1
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Loi S, Salgado R, Schmid P, Cortes J, Cescon DW, Winer EP, Toppmeyer DL, Rugo HS, De Laurentiis M, Nanda R, Iwata H, Awada A, Tan AR, Sun Y, Karantza V, Wang A, Huang L, Saadatpour A, Cristescu R, Yearley J, Lunceford J, Jelinic P, Adams S. Association Between Biomarkers and Clinical Outcomes of Pembrolizumab Monotherapy in Patients With Metastatic Triple-Negative Breast Cancer: KEYNOTE-086 Exploratory Analysis. JCO Precis Oncol 2023; 7:e2200317. [PMID: 37099733 DOI: 10.1200/po.22.00317] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
PURPOSE In the two-cohort phase II KEYNOTE-086 study (ClinicalTrials.gov identifier: NCT02447003), first-line and second-line or later pembrolizumab monotherapy demonstrated antitumor activity in metastatic triple-negative breast cancer (mTNBC; N = 254). This exploratory analysis evaluates the association between prespecified molecular biomarkers and clinical outcomes. METHODS Cohort A enrolled patients with disease progression after one or more systemic therapies for metastatic disease irrespective of PD-L1 status; Cohort B enrolled patients with previously untreated PD-L1-positive (combined positive score [CPS] ≥ 1) metastatic disease. The association between the following biomarkers as continuous variables and clinical outcomes (objective response rate [ORR], progression-free survival [PFS], and overall survival [OS]) was evaluated: PD-L1 CPS (immunohistochemistry), cluster of differentiation 8 (CD8; immunohistochemistry), stromal tumor-infiltrating lymphocyte (sTIL; hematoxylin and eosin staining), tumor mutational burden (TMB; whole-exome sequencing [WES]), homologous recombination deficiency-loss of heterozygosity, mutational signature 3 (WES), mutational signature 2 (apolipoprotein B mRNA editing catalytic polypeptide-like; WES), T-cell-inflamed gene expression profile (TcellinfGEP; RNA sequencing), and 10 non-TcellinfGEP signatures (RNA sequencing); Wald test P values were calculated, and significance was prespecified at α = 0.05. RESULTS In the combined cohorts (A and B), PD-L1 (P = .040), CD8 (P < .001), sTILs (P = .012), TMB (P = .007), and TcellinfGEP (P = .011) were significantly associated with ORR; CD8 (P < .001), TMB (P = .034), Signature 3 (P = .009), and TcellinfGEP (P = .002) with PFS; and CD8 (P < .001), sTILs (P = .004), TMB (P = .025), and TcellinfGEP (P = .001) with OS. None of the non-TcellinfGEP signatures were associated with outcomes of pembrolizumab after adjusting for the TcellinfGEP. CONCLUSION In this exploratory biomarker analysis from KEYNOTE-086, baseline tumor PD-L1, CD8, sTILs, TMB, and TcellinfGEP were associated with improved clinical outcomes of pembrolizumab and may help identify patients with mTNBC who are most likely to respond to pembrolizumab monotherapy.
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Affiliation(s)
- Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne, Parkville, Australia
| | | | - Peter Schmid
- Barts ECMC, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- Barts Health NHS Trust, London, United Kingdom
| | - Javier Cortes
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quironsalud Group, Madrid, Barcelona, Spain
- Faculty of Biomedical and Health Sciences, Department of Medicine, Universidad Europea de Madrid, Madrid, Spain
| | - David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Eric P Winer
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | - Hope S Rugo
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | | | | | - Ahmad Awada
- Medical Oncology Clinic, Institut Jules Bordet, Brussels, Belgium
| | | | | | | | | | | | | | | | | | | | | | - Sylvia Adams
- Perlmutter Cancer Center, NYU Langone Health, New York, NY
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2
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Bellmunt J, de Wit R, Fradet Y, Climent MA, Petrylak DP, Lee JL, Fong L, Necchi A, Sternberg CN, O'Donnell PH, Powles T, Plimack ER, Bajorin DF, Balar AV, Castellano D, Choueiri TK, Culine S, Gerritsen W, Gurney H, Quinn DI, Vuky J, Vogelzang NJ, Cristescu R, Lunceford J, Saadatpour A, Loboda A, Ma J, Rajasagi M, Godwin JL, Homet Moreno B, Grivas P. Putative Biomarkers of Clinical Benefit With Pembrolizumab in Advanced Urothelial Cancer: Results from the KEYNOTE-045 and KEYNOTE-052 Landmark Trials. Clin Cancer Res 2022; 28:2050-2060. [PMID: 35247908 DOI: 10.1158/1078-0432.ccr-21-3089] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE In an exploratory analysis, we investigated the association between programmed death ligand 1 (PD-L1), tumor mutational burden (TMB), T-cell-inflamed gene expression profile (TcellinfGEP), and stromal signature with outcomes of pembrolizumab in urothelial carcinoma (UC). PATIENTS AND METHODS Patients with advanced UC received first-line pembrolizumab 200 mg every 3 weeks in the single-arm phase II KEYNOTE-052 trial (NCT02335424) and salvage pembrolizumab 200 mg every 3 weeks or chemotherapy (paclitaxel/docetaxel/vinflunine) in the randomized phase III KEYNOTE-045 trial (NCT02256436). The association of each biomarker (continuous variable) with objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) was