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Beigi YZ, Lanjanian H, Fayazi R, Salimi M, Hoseyni BHM, Noroozizadeh MH, Masoudi-Nejad A. Heterogeneity and molecular landscape of melanoma: implications for targeted therapy. MOLECULAR BIOMEDICINE 2024; 5:17. [PMID: 38724687 PMCID: PMC11082128 DOI: 10.1186/s43556-024-00182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Uveal cancer (UM) offers a complex molecular landscape characterized by substantial heterogeneity, both on the genetic and epigenetic levels. This heterogeneity plays a critical position in shaping the behavior and response to therapy for this uncommon ocular malignancy. Targeted treatments with gene-specific therapeutic molecules may prove useful in overcoming radiation resistance, however, the diverse molecular makeups of UM call for a patient-specific approach in therapy procedures. We need to understand the intricate molecular landscape of UM to develop targeted treatments customized to each patient's specific genetic mutations. One of the promising approaches is using liquid biopsies, such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), for detecting and monitoring the disease at the early stages. These non-invasive methods can help us identify the most effective treatment strategies for each patient. Single-cellular is a brand-new analysis platform that gives treasured insights into diagnosis, prognosis, and remedy. The incorporation of this data with known clinical and genomics information will give a better understanding of the complicated molecular mechanisms that UM diseases exploit. In this review, we focused on the heterogeneity and molecular panorama of UM, and to achieve this goal, the authors conducted an exhaustive literature evaluation spanning 1998 to 2023, using keywords like "uveal melanoma, "heterogeneity". "Targeted therapies"," "CTCs," and "single-cellular analysis".
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Affiliation(s)
- Yasaman Zohrab Beigi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hossein Lanjanian
- Software Engineering Department, Engineering Faculty, Istanbul Topkapi University, Istanbul, Turkey
| | - Reyhane Fayazi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Behnaz Haji Molla Hoseyni
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Masoudi-Nejad
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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2
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Kidman J, Zemek RM, Sidhom JW, Correa D, Principe N, Sheikh F, Fear VS, Forbes CA, Chopra A, Boon L, Zaitouny A, de Jong E, Holt RA, Jones M, Millward MJ, Lassmann T, Forrest AR, Nowak AK, Watson M, Lake RA, Lesterhuis WJ, Chee J. Immune checkpoint therapy responders display early clonal expansion of tumor infiltrating lymphocytes. Oncoimmunology 2024; 13:2345859. [PMID: 38686178 PMCID: PMC11057660 DOI: 10.1080/2162402x.2024.2345859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Immune checkpoint therapy (ICT) causes durable tumour responses in a subgroup of patients, but it is not well known how T cell receptor beta (TCRβ) repertoire dynamics contribute to the therapeutic response. Using murine models that exclude variation in host genetics, environmental factors and tumour mutation burden, limiting variation between animals to naturally diverse TCRβ repertoires, we applied TCRseq, single cell RNAseq and flow cytometry to study TCRβ repertoire dynamics in ICT responders and non-responders. Increased oligoclonal expansion of TCRβ clonotypes was observed in responding tumours. Machine learning identified TCRβ CDR3 signatures unique to each tumour model, and signatures associated with ICT response at various timepoints before or during ICT. Clonally expanded CD8+ T cells in responding tumours post ICT displayed effector T cell gene signatures and phenotype. An early burst of clonal expansion during ICT is associated with response, and we report unique dynamics in TCRβ signatures associated with ICT response.
