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Ye QW, Liu YJ, Li JQ, Han M, Bian ZR, Chen TY, Li JP, Liu SL, Zou X. GJA4 expressed on cancer associated fibroblasts (CAFs)-A 'promoter' of the mesenchymal phenotype. Transl Oncol 2024; 46:102009. [PMID: 38833783 PMCID: PMC11190749 DOI: 10.1016/j.tranon.2024.102009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 05/09/2024] [Accepted: 05/25/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most common cancer worldwide. Connexin is a transmembrane protein involved in gap junctions (GJs) formation. Our previous study found that connexin 37 (Cx37), encoded by gap junction protein alpha 4 (GJA4), expressed on fibroblasts acts as a promoter of CRC and is closely related to epithelial-mesenchymal transition (EMT) and tumor immune microenvironment. However, to date, the mechanism concerning the malignancy of GJA4 in tumor stroma has not been studied. METHODS Hematoxylin-eosin (HE) and immunohistochemical (IHC) staining were used to validate the expression and localization of GJA4. Using single-cell analysis, enrichment analysis, spatial transcriptomics, immunofluorescence staining (IF), Sirius red staining, wound healing and transwell assays, western blotting (WB), Cell Counting Kit-8 (CCK8) assay and in vivo experiments, we investigated the possible mechanisms of GJA4 in promoting CRC. RESULTS We discovered that in CRC, GJA4 on fibroblasts is involved in promoting fibroblast activation and promoting EMT through a fibroblast-dependent pathway. Furthermore, GJA4 may act synergistically with M2 macrophages to limit T cell infiltration by stimulating the formation of an immune-excluded desmoplasic barrier. Finally, we found a significantly correlation between GJA4 and pathological staging (P < 0.0001) or D2 dimer (R = 0.03, P < 0.05). CONCLUSION We have identified GJA4 expressed on fibroblasts is actually a promoter of the tumor mesenchymal phenotype. Our findings suggest that the interaction between GJA4+ fibroblasts and M2 macrophages may be an effective target for enhancing tumor immunotherapy.
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Affiliation(s)
- Qian-Wen Ye
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Yuan-Jie Liu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Jia-Qi Li
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Mei Han
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Ze-Ren Bian
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Tian-Yuan Chen
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Jie-Pin Li
- Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Shen-Lin Liu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China.
| | - Xi Zou
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, Nanjing, Jiangsu, PR China.
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2
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Nicolas E, Kosmider B, Cukierman E, Borghaei H, Golemis EA, Borriello L. Cancer treatments as paradoxical catalysts of tumor awakening in the lung. Cancer Metastasis Rev 2024:10.1007/s10555-024-10196-5. [PMID: 38963567 DOI: 10.1007/s10555-024-10196-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
Much of the fatality of tumors is linked to the growth of metastases, which can emerge months to years after apparently successful treatment of primary tumors. Metastases arise from disseminated tumor cells (DTCs), which disperse through the body in a dormant state to seed distant sites. While some DTCs lodge in pre-metastatic niches (PMNs) and rapidly develop into metastases, other DTCs settle in distinct microenvironments that maintain them in a dormant state. Subsequent awakening, induced by changes in the microenvironment of the DTC, causes outgrowth of metastases. Hence, there has been extensive investigation of the factors causing survival and subsequent awakening of DTCs, with the goal of disrupting these processes to decrease cancer lethality. We here provide a detailed overview of recent developments in understanding of the factors controlling dormancy and awakening in the lung, a common site of metastasis for many solid tumors. These factors include dynamic interactions between DTCs and diverse epithelial, mesenchymal, and immune cell populations resident in the lung. Paradoxically, among key triggers for metastatic outgrowth, lung tissue remodeling arising from damage induced by the treatment of primary tumors play a significant role. In addition, growing evidence emphasizes roles for inflammation and aging in opposing the factors that maintain dormancy. Finally, we discuss strategies being developed or employed to reduce the risk of metastatic recurrence.
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Affiliation(s)
- Emmanuelle Nicolas
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Beata Kosmider
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine, Temple University, 3500 N Broad St., Philadelphia, PA, 19140, USA
- Department of Microbiology, Immunology, and Inflammation, Lewis Katz School of Medicine, Temple University, 3500 N Broad St., Philadelphia, PA, 19140, USA
| | - Edna Cukierman
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Hossein Borghaei
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Erica A Golemis
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, 3500 N Broad St., Philadelphia, PA, 19140, USA
| | - Lucia Borriello
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, 3500 N Broad St., Philadelphia, PA, 19140, USA.
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3
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Hodgins JJ, Abou-Hamad J, O’Dwyer CE, Hagerman A, Yakubovich E, Tanese de Souza C, Marotel M, Buchler A, Fadel S, Park MM, Fong-McMaster C, Crupi MF, Makinson OJ, Kurdieh R, Rezaei R, Dhillon HS, Ilkow CS, Bell JC, Harper ME, Rotstein BH, Auer RC, Vanderhyden BC, Sabourin LA, Bourgeois-Daigneault MC, Cook DP, Ardolino M. PD-L1 promotes oncolytic virus infection via a metabolic shift that inhibits the type I IFN pathway. J Exp Med 2024; 221:e20221721. [PMID: 38869480 PMCID: PMC11176258 DOI: 10.1084/jem.20221721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/04/2024] [Accepted: 03/14/2024] [Indexed: 06/14/2024] Open
Abstract
While conventional wisdom initially postulated that PD-L1 serves as the inert ligand for PD-1, an emerging body of literature suggests that PD-L1 has cell-intrinsic functions in immune and cancer cells. In line with these studies, here we show that engagement of PD-L1 via cellular ligands or agonistic antibodies, including those used in the clinic, potently inhibits the type I interferon pathway in cancer cells. Hampered type I interferon responses in PD-L1-expressing cancer cells resulted in enhanced efficacy of oncolytic viruses in vitro and in vivo. Consistently, PD-L1 expression marked tumor explants from cancer patients that were best infected by oncolytic viruses. Mechanistically, PD-L1 promoted a metabolic shift characterized by enhanced glycolysis rate that resulted in increased lactate production. In turn, lactate inhibited type I IFN responses. In addition to adding mechanistic insight into PD-L1 intrinsic function, our results will also help guide the numerous ongoing efforts to combine PD-L1 antibodies with oncolytic virotherapy in clinical trials.
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Affiliation(s)
- Jonathan J. Hodgins
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
| | - John Abou-Hamad
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
| | - Colin Edward O’Dwyer
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
| | - Ash Hagerman
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
| | - Edward Yakubovich
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
| | | | - Marie Marotel
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
| | - Ariel Buchler
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
- University of Ottawa Heart Institute, Ottawa, Canada
| | - Saleh Fadel
- The Ottawa Hospital, Ottawa, Canada
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Canada
| | - Maria M. Park
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
| | - Claire Fong-McMaster
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute for Systems Biology, Ottawa, Canada
| | - Mathieu F. Crupi
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Olivia Joan Makinson
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
| | - Reem Kurdieh
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Reza Rezaei
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
| | - Harkirat Singh Dhillon
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
| | - Carolina S. Ilkow
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
| | - John C. Bell
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
- Ottawa Institute for Systems Biology, Ottawa, Canada
| | - Benjamin H. Rotstein
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
- University of Ottawa Heart Institute, Ottawa, Canada
| | - Rebecca C. Auer
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
| | - Barbara C. Vanderhyden
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
| | - Luc A. Sabourin
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
| | - Marie-Claude Bourgeois-Daigneault
- Department of Microbiology, Infectious Diseases, and Immunology, University of Montreal, Montreal, Canada
- Centre Hospitalier de l’Université de Montréal Research Centre, Cancer and Immunopathology axes, Montreal, Canada
| | - David P. Cook
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
| | - Michele Ardolino
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Canada
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4
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Hu M, Chikina M. Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods. Genome Biol 2024; 25:169. [PMID: 38956606 DOI: 10.1186/s13059-024-03292-w] [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: 01/20/2023] [Accepted: 05/29/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Computational cell type deconvolution enables the estimation of cell type abundance from bulk tissues and is important for understanding tissue microenviroment, especially in tumor tissues. With rapid development of deconvolution methods, many benchmarking studies have been published aiming for a comprehensive evaluation for these methods. Benchmarking studies rely on cell-type resolved single-cell RNA-seq data to create simulated pseudobulk datasets by adding individual cells-types in controlled proportions. RESULTS In our work, we show that the standard application of this approach, which uses randomly selected single cells, regardless of the intrinsic difference between them, generates synthetic bulk expression values that lack appropriate biological variance. We demonstrate why and how the current bulk simulation pipeline with random cells is unrealistic and propose a heterogeneous simulation strategy as a solution. The heterogeneously simulated bulk samples match up with the variance observed in real bulk datasets and therefore provide concrete benefits for benchmarking in several ways. We demonstrate that conceptual classes of deconvolution methods differ dramatically in their robustness to heterogeneity with reference-free methods performing particularly poorly. For regression-based methods, the heterogeneous simulation provides an explicit framework to disentangle the contributions of reference construction and regression methods to performance. Finally, we perform an extensive benchmark of diverse methods across eight different datasets and find BayesPrism and a hybrid MuSiC/CIBERSORTx approach to be the top performers. CONCLUSIONS Our heterogeneous bulk simulation method and the entire benchmarking framework is implemented in a user friendly package https://github.com/humengying0907/deconvBenchmarking and https://doi.org/10.5281/zenodo.8206516 , enabling further developments in deconvolution methods.
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Affiliation(s)
- Mengying Hu
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA.
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, USA.
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5
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Choi JE, Qiao Y, Kryczek I, Yu J, Gurkan J, Bao Y, Gondal M, Tien JCY, Maj T, Yazdani S, Parolia A, Xia H, Zhou J, Wei S, Grove S, Vatan L, Lin H, Li G, Zheng Y, Zhang Y, Cao X, Su F, Wang R, He T, Cieslik M, Green MD, Zou W, Chinnaiyan AM. PIKfyve, expressed by CD11c-positive cells, controls tumor immunity. Nat Commun 2024; 15:5487. [PMID: 38942798 PMCID: PMC11213953 DOI: 10.1038/s41467-024-48931-9] [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: 08/17/2023] [Accepted: 05/15/2024] [Indexed: 06/30/2024] Open
Abstract
Cancer treatment continues to shift from utilizing traditional therapies to targeted ones, such as protein kinase inhibitors and immunotherapy. Mobilizing dendritic cells (DC) and other myeloid cells with antigen presenting and cancer cell killing capacities is an attractive but not fully exploited approach. Here, we show that PIKFYVE is a shared gene target of clinically relevant protein kinase inhibitors and high expression of this gene in DCs is associated with poor patient response to immune checkpoint blockade (ICB) therapy. Genetic and pharmacological studies demonstrate that PIKfyve ablation enhances the function of CD11c+ cells (predominantly dendritic cells) via selectively altering the non-canonical NF-κB pathway. Both loss of Pikfyve in CD11c+ cells and treatment with apilimod, a potent and specific PIKfyve inhibitor, restrained tumor growth, enhanced DC-dependent T cell immunity, and potentiated ICB efficacy in tumor-bearing mouse models. Furthermore, the combination of a vaccine adjuvant and apilimod reduced tumor progression in vivo. Thus, PIKfyve negatively regulates the function of CD11c+ cells, and PIKfyve inhibition has promise for cancer immunotherapy and vaccine treatment strategies.
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Affiliation(s)
- Jae Eun Choi
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Yuanyuan Qiao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jiali Yu
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Gurkan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yi Bao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mahnoor Gondal
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jean Ching-Yi Tien
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tomasz Maj
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sahr Yazdani
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Abhijit Parolia
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Houjun Xia
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - JiaJia Zhou
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Shuang Wei
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sara Grove
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Linda Vatan
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Heng Lin
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Gaopeng Li
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tongchen He
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Michael D Green
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Weiping Zou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA.
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA.
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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6
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Tooley K, Jerby L, Escobar G, Krovi SH, Mangani D, Dandekar G, Cheng H, Madi A, Goldschmidt E, Lambden C, Krishnan RK, Rozenblatt-Rosen O, Regev A, Anderson AC. Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity. Cell Rep Med 2024:101640. [PMID: 38959885 DOI: 10.1016/j.xcrm.2024.101640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 01/05/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
CD8+ T cells must persist and function in diverse tumor microenvironments to exert their effects. Thus, understanding common underlying expression programs could better inform the next generation of immunotherapies. We apply a generalizable matrix factorization algorithm that recovers both shared and context-specific expression programs from diverse datasets to a single-cell RNA sequencing (scRNA-seq) compendium of 33,161 CD8+ T cells from 132 patients with seven human cancers. Our meta-single-cell analyses uncover a pan-cancer T cell dysfunction program that predicts clinical non-response to checkpoint blockade in melanoma and highlights CXCR6 as a pan-cancer marker of chronically activated T cells. Cxcr6 is trans-activated by AP-1 and repressed by TCF1. Using mouse models, we show that Cxcr6 deletion in CD8+ T cells increases apoptosis of PD1+TIM3+ cells, dampens CD28 signaling, and compromises tumor growth control. Our study uncovers a TCF1:CXCR6 axis that counterbalances PD1-mediated suppression of CD8+ cell responses and is essential for effective anti-tumor immunity.
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Affiliation(s)
- Katherine Tooley
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Livnat Jerby
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulia Escobar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - S Harsha Krovi
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Davide Mangani
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gitanjali Dandekar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanning Cheng
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Asaf Madi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Goldschmidt
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Conner Lambden
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rajesh K Krishnan
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ana C Anderson
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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7
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Wang L, Izadmehr S, Sfakianos JP, Tran M, Beaumont KG, Brody R, Cordon-Cardo C, Horowitz A, Sebra R, Oh WK, Bhardwaj N, Galsky MD, Zhu J. Single-cell transcriptomic-informed deconvolution of bulk data identifies immune checkpoint blockade resistance in urothelial cancer. iScience 2024; 27:109928. [PMID: 38812546 PMCID: PMC11133924 DOI: 10.1016/j.isci.2024.109928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/23/2023] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
Interactions within the tumor microenvironment (TME) significantly influence tumor progression and treatment responses. While single-cell RNA sequencing (scRNA-seq) and spatial genomics facilitate TME exploration, many clinical cohorts are assessed at the bulk tissue level. Integrating scRNA-seq and bulk tissue RNA-seq data through computational deconvolution is essential for obtaining clinically relevant insights. Our method, ProM, enables the examination of major and minor cell types. Through evaluation against existing methods using paired single-cell and bulk RNA sequencing of human urothelial cancer (UC) samples, ProM demonstrates superiority. Application to UC cohorts treated with immune checkpoint inhibitors reveals pre-treatment cellular features associated with poor outcomes, such as elevated SPP1 expression in macrophage/monocytes (MM). Our deconvolution method and paired single-cell and bulk tissue RNA-seq dataset contribute novel insights into TME heterogeneity and resistance to immune checkpoint blockade.
