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Kaplan HG, Dowdell AK, Berry AB, Shimol RB, Robinson FL, Carney CA, Piening BD. Multi-omic profiling of simultaneous ductal carcinoma in situ and invasive breast cancer. Breast Cancer Res Treat 2024; 205:451-464. [PMID: 38523186 PMCID: PMC11101558 DOI: 10.1007/s10549-024-07270-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/24/2024] [Indexed: 03/26/2024]
Abstract
PURPOSE The progression of ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) in humans is highly variable. To better understand the relationship between them, we performed a multi-omic characterization of co-occurring DCIS and IBC lesions in a cohort of individuals. METHODS Formalin-fixed paraffin-embedded tissue samples from 50 patients with co-occurring DCIS and IBC lesions were subjected to DNA-seq and whole transcriptome RNA-seq. Paired DCIS and IBC multi-omics profiles were then interrogated for DNA mutations, gene expression profiles and pathway analysis. RESULTS Most small variants and copy number variations were shared between co-occurring DCIS and IBC lesions, with IBC exhibiting on average a higher degree of additional mutations. However, 36% of co-occurring lesions shared no common mutations and 49% shared no common copy number variations. The most frequent genomic variants in both DCIS and IBC were PIK3CA, TP53, KMT2C, MAP3K1, GATA3 and SF3B1, with KMT2C being more frequent in DCIS and TP53 and MAP3K1 more frequent in IBC, though the numbers are too small for definitive conclusions. The most frequent copy number variations were seen in MCL1, CKSB1 and ERBB2. ERBB2 changes were not seen in IBC unless present in the corresponding DCIS. Transcriptional profiles were highly distinct between DCIS and IBC, with DCIS exhibiting upregulation of immune-related signatures, while IBC showed significant overexpression in genes and pathways associated with cell division and proliferation. Interestingly, DCIS and IBC exhibited significant differential expression of different components of extracellular matrix (ECM) formation and regulation, with DCIS showing overexpression of ECM-membrane interaction components while IBC showed upregulation of genes associated with fibronectin and invadopodia. CONCLUSION While most co-occurring DCIS and IBC were mutationally similar and suggestive of a common clonal progenitor, transcriptionally the lesions are highly distinct, with IBC expressing key pathways that facilitate invasion and proliferation. These results are suggestive of additional levels of regulation, epigenetic or other, that facilitate the acquisition of invasive properties during tumor evolution.
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MESH Headings
- Humans
- Female
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Mutation
- DNA Copy Number Variations
- Gene Expression Profiling/methods
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/metabolism
- Biomarkers, Tumor/genetics
- Middle Aged
- Neoplasm Invasiveness
- Gene Expression Regulation, Neoplastic
- Transcriptome
- Aged
- Adult
- Genomics/methods
- Multiomics
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Affiliation(s)
- Henry G Kaplan
- Swedish Cancer Institute, 1221 Madison St., Suite 920, Seattle, WA, 98104, USA.
| | - Alexa K Dowdell
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
| | - Anna B Berry
- Swedish Cancer Institute, 1221 Madison St., Suite 920, Seattle, WA, 98104, USA
| | - Racheli Ben Shimol
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
| | - Fred L Robinson
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
| | | | - Brian D Piening
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
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Tang Y, Lan X, Yan M, Fu Z, Li H. CKS1B as a potential target for prognostic assessment and intervention in pancreatic cancer and its role in abnormal proliferation and cellular phenotype through mediation of cell cycle signaling pathways. Saudi Med J 2024; 45:128-138. [PMID: 38309745 PMCID: PMC11115417 DOI: 10.15537/smj.2024.45.2.20230132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 01/04/2024] [Indexed: 02/05/2024] Open
Abstract
OBJECTIVES To investigate the role of cell cycle protein-dependent kinase regulatory subunit 1B (CKS1B) in driving the aggressive and rapid proliferation observed in pancreatic cancer. METHODS A comprehensive analysis was carried out using raw mRNA information and data from 2 databases: the cancer genome atlas and gene expression omnibus. The differential expression of CKS1B at the mRNA and tissue levels in cancer and adjacent paracancerous tissues were assessed. Additionally, the relationship of CKS1B expression and overall survival (OS) rate was investigated using Kaplan-Meier survival curves. Potential molecular mechanisms by which CKS1B may influence the biological characteristics of pancreatic cancer were explored using resources available within the encyclopedia of RNA interactomes database. RESULTS The CKS1B exhibited significant differential expression at the mRNA as well as protein levels. A correlation with statistical significance between CKS1B expression and N stage, age, and alcohol consumption was observed. Notably, high CKS1B expression was determined as a predictive factor for worse OS. Furthermore, the analysis revealed a potential synergistic role between CKS1B and the molecule PKMYT1, which could impact the ATR-Chk1-Cdc25 signaling pathway and disrupt the G2/M checkpoint within the cell cycle, ultimately promoting abnormal tumor proliferation. CONCLUSION The CKS1B may serve as a novel potential prognostic factor in pancreatic cancer and is involved in the abnormal proliferation biology phenotype by mediating cell cycle signaling pathways.
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Affiliation(s)
- Yuzhu Tang
- From the Department of specialty (Yuzhu, Xiaohua), Graduate School of Hebei North University, Zhangjiakou, and from the Department of Radiation Oncology (Yuzhu, Maohui, Zhiguang, Hongqi), Air Force Medical Center, PLA, Beijing, China.
| | - Xiaohua Lan
- From the Department of specialty (Yuzhu, Xiaohua), Graduate School of Hebei North University, Zhangjiakou, and from the Department of Radiation Oncology (Yuzhu, Maohui, Zhiguang, Hongqi), Air Force Medical Center, PLA, Beijing, China.
| | - Maohui Yan
- From the Department of specialty (Yuzhu, Xiaohua), Graduate School of Hebei North University, Zhangjiakou, and from the Department of Radiation Oncology (Yuzhu, Maohui, Zhiguang, Hongqi), Air Force Medical Center, PLA, Beijing, China.
| | - Zhiguang Fu
- From the Department of specialty (Yuzhu, Xiaohua), Graduate School of Hebei North University, Zhangjiakou, and from the Department of Radiation Oncology (Yuzhu, Maohui, Zhiguang, Hongqi), Air Force Medical Center, PLA, Beijing, China.
| | - Hongqi Li
- From the Department of specialty (Yuzhu, Xiaohua), Graduate School of Hebei North University, Zhangjiakou, and from the Department of Radiation Oncology (Yuzhu, Maohui, Zhiguang, Hongqi), Air Force Medical Center, PLA, Beijing, China.
