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Nguyen AT, Kim HK. Recent Progress in Synthesis of 99mTc-labeled Complexes with Nitroimidazoles as SPECT Probes for Targeting Tumor Hypoxia. Nucl Med Mol Imaging 2024; 58:258-278. [PMID: 39036459 PMCID: PMC11255181 DOI: 10.1007/s13139-024-00860-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 07/23/2024] Open
Abstract
The majority of solid tumors have hypoxia, or low oxygen levels, which is one of the hallmarks of cancer. Hypoxia was found to relate to cancer metastases and resistance to therapies, therefore, detection of hypoxia plays an important role in the process of cancer prognosis and treatment. Single-photon emission computed tomography (SPECT) is a non-invasive imaging technique using gamma-emitting radiopharmaceuticals to visualize biological activities within the body. SPECT is also applied for the detection of tumor hypoxia with the development of hypoxia-targeting radiopharmaceuticals. Radiopharmaceuticals containing nitroimidazole moieties have received increasing attention due to their bio-reducible characteristics which make the radiopharmaceuticals accumulate in the hypoxia regions. This review summarizes the recent development of 99mTc-labeled radiopharmaceuticals bearing nitroimidazoles for SPECT imaging of tumor hypoxia including the synthetic methods and results of animal studies.
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Affiliation(s)
- Anh Thu Nguyen
- Department of Nuclear Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, 54907 Republic of Korea
| | - Hee-Kwon Kim
- Department of Nuclear Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, 54907 Republic of Korea
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2
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Song F, Hou C, Huang Y, Liang J, Cai H, Tian G, Jiang Y, Wang Z, Hou J. Lactylome analyses suggest systematic lysine-lactylated substrates in oral squamous cell carcinoma under normoxia and hypoxia. Cell Signal 2024; 120:111228. [PMID: 38750680 DOI: 10.1016/j.cellsig.2024.111228] [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: 03/29/2024] [Revised: 05/05/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Cancer cells tend to live in hypoxic environment characterized by enhanced glycolysis and accumulation of lactate. Intracellular lactate is shown to drive a novel type of post-translational modification (PTM), lysine lactylation (Kla). Kla has been confirmed to affect the malignant progression of tumors such as hepatocellular carcinoma (HCC) and colon cancer, whereas the global lactylomic profiling of oral squamous cell carcinoma (OSCC) is unclear. Here, the integrative lactylome and proteome analyses by using liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 1011 Kla sites within 532 proteins and 1197 Kla sites within 608 proteins in SCC25 cells under normoxic and hypoxic environments, respectively. Among these lactylated proteins, histones accounted for only a small fraction, suggesting the presence of Kla modification of OSCC in a large number of non-histone proteins. Notably, Kla preferred to enrich in spliceosome, ribosome and glycolysis/gluconeogenesis pathway in both normoxic and hypoxic cultures. Compared with normoxia, 589 differential proteins with 898 differentially lactylated sites were detected under hypoxia, which were mainly associated with the glycolysis/gluconeogenesis pathway by KEGG analysis. Importantly, we verified the presence of lactylation modification in the spliceosomal proteins hnRNPA1, SF3A1, hnRNPU and SLU7, as well as in glycolytic enzyme PFKP. In addition, the differential alternative splicing analysis described the divergence of pre-mRNA splicing patterns in the presence or absence of sodium lactate and at different oxygen concentrations. Finally, a negative correlation between tissue Kla levels and the prognosis of OSCC patients was revealed by immunohistochemistry. Our study is the first report to elucidate the lactylome and its biological function in OSCC, which deepens our understanding of the mechanisms underlying OSCC progression and provides a novel strategy for targeted therapy for OSCC.
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Affiliation(s)
- Fan Song
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Chen Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Yingzhao Huang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Jianfeng Liang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Hongshi Cai
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Guoli Tian
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Yaoqi Jiang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Ziyi Wang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Jinsong Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China.
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3
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Abdulghani M, Razavian NB, Burdick JT, Domingo E, Cheung VG, Humphrey TC. Isoform Switching Regulates the Response to Ionizing Radiation Through SRSF1. Int J Radiat Oncol Biol Phys 2024; 119:1517-1529. [PMID: 38447610 DOI: 10.1016/j.ijrobp.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/23/2024] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
PURPOSE This study investigated how isoform switching affects the cellular response to ionizing radiation (IR), an understudied area despite its relevance to radiation therapy in cancer treatment. We aimed to identify changes in transcript isoform expression post-IR exposure and the proteins mediating these changes, with a focus on their potential to modulate radiosensitivity. METHODS AND MATERIALS Using RNA sequencing, we analyzed the B-cell lines derived from 10 healthy individuals at 3 timepoints, applying the mixture of isoforms algorithm to quantify alternative splicing. We examined RNA binding protein motifs within the sequences of IR-responsive isoforms and validated the serine/arginine-rich splicing factor 1 (SRSF1) as a predominant mediator through RNA immunoprecipitation. We further investigated the effects of SRSF1 on radiosensitivity by RNA interference and by analyzing publicly available data on patients with cancer. RESULTS We identified ∼1900 radiation-responsive alternatively spliced isoforms. Many isoforms were differentially expressed without changes in their overall gene expression. Over a third of these transcripts underwent exon skipping, while others used proximal last exons. These IR-responsive isoforms tended to be shorter transcripts missing vital domains for preventing apoptosis and promoting cell division but retaining those necessary for DNA repair. Our combined computational, genetic, and molecular analyses identified the proto-oncogene SRSF1 as a mediator of these radiation-induced isoform-switching events that promote apoptosis. After exposure to DNA double-strand break-inducing agents, SRSF1 expression decreased. A reduction in SRSF1 increased radiosensitivity in vitro and among patients with cancer. CONCLUSIONS We establish a pivotal role for isoform switching in the cellular response to IR and propose SRSF1 as a promising biomarker for assessing radiation therapy effectiveness.
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Affiliation(s)
- Majd Abdulghani
- Rhodes Trust and; Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Niema B Razavian
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Joshua T Burdick
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Enric Domingo
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Vivian G Cheung
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan.
| | - Timothy C Humphrey
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom; Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex, United Kingdom.
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4
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Chetta M, Basile A, Tarsitano M, Rivieccio M, Oro M, Capitanio N, Bukvic N, Priolo M, Rosati A. The Target Therapy Hyperbole: "KRAS (p.G12C)"-The Simplification of a Complex Biological Problem. Cancers (Basel) 2024; 16:2389. [PMID: 39001451 PMCID: PMC11240669 DOI: 10.3390/cancers16132389] [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: 05/26/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) gene variations are linked to the development of numerous cancers, including non-small cell lung cancer (NSCLC), colorectal cancer (CRC), and pancreatic ductal adenocarcinoma (PDAC). The lack of typical drug-binding sites has long hampered the discovery of therapeutic drugs targeting KRAS. Since "CodeBreaK 100" demonstrated Sotorasib's early safety and efficacy and led to its approval, especially in the treatment of non-small cell lung cancer (NSCLC), the subsequent identification of specific inhibitors for the p.G12C mutation has offered hope. However, the CodeBreaK 200 study found no significant difference in overall survival (OS) between patients treated with Docetaxel and Sotorasib (AMG 510), adding another degree of complexity to this ongoing challenge. The current study compares the three-dimensional structures of the two major KRAS isoforms, KRAS4A and KRAS4B. It also investigates the probable structural changes caused by the three major mutations (p.G12C, p.G12D, and p.G12V) within Sotorasib's pocket domain. The computational analysis demonstrates that the wild-type and mutant isoforms have distinct aggregation propensities, resulting in the creation of alternate oligomeric configurations. This study highlights the increased complexity of the biological issue of using KRAS as a therapeutic target. The present study stresses the need for a better understanding of the structural dynamics of KRAS and its mutations to design more effective therapeutic approaches. It also emphasizes the potential of computational approaches to shed light on the complicated molecular pathways that drive KRAS-mediated oncogenesis. This study adds to the ongoing efforts to address the therapeutic hurdles presented by KRAS in cancer treatment.
