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Kim J, Kang JH, Noh MG, Lee B, Choi YD, Kim OJ, Kim Y. New potential diagnostic markers for verrucous hyperplasia and verrucous carcinoma based on RNA-sequencing data. Mol Cell Probes 2024; 77:101980. [PMID: 39127310 DOI: 10.1016/j.mcp.2024.101980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024]
Abstract
Verrucous carcinoma (VC) is a rare subtype of squamous cell carcinoma (SCC) characterized by its histological presentation as a low-grade tumor with no potential for metastasis, setting it apart from invasive SCC. However, distinguishing VC from its benign counterpart, verrucous hyperplasia (VH), is challenging due to their clinical and morphological similarities. Despite the importance of accurate diagnosis for determining treatment strategies, diagnosis of VH and VC relied only on lesion recurrence after resection. To address this challenge, we generated RNA profiling data from tissue samples of VH and VC patients to identify novel diagnostic markers. We analyzed differentially expressed (DE) mRNA and long non-coding RNA (lncRNA) in tissue samples from VH and VC patients. Additionally, ChIP-X Enrichment Analysis 3 (ChEA3) was conducted to identify the top five transcription factors potentially regulating the expression of DE mRNAs in VH and VC. Our analysis of mRNA and lncRNA expression profiles in VH and VC provides insights into the underlying molecular characteristics of these diseases and offers potential new diagnostic markers. The identification of specific DE genes and lncRNAs may enable clinicians to more accurately differentiate between VH and VC, leading to better treatment choices.
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Affiliation(s)
- Janghyun Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea; Hard-Tissue Biointerface Research Center, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jee-Hye Kang
- Deparment of Dental Science, Graduate School, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Myung-Giun Noh
- Department of Pathology, School of Medicine, Ajou University, Gyeonggi-do, 16499, Republic of Korea
| | - Bora Lee
- Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Hwasun 58128, Republic of Korea
| | - Yoo-Duk Choi
- Department of Pathology, Chonnam National University Medical School, Gwangju, 61469, Republic of Korea
| | - Ok Joon Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Young Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea; Hard-Tissue Biointerface Research Center, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea.
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Khazem F, Zetoune AB. Decoding high mobility group A2 protein expression regulation and implications in human cancers. Discov Oncol 2024; 15:322. [PMID: 39085703 PMCID: PMC11291832 DOI: 10.1007/s12672-024-01202-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/29/2024] [Indexed: 08/02/2024] Open
Abstract
High Mobility Group A2 (HMGA2) oncofetal proteins are a distinct category of Transcription Factors (TFs) known as "architectural factors" due to their lack of direct transcriptional activity. Instead, they modulate the three-dimensional structure of chromatin by binding to AT-rich regions in the minor grooves of DNA through their AT-hooks. This binding allows HMGA2 to interact with other proteins and different regions of DNA, thereby regulating the expression of numerous genes involved in carcinogenesis. Consequently, multiple mechanisms exist to finely control HMGA2 protein expression at various transcriptional levels, ensuring precise concentration adjustments to maintain cellular homeostasis. During embryonic development, HMGA2 protein is highly expressed but becomes absent in adult tissues. However, recent studies have revealed its re-elevation in various cancer types. Extensive research has demonstrated the involvement of HMGA2 protein in carcinogenesis at multiple levels. It intervenes in crucial processes such as cell cycle regulation, apoptosis, angiogenesis, epithelial-to-mesenchymal transition, cancer cell stemness, and DNA damage repair mechanisms, ultimately promoting cancer cell survival. This comprehensive review provides insights into the HMGA2 protein, spanning from the genetic regulation to functional protein behavior. It highlights the significant mechanisms governing HMGA2 gene expression and elucidates the molecular roles of HMGA2 in the carcinogenesis process.
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Affiliation(s)
- Farah Khazem
- Department of Biochemistry and Microbiology, Faculty of Pharmacy, Damascus University, Damascus, Syria.