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Huang X, Feng Y, Li Y, Ding H, Huang X, Chen C, Yu Z, Zhang J, Xu X, Ma D, Yu S, Chen C. A novel transcriptomic signature associated with lymphovascular invasion predicts clinical outcomes, tumor microenvironment, and therapeutic response in lung adenocarcinoma. Int Immunopharmacol 2024; 127:111286. [PMID: 38064818 DOI: 10.1016/j.intimp.2023.111286] [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: 09/03/2023] [Revised: 10/31/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024]
Abstract
PURPOSE Since TNM staging has limitations for predicting post-operative outcomes and relapse, more effective prediction tools need to be researched and developed. Lymphovascular invasion, LVI, as a histopathological feature, has been widely shown to have a correlation with poor prognosis and early recurrence of lung adenocarcinoma (LUAD). However, LVI assessment is limited by subjective bias, and therefore its efficacy in practical clinical application needs further clarification. The aim of this study was to formulate a new signature based on LVI-related genes to predict prognosis and recurrence in patients with lung adenocarcinoma. METHODS Clinicopathological information, gene sequencing data and whole slide images (WSIs) of LUAD patients were downloaded from the Cancer Genome Atlas (TCGA) databases. LVI statue were evaluated by professional pathologists, and then the differentially expressed genes (LVI DEGs) associated with LVI were screened. The least absolute shrinkage and selection operator (LASSO) and Step Cox regression models were used to construct LVI-associated risk scores (LVRS), including PAQR4, ARGHEF6, CKS1B, CFTR and SEC14L4. The validity of the LVRS score was evaluated on multiple external datasets and our JSSZL cohort dataset. Using LVRS scores and clinical information, nomogram were constructed for use by clinicians. In addition, we further explored the relationship between LVRS score and clinicopathological features, immune infiltration, tumor mutational load, and immunotherapy response, and confirmed the expression of key genes in LVRS score in lung adenocarcinoma tissues using qRT-PCR and immunohistochemistry (IHC) techniques. RESULTS Based on the LVRS, patients could be classified into high-LVRS and low-LVRS groups. It was found that OS and PFS were significantly worse in the high-LVRS group than in the low-LVRS group (p < 0.001). By ROC curve analysis, it could be found that the nomogram combining LVRS and clinical information could accurately predict the prognosis of LUAD patients with the area under the curve of 1,3,5-year survival rate could reach 0.754, 0.741 and 0.735. The results of univariate and multivariate analysis showed that LVRS was an independent prognostic factor. At the same time, there were significant differences in the mutation profiles and immune microenvironment between the high-LVRS and low-LVRS groups, with the high-LVRS group having a significantly higher mutation rate than the low-LVRS group and exhibiting immunological "cold" features. By the experimental results, higher expression levels of PAQR4 and CKS1B were found in LUAD tissues, while lower expression levels of ARGHEF6, CFTR and SEC14L4 were observed. CONCLUSIONS The LVRS established in this study serves as a valid tool to predict the prognosis and recurrence status of lung adenocarcinoma patients and has a predictive effect on the response to postoperative treatment. The establishment of LVRS may offer some theoretical support to clinical treatment strategies for patients with lung adenocarcinoma following surgical intervention.
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Affiliation(s)
- Xing Huang
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Yipeng Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Yutao Li
- Department of Radiotherapy, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Hanlin Ding
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Xiaochen Huang
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Chen Chen
- School of Control Science and Engineering, Shandong University, Jinan, China
| | - Ziru Yu
- Department of Scientific Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jingyuan Zhang
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Xinyu Xu
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Dawei Ma
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, China.
| | - Shaorong Yu
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, Jiangsu, China.
| | - Chen Chen
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, Jiangsu, China; The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, China.
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4
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Lin X, Ma Q, Chen L, Guo W, Huang Z, Huang T, Cai YD. Identifying genes associated with resistance to KRAS G12C inhibitors via machine learning methods. Biochim Biophys Acta Gen Subj 2023; 1867:130484. [PMID: 37805078 DOI: 10.1016/j.bbagen.2023.130484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Targeted therapy has revolutionized cancer treatment, greatly improving patient outcomes and quality of life. Lung cancer, specifically non-small cell lung cancer, is frequently driven by the G12C mutation at the KRAS locus. The development of KRAS inhibitors has been a breakthrough in the field of cancer research, given the crucial role of KRAS mutations in driving tumor growth and progression. However, over half of patients with cancer bypass inhibition show limited response to treatment. The mechanisms underlying tumor cell resistance to this treatment remain poorly understood. METHODS To address above gap in knowledge, we conducted a study aimed to elucidate the differences between tumor cells that respond positively to KRAS (G12C) inhibitor therapy and those that do not. Specifically, we analyzed single-cell gene expression profiles from KRAS G12C-mutant tumor cell models (H358, H2122, and SW1573) treated with KRAS G12C (ARS-1620) inhibitor, which contained 4297 cells that continued to proliferate under treatment and 3315 cells that became quiescent. Each cell was represented by the expression levels on 8687 genes. We then designed an innovative machine learning based framework, incorporating seven feature ranking algorithms and four classification algorithms to identify essential genes and establish quantitative rules. RESULTS Our analysis identified some top-ranked genes, including H2AFZ, CKS1B, TUBA1B, RRM2, and BIRC5, that are known to be associated with the progression of multiple cancers. CONCLUSION Above genes were relevant to tumor cell resistance to targeted therapy. This study provides important insights into the molecular mechanisms underlying tumor cell resistance to KRAS inhibitor treatment.