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MESH Headings
- Animals
- Immune Checkpoint Inhibitors/pharmacology
- Immune Checkpoint Inhibitors/therapeutic use
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Mice
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/drug effects
- Lymphocytes, Tumor-Infiltrating/metabolism
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/metabolism
- Humans
- Mice, Inbred C57BL
- Female
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Affiliation(s)
- Joel Kidman
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, University of Western Australia, Perth, Australia
| | | | | | - Debora Correa
- Complex Systems Group, Department of Mathematics and Statistics, University of Western Australia, Perth, Australia
| | - Nicola Principe
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, University of Western Australia, Perth, Australia
| | - Fezaan Sheikh
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, University of Western Australia, Perth, Australia
| | | | | | - Abha Chopra
- Medical Genomics Laboratories (IIID), Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Australia
| | | | - Ayham Zaitouny
- Complex Systems Group, Department of Mathematics and Statistics, University of Western Australia, Perth, Australia
- Department of Mathematical Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Emma de Jong
- Telethon Kids Institute, Perth, Australia
- Medical School, University of Western Australia, Perth, Australia
| | | | - Matt Jones
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Australia
| | | | | | - Alistair R.R. Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Australia
| | - Anna K. Nowak
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, University of Western Australia, Perth, Australia
- Medical School, University of Western Australia, Perth, Australia
| | - Mark Watson
- Medical Genomics Laboratories (IIID), Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Australia
| | - Richard A. Lake
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, University of Western Australia, Perth, Australia
| | - W. Joost Lesterhuis
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, University of Western Australia, Perth, Australia
- Telethon Kids Institute, Perth, Australia
| | - Jonathan Chee
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, University of Western Australia, Perth, Australia
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3
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Wong MK, Yee C. Polyomavirus-positive Merkel cell carcinoma: the beginning of the beginning. J Clin Invest 2024; 134:e179749. [PMID: 38618960 PMCID: PMC11014648 DOI: 10.1172/jci179749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Abstract
Merkel cell carcinoma (MCC) is an aggressive, fast-growing, highly metastatic neuroendocrine skin cancer. The Merkel cell polyomavirus (MCPyV) is an oncogenic driver in the majority of MCC tumors. In this issue of the JCI, Hansen and authors report on their tracking of CD8+ T cells reactive to MCPyV T antigen (T-Ag) in the peripheral blood of 26 patients with MCC who were undergoing frontline anti-programmed cell death protein-1 (anti-PD-1) immunotherapy. They discovered unique T cell epitopes and used the power of bar-coded tetramers to portray immune checkpoint inhibitor-induced immunogenicity as a predictor of clinical response. These findings provide the foundation for therapeutic possibilities for MCC, including vaccines and adoptive T cell- and T cell receptor-driven (TCR-driven) treatments.
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Trauet J, Bourgoin P, Schuldt J, Lefèvre G, Labalette M, Busnel JM, Demaret J. Studying antigen-specific T cells through a streamlined, whole blood-based extracellular approach. Cytometry A 2024; 105:288-296. [PMID: 38149360 DOI: 10.1002/cyto.a.24818] [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: 05/16/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
Techniques currently used for the study of antigen-specific T-cell responses are either poorly informative or require a heavy workload. Consequently, many perspectives associated with the broader study of such approaches remain mostly unexplored in translational research. However, these could benefit many fields including but not limited to infectious diseases, oncology, and vaccination. Herein, the main objective of this work was to develop a standardized flow cytometry-based approach that would combine ease of use together with a relevant study of antigen-specific T-cell responses so that they could be more often included in clinical research. To this extent, a streamlined approach relying on 1/ the use of whole blood instead of peripheral blood mononuclear cells and 2/ solely based on the expression of extracellular activation-induced markers (AIMs), called whole blood AIM (WAIM), was developed and further compared to more conventional techniques such as enzyme-linked immunospot (ELISpot) and flow cytometry-based intracellular cytokine staining (ICS). Based on a cohort of 20 individuals receiving the COVID-19 mRNA vaccine and focusing on SARS-CoV-2 and cytomegalovirus (CMV)-derived antigen T-cell-specific responses, a significant level of correlation between the three techniques was found. Based on the use of whole blood and on the expression of extracellular activation-induced markers (CD154, CD137, and CD107a), the WAIM technique appears to be very simple to implement and yet allows interesting patient stratification capabilities as the chosen combination of extracellular markers exhibited higher orthogonality than cytokines that are commonly considered in ICS (IFN-γ, TNF-α, and IL-2).