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Yang Z, Li X, Zhou L, Luo Y, Zhan N, Ye Y, Liu Z, Zhang X, Qiu T, Lin L, Peng L, Hu Y, Pan C, Sun M, Zhang Y. Ferroptosis-related lncRNAs: Distinguishing heterogeneity of the tumour microenvironment and predicting immunotherapy response in bladder cancer. Heliyon 2024; 10:e32018. [PMID: 38867969 PMCID: PMC11168393 DOI: 10.1016/j.heliyon.2024.e32018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024] Open
Abstract
Ferroptosis, a cell death pathway dependent on iron, has been shown in research to play a role in the development, advancement, and outlook of tumours through ferroptosis-related lncRNAs (FRLRs). However, the value of the FRLRs in bladder cancer (BLCA) has not been thoroughly investigated. This research project involved developing a predictive model using ten specific FRLRs (AC099850.4, AL731567.1, AL133415.1, AC021321.1, SPAG5-AS1, HMGA2-AS1, RBMS3-AS3, AC006160.1, AL583785.1, and AL662844.4) through univariate COX and LASSO regression techniques. The validation of this signature as a standalone predictor was confirmed in a group of 65 patients from the urology bladder tumour database at the First Affiliated Hospital of Wenzhou Medical University in Wenzhou, China. Patients were categorized based on their median risk score into either a low-risk group or a high-risk group. Enrichment analysis identified possible molecular mechanisms that could explain the variations in clinical outcomes observed in high-risk and low-risk groups. Moreover, we explored the correlation between FLPS and immunotherapy-related indicators. The ability of FLPS to forecast the effectiveness of immunotherapy was validated by the elevated levels of immune checkpoint genes (PD-L1, CTLA4, and PD-1) in the group at high risk. We also screened the crucial FRLR (HMGA2-AS1) through congruent expression and prognostic conditions and established a ceRNA network, indicating that HMGA2-AS1 may affect epithelial-mesenchymal transition by modulating the Wnt signalling pathway through the ceRNA mechanism. We identified the top five mRNAs (NFIB, NEGR1, JAZF1, JCAD, and ESM1) based on random forest algorithm and analysed the relationship between HMGA2-AS1, the top five mRNAs, and immunotherapy, and their interactions with drug sensitivities. Our results suggest that patients with BLCA have a greater sensitivity to four drugs (dasatinib, pazopanib, erismodegib and olaparib). Our study provides new insights into the TME, key signalling pathways, genome, and potential therapeutic targets of BLCA, with future guidance for immunotherapy and targeted precision drugs.
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Affiliation(s)
- Zhan Yang
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Xiaoqi Li
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Lijun Zhou
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yaxian Luo
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Ning Zhan
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Yifan Ye
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhichao Liu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Xiaoting Zhang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Tao Qiu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Lining Lin
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Lianjie Peng
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Yiming Hu
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Chaoran Pan
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Mouyuan Sun
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Yan Zhang
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
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Patel RS, Krause-Hauch M, Kenney K, Miles S, Nakase-Richardson R, Patel NA. Long Noncoding RNA VLDLR-AS1 Levels in Serum Correlate with Combat-Related Chronic Mild Traumatic Brain Injury and Depression Symptoms in US Veterans. Int J Mol Sci 2024; 25:1473. [PMID: 38338752 PMCID: PMC10855201 DOI: 10.3390/ijms25031473] [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: 12/04/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
More than 75% of traumatic brain injuries (TBIs) are mild (mTBI) and military service members often experience repeated combat-related mTBI. The chronic comorbidities concomitant with repetitive mTBI (rmTBI) include depression, post-traumatic stress disorder or neurological dysfunction. This study sought to determine a long noncoding RNA (lncRNA) expression signature in serum samples that correlated with rmTBI years after the incidences. Serum samples were obtained from Long-Term Impact of Military-Relevant Brain-Injury Consortium Chronic Effects of Neurotrauma Consortium (LIMBIC CENC) repository, from participants unexposed to TBI or who had rmTBI. Four lncRNAs were identified as consistently present in all samples, as detected via droplet digital PCR and packaged in exosomes enriched for CNS origin. The results, using qPCR, demonstrated that the lncRNA VLDLR-AS1 levels were significantly lower among individuals with rmTBI compared to those with no lifetime TBI. ROC analysis determined an AUC of 0.74 (95% CI: 0.6124 to 0.8741; p = 0.0012). The optimal cutoff for VLDLR-AS1 was ≤153.8 ng. A secondary analysis of clinical data from LIMBIC CENC was conducted to evaluate the psychological symptom burden, and the results show that lncRNAs VLDLR-AS1 and MALAT1 are correlated with symptoms of depression. In conclusion, lncRNA VLDLR-AS1 may serve as a blood biomarker for identifying chronic rmTBI and depression in patients.
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Affiliation(s)
- Rekha S. Patel
- Research Service, James A. Haley Veteran’s Hospital, 13000 Bruce B Downs Blvd., Tampa, FL 33612, USA; (R.S.P.); (S.M.)
| | - Meredith Krause-Hauch
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Kimbra Kenney
- Department of Neurology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA;
| | - Shannon Miles
- Research Service, James A. Haley Veteran’s Hospital, 13000 Bruce B Downs Blvd., Tampa, FL 33612, USA; (R.S.P.); (S.M.)
