Preprints:

Single-cell metabolic dynamics of early activated CD8 T cells during the primary immune response to infection

Lauren S. Levine, Kamir J. Hiam, Diana M. Marquez, Iliana Tenvooren, Diana C. Contreras, Jeffrey C. Rathmell, Matthew H. Spitzer

bioRxiv 2020.01.21.911545; doi: https://doi.org/10.1101/2020.01.21.911545

 

SCITO-seq: single-cell combinatorial indexed cytometry sequencing

Byungjin Hwang, David S. Lee, Whitney Tamaki, Yang Sun, Anton Ogorodnikov, George Hartoularos, Aidan Winters, Yun S. Song, Eric D. Chow, Matthew H. Spitzer, Chun Jimmie Ye

bioRxiv 2020.03.27.012633; doi: https://doi.org/10.1101/2020.03.27.012633

 

Mitogen-independent cell cycle progression in B lymphocytes

Amit Singh, Matthew H. Spitzer, Jaimy P. Joy, Mary Kaileh, Xiang Qiu, Garry P. Nolan, Ranjan Sen

bioRxiv 796904; doi: https://doi.org/10.1101/796904

 

Cell type-specific monoclonal antibody cross-reactivity screening in non-human primates and development of comparative immunophenotyping panels for CyTOF

Zachary B Bjornson-Hooper, Gabriela K Fragiadakis, Matthew H Spitzer, Deepthi Madhireddy, Kevin Hu, Kelly Lundsten, Garry P Nolan

bioRxiv 577759; doi: https://doi.org/10.1101/577759

 

A comprehensive atlas of immunological differences between humans, mice and non-human primates

Zachary B Bjornson-Hooper, Gabriela K Fragiadakis, Matthew H Spitzer, Deepthi Madhireddy, Dave McIlwain, Garry P Nolan

bioRxiv 574160; doi: https://doi.org/10.1101/574160

 

Variation of immune cell responses in humans reveals sex-specific coordinated signaling across cell types

Gabriela K. Fragiadakis, Zachary B. Bjornson-Hooper, Deepthi Madhireddy, Karen Sachs, Matthew H. Spitzer, Sean C. Bendall, Garry P. Nolan

bioRxiv 567784; doi: https://doi.org/10.1101/567784

Peer-Reviewed Articles:

Landscape of coordinated immune responses to H1N1 challenge in humans.

Rahil Z, Leylek R, Schürch CM, Chen H, Bjornson-Hooper Z, Christensen SR, Gherardini PF, Bhate SS, Spitzer MH, Fragiadakis GK, Mukherjee N, Kim N, Jiang S, Yo J, Gaudilliere B, Affrime M, Bock B, Hensley SE, Idoyaga J, Aghaeepour N, Kim K, Nolan GP, McIlwain DR.

J Clin Invest. 2020 Oct 12:137265. doi: 10.1172/JCI137265. Online ahead of print.

PMID: 33044226

 

Functional CRISPR dissection of gene networks controlling human regulatory T cell identity.

Schumann K, Raju SS, Lauber M, Kolb S, Shifrut E, Cortez JT, Skartsis N, Nguyen VQ, Woo JM, Roth TL, Yu R, Nguyen MLT, Simeonov DR, Nguyen DN, Targ S, Gate RE, Tang Q, Bluestone JA, Spitzer MH, Ye CJ, Marson A.

Nat Immunol. 2020 Sep 28. doi: 10.1038/s41590-020-0784-4. Online ahead of print.

PMID: 32989329

 

ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network.

Atallah MB, Tandon V, Hiam KJ, Boyce H, Hori M, Atallah W, Spitzer MH, Engleman E, Mallick P.

BMC Bioinformatics. 2020 Aug 10;21(1):346. doi: 10.1186/s12859-020-03702-3.

PMID: 32778050

 

Intratumoral CD4⁺ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer.

Oh DY, Kwek SS, Raju SS, Li T, McCarthy E, Chow E, Aran D, Ilano A, Pai CS, Rancan C, Allaire K, Burra A, Sun Y, Spitzer MH, Mangul S, Porten S, Meng MV, Friedlander TW, Ye CJ, Fong L.

