornson, Zach B, Mukherjee, Nilanjan, Sellers, Brian A, Tran, Nancy, Bauer, Matthew R, Adams, Gordon C, Adams, Ricky, Rinn, John L, Melé, Marta, Schaffner, Stephen F, Nolan, Garry P, Barnes, Kayla G, Hensley, Lisa E, McIlwain, David R, Shalek, Alex K, Sabeti, Pardis C, and Bennett, Richard S

Abstract

© 2020 The Author(s) Single-cell profiling of circulating immune cells during Ebola virus (EBOV) infection in non-human primates resolves molecular correlates of viral tropism, characterizes replication dynamics within infected cells, and distinguishes expression changes that are mediated by viral infection from those due to cytokine signaling.

Published
2022

42. Identification of Highly Cross-Reactive Mimotopes for a Public T Cell Response in Murine Melanoma

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Chemical Engineering, Ragon Institute of MGH, MIT and Harvard, Grace, Beth E., Backlund, Coralie M., Morgan, Duncan M., Kang, Byong H., Singh, Nishant K., Huisman, Brooke D., Rappazzo, C. Garrett, Moynihan, Kelly D., Maiorino, Laura, Dobson, Connor S., Kyung, Taeyoon, Gordon, Khloe S., Holec, Patrick V., Mbah, Overbeck C. Takou, Garafola, Daniel, Wu, Shengwei, Love, J. Christopher, Wittrup, K. Dane, Irvine, Darrell J., Birnbaum, Michael E., Massachusetts Institute of Technology. Department of Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Chemical Engineering, Ragon Institute of MGH, MIT and Harvard, Grace, Beth E., Backlund, Coralie M., Morgan, Duncan M., Kang, Byong H., Singh, Nishant K., Huisman, Brooke D., Rappazzo, C. Garrett, Moynihan, Kelly D., Maiorino, Laura, Dobson, Connor S., Kyung, Taeyoon, Gordon, Khloe S., Holec, Patrick V., Mbah, Overbeck C. Takou, Garafola, Daniel, Wu, Shengwei, Love, J. Christopher, Wittrup, K. Dane, Irvine, Darrell J., and Birnbaum, Michael E.

Abstract

While immune checkpoint blockade results in durable responses for some patients, many others have not experienced such benefits. These treatments rely upon reinvigorating specific T cell-antigen interactions. However, it is often unknown what antigens are being recognized by T cells or how to potently induce antigen-specific responses in a broadly applicable manner. Here, we characterized the CD8+ T cell response to a murine model of melanoma following combination immunotherapy to determine the basis of tumor recognition. Sequencing of tumor-infiltrating T cells revealed a repertoire of highly homologous TCR sequences that were particularly expanded in treated mice and which recognized an antigen from an endogenous retrovirus. While vaccination against this peptide failed to raise a protective T cell response in vivo, engineered antigen mimotopes induced a significant expansion of CD8+ T cells cross-reactive to the original antigen. Vaccination with mimotopes resulted in killing of antigen-loaded cells in vivo yet showed modest survival benefit in a prophylactic vaccine paradigm. Together, this work demonstrates the identification of a dominant tumor-associated antigen and generation of mimotopes which can induce robust functional T cell responses that are cross-reactive to the endogenous antigen across multiple individuals.

