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Bao X, Lin X, Xie M, Yao J, Song J, Ma X, Zhang X, Zhang Y, Liu Y, Han W, Liang Y, Hu H, Xu L, Xue X. Mature tertiary lymphoid structures: important contributors to anti-tumor immune efficacy. Front Immunol 2024; 15:1413067. [PMID: 39026670 PMCID: PMC11254644 DOI: 10.3389/fimmu.2024.1413067] [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: 04/06/2024] [Accepted: 06/06/2024] [Indexed: 07/20/2024] Open
Abstract
Tertiary lymphoid structures (TLS) represent the ectopic aggregations of immune cells arising during chronic inflammation or tumor progression. In cancer, TLS are often associated with beneficial clinical outcomes in patients undergoing immunotherapy, underscoring their prognostic and predictive significance. Mature TLS, characterized by germinal centers and areas of T-cell and B-cell aggregation, are considered primary locations for activating and maintaining both humoral and cellular anti-tumor immune effects. Despite their recognized importance, the mechanisms driving the formation of mature TLS in cancer and their influence on the immune response within tumors remain insufficiently understood. Therefore, this review aims to comprehensively explore the structural composition, development mechanisms, maturity impact factors, immunological function, and innovative therapeutic strategies of mature TLS within the tumor microenvironment. The research summarized herein offers novel insights and considerations for therapeutic approaches to promote TLS generation and maturation in patients with cancer, representing a promising avenue for future cancer therapies.
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Affiliation(s)
- Xinyu Bao
- Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang, China
| | - Xuwen Lin
- Department of Respiratory and Critical Care, Emergency and Critical Care Medical Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mei Xie
- Department of Respiratory and Critical Care, Chinese PLA General Hospital, Beijing, China
| | - Jie Yao
- Department of Respiratory and Critical Care, Emergency and Critical Care Medical Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jialin Song
- Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang, China
| | - Xidong Ma
- Department of Respiratory and Critical Care, Emergency and Critical Care Medical Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Xin Zhang
- Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang, China
| | - Yinguang Zhang
- Department of Thoracic Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yiming Liu
- Department of Thoracic Surgery, Chinese PLA General Hospital, Beijing, China
| | - Wenya Han
- Department of Respiratory and Critical Care, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yiran Liang
- Department of Respiratory and Critical Care, Emergency and Critical Care Medical Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hongling Hu
- Department of Respiratory Medicine, Wuhan Central Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Xu
- Department of Respiratory Endoscopy, The Public Health Clinical Center Affiliated of Shandong University, Jinan, China
| | - Xinying Xue
- Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang, China
- Department of Respiratory and Critical Care, Emergency and Critical Care Medical Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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2
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Robertson BM, Fane ME, Weeraratna AT, Rebecca VW. Determinants of resistance and response to melanoma therapy. NATURE CANCER 2024; 5:964-982. [PMID: 39020103 DOI: 10.1038/s43018-024-00794-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/05/2024] [Indexed: 07/19/2024]
Abstract
Metastatic melanoma is among the most enigmatic advanced cancers to clinically manage despite immense progress in the way of available therapeutic options and historic decreases in the melanoma mortality rate. Most patients with metastatic melanoma treated with modern targeted therapies (for example, BRAFV600E/K inhibitors) and/or immune checkpoint blockade (for example, anti-programmed death 1 therapy) will progress, owing to profound tumor cell plasticity fueled by genetic and nongenetic mechanisms and dichotomous host microenvironmental influences. Here we discuss the determinants of tumor heterogeneity, mechanisms of therapy resistance and effective therapy regimens that hold curative promise.
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Affiliation(s)
- Bailey M Robertson
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mitchell E Fane
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Vito W Rebecca
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
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3
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Li Y, Li H, Sun G, Xu S, Tang X, Zhang L, Wan L, Zhang L, Tang M. Integrative analyses of multi-omics data constructing tumor microenvironment and immune-related molecular prognosis model in human colorectal cancer. Heliyon 2024; 10:e32744. [PMID: 38975206 PMCID: PMC11226854 DOI: 10.1016/j.heliyon.2024.e32744] [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: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 07/09/2024] Open
Abstract
The increasing prevalence and incidence of colorectal cancer (CRC), particularly in young adults, underscore the imperative to comprehend its fundamental mechanisms, discover novel diagnostic and prognostic markers, and enhance therapeutic strategies. Here, we integrated multi-omics data, including gene expression, somatic mutation data and DNA methylation data, to unravel the intricacies of tumor microenvironment (TME) in CRC and search for novel prognostic markers. By calculating the immune score for each patient from the expression profile, we delineated the differential immune cell fraction, constructed an immune-related multi-omics atlas, and identified molecular characteristics. The entire colorectal dataset (n = 343) was randomly divided into training (n = 249) and testing datasets (n = 94). We screened 144 immune-related genes, 6 mutant genes, and 38 methylation probes associated with overall survival (OS). These makers were then incorporated into a 10-gene prognostic model using Lasso and Cox regression in the training dataset, and the model's performance was evaluated in an independent validation dataset. The model exhibited satisfactory results (average concordance index [C-index] = 0.77), with the average 1-year, 3-year, and 5-year AUCs being 0.79, 0.76, and 0.76 in the training dataset and 0.74, 0.80, and 0.90 in the testing dataset. Furthermore, the prognostic model demonstrated applicability in guiding chemotherapy for CRC patients and exhibited a degree of pan-cancer utility in risk stratification. In conclusion, our integrated analysis of multi-omics data revealed immune-related genetic and epigenetic characteristics of the TME. We propose an integrative prognostic model that can stratify risk and guide chemotherapy for CRC patients. The generalizability of the model in risk stratification across different cancer types was validated in Pan-Cancer cohort.
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Affiliation(s)
- Yifei Li
- Clinical Biobank, Institute of Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hexin Li
- Clinical Biobank, Institute of Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Gaoyuan Sun
- Clinical Biobank, Institute of Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Siyuan Xu
- Clinical Biobank, Institute of Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaokun Tang
- Clinical Biobank, Institute of Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lanxin Zhang
- Clinical Biobank, Institute of Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Li Wan
- Clinical Biobank, Institute of Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lili Zhang
- Clinical Biobank, Institute of Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Min Tang
- Department of Medical Oncology, Institute of Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, China
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4
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Su C, Kent CL, Pierpoint M, Floyd W, Luo L, Williams NT, Ma Y, Peng B, Lazarides AL, Subramanian A, Himes JE, Perez VM, Hernansaiz-Ballesteros RD, Roche KE, Modliszewski JL, Selitsky SR, Shinohara ML, Wisdom AJ, Moding EJ, Mowery YM, Kirsch DG. Enhancing radiotherapy response via intratumoral injection of a TLR9 agonist in autochthonous murine sarcomas. JCI Insight 2024; 9:e178767. [PMID: 39133651 DOI: 10.1172/jci.insight.178767] [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: 01/03/2024] [Accepted: 06/11/2024] [Indexed: 08/21/2024] Open
Abstract
Radiation therapy (RT) is frequently used to treat cancers, including soft-tissue sarcomas. Prior studies established that the toll-like receptor 9 (TLR9) agonist cytosine-phosphate-guanine oligodeoxynucleotide (CpG) enhances the response to RT in transplanted tumors, but the mechanisms of this enhancement remain unclear. Here, we used CRISPR/Cas9 and the chemical carcinogen 3-methylcholanthrene (MCA) to generate autochthonous soft-tissue sarcomas with high tumor mutation burden. Treatment with a single fraction of 20 Gy RT and 2 doses of CpG significantly enhanced tumor response, which was abrogated by genetic or immunodepletion of CD8+ T cells. To characterize the immune response to CpG+RT, we performed bulk RNA-Seq, single-cell RNA-Seq, and mass cytometry. Sarcomas treated with 20 Gy and CpG demonstrated increased CD8 T cells expressing markers associated with activation and proliferation, such as Granzyme B, Ki-67, and IFN-γ. CpG+RT also upregulated antigen presentation pathways on myeloid cells. Furthermore, in sarcomas treated with CpG+RT, TCR clonality analysis suggests an increase in clonal T cell dominance. Collectively, these findings demonstrate that CpG+RT significantly delays tumor growth in a CD8 T cell-dependent manner. These results provide a strong rationale for clinical trials evaluating CpG or other TLR9 agonists with RT in patients with soft-tissue sarcoma.
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Affiliation(s)
- Chang Su
- Department of Pharmacology and Cancer Biology and
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Collin L Kent
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Matthew Pierpoint
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Warren Floyd
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Nerissa T Williams
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Brian Peng
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Alexander L Lazarides
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Ajay Subramanian
- Department of Radiation Oncology, Stanford University, Stanford, California, USA
| | - Jonathon E Himes
- Department of Pharmacology and Cancer Biology and
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | | | | | - Kimberly E Roche
- Tempus AI Inc., Durham, North Carolina, USA
- QuantBio LLC, Durham, North Carolina, USA
| | - Jennifer L Modliszewski
- QuantBio LLC, Durham, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Sara R Selitsky
- Tempus AI Inc., Durham, North Carolina, USA
- QuantBio LLC, Durham, North Carolina, USA
| | - Mari L Shinohara
- Department of Integrative Immunology
- Department of Molecular Genetics and Microbiology, and
- Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Amy J Wisdom
- Harvard Radiation Oncology Program, Boston, Massachusetts, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Yvonne M Mowery
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David G Kirsch
- Department of Pharmacology and Cancer Biology and
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Radiation Oncology and
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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5
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Flippot R, Teixeira M, Rey-Cardenas M, Carril-Ajuria L, Rainho L, Naoun N, Jouniaux JM, Boselli L, Naigeon M, Danlos FX, Escudier B, Scoazec JY, Cassard L, Albiges L, Chaput N. B cells and the coordination of immune checkpoint inhibitor response in patients with solid tumors. J Immunother Cancer 2024; 12:e008636. [PMID: 38631710 PMCID: PMC11029261 DOI: 10.1136/jitc-2023-008636] [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: 03/31/2024] [Indexed: 04/19/2024] Open
Abstract
Immunotherapy profoundly changed the landscape of cancer therapy by providing long-lasting responses in subsets of patients and is now the standard of care in several solid tumor types. However, immunotherapy activity beyond conventional immune checkpoint inhibition is plateauing, and biomarkers are overall lacking to guide treatment selection. Most studies have focused on T cell engagement and response, but there is a growing evidence that B cells may be key players in the establishment of an organized immune response, notably through tertiary lymphoid structures. Mechanisms of B cell response include antibody-dependent cellular cytotoxicity and phagocytosis, promotion of CD4+ and CD8+ T cell activation, maintenance of antitumor immune memory. In several solid tumor types, higher levels of B cells, specific B cell subpopulations, or the presence of tertiary lymphoid structures have been associated with improved outcomes on immune checkpoint inhibitors. The fate of B cell subpopulations may be widely influenced by the cytokine milieu, with versatile roles for B-specific cytokines B cell activating factor and B cell attracting chemokine-1/CXCL13, and a master regulatory role for IL-10. Roles of B cell-specific immune checkpoints such as TIM-1 are emerging and could represent potential therapeutic targets. Overall, the expanding field of B cells in solid tumors of holds promise for the improvement of current immunotherapy strategies and patient selection.
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Affiliation(s)
- Ronan Flippot
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Marcus Teixeira
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Macarena Rey-Cardenas
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Lucia Carril-Ajuria
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
- Medical Oncology, CHU Brugmann, Brussels, Belgium
| | - Larissa Rainho
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Natacha Naoun
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Jean-Mehdi Jouniaux
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Lisa Boselli
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Marie Naigeon
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Francois-Xavier Danlos
- LRTI, INSERM U1015, Gustave Roussy, Villejuif, France
- Drug Development Department, Gustave Roussy, Villejuif, France
| | - Bernard Escudier
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
| | | | - Lydie Cassard
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Laurence Albiges
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Nathalie Chaput
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
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Rong D, Su Y, Jia D, Zeng Z, Yang Y, Wei D, Lu H, Cao Y. Experimentally validated oxidative stress -associated prognostic signatures describe the immune landscape and predict the drug response and prognosis of SKCM. Front Immunol 2024; 15:1387316. [PMID: 38660305 PMCID: PMC11039952 DOI: 10.3389/fimmu.2024.1387316] [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: 02/17/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
Background Skin Cutaneous Melanoma (SKCM) incidence is continually increasing, with chemotherapy and immunotherapy being among the most common cancer treatment modalities. This study aims to identify novel biomarkers for chemotherapy and immunotherapy response in SKCM and explore their association with oxidative stress. Methods Utilizing TCGA-SKCM RNA-seq data, we employed Weighted Gene Co-expression Network Analysis (WGCNA) and Protein-Protein Interaction (PPI) networks to identify six core genes. Gene co-expression analysis and immune-related analysis were conducted, and specific markers associated with oxidative stress were identified using Gene Set Variation Analysis (GSVA). Single-cell analysis revealed the expression patterns of Oxidative Stress-Associated Genes (OSAG) in the tumor microenvironment. TIDE analysis was employed to explore the association between immune therapy response and OSAG, while CIBERSORT was used to analyze the tumor immune microenvironment. The BEST database demonstrated the impact of the Oxidative Stress signaling pathway on chemotherapy drug resistance. Immunohistochemical staining and ROC curve evaluation were performed to assess the protein expression levels of core genes in SKCM and normal samples, with survival analysis utilized to determine their diagnostic value. Results We identified six central genes associated with SKCM metastasis, among which the expression of DSC2 and DSC3 involved in the oxidative stress pathway was closely related to immune cell infiltration. DSC2 influenced drug resistance in SKMC patients. Furthermore, downregulation of DSC2 and DSC3 expression enhanced the response of SKCM patients to immunotherapy. Conclusion This study identified two Oxidative Stress-Associated genes as novel biomarkers for SKCM. Additionally, targeting the oxidative stress pathway may serve as a new strategy in clinical practice to enhance SKCM chemotherapy and sensitivity.
