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Wang Q, Yu T, Ke ZH, Wang FF, Yin JN, Shao Y, Lu KH. RB1 aberrations predict outcomes of immune checkpoint inhibitor combination therapy in NSCLC. Front Oncol 2023; 13:1172728. [PMID: 37441425 PMCID: PMC10334286 DOI: 10.3389/fonc.2023.1172728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/06/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Immune checkpoint inhibitors (ICI) have changed the treatment of non-small cell lung cancer (NSCLC). Furthermore, compared with monotherapy, ICI combination therapy had better efficacy and partly different mechanism. Therefore, we aim to investigate and improve biomarkers specialized for ICI combination therapy. Methods We enrolled 53 NSCLC patients treated with ICI combination therapy and collected their tissue and plasma samples to perform next-generation sequencing (NGS) with a 425-gene panel. Results The line of treatment was the only clinical factor significantly affecting objective response rate (ORR) and progression-free survival (PFS). Surprisingly, classical markers PD-L1 and TMB only had limited predictive values in the ICI combination therapy. Instead, we found RB1 mutation was significantly associated with prognosis. Patients with mutated RB1 had shorter PFS than those with wild RB1 (134d vs 219d, p=0.018). Subsequent analysis showed the RB1 related mutated cell cycle and chromosomal instability were also deleterious to prognosis (103d vs 411d, p<0.001; 138d vs 505d, p=0.018). Additionally, patients with more circulating tumor DNA (ctDNA) had significantly shorter PFS (41d vs 194d, p=0.0043). Conclusion This study identified that NSCLC patients with mutated RB1 were less sensitive to ICI combination therapy. RB1 mutations and following cell cycle abnormalities and chromosomal instability can potentially guide clinical management.
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Affiliation(s)
- Qian Wang
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Tao Yu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zi-Hao Ke
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fu-Feng Wang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Jia-Ni Yin
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kai-Hua Lu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Voutsadakis IA. Characteristics and Prognosis of 8p11.23-Amplified Squamous Lung Carcinomas. J Clin Med 2023; 12:jcm12051711. [PMID: 36902501 PMCID: PMC10002535 DOI: 10.3390/jcm12051711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND Copy number alterations are common genetic lesions in cancer. In squamous non-small cell lung carcinomas, the most common copy-number-altered loci are at chromosomes 3q26-27 and 8p11.23. The genes that may be drivers in squamous lung cancers with 8p11.23 amplifications are unclear. METHODS Data pertaining to copy number alterations, mRNA expression and protein expression of genes located in the 8p11.23 amplified region were extracted from various sources including The Cancer Genome Atlas, the Human Protein Atlas and the Kaplan Meier Plotter. Genomic data were analyzed using the cBioportal platform. Survival analysis of cases with amplifications compared to nonamplified cases was performed using the Kaplan Meier Plotter platform. RESULTS The 8p11.23 locus is amplified in 11.5% to 17.7% of squamous lung carcinomas. The most frequently amplified genes include NSD3, FGFR1 and LETM2. Only some of the amplified genes present concomitant overexpression at the mRNA level. These include NSD3, PLPP5, DDHD2, LSM1 and ASH2L, while other genes display lower levels of correlation, and still, some genes in the locus show no mRNA overexpression compared with copy-neutral samples. The protein products of most locus genes are expressed in squamous lung cancers. No significant difference in overall survival in 8p11.23-amplified squamous cell lung cancers versus nonamplified cancers is observed. In addition, there is no adverse effect of mRNA overexpression for relapse-free survival of any of the amplified genes. CONCLUSION Several genes that are part of the commonly amplified locus 8p11.23 in squamous lung carcinomas are putative oncogenic candidates. A subset of genes of the centromeric part of the locus, which is amplified more commonly than the telomeric part, show high concomitant mRNA expression.