Published
2022

43. Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases

Author

Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Computational and Systems Biology Program, Prakadan, Sanjay M, Alvarez-Breckenridge, Christopher A, Markson, Samuel C, Kim, Albert E, Klein, Robert H, Nayyar, Naema, Navia, Andrew W, Kuter, Benjamin M, Kolb, Kellie E, Bihun, Ivanna, Mora, Joana L, Bertalan, Mia Solana, Shaw, Brian, White, Michael, Kaplan, Alexander, Stocking, Jackson H, Wadsworth, Marc H, Lee, Eudocia Q, Chukwueke, Ugonma, Wang, Nancy, Subramanian, Megha, Rotem, Denisse, Cahill, Daniel P, Adalsteinsson, Viktor A, Miller, Jeffrey W, Sullivan, Ryan J, Carter, Scott L, Brastianos, Priscilla K, Shalek, Alex K, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Computational and Systems Biology Program, Prakadan, Sanjay M, Alvarez-Breckenridge, Christopher A, Markson, Samuel C, Kim, Albert E, Klein, Robert H, Nayyar, Naema, Navia, Andrew W, Kuter, Benjamin M, Kolb, Kellie E, Bihun, Ivanna, Mora, Joana L, Bertalan, Mia Solana, Shaw, Brian, White, Michael, Kaplan, Alexander, Stocking, Jackson H, Wadsworth, Marc H, Lee, Eudocia Q, Chukwueke, Ugonma, Wang, Nancy, Subramanian, Megha, Rotem, Denisse, Cahill, Daniel P, Adalsteinsson, Viktor A, Miller, Jeffrey W, Sullivan, Ryan J, Carter, Scott L, Brastianos, Priscilla K, and Shalek, Alex K

Abstract

AbstractLeptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlighting the need for new interventions. To examine the efficacy of immune checkpoint inhibitors (ICI) in patients with LMD, we completed two phase II clinical trials. Here, we investigate the cellular and molecular features underpinning observed patient trajectories in these trials by applying single-cell RNA and cell-free DNA profiling to longitudinal cerebrospinal fluid (CSF) draws from enrolled patients. We recover immune and malignant cell types in the CSF, characterize cell behavior changes following ICI, and identify genomic features associated with relevant clinical phenomena. Overall, our study describes the liquid LMD tumor microenvironment prior to and following ICI treatment and demonstrates clinical utility of cell-free and single-cell genomic measurements for LMD research.

Published
2022

44. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma

Author

Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Holden, Rebecca Lynn, Pentelute, Bradley L., Barouch, Dan H., Massachusetts Institute of Technology. Department of Chemistry, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Holden, Rebecca Lynn, Pentelute, Bradley L., and Barouch, Dan H.

Abstract

© 2021, The Author(s), under exclusive licence to Springer Nature America, Inc. Personal neoantigen vaccines have been envisioned as an effective approach to induce, amplify and diversify antitumor T cell responses. To define the long-term effects of such a vaccine, we evaluated the clinical outcome and circulating immune responses of eight patients with surgically resected stage IIIB/C or IVM1a/b melanoma, at a median of almost 4 years after treatment with NeoVax, a long-peptide vaccine targeting up to 20 personal neoantigens per patient (NCT01970358). All patients were alive and six were without evidence of active disease. We observed long-term persistence of neoantigen-specific T cell responses following vaccination, with ex vivo detection of neoantigen-specific T cells exhibiting a memory phenotype. We also found diversification of neoantigen-specific T cell clones over time, with emergence of multiple T cell receptor clonotypes exhibiting distinct functional avidities. Furthermore, we detected evidence of tumor infiltration by neoantigen-specific T cell clones after vaccination and epitope spreading, suggesting on-target vaccine-induced tumor cell killing. Personal neoantigen peptide vaccines thus induce T cell responses that persist over years and broaden the spectrum of tumor-specific cytotoxicity in patients with melanoma.

Published
2022

46. Cellular and transcriptional diversity over the course of human lactation

Author

Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Ragon Institute of MGH, MIT and Harvard, Koch Institute for Integrative Cancer Research at MIT, Nyquist, Sarah K, Gao, Patricia, Haining, Tessa KJ, Retchin, Michael R, Golan, Yarden, Drake, Riley S, Kolb, Kellie, Mead, Benjamin E, Ahituv, Nadav, Martinez, Micaela E, Shalek, Alex K, Berger, Bonnie, Goods, Brittany A, Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Ragon Institute of MGH, MIT and Harvard, Koch Institute for Integrative Cancer Research at MIT, Nyquist, Sarah K, Gao, Patricia, Haining, Tessa KJ, Retchin, Michael R, Golan, Yarden, Drake, Riley S, Kolb, Kellie, Mead, Benjamin E, Ahituv, Nadav, Martinez, Micaela E, Shalek, Alex K, Berger, Bonnie, and Goods, Brittany A

Abstract

Significance Human breast milk is the nutritional food source evolved specifically to meet the needs of infants, but much remains to be learned about its composition and changes over the course of lactation. Our description of the cellular components of breast milk, their associations with maternal–infant dyad metadata, and quantification of alterations at the gene and pathway levels provide a longitudinal picture of human breast milk cells across lactational time. These results pave the way for improved therapeutic support of healthy lactation and milk production.

