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Ramisetti SV, Patra T, Munirathnam V, Sainath JV, Veeraiyan D, Namani A. NRF2 Signaling Pathway in Chemo/Radio/Immuno-Therapy Resistance of Lung Cancer: Looking Beyond the Tip of the Iceberg. Arch Bronconeumol 2024:S0300-2896(24)00267-9. [PMID: 39060123 DOI: 10.1016/j.arbres.2024.06.021] [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: 05/09/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
Lung cancer is one of the most common causes of cancer death in men and women worldwide. Various combinations of surgery, chemotherapy, radiation therapy and immunotherapy are currently used to treat lung cancer. However, the prognosis remains relatively poor due to the higher frequency of tumor mutational burden (TMB). Nuclear factor E2-related factor 2 (NFE2L2/NRF2) is often considered a primary regulator of the expression of antioxidant enzymes and detoxification proteins and is involved in cytoprotection. On the contrary, NRF2 is even known to induce metastasis and support tumor progression. Kelch-like ECH-associated protein 1 (KEAP1) plays an important role in negatively regulating NRF2 activity via CUL3-mediated ubiquitinylation and successive proteasomal degradation. Extensive research has shown that the genetic alterations of KEAP1/NFE2L2/CUL3 genes lead to increased expression of NRF2 and its target genes in lung cancer. Thus, these studies provide ample evidence for the dual role of NRF2 in lung cancer. In this review, we discussed the mechanistic insights into the role of NRF2 signaling in therapy resistance by focusing on cell lines, mouse models, and translational studies in lung cancer. Finally, we highlighted the potential therapeutic strategies targeting NRF2 inhibition, followed by the discussion of biomarkers related to NRF2 activity in lung cancer. Overall, our article exclusively discusses in detail the NRF2 signaling pathway in resistance to therapy, especially immunotherapy, and its therapeutic avenue in the treatment of lung cancer.
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Affiliation(s)
- Sri Vidya Ramisetti
- Department of Biotechnology, School of Science, GITAM (Deemed to be University), Visakhapatnam 530045, India
| | - Tapas Patra
- Department of Molecular Research, Sri Shankara Cancer Hospital and Research Centre, Sri Shankara National Centre for Cancer Prevention and Research, Sri Shankara Cancer Foundation, Bangalore 560004, India
| | - Vinayak Munirathnam
- Department of Medical Oncology, Sri Shankara Cancer Hospital and Research Centre, Bangalore 560004, India
| | - Jyothi Venkat Sainath
- Department of Head and Neck Oncology, Sri Shankara Cancer Hospital and Research Centre, Bangalore 560004, India
| | - Durgadevi Veeraiyan
- Department of Molecular Research, Sri Shankara Cancer Hospital and Research Centre, Sri Shankara National Centre for Cancer Prevention and Research, Sri Shankara Cancer Foundation, Bangalore 560004, India
| | - Akhileshwar Namani
- Department of Molecular Research, Sri Shankara Cancer Hospital and Research Centre, Sri Shankara National Centre for Cancer Prevention and Research, Sri Shankara Cancer Foundation, Bangalore 560004, India.
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Wang Z, Wang H, Liu M, Ning X, Chen Y, Tang H. Neutrophil in the suppressed immune microenvironment: Critical prognostic factor for lung adenocarcinoma patients with KEAP1 mutation. Front Genet 2024; 15:1382421. [PMID: 38962454 PMCID: PMC11220125 DOI: 10.3389/fgene.2024.1382421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/20/2024] [Indexed: 07/05/2024] Open
Abstract
Purpose It is still unclear whether KEAP1 mutation is detrimental to immunotherapy of lung adenocarcinoma (LUAD) patients, we try to analyse the exact changes in the TME in LUAD patients with KEAP1 mutations and to identify key factors influencing prognosis. Experimental design A total of 1,029 patients with lung squamous carcinoma (LUSC) or LUAD with data obtained from The Cancer Genome Atlas were included in this study. The TME and OS of patients with LUAD stratified by mutant versus wild-type KEAP1 status were comprehensively measured. Moreover, we classified LUAD patients with KEAP1 mutations into three subtypes, by unsupervised consensus clustering. We further analysed the TME, OS, commutated genes and metabolic pathways of different subgroups. A total of 40 LUAD patients underwent immunotherapy were collected and classified into mutant KEAP1 group and wild-type KEAP1 group. We also conducted immunohistochemical staining in KEAP1-MT groups. Result Suppressed TME was observed not only in LUAD patients but also in LUSC patients. LUAD patients with mutant KEAP1 underwent immunotherapy had worse PFS than wild-type KEAP1. Unsupervised consensus clustering analysis suggested that the three subtypes of patients exhibited different densities of neutrophil infiltration and had different OS results: cluster 2 patients had significantly higher levels of neutrophils had significantly worse prognoses than those of patients in clusters 1 and 3 and patients with wild-type KEAP1. Univariate and multivariate Cox analyses proved that a high density of neutrophils was significantly associated with worse OS and immunohistochemical staining proved that shorter PFS showed high density of neutrophils. Conclusion KEAP1 mutation significantly suppresses the tumour immune microenvironment in LUAD patients. LUAD patients with mutant KEAP1 underwent immunotherapy had worse PFS than with wild-type KEAP1. Neutrophils may play an important role in the prognosis of LUAD patients with KEAP1 mutations and may provide a promising therapeutic target.