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Affiliation(s)
- Li Wang
- Department of Precision Medicine, Aitia, Somerville, MA 02143, USA
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
| | - Sudeh Izadmehr
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
| | - John P. Sfakianos
- Department of Urology; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michelle Tran
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristin G. Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rachel Brody
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Cordon-Cardo
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amir Horowitz
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - William K. Oh
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
| | - Nina Bhardwaj
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew D. Galsky
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
| | - Jun Zhu
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
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8
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Desai P, Takahashi N, Kumar R, Nichols S, Malin J, Hunt A, Schultz C, Cao Y, Tillo D, Nousome D, Chauhan L, Sciuto L, Jordan K, Rajapakse V, Tandon M, Lissa D, Zhang Y, Kumar S, Pongor L, Singh A, Schroder B, Sharma AK, Chang T, Vilimas R, Pinkiert D, Graham C, Butcher D, Warner A, Sebastian R, Mahon M, Baker K, Cheng J, Berger A, Lake R, Abel M, Krishnamurthy M, Chrisafis G, Fitzgerald P, Nirula M, Goyal S, Atkinson D, Bateman NW, Abulez T, Nair G, Apolo A, Guha U, Karim B, El Meskini R, Ohler ZW, Jolly MK, Schaffer A, Ruppin E, Kleiner D, Miettinen M, Brown GT, Hewitt S, Conrads T, Thomas A. Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities. Cell Rep Med 2024; 5:101610. [PMID: 38897168 DOI: 10.1016/j.xcrm.2024.101610] [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: 03/02/2023] [Revised: 08/04/2023] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intratumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the cell-extrinsic drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall composition of non-malignant cells in the TME exhibit substantial variability, closely mirroring the tumor phenotype, suggesting TME-driven reprogramming of NE cell states. We identify cancer-associated fibroblasts (CAFs) as a crucial element of SCLC TME heterogeneity, contributing to immune exclusion, and predicting exceptionally poor prognosis. Our work provides a comprehensive map of SCLC tumor and TME ecosystems, emphasizing their pivotal role in SCLC's adaptable nature, opening possibilities for reprogramming the TME-tumor communications that shape SCLC tumor states.
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Affiliation(s)
- Parth Desai
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Medical Oncology, Fox Chase Cancer Center, Temple University Hospital and Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Nobuyuki Takahashi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Medical Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Rajesh Kumar
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samantha Nichols
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin Malin
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison Hunt
- Women's Health Integrated Research Center, Inova Health System, Falls Church, VA, USA
| | - Christopher Schultz
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yingying Cao
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Desiree Tillo
- CCR Collaborative Bioinformatics, Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Darryl Nousome
- CCR Collaborative Bioinformatics, Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lakshya Chauhan
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Linda Sciuto
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kimberly Jordan
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Vinodh Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mayank Tandon
- CCR Collaborative Bioinformatics, Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Delphine Lissa
- Laboratory of Human Carcinogenesis, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yang Zhang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Suresh Kumar
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lorinc Pongor
- HCEMM Cancer Genomics and Epigenetics Research Group, Szeged, Hungary
| | - Abhay Singh
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Brett Schroder
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ajit Kumar Sharma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tiangen Chang
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rasa Vilimas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Danielle Pinkiert
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chante Graham
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Donna Butcher
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Andrew Warner
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Robin Sebastian
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mimi Mahon
- Pain and Palliative care services, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Karen Baker
- Pain and Palliative care services, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Jennifer Cheng
- Pain and Palliative care services, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Ann Berger
- Pain and Palliative care services, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Ross Lake
- Laboratory of Genitourinary cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melissa Abel
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Manan Krishnamurthy
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George Chrisafis
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter Fitzgerald
- CCR Collaborative Bioinformatics, Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Micheal Nirula
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shubhank Goyal
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Devon Atkinson
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Nicholas W Bateman
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Tamara Abulez
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Govind Nair
- National Institute of Neurological Disorders and Stroke, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrea Apolo
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Baktiar Karim
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Rajaa El Meskini
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Zoe Weaver Ohler
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Mohit Kumar Jolly
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Alejandro Schaffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Kleiner
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - G Tom Brown
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Conrads
- Women's Health Integrated Research Center, Inova Health System, Falls Church, VA, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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9
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Jing ZQ, Luo ZQ, Chen SR, Sun ZJ. Heterogeneity of myeloid cells in common cancers: Single cell insights and targeting strategies. Int Immunopharmacol 2024; 134:112253. [PMID: 38735257 DOI: 10.1016/j.intimp.2024.112253] [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: 03/27/2024] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
Tumor microenvironment (TME), is characterized by a complex and heterogenous composition involving a substantial population of immune cells. Myeloid cells comprising over half of the solid tumor mass, are undoubtedly one of the most prominent cell populations associated with tumors. Studies have unambiguously established that myeloid cells play a key role in tumor development, including immune suppression, pro-inflammation, promote tumor metastasis and angiogenesis, for example, tumor-associated macrophages promote tumor progression in a variety of common tumors, including lung cancer, through direct or indirect interactions with the TME. However, due to previous technological constraints, research on myeloid cells often tended to be conducted as studies with low throughput and limited resolution. For example, the conventional categorization of macrophages into M1-like and M2-like subsets based solely on their anti-tumor and pro-tumor roles has disregarded their continuum of states, resulting in an inadequate analysis of the high heterogeneity characterizing myeloid cells. The widespread adoption of single-cell RNA sequencing (scRNA-seq) in tumor immunology has propelled researchers into a new realm of understanding, leading to the establishment of novel subsets and targets. In this review, the origin of myeloid cells in high-incidence cancers, the functions of myeloid cell subsets examined through traditional and single-cell perspectives, as well as specific targeting strategies, are comprehensively outlined. As a result of this endeavor, we will gain a better understanding of myeloid cell heterogeneity, as well as contribute to the development of new therapeutic approaches.
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Affiliation(s)
- Zhi-Qian Jing
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Science, Wuhan University, Wuhan 430079, China
| | - Zhi-Qi Luo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Science, Wuhan University, Wuhan 430079, China
| | - Si-Rui Chen
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Science, Wuhan University, Wuhan 430079, China
| | - Zhi-Jun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Science, Wuhan University, Wuhan 430079, China.
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10
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Zhang JP, Yan BZ, Liu J, Wang W. Action of circulating and infiltrating B cells in the immune microenvironment of colorectal cancer by single-cell sequencing analysis. World J Gastrointest Oncol 2024; 16:2671-2684. [DOI: 10.4251/wjgo.v16.i6.2671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND The complexity of the immune microenvironment has an impact on the treatment of colorectal cancer (CRC), one of the most prevalent malignancies worldwide. In this study, multi-omics and single-cell sequencing techniques were used to investigate the mechanism of action of circulating and infiltrating B cells in CRC. By revealing the heterogeneity and functional differences of B cells in cancer immunity, we aim to deepen our understanding of immune regulation and provide a scientific basis for the development of more effective cancer treatment strategies.
AIM To explore the role of circulating and infiltrating B cell subsets in the immune microenvironment of CRC, explore the potential driving mechanism of B cell development, analyze the interaction between B cells and other immune cells in the immune microenvironment and the functions of communication molecules, and search for possible regulatory pathways to promote the anti-tumor effects of B cells.
METHODS A total of 69 paracancer (normal), tumor and peripheral blood samples were collected from 23 patients with CRC from The Cancer Genome Atlas database (https://portal.gdc.cancer.gov/). After the immune cells were sorted by multicolor flow cytometry, the single cell transcriptome and B cell receptor group library were sequenced using the 10X Genomics platform, and the data were analyzed using bioinformatics tools such as Seurat. The differences in the number and function of B cell infiltration between tumor and normal tissue, the interaction between B cell subsets and T cells and myeloid cell subsets, and the transcription factor regulatory network of B cell subsets were explored and analyzed.
RESULTS Compared with normal tissue, the infiltrating number of CD20+B cell subsets in tumor tissue increased significantly. Among them, germinal center B cells (GCB) played the most prominent role, with positive clone expansion and heavy chain mutation level increasing, and the trend of differentiation into memory B cells increased. However, the number of plasma cells in the tumor microenvironment decreased significantly, and the plasma cells secreting IgA antibodies decreased most obviously. In addition, compared with the immune microenvironment of normal tissues, GCB cells in tumor tissues became more closely connected with other immune cells such as T cells, and communication molecules that positively regulate immune function were significantly enriched.
CONCLUSION The role of GCB in CRC tumor microenvironment is greatly enhanced, and its affinity to tumor antigen is enhanced by its significantly increased heavy chain mutation level. Meanwhile, GCB has enhanced its association with immune cells in the microenvironment, which plays a positive anti-tumor effect.
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Affiliation(s)
- Jing-Po Zhang
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
| | - Bing-Zheng Yan
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
| | - Jie Liu
- Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital, Changsha 410002, Hunan Province, China
| | - Wei Wang
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
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11
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Zhang JP, Yan BZ, Liu J, Wang W. Action of circulating and infiltrating B cells in the immune microenvironment of colorectal cancer by single-cell sequencing analysis. World J Gastrointest Oncol 2024; 16:2683-2696. [DOI: 10.4251/wjgo.v16.i6.2683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The complexity of the immune microenvironment has an impact on the treatment of colorectal cancer (CRC), one of the most prevalent malignancies worldwide. In this study, multi-omics and single-cell sequencing techniques were used to investigate the mechanism of action of circulating and infiltrating B cells in CRC. By revealing the heterogeneity and functional differences of B cells in cancer immunity, we aim to deepen our understanding of immune regulation and provide a scientific basis for the development of more effective cancer treatment strategies.
AIM To explore the role of circulating and infiltrating B cell subsets in the immune microenvironment of CRC, explore the potential driving mechanism of B cell development, analyze the interaction between B cells and other immune cells in the immune microenvironment and the functions of communication molecules, and search for possible regulatory pathways to promote the anti-tumor effects of B cells.
METHODS A total of 69 paracancer (normal), tumor and peripheral blood samples were collected from 23 patients with CRC from The Cancer Genome Atlas database (https://portal.gdc.cancer.gov/). After the immune cells were sorted by multicolor flow cytometry, the single cell transcriptome and B cell receptor group library were sequenced using the 10X Genomics platform, and the data were analyzed using bioinformatics tools such as Seurat. The differences in the number and function of B cell infiltration between tumor and normal tissue, the interaction between B cell subsets and T cells and myeloid cell subsets, and the transcription factor regulatory network of B cell subsets were explored and analyzed.
RESULTS Compared with normal tissue, the infiltrating number of CD20+B cell subsets in tumor tissue increased significantly. Among them, germinal center B cells (GCB) played the most prominent role, with positive clone expansion and heavy chain mutation level increasing, and the trend of differentiation into memory B cells increased. However, the number of plasma cells in the tumor microenvironment decreased significantly, and the plasma cells secreting IgA antibodies decreased most obviously. In addition, compared with the immune microenvironment of normal tissues, GCB cells in tumor tissues became more closely connected with other immune cells such as T cells, and communication molecules that positively regulate immune function were significantly enriched.
CONCLUSION The role of GCB in CRC tumor microenvironment is greatly enhanced, and its affinity to tumor antigen is enhanced by its significantly increased heavy chain mutation level. Meanwhile, GCB has enhanced its association with immune cells in the microenvironment, which plays a positive anti-tumor effect.
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Affiliation(s)
- Jing-Po Zhang
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
| | - Bing-Zheng Yan
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
| | - Jie Liu
- Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital, Changsha 410002, Hunan Province, China
| | - Wei Wang
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
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12
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Choi WS, Kwon HJ, Yi E, Lee H, Kim JM, Park HJ, Choi EJ, Choi ME, Sung YH, Won CH, Sung CO, Kim HS. HPK1 Dysregulation-Associated NK Cell Dysfunction and Defective Expansion Promotes Metastatic Melanoma Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400920. [PMID: 38828677 DOI: 10.1002/advs.202400920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/10/2024] [Indexed: 06/05/2024]
Abstract
Distant metastasis, the leading cause of cancer death, is efficiently kept in check by immune surveillance. Studies have uncovered peripheral natural killer (NK) cells as key antimetastatic effectors and their dysregulation during metastasis. However, the molecular mechanism governing NK cell dysfunction links to metastasis remains elusive. Herein, MAP4K1 encoding HPK1 is aberrantly overexpressed in dysfunctional NK cells in the periphery and the metastatic site. Conditional HPK1 overexpression in NK cells suffices to exacerbate melanoma lung metastasis but not primary tumor growth. Conversely, MAP4K1-deficient mice are resistant to metastasis and further protected by combined immune-checkpoint inhibitors. Mechanistically, HPK1 restrains NK cell cytotoxicity and expansion via activating receptors. Likewise, HPK1 limits human NK cell activation and associates with melanoma NK cell dysfunction couples to TGF-β1 and patient response to immune checkpoint therapy. Thus, HPK1 is an intracellular checkpoint controlling NK-target cell responses, which is dysregulated and hijacked by tumors during metastatic progression.
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Affiliation(s)
- Woo Seon Choi
- Department of Microbiology, Stem Cell Immunomodulation Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hyung-Joon Kwon
- Department of Microbiology, Stem Cell Immunomodulation Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Eunbi Yi
- Department of Microbiology, Stem Cell Immunomodulation Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Haeun Lee
- Department of Microbiology, Stem Cell Immunomodulation Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Jung Min Kim
- Department of Microbiology, Stem Cell Immunomodulation Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hyo Jin Park
- Department of Microbiology, Stem Cell Immunomodulation Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Eun Ji Choi
- Department of Dermatology, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Myoung Eun Choi
- Department of Dermatology, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Young Hoon Sung
- Department of Cell and Genetic Engineering, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Chong Hyun Won
- Department of Dermatology, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Chang Ohk Sung
- Department of Pathology, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hun Sik Kim
- Department of Microbiology, Stem Cell Immunomodulation Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
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13
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Chen ACY, Jaiswal S, Martinez D, Yerinde C, Ji K, Miranda V, Fung ME, Weiss SA, Zschummel M, Taguchi K, Garris CS, Mempel TR, Hacohen N, Sen DR. The aged tumor microenvironment limits T cell control of cancer. Nat Immunol 2024; 25:1033-1045. [PMID: 38745085 DOI: 10.1038/s41590-024-01828-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/27/2024] [Indexed: 05/16/2024]
Abstract
The etiology and effect of age-related immune dysfunction in cancer is not completely understood. Here we show that limited priming of CD8+ T cells in the aged tumor microenvironment (TME) outweighs cell-intrinsic defects in limiting tumor control. Increased tumor growth in aging is associated with reduced CD8+ T cell infiltration and function. Transfer of T cells from young mice does not restore tumor control in aged mice owing to rapid induction of T cell dysfunction. Cell-extrinsic signals in the aged TME drive a tumor-infiltrating age-associated dysfunctional (TTAD) cell state that is functionally, transcriptionally and epigenetically distinct from canonical T cell exhaustion. Altered natural killer cell-dendritic cell-CD8+ T cell cross-talk in aged tumors impairs T cell priming by conventional type 1 dendritic cells and promotes TTAD cell formation. Aged mice are thereby unable to benefit from therapeutic tumor vaccination. Critically, myeloid-targeted therapy to reinvigorate conventional type 1 dendritic cells can improve tumor control and restore CD8+ T cell immunity in aging.