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Affiliation(s)
- Jacques Trauet
- CHU Lille, Institut d'Immunologie, U1286 - INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, Lille, France
| | - Penelope Bourgoin
- Global Research Organization, Beckman Coulter Life Sciences, Marseille, France
| | - Jana Schuldt
- Global Research Organization, Beckman Coulter Life Sciences, Marseille, France
| | - Guillaume Lefèvre
- CHU Lille, Institut d'Immunologie, U1286 - INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, Lille, France
| | - Myriam Labalette
- CHU Lille, Institut d'Immunologie, U1286 - INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, Lille, France
| | - Jean-Marc Busnel
- Global Research Organization, Beckman Coulter Life Sciences, Marseille, France
| | - Julie Demaret
- CHU Lille, Institut d'Immunologie, U1286 - INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, Lille, France
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5
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Roy P, Suthahar SSA, Makings J, Ley K. Identification of apolipoprotein B-reactive CDR3 motifs allows tracking of atherosclerosis-related memory CD4 +T cells in multiple donors. Front Immunol 2024; 15:1302031. [PMID: 38571941 PMCID: PMC10988780 DOI: 10.3389/fimmu.2024.1302031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/02/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Atherosclerosis is a major pathological condition that underlies many cardiovascular diseases (CVDs). Its etiology involves breach of tolerance to self, leading to clonal expansion of autoreactive apolipoprotein B (APOB)-reactive CD4+T cells that correlates with clinical CVD. The T-cell receptor (TCR) sequences that mediate activation of APOB-specific CD4+T cells are unknown. Methods In a previous study, we had profiled the hypervariable complementarity determining region 3 (CDR3) of CD4+T cells that respond to six immunodominant APOB epitopes in most donors. Here, we comprehensively analyze this dataset of 149,065 APOB-reactive and 199,211 non-reactive control CDR3s from six human leukocyte antigen-typed donors. Results We identified 672 highly expanded (frequency threshold > 1.39E-03) clones that were significantly enriched in the APOB-reactive group as compared to the controls (log10 odds ratio ≥1, Fisher's test p < 0.01). Analysis of 114,755 naïve, 91,001 central memory (TCM) and 29,839 effector memory (TEM) CDR3 sequences from the same donors revealed that APOB+ clones can be traced to the complex repertoire of unenriched blood T cells. The fraction of APOB+ clones that overlapped with memory CDR3s ranged from 2.2% to 46% (average 16.4%). This was significantly higher than their overlap with the naïve pool, which ranged from 0.7% to 2% (average 1.36%). CDR3 motif analysis with the machine learning-based in-silico tool, GLIPHs (grouping of lymphocyte interactions by paratope hotspots), identified 532 APOB+ motifs. Analysis of naïve and memory CDR3 sequences with GLIPH revealed that ~40% (209 of 532) of these APOB+ motifs were enriched in the memory pool. Network analysis with Cytoscape revealed extensive sharing of the memory-affiliated APOB+ motifs across multiple donors. We identified six motifs that were present in TCM and TEM CDR3 sequences from >80% of the donors and were highly enriched in the APOB-reactive TCR repertoire. Discussion The identified APOB-reactive expanded CD4+T cell clones and conserved motifs can be used to annotate and track human atherosclerosis-related autoreactive CD4+T cells and measure their clonal expansion.
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Affiliation(s)
- Payel Roy
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, United States
- Immunology Center of Georgia, Augusta University, Augusta, GA, United States
| | | | - Jeffrey Makings
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Klaus Ley
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, United States
- Immunology Center of Georgia, Augusta University, Augusta, GA, United States
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6
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Klobuch S, Seijkens TTP, Schumacher TN, Haanen JBAG. Tumour-infiltrating lymphocyte therapy for patients with advanced-stage melanoma. Nat Rev Clin Oncol 2024; 21:173-184. [PMID: 38191921 DOI: 10.1038/s41571-023-00848-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
Immunotherapy with immune-checkpoint inhibitors (ICIs) and targeted therapy with BRAF and MEK inhibitors have revolutionized the treatment of melanoma over the past decade. Despite these breakthroughs, the 5-year survival rate of patients with advanced-stage melanoma is at most 50%, emphasizing the need for additional therapeutic strategies. Adoptive cell therapy with tumour-infiltrating lymphocytes (TILs) is a therapeutic modality that has, in the past few years, demonstrated long-term clinical benefit in phase II/III trials involving patients with advanced-stage melanoma, including those with disease progression on ICIs and/or BRAF/MEK inhibitors. In this Review, we summarize the current status of TIL therapies for patients with advanced-stage melanoma, including potential upcoming marketing authorization, the characteristics of TIL therapy products, as well as future strategies that are expected to increase the efficacy of this promising cellular immunotherapy.