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Affiliation(s)
- Zhongzhao Wang
- Department of Respiratory and Critical Care Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Haojue Wang
- School of Basic Medicine, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Mingjia Liu
- School of Basic Medicine, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Xinhang Ning
- School of Basic Medicine, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Yang Chen
- Department of Respiratory and Critical Care Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Hao Tang
- Department of Respiratory and Critical Care Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China
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3
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Lu Y, Zhao X, Yuan M, Zhao M, Liu K, Zhang M, Qiu X, Yu X, Liu X, Wei D, Xie J, Cheng Z. KYNU Expression Promotes Cisplatin Resistance in Esophageal Cancer. J Cancer 2024; 15:2475-2485. [PMID: 38577600 PMCID: PMC10988315 DOI: 10.7150/jca.93229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024] Open
Abstract
Background: Chemotherapy resistance is a barrier to effective cancer prognoses. Cisplatin (CDDP) resistance is a major challenge for esophageal cancer (EC) therapy. A deeper understanding of the fundamental mechanisms of cisplatin resistance and improved targeting strategies are required in clinical settings. This study was performed to identify and characterize a marker of cisplatin resistance in EC cells. Method: KYSE140 and Eca-109 cells were subjected to escalating concentrations of cisplatin, resulting in the development of cisplatin-resistant KYSE140/CDDP and Eca-109/CDDP cell lines, respectively. RNA Sequencing (RNA-seq) was utilized to screen for the genes exhibiting differential expression between cisplatin-resistant and parental cells. Reverse transcription quantitative PCR was conducted to assess gene expression, and western blotting was employed to analyze protein levels. A sphere-formation assay was performed to validate tumor cell stemness. Cell counting kit-8 (CCK-8) experiments were conducted to confirm the sensitivity of cells to cisplatin. We examined the relationship between target genes and the clinicopathological features of patients with EC. Furthermore, the expression of target genes in EC tissues was evaluated via western blotting and fluorescence probe in situ hybridization (FISH). Results: KYNU was upregulated in cisplatin-resistant EC cells (KYSE140/CDDP and Eca-109/CDDP cells) and in EC tissues compared to that in the respective parental cell lines (KYSE140 and Eca-109 cells) and non-carcinoma tissues. Downregulation of KYNU increased cell sensitivity to cisplatin and suppressed tumor stemness, whereas abnormal KYNU expression had the opposite effect. KYNU expression was correlated with the expression of tumor stemness-associated factors (SOX2, Nanog, and OCT4) and the tumor size. Conclusions: KYNU may promote drug resistance in EC by regulating cancer stemness, and could serve as a biomarker and therapeutic target for EC.
