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Dong W, Li J, Zhuang Z. Neutrophil-related Signature Characterizes Immune Landscape and Predicts Prognosis of Invasive Breast Cancer. Biochem Genet 2024:10.1007/s10528-024-10940-0. [PMID: 39417978 DOI: 10.1007/s10528-024-10940-0] [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: 09/28/2023] [Accepted: 10/06/2024] [Indexed: 10/19/2024]
Abstract
As a leading prevalent malignancy, breast cancer remains a significant worldwide health issue. Recent research indicates that neutrophils play a crucial role in breast cancer development. The prognostic significance of neutrophil-related genes (NRGs) or the immune landscape of the neutrophil-related signature in invasive breast cancer (IBC) is, nevertheless, unknown. To uncover innovative therapy alternatives, the significance of the neutrophil-related signatures in IBC was evaluated here. Briefly, a prediction model based on neutrophil-related core prognostic genes and The Cancer Genome Atlas data was created (TCGA). The model may assess IBC patients' prognosis. The IBC data from the Gene Expression Omnibus (GEO) confirmed the prognostic accuracy of the model. The overall survival (OS) of patients was worse in the group with a high NRGs score compared to the group with a low NRGs score. In addition, patients with low NRGs scores were considerably more sensitive to vinorelbine, cyclophosphamide, epirubicin, gemcitabine, paclitaxel, 5-fluorouracil, docetaxel, and cisplatin. Patients with low NRGs scores responded better to CTLA-4 and PD-1 treatments. Additionally, the immune microenvironment components were more abundant in patients with low NRGs scores. Moreover, qRT-PCR results confirmed that LEF1 had a higher expression level in tumor samples compared to normal samples, whereas NRG1 and STX11 exhibited lower expression levels in tumor samples than in normal samples. These results suggest that NRGs might be utilized as biomarkers to predict the prognosis of individuals with IBC, thereby paving the way for the creation of customized therapies for IBC.
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Affiliation(s)
- Wenge Dong
- Department of Breast Surgery, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jiejing Li
- Department of Breast Surgery, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Zhigang Zhuang
- Department of Breast Surgery, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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Zhong F, Zeng Y, Yan Y, Guo L, Guo Q, Liu W, Liu C. Comprehensive multi-omics analysis of the prognostic value and immune signature of NCF2 in pan-cancer and its relationship with acute myeloid leukemia. Int Immunopharmacol 2024; 143:113364. [PMID: 39393272 DOI: 10.1016/j.intimp.2024.113364] [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: 07/08/2024] [Revised: 09/28/2024] [Accepted: 10/05/2024] [Indexed: 10/13/2024]
Abstract
BACKGROUND The neutrophil cytoplasmic factor 2 (NCF2) gene encodes the p67phox protein, which has been implicated in the pathogenesis of several diseases. However, its specific role in tumorigenesis remains ambiguous. This study seeks to clarify the prognostic implications, immune profile, and therapeutic responses associated with NCF2 across different cancer types. METHODS We conducted a comprehensive analysis using multi-omics data to investigate tissue-specific and single-cell specific expression, pan-cancer expression patterns, epigenetic modifications, the immune microenvironment, and therapeutic responses. Our study specifically examined NCF2-associated immune signatures, molecular mechanisms, and potential therapeutic targets in acute myeloid leukemia (AML). Additionally, we performed in vitro experiments to assess how NCF2 knockdown influences cell proliferation, apoptosis, and cell cycle dynamics in AML cell lines U937 and KG-1. RESULTS NCF2 is dysregulated in more than two-thirds of cancer types, with elevated expression strongly correlating with poor prognosis in various cancers, including leukemia. Multifactorial Cox analysis has identified NCF2 as an independent prognostic factor for leukemia. Immunological studies have highlighted NCF2's impact on the tumor microenvironment, particularly affecting monocytes and macrophages. Furthermore, NCF2 expression closely correlates with responses to immunotherapy and chemotherapy. In vitro experiments demonstrate that NCF2 knockdown alters proliferation, apoptosis, and cell cycle dynamics of U937 cells and KG-1 cells. Notably, NCF2 is involved in regulating the differentiation of monocytes into macrophages. CONCLUSIONS These findings highlight NCF2 as a promising pan-cancer biomarker that significantly impacts tumor microenvironment, therapeutic response, and is critically associated with cell cycle regulation, apoptosis and macrophage transformation in AML.
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Affiliation(s)
- Fangfang Zhong
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan 646000, PR China.
| | - Yan Zeng
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan 646000, PR China
| | - Yuzhi Yan
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan 646000, PR China
| | - Ling Guo
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan 646000, PR China
| | - Qulian Guo
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan 646000, PR China
| | - Wenjun Liu
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan 646000, PR China.
| | - Chunyan Liu
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan 646000, PR China.
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3
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Li K, Tan SC, Yang Z, Li C. FAS gene expression, prognostic significance and molecular interactions in lung cancer. Front Oncol 2024; 14:1473515. [PMID: 39416461 PMCID: PMC11479862 DOI: 10.3389/fonc.2024.1473515] [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: 07/31/2024] [Accepted: 09/09/2024] [Indexed: 10/19/2024] Open
Abstract
Introduction FAS has been implicated in the development of various cancers, but its involvement in lung cancer has not been systematically characterized. In this study, we performed data mining in online tumor databases to investigate the expression, methylation, alterations, protein interactions, co-expression and prognostic significance of FAS in lung cancer. Method The expression, prognostic significance and molecular interactions of FAS in lung cancer was mined and analyzed using GENT2, GEPIA2, UALCAN, cBioPortal, STRING, GeneMANIA, UCSC Xena, Enrichr, and OSluca databases. FAS expression was subsequently investigated at the protein level in samples from 578 lung cancer patients to understand its protein-level expression. In vitro validation of FAS gene expression was performed on H1299, H1993, A549 and HBE cell lines. Result We found that the expression of FAS was significantly downregulated in both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) compared to normal lung tissue. In addition, we observed a higher level of FAS promoter methylation in LUSC tissue than in normal tissue. FAS alterations were rare (1.9%) in lung cancer samples, with deep deletions being more common than missense mutations, which occurred mainly in the TNFR-like cysteine-rich domain and the death domain. We also identified a list of proteins interacting with FAS and genes co-expressed with FAS, with LUAD having 11 co-expressed genes and LUSC having 90 co-expressed genes. Our results also showed that FAS expression has limited prognostic significance (HR=1.302, 95% CI=0.935-1.139, P=0.530). Protein level investigation revealed that FAS expression varied among individuals, with nTPM values ranging from 5.2 to 67.2. Conclusion This study provides valuable insights into the involvements and characteristics of FAS in lung cancer. Further studies are needed to investigate the clinical significance of FAS alterations in lung cancer and to explore the potential of targeting FAS for therapeutic intervention.
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Affiliation(s)
- Kaimin Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Zhihao Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Chenwei Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
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4
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Xu M, Hong JJ, Zhang X, Sun M, Liu X, Kang J, Stack H, Fang W, Lei H, Lacoste X, Okada R, Jung R, Nguyen R, Shern JF, Thiele CJ, Liu Z. Targeting SWI/SNF ATPases reduces neuroblastoma cell plasticity. EMBO J 2024; 43:4522-4541. [PMID: 39174852 PMCID: PMC11480351 DOI: 10.1038/s44318-024-00206-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 07/01/2024] [Accepted: 07/17/2024] [Indexed: 08/24/2024] Open
Abstract
Tumor cell heterogeneity defines therapy responsiveness in neuroblastoma (NB), a cancer derived from neural crest cells. NB consists of two primary subtypes: adrenergic and mesenchymal. Adrenergic traits predominate in NB tumors, while mesenchymal features becomes enriched post-chemotherapy or after relapse. The interconversion between these subtypes contributes to NB lineage plasticity, but the underlying mechanisms driving this phenotypic switching remain unclear. Here, we demonstrate that SWI/SNF chromatin remodeling complex ATPases are essential in establishing an mesenchymal gene-permissive chromatin state in adrenergic-type NB, facilitating lineage plasticity. Targeting SWI/SNF ATPases with SMARCA2/4 dual degraders effectively inhibits NB cell proliferation, invasion, and notably, cellular plasticity, thereby preventing chemotherapy resistance. Mechanistically, depletion of SWI/SNF ATPases compacts cis-regulatory elements, diminishes enhancer activity, and displaces core transcription factors (MYCN, HAND2, PHOX2B, and GATA3) from DNA, thereby suppressing transcriptional programs associated with plasticity. These findings underscore the pivotal role of SWI/SNF ATPases in driving intrinsic plasticity and therapy resistance in neuroblastoma, highlighting an epigenetic target for combinational treatments in this cancer.
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Affiliation(s)
- Man Xu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jason J Hong
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xiyuan Zhang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ming Sun
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xingyu Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jeeyoun Kang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hannah Stack
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wendy Fang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Haiyan Lei
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xavier Lacoste
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Reona Okada
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Raina Jung
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rosa Nguyen
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Zhihui Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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5
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Grelloni C, Garraffo R, Setti A, Rossi F, Peruzzi G, Cinquanta M, Di Rosa MC, Pierotti MA, Beltran M, Bozzoni I. BRCA1 levels and DNA-damage response are controlled by the competitive binding of circHIPK3 or FMRP to the BRCA1 mRNA. Mol Cell 2024:S1097-2765(24)00773-1. [PMID: 39389065 DOI: 10.1016/j.molcel.2024.09.016] [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: 11/07/2023] [Revised: 08/22/2024] [Accepted: 09/13/2024] [Indexed: 10/12/2024]
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules widely expressed in eukaryotes and deregulated in several pathologies, including cancer. Many studies point to their activity as microRNAs (miRNAs) and protein sponges; however, we propose a function based on circRNA-mRNA interaction to regulate mRNA fate. We show that the widely tumor-associated circHIPK3 directly interacts in vivo with the BRCA1 mRNA through the back-splicing region in human cancer cells. This interaction increases BRCA1 translation by competing for the binding of the fragile-X mental retardation 1 protein (FMRP) protein, which we identified as a BRCA1 translational repressor. CircHIPK3 depletion or disruption of the circRNA-mRNA interaction decreases BRCA1 protein levels and increases DNA damage, sensitizing several cancer cells to DNA-damage-inducing agents and rendering them susceptible to synthetic lethality. Additionally, blocking FMRP interaction with BRCA1 mRNA with locked nucleic acid (LNA) restores physiological protein levels in BRCA1 hemizygous breast cancer cells, underscoring the importance of this circRNA-mRNA interaction in regulating DNA-damage response.
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Affiliation(s)
- Chiara Grelloni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Raffaele Garraffo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesca Rossi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Mario Cinquanta
- Cogentech ltd Benefit C. Registered Office, 20133 Milan, Italy
| | | | | | - Manuel Beltran
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy.
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy; Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy.
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6
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Krishnan N, R L N, Warrier AV, Yadev I, Anandan J, Sundaram S, Rajan A, Kumari P, Ittycheria SS, V G M, Mohammed S, S P, Nair RS, Srinivas P. Direct DNA binding by BRCA1 on β-hCG promoter and its clinical implications. Heliyon 2024; 10:e37064. [PMID: 39286065 PMCID: PMC11403530 DOI: 10.1016/j.heliyon.2024.e37064] [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: 10/27/2023] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024] Open
Abstract
Objective The role of β-hCG in breast cancer is largely unknown, this study aims to analyse the gene expression and clinical implications of β-hCG and its isoforms in various cancers focussing particularly in Breast Invasive Carcinoma (BRCA). A mechanistic approach deciphering the transcriptional regulation of β-hCG by BRCA1 was also explored. Methods Data from various comprehensive gene expression platforms like UALCAN, GEPIA2, GENT2, TIMER2, LinkedOmics, and STRING were used to analyse the expression of β-hCG and its clinical implications; Immunohistochemistry and ELISA for β-hCG expression analysis from human breast cancer patients; Electrophoretic mobility shift assay (EMSA) to analyse the direct binding of BRCA1 on β-hCG; Immunoblotting and Luciferase assay to understand the regulation of β-hCG by p53 were performed. Results Results from UALCAN and GENT2 gene expression cancer database revealed that TNBC subtypes and high-grade metaplastic carcinoma shows elevated expression of β-hCG and infiltration of various immune cells were also identified in BRCA by TIMER2. It was observed that most of the isoforms of β-hCG (CGB) are upregulated in breast cancers irrespective of hormonal status when BRCA1 gene is mutated according to TIMER2. Similar results were observed with Lymphoid neoplasm diffuse large B-cell lymphoma (LGG) and DLBC (Brain lower grade glioma) when BRCA1 is mutated. These results correlate with our earlier reports indicating expression of β-hCG in BRCA1 defective condition. We have also identified direct binding of BRCA1 on β-hCG promoter. Conclusion All these findings demonstrate the importance of β-hCG as a potential target in BRCA1-deficient carcinomas.
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Affiliation(s)
- Neethu Krishnan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Neetha R L
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Arathy V Warrier
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Induprabha Yadev
- Government Medical College, Thiruvananthapuram, Kerala, India
- Government Medical College, Kollam, Kerala, India
| | - Jaimie Anandan
- Government Medical College, Thiruvananthapuram, Kerala, India
| | | | - Arathi Rajan
- Institute of Advanced Virology, Thiruvananthapuram, Kerala, India
| | - Prianka Kumari
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
- DBT-Regional Centre for Biotechnology (RCB), Faridabad, 121001, Haryana, India
| | - Shreya Sara Ittycheria
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Manasa V G
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Serbin Mohammed
- Government Medical College, Thiruvananthapuram, Kerala, India
- Government Medical College, Kollam, Kerala, India
| | - Preethamol S
- Government Medical College, Thiruvananthapuram, Kerala, India
| | - Rakesh Sathish Nair
- Department of Surgery, Division of Surgical Oncology, The University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Priya Srinivas
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
- DBT-Regional Centre for Biotechnology (RCB), Faridabad, 121001, Haryana, India
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7
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Arulkumar R, Jung HJ, Noh SG, Kim HW, Chung HY. 8-Prenylgenistein Isoflavone in Cheonggukjang Acts as a Novel AMPK Activator Attenuating Hepatic Steatosis by Enhancing the SIRT1-Mediated Pathway. Int J Mol Sci 2024; 25:9730. [PMID: 39273677 PMCID: PMC11395689 DOI: 10.3390/ijms25179730] [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: 06/29/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
8-Prenylgenistein (8PG), a genistein derivative, is present in fermented soybeans (Glycine max), including cheonggukjang (CGJ), and exhibits osteoprotective, osteogenic, and antiadipogenic properties. However, the hepatoprotective effects of 8PG and its underlying molecular mechanisms remain largely unexplored. Here, we identified the high binding affinity of 8PG with AMP-activated protein kinase (AMPK) and sirtuin 1 (SIRT1), which acts as a potent AMPK activator that counteracts hepatic steatosis. Notably, 8PG exhibited better pharmacokinetics with greater absorption and higher plasma binding than the positive controls for the target proteins. Moreover, 8PG exerted non-carcinogenic activity in rats and significantly increased AMPK phosphorylation. Compound C, an AMPK inhibitor, did not antagonize 8PG-activated AMPK in HepG2 cells. 8PG significantly attenuated palmitate-induced lipid accumulation and enhanced phosphorylated AMPK and its downstream target, acetyl-CoA carboxylase. Further, 8PG activated nuclear SIRT1 at the protein level, which promoted fatty acid oxidation in palmitate-treated HepG2 cells. Overall, 8PG acts as a potent AMPK activator, further attenuating hepatic steatosis via the SIRT1-mediated pathway and providing new avenues for dietary interventions to treat metabolic dysfunction-associated steatotic liver disease (MASLD).