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Affiliation(s)
- Ioannis A. Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste. Marie, ON P6B 0A8, Canada; or
- Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON P3E 2C6, Canada
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3
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Molecular Alterations and Putative Therapeutic Targeting of Planar Cell Polarity Proteins in Breast Cancer. J Clin Med 2023; 12:jcm12020411. [PMID: 36675340 PMCID: PMC9864096 DOI: 10.3390/jcm12020411] [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: 11/23/2022] [Revised: 12/27/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Treatment and outcomes of breast cancer, one of the most prevalent female cancers, have improved in recent decades. However, metastatic breast cancer remains incurable in most cases, and new therapies are needed to ameliorate prognosis. Planar cell polarity (PCP) is a characteristic of epithelial cells that form layers and is integral to the communication of these cells with neighboring cells. Dysfunction of PCP is observed in cancers and may confer a targetable vulnerability. METHODS The breast cancer cohorts from The Cancer Genome Atlas (TCGA) and the METABRIC study were interrogated for molecular alterations in genes of the PCP pathway. The groups with the most prevalent alterations were characterized, and survival was compared with counterparts not possessing PCP alterations. Breast cancer cell lines with PCP alterations from the Cancer Cell Line Encyclopedia (CCLE) were interrogated for sensitivity to drugs affecting PCP. RESULTS Among genes of the PCP pathway, VANGL2, NOS1AP and SCRIB display amplifications in a sizable minority of breast cancers. Concomitant up-regulation at the mRNA level can be observed mostly in basal cancers, but it does not correlate well with the amplification status of the genes, as it can also be observed in non-amplified cases. In an exploration of cell line models, two of the four breast cancer cell line models with amplifications in VANGL2, NOS1AP and SCRIB display sensitivity to drugs inhibiting acyl-transferase porcupine interfering with the WNT pathway. This sensitivity suggests a possible therapeutic role of these inhibitors in cancers bearing the amplifications. CONCLUSION Molecular alterations in PCP genes can be observed in breast cancers with a predilection for the basal sub-type. An imperfect correlation of copy number alterations with mRNA expression suggests that post-translational modifications are important in PCP regulation. Inhibitors of acyl-transferase porcupine may be rational candidates for combination therapy development in PCP-altered breast cancers.
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Voutsadakis IA. Molecular alterations in anti-apoptotic BCL2 family proteins in breast cancer cell line models, drug sensitivities and dependencies to guide the development of BCL2 inhibitors. Gene X 2022; 847:146881. [PMID: 36100115 DOI: 10.1016/j.gene.2022.146881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/09/2022] [Accepted: 09/05/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Breast cancer is one of the most prevalent cancers and a cause of significant morbidity and mortality. Despite introduction of new therapies that improve control of the disease, metastatic breast cancer remains still incurable in most cases. Further therapies based on a better understanding of the pathogenesis of breast cancers and its sub-types are needed to improve outcomes. Apoptosis has arisen as a potential target in recent years. Research on therapeutic use of apoptosis promoting drugs could be advanced by cell line models of efficacy. METHODS Alterations in antiapoptotic members of the BCL2 family of proteins encoded by genes BCL2, BCL2L1, BCL2L2, MCL1 and BCL2A1 were evaluated in breast cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE). Sensitivities of breast cancer cell lines to apoptosis promoting drugs were evaluated using the Genomics of Drug Sensitivity in Cancer (GDSC) platform. Concomitant molecular aberrations of sensitive and resistant cell lines were examined for recurrent themes. Cell line dependencies were surveyed using publicly available CRISPR and RNAi arrays. RESULTS Breast cancer cell lines, in concordance with breast cancer patient samples, commonly exhibit amplifications in the BCL2 member MCL1 but not other molecular alterations in antiapoptotic family members. The panel of breast cancer cell lines with sensitivity to drugs inhibiting MCL1, with or without inhibition of other family members consists exclusively of cell lines of the basal phenotype. Sensitive cell lines possess fewer amplifications in the commonly amplified in breast cancer loci at 8q23, 11q13, 17q12 and 1q21. Dependency analysis suggests that in some instances activity of cancer related pathways such as PI3K/ AKT and WNT/ β-catenin may affect apoptosis threshold. CONCLUSION Breast cancer cell line models faithfully depict the most common molecular aberration in BCL2 family proteins observed in clinical breast cancer samples, MCL1 amplifications. Basal cell lines may be a preferred target of MCL1 inhibitors. However, concomitant aberrations, as explored in this report, are likely to be involved in ultimate sensitivity to anti-apoptosis targeting therapies.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste. Marie, Ontario, Canada; Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, Ontario, Canada.