evaluated using logistic regression (ORR) and Cox PH (PFS, OS), adjusted for ECOG PS; nominal P values were calculated without multiplicity adjustment (one-sided, pembrolizumab; two-sided, chemotherapy). Significance was prespecified at α = 0.05. RESULTS In KEYNOTE-052, PD-L1, TMB, and TcellinfGEP were significantly associated with improved outcomes; stromal signature was significantly associated with worse outcomes. In KEYNOTE-045, although findings for TMB and TcellinfGEP with pembrolizumab were consistent with those of KEYNOTE-052, PD-L1 was not significantly associated with improved outcomes, nor was stromal signature associated with worse outcomes with pembrolizumab; chemotherapy was not associated with outcomes in a consistent manner for any of the biomarkers. Hazard ratio (HR) estimates at prespecified cutoffs showed an advantage for pembrolizumab versus chemotherapy regardless of PD-L1 or TMB, with a trend toward lower HRs in the combined positive score ≥10 and the TMB ≥175 mutation/exome subgroup. For TcellinfGEP, PFS and OS HRs were lower in the TcellinfGEP-nonlow subgroup regardless of treatment. CONCLUSIONS Multiple biomarkers characterizing the tumor microenvironment may help predict response to pembrolizumab monotherapy in UC, and potential clinical utility of these biomarkers may be context-dependent.
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Affiliation(s)
- Joaquim Bellmunt
- Department of Hematology and Oncology, Beth Israel Deaconess Medical Center, and IMIM-PSMAR Lab Harvard Medical School, Boston, Massachusetts
| | - Ronald de Wit
- Department of MedOnc, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Yves Fradet
- Department of Surgery/Urology, Centre Hospitalier Universitaire de Québec-Université Laval, Quebec City, QC, Canada
| | - Miguel A Climent
- Department of Medical Oncology, Fundación Instituto Valenciano de Oncología, Valencia, Spain
| | - Daniel P Petrylak
- Department of Internal Medicine/Medical Oncology, Yale New Haven Health, Smilow Cancer Hospital, New Haven, Connecticut
| | - Jae-Lyun Lee
- Department of Oncology, Asan Medical Center and University of Ulsan College of Medicine, Seoul, South Korea
| | - Lawrence Fong
- Department of Medicine, UCLA, Los Angeles, California
| | - Andrea Necchi
- Department of Medical Oncology, Vita-Salute San Raffaele University and IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy
| | - Cora N Sternberg
- Englander Institute for Precision Medicine, Department of Hematology and Oncology, Weill Cornell Medicine, Meyer Cancer Center, New York, New York
| | - Peter H O'Donnell
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Thomas Powles
- Department of Genitourinary Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Elizabeth R Plimack
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arjun V Balar
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Daniel Castellano
- Department of Medical Oncology, Hospital Universitario 12 de Octubre (CiberOnc), Madrid, Spain
| | | | - Stephane Culine
- Department of Medical Oncology, Hôpital Saint-Louis, Paris, France
| | - Winald Gerritsen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Howard Gurney
- Department of Medical Oncology, Westmead Hospital and Macquarie University, Sydney, NSW, Australia
| | - David I Quinn
- Department of Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Jacqueline Vuky
- Department of Medicine/Oncology, Oregon Health & Science University, Portland, Oregon
| | - Nicholas J Vogelzang
- Department of Medical Oncology, Comprehensive Cancer Centers of Nevada, Las Vegas, Nevada
| | - Razvan Cristescu
- Department of Translational Medicine, Merck & Co., Inc., Kenilworth, New Jersey
| | - Jared Lunceford
- Department of Translational Oncology Statistics, Merck & Co., Inc., Kenilworth, New Jersey
| | - Assieh Saadatpour
- Department of Genome and Biomarker Sciences, Merck & Co., Inc., Kenilworth, New Jersey
| | - Andrey Loboda
- Department of Translational Medicine, Merck & Co., Inc., Kenilworth, New Jersey
| | - Junshui Ma
- Department of Translational Oncology Statistics, Merck & Co., Inc., Kenilworth, New Jersey
| | - Mohini Rajasagi
- Department of Oncology Early Development, Merck & Co., Inc., Kenilworth, New Jersey
| | | | | | - Petros Grivas
- Department of Medicine, Division of Oncology, University of Washington, Fred Hutchinson Cancer Research Center, Seattle Cancer Care Alliance, Seattle, Washington
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3
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Cartwright ANR, Suo S, Badrinath S, Kumar S, Melms J, Luoma A, Bagati A, Saadatpour A, Izar B, Yuan GC, Wucherpfennig KW. Immunosuppressive Myeloid Cells Induce Nitric Oxide-Dependent DNA Damage and p53 Pathway Activation in CD8 + T Cells. Cancer Immunol Res 2021; 9:470-485. [PMID: 33514509 DOI: 10.1158/2326-6066.cir-20-0085] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 10/13/2020] [Accepted: 01/26/2021] [Indexed: 01/01/2023]
Abstract
