1
|
Kwon H, Joh JY, Hong KU. Human CKAP2L shows a cell cycle-dependent expression pattern and exhibits microtubule-stabilizing properties. FEBS Open Bio 2024. [PMID: 39073037 DOI: 10.1002/2211-5463.13864] [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: 10/31/2023] [Revised: 04/30/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
Cytoskeleton-associated protein 2-like (CKAP2L) is a paralogue of cytoskeleton-associated protein 2 (CKAP2). We characterized the expression pattern, subcellular localization, and microtubule-stabilizing properties of human CKAP2L. The levels of both CKAP2L transcript and protein were cell cycle phase-dependent, peaking during the G2/M phase and relatively high in certain human tissues, including testis, intestine, and spleen. CKAP2L protein was detectable in all human cancer cell lines we tested. CKAP2L localized to the mitotic spindle apparatus during mitosis, as reported previously. During interphase, however, CKAP2L localized mainly to the nucleus. Ectopic overexpression of CKAP2L resulted in 'microtubule bundling', and, consequently, an elevated CKAP2L level led to prolonged mitosis. These findings support the mitotic role of CKAP2L during the human cell cycle.
Collapse
Affiliation(s)
- Hyerim Kwon
- School of Medicine, Sungkyunkwan University, Suwon, Korea
| | - Jonathan Y Joh
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, KY, USA
| | - Kyung U Hong
- College of Pharmacy and Health Sciences, Western New England University, Springfield, MA, USA
| |
Collapse
|
2
|
Sato T, Oshi M, Huang JL, Chida K, Roy AM, Endo I, Takabe K. CD133 expression is associated with less DNA repair, better response to chemotherapy and survival in ER-positive/HER2-negative breast cancer. Breast Cancer Res Treat 2024:10.1007/s10549-024-07434-3. [PMID: 39017815 DOI: 10.1007/s10549-024-07434-3] [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: 03/22/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
PURPOSE CD133, a cancer stem cells (CSC) marker, has been reported to be associated with treatment resistance and worse survival in triple-negative breast cancer (BC). However, the clinical relevance of CD133 expression in ER-positive/HER2-negative (ER + /HER2-) BC, the most abundant subtype, remains unknown. METHODS The BC cohorts from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC, n = 1904) and The Cancer Genome Atlas (TCGA, n = 1065) were used to obtain biological variables and gene expression data. RESULTS Epithelial cells were the exclusive source of CD133 gene expression in a bulk BC. CD133-high ER + /HER2- BC was associated with CD24, NOTCH1, DLL1, and ALDH1A1 gene expressions, as well as with WNT/β-Catenin, Hedgehog, and Notch signaling pathways, all characteristic for CSC. Consistent with a CSC phenotype, CD133-low BC was enriched with gene sets related to cell proliferation, such as G2M Checkpoint, MYC Targets V1, E2F Targets, and Ki67 gene expression. CD133-low BC was also linked with enrichment of genes related to DNA repair, such as BRCA1, E2F1, E2F4, CDK1/2. On the other hand, CD133-high tumors had proinflammatory microenvironment, higher activity of immune cells, and higher expression of genes related to inflammation and immune response. Finally, CD133-high tumors had better pathological complete response after neoadjuvant chemotherapy in GSE25066 cohort and better disease-free survival and overall survival in both TCGA and METABRIC cohorts. CONCLUSION CD133-high ER + /HER2- BC was associated with CSC phenotype such as less cell proliferation and DNA repair, but also with enhanced inflammation, better response to neoadjuvant chemotherapy and better prognosis.
Collapse
Affiliation(s)
- Takumi Sato
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
- University of Tokyo Hospital, Tokyo, 113-8655, Japan
- National Hospital Organization Disaster Medical Center, Tokyo, 190-0014, Japan
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Jing Li Huang
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Kohei Chida
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
- Department of Gastroenterological Surgery, Hirosaki University Graduate School of Medicine, Hirosaki, 036-8562, Japan
| | - Arya Mariam Roy
- Department of Medical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA.
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY, 14263, USA.
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8520, Japan.
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, 960-1295, Japan.
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402, Japan.
| |
Collapse
|
3
|
Chen X, Sun H, Yang C, Wang W, Lyu W, Zou K, Zhang F, Dai Z, He X, Dong H. Bioinformatic analysis and experimental validation of six cuproptosis-associated genes as a prognostic signature of breast cancer. PeerJ 2024; 12:e17419. [PMID: 38912044 PMCID: PMC11192027 DOI: 10.7717/peerj.17419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/28/2024] [Indexed: 06/25/2024] Open
Abstract
Background Breast carcinoma (BRCA) is a life-threatening malignancy in women and shows a poor prognosis. Cuproptosis is a novel mode of cell death but its relationship with BRCA is unclear. This study attempted to develop a cuproptosis-relevant prognostic gene signature for BRCA. Methods Cuproptosis-relevant subtypes of BRCA were obtained by consensus clustering. Differential expression analysis was implemented using the 'limma' package. Univariate Cox and multivariate Cox analyses were performed to determine a cuproptosis-relevant prognostic gene signature. The signature was constructed and validated in distinct datasets. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were also conducted using the prognostic signature to uncover the underlying molecular mechanisms. ESTIMATE and CIBERSORT algorithms were applied to probe the linkage between the gene signature and tumor microenvironment (TME). Immunotherapy responsiveness was assessed using the Tumor Immune Dysfunction and Exclusion (TIDE) web tool. Real-time quantitative PCR (RT-qPCR) was performed to detect the expressions of cuproptosis-relevant prognostic genes in breast cancer cell lines. Results Thirty-eight cuproptosis-associated differentially expressed genes (DEGs) in BRCA were mined by consensus clustering and differential expression analysis. Based on univariate Cox and multivariate Cox analyses, six cuproptosis-relevant prognostic genes, namely SAA1, KRT17, VAV3, IGHG1, TFF1, and CLEC3A, were mined to establish a corresponding signature. The signature was validated using external validation sets. GSVA and GSEA showed that multiple cell cycle-linked and immune-related pathways along with biological processes were associated with the signature. The results ESTIMATE and CIBERSORT analyses revealed significantly different TMEs between the two Cusig score subgroups. Finally, RT-qPCR analysis of cell lines further confirmed the expressional trends of SAA1, KRT17, IGHG1, and CLEC3A. Conclusion Taken together, we constructed a signature for projecting the overall survival of BRCA patients and our findings authenticated the cuproptosis-relevant prognostic genes, which are expected to provide a basis for developing prognostic molecular biomarkers and an in-depth understanding of the relationship between cuproptosis and BRCA.
Collapse
Affiliation(s)
- Xiang Chen
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Hening Sun
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Changcheng Yang
- Department of The First Affiliated Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Wei Wang
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Wenzhi Lyu
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Kejian Zou
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Fan Zhang
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Zhijun Dai
- Department of The First Affiliated Hospital, Zhejiang University, Hangzhou City, Zhejiang Province, China
| | - Xionghui He
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Huaying Dong
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| |
Collapse
|
4
|
Gan D, Zhu Y, Lu X, Li J. SCIPAC: quantitative estimation of cell-phenotype associations. Genome Biol 2024; 25:119. [PMID: 38741183 PMCID: PMC11089691 DOI: 10.1186/s13059-024-03263-1] [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: 01/30/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Numerous algorithms have been proposed to identify cell types in single-cell RNA sequencing data, yet a fundamental problem remains: determining associations between cells and phenotypes such as cancer. We develop SCIPAC, the first algorithm that quantitatively estimates the association between each cell in single-cell data and a phenotype. SCIPAC also provides a p-value for each association and applies to data with virtually any type of phenotype. We demonstrate SCIPAC's accuracy in simulated data. On four real cancerous or noncancerous datasets, insights from SCIPAC help interpret the data and generate new hypotheses. SCIPAC requires minimum tuning and is computationally very fast.
Collapse
Affiliation(s)
- Dailin Gan
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, 46556, IN, USA
| | - Yini Zhu
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, 46556, IN, USA
| | - Xin Lu
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, 46556, IN, USA
- Tumor Microenvironment and Metastasis Program, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, 46202, IN, USA
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, 46556, IN, USA.
| |
Collapse
|
5
|
Mitra S, Biswas P, Bandyopadhyay A, Gadekar VS, Gopalakrishnan AV, Kumar M, Radha, Nandy S. Piperlongumine: the amazing amide alkaloid from Piper in the treatment of breast cancer. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2637-2650. [PMID: 37955690 DOI: 10.1007/s00210-023-02673-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/12/2023] [Indexed: 11/14/2023]
Abstract
Piperlongumine (PL), an alkaloid found primarily in the fruits and roots of the plant Piper longum L. (Piperaceae), is a natural compound that exhibits potent activity against various cancer cell proliferation. The most frequently caused malignancy in women globally, breast cancer (BC), has been demonstrated to be significantly inhibited by PL. Apoptosis, cell cycle arrest, increased ROS generation, and changes in the signalling protein's expression are all caused by the numerous signalling pathways that PL impacts. Since BC cells resist conventional chemotherapeutic drugs (doxorubicin, docetaxel etc.), researchers have shown that the drugs in combination with PL can exhibit a synergistic effect, greater than the effects of the drug or PL alone. Recently, techniques for drug packaging based on nanotechnology have been employed to improve PL release. The review has presented an outline of the chemistry of PL, its molecular basis in BC, its bioavailability, toxicity, and nanotechnological applications. An attempt to understand the future prospects and direction of research about the compound has also been discussed.
Collapse
Affiliation(s)
- Shatakshi Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Protha Biswas
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Anupriya Bandyopadhyay
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | | | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research On Cotton Technology, Mumbai, 400019, India
| | - Radha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173229, Himachal Pradesh, India
| | - Samapika Nandy
- Department of Botany, Vedanta College, 33A, Shiv Krishna Daw Lane, Phool Bagan, Kolkata, 700054, West Bengal, India.
- School of Pharmacy, Graphic Era Hill University, Bell Road, Clement Town, Dehradun, 248002, Uttarakhand, India.
| |
Collapse
|
6
|
Oshi M, Roy AM, Yan L, Kinoshita S, Tamura Y, Kosaka T, Akiyama H, Kunisaki C, Takabe K, Endo I. Enhanced epithelial-mesenchymal transition signatures are linked with adverse tumor microenvironment, angiogenesis and worse survival in gastric cancer. Cancer Gene Ther 2024; 31:746-754. [PMID: 38532115 DOI: 10.1038/s41417-024-00756-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024]
Abstract
Epithelial-mesenchymal transition (EMT) is a crucial mechanism that facilitates cancer cell metastasis. Despite its importance, the clinical significance of EMT in gastric cancer (GC) patients has yet to be clearly demonstrated. For gauging the extent of EMT in GC, we employed gene set variation analysis to score 807 patient samples from two large cohorts: TCGA and GSE84437. In both cohorts, EMT high GC showed a significant association with worse overall survival (hazard ratio (HR) = 1.74, p = 0.011 and HR = 2.01, p < 0.001, respectively). This association was stronger when considering the EMT signature score compared to the individual expressions of EMT-related genes (CDH1, CDH2, VIM, and FN1). While the EMT signature level did not differ among various cancers, high EMT signature specifically correlated with survival in GC alone. Mucinous and diffuse histological types exhibited higher EMT levels compared to others (p < 0.001), and the EMT signature level was correlated with tumor depth and AJCC stage (all p < 0.001). Interestingly, the EMT score was an independent factor for overall and disease-specific survival (multivariate; p = 0.006 and 0.032, respectively). EMT high GC displayed a lower fraction of Th1 cells and a higher fraction of dendritic cells, M1 macrophages and several stromal cells. EMT high GC exhibited an inverse correlation with cell proliferation-related gene sets. While they significantly enriched multiple pro-cancerous gene sets, such as TGF-β signaling, hypoxia, and angiogenesis. The presence of EMT signature in a bulk tumor was linked to TGF-β signaling, hypoxia, and angiogenesis, and was also associated with poorer survival outcomes in GC patients.
Collapse
Affiliation(s)
- Masanori Oshi
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
| | - Arya Mariam Roy
- Department of Medical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Sachika Kinoshita
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Yuko Tamura
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Takashi Kosaka
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Hirotoshi Akiyama
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Chikara Kunisaki
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuaki Takabe
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY, 14263, USA
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, 960-1295, Japan
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| |
Collapse
|
7
|
Wang Z, Zheng Z, Wang B, Zhan C, Yuan X, Lin X, Xin Q, Zhong Z, Qiu X. Characterization of a G2M checkpoint-related gene model and subtypes associated with immunotherapy response for clear cell renal cell carcinoma. Heliyon 2024; 10:e29289. [PMID: 38617927 PMCID: PMC11015143 DOI: 10.1016/j.heliyon.2024.e29289] [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: 02/06/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) presents challenges in early diagnosis and effective treatment. In this study, we aimed to establish a prognostic model based on G2M checkpoint-related genes and identify associated clusters in ccRCC through clinical bioinformatic analysis and experimental validation. Utilizing a single-cell RNA dataset (GSE159115) and bulk-sequencing data from The Cancer Genome Atlas (TCGA) database, we analyzed the G2M checkpoint pathway in ccRCC. Differential expression analysis identified 45 genes associated with the G2M checkpoint, leading to the construction of a predictive model with four key genes (E2F2, GTSE1, RAD54L, and UBE2C). The model demonstrated reliable predictive ability for 1-, 3-, and 5-year overall survival, with AUC values of 0.794, 0.790, and 0.794, respectively. Patients in the high-risk group exhibited a worse prognosis, accompanied by significant differences in immune cell infiltration, immune function, TIDE and IPS scores, and drug sensitivities. Two clusters of ccRCC were identified using the "ConsensusClusterPlus" package, cluster 1 exhibited a worse survival rate and was resistant to chemotherapeutic drugs of Axitinib, Erlotinib, Pazopanib, Sunitinib, and Temsirolimus, but not Sorafenib. Targeted experiments on RAD54L, a gene involved in DNA repair processes, revealed its crucial role in inhibiting proliferation, invasion, and migration in 786-O cells. In conclusion, our study offers valuable insights into the molecular mechanisms underlying ccRCC, identifying potential prognostic genes and molecular subtypes associated with the G2M checkpoint. These findings hold promise for guiding personalized treatment strategies in the management of ccRCC.