- Department of Psychiatry & Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Risa Nakase-Richardson
- Chief of Staff Office, James A. Haley Veteran’s Hospital, Tampa, FL 33612, USA;
- Department of Internal Medicine, Pulmonary, Critical Care and Sleep Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Niketa A. Patel
- Research Service, James A. Haley Veteran’s Hospital, 13000 Bruce B Downs Blvd., Tampa, FL 33612, USA; (R.S.P.); (S.M.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
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Abd El Fattah YK, Abulsoud AI, AbdelHamid SG, AbdelHalim S, Hamdy NM. CCDC144NL-AS1/hsa-miR-143-3p/HMGA2 interaction: In-silico and clinically implicated in CRC progression, correlated to tumor stage and size in case-controlled study; step toward ncRNA precision. Int J Biol Macromol 2023; 253:126739. [PMID: 37690651 DOI: 10.1016/j.ijbiomac.2023.126739] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/06/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
Unravel the regulatory mechanism of lncRNA CCDC144NL-AS1 in CRC hsa-miR-143-3p, downstream protein HMGA2 interaction arm, association with clinicopathological characteristics. Using peripheral blood as liquid biopsy from 60 CRC patients and 30 controls. The expression levels of CCDC144NL-AS1 and hsa-miR-143-3p detected by qRT-PCR. CCDC144NL-AS1 expression was significantly upregulated in CRC patients' sera, associated with worse CRC clinicopathological features regarding the depth of tumor invasion and highly significant difference between tumor stages 3 and 4 and tumor stages 2 and 4. While, hsa-miR-143-3p expression was downregulated in CRC patients by 4.5-fold change when compared to the control subjects (p < 0.0001) and HMGA2 increased in CRC patients than controls 19.59 ng/μL and 5.377 ng/μL, respectively (p < 0.0001) with significant difference between tumor stages 3 and 4 as well as tumor stages 2 and 4. CRC patients with large tumor size showed upregulation in CCDC144NL-AS1 expression and HMGA2 levels compared to those with small tumor size (p-value = 0.0365 and 0.013, respectively). CCDC144NL-AS1 and HMGA2 were positively correlated, whereas lncRNA CCDC144NL-AS1 and hsa-miR-143-3p were negatively correlated. Conclusion: As an interaction arm CCDC144NL-AS1/hsa-miR-143-3p/HMGA2 were correlated to CRC stages 2-4. Therefore, this interaction arm expression clinically and in silico approved, would direct treatment precision in the near future.
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Affiliation(s)
- Yasmine K Abd El Fattah
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, 11785, Cairo, Egypt
| | - Ahmed I Abulsoud
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, 11785, Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy (Boy's Branch), Al-Azhar University, Nasr City, 11884, Cairo, Egypt
| | - Sherihan G AbdelHamid
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Sherif AbdelHalim
- Department of General surgery, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
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Hashemi M, Rashidi M, Hushmandi K, Ten Hagen TLM, Salimimoghadam S, Taheriazam A, Entezari M, Falahati M. HMGA2 regulation by miRNAs in cancer: affecting cancer hallmarks and therapy response. Pharmacol Res 2023; 190:106732. [PMID: 36931542 DOI: 10.1016/j.phrs.2023.106732] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
High mobility group A 2 (HMGA2) is a protein that modulates the structure of chromatin in the nucleus. Importantly, aberrant expression of HMGA2 occurs during carcinogenesis, and this protein is an upstream mediator of cancer hallmarks including evasion of apoptosis, proliferation, invasion, metastasis, and therapy resistance. HMGA2 targets critical signaling pathways such as Wnt/β-catenin and mTOR in cancer cells. Therefore, suppression of HMGA2 function notably decreases cancer progression and improves outcome in patients. As HMGA2 is mainly oncogenic, targeting expression by non-coding RNAs (ncRNAs) is crucial to take into consideration since it affects HMGA2 function. MicroRNAs (miRNAs) belong to ncRNAs and are master regulators of vital cell processes, which affect all aspects of cancer hallmarks. Long ncRNAs (lncRNAs) and circular RNAs (circRNAs), other members of ncRNAs, are upstream mediators of miRNAs. The current review intends to discuss the importance of the miRNA/HMGA2 axis in modulation of various types of cancer, and mentions lncRNAs and circRNAs, which regulate this axis as upstream mediators. Finally, we discuss the effect of miRNAs and HMGA2 interactions on the response of cancer cells to therapy. Regarding the critical role of HMGA2 in regulation of critical signaling pathways in cancer cells, and considering the confirmed interaction between HMGA2 and one of the master regulators of cancer, miRNAs, targeting miRNA/HMGA2 axis in cancer therapy is promising and this could be the subject of future clinical trial experiments.
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Affiliation(s)
- Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran.
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Timo L M Ten Hagen
- Precision Medicine in Oncology (PrMiO), Department of Pathology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, the Netherlands.
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mojtaba Falahati
- Precision Medicine in Oncology (PrMiO), Department of Pathology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, the Netherlands.
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Wang P, Wang Z, Zhu L, Sun Y, Castellano L, Stebbing J, Yu Z, Peng L. A pyroptosis-related lncRNA signature in bladder cancer. Cancer Med 2023; 12:6348-6364. [PMID: 36237132 PMCID: PMC10028168 DOI: 10.1002/cam4.5344] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/13/2022] [Accepted: 09/26/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Pyroptosis, a type of programmed cell death, is implicated in the tumorigenesis, development and migration of cancer, which can be regulated by long non-coding RNAs (lncRNAs). Our research aimed to investigate the prognostic role of pyroptosis-related lncRNAs and the relationship to the tumor immune microenvironment through bioinformatics analysis. METHODS The clinical and RNA-sequencing data of bladder cancer patients were downloaded from The Cancer Genome Atlas (TCGA). And 412 bladder cancer subjects with clinical information were divided into training and testing cohort. And 52 reported pyroptosis-related genes were used to screen pyroptosis-related lncRNAs. A pyroptosis-related lncRNA signature was constructed based on Cox regression analyses. RESULTS A 9-pyroptosis-related-lncRNA signature was identified to separate patients with bladder cancer into two groups. The prognosis of bladder cancer patients in the high-risk group was significantly inferior compared with those in the low-risk group. Risk scores were validated to develop an independent prognostic indicator based on multivariate Cox regression analysis. Receiver operating characteristic curve (ROC) analysis examined the signature on overall survival. The area under time-dependent ROC curve (AUC) at 1-, 3, and 5-years measured 0.747, 0.783, and 0.768, respectively. Analysis of the immune landscape and PD-L1 expression showed that PD-L1 is upregulated in the high-risk group. The immunocyte subtypes of the two groups were different. CONCLUSION A novel pyroptosis-related lncRNA signature was identified with prognostic value for bladder cancer patients. Pyroptosis-related lncRNAs have a potential role in cancer immunology and may serve as prognostic or therapeutic targets.