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Affiliation(s)
- Radha Arulkumar
- Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan 46241, Republic of Korea
| | - Hee Jin Jung
- Department of Pharmacy, College of Pharmacy, Research Institute for Drug Development, Pusan National University, Busan 46241, Republic of Korea
| | - Sang Gyun Noh
- Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan 46241, Republic of Korea
| | - Hyun Woo Kim
- Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan 46241, Republic of Korea
- Department of Pharmacy, College of Pharmacy, Research Institute for Drug Development, Pusan National University, Busan 46241, Republic of Korea
| | - Hae Young Chung
- Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan 46241, Republic of Korea
- Department of Pharmacy, College of Pharmacy, Research Institute for Drug Development, Pusan National University, Busan 46241, Republic of Korea
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8
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Bose GS, Jindal S, Landage KG, Jindal A, Mahale MP, Kulkarni AP, Mittal S. SMAR1 and p53-regulated lncRNA RP11-431M3.1 enhances HIF1A translation via miR-138 in colorectal cancer cells under oxidative stress. FEBS J 2024. [PMID: 39240540 DOI: 10.1111/febs.17253] [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: 11/14/2023] [Revised: 02/16/2024] [Accepted: 08/14/2024] [Indexed: 09/07/2024]
Abstract
Eukaryotic cells respond to stress by altering coding and non-coding gene expression programs. Alongside many approaches and regulatory mechanisms, long non-coding RNAs (lncRNA) are finding a significant place in gene regulation, suggesting an involvement in various cellular processes and pathophysiology. LncRNAs are regulated by many transcription factors, including SMAR1 and p53, which are tumor suppressor genes. SMAR1 inhibits cancer cell metastasis and invasion and is also known to inhibit apoptosis during low-dose stress in coordination with p53. Data mining analysis suggested that these tumor suppressor genes might coregulate the lncRNA RP11-431M3.1 in colon cancer cells. Importantly, RP11-431M3.1 expression was found to be negatively correlated with patient survival rates in a number of cancers. Oxidative stress occurs when an imbalance in the body is caused by reactive oxygen species (ROS). This imbalance is known to be important in the development/pathogenesis of colon cancer. We are researching the role and control of this lncRNA in HCT116 cells under conditions of oxidative stress. We observed a dose-dependent differential expression of lncRNA upon H2O2 treatment and found that p53 and SMAR1 bind differentially to the promoter in response to the dose of stress inducer used. RP11-431M3.1 was observed to sponge miR-138 which has an important target gene, hypoxia-inducible factor (HIF1A). miR-138 was observed to bind differentially to RP11-431M3.1 and HIF1A RNA depending on the dose of oxidative stress. Furthermore, the knockdown of RP11-431M3.1 decreased the migration and proliferation of colon cancer cells. Our results suggest a previously undescribed regulatory mechanism through which RP11-431M3.1 is transcriptionally regulated by SMAR1 and p53, target HIF1A through miR-138, and highlight its potential as a therapeutic and diagnostic marker for cancer.
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Affiliation(s)
- Ganesh Suraj Bose
- Department of Biotechnology, Savitribai Phule Pune University, India
| | - Shruti Jindal
- Department of Biotechnology, Savitribai Phule Pune University, India
| | | | - Aarzoo Jindal
- Department of Biotechnology, Savitribai Phule Pune University, India
| | | | | | - Smriti Mittal
- Department of Biotechnology, Savitribai Phule Pune University, India
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9
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Grafinger OR, Hayward JJ, Meng Y, Geddes-McAlister J, Li Y, Mar S, Sheng M, Su B, Thillainadesan G, Lipsman N, Coppolino MG, Trant JF, Jerzak KJ, Leong HS. Cancer cell extravasation requires iplectin-mediated delivery of MT1-MMP at invadopodia. Br J Cancer 2024; 131:931-943. [PMID: 38969866 PMCID: PMC11369281 DOI: 10.1038/s41416-024-02782-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Invadopodia facilitate cancer cell extravasation, but the molecular mechanism whereby invadopodia-specific proteases such as MT1-MMP are called to invadopodia is unclear. METHODS Mass spectrometry and immunoprecipitation were used to identify interactors of MT1-MMP in metastatic breast cancer cells. After identification, siRNA and small molecule inhibitors were used to assess the effect these interactors had on cellular invasiveness. The chicken embryo chorioallantoic membrane (CAM) model was used to assess extravasation and invadopodia formation in vivo. RESULTS In metastatic breast cancer cells, MT1-MMP was found to associate with plectin, a cytolinker and scaffolding protein. Complex formation between plectin and MT1-MMP launches invadopodia formation, a subtype we termed iplectin (i = invadopodial). iPlectin delivers MT1-MMP to invadopodia and is indispensable for regulating cell surface levels of the enzyme. Genetic depletion of plectin with siRNA reduced invadopodia formation and cell invasion in vitro. In vivo extravasation efficiency assays and intravital imaging revealed iplectin to be a key contributor to invadopodia ultrastructure and essential for extravasation. Pharmacologic inhibition of plectin using the small molecule Plecstatin-1 (PST-1) abrogated MT1-MMP delivery to invadopodia and extravasation efficiency. CONCLUSIONS Anti-metastasis therapeutic approaches that target invadopodia are possible by disrupting interactions between MT1-MMP and iplectin. CLINICAL TRIAL REGISTRATION NUMBER NCT04608357.
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Affiliation(s)
- Olivia R Grafinger
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | - John J Hayward
- Department of Chemistry, University of Windsor, Windsor, ON, Canada
| | - Ying Meng
- Harquail Centre for Neuromodulation, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Division of Neurosurgery, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | | | - Yan Li
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Sara Mar
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Minzhi Sheng
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Boyang Su
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Gobi Thillainadesan
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Nir Lipsman
- Harquail Centre for Neuromodulation, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Division of Neurosurgery, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Marc G Coppolino
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - John F Trant
- Department of Chemistry, University of Windsor, Windsor, ON, Canada
| | - Katarzyna J Jerzak
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology, Sunnybrook Odette Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Hon S Leong
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada.
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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10
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Ferreira JC, Villanueva AJ, Fadl S, Al Adem K, Cinviz ZN, Nedyalkova L, Cardoso THS, Andrade ME, Saksena NK, Sensoy O, Rabeh WM. Residues in the fructose-binding pocket are required for ketohexokinase-A activity. J Biol Chem 2024; 300:107538. [PMID: 38971308 PMCID: PMC11332825 DOI: 10.1016/j.jbc.2024.107538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
Excessive fructose consumption is a primary contributor to the global surges in obesity, cancer, and metabolic syndrome. Fructolysis is not robustly regulated and is initiated by ketohexokinase (KHK). In this study, we determined the crystal structure of KHK-A, one of two human isozymes of KHK, in the apo-state at 1.85 Å resolution, and we investigated the roles of residues in the fructose-binding pocket by mutational analysis. Introducing alanine at D15, N42, or N45 inactivated KHK-A, whereas mutating R141 or K174 reduced activity and thermodynamic stability. Kinetic studies revealed that the R141A and K174A mutations reduced fructose affinity by 2- to 4-fold compared to WT KHK-A, without affecting ATP affinity. Molecular dynamics simulations provided mechanistic insights into the potential roles of the mutated residues in ligand coordination and the maintenance of an open state in one monomer and a closed state in the other. Protein-protein interactome analysis indicated distinct expression patterns and downregulation of partner proteins in different tumor tissues, warranting a reevaluation of KHK's role in cancer development and progression. The connections between different cancer genes and the KHK signaling pathway suggest that KHK is a potential target for preventing cancer metastasis. This study enhances our understanding of KHK-A's structure and function and offers valuable insights into potential targets for developing treatments for obesity, cancer, and metabolic syndrome.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kenana Al Adem
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Zeynep Nur Cinviz
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Lyudmila Nedyalkova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Mario Edson Andrade
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, USA
| | - Nitin K Saksena
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Ozge Sensoy
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey; Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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11
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Yang Y, Gao Y, Liu XS, Huang ZM, Zhang Y, Zhang YH, Liu ZY, Chen YX, Pei ZJ. FASTKD1 as a diagnostic and prognostic biomarker for STAD: Insights into m6A modification and immune infiltration. Exp Ther Med 2024; 28:305. [PMID: 38873045 PMCID: PMC11170332 DOI: 10.3892/etm.2024.12594] [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: 12/15/2023] [Accepted: 04/19/2024] [Indexed: 06/15/2024] Open
Abstract
Fas-activated serine/threonine kinase domain 1 (FASTKD1), a known modulator of mitochondrial-mediated cell death and survival processes, has garnered attention for its potential role in various biological contexts. However, its involvement in gastric cancer remains unclear. Thus, the present study aimed to investigate the relationship between FASTKD1 expression and key factors, including clinicopathological characteristics, immune infiltration and m6A modification in stomach adenocarcinoma (STAD). The expression of FASTKD1 was analyzed in STAD and normal adjacent tissues to assess its association with clinicopathological characteristics and survival prognosis. Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used in this study. Additionally, the findings were validated through immunohistochemical staining. Co-expression analysis of FASTKD1 was performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) enrichment analysis, Gene Set Enrichment Analysis (GSEA) and LinkedOmics database analysis. An in-depth analysis was conducted using databases, such as Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), GEO and TCGA to explore the potential correlation between FASTKD1 expression and immune infiltration and m6A modification in STAD. The results revealed that FASTKD1 was significantly upregulated across different tumor types, including STAD. Notably, FASTKD1 was able to distinguish between tumor and normal tissue samples with accuracy. Furthermore, the expression levels of FASTKD1 were significantly associated with clinical stage and survival. Through GO/KEGG enrichment analysis and GSEA, it was revealed that the genes co-expressed with FASTKD1 were active in a variety of biological processes. Within the TIMER, GEPIA and TCGA databases, a notable inverse correlation was observed between FASTKD1 expression and the abundance of immune cell subsets. Notably, significant correlations were established between FASTKD1 and m6A modification genes, YTHDF1 and LRPPRC, in both TCGA and GEO datasets. In conclusion, FASTKD1 may serve a significant role in m6A modification and immune infiltration processes, making it a potentially valuable diagnostic and prognostic biomarker in STAD.
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Affiliation(s)
- Yi Yang
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yan Gao
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Shiyan, Hubei 442000, P.R. China
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
- Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Xu-Sheng Liu
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Zhong-Min Huang
- Department of Medical Ultrasound, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yu Zhang
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yao-Hua Zhang
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Zi-Yue Liu
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yu-Xuan Chen
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Shiyan, Hubei 442000, P.R. China
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
- Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
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12
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Lv Y, Sun S, Zhang J, Wang C, Chen C, Zhang Q, Zhao J, Qi Y, Zhang W, Wang Y, Li M. Loss of RBM45 inhibits breast cancer progression by reducing the SUMOylation of IRF7 to promote IFNB1 transcription. Cancer Lett 2024; 596:216988. [PMID: 38797234 DOI: 10.1016/j.canlet.2024.216988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 05/11/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Type I interferons exhibit anti-proliferative and anti-cancer activities, but their detailed regulatory mechanisms in cancer have not been fully elucidated yet. RNA binding proteins are master orchestrators of gene regulation, which are closely related to tumor progression. Here we show that the upregulated RNA binding protein RBM45 correlates with poor prognosis in breast cancer. Depletion of RBM45 suppresses breast cancer progression both in cultured cells and xenograft mouse models. Mechanistically, RBM45 ablation inhibits breast cancer progression through regulating type I interferon signaling, particularly by elevating IFN-β production. Importantly, RBM45 recruits TRIM28 to IRF7 and stimulates its SUMOylation, thereby repressing IFNB1 transcription. Loss of RBM45 reduced the SUMOylation of IRF7 by reducing the interaction between TRIM28 and IRF7 to promote IFNB1 transcription, leading to the inhibition of breast cancer progression. Taken together, our finding uncovers a vital role of RBM45 in modulating type I interferon signaling and cancer aggressive progression, implicating RBM45 as a potential therapeutic target in breast cancer.
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Affiliation(s)
- Yuesheng Lv
- Department of Oncology of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116023, China
| | - Siwen Sun
- Department of Oncology & Sino-US Research Center for Cancer Translational Medicine, The Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Jinrui Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Chong Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Chaoqun Chen
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Qianyi Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.
| | - Yang Wang
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116023, China.
| | - Man Li
- Department of Oncology & Sino-US Research Center for Cancer Translational Medicine, The Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
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13
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Kashyap D, Koirala S, Saini V, Bagde PH, Samanta S, Kar P, Jha HC. Prediction of Rab5B inhibitors through integrative in silico techniques. Mol Divers 2024; 28:2547-2562. [PMID: 37505376 DOI: 10.1007/s11030-023-10693-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Rab5B is a small monomeric G protein that regulates early endocytosis and controls signaling pathways related to cell growth, survival, and apoptosis. Dysregulation of Rab5B protein expression has been linked to the development of several cancers such as leukemia, lymphoma, kidney, prostate, ovarian, breast cancer, etc. Our research shows the first attempt to identify inhibitors that can target Rab5B GTPase. In this study, we performed molecular docking using Autodock Vina 1.5.6 and identified eight molecules with docking scores ranging from -9.8 to -10.6 kcal/mol. Thereafter, we examined the pharmacological characteristics of these compounds, and selected compounds were further analyzed for their conformational dynamics and thermodynamic stability using molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA)-based free energy calculations. Notably, our findings revealed that strychnine had the highest binding affinity to Rab5B followed by anonaine, helioxanthin, and taiwanin E, with a ΔGbind value of -21.43, -17.11, -15.11, and -14.09 kcal/mol respectively. The binding free energy calculations showed that Van der Waals interactions are the primary contributor to the binding between Rab5B and the inhibitor. The interaction between the inhibitor and Rab5B was shown to be controlled by certain hot spot residues, including Phe45, Tyr48, Ala64, and Ala30. Overall, we believe that these findings could facilitate the exploration and development of potential hits against Rab5B, subject to optimization and further research.
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Affiliation(s)
- Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Suman Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Vaishali Saini
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Pranit Hemant Bagde
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India.
- Lab No. POD 1B 502, Computational Biophysics Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India.
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India.
- Lab No. POD 1B 602, Infection Bio-Engineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India.
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14
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Zhong F, Song L, li H, Liu J, Liu C, Guo Q, Liu W. Multi-omics evaluation of the prognostic value and immune signature of FCN1 in pan-cancer and its relationship with proliferation and apoptosis in acute myeloid leukemia. Front Genet 2024; 15:1425075. [PMID: 39139822 PMCID: PMC11320419 DOI: 10.3389/fgene.2024.1425075] [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: 04/29/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024] Open
Abstract
Background The FCN1 gene encodes the ficolin-1 protein, implicated in the pathogenesis of various diseases, though its precise role in tumorigenesis remains elusive. This study aims to elucidate the prognostic significance, immune signature, and treatment response associated with FCN1 across diverse cancer types. Methods Employing multi-omics data, we conducted a comprehensive assessment, encompassing tissue-specific and single-cell-specific expression disparities, pan-cancer expression patterns, epigenetic modifications affecting FCN1 expression, and the immune microenvironment. Our investigation primarily focused on the clinical prognostic attributes, immune profiles, potential molecular mechanisms, and candidate therapeutic agents concerning FCN1 and acute myeloid leukemia (AML). Additionally, in vitro experiments were performed to scrutinize the impact of FCN1 knockdown on cell proliferation, apoptosis, and cell cycle dynamics within the AML cell line U937 and NB4. Results FCN1 expression exhibits widespread dysregulation across various cancers. Through both univariate and multivariate Cox regression analyses, FCN1 has been identified as an independent prognostic indicator for AML. Immunological investigations elucidate FCN1's involvement in modulating inflammatory responses within the tumor microenvironment and its correlation with treatment efficacy. Remarkably, the deletion of FCN1 influences the proliferation, apoptosis, and cell cycle dynamics of U937 cells and NB4 cells. Conclusion These findings underscore FCN1 as a promising pan-cancer biomarker indicative of macrophage infiltration, intimately linked with the tumor microenvironment and treatment responsiveness, and pivotal for cellular mechanisms within AML cell lines.