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Affiliation(s)
- Massimiliano Chetta
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Anna Basile
- StressBioLab, Department of Medicine, Surgery and Dentistry “Schola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (A.B.); (A.R.)
| | - Marina Tarsitano
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Maria Rivieccio
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Maria Oro
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Nazzareno Capitanio
- Department of Clinical and Experimental Medicine, University of Foggia, 71121 Foggia, Italy;
| | - Nenad Bukvic
- Medical Genetics Section, University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy;
| | - Manuela Priolo
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Alessandra Rosati
- StressBioLab, Department of Medicine, Surgery and Dentistry “Schola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (A.B.); (A.R.)
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Cappabianca L, Ruggieri M, Sebastiano M, Sbaffone M, Martelli I, Ruggeri P, Di Padova M, Farina AR, Mackay AR. Molecular Characterization and Inhibition of a Novel Stress-Induced Mitochondrial Protecting Role for Misfolded TrkAIII in Human SH-SY5Y Neuroblastoma Cells. Int J Mol Sci 2024; 25:5475. [PMID: 38791513 PMCID: PMC11122047 DOI: 10.3390/ijms25105475] [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: 04/18/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Pediatric neuroblastomas (NBs) are heterogeneous, aggressive, therapy-resistant embryonal tumors that originate from cells of neural crest origin committed to the sympathoadrenal progenitor cell lineage. Stress- and drug-resistance mechanisms drive post-therapeutic relapse and metastatic progression, the characterization and inhibition of which are major goals in improving therapeutic responses. Stress- and drug-resistance mechanisms in NBs include alternative TrkAIII splicing of the neurotrophin receptor tropomyosin-related kinase A (NTRK1/TrkA), which correlates with post-therapeutic relapse and advanced-stage metastatic disease. The TrkAIII receptor variant exerts oncogenic activity in NB models by mechanisms that include stress-induced mitochondrial importation and activation. In this study, we characterize novel targetable and non-targetable participants in this pro-survival mechanism in TrkAIII-expressing SH-SY5Y NB cells, using dithiothreitol (DTT) as an activator and a variety of inhibitors by regular and immunoprecipitation Western blotting of purified mitochondria and IncuCyte cytotoxicity assays. We report that stress-induced TrkAIII misfolding initiates this mechanism, resulting in Grp78, Ca2+-calmodulin, adenosine ribosylating factor (Arf) and Hsp90-regulated mitochondrial importation. TrkAIII imported into inner mitochondrial membranes is cleaved by Omi/high temperature requirement protein A2 (HtrA2) then activated by a mechanism dependent upon calmodulin kinase II (CaMKII), alpha serine/threonine kinase (Akt), mitochondrial Ca2+ uniporter and reactive oxygen species (ROS), involving inhibitory mitochondrial protein tyrosine phosphatase (PTPase) oxidation, resulting in phosphoinositide 3 kinase (PI3K) activation of mitochondrial Akt, which enhances stress resistance. This novel pro-survival function for misfolded TrkAIII mitigates the cytotoxicity of mitochondrial Ca2+ homeostasis disrupted during integrated stress responses, and is prevented by clinically approved Trk and Akt inhibitors and also by inhibitors of 78kDa glucose regulated protein (Grp78), heat shock protein 90 (Hsp90), Ca2+-calmodulin and PI3K. This identifies Grp78, Ca2+-calmodulin, Hsp90, PI3K and Akt as novel targetable participants in this mechanism, in addition to TrkAIII, the inhibition of which has the potential to enhance the stress-induced elimination of TrkAIII-expressing NB cells, with the potential to improve therapeutic outcomes in NBs that exhibit TrkAIII expression and activation.
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Dadgar N, Sherry C, Zimmerman J, Park H, Lewis C, Donnenberg A, Zaidi AH, Fan Y, Xiao K, Bartlett D, Donnenberg V, Wagner PL. Targeting interleukin-6 as a treatment approach for peritoneal carcinomatosis. J Transl Med 2024; 22:402. [PMID: 38689325 PMCID: PMC11061933 DOI: 10.1186/s12967-024-05205-8] [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: 02/05/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Peritoneal carcinomatosis (PC) is a complex manifestation of abdominal cancers, with a poor prognosis and limited treatment options. Recent work identifying high concentrations of the cytokine interleukin-6 (IL-6) and its soluble receptor (sIL-6-Rα) in the peritoneal cavity of patients with PC has highlighted this pathway as an emerging potential therapeutic target. This review article provides a comprehensive overview of the current understanding of the potential role of IL-6 in the development and progression of PC. We discuss mechansims by which the IL-6 pathway may contribute to peritoneal tumor dissemination, mesothelial adhesion and invasion, stromal invasion and proliferation, and immune response modulation. Finally, we review the prospects for targeting the IL-6 pathway in the treatment of PC, focusing on common sites of origin, including ovarian, gastric, pancreatic, colorectal and appendiceal cancer, and mesothelioma.
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Affiliation(s)
- Neda Dadgar
- Translational Hematology & Oncology Research, Enterprise Cancer Institute, Cleveland Clinic, Cleveland, OH, 44106, USA
| | - Christopher Sherry
- Allegheny Health Network Cancer Institute, 314 E. North Ave, Pittsburgh, PA, 15212, USA
| | - Jenna Zimmerman
- Allegheny Health Network Cancer Institute, 314 E. North Ave, Pittsburgh, PA, 15212, USA
| | - Hyun Park
- Allegheny Health Network Cancer Institute, 314 E. North Ave, Pittsburgh, PA, 15212, USA
| | - Catherine Lewis
- Allegheny Health Network Cancer Institute, 314 E. North Ave, Pittsburgh, PA, 15212, USA
| | - Albert Donnenberg
- Allegheny Health Network Cancer Institute, 314 E. North Ave, Pittsburgh, PA, 15212, USA
| | - Ali H Zaidi
- Allegheny Health Network Cancer Institute, 314 E. North Ave, Pittsburgh, PA, 15212, USA
| | - Yong Fan
- Allegheny Health Network Cancer Institute, 314 E. North Ave, Pittsburgh, PA, 15212, USA
| | - Kunhong Xiao
- Center for Proteomics & Artificial Intelligence, Center for Clinical Mass Spectrometry, Allegheny Health Network Cancer Institute, Pittsburgh, PA, 15224, USA
| | - David Bartlett
- Allegheny Health Network Cancer Institute, 314 E. North Ave, Pittsburgh, PA, 15212, USA
| | - Vera Donnenberg
- University of Pittsburgh School of MedicineDepartment of Cardiothoracic SurgeryUPMC Hillman Cancer Center Wagner, Patrick; Allegheny Health Network Cancer Institute, Pittsburgh, USA
| | - Patrick L Wagner
- Allegheny Health Network Cancer Institute, 314 E. North Ave, Pittsburgh, PA, 15212, USA.