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Affiliation(s)
- Alex C Y Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Sneha Jaiswal
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniela Martinez
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Cansu Yerinde
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Keely Ji
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Velita Miranda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Megan E Fung
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah A Weiss
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Maria Zschummel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Kazuhiro Taguchi
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher S Garris
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Thorsten R Mempel
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Nir Hacohen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Debattama R Sen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
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14
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Fan L, Liu J, Hu W, Chen Z, Lan J, Zhang T, Zhang Y, Wu X, Zhong Z, Zhang D, Zhang J, Qin R, Chen H, Zong Y, Zhang J, Chen B, Jiang J, Cheng J, Zhou J, Gao Z, Liu Z, Chai Y, Fan J, Wu P, Chen Y, Zhu Y, Wang K, Yuan Y, Huang P, Zhang Y, Feng H, Song K, Zeng X, Zhu W, Hu X, Yin W, Chen W, Wang J. Targeting pro-inflammatory T cells as a novel therapeutic approach to potentially resolve atherosclerosis in humans. Cell Res 2024; 34:407-427. [PMID: 38491170 PMCID: PMC11143203 DOI: 10.1038/s41422-024-00945-0] [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: 09/24/2023] [Accepted: 02/24/2024] [Indexed: 03/18/2024] Open
Abstract
Atherosclerosis (AS), a leading cause of cardio-cerebrovascular disease worldwide, is driven by the accumulation of lipid contents and chronic inflammation. Traditional strategies primarily focus on lipid reduction to control AS progression, leaving residual inflammatory risks for major adverse cardiovascular events (MACEs). While anti-inflammatory therapies targeting innate immunity have reduced MACEs, many patients continue to face significant risks. Another key component in AS progression is adaptive immunity, but its potential role in preventing AS remains unclear. To investigate this, we conducted a retrospective cohort study on tumor patients with AS plaques. We found that anti-programmed cell death protein 1 (PD-1) monoclonal antibody (mAb) significantly reduces AS plaque size. With multi-omics single-cell analyses, we comprehensively characterized AS plaque-specific PD-1+ T cells, which are activated and pro-inflammatory. We demonstrated that anti-PD-1 mAb, when captured by myeloid-expressed Fc gamma receptors (FcγRs), interacts with PD-1 expressed on T cells. This interaction turns the anti-PD-1 mAb into a substitute PD-1 ligand, suppressing T-cell functions in the PD-1 ligands-deficient context of AS plaques. Further, we conducted a prospective cohort study on tumor patients treated with anti-PD-1 mAb with or without Fc-binding capability. Our analysis shows that anti-PD-1 mAb with Fc-binding capability effectively reduces AS plaque size, while anti-PD-1 mAb without Fc-binding capability does not. Our work suggests that T cell-targeting immunotherapy can be an effective strategy to resolve AS in humans.
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Affiliation(s)
- Lin Fan
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, Zhejiang, China
| | - Junwei Liu
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Wei Hu
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zexin Chen
- Center of Clinical Epidemiology and Biostatistics and Department of Scientific Research, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jie Lan
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, China
- Department of Bioinformatics, The Basic Medical School of Chongqing Medical University, Chongqing, China
| | - Tongtong Zhang
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yang Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xianpeng Wu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Zhiwei Zhong
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Danyang Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jinlong Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Rui Qin
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Frontier Science Center for Brain Science & Brain-machine Integration, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hui Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Zong
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianmin Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bing Chen
- Department of Vascular Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Jiang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jifang Cheng
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jingyi Zhou
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhiwei Gao
- Department of Vascular Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhenjie Liu
- Department of Vascular Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Chai
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Junqiang Fan
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinxuan Chen
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuefeng Zhu
- Department of Vascular Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kai Wang
- Department of Respiratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Yuan
- Department of Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Pintong Huang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Zhang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huiqin Feng
- Department of Clinical Research Center, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kaichen Song
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xun Zeng
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wei Zhu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xinyang Hu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, Zhejiang, China.
| | - Weiwei Yin
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Wei Chen
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China.
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China.
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China.
- The MOE Frontier Science Center for Brain Science & Brain-machine Integration, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Jian'an Wang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, Zhejiang, China.
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15
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Karakousi T, Mudianto T, Lund AW. Lymphatic vessels in the age of cancer immunotherapy. Nat Rev Cancer 2024; 24:363-381. [PMID: 38605228 DOI: 10.1038/s41568-024-00681-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/13/2024]
Abstract
Lymphatic transport maintains homeostatic health and is necessary for immune surveillance, and yet lymphatic growth is often associated with solid tumour development and dissemination. Although tumour-associated lymphatic remodelling and growth were initially presumed to simply expand a passive route for regional metastasis, emerging research puts lymphatic vessels and their active transport at the interface of metastasis, tumour-associated inflammation and systemic immune surveillance. Here, we discuss active mechanisms through which lymphatic vessels shape their transport function to influence peripheral tissue immunity and the current understanding of how tumour-associated lymphatic vessels may both augment and disrupt antitumour immune surveillance. We end by looking forward to emerging areas of interest in the field of cancer immunotherapy in which lymphatic vessels and their transport function are likely key players: the formation of tertiary lymphoid structures, immune surveillance in the central nervous system, the microbiome, obesity and ageing. The lessons learnt support a working framework that defines the lymphatic system as a key determinant of both local and systemic inflammatory networks and thereby a crucial player in the response to cancer immunotherapy.
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Affiliation(s)
- Triantafyllia Karakousi
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Tenny Mudianto
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Amanda W Lund
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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16
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Yang C, Liu Y, Lv C, Xu M, Xu K, Shi J, Tan T, Zhou W, Lv D, Li Y, Xu J, Shao T. CanCellVar: A database for single-cell variants map in human cancer. Am J Hum Genet 2024:S0002-9297(24)00177-0. [PMID: 38838674 DOI: 10.1016/j.ajhg.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
Numerous variants, including both single-nucleotide variants (SNVs) in DNA and A>G RNA edits in mRNA as essential drivers of cellular proliferation and tumorigenesis, are commonly associated with cancer progression and growth. Thus, mining and summarizing single-cell variants will provide a refined and higher-resolution view of cancer and further contribute to precision medicine. Here, we established a database, CanCellVar, which aims to provide and visualize the comprehensive atlas of single-cell variants in tumor microenvironment. The current CanCellVar identified ∼3 million variants (∼1.4 million SNVs and ∼1.4 million A>G RNA edits) involved in 2,754,531 cells of 5 major cell types across 37 cancer types. CanCellVar provides the basic annotation information as well as cellular and molecular function properties of variants. In addition, the clinical relevance of variants can be obtained including tumor grade, treatment, metastasis, and others. Several flexible tools were also developed to aid retrieval and to analyze cell-cell interactions, gene expression, cell-development trajectories, regulation, and molecular structure affected by variants. Collectively, CanCellVar will serve as a valuable resource for investigating the functions and characteristics of single-cell variations and their roles in human tumor evolution and treatment.
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Affiliation(s)
- Changbo Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Yujie Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Chongwen Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Mengjia Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Kang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Jingyi Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Tingting Tan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Dezhong Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Yongsheng Li
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China.
| | - Tingting Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China.
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17
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Li X, Poire A, Jeong KJ, Zhang D, Ozmen TY, Chen G, Sun C, Mills GB. C5aR1 inhibition reprograms tumor associated macrophages and reverses PARP inhibitor resistance in breast cancer. Nat Commun 2024; 15:4485. [PMID: 38802355 PMCID: PMC11130309 DOI: 10.1038/s41467-024-48637-y] [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: 11/21/2022] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Although Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) have been approved in multiple diseases, including BRCA1/2 mutant breast cancer, responses are usually transient requiring the deployment of combination therapies for optimal efficacy. Here we thus explore mechanisms underlying sensitivity and resistance to PARPi using two intrinsically PARPi sensitive (T22) and resistant (T127) syngeneic murine breast cancer models in female mice. We demonstrate that tumor associated macrophages (TAM) potentially contribute to the differential sensitivity to PARPi. By single-cell RNA-sequencing, we identify a TAM_C3 cluster, expressing genes implicated in anti-inflammatory activity, that is enriched in PARPi resistant T127 tumors and markedly decreased by PARPi in T22 tumors. Rps19/C5aR1 signaling is selectively elevated in TAM_C3. C5aR1 inhibition or transferring C5aR1hi cells increases and decreases PARPi sensitivity, respectively. High C5aR1 levels in human breast cancers are associated with poor responses to immune checkpoint blockade. Thus, targeting C5aR1 may selectively deplete pro-tumoral macrophages and engender sensitivity to PARPi and potentially other therapies.
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Affiliation(s)
- Xi Li
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Alfonso Poire
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Kang Jin Jeong
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Dong Zhang
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Tugba Yildiran Ozmen
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gordon B Mills
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
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18
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Ramos C, Gerakopoulos V, Oehler R. Metastasis-associated fibroblasts in peritoneal surface malignancies. Br J Cancer 2024:10.1038/s41416-024-02717-4. [PMID: 38783165 DOI: 10.1038/s41416-024-02717-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Over decades, peritoneal surface malignancies (PSMs) have been associated with limited treatment options and poor prognosis. However, advancements in perioperative systemic chemotherapy, cytoreductive surgery (CRS), and hyperthermic intraperitoneal chemotherapy (HIPEC) have significantly improved clinical outcomes. PSMs predominantly result from the spread of intra-abdominal neoplasia, which then form secondary peritoneal metastases. Colorectal, ovarian, and gastric cancers are the most common contributors. Despite diverse primary origins, the uniqueness of the peritoneum microenvironment shapes the common features of PSMs. Peritoneal metastization involves complex interactions between tumour cells and the peritoneal microenvironment. Fibroblasts play a crucial role, contributing to tumour development, progression, and therapy resistance. Peritoneal metastasis-associated fibroblasts (MAFs) in PSMs exhibit high heterogeneity. Single-cell RNA sequencing technology has revealed that immune-regulatory cancer-associated fibroblasts (iCAFs) seem to be the most prevalent subtype in PSMs. In addition, other major subtypes as myofibroblastic CAFs (myCAFs) and matrix CAFs (mCAFs) were frequently observed across PSMs studies. Peritoneal MAFs are suggested to originate from mesothelial cells, submesothelial fibroblasts, pericytes, endothelial cells, and omental-resident cells. This plasticity and heterogeneity of CAFs contribute to the complex microenvironment in PSMs, impacting treatment responses. Understanding these interactions is crucial for developing targeted and local therapies to improve PSMs patient outcomes.
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Affiliation(s)
- Cristiano Ramos
- Department of General Surgery, Division of Visceral Surgery, Medical University of Vienna, Vienna, Austria
| | - Vasileios Gerakopoulos
- Department of General Surgery, Division of Visceral Surgery, Medical University of Vienna, Vienna, Austria
| | - Rudolf Oehler
- Department of General Surgery, Division of Visceral Surgery, Medical University of Vienna, Vienna, Austria.
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19
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Xu L, Saunders K, Huang SP, Knutsdottir H, Martinez-Algarin K, Terrazas I, Chen K, McArthur HM, Maués J, Hodgdon C, Reddy SM, Roussos Torres ET, Xu L, Chan IS. A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response. Cell Rep Med 2024; 5:101511. [PMID: 38614094 PMCID: PMC11148512 DOI: 10.1016/j.xcrm.2024.101511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 02/20/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024]
Abstract
We present an integrated single-cell RNA sequencing atlas of the primary breast tumor microenvironment (TME) containing 236,363 cells from 119 biopsy samples across eight datasets. In this study, we leverage this resource for multiple analyses of immune and cancer epithelial cell heterogeneity. We define natural killer (NK) cell heterogeneity through six subsets in the breast TME. Because NK cell heterogeneity correlates with epithelial cell heterogeneity, we characterize epithelial cells at the level of single-gene expression, molecular subtype, and 10 categories reflecting intratumoral transcriptional heterogeneity. We develop InteractPrint, which considers how cancer epithelial cell heterogeneity influences cancer-immune interactions. We use T cell InteractPrint to predict response to immune checkpoint inhibition (ICI) in two breast cancer clinical trials testing neoadjuvant anti-PD-1 therapy. T cell InteractPrint was predictive of response in both trials versus PD-L1 (AUC = 0.82, 0.83 vs. 0.50, 0.72). This resource enables additional high-resolution investigations of the breast TME.
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Affiliation(s)
- Lily Xu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kaitlyn Saunders
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shao-Po Huang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hildur Knutsdottir
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Kenneth Martinez-Algarin
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isabella Terrazas
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Heather M McArthur
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | - Sangeetha M Reddy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Evanthia T Roussos Torres
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isaac S Chan
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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20
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Gao ZJ, Fang H, Sun S, Liu SQ, Fang Z, Liu Z, Li B, Wang P, Sun SR, Meng XY, Wu Q, Chen CS. Single-cell analyses reveal evolution mimicry during the specification of breast cancer subtype. Theranostics 2024; 14:3104-3126. [PMID: 38855191 PMCID: PMC11155410 DOI: 10.7150/thno.96163] [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: 03/11/2024] [Accepted: 05/12/2024] [Indexed: 06/11/2024] Open
Abstract
Background: The stem or progenitor antecedents confer developmental plasticity and unique cell identities to cancer cells via genetic and epigenetic programs. A comprehensive characterization and mapping of the cell-of-origin of breast cancer using novel technologies to unveil novel subtype-specific therapeutic targets is still absent. Methods: We integrated 195,144 high-quality cells from normal breast tissues and 406,501 high-quality cells from primary breast cancer samples to create a large-scale single-cell atlas of human normal and cancerous breasts. Potential heterogeneous origin of malignant cells was explored by contrasting cancer cells against reference normal epithelial cells. Multi-omics analyses and both in vitro and in vivo experiments were performed to screen and validate potential subtype-specific treatment targets. Novel biomarkers of identified immune and stromal cell subpopulations were validated by immunohistochemistry in our cohort. Results: Tumor stratification based on cancer cell-of-origin patterns correlated with clinical outcomes, genomic aberrations and diverse microenvironment constitutions. We found that the luminal progenitor (LP) subtype was robustly associated with poor prognosis, genomic instability and dysfunctional immune microenvironment. However, the LP subtype patients were sensitive to neoadjuvant chemotherapy (NAC), PARP inhibitors (PARPi) and immunotherapy. The LP subtype-specific target PLK1 was investigated by both in vitro and in vivo experiments. Besides, large-scale single-cell profiling of breast cancer inspired us to identify a range of clinically relevant immune and stromal cell subpopulations, including subsets of innate lymphoid cells (ILCs), macrophages and endothelial cells. Conclusion: The present single-cell study revealed the cellular repertoire and cell-of-origin patterns of breast cancer. Combining single-cell and bulk transcriptome data, we elucidated the evolution mimicry from normal to malignant subtypes and expounded the LP subtype with vital clinical implications. Novel immune and stromal cell subpopulations of breast cancer identified in our study could be potential therapeutic targets. Taken together, Our findings lay the foundation for the precise prognostic and therapeutic stratification of breast cancer.