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Affiliation(s)
- Yu Lu
- Department of Clinical Research Center, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
- Department of pharmacy, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Xianyang Zhao
- Department of Clinical Research Center, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Mingliang Yuan
- Department of Gastroenterology, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Ming Zhao
- Department of pharmacy, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Kaisheng Liu
- Department of Clinical Research Center, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Miaomiao Zhang
- Department of Clinical Research Center, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Xiaoyan Qiu
- Department of Clinical Research Center, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Xuechun Yu
- Department of Gastroenterology, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Xinliang Liu
- Department of Endocrinology, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Dongping Wei
- Department of Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Jun Xie
- Department of Clinical Research Center, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
- Department of Inspection, Xuyi People's Hospital, Affiliated Xuyi Hospital of Yangzhou University Medical College, Jiangsu, China
| | - Zhongbin Cheng
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
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Dayalan Naidu S, Angelova PR, Knatko EV, Leonardi C, Novak M, de la Vega L, Ganley IG, Abramov AY, Dinkova-Kostova AT. Nrf2 depletion in the context of loss-of-function Keap1 leads to mitolysosome accumulation. Free Radic Biol Med 2023; 208:478-493. [PMID: 37714439 DOI: 10.1016/j.freeradbiomed.2023.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/17/2023]
Abstract
Transcription factor nuclear factor erythroid 2 p45-related factor 2 (Nrf2) is the principal determinant of the cellular redox homeostasis, contributing to mitochondrial function, integrity and bioenergetics. The main negative regulator of Nrf2 is Kelch-like ECH associated protein 1 (Keap1), a substrate adaptor for Cul3/Rbx1 ubiquitin ligase, which continuously targets Nrf2 for ubiquitination and proteasomal degradation. Loss-of-function mutations in Keap1 occur frequently in lung cancer, leading to constitutive Nrf2 activation. We used the human lung cancer cell line A549 and its CRISPR/Cas9-generated homozygous Nrf2-knockout (Nrf2-KO) counterpart to assess the role of Nrf2 on mitochondrial health. To confirm that the observed effects of Nrf2 deficiency are not due to clonal selection or long-term adaptation to the absence of Nrf2, we also depleted Nrf2 by siRNA (siNFE2L2), thus creating populations of Nrf2-knockdown (Nrf2-KD) A549 cells. Nrf2 deficiency decreased mitochondrial respiration, but increased the mitochondrial membrane potential, mass, DNA content, and the number of mitolysosomes. The proportion of ATG7 and ATG3 within their respective LC3B conjugates was increased in Nrf2-deficient cells with mutant Keap1, whereas the formation of new autophagosomes was not affected. Thus, in lung cancer cells with loss-of-function Keap1, Nrf2 facilitates mitolysosome degradation thereby ensuring timely clearance of damaged mitochondria.
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Affiliation(s)
- Sharadha Dayalan Naidu
- Jacqui Wood Cancer Centre, Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, UK
| | | | - Elena V Knatko
- Jacqui Wood Cancer Centre, Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Chiara Leonardi
- Jacqui Wood Cancer Centre, Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Miroslav Novak
- Jacqui Wood Cancer Centre, Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Laureano de la Vega
- Jacqui Wood Cancer Centre, Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Andrey Y Abramov
- UCL Queen Square Institute of Neurology, Queen Square, London, UK.
| | - Albena T Dinkova-Kostova
- Jacqui Wood Cancer Centre, Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, UK; Department of Pharmacology and Molecular Sciences and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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5
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León-Letelier RA, Dou R, Vykoukal J, Sater AHA, Ostrin E, Hanash S, Fahrmann JF. The kynurenine pathway presents multi-faceted metabolic vulnerabilities in cancer. Front Oncol 2023; 13:1256769. [PMID: 37876966 PMCID: PMC10591110 DOI: 10.3389/fonc.2023.1256769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The kynurenine pathway (KP) and associated catabolites play key roles in promoting tumor progression and modulating the host anti-tumor immune response. To date, considerable focus has been on the role of indoleamine 2,3-dioxygenase 1 (IDO1) and its catabolite, kynurenine (Kyn). However, increasing evidence has demonstrated that downstream KP enzymes and their associated metabolite products can also elicit tumor-microenvironment immune suppression. These advancements in our understanding of the tumor promotive role of the KP have led to the conception of novel therapeutic strategies to target the KP pathway for anti-cancer effects and reversal of immune escape. This review aims to 1) highlight the known biological functions of key enzymes in the KP, and 2) provide a comprehensive overview of existing and emerging therapies aimed at targeting discrete enzymes in the KP for anti-cancer treatment.
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Affiliation(s)
- Ricardo A. León-Letelier
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rongzhang Dou
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jody Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ali Hussein Abdel Sater
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Edwin Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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6
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Tanaka I, Koyama J, Itoigawa H, Hayai S, Morise M. Metabolic barriers in non-small cell lung cancer with LKB1 and/or KEAP1 mutations for immunotherapeutic strategies. Front Oncol 2023; 13:1249237. [PMID: 37675220 PMCID: PMC10477992 DOI: 10.3389/fonc.2023.1249237] [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: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023] Open
Abstract
Currently, immune checkpoint inhibitors (ICIs) are widely considered the standard initial treatment for advanced non-small cell lung cancer (NSCLC) when there are no targetable driver oncogenic alternations. NSCLC tumors that have two alterations in tumor suppressor genes, such as liver kinase B1 (LKB1) and/or Kelch-like ECH-associated protein 1 (KEAP1), have been found to exhibit reduced responsiveness to these therapeutic strategies, as revealed by multiomics analyses identifying immunosuppressed phenotypes. Recent advancements in various biological approaches have gradually unveiled the molecular mechanisms underlying intrinsic reprogrammed metabolism in tumor cells, which contribute to the evasion of immune responses by the tumor. Notably, metabolic alterations in glycolysis and glutaminolysis have a significant impact on tumor aggressiveness and the remodeling of the tumor microenvironment. Since glucose and glutamine are essential for the proliferation and activation of effector T cells, heightened consumption of these nutrients by tumor cells results in immunosuppression and resistance to ICI therapies. This review provides a comprehensive summary of the clinical efficacies of current therapeutic strategies against NSCLC harboring LKB1 and/or KEAP1 mutations, along with the metabolic alterations in glycolysis and glutaminolysis observed in these cancer cells. Furthermore, ongoing trials targeting these metabolic alterations are discussed as potential approaches to overcome the extremely poor prognosis associated with this type of cancer.