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Affiliation(s)
- Dongyun Rong
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yushen Su
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Dechao Jia
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhirui Zeng
- Department of anorectal surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
- School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan Yang
- Department of Internal Medicine, The Third Affiliated Hospital of Guizhou Medical University, Duyun, Guizhou, China
| | - Dalong Wei
- Department of Burns, Plastic Surgery and Wound Repair, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Key Laboratory of Tumor Molecular Pathology of Baise, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Honguan Lu
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yu Cao
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
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7
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Bekkat F, Seradj M, Lengagne R, Fiore F, Kato M, Lucas B, Castellano F, Molinier-Frenkel V, Richard Y, Prévost-Blondel A. Upregulation of IL4-induced gene 1 enzyme by B2 cells during melanoma progression impairs their antitumor properties. Eur J Immunol 2024; 54:e2350615. [PMID: 38400692 DOI: 10.1002/eji.202350615] [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: 06/19/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024]
Abstract
B cells present in human cutaneous melanoma have been associated with protective or detrimental effects on disease progression according to their phenotype. By using the RET model of spontaneous melanoma and adoptive transfer of B16 melanoma cells, we show that immature and follicular B2 (B2-FO) cells exert a protective effect on melanoma progression by promoting the generation of effector memory T cells and limiting the recruitment of polymorphonuclear myeloid-derived suppressor cells. Unfortunately, this beneficial effect progressively wanes as a consequence of enhanced expression of the IL4-induced gene 1 (IL4I1) enzyme by immature B cells and B2-FO cells. Endogenous IL4I1 selectively decreases CXCR5 expression in splenic immature B cells, subverting their trafficking to primary tumors and enhancing the production of IL-10 by B2 cells, thereby promoting an immunosuppressive microenvironment. Accordingly, B2 cells from RET IL4I1KO mice more efficiently controlled B16 melanoma growth than B2 cells from IL4I1-competent RET mice. Collectively, immature B cells and B2-FO cells are key actors in the control of melanoma growth, but their mobility and functions are differently impaired by IL4I1 overexpression during melanoma progression. Thus, our present data strongly urge us to associate an IL4I1 antagonist with current immunotherapy to improve the treatment of metastatic melanoma.
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Affiliation(s)
- Fériel Bekkat
- Université Paris Cité, CNRS UMR 8104, INSERM U1016, Institut Cochin, Paris, France
| | - Malvina Seradj
- Université Paris Cité, CNRS UMR 8104, INSERM U1016, Institut Cochin, Paris, France
| | - Renée Lengagne
- Université Paris Cité, CNRS UMR 8104, INSERM U1016, Institut Cochin, Paris, France
| | - Frédéric Fiore
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, INSERM, CNRS, CELPHEDIA, PHENOMIN, Marseille, France
| | - Masashi Kato
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Bruno Lucas
- Université Paris Cité, CNRS UMR 8104, INSERM U1016, Institut Cochin, Paris, France
| | - Flavia Castellano
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- AP-HP, Hôpital Henri Mondor, Département d'Hématologie-Immunologie, Créteil, France
| | - Valérie Molinier-Frenkel
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- AP-HP, Hôpital Henri Mondor, Département d'Hématologie-Immunologie, Créteil, France
| | - Yolande Richard
- Université Paris Cité, CNRS UMR 8104, INSERM U1016, Institut Cochin, Paris, France
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8
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Ding Z, Ding Q, Li H. The prognostic biomarker TPGS2 is correlated with immune infiltrates in pan-cancer: a bioinformatics analysis. Transl Cancer Res 2024; 13:1458-1478. [PMID: 38617524 PMCID: PMC11009813 DOI: 10.21037/tcr-23-113] [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: 01/29/2023] [Accepted: 10/20/2023] [Indexed: 04/16/2024]
Abstract
Background Tubulin polyglutamylase complex subunit 2 (TPGS2) is an element of the neuronal polyglutamylase complex that plays a role in the post-translational addition of glutamate residues to C-terminal tubulin tails. Recent research has shown that TPGS2 is associated with some tumors, but the roles of TPGS2 in tumor immunity remain unclear. Methods The research data were mainly sourced from The Cancer Genome Atlas. The data were analyzed to identify potential correlations between TPGS2 expression and survival, gene alterations, the tumor mutational burden (TMB), microsatellite instability (MSI), immune infiltration, and various immune-related genes across various cancers. The Wilcoxon rank-sum test was used to identify the significance. A log-rank test and univariate Cox regression analysis were performed to assess the survival state of the patients. Spearman's correlation coefficients were used to show the correlations. Results TPGS2 exhibited abnormal expression patterns in most types of cancers, and has promising prognostic potential in adrenocortical carcinoma and liver hepatocellular carcinoma. Further, TPGS2 expression was significantly correlated with molecular and immune subtypes. Moreover, the single-cell analyses showed that the expression of TPGS2 was associated with the cell cycle, metastasis, invasion, inflammation, and DNA damage. In addition, the immune cell infiltration analysis and gene-set enrichment analysis demonstrated that a variety of immune cells and immune processes were associated with TPGS2 expression in various cancers. Further, immune regulators, including immunoinhibitors, immunostimulators, the major histocompatibility complex, chemokines, and chemokine receptors, were correlated with TPGS2 expression in different cancer types. Finally, the TMB and MSI, which have been identified as powerful predictors of immunotherapy, were shown to be correlated with the expression of TPGS2 across human cancers. Conclusions TPGS2 is aberrantly expressed in most cancer tissues and might be associated with immune cell infiltration in the tumor microenvironment. TPGS2 could serve not only as a biomarker for predicting clinical outcomes, but also as a promising biomarker for evaluating and developing new approaches to immunotherapy in many types of cancers, especially colon adenocarcinoma and stomach adenocarcinoma.
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Affiliation(s)
- Zujun Ding
- Department of General Surgery, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Qing Ding
- Department of Pharmacy, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hang Li
- Department of General Surgery, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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9
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Chen C, Zhang Y, Wu X, Shen J. The role of tertiary lymphoid structure and B cells in nasopharyngeal carcinoma: Based on bioinformatics and experimental verification. Transl Oncol 2024; 41:101885. [PMID: 38295746 PMCID: PMC10846412 DOI: 10.1016/j.tranon.2024.101885] [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: 12/02/2023] [Accepted: 01/15/2024] [Indexed: 02/07/2024] Open
Abstract
OBJECTIVE Transcriptomic characteristics and prognosis of tertiary lymphoid structures (TLS) and infiltrating B cells in nasopharyngeal carcinoma (NPC) remain unclear. Here, NPC transcriptomic data and clinical samples were used to investigate the role of infiltrating B cells and TLS in NPC. METHODS We investigated the gene expression and infiltrating immune cells of NPC patients and further investigated the clinical relevance of B cell and TLS signatures. Transcriptional features of infiltrating B cell subsets were revealed by single-cell RNA sequencing (scRNA-seq) analysis. Immunohistochemical (IHC) and HE staining were performed to validate the clinical relevance of infiltrating B cells and TLS in NPC samples. RESULTS 27 differentially expressed immune-related genes (IRGs) associated with prognosis were identified, including B cell marker genes CD19 and CD79B. The higher B cells and TLS signature scores were associated with better outcomes and early pathological staging in 88 NPC patients. ScRNA-seq identified five distinct B cell subsets in NPC, including the BC-4 cluster associated with poor outcomes and the BC-0 cluster associated with better outcomes. EBV infection was positively associated with the formation of TLS. Furthermore, experimental results showed that the infiltration of B cells in NPC tissues was higher than that of normal tissues, and the density of TLS in an early stage of NPC was higher than that in advanced-stage TLS. CONCLUSION Our findings demonstrate the functional importance of distinct B cell subsets in the prognosis of NPC. Additionally, we confirmed that B cells and TLS may serve as prognostic biomarkers of survival for NPC patients.
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Affiliation(s)
- Chujun Chen
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Yan Zhang
- Pathology Dept., The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Xiaoting Wu
- School of Bioscience and Biopharmaceutics, Guangdong Province Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Juan Shen
- School of Bioscience and Biopharmaceutics, Guangdong Province Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, PR China.
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10
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Su C, Kent CL, Pierpoint M, Floyd W, Luo L, Wiliams NT, Ma Y, Peng B, Lazarides AL, Subramanian A, Himes JE, Perez VM, Hernansaiz-Ballesteros RD, Roche KE, Modliszewski JL, Selitsky SR, Mari Shinohara, Wisdom AJ, Moding EJ, Mowery YM, Kirsch DG. Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573968. [PMID: 38260522 PMCID: PMC10802286 DOI: 10.1101/2024.01.03.573968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Radiation therapy is frequently used to treat cancers including soft tissue sarcomas. Prior studies established that the toll-like receptor 9 (TLR9) agonist cytosine-phosphate-guanine oligodeoxynucleotide (CpG) enhances the response to radiation therapy (RT) in transplanted tumors, but the mechanism(s) remain unclear. Here, we used CRISPR/Cas9 and the chemical carcinogen 3-methylcholanthrene (MCA) to generate autochthonous soft tissue sarcomas with high tumor mutation burden. Treatment with a single fraction of 20 Gy RT and two doses of CpG significantly enhanced tumor response, which was abrogated by genetic or immunodepletion of CD8+ T cells. To characterize the immune response to RT + CpG, we performed bulk RNA-seq, single-cell RNA-seq, and mass cytometry. Sarcomas treated with 20 Gy and CpG demonstrated increased CD8 T cells expressing markers associated with activation and proliferation, such as Granzyme B, Ki-67, and interferon-γ. CpG + RT also upregulated antigen presentation pathways on myeloid cells. Furthermore, in sarcomas treated with CpG + RT, TCR clonality analysis suggests an increase in clonal T-cell dominance. Collectively, these findings demonstrate that RT + CpG significantly delays tumor growth in a CD8 T cell-dependent manner. These results provide a strong rationale for clinical trials evaluating CpG or other TLR9 agonists with RT in patients with soft tissue sarcoma.
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Affiliation(s)
- Chang Su
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Collin L. Kent
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Matthew Pierpoint
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Nerissa T. Wiliams
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Brian Peng
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - Ajay Subramanian
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Jonathan E. Himes
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | | | | | | | | | - Mari Shinohara
- Department of Immunology, Duke University, Durham, NC, USA
| | - Amy J. Wisdom
- Department of Radiation Oncology, Harvard University, Cambridge, MA, USA
| | - Everett J. Moding
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Yvonne M. Mowery
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA
| | - David G. Kirsch
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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11
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Kang JY, Yang J, Lee H, Park S, Gil M, Kim KE. Systematic Multiomic Analysis of PKHD1L1 Gene Expression and Its Role as a Predicting Biomarker for Immune Cell Infiltration in Skin Cutaneous Melanoma and Lung Adenocarcinoma. Int J Mol Sci 2023; 25:359. [PMID: 38203530 PMCID: PMC10778817 DOI: 10.3390/ijms25010359] [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: 11/08/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
The identification of genetic factors that regulate the cancer immune microenvironment is important for understanding the mechanism of tumor progression and establishing an effective treatment strategy. Polycystic kidney and hepatic disease 1-like protein 1 (PKHD1L1) is a large transmembrane protein that is highly expressed in immune cells; however, its association with tumor progression remains unclear. Here, we systematically analyzed the clinical relevance of PKHD1L1 in the tumor microenvironment in multiple cancer types using various bioinformatic tools. We found that the PKHD1L1 mRNA expression levels were significantly lower in skin cutaneous melanoma (SKCM) and lung adenocarcinoma (LUAD) than in normal tissues. The decreased expression of PKHD1L1 was significantly associated with unfavorable overall survival (OS) in SKCM and LUAD. Additionally, PKHD1L1 expression was positively correlated with the levels of infiltrating B cells, cluster of differentiation (CD)-8+ T cells, and natural killer (NK) cells, suggesting that the infiltration of immune cells could be associated with a good prognosis due to increased PKHD1L1 expression. Gene ontology (GO) analysis also revealed the relationship between PKHD1L1-co-altered genes and the activation of lymphocytes, including B and T cells. Collectively, this study shows that PKHD1L1 expression is positively correlated with a good prognosis via the induction of immune infiltration, suggesting that PKHD1L1 has potential prognostic value in SKCM and LUAD.
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Affiliation(s)
- Ji Young Kang
- Department of Health Industry, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (J.Y.K.); (M.G.)
| | - Jisun Yang
- Department of Cosmetic Sciences, Sookmyung Women’s University, Seoul 04310, Republic of Korea;
| | - Haeryung Lee
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (H.L.); (S.P.)
| | - Soochul Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (H.L.); (S.P.)
| | - Minchan Gil
- Department of Health Industry, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (J.Y.K.); (M.G.)
| | - Kyung Eun Kim
- Department of Health Industry, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (J.Y.K.); (M.G.)
- Department of Cosmetic Sciences, Sookmyung Women’s University, Seoul 04310, Republic of Korea;
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12
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Rediti M, Fernandez-Martinez A, Venet D, Rothé F, Hoadley KA, Parker JS, Singh B, Campbell JD, Ballman KV, Hillman DW, Winer EP, El-Abed S, Piccart M, Di Cosimo S, Symmans WF, Krop IE, Salgado R, Loi S, Pusztai L, Perou CM, Carey LA, Sotiriou C. Immunological and clinicopathological features predict HER2-positive breast cancer prognosis in the neoadjuvant NeoALTTO and CALGB 40601 randomized trials. Nat Commun 2023; 14:7053. [PMID: 37923752 PMCID: PMC10624889 DOI: 10.1038/s41467-023-42635-2] [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: 12/01/2022] [Accepted: 10/16/2023] [Indexed: 11/06/2023] Open
Abstract
The identification of prognostic markers in patients receiving neoadjuvant therapy is crucial for treatment optimization in HER2-positive breast cancer, with the immune microenvironment being a key factor. Here, we investigate the complexity of B and T cell receptor (BCR and TCR) repertoires in the context of two phase III trials, NeoALTTO and CALGB 40601, evaluating neoadjuvant paclitaxel with trastuzumab and/or lapatinib in women with HER2-positive breast cancer. BCR features, particularly the number of reads and clones, evenness and Gini index, are heterogeneous according to hormone receptor status and PAM50 subtypes. Moreover, BCR measures describing clonal expansion, namely evenness and Gini index, are independent prognostic factors. We present a model developed in NeoALTTO and validated in CALGB 40601 that can predict event-free survival (EFS) by integrating hormone receptor and clinical nodal status, breast pathological complete response (pCR), stromal tumor-infiltrating lymphocyte levels (%) and BCR repertoire evenness. A prognostic score derived from the model and including those variables, HER2-EveNT, allows the identification of patients with 5-year EFS > 90%, and, in those not achieving pCR, of a subgroup of immune-enriched tumors with an excellent outcome despite residual disease.
