1
|
Singh S, Shi X, Haddox S, Elfman J, Ahmad SB, Lynch S, Manley T, Piczak C, Phung C, Sun Y, Sharma A, Li H. RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data. Brief Bioinform 2024; 25:bbae251. [PMID: 38796690 PMCID: PMC11128028 DOI: 10.1093/bib/bbae251] [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: 11/15/2023] [Revised: 03/30/2024] [Accepted: 05/09/2024] [Indexed: 05/28/2024] Open
Abstract
Read-through chimeric RNAs are being recognized as a means to expand the functional transcriptome and contribute to cancer tumorigenesis when mis-regulated. However, current software tools often fail to predict them. We have developed RTCpredictor, utilizing a fast ripgrep tool to search for all possible exon-exon combinations of parental gene pairs. We also added exonic variants allowing searches containing common SNPs. To our knowledge, it is the first read-through chimeric RNA specific prediction method that also provides breakpoint coordinates. Compared with 10 other popular tools, RTCpredictor achieved high sensitivity on a simulated and three real datasets. In addition, RTCpredictor has less memory requirements and faster execution time, making it ideal for applying on large datasets.
Collapse
Affiliation(s)
- Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Xinrui Shi
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Justin Elfman
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Syed Basil Ahmad
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Sarah Lynch
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Tommy Manley
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Claire Piczak
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Christopher Phung
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Yunan Sun
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Aadi Sharma
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| |
Collapse
|
2
|
Elfman J, Goins L, Heller T, Singh S, Wang YH, Li H. Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction. Nucleic Acids Res 2024; 52:4409-4421. [PMID: 38587197 PMCID: PMC11077074 DOI: 10.1093/nar/gkae258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
Gene fusions and their chimeric products are commonly linked with cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. Large-scale efforts to annotate structural variations have identified gene fusions capable of generating chimeric transcripts even in normal tissues. In this study, we present a bottom-up approach targeting population-specific chimeric RNAs, identifying 58 such instances in the GTEx cohort, including notable cases such as SUZ12P1-CRLF3, TFG-ADGRG7 and TRPM4-PPFIA3, which possess distinct patterns across different ancestry groups. We provide direct evidence for an additional 29 polymorphic chimeric RNAs with associated structural variants, revealing 13 novel rare structural variants. Additionally, we utilize the All of Us dataset and a large cohort of clinical samples to characterize the association of the SUZ12P1-CRLF3-causing variant with patient phenotypes. Our study showcases SUZ12P1-CRLF3 as a representative example, illustrating the identification of elusive structural variants by focusing on those producing population-specific fusion transcripts.
Collapse
Affiliation(s)
- Justin Elfman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lynette Goins
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA
| | - Tessa Heller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Sandeep Singh
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
- Department of Pathology, University of Virginia, Charlottesville, VA 22903, USA
| |
Collapse
|
3
|
Pei F, Tao Z, Lu Q, Fang T, Peng S. Octamer-binding transcription factor 4-positive circulating tumor cell predicts worse treatment response and survival in advanced cholangiocarcinoma patients who receive immune checkpoint inhibitors treatment. World J Surg Oncol 2024; 22:110. [PMID: 38664770 PMCID: PMC11044354 DOI: 10.1186/s12957-024-03369-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/28/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Octamer-binding transcription factor 4-positive circulating tumor cell (OCT4+CTC) exhibits high stemness and invasive potential, which may influence the efficacy of immune checkpoint inhibitors (ICI). This study aimed to assess the prognostic role of OCT4+CTC in advanced cholangiocarcinoma (CCA) patients who received ICI treatment. METHODS In total, 40 advanced CCA patients who received ICI treatment were included, and CTC and OCT4 counts were detected via a Canpatrol system and an RNA in situ hybridization method before ICI treatment. Patients were subsequently divided into none CTC, OCT4-CTC, and OCT4+CTC groups. Patients were followed up for a median of 10.4 months. RESULTS The percentages of patients in none CTC, OCT4-CTC, and OCT4+CTC groups were 25.0%, 30.0%, and 45.0%, respectively. The proportion of patients with lymph node metastasis was highest in OCT4+CTC group, followed by none CTC group, and lowest in OCT4-CTC group (P = 0.025). The objective response rate (ORR) was lowest in OCT4+CTC group, moderate in OCT4-CTC group, and highest in none CTC group (P = 0.009), while disease control rate was not different among three groups (P = 0.293). In addition, progression-free survival (PFS) (P < 0.001) and overall survival (OS) (P = 0.001) were shorter in the OCT4+CTC group than in none CTC & OCT4-CTC group. Moreover, OCT4+CTC (versus none CTC) was independently linked with poorer PFS [hazard ratio (HR) = 6.752, P = 0.001] and OS (HR = 6.674, P = 0.003) in advanced CCA patients. CONCLUSION OCT4+CTC relates to lymph node metastasis and shows a good predictive value for poor treatment response and survival in advanced CCA patients who receive ICI treatment.