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Affiliation(s)
- Fangfang Zhong
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Lijun Song
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Hao li
- Department of Pediatrics, Hejiang County People’s Hospital, Luzhou, Sichuan, China
| | - Jing Liu
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Chunyan Liu
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Qulian Guo
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Wenjun Liu
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
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15
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Lee YF, Phua CZJ, Yuan J, Zhang B, Lee MY, Kannan S, Chiu YHJ, Koh CWQ, Yap CK, Lim EKH, Chen J, Lim Y, Lee JJH, Skanderup AJ, Wang Z, Zhai W, Tan NS, Verma CS, Tay Y, Tan DSW, Tam WL. PARP4 interacts with hnRNPM to regulate splicing during lung cancer progression. Genome Med 2024; 16:91. [PMID: 39034402 PMCID: PMC11265163 DOI: 10.1186/s13073-024-01328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/02/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND The identification of cancer driver genes from sequencing data has been crucial in deepening our understanding of tumor biology and expanding targeted therapy options. However, apart from the most commonly altered genes, the mechanisms underlying the contribution of other mutations to cancer acquisition remain understudied. Leveraging on our whole-exome sequencing of the largest Asian lung adenocarcinoma (LUAD) cohort (n = 302), we now functionally assess the mechanistic role of a novel driver, PARP4. METHODS In vitro and in vivo tumorigenicity assays were used to study the functional effects of PARP4 loss and mutation in multiple lung cancer cell lines. Interactomics analysis by quantitative mass spectrometry was conducted to identify PARP4's interaction partners. Transcriptomic data from cell lines and patient tumors were used to investigate splicing alterations. RESULTS PARP4 depletion or mutation (I1039T) promotes the tumorigenicity of KRAS- or EGFR-driven lung cancer cells. Disruption of the vault complex, with which PARP4 is commonly associated, did not alter tumorigenicity, indicating that PARP4's tumor suppressive activity is mediated independently. The splicing regulator hnRNPM is a potentially novel PARP4 interaction partner, the loss of which likewise promotes tumor formation. hnRNPM loss results in splicing perturbations, with a propensity for dysregulated intronic splicing that was similarly observed in PARP4 knockdown cells and in LUAD cohort patients with PARP4 copy number loss. CONCLUSIONS PARP4 is a novel modulator of lung adenocarcinoma, where its tumor suppressive activity is mediated not through the vault complex-unlike conventionally thought, but in association with its novel interaction partner hnRNPM, thus suggesting a role for splicing dysregulation in LUAD tumorigenesis.
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Affiliation(s)
- Yi Fei Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Cheryl Zi Jin Phua
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Ju Yuan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - May Yin Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
| | - Yui Hei Jasper Chiu
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Casslynn Wei Qian Koh
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Choon Kong Yap
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Edwin Kok Hao Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Yuhua Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Jane Jia Hui Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Zhenxun Wang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- Centre for Vision Research, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Weiwei Zhai
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Chandra S Verma
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Daniel Shao Weng Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.
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16
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Keahi DL, Sanders MA, Paul MR, Webster ALH, Fang Y, Wiley TF, Shalaby S, Carroll TS, Chandrasekharappa SC, Sandoval-Garcia C, MacMillan ML, Wagner JE, Hatten ME, Smogorzewska A. G-quadruplexes are a source of vulnerability in BRCA2 deficient granule cell progenitors and medulloblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.20.604431. [PMID: 39091814 PMCID: PMC11291086 DOI: 10.1101/2024.07.20.604431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Biallelic pathogenic variants in the essential DNA repair gene BRCA2 causes Fanconi anemia, complementation group FA-D1. Patients in this group are highly prone to develop embryonal tumors, most commonly medulloblastoma arising from the cerebellar granule cell progenitors (GCPs). GCPs undergo high proliferation in the postnatal cerebellum under SHH activation, but the type of DNA lesions that require the function of the BRCA2 to prevent tumorigenesis remains unknown. To identify such lesions, we assessed both GCP neurodevelopment and tumor formation using a mouse model with deletion of exons three and four of Brca2 in the central nervous system, coupled with global Trp53 loss. Brca2 Δex3-4 ;Trp53 -/- animals developed SHH subgroup medulloblastomas with complete penetrance. Whole-genome sequencing of the tumors identified structural variants with breakpoints enriched in areas overlapping G-quadruplexes (G4s). Brca2-deficient GCPs exhibited decreased replication speed in the presence of the G4-stabilizer pyridostatin. Pif1 helicase, which resolves G4s during replication, was highly upregulated in tumors, and Pif1 knockout in primary MB tumor cells resulted in increased genome instability upon pyridostatin treatment. These data suggest that G4s may represent sites prone to replication stalling in highly proliferative GCPs and without BRCA2, G4s become a source of genome instability. Tumor cells upregulate G4-resolving helicases to facilitate rapid proliferation through G4s highlighting PIF1 helicase as a potential therapeutic target for treatment of BRCA2-deficient medulloblastomas.
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Affiliation(s)
- Danielle L. Keahi
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, USA
| | - Mathijs A. Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Matthew R. Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | | | - Yin Fang
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, USA
| | - Tom F. Wiley
- Comparative Bioscience Center, The Rockefeller University, New York, NY, USA
| | - Samer Shalaby
- Flow Cytometry Resource Center, The Rockefeller University, New York, NY, USA
| | - Thomas S. Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Settara C. Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - John E. Wagner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Mary E. Hatten
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, USA
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17
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Tovar-Parra D, Zammit-Mangion M. Comparative Analysis of the Effect of the BRAF Inhibitor Dabrafenib in 2D and 3D Cell Culture Models of Human Metastatic Melanoma Cells. In Vivo 2024; 38:1579-1593. [PMID: 38936891 PMCID: PMC11215570 DOI: 10.21873/invivo.13608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND/AIM Melanoma, a variant of skin cancer, presents the highest mortality rates among all skin cancers. Despite advancements in targeted therapies, immunotherapies, and tissue culture techniques, the absence of an effective early treatment model remains a challenge. This study investigated the impact of dabrafenib on both 2D and 3D cell culture models with distinct molecular profiles. MATERIALS AND METHODS We developed a high-throughput workflow enabling drug screening on spheroids. Our approach involved cultivating 2D and 3D cultures derived from normal melanocytes and metastatic melanoma cells, treating them with dabrafenib and conducting viability, aggregation, migration, cell cycle, and apoptosis assays. RESULTS Dabrafenib exerted multifaceted influences, particularly on migration at concentrations of 10 and 25 μM. It induced a decrease in cell viability, impeded cellular adhesion to the matrix, inhibited cellular aggregation and spheroid formation, arrested the cell cycle in the G1 phase, and induced apoptosis. CONCLUSION These results confirm the therapeutic potential of dabrafenib in treating melanoma with the BRAF V600E mutation and that 3D models are validated models to study the potential of new molecules for therapeutic purposes. Furthermore, our study underscores the relevance of 3D models in simulating physiological in vivo microenvironments, providing insights into varied treatment responses between normal and tumor cells.
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Affiliation(s)
- David Tovar-Parra
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta;
| | - Marion Zammit-Mangion
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta;
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
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18
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Kaleta K, Janik K, Rydz L, Wróbel M, Jurkowska H. Bridging the Gap in Cancer Research: Sulfur Metabolism of Leukemic Cells with a Focus on L-Cysteine Metabolism and Hydrogen Sulfide-Producing Enzymes. Biomolecules 2024; 14:746. [PMID: 39062461 PMCID: PMC11274876 DOI: 10.3390/biom14070746] [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: 05/17/2024] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
Leukemias are cancers of the blood-forming system, representing a significant challenge in medical science. The development of leukemia cells involves substantial disturbances within the cellular machinery, offering hope in the search for effective selective treatments that could improve the 5-year survival rate. Consequently, the pathophysiological processes within leukemia cells are the focus of critical research. Enzymes such as cystathionine beta-synthase and sulfurtransferases like thiosulfate sulfurtransferase, 3-mercaptopyruvate sulfurtransferase, and cystathionine gamma-lyase play a vital role in cellular sulfur metabolism. These enzymes are essential to maintaining cellular homeostasis, providing robust antioxidant defenses, and supporting cell division. Numerous studies have demonstrated that cancerous processes can alter the expression and activity of these enzymes, uncovering potential vulnerabilities or molecular targets for cancer therapy. Recent laboratory research has indicated that certain leukemia cell lines may exhibit significant changes in the expression patterns of these enzymes. Analysis of the scientific literature and online datasets has confirmed variations in sulfur enzyme function in specific leukemic cell lines compared to normal leukocytes. This comprehensive review collects and analyzes available information on sulfur enzymes in normal and leukemic cell lines, providing valuable insights and identifying new research pathways in this field.
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Affiliation(s)
- Konrad Kaleta
- Students’ Scientific Group of Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, 7 Kopernika St., 31-034 Krakow, Poland;
| | - Klaudia Janik
- Chair of Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, 7 Kopernika St., 31-034 Krakow, Poland; (K.J.); (L.R.); (M.W.)
| | - Leszek Rydz
- Chair of Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, 7 Kopernika St., 31-034 Krakow, Poland; (K.J.); (L.R.); (M.W.)
| | - Maria Wróbel
- Chair of Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, 7 Kopernika St., 31-034 Krakow, Poland; (K.J.); (L.R.); (M.W.)
| | - Halina Jurkowska
- Chair of Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, 7 Kopernika St., 31-034 Krakow, Poland; (K.J.); (L.R.); (M.W.)
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19
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Shenoy US, Basavarajappa DS, Kabekkodu SP, Radhakrishnan R. Pan-cancer exploration of oncogenic and clinical impacts revealed that HOXA9 is a diagnostic indicator of tumorigenesis. Clin Exp Med 2024; 24:134. [PMID: 38904676 PMCID: PMC11192824 DOI: 10.1007/s10238-024-01389-x] [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: 03/01/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
Abstract
Homeodomain transcription factor A9 (HOXA9) is a member of the HOX cluster family of transcription factors that are crucially involved in embryo implantation, morphogenesis, body axis development, and endothelial cell differentiation. Despite numerous reports on its aberrant expression in a few malignancies, the molecular and functional complexity of HOXA9 across cancers remains obscure. We aimed to analyze the dynamic role of HOXA9 across cancers by identifying, analyzing, and understanding its multiple modes of regulation and functional implications and identifying possible therapeutic avenues. We conducted a comprehensive analysis to determine the role of HOXA9 across cancers. This approach involved the integration of large-scale datasets from public repositories such as the Genomic Data Commons, specifically the Cancer Genome Atlas (GDC-TCGA), across 33 different cancer types. The multiple modes of HOXA9 regulation by genetic and epigenetic factors were determined using online tools, which comprised experimentally validated observations. Furthermore, downstream pathways were identified by predicting the targets of HOXA9 and by performing functional enrichment analysis. We also assessed the clinical significance of HOXA9 in terms of prognosis and stage stratification. This study evaluated the correlation between HOXA9 and tumor-infiltrating molecules and discussed its association with therapeutically approved antineoplastic drugs. HOXA9 was significantly upregulated in 9 tumors and downregulated in 2 cancers. The deregulation of HOXA9 is primarily attributed to epigenetic factors, including promoter DNA methylation and noncoding RNAs (ncRNAs). The HOXA9 transcription factor interacts with PBX/MEIS cofactors and regulates multiple genes involved in cancer-associated EMT, autophagy, the cell cycle, metabolic pathways, Wnt signaling, TGF-β signaling, the AMPK pathway, PI3K/AKT signaling, and NF-κB signaling, thereby establishing control over downstream mechanisms. Differential expression in various clinical stages across cancers was shown to have prognostic significance and to be correlated with tumor-infiltrating immune molecules. The assessment of the correlation of HOXA9 expression with approved antineoplastic drugs revealed that targeting HOXA9 could be the most reliable strategy for preventing cancer progression. HOXA9 is upregulated in the majority of malignancies and drives cancer progression by regulating multiple signaling mechanisms. Hence, HOXA9 could be a reliable diagnostic indicator and a potential therapeutic candidate for solid cancer types.
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Affiliation(s)
- U Sangeetha Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Dhanraj Salur Basavarajappa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
- Academic Unit of Oral and Maxillofacial Medicine and Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield,, S10 2TA, UK.
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20
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Hayes V, Gong T, Jiang J, Bornman R, Gheybi K, Stricker P, Weischenfeldt J, Mutambirwa S. Rare pathogenic structural variants show potential to enhance prostate cancer germline testing for African men. RESEARCH SQUARE 2024:rs.3.rs-4531885. [PMID: 38947031 PMCID: PMC11213160 DOI: 10.21203/rs.3.rs-4531885/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Prostate cancer (PCa) is highly heritable, with men of African ancestry at greatest risk and associated lethality. Lack of representation in genomic data means germline testing guidelines exclude for African men. Established that structural variations (SVs) are major contributors to human disease and prostate tumourigenesis, their role is under-appreciated in familial and therapeutic testing. Utilising a clinico-methodologically matched African (n = 113) versus European (n = 57) deep-sequenced PCa resource, we interrogated 42,966 high-quality germline SVs using a best-fit pathogenicity prediction workflow. We identified 15 potentially pathogenic SVs representing 12.4% African and 7.0% European patients, of which 72% and 86% met germline testing standard-of-care recommendations, respectively. Notable African-specific loss-of-function gene candidates include DNA damage repair MLH1 and BARD1 and tumour suppressors FOXP1, WASF1 and RB1. Representing only a fraction of the vast African diaspora, this study raises considerations with respect to the contribution of kilo-to-mega-base rare variants to PCa pathogenicity and African associated disparity.