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Affiliation(s)
- Sebastian Klobuch
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tom T P Seijkens
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - John B A G Haanen
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands.
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands.
- Melanoma Clinic, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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7
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Pulliam T, Jani S, Jing L, Ryu H, Jojic A, Shasha C, Zhang J, Kulikauskas R, Church C, Garnett-Benson C, Gooley T, Chapuis A, Paulson K, Smith KN, Pardoll DM, Newell EW, Koelle DM, Topalian SL, Nghiem P. Circulating cancer-specific CD8 T cell frequency is associated with response to PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101412. [PMID: 38340723 PMCID: PMC10897614 DOI: 10.1016/j.xcrm.2024.101412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/01/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Understanding cancer immunobiology has been hampered by difficulty identifying cancer-specific T cells. Merkel cell polyomavirus (MCPyV) causes most Merkel cell carcinomas (MCCs). All patients with virus-driven MCC express MCPyV oncoproteins, facilitating identification of virus (cancer)-specific T cells. We studied MCPyV-specific T cells from 27 patients with MCC using MCPyV peptide-HLA-I multimers, 26-color flow cytometry, single-cell transcriptomics, and T cell receptor (TCR) sequencing. In a prospective clinical trial, higher circulating MCPyV-specific CD8 T cell frequency before anti-PD-1 treatment was strongly associated with 2-year recurrence-free survival (75% if detectable, 0% if undetectable, p = 0.0018; ClinicalTrial.gov: NCT02488759). Intratumorally, such T cells were typically present, but their frequency did not significantly associate with response. Circulating MCPyV-specific CD8 T cells had increased stem/memory and decreased exhaustion signatures relative to their intratumoral counterparts. These results suggest that cancer-specific CD8 T cells in the blood may play a role in anti-PD-1 responses. Thus, strategies that augment their number or mobilize them into tumors could improve outcomes.
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Affiliation(s)
- Thomas Pulliam
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Saumya Jani
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Heeju Ryu
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ana Jojic
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Carolyn Shasha
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jiajia Zhang
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Rima Kulikauskas
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Candice Church
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | | | - Ted Gooley
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Aude Chapuis
- Department of Medicine, University of Washington, Seattle, WA 98109, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kelly Paulson
- Paul G. Allen Research Center, Providence-Swedish Cancer Institute, Seattle, WA 98104, USA; Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Kellie N Smith
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Evan W Newell
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David M Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98109, USA; Benaroya Research Institute, Seattle, WA 98101, USA
| | - Suzanne L Topalian
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA.
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Vallacchi V, Vergani E, Cossa M, Gargiuli C, Busico A, Devecchi A, Dugo M, Bergamaschi L, De Cecco L, Cavalieri S, Valeri B, Tamborini E, Gallino G, Del Vecchio M, Santinami M, Sensi M, Rivoltini L, Di Guardo L, Rodolfo M. Multistep tumor genetic evolution and changes in immunogenicity trigger immune-mediated disease eradication in stage IV melanoma: lessons from a single case. J Immunother Cancer 2024; 12:e007612. [PMID: 38177075 PMCID: PMC10773440 DOI: 10.1136/jitc-2023-007612] [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] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Durable remissions are observed in 10%-20% of treated patients with advanced metastatic melanoma but the factors associated with long-term complete clinical responses are largely unknown. Here, we report the molecular characteristics of tumor evolution during disease progression along a 9-year clinical course in a patient with advanced disseminated melanoma who received different treatments, including trametinib, ipilimumab, radiation, vemurafenib, surgical tumor debulking and a second ipilimumab course, ultimately achieving complete long-term disease remission.Longitudinal analyses of therapies-resistant metastatic tumors revealed the effects of different treatments on tumor's microenvironment and immunogenicity, ultimately creating a milieu favorable to immunotherapy response. Monitoring of the temporal dynamics of T cells by analysis of the T cell receptor (TCR) repertoire in the tumor and peripheral blood during disease evolution indicated that T-cell clones with common TCR rearrangements, present at low levels at baseline, were maintained and expanded after immunotherapy, and that TCR diversity increased. Analysis of genetic, molecular, and cellular components of the tumor depicted a multistep process in which treatment with kinase inhibitors strongly conditioned the immune microenvironment creating an inflamed milieu converting cold into hot tumors, while ipilimumab impacted and increased the TCR repertoire, a requirement for tumor rejection.Since the optimal sequencing of treatment with antibodies targeting immune checkpoints and kinase inhibitors for advanced melanoma is still clinically debated, this case indicates that immunotherapy success is possible even after progression on targeted therapy.