Collapse
Affiliation(s)
- Zhenwei Wang
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Zongtai Zheng
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Bangqi Wang
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Changxin Zhan
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
- The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, 510317, China
| | - Xuefeng Yuan
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoqi Lin
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Qifan Xin
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Zhihui Zhong
- Center of Stem Cell and Regenerative Medicine, Gaozhou People's Hospital, Gaozhou, 525200, Guangdong, China
| | - Xiaofu Qiu
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
- The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, 510317, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| |
Collapse
|
8
|
Sato T, Oshi M, Huang JL, Chida K, Roy AM, Endo I, Takabe K. CD133 expression is associated with less DNA repair, better response to chemotherapy and survival in ER-positive/HER2-negative breast cancer. RESEARCH SQUARE 2024:rs.3.rs-4148608. [PMID: 38585981 PMCID: PMC10996805 DOI: 10.21203/rs.3.rs-4148608/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: 04/09/2024]
Abstract
Purpose CD133, a cancer stem cells (CSC) marker, has been reported to be associated with treatment resistance and worse survival in triple-negative breast cancer (BC). However, the clinical relevance of CD133 expression in ER-positive/HER2-negative (ER+/HER2-) BC, the most abundant subtype, remains unknown. Methods The BC cohorts from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC, n = 1904) and The Cancer Genome Atlas (TCGA, n = 1065) were used to obtain biological variables and gene expression data. Results Epithelial cells were the exclusive source of CD133 gene expression in a bulk BC. CD133-high ER+/HER2- BC was associated with CD24, NOTCH1, DLL1, and ALDH1A1 gene expressions, as well as with WNT/β-Catenin, Hedgehog, and Notchsignaling pathways, all characteristic for CSC. Consistent with a CSC phenotype, CD133-low BC was enriched with gene sets related to cell proliferation, such as G2M Checkpoint, MYC Targets V1, E2F Targets, and Ki67 gene expression. CD133-low BC was also linked with enrichment of genes related to DNA repair, such as BRCA1, E2F1, E2F4, CDK1/2. On the other hand, CD133-high tumors had proinflammatory microenvironment, higher activity of immune cells, and higher expression of genes related to inflammation and immune response. Finally, CD133-high tumors had better pathological complete response after neoadjuvant chemotherapy in GSE25066 cohort and better disease-free survival and overall survival in both TCGA and METABRIC cohorts. Conclusion CD133-high ER+/HER2- BC was associated with CSC phenotype such as less cell proliferation and DNA repair, but also with enhanced inflammation, better response to neoadjuvant chemotherapy and better prognosis.
Collapse
Affiliation(s)
| | - Masanori Oshi
- Yokohama City University Graduate School of Medicine
| | | | | | | | - Itaru Endo
- Yokohama City University Graduate School of Medicine
| | | |
Collapse
|
9
|
Xie B, Olalekan S, Back R, Ashitey NA, Eckart H, Basu A. Exploring the tumor micro-environment in primary and metastatic tumors of different ovarian cancer histotypes. Front Cell Dev Biol 2024; 11:1297219. [PMID: 38328306 PMCID: PMC10847324 DOI: 10.3389/fcell.2023.1297219] [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: 09/19/2023] [Accepted: 12/06/2023] [Indexed: 02/09/2024] Open
Abstract
Ovarian cancer is a highly heterogeneous disease consisting of at least five different histological subtypes with varying clinical features, cells of origin, molecular composition, risk factors, and treatments. While most single-cell studies have focused on High grade serous ovarian cancer, a comprehensive landscape of the constituent cell types and their interactions within the tumor microenvironment are yet to be established in the different ovarian cancer histotypes. Further characterization of tumor progression, metastasis, and various histotypes are also needed to connect molecular signatures to pathological grading for personalized diagnosis and tailored treatment. In this study, we leveraged high-resolution single-cell RNA sequencing technology to elucidate the cellular compositions on 21 solid tumor samples collected from 12 patients with six ovarian cancer histotypes and both primary (ovaries) and metastatic (omentum, rectum) sites. The diverse collection allowed us to deconstruct the histotypes and tumor site-specific expression patterns of cells in the tumor, and identify key marker genes and ligand-receptor pairs that are active in the ovarian tumor microenvironment. Our findings can be used in improving precision disease stratification and optimizing treatment options.
Collapse
Affiliation(s)
- Bingqing Xie
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, United States
| | | | | | | | | | - Anindita Basu
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, United States
| |
Collapse
|
10
|
Chida K, Oshi M, An N, Kanazawa H, Roy AM, Mann GK, Yan L, Endo I, Hakamada K, Takabe K. Gastric cancer with enhanced myogenesis is associated with less cell proliferation, enriched epithelial-to-mesenchymal transition and angiogenesis, and poor clinical outcomes. Am J Cancer Res 2024; 14:355-367. [PMID: 38323295 PMCID: PMC10839307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Gastric cancer (GC) remains a lethal disease, with over 26,000 new cases and more than 11,000 deaths annually in the US. Thus, a deeper understanding of GC biology is critical to improve survival. Myogenesis is the formation of muscle fibers, which is a mesodermal tissue. In cancer, epithelial-to-mesenchymal transition (EMT) is a known phenomenon that promotes metastasis and poor survival. Given that myogenesis produces mesenchymal cells, we hypothesized that GC with increased myogenesis is linked to aggressive tumor behaviors and less favorable outcomes. In this study, three GC patient cohorts: TCGA (n=375), GSE26253 (n=432), and GSE84437 (n=482), were analyzed. The "MYOGENESIS" set in the Hallmark collection which comprises 200 myogenesis-related genes was analyzed to perform gene set variation analysis to create a score to quantify the myogenesis activity. Our results showed that T category of AJCC cancer staging that reflects the tumor invasion to stomach wall consistently correlated with myogenesis activity in two GC cohorts. High myogenesis GC was associated with lower cell proliferation, evidenced by reduced proliferation scores, decreased Ki67 gene expression, and less enrichment of E2F Targets, G2M checkpoint, MYC Targets V1, and V2 gene sets. High myogenesis tumors showed increased stromal cells (fibroblasts and adipocytes) infiltration within the tumor microenvironment, as well as less silent and non-silent mutation rates and copy number alterations. Higher lymphocyte infiltration, leukocyte fraction, T-cell receptor richness, and B-cell receptor richness were associated with high myogenesis GC. However, infiltration of CD4 cells, T helper type 1 and 2 cells, Natural Killer cells, regulatory T cells, and plasma cells was lower, with increased infiltration of dendritic cells in high myogenesis GC. High myogenesis GC enriched EMT, Hedgehog, TGF-β, and KRAS gene sets. Furthermore, it was associated with enhanced angiogenesis, evidenced by enrichment of Angiogenesis, Coagulation, and Hypoxia gene sets, and increased infiltration of microvascular and lymphatic endothelial cells and pericytes. High myogenesis GC consistently correlated with worse overall survival in all three cohorts, and worse disease-specific and progression-free survival in the TCGA cohort. Hence, our findings suggest that GC with enhanced myogenesis is associated with decreased cell proliferation, increased EMT and angiogenesis, and worse prognosis.
Collapse
Affiliation(s)
- Kohei Chida
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Gastroenterological Surgery, Hirosaki University Graduate School of MedicineHirosaki 036-8562, Japan
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
| | - Nan An
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Hirofumi Kanazawa
- The University of Texas Health Science Center at Tyler School of MedicineTyler, TX 11937, USA
| | - Arya M Roy
- Department of Hematology and Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Gabriella K Mann
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
| | - Kenichi Hakamada
- Department of Gastroenterological Surgery, Hirosaki University Graduate School of MedicineHirosaki 036-8562, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New YorkBuffalo, NY 14263, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata 951-8510, Japan
- Department of Breast Surgery, Fukushima Medical University School of MedicineFukushima 960-1295, Japan
| |
Collapse
|
11
|
Zhu J, Li Q, Wu Z, Xu Y, Jiang R. Curcumin for Treating Breast Cancer: A Review of Molecular Mechanisms, Combinations with Anticancer Drugs, and Nanosystems. Pharmaceutics 2024; 16:79. [PMID: 38258090 PMCID: PMC10819793 DOI: 10.3390/pharmaceutics16010079] [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: 12/01/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Breast cancer (BC) has become the fifth most prevalent cause of cancer-related morbidity, attracting significant attention from researchers due to its heightened malignancy and drug resistance. Conventional chemotherapy approaches have proven inadequate in addressing all BC subtypes, highlighting the urgent need for novel therapeutic approaches or drugs. Curcumin (CUR), a phytochemical derived from Curcuma longa (turmeric), has shown substantial potential in inhibiting BC cell migration, metastasis, and proliferation. However, the use of CUR in this context comes with challenges due to its dynamic and easily degradable nature, poor aqueous solubility, low bioavailability, rapid metabolism, and swift systemic elimination, collectively limiting its clinical applications. As such, we provide an overview of the properties, synthesis, and characterization of the hybridization of CUR and its analogue with chemo-drug building blocks. We reviewed research from the last five years on CUR's biogenesis with respect to the regulation of BC, revealing that CUR participates in arresting BC cells in the cell cycle and significantly induces apoptosis in BC cells. Information on the chemotherapeutic and antitumor mechanisms of CUR in BC, including regulation of the cell cycle, increased cell apoptosis, and inhibition of multidrug resistance (MDR), was compiled. Additionally, we provide an overview of CUR loaded into nanomaterials that are cotreated with other chemotherapeutic drugs, such as paclitaxel, thymoquinone, and tamoxifen. In this review, we discuss different types of nanoparticles that can be used for CUR delivery, such as polymeric nanoparticles, carbon nanotubes, and liposomes. By comparing the size, entrapment efficiency, drug-loading capacity, release time, biocompatibility, pharmaceutical scale, and reproducibility of various nanomaterials, we aimed to determine which formulations are better suited for loading CUR or its analogue. Ultimately, this review is expected to offer inspiring ideas, promising strategies, and potential pathways for developing advanced anti-BC strategy nanosystems in clinical practice.
Collapse
Affiliation(s)
- Jing Zhu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (J.Z.); (Z.W.)
| | - Qian Li
- Medical Department, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China;
| | - Zhongping Wu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (J.Z.); (Z.W.)
| | - Ying Xu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (J.Z.); (Z.W.)
| | - Rilei Jiang
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (J.Z.); (Z.W.)
| |
Collapse
|
12
|
Singh A, Mishra R, Mazumder A. Breast cancer and its therapeutic targets: A comprehensive review. Chem Biol Drug Des 2024; 103:e14384. [PMID: 37919259 DOI: 10.1111/cbdd.14384] [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: 05/20/2023] [Revised: 09/14/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Breast cancer is a common and deadly disease, so there is a constant need for research to find efficient targets and therapeutic approaches. Breast cancer can be classified on a molecular and histological base. Breast cancer can be divided into ER (estrogen receptor)-positive and ER-negative, HER2 (human epidermal growth factor receptor2)-positive and HER2-negative subtypes based on the presence of specific biomarkers. Targeting hormone receptors, such as the HER2, progesterone receptor (PR), and ER, is very significant and plays a vital role in the onset and progression of breast cancer. Endocrine treatments and HER2-targeted drugs are examples of targeted therapies now being used against these receptors. Emerging immune-based medicines with promising outcomes in the treatment of breast cancer include immune checkpoint inhibitors, cancer vaccines, and adoptive T-cell therapy. It is also explored how immune cells and the tumor microenvironment affect breast cancer development and treatment response. The major biochemical pathways, signaling cascades, and DNA repair mechanisms that are involved in the development and progression of breast cancer, include the PI3K/AKT/mTOR system, the MAPK pathway, and others. These pathways are intended to be inhibited by a variety of targeted drugs, which are then delivered with the goal of restoring normal cellular function. This review aims to shed light on types of breast cancer with the summarization of different therapeutic approaches which can target different pathways for tailored medicines and better patient outcomes.
Collapse
Affiliation(s)
- Ayushi Singh
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
| | - Rakhi Mishra
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
| | - Avijit Mazumder
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
| |
Collapse
|
13
|
Cai WL, Cheng M, Wang Y, Xu PH, Yang X, Sun ZW, Wang-Jun Yan. Prediction and related genes of cancer distant metastasis based on deep learning. Comput Biol Med 2024; 168:107664. [PMID: 38000245 DOI: 10.1016/j.compbiomed.2023.107664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/27/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023]
Abstract
Cancer metastasis is one of the main causes of cancer progression and difficulty in treatment. Genes play a key role in the process of cancer metastasis, as they can influence tumor cell invasiveness, migration ability and fitness. At the same time, there is heterogeneity in the organs of cancer metastasis. Breast cancer, prostate cancer, etc. tend to metastasize in the bone. Previous studies have pointed out that the occurrence of metastasis is closely related to which tissue is transferred to and genes. In this paper, we identified genes associated with cancer metastasis to different tissues based on LASSO and Pearson correlation coefficients. In total, we identified 45 genes associated with bone metastases, 89 genes associated with lung metastases, and 86 genes associated with liver metastases. Through the expression of these genes, we propose a CNN-based model to predict the occurrence of metastasis. We call this method MDCNN, which introduces a modulation mechanism that allows the weights of convolution kernels to be adjusted at different positions and feature maps, thereby adaptively changing the convolution operation at different positions. Experiments have proved that MDCNN has achieved satisfactory prediction accuracy in bone metastasis, lung metastasis and liver metastasis, and is better than other 4 methods of the same kind. We performed enrichment analysis and immune infiltration analysis on bone metastasis-related genes, and found multiple pathways and GO terms related to bone metastasis, and found that the abundance of macrophages and monocytes was the highest in patients with bone metastasis.