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Affiliation(s)
- Zhi-Jie Gao
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Huan Fang
- Kunming Institute of Zoology, Chinese Academy of Sciences. Kunming, Yunnan, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Si Sun
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Si-Qing Liu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhou Fang
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhou Liu
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Bei Li
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei. China
| | - Ping Wang
- Medical College, Anhui University of Science and Technology, Huainan, AnHui. China
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Sheng-Rong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiang-Yu Meng
- Health Science Center, Hubei Minzu University, Enshi, Hubei, China
| | - Qi Wu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ce-Shi Chen
- Kunming Institute of Zoology, Chinese Academy of Sciences. Kunming, Yunnan, China
- Academy of Biomedical Engineering, Kunming Medical University, Kunming, Yunnan, China
- The Third Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, China
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21
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Agrawal P, Jain N, Gopalan V, Timon A, Singh A, Rajagopal PS, Hannenhalli S. Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer. iScience 2024; 27:109752. [PMID: 38699227 PMCID: PMC11063905 DOI: 10.1016/j.isci.2024.109752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 05/05/2024] Open
Abstract
Breast cancers (BRCA) exhibit substantial transcriptional heterogeneity, posing a significant clinical challenge. The global transcriptional changes in a disease context, however, are likely mediated by few key genes which reflect disease etiology better than the differentially expressed genes (DEGs). We apply our network-based tool PathExt to 1,059 BRCA tumors across 4 subtypes to identify key mediator genes in each subtype. Compared to conventional differential expression analysis, PathExt-identified genes exhibit greater concordance across tumors, revealing shared and subtype-specific biological processes; better recapitulate BRCA-associated genes in multiple benchmarks, and are more essential in BRCA subtype-specific cell lines. Single-cell transcriptomic analysis reveals a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target key genes potentially mediating drug resistance.
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Affiliation(s)
- Piyush Agrawal
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Vishaka Gopalan
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Annan Timon
- University of Pennsylvania, Philadelphia, PA, USA
| | - Arashdeep Singh
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Padma S. Rajagopal
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
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22
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Zhao Y, Li X, Loscalzo J, Smelik M, Sysoev O, Wang Y, Mahmud AKMF, Mansour Aly D, Benson M. Transcript and protein signatures derived from shared molecular interactions across cancers are associated with mortality. J Transl Med 2024; 22:444. [PMID: 38734658 PMCID: PMC11088765 DOI: 10.1186/s12967-024-05268-7] [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: 02/26/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Characterization of shared cancer mechanisms have been proposed to improve therapy strategies and prognosis. Here, we aimed to identify shared cell-cell interactions (CCIs) within the tumor microenvironment across multiple solid cancers and assess their association with cancer mortality. METHODS CCIs of each cancer were identified by NicheNet analysis of single-cell RNA sequencing data from breast, colon, liver, lung, and ovarian cancers. These CCIs were used to construct a shared multi-cellular tumor model (shared-MCTM) representing common CCIs across cancers. A gene signature was identified from the shared-MCTM and tested on the mRNA and protein level in two large independent cohorts: The Cancer Genome Atlas (TCGA, 9185 tumor samples and 727 controls across 22 cancers) and UK biobank (UKBB, 10,384 cancer patients and 5063 controls with proteomics data across 17 cancers). Cox proportional hazards models were used to evaluate the association of the signature with 10-year all-cause mortality, including sex-specific analysis. RESULTS A shared-MCTM was derived from five individual cancers. A shared gene signature was extracted from this shared-MCTM and the most prominent regulatory cell type, matrix cancer-associated fibroblast (mCAF). The signature exhibited significant expression changes in multiple cancers compared to controls at both mRNA and protein levels in two independent cohorts. Importantly, it was significantly associated with mortality in cancer patients in both cohorts. The highest hazard ratios were observed for brain cancer in TCGA (HR [95%CI] = 6.90[4.64-10.25]) and ovarian cancer in UKBB (5.53[2.08-8.80]). Sex-specific analysis revealed distinct risks, with a higher mortality risk associated with the protein signature score in males (2.41[1.97-2.96]) compared to females (1.84[1.44-2.37]). CONCLUSION We identified a gene signature from a comprehensive shared-MCTM representing common CCIs across different cancers and revealed the regulatory role of mCAF in the tumor microenvironment. The pathogenic relevance of the gene signature was supported by differential expression and association with mortality on both mRNA and protein levels in two independent cohorts.
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Affiliation(s)
- Yelin Zhao
- Medical Digital Twin Research Group, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Xinxiu Li
- Medical Digital Twin Research Group, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Joseph Loscalzo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin Smelik
- Medical Digital Twin Research Group, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Oleg Sysoev
- Division of Statistics and Machine Learning, Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Yunzhang Wang
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - A K M Firoj Mahmud
- Medical Digital Twin Research Group, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Dina Mansour Aly
- Medical Digital Twin Research Group, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Mikael Benson
- Medical Digital Twin Research Group, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden.
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23
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Plebanek MP, Xue Y, Nguyen YV, DeVito NC, Wang X, Holtzhausen A, Beasley GM, Theivanthiran B, Hanks BA. A lactate-SREBP2 signaling axis drives tolerogenic dendritic cell maturation and promotes cancer progression. Sci Immunol 2024; 9:eadi4191. [PMID: 38728412 DOI: 10.1126/sciimmunol.adi4191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024]
Abstract
Conventional dendritic cells (DCs) are essential mediators of antitumor immunity. As a result, cancers have developed poorly understood mechanisms to render DCs dysfunctional within the tumor microenvironment (TME). After identification of CD63 as a specific surface marker, we demonstrate that mature regulatory DCs (mregDCs) migrate to tumor-draining lymph node tissues and suppress DC antigen cross-presentation in trans while promoting T helper 2 and regulatory T cell differentiation. Transcriptional and metabolic studies showed that mregDC functionality is dependent on the mevalonate biosynthetic pathway and its master transcription factor, SREBP2. We found that melanoma-derived lactate activates SREBP2 in tumor DCs and drives conventional DC transformation into mregDCs via homeostatic or tolerogenic maturation. DC-specific genetic silencing and pharmacologic inhibition of SREBP2 promoted antitumor CD8+ T cell activation and suppressed melanoma progression. CD63+ mregDCs were found to reside within the lymph nodes of several preclinical tumor models and in the sentinel lymph nodes of patients with melanoma. Collectively, this work suggests that a tumor lactate-stimulated SREBP2-dependent program promotes CD63+ mregDC development and function while serving as a promising therapeutic target for overcoming immune tolerance in the TME.
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Affiliation(s)
- Michael P Plebanek
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Yue Xue
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Y-Van Nguyen
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Nicholas C DeVito
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Xueying Wang
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708, USA
| | - Alisha Holtzhausen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Georgia M Beasley
- Department of Surgery, Division of Surgical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Balamayooran Theivanthiran
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Brent A Hanks
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708, USA
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24
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Ma J, Wu Y, Ma L, Yang X, Zhang T, Song G, Li T, Gao K, Shen X, Lin J, Chen Y, Liu X, Fu Y, Gu X, Chen Z, Jiang S, Rao D, Pan J, Zhang S, Zhou J, Huang C, Shi S, Fan J, Guo G, Zhang X, Gao Q. A blueprint for tumor-infiltrating B cells across human cancers. Science 2024; 384:eadj4857. [PMID: 38696569 DOI: 10.1126/science.adj4857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 03/06/2024] [Indexed: 05/04/2024]
Abstract
B lymphocytes are essential mediators of humoral immunity and play multiple roles in human cancer. To decode the functions of tumor-infiltrating B cells, we generated a B cell blueprint encompassing single-cell transcriptome, B cell-receptor repertoire, and chromatin accessibility data across 20 different cancer types (477 samples, 269 patients). B cells harbored extraordinary heterogeneity and comprised 15 subsets, which could be grouped into two independent developmental paths (extrafollicular versus germinal center). Tumor types grouped into the extrafollicular pathway were linked with worse clinical outcomes and resistance to immunotherapy. The dysfunctional extrafollicular program was associated with glutamine-derived metabolites through epigenetic-metabolic cross-talk, which promoted a T cell-driven immunosuppressive program. These data suggest an intratumor B cell balance between extrafollicular and germinal-center responses and suggest that humoral immunity could possibly be harnessed for B cell-targeting immunotherapy.
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Affiliation(s)
- Jiaqiang Ma
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yingcheng Wu
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xupeng Yang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Tiancheng Zhang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guohe Song
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Teng Li
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xia Shen
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Lin
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yamin Chen
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoshan Liu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xixi Gu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zechuan Chen
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shan Jiang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaomeng Pan
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Shanghai General Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200080, China
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaoming Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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25
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Hu R, Yang W, Li J, Jiang L, Li M, Zhang M, Kang Y, Cheng X, Zhu S, Zhao L, He W, Guo M, Ding S, Wu H, Cheng W. Multiple RNA Rapid In Situ Imaging Based on Cas9 Code Key System. SMALL METHODS 2024:e2400195. [PMID: 38699929 DOI: 10.1002/smtd.202400195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/29/2024] [Indexed: 05/05/2024]
Abstract
Existing RNA in situ imaging strategies mostly utilize parallel repetitive nucleic acid self-assembly to achieve multiple analysis, with limitations of complicated systems and cumbersome steps. Here, a Cas9 code key system with key probe (KP) encoder and CRISPR/Cas9 signal exporter is developed. This system triggers T-protospacer adjacent motif (T-PAM structural transitions of multiple KP encoders to form coding products with uniform single-guide RNA (sgRNA) target sequences as tandem nodes. Only single sgRNA/Cas9 complex is required to cleave multiple coding products, enabling efficient "many-to-one" tandem signaling, and non-collateral cleavage activity-dependent automatic signaling output through active introduction of mismatched bases. Compared with conventional parallel multiple signaling analysis model, the proposed system greatly simplifies reaction process and enhances detection efficiency. Further, a rapid multiple RNA in situ imaging system is developed by combining the Cas9 code key system with a T-strand displacement amplification (T-SDA) signal amplifier. The constructed system is applied to tumor cells and clinicopathology slices, generating clear multi-mRNA imaging profiles in less than an hour with just one step. Therefore, this work provides reliable technical support for clinical tumor typing and molecular mechanism investigation.
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Affiliation(s)
- Ruiwei Hu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Wei Yang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, China
| | - Jia Li
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Lanxin Jiang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Menghan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Mengxuan Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yuexi Kang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Xiaoxue Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Shasha Zhu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Lina Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Wen He
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Minghui Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
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26
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Mills GB, Labrie M. Enhancing anticancer activity of macrophages through rational drug combinations. J Clin Invest 2024; 134:e180512. [PMID: 38690738 PMCID: PMC11060729 DOI: 10.1172/jci180512] [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: 05/03/2024] Open
Abstract
Targeting tumor-associated macrophages (TAMs) is an emerging approach being tested in multiple clinical trials. TAMs, depending on their differentiation state, can exhibit pro- or antitumorigenic functions. For example, the M2-like phenotype represents a protumoral state that can stimulate tumor growth, angiogenesis, metastasis, therapy resistance, and immune evasion by expressing immune checkpoint proteins. In this issue of the JCI, Vaccaro and colleagues utilized an innovative drug screen approach to demonstrate that targeting driver oncogenic signaling pathways concurrently with anti-CD47 sensitizes tumor cells, causing them to undergo macrophage-induced phagocytosis. The combination treatment altered expression of molecules on the tumor cells that typically limit phagocytosis. It also reprogrammed macrophages to an M1-like antitumor state. Moreover, the approach was generalizable to tumor cells with different oncogenic pathways, opening the door to precision oncology-based rationale combination therapies that have the potential to improve outcomes for patients with oncogene-driven lung cancers and likely other cancer types.
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Affiliation(s)
- Gordon B. Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Marilyne Labrie
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke (CRCHUS), Sherbrooke, Quebec, Canada
- Institut de Recherche sur le Cancer de l’Université de Sherbrooke (IRCUS), Sherbrooke, Quebec, Canada
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27
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Dobner S, Tóth F, de Rooij LPMH. A high-resolution view of the heterogeneous aging endothelium. Angiogenesis 2024; 27:129-145. [PMID: 38324119 PMCID: PMC11021252 DOI: 10.1007/s10456-023-09904-6] [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: 08/21/2023] [Accepted: 12/28/2023] [Indexed: 02/08/2024]
Abstract
Vascular endothelial cell (EC) aging has a strong impact on tissue perfusion and overall cardiovascular health. While studies confined to the investigation of aging-associated vascular readouts in one or a few tissues have already drastically expanded our understanding of EC aging, single-cell omics and other high-resolution profiling technologies have started to illuminate the intricate molecular changes underlying endothelial aging across diverse tissues and vascular beds at scale. In this review, we provide an overview of recent insights into the heterogeneous adaptations of the aging vascular endothelium. We address critical questions regarding tissue-specific and universal responses of the endothelium to the aging process, EC turnover dynamics throughout lifespan, and the differential susceptibility of ECs to acquiring aging-associated traits. In doing so, we underscore the transformative potential of single-cell approaches in advancing our comprehension of endothelial aging, essential to foster the development of future innovative therapeutic strategies for aging-associated vascular conditions.
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Affiliation(s)
- Sarah Dobner
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fanni Tóth
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Laura P M H de Rooij
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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28
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George B, Kudryashova O, Kravets A, Thalji S, Malarkannan S, Kurzrock R, Chernyavskaya E, Gusakova M, Kravchenko D, Tychinin D, Savin E, Alekseeva L, Butusova A, Bagaev A, Shin N, Brown JH, Sethi I, Wang D, Taylor B, McFall T, Kamgar M, Hall WA, Erickson B, Christians KK, Evans DB, Tsai S. Transcriptomic-Based Microenvironment Classification Reveals Precision Medicine Strategies for Pancreatic Ductal Adenocarcinoma. Gastroenterology 2024; 166:859-871.e3. [PMID: 38280684 DOI: 10.1053/j.gastro.2024.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 12/11/2023] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND & AIMS The complex tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) has hindered the development of reliable predictive biomarkers for targeted therapy and immunomodulatory strategies. A comprehensive characterization of the TME is necessary to advance precision therapeutics in PDAC. METHODS A transcriptomic profiling platform for TME classification based on functional gene signatures was applied to 14 publicly available PDAC datasets (n = 1657) and validated in a clinically annotated independent cohort of patients with PDAC (n = 79). Four distinct subtypes were identified using unsupervised clustering and assessed to evaluate predictive and prognostic utility. RESULTS TME classification using transcriptomic profiling identified 4 biologically distinct subtypes based on their TME immune composition: immune enriched (IE); immune enriched, fibrotic (IE/F); fibrotic (F); and immune depleted (D). The IE and IE/F subtypes demonstrated a more favorable prognosis and potential for response to immunotherapy compared with the F and D subtypes. Most lung metastases and liver metastases were subtypes IE and D, respectively, indicating the role of clonal phenotype and immune milieu in developing personalized therapeutic strategies. In addition, distinct TMEs with potential therapeutic implications were identified in treatment-naive primary tumors compared with tumors that underwent neoadjuvant therapy. CONCLUSIONS This novel approach defines a distinct subgroup of PADC patients that may benefit from immunotherapeutic strategies based on their TME subtype and provides a framework to select patients for prospective clinical trials investigating precision immunotherapy in PDAC. Further, the predictive utility and real-world clinical applicability espoused by this transcriptomic-based TME classification approach will accelerate the advancement of precision medicine in PDAC.