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Affiliation(s)
- Viviana Vallacchi
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elisabetta Vergani
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mara Cossa
- Pathology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara Gargiuli
- Applied Research and Technology Development Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Adele Busico
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Devecchi
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Dugo
- Department of Medical Oncology, San Raffaele Hospital, Milan, Italy
| | - Laura Bergamaschi
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Integrated Biology of Rare Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano Cavalieri
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Barbara Valeri
- Pathology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Tamborini
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Michele Del Vecchio
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mario Santinami
- Melanoma Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marialuisa Sensi
- Applied Research and Technology Development Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Licia Rivoltini
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lorenza Di Guardo
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Rodolfo
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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9
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Huuhtanen J, Adnan-Awad S, Theodoropoulos J, Forstén S, Warfvinge R, Dufva O, Bouhlal J, Dhapola P, Duàn H, Laajala E, Kasanen T, Klievink J, Ilander M, Jaatinen T, Olsson-Strömberg U, Hjorth-Hansen H, Burchert A, Karlsson G, Kreutzman A, Lähdesmäki H, Mustjoki S. Single-cell analysis of immune recognition in chronic myeloid leukemia patients following tyrosine kinase inhibitor discontinuation. Leukemia 2024; 38:109-125. [PMID: 37919606 PMCID: PMC10776410 DOI: 10.1038/s41375-023-02074-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/19/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Immunological control of residual leukemia cells is thought to occur in patients with chronic myeloid leukemia (CML) that maintain treatment-free remission (TFR) following tyrosine kinase inhibitor (TKI) discontinuation. To study this, we analyzed 55 single-cell RNA and T cell receptor (TCR) sequenced samples (scRNA+TCRαβ-seq) from patients with CML (n = 13, N = 25), other cancers (n = 28), and healthy (n = 7). The high number and active phenotype of natural killer (NK) cells in CML separated them from healthy and other cancers. Most NK cells in CML belonged to the active CD56dim cluster with high expression of GZMA/B, PRF1, CCL3/4, and IFNG, with interactions with leukemic cells via inhibitory LGALS9-TIM3 and PVR-TIGIT interactions. Accordingly, upregulation of LGALS9 was observed in CML target cells and TIM3 in NK cells when co-cultured together. Additionally, we created a classifier to identify TCRs targeting leukemia-associated antigen PR1 and quantified anti-PR1 T cells in 90 CML and 786 healthy TCRβ-sequenced samples. Anti-PR1 T cells were more prevalent in CML, enriched in bone marrow samples, and enriched in the mature, cytotoxic CD8 + TEMRA cluster, especially in a patient maintaining TFR. Our results highlight the role of NK cells and anti-PR1 T cells in anti-leukemic immune responses in CML.