Published
2022

47. Striosomes Mediate Value-Based Learning Vulnerable in Age and a Huntington’s Disease Model

Author

Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research at MIT, Ragon Institute of MGH, MIT and Harvard, Friedman, Alexander, Hueske, Emily, Drammis, Sabrina M, Toro Arana, Sebastian E, Nelson, Erik D, Carter, Cody W, Delcasso, Sebastien, Rodriguez, Raimundo X, Lutwak, Hope, DiMarco, Kaden S, Zhang, Qingyang, Rakocevic, Lara I, Hu, Dan, Xiong, Joshua K, Zhao, Jiajia, Gibb, Leif G, Yoshida, Tomoko, Siciliano, Cody A, Diefenbach, Thomas J, Ramakrishnan, Charu, Deisseroth, Karl, Graybiel, Ann M, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research at MIT, Ragon Institute of MGH, MIT and Harvard, Friedman, Alexander, Hueske, Emily, Drammis, Sabrina M, Toro Arana, Sebastian E, Nelson, Erik D, Carter, Cody W, Delcasso, Sebastien, Rodriguez, Raimundo X, Lutwak, Hope, DiMarco, Kaden S, Zhang, Qingyang, Rakocevic, Lara I, Hu, Dan, Xiong, Joshua K, Zhao, Jiajia, Gibb, Leif G, Yoshida, Tomoko, Siciliano, Cody A, Diefenbach, Thomas J, Ramakrishnan, Charu, Deisseroth, Karl, and Graybiel, Ann M

Abstract

© 2020 Elsevier Inc. Friedman et al. find that specialized regions of the striatum, a key part of the brain's movement and motivation control system, are essential for learning about the values of good and bad outcomes of decisions. The learning signals in striosomes scale according to subjective value and are vulnerable to decline with aging and in neurodegenerative disorders.

Published
2021

48. Evolution of Toll-like receptor 7/8 agonist therapeutics and their delivery approaches: From antiviral formulations to vaccine adjuvants

Author

Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Department of Chemical Engineering, Broad Institute of MIT and Harvard, Ragon Institute of MGH, MIT and Harvard, Bhagchandani, Sachin Haresh, Johnson, Jeremiah A., Irvine, Darrell J, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Department of Chemical Engineering, Broad Institute of MIT and Harvard, Ragon Institute of MGH, MIT and Harvard, Bhagchandani, Sachin Haresh, Johnson, Jeremiah A., and Irvine, Darrell J

Abstract

Imidazoquinoline derivatives (IMDs) and related compounds function as synthetic agonists of Toll-like receptors 7 and 8 (TLR7/8) and one is FDA approved for topical antiviral and skin cancer treatments. Nevertheless, these innate immune system-activating drugs have potentially much broader therapeutic utility; they have been pursued as antitumor immunomodulatory agents and more recently as candidate vaccine adjuvants for cancer and infectious disease. The broad expression profiles of TLR7/8, poor pharmacokinetic properties of IMDs, and toxicities associated with systemic administration, however, are formidable barriers to successful clinical translation. Herein, we review IMD formulations that have advanced to the clinic and discuss issues related to biodistribution and toxicity that have hampered the further development of these compounds. Recent strategies aimed at enhancing safety and efficacy, particularly through the use of bioconjugates and nanoparticle formulations that alter pharmacokinetics, biodistribution, and cellular targeting, are described. Finally, key aspects of the biology of TLR7 signaling, such as TLR7 tolerance, that may need to be considered in the development of new IMD therapeutics are discussed., NIH (UM1 AI144462), NIH (1R01CA22046801)