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Affiliation(s)
| | | | - Jue Jiang
- Garvan Institute of Medical Research
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21
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Manjunath M, Ravindran F, Sharma S, Siddiqua H, Raghavan SC, Choudhary B. Disarib, a Specific BCL2 Inhibitor, Induces Apoptosis in Triple-Negative Breast Cancer Cells and Impedes Tumour Progression in Xenografts by Altering Mitochondria-Associated Processes. Int J Mol Sci 2024; 25:6485. [PMID: 38928195 PMCID: PMC11203414 DOI: 10.3390/ijms25126485] [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: 04/03/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Targeted cancer therapy aims to disrupt the functions of proteins that regulate cancer progression, mainly by using small molecule inhibitors (SMIs). SMIs exert their effect by modulating signalling pathways, organelle integrity, chromatin components, and several biosynthetic processes essential for cell division and survival. Antiapoptotic protein BCL2 is highly upregulated in many cancers compared with normal cells, making it an ideal target for cancer therapy. Around 75% of primary breast cancers overexpress BCL2, providing an opportunity to explore BCL2 inhibitors as a therapeutic option. Disarib is an SMI that has been developed as a selective BCL2 inhibitor. Disarib works by disrupting BCL2-BAK interaction and activating intrinsic apoptotic pathways in leukemic cells while sparing normal cells. We investigated the effects of Disarib, a BCL2 specific inhibitor, on breast cancer cells and xenografts. Cytotoxicity and fluorometric assays revealed that Disarib induced cell death by increasing reactive oxygen species and activating intrinsic apoptotic pathways in Triple-Negative Breast Cancer cells (MDA-MB-231 and MDA-MB-468). Disarib also affected the colony-forming properties of these cells. MDA-MB-231- and MDA-MB-468-derived xenografts showed a significant reduction in tumours upon Disarib treatment. Through the transcriptomics approach, we also explored the influence of BCL2 inhibitors on energy metabolism, mitochondrial dynamics, and epithelial-to-mesenchymal transition (EMT). Mitochondrial dynamics and glucose metabolism mainly regulate energy metabolism. The change in energetics regulates tumour growth through epithelial-mesenchymal transition, and angiogenesis. RNA sequencing (RNAseq) analysis revealed that BCL2 inhibitors ABT-199 and Disarib maintain Oxphos levels in MDA-MB-231. However, key glycolytic genes were significantly downregulated. Mitochondrial fission genes were seen to be downregulated both in RNAseq data and semi quantitative real time polymerase chain reaction (qRTPCR) in Disarib-treated TNBC cells and xenografts. Lastly, Disarib inhibited wound healing and epithelial-to-mesenchymal transition. This study showed that Disarib disrupts mitochondrial function, activates the intrinsic apoptotic pathway in breast cancer, and inhibits epithelial-to-mesenchymal transition both in vitro and in vivo. These findings highlight Disarib's potential as a multifaceted therapeutic strategy for patients with Triple-Negative Breast Cancer.
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Affiliation(s)
- Meghana Manjunath
- Department of Biotechnology and Applied Bioinformatics, Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bengaluru 560100, India
| | - Febina Ravindran
- Department of Biotechnology and Applied Bioinformatics, Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bengaluru 560100, India
| | - Shivangi Sharma
- Department of Biotechnology and Applied Bioinformatics, Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bengaluru 560100, India
- Indian Institute of Science, Bengaluru 560012, India; (H.S.); (S.C.R.)
| | - Humaira Siddiqua
- Indian Institute of Science, Bengaluru 560012, India; (H.S.); (S.C.R.)
| | | | - Bibha Choudhary
- Department of Biotechnology and Applied Bioinformatics, Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bengaluru 560100, India
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22
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Bachus S, Akkerman N, Fulham L, Graves D, Helwer R, Rempel J, Pelka P. ARGLU1 enhances promoter-proximal pausing of RNA polymerase II and stimulates DNA damage repair. Nucleic Acids Res 2024; 52:5658-5675. [PMID: 38520408 PMCID: PMC11162773 DOI: 10.1093/nar/gkae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
Arginine and glutamate rich 1 (ARGLU1) is a poorly understood cellular protein with functions in RNA splicing and transcription. Computational prediction suggests that ARGLU1 contains intrinsically disordered regions and lacks any known structural or functional domains. We used adenovirus Early protein 1A (E1A) to probe for critical regulators of important cellular pathways and identified ARGLU1 as a significant player in transcription and the DNA damage response pathway. Transcriptional effects induced by ARGLU1 occur via enhancement of promoter-proximal RNA polymerase II pausing, likely by inhibiting the interaction between JMJD6 and BRD4. When overexpressed, ARGLU1 increases the growth rate of cancer cells, while its knockdown leads to growth arrest. Significantly, overexpression of ARGLU1 increased cancer cell resistance to genotoxic drugs and promoted DNA damage repair. These results identify new roles for ARGLU1 in cancer cell survival and the DNA damage repair pathway, with potential clinical implications for chemotherapy resistance.
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Affiliation(s)
- Scott Bachus
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Nikolas Akkerman
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Lauren Fulham
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Drayson Graves
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Rafe Helwer
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Jordan Rempel
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Peter Pelka
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
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23
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Coleman MF, Cotul EK, Pfeil AJ, Devericks EN, Safdar MH, Monteiro M, Chen H, Ho AN, Attaar N, Malian HM, Kiesel VA, Ramos A, Smith M, Panchal H, Mailloux A, Teegarden D, Hursting SD, Wendt MK. Hypoxia-mediated repression of pyruvate carboxylase drives immunosuppression. Breast Cancer Res 2024; 26:96. [PMID: 38849928 PMCID: PMC11161980 DOI: 10.1186/s13058-024-01854-1] [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: 11/20/2023] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Metabolic plasticity mediates breast cancer survival, growth, and immune evasion during metastasis. However, how tumor cell metabolism is influenced by and feeds back to regulate breast cancer progression are not fully understood. We identify hypoxia-mediated suppression of pyruvate carboxylase (PC), and subsequent induction of lactate production, as a metabolic regulator of immunosuppression. METHODS We used qPCR, immunoblot, and reporter assays to characterize repression of PC in hypoxic primary tumors. Steady state metabolomics were used to identify changes in metabolite pools upon PC depletion. In vivo tumor growth and metastasis assays were used to evaluate the impact of PC manipulation and pharmacologic inhibition of lactate transporters. Immunohistochemistry, flow cytometry, and global gene expression analyzes of tumor tissue were employed to characterize the impact of PC depletion on tumor immunity. RESULTS PC is essential for metastatic colonization of the lungs. In contrast, depletion of PC in tumor cells promotes primary tumor growth. This effect was only observed in immune competent animals, supporting the hypothesis that repression of PC can suppress anti-tumor immunity. Exploring key differences between the pulmonary and mammary environments, we demonstrate that hypoxia potently downregulated PC. In the absence of PC, tumor cells produce more lactate and undergo less oxidative phosphorylation. Inhibition of lactate metabolism was sufficient to restore T cell populations to PC-depleted mammary tumors. CONCLUSIONS We present a dimorphic role for PC in primary mammary tumors vs. pulmonary metastases. These findings highlight a key contextual role for PC-directed lactate production as a metabolic nexus connecting hypoxia and antitumor immunity.
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Affiliation(s)
- Michael F Coleman
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eylem Kulkoyluoglu Cotul
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Alexander J Pfeil
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily N Devericks
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Muhammad H Safdar
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Marvis Monteiro
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Hao Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Alyssa N Ho
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Numair Attaar
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hannah M Malian
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Violet A Kiesel
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexis Ramos
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Matthew Smith
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Heena Panchal
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Adam Mailloux
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Dorothy Teegarden
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Stephen D Hursting
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, IN, USA.
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA.
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA.
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24
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Ala U, Fagoonee S. RNA-binding protein transcripts as potential biomarkers for detecting Primary Sclerosing Cholangitis and for predicting its progression to Cholangiocarcinoma. Front Mol Biosci 2024; 11:1388294. [PMID: 38903178 PMCID: PMC11187294 DOI: 10.3389/fmolb.2024.1388294] [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: 02/19/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Primary Sclerosing Cholangitis (PSC) is a persistent inflammatory liver condition that affects the bile ducts and is commonly diagnosed in young individuals. Despite efforts to incorporate various clinical, biochemical and molecular parameters for diagnosing PSC, it remains challenging, and no biomarkers characteristic of the disease have been identified hitherto. PSC is linked with an uncertain prognosis, and there is a pressing need to explore multiomics databases to establish a new biomarker panel for the early detection of PSC's gradual progression into Cholangiocarcinoma (CCA) and for the development of effective therapeutic interventions. Apart from non-coding RNAs, other components of the Ribonucleoprotein (RNP) complex, such as RNA-Binding Proteins (RBPs), also hold great promise as biomarkers due to their versatile expression in pathological conditions. In the present review, an update on the RBP transcripts that show dysregulated expression in PSC and CCA is provided. Moreover, by utilizing a bioinformatic data mining approach, we give insight into those RBP transcripts that also exhibit differential expression in liver and gall bladder, as well as in body fluids, and are promising as biomarkers for diagnosing and predicting the prognosis of PSC. Expression data were bioinformatically extracted from public repositories usingTCGA Bile Duct Cancer dataset for CCA and specific NCBI GEO datasets for both PSC and CCA; more specifically, RBPs annotations were obtained from RBP World database. Interestingly, our comprehensive analysis shows an elevated expression of the non-canonical RBPs, FANCD2, as well as the microtubule dynamics regulator, ASPM, transcripts in the body fluids of patients with PSC and CCA compared with their respective controls, with the same trend in expression being observed in gall bladder and liver cancer tissues. Consequently, the manipulation of tissue expression of RBP transcripts might be considered as a strategy to mitigate the onset of CCA in PSC patients, and warrants further experimental investigation. The analysis performed herein may be helpful in the identification of non-invasive biomarkers for the early detection of PSC and for predicting its progression into CCA. In conclusion, future clinical research should investigate in more depth the full potential of RBP transcripts as biomarkers for human pathologies.
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Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Sharmila Fagoonee
- Institute of Biostructure and Bioimaging (CNR), Molecular Biotechnology Center “Guido Tarone”, Turin, Italy
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25
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Laham AJ, El-Awady R, Saber-Ayad M, Wang N, Yan G, Boudreault J, Ali S, Lebrun JJ. Targeting the DYRK1A kinase prevents cancer progression and metastasis and promotes cancer cells response to G1/S targeting chemotherapy drugs. NPJ Precis Oncol 2024; 8:128. [PMID: 38839871 PMCID: PMC11153725 DOI: 10.1038/s41698-024-00614-w] [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: 08/23/2023] [Accepted: 05/17/2024] [Indexed: 06/07/2024] Open
Abstract
Metastatic cancer remains incurable as patients eventually loose sensitivity to targeted therapies and chemotherapies, further leading to poor clinical outcome. Thus, there is a clear medical gap and urgent need to develop efficient and improved targeted therapies for cancer patients. In this study, we investigated the role of DYRK1A kinase in regulating cancer progression and evaluated the therapeutic potential of DYRK1A inhibition in invasive solid tumors, including colon and triple-negative breast cancers. We uncovered new roles played by the DYRK1A kinase. We found that blocking DYRK1A gene expression or pharmacological inhibition of its kinase activity via harmine efficiently blocked primary tumor formation and the metastatic tumor spread in preclinical models of breast and colon cancers. Further assessing the underlying molecular mechanisms, we found that DYRK1A inhibition resulted in increased expression of the G1/S cell cycle regulators while decreasing expression of the G2/M regulators. Combined, these effects release cancer cells from quiescence, leading to their accumulation in G1/S and further delaying/preventing their progression toward G2/M, ultimately leading to growth arrest and tumor growth inhibition. Furthermore, we show that accumulation of cancer cells in G1/S upon DYRK1A inhibition led to significant potentiation of G1/S targeting chemotherapy drug responses in vitro and in vivo. This study underscores the potential for developing novel DYRK1A-targeting therapies in colon and breast cancers and, at the same time, further defines DYRK1A pharmacological inhibition as a viable and powerful combinatorial treatment approach for improving G1/S targeting chemotherapy drugs treatments in solid tumors.
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Affiliation(s)
- Amina Jamal Laham
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
- College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Raafat El-Awady
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates.
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates.
| | - Maha Saber-Ayad
- College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Ni Wang
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
| | - Gang Yan
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
| | - Julien Boudreault
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
| | - Suhad Ali
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
| | - Jean-Jacques Lebrun
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada.
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26
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Jiang M, Salari A, Stock C, Nikolovska K, Boedtkjer E, Amiri M, Seidler UE. The electroneutral Na +-HCO 3- cotransporter NBCn1 (SLC4A7) modulates colonic enterocyte pH i, proliferation, and migration. Am J Physiol Cell Physiol 2024; 326:C1625-C1636. [PMID: 38646790 PMCID: PMC11371319 DOI: 10.1152/ajpcell.00079.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/23/2024]
Abstract
NBCn1 (SLC4A7) is one of the two major Na+-HCO3- cotransporters in the human colonic epithelium, expressed predominantly in the highly proliferating colonocytes at the cryptal base. Increased NBCn1 expression levels are reported in tumors, including colorectal cancer. The study explores its importance for maintenance of the intracellular pH (pHi), as well as the proliferative, adhesive, and migratory behavior of the self-differentiating Caco2BBe colonic tumor cell line. In the self-differentiating Caco2BBe cells, NBCn1 mRNA was highly expressed from the proliferative stage until full differentiation. The downregulation of NBCn1 expression by RNA interference affected proliferation and differentiation and decreased intracellular pH (pHi) of the cells in correlation with the degree of knockdown. In addition, a disturbed cell adhesion and reduced migratory speed were associated with NBCn1 knockdown. Murine colonic Nbcn1-/- enteroids also displayed reduced proliferative activity. In the migrating Caco2BBe cells, NBCn1 was found at the leading edge and in colocalization with the focal adhesion markers vinculin and paxillin, which suggests that NBCn1 is involved in the establishment of cell-matrix adhesion. Our data highlight the physiological significance of NBCn1 in modulating epithelial pH homeostasis and cell-matrix interactions in the proliferative region of the colonic epithelium and unravel the molecular mechanism behind pathological overexpression of this transporter in human colorectal cancers.NEW & NOTEWORTHY The transporter NBCn1 plays a central role in maintaining homeostasis within Caco2BBe colonic epithelial cells through its regulation of intracellular pH, matrix adhesion, migration, and proliferation. These observations yield valuable insights into the molecular mechanism of the aberrant upregulation of this transporter in human colorectal cancers.
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Affiliation(s)
- Min Jiang
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Azam Salari
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Christian Stock
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Katerina Nikolovska
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Ebbe Boedtkjer
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Mahdi Amiri
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Ursula E Seidler
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
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Keuper K, Bartek J, Maya-Mendoza A. The nexus of nuclear envelope dynamics, circular economy and cancer cell pathophysiology. Eur J Cell Biol 2024; 103:151394. [PMID: 38340500 DOI: 10.1016/j.ejcb.2024.151394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
The nuclear envelope (NE) is a critical component in maintaining the function and structure of the eukaryotic nucleus. The NE and lamina are disassembled during each cell cycle to enable an open mitosis. Nuclear architecture construction and deconstruction is a prime example of a circular economy, as it fulfills a highly efficient recycling program bound to continuous assessment of the quality and functionality of the building blocks. Alterations in the nuclear dynamics and lamina structure have emerged as important contributors to both oncogenic transformation and cancer progression. However, the knowledge of the NE breakdown and reassembly is still limited to a fraction of participating proteins and complexes. As cancer cells contain highly diverse nuclei in terms of DNA content, but also in terms of nuclear number, size, and shape, it is of great interest to understand the intricate relationship between these nuclear features in cancer cell pathophysiology. In this review, we provide insights into how those NE dynamics are regulated, and how lamina destabilization processes may alter the NE circular economy. Moreover, we expand the knowledge of the lamina-associated domain region by using strategic algorithms, including Artificial Intelligence, to infer protein associations, assess their function and location, and predict cancer-type specificity with implications for the future of cancer diagnosis, prognosis and treatment. Using this approach we identified NUP98 and MECP2 as potential proteins that exhibit upregulation in Acute Myeloid Leukemia (LAML) patients with implications for early diagnosis.