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Affiliation(s)
- Ben George
- LaBahn Pancreatic Cancer Program, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin.
| | | | | | - Samih Thalji
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Subramaniam Malarkannan
- Versiti Blood Research Institute, Department of Medicine, Microbiology & Molecular Genetics, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Razelle Kurzrock
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | | | | | | | | | - Egor Savin
- BostonGene Corporation, Waltham, Massachusetts
| | | | | | | | - Nara Shin
- BostonGene Corporation, Waltham, Massachusetts
| | | | - Isha Sethi
- BostonGene Corporation, Waltham, Massachusetts
| | - Dandan Wang
- Versiti Blood Research Institute, Department of Medicine, Microbiology & Molecular Genetics, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Bradley Taylor
- Clinical and Translational Science Institute, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Thomas McFall
- LaBahn Pancreatic Cancer Program, Department of Biochemistry, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Mandana Kamgar
- LaBahn Pancreatic Cancer Program, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - William A Hall
- LaBahn Pancreatic Cancer Program, Department of Radiation Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Beth Erickson
- LaBahn Pancreatic Cancer Program, Department of Radiation Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Kathleen K Christians
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Douglas B Evans
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Susan Tsai
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
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De Wispelaere W, Annibali D, Tuyaerts S, Messiaen J, Antoranz A, Shankar G, Dubroja N, Herreros‐Pomares A, Baiden‐Amissah REM, Orban M, Delfini M, Berardi E, Van Brussel T, Schepers R, Philips G, Boeckx B, Baietti MF, Congedo L, HoWangYin KY, Bayon E, Van Rompuy A, Leucci E, Tabruyn SP, Bosisio F, Mazzone M, Lambrechts D, Amant F. PI3K/mTOR inhibition induces tumour microenvironment remodelling and sensitises pS6 high uterine leiomyosarcoma to PD-1 blockade. Clin Transl Med 2024; 14:e1655. [PMID: 38711203 PMCID: PMC11074386 DOI: 10.1002/ctm2.1655] [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: 10/16/2023] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Uterine leiomyosarcomas (uLMS) are aggressive tumours with poor prognosis and limited treatment options. Although immune checkpoint blockade (ICB) has proven effective in some 'challenging-to-treat' cancers, clinical trials showed that uLMS do not respond to ICB. Emerging evidence suggests that aberrant PI3K/mTOR signalling can drive resistance to ICB. We therefore explored the relevance of the PI3K/mTOR pathway for ICB treatment in uLMS and explored pharmacological inhibition of this pathway to sensitise these tumours to ICB. METHODS We performed an integrated multiomics analysis based on TCGA data to explore the correlation between PI3K/mTOR dysregulation and immune infiltration in 101 LMS. We assessed response to PI3K/mTOR inhibitors in immunodeficient and humanized uLMS patient-derived xenografts (PDXs) by evaluating tumour microenvironment modulation using multiplex immunofluorescence. We explored response to single-agent and a combination of PI3K/mTOR inhibitors with PD-1 blockade in humanized uLMS PDXs. We mapped intratumoural dynamics using single-cell RNA/TCR sequencing of serially collected biopsies. RESULTS PI3K/mTOR over-activation (pS6high) associated with lymphocyte depletion and wound healing immune landscapes in (u)LMS, suggesting it contributes to immune evasion. In contrast, PI3K/mTOR inhibition induced profound tumour microenvironment remodelling in an ICB-resistant humanized uLMS PDX model, fostering adaptive anti-tumour immune responses. Indeed, PI3K/mTOR inhibition induced macrophage repolarisation towards an anti-tumourigenic phenotype and increased antigen presentation on dendritic and tumour cells, but also promoted infiltration of PD-1+ T cells displaying an exhausted phenotype. When combined with anti-PD-1, PI3K/mTOR inhibition led to partial or complete tumour responses, whereas no response to single-agent anti-PD-1 was observed. Combination therapy reinvigorated exhausted T cells and induced clonal hyper-expansion of a cytotoxic CD8+ T-cell population supported by a CD4+ Th1 niche. CONCLUSIONS Our findings indicate that aberrant PI3K/mTOR pathway activation contributes to immune escape in uLMS and provides a rationale for combining PI3K/mTOR inhibition with ICB for the treatment of this patient population.
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Affiliation(s)
- Wout De Wispelaere
- Department of OncologyLaboratory of Gynecological OncologyUniversity of LeuvenLeuvenBelgium
- Department of Human GeneticsLaboratory for Translational GeneticsUniversity of LeuvenLeuvenBelgium
- Laboratory for Translational GeneticsCenter for Cancer Biology (CCB)Flemish Institute of Biotechnology (VIB)LeuvenBelgium
| | - Daniela Annibali
- Department of OncologyLaboratory of Gynecological OncologyUniversity of LeuvenLeuvenBelgium
- Department of Gynecological OncologyAntoni Van Leeuwenhoek – Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sandra Tuyaerts
- Department of Medical OncologyLaboratory of Medical and Molecular Oncology (LMMO)Vrije Universiteit Brussel – UZ BrusselBrusselsBelgium
| | - Julie Messiaen
- Department of Imaging and PathologyTranslational Cell and Tissue ResearchUniversity of LeuvenLeuvenBelgium
- Department of PediatricsUniversity Hospitals LeuvenLeuvenBelgium
| | - Asier Antoranz
- Department of Imaging and PathologyTranslational Cell and Tissue ResearchUniversity of LeuvenLeuvenBelgium
| | - Gautam Shankar
- Department of Imaging and PathologyTranslational Cell and Tissue ResearchUniversity of LeuvenLeuvenBelgium
| | - Nikolina Dubroja
- Department of Imaging and PathologyTranslational Cell and Tissue ResearchUniversity of LeuvenLeuvenBelgium
| | - Alejandro Herreros‐Pomares
- Department of OncologyLaboratory of Gynecological OncologyUniversity of LeuvenLeuvenBelgium
- Department of BiotechnologyUniversitat Politècnica de ValenciaValenciaSpain
| | | | - Marie‐Pauline Orban
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)Flemish Institute of Biotechnology (VIB)LeuvenBelgium
- Department of OncologyLaboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)University of LeuvenLeuvenBelgium
| | - Marcello Delfini
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)Flemish Institute of Biotechnology (VIB)LeuvenBelgium
- Department of OncologyLaboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)University of LeuvenLeuvenBelgium
| | - Emanuele Berardi
- Department of Development and RegenerationLaboratory of Tissue EngineeringUniversity of LeuvenKortrijkBelgium
| | - Thomas Van Brussel
- Department of Human GeneticsLaboratory for Translational GeneticsUniversity of LeuvenLeuvenBelgium
- Laboratory for Translational GeneticsCenter for Cancer Biology (CCB)Flemish Institute of Biotechnology (VIB)LeuvenBelgium
| | - Rogier Schepers
- Department of Human GeneticsLaboratory for Translational GeneticsUniversity of LeuvenLeuvenBelgium
- Laboratory for Translational GeneticsCenter for Cancer Biology (CCB)Flemish Institute of Biotechnology (VIB)LeuvenBelgium
| | - Gino Philips
- Department of Human GeneticsLaboratory for Translational GeneticsUniversity of LeuvenLeuvenBelgium
- Laboratory for Translational GeneticsCenter for Cancer Biology (CCB)Flemish Institute of Biotechnology (VIB)LeuvenBelgium
| | - Bram Boeckx
- Department of Human GeneticsLaboratory for Translational GeneticsUniversity of LeuvenLeuvenBelgium
- Laboratory for Translational GeneticsCenter for Cancer Biology (CCB)Flemish Institute of Biotechnology (VIB)LeuvenBelgium
| | | | - Luigi Congedo
- Department of OncologyLaboratory of Gynecological OncologyUniversity of LeuvenLeuvenBelgium
| | | | | | | | - Eleonora Leucci
- TRACE, Department of OncologyUniversity of LeuvenLeuvenBelgium
| | | | - Francesca Bosisio
- Department of Imaging and PathologyTranslational Cell and Tissue ResearchUniversity of LeuvenLeuvenBelgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)Flemish Institute of Biotechnology (VIB)LeuvenBelgium
- Department of OncologyLaboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)University of LeuvenLeuvenBelgium
| | - Diether Lambrechts
- Department of Human GeneticsLaboratory for Translational GeneticsUniversity of LeuvenLeuvenBelgium
- Laboratory for Translational GeneticsCenter for Cancer Biology (CCB)Flemish Institute of Biotechnology (VIB)LeuvenBelgium
| | - Frédéric Amant
- Department of OncologyLaboratory of Gynecological OncologyUniversity of LeuvenLeuvenBelgium
- Department of Gynecological OncologyAntoni Van Leeuwenhoek – Netherlands Cancer InstituteAmsterdamThe Netherlands
- Department of Obstetrics and GynecologyUniversity Hospitals LeuvenLeuvenBelgium
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Elst L, Philips G, Vandermaesen K, Bassez A, Lodi F, Vreeburg MTA, Brouwer OR, Schepers R, Van Brussel T, Mohanty SK, Parwani AV, Spans L, Vanden Bempt I, Jacomen G, Baldewijns M, Lambrechts D, Albersen M. Single-cell Atlas of Penile Cancer Reveals TP53 Mutations as a Driver of an Aggressive Phenotype, Irrespective of Human Papillomavirus Status, and Provides Clues for Treatment Personalization. Eur Urol 2024:S0302-2838(24)02266-8. [PMID: 38670879 DOI: 10.1016/j.eururo.2024.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/11/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND AND OBJECTIVE TP53 loss-of-function (TP53LOF) mutations might be a driver of poor prognosis and chemoresistance in both human papillomavirus (HPV)-independent (HPV-) and HPV-associated (HPV+) penile squamous cell carcinoma (PSCC). Here, we aim to describe transcriptomic differences in the PSCC microenvironment stratified by TP53LOF and HPV status. METHODS We used single-cell RNA sequencing (scRNA-seq) and T-cell receptor sequencing to obtain a comprehensive atlas of the cellular architecture of PSCC. TP53LOF and HPV status were determined by targeted next-generation sequencing and sequencing HPV-DNA reads. Six HPV+ TP53 wild type (WT), six HPV- TP53WT, and four TP53LOF PSCC samples and six controls were included. Immunohistochemistry and hematoxylin-eosin confirmed the morphological context of the observed signatures. Prognostic differences between patient groups were validated in 541 PSCC patients using Kaplan-Meier survival estimates. KEY FINDINGS AND LIMITATIONS Patients with aberrant p53 staining fare much worse than patients with either HPV- or HPV+ tumors and WT p53 expression. Using scRNA-seq, we revealed 65 cell subtypes within 83 682 cells. TP53LOF tumors exhibit a partial epithelial-to-mesenchymal transition, immune-excluded, angiogenic, and morphologically invasive environment, underlying their aggressive phenotype. HPV- TP53WT tumors show stemness and immune exhaustion. HPV+ TP53WT tumors mirror normal epithelial maturation with upregulation of antibody-drug-conjugate targets and activation of innate immunity. Inherent to the scRNA-seq analysis, low sample size is a limitation and validation of signatures in large PSCC cohorts is needed. CONCLUSIONS AND CLINICAL IMPLICATIONS This first scRNA-seq atlas offers unprecedented in-depth insights into PSCC biology underlying prognostic differences based on TP53 and HPV status. Our findings provide clues for testing novel biomarker-driven therapies in PSCC. PATIENT SUMMARY Here, we analyzed tissues of penile cancer at the level of individual cells, which helps us understand why patients who harbor a deactivating mutation in the TP53 gene do much worse than patients lacking such a mutation. Such an analysis may help us tailor future therapies based on TP53 gene mutations and human papillomavirus status of these tumors.
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Affiliation(s)
- Laura Elst
- Center for Cancer Biology, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Leuven, Belgium; Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Gino Philips
- Center for Cancer Biology, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Kaat Vandermaesen
- Center for Cancer Biology, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Leuven, Belgium; Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Ayse Bassez
- Center for Cancer Biology, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Francesca Lodi
- Center for Cancer Biology, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Manon T A Vreeburg
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Oscar R Brouwer
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Rogier Schepers
- Center for Cancer Biology, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Thomas Van Brussel
- Center for Cancer Biology, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Sambit K Mohanty
- Department of Pathology and Laboratory Medicine, Advanced Medical Research Institute, Bhubaneswar, India; Department of Pathology and Laboratory Medicine, CORE Diagnostics, Gurgaon, India
| | - Anil V Parwani
- Department of Pathology, Wexner Medical Center, Columbus, OH, USA
| | - Lien Spans
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Gerd Jacomen
- Laboratory of Pathological Anatomy, AZ Sint-Maarten, Mechelen, Belgium
| | | | - Diether Lambrechts
- Center for Cancer Biology, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Maarten Albersen
- Department of Urology, University Hospitals Leuven, Leuven, Belgium; Department of Development and Regeneration, KU Leuven, Leuven, Belgium.
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Hu S, Xiao Q, Gao R, Qin J, Nie J, Chen Y, Lou J, Ding M, Pan Y, Wang S. Identification of BGN positive fibroblasts as a driving factor for colorectal cancer and development of its related prognostic model combined with machine learning. BMC Cancer 2024; 24:516. [PMID: 38654221 PMCID: PMC11041013 DOI: 10.1186/s12885-024-12251-4] [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: 12/29/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Numerous studies have indicated that cancer-associated fibroblasts (CAFs) play a crucial role in the progression of colorectal cancer (CRC). However, there are still many unknowns regarding the exact role of CAF subtypes in CRC. METHODS The data for this study were obtained from bulk, single-cell, and spatial transcriptomic sequencing data. Bioinformatics analysis, in vitro experiments, and machine learning methods were employed to investigate the functional characteristics of CAF subtypes and construct prognostic models. RESULTS Our study demonstrates that Biglycan (BGN) positive cancer-associated fibroblasts (BGN + Fib) serve as a driver in colorectal cancer (CRC). The proportion of BGN + Fib increases gradually with the progression of CRC, and high infiltration of BGN + Fib is associated with poor prognosis in terms of overall survival (OS) and recurrence-free survival (RFS) in CRC. Downregulation of BGN expression in cancer-associated fibroblasts (CAFs) significantly reduces migration and proliferation of CRC cells. Among 101 combinations of 10 machine learning algorithms, the StepCox[both] + plsRcox combination was utilized to develop a BGN + Fib derived risk signature (BGNFRS). BGNFRS was identified as an independent adverse prognostic factor for CRC OS and RFS, outperforming 92 previously published risk signatures. A Nomogram model constructed based on BGNFRS and clinical-pathological features proved to be a valuable tool for predicting CRC prognosis. CONCLUSION In summary, our study identified BGN + Fib as drivers of CRC, and the derived BGNFRS was effective in predicting the OS and RFS of CRC patients.