Collapse
Affiliation(s)
- Fei Pei
- Department of Hepatobiliary Pancreatic Surgery, Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, No. 141 Tianjin Road, Huangshi, 435200, Hubei, China
| | - Zhen Tao
- Department of Hepatobiliary Pancreatic Surgery, Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, No. 141 Tianjin Road, Huangshi, 435200, Hubei, China.
| | - Qi Lu
- Department of Hepatobiliary Pancreatic Surgery, Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, No. 141 Tianjin Road, Huangshi, 435200, Hubei, China
| | - Tao Fang
- Department of Hepatobiliary Pancreatic Surgery, Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, No. 141 Tianjin Road, Huangshi, 435200, Hubei, China
| | - Shasha Peng
- Department of Hepatobiliary Pancreatic Surgery, Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, No. 141 Tianjin Road, Huangshi, 435200, Hubei, China
| |
Collapse
|
4
|
Liu S, Yang P, Wang L, Zou X, Zhang D, Chen W, Hu C, Xiao D, Ren H, Zhang H, Cai S. Targeting PAK4 reverses cisplatin resistance in NSCLC by modulating ER stress. Cell Death Discov 2024; 10:36. [PMID: 38238316 PMCID: PMC10796919 DOI: 10.1038/s41420-024-01798-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
Chemoresistance poses a significant impediment to effective treatments for non-small-cell lung cancer (NSCLC). P21-activated kinase 4 (PAK4) has been implicated in NSCLC progression by invasion and migration. However, the involvement of PAK4 in cisplatin resistance is not clear. Here, we presented a comprehensive investigation into the involvement of PAK4 in cisplatin resistance within NSCLC. Our study revealed enhanced PAK4 expression in both cisplatin-resistant NSCLC tumors and cell lines. Notably, PAK4 silencing led to a remarkable enhancement in the chemosensitivity of cisplatin-resistant NSCLC cells. Cisplatin evoked endoplasmic reticulum stress in NSCLC. Furthermore, inhibition of PAK4 demonstrated the potential to sensitize resistant tumor cells through modulating endoplasmic reticulum stress. Mechanistically, we unveiled that the suppression of the MEK1-GRP78 signaling pathway results in the sensitization of NSCLC cells to cisplatin after PAK4 knockdown. Our findings establish PAK4 as a promising therapeutic target for addressing chemoresistance in NSCLC, potentially opening new avenues for enhancing treatment efficacy and patient outcomes.
Collapse
Affiliation(s)
- Shixin Liu
- Department of Thoracic Surgery, the First Affiliated Hospital of Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, and Minister of Education Key Laboratory of Tumor Molecular Biology, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Pingshan Yang
- Department of Thoracic Surgery, the First Affiliated Hospital of Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
| | - Lu Wang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, and Minister of Education Key Laboratory of Tumor Molecular Biology, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Xiaofang Zou
- Department of Medical Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Dongdong Zhang
- Department of Thoracic Surgery, the First Affiliated Hospital of Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
| | - Wenyou Chen
- Department of Thoracic Surgery, the First Affiliated Hospital of Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
| | - Chuang Hu
- Department of Thoracic Surgery, the First Affiliated Hospital of Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
| | - Duqing Xiao
- Department of Thoracic Surgery, the First Affiliated Hospital of Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
| | - Hongzheng Ren
- Department of Pathology, Gongli Hospital, Naval Medical University, Shanghai, 200135, China.
- Department of Pathology, Heping Hospital, Changzhi Medical College, Changzhi, 000465, China.
| | - Hao Zhang
- Department of Thoracic Surgery, the First Affiliated Hospital of Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China.
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, and Minister of Education Key Laboratory of Tumor Molecular Biology, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou; The Second Affiliated Hospital of Shantou University Medical College, Shantou, China.
| | - Songwang Cai
- Department of Thoracic Surgery, the First Affiliated Hospital of Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China.
| |
Collapse
|
5
|
Wang Q, Cheng B, Singh S, Tao Y, Xie Z, Qin F, Shi X, Xu J, Hu C, Tan W, Li H, Huang H. A protein-encoding CCDC7 circular RNA inhibits the progression of prostate cancer by up-regulating FLRT3. NPJ Precis Oncol 2024; 8:11. [PMID: 38225404 PMCID: PMC10789799 DOI: 10.1038/s41698-024-00503-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Circular RNAs (circRNAs) are a family of endogenous RNAs that have become a focus of biological research in recent years. Emerging evidence has revealed that circRNAs exert biological functions by acting as transcriptional regulators, microRNA sponges, and binding partners with RNA-binding proteins. However, few studies have identified coding circRNAs, which may lead to a hidden repertoire of proteins. In this study, we unexpectedly discovered a protein-encoding circular RNA circCCDC7(15,16,17,18,19) while we were searching for prostate cancer related chimeric RNAs. circCCDC7(15,16,17,18,19) is derived from exon 19 back spliced to exon 15 of the CCDC7 gene. It is significantly downregulated in patients with high Gleason score. Prostate cancer patients with decreased circCCDC7(15,16,17,18,19) expression have a worse prognosis, while linear CCDC7 had no such association. Overexpressed circCCDC7(15,16,17,18,19) inhibited prostate cancer cell migration, invasion, and viability, supporting classification of circCCDC7(15,16,17,18,19) as a bona fide tumor suppressor gene. We provide evidence that its tumor suppressive activity is driven by the protein it encodes, and that circCCDC7(15,16,17,18,19) encodes a secretory protein. Consistently, conditioned media from circCCDC7(15,16,17,18,19) overexpressing cells has the same tumor suppressive activity. We further demonstrate that the tumor suppressive activity of circCCDC7(15,16,17,18,19) is at least partially mediated by FLRT3, whose expression also negatively correlates with Gleason score and clinical prognosis. In conclusion, circCCDC7(15,16,17,18,19) functions as a tumor suppressor in prostate cancer cells through the circCCDC7-180aa secretory protein it encodes, and is a promising therapeutic peptide for prostate cancer.