Published
2021

49. Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers

Author

National Institutes of Health (US), Bill & Melinda Gates Foundation, Foundation for AIDS Research, Consejo Superior de Investigaciones Científicas (España), Instituto de Salud Carlos III, European Commission, Junta de Andalucía, Harvard University, University of California, Centers for AIDS Research (US), National Institute of Allergy and Infectious Diseases (US), National Cancer Institute (US), Eunice Kennedy Shriver National Institute of Child Health and Human Development (US), National Heart, Lung, and Blood Institute (US), National Institute on Drug Abuse (US), National Institute of Mental Health (US), Delaney AIDS Research Enterprise, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology, Schwartz Family Foundation, Frederick National Laboratory for Cancer Research (US), Lian, Xiaodong, Gao, Ce, Sun, Xiaoming, Jiang, Chenyang, Einkauf, Kevin B., Seiger, Kyra W., Chevalier, Joshua M., Yuki, Yuko, Martin, Maureen, Hoh, Rebecca, Peluso, Michael J., Carrington, Mary, Ruiz-Mateos, Ezequiel, Deeks, Steven G., Rosenberg, Eric S, Walker, Bruce D., Lichterfeld, Mathias, Yu, Xu G., National Institutes of Health (US), Bill & Melinda Gates Foundation, Foundation for AIDS Research, Consejo Superior de Investigaciones Científicas (España), Instituto de Salud Carlos III, European Commission, Junta de Andalucía, Harvard University, University of California, Centers for AIDS Research (US), National Institute of Allergy and Infectious Diseases (US), National Cancer Institute (US), Eunice Kennedy Shriver National Institute of Child Health and Human Development (US), National Heart, Lung, and Blood Institute (US), National Institute on Drug Abuse (US), National Institute of Mental Health (US), Delaney AIDS Research Enterprise, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology, Schwartz Family Foundation, Frederick National Laboratory for Cancer Research (US), Lian, Xiaodong, Gao, Ce, Sun, Xiaoming, Jiang, Chenyang, Einkauf, Kevin B., Seiger, Kyra W., Chevalier, Joshua M., Yuki, Yuko, Martin, Maureen, Hoh, Rebecca, Peluso, Michael J., Carrington, Mary, Ruiz-Mateos, Ezequiel, Deeks, Steven G., Rosenberg, Eric S, Walker, Bruce D., Lichterfeld, Mathias, and Yu, Xu G.

Abstract

Increasing evidence suggests that durable drug-free control of HIV-1 replication is enabled by effective cellular immune responses that may induce an attenuated viral reservoir configuration with a weaker ability to drive viral rebound. Here, we comprehensively tracked effects of antiviral immune responses on intact and defective proviral sequences from elite controllers (ECs), analyzing both classical escape mutations and HIV-1 chromosomal integration sites as biomarkers of antiviral immune selection pressure. We observed that, within ECs, defective proviruses were commonly located in permissive genic euchromatin positions, which represented an apparent contrast to autologous intact proviruses that were frequently located in heterochromatin regions; this suggests differential immune selection pressure on intact versus defective proviruses in ECs. In comparison to individuals receiving antiretroviral therapy, intact and defective proviruses from ECs showed reduced frequencies of escape mutations in cytotoxic T cell epitopes and antibody contact regions, possibly due to the small and poorly inducible reservoir that may be insufficient to drive effective viral escape in ECs. About 15% of ECs harbored nef deletions in intact proviruses, consistent with increased viral vulnerability to host immunity in the setting of nef dysfunction. Together, these results suggest a distinct signature of immune footprints in proviral sequences from ECs.

Published
2021

50. Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Biological Engineering, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Mathematics, Hie, Brian, Bryson, Bryan D, Berger, Bonnie, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Biological Engineering, Ragon Institute of MGH, MIT and Harvard, Massachusetts Institute of Technology. Department of Mathematics, Hie, Brian, Bryson, Bryan D, and Berger, Bonnie

Abstract

© 2020 The Author(s) A machine learning algorithm that also reports its certainty about a prediction can help a researcher design new experiments. Algorithms called Gaussian processes trained with modern data can make accurate predictions with informative uncertainty. We leverage this approach to find nanomolar kinase binders, Mycobacterium tuberculosis inhibitors, mutations that enhance protein fluorescence, and genes important for cell development.

Published
2021

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