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Affiliation(s)
- Xiandong Lin
- Laboratory of Radiation Oncology and Radiobiology, Clinical Oncology School of Fujian Medical University and Fujian Cancer Hospital, Fuzhou 350014, China.
| | - QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - Zhiyi Huang
- College of Chemistry, Fuzhou University, Fuzhou 350000, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
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5
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Nakamura-García AK, Espinal-Enríquez J. The network structure of hematopoietic cancers. Sci Rep 2023; 13:19837. [PMID: 37963971 PMCID: PMC10645882 DOI: 10.1038/s41598-023-46655-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023] Open
Abstract
Hematopoietic cancers (HCs) are a heterogeneous group of malignancies that affect blood, bone marrow and lymphatic system. Here, by analyzing 1960 RNA-Seq samples from three independent datasets, we explored the co-expression landscape in HCs, by inferring gene co-expression networks (GCNs) with four cancer phenotypes (B and T-cell acute leukemia -BALL, TALL-, acute myeloid leukemia -AML-, and multiple myeloma -MM-) as well as non-cancer bone marrow. We characterized their structure (topological features) and function (enrichment analyses). We found that, as in other types of cancer, the highest co-expression interactions are intra-chromosomal, which is not the case for control GCNs. We also detected a highly co-expressed group of overexpressed pseudogenes in HC networks. The four GCNs present only a small fraction of common interactions, related to canonical functions, like immune response or erythrocyte differentiation. With this approach, we were able to reveal cancer-specific features useful for detection of disease manifestations.
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Affiliation(s)
| | - Jesús Espinal-Enríquez
- National Institute of Genomic Medicine, Computational Genomics, 14610, Mexico City, Mexico.
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6
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Zhou Y, Miao Y, Huang Q, Shi W, Xie J, Lin J, Huang P, Yue C, Qin Y, Yu X, Wang H, Qin L, Chen J. A redox-responsive self-assembling COA-4-arm PEG prodrug nanosystem for dual drug delivery suppresses cancer metastasis and drug resistance by downregulating hsp90 expression. Acta Pharm Sin B 2023; 13:3153-3167. [PMID: 37521875 PMCID: PMC10372829 DOI: 10.1016/j.apsb.2022.11.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/09/2022] [Accepted: 11/04/2022] [Indexed: 11/26/2022] Open
Abstract
Metastasis and resistance are main causes to affect the outcome of the current anticancer therapies. Heat shock protein 90 (Hsp90) as an ATP-dependent molecular chaperone takes important role in the tumor metastasis and resistance. Targeting Hsp90 and downregulating its expression show promising in inhibiting tumor metastasis and resistance. In this study, a redox-responsive dual-drug nanocarrier was constructed for the effective delivery of a commonly used chemotherapeutic drug PTX, and a COA-modified 4-arm PEG polymer (4PSC) was synthesized. COA, an active component in oleanolic acid that exerts strong antitumor activity by downregulating Hsp90 expression, was used as a structural and functional element to endow 4PSC with redox responsiveness and Hsp90 inhibitory activity. Our results showed that 4PSC/PTX nanomicelles efficiently delivered PTX and COA to tumor locations without inducing systemic toxicity. By blocking the Hsp90 signaling pathway, 4PSC significantly enhanced the antitumor effect of PTX, inhibiting tumor proliferation and invasiveness as well as chemotherapy-induced resistance in vitro. Remarkable results were further confirmed in vivo with two preclinical tumor models. These findings demonstrate that the COA-modified 4PSC drug delivery nanosystem provides a potential platform for enhancing the efficacy of chemotherapies.
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Affiliation(s)
- Yi Zhou
- Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Yingling Miao
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Qiudi Huang
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Wenwen Shi
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Jiacui Xie
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jiachang Lin
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Pei Huang
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Chengfeng Yue
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
- Center of Cancer Research, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Yuan Qin
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Xiyong Yu
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease and the Fifth Affiliated Hospital, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - He Wang
- Center of Cancer Research, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Linghao Qin
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jianhai Chen
- Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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7
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MicroRNA-148a Controls Epidermal and Hair Follicle Stem/Progenitor Cells by Modulating the Activities of ROCK1 and ELF5. J Invest Dermatol 2023; 143:480-491.e5. [PMID: 36116511 DOI: 10.1016/j.jid.2022.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/09/2022] [Accepted: 06/16/2022] [Indexed: 11/22/2022]
Abstract
Skin and hair development is regulated by complex programs of gene activation and silencing and microRNA-dependent modulation of gene expression to maintain normal skin and hair follicle development, homeostasis, and cycling. In this study, we show that miR-148a, through its gene targets, plays an important role in regulating skin homeostasis and hair follicle cycling. RNA and protein analysis of miR-148a and its gene targets were analyzed using a combination of in vitro and in vivo experiments. We show that the expression of miR-148a markedly increases during telogen (bulge and hair germ stem cell compartments). Administration of antisense miR-148a inhibitor into mouse skin during the telogen phases of the postnatal hair cycle results in accelerated anagen development and altered stem cell activity in the skin. We also show that miR-148a can regulate colony-forming abilities of hair follicle bulge stem cells as well as control keratinocyte proliferation/differentiation processes. RNA and protein analysis revealed that miR-148a may control these processes by regulating the expression of Rock1 and Elf5 in vitro and in vivo. These data provide an important foundation for further analyses of miR-148a as a crucial regulator of these genes target in the skin and hair follicles and its importance in maintaining stem/progenitor cell functions during normal tissue homeostasis and regeneration.
