Grimes Lab

Publications

Li, G; Song, B; Singh, H; Prasath, S; Grimes, L; Salomonis, N. scTriangulate, a game-theory based framework for optimal solutions of uni- and multimodal single-cell data. 2021; 2021.10.16.464640.

Muench, DE; Olsson, A; Ferchen, K; Pham, G; Serafin, RA; Chutipongtanate, S; Dwivedi, P; Song, B; Hay, S; Chetal, K; Kappes, DJ; Way, SS; Salomonis, N; Grimes, HL. Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020; 582:109-114.

Olsson, A; Venkatasubramanian, M; Chaudhri, VK; Aronow, BJ; Salomonis, N; Singh, H; Grimes, HL. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016; 537:698-702.

Herro, R; Grimes, HL. The diverse roles of neutrophils from protection to pathogenesis. Nature Immunology. 2024; 25:2209-2219.

Sezaki, M; Yokota, A; Zhang, X; Pan, M; Wang, Z; Hashimoto, M; Nooruddin, Z; Pietras, EM; Salomonis, N; Grimes, HL; Huang, G. Luspatercept Promotes Heme Biosynthesis and Erythroblast Island Formation in a Novel Low-Risk MDS Mouse Model. Blood. 2024; 144:877.

Zhang, X; Li, G; Oliverio, A; VanOudenhove, J; DeZern, AE; Ghiaur, G; Halene, S; Grimes, HL; Salomonis, N. Clonal Dissection of MDS and Secondary AML Resolves Shared Splicing Neoantigens and Mechanistic Underpinnings of Hypomethylating Agent Therapeutic Response. Blood. 2024; 144:1810.

Ujoatu, E; Mukhopadhyay, S; Gurnari, C; Visconte, V; Maciejewski, J; Basu, J; Jha, BK; Grimes, HL; Sykes, S; Kappes, D. Oncogenic Nexus of TET2 with Thpok in Myeloid Neoplasia. Blood. 2024; 144:2716.

Oelschläger, L; Nicolet, D; Mrózek, K; Schnell, D; Alotaibi, N; Walker, CJ; Mims, A; Blachly, JS; Powell, BL; Kolitz, JE; Salomonis, N; Grimes, HL; Fornerod, M; Eisfeld, A. Transcriptomically Defined Acute Myeloid Leukemia, Myelodysplasia-Related (AML-MR) Phenotype Governs Mutation-Based Disease Group Assignment. Blood. 2024; 144:641.

Baassiri, A; Maziarz, J; Blackburn, HN; Maul-Newby, H; VanOudenhove, J; Zhang, X; Matthews, M; Paul, S; Liu, W; Sefik, E; Salomonis, N; Grimes, HL; Flavell, R; Halene, S. MISTRG6kitW41: Enhanced Engraftment in a Cytokine Humanized Patient-Derived Xenotransplantation Mouse Model. Blood. 2024; 144:1815.

Kain, BN; Sen, S; Nicolet, D; Bennett, SN; Bernardicius, D; Hu, Y; Walker, C; Eisfeld, A; Salomonis, N; Grimes, HL. Phip Is a Potent Leukemia Oncogene Identified in Acute Myeloid Leukemia (AML) Patients of African Ancestry. Blood. 2024; 144:327.

Stiff, A; Fornerod, M; Kain, BN; Nicolet, D; Kelly, BJ; Miller, KE; Mrózek, K; Boateng, I; Bollas, A; Garfinkle, EA R; Salomonis, N; Grimes, HL; Mardis, ER; Eisfeld, AK. Multiomic profiling identifies predictors of survival in African American patients with acute myeloid leukemia. Nature Genetics. 2024; 56:2434-2446.

Samer, EK; Morris, SA; Hutter, CM; Gilchrist, DA; Calluori, S; Bly, Z; Osorio, D; Zhang, L; He, W; Fu, R; Borsari, B; Assis, PR; Andreeva, K; Gerstein, MB. Deciphering the impact of genomic variation on function. Nature. 2024; 633:47-57.

Grimes, HL; Ferchen, K; Salomonis, N. 1008 – UNIFIED SINGLE-CELL METHODS SORT DIVERGENT FATES THROUGH GENE REGULATION. Experimental Hematology. 2024; 137:104309.

Zhang, X; Song, B; Carlino, MJ; Li, G; Ferchen, K; Chen, M; Thompson, EN; Kain, BN; Schnell, D; Thakkar, K; Singh, H; Krause, DS; Salomonis, N; Grimes, HL. An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors. Nature Immunology. 2024; 25:703-715.