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Affiliation(s)
- Kristina Keuper
- DNA Replication and Cancer Group, Danish Cancer Institute, Copenhagen, Denmark; Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SciLifeLab, Stockholm, Sweden
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Wang C, Yang Y, Li D, Guan Y, Cao M, Nie M, Sun C, Fu W, Kong X. Immunological Roles of CCL18 in Pan‑Cancer and Its Potential Value in Endometrial Cancer. Mol Biotechnol 2024:10.1007/s12033-024-01205-7. [PMID: 38816548 DOI: 10.1007/s12033-024-01205-7] [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] [Received: 12/21/2023] [Accepted: 05/14/2024] [Indexed: 06/01/2024]
Abstract
Endometrial cancer (EC) is one of the most prevalent malignancies in the female reproductive system. However, the potential functions and mechanisms of immune-related genes in the onset and progression of EC remain unclear. The immune-related gene CCL18 has been implicated in apoptosis, proliferation, invasion, metastasis, and drug resistance in various types of tumors. Nevertheless, its role in pan-cancer has been poorly investigated, and its expression value and prognostic significance in endometrial cancer (EC) have not been explored. Therefore, the objective of this study was to identify potential immune-related prognostic biomarkers for EC by utilizing the cancer genome atlas (TCGA), immunology database and analysis portal (ImmPort) database, and Gene Expression Omnibus (GEO). Immunohistochemistry staining results from EC tissue chips demonstrated elevated expression levels of inflammatory chemokine protein 18 (CCL18) in EC compared to normal endometrium. This study offers a potential therapeutic strategy for EC treatment by identifying regulatory targets through microRNA sequencing data. Additionally, drug prediction was based on CCL18 targets. Furthermore, an analysis of CCL18 expression in pan-cancer was conducted, and the results revealed its high expression in various types of cancer, including EC and bladder cancer. Through analysis of the ATAC-seq data, we found that SIX1, SOX3, and TWIST2 may regulate CCL18 transcription by binding to the gene promoter of CCL18 in EC. This study indicated that CCL18 could be a potential biomarker in pan-cancer and EC.
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Affiliation(s)
- Cangxue Wang
- School of Basic Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yuxiang Yang
- School of Basic Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Donghao Li
- School of Basic Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yihao Guan
- School of Basic Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - MengYuan Cao
- School of Basic Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Manjie Nie
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Caowei Sun
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Wenke Fu
- School of Basic Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xuhui Kong
- School of Basic Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China.
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Jiang YZ, Hu LY, Chen MS, Wang XJ, Tan CN, Xue PP, Yu T, He XY, Xiang LX, Xiao YN, Li XL, Ran Q, Li ZJ, Chen L. GATA binding protein 2 mediated ankyrin repeat domain containing 26 high expression in myeloid-derived cell lines. World J Stem Cells 2024; 16:538-550. [PMID: 38817334 PMCID: PMC11135246 DOI: 10.4252/wjsc.v16.i5.538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/12/2024] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Thrombocytopenia 2, an autosomal dominant inherited disease characterized by moderate thrombocytopenia, predisposition to myeloid malignancies and normal platelet size and function, can be caused by 5'-untranslated region (UTR) point mutations in ankyrin repeat domain containing 26 (ANKRD26). Runt related transcription factor 1 (RUNX1) and friend leukemia integration 1 (FLI1) have been identified as negative regulators of ANKRD26. However, the positive regulators of ANKRD26 are still unknown. AIM To prove the positive regulatory effect of GATA binding protein 2 (GATA2) on ANKRD26 transcription. METHODS Human induced pluripotent stem cells derived from bone marrow (hiPSC-BM) and urothelium (hiPSC-U) were used to examine the ANKRD26 expression pattern in the early stage of differentiation. Then, transcriptome sequencing of these iPSCs and three public transcription factor (TF) databases (Cistrome DB, animal TFDB and ENCODE) were used to identify potential TF candidates for ANKRD26. Furthermore, overexpression and dual-luciferase reporter experiments were used to verify the regulatory effect of the candidate TFs on ANKRD26. Moreover, using the GENT2 platform, we analyzed the relationship between ANKRD26 expression and overall survival in cancer patients. RESULTS In hiPSC-BMs and hiPSC-Us, we found that the transcription levels of ANKRD26 varied in the absence of RUNX1 and FLI1. We sequenced hiPSC-BM and hiPSC-U and identified 68 candidate TFs for ANKRD26. Together with three public TF databases, we found that GATA2 was the only candidate gene that could positively regulate ANKRD26. Using dual-luciferase reporter experiments, we showed that GATA2 directly binds to the 5'-UTR of ANKRD26 and promotes its transcription. There are two identified binding sites of GATA2 that are located 2 kb upstream of the TSS of ANKRD26. In addition, we discovered that high ANKRD26 expression is always related to a more favorable prognosis in breast and lung cancer patients. CONCLUSION We first discovered that the transcription factor GATA2 plays a positive role in ANKRD26 transcription and identified its precise binding sites at the promoter region, and we revealed the importance of ANKRD26 in many tissue-derived cancers.
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Affiliation(s)
- Yang-Zhou Jiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Lan-Yue Hu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Mao-Shan Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Xiao-Jie Wang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Cheng-Ning Tan
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Pei-Pei Xue
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Teng Yu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Xiao-Yan He
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Li-Xin Xiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Yan-Ni Xiao
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Xiao-Liang Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Qian Ran
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Zhong-Jun Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Li Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China.
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Hernandez-Gamarra M, Salgado-Roo A, Dominguez E, Goiricelaya Seco EM, Veiga-Rúa S, Pedrera-Garbayo LF, Carracedo Á, Allegue C. CARTAR: a comprehensive web tool for identifying potential targets in chimeric antigen receptor therapies using TCGA and GTEx data. Brief Bioinform 2024; 25:bbae326. [PMID: 38975894 PMCID: PMC11229032 DOI: 10.1093/bib/bbae326] [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: 04/16/2024] [Revised: 05/24/2024] [Accepted: 06/26/2024] [Indexed: 07/09/2024] Open
Abstract
Chimeric antigen receptor (CAR) therapy has emerged as a ground-breaking advancement in cancer treatment, harnessing the power of engineered human immune cells to target and eliminate cancer cells. The escalating interest and investment in CAR therapy in recent years emphasize its profound significance in clinical research, positioning it as a rapidly expanding frontier in the field of personalized cancer therapies. A crucial step in CAR therapy design is choosing the right target as it determines the therapy's effectiveness, safety and specificity against cancer cells, while sparing healthy tissues. Herein, we propose a suite of tools for the identification and analysis of potential CAR targets leveraging expression data from The Cancer Genome Atlas and Genotype-Tissue Expression Project, which are implemented in CARTAR website. These tools focus on pinpointing tumor-associated antigens, ensuring target selectivity and assessing specificity to avoid off-tumor toxicities and can be used to rationally designing dual CARs. In addition, candidate target expression can be explored in cancer cell lines using the expression data for the Cancer Cell Line Encyclopedia. To our best knowledge, CARTAR is the first website dedicated to the systematic search of suitable candidate targets for CAR therapy. CARTAR is publicly accessible at https://gmxenomica.github.io/CARTAR/.
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Affiliation(s)
- Miguel Hernandez-Gamarra
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, Av. Barcelona, 15706 A Coruña, Spain
- C005, Instituto de Investigación Sanitaria de Santiago (IDIS), Travesía da Choupana, 15706 A Coruña, Spain
| | - Alba Salgado-Roo
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, Av. Barcelona, 15706 A Coruña, Spain
- C005, Instituto de Investigación Sanitaria de Santiago (IDIS), Travesía da Choupana, 15706 A Coruña, Spain
| | - Eduardo Dominguez
- C005, Instituto de Investigación Sanitaria de Santiago (IDIS), Travesía da Choupana, 15706 A Coruña, Spain
| | | | - Sara Veiga-Rúa
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, Av. Barcelona, 15706 A Coruña, Spain
- C005, Instituto de Investigación Sanitaria de Santiago (IDIS), Travesía da Choupana, 15706 A Coruña, Spain
| | - Lucía F Pedrera-Garbayo
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, Av. Barcelona, 15706 A Coruña, Spain
- C005, Instituto de Investigación Sanitaria de Santiago (IDIS), Travesía da Choupana, 15706 A Coruña, Spain
| | - Ángel Carracedo
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, Av. Barcelona, 15706 A Coruña, Spain
- C005, Instituto de Investigación Sanitaria de Santiago (IDIS), Travesía da Choupana, 15706 A Coruña, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Travesía da Choupana, 15706 A Coruña, Spain
- CB06/07/0088, Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Av. Monforte de Lemos, 28029 Madrid, Spain
| | - Catarina Allegue
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, Av. Barcelona, 15706 A Coruña, Spain
- C005, Instituto de Investigación Sanitaria de Santiago (IDIS), Travesía da Choupana, 15706 A Coruña, Spain
- CB06/07/0088, Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Av. Monforte de Lemos, 28029 Madrid, Spain
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Sanvicente García A, Pedregal M, Paniagua-Herranz L, Díaz-Tejeiro C, Nieto-Jiménez C, Pérez Segura P, Munkácsy G, Győrffy B, Calvo E, Moreno V, Ocaña A. Clinical and Immunologic Characteristics of Colorectal Cancer Tumors Expressing LY6G6D. Int J Mol Sci 2024; 25:5345. [PMID: 38791382 PMCID: PMC11121234 DOI: 10.3390/ijms25105345] [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: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The identification of targets that are expressed on the cell membrane is a main goal in cancer research. The Lymphocyte Antigen 6 Family Member G6D (LY6G6D) gene codes for a protein that is mainly present on the surface of colorectal cancer (CRC) cells. Therapeutic strategies against this protein like the development of T cell engagers (TCE) are currently in the early clinical stage. In the present work, we interrogated public genomic datasets including TCGA to evaluate the genomic and immunologic cell profile present in tumors with high expression of LY6G6D. We used data from TCGA, among others, and the Tumor Immune Estimation Resource (TIMER2.0) platform for immune cell estimations and Spearman correlation tests. LY6G6D expression was exclusively present in CRC, particularly in the microsatellite stable (MSS) subtype, and was associated with left-side tumors and the canonical genomic subgroup. Tumors with mutations of APC and p53 expressed elevated levels of LY6G6D. This protein was expressed in tumors with an inert immune microenvironment with an absence of immune cells and co-inhibitory molecules. In conclusion, we described clinical, genomic and immune-pathologic characteristics that can be used to optimize the clinical development of agents against this target. Future studies should be performed to confirm these findings and potentially explore the suggested clinical development options.
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Affiliation(s)
- Adrián Sanvicente García
- Experimental Therapeutics in Cancer Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (A.S.G.); (L.P.-H.); (C.D.-T.); (C.N.-J.)
- Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Manuel Pedregal
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, 28040 Madrid, Spain; (M.P.); (E.C.); (V.M.)
| | - Lucía Paniagua-Herranz
- Experimental Therapeutics in Cancer Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (A.S.G.); (L.P.-H.); (C.D.-T.); (C.N.-J.)
| | - Cristina Díaz-Tejeiro
- Experimental Therapeutics in Cancer Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (A.S.G.); (L.P.-H.); (C.D.-T.); (C.N.-J.)
| | - Cristina Nieto-Jiménez
- Experimental Therapeutics in Cancer Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (A.S.G.); (L.P.-H.); (C.D.-T.); (C.N.-J.)
| | - Pedro Pérez Segura
- Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain;
| | - Gyöngyi Munkácsy
- Department of Bioinformatics, Semmelweis University, H-1094 Budapest, Hungary; (G.M.); (B.G.)
- Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, H-1094 Budapest, Hungary; (G.M.); (B.G.)
- Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
- Research Centre for Natural Sciences, Institute of Enzymology, H-1117 Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, H-7624 Pecs, Hungary
| | - Emiliano Calvo
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, 28040 Madrid, Spain; (M.P.); (E.C.); (V.M.)
- START Madrid-HM Centro Integral Oncológico Clara Campal (CIOCC), Early Phase Program, HM Sanchinarro University Hospital, 28050 Madrid, Spain
| | - Víctor Moreno
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, 28040 Madrid, Spain; (M.P.); (E.C.); (V.M.)
| | - Alberto Ocaña
- Experimental Therapeutics in Cancer Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (A.S.G.); (L.P.-H.); (C.D.-T.); (C.N.-J.)
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, 28040 Madrid, Spain; (M.P.); (E.C.); (V.M.)
- Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain;
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
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Xu H, Zhang H, Sun S, Zhang J, Huo J, Zhou C. Integrated Analysis of CD1A Immune Infiltration and Competing Endogenous RNA Networks in COAD. Int J Gen Med 2024; 17:2037-2053. [PMID: 38751492 PMCID: PMC11095400 DOI: 10.2147/ijgm.s455546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
Background The CD1A gene, a key component of the human immune system and part of the CD1 family, plays a crucial role in presenting lipid antigens to T cells. Abnormal CD1A expression is associated with various immune-related diseases and tumors. However, the biological function of CD1A in COAD is unclear. Methods Multiple databases were systematically employed to conduct an analysis of CD1A expression in pan-cancer and COAD, along with its clinical-pathological features. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses of CD1A were performed using the 'clusterProfiler' package. The Protein-protein interaction (PPI) analysis of CD1A was used the STRING database. Additionally, TIMER and ssGSEA tools were used to explore the relationship between CD1A expression in COAD and immune cell infiltration. The study also investigated the association between CD1A expression and N6-methyladenosine (m6A) modification genes in the TCGA COAD cohort and constructed a CD1A-centric competing endogenous RNA (ceRNA) regulatory network. Results CD1A displays varying expression levels in various tumors, including COAD, and is closely linked to clinical-pathological characteristics. GO analysis suggests that CD1A plays a role in important processes like antigen processing and presentation, leukocyte-mediated immunity, and lymphocyte-mediated immunity. KEGG analysis identifies CD1A's involvement in key pathways such as the Chemokine signaling pathway and Cytokine-cytokine receptor interaction. PPI analysis highlights CD1A's interactions with CD207, CD1C, CD1E, FOXP3, and ITGB2. ssGSEA analysis indicates a significant relationship between CD1A expression and the infiltration of various immune cells in COAD. Significant associations were found between CD1A and m6A modification genes in COAD. Furthermore, a CD1A-centered ceRNA regulatory network has been constructed. Conclusion CD1A emerges as a potential biomarker for the diagnosis and treatment of COAD, showing a strong association with tumor immune infiltration, m6A modification, and the ceRNA network.