Collapse
Affiliation(s)
- Wei-Luo Cai
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, China
| | - Mo Cheng
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, China
| | - Yi Wang
- Department of Gastrointestinal Surgical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, China
| | - Pei-Hang Xu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, China
| | - Xi Yang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, China; Department of Oncology, Shanghai Medical College, Fudan University, China.
| | - Zheng-Wang Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, China.
| | - Wang-Jun Yan
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, China.
| |
Collapse
|
14
|
Giordano C, Accattatis FM, Gelsomino L, Del Console P, Győrffy B, Giuliano M, Veneziani BM, Arpino G, De Angelis C, De Placido P, Pietroluongo E, Zinno F, Bonofiglio D, Andò S, Barone I, Catalano S. miRNAs in the Box: Potential Diagnostic Role for Extracellular Vesicle-Packaged miRNA-27a and miRNA-128 in Breast Cancer. Int J Mol Sci 2023; 24:15695. [PMID: 37958677 PMCID: PMC10649351 DOI: 10.3390/ijms242115695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Circulating extracellular vesicle (EV)-derived microRNAs (miRNAs) are now considered the next generation of cancer "theranostic" tools, with strong clinical relevance. Although their potential in breast cancer diagnosis has been widely reported, further studies are still required to address this challenging issue. The present study examined the expression profiles of EV-packaged miRNAs to identify novel miRNA signatures in breast cancer and verified their diagnostic accuracy. Circulating EVs were isolated from healthy controls and breast cancer patients and characterized following the MISEV 2018 guidelines. RNA-sequencing and real-time PCR showed that miRNA-27a and miRNA-128 were significantly down-regulated in patient-derived EVs compared to controls in screening and validation cohorts. Bioinformatics analyses of miRNA-target genes indicated several enriched biological processes/pathways related to breast cancer. Receiver operating characteristic (ROC) curves highlighted the ability of these EV-miRNAs to distinguish breast cancer patients from non-cancer controls. According to other reports, the levels of EV-miRNA-27a and EV-miRNA-128 are not associated with their circulating ones. Finally, evidence from the studies included in our systematic review underscores how the expression of these miRNAs in biofluids is still underinvestigated. Our findings unraveled the role of serum EV-derived miRNA-27a and miRNA-128 in breast cancer, encouraging further investigation of these two miRNAs within EVs towards improved breast cancer detection.
Collapse
Affiliation(s)
- Cinzia Giordano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Clinical Laboratory Unit, A.O. “Annunziata”, 87100 Cosenza, Italy
| | - Felice Maria Accattatis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Luca Gelsomino
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Piercarlo Del Console
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Balázs Győrffy
- Departments of Bioinformatics and Pediatrics, Semmelweis University, 1094 Budapest, Hungary;
- TTK Cancer Biomarker Research Group, 1117 Budapest, Hungary
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Bianca Maria Veneziani
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80133 Naples, Italy;
| | - Grazia Arpino
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Pietro De Placido
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Erica Pietroluongo
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Francesco Zinno
- Immunohaematology and Transfusion Medicine, A.O. “Annunziata”, 87100 Cosenza, Italy;
| | - Daniela Bonofiglio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Ines Barone
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Stefania Catalano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Clinical Laboratory Unit, A.O. “Annunziata”, 87100 Cosenza, Italy
| |
Collapse
|
15
|
Navarro-Yepes J, Kettner NM, Rao X, Bishop CS, Bui TN, Wingate HF, Raghavendra AS, Wang Y, Wang J, Sahin AA, Meric-Bernstam F, Hunt KK, Damodaran S, Tripathy D, Keyomarsi K. Abemaciclib Is Effective in Palbociclib-Resistant Hormone Receptor-Positive Metastatic Breast Cancers. Cancer Res 2023; 83:3264-3283. [PMID: 37384539 PMCID: PMC10592446 DOI: 10.1158/0008-5472.can-23-0705] [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: 04/21/2023] [Revised: 05/31/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023]
Abstract
Cyclin-dependent kinases 4/6 inhibitor (CDK4/6i) plus endocrine therapy (ET) is standard of care for patients with hormone receptor (HR)-positive, HER2-negative metastatic breast cancer (MBC). However, resistance to CDK4/6is plus ET remains a clinical problem with limited therapeutic options following disease progression. Different CDK4/6is might have distinct mechanisms of resistance, and therefore using them sequentially or targeting their differentially altered pathways could delay disease progression. To understand pathways leading to resistance to the CDK4/6is palbociclib and abemaciclib, we generated multiple in vitro models of palbociclib-resistant (PR) and abemaciclib-resistant (AR) cell lines as well as in vivo patient-derived xenografts (PDX) and ex vivo PDX-derived organoids (PDxO) from patients who progressed on CDK4/6i. PR and AR breast cancer cells exhibited distinct transcriptomic and proteomic profiles that sensitized them to different classes of inhibitors; PR cells upregulated G2-M pathways and responded to abemaciclib, while AR cells upregulated mediators of the oxidative phosphorylation pathway (OXPHOS) and responded to OXPHOS inhibitors. PDX and organoid models derived from patients with PR breast cancer remained responsive to abemaciclib. Resistance to palbociclib while maintaining sensitivity to abemaciclib was associated with pathway-specific transcriptional activity but was not associated with any individual genetic alterations. Finally, data from a cohort of 52 patients indicated that patients with HR-positive/HER2-negative MBC who progressed on palbociclib-containing regimens can exhibit a meaningful overall clinical benefit from abemaciclib-based therapy when administered after palbociclib. These findings provide the rationale for clinical trials evaluating the benefit of abemaciclib treatment following progression on a prior CDK4/6i. SIGNIFICANCE Palbociclib-resistant breast cancers respond to abemaciclib and express pathway-specific signatures of sensitivity, providing a biomarker-driven therapeutic option for patients with metastatic breast cancer following disease progression on cyclin-dependent kinases 4/6 inhibitors.
Collapse
Affiliation(s)
- Juliana Navarro-Yepes
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicole M. Kettner
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiayu Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cassandra Santaella Bishop
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tuyen N. Bui
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hannah F. Wingate
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Yan Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aysegul A. Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kelly K. Hunt
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Senthil Damodaran
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Debasish Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
16
|
Swapna LS, Huang M, Li Y. GTM-decon: guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes. Genome Biol 2023; 24:190. [PMID: 37596691 PMCID: PMC10436670 DOI: 10.1186/s13059-023-03034-4] [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: 12/22/2022] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
Cell-type composition is an important indicator of health. We present Guided Topic Model for deconvolution (GTM-decon) to automatically infer cell-type-specific gene topic distributions from single-cell RNA-seq data for deconvolving bulk transcriptomes. GTM-decon performs competitively on deconvolving simulated and real bulk data compared with the state-of-the-art methods. Moreover, as demonstrated in deconvolving disease transcriptomes, GTM-decon can infer multiple cell-type-specific gene topic distributions per cell type, which captures sub-cell-type variations. GTM-decon can also use phenotype labels from single-cell or bulk data to infer phenotype-specific gene distributions. In a nested-guided design, GTM-decon identified cell-type-specific differentially expressed genes from bulk breast cancer transcriptomes.
Collapse
Affiliation(s)
| | - Michael Huang
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - Yue Li
- School of Computer Science, McGill University, Montreal, QC, Canada.
| |
Collapse
|
17
|
Chida K, Oshi M, Roy AM, Yachi T, Nara M, Yamada K, Matsuura O, Hashizume T, Endo I, Takabe K. E2F target score is associated with cell proliferation and survival of patients with hepatocellular carcinoma. Surgery 2023; 174:307-314. [PMID: 37198038 PMCID: PMC10524872 DOI: 10.1016/j.surg.2023.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/28/2023] [Accepted: 04/09/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND E2F target genes are essential for the cell cycle. A score that quantifies its activity is expected to reflect the aggressiveness and prognosis of hepatocellular carcinoma. METHODS Cohorts of hepatocellular carcinoma patients (total n = 655) from The Cancer Genome Atlas, GSE89377, GSE76427, and GSE6764 were analyzed. The cohorts were divided into high versus low by the median. RESULTS All the Hallmark cell proliferation-related gene sets were consistently enriched in hepatocellular carcinoma with high E2F targets score, and E2F score was associated with grade, tumor size, American Joint Committee on Cancer staging, proliferation score, and MKI67 expression, as well as with less abundance of hepatocytes and stromal cells. E2F targets enriched DNA repair, mTORC1 signaling, glycolysis, and unfolded protein response gene sets and were significantly associated with the higher intratumoral genomic heterogeneity, homologous recombination deficiency, and progression of hepatocellular carcinoma. On the other hand, there was no relationship between E2F targets and mutation rates or neoantigens. High E2F hepatocellular carcinoma did not enrich any of the immune-response-related gene sets but was associated with high infiltration of Th1, Th2 cells, and M2 macrophage; however, there was no difference in cytolytic activity. In both early (I and II) and late (III and IV) stages of hepatocellular carcinoma, a high E2F score was associated with worse survival and was an independent prognostic factor for overall and disease-specific survival in patients with hepatocellular carcinoma. CONCLUSION The E2F target score, associated with cancer aggressiveness and worse survival, could be used as a prognostic biomarker in patients with hepatocellular carcinoma.
Collapse
Affiliation(s)
- Kohei Chida
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY; Department of Surgery, Mutsu General Hospital, Aomori, Japan. http://www.twitter.com/koheichida1
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY; Department of Gastroenterological Surgery, Yokohama, Kanagawa, Japan
| | - Arya Mariam Roy
- Department of Medical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Takafumi Yachi
- Department of Surgery, Mutsu General Hospital, Aomori, Japan
| | - Masaki Nara
- Department of Surgery, Mutsu General Hospital, Aomori, Japan
| | - Kyogo Yamada
- Department of Surgery, Mutsu General Hospital, Aomori, Japan
| | - Osamu Matsuura
- Department of Surgery, Mutsu General Hospital, Aomori, Japan
| | | | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama, Kanagawa, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY; Department of Gastroenterological Surgery, Yokohama, Kanagawa, Japan; Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, NY; Department of Breast Surgery and Oncology, Tokyo Medical University, Japan; Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Japan; Department of Breast Surgery, Fukushima Medical University School of Medicine, Japan; Department of Breast Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY.
| |
Collapse
|
18
|
Wörthmüller J, Disler S, Pradervand S, Richard F, Haerri L, Ruiz Buendía GA, Fournier N, Desmedt C, Rüegg C. MAGI1 Prevents Senescence and Promotes the DNA Damage Response in ER + Breast Cancer. Cells 2023; 12:1929. [PMID: 37566008 PMCID: PMC10417439 DOI: 10.3390/cells12151929] [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: 05/09/2023] [Revised: 06/30/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
MAGI1 acts as a tumor suppressor in estrogen receptor-positive (ER+) breast cancer (BC), and its loss correlates with a more aggressive phenotype. To identify the pathways and events affected by MAGI1 loss, we deleted the MAGI1 gene in the ER+ MCF7 BC cell line and performed RNA sequencing and functional experiments in vitro. Transcriptome analyses revealed gene sets and biological processes related to estrogen signaling, the cell cycle, and DNA damage responses affected by MAGI1 loss. Upon exposure to TNF-α/IFN-γ, MCF7 MAGI1 KO cells entered a deeper level of quiescence/senescence compared with MCF7 control cells and activated the AKT and MAPK signaling pathways. MCF7 MAGI1 KO cells exposed to ionizing radiations or cisplatin had reduced expression of DNA repair proteins and showed increased sensitivity towards PARP1 inhibition using olaparib. Treatment with PI3K and AKT inhibitors (alpelisib and MK-2206) restored the expression of DNA repair proteins and sensitized cells to fulvestrant. An analysis of human BC patients' transcriptomic data revealed that patients with low MAGI1 levels had a higher tumor mutational burden and homologous recombination deficiency. Moreover, MAGI1 expression levels negatively correlated with PI3K/AKT and MAPK signaling, which confirmed our in vitro observations. Pharmacological and genomic evidence indicate HDACs as regulators of MAGI1 expression. Our findings provide a new view on MAGI1 function in cancer and identify potential treatment options to improve the management of ER+ BC patients with low MAGI1 levels.
Collapse
Affiliation(s)
- Janine Wörthmüller
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Simona Disler
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Sylvain Pradervand
- Lausanne Genomic Technologies Facility (LGTF), University of Lausanne, 1015 Lausanne, Switzerland
| | - François Richard
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Lisa Haerri
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Gustavo A. Ruiz Buendía
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Nadine Fournier
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Curzio Rüegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| |
Collapse
|
19
|
Azher ZL, Suvarna A, Chen JQ, Zhang Z, Christensen BC, Salas LA, Vaickus LJ, Levy JJ. Assessment of emerging pretraining strategies in interpretable multimodal deep learning for cancer prognostication. BioData Min 2023; 16:23. [PMID: 37481666 PMCID: PMC10363299 DOI: 10.1186/s13040-023-00338-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/05/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Deep learning models can infer cancer patient prognosis from molecular and anatomic pathology information. Recent studies that leveraged information from complementary multimodal data improved prognostication, further illustrating the potential utility of such methods. However, current approaches: 1) do not comprehensively leverage biological and histomorphological relationships and 2) make use of emerging strategies to "pretrain" models (i.e., train models on a slightly orthogonal dataset/modeling objective) which may aid prognostication by reducing the amount of information required for achieving optimal performance. In addition, model interpretation is crucial for facilitating the clinical adoption of deep learning methods by fostering practitioner understanding and trust in the technology. METHODS Here, we develop an interpretable multimodal modeling framework that combines DNA methylation, gene expression, and histopathology (i.e., tissue slides) data, and we compare performance of crossmodal pretraining, contrastive learning, and transfer learning versus the standard procedure. RESULTS Our models outperform the existing state-of-the-art method (average 11.54% C-index increase), and baseline clinically driven models (average 11.7% C-index increase). Model interpretations elucidate consideration of biologically meaningful factors in making prognosis predictions. DISCUSSION Our results demonstrate that the selection of pretraining strategies is crucial for obtaining highly accurate prognostication models, even more so than devising an innovative model architecture, and further emphasize the all-important role of the tumor microenvironment on disease progression.
