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Campbell KM, Amouzgar M, Pfeiffer SM, Howes TR, Medina E, Travers M, Steiner G, Weber JS, Wolchok JD, Larkin J, Hodi FS, Boffo S, Salvador L, Tenney D, Tang T, Thompson MA, Spencer CN, Wells DK, Ribas A. Prior anti-CTLA-4 therapy impacts molecular characteristics associated with anti-PD-1 response in advanced melanoma. Cancer Cell 2023; 41:791-806.e4. [PMID: 37037616 PMCID: PMC10187051 DOI: 10.1016/j.ccell.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 01/16/2023] [Accepted: 03/08/2023] [Indexed: 04/12/2023]
Abstract
Immune checkpoint inhibitors (ICIs), including CTLA-4- and PD-1-blocking antibodies, can have profound effects on tumor immune cell infiltration that have not been consistent in biopsy series reported to date. Here, we analyze seven molecular datasets of samples from patients with advanced melanoma (N = 514) treated with ICI agents to investigate clinical, genomic, and transcriptomic features of anti-PD-1 response in cutaneous melanoma. We find that prior anti-CTLA-4 therapy is associated with differences in genomic, individual gene, and gene signatures in anti-PD-1 responders. Anti-CTLA-4-experienced melanoma tumors that respond to PD-1 blockade exhibit increased tumor mutational burden, inflammatory signatures, and altered cell cycle processes compared with anti-CTLA-4-naive tumors or anti-CTLA-4-experienced, anti-PD-1-nonresponsive melanoma tumors. We report a harmonized, aggregate resource and suggest that prior CTLA-4 blockade therapy is associated with marked differences in the tumor microenvironment that impact the predictive features of PD-1 blockade therapy response.
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Affiliation(s)
- Katie M Campbell
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Meelad Amouzgar
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | | | - Timothy R Howes
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Egmidio Medina
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Travers
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Gabriela Steiner
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Jeffrey S Weber
- Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Jedd D Wolchok
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medicine, New York, NY 10065, USA
| | - James Larkin
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Silvia Boffo
- Bristol Myers Squibb Corp., Princeton, NJ 08540, USA
| | - Lisa Salvador
- Bristol Myers Squibb Corp., Princeton, NJ 08540, USA
| | - Daniel Tenney
- Bristol Myers Squibb Corp., Princeton, NJ 08540, USA
| | - Tracy Tang
- Bristol Myers Squibb Corp., Princeton, NJ 08540, USA
| | | | | | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Antoni Ribas
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of Surgical Oncology, Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90024, USA.
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Wucherpfennig JI, Howes TR, Au JN, Au EH, Roberts Kingman GA, Brady SD, Herbert AL, Reimchen TE, Bell MA, Lowe CB, Dalziel AC, Kingsley DM. Evolution of stickleback spines through independent cis-regulatory changes at HOXDB. Nat Ecol Evol 2022; 6:1537-1552. [PMID: 36050398 PMCID: PMC9525239 DOI: 10.1038/s41559-022-01855-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 02/02/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022]
Abstract
Understanding the mechanisms leading to new traits or additional features in organisms is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different fish genera to alter the length and number of the prominent dorsal spines used to classify stickleback species. In Gasterosteus aculeatus (typically 'three-spine sticklebacks'), a variant HOXDB allele is genetically linked to shortening an existing spine and adding an additional spine. In Apeltes quadracus (typically 'four-spine sticklebacks'), a variant HOXDB allele is associated with lengthening a spine and adding an additional spine in natural populations. The variant alleles alter the same non-coding enhancer region in the HOXDB locus but do so by diverse mechanisms, including single-nucleotide polymorphisms, deletions and transposable element insertions. The independent regulatory changes are linked to anterior expansion or contraction of HOXDB expression. We propose that associated changes in spine lengths and numbers are partial identity transformations in a repeating skeletal series that forms major defensive structures in fish. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.