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Voutsadakis IA. Loss of genes in chromosome arms 5q and 16q in breast cancer. Breast Dis 2022; 41:331-341. [PMID: 35964165 DOI: 10.3233/bd-210047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Losses of genetic material from chromosomes 5q and 16q commonly occur in sub-sets of breast cancer. Their significance from a pathophysiologic point of view is not well-defined. METHODS This study uses publicly available genomic data from extensive breast cancer datasets to define the landscape of losses in chromosomal arms 5q and 16q in the two sub-types of breast cancer they most commonly occur, basal-like and luminal A cancers, respectively. RESULTS It is shown that dozens of genes from these chromosomal arms are putatively hemi-deleted in few samples each. No individual gene from either 5q or 16q shows an incidence of deep deletion above 10% in the cohorts with basal-like and luminal A cancers or in the whole cohorts. A few tumor suppressor genes are deleted in a small number of samples, less than 5% in each cohort. Losses of 5q or 16q confer no survival advantage in either the basal-like or the luminal A cohorts from TCGA that harbor them. CONCLUSION Results suggest that there are no individual genes in chromosomes 5q and 16q whose loss can be implicated in a dominant pathophysiologic sequence of events in breast cancer or its sub-sets.
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Affiliation(s)
- Ioannis A Voutsadakis
- Sault Area Hospital, Algoma District Cancer Program, Sault Ste. Marie, ON, Canada.,Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON, Canada
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6
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Zhang R, Liu Z, Chang X, Gao Y, Han H, Liu X, Cai H, Fu Q, Liu L, Yin K. Clinical significance of chromosomal integrity in gastric cancers. Int J Biol Markers 2022; 37:296-305. [PMID: 35722719 DOI: 10.1177/03936155221106217] [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] [Indexed: 11/15/2022]
Abstract
BACKGROUND A whole-exome or targeted cancer genes panel by next-generation sequencing has been used widely in assisting individualized treatment decisions. Currently, multiple algorithms are developed to estimate DNA copy numbers based on sequencing data, which makes a comprehensive global glance at chromosomal integrity possible. We aim to classify gastric cancers based on chromosomal integrity to guide personalized therapy. METHODS We investigated copy number variations (CNV) across the entire genome of 124 gastric carcinomas via exome or targeted sequencing. Chromosomal integrity was classified as chromosomal stability (CS), chromosomal instability (CIN) and intermediate state (CIN/CS) based on CNV results. Chromosomal integrity was correlated to molecular features and clinical characteristics. RESULTS According the states of chromosomal integrity, gastric carcinomas can be stratified into two cohorts: CS and CIN. Our results showed a significant relationship between CIN status and TP53 mutation, but not RB1, phosphatase and tensin homolog (PTEN), or other reported DNA damage repair genes. The mutation frequency of the TP53 gene had great relevance. Our study initially revealed clinical significance of chromosomal integrity that CIN patients were prone to HER2-positive and mucinous adenocarcinoma, while CS patients were a diffuse subtype and poorly differentiated but had longer overall survival. CONCLUSIONS We classified gastric carcinomas into two states of chromosomal integrity with clinical implications. The dichotomy is applicable to clinical transformation. We proposed that classifying gastric cancers based on chromosomal integrity would enable us to achieve personalized therapy for patients and may be beneficial to patient stratification in future clinical trials.
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Affiliation(s)
- Rukui Zhang
- Institutes of Biomedical Sciences, 262117Fudan University, Shanghai, China
| | - Zhaorui Liu
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xusheng Chang
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Yuan Gao
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Huan Han
- Department of Pathology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiaona Liu
- Institutes of Biomedical Sciences, 262117Fudan University, Shanghai, China
| | - Hui Cai
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Qiqing Fu
- Institutes of Biomedical Sciences, 262117Fudan University, Shanghai, China
| | - Lei Liu
- Institutes of Biomedical Sciences, 262117Fudan University, Shanghai, China.,School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kai Yin
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
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Zaker SR, Ghaedi K. Downregulation of LINC02615 Is Correlated with The Breast Cancer Progress: A Novel Biomarker for Differential Identification of Breast Cancer Tissues. CELL JOURNAL 2021; 23:414-420. [PMID: 34455716 PMCID: PMC8405088 DOI: 10.22074/cellj.2021.7283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/27/2020] [Indexed: 11/26/2022]
Abstract
Objective Breast cancer is one of the most frequent types of cancer with a gradually increasing incidence in developing
countries. The aim of this study was to assess modulation of LINC02615 levels in breast cancer progress, using
pairwise breast cancer and healthy control tissue samples with regard to the obesity and other conditions, as estrogen
receptor (ER) expression.