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Geng DY, Chen QS, Chen WX, Zhou LS, Han XS, Xie QH, Guo GH, Chen XF, Chen JS, Zhong XP. Molecular targets and mechanisms of different aberrant alternative splicing in metastatic liver cancer. World J Clin Oncol 2024; 15:531-539. [PMID: 38689626 PMCID: PMC11056863 DOI: 10.5306/wjco.v15.i4.531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/29/2024] [Accepted: 03/07/2024] [Indexed: 04/22/2024] Open
Abstract
Metastasis remains a major challenge in the successful management of malignant diseases. The liver is a major site of metastatic disease and a leading cause of death from gastrointestinal malignancies such as colon, stomach, and pancreatic cancers, as well as melanoma, breast cancer, and sarcoma. As an important factor that influences the development of metastatic liver cancer, alternative splicing drives the diversity of RNA transcripts and protein subtypes, which may provide potential to broaden the target space. In particular, the dysfunction of splicing factors and abnormal expression of splicing variants are associated with the occurrence, progression, aggressiveness, and drug resistance of cancers caused by the selective splicing of specific genes. This review is the first to provide a detailed summary of the normal splicing process and alterations that occur during metastatic liver cancer. It will cover the role of alternative splicing in the mechanisms of metastatic liver cancer by examining splicing factor changes, abnormal splicing, and the contribution of hypoxia to these changes during metastasis.
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Affiliation(s)
- De-Yi Geng
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Qing-Shan Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Wan-Xian Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Lin-Sa Zhou
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Xiao-Sha Han
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Qi-Hu Xie
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Geng-Hong Guo
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Xue-Fen Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Jia-Sheng Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Xiao-Ping Zhong
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
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8
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Sbaffone M, Jaffrain-Rea ML, Cappabianca L, Carbonara F, Gianno F, Feola T, Ruggieri M, Zelli V, Maccarone R, Guadagni S, Clementi M, Arcella A, Esposito V, Carozza G, Martelli I, Farina AR, Mackay AR. A Study of Alternative TrkA Splicing Identifies TrkAIII as a Novel Potentially Targetable Participant in PitNET Progression. BIOLOGY 2024; 13:171. [PMID: 38534441 DOI: 10.3390/biology13030171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
Pituitary neuroendocrine tumors (PitNETs) are generally benign but comprise an aggressive, invasive, therapy-resistant, metastatic subset, underpinning a need for novel therapeutic targets. PitNETs exhibit low mutation rates but are associated with conditions linked to alternative splicing, an alternative oncogene pathway activation mechanism. PitNETs express the neurotrophin receptor TrkA, which exhibits oncogenic alternative TrkAIII splicing in other neuroendocrine tumors. We, therefore, assessed whether TrkAIII splicing represents a potential oncogenic participant in PitNETs. TrkAIII splicing was RT-PCR assessed in 53 PitNETs and TrkA isoform(s) expression and activation were assessed by confocal immunofluorescence. TrkAIII splicing was also compared to HIF1α, HIF2α, SF3B1, SRSF2, U2AF1, and JCPyV large T antigen mRNA expression, Xbp1 splicing, and SF3B1 mutation. TrkAIII splicing was detected in all invasive and most non-invasive PitNETs and was significantly elevated in invasive cases. In PitNET lineages, TrkAIII splicing was significantly elevated in invasive PIT1 PitNETs and high in invasive and non-invasive SF1 and TPIT lineages. Immunoreactivity consistent with TrkAIII activation characterized PitNET expressing TrkAIII mRNA, and invasive Pit1 PitNETs exhibited elevated HIF2α expression. TrkAIII splicing did not associate with SF3B1 mutations, altered SF3B1, SRSF2, and U2AF1 or JCPyV large T antigen expression, or Xbp1 splicing. Therefore, TrkAIII splicing is common in PitNETs, is elevated in invasive, especially PIT1 tumors, can result in intracellular TrkAIII activation, and may involve hypoxia. The data support a role for TrkAIII splicing in PitNET pathogenesis and progression and identify TrkAIII as a novel potential target in refractory PitNETs.
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Affiliation(s)
- Maddalena Sbaffone
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Marie-Lise Jaffrain-Rea
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
- Neuromed, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 86077 Pozzilli, Italy
| | - Lucia Cappabianca
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Francesca Carbonara
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Francesca Gianno
- Neuromed, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 86077 Pozzilli, Italy
- Department of Radiological, Oncological and Pathological Sciences, La Sapienza University of Rome, 00185 Rome, Italy
| | - Tiziana Feola
- Neuromed, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 86077 Pozzilli, Italy
- Department of Experimental Medicine, La Sapienza University of Rome, 00185 Rome, Italy
| | - Marianna Ruggieri
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Rita Maccarone
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Stefano Guadagni
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Marco Clementi
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Antonietta Arcella
- Neuromed, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 86077 Pozzilli, Italy
| | - Vincenzo Esposito
- Neuromed, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 86077 Pozzilli, Italy
- Department of Neurology and Psychiatry, La Sapienza University of Rome, 00185 Rome, Italy
| | - Giulia Carozza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Ilaria Martelli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Antonietta Rosella Farina
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Andrew Reay Mackay
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
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9
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Kerry J, Specker EJ, Mizzoni M, Brumwell A, Fell L, Goodbrand J, Rosen MN, Uniacke J. Autophagy-dependent alternative splicing of ribosomal protein S24 produces a more stable isoform that aids in hypoxic cell survival. FEBS Lett 2024; 598:503-520. [PMID: 38281767 DOI: 10.1002/1873-3468.14804] [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: 11/05/2023] [Revised: 12/08/2023] [Accepted: 12/24/2023] [Indexed: 01/30/2024]
Abstract
Cells remodel splicing and translation machineries to mount specialized gene expression responses to stress. Here, we show that hypoxic human cells in 2D and 3D culture models increase the relative abundance of a longer mRNA variant of ribosomal protein S24 (RPS24L) compared to a shorter mRNA variant (RPS24S) by favoring the inclusion of a 22 bp cassette exon. Mechanistically, RPS24L and RPS24S are induced and repressed, respectively, by distinct pathways in hypoxia: RPS24L is induced in an autophagy-dependent manner, while RPS24S is reduced by mTORC1 repression in a hypoxia-inducible factor-dependent manner. RPS24L produces a more stable protein isoform that aids in hypoxic cell survival and growth, which could be exploited by cancer cells in the tumor microenvironment.