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Affiliation(s)
- Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Timothy R Howes
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jessica N Au
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric H Au
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Amy L Herbert
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Anne C Dalziel
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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Santos PM, Adamik J, Howes TR, Du S, Vujanovic L, Warren S, Gambotto A, Kirkwood JM, Butterfield LH. Impact of checkpoint blockade on cancer vaccine-activated CD8+ T cell responses. J Exp Med 2021; 217:151736. [PMID: 32369107 PMCID: PMC7336310 DOI: 10.1084/jem.20191369] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/04/2019] [Accepted: 03/23/2020] [Indexed: 12/19/2022] Open
Abstract
Immune and molecular profiling of CD8 T cells of patients receiving DC vaccines expressing three full-length melanoma antigens (MAs) was performed. Antigen expression levels in DCs had no significant impact on T cell or clinical responses. Patients who received checkpoint blockade before DC vaccination had higher baseline MA-specific CD8 T cell responses but no evidence for improved functional responses to the vaccine. Patients who showed the best clinical responses had low PD-1 expression on MA-specific T cells before and after DC vaccination; however, blockade of PD-1 during antigen presentation by DC had minimal functional impact on PD-1high MA-specific T cells. Gene and protein expression analyses in lymphocytes and tumor samples identified critical immunoregulatory pathways, including CTLA-4 and PD-1. High immune checkpoint gene expression networks correlated with inferior clinical outcomes. Soluble serum PD-L2 showed suggestive positive association with improved outcome. These findings show that checkpoint molecular pathways are critical for vaccine outcomes and suggest specific sequencing of vaccine combinations.
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Affiliation(s)
- Patricia M Santos
- University of Pittsburgh Medical Center, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA
| | - Juraj Adamik
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Timothy R Howes
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Samuel Du
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA
| | - Lazar Vujanovic
- University of Pittsburgh Medical Center, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA
| | | | - Andrea Gambotto
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA
| | - John M Kirkwood
- University of Pittsburgh Medical Center, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA.,Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Lisa H Butterfield
- University of Pittsburgh Medical Center, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA.,Department of Surgery, University of Pittsburgh, Pittsburgh, PA.,Department of Medicine, University of Pittsburgh, Pittsburgh, PA
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Howes TR, Summers BR, Kingsley DM. Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A. BMC Biol 2017; 15:115. [PMID: 29212540 PMCID: PMC5719529 DOI: 10.1186/s12915-017-0456-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 11/09/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Dorsal spine reduction in threespine sticklebacks (Gasterosteus aculeatus) is a classic example of recurrent skeletal evolution in nature. Sticklebacks in marine environments typically have long spines that form part of their skeletal armor. Many derived freshwater populations have evolved shorter spines. Changes in spine length are controlled in part by a quantitative trait locus (QTL) previously mapped to chromosome 4, but the causative gene and mutations underlying the repeated evolution of this interesting skeletal trait have not been identified. RESULTS Refined mapping of the spine length QTL shows that it lies near the MSX2A transcription factor gene. MSX2A is expressed in developing spines. In F1 marine × freshwater fish, the marine allele is preferentially expressed. Differences in expression can be attributed to splicing regulation. Due to the use of an alternative 5 ' splice site within the first exon, the freshwater allele produces greater amounts of a shortened, non-functional transcript and makes less of the full-length transcript. Sequence changes in the MSX2A region are shared by many freshwater fish, suggesting that repeated evolution occurs by reuse of a spine-reduction variant. To demonstrate the effect of full-length MSX2A on spine length, we produced transgenic freshwater fish expressing a copy of marine MSX2A. The spines of the transgenic fish were significantly longer on average than those of their non-transgenic siblings, partially reversing the reduced spine lengths that have evolved in freshwater populations. CONCLUSIONS MSX2A is a major gene underlying dorsal spine reduction in freshwater sticklebacks. The gene is linked to a separate gene controlling bony plate loss, helping explain the concerted effects of chromosome 4 on multiple armor-reduction traits. The nature of the molecular changes provides an interesting example of morphological evolution occurring not through a simple amino acid change, nor through a change only in gene expression levels, but through a change in the ratio of splice products encoding both normal and truncated proteins.
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Affiliation(s)
- Timothy R Howes
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian R Summers
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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