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Tomkova M, Tomek J, Chow J, McPherson JD, Segal DJ, Hormozdiari F. Dr.Nod: computational framework for discovery of regulatory non-coding drivers in tissue-matched distal regulatory elements. Nucleic Acids Res 2023; 51:e23. [PMID: 36625266 PMCID: PMC9976879 DOI: 10.1093/nar/gkac1251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
The discovery of cancer driver mutations is a fundamental goal in cancer research. While many cancer driver mutations have been discovered in the protein-coding genome, research into potential cancer drivers in the non-coding regions showed limited success so far. Here, we present a novel comprehensive framework Dr.Nod for detection of non-coding cis-regulatory candidate driver mutations that are associated with dysregulated gene expression using tissue-matched enhancer-gene annotations. Applying the framework to data from over 1500 tumours across eight tissues revealed a 4.4-fold enrichment of candidate driver mutations in regulatory regions of known cancer driver genes. An overarching conclusion that emerges is that the non-coding driver mutations contribute to cancer by significantly altering transcription factor binding sites, leading to upregulation of tissue-matched oncogenes and down-regulation of tumour-suppressor genes. Interestingly, more than half of the detected cancer-promoting non-coding regulatory driver mutations are over 20 kb distant from the cancer-associated genes they regulate. Our results show the importance of tissue-matched enhancer-gene maps, functional impact of mutations, and complex background mutagenesis model for the prediction of non-coding regulatory drivers. In conclusion, our study demonstrates that non-coding mutations in enhancers play a previously underappreciated role in cancer and dysregulation of clinically relevant target genes.
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Affiliation(s)
- Marketa Tomkova
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA.,Ludwig Cancer Research, University of Oxford, Oxford, OX3 7DQ, UK.,UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Jakub Tomek
- Department of Pharmacology, University of California, Davis, CA 95616, USA
| | - Julie Chow
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - David J Segal
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA.,UC Davis Genome Center, University of California, Davis, CA 95616, USA.,UC Davis MIND Institute, University of California, Davis, CA 95616, USA
| | - Fereydoun Hormozdiari
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA.,UC Davis Genome Center, University of California, Davis, CA 95616, USA.,UC Davis MIND Institute, University of California, Davis, CA 95616, USA
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9
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D'costa M, Bothe A, Das S, Udhaya Kumar S, Gnanasambandan R, George Priya Doss C. CDK regulators—Cell cycle progression or apoptosis—Scenarios in normal cells and cancerous cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:125-177. [PMID: 37061330 DOI: 10.1016/bs.apcsb.2022.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Serine/threonine kinases called cyclin-dependent kinases (CDKs) interact with cyclins and CDK inhibitors (CKIs) to control the catalytic activity. CDKs are essential controllers of RNA transcription and cell cycle advancement. The ubiquitous overactivity of the cell cycle CDKs is caused by a number of genetic and epigenetic processes in human cancer, and their suppression can result in both cell cycle arrest and apoptosis. This review focused on CDKs, describing their kinase activity, their role in phosphorylation inhibition, and CDK inhibitory proteins (CIP/KIP, INK 4, RPIC). We next compared the role of different CDKs, mainly p21, p27, p57, p16, p15, p18, and p19, in the cell cycle and apoptosis in cancer cells with respect to normal cells. The current work also draws attention to the use of CDKIs as therapeutics, overcoming the pharmacokinetic barriers of pan-CDK inhibitors, analyze new chemical classes that are effective at attacking the CDKs that control the cell cycle (cdk4/6 or cdk2). It also discusses CDKI's drawbacks and its combination therapy against cancer patients. These findings collectively demonstrate the complexity of cancer cell cycles and the need for targeted therapeutic intervention. In order to slow the progression of the disease or enhance clinical outcomes, new medicines may be discovered by researching the relationship between cell death and cell proliferation.
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Affiliation(s)
- Maria D'costa
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Anusha Bothe
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Soumik Das
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - R Gnanasambandan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
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10
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Oh ET, Kim HG, Kim CH, Lee J, Kim C, Lee JS, Cho Y, Park HJ. NQO1 regulates cell cycle progression at the G2/M phase. Theranostics 2023; 13:873-895. [PMID: 36793872 PMCID: PMC9925316 DOI: 10.7150/thno.77444] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023] Open
Abstract
Rationale: Overexpression of NAD(P)H:quinone oxidoreductase 1 (NQO1) is associated with tumor cell proliferation and growth in several human cancer types. However, the molecular mechanisms underlying the activity of NQO1 in cell cycle progression are currently unclear. Here, we report a novel function of NQO1 in modulation of the cell cycle regulator, cyclin-dependent kinase subunit-1 (CKS1), at the G2/M phase through effects on the stability of c‑Fos. Methods: The roles of the NQO1/c-Fos/CKS1 signaling pathway in cell cycle progression were analyzed in cancer cells using synchronization of the cell cycle and flow cytometry. The mechanisms underlying NQO1/c-Fos/CKS1-mediated regulation of cell cycle progression in cancer cells were studied using siRNA approaches, overexpression systems, reporter assays, co-immunoprecipitation, pull-down assays, microarray analysis, and CDK1 kinase assays. In addition, publicly available data sets and immunohistochemistry were used to investigate the correlation between NQO1 expression levels and clinicopathological features in cancer patients. Results: Our results suggest that NQO1 directly interacts with the unstructured DNA-binding domain of c-Fos, which has been implicated in cancer proliferation, differentiation, and development as well as patient survival, and inhibits its proteasome-mediated degradation, thereby inducing CKS1 expression and regulation of cell cycle progression at the G2/M phase. Notably, a NQO1 deficiency in human cancer cell lines led to suppression of c-Fos-mediated CKS1 expression and cell cycle progression. Consistent with this, high NQO1 expression was correlated with increased CKS1 and poor prognosis in cancer patients. Conclusions: Collectively, our results support a novel regulatory role of NQO1 in the mechanism of cell cycle progression at the G2/M phase in cancer through effects on c‑Fos/CKS1 signaling.