Collapse
Affiliation(s)
- Zarif L Azher
- Thomas Jefferson High School for Science and Technology, Alexandria, VA, USA
| | - Anish Suvarna
- Thomas Jefferson High School for Science and Technology, Alexandria, VA, USA
| | - Ji-Qing Chen
- Cancer Biology Graduate Program, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
- Program in Quantitative Biomedical Sciences, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
- Department of Epidemiology, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
| | - Ze Zhang
- Program in Quantitative Biomedical Sciences, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
- Department of Epidemiology, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
- Department of Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
- Department of Community and Family Medicine, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
- Department of Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
- Integrative Neuroscience at Dartmouth (IND) Graduate Program, Dartmouth College Geisel School of Medicine, Hanover, NH, USA
| | - Louis J Vaickus
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Health, Lebanon, NH, USA
| | - Joshua J Levy
- Program in Quantitative Biomedical Sciences, Dartmouth College Geisel School of Medicine, Hanover, NH, USA.
- Department of Epidemiology, Dartmouth College Geisel School of Medicine, Hanover, NH, USA.
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Health, Lebanon, NH, USA.
- Department of Dermatology, Dartmouth Health, Lebanon, NH, USA.
| |
Collapse
|
20
|
Oshi M, Roy AM, Yan L, Sasamoto M, Tokumaru Y, Wu R, Yamada A, Yamamoto S, Chishima T, Narui K, Endo I, Takabe K. Accelerated glycolysis in tumor microenvironment is associated with worse survival in triple-negative but not consistently with ER+/HER2- breast cancer. Am J Cancer Res 2023; 13:3041-3054. [PMID: 37559984 PMCID: PMC10408485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/06/2023] [Indexed: 08/11/2023] Open
Abstract
Metabolic reprogramming to sustain immortality is a hallmark of cancer and glycolysis is an important way to attain this. Thus, we investigate the association of glycolysis and associated pathways in the survival of breast cancer. A total of 5,176 breast cancer patients from multiple independent cohorts were analyzed. We determined the glycolytic signaling score by the degree of enrichment by Gene Set Variant Analysis and the median was used to divide each cohort into high vs low score groups. Glycolysis high breast cancer significantly enriched the hallmark cell proliferation-related gene sets (E2F targets, G2M checkpoint, and MYC targets v1 and v2) and was associated with high MKI67 expression. In all cohorts, triple-negative breast cancer (TNBC) was associated with the highest glycolysis score. It was found that in TNBC, glycolysis high breast cancer was associated with worse survival but in ER-positive/HER2-negative breast cancer this was not observed consistently. The glycolysis high TNBC enriched multiple pro-cancerous gene sets and was infiltrated with a low level of B-cells and anti-cancerous immune cells, and significantly associated with a decreased level of cytolytic activity. It was also observed that the glycolysis was higher in the metastatic sites than in the primary breast cancer and the survival was not affected by the metastatic sites. In conclusion, accelerated glycolysis is associated with cancer cell proliferation and worse survival in TNBC.
Collapse
Affiliation(s)
- Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Arya Mariam Roy
- Department of Medical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
| | - Mahato Sasamoto
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Yoshihisa Tokumaru
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
| | - Rongrong Wu
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
| | - Akimitsu Yamada
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Shinya Yamamoto
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Takashi Chishima
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Kazutaka Narui
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo, New York 14263, USA
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata 951-8520, Japan
- Department of Breast Surgery, Fukushima Medical University School of MedicineFukushima 960-1295, Japan
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| |
Collapse
|
21
|
Shichiri K, Oshi M, Ziazadeh D, Endo I, Takabe K. High miR-200c expression is associated with suppressed epithelial-mesenchymal transition, TGF-β signaling and better survival despite enhanced cell proliferation in gastric cancer patients. Am J Cancer Res 2023; 13:3027-3040. [PMID: 37560006 PMCID: PMC10408478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/20/2023] [Indexed: 08/11/2023] Open
Abstract
MicroRNAs are small non-coding RNAs that epigenetically regulate gene expression. MiR-200c is a known tumor suppressive microRNA found in many types of cancer, and its high expression has been associated with improved prognosis. However, the association between miR-200c expression and its clinical relevance in gastric cancer (GC) patients remains controversial. Here, we hypothesized that gastric cancer patients with high miR-200c gene expression translated to better overall survival. A total of 372 GC patients from the Cancer Genome Atlas (TCGA) were analyzed. The top three quartiles were defined as a high miR-200c expression group. High miR-200c expression was associated with decreased invasion, favorable histological type, and improved overall survival in gastric cancer patients. Unexpectedly, high miR-200c expression GC was also associated with enhanced cell proliferation, shown by MKi67 expression, proliferation score, and enrichment of Hallmark cell proliferation-related gene sets (E2F targets, G2M checkpoints, MYC targets v1 and v2) by gene set enrichment assay (GSEA). High miR-200c GC was also associated with a high mutation rate and homologous recombination deficiency. Despite the association with elevated neoantigens, high miR-200c GC was associated with significantly low infiltration of anti-cancer immune cells, decreased immune response, and with suppressed IL2, TNF-α, and IFN-γ pathways. On the other hand, GC with low miR-200c expression significantly enriched hypoxia, angiogenesis, epithelial-mesenchymal transition (EMT), and TGF-β signaling gene sets, all of which promote cancer progression and metastasis in GSEA. In conclusion, patients with high miR-200c expression GC had better survival despite association with aggressive tumor biology, such as high mutation rates, cell proliferation, and low cancer immunity. Given that low miR-200c GC was associated with hypoxia, angiogenesis, EMT and TGF-β signaling, we cannot help but speculate that the difference in survival by miR-200c expression may be at least partly due to the association between low miR-200c expression and aggressive biology.
Collapse
Affiliation(s)
- Keiko Shichiri
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- U.S. Naval Hospital OkinawaOkinawa, FPO, AP 96362, Japan
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
| | - Danya Ziazadeh
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New YorkBuffalo, NY 14203, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New YorkBuffalo, NY 14203, USA
- Department of Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata 950-0883, Japan
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
- Department of Breast Surgery, Fukushima Medical UniversityFukushima 960-8074, Japan
| |
Collapse
|
22
|
Oshi M, Ziazadeh D, Wu R, Chida K, Yamada A, Yamamoto S, Narui K, Yan L, Ishikawa T, Endo I, Takabe K. GALNT1 Expression Is Associated with Angiogenesis and Is a Prognostic Biomarker for Breast Cancer in Adolescents and Young Adults (AYA). Cancers (Basel) 2023; 15:3489. [PMID: 37444599 PMCID: PMC10341315 DOI: 10.3390/cancers15133489] [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: 06/01/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
It is well established that genetic information differs amongst the adolescent and young adult population (AYA) and older patients. Although several studies on genetic information have been conducted, no current prognostic biomarker exists to help differentiate survival outcomes amongst AYA patients. The GALNT family of genes have been associated with several cancer etiologies, such as the Tn antigen and epithelial-mesenchymal transition (EMT); however, the clinical significance of GALNT1 expression in breast cancer (BC) remains unclear. We investigated the clinical relevance of GALNT1 expression in BC using two large independent cohorts. We found that, although triple-negative BC (TNBC) had the highest GALNT1 expression compared to ER-positive/HER2-negative BC, GALNT1 levels in BC were not associated with clinical aggressiveness, including histological grade, AJCC stage and N-category, and patient survival, consistently in both the METABRIC and GSE96058 cohorts. There was also no biological difference between low- and high-GALNT1 expression BC, as analyzed by hallmark gene sets via gene set enrichment analysis (GSEA). Further, no significant difference was found in GALNT1 expression levels among AYAs and older patients. However, high GALNT1 expression was associated with significantly worse survival in AYA patients, in both cohorts. Furthermore, high GALNT1 expression was found to be an independent factor among several clinical features, including subtype, histological grade, AJCC T and N-category, in AYA patients. In both cohorts, BC with high GALNT1 expression demonstrated low levels of CD8+ T-cell infiltration, but not other anti-cancerous or pro-cancerous immune cells. Finally, high levels of GALNT1 BC demonstrated increased EMT, angiogenesis, and protein secretion in the AYA population, but not in older patients. In conclusion, our findings demonstrate that GALNT1 expression was found to be associated with angiogenesis and EMT, and may have potential as prognostic biomarker, specifically in AYA patients.
Collapse
Affiliation(s)
- Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (D.Z.); (K.C.)
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; (A.Y.)
| | - Danya Ziazadeh
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (D.Z.); (K.C.)
| | - Rongrong Wu
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan; (R.W.); (T.I.)
| | - Kohei Chida
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (D.Z.); (K.C.)
| | - Akimitsu Yamada
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; (A.Y.)
| | - Shinya Yamamoto
- Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama 232-0024, Japan; (S.Y.); (K.N.)
| | - Kazutaka Narui
- Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama 232-0024, Japan; (S.Y.); (K.N.)
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan; (R.W.); (T.I.)
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; (A.Y.)
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (D.Z.); (K.C.)
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; (A.Y.)
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan; (R.W.); (T.I.)
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY 14263, USA
| |
Collapse
|
23
|
He X, Zhao D, Zhang X, Ma Y, Zhang R, Huang Z, Wang G, Guo G, Wang W, Wen Y, Zhang L. Intrinsic Immunogenic Tumor Cell Death Subtypes Delineate Prognosis and Responsiveness to Immunotherapy in Lung Adenocarcinoma. BIOLOGY 2023; 12:808. [PMID: 37372093 DOI: 10.3390/biology12060808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
Recent studies have highlighted the combination of activation of host immunogenic cell death (ICD) and tumor-directed cytotoxic strategies. However, overall multiomic analysis of the intrinsic ICD property in lung adenocarcinoma (LUAD) has not been performed. Therefore, the aim of this study was to develop an ICD-based risk scoring system to predict overall survival (OS) and immunotherapeutic efficacy in patients. In our study, both weighted gene co-expression network analysis (WGCNA) and LASSO-Cox analysis were utilized to identify ICDrisk subtypes (ICDrisk). Moreover, we identify genomic alterations and differences in biological processes, analyze the immune microenvironment, and predict the response to immunotherapy in patients with pan-cancer. Importantly, immunogenicity subgroup typing was performed based on the immune score (IS) and microenvironmental tumor neoantigens (meTNAs). Our results demonstrate that ICDrisk subtypes were identified based on 16 genes. Furthermore, high ICDrisk was proved to be a poor prognostic factor in LUAD patients and indicated poor efficacy of immune checkpoint inhibitor (ICI) treatment in patients with pan-cancer. The two ICDrisk subtypes displayed distinct clinicopathologic features, tumor-infiltrating immune cell patterns, and biological processes. The ISlowmeTNAhigh subtype showed low intratumoral heterogeneity (ITH) and immune-activated phenotypes and correlated with better survival than the other subtypes within the high ICDrisk group. This study suggests effective biomarkers for the prediction of OS in LUAD patients and immunotherapeutic response across Pan-cancer and contributes to enhancing our understanding of intrinsic immunogenic tumor cell death.
Collapse
Affiliation(s)
- Xiaotian He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Dechang Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xuewen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yiyang Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Rusi Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Zirui Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Gongming Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Guangran Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Weidong Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yingsheng Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Lanjun Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| |
Collapse
|
24
|
Song X, Wang P, Feng R, Chetry M, Li E, Wu X, Liu Z, Liao S, Lin J. Pan-Cancer Analysis of Prognostic and Immune Infiltrates for the TMEM65, Especially for the Breast Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2023; 2023:9349494. [PMID: 37101716 PMCID: PMC10125759 DOI: 10.1155/2023/9349494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/10/2022] [Accepted: 07/23/2022] [Indexed: 04/28/2023]
Abstract
Introduction Transmembrane protein 65 (TMEM65) is an inner mitochondrial membrane protein, which played important role in mediating autophagy, smooth muscle contraction, protein glycosylation, and immune response. In recent years, the interest had risen for exploring the function of the TMEM genes in the cancer fields. As a consequence, in our pan-cancer research of the TMEM65, we explored the function of the gene in kinds of database and tried to apply the finding in the clinical practice. Methods In this research, we provide a comprehensive investigation of TMEM65 expression in a pan-cancer manner containing 33 cancer types. We evaluated the association of TMEM65 with the prognosis, immune infiltration, drug sensitivity analysis, GSVA enrichment analysis, TMB, MSI, NEO, and hotspot mechanisms. Results TMEM65 was abnormally expressed in 24 types of cancers and showed correlation with the OS for 6 cancers and PFI for 9 cancers and kpI for 3 types. Moreover, the TME score, CD8 T effector, and immune checkpoint scoring systems showed a close correlation with the TMEM65. Moreover, TMEM65 was strongly correlated with some of the most common tumor-related genes and certain pathways (TGF beta signaling, TNFA signaling, hypoxia, pyroptosis, DNA repairing, autophagy, ferroptosis, and other related genes). Additionally, the TMEM65 showed correlations with the tumor mutational burden (TMB), microsatellite instability (MSI), NEO, and drug sensitivity. Finally, we confirmed several pathways by the GSEA and GSVA for the TMEM65 at the breast cancer aspects. Nomogram prediction model was also established for the breast tumors based on the TMEM65 level and other variables. Conclusion Above all, the TMEM65 played important roles in predicting the prognosis of the cancers and correlated with the tumor immunity in the pan-cancer analysis.
Collapse
Affiliation(s)
- Xinming Song
- Department of Oncology, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Pintian Wang
- Department of Oncology, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Ruiling Feng
- Department of Oncology, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Mandika Chetry
- Department of Oncology, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - E Li
- Department of Oncology, Shantou Longhu People's Hospital, Shantou, Guangdong, China
| | - Xiaohua Wu
- Department of Oncology, Shantou Longhu People's Hospital, Shantou, Guangdong, China
| | - Zewa Liu
- Department of Oncology, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Shasha Liao
- Department of Oncology, Shantou Longhu People's Hospital, Shantou, Guangdong, China
| | - Jing Lin
- Department of Oncology, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| |
Collapse
|
25
|
Shibata MA, Taniguchi K. Metastasis Inhibition. Int J Mol Sci 2023; 24:ijms24087123. [PMID: 37108286 PMCID: PMC10138681 DOI: 10.3390/ijms24087123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
Cancer metastasis is a common biological phenomenon observed in malignant tumors that can lead to death in affected individuals [...].