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Affiliation(s)
- Mattia Rediti
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - David Venet
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jordan D Campbell
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Karla V Ballman
- Alliance Statistics and Data Management Center, Weill Cornell Medicine, New York, NY, USA
| | - David W Hillman
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Eric P Winer
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | | | - Martine Piccart
- Medical Oncology Department, Institut Jules Bordet and l'Université Libre de Bruxelles (U.L.B.), Brussels, Belgium
| | - Serena Di Cosimo
- Integrated biology platform unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - William Fraser Symmans
- Department of Pathology, University of Texas, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ian E Krop
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Ziekenhuizen, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Lajos Pusztai
- Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Lisa A Carey
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium.
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13
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Liu Y, Liu Z, Yang Y, Cui J, Sun J, Liu Y. The prognostic and biology of tumour-infiltrating lymphocytes in the immunotherapy of cancer. Br J Cancer 2023; 129:1041-1049. [PMID: 37452117 PMCID: PMC10539364 DOI: 10.1038/s41416-023-02321-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/04/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Tumour immunotherapy has achieved remarkable clinical success in many different types of cancer in the past two decades. The outcome of immune checkpoint inhibitors in cancer patients has been linked to the quality and magnitude of T cell, NK cell, and more recently, B cell within the tumour microenvironment, suggesting that the immune landscape of a tumour is highly connected to patient response and prognosis. It is critical to understanding tumour immune microenvironments for identifying immune modifiers of cancer progression and developing cancer immunotherapies. The infiltration of solid tumours by immune cells with anti-tumour activity is both a strong prognostic factor and a therapeutic goal. Recent approaches and applications of new technologies, especially single-cell mRNA analysis in dissecting tumour microenvironments have brought important insights into the biology of tumour-infiltrating immune cells, revealed a remarkable degree of cellular heterogeneity and distinct patterns of immune response. In this review, we will discuss recent advances in the understanding of tumour infiltrated lymphocytes, their prognostic benefit, and predictive value for immunotherapy.
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Affiliation(s)
- Yanbin Liu
- Grit Biotechnology Ltd., Building 25, Area C, Sangtian Island Biological Industrial Park, Suzhou Industrial Park, Suzhou, Jiangsu Province, China
| | - Zhenjiang Liu
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China
| | - Yixiao Yang
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China
| | - Jun Cui
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China
| | - Jingwei Sun
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China
| | - Yarong Liu
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China.
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14
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Feng W, Jiang D, Xu Y, Li Y, Chen L, Zhao M, Shen Y, Liao W, Yang H, Li J. CDK4/6i enhances the antitumor effect of PD1 antibody by promoting TLS formation in ovarian cancer. Heliyon 2023; 9:e19760. [PMID: 37809574 PMCID: PMC10559077 DOI: 10.1016/j.heliyon.2023.e19760] [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: 03/28/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
Ovarian cancer is insensitive to immunotherapy and has a high mortality rate. CDK4/6 inhibitors (CDK4/6i) regulate the tumor microenvironment and play an antitumor role. Our previous research demonstrated that lymphocyte aggregation (tertiary lymphoid structures, TLSs) was observed after CDK4/6i treatment. This may explain the synergistic action of CDK4/6i with the anti-PD1 antibody. However, the key mechanism by which CDK4/6i promotes TLS formation has not been elucidated. We examine the link between TLS and prognosis. Animal models and high-throughput sequencing were used to explore the potential mechanism by which CDK4/6i promotes TLS formation. Our results showed the presence of TLSs was associated with a favorable prognosis for ovarian cancer. CDK4/6i promoted TLS formation and enhanced the immunotherapeutic effect of the anti-PD1 antibody. The potential mechanism of CDK4/6i affecting the formation of TLS may be through modulating SCD1 and its regulatory molecules ATF3 and CCL4. Our findings provide a theoretical basis for the application of CDK4/6i in ovarian cancer.
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Affiliation(s)
- Wangyou Feng
- Department of Gynaecology and Obstetrics, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), 15 Changle Western Road, Xi'an, 710032, Shaanxi, China
| | - Dongbo Jiang
- Department of Immunology, School of Basic Medicine, Air Force Medical University (the Fourth Military Medical University), 169 Changle Western Road, Xi'an, 710032, Shaanxi, China
| | - Ying Xu
- Department of Gynaecology and Obstetrics, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), 15 Changle Western Road, Xi'an, 710032, Shaanxi, China
| | - Yuanfeng Li
- Department of Gynaecology and Obstetrics, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), 15 Changle Western Road, Xi'an, 710032, Shaanxi, China
| | - Lin Chen
- Department of Gynaecology and Obstetrics, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), 15 Changle Western Road, Xi'an, 710032, Shaanxi, China
| | - Minye Zhao
- Department of Gynaecology and Obstetrics, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), 15 Changle Western Road, Xi'an, 710032, Shaanxi, China
| | - Yujie Shen
- Department of Gynaecology and Obstetrics, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), 15 Changle Western Road, Xi'an, 710032, Shaanxi, China
| | - Wenjing Liao
- Department of Gynaecology and Obstetrics, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), 15 Changle Western Road, Xi'an, 710032, Shaanxi, China
| | - Hong Yang
- Department of Gynaecology and Obstetrics, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), 15 Changle Western Road, Xi'an, 710032, Shaanxi, China
| | - Jia Li
- Department of Gynaecology and Obstetrics, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), 15 Changle Western Road, Xi'an, 710032, Shaanxi, China
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15
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Li J, Ren H, Huai H, Li J, Xie P, Li X. The evaluation of tumor microenvironment infiltration and the identification of angiogenesis-related subgroups in skin cutaneous melanoma. J Cancer Res Clin Oncol 2023; 149:7259-7273. [PMID: 36912943 DOI: 10.1007/s00432-023-04680-8] [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: 10/31/2022] [Accepted: 03/04/2023] [Indexed: 03/14/2023]
Abstract
BACKGROUND There are limited studies on the association between angiogenesis-related genes (ARGs) and the predictive risk of melanoma, even though angiogenic factors, which are essential for tumor growth and metastasis, might be secreted by angiogenesis-related protein in skin cutaneous melanoma (SKCM). To forecast patient outcomes, this study attempts to develop a predictive risk signature linked to angiogenesis in cutaneous melanoma. METHODS In 650 patients with SKCM, the expression and mutation of ARGs were examined, and this information was related to the clinical prognosis. SKCM patients were split into two groups based on how well they performed on the ARG. The link between ARGs, risk genes, and immunological microenvironment was examined using a range of algorithmic analysis techniques. Based on these five risk genes, an angiogenesis risk signature was created. We developed a nomogram and examined the sensitivity of antineoplastic medications to help the proposed risk model's clinical applicability. RESULTS The risk model developed by ARGs revealed that the prognosis for the two groups was significantly different. The predictive risk score was negatively connected with memory B cells, activated memory CD4 + T cells, M1 macrophages, and CD8 + T cells, and favorably correlated with dendritic cells, mast cells, and neutrophils. CONCLUSIONS Our findings offer fresh perspectives on prognostic evaluation and imply that ARG modulation is implicated in SKCM. Potential medications for the treatment of individuals with various SKCM subtypes were predicted by drug sensitivity analysis.
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Affiliation(s)
- Junpeng Li
- Department of Plastic and Burns Surgery, National Key Clinical Construction Specialty, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Institute for Translational Chinese Medicine, Sichuan Academy of Chinese Medicine Sciences, Chengdu, Sichuan, China
| | - Hangjun Ren
- Department of General Surgery, First People's Hospital of Yuhang District, Hangzhou, Zhejiang, China
| | - Hongyu Huai
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, China
| | - Junliang Li
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Pan Xie
- Department of Plastic and Burns Surgery, National Key Clinical Construction Specialty, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Institute for Translational Chinese Medicine, Sichuan Academy of Chinese Medicine Sciences, Chengdu, Sichuan, China
| | - Xiaolu Li
- Department of Plastic and Burns Surgery, National Key Clinical Construction Specialty, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Institute for Translational Chinese Medicine, Sichuan Academy of Chinese Medicine Sciences, Chengdu, Sichuan, China.
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16
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Yang L, Wang J, Altreuter J, Jhaveri A, Wong CJ, Song L, Fu J, Taing L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qiu X, Long HW, Michor F, Liu Y, Liu XS. Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nat Protoc 2023; 18:2404-2414. [PMID: 37391666 DOI: 10.1038/s41596-023-00841-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/22/2023] [Indexed: 07/02/2023]
Abstract
RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique for molecular profiling and immune characterization of tumors. In the past decade, many computational tools have been developed to characterize tumor immunity from gene expression data. However, the analysis of large-scale RNA-seq data requires bioinformatics proficiency, large computational resources and cancer genomics and immunology knowledge. In this tutorial, we provide an overview of computational analysis of bulk RNA-seq data for immune characterization of tumors and introduce commonly used computational tools with relevance to cancer immunology and immunotherapy. These tools have diverse functions such as evaluation of expression signatures, estimation of immune infiltration, inference of the immune repertoire, prediction of immunotherapy response, neoantigen detection and microbiome quantification. We describe the RNA-seq IMmune Analysis (RIMA) pipeline integrating many of these tools to streamline RNA-seq analysis. We also developed a comprehensive and user-friendly guide in the form of a GitBook with text and video demos to assist users in analyzing bulk RNA-seq data for immune characterization at both individual sample and cohort levels by using RIMA.
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Affiliation(s)
- Lin Yang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Li Song
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- School of Life Science and Technology, Tongji University, Shanghai, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Avinash Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Gali Bai
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
- The Ludwig Center at Harvard, Boston, MA, USA
| | - Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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17
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Ostojić M, Jevrić M, Mitrović-Ajtić O, Živić K, Tanić M, Čavić M, Srdić-Rajić T, Grahovac J. Nischarin expression may have differing roles in male and female melanoma patients. J Mol Med (Berl) 2023; 101:1001-1014. [PMID: 37382661 DOI: 10.1007/s00109-023-02339-y] [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: 06/27/2022] [Revised: 05/23/2023] [Accepted: 06/13/2023] [Indexed: 06/30/2023]
Abstract
Due to the development of resistance to previously effective therapies, there is a constant need for novel treatment modalities for metastatic melanoma. Nischarin (NISCH) is a druggable scaffolding protein reported as a tumor suppressor and a positive prognostic marker in breast and ovarian cancers through regulation of cancer cell survival, motility and invasion. The aim of this study was to examine the expression and potential role of nischarin in melanoma. We found that nischarin expression was decreased in melanoma tissues compared to the uninvolved skin, and this was attributed to the presence of microdeletions and hyper-methylation of the NISCH promoter in the tumor tissue. In addition to the previously reported cytoplasmic and membranous localization, we observed nischarin in the nuclei in melanoma patients' tissues. NISCH expression in primary melanoma had favorable prognostic value for female patients, but, unexpectedly, high NISCH expression predicted worse prognosis for males. Gene set enrichment analysis suggested significant sex-related disparities in predicted association of NISCH with several signaling pathways, as well as with different tumor immune infiltrate composition in male and female patients. Taken together, our results imply that nischarin may have a role in melanoma progression, but that fine-tuning of the pathways it regulates is sex-dependent. KEY MESSAGES: Nischarin is a tumor suppressor whose role has not been investigated in melanoma. Nischarin expression was downregulated in melanoma tissue compared to the normal skin. Nischarin had the opposite prognostic value in male and female melanoma patients. Nischarin association with signaling pathways differed in females and males. Our findings challenge the current view of nischarin as a universal tumor suppressor.
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Affiliation(s)
- Marija Ostojić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, 11000, Serbia
| | - Marko Jevrić
- Department of Surgery, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, 11000, Serbia
| | - Olivera Mitrović-Ajtić
- Department of Molecular Oncology, Institute for Medical Research, Dr Subotića 4, Belgrade, 11000, Serbia
| | - Kristina Živić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, 11000, Serbia
| | - Miljana Tanić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, 11000, Serbia
| | - Milena Čavić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, 11000, Serbia
| | - Tatjana Srdić-Rajić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, 11000, Serbia.
| | - Jelena Grahovac
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, 11000, Serbia.
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18
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Xue L, Zhang W, Ju Y, Xu X, Bo H, Zhong X, Hu Z, Zheng C, Fang B, Tang S. TNFSF10, an autophagy related gene, was a prognostic and immune infiltration marker in skin cutaneous melanoma. J Cancer 2023; 14:2417-2430. [PMID: 37670976 PMCID: PMC10475358 DOI: 10.7150/jca.86735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/09/2023] [Indexed: 09/07/2023] Open
Abstract
Autophagy exerts a pivotal effect on skin cutaneous melanoma (SKCM). This study was aimed to investigate the expression of autophagy related genes (ARGs) in SKCM as well as its clinical value. Differentially expressed (DE) ARGs were downloaded from the intersection of SKCM data in GEPIA2 database and ARGs in Human Autophagy Database (HADB) database, and were verified in SKCM datasets GSE46517 and GSE15605. DE ARGs were enriched by Metascape online tools. According to GEPIA2 database, tumor necrosis factor-related apoptosis-inducing ligand (TNFSF10) was identified as a closely related factor and prognostic marker of SKCM. Then the correlation analysis of clinicopathological characteristics between TNFSF10 and SKCM was completed by several online tools such as TISCH, HPA, BEST and qRT-PCR. Subsequently, we investigated TNFSF10 related functions and signal pathways with LinkedOmics online tool, and immune infiltration using Assistant for Clinical Bioinformatics online tool. Furthermore, correlation analysis between TNFSF10 expression and immunotherapy response was performed by TIDE algorithm and BEST online tool. And Kaplan-Meier Plotter was used to assessing the prognosis of SKCM patients receiving immunotherapy. Finally, the correlation analysis among TNFSF10 methylation, TNFSF10 expression and patient prognosis was completed by the DiseaseMeth version 2.0, UCSC XENA and qRT-PCR. ARGs are DE in SKCM and participate in the ERBB signaling pathway, as well as the processing and presentation of antigens. Moreover, TNFSF10's expression along with methylation expression were significantly associated with the prognosis. Low expression of TNFSF10 was associated with malignant clinicopathological features, lower immune signal activity and lower immunocytes abundance in patients with SKCM. As an ARG, TNFSF10 has a potential capacity in predicting the prognosis of SKCM patients, meanwhile, may be a novel immunotherapy marker for SKCM.