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Affiliation(s)
- Peng Wang
- Department of Medical Oncology, Yidu Central Hospital of Weifang, Weifang, China
| | - Zhiqiang Wang
- Department of Urology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Liping Zhu
- Department of Medical Oncology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Yilan Sun
- Department of Respiratory Disease, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Zhejiang, China
| | - Leandro Castellano
- Department of Biochemistry, School of Life Sciences, University of Sussex, Brighton, UK
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Justin Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
- Department of Biomedical Sciences, Anglia Ruskin University, Cambridge, UK
| | - Zhentao Yu
- Department of Thoracic Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Ling Peng
- Department of Respiratory Disease, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Zhejiang, China
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Jiang K, Wu L, Yin X, Tang Q, Yin J, Zhou Z, Yu H, Yan S. Prognostic implications of necroptosis-related long noncoding RNA signatures in muscle-invasive bladder cancer. Front Genet 2022; 13:1036098. [PMID: 36531246 PMCID: PMC9755502 DOI: 10.3389/fgene.2022.1036098] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/15/2022] [Indexed: 09/22/2023] Open
Abstract
Background: Bladder cancer (BLCA) is the sixth most common cancer in men, with an increasing incidence of morbidity and mortality. Necroptosis is a type of programmed cell death and plays a critical role in the biological processes of bladder cancer (BLCA). However, current studies focusing on long noncoding RNA (lncRNA) and necroptosis in cancer are limited, and there is no research about necroptosis-related lncRNAs (NRLs) in BLCA. Methods: We obtained the RNA-seq data and corresponding clinical information of BLCA from The Cancer Genome Atlas (TCGA) database. The seven determined prognostic NLRs were analyzed by several methods and verified by RT-qPCR. Then, a risk signature was established based on the aforementioned prognostic NLRs. To identify it, we evaluated its prognostic value by Kaplan-Meier (K-M) survival curve and receiver operating characteristics (ROC) curve analysis. Moreover, the relationships between risk signature and clinical features, functional enrichment, immune landscape, and drug resistance were explored as well. Results: We constructed a signature based on seven defined NLRs (HMGA2-AS1, LINC02489, ETV7-AS1, EMSLR, AC005954.1, STAG3L5P-PVRIG2P-PILRB, and LINC02178). Patients in the low-risk cohort had longer survival times than those in the high-risk cohort, and the area under the ROC curve (AUC) value of risk signature was higher than other clinical variables. Functional analyses, the infiltrating level of immune cells and functions, ESTIMATE score, and immune checkpoint analysis all indicated that the high-risk group was in a relatively immune-activated state. In terms of treatments, patients in the high-risk group were more sensitive to immunotherapy, especially anti-PD1/PD-L1 immunotherapy and conventional chemotherapy. Conclusion: The novel NLR signature acts as an invaluable tool for predicting prognosis, immune microenvironment, and drug resistance in muscle-invasive bladder cancer (MIBC) patients.
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Affiliation(s)
- Kan Jiang
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Lingyun Wu
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Xin Yin
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Qiuying Tang
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Jie Yin
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Ziyang Zhou
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Hao Yu
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Senxiang Yan
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
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9
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Santos F, Capela AM, Mateus F, Nóbrega-Pereira S, Bernardes de Jesus B. Non-coding antisense transcripts: fine regulation of gene expression in cancer. Comput Struct Biotechnol J 2022; 20:5652-5660. [PMID: 36284703 PMCID: PMC9579725 DOI: 10.1016/j.csbj.2022.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/14/2022] Open
Abstract
Natural antisense transcripts (NATs) are coding or non-coding RNA sequences transcribed on the opposite direction from the same genomic locus. NATs are widely distributed throughout the human genome and seem to play crucial roles in physiological and pathological processes, through newly described and targeted mechanisms. NATs represent the intricate complexity of the genome organization and constitute another layer of potential targets in disease. Here, we focus on the interesting and unique role of non-coding NATs in cancer, paying particular attention to those acting as miRNA sponges.