Cell. 2020 Jun 25;181(7):1612-1625.e13. doi: 10.1016/j.cell.2020.05.017. Epub 2020 Jun 3.

PMID: 32497499

 

Tumor Immune Profiling-Based Neoadjuvant Immunotherapy for Locally Advanced Melanoma.

Levine LS, Mahuron KM, Tsai KK, Wu C, Mattis DM, Pauli ML, Oglesby A, Lee JC, Spitzer MH, Krummel MF, Algazi AP, Rosenblum MD, Alvarado M, Daud AI.

Ann Surg Oncol. 2020 Jun 2. doi: 10.1245/s10434-020-08648-7. Online ahead of print.

PMID: 32488521

 

Systemic dysfunction and plasticity of the immune macroenvironment in cancer models.

Allen BM, Hiam KJ, Burnett CE, Venida A, DeBarge R, Tenvooren I, Marquez DM, Cho NW, Carmi Y, Spitzer MH.

Nat Med. 2020 May 25. doi: 10.1038/s41591-020-0892-6. Online ahead of print.

PMID: 32451499

 

Depletion of microbiome-derived molecules in the host using Clostridium genetics.

Guo CJ, Allen BM, Hiam KJ, Dodd D, Van Treuren W, Higginbottom S, Nagashima K, Fischer CR, Sonnenburg JL, Spitzer MH*, Fischbach MA*.

Science. 2019 Dec 13;366(6471). pii: eaav1282. doi: 10.1126/science.aav1282.

PMID: 31831639

 

Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity.

Zammit NW, Siggs OM, Gray PE, Horikawa K, Langley DB, Walters SN, Daley SR, Loetsch C, Warren J, Yap JY, Cultrone D, Russell A, Malle EK, Villanueva JE, Cowley MJ, Gayevskiy V, Dinger ME, Brink R, Zahra D, Chaudhri G, Karupiah G, Whittle B, Roots C, Bertram E, Yamada M, Jeelall Y, Enders A, Clifton BE, Mabbitt PD, Jackson CJ, Watson SR, Jenne CN, Lanier LL, Wiltshire T, Spitzer MH, Nolan GP, Schmitz F, Aderem A, Porebski BT, Buckle AM, Abbott DW, Ziegler JB, Craig ME, Benitez-Aguirre P, Teo J, Tangye SG, King C, Wong M, Cox MP, Phung W, Tang J, Sandoval W, Wertz IE, Christ D, Goodnow CC, Grey ST.

Nat Immunol. 2019 Oct;20(10):1299-1310. doi: 10.1038/s41590-019-0492-0. Epub 2019 Sep 18.

PMID: 31534238

 

De novo mutations in mitochondrial DNA of iPSCs produce immunogenic neoepitopes in mice and humans.

Deuse T, Hu X, Agbor-Enoh S, Koch M, Spitzer MH, Gravina A, Alawi M, Marishta A, Peters B, Kosaloglu-Yalcin Z, Yang Y, Rajalingam R, Wang D, Nashan B, Kiefmann R, Reichenspurner H, Valantine H, Weissman IL, Schrepfer S.

Nat Biotechnol. 2019 Oct;37(10):1137-1144. doi: 10.1038/s41587-019-0227-7. Epub 2019 Aug 19.

PMID: 31427818

 

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy.

Hartmann FJ, Babdor J, Gherardini PF, Amir ED, Jones K, Sahaf B, Marquez DM, Krutzik P, O'Donnell E, Sigal N, Maecker HT, Meyer E, Spitzer MH, Bendall SC.

Cell Rep. 2019 Jul 16;28(3):819-831.e4. doi: 10.1016/j.celrep.2019.06.049.

PMID: 31315057

 

Scalable Conjugation and Characterization of Immunoglobulins with Stable Mass Isotope Reporters for Single-Cell Mass Cytometry Analysis.

Hartmann FJ, Simonds EF, Vivanco N, Bruce T, Borges L, Nolan GP, Spitzer MH, Bendall SC.