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Affiliation(s)
- Houxi Xu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing, University of Chinese Medicine, Nanjing, People’s Republic of China
- School of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Hongqun Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing, University of Chinese Medicine, Nanjing, People’s Republic of China
- The Third School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Songxian Sun
- School of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Jingyuan Zhang
- School of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Jiege Huo
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing, University of Chinese Medicine, Nanjing, People’s Republic of China
- The Third School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Chunxiang Zhou
- School of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
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Torshizi Esfahani A, Mohammadpour S, Jalali P, Yaghoobi A, Karimpour R, Torkamani S, Pardakhtchi A, Salehi Z, Nazemalhosseini-Mojarad E. Differential expression of angiogenesis-related genes 'VEGF' and 'angiopoietin-1' in metastatic and EMAST-positive colorectal cancer patients. Sci Rep 2024; 14:10539. [PMID: 38719941 PMCID: PMC11079037 DOI: 10.1038/s41598-024-61000-x] [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: 11/11/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Abnormal angiogenesis leads to tumor progression and metastasis in colorectal cancer (CRC). This study aimed to elucidate the association between angiogenesis-related genes, including VEGF-A, ANGPT-1, and ANGPT-2 with both metastatic and microsatellite alterations at selected tetranucleotide repeats (EMAST) subtypes of CRC. We conducted a thorough assessment of the ANGPT-1, ANGPT-2, and VEGF-A gene expression utilizing publicly available RNA sequencing and microarray datasets. Then, the experimental validation was performed in 122 CRC patients, considering their disease metastasis and EMAST+/- profile by using reverse transcription polymerase chain reaction (RT-PCR). Subsequently, a competing endogenous RNA (ceRNA) network associated with these angiogenesis-related genes was constructed and analyzed. The expression level of VEGF-A and ANGPT-2 genes were significantly higher in tumor tissues as compared with normal adjacent tissues (P-value < 0.001). Nevertheless, ANGPT-1 had a significantly lower expression in tumor samples than in normal colon tissue (P-value < 0.01). We identified a significantly increased VEGF-A (P-value = 0.002) and decreased ANGPT-1 (P-value = 0.04) expression in EMAST+ colorectal tumors. Regarding metastasis, a significantly increased VEGF-A and ANGPT-2 expression (P-value = 0.001) and decreased ANGPT-1 expression (P-value < 0.05) were established in metastatic CRC patients. Remarkably, co-expression analysis also showed a strong correlation between ANGPT-2 and VEGF-A gene expressions. The ceRNA network was constructed by ANGPT-1, ANGPT-2, VEGF-A, and experimentally validated miRNAs (hsa-miR-190a-3p, hsa-miR-374c-5p, hsa-miR-452-5p, and hsa-miR-889-3p), lncRNAs (AFAP1-AS1, KCNQ1OT1 and MALAT1), and TFs (Sp1, E2F1, and STAT3). Network analysis revealed that colorectal cancer is amongst the 82 significant pathways. We demonstrated a significant differential expression of VEGF-A and ANGPT-1 in colorectal cancer patients exhibiting the EMAST+ phenotype. This finding provides novel insights into the molecular pathogenesis of colorectal cancer, specifically in EMAST subtypes. Yet, the generalization of in silico findings to EMAST+ colorectal cancer warrants future experimental investigations. In the end, this study proposes that the EMAST biomarker could serve as an additional perspective on CMS4 biology which is well-defined by activated angiogenesis and worse overall survival.
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Affiliation(s)
- Amir Torshizi Esfahani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mohammadpour
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pooya Jalali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Yaghoobi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Raana Karimpour
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Soha Torkamani
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Pardakhtchi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands.
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Chen X, Wang S, Jiang X, Zhang M, Ding Y. Long non-coding RNA HOTAIR: from pan-cancer analysis to colorectal cancer-related uridine metabolism. Aging (Albany NY) 2024; 16:7752-7773. [PMID: 38696320 PMCID: PMC11132002 DOI: 10.18632/aging.205781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/29/2024] [Indexed: 05/04/2024]
Abstract
Long non-coding RNAs (lncRNAs) are involved significantly in the development of human cancers. lncRNA HOTAIR has been reported to play an oncogenic role in many human cancers. Its specific regulatory role is still elusive. And it might have enormous potential to interpret the malignant progression of tumors in a broader perspective, that is, in pan-cancer. We comprehensively investigated the effect of HOTAIR expression on tumor prognosis across human malignancies by analyzing multiple cancer-related databases like The Cancer Genome Atlas (TCGA) and Tumor Immune Estimation Resource (TIMER). Bioinformatics data indicated that HOTAIR was overexpressed in most of these human malignancies and was significantly associated with the prognosis of patients with cancer, especially in colorectal cancer (CRC). Subsequently, this study further clarified the utility of HOTAIR that downregulation of its expression could result in reduced proliferation and invasion of CRC cells. Mechanistically, HOTAIR upregulated the metabolic enzymes UPP1 by recruiting histone methyltransferase EZH2, thereby increasing the tumor progression. Our results highlight the essential role of HOTAIR in pan-cancer and uridine bypass, suggesting that the HOTAIR/EZH2/UPP1 axis might be a novel target for overcoming CRC. We anticipate that the role of HOTAIR in metabolism could be important in the context of CRC and even exploited for therapeutic purposes.
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Affiliation(s)
- Xuyu Chen
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Siying Wang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Jiang
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Min Zhang
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yanbing Ding
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
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Mohajeri Khorasani A, Mohammadi S, Raghibi A, Haj Mohammad Hassani B, Bazghandi B, Mousavi P. miR-17-92a-1 cluster host gene: a key regulator in colorectal cancer development and progression. Clin Exp Med 2024; 24:85. [PMID: 38662056 PMCID: PMC11045601 DOI: 10.1007/s10238-024-01331-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
Colorectal cancer (CRC), recognized among the five most prevalent malignancies and most deadly cancers, manifests multifactorial influences stemming from environmental exposures, dietary patterns, age, and genetic predisposition. Although substantial progress has been made in comprehending the etiology of CRC, the precise genetic components driving its pathogenesis remain incompletely elucidated. Within the expansive repertoire of non-coding RNAs, particular focus has centered on the miR-17-92a-1 cluster host gene (MIR17HG) and its associated miRNAs, which actively participate in diverse cellular processes and frequently exhibit heightened expression in various solid tumors, notably CRC. Therefore, the primary objective of this research is to undertake an extensive inquiry into the regulatory mechanisms, structural features, functional attributes, and potential diagnostic and therapeutic implications associated with this cluster in CRC. Furthermore, the intricate interplay between this cluster and the development and progression of CRC will be explored. Our findings underscore the upregulation of the miR-17-92a-1 cluster host gene (MIR17HG) and its associated miRNAs in CRC compared to normal tissues, thus implying their profound involvement in the progression of CRC. Collectively, these molecules are implicated in critical oncogenic processes, encompassing metastatic activity, regulation of apoptotic pathways, cellular proliferation, and drug resistance. Consequently, these findings shed illuminating insights into the potential of MIR17HG and its associated miRNAs as promising targets for therapeutic interventions in the management of CRC.
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Affiliation(s)
- Amirhossein Mohajeri Khorasani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Samane Mohammadi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Alireza Raghibi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Behzad Haj Mohammad Hassani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Behina Bazghandi
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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Rose M, Burgess JT, Cheong CM, Adams MN, Shahrouzi P, O’Byrne KJ, Richard DJ, Bolderson E. The expression and role of the Lem-D proteins Ankle2, Emerin, Lemd2, and TMPO in triple-negative breast cancer cell growth. Front Oncol 2024; 14:1222698. [PMID: 38720803 PMCID: PMC11076778 DOI: 10.3389/fonc.2024.1222698] [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: 05/15/2023] [Accepted: 02/28/2024] [Indexed: 05/12/2024] Open
Abstract
Background Triple-negative breast cancer (TNBC) is a sub-classification of breast carcinomas, which leads to poor survival outcomes for patients. TNBCs do not possess the hormone receptors that are frequently targeted as a therapeutic in other cancer subtypes and, therefore, chemotherapy remains the standard treatment for TNBC. Nuclear envelope proteins are frequently dysregulated in cancer cells, supporting their potential as novel cancer therapy targets. The Lem-domain (Lem-D) (LAP2, Emerin, MAN1 domain, and Lem-D) proteins are a family of inner nuclear membrane proteins, which share a ~45-residue Lem-D. The Lem-D proteins, including Ankle2, Lemd2, TMPO, and Emerin, have been shown to be associated with many of the hallmarks of cancer. This study aimed to define the association between the Lem-D proteins and TNBC and determine whether these proteins could be promising therapeutic targets. Methods GENT2, TCGA, and KM plotter were utilized to investigate the expression and prognostic implications of several Lem-D proteins: Ankle2, TMPO, Emerin, and Lemd2 in publicly available breast cancer patient data. Immunoblotting and immunofluorescent analysis of immortalized non-cancerous breast cells and a panel of TNBC cells were utilized to establish whether protein expression of the Lem-D proteins was significantly altered in TNBC. SiRNA was used to decrease individual Lem-D protein expression, and functional assays, including proliferation assays and apoptosis assays, were conducted. Results The Lem-D proteins were generally overexpressed in TNBC patient samples at the mRNA level and showed variable expression at the protein level in TNBC cell lysates. Similarly, protein levels were generally negatively correlated with patient survival outcomes. siRNA-mediated depletion of the individual Lem-D proteins in TNBC cells induced aberrant nuclear morphology, decreased proliferation, and induced cell death. However, minimal effects on nuclear morphology or cell viability were observed following Lem-D depletion in non-cancerous MCF10A cells. Conclusion There is evidence to suggest that Ankle2, TMPO, Emerin, and Lemd2 expressions are correlated with breast cancer patient outcomes, but larger patient sample numbers are required to confirm this. siRNA-mediated depletion of these proteins was shown to specifically impair TNBC cell growth, suggesting that the Lem-D proteins may be a specific anti-cancer target.
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Affiliation(s)
- Maddison Rose
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Joshua T. Burgess
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Chee Man Cheong
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mark N. Adams
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Parastoo Shahrouzi
- Department of Medical Genetics, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Kenneth J. O’Byrne
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Services, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Derek J. Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Emma Bolderson
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
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Kwiatkowski M, Krajewski A, Durślewicz J, Buchholz K, Grzanka D, Gagat M, Zabrzyński J, Klimaszewska-Wiśniewska A. Overexpression of cyclin F/CCNF as an independent prognostic factor for poor survival in clear cell renal cell carcinoma. Sci Rep 2024; 14:9280. [PMID: 38654021 PMCID: PMC11039610 DOI: 10.1038/s41598-024-59437-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Cyclin F (encoded by CCNF gene) has been reported to be implicated in the pathobiology of several human cancers. However, its potential clinical significance in clear cell renal cell carcinoma (ccRCC) remains unknown. The present study aimed to evaluate the potential significance of cyclin F, assessed by immunohistochemical (IHC) staining and molecular (bioinformatics) techniques, as a prognostic marker in ccRCC in relation to clinicopathological features and outcomes. IHC staining was performed using two independent ccRCC tissue array cohorts, herein called tissue macroarray (TMA)_1 and tissue microarray (TMA)_2, composed of 108 ccRCCs and 37 histologically normal tissues adjacent to the tumor (NAT) and 192 ccRCCs and 16 normal kidney samples, respectively. The mRNA expression data were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) public datasets, followed by bioinformatics analysis of biological mechanisms underlying prognosis. The relationship between immune cell infiltration level and CCNF expression in ccRCC was investigated using the Tumor Immune Estimation Resource 2.0 (TIMER2) and Gene Expression Profiling Interactive Analysis 2 (GEPIA2). Cyclin F expression was significantly elevated in ccRCC lesions compared to both NAT and normal renal tissues. Likewise, CCNF mRNA was markedly increased in ccRCCs relative to non-cancerous tissues. In all analyzed cohorts, tumors with features of more aggressive behavior were more likely to display cyclin F/CCNF-high expression than low. Furthermore, patients with high cyclin F/CCNF expression had shorter overall survival (OS) times than those with low expression. In addition, multivariable analysis revealed that cyclin F/CCNF-high expression was an independent prognostic factor for poor OS in ccRCC. Enrichment analysis for mechanistically relevant processes showed that CCNF and its highly correlated genes initiate the signaling pathways that eventually result in uncontrolled cell proliferation. CCNF expression was also correlated with immune cell infiltration and caused poor outcomes depending on the abundance of tumor-infiltrating immune cells in ccRCC. Our findings suggest that cyclin F/CCNF expression is likely to have an essential role in ccRCC pathobiology through regulating multiple oncogenic signaling pathways and affecting the tumor immune microenvironment and may serve as prognostic biomarker and promising therapeutic target in ccRCC.
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Affiliation(s)
- Maciej Kwiatkowski
- Department of Urology and Urological Oncology, Multidisciplinary Hospital of Ludwik Blażek, Inowrocław, Poland
| | - Adrian Krajewski
- Department of Histology and Embryology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Justyna Durślewicz
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Karolina Buchholz
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
- Department of Histology and Embryology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Dariusz Grzanka
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Maciej Gagat
- Department of Histology and Embryology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
- Faculty of Medicine, Collegium Medicum, Mazovian Academy, Płock, Poland
| | - Jan Zabrzyński
- Department of Orthopaedics and Traumatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Anna Klimaszewska-Wiśniewska
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
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Peng L, Zhou L, Li H, Zhang X, Li S, Wang K, Yang M, Ma X, Zhang D, Xiang S, Duan Y, Wang T, Sun C, Wang C, Lu D, Qian M, Wang Z. Hippo-signaling-controlled MHC class I antigen processing and presentation pathway potentiates antitumor immunity. Cell Rep 2024; 43:114003. [PMID: 38527062 DOI: 10.1016/j.celrep.2024.114003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 02/05/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024] Open
Abstract
The major histocompatibility complex class I (MHC class I)-mediated tumor antigen processing and presentation (APP) pathway is essential for the recruitment and activation of cytotoxic CD8+ T lymphocytes (CD8+ CTLs). However, this pathway is frequently dysregulated in many cancers, thus leading to a failure of immunotherapy. Here, we report that activation of the tumor-intrinsic Hippo pathway positively correlates with the expression of MHC class I APP genes and the abundance of CD8+ CTLs in mouse tumors and patients. Blocking the Hippo pathway effector Yes-associated protein/transcriptional enhanced associate domain (YAP/TEAD) potently improves antitumor immunity. Mechanistically, the YAP/TEAD complex cooperates with the nucleosome remodeling and deacetylase complex to repress NLRC5 transcription. The upregulation of NLRC5 by YAP/TEAD depletion or pharmacological inhibition increases the expression of MHC class I APP genes and enhances CD8+ CTL-mediated killing of cancer cells. Collectively, our results suggest a crucial tumor-promoting function of YAP depending on NLRC5 to impair the MHC class I APP pathway and provide a rationale for inhibiting YAP activity in immunotherapy for cancer.
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Affiliation(s)
- Linyuan Peng
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Liang Zhou
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Cancer Research Center, Department of Pharmacology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Huan Li
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Cancer Research Center, Department of Pharmacology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xin Zhang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Su Li
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Kai Wang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Mei Yang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaoyu Ma
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Danlan Zhang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Cancer Research Center, Department of Pharmacology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Siliang Xiang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Yajun Duan
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Tianzhi Wang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Chunmeng Sun
- State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Chen Wang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Desheng Lu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Cancer Research Center, Department of Pharmacology, Shenzhen University Medical School, Shenzhen 518055, China.
| | - Minxian Qian
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China.
| | - Zhongyuan Wang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China.