Collapse
Affiliation(s)
- Masa-Aki Shibata
- Department of Anatomy and Cell Biology, Division of Life Sciences, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Osaka, Japan
| | - Kohei Taniguchi
- Translational Research Program, Department of General and Gastroenterological Surgery, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Osaka, Japan
| |
Collapse
|
26
|
Kula A, Dawidowicz M, Mielcarska S, Kiczmer P, Skiba H, Krygier M, Chrabańska M, Piecuch J, Szrot M, Robotycka J, Ochman B, Strzałkowska B, Czuba Z, Świętochowska E, Waniczek D. Overexpression and Role of HHLA2, a Novel Immune Checkpoint, in Colorectal Cancer. Int J Mol Sci 2023; 24:ijms24065876. [PMID: 36982953 PMCID: PMC10057377 DOI: 10.3390/ijms24065876] [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: 02/10/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The study aimed to investigate correlations between HHLA2 levels and parameters, including microsatellite instability (MSI) status, CD8+ cells, and histopathological features: budding, tumor-infiltrating lymphocytes (TILs), TNM scale, grading, cytokines, chemokines, and cell signaling moleculesin colorectal cancer (CRC). Furthermore, the immune infiltration landscape and HHLA2-related pathways in colorectal cancer using available online datasets were analyzed. The study included 167 patients diagnosed with CRC. Expression of HHLA2 was detected by immunohistochemistry method (IHC) and enzyme-linked immunosorbent assay (ELISA). The IHC was used to evaluate the MSI and CD8+ status. The budding and TILs were measured using a light microscope. The concentrations of cytokines, chemokines, and cell signaling molecules were measured to analyze the data by the Bio-Plex Pro Human cytokine screening panel, 48 cytokine assay, and principal component analysis (PCA). Geneset enrichment analysis (GSEA) was conducted to identify HHLA2-related pathways. The biological function of HHLA2 was predicted by Gene Ontology (GO). Analysis of the immune infiltration landscape of HHLA2 in colorectal cancer was made by the web-based tool Camoip. High HHLA2 expression was detected in CRC tumor tissues compared to the adjacent noncancerous tissues. The percentage of HHLA2-positive tumors was 97%. GSEA and GO showed that HHLA2 upregulation correlated with cancer-related pathways and several biological functions. Tumor-infiltrating lymphocytes score correlated positively with IHC HHLA2 expression level percentage. There was a negative correlation between HHLA2, anti-tumor cytokines and pro-tumor growth factors. This study provides a valuable insight into the role of HHLA2 in CRC. We reveal the role of HHLA2 expression as well as a stimulatory and inhibitory immune checkpoint in colorectal cancer. Further research may verify the therapeutic values of the HHLA2-KIR3DL3/TMIGD2 pathway in colorectal cancer.
Collapse
Affiliation(s)
- Agnieszka Kula
- Department of Oncological Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
| | - Miriam Dawidowicz
- Department of Oncological Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
| | - Sylwia Mielcarska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Paweł Kiczmer
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 13-15 3 Maja, 41-800 Zabrze, Poland
| | - Hanna Skiba
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 13-15 3 Maja, 41-800 Zabrze, Poland
| | - Małgorzata Krygier
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 13-15 3 Maja, 41-800 Zabrze, Poland
| | - Magdalena Chrabańska
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 13-15 3 Maja, 41-800 Zabrze, Poland
| | - Jerzy Piecuch
- Department of General and Bariatric Surgery and Emergency Medicine, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
| | - Monika Szrot
- Department of General and Bariatric Surgery and Emergency Medicine, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
| | - Julia Robotycka
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Błażej Ochman
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Bogumiła Strzałkowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Zenon Czuba
- Department of Microbiology and Immunology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | - Elżbieta Świętochowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Dariusz Waniczek
- Department of Oncological Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
| |
Collapse
|
27
|
Woldmar N, Schwendenwein A, Kuras M, Szeitz B, Boettiger K, Tisza A, László V, Reiniger L, Bagó AG, Szállási Z, Moldvay J, Szász AM, Malm J, Horvatovich P, Pizzatti L, Domont GB, Rényi-Vámos F, Hoetzenecker K, Hoda MA, Marko-Varga G, Schelch K, Megyesfalvi Z, Rezeli M, Döme B. Proteomic analysis of brain metastatic lung adenocarcinoma reveals intertumoral heterogeneity and specific alterations associated with the timing of brain metastases. ESMO Open 2023; 8:100741. [PMID: 36527824 PMCID: PMC10024110 DOI: 10.1016/j.esmoop.2022.100741] [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: 05/25/2022] [Revised: 09/07/2022] [Accepted: 11/02/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Brain metastases are associated with considerable negative effects on patients' outcome in lung adenocarcinoma (LADC). Here, we investigated the proteomic landscape of primary LADCs and their corresponding brain metastases. MATERIALS AND METHODS Proteomic profiling was conducted on 20 surgically resected primary and brain metastatic LADC samples via label-free shotgun proteomics. After sample processing, peptides were analyzed using an Ultimate 3000 pump coupled to a QExactive HF-X mass spectrometer. Raw data were searched using PD 2.4. Further data analyses were carried out using Perseus, RStudio and GraphPad Prism. Proteomic data were correlated with clinical and histopathological parameters and the timing of brain metastases. Mass spectrometry-based proteomic data are available via ProteomeXchange with identifier PXD027259. RESULTS Out of the 6821 proteins identified and quantified, 1496 proteins were differentially expressed between primary LADCs and corresponding brain metastases. Pathways associated with the immune system, cell-cell/matrix interactions and migration were predominantly activated in the primary tumors, whereas pathways related to metabolism, translation or vesicle formation were overrepresented in the metastatic tumors. When comparing fast- versus slow-progressing patients, we found 454 and 298 differentially expressed proteins in the primary tumors and brain metastases, respectively. Metabolic reprogramming and ribosomal activity were prominently up-regulated in the fast-progressing patients (versus slow-progressing individuals), whereas expression of cell-cell interaction- and immune system-related pathways was reduced in these patients and in those with multiple brain metastases. CONCLUSIONS This is the first comprehensive proteomic analysis of paired primary tumors and brain metastases of LADC patients. Our data suggest a malfunction of cellular attachment and an increase in ribosomal activity in LADC tissue, promoting brain metastasis. The current study provides insights into the biology of LADC brain metastases and, moreover, might contribute to the development of personalized follow-up strategies in LADC.
Collapse
Affiliation(s)
- N Woldmar
- Department of Biomedical Engineering, Lund University, Lund, Sweden; Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A Schwendenwein
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - M Kuras
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - B Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - K Boettiger
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - A Tisza
- National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - V László
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria; National Korányi Institute of Pulmonology, Budapest, Hungary
| | - L Reiniger
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary; Department of Pathology, Forensic and Insurance Medicine, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - A G Bagó
- Department of Neurooncology, National Institute of Clinical Neurosciences, Budapest, Hungary
| | - Z Szállási
- Department of Pathology, Forensic and Insurance Medicine, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Budapest, Hungary; Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, USA; Danish Cancer Society Research Center, Copenhagen, Denmark
| | - J Moldvay
- National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Pathology, Forensic and Insurance Medicine, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - A M Szász
- National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - J Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - P Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - L Pizzatti
- Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - G B Domont
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - F Rényi-Vámos
- National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
| | - K Hoetzenecker
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - M A Hoda
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - G Marko-Varga
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - K Schelch
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - Z Megyesfalvi
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria; National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
| | - M Rezeli
- Department of Biomedical Engineering, Lund University, Lund, Sweden.
| | - B Döme
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria; Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden; National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary.
| |
Collapse
|
28
|
Qi TF, Tang F, Yin J, Miao W, Wang Y. Parallel-reaction monitoring revealed altered expression of a number of epitranscriptomic reader, writer, and eraser proteins accompanied with colorectal cancer metastasis. Proteomics 2023; 23:e2200059. [PMID: 35443089 PMCID: PMC9582037 DOI: 10.1002/pmic.202200059] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 11/09/2022]
Abstract
RNA contains more than 170 types of chemical modifications, and these modified nucleosides are recognized, installed and removed by their reader, writer, and eraser (RWE) proteins, respectively. Here, we employed a parallel-reaction monitoring (PRM)-based targeted proteomic method, in conjunction with stable isotope labeling by amino acids in cell culture (SILAC), to examine comprehensively the differential expression of epitranscriptomic RWE proteins in a matched pair of primary/metastatic colorectal cancer (CRC) cells, namely SW480/SW620. We were able to quantify 113 nonredundant epitranscriptomic RWE proteins; among them, 48 and 5 were up- and down-regulated by >1.5-fold in SW620 over SW480 cells, respectively. Some of those proteins with marked up-regulation in metastatic CRC cells, including NAT10, hnRNPC, and DKC1, were documented to assume important roles in the metastasis of CRC and other types of cancer. Interrogation of the Clinical Proteomic Tumor Analysis Consortium data revealed the involvement of DUS1L in the initiation and metastatic transformation of CRC. It can be envisaged that the PRM method can be utilized, in the future, to identify epitranscriptomic RWE proteins involved in the metastatic transformations of other types of cancer.
Collapse
Affiliation(s)
- Tianyu F Qi
- Environmental Toxicology Graduate Program, Riverside, California, USA
| | - Feng Tang
- Department of Chemistry, University of California, Riverside, California, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, Riverside, California, USA
| | - Weili Miao
- Department of Chemistry, University of California, Riverside, California, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, Riverside, California, USA
- Department of Chemistry, University of California, Riverside, California, USA
| |
Collapse
|
29
|
Takabe K, Benesch MGK. Biomarker Research in World Journal of Oncology. World J Oncol 2023; 14:1-3. [PMID: 36895990 PMCID: PMC9990739 DOI: 10.14740/wjon1577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023] Open
Affiliation(s)
- Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.,Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY 14263, USA.,Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan.,Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan.,Department of Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Department of Breast Surgery, Fukushima Medical University, Fukushima, Japan
| | - Matthew G K Benesch
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| |
Collapse
|
30
|
Zengin ZB, Govindarajan A, Salgia N, Sayegh N, Tripathi N, Muddasani R, Chehrazi-Raffle A, Feng M, Mercier BD, Ladbury C, Hao C, Salgia S, Chawla N, Meza L, Malhotra J, Dizman N, Hsu J, Castro DV, Barragan-Carrillo R, Ebrahimi H, Philip EJ, Chang M, Zhang J, Byron S, Lyou Y, Dorff T, Pal SK, Dandapani S. Genomic and Transcriptomic Predictors of Response from Stereotactic Body Radiation Therapy in Patients with Oligoprogressive Renal Cell Carcinoma. Eur Urol Oncol 2023:S2588-9311(22)00203-6. [PMID: 36609061 DOI: 10.1016/j.euo.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/17/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023]
Abstract
Stereotactic body radiation therapy (SBRT) has been shown to be safe and effective for delaying systemic treatment change among patients with metastatic renal cell carcinoma (mRCC). In this study, we sought to assess the genomic signatures of patients with mRCC who underwent SBRT for oligoprogression. A total of 30 patients with oligoprogressive disease were identified, the majority of whom had clear cell renal cell carcinoma (83.3%) and were receiving first-line treatment (53.3%). Genomic and transcriptomic sequencing were available in 20 and 16 patients, respectively. Duration of systemic treatment (DOT) was categorized as that prior (DOT[P]) and subsequent (DOT[S]) to radiation treatment. The median DOT(P) and DOT(S) were 15.1 and 18.3 mo, respectively, with a median DOT(S)/DOT(P) ratio of 1.4. Patients who had a DOT(S)/DOT(P) ratio of ≥1 had increased expression in pathways related to cell proliferation and development. In contrast, among patients with a ratio of ≤1, the reactive oxygen species pathway was enriched. This study highlights the potential role of genomics and transcriptomics to refine radiation treatment selection in patients with mRCC. PATIENT SUMMARY: In this study, we looked at mutations and genomic expressions among kidney cancer patients who responded better to stereotactic body radiotherapy. We found that enriched expression of certain pathways might play a role in response to radiotherapy.
Collapse
Affiliation(s)
- Zeynep B Zengin
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ameish Govindarajan
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Nicholas Salgia
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Nicolas Sayegh
- Division of Medical Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Nishita Tripathi
- Division of Medical Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Ramya Muddasani
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Alex Chehrazi-Raffle
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Matthew Feng
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Benjamin D Mercier
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Colton Ladbury
- Department of Radiation Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Claire Hao
- Department of Radiation Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sabrina Salgia
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Neal Chawla
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Luis Meza
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jasnoor Malhotra
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Nazli Dizman
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - JoAnn Hsu
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Daniela V Castro
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | - Hedyeh Ebrahimi
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Errol J Philip
- University of California-San Francisco, San Francisco, CA, USA
| | - Mark Chang
- Kerk Kerkorian School of Medicine at UNLV, Las Vegas, NV, USA
| | - Jiaming Zhang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sara Byron
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Yung Lyou
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Tanya Dorff
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sumanta K Pal
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
| | - Savita Dandapani
- Department of Radiation Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
| |
Collapse
|
31
|
Crocamo S, Binato R, dos Santos EC, de Paula B, Abdelhay E. Translational Results of Zo-NAnTax: A Phase II Trial of Neoadjuvant Zoledronic Acid in HER2-Positive Breast Cancer. Int J Mol Sci 2022; 23:ijms232415515. [PMID: 36555156 PMCID: PMC9779412 DOI: 10.3390/ijms232415515] [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: 10/12/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is a heterogeneous disease with distinct clinical and molecular characteristics. Scientific advances in molecular subtype differentiation support the understanding of cellular signaling, crosstalk, proliferation, survival, migration, and invasion mechanisms, allowing the development of new molecular drug targets. The breast cancer subtype with super expression and/or amplification of human growth factor receptor 2 (HER2) is clinically aggressive, but prognosis significantly shifted with the advent of anti-HER2 targeted therapy. Zoledronic-acid (ZOL) combined with a neoadjuvant Trastuzumab-containing chemotherapy regimen (Doxorubicin, Cyclophosphamide followed by Docetaxel, Trastuzumab) increased the pCR rate in a RH-positive/ HER2-positive subgroup, according to the phase II Zo-NAnTax trial. To verify genes that could be related to this response, a microarray assay was performed finding 164 differentially expressed genes. Silico analysis of these genes showed signaling pathways related to growth factors, apoptosis, invasion, and metabolism, as well as differentially expressed genes related to estrogen response. In addition, the RAC3 gene was found to interact with the MVD gene, a member of the mevalonate pathway. Taken together, these results indicate that RH-positive/ HER2-positive patients present gene alterations before treatment, and these could be related to the improvement of pCR.