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Affiliation(s)
- Lei Xue
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Wancong Zhang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
| | - Yikun Ju
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xuezheng Xu
- Department of Orthopaedics, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Hao Bo
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xiaoping Zhong
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhexiao Hu
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
| | - Congyuan Zheng
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
| | - Bairong Fang
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shijie Tang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
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19
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Shuptrine CW, Perez VM, Selitsky SR, Schreiber TH, Fromm G. Shining a LIGHT on myeloid cell targeted immunotherapy. Eur J Cancer 2023; 187:147-160. [PMID: 37167762 DOI: 10.1016/j.ejca.2023.03.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023]
Abstract
Despite over a decade of clinical trials combining inhibition of emerging checkpoints with a PD-1/L1 inhibitor backbone, meaningful survival benefits have not been shown in PD-1/L1 inhibitor resistant or refractory solid tumours, particularly tumours dominated by a myelosuppressive microenvironment. Achieving durable anti-tumour immunity will therefore likely require combination of adaptive and innate immune stimulation, myeloid repolarisation, enhanced APC activation and antigen processing/presentation, lifting of the CD47/SIRPα (Cluster of Differentiation 47/signal regulatory protein alpha) 'do not eat me' signal, provision of an apoptotic 'pro-eat me' or 'find me' signal, and blockade of immune checkpoints. The importance of effectively targeting mLILRB2 and SIRPAyeloid cells to achieve improved response rates has recently been emphasised, given myeloid cells are abundant in the tumour microenvironment of most solid tumours. TNFSF14, or LIGHT, is a tumour necrosis superfamily ligand with a broad range of adaptive and innate immune activities, including (1) myeloid cell activation through Lymphotoxin Beta Receptor (LTβR), (2) T/NK (T cell and natural killer cell) induced anti-tumour immune activity through Herpes virus entry mediator (HVEM), (3) potentiation of proinflammatory cytokine/chemokine secretion through LTβR on tumour stromal cells, (4) direct induction of tumour cell apoptosis in vitro, and (5) the reorganisation of lymphatic tissue architecture, including within the tumour microenvironment (TME), by promoting high endothelial venule (HEV) formation and induction of tertiary lymphoid structures. LTBR (Lymphotoxin beta receptor) and HVEM rank highly amongst a range of costimulatory receptors in solid tumours, which raises interest in considering how LIGHT-mediated costimulation may be distinct from a growing list of immunotherapy targets which have failed to provide survival benefit as monotherapy or in combination with PD-1 inhibitors, particularly in the checkpoint acquired resistant setting.
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Affiliation(s)
- Casey W Shuptrine
- Shattuck Labs Inc., Austin, TX, USA; Shattuck Labs Inc., Durham, NC, USA
| | | | | | - Taylor H Schreiber
- Shattuck Labs Inc., Austin, TX, USA; Shattuck Labs Inc., Durham, NC, USA
| | - George Fromm
- Shattuck Labs Inc., Austin, TX, USA; Shattuck Labs Inc., Durham, NC, USA.
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20
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Kumar V, Stewart JH. Immunometabolic reprogramming, another cancer hallmark. Front Immunol 2023; 14:1125874. [PMID: 37275901 PMCID: PMC10235624 DOI: 10.3389/fimmu.2023.1125874] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Molecular carcinogenesis is a multistep process that involves acquired abnormalities in key biological processes. The complexity of cancer pathogenesis is best illustrated in the six hallmarks of the cancer: (1) the development of self-sufficient growth signals, (2) the emergence of clones that are resistant to apoptosis, (3) resistance to the antigrowth signals, (4) neo-angiogenesis, (5) the invasion of normal tissue or spread to the distant organs, and (6) limitless replicative potential. It also appears that non-resolving inflammation leads to the dysregulation of immune cell metabolism and subsequent cancer progression. The present article delineates immunometabolic reprogramming as a critical hallmark of cancer by linking chronic inflammation and immunosuppression to cancer growth and metastasis. We propose that targeting tumor immunometabolic reprogramming will lead to the design of novel immunotherapeutic approaches to cancer.
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Affiliation(s)
- Vijay Kumar
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Science Center (LSUHSC), New Orleans, LA, United States
| | - John H. Stewart
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Science Center (LSUHSC), New Orleans, LA, United States
- Louisiana State University- Louisiana Children’s Medical Center, Stanley S. Scott, School of Medicine, Louisiana State University Health Science Center (LSUHSC), New Orleans, LA, United States
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21
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Xiong K, Wang Z, Hounye AH, Peng L, Zhang J, Qi M. Development and validation of ferroptosis-related lncRNA signature and immune-related gene signature for predicting the prognosis of cutaneous melanoma patients. Apoptosis 2023; 28:840-859. [PMID: 36964478 DOI: 10.1007/s10495-023-01831-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 03/26/2023]
Abstract
Ferroptosis, a form of cell death caused by iron-dependent peroxidation of lipids, plays an important role in cancer. Recent studies have shown that long noncoding RNAs (lncRNAs) are involved in the regulation of ferroptosis in tumor cells and are also closely related to tumor immunity. Immune cell infiltration in the tumor microenvironment affects the prognosis and clinical outcome of immunotherapy in melanoma patients, and immune cell classification may be able to accurately predict the prognosis of melanoma patients. However, the prognostic value of ferroptosis-related lncRNAs (FRLs) in melanoma has not been thoroughly explored, and it is difficult to define the immune characteristics of melanoma. We used The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) database, and the FerrDb database to identify FRLs. FRLs with prognostic value were evaluated in an experimental cohort utilizing univariate, LASSO (least absolute shrinkage and selection operator) and multivariate Cox regression, followed by in vitro assays evaluating the expression levels and the biological functions of three candidate FRLs. Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curve analyses were used to assess the validity of the risk model, and the drug sensitivity of FRLs was examined by drug sensitivity analysis. The differentially expressed genes between the high- and low-risk groups in the risk model were enriched in the immune pathway, and we further found immune gene signatures (IRGs) that could predict the prognosis of melanoma patients through a series of methods including single-sample Gene Set Enrichment Analysis (ssGSEA). Finally, two GEO cohorts were used to validate the predictive accuracy and reliability of these two signature models. Our findings suggest that FRLs and IRGs have the potential to predict the prognosis of patients with cutaneous melanoma.
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Affiliation(s)
- Kaifen Xiong
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zheng Wang
- School of Computer Science, Hunan First Normal University, Changsha, 410205, China
| | | | - Li Peng
- School of Computer Science, Hunan First Normal University, Changsha, 410205, China.
| | - Jianglin Zhang
- Department of Dermatology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
- Candidate Branch of National Clinical Research Center for Skin Diseases, Shenzhen, 518020, Guangdong, China.
- Department of Geriatrics, Shenzhen People's Hospital(The Second Clinical Medical College, Jinan UniversityThe First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
| | - Min Qi
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China.
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22
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Xu X, Ju Y, Zhao X, Yang P, Zhu F, Fang B. SMG7-AS1 as a prognostic biomarker and predictor of immunotherapy responses for skin cutaneous melanoma. Genomics 2023; 115:110614. [PMID: 36931476 DOI: 10.1016/j.ygeno.2023.110614] [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: 11/04/2022] [Revised: 02/14/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Skin cutaneous melanoma (SKCM) is the most life-threatening skin cancer and lacks early detection and effective treatment strategies. Many long noncoding RNAs are associated with the development of tumors and may serve as potential immunotherapeutic targets. In this study, microarray analysis was performed to screen for differentially expressed lncRNAs between SKCM and normal tissues, and SMG7-AS1 was identified as an upregulated lncRNA in SKCM. Subsequently, bioinformatic analysis revealed that dysregulation of SMG7-AS1 influences metastasis and immune infiltration. qRT-PCR of clinical samples demonstrated that the expression of SMG7-AS1 was higher in melanoma tissues. Flow cytometry showed that SMG7-AS1 plays a vital role in the cell cycle. Additionally, SMG7-AS1 was found to be associated with immunotherapy responses. To the best of our knowledge, this study is the first to report that SMG7-AS1 is associated with SKCM and may serve as a prognostic biomarker and predictor of immunotherapy responses in SKCM.
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Affiliation(s)
- Xuezheng Xu
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Yikun Ju
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Xueheng Zhao
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha 410078, People's Republic of China
| | - Pu Yang
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Fang Zhu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha 410078, People's Republic of China
| | - Bairong Fang
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China.
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23
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Zhang E, Ding C, Li S, Zhou X, Aikemu B, Fan X, Sun J, Zheng M, Yang X. Roles and mechanisms of tumour-infiltrating B cells in human cancer: a new force in immunotherapy. Biomark Res 2023; 11:28. [PMID: 36890557 PMCID: PMC9997025 DOI: 10.1186/s40364-023-00460-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/28/2023] [Indexed: 03/10/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) targeting PD-1 or PD-L1 have emerged as a revolutionary treatment strategy for human cancer patients. However, as the response rate to ICI therapy varies widely among different types of tumours, we are beginning to gain insight into the mechanisms as well as biomarkers of therapeutic response and resistance. Numerous studies have highlighted the dominant role of cytotoxic T cells in determining the treatment response to ICIs. Empowered by recent technical advances, such as single-cell sequencing, tumour-infiltrating B cells have been identified as a key regulator in several solid tumours by affecting tumour progression and the response to ICIs. In the current review, we summarized recent advances regarding the role and underlying mechanisms of B cells in human cancer and therapy. Some studies have shown that B-cell abundance in cancer is positively associated with favourable clinical outcomes, while others have indicated that they are tumour-promoting, implying that the biological function of B cells is a complex landscape. The molecular mechanisms involved multiple aspects of the functions of B cells, including the activation of CD8+ T cells, the secretion of antibodies and cytokines, and the facilitation of the antigen presentation process. In addition, other crucial mechanisms, such as the functions of regulatory B cells (Bregs) and plasma cells, are discussed. Here, by summarizing the advances and dilemmas of recent studies, we depicted the current landscape of B cells in cancers and paved the way for future research in this field.
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Affiliation(s)
- Enkui Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chengsheng Ding
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shuchun Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xueliang Zhou
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Batuer Aikemu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaodong Fan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Minhua Zheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Department of General Surgery & Carson International Cancer Research Center, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy, Shenzhen, 518055, China.
| | - Xiao Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Department of General Surgery & Carson International Cancer Research Center, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy, Shenzhen, 518055, China.
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24
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Taylor J, Gandhi A, Gray E, Zaenker P. Checkpoint inhibitor immune-related adverse events: A focused review on autoantibodies and B cells as biomarkers, advancements and future possibilities. Front Immunol 2023; 13:991433. [PMID: 36713389 PMCID: PMC9874109 DOI: 10.3389/fimmu.2022.991433] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/07/2022] [Indexed: 01/13/2023] Open
Abstract
The use of immune checkpoint inhibitors (ICIs) has evolved rapidly with unprecedented treatment benefits being obtained for cancer patients, including improved patient survival. However, over half of the patients experience immune related adverse events (irAEs) or toxicities, which can be fatal, affect the quality of life of patients and potentially cause treatment interruption or cessation. Complications from these toxicities can also cause long term irreversible organ damage and other chronic health conditions. Toxicities can occur in various organ systems, with common observations in the skin, rheumatologic, gastrointestinal, hepatic, endocrine system and the lungs. These are not only challenging to manage but also difficult to detect during the early stages of treatment. Currently, no biomarker exists to predict which patients are likely to develop toxicities from ICI therapy and efforts to identify robust biomarkers are ongoing. B cells and antibodies against autologous antigens (autoantibodies) have shown promise and are emerging as markers to predict the development of irAEs in cancer patients. In this review, we discuss the interplay between ICIs and toxicities in cancer patients, insights into the underlying mechanisms of irAEs, and the involvement of the humoral immune response, particularly by B cells and autoantibodies in irAE development. We also provide an appraisal of the progress, key empirical results and advances in B cell and autoantibody research as biomarkers for predicting irAEs. We conclude the review by outlining the challenges and steps required for their potential clinical application in the future.
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Affiliation(s)
- John Taylor
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia,*Correspondence: John Taylor,
| | - Aesha Gandhi
- Sir Charles Gairdner Hospital, Department of Medical Oncology, Nedlands, WA, Australia
| | - Elin Gray
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Pauline Zaenker
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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25
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Katoh H, Komura D, Furuya G, Ishikawa S. Immune repertoire profiling for disease pathobiology. Pathol Int 2023; 73:1-11. [PMID: 36342353 PMCID: PMC10099665 DOI: 10.1111/pin.13284] [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: 05/24/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Lymphocytes consist of highly heterogeneous populations, each expressing a specific cell surface receptor corresponding to a particular antigen. Lymphocytes are both the cause and regulator of various diseases, including autoimmune/allergic diseases, lifestyle diseases, neurodegenerative diseases, and cancers. Recently, immune repertoire sequencing has attracted much attention because it helps obtain global profiles of the immune receptor sequences of infiltrating T and B cells in specimens. Immune repertoire sequencing not only helps deepen our understanding of the molecular mechanisms of immune-related pathology but also assists in discovering novel therapeutic modalities for diseases, thereby shedding colorful light on otherwise tiny monotonous cells when observed under a microscope. In this review article, we introduce and detail the background and methodology of immune repertoire sequencing and summarize recent scientific achievements in association with human diseases. Future perspectives on this genetic technique in the field of histopathological research will also be discussed.