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Affiliation(s)
- Jani Huuhtanen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
- Department of Computer Science, Aalto University, Espoo, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Shady Adnan-Awad
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Jason Theodoropoulos
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Sofia Forstén
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Rebecca Warfvinge
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Olli Dufva
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jonas Bouhlal
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Parashar Dhapola
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Hanna Duàn
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Essi Laajala
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Tiina Kasanen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jay Klievink
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Mette Ilander
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Taina Jaatinen
- Histocompatibility Testing Laboratory, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Ulla Olsson-Strömberg
- Department of Medical Sciences, Uppsala University and Hematology Section, Uppsala University Hospital, Uppsala, Sweden
| | - Henrik Hjorth-Hansen
- Department of Hematology, St. Olavs Hospital, Trondheim, Norway
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Andreas Burchert
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, and University Medical Center Giessen and Marburg, Marburg, Germany
| | - Göran Karlsson
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Anna Kreutzman
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Satu Mustjoki
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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10
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Lee MH, Theodoropoulos J, Huuhtanen J, Bhattacharya D, Järvinen P, Tornberg S, Nísen H, Mirtti T, Uski I, Kumari A, Peltonen K, Draghi A, Donia M, Kreutzman A, Mustjoki S. Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:1260-1276. [PMID: 37484198 PMCID: PMC10361538 DOI: 10.1158/2767-9764.crc-22-0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
The successful use of expanded tumor-infiltrating lymphocytes (TIL) in adoptive TIL therapies has been reported, but the effects of the TIL expansion, immunophenotype, function, and T cell receptor (TCR) repertoire of the infused products relative to the tumor microenvironment (TME) are not well understood. In this study, we analyzed the tumor samples (n = 58) from treatment-naïve patients with renal cell carcinoma (RCC), "pre-rapidly expanded" TILs (pre-REP TIL, n = 15) and "rapidly expanded" TILs (REP TIL, n = 25) according to a clinical-grade TIL production protocol, with single-cell RNA (scRNA)+TCRαβ-seq (TCRαβ sequencing), TCRβ-sequencing (TCRβ-seq), and flow cytometry. REP TILs encompassed a greater abundance of CD4+ than CD8+ T cells, with increased LAG-3 and low PD-1 expressions in both CD4+ and CD8+ T cell compartments compared with the pre-REP TIL and tumor T cells. The REP protocol preferentially expanded small clones of the CD4+ phenotype (CD4, IL7R, KLRB1) in the TME, indicating that the largest exhausted T cell clones in the tumor do not expand during the expansion protocol. In addition, by generating a catalog of RCC-associated TCR motifs from >1,000 scRNA+TCRαβ-seq and TCRβ-seq RCC, healthy and other cancer sample cohorts, we quantified the RCC-associated TCRs from the expansion protocol. Unlike the low-remaining amount of anti-viral TCRs throughout the expansion, the quantity of the RCC-associated TCRs was high in the tumors and pre-REP TILs but decreased in the REP TILs. Our results provide an in-depth understanding of the origin, phenotype, and TCR specificity of RCC TIL products, paving the way for a more rationalized production of TILs. Significance TILs are a heterogenous group of immune cells that recognize and attack the tumor, thus are utilized in various clinical trials. In our study, we explored the TILs in patients with kidney cancer by expanding the TILs using a clinical-grade protocol, as well as observed their characteristics and ability to recognize the tumor using in-depth experimental and computational tools.
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Affiliation(s)
- Moon Hee Lee
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Dipabarna Bhattacharya
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Petrus Järvinen
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Sara Tornberg
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Harry Nísen
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Mirtti
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biomedical Engineering, School of Medicine, Emory University, Atlanta, Georgia
| | - Ilona Uski
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Anita Kumari
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Karita Peltonen
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Arianna Draghi
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Anna Kreutzman
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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11
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Luo J, Wang X, Zou Y, Chen L, Liu W, Zhang W, Li SC. Quantitative annotations of T-Cell repertoire specificity. Brief Bioinform 2023; 24:bbad175. [PMID: 37150761 DOI: 10.1093/bib/bbad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/17/2023] [Indexed: 05/09/2023] Open
Abstract
The specificity of a T-cell receptor (TCR) repertoire determines personalized immune capacity. Existing methods have modeled the qualitative aspects of TCR specificity, while the quantitative aspects remained unaddressed. We developed a package, TCRanno, to quantify the specificity of TCR repertoires. We created deep-learning-based, epitope-aware vector embeddings to infer individual TCR specificity. Then we aggregated clonotype frequencies of TCRs to obtain a quantitative profile of repertoire specificity at epitope, antigen and organism levels. Applying TCRanno to 4195 TCR repertoires revealed quantitative changes in repertoire specificity upon infections, autoimmunity and cancers. Specifically, TCRanno found cytomegalovirus-specific TCRs in seronegative healthy individuals, supporting the possibility of abortive infections. TCRanno discovered age-accumulated fraction of severe acute respiratory syndrome coronavirus 2 specific TCRs in pre-pandemic samples, which may explain the aggressive symptoms and age-related severity of coronavirus disease 2019. TCRanno also identified the encounter of Hepatitis B antigens as a potential trigger of systemic lupus erythematosus. TCRanno annotations showed capability in distinguishing TCR repertoires of healthy and cancers including melanoma, lung and breast cancers. TCRanno also demonstrated usefulness to single-cell TCRseq+gene expression data analyses by isolating T-cells with the specificity of interest.