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Affiliation(s)
- Shangshang Hu
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China
| | - Qianni Xiao
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Rui Gao
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Jian Qin
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China
| | - Junjie Nie
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China
| | - Yuhan Chen
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Jinwei Lou
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Muzi Ding
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Yuqin Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China.
- Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, 211100, Nanjing, Jiangsu, China.
| | - Shukui Wang
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China.
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China.
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China.
- Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, 211100, Nanjing, Jiangsu, China.
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Roller A, Davydov II, Schwalie PC, Serrano-Serrano ML, Heller A, Staedler N, Ferreira CS, Dietmann G, Klaman I, Valdeolivas A, Korski K, Cannarile MA. Tumor-agnostic transcriptome-based classifier identifies spatial infiltration patterns of CD8+T cells in the tumor microenvironment and predicts clinical outcome in early-phase and late-phase clinical trials. J Immunother Cancer 2024; 12:e008185. [PMID: 38649280 PMCID: PMC11043740 DOI: 10.1136/jitc-2023-008185] [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: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The immune status of a patient's tumor microenvironment (TME) may guide therapeutic interventions with cancer immunotherapy and help identify potential resistance mechanisms. Currently, patients' immune status is mostly classified based on CD8+tumor-infiltrating lymphocytes. An unmet need exists for comparable and reliable precision immunophenotyping tools that would facilitate clinical treatment-relevant decision-making and the understanding of how to overcome resistance mechanisms. METHODS We systematically analyzed the CD8 immunophenotype of 2023 patients from 14 phase I-III clinical trials using immunohistochemistry (IHC) and additionally profiled gene expression by RNA-sequencing (RNA-seq). CD8 immunophenotypes were classified by pathologists into CD8-desert, CD8-excluded or CD8-inflamed tumors using CD8 IHC staining in epithelial and stromal areas of the tumor. Using regularized logistic regression, we developed an RNA-seq-based classifier as a surrogate to the IHC-based spatial classification of CD8+tumor-infiltrating lymphocytes in the TME. RESULTS The CD8 immunophenotype and associated gene expression patterns varied across indications as well as across primary and metastatic lesions. Melanoma and kidney cancers were among the strongest inflamed indications, while CD8-desert phenotypes were most abundant in liver metastases across all tumor types. A good correspondence between the transcriptome and the IHC-based evaluation enabled us to develop a 92-gene classifier that accurately predicted the IHC-based CD8 immunophenotype in primary and metastatic samples (area under the curve inflamed=0.846; excluded=0.712; desert=0.855). The newly developed classifier was prognostic in The Cancer Genome Atlas (TCGA) data and predictive in lung cancer: patients with predicted CD8-inflamed tumors showed prolonged overall survival (OS) versus patients with CD8-desert tumors (HR 0.88; 95% CI 0.80 to 0.97) across TCGA, and longer OS on immune checkpoint inhibitor administration (phase III OAK study) in non-small-cell lung cancer (HR 0.75; 95% CI 0.58 to 0.97). CONCLUSIONS We provide a new precision immunophenotyping tool based on gene expression that reflects the spatial infiltration patterns of CD8+ lymphocytes in tumors. The classifier enables multiplex analyses and is easy to apply for retrospective, reverse translation approaches as well as for prospective patient enrichment to optimize the response to cancer immunotherapy.
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Affiliation(s)
- Andreas Roller
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Iakov I Davydov
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Petra C Schwalie
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Martha L Serrano-Serrano
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Astrid Heller
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
| | - Nicolas Staedler
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Cláudia S Ferreira
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
| | - Gabriele Dietmann
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
| | - Irina Klaman
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
| | - Alberto Valdeolivas
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Konstanty Korski
- Roche Product Development, PHC Data, Analytics and Imaging, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Michael A Cannarile
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
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Cong Y, Cai G, Ding C, Zhang H, Chen J, Luo S, Liu J. Disulfidptosis-related signature elucidates the prognostic, immunologic, and therapeutic characteristics in ovarian cancer. Front Genet 2024; 15:1378907. [PMID: 38694875 PMCID: PMC11061395 DOI: 10.3389/fgene.2024.1378907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/02/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Ovarian cancer (OC) is the deadliest malignancy in gynecology, but the mechanism of its initiation and progression is poorly elucidated. Disulfidptosis is a novel discovered type of regulatory cell death. This study aimed to develop a novel disulfidptosis-related prognostic signature (DRPS) for OC and explore the effects and potential treatment by disulfidptosis-related risk stratification. Methods The disulfidptosis-related genes were first analyzed in bulk RNA-Seq and a prognostic nomogram was developed and validated by LASSO algorithm and multivariate cox regression. Then we systematically assessed the clinicopathological and mutational characteristics, pathway enrichment analysis, immune cell infiltration, single-cell-level expression, and drug sensitivity according to DRPS. Results The DRPS was established with 6 genes (MYL6, PDLIM1, ACTN4, FLNB, SLC7A11, and CD2AP) and the corresponding prognostic nomogram was constructed based on the DRPS, FIGO stage, grade, and residual disease. Stratified by the risk score derived from DRPS, patients in high-risk group tended to have worse prognosis, lower level of disulfidptosis, activated oncogenic pathways, inhibitory tumor immune microenvironment, and higher sensitivity to specific drugs including epirubicin, stauroporine, navitoclax, and tamoxifen. Single-cell transcriptomic analysis revealed the expression level of genes in the DRPS significantly varied in different cell types between tumor and normal tissues. The protein-level expression of genes in the DRPS was validated by the immunohistochemical staining analysis. Conclusion In this study, the DRPS and corresponding prognostic nomogram for OC were developed, which was important for OC prognostic assessment, tumor microenvironment modification, drug sensitivity prediction, and exploration of potential mechanisms in tumor development.
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Affiliation(s)
- Yunyan Cong
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Guangyao Cai
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Chengcheng Ding
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Han Zhang
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Jieping Chen
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Shiwei Luo
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Jihong Liu
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
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Deng Y, Xia L, Zhang J, Deng S, Wang M, Wei S, Li K, Lai H, Yang Y, Bai Y, Liu Y, Luo L, Yang Z, Chen Y, Kang R, Gan F, Pu Q, Mei J, Ma L, Lin F, Guo C, Liao H, Zhu Y, Liu Z, Liu C, Hu Y, Yuan Y, Zha Z, Yuan G, Zhang G, Chen L, Cheng Q, Shen S, Liu L. Multicellular ecotypes shape progression of lung adenocarcinoma from ground-glass opacity toward advanced stages. Cell Rep Med 2024; 5:101489. [PMID: 38554705 PMCID: PMC11031428 DOI: 10.1016/j.xcrm.2024.101489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/26/2024] [Accepted: 03/06/2024] [Indexed: 04/02/2024]
Abstract
Lung adenocarcinoma is a type of cancer that exhibits a wide range of clinical radiological manifestations, from ground-glass opacity (GGO) to pure solid nodules, which vary greatly in terms of their biological characteristics. Our current understanding of this heterogeneity is limited. To address this gap, we analyze 58 lung adenocarcinoma patients via machine learning, single-cell RNA sequencing (scRNA-seq), and whole-exome sequencing, and we identify six lung multicellular ecotypes (LMEs) correlating with distinct radiological patterns and cancer cell states. Notably, GGO-associated neoantigens in early-stage cancers are recognized by CD8+ T cells, indicating an immune-active environment, while solid nodules feature an immune-suppressive LME with exhausted CD8+ T cells, driven by specific stromal cells such as CTHCR1+ fibroblasts. This study also highlights EGFR(L858R) neoantigens in GGO samples, suggesting potential CD8+ T cell activation. Our findings offer valuable insights into lung adenocarcinoma heterogeneity, suggesting avenues for targeted therapies in early-stage disease.
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Affiliation(s)
- Yulan Deng
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Liang Xia
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Jian Zhang
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Senyi Deng
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Mengyao Wang
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China; Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong, China
| | - Shiyou Wei
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Kaixiu Li
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China; Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong, China
| | - Hongjin Lai
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Yunhao Yang
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Yuquan Bai
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Yongcheng Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Lanzhi Luo
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Zhenyu Yang
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Yaohui Chen
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Ran Kang
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Fanyi Gan
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Qiang Pu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Jiandong Mei
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Lin Ma
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Feng Lin
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Chenglin Guo
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Hu Liao
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Yunke Zhu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Zheng Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Chengwu Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Yang Hu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Yong Yuan
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Zhengyu Zha
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Gang Yuan
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Gao Zhang
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong, China
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Qing Cheng
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Shensi Shen
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China.
| | - Lunxu Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China; Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China.
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Kong D, Wu Y, Liu Q, Huang C, Wang T, Huang Z, Gao Y, Li Y, Guo H. Functional analysis and validation of oncodrive gene AP3S1 in ovarian cancer through filtering of mutation data from whole-exome sequencing. Eur J Med Res 2024; 29:231. [PMID: 38609993 PMCID: PMC11015698 DOI: 10.1186/s40001-024-01814-7] [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: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND High-grade serous ovarian carcinoma (HGSOC) is the most aggressive and prevalent subtype of ovarian cancer and accounts for a significant portion of ovarian cancer-related deaths worldwide. Despite advancements in cancer treatment, the overall survival rate for HGSOC patients remains low, thus highlighting the urgent need for a deeper understanding of the molecular mechanisms driving tumorigenesis and for identifying potential therapeutic targets. Whole-exome sequencing (WES) has emerged as a powerful tool for identifying somatic mutations and alterations across the entire exome, thus providing valuable insights into the genetic drivers and molecular pathways underlying cancer development and progression. METHODS Via the analysis of whole-exome sequencing results of tumor samples from 90 ovarian cancer patients, we compared the mutational landscape of ovarian cancer patients with that of TCGA patients to identify similarities and differences. The sequencing data were subjected to bioinformatics analysis to explore tumor driver genes and their functional roles. Furthermore, we conducted basic medical experiments to validate the results obtained from the bioinformatics analysis. RESULTS Whole-exome sequencing revealed the mutational profile of HGSOC, including BRCA1, BRCA2 and TP53 mutations. AP3S1 emerged as the most weighted tumor driver gene. Further analysis of AP3S1 mutations and expression demonstrated their associations with patient survival and the tumor immune response. AP3S1 knockdown experiments in ovarian cancer cells demonstrated its regulatory role in tumor cell migration and invasion through the TGF-β/SMAD pathway. CONCLUSION This comprehensive analysis of somatic mutations in HGSOC provides insight into potential therapeutic targets and molecular pathways for targeted interventions. AP3S1 was identified as being a key player in tumor immunity and prognosis, thus providing new perspectives for personalized treatment strategies. The findings of this study contribute to the understanding of HGSOC pathogenesis and provide a foundation for improved outcomes in patients with this aggressive disease.
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Affiliation(s)
- Deshui Kong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Yu Wu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Qiyu Liu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Cuiyu Huang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Tongxia Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Zongyao Huang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Yan Gao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Yuan Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China.
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China.
| | - Hongyan Guo
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China.
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China.
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Badillo O, Helfridsson L, Niemi J, Hellström M. Exploring dendritic cell subtypes in cancer immunotherapy: unraveling the role of mature regulatory dendritic cells. Ups J Med Sci 2024; 129:10627. [PMID: 38716077 PMCID: PMC11075441 DOI: 10.48101/ujms.v129.10627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 05/24/2024] Open
Abstract
Dendritic cells (DCs) possess a specialized function in presenting antigens and play pivotal roles in both innate and adaptive immune responses. Their ability to cross-present antigens from tumor cells to naïve T cells is instrumental in generating specific T-cell-mediated antitumor responses, crucial for controlling tumor growth and preventing tumor cell dissemination. However, within a tumor immune microenvironment (TIME), the functions of DCs can be significantly compromised. This review focuses on the profile, function, and activation of DCs, leveraging recent studies that reveal insights into their phenotype acquisition, transcriptional state, and functional programs through single-cell RNA sequence (scRNA-seq) analysis. Additionally, the therapeutic potential of DC-mediated tumor antigen sensing in priming antitumor immunity is discussed.
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Affiliation(s)
- Oscar Badillo
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Liam Helfridsson
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jenni Niemi
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mats Hellström
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Zhu X, Huang X, Hu M, Sun R, Li J, Wang H, Pan X, Ma Y, Ning L, Tong T, Zhou Y, Ding J, Zhao Y, Xuan B, Fang JY, Hong J, Hon Wong JW, Zhang Y, Chen H. A specific enterotype derived from gut microbiome of older individuals enables favorable responses to immune checkpoint blockade therapy. Cell Host Microbe 2024; 32:489-505.e5. [PMID: 38513657 DOI: 10.1016/j.chom.2024.03.002] [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: 09/28/2023] [Revised: 12/15/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Immunotherapy has revolutionized cancer treatment, but inconsistent responses persist. Our study delves into the intriguing phenomenon of enhanced immunotherapy sensitivity in older individuals with cancers. Through a meta-analysis encompassing 25 small-to-mid-sized trials of immune checkpoint blockade (ICB), we demonstrate that older individuals exhibit heightened responsiveness to ICB therapy. To understand the underlying mechanism, we reanalyze single-cell RNA sequencing (scRNA-seq) data from multiple studies and unveil distinct upregulation of exhausted and cytotoxic T cell markers within the tumor microenvironment (TME) of older patients. Recognizing the potential role of gut microbiota in modulating the efficacy of immunotherapy, we identify an aging-enriched enterotype linked to improved immunotherapy outcomes in older patients. Fecal microbiota transplantation experiments in mice confirm the therapeutic potential of the aging-enriched enterotype, enhancing treatment sensitivity and reshaping the TME. Our discoveries confront the prevailing paradox and provide encouraging paths for tailoring cancer immunotherapy strategies according to an individual's gut microbiome profile.