Wu, Q; Zhang, J; Kumar, S; Shen, S; Kincaid, M; Johnson, CB; Zhang, YS; Turcotte, R; Alt, C; Ito, K; Ito, K; Way, SS; Kofron, JM; Lucas, D. Resilient anatomy and local plasticity of naive and stress haematopoiesis. Nature. 2024; 627:839-846.

Li, G; Mahajan, S; Ma, S; Jeffery, ED; Zhang, X; Bhattacharjee, A; Venkatasubramanian, M; Weirauch, MT; Miraldi, ER; Grimes, HL; Sheynkman, GM; Tilburgs, T; Salomonis, N. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science Translational Medicine. 2024; 16:eade2886.

Govindarajah, V; Sakabe, M; Good, S; Solomon, M; Arasu, A; Chen, N; Zhang, X; Grimes, HL; Kendler, A; Xin, M; Reynaud, D. Gestational diabetes in mice induces hematopoietic memory that affects the long-term health of the offspring. The Journal of Clinical Investigation. 2024; 134:e169730.

Ozga, M; Nicolet, D; Mrózek, K; Yilmaz, AS; Kohlschmidt, J; Larkin, KT; Blachly, JS; Oakes, CC; Buss, J; Walker, CJ; Salomonis, N; Herold, T; Mims, AS; Eisfeld, AK. Sex-associated differences in frequencies and prognostic impact of recurrent genetic alterations in adult acute myeloid leukemia (Alliance, AMLCG). Leukemia. 2024; 38:45-57.

Solomon, M; Song, B; Govindarajah, V; Good, S; Arasu, A; Hinton, EB; Thakkar, K; Bartram, J; Filippi, MD; Cancelas, JA; Salomonis, N; Grimes, HL; Reynaud, D. Slow cycling and durable Flt3+ progenitors contribute to hematopoiesis under native conditions. The Journal of Experimental Medicine. 2024; 221:e20231035.

Li, G; Song, B; Singh, H; Surya Prasath, VB; Leighton Grimes, H; Salomonis, N. Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nature Communications. 2023; 14:406.

Walulik, S; Dean, S; Vick, EJ; Zhu, X; Wunderlich, M; Chou, C; Choi, K; Grimes, HL; Starczynowski, DT; Miles, LA; Volk, A. The Mechanism of Therapy Resistance By Lineage Plasticity in AML and How to Overcome It. Blood. 2023; 142:1410.

Sezaki, M; Hashimoto, M; Yokota, A; Salomonis, N; Grimes, HL; Huang, G. Downregulation of Mitochondrial Complex II (MC II) in Myelodysplastic Syndromes. Blood. 2023; 142:4583.

Stiff, A; Nicolet, D; Fornerod, M; Kelly, B; Miller, K; Mrózek, K; Boateng, I; Kain, BN; Garfinkle, E; Hu, EY; Byrd, JC; Grimes, HL; Mardis, ER; Eisfeld, A. Genomic Profiles and Associated Survival Prognosticators in Black Patients with Acute Myeloid Leukemia. Blood. 2023; 142:837.

Zhang, X; Leighton Grimes, H. Improved detection of measurable residual disease in acute myeloid leukemia. Science Advances. 2023; 9:eadk2533.

Thompson, EN; Carlino, MJ; Scanlon, VM; Grimes, HL; Krause, DS. Assay optimization for the objective quantification of human multilineage colony-forming units. Experimental Hematology. 2023; 124:36-44.e3.

Basu, J; Olsson, A; Ferchen, K; Titerina, EK; Chetal, K; Nicolas, E; Czyzewicz, P; Levchenko, D; Ge, L; Hua, X; Grimes, HL; Salomonis, N; Kappes, DJ. ThPOK is a critical multifaceted regulator of myeloid lineage development. Nature Immunology. 2023; 24:1295-1307.

Kesarwani, M; Kincaid, Z; Azhar, M; Menke, J; Schwieterman, J; Ansari, S; Reaves, A; Deininger, ME; Levine, R; Grimes, HL; Azam, M. MAPK-negative feedback regulation confers dependence to JAK2V617F signaling. Leukemia. 2023; 37:1686-1697.

Ferchen, K; Salomonis, N; Grimes, HL. pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells. Editor, Kelso J. Bioinformatics. 2023; 39:btad287.