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Affiliation(s)
| | | | | | | | - Bruno Bernardes de Jesus
- Corresponding author at: Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
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10
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He C, Liu Y, Li J, Zheng X, Liang J, Cui G, Chang H. LncRNA RPSAP52 promotes cell proliferation and inhibits cell apoptosis via modulating miR-665/STAT3 in gastric cancer. Bioengineered 2022; 13:8699-8711. [PMID: 35322746 PMCID: PMC9161851 DOI: 10.1080/21655979.2022.2054754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 12/19/2022] Open
Abstract
LncRNA RPSAP52 is a newly identified functional molecular in several cancers, but its role in gastric cancer (GC) is currently unclear. This study aimed to investigate the biofunction of lncRNA RPSAP52 in GC. Quantitative polymerase-chain reaction (RT-qPCR) was employed to analyze the gene level of lncRNA RPSAP52 and miR-665. Cell proliferation capacity was evaluated via CCK-8 and colony formation assay. Flow cytometry was applied to detect cell cycle and cell apoptosis. Hematoxylin-eosin staining was conducted for histopathological analysis. Immunochemical staining was carried out to detect expression level of ki-67. Subcellular fractionation was performed to explore the position of lncRNA RPSAP52. The binding relationship among lncRNA RPSAP52, miR-665 and STAT3 was verified via luciferase reporter assay. RNA pull down experiments were used to verify the binding relationship between lncRNA RPSAP52 and miR-665. The STAT3 level was evaluated via Western blot. LncRNA RPSAP52 is significantly elevated in GC cells. Deletion of lncRNA RPSAP52 restrained cell proliferation and induced G0-G1 phase arrest, while expediting apoptosis in GC cells. Tumor growth in vivo was suppressed following lncRNA RPSAP52 depletion. MiR-665 was verified as the target of lncRNA RPSAP52. A ceRNA-sponge mechanism of lncRNA RPSAP52 on miR-665 was identified. Meanwhile, miR-665 functions as STAT3 sponge. MiR-665 overexpression and STAT3 depletion served the same functions as lncRNA RPSAP52 depletion in GC cells. LncRNA RPSAP52 exerted anti-cancer effects via modulating miR-665/STAT3 in GC.Abbreviations: Gastric cancer (GC); Quantitative polymerase-chain reaction (RT-qPCR); Helicobacter pylori (H. pylori); Roswell Park Memorial Institute 1640 (RPMI 1640); fetal bovine serum (FBS); glyceraldheyde 3-phosphate dehydrogenase (GAPDH); propidium iodide (PI); Cell counting kit-8 (CCK-8); radioimmunoprecipitation assay (RIPA); sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE); polyvinylidene fluoride (PVDF); enhanced chemiluminescence (ECL); Statistical Product and Service Solutions (SPSS); standard deviation (SD).
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Affiliation(s)
- Chao He
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, JinanChina
- Department of Gastrointestinal Surgery, Taian Central Hospital, TaianChina
| | - Yuanyuan Liu
- Department of Respiratory Medicine, The Second Affiliated Hospital of Shandong First Medical University, TaianChina
| | - Jinhou Li
- Department of Hepatobiliary and Pancreatic, Taian Central Hospital, TaianChina
| | - Xiao Zheng
- Department of Gastrointestinal Surgery, Taian Central Hospital, TaianChina
| | - Jianwei Liang
- Department of Gastrointestinal Surgery, Taian Central Hospital, TaianChina
| | - Gang Cui
- Department of Gastrointestinal Surgery, Taian Central Hospital, TaianChina
| | - Hong Chang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, JinanChina
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11
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Nai A, Zeng H, Wu Q, He Z, Zeng S, Bashir S, Ma F, He J, Wan W, Xu M. lncRNA/miR-29c-Mediated High Expression of LOX Can Influence the Immune Status and Chemosensitivity and Can Forecast the Poor Prognosis of Gastric Cancer. Front Cell Dev Biol 2022; 9:760470. [PMID: 35047494 PMCID: PMC8762233 DOI: 10.3389/fcell.2021.760470] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/22/2021] [Indexed: 12/20/2022] Open
Abstract
Gastric carcinoma is the fourth most prevalent cause of cancer-related deaths worldwide because of dismal prognosis and few therapeutic options. Accumulated studies have indicated that targeting lysyl oxidase (LOX) family members may serve as an anticancer strategy. Nevertheless, the specific mechanisms of LOX in stomach carcinoma are still unclear. In this study, we demonstrated that LOX is significantly different in 13 types of cancers and may act as a potential therapeutic target, especially in stomach carcinoma. Moreover, overexpression of LOX in gastric carcinoma was validated by multiple databases and contributed to the poor overall survival (OS), progression-free survival (PFS) and post-progression survival (PPS) of stomach adenocarcinoma (STAD) patients. Next, based on the ceRNA hypothesis, the HIF1A-AS2/RP11-366L20.2-miR-29c axis was characterized as the upstream regulatory mechanism of LOX gene overexpression in gastric cancer by combining correlation analysis, expression analysis, and survival analysis. Finally, we illustrated that LOX gene overexpression leads to dismal prognosis of gastric cancer, perhaps through promoting M2 macrophage polarization and tumor immune escape and enhancing drug resistance of tumor cells to chemotherapeutic drugs. Our research demonstrate that LOX may be potentially applied as a novel prognostic marker and targeting inhibition of LOX holds promise as a treatment strategy for gastric cancer.