Collapse
Affiliation(s)
- Qiong Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Bisheng Cheng
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yiran Tao
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Xinrui Shi
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jingjing Xu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chenxi Hu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wanlong Tan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
| | - Hai Huang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
- Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China.
| |
Collapse
|
6
|
Chen C, Qin F, Singh S, Tang Y, Li H. CTNNBIP1-CLSTN1 functions as a housekeeping chimeric RNA and regulates cell proliferation through SERPINE2. Cell Death Discov 2023; 9:369. [PMID: 37805599 PMCID: PMC10560238 DOI: 10.1038/s41420-023-01668-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023] Open
Abstract
The conventional understanding that chimeric RNAs are unique to carcinoma and are the products of chromosomal rearrangement is being challenged. However, experimental evidence supporting the function of chimeric RNAs in normal physiology is scarce. We decided to focus on one particular chimeric RNA, CTNNBIP1-CLSTN1. We examined its expression in various tissues and cell types and compared it quantitatively among cancer and noncancer cells. We further investigated its role in a panel of noncancer cells and investigated the functional mechanism. We found that this fusion transcript is expressed in almost all tissues and a wide range of cell types, including fibroblasts, epithelial cells, stem cells, vascular endothelial cells, and hepatocytes. In addition, the CTNNBIP1-CLSTN1 expression level in noncancerous cell lines was not evidently different from that in cancer cell lines. Furthermore, in at least three cell types, silencing CTNNBIP1-CLSTN1 significantly reduced the cell proliferation rate by inducing G2/M arrest and apoptosis. Importantly, rescue experiments confirmed that cell cycle arrest was restored by exogenous expression of the chimera but not the wild-type parental gene. Further evidence is provided that CTNNBIP1-CLSTN1 regulates cell proliferation through SERPINE2. Thus, CTNNBIP1-CLSTN1 is an example of a new class of fusion RNAs, dubbed "housekeeping chimeric RNAs".
Collapse
Affiliation(s)
- Chen Chen
- School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Department of Clinical Laboratory, Qilu Hospital of Shandong University Dezhou Hospital, Dezhou, 253000, Shandong, China
| | - Fujun Qin
- School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
- ICMR-Center for Research, Management and Control of Haemoglobinopathies (Unit of ICMR-National Institute of Immunohaematology, Mumbai), Chandrapur, Maharashtra, 442406, India
| | - Yue Tang
- School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
| |
Collapse
|
7
|
Li H, Chen C, Tang Y, Qin F, Singh S. CTNNBIP1-CLSTN1 Functions as a Housekeeping Chimeric RNA, and Regulates Cell Proliferation through SERPINE2. RESEARCH SQUARE 2023:rs.3.rs-3112431. [PMID: 37503100 PMCID: PMC10371161 DOI: 10.21203/rs.3.rs-3112431/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The conventional wisdom that chimeric RNAs being peculiarity of carcinoma, and the products of chromosomal rearrangement is being challenged, However, experimental evidence supporting chimeric RNAs in normal physiology being functional is scarce. We decided to focus on one particular chimeric RNA, CTNNBIP1-CLSTN1 . We examined its expression among various tissues and cell types, and compared quantitatively among cancer and non-cancer cells. We further investigated its role in a panel of non-cancer cells and probed the functional mechanism. We found that this fusion transcript is expressed in almost all tissues, and a wide range of cell types including fibroblasts, epithelial, stem, vascular endothelial cells, and hepatocytes. The expression level in non-cancerous cell lines is also not evidently different from that in the cancer cell lines. Furthermore, silencing CTNNBIP1-CLSTN1 significantly reduces cell proliferation rate, by inducing G2/M arrest in cell cycle progress and apoptosis in at least three cell types. Importantly, rescue experiments confirmed that the cell cycle arrest can be regained by exogenous expression of the chimera, but not the wild type parental gene. Further evidence is provided that CTNNBIP1-CLSTN1 regulates cell proliferation through SERPINE2 . Thus, CTNNBIP1-CLSTN1 represents an example of a new class of fusion RNA, dubbed "housekeeping chimeric RNAs".
Collapse
|
8
|
许 云, 苏 征, 郑 林, 张 孟, 谭 珺, 杨 亚, 张 梦, 徐 苗, 陈 铌, 陈 雪, 周 桥. [Read-through circular RNA rt-circ-HS promotes hypoxia inducible factor 1α expression and renal carcinoma cell proliferation, migration and invasiveness]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2023; 55:217-227. [PMID: 37042131 PMCID: PMC10091263 DOI: 10.19723/j.issn.1671-167x.2023.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Indexed: 04/07/2024]
Abstract
OBJECTIVE To identify and characterize read-through RNAs and read-through circular RNAs (rt-circ-HS) derived from transcriptional read-through hypoxia inducible factor 1α (HIF1α) and small nuclear RNA activating complex polypeptide 1 (SNAPC1) the two adjacent genes located on chromosome 14q23, in renal carcinoma cells and renal carcinoma tissues, and to study the effects of rt-circ-HS on biological behavior of renal carcinoma cells and on regulation of HIF1α. METHODS Reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing were used to examine expression of read-through RNAs HIF1α-SNAPC1 and rt-circ-HS in different tumor cells. Tissue microarrays of 437 different types of renal cell carcinoma (RCC) were constructed, and chromogenic in situ hybridization (ISH) was used to investigate expression of rt-circ-HS in different RCC types. Small interference RNA (siRNA) and artificial overexpression plasmids were designed to examine the effects of rt-circ-HS on 786-O and A498 renal carcinoma cell proliferation, migration and invasiveness by cell counting kit 8 (CCK8), EdU incorporation and Transwell cell migration and invasion assays. RT-PCR and Western blot were used to exa-mine expression of HIF1α and SNAPC1 RNA and proteins after interference of rt-circ-HS with siRNA, respectively. The binding of rt-circ-HS with microRNA 539 (miR-539), and miR-539 with HIF1α 3' untranslated region (3' UTR), and the effects of these interactions were investigated by dual luciferase reporter gene assays. RESULTS We discovered a novel 1 144 nt rt-circ-HS, which was derived from read-through RNA HIF1α-SNAPC1 and consisted of HIF1α exon 2-6 and SNAPC1 exon 2-4. Expression of rt-circ-HS was significantly upregulated in 786-O renal carcinoma cells. ISH showed that the overall positive expression rate of rt-circ-HS in RCC tissue samples was 67.5% (295/437), and the expression was different in different types of RCCs. Mechanistically, rt-circ-HS promoted renal carcinoma cell proliferation, migration and invasiveness by functioning as a competitive endogenous inhibitor of miR-539, which we found to be a potent post-transcriptional suppressor of HIF1α, thus promoting expression of HIF1α. CONCLUSION The novel rt-circ-HS is highly expressed in different types of RCCs and acts as a competitive endogenous inhibitor of miR-539 to promote expression of its parental gene HIF1α and thus the proliferation, migration and invasion of renal cancer cells.