Song, B; Zhang, X; Bennett, S; Ma, S; Ferchen, K; Salomonis, N; Grimes, HL. High-throughput workflow leveraging spectral flow cytometry and CITE-seq to characterize human bone marrow across race and gender. Journal of immunology (Baltimore, Md. : 1950). 2023; 210:250.13.

Ferchen, K; Song, B; Potter, C; Zhang, X; Chou, C; Khodoun, M; Finkelman, FD; Salomonis, N; Grimes, HL. Th2 immune responses induced by helminth infection reprogram multilineage progenitors to produce successive waves of neutrophils, basophils, and eosinophils. Journal of immunology (Baltimore, Md. : 1950). 2023; 210:65.01.

Song, B; Zhang, X; Steele, H; Chou, C; Ferchen, K; Salomonis, N; Herro, R; Grimes, HL. Live bacterial ligands universally regulate mTOR activity but are not essential for homeostatic innate immunity. Journal of immunology (Baltimore, Md. : 1950). 2023; 210:65.05.

Solomon, M; Song, BA; Govindarajah, V; Good, S; Bartram, J; Cancelas, J; Filippi, M; Salomonis, N; Grimes, HL; Reynaud, D. Hematopoietic Flt3+ Multipotent Progenitors Are Organized in Discrete Functionally and Hierarchically Distinct Populations. Blood. 2022; 140:1981-1982.

Colom Diaz, PA; Chou, C; Mistry, JJ; Salomonis, N; Daud Khan, M; Grimes, HL; Trowbridge, JJ. Metallothionein 1 (MT1) Is Selectively Required for DNMT3A;NPM1-Mutant Acute Myeloid Leukemia Proliferation. Blood. 2022; 140:9103-9104.

Ozga, MP; Nicolet, D; Mrózek, K; Yilmaz, S; Kohlschmidt, J; Larkin, KT; Blachly, JS; Oakes, CC; Buss, J; Walker, CJ; Salomonis, N; Herold, T; Mims, AS; Eisfeld, A. Sex-Associated Differences in Frequencies and Outcome Prognostication of Recurrent Molecular Features in Adults with Acute Myeloid Leukemia (AML) (AMLCG, CALGB [Alliance]). Blood. 2022; 140:936-939.

Ferchen, K; Song, BA; Chou, C; Zhang, X; Salomonis, N; Grimes, HL. Identification and Isolation of Hematopoietic Stem Cells and Progenitors with Discrete Developmental Gene Expression Programs. Blood. 2022; 140:2856.

Zhang, X; Song, BA; Khan, MD; Ferchen, K; Chou, C; Li, G; DeZern, AE; Ghiaur, G; Halene, S; Salomonis, N; Grimes, HL. Single-Cell Multiomics Reveal Hypomethylating Agent Partially Restores Hematopoiesis in a LR-MDS Patient at the Cost of Leukemic Transformation. Blood. 2022; 140:9759-9760.

Romano, L; Seu, KG; Papoin, J; Muench, DE; Konstantinidis, D; Olsson, A; Schlum, K; Chetal, K; Chasis, JA; Mohandas, N; Grimes, HL; Salomonis, N; Blanc, L; Kalfa, TA. Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis. Blood. 2022; 140:1621-1634.

Avellino, R; Mulet-Lazaro, R; Havermans, M; Hoogenboezem, R; Smeenk, L; Salomonis, N; Schneider, RK; Rombouts, E; Bindels, E; Grimes, L; Delwel, R. Induced cell-autonomous neutropenia systemically perturbs hematopoiesis in Cebpa enhancer-null mice. Blood Advances. 2022; 6:1406-1419.

Díaz, PC; Chou, C; Mistry, J; Khan, MD; Salomonis, N; Grimes, HL; Trowbridge, J. 3055 – METALLOTHIONEIN 1 (MT1) AS A TARGETABLE DEPENDENCY IN ACUTE MYELOID LEUKEMIA. Experimental Hematology. 2022; 111:s72.

Leighton Grimes, H; Ferchen, K; Salomonis, N; Song, B; Zhang, X. 2007 – IDENTIFICATION AND ISOLATION OF HEMATOPOIETIC STEM CELLS AND PROGENITORS WITH DISCRETE DEVELOPMENTAL GENE EXPRESSION PROGRAMS. Experimental Hematology. 2022; 111:s35.