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Affiliation(s)
- Jiaqi Luo
- Department of Computer Science, City University of Hong Kong, 83 Tat Tree Ave, Kowloon Tong, Hong Kong, China
| | - Xueying Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Tree Ave, Kowloon Tong, Hong Kong, China
| | - Yiping Zou
- Department of Computer Science, City University of Hong Kong, 83 Tat Tree Ave, Kowloon Tong, Hong Kong, China
| | - Lingxi Chen
- Department of Computer Science, City University of Hong Kong, 83 Tat Tree Ave, Kowloon Tong, Hong Kong, China
| | - Wei Liu
- Department of Computer Science, City University of Hong Kong, 83 Tat Tree Ave, Kowloon Tong, Hong Kong, China
| | - Wei Zhang
- Department of Computer Science, City University of Hong Kong, 83 Tat Tree Ave, Kowloon Tong, Hong Kong, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, 83 Tat Tree Ave, Kowloon Tong, Hong Kong, China
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Tree Ave, Kowloon Tong, Hong Kong, China
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12
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Huuhtanen J, Kasanen H, Peltola K, Lönnberg T, Glumoff V, Brück O, Dufva O, Peltonen K, Vikkula J, Jokinen E, Ilander M, Lee MH, Mäkelä S, Nyakas M, Li B, Hernberg M, Bono P, Lähdesmäki H, Kreutzman A, Mustjoki S. Single-cell characterization of anti-LAG-3 and anti-PD-1 combination treatment in patients with melanoma. J Clin Invest 2023; 133:164809. [PMID: 36719749 PMCID: PMC10014104 DOI: 10.1172/jci164809] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
BackgroundRelatlimab plus nivolumab (anti-lymphocyte-activation gene 3 plus anti-programmed death 1 [anti-LAG-3+anti-PD-1]) has been approved by the FDA as a first-line therapy for stage III/IV melanoma, but its detailed effect on the immune system is unknown.MethodsWe evaluated blood samples from 40 immunotherapy-naive or prior immunotherapy-refractory patients with metastatic melanoma treated with anti-LAG-3+anti-PD-1 in a phase I trial using single-cell RNA and T cell receptor sequencing (scRNA+TCRαβ-Seq) combined with other multiomics profiling.ResultsThe highest LAG3 expression was noted in NK cells, Tregs, and CD8+ T cells, and these cell populations underwent the most significant changes during the treatment. Adaptive NK cells were enriched in responders and underwent profound transcriptomic changes during the therapy, resulting in an active phenotype. LAG3+ Tregs expanded, but based on the transcriptome profile, became metabolically silent during the treatment. Last, higher baseline TCR clonality was observed in responding patients, and their expanding CD8+ T cell clones gained a more cytotoxic and NK-like phenotype.ConclusionAnti-LAG-3+anti-PD-1 therapy has profound effects on NK cells and Tregs in addition to CD8+ T cells.Trial registrationClinicalTrials.gov (NCT01968109)FundingCancer Foundation Finland, Sigrid Juselius Foundation, Signe and Ane Gyllenberg Foundation, Relander Foundation, State funding for university-level health research in Finland, a Helsinki Institute of Life Sciences Fellow grant, Academy of Finland (grant numbers 314442, 311081, 335432, and 335436), and an investigator-initiated research grant from BMS.
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Affiliation(s)
- Jani Huuhtanen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Department of Computer Science, Aalto University, Espoo, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Henna Kasanen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Katriina Peltola
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.,Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Virpi Glumoff
- Research Unit of Biomedicine, Medical Microbiology and Immunology, University of Oulu, Oulu, Finland
| | - Oscar Brück
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Olli Dufva
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Karita Peltonen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Johanna Vikkula
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Emmi Jokinen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Department of Computer Science, Aalto University, Espoo, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Mette Ilander
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Moon Hee Lee
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Siru Mäkelä
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Marta Nyakas
- Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Bin Li
- Bristol Myers Squibb (BMS) Research and Development, Princeton, New Jersey, USA
| | - Micaela Hernberg
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Petri Bono
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Anna Kreutzman
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Satu Mustjoki
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
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