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Affiliation(s)
- Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Genta Furuya
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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26
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Jumaniyazova E, Lokhonina A, Dzhalilova D, Kosyreva A, Fatkhudinov T. Immune Cells in Head-and-Neck Tumor Microenvironments. J Pers Med 2022; 12:jpm12091521. [PMID: 36143308 PMCID: PMC9506052 DOI: 10.3390/jpm12091521] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Head-and-neck cancers constitute a heterogeneous group of aggressive tumors with high incidence and low survival rates, collectively being the sixth most prevalent cancer type globally. About 90% of head-and-neck cancers are classified as squamous cell carcinomas (HNSCC). The innate and adaptive immune systems, indispensable for anti-cancer immune surveillance, largely define the rates of HNSCC emergence and progression. HNSCC microenvironments harbor multiple cell types that infiltrate the tumors and interact both with tumor cells and among themselves. Gradually, tumor cells learn to manipulate the immune system, either by adapting their own immunogenicity or through the release of immunosuppressive molecules. These interactions continuously evolve and shape the tumor microenvironment, both structurally and functionally, facilitating angiogenesis, proliferation and metastasis. Our understanding of this evolution is directly related to success in the development of advanced therapies. This review focuses on the key mechanisms that rule HNSCC infiltration, featuring particular immune cell types and their roles in the pathogenesis. A close focus on the tumor-immunity interactions will help identify new immunotherapeutic targets in patients with HNSCC.
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Affiliation(s)
- Enar Jumaniyazova
- Department of Histology, Cytology and Embryology, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
- Correspondence: ; Tel.: +7-9254258360
| | - Anastasiya Lokhonina
- Department of Histology, Cytology and Embryology, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 4 Oparina Street, 117997 Moscow, Russia
| | - Dzhuliia Dzhalilova
- Department of Histology, Cytology and Embryology, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
- Avtsyn Research Institute of Human Morphology of Petrovsky National Research Centre of Surgery, 3 Tsyurupy Street, 117418 Moscow, Russia
| | - Anna Kosyreva
- Department of Histology, Cytology and Embryology, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
- Avtsyn Research Institute of Human Morphology of Petrovsky National Research Centre of Surgery, 3 Tsyurupy Street, 117418 Moscow, Russia
| | - Timur Fatkhudinov
- Department of Histology, Cytology and Embryology, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
- Avtsyn Research Institute of Human Morphology of Petrovsky National Research Centre of Surgery, 3 Tsyurupy Street, 117418 Moscow, Russia
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27
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Yang X, Wang X, Sun X, Xiao M, Fan L, Su Y, Xue L, Luo S, Hou S, Wang H. Construction of five cuproptosis-related lncRNA signature for predicting prognosis and immune activity in skin cutaneous melanoma. Front Genet 2022; 13:972899. [PMID: 36160015 PMCID: PMC9490379 DOI: 10.3389/fgene.2022.972899] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Cuproptosis is a newly discovered new mechanism of programmed cell death, and its unique pathway to regulate cell death is thought to have a unique role in understanding cancer progression and guiding cancer therapy. However, this regulation has not been studied in SKCM at present. In this study, data on Skin Cutaneous Melanoma (SKCM) patients were downloaded from the TCGA database. We screened the genes related to cuproptosis from the published papers and confirmed the lncRNAs related to them. We applied Univariate/multivariate and LASSO Cox regression algorithms, and finally identified 5 cuproptosis-related lncRNAs for constructing prognosis prediction models (VIM-AS1, AC012443.2, MALINC1, AL354696.2, HSD11B1-AS1). The reliability and validity test of the model indicated that the model could well distinguish the prognosis and survival of SKCM patients. Next, immune microenvironment, immunotherapy analysis, and functional enrichment analysis were also performed. In conclusion, this study is the first analysis based on cuproptosis-related lncRNAs in SKCM and aims to open up new directions for SKCM therapy.
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Affiliation(s)
- Xiaojing Yang
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, China
- *Correspondence: Xiaojing Yang, ; Huiping Wang,
| | - Xing Wang
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xinti Sun
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Meng Xiao
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, China
| | - Liyun Fan
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yunwei Su
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, China
| | - Lu Xue
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, China
| | - Suju Luo
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shuping Hou
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, China
| | - Huiping Wang
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, China
- *Correspondence: Xiaojing Yang, ; Huiping Wang,
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Yang H, Che D, Gu Y, Cao D. Prognostic and immune-related value of complement C1Q (C1QA, C1QB, and C1QC) in skin cutaneous melanoma. Front Genet 2022; 13:940306. [PMID: 36110204 PMCID: PMC9468976 DOI: 10.3389/fgene.2022.940306] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Skin cutaneous melanoma (SKCM) is a common malignancy that is associated with increased morbidity and mortality. Complement C1Q is composed of C1QA, C1QB, and C1QC and is involved in the occurrence and development of many malignant tumours. However, the effect of C1QA, C1QB, and C1QC expression on tumour immunity and prognosis of cutaneous melanoma remains unclear.Methods: First, we analysed C1QA, C1QB, and C1QC expression levels and prognostic values using Gene Expression Profiling Interactive Analysis (GEPIA) and Tumour Immune Estimation Resource (TIMER) analysis, and further validation was performed using RT-qPCR, The Human Protein Atlas, The Cancer Genome Atlas (TCGA) dataset, and Gene Expression Omnibus dataset. We then performed univariate/multivariate Cox proportional hazard model, clinicopathological correlation, and receiver operating characteristic curve analysis using TCGA dataset and established a nomogram model. Differentially expressed genes associated with C1QA, C1QB, and C1QC in SKCM were identified and analysed using LinkedOmics, TIMER, the Search Tool for the Retrieval of Interacting Genes database, and Metascape and Cytoscape software platforms. We used TIMER, GEPIA, and single-sample gene set enrichment analysis (ssGSEA) to analyse the relationship between the three genes and the level of immune cell infiltration, biomarkers, and checkpoint expression in SKCM. Finally, GSEA was utilized to study the functional pathways of C1QA, C1QB, and C1QC enrichment in SKCM.Results: The overexpression of C1QA, C1QB, and C1QC provided significant value in the diagnosis of SKCM and has been associated with better overall survival (OS). Multivariate Cox regression analysis indicated that C1QA, C1QB, and C1QC are independent prognostic biomarkers for patients with SKCM. Immune cell infiltration, biomarkers, and checkpoints were positively correlated with the expression of C1QA, C1QB, and C1QC. Furthermore, the results of functional and pathway enrichment analysis showed that immune-related and apoptotic pathways were significantly enriched in the high-expression group of C1QA, C1QB, and C1QC.Conclusion: We found that C1QA, C1QB, and C1QC can be used as biomarkers for the diagnosis and prognosis of SKCM patients. The upregulated expression levels of these three complement components benefit patients from OS and may increase the effect of immunotherapy. This result may be due to the dual effects of anti-tumour immunity and apoptosis.
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Reddy R, Mintz J, Golan R, Firdaus F, Ponce R, Van Booven D, Manoharan A, Issa I, Blomberg BB, Arora H. Antibody Diversity in Cancer: Translational Implications and Beyond. Vaccines (Basel) 2022; 10:vaccines10081165. [PMID: 35893814 PMCID: PMC9331493 DOI: 10.3390/vaccines10081165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/14/2022] [Accepted: 06/22/2022] [Indexed: 12/10/2022] Open
Abstract
Patients with cancer tend to develop antibodies to autologous proteins. This phenomenon has been observed across multiple cancer types, including bladder, lung, colon, prostate, and melanoma. These antibodies potentially arise due to induced inflammation or an increase in self-antigens. Studies focusing on antibody diversity are particularly attractive for their diagnostic value considering antibodies are present at an early diseased stage, serum samples are relatively easy to obtain, and the prevalence of antibodies is high even when the target antigen is minimally expressed. Conversely, the surveillance of serum proteins in cancer patients is relatively challenging because they often show variability in expression and are less abundant. Moreover, an antibody’s presence is also useful as it suggests the relative immunogenicity of a given antigen. For these reasons, profiling antibodies’ responses is actively considered to detect the spread of antigens following immunotherapy. The current review focuses on expanding the knowledge of antibodies and their diversity, and the impact of antibody diversity on cancer regression and progression.
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Affiliation(s)
- Raghuram Reddy
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (R.R.); (F.F.); (A.M.)
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Joel Mintz
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Davie, FL 33328, USA;
| | - Roei Golan
- College of Medicine, Florida State University, Tallahassee FL 32304, USA;
| | - Fakiha Firdaus
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (R.R.); (F.F.); (A.M.)
| | - Roxana Ponce
- Department of Biology, Florida International University, Miami, FL 33199, USA;
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33143, USA; (D.V.B.); (I.I.)
| | - Aysswarya Manoharan
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (R.R.); (F.F.); (A.M.)
| | - Isabelle Issa
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33143, USA; (D.V.B.); (I.I.)
| | - Bonnie B. Blomberg
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Himanshu Arora
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (R.R.); (F.F.); (A.M.)
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33143, USA; (D.V.B.); (I.I.)
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- The Interdisciplinary Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Correspondence:
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30
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Zhang S, Chen K, Zhao Z, Zhang X, Xu L, Liu T, Yu S. Lower Expression of GBP2 Associated With Less Immune Cell Infiltration and Poor Prognosis in Skin Cutaneous Melanoma (SKCM). J Immunother 2022; 45:274-283. [PMID: 35543550 DOI: 10.1097/cji.0000000000000421] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/22/2022] [Indexed: 11/26/2022]
Abstract
Guanylate binding protein 2 (GBP2) could bind to guanine nucleotides (GMP, GDP, and GTP) and exhibits antiviral activity against influenza virus through the innate immune response. Some researchers have demonstrated that the value of GBP2 in predicting the prognosis of multiple cancers and the complex correlation with immune response. However, the correlation of GBP2 to prognosis and immune cell infiltration level were unknown in skin cutaneous melanoma (SKCM). The GBP2 expression in multiple cancers were evaluated through Tumor Immune Estimation Resource (TIMER) and Oncomine. We also evaluated the influence of GBP2 on overall survival in multiple caners through GEPIA, TIMER, and tissue microarray. The correlation between GBP2 expression level and immune cell or gene markers of immune infiltration level was explored on TIMER and GEPIA. Gene set enrichment analysis was performed using the TCGA dataset. The GBP2 expression level represented a significant reduction and the GBP2 expression was lower compared with the SKCM-Metastasis with P<0.01. Lower GBP2 expression was significantly correlated with the poor overall survival of SKCM patients. Simultaneously, higher GBP2 expression predicted the better SKCM-free survival with P=0.019. GBP2 expression was positively correlated with the infiltration cells of B-cell, CD8+ T-cell, CD4+ T-cell, macrophage, neutrophil, and dendritic cell in SKCM. And there was a significant negative correlation between the expression of GBP2 and DNA methylation in the cBioPortal database (P=3.39e-42). Gene set enrichment analysis revealed that GBP2 was closely correlated with multiple pathways of immune response in cancer. In conclusion, Lower expression of GBP2 associated with less immune cell infiltration and poor prognosis in SKCM and the high promoter methylation of GBP2 represented a promising biomarker for poor prognostication in SKCM.
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Affiliation(s)
| | - Kun Chen
- State Key Lab of Molecular Oncology and Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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31
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Wang Z, Cheng Z, Lu S, Chard Dunmall LS, Wang J, Guo Y, Wang Y. Characterization of the Intra-tumoral B Cell Immunoglobulin Repertoire Is of Prognostic Value for Esophageal Squamous Cell Carcinoma. Front Immunol 2022; 13:896627. [PMID: 35812448 PMCID: PMC9257635 DOI: 10.3389/fimmu.2022.896627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Esophageal Squamous Cell carcinomas (ESCC) is a highly heterogeneous malignancy that is among the leading cause of cancer-related death worldwide. B cells play pivotal roles in the immune defense system and cancer progression and regression, yet the repertoire of tumor infiltrating B cells (TIBs) and its association with clinical outcome remains unexplored in ESCC. Here we collected bulk RNA-seq sequencing data from 119 ESCC tumors and matched adjacent normal samples to delineate the B cell repertoire. We found that ESCC is more heavily infiltrated by B cells and plasma cells compared to activated T cells. The immunoglobulin heavy chain variable region (IGHV) gene usage was remarkably biased and IGHV3-74 was under-represented in ESCC tumors. The TIBs showed a more oligoclonal profile along with widespread clonal expansion and IgG subclass switch events (CSRs). Survival analysis revealed several unexpected associations between tumor infiltrating B cells and prognosis. Higher levels of immunoglobulin expression (IGH), CD138 expression, IGH to MS4A1 ratio, CSR events and clone diversity are all associated with better survival. Notably, we found that the abundance of CD20-negative IgG2-producing plasma cells has a strong positive effect on overall survival with a hazard ratio (HR) of 0.40 (log-rank p: 0.002). Combing molecular subtyping, the IgG2-producing plasma cells could stratify high-risk patients more accurately with a HR of 0.253 (log-rank p: 0.0006). The direct link between protective B cell populations and ESCC prognosis provides biomarkers for high-risk patient selection and holds great promise for developing strategies for immunotherapy targeting B cells in ESCC patients.