Collapse
Affiliation(s)
- Susanne Crocamo
- Núcleo de Pesquisa Clínica, Hospital de Câncer III, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro 20560-121, Brazil
- Correspondence:
| | - Renata Binato
- Laboratório de Célula-Tronco, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro 20230-130, Brazil
| | - Everton Cruz dos Santos
- Laboratório de Célula-Tronco, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro 20230-130, Brazil
| | - Bruno de Paula
- Núcleo de Pesquisa Clínica, Hospital de Câncer III, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro 20560-121, Brazil
| | - Eliana Abdelhay
- Laboratório de Célula-Tronco, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro 20230-130, Brazil
| |
Collapse
|
32
|
Zhong Y, Xu S, Liu Z. The potential of glutamine metabolism-related long non-coding RNAs (lncRNAs) as prognostic biomarkers in multiple myeloma patients. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1362. [PMID: 36660731 PMCID: PMC9843343 DOI: 10.21037/atm-22-6190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/01/2023]
Abstract
Background Glutamine (Gln) metabolism has been confirmed as an important fuel in cancer metabolism. This study aimed to uncover potential links of Gln with long non-coding RNAs (lncRNAs) and the prognostic value of Gln-associated lncRNAs in multiple myeloma (MM) patients. Methods The RNA-seq expression profile and corresponding clinical data of gastric cancer obtained from Gene Expression Omnibus (GEO) database. Unsupervised consensus clustering was used to cluster MM samples based on Gln-associated lncRNAs. The overall survival (OS), biological pathways, and immune microenvironment were compared in different subtypes. Differential analysis was utilized to identify differentially expressed lncRNAs (DElncRNAs) in different subtypes. A risk model was constructed based on DElncRNAs by using Cox regression, least absolute shrinkage and selection operator (LASSO), and the stepAIC algorithm. Results We screened 50 Gln-associated lncRNAs and identified 3 molecular subtypes (clust1, clust2, and clust3) based on lncRNA expression profiles. Clust3 subtype showed the worst prognosis and highest enrichment of Gln metabolism pathway. Angiogenesis, epithelial-mesenchymal transition (EMT), and cell cycle-related pathways were relatively activated in clust3. Then, we identified 11 prognostic DElncRNAs for constructing the risk model. The MM samples were divided into high- and low-risk groups with distinct prognosis according to the risk score. The risk score was significantly associated with cell cycle and infiltration of many immune cells. Conclusions This study characterized the role of Gln-associated lncRNAs in Gln metabolism contributing for tumor-related pathways and immune microenvironment in MM patients. The 11 lncRNAs in the risk model may serve as potential targets for exploring the mechanism of Gln metabolism or serve as potential biomarkers for MM prognosis.
Collapse
Affiliation(s)
- Yun Zhong
- Department of Lymphohematology and Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Shenghua Xu
- Department of Lymphohematology and Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Zhe Liu
- Department of Orthopedics, Jiangxi Cancer Hospital, Nanchang, China
| |
Collapse
|
33
|
Mosquim Junior S, Siino V, Rydén L, Vallon-Christersson J, Levander F. Choice of High-Throughput Proteomics Method Affects Data Integration with Transcriptomics and the Potential Use in Biomarker Discovery. Cancers (Basel) 2022; 14:cancers14235761. [PMID: 36497242 PMCID: PMC9736226 DOI: 10.3390/cancers14235761] [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: 09/30/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
In recent years, several advances have been achieved in breast cancer (BC) classification and treatment. However, overdiagnosis, overtreatment, and recurrent disease are still significant causes of complication and death. Here, we present the development of a protocol aimed at parallel transcriptome and proteome analysis of BC tissue samples using mass spectrometry, via Data Dependent and Independent Acquisitions (DDA and DIA). Protein digestion was semi-automated and performed on flowthroughs after RNA extraction. Data for 116 samples were acquired in DDA and DIA modes and processed using MaxQuant, EncyclopeDIA, or DIA-NN. DIA-NN showed an increased number of identified proteins, reproducibility, and correlation with matching RNA-seq data, therefore representing the best alternative for this setup. Gene Set Enrichment Analysis pointed towards complementary information being found between transcriptomic and proteomic data. A decision tree model, designed to predict the intrinsic subtypes based on differentially abundant proteins across different conditions, selected protein groups that recapitulate important clinical features, such as estrogen receptor status, HER2 status, proliferation, and aggressiveness. Taken together, our results indicate that the proposed protocol performed well for the application. Additionally, the relevance of the selected proteins points to the possibility of using such data as a biomarker discovery tool for personalized medicine.
Collapse
Affiliation(s)
| | - Valentina Siino
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences Lund, Lund University, 223 81 Lund, Sweden
- Department of Surgery and Gastroenterology, Skåne University Hospital, 214 28 Malmö, Sweden
| | | | - Fredrik Levander
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, 223 81 Lund, Sweden
- Correspondence:
| |
Collapse
|
34
|
Wu R, Yu I, Tokumaru Y, Asaoka M, Oshi M, Yan L, Okuda S, Ishikawa T, Takabe K. Elevated bile acid metabolism and microbiome are associated with suppressed cell proliferation and better survival in breast cancer. Am J Cancer Res 2022; 12:5271-5285. [PMID: 36504906 PMCID: PMC9729904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
Bile acids are metabolized by the gut microbiome and are involved in fat absorption. Contrary to their carcinogenic role in gastrointestinal cancers, bile acids have been reported to inhibit cancer cell proliferation in breast cancer. The microbiome of breast cancer tissues may also influence cancer proliferation. We hypothesized that bile acid metabolism reflects its accumulation and is associated with certain microbiomes, breast cancer biology, and patient survival. Transcriptomic and clinicopathological information of a total of 6050 patients in three large open primary breast cancer cohorts (GSE96058, METABRIC, TCGA) and 16S rRNA gene sequence microbiome data of breast cancer tissues in TCGA were analyzed by high and low bile acid metabolism scores calculated by gene set variation analysis (GSVA). Breast cancers with high bile acid metabolism had a significantly improved survival across all three cohorts. Metabolic pathways related to the production and regulation of bile acids were consistently enriched in high bile acid metabolism groups across all cohorts. On the other hand, the low bile acid metabolism group was associated with higher Ki67 expression and Nottingham histological grade, as well as enrichment of cell proliferation-related gene sets. Intratumoral heterogeneity, homologous recombination deficiency, mutational load, activation of cancer immunity, and infiltration of anticancer immune cells were also higher in this group. Gammaretrovirus, Hymenobacter, Anaerococcus, and Collimonas were significantly more abundant in the high bile acid metabolism group compared to Lactobacillus, Ruegeria, and Marichromatium in the low metabolism group. Surprisingly, almost all Hallmark cell proliferation-associated gene sets were highly enriched in all three microorganisms that were abundant in the low bile acid metabolism group. In conclusion, microorganisms abundant in the breast tumor microenvironment with low bile acid metabolism are associated with aggressive cancer biology, including increased cell proliferation and poor survival.
Collapse
Affiliation(s)
- Rongrong Wu
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA,Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| | - Irene Yu
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New YorkBuffalo, New York 14263, USA
| | - Yoshihisa Tokumaru
- Department of Surgical Oncology, Graduate School of Medicine, Gifu UniversityGifu 501-1193, Japan
| | - Mariko Asaoka
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA,Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
| | - Shujiro Okuda
- Medical AI Center, Niigata University School of MedicineNiigata, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA,Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan,Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New YorkBuffalo, New York 14263, USA,Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan,Department of Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata, Japan,Department of Breast Surgery, Fukushima Medical UniversityFukushima, Japan
| |
Collapse
|
35
|
Oshi M, Gandhi S, Wu R, Asaoka M, Yan L, Yamada A, Yamamoto S, Narui K, Chishima T, Ishikawa T, Endo I, Takabe K. Development of a novel BRCAness score that predicts response to PARP inhibitors. Biomark Res 2022; 10:80. [PMID: 36371386 PMCID: PMC9652967 DOI: 10.1186/s40364-022-00427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/30/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND BRCAness is a characteristic feature of homologous recombination deficiency (HRD) mimicking BRCA gene mutation in breast cancer. We hypothesized that a measure to quantify BRCAness that causes synthetic lethality in BRCA mutated tumors will identify responders to PARP inhibitors. METHODS A total of 6753 breast cancer patients from 3 large independent cohorts were analyzed. A score was generated by transcriptomic profiling using gene set variation analysis algorithm on 34 BRCA1-mutation related genes selected by high AUC levels in ROC curve between BRCA1 mutation and wildtype breast cancer. RESULTS The score was significantly associated with BRCA1 mutation, high mutation load and intratumoral heterogeneity as expected, as well as with high HRD, DNA repair and MKi67 expression regardless of BRCA mutations. High BRCAness tumors enriched not only DNA repair, but also all five Hallmark cell proliferation-related gene sets. High BRCAness tumors were significantly associated with higher cytolytic activity and with higher anti-cancerous immune cell infiltration. Not only did the breast cancer cell lines with BRCA-mutation show high score, but even the other cells in human breast cancer tumor microenvironment were contributing to the score. The BRCAness score was the highest in triple-negative breast cancer consistently in all 3 cohorts. BRCAness was associated with response to chemotherapy and correlated strongly with response to PARP inhibitor in both triple-negative and ER-positive/HER2-negative breast cancer. CONCLUSIONS We established a novel BRCAness score using BRCA-mutation-related gene expressions and found that it associates with DNA repair and predicts response to PARP inhibitors regardless of BRCA mutation.
Collapse
Affiliation(s)
- Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263 USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Shipra Gandhi
- Department of Medical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263 USA
| | - Rongrong Wu
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263 USA
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402 Japan
| | - Mariko Asaoka
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402 Japan
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263 USA
| | - Akimitsu Yamada
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Shinya Yamamoto
- Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama, Kanagawa Japan
| | - Kazutaka Narui
- Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama, Kanagawa Japan
| | - Takashi Chishima
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402 Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263 USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8520 Japan
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, 960-1295 Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY 14263 USA
- Department of Breast Surgery, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY 14263 USA
| |
Collapse
|
36
|
Oshi M, Tokumaru Y, Benesch MGK, Sugito N, Wu R, Yan L, Yamada A, Chishima T, Ishikawa T, Endo I, Takabe K. High miR-99b expression is associated with cell proliferation and worse patient outcomes in breast cancer. Am J Cancer Res 2022; 12:4840-4852. [PMID: 36381329 PMCID: PMC9641402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023] Open
Abstract
Although miR-99b is a known suppressive microRNA (miRNA) in several cancers, its role in breast cancer has not been elucidated. In this study, we examined the clinical relevance of miR-99b expression in breast cancer. We analyzed miRNA and mRNA expression and their relationships with clinical parameters in 1,961 breast cancer samples from two independent large cohorts, the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and The Cancer Genome Atlas (TCGA). Several algorithms, including gene set enrichment analysis (GSEA) and xCell, have been used to investigate biological functions and the tumor microenvironment. High miR-99b expression significantly enriched the mTORC1 signaling gene set in breast cancer (NES = 1.63, FDR = 0.03, and NES = 1.58, FDR = 0.10, in METABRIC and TCGA, respectively). No other mechanisms, including the epithelial mesenchymal transition, NFκB, and TGF-β signaling, were consistently enriched in both cohorts. MiR-99b-high breast cancer was associated with high homologous recombination deficiencies, intratumor heterogeneity, and high rates of mutation and neoantigens. In agreement, miR-99b-high breast cancer was associated with increased cell proliferation, correlating with Nottingham histological grade, and significant enrichment of E2F targets, G2/M checkpoint, and mitotic spindle gene sets consistently in both cohorts (P = 0.01, P < 0.001). High miR-99b levels were also associated with low stromal cell fractions in the tumor microenvironment, including adipocytes, keratinocytes, and lymphatic endothelial cells (P < 0.001). However, in both cohorts, miR-99b expression was not associated with significant infiltration of immune cells, except dendritic cells (P = 0.006, 0.020). Finally, in both cohorts, breast cancer with high miR-99b expression was significantly associated with worse disease-free survival (DSS) and overall survival (OS), particularly in estrogen receptor (ER)-positive/human epidermal growth factor (HER)2-negative breast cancer (DSS hazard ratio (HR) 1.29, 95% confidence interval (CI) 1.10-1.51, P < 0.001 in the METABRIC cohort and HR 1.82, 95% CI 1.12-2.98, P = 0.017 in the TCGA cohort). In conclusion, breast cancer with high miR-99b expression was significantly associated with mTORC1 signaling, cell proliferation, and decreased patient survival, particularly in the ER-positive/HER2-negative subtype.
Collapse
Affiliation(s)
- Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Yoshihisa Tokumaru
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
- Department of Surgical Oncology, Graduate School of Medicine, Gifu University1-1 Yanagido, Gifu 501-1194, Japan
| | - Matthew GK Benesch
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
| | - Nobuhiko Sugito
- Department of Surgical Oncology, Graduate School of Medicine, Gifu University1-1 Yanagido, Gifu 501-1194, Japan
| | - Rongrong Wu
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
| | - Akimitsu Yamada
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Takashi Chishima
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata 951-8520, Japan
- Department of Breast Surgery, Fukushima Medical University School of MedicineFukushima 960-1295, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo 14263, New York, USA
| |
Collapse
|
37
|
Mammography radiomics features at diagnosis and progression-free survival among patients with breast cancer. Br J Cancer 2022; 127:1886-1892. [PMID: 36050449 DOI: 10.1038/s41416-022-01958-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The associations between mammographic radiomics and breast cancer clinical endpoints are unclear. We aimed to identify mammographic radiomics features associated with breast cancer prognosis. METHODS Nested from a large breast cancer cohort in our institution, we conducted an extreme case-control study consisting of 207 cases with any invasive disease-free survival (iDFS) endpoint <5 years and 207 molecular subtype-matched controls with >5-year iDFS. A total of 632 radiomics features in craniocaudal (CC) and mediolateral oblique (MLO) views were extracted from pre-treatment mammography. Logistic regression was used to identify iDFS-associated features with multiple testing corrections (Benjamini-Hochberg method). In a subsample with RNA-seq data (n = 96), gene set enrichment analysis was employed to identify pathways associated with lead features. RESULTS We identified 15 iDFS-associated features from CC-view yet none from MLO-view. S(1,-1)SumAverg and WavEnLL_s-6 were the lead ones and associated with favourable (OR 0.64, 95% CI 0.42-0.87, P = 0.01) and poor iDFS (OR 1.53, 95% CI 1.31-1.76, P = 0.01), respectively. Both features were associated with eight pathways (primarily involving cell cycle regulation) in tumour but not adjacent normal tissues. CONCLUSION Our findings suggest mammographic radiomics features are associated with breast cancer iDFS, potentially through pathways involving cell cycle regulation.