Tumor-infiltrating myeloid-derived suppressor cells (MDSC) are associated with poor survival outcomes in many human cancers. MDSCs inhibit T cell-mediated tumor immunity in part because they strongly inhibit T-cell function. However, whether MDSCs inhibit early or later steps of T-cell activation is not well established. Here we show that MDSCs inhibited proliferation and induced apoptosis of CD8+ T cells even in the presence of dendritic cells (DC) presenting a high-affinity cognate peptide. This inhibitory effect was also observed with delayed addition of MDSCs to cocultures, consistent with functional data showing that T cells expressed multiple early activation markers even in the presence of MDSCs. Single-cell RNA-sequencing analysis of CD8+ T cells demonstrated a p53 transcriptional signature in CD8+ T cells cocultured with MDSCs and DCs. Confocal microscopy showed induction of DNA damage and nuclear accumulation of activated p53 protein in a substantial fraction of these T cells. DNA damage in T cells was dependent on the iNOS enzyme and subsequent nitric oxide release by MDSCs. Small molecule-mediated inhibition of iNOS or inactivation of the Nos2 gene in MDSCs markedly diminished DNA damage in CD8+ T cells. DNA damage in CD8+ T cells was also observed in KPC pancreatic tumors but was reduced in tumors implanted into Nos2-deficient mice compared with wild-type mice. These data demonstrate that MDSCs do not block early steps of T-cell activation but rather induce DNA damage and p53 pathway activation in CD8+ T cells through an iNOS-dependent pathway.
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Affiliation(s)
- Adam N R Cartwright
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Shengbao Suo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Soumya Badrinath
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Sushil Kumar
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Johannes Melms
- Columbia Center for Translational Immunology, New York, New York.,Columbia University Medical Center, Division of Hematology and Oncology, New York, New York
| | - Adrienne Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Archis Bagati
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Assieh Saadatpour
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Benjamin Izar
- Columbia Center for Translational Immunology, New York, New York.,Columbia University Medical Center, Division of Hematology and Oncology, New York, New York
| | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Immunology, Harvard Medical School, Boston, Massachusetts.,Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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4
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Ledermann J, Shapira-Frommer R, Santin A, Lisyanskaya A, Pignata S, Vergote I, Raspagliesi F, Sonke G, Birrer M, Provencher D, Sehouli J, Colombo N, González Martín A, Oaknin A, Saadatpour A, Kobie J, Jelinic P, Stein K, Matulonis U. 843P Association of gene expression signatures and TMB with response to pembrolizumab (pembro) in patients (pts) with recurrent ovarian cancer (ROC) enrolled in KEYNOTE-100. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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5
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Grivas P, Balar A, Vuky J, de Wit R, Vogelzang N, Choueiri T, Bajorin D, Castellano Gauna D, Gerritsen W, Gurney H, Quinn D, Culine S, Fradet Y, Saadatpour A, Loboda A, Ma J, Rajasagi M, Godwin J, Moreno B, Bellmunt J. 744P Association between gene expression signatures (sigs) and pembrolizumab (pembro) efficacy in patients (pts) with advanced urothelial cancer (UC). Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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6
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McCarthy N, Manieri E, Storm EE, Saadatpour A, Luoma AM, Kapoor VN, Madha S, Gaynor LT, Cox C, Keerthivasan S, Wucherpfennig K, Yuan GC, de Sauvage FJ, Turley SJ, Shivdasani RA. Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient. Cell Stem Cell 2020; 26:391-402.e5. [PMID: 32084389 DOI: 10.1016/j.stem.2020.01.008] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/27/2019] [Accepted: 01/15/2020] [Indexed: 12/13/2022]
Abstract
Intestinal stem cells (ISCs) are confined to crypt bottoms and their progeny differentiate near crypt-villus junctions. Wnt and bone morphogenic protein (BMP) gradients drive this polarity, and colorectal cancer fundamentally reflects disruption of this homeostatic signaling. However, sub-epithelial sources of crucial agonists and antagonists that organize this BMP gradient remain obscure. Here, we couple whole-mount high-resolution microscopy with ensemble and single-cell RNA sequencing (RNA-seq) to identify three distinct PDGFRA+ mesenchymal cell types. PDGFRA(hi) telocytes are especially abundant at the villus base and provide a BMP reservoir, and we identified a CD81+ PDGFRA(lo) population present just below crypts that secretes the BMP antagonist Gremlin1. These cells, referred to as trophocytes, are sufficient to expand ISCs in vitro without additional trophic support and contribute to ISC maintenance in vivo. This study reveals intestinal mesenchymal structure at fine anatomic, molecular, and functional detail and the cellular basis for a signaling gradient necessary for tissue self-renewal.