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Affiliation(s)
- Zhizhong Wang
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Zhenguo Cheng
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shuangshuang Lu
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Louisa S. Chard Dunmall
- Centre for Biomarkers Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jun Wang
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Yongjun Guo
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Yaohe Wang, ; Yongjun Guo,
| | - Yaohe Wang
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Centre for Biomarkers Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- *Correspondence: Yaohe Wang, ; Yongjun Guo,
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Wu S, Liang Y, Zang Q, Xing Z, Yin P, Sun R, Dai B. FLG Is a Potential Biomarker of Prognosis and Immunotherapy in Skin Cutaneous Melanoma. Appl Bionics Biomech 2022; 2022:5160748. [PMID: 35607429 PMCID: PMC9124147 DOI: 10.1155/2022/5160748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022] Open
Abstract
Background Skin cutaneous melanoma is one of most aggressive type of cancers worldwide. Therefore, the identification of SKCM biomarkers is of great importance. FLG gene is one of the genes that encode proteins involved in epidermal formation. This was the first time to study the role of FLG in the prognosis and immune infiltrates of skin cutaneous melanoma. Methods We downloaded the somatic mutation data of 471 SKCM patients from the Cancer Genome Atlas (TCGA) database and analyzed the mutation profiles with "MafTools" package. The expression of FLG and the overall survival in SKCM were analyzed by GEPIA. Additionally, univariate and multivariate Cox analyses were used to compare several clinical features with survival rates. We used TIMER to investigate FLG expression and collection of immune infiltration levels in SKCM, as well as cumulative survival in SKCM. Meanwhile, we also used CIBERSORT to investigate the association between FLG and cancer immune infiltration. In addition, gene set enrichment analysis (GSEA) was performed using the TCGA dataset. Furthermore, data from GEO and HPA was used to validate the results. Results Single nucleotide polymorphism (SNP) happened more frequently than insertion or deletion, and C > T was the most common of SNV in SKCM. We selected the first 15 mutated genes by analyzing 471 melanoma samples, and the prognosis analysis showed that only the high expression of mutated FLG gene was significantly correlated with the poor prognosis of SKCM. Multivariate Cox analysis showed that age, the worse tumor status, less lymph node metastasis, and FLG expression were independent factors for prognosis. Specifically, lower infiltration levels of B cell, CD8+ T cells, neutrophils, and dendritic cells correlated with poor survival outcomes in SKCM. GSEA revealed that FLG is closely related to cancer pathways and epidermal cell proliferation. In addition, the previous conclusions can be verified from external data from GEO and HPA. Conclusion The discovery of mutant gene FLG as a biomarker of SKCM helps elucidate how changes in the immune environment promote the occurrence of cutaneous melanoma. Further analysis suggested that FLG might be a new predictor of SKCM prognosis.
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Affiliation(s)
- Shaobo Wu
- Health Science Center, Xi'an Jiaotong University, Shaanxi, Xi'an 710061, China
| | - Yuxia Liang
- Department of Imaging, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, Xi'an 710061, China
| | - Qijuan Zang
- Health Science Center, Xi'an Jiaotong University, Shaanxi, Xi'an 710061, China
| | - Zixuan Xing
- Health Science Center, Xi'an Jiaotong University, Shaanxi, Xi'an 710061, China
| | - Pan Yin
- Health Science Center, Xi'an Jiaotong University, Shaanxi, Xi'an 710061, China
| | - Ruifang Sun
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University, Shaanxi, Xi'an 710061, China
| | - Bingling Dai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Shaanxi, Xi'an 710061, China
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Rodgers CB, Mustard CJ, McLean RT, Hutchison S, Pritchard AL. A B-cell or a key player? The different roles of B-cells and antibodies in melanoma. Pigment Cell Melanoma Res 2022; 35:303-319. [PMID: 35218154 PMCID: PMC9314792 DOI: 10.1111/pcmr.13031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 02/01/2022] [Accepted: 02/21/2022] [Indexed: 12/17/2022]
Abstract
The B‐cell system plays an important role in the melanoma immune response; however, consensus has yet to be reached in many facets. Here, we comprehensively review human studies only, due to fundamental differences in the humoral response with animal models. Tumour‐infiltrating B‐cells are associated with contradictory prognostic values, reflecting a lack of agreement between studies on cell subset classification and differences in the markers used, particularly the common use of a single marker not differentiating multiple subsets. Tertiary lymphoid structures (TLS) organise T‐cells and B‐cells within tumours to generate a local anti‐tumour response and TLS presence associates with improved survival in response to immune checkpoint blockade, in late‐stage disease. Autoantibody production is increased in melanoma patients and has been proposed as biomarkers for diagnosis, prognosis and treatment/toxicity response; however, no consistent targets are yet identified. The function of antibodies in an anti‐tumour response is determined by its isotype and subclass; IgG4 is immune‐suppressive and robustly correlate with poor patient survival in melanoma. We conclude that the current B‐cell literature needs careful interpretation based on the methods used and that we need a consensus of markers to define B‐cells and associated lymphoid organs. Furthermore, future studies need to not only examine antibody targets, but also isotypes when considering functional roles.
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Affiliation(s)
- Chloe B Rodgers
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
| | - Colette J Mustard
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
| | - Ryan T McLean
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
| | - Sharon Hutchison
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
| | - Antonia L Pritchard
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
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Abstract
The tumor microenvironment (TME) is a heterogeneous, complex organization composed of tumor, stroma, and endothelial cells that is characterized by cross talk between tumor and innate and adaptive immune cells. Over the last decade, it has become increasingly clear that the immune cells in the TME play a critical role in controlling or promoting tumor growth. The function of T lymphocytes in this process has been well characterized. On the other hand, the function of B lymphocytes is less clear, although recent data from our group and others have strongly indicated a critical role for B cells in antitumor immunity. There are, however, a multitude of populations of B cells found within the TME, ranging from naive B cells all the way to terminally differentiated plasma cells and memory B cells. Here, we characterize the role of B cells in the TME in both animal models and patients, with an emphasis on dissecting how B cell heterogeneity contributes to the immune response to cancer.
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Affiliation(s)
- Stephanie M Downs-Canner
- Department of Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jeremy Meier
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA;
| | - Benjamin G Vincent
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; .,Bioinformatics and Computational Biology Program, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jonathan S Serody
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; .,Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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Shepherd JH, Ballman K, Polley MYC, Campbell JD, Fan C, Selitsky S, Fernandez-Martinez A, Parker JS, Hoadley KA, Hu Z, Li Y, Soloway MG, Spears PA, Singh B, Tolaney SM, Somlo G, Port ER, Ma C, Kuzma C, Mamounas E, Golshan M, Bellon JR, Collyar D, Hahn OM, Hudis CA, Winer EP, Partridge A, Hyslop T, Carey LA, Perou CM, Sikov WM. CALGB 40603 (Alliance): Long-Term Outcomes and Genomic Correlates of Response and Survival After Neoadjuvant Chemotherapy With or Without Carboplatin and Bevacizumab in Triple-Negative Breast Cancer. J Clin Oncol 2022; 40:1323-1334. [PMID: 35044810 PMCID: PMC9015203 DOI: 10.1200/jco.21.01506] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/10/2021] [Accepted: 12/13/2021] [Indexed: 12/14/2022] Open
Abstract
PURPOSE CALGB 40603 (NCT00861705), a 2 × 2 randomized phase II trial, demonstrated that adding carboplatin or bevacizumab to weekly paclitaxel (wP) followed by doxorubicin and cyclophosphamide significantly increased the pathologic complete response (pCR) rate in stage II-III triple-negative breast cancer. We now report long-term outcomes (LTOs) and correlative science end points. PATIENTS AND METHODS The Kaplan-Meier method was used to estimate LTOs in 443 patients who initiated study treatment. Log-rank tests and Cox proportional hazards models evaluated the impact of clinical characteristics, pathologic response, calculated residual cancer burden (RCB) in patients with residual disease (RD), treatment assignment, and dose delivery during wP on LTOs, including event-free survival (EFS). Genomic predictors of treatment response and outcomes were assessed on pretreatment tumor samples by mRNA sequencing. RESULTS Among baseline characteristics, only the clinical stage was associated with LTOs. At a median follow-up of 7.9 years, LTOs were not significantly improved with either carboplatin or bevacizumab, overall or in patients with basal-like subtype cancers by genomic analysis. Patients with pCR (n = 205, 46.3%) had significantly higher 5-year EFS (85.5% v 56.6%, log-rank P < .0001) and overall survival (87.9% v 63.4%, P < .0001) rates compared with patients with RD, even those with RCB class I. Among clinical and genomic features, evidence of immune activation, including tumor-infiltrating lymphocytes and low B-cell receptor evenness, was associated with pCR and improved EFS. CONCLUSION Despite higher pCR rates, neither carboplatin nor bevacizumab appeared to improve LTOs although the study was not powered to assess these secondary end points. pCR was associated with superior LTOs even when compared with minimal RD. Markers of immune activation in pretreatment tumor biopsies were independently associated with higher pCR rates and improved survival.
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Affiliation(s)
- Jonathan H. Shepherd
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Karla Ballman
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | - Mei-Yin C. Polley
- Department of Public Health Sciences, University of Chicago, Chicago, IL
| | - Jordan D. Campbell
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Zhiyuan Hu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yan Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew G. Soloway
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Patricia A. Spears
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - George Somlo
- City of Hope Comprehensive Cancer Center, Duarte, CA
| | | | - Cynthia Ma
- Washington University School of Medicine, St Louis, MO
| | - Charles Kuzma
- FirstHealth Sanford Hematology and Oncology, Sanford, NC
| | | | - Mehra Golshan
- Yale Cancer Center, Yale School of Medicine, New Haven, CT
| | | | | | | | | | | | | | - Terry Hyslop
- Department of Biostatistics & Bioinformatics, School of Medicine, Duke University, Durham, NC
| | - Lisa A. Carey
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - William M. Sikov
- Program in Women's Oncology, Women and Infants Hospital of Rhode Island and Warren Alpert Medical School of Brown University, Providence, RI
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Fridman WH, Meylan M, Petitprez F, Sun CM, Italiano A, Sautès-Fridman C. B cells and tertiary lymphoid structures as determinants of tumour immune contexture and clinical outcome. Nat Rev Clin Oncol 2022; 19:441-457. [PMID: 35365796 DOI: 10.1038/s41571-022-00619-z] [Citation(s) in RCA: 206] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2022] [Indexed: 02/08/2023]
Abstract
B cells are a major component of the tumour microenvironment, where they are predominantly associated with tertiary lymphoid structures (TLS). In germinal centres within mature TLS, B cell clones are selectively activated and amplified, and undergo antibody class switching and somatic hypermutation. Subsequently, these B cell clones differentiate into plasma cells that can produce IgG or IgA antibodies targeting tumour-associated antigens. In tumours without mature TLS, B cells are either scarce or differentiate into regulatory cells that produce immunosuppressive cytokines. Indeed, different tumours vary considerably in their TLS and B cell content. Notably, tumours with mature TLS, a high density of B cells and plasma cells, as well as the presence of antibodies to tumour-associated antigens are typically associated with favourable clinical outcomes and responses to immunotherapy compared with those lacking these characteristics. However, polyclonal B cell activation can also result in the formation of immune complexes that trigger the production of pro-inflammatory cytokines by macrophages and neutrophils. In complement-rich tumours, IgG antibodies can also activate the complement cascade, resulting in the production of anaphylatoxins that sustain tumour-promoting inflammation and angiogenesis. Herein, we review the phenotypic heterogeneity of intratumoural B cells and the importance of TLS in their generation as well as the potential of B cells and TLS as prognostic and predictive biomarkers. We also discuss novel therapeutic approaches that are being explored with the aim of increasing mature TLS formation, B cell differentiation and anti-tumour antibody production within tumours.
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Affiliation(s)
- Wolf H Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, Equipe inflammation, complément et cancer, Paris, France. .,Equipe labellisée Ligue contre le Cancer, Paris, France.
| | - Maxime Meylan
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, Equipe inflammation, complément et cancer, Paris, France.,Equipe labellisée Ligue contre le Cancer, Paris, France
| | - Florent Petitprez
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Cheng-Ming Sun
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, Equipe inflammation, complément et cancer, Paris, France.,Equipe labellisée Ligue contre le Cancer, Paris, France
| | - Antoine Italiano
- Faculty of Medicine, University of Bordeaux, Bordeaux, France.,Department of Medicine, Institute Bergonié, Bordeaux, France
| | - Catherine Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, Equipe inflammation, complément et cancer, Paris, France.,Equipe labellisée Ligue contre le Cancer, Paris, France
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Zhang H, Liu Y, Hu D, Liu S. Identification of Novel Molecular Therapeutic Targets and Their Potential Prognostic Biomarkers Based on Cytolytic Activity in Skin Cutaneous Melanoma. Front Oncol 2022; 12:844666. [PMID: 35345444 PMCID: PMC8957259 DOI: 10.3389/fonc.2022.844666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/09/2022] [Indexed: 12/13/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) attracts attention worldwide for its extremely high malignancy. A novel term cytolytic activity (CYT) has been introduced as a potential immunotherapy biomarker associated with counter-regulatory immune responses and enhanced prognosis in tumors. In this study, we extracted all datasets of SKCM patients, namely, RNA sequencing data and clinical information from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database, conducted differential expression analysis to yield 864 differentially expressed genes (DEGs) characteristic of CYT and used non-negative matrix factorization (NMF) method to classify molecular subtypes of SKCM patients. Among all genes, 14 hub genes closely related to prognosis for SKCM were finally screen out. Based on these genes, we constructed a 14-gene prognostic risk model and its robustness and strong predictive performance were further validated. Subsequently, the underlying mechanisms in tumor pathogenesis and prognosis have been defined from a number of perspectives, namely, tumor mutation burden (TMB), copy number variation (CNV), tumor microenvironment (TME), infiltrating immune cells, gene set enrichment analysis (GSEA) and immune checkpoint inhibitors (ICIs). Furthermore, combined with GTEx database and HPA database, the expression of genes in the model was verified at the transcriptional level and protein level, and the relative importance of genes in the model was described by random forest algorithm. In addition, the model was used to predict the difference in sensitivity of SKCM patients to chemotherapy and immunotherapy. Finally, a nomogram was constructed to better aid clinical diagnosis.