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Affiliation(s)
- Jenna Kerry
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Erin J Specker
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Morgan Mizzoni
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Andrea Brumwell
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Leslie Fell
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Jenna Goodbrand
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Michael N Rosen
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - James Uniacke
- Department of Molecular and Cellular Biology, University of Guelph, Canada
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10
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Perales S, Sigamani V, Rajasingh S, Gurusamy N, Bittel D, Czirok A, Radic M, Rajasingh J. scaRNA20 promotes pseudouridylatory modification of small nuclear snRNA U12 and improves cardiomyogenesis. Exp Cell Res 2024; 436:113961. [PMID: 38341080 PMCID: PMC10964393 DOI: 10.1016/j.yexcr.2024.113961] [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: 12/23/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Non-coding RNAs, particularly small Cajal-body associated RNAs (scaRNAs), play a significant role in spliceosomal RNA modifications. While their involvement in ischemic myocardium regeneration is known, their role in cardiac development is unexplored. We investigated scaRNA20's role in iPSC differentiation into cardiomyocytes (iCMCs) via overexpression and knockdown assays. We measured scaRNA20-OE-iCMCs and scaRNA20-KD-iCMCs contractility using Particle Image Velocimetry (PIV), comparing them to control iCMCs. We explored scaRNA20's impact on alternative splicing via pseudouridylation (Ψ) of snRNA U12, analyzing its functional consequences in cardiac differentiation. scaRNA20-OE-iPSC differentiation increased beating colonies, upregulated cardiac-specific genes, activated TP53 and STAT3, and preserved contractility under hypoxia. Conversely, scaRNA20-KD-iCMCs exhibited poor differentiation and contractility. STAT3 inhibition in scaRNA20-OE-iPSCs hindered cardiac differentiation. RNA immunoprecipitation revealed increased Ψ at the 28th uridine of U12 RNA in scaRNA20-OE iCMCs. U12-KD iCMCs had reduced cardiac differentiation, which improved upon U12 RNA introduction. In summary, scaRNA20-OE in iPSCs enhances cardiomyogenesis, preserves iCMC function under hypoxia, and may have implications for ischemic myocardium regeneration.
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Affiliation(s)
- Selene Perales
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Vinoth Sigamani
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sheeja Rajasingh
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Narasimman Gurusamy
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Douglas Bittel
- Department of Biosciences, Kansas City University of Medicine and Biosciences, Kansas City, MO, USA
| | - Andras Czirok
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Marko Radic
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Johnson Rajasingh
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Medicine-Cardiology, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA.
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11
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Mierke CT. Phenotypic Heterogeneity, Bidirectionality, Universal Cues, Plasticity, Mechanics, and the Tumor Microenvironment Drive Cancer Metastasis. Biomolecules 2024; 14:184. [PMID: 38397421 PMCID: PMC10887446 DOI: 10.3390/biom14020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Tumor diseases become a huge problem when they embark on a path that advances to malignancy, such as the process of metastasis. Cancer metastasis has been thoroughly investigated from a biological perspective in the past, whereas it has still been less explored from a physical perspective. Until now, the intraluminal pathway of cancer metastasis has received the most attention, while the interaction of cancer cells with macrophages has received little attention. Apart from the biochemical characteristics, tumor treatments also rely on the tumor microenvironment, which is recognized to be immunosuppressive and, as has recently been found, mechanically stimulates cancer cells and thus alters their functions. The review article highlights the interaction of cancer cells with other cells in the vascular metastatic route and discusses the impact of this intercellular interplay on the mechanical characteristics and subsequently on the functionality of cancer cells. For instance, macrophages can guide cancer cells on their intravascular route of cancer metastasis, whereby they can help to circumvent the adverse conditions within blood or lymphatic vessels. Macrophages induce microchannel tunneling that can possibly avoid mechanical forces during extra- and intravasation and reduce the forces within the vascular lumen due to vascular flow. The review article highlights the vascular route of cancer metastasis and discusses the key players in this traditional route. Moreover, the effects of flows during the process of metastasis are presented, and the effects of the microenvironment, such as mechanical influences, are characterized. Finally, the increased knowledge of cancer metastasis opens up new perspectives for cancer treatment.
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Affiliation(s)
- Claudia Tanja Mierke
- Faculty of Physics and Earth System Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, Leipzig University, 04103 Leipzig, Germany
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12
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Jayashree P, Kalpita M, Judith T, Singh AS, Ashwin K. Role of MicroRNA in Hypoxic Tumours and their Potential as Biomarkers for Early Detection of Cancer. Curr Mol Med 2024; 24:525-536. [PMID: 38310548 DOI: 10.2174/0115665240268661231128094831] [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: 07/06/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 02/06/2024]
Abstract
Hypoxia is a pathophysiological condition characterized by oxygen deficiency in tissues, which negatively affects normal biological functions. It is a typical microenvironment character of almost all solid tumours. Noncoding RNA are small functional RNA molecules that regulate gene expression at chromatin and posttranscriptional levels. Micro-RNAs (miRNAs) are a type of noncoding RNA and are ~12-22 nucleotides long that are crucial in regulating gene expression by partnering with the mRNAs of protein-coding genes. It is widely reported that miRs play an important role in various key processes and pathways during tumour formation, as well as advancement in hypoxic tumors by influencing the HIF pathway. The role of miRNAs in hypoxic tumours, namely in pancreatic, kidney, breast, lung and colorectal, are described. These miRNAs have immense potential as diagnostic and prognostic biomarkers for early cancer detection.
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Affiliation(s)
- Pawar Jayashree
- Department of Biotechnology and Microbiology, VPM's B. N. Bandodkar College of Science, Mumbai University, Mumbai, Maharashtra, India
| | - Mulye Kalpita
- Department of Biotechnology and Microbiology, VPM's B. N. Bandodkar College of Science, Mumbai University, Mumbai, Maharashtra, India
| | - Talker Judith
- Department of Biotechnology and Microbiology, VPM's B. N. Bandodkar College of Science, Mumbai University, Mumbai, Maharashtra, India
| | - Ahirwar Sonu Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, (M.P.), India
| | - Kotnis Ashwin
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, (M.P.), India
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13
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Khalifah BA, Alghamdi SA, Alhasan AH. Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts. Front Bioeng Biotechnol 2023; 11:1244377. [PMID: 38047291 PMCID: PMC10690607 DOI: 10.3389/fbioe.2023.1244377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
Human transcriptome can undergo RNA mis-splicing due to spliceopathies contributing to the increasing number of genetic diseases including muscular dystrophy (MD), Alzheimer disease (AD), Huntington disease (HD), myelodysplastic syndromes (MDS). Intron retention (IR) is a major inducer of spliceopathies where two or more introns remain in the final mature mRNA and account for many intronic expansion diseases. Potential removal of such introns for therapeutic purposes can be feasible when utilizing bioinformatics, catalytic RNAs, and nano-drug delivery systems. Overcoming delivery challenges of catalytic RNAs was discussed in this review as a future perspective highlighting the significance of utilizing synthetic biology in addition to high throughput deep sequencing and computational approaches for the treatment of mis-spliced transcripts.