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Affiliation(s)
- Xiaoqiang Zhu
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Centre for Oncology and Immunology, Hong Kong Science Park. Hong Kong, Hong Kong SAR, China; Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowen Huang
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Muni Hu
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rongrong Sun
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Jiantao Li
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University
| | - Hai Wang
- Department of Endoscopy, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Xuefeng Pan
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Yanru Ma
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lijun Ning
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tianying Tong
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yilu Zhou
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jinmei Ding
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhao
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Baoqin Xuan
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Yuan Fang
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jason Wing Hon Wong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Centre for Oncology and Immunology, Hong Kong Science Park. Hong Kong, Hong Kong SAR, China.
| | - Youwei Zhang
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, China.
| | - Haoyan Chen
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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38
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Wasson MCD, Venkatesh J, Cahill HF, McLean ME, Dean CA, Marcato P. LncRNAs exhibit subtype-specific expression, survival associations, and cancer-promoting effects in breast cancer. Gene 2024; 901:148165. [PMID: 38219875 DOI: 10.1016/j.gene.2024.148165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/25/2023] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in cancer progression, influencing processes such as invasion, metastasis, and drug resistance. Their reported cell type-dependent expression patterns suggest the potential for specialized functions in specific contexts. In breast cancer, lncRNA expression has been associated with different subtypes, highlighting their relevance in disease heterogeneity. However, our understanding of lncRNA function within breast cancer subtypes remains limited, warranting further investigation. We conducted a comprehensive analysis using the TANRIC dataset derived from the TCGA-BRCA cohort, profiling the expression, patient survival associations and immune cell type correlations of 12,727 lncRNAs across subtypes. Our findings revealed subtype-specific associations of lncRNAs with patient survival, tumor infiltrating lymphocytes and other immune cells. Targeting of lncRNAs exhibiting subtype-specific survival associations and expression in a panel of breast cancer cells demonstrated a selective reduction in cell proliferation within their associated subtype, supporting subtype-specific functions of certain lncRNAs. Characterization of HER2 + -specific lncRNA LINC01269 and TNBC-specific lncRNA AL078604.2 showed nuclear localization and altered expression of hundreds of genes enriched in cancer-promoting processes, including apoptosis, cell proliferation and immune cell regulation. This work emphasizes the importance of considering the heterogeneity of breast cancer subtypes and the need for subtype-specific analyses to fully uncover the relevance and potential impact of lncRNAs. Collectively, these findings demonstrate the contribution of lncRNAs to the distinct molecular, prognostic, and cellular composition of breast cancer subtypes.
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Affiliation(s)
| | | | - Hannah F Cahill
- Department of Pathology, Dalhousie University, Halifax, NS B3H4R2, Canada
| | - Meghan E McLean
- Department of Pathology, Dalhousie University, Halifax, NS B3H4R2, Canada
| | - Cheryl A Dean
- Department of Pathology, Dalhousie University, Halifax, NS B3H4R2, Canada
| | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, NS B3H4R2, Canada; Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H4R2, Canada; Nova Scotia Health Authority, Halifax, NS B3H1V8, Canada.
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39
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Denisenko E, de Kock L, Tan A, Beasley AB, Beilin M, Jones ME, Hou R, Muirí DÓ, Bilic S, Mohan GRKA, Salfinger S, Fox S, Hmon KPW, Yeow Y, Kim Y, John R, Gilderman TS, Killingbeck E, Gray ES, Cohen PA, Yu Y, Forrest ARR. Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones. Nat Commun 2024; 15:2860. [PMID: 38570491 PMCID: PMC10991508 DOI: 10.1038/s41467-024-47271-y] [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: 10/05/2022] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is genetically unstable and characterised by the presence of subclones with distinct genotypes. Intratumoural heterogeneity is linked to recurrence, chemotherapy resistance, and poor prognosis. Here, we use spatial transcriptomics to identify HGSOC subclones and study their association with infiltrating cell populations. Visium spatial transcriptomics reveals multiple tumour subclones with different copy number alterations present within individual tumour sections. These subclones differentially express various ligands and receptors and are predicted to differentially associate with different stromal and immune cell populations. In one sample, CosMx single molecule imaging reveals subclones differentially associating with immune cell populations, fibroblasts, and endothelial cells. Cell-to-cell communication analysis identifies subclone-specific signalling to stromal and immune cells and multiple subclone-specific autocrine loops. Our study highlights the high degree of subclonal heterogeneity in HGSOC and suggests that subclone-specific ligand and receptor expression patterns likely modulate how HGSOC cells interact with their local microenvironment.
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Affiliation(s)
- Elena Denisenko
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia.
| | - Leanne de Kock
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Adeline Tan
- Anatomical Pathology Department, Clinipath, Sonic Healthcare, Perth, WA, 6017, Australia
| | - Aaron B Beasley
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Maria Beilin
- Department of Gynaecological Oncology, Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, 12 Salvado Rd, Subiaco, WA, 6008, Australia
| | - Matthew E Jones
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Rui Hou
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Dáithí Ó Muirí
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Sanela Bilic
- Department of Gynaecological Oncology, Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, 12 Salvado Rd, Subiaco, WA, 6008, Australia
| | - G Raj K A Mohan
- Department of Gynaecological Oncology, Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, 12 Salvado Rd, Subiaco, WA, 6008, Australia
- School of Medicine, University of Notre Dame, Fremantle, WA, 6160, Australia
| | | | - Simon Fox
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Khaing P W Hmon
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Yen Yeow
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | | | - Rhea John
- NanoString Technologies, Seattle, WA, USA
| | | | | | - Elin S Gray
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Paul A Cohen
- Division of Obstetrics and Gynaecology, Medical School, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- Institute for Health Research, The University of Notre Dame Australia, 32 Mouat Street Fremantle, Fremantle, WA, 6160, Australia.
| | - Yu Yu
- Division of Obstetrics and Gynaecology, Medical School, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- Curtin Medical School, Curtin University, 410 Koorliny Way, Bentley, WA, 6102, Australia.
- Curtin Health Innovation Research Institute, Curtin University B305, Bentley, WA, 6102, Australia.
| | - Alistair R R Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia.
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Xu L, Chen Y, Liu L, Hu X, He C, Zhou Y, Ding X, Luo M, Yan J, Liu Q, Li H, Lai D, Zou Z. Tumor-associated macrophage subtypes on cancer immunity along with prognostic analysis and SPP1-mediated interactions between tumor cells and macrophages. PLoS Genet 2024; 20:e1011235. [PMID: 38648200 PMCID: PMC11034676 DOI: 10.1371/journal.pgen.1011235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Tumor-associated macrophages (TAM) subtypes have been shown to impact cancer prognosis and resistance to immunotherapy. However, there is still a lack of systematic investigation into their molecular characteristics and clinical relevance in different cancer types. Single-cell RNA sequencing data from three different tumor types were used to cluster and type macrophages. Functional analysis and communication of TAM subpopulations were performed by Gene Ontology-Biological Process and CellChat respectively. Differential expression of characteristic genes in subpopulations was calculated using zscore as well as edgeR and Wilcoxon rank sum tests, and subsequently gene enrichment analysis of characteristic genes and anti-PD-1 resistance was performed by the REACTOME database. We revealed the heterogeneity of TAM, and identified eleven subtypes and their impact on prognosis. These subtypes expressed different molecular functions respectively, such as being involved in T cell activation, apoptosis and differentiation, or regulating viral bioprocesses or responses to viruses. The SPP1 pathway was identified as a critical mediator of communication between TAM subpopulations, as well as between TAM and epithelial cells. Macrophages with high expression of SPP1 resulted in poorer survival. By in vitro study, we showed SPP1 mediated the interactions between TAM clusters and between TAM and tumor cells. SPP1 promoted the tumor-promoting ability of TAM, and increased PDL1 expression and stemness of tumor cells. Inhibition of SPP1 attenuated N-cadherin and β-catenin expression and the activation of AKT and STAT3 pathway in tumor cells. Additionally, we found that several subpopulations could decrease the sensitivity of anti-PD-1 therapy in melanoma. SPP1 signal was a critical pathway of communication between macrophage subtypes. Some specific macrophage subtypes were associated with immunotherapy resistance and prognosis in some cancer types.
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Affiliation(s)
- Liu Xu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yibing Chen
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Lingling Liu
- Department of Hematology, The Third Affiliated Hospital of Sun Yat-sen University & Sun Yat-sen Institute of Hematology, Guangzhou, China
| | - Xinyu Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Chengsi He
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yuan Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Xinyi Ding
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Minhua Luo
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Jiajing Yan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Quentin Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Hongsheng Li
- Department of Breast Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Dongming Lai
- Shenshan Medical Center and Department of Gastrointestinal Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhengzhi Zou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
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Song X, Wei J, Li Y, Zhu W, Cai Z, Li K, Wei J, Lu J, Pan W, Li M. An integrative pan-cancer analysis of the molecular characteristics of dietary restriction in tumour microenvironment. EBioMedicine 2024; 102:105078. [PMID: 38507875 PMCID: PMC10965464 DOI: 10.1016/j.ebiom.2024.105078] [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: 11/14/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Dietary restriction (DR), a general term for dieting, has been demonstrated as an effective intervention in reducing the occurrence of cancers. Molecular activities associated with DR are crucial in mediating its anti-cancer effects, yet a comprehensive exploration of the landscape of these activities at the pan-cancer level is still lacking. METHODS We proposed a computational approach for quantifying DR-related molecular activities and delineating the landscape of these activities across 33 cancer types and 30 normal tissues within 27,320 samples. We thoroughly examined the associations between DR-related molecular activities and various factors, including the tumour microenvironment, immunological phenotypes, genomic features, and clinical prognosis. Meanwhile, we identified two DR genes that show potential as prognostic predictors in hepatocellular carcinoma and verified them by immunohistochemical assays in 90 patients. FINDINGS We found that DR-related molecular activities showed a close association with tumour immunity and hold potential for predicting immunotherapy responses in various cancers. Importantly, a higher level of DR-related molecular activities is associated with improved overall survival and cancer-specific survival. FZD1 and G6PD are two DR genes that serve as biomarkers for predicting the prognosis of patients with hepatocellular carcinoma. INTERPRETATION This study presents a robust link between DR-related molecular activities and tumour immunity across multiple cancer types. Our research could open the path for further investigation of DR-related molecular processes in cancer treatment. FUNDING National Natural Science Foundation of China (Grant No. 82000628) and the Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine Foundation of Guangdong Province (Grant No. 2023LSYS001).
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Affiliation(s)
- Xiaoyi Song
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jiaxing Wei
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Yang Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Wen Zhu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Zhiyuan Cai
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Kunwei Li
- Department of Radiology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jingyue Wei
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jieyu Lu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Wanping Pan
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Man Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Biobank, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Department of Information Technology and Data Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China.
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Heras-Murillo I, Adán-Barrientos I, Galán M, Wculek SK, Sancho D. Dendritic cells as orchestrators of anticancer immunity and immunotherapy. Nat Rev Clin Oncol 2024; 21:257-277. [PMID: 38326563 DOI: 10.1038/s41571-024-00859-1] [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: 01/09/2024] [Indexed: 02/09/2024]
Abstract
Dendritic cells (DCs) are a heterogeneous group of antigen-presenting innate immune cells that regulate adaptive immunity, including against cancer. Therefore, understanding the precise activities of DCs in tumours and patients with cancer is important. The classification of DC subsets has historically been based on ontogeny; however, single-cell analyses are now additionally revealing a diversity of functional states of DCs in cancer. DCs can promote the activation of potent antitumour T cells and immune responses via numerous mechanisms, although they can also be hijacked by tumour-mediated factors to contribute to immune tolerance and cancer progression. Consequently, DC activities are often key determinants of the efficacy of immunotherapies, including immune-checkpoint inhibitors. Potentiating the antitumour functions of DCs or using them as tools to orchestrate short-term and long-term anticancer immunity has immense but as-yet underexploited therapeutic potential. In this Review, we outline the nature and emerging complexity of DC states as well as their functions in regulating adaptive immunity across different cancer types. We also describe how DCs are required for the success of current immunotherapies and explore the inherent potential of targeting DCs for cancer therapy. We focus on novel insights on DCs derived from patients with different cancers, single-cell studies of DCs and their relevance to therapeutic strategies.
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Affiliation(s)
- Ignacio Heras-Murillo
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Irene Adán-Barrientos
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Miguel Galán
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Stefanie K Wculek
- Innate Immune Biology Laboratory, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - David Sancho
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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Ding B, Ye Z, Yin H, Hong XY, Feng SW, Xu JY, Shen Y. Comprehensive single-cell analysis reveals heterogeneity of fibroblast subpopulations in ovarian cancer tissue microenvironment. Heliyon 2024; 10:e27873. [PMID: 38533040 PMCID: PMC10963331 DOI: 10.1016/j.heliyon.2024.e27873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Background Ovarian cancer, as a highly malignant tumor, features the critical involvement of tumor-associated fibroblasts in the ovarian cancer tissue microenvironment. However, due to the apparent heterogeneity within fibroblast subpopulations, the specific functions of these subpopulations in the ovarian cancer tissue microenvironment remain insufficiently elucidated. Methods In this study, we integrated single-cell sequencing data from 32 ovarian cancer samples derived from four distinct cohorts and 3226 bulk RNA-seq data from GEO and TCGA-OV cohorts. Utilizing computational frameworks such as Seurat, Monocle 2, Cellchat, and others, we analyzed the characteristics of the ovarian cancer tissue microenvironment, focusing particularly on fibroblast subpopulations and their differentiation trajectories. Employing the CIBERSORTX computational framework, we assessed various cellular components within the ovarian cancer tissue microenvironment and evaluated their associations with ovarian cancer prognosis. Additionally, we conducted Mendelian randomization analysis based on cis-eQTL to investigate causal relationships between gene expression and ovarian cancer. Results Through integrative analysis, we identified 13 major cell types present in ovarian cancer tissues, including CD8+ T cells, malignant cells, and fibroblasts. Analysis of the tumor microenvironment (TME) cell proportions revealed a significant increase in the proportion of CD8+ T cells and CD4+ T cells in tumor tissues compared to normal tissues, while fibroblasts predominated in normal tissues. Further subgroup analysis of fibroblasts identified seven subgroups, with the MMP11+Fib subgroup showing the highest activity in the TGFβ signaling pathway. Single-cell analysis suggested that oxidative phosphorylation could be a key pathway driving fibroblast differentiation, and the ATRNL1+KCN + Fib subgroup exhibited chromosomal copy number variations. Prognostic analysis using a large sample size indicated that high infiltration of MMP11+ fibroblasts was associated with poor prognosis in ovarian cancer. SMR analysis identified 132 fibroblast differentiation-related genes, which were linked to pathways such as platinum drug resistance. Conclusions In the context of ovarian cancer, fibroblasts expressing MMP11 emerge as the primary drivers of the TGF-beta signaling pathway. Their presence correlates with an increased risk of adverse ovarian prognoses. Additionally, the genetic regulation governing the differentiation of fibroblasts associated with ovarian cancer correlates with the emergence of drug resistance.