Materials and Methods In this cohort study, the genes, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs)
in several important pathways of chromosomal instability, apoptosis and proliferation were analyzed through in silico
studies pinpointing the important genes which were responsible for the breast cancer incidence. Then, the respective
miRNAs and lncRNAs were selected by relevant databases. At the next step, Lncbase was used for interaction analysis
of selected miRNAs and LncRNAs, which resulted in final selection of LINC02615. Total RNA was isolated from 24
pairwise breast cancer and healthy control tissue samples. Expression profile of LINC02615 was assessed using
quantitative reverse transcription polymerase chain reaction (qRT-PCR). Correlation between LINC02615 expression
and clinicopathological characteristics were analyzed using Pearson’s Chi-square test in breast cancer patients.
Results Data demonstrated that expression of LINC02615 was significantly downregulated in breast cancer tissues
compared to the healthy controls (P=0.046). In particular, the relative LINC02615 expression was significantly different in
breast cancer tissues especially in obese patients compared to those persons without obesity (P=0.047). Furthermore,
a significant difference in LINC02615 level was found between the high and low ER expressions (P=0.014). However,
the aberrant expression of LINC02615 was significantly related to physical activity and diabetes disease as well as the
stress and age at menopause (P=0.028, P=0.046, P=0.047 and P=0.025, respectively).
Conclusion Taken together, we suggest that LINC02615 downregulation may be related to the risk of breast cancer in
Iranian patients. Thus, it may serve as a novel biomarker for identification of breast cancer tissues.
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Affiliation(s)
- Sayed Rasoul Zaker
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Kamran Ghaedi
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.,Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Iran
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Impaired Expression of Cytoplasmic Actins Leads to Chromosomal Instability of MDA-MB-231 Basal-Like Mammary Gland Cancer Cell Line. Molecules 2021; 26:molecules26082151. [PMID: 33917969 PMCID: PMC8068389 DOI: 10.3390/molecules26082151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 12/03/2022] Open
Abstract
We have shown previously that two cytoplasmic actin isoforms play different roles in neoplastic cell transformation. Namely, β-cytoplasmic actin acts as a tumor suppressor, whereas γ-cytoplasmic actin enhances malignant features of tumor cells. The distinct participation of each cytoplasmic actin in the cell cycle driving was also observed. The goal of this study was to describe the diverse roles of cytoplasmic actins in the progression of chromosomal instability of MDA-MB-231 basal-like human carcinoma cell line. We performed traditional methods of chromosome visualization, as well as 3D-IF microscopy and western blotting for CENP-A detection/quantification, to investigate chromosome morphology. Downregulation of cytoplasmic actin isoforms alters the phenotype and karyotype of MDA-MB-231 breast cancer cells. Moreover, β-actin depletion leads to the progression of chromosomal instability with endoreduplication and aneuploidy increase. On the contrary, γ-actin downregulation results not only in reduced percentage of mitotic carcinoma cells, but leads to chromosome stability, reduced polyploidy, and aneuploidy.
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Voutsadakis IA. The Landscape of Chromosome Instability in Breast Cancers and Associations with the Tumor Mutation Burden: An Analysis of Data from TCGA. Cancer Invest 2020; 39:25-38. [PMID: 33306412 DOI: 10.1080/07357907.2020.1863418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Chromosomal instability (CIN) is a defining characteristic of cancer and is part of the genetic instability of cancer. CIN results in both numeric alterations of chromosomes also called aneuploidy and in gains or losses of parts of chromosome arms but both usually coexist. The frequency and distribution of CIN varies between cancer types and even in the same cancer and breast cancer is no exception. Its presence may provide prognostic and therapeutic opportunities. METHODS CIN as measured with a score named Aneuploidy Score (AS) derived from single nucleotide polymorphism array studies was examined using the breast cancer study from the Cancer Genome Atlas (TCGA). Correlations of the AS with sub-types of breast cancer and with the tumor mutation burden (TMB) were examined. Specific copy number alterations contributing to the AS and their associations with sub-types were also investigated. RESULTS Most breast cancers (about 75% in the series) present some degree of CIN, having an AS of above 5. The remaining 25% have AS of 5 or below. Luminal A sub-type is over-represented in cancers with low AS while the reverse is true for cancers with high AS where the percentage of the three other sub-types, luminal B, Her2 positive and basal is higher. Common gains of chromosomal arms are observed in 1q, 8q and 16p and losses are commonly present in 16q, 17p and 8p but with variability among sub-types. A chromosome loss characterizing basal cancers is observed at 5q. No association of AS with TMB is observed in breast cancer. AS was not predictive for survival outcomes in the entire cohort of breast cancers, but PFS was significant worse in luminal B cancers with high AS. CONCLUSION The copy number alterations landscape of breast cancer reveals specific abnormalities in each sub-type and may help further characterize these sub-types in order to refine classification of these cancers and promote prognostic and therapeutic advancements in the clinic.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste. Marie, Ontario, Canada.,Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, Ontario, Canada
