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Penter L, Borji M, Nagler A, Lyu H, Lu WS, Cieri N, Maurer K, Oliveira G, Al'Khafaji AM, Garimella KV, Li S, Neuberg DS, Ritz J, Soiffer RJ, Garcia JS, Livak KJ, Wu CJ. Integrative genotyping of cancer and immune phenotypes by long-read sequencing. Nat Commun 2024; 15:32. [PMID: 38167262 PMCID: PMC10762175 DOI: 10.1038/s41467-023-44137-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current methods to detect natural genetic barcodes often require cumbersome primer panels and early commitment to targets. Here we devise a flexible long-read sequencing workflow and analysis pipeline, termed nanoranger, that starts from intermediate single-cell cDNA libraries to detect cell lineage-defining features, including single-nucleotide variants, fusion genes, isoforms, sequences of chimeric antigen and TCRs. Through systematic analysis of these classes of natural 'barcodes', we define the optimal targets for nanoranger, namely those loci close to the 5' end of highly expressed genes with transcript lengths shorter than 4 kB. As proof-of-concept, we apply nanoranger to longitudinal tracking of subclones of acute myeloid leukemia (AML) and describe the heterogeneous isoform landscape of thousands of marrow-infiltrating immune cells. We propose that enhanced cellular genotyping using nanoranger can improve the tracking of single-cell tumor and immune cell co-evolution.
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Grants
- P01 CA229092 NCI NIH HHS
- P50 CA101942 NCI NIH HHS
- UM1 CA186709 NCI NIH HHS
- U24 CA224316 NCI NIH HHS
- U24 CA224331 NCI NIH HHS
- U24 CA224285 NCI NIH HHS
- R50 CA251956 NCI NIH HHS
- U24 CA224309 NCI NIH HHS
- U24 CA224319 NCI NIH HHS
- K08 CA245209 NCI NIH HHS
- This work was supported by National Institutes of Health, National Cancer Institute grant P01CA229092 (CJW), UM1CA186709 (Principal Investigator: Geoffrey Shapiro), National Cancer Institute Cancer Therapy Evaluation Program, Bristol-Myers Squibb, and LLS Therapy Accelerator Program. L.P. was supported by a research fellowship from the German Research Foundation (DFG, PE 3127/1-1) and is a Scholar of the American Society of Hematology, participant in the BIH Charité Digital Clinician Scientist Program funded by the DFG, the Charité – Universitätsmedizin Berlin, and the Berlin Institute of Health at Charité (BIH) and is supported by the Max-Eder program of the German Cancer Aid. A.A. is supported by the Broad Institute IGNITE award. K.M. is suppored by the ASCO YIA award. G.O. was supported by the Claudia Adams Barr Program for Innovative Cancer Research and by DF/HCC Kidney Cancer SPORE P50 CA101942. S.L. is supported by the National Institutes of Health, National Cancer Institute Research Specialist Award (R50CA251956). JSG is supported by the Conquer Cancer Foundation Career Development Award, Leukemia and Lymphoma Society Translational Research Program Award, and NIH K08CA245209. NCI CTEP provided study drug (Ipilimumab) support. This work was further supported by the CIMAC-CIDC Network. Scientific and financial support for the CIMAC-CIDC Network is provided through National Institutes of Health, National Cancer Institute Cooperative Agreements U24CA224319 (to the Icahn School of Medicine at Mount Sinai CIMAC), U24CA224331 (to the Dana-Farber Cancer Institute CIMAC), U24CA224285 (to the MD Anderson Cancer Center CIMAC), U24CA224309 (to the Stanford University CIMAC), and U24CA224316 (to the CIDC at Dana-Farber Cancer Institute). The CIMAC-CIDC website is found at https://cimac-network.org/.
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Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Mehdi Borji
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adi Nagler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Haoxiang Lyu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wesley S Lu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katie Maurer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aziz M Al'Khafaji
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Kiran V Garimella
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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Li Y, Xu R, Wu Y, Guo J, Quan F, Pei Y, Huang D, Zhao X, Gao H, Liu J, Zhang Z, Shi J, Zhang K. Genotype-specific precision tumor therapy using mitochondrial DNA mutation-induced drug release system. SCIENCE ADVANCES 2023; 9:eadi1965. [PMID: 37756407 PMCID: PMC10530102 DOI: 10.1126/sciadv.adi1965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Precise killing of tumor cells without affecting surrounding normal cells is a challenge. Mitochondrial DNA (mtDNA) mutations, a common genetic variant in cancer, can directly affect metabolic homeostasis, serving as an ideal regulatory switch for precise tumor therapy. Here, we designed a mutation-induced drug release system (MIDRS), using the single-nucleotide variation (SNV) recognition ability and trans-cleavage activity of Cas12a to convert tumor-specific mtDNA mutations into a regulatory switch for intracellular drug release, realizing precise tumor cell killing. Using Ce6 as a model drug, MIDRS enabled organelle-level photodynamic therapy, triggering innate and adaptive immunity simultaneously. In vivo evaluation showed that MIDRSMT could identify tumor tissue carrying SNVs in mtDNA in unilateral, bilateral, and heterogeneous tumor models, producing an excellent antitumor effect (~82.6%) without affecting normal cells and thus resulting in a stronger systemic antitumor immune response. Additionally, MIDRS was suitable for genotype-specific precision drug release of chemotherapeutic drugs. This strategy holds promise for mutation-specific personalized tumor treatment approaches.
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Affiliation(s)
- Yanan Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Ru Xu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Yonghua Wu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jialing Guo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Fenglei Quan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Yiran Pei
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Di Huang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Xiu Zhao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Hua Gao
- Department of Pathogen Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Junjie Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou 450001, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou 450001, P. R. China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou 450001, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou 450001, P. R. China
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou 450001, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou 450001, P. R. China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou 450001, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou 450001, P. R. China
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Goyette MA, Lipsyc-Sharf M, Polyak K. Clinical and translational relevance of intratumor heterogeneity. Trends Cancer 2023; 9:726-737. [PMID: 37248149 PMCID: PMC10524913 DOI: 10.1016/j.trecan.2023.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023]
Abstract
Intratumor heterogeneity (ITH) is a driver of tumor evolution and a main cause of therapeutic resistance. Despite its importance, measures of ITH are still not incorporated into clinical practice. Consequently, standard treatment is frequently ineffective for patients with heterogeneous tumors as changes to treatment regimens are made only after recurrence and disease progression. More effective combination therapies require a mechanistic understanding of ITH and ways to assess it in clinical samples. The growth of technologies enabling the spatially intact analysis of tumors at the single-cell level and the development of sophisticated preclinical models give us hope that ITH will not simply be used as a predictor of a poor outcome but will guide treatment decisions from diagnosis through treatment.
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Affiliation(s)
- Marie-Anne Goyette
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marla Lipsyc-Sharf
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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