Collapse
Affiliation(s)
- 云屹 许
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 征征 苏
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 林茂 郑
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 孟尼 张
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 珺娅 谭
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院病理研究室,成都 610041Research Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 亚蓝 杨
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 梦鑫 张
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 苗 徐
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 铌 陈
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院病理研究室,成都 610041Research Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 雪芹 陈
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院病理研究室,成都 610041Research Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 桥 周
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院病理研究室,成都 610041Research Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
9
|
Elfman J, Goins L, Heller T, Singh S, Wang YH, Li H. Discovery of A Polymorphic Gene Fusion via Bottom-Up Chimeric RNA Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526864. [PMID: 36778239 PMCID: PMC9915695 DOI: 10.1101/2023.02.02.526864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gene fusions and their chimeric products are typically considered hallmarks of cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. In addition, efforts to annotate structural variation at large scale have found examples of gene fusions with potential to produce chimeric transcripts in normal tissues. In this report, we provide a means for targeting population-specific chimeric RNAs to enrich for those generated by gene fusion events. We identify 57 such chimeric RNAs from the GTEx cohort, including SUZ12P1-CRLF3 and TFG-ADGRG7 , whose distribution we assessed across the populations of the 1000 Genomes Project. We reveal that SUZ12P1-CRLF3 results from a common complex structural variant in populations with African heritage, and identify its likely mechanism for formation. Additionally, we utilize a large cohort of clinical samples to characterize the SUZ12P1-CRLF3 chimeric RNA, and find an association between the variant and indications of Neurofibramatosis Type I. We present this gene fusion as a case study for identifying hard-to-find and potentially functional structural variants by selecting for those which produce population-specific fusion transcripts. KEY POINTS - Discovery of 57 polymorphic chimeric RNAs- Characterization of SUZ12P1-CRLF3 polymorphic chimeric RNA and corresponding rearrangement- Novel bottom-up approach to identify structural variants which produce transcribed gene fusions.
Collapse
|
10
|
Singh S, Shi X, Ahmad SB, Manley T, Piczak C, Phung C, Sun Y, Lynch S, Sharma A, Li H. RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526869. [PMID: 36778443 PMCID: PMC9915620 DOI: 10.1101/2023.02.02.526869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Read-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor ( https://github.com/sandybioteck/RTCpredictor ) has less memory requirements and faster execution time.
Collapse
|
11
|
Xiong X, Ke X, Wang L, Lin Y, Wang S, Yao Z, Li K, Luo Y, Liu F, Pan Y, Yeung SJ, Helfrich W, Zhang H. Neoantigen-based cancer vaccination using chimeric RNA-loaded dendritic cell-derived extracellular vesicles. J Extracell Vesicles 2022; 11:e12243. [PMID: 35927827 PMCID: PMC9451527 DOI: 10.1002/jev2.12243] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/09/2022] [Accepted: 06/21/2022] [Indexed: 02/05/2023] Open
Abstract
Cancer vaccines critically rely on the availability of targetable immunogenic cancer-specific neoepitopes. However, mutation-based immunogenic neoantigens are rare or even non-existent in subgroups of cancer types. To address this issue, we exploited a cancer-specific aberrant transcription-induced chimeric RNA, designated A-Pas chiRNA, as a possible source of clinically relevant and targetable neoantigens. A-Pas chiRNA encodes a recently discovered cancer-specific chimeric protein that comprises full-length astrotactin-2 (ASTN2) C-terminally fused in-frame to the antisense sequence of the 18th intron of pregnancy-associated plasma protein-A (PAPPA). We used extracellular vesicles (EVs) from A-Pas chiRNA-transfected dendritic cells (DCs) to produce the cell-free anticancer vaccine DEXA-P . Treatment of immunocompetent cancer-bearing mice with DEXA-P inhibited tumour growth and prolonged animal survival. In summary, we demonstrate for the first time that cancer-specific transcription-induced chimeric RNAs can be exploited to produce a cell-free cancer vaccine that induces potent CD8+ T cell-mediated anticancer immunity. Our novel approach may be particularly useful for developing cancer vaccines to treat malignancies with low mutational burden or without mutation-based antigens. Moreover, this cell-free anticancer vaccine approach may offer several practical advantages over cell-based vaccines, such as ease of scalability and genetic modifiability as well as enhanced shelf life.