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10
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8p11.23 Amplification in Breast Cancer: Molecular Characteristics, Prognosis and Targeted Therapy. J Clin Med 2020; 9:jcm9103079. [PMID: 32987805 PMCID: PMC7598661 DOI: 10.3390/jcm9103079] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Amplification of the locus 8p11.23 has been observed in cancer and genes of this locus, including ZNF703 (Zinc finger protein 703), NSD3 (Nuclear receptor binding SET domain protein 3) and FGFR1 (Fibroblast growth factor receptor 1), have been put forward as dominant oncogenes conferring pathophysiologic benefit in cancers with amplifications. However, there is no consensus on the importance of each of them or any other genes of the amplicon or even a consensus on which genes are part of the amplicon. METHODS Publicly available data were used to characterize the locus amplified at 8p11.23 and derive information on each of the genes and roles as oncogenes. The frequency of the amplifications in the locus was examined in the cBioportal platform, and expression levels of the amplicon genes in amplified cases were derived from genomic studies reported in the platform. Examination of the influence of mRNA expressions of each gene of the locus for Recurrence-free survival in breast cancer was performed using K-M plotter. RESULTS The 8p11.23 amplicon is present in higher frequency in squamous cell lung carcinomas, breast cancers and bladder carcinomas and is only rarely observed in other cancers. The most frequently amplified genes within the amplicon vary between different types of cancers. In breast cancer, amplified cases are most commonly of the luminal B type. Amplified genes are not always over-expressed and there is a low correlation of amplification with over-expression in amplicon genes with variation between genes. The presence of the amplicon does not influence the aneuploidy score or the tumor mutation burden of breast cancers. Regarding prognosis, the two genes of the amplicon whose mRNA hyper-expression portends adverse relapse-free survival in breast cancer are EIF4EBP1 (Eukaryotic transcription initiation factor 4E binding protein 1) and LSM1 (LSM1 homolog, mRNA degradation associated). CONCLUSION Besides the previously proposed genes to play a role as dominant oncogenes in the 8p11.23 cancer amplified locus, other genes may also be important in breast cancer based on the high correlation of their amplification and mRNA expression and adverse prognosis conferred by over-expression, consistent with an oncogenic role.
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11
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Zhou H, Yang Z, Yue J, Chen Y, Chen T, Mu T, Liu H, Bi X. Identification of potential hub genes via bioinformatics analysis combined with experimental verification in colorectal cancer. Mol Carcinog 2020; 59:425-438. [PMID: 32064687 DOI: 10.1002/mc.23165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/23/2020] [Accepted: 01/31/2020] [Indexed: 12/18/2022]
Abstract
Colorectal cancer (CRC) is a kind of malignant cancer with high morbidity and mortality. The purpose of this study was to explore potential regulated key genes involved in CRC through bioinformatics analysis and experimental verification. The gene expression profile data were downloaded from the Gene Expression Omnibus, and the differential expression genes were detected in cancerous and paracancerous samples of CRC patients, respectively. Then functional enrichment analysis, such as the Kyoto Encyclopedia of Genes and Genomes pathway analysis as well as the protein-protein interaction network were constructed, and the highly related genes were clustered by Molecular COmplex DEtection algorithm to find out the core interaction in different genes' crosstalk. The genes affecting CRC prognosis were screened by the Human Protein Atlas database. In addition, the expression level of core genes was detected by GEPIA database, and the core genes' changes in large-scale cancer genome data set were directly analyzed by cBioPortal database. The expression of the predicted hub genes DSN1, AHCY, and ERCC6L was verified by reverse-transcription quantitative polymerase chain reaction in CRC cells. The gene function of DSN1 was analyzed by wound healing and colony formation assays. The results showed that silencing of DSN1 could significantly reduce the migration and proliferation of CRC cells. Further, BUB1B, the potential interacting protein of DSN1, was also predicted via bioinformatics analysis. Above all, this study shows that bioinformatics analysis combined with experimental method verification provide more potential vital genes for the prevention and therapy of CRC.