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Affiliation(s)
- Neil McCarthy
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Elisa Manieri
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Elaine E Storm
- Department of Molecular Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Assieh Saadatpour
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Varun N Kapoor
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Shariq Madha
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Liam T Gaynor
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Graduate Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Christian Cox
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Shilpa Keerthivasan
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Kai Wucherpfennig
- Department of Molecular Oncology, Genentech, South San Francisco, CA 94080, USA; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Guo-Cheng Yuan
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | | | - Shannon J Turley
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA.
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7
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Joyce CE, Saadatpour A, Ruiz-Gutierrez M, Bolukbasi OV, Jiang L, Thomas DD, Young S, Hofmann I, Sieff CA, Myers KC, Whangbo J, Libermann TA, Nusbaum C, Yuan GC, Shimamura A, Novina CD. TGFβ signaling underlies hematopoietic dysfunction and bone marrow failure in Shwachman-Diamond Syndrome. J Clin Invest 2019; 129:3821-3826. [PMID: 31211692 DOI: 10.1172/jci125375] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Shwachman-Diamond Syndrome (SDS) is a rare and clinically-heterogeneous bone marrow (BM) failure syndrome caused by mutations in the Shwachman-Bodian-Diamond Syndrome (SBDS) gene. Although SDS was described over 50 years ago, the molecular pathogenesis is poorly understood due, in part, to the rarity and heterogeneity of the affected hematopoietic progenitors. To address this, we used single cell RNA sequencing to profile scant hematopoietic stem and progenitor cells from SDS patients. We generated a single cell map of early lineage commitment and found that SDS hematopoiesis was left-shifted with selective loss of granulocyte-monocyte progenitors. Transcriptional targets of transforming growth factor-beta (TGFβ) were dysregulated in SDS hematopoietic stem cells and multipotent progenitors, but not in lineage-committed progenitors. TGFβ inhibitors (AVID200 and SD208) increased hematopoietic colony formation of SDS patient BM. Finally, TGFβ3 and other TGFβ pathway members were elevated in SDS patient blood plasma. These data establish the TGFβ pathway as a novel candidate biomarker and therapeutic target in SDS and translate insights from single cell biology into a potential therapy.
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Affiliation(s)
- Cailin E Joyce
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Melisa Ruiz-Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ozge Vargel Bolukbasi
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Lan Jiang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Dolly D Thomas
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah Young
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Inga Hofmann
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Colin A Sieff
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kasiani C Myers
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jennifer Whangbo
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Towia A Libermann
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Beth Israel Deaconess Medical Center Genomics, Proteomics, Bioinformatics and Systems Biology Center, Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Chad Nusbaum
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Akiko Shimamura
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Carl D Novina
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
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8
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Cartwright AN, Jiang P, Saadatpour A, Yuan GC, Liu SX, Wucherpfennig KW. Abstract A176: Overcoming CD8 T-cell suppression in the tumor microenvironment. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-a176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
CD8 T-cell-mediated antitumor immunity is required for the control and elimination of tumors. However, tumors are able to overcome immune response resulting in immunosuppression, tumor growth, and metastatic spread. CD8 T-cells are controlled through a homeostatic network of positive and negative feedback loops. These negative signals are exploited by the tumor and associated suppressive cell populations in the tumor microenvironment. Immunotherapies targeted to receptors that control these negative signals, termed immune checkpoint inhibitors, have provided robust and durable responses to a number of cancers. Unfortunately, only a subset of patients will respond to current immunotherapies. This is due to the accruement of suppressive and inhibitory mechanisms employed by the tumor and its microenvironment. These include expression of inhibitory ligands, release of immune-suppressive factors, and the recruitment of suppressive cell populations. Furthermore, the administration of immune checkpoint inhibitors can enhance tumor acquisition of a more suppressive phenotype, diminishing immune responses through additional inhibitory pathways. We therefore propose that further CD8 T-cell-intrinsic negative regulators most likely exist, which can be targeted to improve antitumor responses. Here, we have used functional genomic approaches to identify pathways that can be targeted to advance anti-tumor responses, either in combination with anti-PD-1 or to overcome suppressive mechanisms employed by the tumor microenvironment. Using both in vivo and in vitro assays, we have identified both a novel target that provides an enhancement to CD8 T-cell effector function when in combination with PD-1 checkpoint blockade, and CD8 T-cell-intrinsic pathways that are modulated by the presence of suppressive cells associated with the tumor microenvironment.