Methods Mol Biol. 2019;1989:55-81. doi: 10.1007/978-1-4939-9454-0_5.

PMID: 31077099

 

Autocrine TGFβ Is a Survival Factor for Monocytes and Drives Immunosuppressive Lineage Commitment.

Gonzalez-Junca A, Driscoll KE, Pellicciotta I, Du S, Lo CH, Roy R, Parry R, Tenvooren I, Marquez DM, Spitzer MH, Barcellos-Hoff MH.

Cancer Immunol Res. 2019 Feb;7(2):306-320. doi: 10.1158/2326-6066.CIR-18-0310. Epub 2018 Dec 11.

PMID: 30538091

 

Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry.

Han G, Spitzer MH, Bendall SC, Fantl WJ, Nolan GP.

Nat Protoc. 2018 Oct;13(10):2121-2148. doi: 10.1038/s41596-018-0016-7.

PMID: 30258176

 

MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data.

Hu Z, Jujjavarapu C, Hughey JJ, Andorf S, Lee HC, Gherardini PF, Spitzer MH, Thomas CG, Campbell J, Dunn P, Wiser J, Kidd BA, Dudley JT, Nolan GP, Bhattacharya S, Butte AJ.

Cell Rep. 2018 Jul 31;24(5):1377-1388. doi: 10.1016/j.celrep.2018.07.003.

PMID: 30067990

 

Engineered Tumor-Targeted T Cells Mediate Enhanced Anti-Tumor Efficacy Both Directly and through Activation of the Endogenous Immune System.

Avanzi MP, Yeku O, Li X, Wijewarnasuriya DP, van Leeuwen DG, Cheung K, Park H, Purdon TJ, Daniyan AF, Spitzer MH, Brentjens RJ.

Cell Rep. 2018 May 15;23(7):2130-2141. doi: 10.1016/j.celrep.2018.04.051.

PMID: 29768210

 

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites.

Dodd D, Spitzer MH, Van Treuren W, Merrill BD,  Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA, Sonnenburg JL. 

Nature. 2017 Nov 30;551(7682):648-652. doi: 10.1038/nature24661.

PMID: 29168502

 

Jak1 Integrates Cytokine Sensing to Regulate Hematopoietic Stem Cell Function and Stress Hematopoiesis.

Kleppe M, Spitzer MH, Li S, Hill CE, Dong, Papalexi, De Groote S, Bowman RL, Keller M, Koppikar P, Rapaport FT, Teruya-Feldstein J, Gandara J, Mason CE, Nolan GP, Levine RL.

Cell Stem Cell. 2017 Sep 20. pii: S1934-5909(17)30329-6. doi: 10.1016/j.stem.2017.08.011.

PMID: 28965767

 

Mass Cytometric Analysis of HIV Entry, Replication, and Remodeling in Tissue CD4+ T Cells.

Cavrois M, Banerjee T, Mukherjee G, Raman N, Hussien R, Rodriguez BA, Vasquez J, Spitzer MH, Lazarus NH, Jones JJ, Ochsenbauer C, McCune JM, Butcher EC, Arvin AM, Sen N, Greene WC, Roan NR.

Cell Rep. 2017 Jul 25;20(4):984-998. doi: 10.1016/j.celrep.2017.06.087.

PMID: 28746881

 

Systemic Immunity Is Required for Effective Cancer Immunotherapy.

Spitzer MH, Carmi Y, Reticker-Flynn NE, Kwek SS, Madhireddy D, Martins MM, Gherardini PF, Prestwood TR, Chabon J, Bendall SC, Fong L, Nolan GP, Engleman EG.

Cell. 2017 Jan 10. pii: S0092-8674(16)31738-X. doi: 10.1016/j.cell.2016.12.022. [Epub ahead of print]

PMID: 28111070

 

Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states.

Furman D, Chang J, Lartigue L, Bolen CR, Haddad F, Gaudilliere B, Ganio EA, Fragiadakis GK, Spitzer MH, Douchet I, Daburon S, Moreau JF, Nolan GP, Blanco P, Déchanet-Merville J, Dekker CL, Jojic V, Kuo CJ, Davis MM, Faustin B.