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Affiliation(s)
- Hongrui Zhou
- College of Life Science, Liaoning University, Shenyang, China
| | - Zhe Yang
- College of Life Science, Liaoning University, Shenyang, China
| | - Jiaxin Yue
- College of Life Science, Liaoning University, Shenyang, China
| | - Yang Chen
- College of Life Science, Liaoning University, Shenyang, China
| | - Tianqiao Chen
- College of Life Science, Liaoning University, Shenyang, China
| | - Teng Mu
- College of Life Science, Liaoning University, Shenyang, China
| | - Hongsheng Liu
- College of Life Science, Liaoning University, Shenyang, China
- Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning Province, Liaoning University, Shenyang, China
| | - Xiuli Bi
- College of Life Science, Liaoning University, Shenyang, China
- Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning Province, Liaoning University, Shenyang, China
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12
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Davies V, Voutsadakis IA. Amplification of Chromosome 17 Centromere (CEP17) in Breast Cancer Patients with a Result of HER2 2± by Immunohistochemistry. Cancer Invest 2020; 38:94-101. [PMID: 31977265 DOI: 10.1080/07357907.2020.1720223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Background: Amplification of the centromeric region of chromosome 17 (CEP17) as measured by In Situ Hybridization (ISH) of the CEP17 probe is used clinically as part of the ISH assay for HER2 status determination in breast cancer. The value of amplification of CEP17 beyond its use in the HER2 ISH test has not been fully explored.Methods: A retrospective review of patients with breast cancer that had a dual probe HER2/CEP17 FISH test during an eight-year period was performed. Data on demographic and cancer-specific characteristics of the included patients were extracted. The group of patients with an amplified CEP17 defined as mean copy number of ≥3 per nucleus was compared with the group without amplification.Results: Two hundred and twelve patients were eligible and included in the analysis. Amplification of CEP17 was observed in 39 patients (18.4%). All patients in the amplified group had a concomitant amplification of HER2 (mean copy number ≥3 per nucleus). In the CEP17 non-amplified group 82 of 172 patients (47.7%) had an amplified HER2 status. More patients in the amplified group had a clinical HER2+ status according to the 3-protein classifier (30.8% versus 12.3% in the non-amplified group) and fewer patients in the amplified group had a clinical ER+/HER2- status (66.7% versus 81.3% in the non-amplified group, x2 p = .01). Other significant differences between the amplified and CEP17 non-amplified groups were observed in their lymph node (LN) status (56.4% of patients in the amplified group versus 38.8% in the non-amplified group were lymph node positive, p = .04) and in the nuclear heterogeneity component of grade (91.2% of patients in the amplified group were nuclear grade 3 versus 67.1% in the non-amplified group, p = .005). There were no statistically significant differences between the groups in overall stage, grade, menopause status or histology. Recurrence Free Survival (RFS) was shorter in stage I to III patients with an amplified CEP17 compared with the non-amplified group.Conclusion: Patients with amplification of CEP17 had a co-amplified HER2 and were more commonly HER2+, LN positive and grade 3 in the nuclear component of grade.
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Affiliation(s)
| | - Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste Marie, Canada.,Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, Canada
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13
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Kouprina N, Liskovykh M, Petrov N, Larionov V. Human artificial chromosome (HAC) for measuring chromosome instability (CIN) and identification of genes required for proper chromosome transmission. Exp Cell Res 2019; 387:111805. [PMID: 31877307 DOI: 10.1016/j.yexcr.2019.111805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 01/24/2023]
Abstract
Chromosomal instability (CIN) is one of the characteristics of cancer inherent for tumor initiation and progression, which is defined as a persistent, high rate of gain/loss of whole chromosomes. In the vast majority of human tumors the molecular basis of CIN remains unknown. The development of a conceptually simple colony color sectoring assay that measures yeast artificial chromosome (YAC) loss provided a powerful genetic tool to assess the rate of chromosome mis-segregation and also identified 937 yeast genes involved in this process. Similarly, a human artificial chromosome (HAC)-based assay has been recently developed and applied to quantify chromosome mis-segregation events in human cells. This assay allowed identification of novel human CIN genes in the library of protein kinases. Among them are PINK1, TRIO, IRAK1, PNCK, and TAOK1. The HAC-based assay may be applied to screen siRNA, shRNA and CRISPR-based libraries to identify the complete spectrum of CIN genes. This will reveal new insights into mechanisms of chromosome segregation and may expedite the development of novel therapeutic strategies to target the CIN phenotype in cancer cells.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Nikolai Petrov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
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