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Affiliation(s)
- Bashayer A. Khalifah
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ali H. Alhasan
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
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14
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Liu L, Han L, Dong L, He Z, Gao K, Chen X, Guo JC, Zhao Y. The hypoxia-associated genes in immune infiltration and treatment options of lung adenocarcinoma. PeerJ 2023; 11:e15621. [PMID: 37576511 PMCID: PMC10414028 DOI: 10.7717/peerj.15621] [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: 03/23/2023] [Accepted: 06/01/2023] [Indexed: 08/15/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a common lung cancer with a poor prognosis under standard chemotherapy. Hypoxia is a crucial factor in the development of solid tumors, and hypoxia-related genes (HRGs) are closely associated with the proliferation of LUAD cells. Methods In this study, LUAD HRGs were screened, and bioinformatics analysis and experimental validation were conducted. The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases were used to gather LUAD RNA-seq data and accompanying clinical information. LUAD subtypes were identified by unsupervised cluster analysis, and immune infiltration analysis of subtypes was conducted by GSVA and ssGSEA. Cox regression and LASSO regression analyses were used to obtain prognosis-related HRGs. Prognostic analysis was used to evaluate HRGs. Differences in enrichment pathways and immunotherapy were observed between risk groups based on GSEA and the TIDE method. Finally, RT-PCR and in vitro experiments were used to confirm prognosis-related HRG expression in LUAD cells. Results Two hypoxia-associated subtypes of LUAD were distinguished, demonstrating significant differences in prognostic analysis and immunological characteristics between subtypes. A prognostic model based on six HRGs (HK1, PDK3, PFKL, SLC2A1, STC1, and XPNPEP1) was developed for LUAD. HK1, SLC2A1, STC1, and XPNPEP1 were found to be risk factors for LUAD. PDK3 and PFKL were protective factors in LUAD patients. Conclusion This study demonstrates the effect of hypoxia-associated genes on immune infiltration in LUAD and provides options for immunotherapy and therapeutic strategies in LUAD.
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Affiliation(s)
- Liu Liu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Lina Han
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Dong
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Zihao He
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Kai Gao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xu Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jin-Cheng Guo
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yi Zhao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- The Research Center for Ubiquitous Computing Systems (CUbiCS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
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15
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Dery KJ, Kojima H, Kageyama S, Kadono K, Hirao H, Cheng B, Zhai Y, Farmer DG, Kaldas FM, Yuan X, Eltzschiasg HK, Kupiec-Weglinski JW. Alternative splicing of CEACAM1 by hypoxia-inducible factor-1α enhances tolerance to hepatic ischemia in mice and humans. Sci Transl Med 2023; 15:eadf2059. [PMID: 37531413 PMCID: PMC11164245 DOI: 10.1126/scitranslmed.adf2059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 07/13/2023] [Indexed: 08/04/2023]
Abstract
Although alternative splicing (AS) drives transcriptional responses and cellular adaptation to environmental stresses, its contributions in organ transplantation have not been appreciated. We have shown that carcinoembryonic antigen-related cell adhesion molecule (Ceacam1; CD66a), a transmembrane biliary glycoprotein expressed in epithelial, endothelial, and immune cells, determines donor liver transplant quality. Here, we studied how AS of Ceacam1 affects ischemia-reperfusion injury (IRI) in mouse and human livers. We found that the short cytoplasmic isoform Ceacam1-S increased during early acute and late resolution phases of warm IRI injury in mice. Transfection of Ceacam1-deficient mouse hepatocytes with adenoviral Ceacam1-S mitigated hypoxia-induced loss of cellular adhesion by repressing the Ask1/p-p38 cell death pathway. Nucleic acid-blocking morpholinos, designed to selectively induce Ceacam1-S, protected hepatocyte cultures against temperature-induced stress in vitro. Luciferase and chromatin immunoprecipitation assays identified direct binding of hypoxia-inducible factor-1α (Hif-1α) to the mouse polypyrimidine tract binding protein 1 (Ptbp1) promoter region. Dimethyloxalylglycine protected mouse livers from warm IR stress and hepatocellular damage by inhibiting prolyl hydroxylase domain-containing protein 1 and promoting AS of Ceacam1-S. Last, analysis of 46 human donor liver grafts revealed that CEACAM1-S positively correlated with pretransplant HIF1A expression. This also correlated with better transplant outcomes, including reduced TIMP1, total bilirubin, proinflammatory MCP1, CXCL10 cytokines, immune activation markers IL17A, and incidence of delayed complications from biliary anastomosis. This translational study identified mouse Hif-1α-controlled AS of Ceacam1, through transcriptional regulation of Ptbp1 promoter region, as a functional underpinning of hepatoprotection against IR stress and tissue damage in liver transplantation.
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Affiliation(s)
- Kenneth J. Dery
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
| | - Hidenobu Kojima
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
| | - Shoichi Kageyama
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
| | - Kentaro Kadono
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
| | - Hirofumi Hirao
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
| | - Brian Cheng
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
| | - Yuan Zhai
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
| | - Douglas G. Farmer
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
| | - Fady M. Kaldas
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
| | - Xiaoyi Yuan
- Department of Anesthesiology, McGovern Medical School at UTHealth; Houston, TX, 77030 USA
| | - Holger K. Eltzschiasg
- Department of Anesthesiology, McGovern Medical School at UTHealth; Houston, TX, 77030 USA
| | - Jerzy W. Kupiec-Weglinski
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095 USA
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16
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Huang Y, Ping X, Cui Y, Yang H, Bao J, Yin Q, Ailifeire H, Shentu X. Glycolysis Aids in Human Lens Epithelial Cells' Adaptation to Hypoxia. Antioxidants (Basel) 2023; 12:1304. [PMID: 37372033 DOI: 10.3390/antiox12061304] [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: 05/06/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Hypoxic environments are known to trigger pathological damage in multiple cellular subtypes. Interestingly, the lens is a naturally hypoxic tissue, with glycolysis serving as its main source of energy. Hypoxia is essential for maintaining the long-term transparency of the lens in addition to avoiding nuclear cataracts. Herein, we explore the complex mechanisms by which lens epithelial cells adapt to hypoxic conditions while maintaining their normal growth and metabolic activity. Our data show that the glycolysis pathway is significantly upregulated during human lens epithelial (HLE) cells exposure to hypoxia. The inhibition of glycolysis under hypoxic conditions incited endoplasmic reticulum (ER) stress and reactive oxygen species (ROS) production in HLE cells, leading to cellular apoptosis. After ATP was replenished, the damage to the cells was not completely recovered, and ER stress, ROS production, and cell apoptosis still occurred. These results suggest that glycolysis not only performs energy metabolism in the process of HLE cells adapting to hypoxia, but also helps them continuously resist cell apoptosis caused by ER stress and ROS production. Furthermore, our proteomic atlas provides possible rescue mechanisms for cellular damage caused by hypoxia.