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Affiliation(s)
- Ichidai Tanaka
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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7
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Capoferri D, Chiodelli P, Corli M, Belleri M, Scalvini E, Mignani L, Guerra J, Grillo E, De Giorgis V, Manfredi M, Presta M. The Pro-Oncogenic Sphingolipid-Metabolizing Enzyme β-Galactosylceramidase Modulates the Proteomic Landscape in BRAF(V600E)-Mutated Human Melanoma Cells. Int J Mol Sci 2023; 24:10555. [PMID: 37445731 DOI: 10.3390/ijms241310555] [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] [Received: 05/18/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
β-Galactosylceramidase (GALC) is a lysosomal enzyme involved in sphingolipid metabolism by removing β-galactosyl moieties from β-galactosylceramide and β-galactosylsphingosine. Previous observations have shown that GALC may exert pro-oncogenic functions in melanoma and Galc silencing, leading to decreased oncogenic activity in murine B16 melanoma cells. The tumor-driving BRAF(V600E) mutation is present in approximately 50% of human melanomas and represents a major therapeutic target. However, such mutation is missing in melanoma B16 cells. Thus, to assess the impact of GALC in human melanoma in a more relevant BRAF-mutated background, we investigated the effect of GALC overexpression on the proteomic landscape of A2058 and A375 human melanoma cells harboring the BRAF(V600E) mutation. The results obtained by liquid chromatography-tandem mass spectrometry (LC-MS/MS) demonstrate that significant differences exist in the protein landscape expressed under identical cell culture conditions by A2058 and A375 human melanoma cells, both harboring the same BRAF(V600E)-activating mutation. GALC overexpression resulted in a stronger impact on the proteomic profile of A375 cells when compared to A2058 cells (261 upregulated and 184 downregulated proteins versus 36 and 14 proteins for the two cell types, respectively). Among them, 25 proteins appeared to be upregulated in both A2058-upGALC and A375-upGALC cells, whereas two proteins were significantly downregulated in both GALC-overexpressing cell types. These proteins appear to be involved in melanoma biology, tumor invasion and metastatic dissemination, tumor immune escape, mitochondrial antioxidant activity, endoplasmic reticulum stress responses, autophagy, and/or apoptosis. Notably, analysis of the expression of the corresponding genes in human skin cutaneous melanoma samples (TCGA, Firehose Legacy) using the cBioPortal for Cancer Genomics platform demonstrated a positive correlation between GALC expression and the expression levels of 14 out of the 27 genes investigated, thus supporting the proteomic findings. Overall, these data indicate for the first time that the expression of the lysosomal sphingolipid-metabolizing enzyme GALC may exert a pro-oncogenic impact on the proteomic landscape in BRAF-mutated human melanoma.
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Affiliation(s)
- Davide Capoferri
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Paola Chiodelli
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Marzia Corli
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Mirella Belleri
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Elisa Scalvini
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Luca Mignani
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Jessica Guerra
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Elisabetta Grillo
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Veronica De Giorgis
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Allergic and Autoimmune Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Allergic and Autoimmune Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Marco Presta
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Consorzio Interuniversitario Biotecnologie (CIB), Unit of Brescia, 25123 Brescia, Italy
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8
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Otegui N, Houry M, Arozarena I, Serrano D, Redin E, Exposito F, Leon S, Valencia K, Montuenga L, Calvo A. Cancer Cell-Intrinsic Alterations Associated with an Immunosuppressive Tumor Microenvironment and Resistance to Immunotherapy in Lung Cancer. Cancers (Basel) 2023; 15:3076. [PMID: 37370686 PMCID: PMC10295869 DOI: 10.3390/cancers15123076] [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] [Received: 05/01/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Despite the great clinical success of immunotherapy in lung cancer patients, only a small percentage of them (<40%) will benefit from this therapy alone or combined with other strategies. Cancer cell-intrinsic and cell-extrinsic mechanisms have been associated with a lack of response to immunotherapy. The present study is focused on cancer cell-intrinsic genetic, epigenetic, transcriptomic and metabolic alterations that reshape the tumor microenvironment (TME) and determine response or refractoriness to immune checkpoint inhibitors (ICIs). Mutations in KRAS, SKT11(LKB1), KEAP1 and TP53 and co-mutations of these genes are the main determinants of ICI response in non-small-cell lung cancer (NSCLC) patients. Recent insights into metabolic changes in cancer cells that impose restrictions on cytotoxic T cells and the efficacy of ICIs indicate that targeting such metabolic restrictions may favor therapeutic responses. Other emerging pathways for therapeutic interventions include epigenetic modulators and DNA damage repair (DDR) pathways, especially in small-cell lung cancer (SCLC). Therefore, the many potential pathways for enhancing the effect of ICIs suggest that, in a few years, we will have much more personalized medicine for lung cancer patients treated with immunotherapy. Such strategies could include vaccines and chimeric antigen receptor (CAR) cells.