Collapse
|
38
|
Kuilman MM, Ellappalayam A, Barcaru A, Haan JC, Bhaskaran R, Wehkamp D, Menicucci AR, Audeh WM, Mittempergher L, Glas AM. BluePrint breast cancer molecular subtyping recognizes single and dual subtype tumors with implications for therapeutic guidance. Breast Cancer Res Treat 2022; 195:263-274. [PMID: 35984580 PMCID: PMC9464757 DOI: 10.1007/s10549-022-06698-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/27/2022] [Indexed: 12/05/2022]
Abstract
Purpose BluePrint (BP) is an 80-gene molecular subtyping test that classifies early-stage breast cancer (EBC) into Basal, Luminal, and HER2 subtypes. In most cases, breast tumors have one dominant subtype, representative of a single activated pathway. However, some tumors show a statistically equal representation of more than one subtype, referred to as dual subtype. This study aims to identify and examine dual subtype tumors by BP to understand their biology and possible implications for treatment guidance. Methods The BP scores of over 15,000 tumor samples from EBC patients were analyzed, and the differences between the highest and the lowest scoring subtypes were calculated. Based upon the distribution of the differences between BP scores, a threshold was determined for each subtype to identify dual versus single subtypes. Results Approximately 97% of samples had one single activated BluePrint molecular subtype, whereas ~ 3% of samples were classified as BP dual subtype. The most frequently occurring dual subtypes were the Luminal-Basal-type and Luminal-HER2-type. Luminal-Basal-type displays a distinct biology from the Luminal single type and Basal single type. Burstein’s classification of the single and dual Basal samples showed that the Luminal-Basal-type is mostly classified as ‘luminal androgen receptor’ and ‘mesenchymal’ subtypes, supporting molecular evidence of AR activation in the Luminal-Basal-type tumors. Tumors classified as Luminal-HER2-type resemble features of both Luminal-single-type and HER2-single-type. However, patients with dual Luminal-HER2-type have a lower pathological complete response after receiving HER2-targeted therapies in addition to chemotherapy in comparison with patients with a HER2-single-type. Conclusion This study demonstrates that BP identifies tumors with two active functional pathways (dual subtype) with specific transcriptional characteristics and highlights the added value of distinguishing BP dual from single subtypes as evidenced by distinct treatment response rates. Supplementary Information The online version contains supplementary material available at 10.1007/s10549-022-06698-x.
Collapse
Affiliation(s)
- Midas M Kuilman
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Architha Ellappalayam
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Andrei Barcaru
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Josien C Haan
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Rajith Bhaskaran
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Diederik Wehkamp
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Andrea R Menicucci
- Department of Medical Affairs, Agendia Inc, 22 Morgan, Irvine, CA, 92618, USA
| | - William M Audeh
- Department of Medical Affairs, Agendia Inc, 22 Morgan, Irvine, CA, 92618, USA
| | - Lorenza Mittempergher
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands.
| | - Annuska M Glas
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands.
| |
Collapse
|
39
|
Identification and Validation of Prognostic Markers for Lung Squamous Cell Carcinoma Associated with Chronic Obstructive Pulmonary Disease. JOURNAL OF ONCOLOGY 2022; 2022:4254195. [PMID: 36035311 PMCID: PMC9402374 DOI: 10.1155/2022/4254195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/28/2022] [Accepted: 07/03/2022] [Indexed: 12/04/2022]
Abstract
Background Globally, the incidence and associated mortality of chronic obstructive pulmonary disease (COPD) and lung carcinoma are showing a worsening trend. There is increasing evidence that COPD is an independent risk factor for the occurrence and progression of lung carcinoma. This study aimed to identify and validate the gene signatures associated with COPD, which may serve as potential new biomarkers for the prediction of prognosis in patients with lung carcinoma. Methods A total of 111 COPD patient samples and 40 control samples were obtained from the GSE76925 cohort, and a total of 4933 genes were included in the study. The weighted gene coexpression network analysis (WGCNA) was performed to identify the modular genes that were significantly associated with COPD. The KEGG pathway and GO functional enrichment analyses were also performed. The RNAseq and clinicopathological data of 490 lung squamous cell carcinoma patients were obtained from the TCGA database. Further, univariate Cox regression and Lasso analyses were performed to screen for marker genes and construct a survival analysis model. Finally, the Human Protein Atlas (HPA) database was used to assess the gene expression in normal and tumor tissues of the lungs. Results A 6-gene signature (DVL1, MRPL4, NRTN, NSUN3, RPH3A, and SNX32) was identified based on the Cox proportional risk analysis to construct the prognostic RiskScore survival model associated with COPD. Kaplan–Meier survival analysis indicated that the model could significantly differentiate between the prognoses of patients with lung carcinoma, wherein higher RiskScore samples were associated with a worse prognosis. Additionally, the model had a good predictive performance and reliability, as indicated by a high AUC, and these were validated in both internal and external sets. The 6-gene signature had a good predictive ability across clinical signs and could be considered an independent factor of prognostic risk. Finally, the protein expressions of the six genes were analyzed based on the HPA database. The expressions of DVL1, MRPL4, and NSUN3 were relatively higher, while that of RPH3A was relatively lower in the tumor tissues. The expression of SNX32 was high in both the tumor and paracarcinoma tissues. Results of the analyses using TCGA and GSE31446 databases were consistent with the expressions reported in the HPA database. Conclusion Novel COPD-associated gene markers for lung carcinoma were identified and validated in this study. The genes may be considered potential biomarkers to evaluate the prognostic risk of patients with lung carcinoma. Furthermore, some of these genes may have implications as new therapeutic targets and can be used to guide clinical applications.
Collapse
|
40
|
Oshi M, Patel A, Wu R, Le L, Tokumaru Y, Yamada A, Yan L, Matsuyama R, Ishikawa T, Endo I, Takabe K. Enhanced immune response outperform aggressive cancer biology and is associated with better survival in triple-negative breast cancer. NPJ Breast Cancer 2022; 8:92. [PMID: 35945417 PMCID: PMC9363489 DOI: 10.1038/s41523-022-00466-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/28/2022] [Indexed: 11/24/2022] Open
Abstract
Although the value of tumor-infiltrating lymphocytes is well known, the clinical relevance of an increased immune response, specifically in breast cancer, has not been investigated across large cohorts of patients using computational algorithms. Our hypothesis stated that an enhanced immune response is associated with an improvement in outcomes. To quantify the immune response, we utilized the allograft rejection score correlated with cytolytic activity and with all the other Hallmark immune-related gene sets. The score reflected the amount of infiltrating immune cells that correlated with the immune checkpoint molecule expressions, including CD4+ and CD8+ T cells, T helper type 1 (Th1) and type 2 (Th2) cells, M1 macrophages, B cells, and plasmacytoid dendritic cells (pDC). A high score was associated with high levels of intratumor heterogeneity, homologous recombination defects, mutation rate, histological grade, advanced stage, and lymph node metastasis. Breast malignancy with a high score enriched immune-related gene sets and pro-cancer-related gene sets, including epithelial–mesenchymal transition and KRAS pathway, in ER-positive/HER2-negative and triple-negative breast cancer (TNBC) groups. TNBC had the highest score compared to other subtypes, and was associated with better survival. In conclusion, we found that breast cancer with a high immune response is associated with aggressive cancer biology, but with better survival in TNBC.
Collapse
Affiliation(s)
- Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.,Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Ankit Patel
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Rongrong Wu
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.,Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Lan Le
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Yoshihisa Tokumaru
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.,Department of Surgical Oncology, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Akimitsu Yamada
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Ryusei Matsuyama
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA. .,Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan. .,Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402, Japan. .,Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8520, Japan. .,Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, 960-1295, Japan. .,Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY, 14263, USA.
| |
Collapse
|
41
|
Comprehensive Analysis on the Specific Role and Function of Mitochondrial Inner Membrane Protein MPV17 in Liver Hepatocellular Carcinoma. Genet Res (Camb) 2022; 2022:7236823. [PMID: 35919033 PMCID: PMC9325347 DOI: 10.1155/2022/7236823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Background Liver hepatocellular carcinoma (LIHC) is the predominant type of liver cancer, and its treatment still faces great challenges presently. Mitochondrial inner membrane protein MPV17 is reported to be involved in multiple biological activities of cancers. Here, we seek to investigate the specific role and functions of MPV17 in LIHC progression. Methods Firstly, MPV17 expressions in various tumors and corresponding normal samples and LIHC groups with various clinical features were analyzed, respectively. Next, the relationship between MPV17 expression and LIHC survival was analyzed and verified by AUC curves. Besides, differentially expressed genes (DEGs) for LIHC were screened from TCGA and then analyzed by GO and KEGG. Then, MPV17 was analyzed by prognostic model, Cox analysis, predictive nomogram, pathway correlation, and immunoassay. Finally, the functions of MPV17 were determined by CCK-8 and Tranwell assays. Results In most tumors, MPV17 expression was higher than that in the normal group, and it was related to LIHC clinical features. In the LIHC survival analysis, highly expressed MPV17 was associated with a poor prognosis. Besides, 314 upregulated and 193 downregulated DEGs are mainly involved in the TNF signaling pathway and tyrosine metabolism. Through prognostic model, Cox analysis, and predictive nomogram, MPV17 had the prognostic value for LIHC. Gene-pathway correlation analysis showed that MPV17 had the strongest correlation with the G2M_checkpoint pathway. In an immunoassay, MPV17 had a strong correlation with many immune cells. Functional assays showed that MPV17 reduction in LIHC cells could inhibit cell invasion, migration, and proliferation. Conclusion MPV17, as a tumor promoter, could be a new biomarker for LIHC diagnosis and prognosis and probably shed new light on the exploration of LIHC therapies.
Collapse
|
42
|
Cherkassky L, Oshi M, Abdelfatah E, Wu R, Takabe Y, Yan L, Endo I, Takabe K. An immune-inflamed tumor microenvironment as defined by CD8 score is associated with favorable oncologic outcomes in hepatocellular carcinoma independent of measures of tumor mutational burden. Am J Cancer Res 2022; 12:3099-3110. [PMID: 35968349 PMCID: PMC9360211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023] Open
Abstract
Despite low mutational burden, immune checkpoint inhibitors have demonstrated promising results in a significant minority of hepatocellular carcinoma (HCC) patients with advanced disease. We hypothesized that HCC patients with higher levels of CD8+ T cell infiltration reflect an immune-inflamed cohort which has improved oncologic outcomes. 355 HCC patients with clinical and transcriptome data in the Cancer Genome Atlas (TCGA) and 151 HCC patients from cohort GSE7624 were analyzed. xCell computational algorithm was used to analyze immune cell infiltration in these patients. Each cohort was divided into high and low expression by the highest 2 terciles value. Gene Set Enrichment Analysis was performed to identify enriched gene sets. High CD8 score associated with improved overall survival in both cohorts (both P < 0.05). High score correlates with early BCLC stage (P = 0.035) but not AJCC stage. High CD8 also correlated with increased IFN-γ response (p = 0.038), lymphocyte infiltration (P < 0.001), and leukocyte fraction (P < 0.001). It was associated with increased polyclonality of T cell (P < 0.001) and B cell response (P = 0.017). High CD8 score correlated with increased cytolytic activity score (P < 0.001) and expression of multiple immune checkpoints including PD-1, PD-L1, CTLA-4 and Lag3 (all P < 0.001). There was no correlation to tumor mutational burden and neoantigens. GSEA demonstrated upregulation of several gene sets involved in inflammatory response and IFN-γ response. In conclusion, HCC patients with high CD8 score demonstrated favorable oncologic outcomes, which may be due to immune-mediated tumor cell attack. Furthermore, CD8 score may be a potentially useful biomarker to select patients for immune checkpoint inhibition.
Collapse
Affiliation(s)
- Leonid Cherkassky
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14203, USA
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14203, USA
- Department of Gastroenterological Surgery, Graduate School of Medicine, Yokohama City UniversityYokohama 236-0004, Japan
| | - Eihab Abdelfatah
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14203, USA
| | - Rongrong Wu
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14203, USA
| | - Yamato Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14203, USA
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14203, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Graduate School of Medicine, Yokohama City UniversityYokohama 236-0004, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14203, USA
- Department of Gastroenterological Surgery, Graduate School of Medicine, Yokohama City UniversityYokohama 236-0004, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo, NY 14263, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
- Department of Digestive and General Surgery, Graduate School of Medicine and Dental Sciences, Niigata UniversityNiigata 951-8520, Japan
- Department of Breast Surgery, School of Medicine, Fukushima Medical UniversityFukushima 960-1295, Japan
| |
Collapse
|
43
|
Wu R, Gandhi S, Tokumaru Y, Asaoka M, Oshi M, Yan L, Ishikawa T, Takabe K. Intratumoral PDGFB gene predominantly expressed in endothelial cells is associated with angiogenesis and lymphangiogenesis, but not with metastasis in breast cancer. Breast Cancer Res Treat 2022; 195:17-31. [DOI: 10.1007/s10549-022-06661-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/15/2022] [Indexed: 11/02/2022]
|
44
|
Abundance of reactive oxygen species (ROS) is associated with tumor aggressiveness, immune response, and worse survival in breast cancer. Breast Cancer Res Treat 2022; 194:231-241. [PMID: 35639264 PMCID: PMC9987174 DOI: 10.1007/s10549-022-06633-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023]
Abstract
PURPOSE Reactive oxygen species (ROS) are oxygen-containing molecules that have high reactivity and play roles in protection or harm the cancer cells. We aimed to clarify the clinical relevance of ROS in breast cancer (BC) tumor microenvironment (TME). We hypothesized that it is associated with worse BC patient outcomes. METHODS ROS score was generated by Gene Set Variation Analysis of Hallmark ROS pathway gene set and a total of 6245 BC patients were analyzed. RESULTS High ROS BC significantly enriched cell proliferation-related gene sets (MYC targets v1 and v2, G2M checkpoint, E2F targets), pro-cancer-related gene sets (DNA repair, unfolded protein response, MTORC1 signaling, PI3K/AKT/MTOR signaling, glycolysis, and oxidative phosphorylation), immune-related gene sets (inflammatory response, allograft rejection, interferon-α and γ responses, complement, and IL6/JAK/STAT3 signaling), and infiltrated immune cells (CD4+ memory and CD8+ T cells, Th1 and Th2, dendritic cells, Tregs, M1 and M2 macrophages) and B cells, as well as elevated cytolytic activity consistently in both METABRIC and GSE96058 cohorts. Cancer cells were the major source of ROS in BC TME of single-cell sequence (GSE75688) cohort. High ROS was associated with intratumor heterogeneity, homologous recombination defects, mutation rates, and neoantigens, and with clinical aggressiveness in AJCC stage, Nottingham grade and Ki67 expression, as well as worse overall survival in both GSE96058 and METABRIC, and with worse disease-specific survival in METABRIC. CONCLUSION Abundant ROS in BC patients is associated with abundant mutations, aggressive cancer biology, immune response, and worse survival.