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Affiliation(s)
- Eun-Taex Oh
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon 22212, Republic of Korea
| | - Ha Gyeong Kim
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Chul Hoon Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jeonghun Lee
- Department of Polymer Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Chulhee Kim
- Department of Polymer Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Jae-Seon Lee
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea.,Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea.,Research Center for Controlling Intracellular Communication, College of Medicine, Inha University, Incheon 22212, Republic of Korea
| | - Yunmi Cho
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Heon Joo Park
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea.,Research Center for Controlling Intracellular Communication, College of Medicine, Inha University, Incheon 22212, Republic of Korea.,Department of Microbiology, College of Medicine, Inha University, Incheon 22212, Republic of Korea
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11
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Li L, Wang J, Zhang Z, Yang Q, Deng Z, Zou W, Ge X, Pan K, Li C, Liu R. Identification of CKS1B as a prognostic indicator and a predictive marker for immunotherapy in pancreatic cancer. Front Immunol 2022; 13:1052768. [PMID: 36405738 PMCID: PMC9668883 DOI: 10.3389/fimmu.2022.1052768] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/19/2022] [Indexed: 01/10/2024] Open
Abstract
As a regulatory subunit of cyclin kinase, CKS1B promotes cancer development and is associated with poor prognosis in multiple cancer patients. However, the intrinsic role of CKS1B in pancreatic cancer remains elusive. In our research, CKS1B expression in pancreatic tumor tissue was higher than that in normal tissue by TCGA, Oncomine and CPTAC databases analysis. Similar result was verified in our center tissues by qRT-PCR. CKS1B expression was closely relevant to histologic grading, prognosis, and TMB. GSEA showed that CKS1B mainly participated in the regulation of autophagy and T cell receptor signaling pathway. Furthermore, CIBERSORT analysis showed that there was a strong correlation between CKS1B expression and tumor immune cells infiltration. Drug sensitivity analysis showed that patients with high CKS1B expression appeared to be more sensitive to gemcitabine, 5-fluorouracil, and paclitaxel. We then investigated cell viability and migratory ability by CCK8 and transwell assay, respectively. Results indicated that CKS1B knockdown by short hairpin RNA significantly reduced pancreatic cancer cell viability and invasion via regulating PD-L1 expression. In conclusion, our research further demonstrates the role of CKS1B in pancreatic cancer and the signaling pathways involved. The association of CKS1B with immune infiltration and immune checkpoint may provide a new direction for immunotherapy of pancreatic cancer.
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Affiliation(s)
- Lincheng Li
- Medical School of Chinese PLA, Beijing, China
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jing Wang
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Key Laboratory of Digital Hepetobiliary Surgery, PLA, Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China
| | - Zhuochao Zhang
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qiyue Yang
- Key Laboratory of Digital Hepetobiliary Surgery, PLA, Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China
| | - Zhaoda Deng
- Medical School of Chinese PLA, Beijing, China
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Wenbo Zou
- Department of General Surgery, No.924 Hospital of PLA Joint Logistic Support Force, Guilin, China
| | - Xinlan Ge
- Key Laboratory of Digital Hepetobiliary Surgery, PLA, Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China
| | - Ke Pan
- Key Laboratory of Digital Hepetobiliary Surgery, PLA, Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China
| | - Chonghui Li
- Key Laboratory of Digital Hepetobiliary Surgery, PLA, Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China
| | - Rong Liu
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
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12
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Yang ZK, Huang XL, Peng L. Transcriptome analysis reveals gene expression changes of the basidiomycetous yeast Apiotrichum mycotoxinivorans in response to ochratoxin A exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114146. [PMID: 36215880 DOI: 10.1016/j.ecoenv.2022.114146] [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: 06/19/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Ochratoxin A (OTA) is one of the most common and deleterious mycotoxins found in food and feedstuffs worldwide; however, Apiotrichum mycotoxinivorans can detoxify OTA. Our results show that A. mycotoxinivorans GUM1709 efficiently degraded OTA, but it caused the accumulation of intracellular reactive oxygen species. The main aim of this study was to identify potential OTA-detoxifying enzymes and to explore the effects of OTA on A. mycotoxinivorans GMU1709. RNA-seq data revealed that 1643 and 1980 genes were significantly upregulated and downregulated, respectively, after OTA exposure. Functional enrichment analyses indicated that OTA exposure enhanced defense capability, protein transport, endocytosis, and energy metabolism; caused ribosomal stress; suppressed DNA replication and transcription; inhibited cell growth and division; and promoted cell death. The integration of secretome, gene expression, and molecular docking analyses revealed that two carboxypeptidase homologues (members of the metallocarboxypeptidase family) were most likely responsible for the detoxification of both extracellular and intracellular OTA. Superoxide dismutase and catalase were the main genes activated in response to oxidative stress. In addition, analysis of key genes associated with cell division and apoptosis showed that OTA exposure inhibited mitosis and promoted cell death. This study revealed the possible OTA response and detoxification mechanisms in A. mycotoxinivorans.
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Affiliation(s)
- Zhi-Kai Yang
- Innovation centre for Advanced Interdisciplinary Medicine, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xue-Ling Huang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Liang Peng
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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13
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Yang ZK, Li DW, Peng L, Liu CF, Wang ZY. Transcriptomic responses of the zearalenone (ZEN)-detoxifying yeast Apiotrichum mycotoxinivorans to ZEN exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113756. [PMID: 35691196 DOI: 10.1016/j.ecoenv.2022.113756] [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: 02/05/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Zearalenone (ZEN) is a potent oestrogenic mycotoxin that is mainly produced by Fusarium species and is a serious environmental pollutant in animal feeds. Apiotrichum mycotoxinivorans has been widely used as a feed additive to detoxify ZEN. However, the effects of ZEN on A. mycotoxinivorans and its detoxification mechanisms remain unclear. In this study, transcriptomic and bioinformatic analyses were used to investigate the molecular responses of A. mycotoxinivorans to ZEN exposure and the genetic basis of ZEN detoxification. We detected 1424 significantly differentially expressed genes (DEGs), of which 446 were upregulated and 978 were downregulated. Functional and enrichment analyses showed that ZEN-induced genes were significantly associated with xenobiotic metabolism, oxidative stress response, and active transport systems. However, ZEN-inhibited genes were mainly related to cell division, cell cycle, and fungal development. Subsequently, bioinformatic analysis identified candidate ZEN-detoxification enzymes. The Baeyer-Villiger monooxygenases and carboxylesterases, which are responsible for the formation and subsequent hydrolysis of a new ZEN lactone, respectively, were significantly upregulated. In addition, the expression levels of genes related to conjugation and transport involved in the xenobiotic detoxification pathway were significantly upregulated. Moreover, the expression levels of genes encoding enzymatic antioxidants and those related to growth and apoptosis were significantly upregulated and downregulated, respectively, which made it possible for A. mycotoxinivorans to survive in a highly toxic environment and efficiently detoxify ZEN. This is the first systematic report of ZEN tolerance and detoxification in A. mycotoxinivorans. We identified the metabolic enzymes that were potentially involved in detoxifying ZEN in the GMU1709 strain and found that ZEN-induced transcriptional regulation of genes is key to withstanding highly toxic environments. Hence, our results provide valuable information for developing enzymatic detoxification systems or engineering this detoxification pathway in other species.