Citation Format: Adam N.R Cartwright, Peng Jiang, Assieh Saadatpour, Guo-Cheng Yuan, Shirley X. Liu, Kai W. Wucherpfennig. Overcoming CD8 T-cell suppression in the tumor microenvironment [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A176.
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Affiliation(s)
| | - Peng Jiang
- Dana-Farber Cancer Institute, Boston, MA
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9
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Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, Huang D, Xu Y, Huang W, Jiang M, Jiang X, Mao J, Chen Y, Lu C, Xie J, Fang Q, Wang Y, Yue R, Li T, Huang H, Orkin SH, Yuan GC, Chen M, Guo G. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 2019; 172:1091-1107.e17. [PMID: 29474909 DOI: 10.1016/j.cell.2018.02.001] [Citation(s) in RCA: 776] [Impact Index Per Article: 155.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/15/2017] [Accepted: 01/30/2018] [Indexed: 12/28/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies are poised to reshape the current cell-type classification system. However, a transcriptome-based single-cell atlas has not been achieved for complex mammalian systems. Here, we developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we analyzed more than 400,000 single cells covering all of the major mouse organs and constructed a basic scheme for a mouse cell atlas (MCA). We reveal a single-cell hierarchy for many tissues that have not been well characterized previously. We built a web-based "single-cell MCA analysis" pipeline that accurately defines cell types based on single-cell digital expression. Our study demonstrates the wide applicability of the Microwell-seq technology and MCA resource.
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Affiliation(s)
- Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
| | - Renying Wang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Yincong Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Huiyu Sun
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Ziming Zhou
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Fang Ye
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Daosheng Huang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yang Xu
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Wentao Huang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xinyi Jiang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Jie Mao
- Institute of Applied Mechanics, Zhejiang University, Hangzhou 310027, China
| | - Yao Chen
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chenyu Lu
- Research Center of Infection and Immunity, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jin Xie
- State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yibin Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Rui Yue
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Tiefeng Li
- Institute of Applied Mechanics, Zhejiang University, Hangzhou 310027, China
| | - He Huang
- Institute of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Stuart H Orkin
- Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Institute of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
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10
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Suo S, Zhu Q, Saadatpour A, Fei L, Guo G, Yuan GC. Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas. Cell Rep 2018; 25:1436-1445.e3. [PMID: 30404000 PMCID: PMC6281296 DOI: 10.1016/j.celrep.2018.10.045] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/06/2018] [Accepted: 10/11/2018] [Indexed: 12/19/2022] Open
Abstract
Recent progress in single-cell technologies has enabled the identification of all major cell types in mouse. However, for most cell types, the regulatory mechanism underlying their identity remains poorly understood. By computational analysis of the recently published mouse cell atlas data, we have identified 202 regulons whose activities are highly variable across different cell types, and more importantly, predicted a small set of essential regulators for each major cell type in mouse. Systematic validation by automated literature and data mining provides strong additional support for our predictions. Thus, these predictions serve as a valuable resource that would be useful for the broad biological community. Finally, we have built a user-friendly, interactive web portal to enable users to navigate this mouse cell network atlas.
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Affiliation(s)
- Shengbao Suo
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Qian Zhu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.
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11
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Beyaz S, Mana MD, Roper J, Kedrin D, Saadatpour A, Hong SJ, Bauer-Rowe KE, Xifaras ME, Akkad A, Arias E, Pinello L, Katz Y, Shinagare S, Abu-Remaileh M, Mihaylova MM, Lamming DW, Dogum R, Guo G, Bell GW, Selig M, Nielsen GP, Gupta N, Ferrone CR, Deshpande V, Yuan GC, Orkin SH, Sabatini DM, Yilmaz ÖH. Author Correction: High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature 2018; 560:E26. [DOI: 10.1038/s41586-018-0187-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, Huang D, Xu Y, Huang W, Jiang M, Jiang X, Mao J, Chen Y, Lu C, Xie J, Fang Q, Wang Y, Yue R, Li T, Huang H, Orkin SH, Yuan GC, Chen M, Guo G. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 2018; 173:1307. [PMID: 29775597 DOI: 10.1016/j.cell.2018.05.012] [Citation(s) in RCA: 207] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Jadhav U, Saxena M, O'Neill NK, Saadatpour A, Yuan GC, Herbert Z, Murata K, Shivdasani RA. Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells. Cell Stem Cell 2017. [PMID: 28648363 DOI: 10.1016/j.stem.2017.05.001] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Replicating Lgr5+ stem cells and quiescent Bmi1+ cells behave as intestinal stem cells (ISCs) in vivo. Disrupting Lgr5+ ISCs triggers epithelial renewal from Bmi1+ cells, from secretory or absorptive progenitors, and from Paneth cell precursors, revealing a high degree of plasticity within intestinal crypts. Here, we show that GFP+ cells from Bmi1GFP mice are preterminal enteroendocrine cells and we identify CD69+CD274+ cells as related goblet cell precursors. Upon loss of native Lgr5+ ISCs, both populations revert toward an Lgr5+ cell identity. While active histone marks are distributed similarly between Lgr5+ ISCs and progenitors of both major lineages, thousands of cis elements that control expression of lineage-restricted genes are selectively open in secretory cells. This accessibility signature dynamically converts to that of Lgr5+ ISCs during crypt regeneration. Beyond establishing the nature of Bmi1GFP+ cells, these findings reveal how chromatin status underlies intestinal cell diversity and dedifferentiation to restore ISC function and intestinal homeostasis.
