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Lin M, Du T, Tang X, Liao Y, Cao L, Zhang Y, Zheng W, Zhou J. An estrogen response-related signature predicts response to immunotherapy in melanoma. Front Immunol 2023; 14:1109300. [PMID: 37251404 PMCID: PMC10213284 DOI: 10.3389/fimmu.2023.1109300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
Background Estrogen/estrogen receptor signaling influences the tumor microenvironment and affects the efficacy of immunotherapy in some tumors, including melanoma. This study aimed to construct an estrogen response-related gene signature for predicting response to immunotherapy in melanoma. Methods RNA sequencing data of 4 immunotherapy-treated melanoma datasets and TCGA melanoma was obtained from open access repository. Differential expression analysis and pathway analysis were performed between immunotherapy responders and non-responders. Using dataset GSE91061 as the training group, a multivariate logistic regression model was built from estrogen response-related differential expression genes to predict the response to immunotherapy. The other 3 datasets of immunotherapy-treated melanoma were used as the validation group. The correlation was also examined between the prediction score from the model and immune cell infiltration estimated by xCell in the immunotherapy-treated and TCGA melanoma cases. Results "Hallmark Estrogen Response Late" was significantly downregulated in immunotherapy responders. 11 estrogen response-related genes were significantly differentially expressed between immunotherapy responders and non-responders, and were included in the multivariate logistic regression model. The AUC was 0.888 in the training group and 0.654-0.720 in the validation group. A higher 11-gene signature score was significantly correlated to increased infiltration of CD8+ T cells (rho=0.32, p=0.02). TCGA melanoma with a high signature score showed a significantly higher proportion of immune-enriched/fibrotic and immune-enriched/non-fibrotic microenvironment subtypes (p<0.001)-subtypes with better response to immunotherapy-and significantly better progression-free interval (p=0.021). Conclusion In this study, we identified and verified an 11-gene signature that could predict response to immunotherapy in melanoma and was correlated with tumor-infiltrating lymphocytes. Our study suggests targeting estrogen-related pathways may serve as a combination strategy for immunotherapy in melanoma.
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Affiliation(s)
- Min Lin
- Department of Ultrasound, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Tian Du
- Department of Breast Surgery, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Xiaofeng Tang
- Department of Ultrasound, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Ying Liao
- Department of Ultrasound, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Lan Cao
- Department of Ultrasound, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Yafang Zhang
- Department of Ultrasound, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Wei Zheng
- Department of Ultrasound, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Jianhua Zhou
- Department of Ultrasound, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
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2
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Chikhaoui A, Jones M, Režen T, Ben Ahmed M, Naouali C, Komel R, Zghal M, Boubaker S, Abdelhak S, Yacoub-Youssef H. Inflammatory landscape in Xeroderma pigmentosum patients with cutaneous melanoma. Sci Rep 2022; 12:13854. [PMID: 35974070 PMCID: PMC9381529 DOI: 10.1038/s41598-022-17928-z] [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: 03/25/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a DNA repair disease that predisposes to early skin cancers as cutaneous melanoma. Melanoma microenvironment contains inflammatory mediators, which would be interesting biomarkers for the prognosis or for the identification of novel therapeutic targets. We used a PCR array to evaluate the transcriptional pattern of 84 inflammatory genes in melanoma tumors obtained from XP patients (XP-Mel) and in sporadic melanoma (SP-Mel) compared to healthy skin. Commonly expressed inflammatory genes were further explored via GTEx and GEPIA databases. The differentially expressed inflammatory genes in XP were compared to their expression in skin exposed to UVs, and evaluated on the basis of the overall survival outcomes of patients with melanoma. Monocyte subsets of patients with SP-Mel, XP and healthy donors were also assessed. PCR array data revealed that 34 inflammatory genes were under-expressed in XP-Mel compared to SP-Mel. Differentially expressed genes that were common in XP-Mel and SP-Mel were correlated with the transcriptomic datasets from GEPIA and GTEx and highlighted the implication of KLK1 and IL8 in the tumorigenesis. We showed also that in XP-Mel tumors, there was an overexpression of KLK6 and KLK10 genes, which seems to be associated with a bad survival rate. As for the innate immunity, we observed a decrease of intermediate monocytes in patients with SP-Mel and in XP. We highlight an alteration in the immune response in XP patients. We identified candidate biomarkers involved in the tumorigenesis, and in the survival of patients with melanoma. Intermediate monocyte's in patients at risk could be a prognostic biomarker for melanoma outcome.
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Affiliation(s)
- Asma Chikhaoui
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Meriem Jones
- Département de Dermatologie, Hôpital Charles Nicolle de Tunis, Tunis, Tunisia
| | - Tadeja Režen
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips and Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Melika Ben Ahmed
- Laboratoire de Transmission, Contrôle Et Immunobiologie de L'infection, LR16IPT02, Institut Pasteur de Tunis Université de Tunis El Manar I, 2092, Tunis, Tunisia
| | - Chokri Naouali
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Radovan Komel
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips and Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Mohamed Zghal
- Département de Dermatologie, Hôpital Charles Nicolle de Tunis, Tunis, Tunisia
| | - Samir Boubaker
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Houda Yacoub-Youssef
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia. .,Université Tunis El Manar, Tunis, Tunisia.
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3
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Srinivasan S, Kryza T, Batra J, Clements J. Remodelling of the tumour microenvironment by the kallikrein-related peptidases. Nat Rev Cancer 2022; 22:223-238. [PMID: 35102281 DOI: 10.1038/s41568-021-00436-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 02/07/2023]
Abstract
Kallikrein-related peptidases (KLKs) are critical regulators of the tumour microenvironment. KLKs are proteolytic enzymes regulating multiple functions of bioactive molecules including hormones and growth factors, membrane receptors and the extracellular matrix architecture involved in cancer progression and metastasis. Perturbations of the proteolytic cascade generated by these peptidases, and their downstream signalling actions, underlie tumour emergence or blockade of tumour growth. Recent studies have also revealed their role in tumour immune suppression and resistance to cancer therapy. Here, we present an overview of the complex biology of the KLK family and its context-dependent nature in cancer, and discuss the different therapeutic strategies available to potentially target these proteases.
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Affiliation(s)
- Srilakshmi Srinivasan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
- Mater Research Institute, The University of Queensland, Woolloongabba, Brisbane, Queensland, Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
- Centre for Genomics and Personalised Medicine, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia.
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4
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Ge D, Feijó A, Wen Z, Abramov AV, Lu L, Cheng J, Pan S, Ye S, Xia L, Jiang X, Vogler AP, Yang Q. Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats. Mol Biol Evol 2021; 38:1905-1923. [PMID: 33386846 PMCID: PMC8097305 DOI: 10.1093/molbev/msaa334] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia.,Joint Russian-Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Shengkai Pan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Sicheng Ye
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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5
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Petrova E, Hovnanian A. Advances in understanding of Netherton syndrome and therapeutic implications. Expert Opin Orphan Drugs 2020. [DOI: 10.1080/21678707.2020.1857724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Evgeniya Petrova
- Laboratory of genetic skin diseases, Université de Paris, Imagine Institute, INSERM UMR1163, Paris, France
| | - Alain Hovnanian
- Laboratory of genetic skin diseases, Université de Paris, Imagine Institute, INSERM UMR1163, Paris, France
- Departement of Genetics, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
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