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Affiliation(s)
- Yuxin Huang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, China
| | - Xiyuan Ping
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, China
| | - Yilei Cui
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, China
| | - Hao Yang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, China
| | - Jing Bao
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, China
| | - Qichuan Yin
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, China
| | - Hailaiti Ailifeire
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, China
| | - Xingchao Shentu
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, China
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17
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Yadav P, Pandey A, Kakani P, Mutnuru SA, Samaiya A, Mishra J, Shukla S. Hypoxia-induced loss of SRSF2-dependent DNA methylation promotes CTCF-mediated alternative splicing of VEGFA in breast cancer. iScience 2023; 26:106804. [PMID: 37235058 PMCID: PMC10206493 DOI: 10.1016/j.isci.2023.106804] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/21/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Alternative splicing of vascular endothelial growth factor A (VEGFA) generates numerous isoforms with unique roles in tumor angiogenesis, and investigating the underlying mechanism during hypoxia necessitates diligent pursuance. Our research systematically demonstrated that the splicing factor SRSF2 causes the inclusion of exon-8b, leading to the formation of the anti-angiogenic VEGFA-165b isoform under normoxic conditions. Additionally, SRSF2 interacts with DNMT3A and maintains methylation on exon-8a, inhibiting CCCTC-binding factor (CTCF) recruitment and RNA polymerase II (pol II) occupancy, causing exon-8a exclusion and decreased expression of pro-angiogenic VEGFA-165a. Conversely, SRSF2 is downregulated by HIF1α-induced miR-222-3p under hypoxic conditions, which prevents exon-8b inclusion and reduces VEGFA-165b expression. Furthermore, reduced SRSF2 under hypoxia promotes hydroxymethylation on exon-8a, increasing CTCF recruitment, pol II occupancy, exon-8a inclusion, and VEGFA-165a expression. Overall, our findings unveil a specialized dual mechanism of VEGFA-165 alternative splicing, instrumented by the cross-talk between SRSF2 and CTCF, which promotes angiogenesis under hypoxic conditions.
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Affiliation(s)
- Pooja Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Anchala Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Parik Kakani
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Srinivas Abhishek Mutnuru
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Atul Samaiya
- Department of Surgical Oncology, BH, Bhopal, Madhya Pradesh 462016, India
| | - Jharna Mishra
- Department of Pathology, Bansal Hospital (BH), Bhopal, Madhya Pradesh 462016, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
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18
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Liu M, Zhang S, Zhou H, Hu X, Li J, Fu B, Wei M, Huang H, Wu H. The interplay between non-coding RNAs and alternative splicing: from regulatory mechanism to therapeutic implications in cancer. Theranostics 2023; 13:2616-2631. [PMID: 37215575 PMCID: PMC10196821 DOI: 10.7150/thno.83920] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
Alternative splicing (AS) is a common and conserved process in eukaryotic gene regulation. It occurs in approximately 95% of multi-exon genes, greatly enriching the complexity and diversity of mRNAs and proteins. Recent studies have found that in addition to coding RNAs, non-coding RNAs (ncRNAs) are also inextricably linked with AS. Multiple different types of ncRNAs are generated by AS of precursor long non-coding (pre-lncRNAs) or precursor messenger RNAs (pre-mRNAs). Furthermore, ncRNAs, as a novel class of regulators, can participate in AS regulation by interacting with the cis-acting elements or trans-acting factors. Several studies have implicated abnormal expression of ncRNAs and ncRNA-related AS events in the initiation, progression, and therapy resistance in various types of cancers. Therefore, owing to their roles in mediating drug resistance, ncRNAs, AS-related factors and AS-related novel antigens may serve as promising therapeutic targets in cancer treatment. In this review, we summarize the interaction between ncRNAs and AS processes, emphasizing their great influences on cancer, especially on chemoresistance, and highlighting their potential values in clinical treatment.
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Affiliation(s)
- Min Liu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Subo Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Heng Zhou
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P. R. China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Jianing Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Boshi Fu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Shenyang Kangwei Medical Laboratory Analysis Co. LTD, Shenyang, Liaoning, P. R. China
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
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19
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Qian DC, Ulrich BC, Peng G, Zhao H, Conneely KN, Miller AH, Bruner DW, Eldridge RC, Wommack EC, Higgins KA, Shin DM, Saba NF, Smith AK, Burtness B, Park HS, Stokes WA, Beitler JJ, Xiao C. Outcomes Stratification of Head and Neck Cancer Using Pre- and Post-treatment DNA Methylation From Peripheral Blood. Int J Radiat Oncol Biol Phys 2023; 115:1217-1228. [PMID: 36410685 DOI: 10.1016/j.ijrobp.2022.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 10/13/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022]
Abstract
PURPOSE Established prognostic factors for head and neck squamous cell carcinoma (HNSCC) mostly consist of clinical and tumor features assessed before treatment. We report a novel application of DNA methylation in peripheral blood before and after radiation therapy to further improve outcomes stratification. METHODS AND MATERIALS Peripheral blood samples from patients with nonmetastatic HNSCC were obtained for methylation analysis 1 week before and 1 month after radiation therapy. Patients were randomized 1:1 to a Discovery Cohort or a Validation Cohort. In the Discovery Cohort, associations between genome-wide methylation change (posttreatment minus pretreatment) and recurrence-free survival (RFS) as well as overall survival (OS) were evaluated using Cox regression. A methylation risk score (MRS) was then constructed from methylation levels at the top associated sites, filtered for residing within the regulatory regions of genes expressed in cells of hematopoietic lineage. The prognostic value of MRS was separately assessed in the Discovery and Validation Cohorts. RESULTS Between December 2013 and September 2018, 115 patients participated in this study. Human papilloma virus negative status, oral cavity cancer, gastrostomy tube insertion, and higher neutrophil count before radiation therapy were associated with shorter RFS and OS (P < .05). Genes downstream of the methylation sites comprising MRS are HIF1A, SF1, LGALS9, and FUT5, involved in hypoxia response, blood cell maturation, and immune modulation. High MRS (in the top third) was significantly associated with worse RFS (hazard ratio [HR], 7.1; 95% confidence interval [CI], 1.4-35.5; P = .016) and OS (HR, 15.9; 95% CI, 1.6-153.6; P = .017) in the Discovery Cohort, independent of the aforementioned risk factors. These findings were replicated in the Validation Cohort, for which high MRS also independently predicted worse RFS (HR, 10.2; 95%, CI 2.4-43.4; P = .002) and OS (HR, 3.7; 95% CI, 1.3-10.4; P = .015). CONCLUSIONS We successfully trained and validated a signature of DNA methylation in peripheral blood before and after radiation therapy that stratified outcomes among patients with HNSCC, implicating the potential for genomics-tailored surveillance and consolidation treatment.
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Affiliation(s)
- David C Qian
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, GA
| | - Bryan C Ulrich
- Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Gang Peng
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Andrew H Miller
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA
| | - Deborah W Bruner
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA
| | - Ronald C Eldridge
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA
| | - Evanthia C Wommack
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA
| | - Kristin A Higgins
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, GA
| | - Dong M Shin
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA
| | - Nabil F Saba
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA
| | - Barbara Burtness
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Henry S Park
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT
| | - William A Stokes
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, GA
| | - Jonathan J Beitler
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, GA
| | - Canhua Xiao
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA.