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Affiliation(s)
- Nerea Otegui
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Maeva Houry
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Imanol Arozarena
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain;
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), 31008 Pamplona, Spain
| | - Diego Serrano
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Francisco Exposito
- Yale Cancer Center, New Haven, CT 06519, USA;
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sergio Leon
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
| | - Luis Montuenga
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
| | - Alfonso Calvo
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
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9
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Adinolfi S, Patinen T, Jawahar Deen A, Pitkänen S, Härkönen J, Kansanen E, Küblbeck J, Levonen AL. The KEAP1-NRF2 pathway: Targets for therapy and role in cancer. Redox Biol 2023; 63:102726. [PMID: 37146513 DOI: 10.1016/j.redox.2023.102726] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
The KEAP1-NRF2 pathway is the key regulator of cellular defense against both extrinsic and intrinsic oxidative and electrophilic stimuli. Since its discovery in the 1990s, its seminal role in various disease pathologies has become well appreciated, motivating research to elucidate the intricacies of NRF2 signaling and its downstream effects to identify novel targets for therapy. In this graphical review, we present an updated overview of the KEAP1-NRF2 signaling, focusing on the progress made within the past ten years. Specifically, we highlight the advances made in understanding the mechanism of activation of NRF2, resulting in novel discoveries in its therapeutic targeting. Furthermore, we will summarize new findings in the rapidly expanding field of NRF2 in cancer, with important implications for its diagnostics and treatment.
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Affiliation(s)
- Simone Adinolfi
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Tommi Patinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Ashik Jawahar Deen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Sini Pitkänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Jouni Härkönen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland; Department of Pathology, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland
| | - Emilia Kansanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland; Science Service Center, Kuopio University Hospital, Kuopio, Finland
| | - Jenni Küblbeck
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Anna-Liisa Levonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland.
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10
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Feng J, Read OJ, Dinkova-Kostova AT. Nrf2 in TIME: The Emerging Role of Nuclear Factor Erythroid 2-Related Factor 2 in the Tumor Immune Microenvironment. Mol Cells 2023; 46:142-152. [PMID: 36927604 PMCID: PMC10070167 DOI: 10.14348/molcells.2023.2183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/12/2022] [Indexed: 03/18/2023] Open
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) mediates the cellular antioxidant response, allowing adaptation and survival under conditions of oxidative, electrophilic and inflammatory stress, and has a role in metabolism, inflammation and immunity. Activation of Nrf2 provides broad and long-lasting cytoprotection, and is often hijacked by cancer cells, allowing their survival under unfavorable conditions. Moreover, Nrf2 activation in established human tumors is associated with resistance to chemo-, radio-, and immunotherapies. In addition to cancer cells, Nrf2 activation can also occur in tumor-associated macrophages (TAMs) and facilitate an anti-inflammatory, immunosuppressive tumor immune microenvironment (TIME). Several cancer cell-derived metabolites, such as itaconate, L-kynurenine, lactic acid and hyaluronic acid, play an important role in modulating the TIME and tumor-TAMs crosstalk, and have been shown to activate Nrf2. The effects of Nrf2 in TIME are context-depended, and involve multiple mechanisms, including suppression of pro-inflammatory cytokines, increased expression of programmed cell death ligand 1 (PD-L1), macrophage colony-stimulating factor (M-CSF) and kynureninase, accelerated catabolism of cytotoxic labile heme, and facilitating the metabolic adaptation of TAMs. This understanding presents both challenges and opportunities for strategic targeting of Nrf2 in cancer.