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Sanvicente A, Díaz-Tejeiro C, Nieto-Jiménez C, Paniagua-Herranz L, López Cade I, Balázs G, Moreno V, Pérez-Segura P, Calvo E, Ocaña A. In Silico Transcriptomic Expression of MSR1 in Solid Tumors Is Associated with Responses to Anti-PD1 and Anti-CTLA4 Therapies. Int J Mol Sci 2024; 25:3987. [PMID: 38612803 PMCID: PMC11012116 DOI: 10.3390/ijms25073987] [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: 03/05/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Immuno-oncology has gained momentum with the approval of antibodies with clinical activities in different indications. Unfortunately, for anti-PD (L)1 agents in monotherapy, only half of the treated population achieves a clinical response. For other agents, such as anti-CTLA4 antibodies, no biomarkers exist, and tolerability can limit administration. In this study, using publicly available genomic datasets, we evaluated the expression of the macrophage scavenger receptor-A (SR-A) (MSR1) and its association with a response to check-point inhibitors (CPI). MSR1 was associated with the presence of macrophages, dendritic cells (DCs) and neutrophils in most of the studied indications. The presence of MSR1 was associated with macrophages with a pro-tumoral phenotype and correlated with TIM3 expression. MSR1 predicted favorable overall survival in patients treated with anti-PD1 (HR: 0.56, FDR: 1%, p = 2.6 × 10-5), anti PD-L1 (HR: 0.66, FDR: 20%, p = 0.00098) and anti-CTLA4 (HR: 0.37, FDR: 1%, p = 4.8 × 10-5). When specifically studying skin cutaneous melanoma (SKCM), we observed similar effects for anti-PD1 (HR: 0.65, FDR: 50%, p = 0.0072) and anti-CTLA4 (HR: 0.35, FDR: 1%, p = 4.1 × 10-5). In a different dataset of SKCM patients, the expression of MSR1 predicted a clinical response to anti-CTLA4 (AUC: 0.61, p = 2.9 × 10-2). Here, we describe the expression of MSR1 in some solid tumors and its association with innate cells and M2 phenotype macrophages. Of note, the presence of MSR1 predicted a response to CPI and, particularly, anti-CTLA4 therapies in different cohorts of patients. Future studies should prospectively explore the association of MSR1 expression and the response to anti-CTLA4 strategies in solid tumors.
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Affiliation(s)
- Adrián Sanvicente
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), 28040 Madrid, Spain; (A.S.); (C.D.-T.); (C.N.-J.); (L.P.-H.); (I.L.C.)
- Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Cristina Díaz-Tejeiro
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), 28040 Madrid, Spain; (A.S.); (C.D.-T.); (C.N.-J.); (L.P.-H.); (I.L.C.)
| | - Cristina Nieto-Jiménez
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), 28040 Madrid, Spain; (A.S.); (C.D.-T.); (C.N.-J.); (L.P.-H.); (I.L.C.)
| | - Lucia Paniagua-Herranz
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), 28040 Madrid, Spain; (A.S.); (C.D.-T.); (C.N.-J.); (L.P.-H.); (I.L.C.)
| | - Igor López Cade
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), 28040 Madrid, Spain; (A.S.); (C.D.-T.); (C.N.-J.); (L.P.-H.); (I.L.C.)
- Molecular Oncology Laboratory, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain
| | - Győrffy Balázs
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7-9, H-1094 Budapest, Hungary;
- Research Centre for Natural Sciences, Hungarian Research Network, Magyar Tudosok Korutja 2, H-1117 Budapest, Hungary
| | - Víctor Moreno
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, 28040 Madrid, Spain; (V.M.); (E.C.)
| | - Pedro Pérez-Segura
- Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain;
| | - Emiliano Calvo
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, 28040 Madrid, Spain; (V.M.); (E.C.)
- START Madrid-HM Centro Integral Oncológico Clara Campal (CIOCC), Early Phase Program, HM Sanchinarro University Hospital, 28050 Madrid, Spain
| | - Alberto Ocaña
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), 28040 Madrid, Spain; (A.S.); (C.D.-T.); (C.N.-J.); (L.P.-H.); (I.L.C.)
- Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain;
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), 28029 Madrid, Spain
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Murthy D, Attri KS, Shukla SK, Thakur R, Chaika NV, He C, Wang D, Jha K, Dasgupta A, King RJ, Mulder SE, Souchek J, Gebregiworgis T, Rai V, Patel R, Hu T, Rana S, Kollala SS, Pacheco C, Grandgenett PM, Yu F, Kumar V, Lazenby AJ, Black AR, Ulhannan S, Jain A, Edil BH, Klinkebiel DL, Powers R, Natarajan A, Hollingsworth MA, Mehla K, Ly Q, Chaudhary S, Hwang RF, Wellen KE, Singh PK. Cancer-associated fibroblast-derived acetate promotes pancreatic cancer development by altering polyamine metabolism via the ACSS2-SP1-SAT1 axis. Nat Cell Biol 2024; 26:613-627. [PMID: 38429478 PMCID: PMC11021164 DOI: 10.1038/s41556-024-01372-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
The ability of tumour cells to thrive in harsh microenvironments depends on the utilization of nutrients available in the milieu. Here we show that pancreatic cancer-associated fibroblasts (CAFs) regulate tumour cell metabolism through the secretion of acetate, which can be blocked by silencing ATP citrate lyase (ACLY) in CAFs. We further show that acetyl-CoA synthetase short-chain family member 2 (ACSS2) channels the exogenous acetate to regulate the dynamic cancer epigenome and transcriptome, thereby facilitating cancer cell survival in an acidic microenvironment. Comparative H3K27ac ChIP-seq and RNA-seq analyses revealed alterations in polyamine homeostasis through regulation of SAT1 gene expression and enrichment of the SP1-responsive signature. We identified acetate/ACSS2-mediated acetylation of SP1 at the lysine 19 residue that increased SP1 protein stability and transcriptional activity. Genetic or pharmacologic inhibition of the ACSS2-SP1-SAT1 axis diminished the tumour burden in mouse models. These results reveal that the metabolic flexibility imparted by the stroma-derived acetate enabled cancer cell survival under acidosis via the ACSS2-SP1-SAT1 axis.
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Affiliation(s)
- Divya Murthy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kuldeep S Attri
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Surendra K Shukla
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Ravi Thakur
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Nina V Chaika
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Chunbo He
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Dezhen Wang
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kanupriya Jha
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Greater Noida, Uttar Pradesh, India
| | - Aneesha Dasgupta
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ryan J King
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Scott E Mulder
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Joshua Souchek
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Teklab Gebregiworgis
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Vikant Rai
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rohit Patel
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Tuo Hu
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sandeep Rana
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sai Sundeep Kollala
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Camila Pacheco
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Paul M Grandgenett
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Fang Yu
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Vikas Kumar
- Department of Cell Biology, Genetics and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Audrey J Lazenby
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Adrian R Black
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Susanna Ulhannan
- Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Ajay Jain
- Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Barish H Edil
- Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - David L Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kamiya Mehla
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Quan Ly
- Department of Surgical Oncology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sarika Chaudhary
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Greater Noida, Uttar Pradesh, India
| | - Rosa F Hwang
- Department of Surgical Oncology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Pankaj K Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- OU Health Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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LI KUNLUN, LI DANDAN, HAFEZ BARBOD, BEKHIT MOUNIRMSALEM, JARDAN YOUSEFABIN, ALANAZI FARSKAED, TAHA EHABI, AUDA SAYEDH, RAMZAN FAIQAH, JAMIL MUHAMMAD. Identifying and validating MMP family members (MMP2, MMP9, MMP12, and MMP16) as therapeutic targets and biomarkers in kidney renal clear cell carcinoma (KIRC). Oncol Res 2024; 32:737-752. [PMID: 38560573 PMCID: PMC10972725 DOI: 10.32604/or.2023.042925] [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: 06/16/2023] [Accepted: 10/11/2023] [Indexed: 04/04/2024] Open
Abstract
Kidney Renal Clear Cell Carcinoma (KIRC) is a malignant tumor that carries a substantial risk of morbidity and mortality. The MMP family assumes a crucial role in tumor invasion and metastasis. This study aimed to uncover the mechanistic relevance of the MMP gene family as a therapeutic target and diagnostic biomarker in Kidney Renal Clear Cell Carcinoma (KIRC) through a comprehensive approach encompassing both computational and molecular analyses. STRING, Cytoscape, UALCAN, GEPIA, OncoDB, HPA, cBioPortal, GSEA, TIMER, ENCORI, DrugBank, targeted bisulfite sequencing (bisulfite-seq), conventional PCR, Sanger sequencing, and RT-qPCR based analyses were used in the present study to analyze MMP gene family members to accurately determine a few hub genes that can be utilized as both therapeutic targets and diagnostic biomarkers for KIRC. By performing STRING and Cytohubba analyses of the 24 MMP gene family members, MMP2 (matrix metallopeptidase 2), MMP9 (matrix metallopeptidase 9), MMP12 (matrix metallopeptidase 12), and MMP16 (matrix metallopeptidase 16) genes were denoted as hub genes having highest degree scores. After analyzing MMP2, MMP9, MMP12, and MMP16 via various TCGA databases and RT-qPCR technique across clinical samples and KIRC cell lines, interestingly, all these hub genes were found significantly overexpressed at mRNA and protein levels in KIRC samples relative to controls. The notable effect of the up-regulated MMP2, MMP9, MMP12, and MMP16 was also documented on the overall survival (OS) of the KIRC patients. Moreover, targeted bisulfite-sequencing (bisulfite-seq) analysis revealed that promoter hypomethylation pattern was associated with up-regulation of hub genes (MMP2, MMP9, MMP12, and MMP16). In addition to this, hub genes were involved in various diverse oncogenic pathways. The MMP gene family members (MMP2, MMP9, MMP12, and MMP16) may serve as therapeutic targets and prognostic biomarkers in KIRC.
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Affiliation(s)
- KUNLUN LI
- The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - DANDAN LI
- Department of Pharmaceutical Engineering, Jiangsu Ocean University, Lianyungang, China
| | - BARBOD HAFEZ
- Department of Biological Engineering, University of Salford, Salford, UK
| | - MOUNIR M. SALEM BEKHIT
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - YOUSEF A. BIN JARDAN
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - FARS KAED ALANAZI
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - EHAB I. TAHA
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - SAYED H. AUDA
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - FAIQAH RAMZAN
- Department of Animal and Poultry Production, Faculty of Veterinary and Animal Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - MUHAMMAD JAMIL
- Department of Arid Zone Research, PARC institute, Dera Ismail Khan, Pakistan
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Al-Shar'i NA. The design of TOPK inhibitors using similarity search, molecular docking, and MD simulations. J Biomol Struct Dyn 2024:1-12. [PMID: 38358833 DOI: 10.1080/07391102.2024.2319107] [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: 12/06/2023] [Accepted: 02/10/2024] [Indexed: 02/17/2024]
Abstract
Cancer is still a major cause of death worldwide. Unfortunately, the majority of current anticancer treatments suffer many limitations, mainly emergence of resistance and lack of selectivity which necessitate the search for new therapeutics. The TOPK enzyme emerges as a promising target due to its overexpression in many cancer types while being rarely detected in normal tissues. Therefore, targeting TOPK would affect the malignant activity of cancerous cells while sparing normal ones. Further, its vital role in cell division, particularly in cytokinesis, adds to its safety to normal non-multiplying cells. In this study, a combined ligand and structure-based approach was utilized to identify potential TOPK inhibitors. Previously, we identified TOPK inhibitors using a structure-based approach following the construction of a 3D homology model of the TOPK enzyme. Herein, the most active identified inhibitor (lead) was used as a search query to conduct similarity search against PubChem and ChemBridge databases. Retrieved hits were filtered using drug-like filters, docked into the ATP binding site of the enzyme, and finally, the binding free energies of all docked poses were calculated. Based on the computational scores, eight hits were selected as potential TOPK inhibitors. The predicted ADMET descriptors of the eight selected hits were generally favorable. Further, MD simulations of the top scoring hit were conducted to investigate its binding dynamics compared to the lead compound and OTS964 which agreed with the docking results and propose the selected hits as potential TOPK inhibitors. Yet, biochemical testing is still needed to validate these results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nizar A Al-Shar'i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
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Wang M, Liu C, Wang Y, Jamil M, Alhomrani M, Alamri AS, Alsanie WF, Alsharif A, Ali M, Jabeen N. Bone morphogenetic protein 1: a prognostic indicator and potential biomarker in three cancer types. Am J Transl Res 2024; 16:400-414. [PMID: 38463598 PMCID: PMC10918118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/10/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND Bone morphogenetic protein 1 (BMP1) is a metalloprotease that plays a role in activating both transforming growth factor-β (TGF-β) and BMP signaling pathways. TGF-β has been identified as a factor initiating and facilitating cancer development. Consequently, we propose the hypothesis that dysregulation of BMP1 could potentially contribute to the onset and advancement of human cancers. METHODS In this research, we aimed to analyze BMP1 expression level and the associated clinical outcomes across various cancers using online cancer OMICS databases, advanced Bioinformatics tools, and molecular analyses. RESULTS The outcomes of our web server-based expression analysis indicated an up-regulation of BMP1 in a majority of the human cancers examined. External validation using clinical samples also showed higher expression of BMP1. Moreover, heightened BMP1 expression exhibited a noteworthy correlation with reduced overall survival (OS) duration in Bladder Cancer (BLCA), Kidney Renal Clear Cell Carcinoma (KIRC), and Lung Adenocarcinoma (LUAD) patients. This suggests a substantial involvement of the BMP1 gene in the development and progression of these three types of cancers. The major signaling pathways related with BMP1 enriched genes were "ECM-receptor interaction, Amoebiasis, Focal adhesion, Protein digestion and absorption, progesterone-mediated, PI3K-Akt signaling pathway, and platelet activation". Moreover, we also explored some interesting correlations among BMP1 expression and its DNA promoter methylation level, CD8+ T immune cells level, and genetic variations. CONCLUSION In conclusion, our study has provided some solid basis for BMP1 to be used as a reliable common biomarker for BLCA, KIRC, and LUAD patients.
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Affiliation(s)
- Ming Wang
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Chunmei Liu
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Yingjie Wang
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Muhammad Jamil
- PARC Arid Zone Research CentreDera Ismail Khan 29050, Pakistan
| | - Majid Alhomrani
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Abdulhakeem S Alamri
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Walaa F Alsanie
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Abdulaziz Alsharif
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Mubarik Ali
- Animal Science Institute, National Agricultural Research CenterIslamabad 54000, Pakistan
| | - Norina Jabeen
- Department of Rural Sociology, University of Agriculture FaisalabadFaisalabad 38040, Punjab, Pakistan
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Zhang Z, Li B, Wang Z, Yang L, Peng J, Wang H, Wang Y, Hong L. Novel LncRNA LINC02936 Suppresses Ferroptosis and Promotes Tumor Progression by Interacting with SIX1/CP Axis in Endometrial Cancer. Int J Biol Sci 2024; 20:1356-1374. [PMID: 38385087 PMCID: PMC10878161 DOI: 10.7150/ijbs.86256] [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: 05/16/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Endometrial cancer (EC) is a prevalent gynecological malignancy, and metabolic disorders are among its most significant risk factors. Abnormal iron metabolism is associated with the progression of cancer malignancy. Nevertheless, the involvement of iron metabolism in the EC remains uncertain. Ceruloplasmin (CP) functions as a multicopper oxidase and ferroxidase, playing a crucial role in maintaining the metabolic balance between copper and iron. Prior research has demonstrated that the dysregulated expression of CP has important clinical implications in EC. However, the specific underlying molecular mechanisms remains uncertain. This research examined the impact of CP on the malignant advancement of EC by suppressing ferroptosis. Next, we explored the possibility that Long non-coding RNA (lncRNA) LINC02936/SIX1/CP axis may be a key pathway for inhibiting ferroptosis and promoting cancer progression in EC. Mechanistically, SIX1 modulates the expression of CP, whereas LINC02936 interacts with SIX1 and recruits SIX1 to the CP promoter, leading to upregulation of CP, inhibition of ferroptosis, and promotion of EC progression. Administration of a small peptide cloud block the LINC02936-SIX1 interaction, thereby inhibits EC progression by promoting ferroptosis. Altogether, this is the first report on the lncRNA regulation of ferroptosis in EC. Our research enhances the knowledge of the lncRNA-mediated regulation of ferroptosis in EC progression and indicates the potential therapeutic significance of the LINC02936/SIX1/CP axis in treating EC.