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Affiliation(s)
- Zhi-Kai Yang
- Innovation centre for Advanced Interdisciplinary Medicine, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Da-Wei Li
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Liang Peng
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chen-Fei Liu
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhi-Yuan Wang
- Innovation Centre for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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14
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Ming T, Dong M, Song X, Li X, Kong Q, Fang Q, Wang J, Wu X, Xia Z. Integrated Analysis of Gene Co-Expression Network and Prediction Model Indicates Immune-Related Roles of the Identified Biomarkers in Sepsis and Sepsis-Induced Acute Respiratory Distress Syndrome. Front Immunol 2022; 13:897390. [PMID: 35844622 PMCID: PMC9281548 DOI: 10.3389/fimmu.2022.897390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Sepsis is a series of clinical syndromes caused by immunological response to severe infection. As the most important and common complication of sepsis, acute respiratory distress syndrome (ARDS) is associated with poor outcomes and high medical expenses. However, well-described studies of analysis-based researches, especially related bioinformatics analysis on revealing specific targets and underlying molecular mechanisms of sepsis and sepsis-induced ARDS (sepsis/se-ARDS), still remain limited and delayed despite the era of data-driven medicine. In this report, weight gene co-expression network based on data from a public database was constructed to identify the key modules and screen the hub genes. Functional annotation by enrichment analysis of the modular genes also demonstrated the key biological processes and signaling pathway; among which, extensive immune-involved enrichment was remarkably associated with sepsis/se-ARDS. Based on the differential expression analysis, least absolute shrink and selection operator, and multivariable logistic regression analysis of the screened hub genes, SIGLEC9, TSPO, CKS1B and PTTG3P were identified as the candidate biomarkers for the further analysis. Accordingly, a four-gene-based model for diagnostic prediction assessment was established and then developed by sepsis/se-ARDS risk nomogram, whose efficiency was verified by calibration curves and decision curve analyses. In addition, various machine learning algorithms were also applied to develop extra models based on the four genes. Receiver operating characteristic curve analysis proved the great diagnostic and predictive performance of these models, and the multivariable logistic regression of the model was still found to be the best as further verified again by the internal test, training, and external validation cohorts. During the development of sepsis/se-ARDS, the expressions of the identified biomarkers including SIGLEC9, TSPO, CKS1B and PTTG3P were all regulated remarkably and generally exhibited notable correlations with the stages of sepsis/se-ARDS. Moreover, the expression levels of these four genes were substantially correlated during sepsis/se-ARDS. Analysis of immune infiltration showed that multiple immune cells, neutrophils and monocytes in particular, might be closely involved in the process of sepsis/se-ARDS. Besides, SIGLEC9, TSPO, CKS1B and PTTG3P were considerably correlated with the infiltration of various immune cells including neutrophils and monocytes during sepsis/se-ARDS. The discovery of relevant gene co-expression network and immune signatures might provide novel insights into the pathophysiology of sepsis/se-ARDS.
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Affiliation(s)
- Tingqian Ming
- Department of Anesthesiology, Renmin Hospital, Wuhan University, Wuhan, China
| | - Mingyou Dong
- College of Medical Laboratory Science, Youjiang Medical College for Nationalities, Baise, China
| | - Xuemin Song
- Department of Anesthesiology and Critical Care Medicine, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Xingqiao Li
- School of Computer, Wuhan University, Wuhan, China
| | - Qian Kong
- Department of Anesthesiology, Renmin Hospital, Wuhan University, Wuhan, China
| | - Qing Fang
- Department of Anesthesiology and Critical Care Medicine, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Jie Wang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital, Wuhan University, Wuhan, China
| | - Xiaojing Wu
- Department of Anesthesiology, Renmin Hospital, Wuhan University, Wuhan, China
- *Correspondence: Zhongyuan Xia, ; Xiaojing Wu,
| | - Zhongyuan Xia
- Department of Anesthesiology, Renmin Hospital, Wuhan University, Wuhan, China
- *Correspondence: Zhongyuan Xia, ; Xiaojing Wu,
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15
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Agonists of prostaglandin E 2 receptors as potential first in class treatment for nephronophthisis and related ciliopathies. Proc Natl Acad Sci U S A 2022; 119:e2115960119. [PMID: 35482924 PMCID: PMC9170064 DOI: 10.1073/pnas.2115960119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceJuvenile nephronophthisis (NPH) is a renal ciliopathy due to a dysfunction of primary cilia for which no curative treatment is available. This paper describes the identification of agonists of prostaglandin E2 receptors as a potential therapeutic approach for the most common NPHP1-associated ciliopathies. We demonstrated that prostaglandin E1 rescues defective ciliogenesis and ciliary composition in NPHP1 patient urine-derived renal tubular cells and improves ciliary and kidney phenotypes in our NPH zebrafish and Nphp1-/- mouse models. In addition, Taprenepag alleviates the severe retinopathy observed in Nphp1-/- mice. Finally, transcriptomic analyses pointed out several pathways downstream the prostaglandin receptors as cell cycle progression, extracellular matrix, or actin cytoskeleton organization. Altogether, our findings provide an alternative for treatment of NPH.