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Affiliation(s)
- Jialin Feng
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Oliver J. Read
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Albena T. Dinkova-Kostova
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
- Department of Pharmacology and Molecular Sciences and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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11
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Pérez de la Cruz G, Pérez de la Cruz V, Navarro Cossio J, Vázquez Cervantes GI, Salazar A, Orozco Morales M, Pineda B. Kynureninase Promotes Immunosuppression and Predicts Survival in Glioma Patients: In Silico Data Analyses of the Chinese Glioma Genome Atlas (CGGA) and of the Cancer Genome Atlas (TCGA). Pharmaceuticals (Basel) 2023; 16:ph16030369. [PMID: 36986469 PMCID: PMC10051585 DOI: 10.3390/ph16030369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Kynureninase (KYNU) is a kynurenine pathway (KP) enzyme that produces metabolites with immunomodulatory properties. In recent years, overactivation of KP has been associated with poor prognosis of several types of cancer, in particular by promoting the invasion, metastasis, and chemoresistance of cancer cells. However, the role of KYNU in gliomas remains to be explored. In this study, we used the available data from TCGA, CGGA and GTEx projects to analyze KYNU expression in gliomas and healthy tissue, as well as the potential contribution of KYNU in the tumor immune infiltrate. In addition, immune-related genes were screened with KYNU expression. KYNU expression correlated with the increased malignancy of astrocytic tumors. Survival analysis in primary astrocytomas showed that KYNU expression correlated with poor prognosis. Additionally, KYNU expression correlated positively with several genes related to an immunosuppressive microenvironment and with the characteristic immune tumor infiltrate. These findings indicate that KYNU could be a potential therapeutic target for modulating the tumor microenvironment and enhancing an effective antitumor immune response.
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Affiliation(s)
- Gonzalo Pérez de la Cruz
- Department of Mathematics, Faculty of Sciences, Universidad Nacional Autónoma de México, UNAM, Mexico City 04510, Mexico
| | - Verónica Pérez de la Cruz
- Neurobiochemistry and Behavior Laboratory, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Mexico City 14269, Mexico
| | - Javier Navarro Cossio
- Neuroimmunology Unit, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Mexico City 14269, Mexico
| | - Gustavo Ignacio Vázquez Cervantes
- Neurobiochemistry and Behavior Laboratory, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Mexico City 14269, Mexico
| | - Aleli Salazar
- Neuroimmunology Unit, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Mexico City 14269, Mexico
| | - Mario Orozco Morales
- Neuroimmunology Unit, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Mexico City 14269, Mexico
| | - Benjamin Pineda
- Neuroimmunology Unit, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Mexico City 14269, Mexico
- Correspondence: ; Tel.: +52-55-5606-4040
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12
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León-Letelier RA, Abdel Sater AH, Chen Y, Park S, Wu R, Irajizad E, Dennison JB, Katayama H, Vykoukal JV, Hanash S, Ostrin EJ, Fahrmann JF. Kynureninase Upregulation Is a Prominent Feature of NFR2-Activated Cancers and Is Associated with Tumor Immunosuppression and Poor Prognosis. Cancers (Basel) 2023; 15:cancers15030834. [PMID: 36765792 PMCID: PMC9913753 DOI: 10.3390/cancers15030834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
The nuclear factor erythroid 2-related factor 2 (NRF2) pathway is frequently activated in various cancer types. Aberrant activation of NRF2 in cancer is attributed to gain-of-function mutations in the NRF2-encoding gene NFE2L2 or a loss of function of its suppressor, Kelch-like ECH-associated protein 1 (KEAP1). NRF2 activation exerts pro-tumoral effects in part by altering cancer cell metabolism. Previously, we reported a novel mechanism of NRF2 tumoral immune suppression through the selective upregulation of the tryptophan-metabolizing enzyme kynureninase (KYNU) in lung adenocarcinoma. In the current study, we explored the relevance of NRF2-mediated KYNU upregulation across multiple cancer types. Specifically, using a gene expression dataset for 9801 tumors representing 32 cancer types from The Cancer Genome Atlas (TCGA), we demonstrated that elevated KYNU parallels increased gene-based signatures of NRF2-activation and that elevated tumoral KYNU mRNA expression is strongly associated with an immunosuppressive tumor microenvironment, marked by high expression of gene-based signatures of Tregs as well as the immune checkpoint blockade-related genes CD274 (PDL-1), PDCD1 (PD-1), and CTLA4, regardless of the cancer type. Cox proportional hazard models further revealed that increased tumoral KYNU gene expression was prognostic for poor overall survival in several cancer types, including thymoma, acute myeloid leukemia, low-grade glioma, kidney renal papillary cell carcinoma, stomach adenocarcinoma, and pancreatic ductal adenocarcinoma (PDAC). Using PDAC as a model system, we confirmed that siRNA-mediated knockdown of NRF2 reduced KYNU mRNA expression, whereas activation of NFE2L2 (the coding gene for NRF2) through either small-molecule agonists or siRNA-mediated knockdown of KEAP1 upregulated KYNU in PDAC cells. Metabolomic analyses of the conditioned medium from PDAC cell lines revealed elevated levels of KYNU-derived anthranilate, confirming that KYNU was enzymatically functional. Collectively, our study highlights the activation of the NRF2-KYNU axis as a multi-cancer phenomenon and supports the relevance of tumoral KYNU as a marker of tumor immunosuppression and as a prognostic marker for poor overall survival.