Collapse
Affiliation(s)
- Xiao Xiong
- Institute of Precision Cancer Medicine and Pathology, and Department of PathologySchool of Medicineand Department of General SurgeryThe First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
| | - Xiurong Ke
- Department of SurgeryLaboratory for Translational Surgical OncologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
- Shantou University Medical CollegeShantouGuangdongChina
| | - Lu Wang
- Institute of Precision Cancer Medicine and Pathology, and Department of PathologySchool of Medicineand Department of General SurgeryThe First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
| | - Yusheng Lin
- Institute of Precision Cancer Medicine and Pathology, and Department of PathologySchool of Medicineand Department of General SurgeryThe First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
- Shantou University Medical CollegeShantouGuangdongChina
- Department of HematologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Shuhong Wang
- Institute of Precision Cancer Medicine and Pathology, and Department of PathologySchool of Medicineand Department of General SurgeryThe First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
| | - Zhimeng Yao
- Institute of Precision Cancer Medicine and Pathology, and Department of PathologySchool of Medicineand Department of General SurgeryThe First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
| | - Kai Li
- Institute of Precision Cancer Medicine and Pathology, and Department of PathologySchool of Medicineand Department of General SurgeryThe First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
| | - Yichen Luo
- Institute of Precision Cancer Medicine and Pathology, and Department of PathologySchool of Medicineand Department of General SurgeryThe First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
| | - Fan Liu
- Institute of Precision Cancer Medicine and Pathology, and Department of PathologySchool of Medicineand Department of General SurgeryThe First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
| | - Yunlong Pan
- Department of General SurgeryThe First Affiliated Hospital of Jinan University, and Institute of Precision Cancer Medicine and PathologySchool of MedicineJinan UniversityGuangzhouGuangdongChina
| | - Sai‐Ching J. Yeung
- Department of Emergency MedicineUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Department of Endocrine Neoplasia and Hormonal DisordersUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Wijnand Helfrich
- Department of SurgeryLaboratory for Translational Surgical OncologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Hao Zhang
- Department of General SurgeryThe First Affiliated Hospital of Jinan University, and Institute of Precision Cancer Medicine and PathologySchool of MedicineJinan UniversityGuangzhouGuangdongChina
- Minister of Education Key Laboratory of Tumor Molecular BiologyJinan UniversityGuangzhouGuangdongChina
| |
Collapse
|
12
|
Arconada-Luque E, Jiménez-Suarez J, Pascual-Serra R, Nam-Cha SH, Moline T, Cimas FJ, Fliquete G, Ortega-Muelas M, Roche O, Fernández-Aroca DM, Muñoz Velasco R, García-Flores N, Garnés-García C, Sánchez-Fdez A, Matilla-Almazán S, Sánchez-Arévalo Lobo VJ, Hernández-Losa J, Belandia B, Pandiella A, Esparís-Ogando A, Ramón y Cajal S, del Peso L, Sánchez-Prieto R, Ruiz-Hidalgo MJ. ERK5 Is a Major Determinant of Chemical Sarcomagenesis: Implications in Human Pathology. Cancers (Basel) 2022; 14:cancers14143509. [PMID: 35884568 PMCID: PMC9316148 DOI: 10.3390/cancers14143509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/11/2022] [Accepted: 07/16/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Sarcoma is a heterogeneous group of tumors poorly studied with few therapeutic opportunities. Interestingly, the role of MAPKs still remains unclear in sarcomatous pathology. Here, we describe for the first time the critical role of ERK5 in the biology of soft tissue sarcoma by using in vitro and in vivo approaches in a murine experimental model of chemical sarcomagenesis. Indeed, our observations were extrapolated to a short series of human leiomyosarcoma and rhabdomyosarcomas. Furthermore, transcriptome analysis allows us to demonstrate the critical role of KLF2 in the biological effects of ERK5. Therefore, the data presented here open new windows in the diagnosis and therapy of soft tissue sarcomas. Abstract Sarcomas are a heterogeneous group of tumors in which the role of ERK5 is poorly studied. To clarify the role of this MAPK in sarcomatous pathology, we used a murine 3-methyl-cholanthrene (3MC)-induced sarcoma model. Our data show that 3MC induces pleomorphic sarcomas with muscle differentiation, showing an increased expression of ERK5. Indeed, this upregulation was also observed in human sarcomas of muscular origin, such as leiomyosarcoma or rhabdomyosarcoma. Moreover, in cell lines derived from these 3MC-induced tumors, abrogation of Mapk7 expression by using specific shRNAs decreased in vitro growth and colony-forming capacity and led to a marked loss of tumor growth in vivo. In fact, transcriptomic profiling in ERK5 abrogated cell lines by RNAseq showed a deregulated gene expression pattern for key biological processes such as angiogenesis, migration, motility, etc., correlating with a better prognostic in human pathology. Finally, among the various differentially expressed genes, Klf2 is a key mediator of the biological effects of ERK5 as indicated by its specific interference, demonstrating that the ERK5–KLF2 axis is an important determinant of sarcoma biology that should be further studied in human pathology.
Collapse
Affiliation(s)
- Elena Arconada-Luque
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Jaime Jiménez-Suarez
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Raquel Pascual-Serra
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Syong Hyun Nam-Cha
- Servicio de Anatomía Patológica, Hospital General de Albacete, 02008 Albacete, Spain;
| | - Teresa Moline
- Grupo de Patología Molecular Traslacional, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona Centro de Investigación Biomédica en RED de Cancer CIBERONC, 08035 Barcelona, Spain; (T.M.); (G.F.); (J.H.-L.); (S.R.y.C.)
| | - Francisco J. Cimas
- Unidad de Bioquímica y Biología Molecular, Servicio de Instrumentación Biomédica, Universidad de Castilla-La Mancha, 02008 Albacete, Spain;
| | - Germán Fliquete
- Grupo de Patología Molecular Traslacional, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona Centro de Investigación Biomédica en RED de Cancer CIBERONC, 08035 Barcelona, Spain; (T.M.); (G.F.); (J.H.-L.); (S.R.y.C.)
| | - Marta Ortega-Muelas
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Olga Roche
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
- Departamento de Ciencias Médicas, Facultad de Medicina, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
| | - Diego M. Fernández-Aroca
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Raúl Muñoz Velasco
- Grupo de Oncología Molecular, Facultad de Ciencias Experimentales, Instituto de Investigación Biosanitaria, Universidad Francisco de Vitoria, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.M.V.); (V.J.S.-A.L.)