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16
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Distinct and Common Features of Numerical and Structural Chromosomal Instability across Different Cancer Types. Cancers (Basel) 2022; 14:cancers14061424. [PMID: 35326573 DOI: 10.3390/cancers14061424] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/27/2023] Open
Abstract
A large proportion of tumours is characterised by numerical or structural chromosomal instability (CIN), defined as an increased rate of gaining or losing whole chromosomes (W-CIN) or of accumulating structural aberrations (S-CIN). Both W-CIN and S-CIN are associated with tumourigenesis, cancer progression, treatment resistance and clinical outcome. Although W-CIN and S-CIN can co-occur, they are initiated by different molecular events. By analysing tumour genomic data from 33 cancer types, we show that the majority of tumours with high levels of W-CIN underwent whole genome doubling, whereas S-CIN levels are strongly associated with homologous recombination deficiency. Both CIN phenotypes are prognostic in several cancer types. Most drugs are less efficient in high-CIN cell lines, but we also report compounds and drugs which should be investigated as targets for W-CIN or S-CIN. By analysing associations between CIN and bio-molecular entities with pathway and gene expression levels, we complement gene signatures of CIN and report that the drug resistance gene CKS1B is strongly associated with S-CIN. Finally, we propose a potential copy number-dependent mechanism to activate the PI3K pathway in high-S-CIN tumours.
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17
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Deng T, Liu Y, Yang Y, Yuan L, Liu F, Wang X, Zhang Q, Xie M. Regulation of microRNA miR-197-3p/CDC28 protein kinase regulatory subunit 1B (CKS1B) axis by Circular RNA hsa_circ_0000285 promotes glioma progression. Bioengineered 2022; 13:4757-4772. [PMID: 35174774 PMCID: PMC8974215 DOI: 10.1080/21655979.2022.2031673] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Circular RNA circ_0000285 is differentially expressed in several malignancies; however, its role in gliomas is under investigation. Reverse transcription quantitative polymerase chain reaction was conducted to evaluate the expression of circ_0000285, miR-197-3p, and CDC28 protein kinase regulatory subunit 1B (CKS1B) in glioma tissues and cells. Cell Counting Kit-8 and Transwell invasion assays coupled with Western blotting analysis using anti-Bax and anti-Bcl-2 antibodies were performed to evaluate cell proliferation, invasion, and apoptosis. Luciferase reporter and AGO2 RNA immunoprecipitation assays were conducted to verify the interaction between miR-197-3p and circ_0000285 or CKS1B. Xenograft tumor growth was evaluated in mice. We noted that circ_0000285 was highly expressed in glioma tissues and cells and that circ_0000285-silencing retarded tumor growth both in vitro and in vivo. This effect was mediated by the binding of circ_0000285 to miR-197-3p, which silenced CKS1B, an essential driver of glioma cell proliferation and invasion. Thus, circ_0000285 boosted glioma progression by regulating the miR-197-3p/CKS1B axis, highlighting a novel competing endogenous RNA circuit of glioma progression.
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Affiliation(s)
- Tao Deng
- Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, China
| | - Yang Liu
- Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, China
| | - Yanlong Yang
- Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, China
| | - Leyong Yuan
- School of Basic Medical Sciences, Hubei University of Medicine, Suizhou, China
| | - Fangfang Liu
- Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, China
| | - Xiaobo Wang
- Medical Transformation Center, Suizhou Hospital, Hubei University of Medicine, Suizhou, China
| | - Qiuying Zhang
- Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, China
| | - Mingshui Xie
- Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, China
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18
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Fei X, Hu C, Wang X, Lu C, Chen H, Sun B, Li C. Construction of a Ferroptosis-Related Long Non-coding RNA Prognostic Signature and Competing Endogenous RNA Network in Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:751490. [PMID: 34820377 PMCID: PMC8606539 DOI: 10.3389/fcell.2021.751490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022] Open
Abstract
Ferroptosis-related genes play an important role in the progression of lung adenocarcinoma (LUAD). However, the potential function of ferroptosis-related lncRNAs in LUAD has not been fully elucidated. Thus, to explore the potential role of ferroptosis-related lncRNAs in LUAD, the transcriptome RNA-seq data and corresponding clinical data of LUAD were downloaded from the TCGA dataset. Pearson correlation was used to mine ferroptosis-related lncRNAs. Differential expression and univariate Cox analysis were performed to screen prognosis related lncRNAs. A ferroptosis-related lncRNA prognostic signature (FLPS), which included six ferroptosis-related lncRNAs, was constructed by the least absolute shrinkage and selection operator (LASSO) Cox regression. Patients were divided into a high risk-score group and low risk-score group by the median risk score. Receiver operating characteristic (ROC) curves, principal component analysis (PCA), and univariate and multivariate Cox regression were performed to confirm the validity of FLPS. Enrichment analysis showed that the biological processes, pathways and markers associated with malignant tumors were more common in high-risk subgroups. There were significant differences in immune microenvironment and immune cells between high- and low-risk groups. Then, a nomogram was constructed. We further investigated the relationship between six ferroptosis-related lncRNAs and tumor microenvironment and tumor stemness. A competing endogenous RNA (ceRNA) network was established based on the six ferroptosis-related lncRNAs. Finally, we detected the expression levels of ferroptosis-related lncRNAs in clinical samples through quantitative real-time polymerase chain reaction assay (qRT-PCR). In conclusion, we identified the prognostic ferroptosis-related lncRNAs in LUAD and constructed a prognostic signature which provided a new strategy for the evaluation and prediction of prognosis in LUAD.