Nat Med. 2017 Jan 16. doi: 10.1038/nm.4267.

 

Akt and SHP-1 are DC-intrinsic checkpoints for tumor immunity.

Carmi Y, Prestwood TR, Spitzer MH, Linde IL, Chabon J, Reticker-Flynn NE, Bhattacharya N, Zhang H, Zhang X, Basto PA, Burt BM, Alonso MN, Engleman EG.

JCI Insight. 2016 Nov 3;1(18):e89020.

PMID: 27812544

 

Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy.

Fragiadakis GK, Baca QJ, Gherardini PF, Ganio EA, Gaudilliere DK, Tingle M, Lancero HL, McNeil LS, Spitzer MH, Wong RJ, Shaw GM, Darmstadt GL, Sylvester KG, Winn VD, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MS, Gaudilliere BL. 

J Immunol. 2016 Oct 28. pii: 1601195.

PMID: 27793998

 

Automated mapping of phenotype space with single-cell data.

Samusik N, Good Z, Spitzer MH, Davis KL, Nolan GP.

Nat Methods. 2016 Jun;13(6):493-6. doi: 10.1038/nmeth.3863. Epub 2016 May 16.

PMID: 27183440

 

Mass Cytometry: Single Cells, Many Features.

Spitzer MH, Nolan GP.

Cell. 2016 May 5;165(4):780-91. doi: 10.1016/j.cell.2016.04.019. Review.

PMID: 27153492

 

An interactive reference framework for modeling a dynamic immune system.

Spitzer MH, Gherardini PF, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP.

Science. 2015 Jul 10;349(6244):1259425. doi: 10.1126/science.1259425.

PMID: 26160952

 

Allogeneic IgG combined with dendritic cell stimuli induce antitumour T-cell immunity.

Carmi Y, Spitzer MH, Linde IL, Burt BM, Prestwood TR, Perlman N, Davidson MG, Kenkel JA, Segal E, Pusapati GV, Bhattacharya N, Engleman EG.

Nature. 2015 May 7;521(7550):99-104. doi: 10.1038/nature14424. Epub 2015 Apr 29.

PMID: 25924063

 

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.

Zunder ER, Finck R, Behbehani GK, Amir el-AD, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, Fantl WJ, Pe'er D, Nolan GP.

Nat Protoc. 2015 Feb;10(2):316-33. doi: 10.1038/nprot.2015.020. Epub 2015 Jan 22.

PMID: 25612231

 

Single-cell mass cytometry of TCR signaling: amplification of small initial differences results in low ERK activation in NOD mice.

Mingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe'er D, Mathis D, Nolan GP, Benoist C.

Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16466-71. doi: 10.1073/pnas.1419337111. Epub 2014 Oct 31.

PMID: 25362052

 

Systems biology. Conditional density-based analysis of T cell signaling in single-cell data.

Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe'er D, Nolan GP.

Science. 2014 Nov 28;346(6213):1250689. doi: 10.1126/science.1250689. Epub 2014 Oct 23.

PMID: 25342659

 

A tetra(ethylene glycol) derivative of benzothiazole aniline enhances Ras-mediated spinogenesis.

Megill A, Lee T, DiBattista AM, Song JM, Spitzer MH, Rubinshtein M, Habib LK, Capule CC, Mayer M, Turner RS, Kirkwood A, Yang J, Pak DT, Lee HK, Hoe HS.

J Neurosci. 2013 May 29;33(22):9306-18. doi: 10.1523/JNEUROSCI.1615-12.2013. Erratum in: J Neurosci. 2014 Oct 1;34(40):13567. 

PMID: 23719799

 

The transcriptional landscape of αβ T cell differentiation.

Mingueneau M, Kreslavsky T, Gray D, Heng T, Cruse R, Ericson J, Bendall S, Spitzer MH, Nolan GP, Kobayashi K, von Boehmer H, Mathis D, Benoist C; Immunological Genome Consortium.

Nat Immunol. 2013 Jun;14(6):619-32. doi: 10.1038/ni.2590. Epub 2013 May 5.

PMID: 23644507