- Departamento de Anatomía Patológica, Instituto de Investigación Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain
| | - Natalia García-Flores
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Cristina Garnés-García
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Adrián Sánchez-Fdez
- Instituto de Biología Molecular y Celular del Cáncer-CSIC, 37007 Salamanca, Spain; (A.S.-F.); (S.M.-A.); (A.P.); (A.E.-O.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en RED de Cancer CIBERONC, 37007 Salamanca, Spain
| | - Sofía Matilla-Almazán
- Instituto de Biología Molecular y Celular del Cáncer-CSIC, 37007 Salamanca, Spain; (A.S.-F.); (S.M.-A.); (A.P.); (A.E.-O.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en RED de Cancer CIBERONC, 37007 Salamanca, Spain
| | - Víctor J. Sánchez-Arévalo Lobo
- Grupo de Oncología Molecular, Facultad de Ciencias Experimentales, Instituto de Investigación Biosanitaria, Universidad Francisco de Vitoria, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.M.V.); (V.J.S.-A.L.)
- Departamento de Anatomía Patológica, Instituto de Investigación Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain
| | - Javier Hernández-Losa
- Grupo de Patología Molecular Traslacional, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona Centro de Investigación Biomédica en RED de Cancer CIBERONC, 08035 Barcelona, Spain; (T.M.); (G.F.); (J.H.-L.); (S.R.y.C.)
| | - Borja Belandia
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, 28029 Madrid, Spain;
| | - Atanasio Pandiella
- Instituto de Biología Molecular y Celular del Cáncer-CSIC, 37007 Salamanca, Spain; (A.S.-F.); (S.M.-A.); (A.P.); (A.E.-O.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en RED de Cancer CIBERONC, 37007 Salamanca, Spain
| | - Azucena Esparís-Ogando
- Instituto de Biología Molecular y Celular del Cáncer-CSIC, 37007 Salamanca, Spain; (A.S.-F.); (S.M.-A.); (A.P.); (A.E.-O.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en RED de Cancer CIBERONC, 37007 Salamanca, Spain
| | - Santiago Ramón y Cajal
- Grupo de Patología Molecular Traslacional, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona Centro de Investigación Biomédica en RED de Cancer CIBERONC, 08035 Barcelona, Spain; (T.M.); (G.F.); (J.H.-L.); (S.R.y.C.)
| | - Luis del Peso
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain;
- Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias CIBERES, 28029 Madrid, Spain
| | - Ricardo Sánchez-Prieto
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
- Departamento de Ciencias Médicas, Facultad de Medicina, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, 28029 Madrid, Spain;
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’, Consejo Superior de Investigaciones Científicas (IIBM-CSIC)-Universidad de Castilla-La Mancha, 02008 Albacete, Spain
- Correspondence:
| | - María José Ruiz-Hidalgo
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
- Departamento de Química Inorgánica, Orgánica y Bioquímica, Área de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
| |
Collapse
|
13
|
Sun Y, Li H. Chimeric RNAs Discovered by RNA Sequencing and Their Roles in Cancer and Rare Genetic Diseases. Genes (Basel) 2022; 13:genes13050741. [PMID: 35627126 PMCID: PMC9140685 DOI: 10.3390/genes13050741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
Chimeric RNAs are transcripts that are generated by gene fusion and intergenic splicing events, thus comprising nucleotide sequences from different parental genes. In the past, Northern blot analysis and RT-PCR were used to detect chimeric RNAs. However, they are low-throughput and can be time-consuming, labor-intensive, and cost-prohibitive. With the development of RNA-seq and transcriptome analyses over the past decade, the number of chimeric RNAs in cancer as well as in rare inherited diseases has dramatically increased. Chimeric RNAs may be potential diagnostic biomarkers when they are specifically expressed in cancerous cells and/or tissues. Some chimeric RNAs can also play a role in cell proliferation and cancer development, acting as tools for cancer prognosis, and revealing new insights into the cell origin of tumors. Due to their abilities to characterize a whole transcriptome with a high sequencing depth and intergenically identify spliced chimeric RNAs produced with the absence of chromosomal rearrangement, RNA sequencing has not only enhanced our ability to diagnose genetic diseases, but also provided us with a deeper understanding of these diseases. Here, we reviewed the mechanisms of chimeric RNA formation and the utility of RNA sequencing for discovering chimeric RNAs in several types of cancer and rare inherited diseases. We also discussed the diagnostic, prognostic, and therapeutic values of chimeric RNAs.
Collapse
Affiliation(s)
- Yunan Sun
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA;
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA;
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
| |
Collapse
|
14
|
Luo Y, Du L, Yao Z, Liu F, Li K, Li F, Zhu J, Coppes RP, Zhang D, Pan Y, Gao S, Zhang H. Generation and Application of Inducible Chimeric RNA ASTN2-PAPPAas Knockin Mouse Model. Cells 2022; 11:277. [PMID: 35053393 PMCID: PMC8773765 DOI: 10.3390/cells11020277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 02/05/2023] Open
Abstract
Chimeric RNAs (chiRNAs) play many previously unrecognized roles in different diseases including cancer. They can not only be used as biomarkers for diagnosis and prognosis of various diseases but also serve as potential therapeutic targets. In order to better understand the roles of chiRNAs in pathogenesis, we inserted human sequences into mouse genome and established a knockin mouse model of the tamoxifen-inducible expression of ASTN2-PAPPA antisense chimeric RNA (A-PaschiRNA). Mice carrying the A-PaschiRNA knockin gene do not display any apparent abnormalities in growth, fertility, histological, hematopoietic, and biochemical indices. Using this model, we dissected the role of A-PaschiRNA in chemical carcinogen 4-nitroquinoline 1-oxide (4NQO)-induced carcinogenesis of esophageal squamous cell carcinoma (ESCC). To our knowledge, we are the first to generate a chiRNA knockin mouse model using the Cre-loxP system. The model could be used to explore the roles of chiRNA in pathogenesis and potential targeted therapies.