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Affiliation(s)
- Bo Ding
- Department of Obstetrics and Gynecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Zheng Ye
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, 510006, Guangdong, China
| | - Han Yin
- Department of Obstetrics and Gynecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Xin-Yi Hong
- Department of Obstetrics and Gynecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Song-wei Feng
- Department of Obstetrics and Gynecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Jing-Yun Xu
- Department of Obstetrics and Gynecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Yang Shen
- Department of Obstetrics and Gynecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
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Qian ZY, Pan YQ, Li XX, Chen YX, Wu HX, Liu ZX, Kosar M, Bartek J, Wang ZX, Xu RH. Modulator of TMB-associated immune infiltration (MOTIF) predicts immunotherapy response and guides combination therapy. Sci Bull (Beijing) 2024; 69:803-822. [PMID: 38320897 DOI: 10.1016/j.scib.2024.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/04/2023] [Accepted: 12/07/2023] [Indexed: 02/08/2024]
Abstract
Patients with high tumor mutational burden (TMB) levels do not consistently respond to immune checkpoint inhibitors (ICIs), possibly because a high TMB level does not necessarily result in adequate infiltration of CD8+ T cells. Using bulk ribonucleic acid sequencing (RNA-seq) data from 9311 tumor samples across 30 cancer types, we developed a novel tool called the modulator of TMB-associated immune infiltration (MOTIF), which comprises genes that can determine the extent of CD8+ T cell infiltration prompted by a certain TMB level. We confirmed that MOTIF can accurately reflect the integrity and defects of the cancer-immunity cycle. By analyzing 84 human single-cell RNA-seq datasets from 32 types of solid tumors, we revealed that MOTIF can provide insights into the diverse roles of various cell types in the modulation of CD8+ T cell infiltration. Using pretreatment RNA-seq data from 13 ICI-treated cohorts, we validated the use of MOTIF in predicting CD8+ T cell infiltration and ICI efficacy. Among the components of MOTIF, we identified EMC3 as a negative regulator of CD8+ T cell infiltration, which was validated via in vivo studies. Additionally, MOTIF provided guidance for the potential combinations of programmed death 1 blockade with certain immunostimulatory drugs to facilitate CD8+ T cell infiltration and improve ICI efficacy.
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Affiliation(s)
- Zheng-Yu Qian
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, China
| | - Yi-Qian Pan
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, China
| | - Xue-Xin Li
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm S-171 21, Sweden; Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang 110032, China
| | - Yan-Xing Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, China
| | - Hao-Xiang Wu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, China
| | - Ze-Xian Liu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, China; Bioinformatics Platform, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Laboratory of Artificial Intelligence and Data Science, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Martin Kosar
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm S-171 21, Sweden; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining 314400, China; Edinburgh Medical School, Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh EH1 1LT, UK
| | - Jiri Bartek
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm S-171 21, Sweden; Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark.
| | - Zi-Xian Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, China; Laboratory of Artificial Intelligence and Data Science, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
| | - Rui-Hua Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, China; Laboratory of Artificial Intelligence and Data Science, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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Li Y, Gao W, Yang Z, Hu Z, Li J. Multi-omics pan-cancer analyses identify MCM4 as a promising prognostic and diagnostic biomarker. Sci Rep 2024; 14:6517. [PMID: 38499612 PMCID: PMC10948783 DOI: 10.1038/s41598-024-57299-1] [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: 10/04/2023] [Accepted: 03/16/2024] [Indexed: 03/20/2024] Open
Abstract
Minichromosome Maintenance Complex Component 4 (MCM4) is a vital component of the mini-chromosome maintenance complex family, crucial for initiating the replication of eukaryotic genomes. Recently, there has been a growing interest in investigating the significance of MCM4 in different types of cancer. Despite the existing research on this topic, a comprehensive analysis of MCM4 across various cancer types has been lacking. This study aims to bridge this knowledge gap by presenting a thorough pan-cancer analysis of MCM4, shedding light on its functional implications and potential clinical applications. The study utilized multi-omics samples from various databases. Bioinformatic tools were employed to explore the expression profiles, genetic alterations, phosphorylation states, immune cell infiltration patterns, immune subtypes, functional enrichment, disease prognosis, as well as the diagnostic potential of MCM4 and its responsiveness to drugs in a range of cancers. Our research demonstrates that MCM4 is closely associated with the oncogenesis, prognosis and diagnosis of various tumors and proposes that MCM4 may function as a potential biomarker in pan-cancer, providing a deeper understanding of its potential role in cancer development and treatment.
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Affiliation(s)
- Yanxing Li
- Xi'an Jiaotong University Health Science Center, Xi'an, 710000, Shaanxi, People's Republic of China
| | - Wentao Gao
- Xi'an Jiaotong University Health Science Center, Xi'an, 710000, Shaanxi, People's Republic of China
| | - Zhen Yang
- Xi'an Jiaotong University Health Science Center, Xi'an, 710000, Shaanxi, People's Republic of China
| | - Zhenwei Hu
- Xi'an Jiaotong University Health Science Center, Xi'an, 710000, Shaanxi, People's Republic of China
| | - Jianjun Li
- Department of Cardiology, Jincheng People's Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi, People's Republic of China.
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Brand J, Haro M, Lin X, Rimel B, McGregor SM, Lawrenson K, Dinh HQ. Fallopian tube single cell analysis reveals myeloid cell alterations in high-grade serous ovarian cancer. iScience 2024; 27:108990. [PMID: 38384837 PMCID: PMC10879678 DOI: 10.1016/j.isci.2024.108990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
Most high-grade serous ovarian cancers (HGSCs) likely initiate from fallopian tube (FT) epithelia. While epithelial subtypes have been characterized using single-cell RNA-sequencing (scRNA-Seq), heterogeneity of other compartments and their involvement in tumor progression are poorly defined. Integrated analysis of human FT scRNA-Seq and HGSC-related tissues, including tumors, revealed greater immune and stromal transcriptional diversity than previously reported. We identified abundant monocytes in FTs across two independent cohorts. The ratio of macrophages to monocytes is similar between benign FTs, ovaries, and adjacent normal tissues but significantly greater in tumors. FT-defined monocyte and macrophage signatures, cell-cell communication, and gene set enrichment analyses identified monocyte- and macrophage-specific interactions and functional pathways in paired tumors and adjacent normal tissues. Further reanalysis of HGSC scRNA-Seq identified monocyte and macrophage subsets associated with neoadjuvant chemotherapy. Taken together, our work provides data that an altered FT myeloid cell composition could inform the discovery of early detection markers for HGSC.
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Affiliation(s)
- Joshua Brand
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI 53705, USA
| | - Marcela Haro
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xianzhi Lin
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- RNA Biology Group, Division of Natural and Applied Sciences and Global Health Research Center, Duke Kunshan University, Kunshan 215316, Jiangsu Province, China
| | - B.J. Rimel
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stephanie M. McGregor
- Department of Pathology and Laboratory Medicine, University of Wisconsin – Madison, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Kate Lawrenson
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI 53705, USA
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Wu Y, Ma J, Yang X, Nan F, Zhang T, Ji S, Rao D, Feng H, Gao K, Gu X, Jiang S, Song G, Pan J, Zhang M, Xu Y, Zhang S, Fan Y, Wang X, Zhou J, Yang L, Fan J, Zhang X, Gao Q. Neutrophil profiling illuminates anti-tumor antigen-presenting potency. Cell 2024; 187:1422-1439.e24. [PMID: 38447573 DOI: 10.1016/j.cell.2024.02.005] [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: 04/11/2023] [Revised: 09/20/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
Neutrophils, the most abundant and efficient defenders against pathogens, exert opposing functions across cancer types. However, given their short half-life, it remains challenging to explore how neutrophils adopt specific fates in cancer. Here, we generated and integrated single-cell neutrophil transcriptomes from 17 cancer types (225 samples from 143 patients). Neutrophils exhibited extraordinary complexity, with 10 distinct states including inflammation, angiogenesis, and antigen presentation. Notably, the antigen-presenting program was associated with favorable survival in most cancers and could be evoked by leucine metabolism and subsequent histone H3K27ac modification. These neutrophils could further invoke both (neo)antigen-specific and antigen-independent T cell responses. Neutrophil delivery or a leucine diet fine-tuned the immune balance to enhance anti-PD-1 therapy in various murine cancer models. In summary, these data not only indicate the neutrophil divergence across cancers but also suggest therapeutic opportunities such as antigen-presenting neutrophil delivery.
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Affiliation(s)
- Yingcheng Wu
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaqiang Ma
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xupeng Yang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Fang Nan
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Tiancheng Zhang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shuyi Ji
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai 200123, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hua Feng
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ke Gao
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xixi Gu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shan Jiang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guohe Song
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaomeng Pan
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Mao Zhang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yanan Xu
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yihui Fan
- Department of Pathogenic Biology and Basic Medical Research Center, School of Medicine, Nantong University, Nantong 226001, China
| | - Xiaoying Wang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Jia Fan
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
| | - Xiaoming Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Qiang Gao
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
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48
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Ng II, Zhang J, Tian T, Peng Q, Huang Z, Xiao K, Yao X, Ng L, Zeng J, Tang H. Network-based screening identifies sitagliptin as an antitumor drug targeting dendritic cells. J Immunother Cancer 2024; 12:e008254. [PMID: 38458637 PMCID: PMC10921530 DOI: 10.1136/jitc-2023-008254] [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: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Dendritic cell (DC)-mediated antigen presentation is essential for the priming and activation of tumor-specific T cells. However, few drugs that specifically manipulate DC functions are available. The identification of drugs targeting DC holds great promise for cancer immunotherapy. METHODS We observed that type 1 conventional DCs (cDC1s) initiated a distinct transcriptional program during antigen presentation. We used a network-based approach to screen for cDC1-targeting therapeutics. The antitumor potency and underlying mechanisms of the candidate drug were investigated in vitro and in vivo. RESULTS Sitagliptin, an oral gliptin widely used for type 2 diabetes, was identified as a drug that targets DCs. In mouse models, sitagliptin inhibited tumor growth by enhancing cDC1-mediated antigen presentation, leading to better T-cell activation. Mechanistically, inhibition of dipeptidyl peptidase 4 (DPP4) by sitagliptin prevented the truncation and degradation of chemokines/cytokines that are important for DC activation. Sitagliptin enhanced cancer immunotherapy by facilitating the priming of antigen-specific T cells by DCs. In humans, the use of sitagliptin correlated with a lower risk of tumor recurrence in patients with colorectal cancer undergoing curative surgery. CONCLUSIONS Our findings indicate that sitagliptin-mediated DPP4 inhibition promotes antitumor immune response by augmenting cDC1 functions. These data suggest that sitagliptin can be repurposed as an antitumor drug targeting DC, which provides a potential strategy for cancer immunotherapy.
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Affiliation(s)
- Ian-Ian Ng
- State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jiaqi Zhang
- State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Tingzhong Tian
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Qi Peng
- State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zheng Huang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kaimin Xiao
- State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiyue Yao
- State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Lui Ng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Haidong Tang
- State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
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49
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Choi JE, Qiao Y, Kryczek I, Yu J, Gurkan J, Bao Y, Gondal M, Tien JCY, Maj T, Yazdani S, Parolia A, Xia H, Zhou J, Wei S, Grove S, Vatan L, Lin H, Li G, Zheng Y, Zhang Y, Cao X, Su F, Wang R, He T, Cieslik M, Green MD, Zou W, Chinnaiyan AM. PIKfyve controls dendritic cell function and tumor immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582543. [PMID: 38464258 PMCID: PMC10925294 DOI: 10.1101/2024.02.28.582543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The modern armamentarium for cancer treatment includes immunotherapy and targeted therapy, such as protein kinase inhibitors. However, the mechanisms that allow cancer-targeting drugs to effectively mobilize dendritic cells (DCs) and affect immunotherapy are poorly understood. Here, we report that among shared gene targets of clinically relevant protein kinase inhibitors, high PIKFYVE expression was least predictive of complete response in patients who received immune checkpoint blockade (ICB). In immune cells, high PIKFYVE expression in DCs was associated with worse response to ICB. Genetic and pharmacological studies demonstrated that PIKfyve ablation enhanced DC function via selectively altering the alternate/non-canonical NF-κB pathway. Both loss of Pikfyve in DCs and treatment with apilimod, a potent and specific PIKfyve inhibitor, restrained tumor growth, enhanced DC-dependent T cell immunity, and potentiated ICB efficacy in tumor-bearing mouse models. Furthermore, the combination of a vaccine adjuvant and apilimod reduced tumor progression in vivo. Thus, PIKfyve negatively controls DCs, and PIKfyve inhibition has promise for cancer immunotherapy and vaccine treatment strategies.
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Affiliation(s)
- Jae Eun Choi
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuanyuan Qiao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jiali Yu
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Gurkan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Bao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mahnoor Gondal
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jean Ching-Yi Tien
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tomasz Maj
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sahr Yazdani
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Abhijit Parolia
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Houjun Xia
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - JiaJia Zhou
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Shuang Wei
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sara Grove
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Linda Vatan
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Heng Lin
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Gaopeng Li
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tongchen He
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Michael D. Green
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Weiping Zou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
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50
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Zhong Z, Hou J, Yao Z, Dong L, Liu F, Yue J, Wu T, Zheng J, Ouyang G, Yang C, Song J. Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics. Nat Commun 2024; 15:1929. [PMID: 38431724 PMCID: PMC10908802 DOI: 10.1038/s41467-024-46413-6] [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: 06/09/2023] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Single-cell and spatial transcriptome sequencing, two recently optimized transcriptome sequencing methods, are increasingly used to study cancer and related diseases. Cell annotation, particularly for malignant cell annotation, is essential and crucial for in-depth analyses in these studies. However, current algorithms lack accuracy and generalization, making it difficult to consistently and rapidly infer malignant cells from pan-cancer data. To address this issue, we present Cancer-Finder, a domain generalization-based deep-learning algorithm that can rapidly identify malignant cells in single-cell data with an average accuracy of 95.16%. More importantly, by replacing the single-cell training data with spatial transcriptomic datasets, Cancer-Finder can accurately identify malignant spots on spatial slides. Applying Cancer-Finder to 5 clear cell renal cell carcinoma spatial transcriptomic samples, Cancer-Finder demonstrates a good ability to identify malignant spots and identifies a gene signature consisting of 10 genes that are significantly co-localized and enriched at the tumor-normal interface and have a strong correlation with the prognosis of clear cell renal cell carcinoma patients. In conclusion, Cancer-Finder is an efficient and extensible tool for malignant cell annotation.
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Affiliation(s)
- Zhixing Zhong
- Institute of Artificial Intelligence, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361102, China
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Junchen Hou
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhixian Yao
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Lei Dong
- Department of Pathology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Feng Liu
- School of Computing and Information Systems, The University of Melbourne, Carlton, Melbourne, VIC, 3053, Australia
| | - Junqiu Yue
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tiantian Wu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Junhua Zheng
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Gaoliang Ouyang
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Chaoyong Yang
- Institute of Artificial Intelligence, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361102, China
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen, 361005, China
| | - Jia Song
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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