Collapse
|
45
|
Oshi M, Roy AM, Gandhi S, Tokumaru Y, Yan L, Yamada A, Endo I, Takabe K. The clinical relevance of unfolded protein response signaling in breast cancer. Am J Cancer Res 2022; 12:2627-2640. [PMID: 35812054 PMCID: PMC9251678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023] Open
Abstract
Protein homeostasis regulated by the Endoplasmic Reticulum (ER) is a recognized process involved in cancer progression. ER stress activates the Unfolded Protein Response (UPR) and has been implicated in a variety of cancers. Given the role of the UPR activation in carcinogenesis, we hypothesized that UPR activation could be associated with pathological progression, higher clinical stage, and worse survival in breast cancer. A total of 4,416 breast cancer patients from multiple independent cohorts were analyzed. We defined the UPR pathway score by the degree of enrichment by Gene Set Variant Analysis and median was used to divide high vs. low score groups in each cohort. High UPR breast cancer significantly enriched not only cell proliferation-related but also other pro-cancerous gene sets consistently in both METABIC and GSE96058 cohort. Majority of UPR pathway score high cells in the bulk tumor were tumor cells compared to other cells, including stromal, T-, B-, and myeloid-cells (P<0.001). UPR score was significantly associated with advanced stage, high grade, and triple negative breast cancer (TNBC) (all P<0.001). High UPR breast cancer was associated with worse patient survival in both cohorts (all P<0.001). Among breast cancer subtype, ER-positive/HER2-negative breast cancer with high UPR was significantly associated with worse survival, but neither HER-positive nor TNBC. High UPR ER-positive/HER2-negative breast cancer was infiltrated with high level of Th1 and Th2 cells, M1 macrophage, and plasma cells. On the other hand, they were significantly infiltrated with high level of several types of stromal cells in tumor microenvironment (all P<0.001). Finally, high UPR metastatic breast cancer was also associated with worse patient survival (P=0.041). UPR signaling is associated with cancer aggressiveness, and worse survival, especially ER-positive/HER2-negative breast cancer subtype.
Collapse
Affiliation(s)
- Masanori Oshi
- Breast Surgery, Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Arya Mariam Roy
- Department of Medical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
| | - Shipra Gandhi
- Department of Medical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
| | - Yoshihisa Tokumaru
- Breast Surgery, Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
| | - Akimitsu Yamada
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Kazuaki Takabe
- Breast Surgery, Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, New York 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo, New York 14263, USA
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata 951-8520, Japan
- Department of Breast Surgery, Fukushima Medical University School of MedicineFukushima 960-1295, Japan
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| |
Collapse
|
46
|
Takahashi H, Oshi M, Yan L, Endo I, Takabe K. Gastric cancer with enhanced apical junction pathway has increased metastatic potential and worse clinical outcomes. Am J Cancer Res 2022; 12:2146-2159. [PMID: 35693068 PMCID: PMC9185607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023] Open
Abstract
Excessive intercellular connection at confluency may be limiting further cell growth or a sign of aggressive biology in the cell culture. As apical junction complex is a main component of cell-to-cell connection, we aimed to investigate gastric cancer biology using Apical Junction Pathway score that we generated using Gene set variant analysis (GSVA) of the "Hallmark Apical Junction" gene set. 1,239 gastric cancer patients from the Cancer Genome Atlas (TCGA) and two GSE cohorts were included in this study. The cohorts were dichotomized using the median of the score. Apical Junction Pathway score high gastric cancer was not consistently associated with increased cell proliferation or immune cell infiltration. On the other hand, Apical Junction Pathway score high gastric cancer was associated with significantly higher infiltration of stromal cells, such as endothelial cells; hence, increased neovascularization and angiogenesis in the tumor microenvironment (TME) were speculated. Gene set enrichment analysis (GSEA) confirmed increased expression of epithelial mesenchymal transition (EMT) and angiogenesis in the high Apical Junction Pathway score group (false discovery rate (FDR) <0.25). Lastly, the high Apical Junction Pathway score group was associated with more aggressive clinicopathological characteristics, such as significantly higher American Joint Committee on Cancer (AJCC) T-category and higher pathological stage, leading to worse disease-specific survival and overall survival (P<0.05, respectively). In conclusion, enhanced Apical Junction Pathway score gastric cancer was associated with aggressive clinical characteristics leading to shorter survival likely due to increased metastatic potential from EMT and angiogenesis.
Collapse
Affiliation(s)
- Hideo Takahashi
- Department of SurgeryMount Sinai South Nassau, NY, USA
- Department of Surgery, Section of Hepatobiliary Surgery, Icahn School of Medicine at Mount SinaiNew York, NY, USA
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterNY, USA
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterNY, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Japan
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer CenterNY, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterNY, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Japan
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
- Department of Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata, Japan
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, the State University of New YorkBuffalo, NY, USA
| |
Collapse
|
47
|
Zhou Y, Lei D, Hu G, Luo F. A Cell Cycle-Related 13-mRNA Signature to Predict Prognosis in Hepatocellular Carcinoma. Front Oncol 2022; 12:760190. [PMID: 35419294 PMCID: PMC8995863 DOI: 10.3389/fonc.2022.760190] [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: 08/17/2021] [Accepted: 02/17/2022] [Indexed: 12/02/2022] Open
Abstract
We aimed to propose a cell cycle-related multi/mRNA signature (CCS) for prognosis prediction and uncover new tumor-driver genes for hepatocellular carcinoma (HCC). Cell cycle-related gene sets and HCC samples with mRNA-Seq data were retrieved from public sources. The genes differentially expressed in HCCs relative to normal peritumoral tissues were extracted through statistical analysis. The CCS was constructed by Cox regression analyses. Predictive capacity and clinical practicality of the signature were evaluated and validated. The expression of the function-unknown genes in the CCS was determined by RT-qPCR. Candidate gene TICRR was selected for subsequent validation through functional experiments. A cell cycle-related 13-mRNA signature was generated from the exploratory cohort [The Cancer Genome Atlas (TCGA), n = 371)]. HCC cases were classified as high- vs. low-risk groups per overall survival (OS) [hazard ratio (HR) = 2.699]. Significantly, the CCS exhibited great predictive value for prognosis in three independent cohorts, particularly in GSE76427 cohort [area under the curve (AUC) = 0.835/0.822/0.808/0.821/0.826 at 1/2/3/4/5 years]. The nomogram constructed by integrating clinicopathological features with the CCS indicated high accuracy and practicability. Significant enrichment of tumorigenesis-associated pathways was observed in the high-risk patients by Gene Set Enrichment Analysis (GSEA). RT-qPCR revealed that TICRR was overexpressed in HCC samples. Increased TICRR expression implied poor prognosis in HCC patients. Furthermore, depletion of TICRR in HCC cells decreased cell proliferation and the G1/S transition. In conclusion, the established 13-CCS had efficacy in prognostic prediction of HCC patients. Additionally, TICRR was demonstrated as a tumor-driver gene for this deadly disease.
Collapse
Affiliation(s)
- Yang Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Central Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dengliang Lei
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Central Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Gangli Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Central Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fang Luo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
48
|
Leng X, Kan H, Wu Q, Li C, Zheng Y, Peng G. Inhibitory Effect of Salvia miltiorrhiza Extract and Its Active Components on Cervical Intraepithelial Neoplastic Cells. Molecules 2022; 27:1582. [PMID: 35268683 PMCID: PMC8911905 DOI: 10.3390/molecules27051582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/16/2022] Open
Abstract
The effective treatment of cervical intraepithelial neoplasia (CIN) can prevent cervical cancer. Salvia miltiorrhiza is a medicinal and health-promoting plant. To identify a potential treatment for CIN, the effect of S. miltiorrhiza extract and its active components on immortalized cervical epithelial cells was studied in vitro. The H8 cell was used as a CIN model. We found that S. miltiorrhiza extract effectively inhibited H8 cells through the CCK8 method. An HPLC-MS analysis revealed that S. miltiorrhiza extract contained salvianolic acid H, salvianolic acid A, salvianolic acid B, monomethyl lithospermate, 9‴-methyl lithospermate B, and 9‴-methyl lithospermate B/isomer. Salvianolic acid A had the best inhibitory effect on H8 cells with an IC50 value of 5.74 ± 0.63 μM. We also found that the combination of salvianolic acid A and oxysophoridine had a synergistic inhibitory effect on H8 cells at molar ratios of 4:1, 2:1, 1:1, 1:2, and 1:4, with salvianolic acid A/oxysophoridine = 1:2 having the best synergistic effect. Using Hoechst33342, flow cytometry, and Western blotting analysis, we found that the combination of salvianolic acid A and oxysophoridine can induce programmed apoptosis of H8 cells and block the cell cycle in the G2/M phase, which was correlated with decreased cyclinB1 and CDK1 protein levels. In conclusion, S. miltiorrhiza extract can inhibit the growth of H8 cells, and the combination of salvianolic acid A (its active component) and oxysophoridine has a synergistic inhibitory effect on H8 cells and may be a potential treatment for cervical intraepithelial neoplasia.
Collapse
Affiliation(s)
| | | | | | | | | | - Guoping Peng
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China; (X.L.); (H.K.); (Q.W.); (C.L.); (Y.Z.)
| |
Collapse
|
49
|
Angarita FA, Oshi M, Yamada A, Yan L, Matsuyama R, Edge SB, Endo I, Takabe K. Low RUFY3 expression level is associated with lymph node metastasis in older women with invasive breast cancer. Breast Cancer Res Treat 2022; 192:19-32. [PMID: 35018543 PMCID: PMC8844209 DOI: 10.1007/s10549-021-06482-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/03/2021] [Indexed: 02/03/2023]
Abstract
PURPOSE Sentinel lymph node biopsy is omitted in older women (≥ 70 years old) with clinical lymph node (LN)-negative hormone receptor-positive breast cancer as it does not influence adjuvant treatment decision-making. However, older women are heterogeneous in frailty while the chance of recurrence increase with improving longevity. Therefore, a biomarker that identifies LN metastasis may facilitate treatment decision-making. RUFY3 is associated with cancer progression. We evaluated RUFY3 expression level as a biomarker for LN-positive breast cancer in older women. METHODS Clinical and transcriptomic data of breast cancer patients were obtained from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC, n = 1903) and The Cancer Genome Atlas (TCGA, n = 1046) Pan-cancer study cohorts. RESULTS A total of 510 (METABRIC) and 211 (TCGA) older women were identified. LN-positive breast cancer, which represented 51.4% (METABRIC) and 48.4% (TCGA), demonstrated worse disease-free, disease-specific, and overall survival. RUFY3 levels were significantly lower in LN-positive tumors regardless of age. The area under the curve for the receiver operator characteristic (AUC-ROC) curves showed RUFY3-predicted LN metastasis. Low RUFY3 enriched oxidative phosphorylation, DNA repair, MYC targets, unfolded protein response, and mtorc1 signaling gene sets, was associated with T helper type 1 cell infiltration, and with intratumor heterogeneity and fraction altered. Low RUFY3 expression was associated with LN-positive breast cancer and with worse disease-specific survival among older women. CONCLUSION Older women with breast cancers who had low expression level of RUFY3 were more frequently diagnosed with LN-positive tumors, which translated into worse prognosis.
Collapse
Affiliation(s)
- Fernando A. Angarita
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA;,Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Akimitsu Yamada
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Ryusei Matsuyama
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Stephen B. Edge
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA;,Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA;,Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan;,Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York, USA;,Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan;,Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
| |
Collapse
|
50
|
Yuan X, Dong Z, Shen S. LncRNA GACAT3: A Promising Biomarker and Therapeutic Target in Human Cancers. Front Cell Dev Biol 2022; 10:785030. [PMID: 35127682 PMCID: PMC8811307 DOI: 10.3389/fcell.2022.785030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/05/2022] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a class of functional RNA molecules that do not encode proteins and are composed of more than 200 nucleotides. LncRNAs play important roles in epigenetic and gene expression regulation. The oncogenic lncRNA GACAT3 was recently discovered to be dysregulated in many tumors. Aberrant expression of GACAT3 contributes to clinical characteristics and regulates multiple oncogenic processes. The association of GACAT3 with a variety of tumors makes it a promising biomarker for diagnosis, prognosis, and targeted therapy. In this review, we integrate the current understanding of the pathological features, biological functions, and molecular mechanisms of GACAT3 in cancer. Additionally, we provide insight into the utility of GACAT3 as an effective diagnostic and prognostic marker for specific tumors, which offers novel opportunities for targeted therapeutic intervention.
Collapse
Affiliation(s)
- Xin Yuan
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zihui Dong
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, The First Affifiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shen Shen
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, The First Affifiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Shen Shen,
| |
Collapse
|