Collapse
Affiliation(s)
- Yichen Luo
- Institute of Precision Cancer Medicine and Pathology, School of Medicine and Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Liang Du
- Department of Biomedical Sciences of Cells &
- Systems, Section Molecular Cell Biology and Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
- Graduate School, Shantou University Medical College, Shantou 515041, China
| | - Zhimeng Yao
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Fan Liu
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Kai Li
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Feifei Li
- Department of Oncology, People’s Hospital of Leshan, Leshan 614099, China;
| | - Jianlin Zhu
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Robert P. Coppes
- Department of Biomedical Sciences of Cells &
- Systems, Section Molecular Cell Biology and Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Dianzheng Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, 4170 City Avenue, Philadelphia, PA 19131, USA
| | - Yunlong Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Shegan Gao
- Henan Key Laboratory of Cancer Epigenetics, College of Clinical Medicine, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471000, China
| | - Hao Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China
- Minister of Education Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| |
Collapse
|
15
|
Targeting PELP1 Attenuates Angiogenesis and Enhances Chemotherapy Efficiency in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14020383. [PMID: 35053547 PMCID: PMC8773490 DOI: 10.3390/cancers14020383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 02/01/2023] Open
Abstract
Abnormal angiogenesis is one of the important hallmarks of colorectal cancer as well as other solid tumors. Optimally, anti-angiogenesis therapy could restrain malignant angiogenesis to control tumor expansion. PELP1 is as a scaffolding oncogenic protein in a variety of cancer types, but its involvement in angiogenesis is unknown. In this study, PELP1 was found to be abnormally upregulated and highly coincidental with increased MVD in CRC. Further, treatment with conditioned medium (CM) from PELP1 knockdown CRC cells remarkably arrested the function of human umbilical vein endothelial cells (HUVECs) compared to those treated with CM from wildtype cells. Mechanistically, the STAT3/VEGFA axis was found to mediate PELP1-induced angiogenetic phenotypes of HUVECs. Moreover, suppression of PELP1 reduced tumor growth and angiogenesis in vivo accompanied by inactivation of STAT3/VEGFA pathway. Notably, in vivo, PELP1 suppression could enhance the efficacy of chemotherapy, which is caused by the normalization of vessels. Collectively, our findings provide a preclinical proof of concept that targeting PELP1 to decrease STAT3/VEGFA-mediated angiogenesis and improve responses to chemotherapy due to normalization of vessels. Given the newly defined contribution to angiogenesis of PELP1, targeting PELP1 may be a potentially ideal therapeutic strategy for CRC as well as other solid tumors.
Collapse
|
16
|
Dong H, Du L, Cai S, Lin W, Chen C, Still M, Yao Z, Coppes RP, Pan Y, Zhang D, Gao S, Zhang H. Tyrosine Phosphatase PTPRO Deficiency in ERBB2-Positive Breast Cancer Contributes to Poor Prognosis and Lapatinib Resistance. Front Pharmacol 2022; 13:838171. [PMID: 35431974 PMCID: PMC9010868 DOI: 10.3389/fphar.2022.838171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/07/2022] [Indexed: 02/05/2023] Open
Abstract
Despite the initial benefit from treating ERBB2-positive breast cancer with tyrosine kinase inhibitor lapatinib, resistance develops inevitably. Since the expression of protein tyrosine phosphatase receptor-type O (PTPRO), a member of the R3 subfamily of receptor protein tyrosine phosphatases (PTPs), is inversely correlated with the aggressiveness of multiple malignancies, we decided to explore the correlation between PTPRO and lapatinib resistance in ERBB2-positive breast cancer. Results of immunohistochemical (IHC) staining and the correlation analysis between the expression levels of PTPRO and the clinicopathological parameters indicate that PTPRO is downregulated in cancer tissues as compared with normal tissues and negatively associated with differentiation, tumor size, tumor depth, as well as the expression of ERBB2 and Ki67. Results from Kaplan-Meier analyses indicate that lower expression of PTPRO is correlated with shorter relapse-free survival for patients with ERBB2-positive breast cancer, and multivariable Cox regression analysis found that PTPRO can potentially serve as an independent prognostic indicator for ERBB2-positive breast cancer. Results from both human breast cancer cells with PTPRO knockdown or overexpression and mouse embryonic fibroblasts (MEFs) which derived from Ptpro +/+ and Ptpro -/- mice with then stably transfected plasmid FUGW-Erbb2 consistently demonstrated the essentiality of PTPRO in the lapatinib-mediated anticancer process. Our findings suggest that PTPRO is not only able to serve as an independent prognostic indicator, but upregulating PTPRO can also reverse the lapatinib resistance of ERBB2-positive breast cancer.