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20
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Filipek K, Deryło K, Michalec-Wawiórka B, Zaciura M, González-Ibarra A, Krokowski D, Latoch P, Starosta AL, Czapiński J, Rivero-Müller A, Wawiórka L, Tchórzewski M. Identification of a novel alternatively spliced isoform of the ribosomal uL10 protein. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194890. [PMID: 36328276 DOI: 10.1016/j.bbagrm.2022.194890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
Alternative splicing is one of the key mechanisms extending the complexity of genetic information and at the same time adaptability of higher eukaryotes. As a result, the broad spectrum of isoforms produced by alternative splicing allows organisms to fine-tune their proteome; however, the functions of the majority of alternatively spliced protein isoforms are largely unknown. Ribosomal protein isoforms are one of the groups for which data are limited. Here we report characterization of an alternatively spliced isoform of the ribosomal uL10 protein, named uL10β. The uL10 protein constitutes the core element of the ribosomal stalk structure within the GTPase associated center, which represents the landing platform for translational GTPases - trGTPases. The stalk plays an important role in the ribosome-dependent stimulation of GTP by trGTPases, which confer unidirectional trajectory for the ribosome, allosterically contributing to the speed and accuracy of translation. We have shown that the newly identified uL10β protein is stably expressed in mammalian cells and is primarily located within the nuclear compartment with a minor signal within the cytoplasm. Importantly, uL10β is able to bind to the ribosomal particle, but is mainly associated with 60S and 80S particles; additionally, the uL10β undergoes re-localization into the mitochondria upon endoplasmic reticulum stress induction. Our results suggest a specific stress-related dual role of uL10β, supporting the idea of existence of specialized ribosomes with an altered GTPase associated center.
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Affiliation(s)
- Kamil Filipek
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Barbara Michalec-Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Monika Zaciura
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Alan González-Ibarra
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Przemysław Latoch
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland; Polish-Japanese Academy of Information Technology, Warsaw 02-008, Poland
| | - Agata L Starosta
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Leszek Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
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21
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de Oliveira Freitas Machado C, Schafranek M, Brüggemann M, Hernández Cañás M, Keller M, Di Liddo A, Brezski A, Blümel N, Arnold B, Bremm A, Wittig I, Jaé N, McNicoll F, Dimmeler S, Zarnack K, Müller-McNicoll M. Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia. Nucleic Acids Res 2023; 51:870-890. [PMID: 36620874 PMCID: PMC9881134 DOI: 10.1093/nar/gkac1225] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 01/10/2023] Open
Abstract
Hypoxia induces massive changes in alternative splicing (AS) to adapt cells to the lack of oxygen. Here, we identify the splicing factor SRSF6 as a key factor in the AS response to hypoxia. The SRSF6 level is strongly reduced in acute hypoxia, which serves a dual purpose: it allows for exon skipping and triggers the dispersal of nuclear speckles. Our data suggest that cells use dispersal of nuclear speckles to reprogram their gene expression during hypoxic adaptation and that SRSF6 plays an important role in cohesion of nuclear speckles. Down-regulation of SRSF6 is achieved through inclusion of a poison cassette exon (PCE) promoted by SRSF4. Removing the PCE 3' splice site using CRISPR/Cas9 abolishes SRSF6 reduction in hypoxia. Aberrantly high SRSF6 levels in hypoxia attenuate hypoxia-mediated AS and impair dispersal of nuclear speckles. As a consequence, proliferation and genomic instability are increased, while the stress response is suppressed. The SRSF4-PCE-SRSF6 hypoxia axis is active in different cancer types, and high SRSF6 expression in hypoxic tumors correlates with a poor prognosis. We propose that the ultra-conserved PCE of SRSF6 acts as a tumor suppressor and that its inclusion in hypoxia is crucial to reduce SRSF6 levels. This may prevent tumor cells from entering the metastatic route of hypoxia adaptation.
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Affiliation(s)
- Camila de Oliveira Freitas Machado
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - Michal Schafranek
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Mirko Brüggemann
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | | | - Mario Keller
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Antonella Di Liddo
- Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Andre Brezski
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Nicole Blümel
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Benjamin Arnold
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Anja Bremm
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Nicolas Jaé
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - François McNicoll
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - Kathi Zarnack
- Correspondence may also be addressed to Kathi Zarnack.
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22
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The Alternative TrkAIII Splice Variant, a Targetable Oncogenic Participant in Human Cutaneous Malignant Melanoma. Cells 2023; 12:cells12020237. [PMID: 36672171 PMCID: PMC9856487 DOI: 10.3390/cells12020237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Post-therapeutic relapse, poor survival rates and increasing incidence justify the search for novel therapeutic targets and strategies in cutaneous malignant melanoma (CMM). Within this context, a potential oncogenic role for TrkA in CMM is suggested by reports of NTRK1 amplification, enhanced TrkA expression and intracellular TrkA activation associated with poor prognosis. TrkA, however, exhibits tumour-suppressing properties in melanoma cell lines and has recently been reported not to be associated with CMM progression. To better understand these contradictions, we present the first analysis of potential oncogenic alternative TrkA mRNA splicing, associated with TrkA immunoreactivity, in CMMs, and compare the behaviour of fully spliced TrkA and the alternative TrkAIII splice variant in BRAF(V600E)-mutated A375 melanoma cells. Alternative TrkA splicing in CMMs was associated with unfolded protein response (UPR) activation. Of the several alternative TrkA mRNA splice variants detected, TrkAIII was the only variant with an open reading frame and, therefore, oncogenic potential. TrkAIII expression was more frequent in metastatic CMMs, predominated over fully spliced TrkA mRNA expression in ≈50% and was invariably linked to intracellular phosphorylated TrkA immunoreactivity. Phosphorylated TrkA species resembling TrkAIII were also detected in metastatic CMM extracts. In A375 cells, reductive stress induced UPR activation and promoted TrkAIII expression and, in transient transfectants, promoted TrkAIII and Akt phosphorylation, enhancing resistance to reductive stress-induced death, which was prevented by lestaurtinib and entrectinib. In contrast, fully spliced TrkA was dysfunctional in A375 cells. The data identify fully spliced TrkA dysfunction as a novel mechanism for reducing melanoma suppression, support a causal relationship between reductive stress, UPR activation, alternative TrkAIII splicing and TrkAIII activation and characterise a targetable oncogenic pro-survival role for TrkAIII in CMM.
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23
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Taze C, Drakouli S, Samiotaki M, Panayotou G, Simos G, Georgatsou E, Mylonis I. Short-term hypoxia triggers ROS and SAFB mediated nuclear matrix and mRNA splicing remodeling. Redox Biol 2022; 58:102545. [PMID: 36427398 PMCID: PMC9692040 DOI: 10.1016/j.redox.2022.102545] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022] Open
Abstract
The cellular response to hypoxia, in addition to HIF-dependent transcriptional reprogramming, also involves less characterized transcription-independent processes, such as alternative splicing of the VEGFA transcript leading to the production of the proangiogenic VEGF form. We now show that this event depends on reorganization of the splicing machinery, triggered after short-term hypoxia by ROS production and intranuclear redistribution of the nucleoskeletal proteins SAFB1/2. Exposure to low oxygen causes fast dissociation of SAFB1/2 from the nuclear matrix, which is reversible, inhibited by antioxidant treatment, and also observed under normoxia when the mitochondrial electron transport chain is blocked. This is accompanied by altered interactions between SAFB1/2 and the splicing machinery, translocation of kinase SRPK1 to the cytoplasm, and dephosphorylation of RS-splicing factors. Depletion of SAFB1/2 under normoxia phenocopies the hypoxic and ROS-mediated switch in VEGF mRNA splicing. These data suggest that ROS-dependent remodeling of the nuclear architecture can promote production of splicing variants that facilitate adaptation to hypoxia.