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Affiliation(s)
- Xiang Fei
- Department of Thoracic Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Congli Hu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Xinyu Wang
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaojing Lu
- Department of Thoracic Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Hezhong Chen
- Department of Thoracic Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Bin Sun
- Department of Molecular Oncology, Eastern Hepatobiliary Surgical Hospital & National Center for Liver Cancer, Navy Military Medical University, Shanghai, China
| | - Chunguang Li
- Department of Thoracic Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
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19
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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20
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Jia Y, Tian Q, Yang K, Liu Y, Liu Y. A Pan-Cancer Analysis of Clinical Prognosis and Immune Infiltration of CKS1B in Human Tumors. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5862941. [PMID: 34845438 PMCID: PMC8627364 DOI: 10.1155/2021/5862941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022]
Abstract
Although more and more evidence supports CDC28 protein kinase subunit 1B (CKS1B) is involved significantly in the development of human cancers, most of the researches have focused on a single disease, and pan-cancer studies conducted from a holistic perspective of different tumor sources have not been reported yet. Here, for the first time, we investigated the potential oncogenic and prognostic role of CKS1B across 33 tumors based on public databases and further verified it in a small scale by RNA sequencing or quantitative real-time PCR. CKS1B was generally highly expressed in a majority of tumors and had a notable correlation with the prognosis of patients, but its prognostic significance in different tumors was not exactly the same. In addition, CKS1B expression was also closely related to the infiltration of cancer-associated fibroblasts in tumors such as breast invasive carcinoma, kidney chromophobe, lung adenocarcinoma, and tumor-infiltrating lymphocytes in tumors such as glioblastoma multiforme, bladder urothelial carcinoma, and brain lower grade glioma. Moreover, reduced CKS1B methylation was observed in certain tumors, for example, adrenocortical carcinoma. Cell cycle and kinase activity regulation and PI3K-Akt signaling pathway were found to be involved in the functional mechanism of CKS1B. In conclusion, our first pan-cancer analysis of CKS1B contributes to a better overall understanding of CKS1B and may provide a new target for future cancer therapy.
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Affiliation(s)
- Yan Jia
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Quan Tian
- Department of Reproductive Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Kaitai Yang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Liu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Yanfeng Liu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
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21
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Wang K, Zhang M, Wang J, Sun P, Luo J, Jin H, Li R, Pan C, Lu L. A Systematic Analysis Identifies Key Regulators Involved in Cell Proliferation and Potential Drugs for the Treatment of Human Lung Adenocarcinoma. Front Oncol 2021; 11:737152. [PMID: 34650921 PMCID: PMC8505978 DOI: 10.3389/fonc.2021.737152] [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: 07/06/2021] [Accepted: 09/06/2021] [Indexed: 11/23/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most common and malignant cancer types. Abnormal cell proliferation, exemplified by cell cycle and cell division dysregulation, is one of the most prominent hallmarks of cancer and is responsible for recurrence, metastasis, and resistance to cancer therapy. However, LUAD-specific gene regulation and clinical significance remain obscure. Here, by using both tissues and cells from LUAD and normal lung samples, 434 increased and 828 decreased genes of biological significance were detected, including 127 cell cycle-associated genes (95 increased and 32 decreased), 66 cell division-associated genes (56 increased and 10 decreased), and 81 cell proliferation-associated genes (34 increased and 47 decreased). Among them, 12 increased genes (TPX2, CENPF, BUB1, PLK1, KIF2C, AURKB, CDKN3, BUB1B, HMGA2, CDK1, ASPM, and CKS1B) and 2 decreased genes (TACC1 and MYH10) were associated with all the three above processes. Importantly, 2 (CDKN3 and CKS1B) out of the 11 increased genes (except HMGA2) are previously uncharacterized ones in LUAD and can potentially be prognostic markers. Moreover, PLK1 could be a promising therapeutic target for LUAD. Besides, protein–protein interaction network analysis showed that CDK1 and CDC20 were the hub genes, which might play crucial roles in cell proliferation of LUAD. Furthermore, transcriptional regulatory network analysis suggested that the transcription factor E2F1 could be a key regulator in controlling cell proliferation of LUAD via expression modulation of most cell cycle-, cell division-, and cell proliferation-related DEGs. Finally, trichostatin A, hycanthone, vorinostat, and mebeverine were identified as four potential therapeutic agents for LUAD. This work revealed key regulators contributing to cell proliferation in human LUAD and identified four potential therapeutic agents for treatment strategy.
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Affiliation(s)
- Kai Wang
- Clinical Research Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Man Zhang
- Department of Radiology, Xiangyang Hospital of Traditional Chinese Medicine, Hubei University of Traditional Chinese Medicine, Xiangyang, China
| | - Jiao Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Pan Sun
- Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jizhuang Luo
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haizhen Jin
- Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Rong Li
- Clinical Research Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,China Hospital Development Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Changqing Pan
- General Surgery Department, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Liming Lu
- Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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22
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Schmidt TM, Fonseca R, Usmani SZ. Chromosome 1q21 abnormalities in multiple myeloma. Blood Cancer J 2021; 11:83. [PMID: 33927196 PMCID: PMC8085148 DOI: 10.1038/s41408-021-00474-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/15/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Gain of chromosome 1q (+1q) is one of the most common recurrent cytogenetic abnormalities in multiple myeloma (MM), occurring in approximately 40% of newly diagnosed cases. Although it is often considered a poor prognostic marker in MM, +1q has not been uniformly adopted as a high-risk cytogenetic abnormality in guidelines. Controversy exists regarding the importance of copy number, as well as whether +1q is itself a driver of poor outcomes or merely a common passenger genetic abnormality in biologically unstable disease. Although the identification of a clear pathogenic mechanism from +1q remains elusive, many genes at the 1q21 locus have been proposed to cause early progression and resistance to anti-myeloma therapy. The plethora of potential drivers suggests that +1q is not only a causative factor or poor outcomes in MM but may be targetable and/or predictive of response to novel therapies. This review will summarize our current understanding of the pathogenesis of +1q in plasma cell neoplasms, the impact of 1q copy number, identify potential genetic drivers of poor outcomes within this subset, and attempt to clarify its clinical significance and implications for the management of patients with multiple myeloma.
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Affiliation(s)
| | - Rafael Fonseca
- Department of Hematology, Mayo Clinic, Scottsdale, AZ, USA
| | - Saad Z Usmani
- Plasma Cell Disorders Division, Levine Cancer Institute/Atrium Health, Charlotte, NC, USA.
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