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Affiliation(s)
- Aitao Nai
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Huihui Zeng
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Qiong Wu
- Key Laboratory of Brain Science Research and Transformation in Tropical Environment of Hainan Province, Hainan Medical University, Haikou, China
| | - Zirui He
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Shuwen Zeng
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Shoaib Bashir
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Feng Ma
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jie He
- Key Laboratory of Brain Science Research and Transformation in Tropical Environment of Hainan Province, Hainan Medical University, Haikou, China
| | - Wei Wan
- Key Laboratory of Brain Science Research and Transformation in Tropical Environment of Hainan Province, Hainan Medical University, Haikou, China
| | - Meng Xu
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
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12
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Krappinger JC, Bonstingl L, Pansy K, Sallinger K, Wreglesworth NI, Grinninger L, Deutsch A, El-Heliebi A, Kroneis T, Mcfarlane RJ, Sensen CW, Feichtinger J. Non-coding Natural Antisense Transcripts: Analysis and Application. J Biotechnol 2021; 340:75-101. [PMID: 34371054 DOI: 10.1016/j.jbiotec.2021.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Non-coding natural antisense transcripts (ncNATs) are regulatory RNA sequences that are transcribed in the opposite direction to protein-coding or non-coding transcripts. These transcripts are implicated in a broad variety of biological and pathological processes, including tumorigenesis and oncogenic progression. With this complex field still in its infancy, annotations, expression profiling and functional characterisations of ncNATs are far less comprehensive than those for protein-coding genes, pointing out substantial gaps in the analysis and characterisation of these regulatory transcripts. In this review, we discuss ncNATs from an analysis perspective, in particular regarding the use of high-throughput sequencing strategies, such as RNA-sequencing, and summarize the unique challenges of investigating the antisense transcriptome. Finally, we elaborate on their potential as biomarkers and future targets for treatment, focusing on cancer.
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Affiliation(s)
- Julian C Krappinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Lilli Bonstingl
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Katrin Pansy
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Katja Sallinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Nick I Wreglesworth
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Lukas Grinninger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Austrian Biotech University of Applied Sciences, Konrad Lorenz-Straße 10, 3430 Tulln an der Donau, Austria
| | - Alexander Deutsch
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Thomas Kroneis
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Ramsay J Mcfarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Christoph W Sensen
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria; Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; HCEMM Kft., Római blvd. 21, 6723 Szeged, Hungary
| | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
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13
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Ma G, Li G, Fan W, Xu Y, Song S, Guo K, Liu Z. The Role of Long Noncoding RNA AL161431.1 in the Development and Progression of Pancreatic Cancer. Front Oncol 2021; 11:666313. [PMID: 34395245 PMCID: PMC8363261 DOI: 10.3389/fonc.2021.666313] [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: 06/01/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer is known for its notorious fast progression and poor prognosis. Long noncoding RNA (lncRNA) AL161431.1 has been reported to be involved in the pathogenesis of different cancers. In this study, we explored the role of lncRNA AL161431.1 in the development and progression of pancreatic cancer by bioinformatic analysis, in vitro and in vivo experiments in pancreatic cancer BxPC-3 and SW1990 cells, as well as clinical samples. We found that lncRNA AL161431.1 was highly expressed in pancreatic cancer cells and tissues. Knock down of lncRNA AL161431.1 led to increased cancer cell death and cell cycle arrest. Xenograft growth of SW1990 cells with stable knockdown of lncRNA AL161431.1 in mice was significantly slower than that of SW1990 cells with scrambled control shRNA. Finally, we showed the involvement of lncRNA AL161431.1 in pancreatic cancer was related to its promotion of epithelial mesenchymal transition process.
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Affiliation(s)
- Gang Ma
- Department of Pancreatic-Biliary Surgery, First Hospital of China Medical University, Shenyang, China
| | - Guichen Li
- Department of Pancreatic-Biliary Surgery, First Hospital of China Medical University, Shenyang, China
| | - Wufeng Fan
- Department of Pancreatic-Biliary Surgery, First Hospital of China Medical University, Shenyang, China
| | - Yuanhong Xu
- Department of Pancreatic-Biliary Surgery, First Hospital of China Medical University, Shenyang, China
| | - Shaowei Song
- Department of Pancreatic-Biliary Surgery, First Hospital of China Medical University, Shenyang, China
| | - Kejian Guo
- Department of Pancreatic-Biliary Surgery, First Hospital of China Medical University, Shenyang, China
| | - Zhe Liu
- Department of Pancreatic-Biliary Surgery, First Hospital of China Medical University, Shenyang, China
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14
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Rothzerg E, Ho XD, Xu J, Wood D, Märtson A, Kõks S. Upregulation of 15 Antisense Long Non-Coding RNAs in Osteosarcoma. Genes (Basel) 2021; 12:genes12081132. [PMID: 34440306 PMCID: PMC8394133 DOI: 10.3390/genes12081132] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022] Open
Abstract
The human genome encodes thousands of natural antisense long noncoding RNAs (lncRNAs); they play the essential role in regulation of gene expression at multiple levels, including replication, transcription and translation. Dysregulation of antisense lncRNAs plays indispensable roles in numerous biological progress, such as tumour progression, metastasis and resistance to therapeutic agents. To date, there have been several studies analysing antisense lncRNAs expression profiles in cancer, but not enough to highlight the complexity of the disease. In this study, we investigated the expression patterns of antisense lncRNAs from osteosarcoma and healthy bone samples (24 tumour-16 bone samples) using RNA sequencing. We identified 15 antisense lncRNAs (RUSC1-AS1, TBX2-AS1, PTOV1-AS1, UBE2D3-AS1, ERCC8-AS1, ZMIZ1-AS1, RNF144A-AS1, RDH10-AS1, TRG-AS1, GSN-AS1, HMGA2-AS1, ZNF528-AS1, OTUD6B-AS1, COX10-AS1 and SLC16A1-AS1) that were upregulated in tumour samples compared to bone sample controls. Further, we performed real-time polymerase chain reaction (RT-qPCR) to validate the expressions of the antisense lncRNAs in 8 different osteosarcoma cell lines (SaOS-2, G-292, HOS, U2-OS, 143B, SJSA-1, MG-63, and MNNG/HOS) compared to hFOB (human osteoblast cell line). These differentially expressed IncRNAs can be considered biomarkers and potential therapeutic targets for osteosarcoma.