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Affiliation(s)
- Unmesh Jadhav
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Madhurima Saxena
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Nicholas K O'Neill
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard TH Chan School of Public Health, Boston, MA 02215, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard TH Chan School of Public Health, Boston, MA 02215, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Zachary Herbert
- Molecular Biology Core Facility, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kazutaka Murata
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA.
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14
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Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res 2017; 27:843. [PMID: 28572571 DOI: 10.1038/cr.2017.78] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Dr. Li Dak Sum &Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hao Yu
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Daosheng Huang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Xu
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Xia Li
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lengmei Wang
- The 2 Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Yu
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Luca Pinello
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xueying Tian
- The State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China
| | - Fen Zhang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yanhong Cen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yuko Fujiwara
- Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Zhu
- The 2 Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China
| | - Tianhua Zhou
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Hongwei Ouyang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Dr. Li Dak Sum &Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jianan Wang
- The 2 Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Shumin Duan
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Stuart H Orkin
- Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,The 2 Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Dr. Li Dak Sum &Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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15
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Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res 2017; 27:842. [PMID: 28572570 DOI: 10.1038/cr.2017.77] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Dr. Li Dak Sum &Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hao Yu
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Daosheng Huang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Xu
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Xia Li
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lengmei Wang
- The 2 Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Yu
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Luca Pinello
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xueying Tian
- The State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China
| | - Fen Zhang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yanhong Cen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yuko Fujiwara
- Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Zhu
- The 2 Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China
| | - Tianhua Zhou
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Hongwei Ouyang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Dr. Li Dak Sum &Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jianan Wang
- The 2 Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Shumin Duan
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Stuart H Orkin
- Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,The 2 Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Dr. Li Dak Sum &Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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16
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Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biol 2017; 18:84. [PMID: 28482897 PMCID: PMC5421338 DOI: 10.1186/s13059-017-1218-y] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/21/2017] [Indexed: 12/15/2022] Open
Abstract
Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enabled systematic investigation of cellular heterogeneity in a wide range of tissues and cell populations, yielding fresh insights into the composition, dynamics, and regulatory mechanisms of cell states in development and disease. Despite substantial advances, significant challenges remain in the analysis, integration, and interpretation of single-cell omics data. Here, we discuss the state of the field and recent advances and look to future opportunities.
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Affiliation(s)
- Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Long Cai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tariq Enver
- Cancer Institute, University College London, London, UK
| | - Guoping Fan
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
| | - Rafael Irizarry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Peter Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Stuart Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ramesh Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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17
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Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res 2017; 27:386-401. [PMID: 28128194 DOI: 10.1038/cr.2017.17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 09/03/2016] [Accepted: 12/20/2016] [Indexed: 12/19/2022] Open
Abstract
Recent advances have demonstrated the power of small molecules in promoting cellular reprogramming. Yet, the full potential of such chemicals in cell fate manipulation and the underlying mechanisms require further characterization. Through functional screening assays, we find that mouse embryonic fibroblast cells can be induced to trans-differentiate into a wide range of somatic lineages simultaneously by treatment with a combination of four chemicals. Genomic analysis of the process indicates activation of multi-lineage modules and relaxation of epigenetic silencing programs. In addition, we identify Sox2 as an important regulator within the induced network. Single cell analysis uncovers a novel priming state that enables transition from fibroblast cells to diverse somatic lineages. Finally, we demonstrate that modification of the culture system enables directional trans-differentiation towards myocytic, glial or adipocytic lineages. Our study describes a cell fate control system that may be harnessed for regenerative medicine.
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Affiliation(s)
- Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hao Yu
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Daosheng Huang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Xu
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Xia Li
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lengmei Wang
- The 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Yu
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Luca Pinello
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xueying Tian
- The State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China
| | - Fen Zhang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yanhong Cen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yuko Fujiwara
- Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Zhu
- The 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Bin Zhou
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Tianhua Zhou
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Hongwei Ouyang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jianan Wang
- The 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Shumin Duan
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Stuart H Orkin
- Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,The 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Saadatpour A, Lai S, Guo G, Yuan GC. Single-Cell Analysis in Cancer Genomics. Trends Genet 2016; 31:576-586. [PMID: 26450340 DOI: 10.1016/j.tig.2015.07.003] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/26/2015] [Accepted: 07/20/2015] [Indexed: 02/04/2023]
Abstract
Genetic changes and environmental differences result in cellular heterogeneity among cancer cells within the same tumor, thereby complicating treatment outcomes. Recent advances in single-cell technologies have opened new avenues to characterize the intra-tumor cellular heterogeneity, identify rare cell types, measure mutation rates, and, ultimately, guide diagnosis and treatment. In this paper we review the recent single-cell technological and computational advances at the genomic, transcriptomic, and proteomic levels, and discuss their applications in cancer research.