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Affiliation(s)
- Ricardo A. León-Letelier
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ali H. Abdel Sater
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yihui Chen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Soyoung Park
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ranran Wu
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ehsan Irajizad
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer B. Dennison
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jody V. Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin J. Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (E.J.O.); (J.F.F.)
| | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (E.J.O.); (J.F.F.)
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13
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Jiang Z, Wang X, Huang J, Li G, Li S. Pyroptosis-based risk score predicts prognosis and drug sensitivity in lung adenocarcinoma. Open Med (Wars) 2023; 18:20230663. [PMID: 36941988 PMCID: PMC10024350 DOI: 10.1515/med-2023-0663] [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: 09/27/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 03/14/2023] Open
Abstract
Pyroptosis is a recently identified form of programmed cell death; however, its role in lung adenocarcinoma (LUAD) remains unclear. Therefore, we set out to explore the prognostic potential of pyroptosis-related genes in LUAD. The pyroptosis-related risk score (PRRS) was developed by least absolute shrinkage and selection operator Cox regression and multivariate Cox regression. We found that PRRS was an independent prognostic factor for LUAD. LUAD patients in the high-PRRS group showed a significantly shorter overall survival (OS) and enriched in cell proliferation-related pathways. Then pathway enrichment analyses, mutation profile, tumor microenvironment, and drug sensitivity analysis were further studied in PRRS stratified LUAD patients. Tumor purity (TP) analyses revealed that L-PRRS LUAD patients had a lower TP, and patients in L-TP + L-PRRS subgroup had the most prolonged OS. Mutation analyses suggested that the L-PRRS LUAD patients had a lower tumor mutation burden (TMB), and patients in H-TMB + L-PRRS subgroup had the most prolonged OS. Drug sensitivity analyses showed that PRRS was significantly negatively correlated with the sensitivity of cisplatin, besarotene, etc., while it was significantly positively correlated with the sensitivity of kin001-135. Eventually, a nomogram was constructed based on PRRS and clinical characters of LUAD. Overall, the pyroptosis-related signature is helpful for prognostic prediction and in guiding treatment for LUAD patients.
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Affiliation(s)
- Zhengsong Jiang
- Department of Laboratory Medicine, The First Hospital of Jiujiang, Jiujiang, Jiangxi, China
| | - Xiang Wang
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | | | - Guoyin Li
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Shaanxi Normal University, Xi’an, 710061, China
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Shangfu Li
- Department of Oncology, Yueyang Second People’s Hospital, Yueyang, Hunan, 414022, China
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14
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Identification of Cuproptosis-Related Subtypes in Lung Cancer, Characterization of Tumor Microenvironment Infiltration, and Establishment of a Prognostic Model. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7406636. [PMID: 36588537 PMCID: PMC9797313 DOI: 10.1155/2022/7406636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/21/2022] [Accepted: 11/07/2022] [Indexed: 12/24/2022]
Abstract
Cuproptosis, a recently found kind of programmed cell death, has been linked to tumor development, prognosis, and therapeutic response. The roles of cuproptosis-related genes (CRG) in the tumor microenvironment (TME) are, nevertheless, unknown. We evaluated alterations in CRG and assessed the related expression patterns in 1445 lung cancer (LC) samples from three separate datasets, analyzing genetic, and transcriptional domains. We discovered two separate molecular subtypes of CRG and discovered that various subtypes of CRG were connected with patient clinical features and prognosis. Furthermore, we discovered connections between distinct CRG subtypes and TME cell infiltration features. The CRG_score was then developed and validated for predicting overall survival (OS). Following that, we investigated the relationship between CRG_score and the cancer stem cell (CSC) index and chemotherapeutic treatment sensitivity. In addition, we created a very accurate nomogram to increase the clinical usefulness of CRG_score. The potential roles of CRG in the tumor-immune-microenvironment, clinical characteristics, and prognosis in LC are demonstrated by our multiplex study. These findings expand our understanding of CRG in LC and may open up new options for assessing LC patients' prognosis and generating more effective immunotherapeutic treatments.