Song, B; Ferchen, K; Chou, C; Zhang, X; Steele, H; Herro, R; Salomonis, N; Grimes, HL. 3194 – LIVE BACTERIAL LIGANDS PROGRAM CORE HEMATOPOIETIC GENE EXPRESSION. Experimental Hematology. 2022; 111:s142.

Bono, C; Guerrero, P; Jordán-Pla, A; Erades, A; Salomonis, N; Grimes, HL; Gil, ML; Yáñez, A. GM-CSF Programs Hematopoietic Stem and Progenitor Cells During Candida albicans Vaccination for Protection Against Reinfection. Frontiers in Immunology. 2021; 12:790309.

Zhang, X; Grimes, HL. Why Single-Cell Sequencing Has Promise in MDS. Frontiers in Oncology. 2021; 11:769753.

Li, G; Song, B; Singh, H; Prasath, S; Grimes, L; Salomonis, N. scTriangulate, a game-theory based framework for optimal solutions of uni- and multimodal single-cell data. 2021; 2021.10.16.464640.

Steele, H; Song, B; Willicut, A; Grimes, HL; Herro, R. Isolation of primary immune cells from fibrotic skin, esophageal, and gut tissue. Journal of Immunological Methods. 2021; 497:113107.

Basu, J; Reis, BS; Peri, S; Zha, J; Hua, X; Ge, L; Ferchen, K; Nicolas, E; Czyzewicz, P; Cai, KQ; Grimes, HL; Grivennikov, SI; Mucida, D; Kappes, DJ. Essential role of a ThPOK autoregulatory loop in the maintenance of mature CD4+ T cell identity and function. Nature Immunology. 2021; 22:969-982.

Serrano-Lopez, J; Hegde, S; Kumar, S; Serrano, J; Fang, J; Wellendorf, AM; Roche, PA; Rangel, Y; Carrington, LJ; Geiger, H; Maillard, I; Sanchez-Garcia, J; Starczynowski, DT; Cancelas, JA. Systemic inflammation recruits fast-acting anti-inflammatory innate myeloid progenitors from BM into lymphatics. eLife. 2021; 10:1-60.

Serrano-Lopez, J; Hegde, S; Kumar, S; Serrano, J; Fang, J; Wellendorf, AM; Roche, PA; Rangel, Y; Carrington, LJ; Geiger, H; Maillard, I; Sanchez-Garcia, J; Starczynowski, DT; Cancelas, JA. Inflammation rapidly recruits mammalian GMP and MDP from bone marrow into regional lymphatics. eLife. 2021; 10:e66190.

Zhang, J; Wu, Q; Johnson, CB; Pham, G; Kinder, JM; Olsson, A; Slaughter, A; May, M; Weinhaus, B; D’Alessandro, A; Way, SS; Salomonis, N; Grimes, HL; Lucas, D. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature. 2021; 590:457-462.

Ye, H; Minhajuddin, M; Krug, A; Pei, S; Chou, C; Culp-Hill, R; Ponder, J; De Bloois, E; Schniedewind, B; Amaya, ML; Christians, U; Grimes, HL; D'Alessandro, A; Jordan, CT. The Hepatic Microenvironment Uniquely Protects Leukemia Cells through Induction of Growth and Survival Pathways Mediated by LIPG. Cancer Discovery. 2021; 11:500-519.

Dwivedi, P; Chutipongtanate, S; Muench, DE; Azam, M; Grimes, HL; Greis, KD. SWATH-Proteomics of Ibrutinib's Action in Myeloid Leukemia Initiating Mutated G-CSFR Signaling. Proteomics: Clinical Applications. 2020; 14:e1900144.

Kwok, I; Becht, E; Xia, Y; Ng, M; Teh, YC; Tan, L; Evrard, M; Li, JL Y; Tran, HT N; Tan, Y; Newell, EW; Cheng, T; Ginhoux, F; Ng, LG. Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor. Immunity. 2020; 53:303-318.e5.

Muench, DE; Olsson, A; Ferchen, K; Pham, G; Serafin, RA; Chutipongtanate, S; Dwivedi, P; Song, B; Hay, S; Chetal, K; Kappes, DJ; Way, SS; Salomonis, N; Grimes, HL. Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020; 582:109-114.

Hinge, A; He, J; Bartram, J; Javier, J; Xu, J; Fjellman, E; Sesaki, H; Li, T; Yu, J; Wunderlich, M; Mulloy, J; Kofron, M; Salomonis, N; Grimes, HL; Filippi, M. Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition. Cell Stem Cell. 2020; 26:420-430.e6.