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Affiliation(s)
- Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biol 2014; 15:525. [PMID: 25517911 PMCID: PMC4262970 DOI: 10.1186/s13059-014-0525-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 11/03/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A fundamental challenge for cancer therapy is that each tumor contains a highly heterogeneous cell population whose structure and mechanistic underpinnings remain incompletely understood. Recent advances in single-cell gene expression profiling have created new possibilities to characterize this heterogeneity and to dissect the potential intra-cancer cellular hierarchy. RESULTS Here, we apply single-cell analysis to systematically characterize the heterogeneity within leukemic cells using the MLL-AF9 driven mouse model of acute myeloid leukemia. We start with fluorescence-activated cell sorting analysis with seven surface markers, and extend by using a multiplexing quantitative polymerase chain reaction approach to assay the transcriptional profile of a panel of 175 carefully selected genes in leukemic cells at the single-cell level. By employing a set of computational tools we find striking heterogeneity within leukemic cells. Mapping to the normal hematopoietic cellular hierarchy identifies two distinct subtypes of leukemic cells; one similar to granulocyte/monocyte progenitors and the other to macrophage and dendritic cells. Further functional experiments suggest that these subtypes differ in proliferation rates and clonal phenotypes. Finally, co-expression network analysis reveals similarities as well as organizational differences between leukemia and normal granulocyte/monocyte progenitor networks. CONCLUSIONS Overall, our single-cell analysis pinpoints previously uncharacterized heterogeneity within leukemic cells and provides new insights into the molecular signatures of acute myeloid leukemia.
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Riddell J, Gazit R, Garrison BS, Guo G, Saadatpour A, Mandal PK, Ebina W, Volchkov P, Yuan GC, Orkin SH, Rossi DJ. Reprogramming committed murine blood cells to induced hematopoietic stem cells with defined factors. Cell 2014; 157:549-64. [PMID: 24766805 DOI: 10.1016/j.cell.2014.04.006] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/13/2014] [Accepted: 04/03/2014] [Indexed: 01/17/2023]
Abstract
Hematopoietic stem cells (HSCs) sustain blood formation throughout life and are the functional units of bone marrow transplantation. We show that transient expression of six transcription factors Run1t1, Hlf, Lmo2, Prdm5, Pbx1, and Zfp37 imparts multilineage transplantation potential onto otherwise committed lymphoid and myeloid progenitors and myeloid effector cells. Inclusion of Mycn and Meis1 and use of polycistronic viruses increase reprogramming efficacy. The reprogrammed cells, designated induced-HSCs (iHSCs), possess clonal multilineage differentiation potential, reconstitute stem/progenitor compartments, and are serially transplantable. Single-cell analysis revealed that iHSCs derived under optimal conditions exhibit a gene expression profile that is highly similar to endogenous HSCs. These findings demonstrate that expression of a set of defined factors is sufficient to activate the gene networks governing HSC functional identity in committed blood cells. Our results raise the prospect that blood cell reprogramming may be a strategy for derivation of transplantable stem cells for clinical application.
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Affiliation(s)
- Jonah Riddell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA
| | - Roi Gazit
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA
| | - Brian S Garrison
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA
| | - Guoji Guo
- Dana Farber/Boston Children's Hospital Cancer and Blood Disorders Center, Boston, MA 02116, USA
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Pankaj K Mandal
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA
| | - Wataru Ebina
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA
| | - Pavel Volchkov
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Stuart H Orkin
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Dana Farber/Boston Children's Hospital Cancer and Blood Disorders Center, Boston, MA 02116, USA; Howard Hughes Medical Institute; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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Riddell J, Gazit R, Garrison B, Guo G, Saadatpour A, Mandal P, Ebina W, Volchkov P, Yuan GC, Orkin S, Rossi D. Reprogramming Committed Murine Blood Cells to Induced Hematopoietic Stem Cells with Defined Factors. Cell 2014. [DOI: 10.1016/j.cell.2014.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
Given the complexity and interactive nature of biological systems, constructing informative and coherent network models of these systems and subsequently developing efficient approaches to analyze the assembled networks is of immense importance. The integration of network analysis and dynamic modeling enables one to investigate the behavior of the underlying system as a whole and to make experimentally testable predictions about less-understood aspects of the processes involved. In this paper, we present a tutorial on the fundamental steps of Boolean modeling of biological regulatory networks. We demonstrate how to infer a Boolean network model from the available experimental data, analyze the network using graph-theoretical measures, and convert it into a predictive dynamic model. For each step, the pitfalls one may encounter and possible ways to circumvent them are also discussed. We illustrate these steps on a toy network as well as in the context of the Drosophila melanogaster segment polarity gene network.