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Affiliation(s)
- Haoxue Zhang
- Department of Dermatovenerology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Yuyao Liu
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Delin Hu
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shengxiu Liu
- Department of Dermatovenerology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
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Dual Effect of Immune Cells within Tumour Microenvironment: Pro- and Anti-Tumour Effects and Their Triggers. Cancers (Basel) 2022; 14:cancers14071681. [PMID: 35406451 PMCID: PMC8996887 DOI: 10.3390/cancers14071681] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Our body is constantly exposed to pathogens or external threats, but with the immune response that our body can develop, we can fight off and defeat possible attacks or infections. Nevertheless, sometimes this threat comes from an internal factor. Situations such as the existence of a tumour also cause our immune system (IS) to be put on alert. Indeed, the link between immunology and cancer is evident these days, with IS being used as one of the important targets for treating cancer. Our IS is able to eliminate those abnormal or damaged cells found in our body, preventing the uncontrolled proliferation of tumour cells that can lead to cancer. However, in several cases, tumour cells can escape from the IS. It has been observed that immune cells, the extracellular matrix, blood vessels, fat cells and various molecules could support tumour growth and development. Thus, the developing tumour receives structural support, irrigation and energy, among other resources, making its survival and progression possible. All these components that accompany and help the tumour to survive and to grow are called the tumour microenvironment (TME). Given the importance of its presence in the tumour development process, this review will focus on one of the components of the TME: immune cells. Immune cells can support anti-tumour immune response protecting us against tumour cells; nevertheless, they can also behave as pro-tumoural cells, thus promoting tumour progression and survival. In this review, the anti-tumour and pro-tumour immunity of several immune cells will be discussed. In addition, the TME influence on this dual effect will be also analysed.
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Zou S, Zhang Y, Zhang L, Wang D, Xu S. Construction and validation of a prognostic risk model of angiogenesis factors in skin cutaneous melanoma. Aging (Albany NY) 2022; 14:1529-1548. [PMID: 35157610 PMCID: PMC8876895 DOI: 10.18632/aging.203895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022]
Abstract
Melanoma can secrete tumor angiogenesis factors, which is the essential factor for tumor growth and metastasis. However, there are few reports on the relationship between angiogenesis factors and prognosis risk in melanoma. This study aimed to develop a prognostic risk model of angiogenesis for melanoma. Forty-nine differentially expressed angiogenesis were identified from the TCGA database, which were mainly involved in PI3K/Akt pathway, focal adhesion, and MAPK signaling pathway. We then establish an eleven-gene signature. The model indicated a strong prognostic capability in both the discovery cohort and the validation cohort. Patients of smaller height (<170 cm) and lower weight (<80 kg) and those with advanced-stage and ulcerated melanoma had higher risk scores. The risk score was positively correlated with mutation load, homologous recombination defect, neoantigen load and chromosome instability. In addition, the high-risk group had a higher degree of immune cell infiltration, better response to immunotherapy and lower immune score. Therefore, these results indicate that the risk model is an effective method to predict the prognosis of melanoma.
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Affiliation(s)
- Songyun Zou
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Yonggang Zhang
- Department of Clinical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Limei Zhang
- Oncology Department, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Dengchuan Wang
- Office of Medical Ethics, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Shi Xu
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
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Shi Y, Li Z, Zhou Z, Liao S, Wu Z, Li J, Yin J, Wang M, Weng M. Identification and validation of an epithelial mesenchymal transition-related gene pairs signature for prediction of overall survival in patients with skin cutaneous melanoma. PeerJ 2022; 10:e12646. [PMID: 35116193 PMCID: PMC8785661 DOI: 10.7717/peerj.12646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND We aimed to construct a novel epithelial-mesenchymal transition (EMT)-related gene pairs (ERGPs) signature to predict overall survival (OS) in skin cutaneous melanoma (CM) patients. METHODS Expression data of the relevant genes, corresponding clinicopathological parameters, and follow-up data were obtained from The Cancer Genome Atlas database. Univariate Cox regression analysis was utilized to identify ERGPs significantly associated with OS, and LASSO analysis was used to identify the genes used for the construction of the ERGPs signature. The optimal cutoff value determined by the receiver operating characteristic curve was used to classify patients into high-risk and low-risk groups. Survival curves were generated using the Kaplan-Meier method, and differences between the two groups were estimated using the log-rank test. The independent external datasets GSE65904 and GSE19234 were used to verify the performance of the ERGPs signature using the area under the curve (AUC) values. In addition, we also integrated clinicopathological parameters and risk scores to develop a nomogram that can individually predict the prognosis of patients with CM. RESULTS A total of 104 ERGPs related to OS were obtained, of which 21 ERGPs were selected for the construction of the signature. All CM patients were stratified into high-and low-risk groups based on an optimal risk score cutoff value of 0.281. According to the Kaplan-Meier analysis, the mortality rate in the low-risk group was lower than that in the high-risk group in the TCGA cohort (P < 0.001), GSE65904 cohort (P = 0.006), and GSE19234 cohort (P = 0.002). Multivariate Cox regression analysis indicated that our ERGP signature was an independent risk factor for OS in CM patients in the three cohorts (for TCGA: HR, 2.560; 95% CI [1.907-3.436]; P < 0.001; for GSE65904: HR = 2.235, 95% CI [1.492-3.347], P < 0.001; for GSE19234: HR = 2.458, 95% CI [1.065-5.669], P = 0.035). The AUC value for predicting the 5-year survival rate of patients with CM of our developed model was higher than that of two previously established prognostic signatures. Both the calibration curve and the C-index (0.752, 95% CI [0.678-0.826]) indicated that the developed nomogram was highly accurate. Most importantly, the decision curve analysis results showed that the nomogram had a higher net benefit than that of the American Joint Committee on Cancer stage system. CONCLUSION Our study established an ERGPs signature that could be potentially used in a clinical setting as a genetic biomarker for risk stratification of CM patients. In addition, the ERGPs signature could also predict which CM patients will benefit from PD-1 and PD-L1 inhibitors.
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Affiliation(s)
- Yucang Shi
- Department of Plastic Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zhanpeng Li
- Graduate School of Guangdong Medical University, Zhanjiang, China
| | - Zhihong Zhou
- Graduate School of Guangdong Medical University, Zhanjiang, China
| | - Simu Liao
- Department of Plastic Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zhiyuan Wu
- Department of Plastic Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jie Li
- Graduate School of Guangdong Medical University, Zhanjiang, China
| | - Jiasheng Yin
- Graduate School of Guangdong Medical University, Zhanjiang, China
| | - Meng Wang
- Department of Plastic Surgery, Longhua District People’s Hospital, Shenzhen, China
| | - Meilan Weng
- Graduate School of Guangdong Medical University, Zhanjiang, China
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Yu K, Ravoor A, Malats N, Pineda S, Sirota M. A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires. Front Immunol 2022; 12:790119. [PMID: 35069569 PMCID: PMC8767103 DOI: 10.3389/fimmu.2021.790119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/06/2021] [Indexed: 12/22/2022] Open
Abstract
Tumor-infiltrating B cells can play an important role in anti-tumor responses but their presence is not well understood. In this study, we extracted the B cell receptor repertoires from 9522 tumor and adjacent non-tumor samples across 28 tumor types in the Cancer Genome Atlas project and performed diversity and network analysis. We identified differences in diversity and network statistics across tumor types and subtypes and observed a trend towards increased clonality in primary tumors compared to adjacent non-tumor tissues. We also found significant associations between the repertoire features and mutation load, tumor stage, and age. Our V-gene usage analysis identified similar V-gene usage patterns in colorectal and endometrial cancers. Lastly, we evaluated the prognostic value of the repertoire features and identified significant associations with survival in seven tumor types. This study warrants further research into better understanding the role of tumor-infiltrating B cells across a wide range of tumor types.
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Affiliation(s)
- Katharine Yu
- Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United States
- Department of Pediatrics, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Akshay Ravoor
- Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Silvia Pineda
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United States
- Department of Pediatrics, University of California, San Francisco (UCSF), San Francisco, CA, United States
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42
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Lue JK, Downs-Canner S, Chaudhuri J. The role of B cells in the development, progression, and treatment of lymphomas and solid tumors. Adv Immunol 2022; 154:71-117. [PMID: 36038195 DOI: 10.1016/bs.ai.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
B cells are integral components of the mammalian immune response as they have the ability to generate antibodies against an almost infinite array of antigens. Over the past several decades, significant scientific progress has been made in understanding that this enormous B cell diversity contributes to pathogen clearance. However, our understanding of the humoral response to solid tumors and to tumor-specific antigens is unclear. In this review, we first discuss how B cells interact with other cells in the tumor microenvironment and influence the development and progression of various solid tumors. The ability of B lymphocytes to generate antibodies against a diverse repertoire of antigens and subsequently tailor the humoral immune response to specific pathogens relies on their ability to undergo genomic alterations during their development and differentiation. We will discuss key transforming events that lead to the development of B cell lymphomas. Overall, this review provides a foundation for innovative therapeutic interventions for both lymphoma and solid tumor malignancies.
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Affiliation(s)
- Jennifer K Lue
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
| | - Stephanie Downs-Canner
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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Niu Z, Xu Y, Li Y, Chen Y, Han Y. Construction and validation of a novel pyroptosis-related signature to predict prognosis in patients with cutaneous melanoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:688-706. [PMID: 34903008 DOI: 10.3934/mbe.2022031] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Skin cutaneous melanoma (SKCM) is one of the most malignant skin cancers and remains a health concern worldwide. Pyroptosis is a newly recognized form of programmed cell death and plays a vital role in cancer progression. We aim to construct a prognostic model for SKCM patients based on pyroptosis-related genes (PRGs). SKCM patients from The Cancer Genome Atlas (TCGA) were divided into training and validation cohorts. We used GSE65904 downloaded from GEO database as an external validation cohort. We performed Cox regression and the least absolute shrinkage and selection operator (LASSO) regression to identify prognostic genes and built a risk score. Patients were divided into high- and low-risk groups based on the risk score. Differently expressed genes (DEGs), immune cell infiltration and immune-related pathways activation were compared between the two groups. We established a model containing 4 PRGs, i.e., GSDMA, GSDMC, AIM2 and NOD2. The overall survival (OS) time was significantly different between the 2 groups. The risk score was an independent predictor for prognosis in both the uni- and multi-variable Cox regressions. Gene ontology (GO) and Kyoto Encylopedia of Genes and Genomes (KEGG) analyses showed that DEGs were enriched in immune-related pathways. Most types of immune cells were highly expressed in the low risk group. All immune pathways were significantly up-regulated in the low-risk group. In addition, low-risk patients had a better response to immune checkpoint inhibitors. Our novel pyroptosis-related gene signature could predict the prognosis of SKCM patients and their response to immune checkpoint inhibitors.
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Affiliation(s)
- Zehao Niu
- Medical School of Chinese PLA, Beijing 100853, China
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yujian Xu
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yan Li
- Medical School of Chinese PLA, Beijing 100853, China
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Youbai Chen
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yan Han
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
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Zhou X, Li W, Yang J, Qi X, Chen Y, Yang H, Chu L. Tertiary lymphoid structure stratifies glioma into three distinct tumor subtypes. Aging (Albany NY) 2021; 13:26063-26094. [PMID: 34954691 PMCID: PMC8751592 DOI: 10.18632/aging.203798] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/11/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Tertiary lymphoid structure (TLS), also known as ectopic lymphoid organs, are found in cancer, chronic inflammation, and autoimmune diseases. However, the heterogeneity of TLS in gliomas is unclear. Therefore, it is necessary to identify TLS differences and define TLS subtypes. METHODS The TLS gene profile of 697 gliomas from The Cancer Genome Atlas (TCGA) was used for consensus clustering to identify robust clusters, and the reproducibility of the stratification method was assessed in Chinese Glioma Genome Atlas (CGGA) cohort1, CGGA_cohort2, and GSE16011. Analyses of clinical characteristics, immune infiltration, and potential biological functions were performed for each subtype. RESULTS Three resulting clusters (A, B, and C) were identified based on consensus clustering on the gene expression profile of TLS genes. There was a significant prognostic difference among the clusters, with a shorter survival for C than B and A. In comparison with the A and B subtypes, the C subtype was significantly enriched in primary immunodeficiency, intestinal immune network for lgG production, antigen processing and presentation, natural killer cell-mediated cytotoxicity, complement and coagulation cascades, cytokine-cytokine receptor interaction, leukocyte transendothelial migration, and some immune-related diseases. The levels of 23 immune cell types were higher in the C subtype than in the A and B subtypes. Finally, we developed and validated a riskscore based on TLS subtypes with better performance of prognosis prediction. CONCLUSIONS This study presents a new stratification method according to the TLS gene profile and highlights TLS heterogeneity in gliomas.