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Affiliation(s)
| | | | | | | | | | | | | | - Li Hong
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei Province People's Republic of China
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Tsai YC, Huang SP, Cheng WC, Fan YC, Lin YC, Tsai SY, Huang CY, Yu CC, Lin VC, Geng JH, Li CY, Lu TL, Bao BY. Identifying the role of MTHFD1L in prostate cancer progression from genetic analysis and experimental validation. Am J Cancer Res 2024; 14:169-181. [PMID: 38323273 PMCID: PMC10839318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/15/2023] [Indexed: 02/08/2024] Open
Abstract
One-carbon metabolism plays a crucial role in tumorigenesis as it supplies the one-carbon units necessary for nucleotide synthesis, epigenetic regulation, and redox metabolism, ensuring the rapid proliferation of cancer cells. However, their roles in prostate cancer progression remain poorly understood. In this study, we investigated the association between genetic variants in the one-carbon metabolism pathway and clinical outcomes in patients receiving androgen deprivation therapy for prostate cancer. The associations of 130 single-nucleotide polymorphisms located within 14 genes involved in the one-carbon metabolism pathway with cancer-specific survival (CSS), overall survival, and progression-free survival were assessed using Cox regression in 630 patients with prostate cancer. Subsequently, functional studies were performed using prostate cancer cell lines. After adjusting for covariates and multiple testing, MTHFD1L rs2073190 was found to be significantly associated with CSS (P = 0.000184). Further pooled analysis of multiple datasets demonstrated that MTHFD1L was upregulated in prostate cancer and increased MTHFD1L expression was positively correlated with tumor aggressiveness and poor patient prognosis. Functionally, MTHFD1L knockdown suppressed prostate cancer cell proliferation and colony formation. RNA sequencing and pathway analysis revealed that differentially expressed genes were predominantly enriched in the cell cycle pathway. In conclusion, genetic variants in MTHFD1L of one-carbon metabolism may serve as promising predictors, and our findings offer valuable insights into the underlying genetic mechanisms of prostate cancer progression.
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Affiliation(s)
- Yuan-Chin Tsai
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipei 110, Taiwan
| | - Shu-Pin Huang
- Department of Urology, Kaohsiung Medical University HospitalKaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical UniversityKaohsiung 807, Taiwan
- Ph.D. Program in Environmental and Occupational Medicine, College of Medicine, Kaohsiung Medical UniversityKaohsiung 807, Taiwan
- Institute of Medical Science and Technology, College of Medicine, National Sun Yat-Sen UniversityKaohsiung 804, Taiwan
| | - Wei-Chung Cheng
- Ph.D. Program for Cancer Biology and Drug Discovery, Cancer Biology and Precision Therapeutics Center, China Medical UniversityTaichung 404, Taiwan
| | - Yu-Ching Fan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipei 110, Taiwan
| | - Ya-Ching Lin
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
| | - Shin-Yu Tsai
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
| | - Chao-Yuan Huang
- Department of Urology, National Taiwan University Hospital, College of Medicine, National Taiwan UniversityTaipei 100, Taiwan
| | - Chia-Cheng Yu
- Division of Urology, Department of Surgery, Kaohsiung Veterans General HospitalKaohsiung 813, Taiwan
- Department of Urology, School of Medicine, National Yang-Ming UniversityTaipei 112, Taiwan
- Department of Pharmacy, Tajen UniversityPingtung 907, Taiwan
| | - Victor C Lin
- Department of Urology, E-Da HospitalKaohsiung 824, Taiwan
- School of Medicine for International Students, I-Shou UniversityKaohsiung 840, Taiwan
| | - Jiun-Hung Geng
- Department of Urology, Kaohsiung Medical University HospitalKaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical UniversityKaohsiung 807, Taiwan
- Department of Urology, Kaohsiung Municipal Hsiao-Kang HospitalKaohsiung 812, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical UniversityKaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University HospitalKaohsiung 807, Taiwan
| | - Te-Ling Lu
- Department of Pharmacy, China Medical UniversityTaichung 406, Taiwan
| | - Bo-Ying Bao
- Department of Pharmacy, China Medical UniversityTaichung 406, Taiwan
- Sex Hormone Research Center, China Medical University HospitalTaichung 404, Taiwan
- Department of Nursing, Asia UniversityTaichung 413, Taiwan
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Gao M, Tuo Z, Jiang Z, Chen Z, Wang J. Dysregulated ANLN reveals immune cell landscape and promotes carcinogenesis by regulating the PI3K/Akt/mTOR pathway in clear cell renal cell carcinoma. Heliyon 2024; 10:e23522. [PMID: 38173514 PMCID: PMC10761583 DOI: 10.1016/j.heliyon.2023.e23522] [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: 08/25/2023] [Revised: 11/17/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Background Abnormal anillin (ANLN) expression has been observed in multiple tumours and is closely associated with patient prognosis and clinical features. In this study, we systematically elucidated the clinical significance and biological roles of ANLN in patients with clear cell renal cell carcinoma (ccRCC). Methods We obtained transcriptome and clinical data of patients with ccRCC from public databases. Multi-omics data and clinical samples were combined to analyse the correlation between ANLN expression and the clinical characteristics of patients with renal cancer. Additionally, the immune cell landscape of ANLN expression was evaluated using different immune algorithms in the tumour microenvironment. The tumour-promoting potential of ANLN was confirmed using in vitro assays, including CCK8 and Transwell assays. Results Bioinformatics analysis showed that ANLN is over-expressed in patients with ccRCC, as validated by clinical samples. Publicly available clinical data suggest that high ANLN expression may indicate poor outcomes in patients with ccRCC. Moreover, biological function analysis revealed a marked enrichment of the cell cycle and PI3K-Akt pathways. The distribution of immune cells, particularly M2 macrophages, differed in patients with ccRCC. Furthermore, ANLN silencing inhibited the proliferation, migration, and invasion of renal cancer cells in vitro. After ANLN expression was knocked down in 786-O cells, the protein levels of important PI3K signalling pathway components, including PI3K, Akt, and mTOR, drastically decreased. Conclusions These findings suggest that ANLN is dysregulated in renal cancer tissues and promotes tumour progression by activating the PI3K/Akt/mTOR signalling pathway.
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Affiliation(s)
- Mingzhu Gao
- Department of Oncology, Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Zhouting Tuo
- Department of Urology, Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Zhiwei Jiang
- Department of Urology, Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Zhendong Chen
- Department of Oncology, Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jinyou Wang
- Department of Urology, Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
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Zamora-Salas SX, Macías-Silva M, Tecalco-Cruz AC. Upregulation of the canonical signaling pathway of interferon-gamma is associated with glioblastoma progression. Mol Biol Rep 2024; 51:64. [PMID: 38170343 DOI: 10.1007/s11033-023-09062-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/10/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Glioblastoma is a brain malignant tumor grade IV, highly invasive. Alterations in several signaling pathways are involved in glioblastoma development. In this work, we evaluated the IFN-γ canonical signaling pathway in glioblastoma cells and its effect on cell viability and migration. METHODS The levels of STAT1/pSTAT1, IRF1, and PD-L1 in LN-18 glioblastoma cells were analyzed using western blotting. Cell viability was evaluated by calcein-AM/propidium iodide assays, and a wound healing assay was used to study the migration of glioblastoma cells treated with IFN-γ. Our aim was to determine the expression of IFN-γ signaling elements in cell lines and tissue from glioblastoma samples and examine the relationship between these elements and the survival of glioblastoma patients. The following platforms were utilized for analysis: the CCLE (Cancer Cell Line Encyclopedia), UALCAN (University of Alabama at Birmingham Cancer data analysis Portal), GEPIA (Gene Expression Profiling Interactive Analysis), and GENT2 (Gene Expression patterns across Normal and Tumor tissues). RESULTS Our results evidenced that IFN-γ signaling increases non-phosphorylated and phosphorylated STAT1 levels and promotes the upregulation of IRF1 and PD-L1 in glioblastoma cells. The activation of IFN-γ signaling increased cell migration without affecting the viability of glioblastoma cells. Furthermore, in silico analysis showed that the elements of IFN-γ signaling pathways (IFNGR1/IFNGR2/STAT1/IRF1) are upregulated in human glioblastoma samples. The upregulation of IFN-γ signaling was associated with shorter survival in glioblastoma patients. CONCLUSION IFN-γ signaling pathway is upregulated in glioblastoma, displaying pro-tumor activity. Thus, IFN-γ signaling elements may be potential biomarkers and targets for treating glioblastoma.
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Toner J, Gordon JAR, Greenyer H, Kaufman P, Stein JL, Stein GS, Lian JB. RUNX2 as a Prognostic Factor in Human Cancers. Crit Rev Eukaryot Gene Expr 2024; 34:51-66. [PMID: 39072409 DOI: 10.1615/critreveukaryotgeneexpr.2024054162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The RUNX2 transcription factor was discovered as an essential transcriptional regulator for commitment to osteoblast lineage cells and bone formation. Expression of RUNX2 in other tissues, such as breast, prostate, and lung, has been linked to oncogenesis, cancer progression, and metastasis. In this study, we sought to determine the extent of RUNX2 involvement in other tumors using a pan-cancer analysis strategy. We correlated RUNX2 expression and clinical-pathological parameters in human cancers by interrogating publicly available multiparameter clinical data. Our analysis demonstrated that altered RUNX2 expression or function is associated with several cancer types from different tissues. We identified three tumor types associated with increased RUNX2 expression and four other tumor types associated with decreased RUNX2 expression. Our pan-cancer analysis for RUNX2 revealed numerous other discoveries for RUNX2 regulation of different cancers identified in each of the pan-cancer databases. Both up and down regulation of RUNX2 was observed during progression of specific types of cancers in promoting the distinct types of cancers.
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Affiliation(s)
- J Toner
- Department of Biochemistry, University of Vermont, Larner College of Medicine, Burlington, VT, 05405, USA
| | - Johnathan A R Gordon
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA; University of Vermont Cancer Center, Burlington, Vermont, USA
| | - H Greenyer
- Department of Biochemistry, University of Vermont, Larner College of Medicine, Burlington, VT, 05405, USA
| | - Peter Kaufman
- Hematology/Oncology Division, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Janet L Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405; University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Gary S Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405; University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Jane B Lian
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405; University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
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ZENG SHUANGSHUANG, CHEN XI, YI QIAOLI, THAKUR ABHIMANYU, YANG HUI, YAN YUANLIANG, LIU SHAO. CRABP2 regulates infiltration of cancer-associated fibroblasts and immune response in melanoma. Oncol Res 2023; 32:261-272. [PMID: 38186580 PMCID: PMC10765133 DOI: 10.32604/or.2023.042345] [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: 05/26/2023] [Accepted: 07/31/2023] [Indexed: 01/09/2024] Open
Abstract
Finding biomarkers for immunotherapy is an urgent issue in cancer treatment. Cellular retinoic acid-binding protein 2 (CRABP2) is a controversial factor in the occurrence and development of human tumors. However, there is limited research on the relationship between CRABP2 and immunotherapy response. This study found that negative correlations of CRABP2 and immune checkpoint markers (PD-1, PD-L1, and CTLA-4) were observed in breast invasive carcinoma (BRCA), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD) and testicular germ cell tumors (TGCT). In particular, in SKCM patients who were treated with PD-1 inhibitors, high levels of CRABP2 predicted poor prognosis. Additionally, CRABP2 expression was elevated in cancer-associated fibroblasts (CAFs) at the single-cell level. The expression of CRABP2 was positively correlated with markers of CAFs, such as MFAP5, PDPN, ITGA11, PDGFRα/β and THY1 in SKCM. To validate the tumor-promoting effect of CRABP2 in vivo, SKCM xenograft mice models with CRABP2 overexpression have been constructed. These models showed an increase in tumor weight and volume. Enrichment analysis indicated that CRABP2 may be involved in immune-related pathways of SKCM, such as extracellular matrix (ECM) receptor interaction and epithelial-mesenchymal transition (EMT). The study suggests that CRABP2 may regulate immunotherapy in SKCM patients by influencing infiltration of CAFs. In conclusion, this study provides new insights into the role of CRABP2 in immunotherapy response. The findings suggest that CRABP2 may be a promising biomarker for PD-1 inhibitors in SKCM patients. Further research is needed to confirm these findings and to explore the clinical implications of CRABP2 in immunotherapy.
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Affiliation(s)
- SHUANGSHUANG ZENG
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - XI CHEN
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - QIAOLI YI
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - ABHIMANYU THAKUR
- Pritzker School of Molecular Engineering, Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - HUI YANG
- Department of Pathology, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - YUANLIANG YAN
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - SHAO LIU
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
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50
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Fontana F, Esser AK, Egbulefu C, Karmakar P, Su X, Allen JS, Xu Y, Davis JL, Gabay A, Xiang J, Kwakwa KA, Manion B, Bakewell S, Li S, Park H, Lanza GM, Achilefu S, Weilbaecher KN. Transferrin receptor in primary and metastatic breast cancer: Evaluation of expression and experimental modulation to improve molecular targeting. PLoS One 2023; 18:e0293700. [PMID: 38117806 PMCID: PMC10732420 DOI: 10.1371/journal.pone.0293700] [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: 08/09/2023] [Accepted: 10/17/2023] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Conjugation of transferrin (Tf) to imaging or nanotherapeutic agents is a promising strategy to target breast cancer. Since the efficacy of these biomaterials often depends on the overexpression of the targeted receptor, we set out to survey expression of transferrin receptor (TfR) in primary and metastatic breast cancer samples, including metastases and relapse, and investigate its modulation in experimental models. METHODS Gene expression was investigated by datamining in twelve publicly-available datasets. Dedicated Tissue microarrays (TMAs) were generated to evaluate matched primary and bone metastases as well as and pre and post chemotherapy tumors from the same patient. TMA were stained with the FDA-approved MRQ-48 antibody against TfR and graded by staining intensity (H-score). Patient-derived xenografts (PDX) and isogenic metastatic mouse models were used to study in vivo TfR expression and uptake of transferrin. RESULTS TFRC gene and protein expression were high in breast cancer of all subtypes and stages, and in 60-85% of bone metastases. TfR was detectable after neoadjuvant chemotherapy, albeit with some variability. Fluorophore-conjugated transferrin iron chelator deferoxamine (DFO) enhanced TfR uptake in human breast cancer cells in vitro and proved transferrin localization at metastatic sites and correlation of tumor burden relative to untreated tumor mice. CONCLUSIONS TfR is expressed in breast cancer, primary, metastatic, and after neoadjuvant chemotherapy. Variability in expression of TfR suggests that evaluation of the expression of TfR in individual patients could identify the best candidates for targeting. Further, systemic iron chelation with DFO may upregulate receptor expression and improve uptake of therapeutics or tracers that use transferrin as a homing ligand.
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Affiliation(s)
- Francesca Fontana
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alison K. Esser
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Christopher Egbulefu
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Partha Karmakar
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Xinming Su
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - John S. Allen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Yalin Xu
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jennifer L. Davis
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Ariel Gabay
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jingyu Xiang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Kristin A. Kwakwa
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Brad Manion
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Suzanne Bakewell
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Shunqiang Li
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Haeseong Park
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Gregory M. Lanza
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Samuel Achilefu
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Katherine N. Weilbaecher
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
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