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15
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Bioinformatic Analysis of Kynurenine Pathway Enzymes and Their Relationship with Glioma Hallmarks. Metabolites 2022; 12:metabo12111054. [PMID: 36355137 PMCID: PMC9699055 DOI: 10.3390/metabo12111054] [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: 10/04/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Indoleamine dioxygenase (IDO), a rate limiting enzyme of the tryptophan catabolism through the kynurenine pathway (KP), has been related with a lower survival and a poor patient prognosis on several solid tumors, including gliomas. However, the use of IDO inhibitors as a therapeutic strategy for tumor treatment remains controversial in clinical trials and the role of other KP enzymes on tumor progression has remained poorly understood so far. Recently, different studies on different types of cancer have pointed out the importance of KP enzymes downstream IDO. Because of this, we conducted a bioinformatic analysis of the expression of different KP enzymes and their correlation with the gene expression of molecules related to the hallmarks of cancer in transcriptomic datasets from patients with different types of brain tumors including low grade gliomas, glioblastoma multiforme, neuroblastoma, and paraganglioma and pheochromocytoma. We found that KP enzymes that drive to NAD+ synthesis are overexpressed on different brain tumors compared to brain cortex data. Moreover, these enzymes presented positive correlations with the expression of genes related to immune response modulation, angiogenesis, Signal Transducer and Activator of Transcription (STAT) signaling, and Rho GTPase expression. These correlations suggest the relevance of the expression of the KP enzymes in brain tumor pathogenesis.
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16
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Irajizad E, Fahrmann JF, Long JP, Vykoukal J, Kobayashi M, Capello M, Yu CY, Cai Y, Hsiao FC, Patel N, Park S, Peng Q, Dennison JB, Kato T, Tai MC, Taguchi A, Kadara H, Wistuba II, Katayama H, Do KA, Hanash SM, Ostrin EJ. A Comprehensive Search of Non-Canonical Proteins in Non-Small Cell Lung Cancer and Their Impact on the Immune Response. Int J Mol Sci 2022; 23:ijms23168933. [PMID: 36012199 PMCID: PMC9409146 DOI: 10.3390/ijms23168933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022] Open
Abstract
There is substantial interest in mining neoantigens for cancer applications. Non-canonical proteins resulting from frameshift mutations have been identified as neoantigens in cancer. We investigated the landscape of non-canonical proteins in non-small cell lung cancer (NSCLC) and their induced immune response in the form of autoantibodies. A database of cryptoproteins was computationally constructed and comprised all alternate open reading frames (altORFs) and ORFs identified in pseudogenes, noncoding RNAs, and untranslated regions of mRNAs that did not align with known canonical proteins. Proteomic profiles of seventeen lung adenocarcinoma (LUAD) cell lines were searched to evaluate the occurrence of cryptoproteins. To assess the immunogenicity, immunoglobulin (Ig)-bound cryptoproteins in plasmas were profiled by mass spectrometry. The specimen set consisted of plasmas from 30 newly diagnosed NSCLC cases, pre-diagnostic plasmas from 51 NSCLC cases, and 102 control plasmas. An analysis of LUAD cell lines identified 420 cryptoproteins. Plasma Ig-bound analyses revealed 90 cryptoproteins uniquely found in cases and 14 cryptoproteins that had a fold-change >2 compared to controls. In pre-diagnostic samples, 17 Ig-bound cryptoproteins yielded an odds ratio ≥2. Eight Ig-bound cryptoproteins were elevated in both pre-diagnostic and newly diagnosed cases compared to controls. Cryptoproteins represent a class of neoantigens that induce an autoantibody response in NSCLC.
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Affiliation(s)
- Ehsan Irajizad
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - James P. Long
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Jody Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Makoto Kobayashi
- Department of Basic Pathology, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima 960-1247, Japan
| | - Michela Capello
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Chuan-Yih Yu
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Yining Cai
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Fu Chung Hsiao
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Nikul Patel
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Soyoung Park
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Qian Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Jennifer B. Dennison
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Taketo Kato
- Department of Thoracic Surgery, Nagoya University, Nagoya 464-8601, Japan
| | - Mei Chee Tai
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Ayumu Taguchi
- Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya 464-8601, Japan
- Division of Advanced Cancer Diagnostics, Nagoya University Graduate School of Medicine, Nagoya 464-8601, Japan
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Kim-Anh Do
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
- Correspondence: (K.-A.D.); (S.M.H.); (E.J.O.); Tel.: +1-713-745-5242 (S.M.H.)
| | - Samir M. Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
- Correspondence: (K.-A.D.); (S.M.H.); (E.J.O.); Tel.: +1-713-745-5242 (S.M.H.)
| | - Edwin J. Ostrin
- Departments of General Internal Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
- Correspondence: (K.-A.D.); (S.M.H.); (E.J.O.); Tel.: +1-713-745-5242 (S.M.H.)
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