Collapse
Affiliation(s)
- Hongmei Dong
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Department of General Surgery, The First Affiliated Hospital of Jinan University, Minister of Education Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China
| | - Liang Du
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Department of General Surgery, The First Affiliated Hospital of Jinan University, Minister of Education Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China
- Departments of Biomedical Sciences of Cells and Systems, Section Molecular Cell Biology and Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Graduate School, Shantou University Medical College, Shantou, China
| | - Songwang Cai
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Wan Lin
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Chaoying Chen
- Graduate School, Shantou University Medical College, Shantou, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Hunan Traditional Chinese Medical College (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, China
| | - Matthew Still
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, United States
| | - Zhimeng Yao
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Department of General Surgery, The First Affiliated Hospital of Jinan University, Minister of Education Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China
| | - Robert P. Coppes
- Departments of Biomedical Sciences of Cells and Systems, Section Molecular Cell Biology and Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yunlong Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Dianzheng Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, United States
| | - Shegan Gao
- Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medicine) of Henan University of Science and Technology, Luoyang, China
- *Correspondence: Hao Zhang, ; Shegan Gao,
| | - Hao Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Minister of Education Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China
- *Correspondence: Hao Zhang, ; Shegan Gao,
| |
Collapse
|
17
|
Lozinski M, Bowden NA, Graves MC, Fay M, Tooney PA. DNA damage repair in glioblastoma: current perspectives on its role in tumour progression, treatment resistance and PIKKing potential therapeutic targets. Cell Oncol (Dordr) 2021; 44:961-981. [PMID: 34057732 DOI: 10.1007/s13402-021-00613-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/17/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The aggressive, invasive and treatment resistant nature of glioblastoma makes it one of the most lethal cancers in humans. Total surgical resection is difficult, and a combination of radiation and chemotherapy is used to treat the remaining invasive cells beyond the tumour border by inducing DNA damage and activating cell death pathways in glioblastoma cells. Unfortunately, recurrence is common and a major hurdle in treatment, often met with a more aggressive and treatment resistant tumour. A mechanism of resistance is the response of DNA repair pathways upon treatment-induced DNA damage, which enact cell-cycle arrest and repair of DNA damage that would otherwise cause cell death in tumour cells. CONCLUSIONS In this review, we discuss the significance of DNA repair mechanisms in tumour formation, aggression and treatment resistance. We identify an underlying trend in the literature, wherein alterations in DNA repair pathways facilitate glioma progression, while established high-grade gliomas benefit from constitutively active DNA repair pathways in the repair of treatment-induced DNA damage. We also consider the clinical feasibility of inhibiting DNA repair in glioblastoma and current strategies of using DNA repair inhibitors as agents in combination with chemotherapy, radiation or immunotherapy. Finally, the importance of blood-brain barrier penetrance when designing novel small-molecule inhibitors is discussed.
Collapse
Affiliation(s)
- Mathew Lozinski
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Nikola A Bowden
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, Newcastle, NSW, Australia
- School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - Moira C Graves
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, Newcastle, NSW, Australia
- School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - Michael Fay
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, Newcastle, NSW, Australia
- Genesis Cancer Care, Gateshead, New South Wales, Australia
| | - Paul A Tooney
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia.
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia.
- Hunter Medical Research Institute, Newcastle, NSW, Australia.
| |
Collapse
|
18
|
Dong H, Xie C, Jiang Y, Li K, Lin Y, Pang X, Xiong X, Zheng J, Ke X, Chen Y, Li Y, Zhang H. Tumor-Derived Exosomal Protein Tyrosine Phosphatase Receptor Type O Polarizes Macrophage to Suppress Breast Tumor Cell Invasion and Migration. Front Cell Dev Biol 2021; 9:703537. [PMID: 34650968 PMCID: PMC8505750 DOI: 10.3389/fcell.2021.703537] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/09/2021] [Indexed: 02/05/2023] Open
Abstract
Tumor-derived exosomes, containing multiple nucleic acids and proteins, have been implicated to participate in the interaction between tumor cells and microenvironment. However, the functional involvement of phosphatases in tumor-derived exosomes is not fully understood. We and others previously demonstrated that protein tyrosine phosphatase receptor type O (PTPRO) acts as a tumor suppressor in multiple cancer types. In addition, its role in tumor immune microenvironment remains elusive. Bioinformatical analyses revealed that PTPRO was closely associated with immune infiltration, and positively correlated to M1-like macrophages, but negatively correlated to M2-like macrophages in breast cancer tissues. Co-cultured with PTPRO-overexpressing breast cancer cells increased the proportion of M1-like tumor-associated macrophages (TAMs) while decreased that of M2-like TAMs. Further, we observed that tumor-derived exosomal PTPRO induced M1-like macrophage polarization, and regulated the corresponding functional phenotypes. Moreover, tumor cell-derived exosomal PTPRO inhibited breast cancer cell invasion and migration, and inactivated STAT signaling in macrophages. Our data suggested that exosomal PTPRO inhibited breast cancer invasion and migration by modulating macrophage polarization. Anti-tumoral effect of exosomal PTPRO was mediated by inactivating STAT family in macrophages. These findings highlight a novel mechanism of tumor invasion regulated by tumor-derived exosomal tyrosine phosphatase, which is of translational potential for the therapeutic strategy against breast cancer.
Collapse
Affiliation(s)
- Hongmei Dong
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China
| | - Chaoyu Xie
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China
| | - Yuchen Jiang
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China
| | - Kai Li
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China
| | - Yusheng Lin
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Graduate School, Shantou University Medical College, Shantou, China
| | - Xijiao Pang
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiao Xiong
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China
| | - Jiehua Zheng
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xiurong Ke
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China
- Graduate School, Shantou University Medical College, Shantou, China
- Laboratory for Translational Surgical Oncology, Department of Surgery, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yexi Chen
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yong Li
- St George and Sutherland Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, Australia
- Cancer Care Centre, St George Hospital, Kogarah, NSW, Australia
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hao Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| |
Collapse
|
19
|
Landscape of Chimeric RNAs in Non-Cancerous Cells. Genes (Basel) 2021; 12:genes12040466. [PMID: 33805149 PMCID: PMC8064075 DOI: 10.3390/genes12040466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/21/2022] Open
Abstract
Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splicing can also be found in normal cells and tissues. In this study, we aim to identify chimeric RNAs in different non-neoplastic cell lines and investigate the landscape and expression of these novel candidate chimeric RNAs. To do so, we used HEK-293T, HUVEC, and LO2 cell lines as models, performed paired-end RNA sequencing, and conducted analyses for chimeric RNA profiles. Several filtering criteria were applied, and the landscape of chimeric RNAs was characterized at multiple levels and from various angles. Further, we experimentally validated 17 chimeric RNAs from different classifications. Finally, we examined a number of validated chimeric RNAs in different cancer and non-cancer cells, including blood from healthy donors, and demonstrated their ubiquitous expression pattern.
Collapse
|