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Affiliation(s)
- Emel Rothzerg
- School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia; (E.R.); (J.X.); (D.W.)
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Xuan Dung Ho
- Department of Oncology, College of Medicine and Pharmacy, Hue University, Hue 53000, Vietnam;
| | - Jiake Xu
- School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia; (E.R.); (J.X.); (D.W.)
| | - David Wood
- School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia; (E.R.); (J.X.); (D.W.)
| | - Aare Märtson
- Department of Traumatology and Orthopaedics, University of Tartu, Tartu University Hospital, 50411 Tartu, Estonia;
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: ; Tel.: +61-(0)-8-6457-0313
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15
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Wang Q, Wang G, Xu X, Chen Z. miR-760 mediated the proliferation and metastasis of hepatocellular carcinoma cells by regulating HMGA2. Pathol Res Pract 2021; 222:153420. [PMID: 33887625 DOI: 10.1016/j.prp.2021.153420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND The purpose of our study was to investigate the roles of miR-760 and its potential mechanisms in HCC. METHODS The functions of miR-760 were identified and measured by MTT, colony formation, transwell, and flow cytometry assays. Luciferase assay was applied to verify the direct binding of miR-760 on HMGA2 3'untranslated region (3'UTR). Then, in vitro experiment was used to investigate the biological effects of miR-760 and HMGA2. Luciferase and ChIP assays were used to detect the validity of SP1 binding sites on the miR-760 promoter. RESULTS We demonstrated that miR-760 overexpression suppressed cell proliferation, migration, and invasion in HCC. Besides, HMGA2 was demonstrated as a direct target gene of miR-760. Furthermore, we found that methylation may result in the downregulation of miR-760, and SP1 could inhibit the transcription of miR-760. CONCLUSIONS Our study demonstrated that SP1/miR-760/HMGA2 may serve as a molecular regulatory axis for HCC treatment.
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Affiliation(s)
- Quhui Wang
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, China
| | - Gang Wang
- Department of Anesthesiology, Union Hospital Affiliated With Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Xiaodong Xu
- Department of General Surgery, The 4th Affiliated Hospital of Nantong University, Yancheng, 224000, China
| | - Zhong Chen
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, China; Department of General Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China.
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16
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Zhang X, Deng HW, Shen H, Ehrlich M. Prioritization of Osteoporosis-Associated Genome-wide Association Study (GWAS) Single-Nucleotide Polymorphisms (SNPs) Using Epigenomics and Transcriptomics. JBMR Plus 2021; 5:e10481. [PMID: 33977200 PMCID: PMC8101624 DOI: 10.1002/jbm4.10481] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/10/2021] [Accepted: 02/19/2021] [Indexed: 12/15/2022] Open
Abstract
Genetic risk factors for osteoporosis, a prevalent disease associated with aging, have been examined in many genome-wide association studies (GWASs). A major challenge is to prioritize transcription-regulatory GWAS-derived variants that are likely to be functional. Given the critical role of epigenetics in gene regulation, we have used an unusual epigenetics-based and transcription-based approach to identify some of the credible regulatory single-nucleotide polymorphisms (SNPs) relevant to osteoporosis from 38 reported bone mineral density (BMD) GWASs. Using Roadmap databases, we prioritized SNPs based upon their overlap with strong enhancer or promoter chromatin preferentially in osteoblasts relative to 12 heterologous cell culture types. We also required that these SNPs overlap open chromatin (Deoxyribonuclease I [DNaseI]-hypersensitive sites) and DNA sequences predicted to bind to osteoblast-relevant transcription factors in an allele-specific manner. From >50,000 GWAS-derived SNPs, we identified 14 novel and credible regulatory SNPs (Tier-1 SNPs) for osteoporosis risk. Their associated genes, BICC1, LGR4, DAAM2, NPR3, or HMGA2, are involved in osteoblastogenesis or bone homeostasis and regulate cell signaling or enhancer function. Four of these genes are preferentially expressed in osteoblasts. BICC1, LGR4, and DAAM2 play important roles in canonical Wnt signaling, a pathway critical for bone formation and repair. The transcription factors predicted to bind to the Tier-1 SNP-containing DNA sequences also have bone-related functions. We present evidence that some of the Tier-1 SNPs exert their effects on BMD risk indirectly through little-studied long noncoding RNA (lncRNA) genes, which may, in turn, control the nearby bone-related protein-encoding gene. Our study illustrates a method to identify novel BMD-related causal regulatory SNPs for future study and to prioritize candidate regulatory GWAS-derived SNPs, in general. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Xiao Zhang
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine Tulane University New Orleans LA USA