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Affiliation(s)
- Assieh Saadatpour
- Department of Mathematics, The Pennsylvania State University, University Park, PA 16802, USA
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Saadatpour A, Wang RS, Liao A, Liu X, Loughran TP, Albert I, Albert R. Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol 2011; 7:e1002267. [PMID: 22102804 PMCID: PMC3213185 DOI: 10.1371/journal.pcbi.1002267] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 09/22/2011] [Indexed: 11/18/2022] Open
Abstract
The blood cancer T cell large granular lymphocyte (T-LGL) leukemia is a chronic disease characterized by a clonal proliferation of cytotoxic T cells. As no curative therapy is yet known for this disease, identification of potential therapeutic targets is of immense importance. In this paper, we perform a comprehensive dynamical and structural analysis of a network model of this disease. By employing a network reduction technique, we identify the stationary states (fixed points) of the system, representing normal and diseased (T-LGL) behavior, and analyze their precursor states (basins of attraction) using an asynchronous Boolean dynamic framework. This analysis identifies the T-LGL states of 54 components of the network, out of which 36 (67%) are corroborated by previous experimental evidence and the rest are novel predictions. We further test and validate one of these newly identified states experimentally. Specifically, we verify the prediction that the node SMAD is over-active in leukemic T-LGL by demonstrating the predominant phosphorylation of the SMAD family members Smad2 and Smad3. Our systematic perturbation analysis using dynamical and structural methods leads to the identification of 19 potential therapeutic targets, 68% of which are corroborated by experimental evidence. The novel therapeutic targets provide valuable guidance for wet-bench experiments. In addition, we successfully identify two new candidates for engineering long-lived T cells necessary for the delivery of virus and cancer vaccines. Overall, this study provides a bird's-eye-view of the avenues available for identification of therapeutic targets for similar diseases through perturbation of the underlying signal transduction network. T-LGL leukemia is a blood cancer characterized by an abnormal increase in the abundance of a type of white blood cell called T cell. Since there is no known curative therapy for this disease, identification of potential therapeutic targets is of utmost importance. Experimental identification of manipulations capable of reversing the disease condition is usually a long, arduous process. Mathematical modeling can aid this process by identifying potential therapeutic interventions. In this work, we carry out a systematic analysis of a network model of T cell survival in T-LGL leukemia to get a deeper insight into the unknown facets of the disease. We identify the T-LGL status of 54 components of the system, out of which 36 (67%) are corroborated by previous experimental evidence and the rest are novel predictions, one of which we validate by follow-up experiments. By deciphering the structure and dynamics of the underlying network, we identify component perturbations that lead to programmed cell death, thereby suggesting several novel candidate therapeutic targets for future experiments.
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Affiliation(s)
- Assieh Saadatpour
- Department of Mathematics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Rui-Sheng Wang
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Aijun Liao
- Penn State Hershey Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Xin Liu
- Penn State Hershey Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Thomas P. Loughran
- Penn State Hershey Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - István Albert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Réka Albert
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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Saadatpour A, Albert I, Albert R. Attractor analysis of asynchronous Boolean models of signal transduction networks. J Theor Biol 2010; 266:641-56. [PMID: 20659480 DOI: 10.1016/j.jtbi.2010.07.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Revised: 05/28/2010] [Accepted: 07/21/2010] [Indexed: 02/07/2023]
Abstract
Prior work on the dynamics of Boolean networks, including analysis of the state space attractors and the basin of attraction of each attractor, has mainly focused on synchronous update of the nodes' states. Although the simplicity of synchronous updating makes it very attractive, it fails to take into account the variety of time scales associated with different types of biological processes. Several different asynchronous update methods have been proposed to overcome this limitation, but there have not been any systematic comparisons of the dynamic behaviors displayed by the same system under different update methods. Here we fill this gap by combining theoretical analysis such as solution of scalar equations and Markov chain techniques, as well as numerical simulations to carry out a thorough comparative study on the dynamic behavior of a previously proposed Boolean model of a signal transduction network in plants. Prior evidence suggests that this network admits oscillations, but it is not known whether these oscillations are sustained. We perform an attractor analysis of this system using synchronous and three different asynchronous updating schemes both in the case of the unperturbed (wild-type) and perturbed (node-disrupted) systems. This analysis reveals that while the wild-type system possesses an update-independent fixed point, any oscillations eventually disappear unless strict constraints regarding the timing of certain processes and the initial state of the system are satisfied. Interestingly, in the case of disruption of a particular node all models lead to an extended attractor. Overall, our work provides a roadmap on how Boolean network modeling can be used as a predictive tool to uncover the dynamic patterns of a biological system under various internal and environmental perturbations.
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Affiliation(s)
- Assieh Saadatpour
- Department of Mathematics, The Pennsylvania State University, University Park, PA 16802, USA
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