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Affiliation(s)
- Xingwang Zhou
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou Province, PR China
| | - Wenyan Li
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou Province, PR China
| | - Jie Yang
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou Province, PR China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang 550004, Guizhou Province, PR China
| | - Yimin Chen
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou Province, PR China
| | - Hua Yang
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou Province, PR China
| | - Liangzhao Chu
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou Province, PR China
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Roufas C, Georgakopoulos-Soares I, Zaravinos A. Distinct genomic features across cytolytic subgroups in skin melanoma. Cancer Immunol Immunother 2021; 70:3137-3154. [PMID: 33779796 PMCID: PMC8505325 DOI: 10.1007/s00262-021-02918-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Skin melanoma is a highly immunogenic cancer. The intratumoral immune cytolytic activity (CYT) reflects the ability of cytotoxic T and NK cells to eliminate cancer cells, and is associated with improved patient survival. Despite the enthusiastic clinical results seen in advanced-stage metastatic melanoma patients treated with immune checkpoint inhibitors, a subgroup of them will later relapse and develop acquired resistance. We questioned whether CYT associates with different genomic profiles and thus, patient outcome, in skin melanoma. METHODS We explored the TCGA-SKCM dataset and stratified patients to distinct subgroups of cytolytic activity. The tumor immune contexture, somatic mutations and recurrent copy number aberrations were calculated using quanTIseq, MutSigCV and GISTIC2. Chromothriptic events were explored using CTLPScanner and cancer neoepitopes were predicted with antigen garnish. Each tumor's immunophenoscore was calculated using Immunophenogram. Mutational signatures and kataegis were explored using SigProfiler and compared to the known single or doublet base substitution signatures from COSMIC. RESULTS Metastatic skin melanomas had significantly higher CYT levels compared to primary tumors. We assessed enrichment for immune-related gene sets within CYT-high tumors, whereas, CYT-low tumors were enriched for non-immune related gene sets. In addition, distinct mutational and neoantigen loads, primarily composed of C > T transitions, along with specific types of copy number aberrations, characterized each cytolytic subgroup. We found a broader pattern of chromothripsis across CYT-low tumors, where chromosomal regions harboring chromothriptic events, contained a higher number of cancer genes. SBS7a/b, SBS5 and SBS1 were the most prevalent mutational signatures across both cytolytic subgroups, but SBS1 differed significantly between them. SBS7a/b was mutually exclusive with SBS5 and SBS1 in both CYT subgroups. CYT-high patients had markedly higher immunophenoscore, suggesting that they should display a clinical benefit upon treatment with immune checkpoint inhibition therapy, compared to CYT-low patients. CONCLUSIONS Overall, our data highlight the existence of distinct genomic features across cytolytic subgroups in skin melanoma, which might affect the patients' relapse rate or their acquisition of resistance to immune checkpoint inhibition therapies.
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Affiliation(s)
- Constantinos Roufas
- Department of Life Sciences, School of Sciences, European University Cyprus, 1516 Nicosia, Cyprus
| | - Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 USA
- Institute for Human Genetics, University of California, San Francisco, CA 94143 USA
| | - Apostolos Zaravinos
- Department of Basic Medical Sciences, College of Medicine, Member of QU Health, Qatar University, 2713 Doha, Qatar
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Gavrielatou N, Vathiotis I, Economopoulou P, Psyrri A. The Role of B Cells in Head and Neck Cancer. Cancers (Basel) 2021; 13:cancers13215383. [PMID: 34771546 PMCID: PMC8582491 DOI: 10.3390/cancers13215383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023] Open
Abstract
Simple Summary Host immunity has established its role in deciding the course of cancer evolution. As cellular and molecular components in the tumor microenvironment peripherally appear to be at a constant interplay, favoring either tumor control or progression, it is vital to decrypt the immunity elements, which demonstrate the potential to be harnessed towards cancer elimination. Head and neck cancer has been characterized as densely immune infiltrated but at the same time a highly immunosuppressive malignancy due to a negative equilibrium between active and dysfunctional immune cell populations. B-cells constitute the cornerstone of humoral immunity; however, their role in cancer has been vastly overlooked in comparison to other immune subtypes and reports from multiple studies fail to show agreement on their prognostic impact. This review focuses on the role of B-cells on head and neck cancer with the aim to highlight their effect on anti-cancer immunity, as well as their possible impact on immunotherapy outcomes. Abstract Head and neck cancer comprises a heterogenous, highly immune infiltrated malignancy, defined by a predominantly immunosuppressive tumor microenvironment (TME). In recent years, PD-1/PD-L1 immune checkpoint inhibitors have become the standard of care treatment, either as monotherapy or in combination with chemotherapy agents, thus revolutionizing the therapeutic landscape of recurrent/metastatic disease. As a result, preclinical research is increasingly focusing on TME composition and pathophysiology, aiming to comprehensively characterize the specific elements and interactions affecting anti-tumor immunity, as well as to unveil novel predictive biomarkers of immunotherapy outcomes. While T lymphocytic populations have been vastly explored regarding their effect on cancer development, B-cells constitute a far less investigated, yet possibly equally important, aspect of cancer immunity. B-cell presence, either as single cells or as part of tertiary lymphoid structures within the TME, has been associated with several anti-tumor defense mechanisms, such as antigen presentation, antibody production and participation in antibody-dependent cellular cytotoxicity, and has demonstrated prognostic significance for multiple types of malignancies. However, immunoregulatory B-cell phenotypes have also been identified both peripherally and within malignant tissue, bearing inhibitory effects on numerous immune response processes. Consequently, B-cells and their subsets demonstrate the potential to become valuable cancer biomarkers and acquire a leading role in future therapeutic strategies.
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Affiliation(s)
- Niki Gavrielatou
- Department of Pathology, School of Medicine, Yale University, New Haven, CT 06510, USA; (N.G.); (I.V.)
| | - Ioannis Vathiotis
- Department of Pathology, School of Medicine, Yale University, New Haven, CT 06510, USA; (N.G.); (I.V.)
| | - Panagiota Economopoulou
- Section of Medical Oncology, Second Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, 12462 Athens, Greece;
| | - Amanda Psyrri
- Section of Medical Oncology, Second Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, 12462 Athens, Greece;
- Correspondence:
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Kutlay A, Aydin Son Y. Integrative Predictive Modeling of Metastasis in Melanoma Cancer Based on MicroRNA, mRNA, and DNA Methylation Data. Front Mol Biosci 2021; 8:637355. [PMID: 34631789 PMCID: PMC8495312 DOI: 10.3389/fmolb.2021.637355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/30/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction: Despite the significant progress in understanding cancer biology, the deduction of metastasis is still a challenge in the clinic. Transcriptional regulation is one of the critical mechanisms underlying cancer development. Even though mRNA, microRNA, and DNA methylation mechanisms have a crucial impact on the metastatic outcome, there are no comprehensive data mining models that combine all transcriptional regulation aspects for metastasis prediction. This study focused on identifying the regulatory impact of genetic biomarkers for monitoring metastatic molecular signatures of melanoma by investigating the consolidated effect of miRNA, mRNA, and DNA methylation. Method: We developed multiple machine learning models to distinguish the metastasis by integrating miRNA, mRNA, and DNA methylation markers. We used the TCGA melanoma dataset to differentiate between metastatic melanoma samples by assessing a set of predictive models. For this purpose, machine learning models using a support vector machine with different kernels, artificial neural networks, random forests, AdaBoost, and Naïve Bayes are compared. An iterative combination of differentially expressed miRNA, mRNA, and methylation signatures is used as a candidate marker to reveal each new biomarker category’s impact. In each iteration, the performances of the combined models are calculated. During all comparisons, the choice of the feature selection method and under and oversampling approaches are analyzed. Selected biomarkers of the highest performing models are further analyzed for the biological interpretation of functional enrichment. Results: In the initial model, miRNA biomarkers can identify metastatic melanoma with an 81% F-score. The addition of mRNA markers upon miRNA increased the F-score to 92%. In the final integrated model, the addition of the methylation data resulted in a similar F-score of 92% but produced a stable model with low variance across multiple trials. Conclusion: Our results support the role of miRNA regulation in metastatic melanoma as miRNA markers model metastasis outcomes with high accuracy. Moreover, the integrated evaluation of miRNA with mRNA and methylation biomarkers increases the model’s power. It populates selected biomarkers on the metastasis-associated pathways of melanoma, such as the “osteoclast”, “Rap1 signaling”, and “chemokine signaling” pathways. Source Code:https://github.com/aysegul-kt/MelonomaMetastasisPrediction/
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Affiliation(s)
- Ayşegül Kutlay
- Department of Health Informatics, Graduate School of Informatics, METU, Ankara, Turkey
| | - Yeşim Aydin Son
- Department of Health Informatics, Graduate School of Informatics, METU, Ankara, Turkey
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Fan Y, Liang X, Yu D. Low expression of endoplasmic reticulum stress-related gene SERP1 is associated with poor prognosis and immune infiltration in skin cutaneous melanoma. Aging (Albany NY) 2021; 13:23036-23071. [PMID: 34613934 PMCID: PMC8544316 DOI: 10.18632/aging.203594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023]
Abstract
Stress-associated endoplasmic reticulum protein 1 (SERP1) is a gene induced by endoplasmic reticulum (ER) stress and a major contributor to multiple tumor types. Skin cutaneous melanoma (SKCM) is a highly aggressive and fatal cancer with poor treatment outcomes after progression. In this study, we evaluated SERP1's role in tumorigenesis, prognosis, and immune infiltration in SKCM. Patients with SKCM had low SERP1 expression. We identified differentially expressed genes between high- and low-SERP1 expression groups and conducted functional, pathway, and gene enrichment analyses. Protein-protein (PPI) and gene-gene interaction (GGI) networks were constructed via STRING and GeneMANIA, respectively. SERP1 mutation information was obtained through cBioPortal; location in the skin was identified through the Human Protein Atlas. Kaplan-Meier analysis revealed an association between low SERP1 expression and overall survival (OS), disease-specific survival (DSS), progress-free interval (PFI) rates, and worse prognosis in patients with multiple clinicopathological features. Cox regression analysis and nomograms further presented SERP1 level as an independent prognostic factor for patients with SKCM. Furthermore, there were significant correlations between SERP1 expression and immune infiltrates; thus, low SERP1 expression is associated with immune cell infiltration and can be considered a poor prognostic biomarker in patients with SKCM. Stress-associated endoplasmic reticulum protein 1 (SERP1) is a gene induced by endoplasmic reticulum (ER) stress and a major contributor to multiple tumor types. Skin cutaneous melanoma (SKCM) is a highly aggressive and fatal cancer with poor treatment outcomes after progression. In this study, we evaluated SERP1's role in tumorigenesis, prognosis, and immune infiltration in SKCM. Patients with SKCM had low SERP1 expression. We identified differentially expressed genes between high- and low-SERP1 expression groups and conducted functional, pathway, and gene enrichment analyses. Protein-protein (PPI) and gene-gene interaction (GGI) networks were constructed via STRING and GeneMANIA, respectively. SERP1 mutation information was obtained through cBioPortal; location in the skin were identified through the Human Protein Atlas. Kaplan-Meier analysis revealed an association between low SERP1 expression and overall survival (OS), disease-specific survival (DSS), progress-free interval (PFI) rates, and worse prognosis in patients with multiple clinicopathological features. Cox regression analysis and nomograms further presented SERP1 level as an independent prognostic factor for patients with SKCM. Furthermore, there were significant correlations between SERP1 expression and immune infiltrates; thus, low SERP1 expression is associated with immune cell infiltration and can be considered a poor prognostic biomarker in patients with SKCM.
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Affiliation(s)
- Yuchao Fan
- Department of Anesthesiology, Sichuan Cancer Center, Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Xiao Liang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Deshui Yu
- Department of Anesthesiology, The Second People’s Hospital of Yibin, Yibin, Sichuan Province, China
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Fridman WH, Petitprez F, Meylan M, Chen TWW, Sun CM, Roumenina LT, Sautès-Fridman C. B cells and cancer: To B or not to B? J Exp Med 2021; 218:211614. [PMID: 33601413 PMCID: PMC7754675 DOI: 10.1084/jem.20200851] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/02/2020] [Accepted: 09/17/2020] [Indexed: 12/21/2022] Open
Abstract
Whereas T cells have been considered the major immune cells of the tumor microenvironment able to induce tumor regression and control cancer clinical outcome, a burst of recent publications pointed to the fact that B cells may also play a prominent role. Activated in germinal centers of tertiary lymphoid structures, B cells can directly present tumor-associated antigens to T cells or produce antibodies that increase antigen presentation to T cells or kill tumor cells, resulting in a beneficial clinical impact. Immune complexes can also increase inflammation, angiogenesis, and immunosuppression via macrophage and complement activation, resulting in deleterious impact.
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Affiliation(s)
- Wolf Herman Fridman
- Centre de Recherche des Cordeliers, Sorbonne Université, Institut national de la santé et de la recherche médicale, Université de Paris, Paris, France
| | - Florent Petitprez
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale contre le Cancer, Paris, France
| | - Maxime Meylan
- Centre de Recherche des Cordeliers, Sorbonne Université, Institut national de la santé et de la recherche médicale, Université de Paris, Paris, France
| | - Tom Wei-Wu Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Cheng-Ming Sun
- Centre de Recherche des Cordeliers, Sorbonne Université, Institut national de la santé et de la recherche médicale, Université de Paris, Paris, France
| | - Lubka T Roumenina
- Centre de Recherche des Cordeliers, Sorbonne Université, Institut national de la santé et de la recherche médicale, Université de Paris, Paris, France
| | - Catherine Sautès-Fridman
- Centre de Recherche des Cordeliers, Sorbonne Université, Institut national de la santé et de la recherche médicale, Université de Paris, Paris, France
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Kang W, Feng Z, Luo J, He Z, Liu J, Wu J, Rong P. Tertiary Lymphoid Structures in Cancer: The Double-Edged Sword Role in Antitumor Immunity and Potential Therapeutic Induction Strategies. Front Immunol 2021; 12:689270. [PMID: 34394083 PMCID: PMC8358404 DOI: 10.3389/fimmu.2021.689270] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/05/2021] [Indexed: 12/14/2022] Open
Abstract
The complex tumor microenvironment (TME) plays a vital role in cancer development and dramatically determines the efficacy of immunotherapy. Tertiary lymphoid structures (TLSs) within the TME are well recognized and consist of T cell-rich areas containing dendritic cells (DCs) and B cell-rich areas containing germinal centers (GCs). Accumulating research has indicated that there is a close association between tumor-associated TLSs and favorable clinical outcomes in most types of cancers, though a minority of studies have reported an association between TLSs and a poor prognosis. Overall, the double-edged sword role of TLSs in the TME and potential mechanisms need to be further investigated, which will provide novel therapeutic perspectives for antitumor immunoregulation. In this review, we focus on discussing the main functions of TLSs in the TME and recent advances in the therapeutic manipulation of TLSs through multiple strategies to enhance local antitumor immunity.
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Affiliation(s)
- Wendi Kang
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhichao Feng
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China.,Molecular Imaging Research Center, Central South University, Changsha, China
| | - Jianwei Luo
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhenhu He
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jun Liu
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jianzhen Wu
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China.,Molecular Imaging Research Center, Central South University, Changsha, China
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