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine Tulane University New Orleans LA USA
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine Tulane University New Orleans LA USA
| | - Melanie Ehrlich
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine Tulane University New Orleans LA USA.,Tulane Cancer Center and Hayward Genetics Center Tulane University New Orleans LA USA
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17
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Meireles Da Costa N, Palumbo A, De Martino M, Fusco A, Ribeiro Pinto LF, Nasciutti LE. Interplay between HMGA and TP53 in cell cycle control along tumor progression. Cell Mol Life Sci 2021; 78:817-831. [PMID: 32920697 PMCID: PMC11071717 DOI: 10.1007/s00018-020-03634-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/05/2020] [Accepted: 09/03/2020] [Indexed: 01/27/2023]
Abstract
The high mobility group A (HMGA) proteins are found to be aberrantly expressed in several tumors. Studies (in vitro and in vivo) have shown that HMGA protein overexpression has a causative role in carcinogenesis process. HMGA proteins regulate cell cycle progression through distinct mechanisms which strongly influence its normal dynamics along malignant transformation. Tumor protein p53 (TP53) is the most frequently altered gene in cancer. The loss of its activity is recognized as the fall of a barrier that enables neoplastic transformation. Among the different functions, TP53 signaling pathway is tightly involved in control of cell cycle, with cell cycle arrest being the main biological outcome observed upon p53 activation, which prevents accumulation of damaged DNA, as well as genomic instability. Therefore, the interaction and opposing effects of HMGA and p53 proteins on regulation of cell cycle in normal and tumor cells are discussed in this review. HMGA proteins and p53 may reciprocally regulate the expression and/or activity of each other, leading to the counteraction of their regulation mechanisms at different stages of the cell cycle. The existence of a functional crosstalk between these proteins in the control of cell cycle could open the possibility of targeting HMGA and p53 in combination with other therapeutic strategies, particularly those that target cell cycle regulation, to improve the management and prognosis of cancer patients.
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Affiliation(s)
- Nathalia Meireles Da Costa
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer-INCA, Rua André Cavalcanti, 37-6th floor-Centro, 20231-050, Rio de Janeiro, RJ, Brazil.
| | - Antonio Palumbo
- Laboratório de Interações Celulares, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro Prédio de Ciências da Saúde-Cidade Universitária, Ilha do Fundão, A. Carlos Chagas, 373-Bloco F, Sala 26, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Marco De Martino
- Istituto di Endocrinologia e Oncologia Sperimentale-CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia e Oncologia Sperimentale-CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Luis Felipe Ribeiro Pinto
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer-INCA, Rua André Cavalcanti, 37-6th floor-Centro, 20231-050, Rio de Janeiro, RJ, Brazil
| | - Luiz Eurico Nasciutti
- Laboratório de Interações Celulares, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro Prédio de Ciências da Saúde-Cidade Universitária, Ilha do Fundão, A. Carlos Chagas, 373-Bloco F, Sala 26, 21941-902, Rio de Janeiro, RJ, Brazil.
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18
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Huang W, Weng W, Wu B, Ye T, Lin Z, Zhang Z, Shi K. Development and validation of the trans-omics model for pancreatic adenocarcinoma. Epigenomics 2021; 13:15-30. [PMID: 33356543 DOI: 10.2217/epi-2020-0184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aim: To develop a trans-omics-based molecular clinicopathological algorithm for predicting pancreatic adenocarcinoma prognosis, we performed a comprehensive analysis of the expression levels of mRNA, DNA methylation and DNA copy number in The Cancer Genome Atlas dataset. Materials & methods: Based on the least absolute shrinkage and selection operator method - COX regression analysis, a trans-omics-based classifier was established to predict overall survival. Nomogram was constructed by combining the classifier band clinical pathological characterization. Results: Based on trans-omics, we developed a 10-gene-based classifier and a molecular-clinicopathologic nomogram for predicting overall survival with satisfactory accuracy. Conclusion: Trans-omics-based classifier and molecule-clinicopathological nomogram based on the classifier can accurately predict the prognosis of pancreatic adenocarcinoma patients.
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Affiliation(s)
- Weiguo Huang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Wanqing Weng
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Boda Wu
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Tingbo Ye
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Zhuo Lin
- Department of Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Zhongjing Zhang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Keqing Shi
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
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