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Affiliation(s)
- Chrysa Taze
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 41500, Greece
| | - Sotiria Drakouli
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 41500, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, BSRC “Alexander Fleming”, Vari, 16672, Greece
| | - George Panayotou
- Institute for Bioinnovation, BSRC “Alexander Fleming”, Vari, 16672, Greece
| | - George Simos
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 41500, Greece,Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, H4A 3T2, Canada
| | - Eleni Georgatsou
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 41500, Greece
| | - Ilias Mylonis
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 41500, Greece,Corresponding author.
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24
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Bartoszewska S, Collawn JF, Bartoszewski R. The Role of the Hypoxia-Related Unfolded Protein Response (UPR) in the Tumor Microenvironment. Cancers (Basel) 2022; 14:4870. [PMID: 36230792 PMCID: PMC9562011 DOI: 10.3390/cancers14194870] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/19/2022] Open
Abstract
Despite our understanding of the unfolded protein response (UPR) pathways, the crosstalk between the UPR and the complex signaling networks that different cancers utilize for cell survival remains to be, in most cases, a difficult research barrier. A major problem is the constant variability of different cancer types and the different stages of cancer as well as the complexity of the tumor microenvironments (TME). This complexity often leads to apparently contradictory results. Furthermore, the majority of the studies that have been conducted have utilized two-dimensional in vitro cultures of cancer cells that were exposed to continuous hypoxia, and this approach may not mimic the dynamic and cyclic conditions that are found in solid tumors. Here, we discuss the role of intermittent hypoxia, one of inducers of the UPR in the cellular component of TME, and the way in which intermittent hypoxia induces high levels of reactive oxygen species, the activation of the UPR, and the way in which cancer cells modulate the UPR to aid in their survival. Although the past decade has resulted in defining the complex, novel non-coding RNA-based regulatory networks that modulate the means by which hypoxia influences the UPR, we are now just to beginning to understand some of the connections between hypoxia, the UPR, and the TME.
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Affiliation(s)
- Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - James F. Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rafal Bartoszewski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a Street, 50-383 Wroclaw, Poland
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25
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Yuan H, Liu X, Wang Z, Ren Y, Li Y, Gao C, Jiao T, Cai Y, Yang Y, Zhao S. Alternative splicing signature of alveolar type II epithelial cells of Tibetan pigs under hypoxia-induced. Front Vet Sci 2022; 9:984703. [PMID: 36187824 PMCID: PMC9523697 DOI: 10.3389/fvets.2022.984703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) allows the generation of multiple transcript variants from a single gene and affects biological processes by generating protein diversity in organisms. In total, 41,642 AS events corresponding to 9,924 genes were identified, and SE is the most abundant alternatively spliced type. The analysis of functional categories demonstrates that alternatively spliced differentially expressed genes (DEGs) were enriched in the MAPK signaling pathway and hypoxia-inducible factor 1 (HIF-1) signaling pathway. Proteoglycans in cancer between the normoxic (21% O2, TN and LN) and hypoxic (2% O2, TL and LL) groups, such as SLC2A1, HK1, HK2, ENO3, and PFKFB3, have the potential to rapidly proliferate alveolar type II epithelial (ATII) cells by increasing the intracellular levels of glucose and quickly divert to anabolic pathways by glycolysis intermediates under hypoxia. ACADL, EHHADH, and CPT1A undergo one or two AS types with different frequencies in ATII cells between TN and TL groups (excluding alternatively spliced DEGs shared between normoxic and hypoxic groups), and a constant supply of lipids might be obtained either from the circulation or de novo synthesis for better growth of ATII cells under hypoxia condition. MCM7 and MCM3 undergo different AS types between LN and LL groups (excluding alternatively spliced DEGs shared between normoxic and hypoxic groups), which may bind to the amino-terminal PER-SIM-ARNT domain and the carboxyl terminus of HIF-1α to maintain their stability. Overall, AS and expression levels of candidate mRNAs between Tibetan pigs and Landrace pigs revealed by RNA-seq suggest their potential involvement in the ATII cells grown under hypoxia conditions.
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Affiliation(s)
- Haonan Yuan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xuanbo Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zhengwen Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yue Ren
- Academy of Agriculture and Animal Husbandry Sciences, Institute of Animal Husbandry and Veterinary Medicine, Lhasa, China
| | - Yongqing Li
- Xinjiang Academy of Animal Sciences, Xinjiang, China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ting Jiao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Yuan Cai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yanan Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Yanan Yang
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Shengguo Zhao
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26
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Venkatakrishnan G, Parvathi VD. Decoding the mechanism of vascular morphogenesis to explore future prospects in targeted tumor therapy. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:178. [PMID: 36036322 DOI: 10.1007/s12032-022-01810-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/26/2022] [Indexed: 11/27/2022]
Abstract
The growth and formation of blood vessels is an undeniably fundamental biological process crucial to controlling overall development of an organism. This phenomenon consists of two separate processes, commencing with vasculogenesis, which refers to the process of blood vessel formation strictly in embryonic stages, via de novo endothelial cell synthesis. Angiogenesis continues the formation of the vascular network via sprouting and splitting. Tumor growth is dependent on the growth and supply of blood vessels around the tumor mass. Extracellular matrix (ECM) molecules can promote angiogenesis by establishing a vascular network and sequestering pro-angiogenic growth factors. Although the methods by which tumor-associated fibroblasts (which differ in phenotype from normal fibroblasts) influence angiogenesis are unknown, they are thought to be a major source of growth factors and cytokines that attract endothelial cells. Chemokines and growth factors (sourced from macrophages and neutrophils) are also regulators of angiogenesis. When considered as a whole, the tumor microenvironment is a heterogenous and dynamic mass of tissue, composed of a plethora of cell types and an ECM that can fundamentally control the pathological angiogenic switch. Angiogenesis is involved in numerous diseases, and understanding the various mechanisms surrounding this phenomenon is key to finding cures.
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Affiliation(s)
- Gayathri Venkatakrishnan
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, 600116, India
| | - Venkatachalam Deepa Parvathi
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, 600116, India.
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27
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Zhou L, Jiang J, Huang Z, Jin P, Peng L, Luo M, Zhang Z, Chen Y, Xie N, Gao W, Nice EC, Li JQ, Chen HN, Huang C. Hypoxia-induced lncRNA STEAP3-AS1 activates Wnt/β-catenin signaling to promote colorectal cancer progression by preventing m6A-mediated degradation of STEAP3 mRNA. Mol Cancer 2022; 21:168. [PMID: 35986274 PMCID: PMC9392287 DOI: 10.1186/s12943-022-01638-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background Hypoxia, a typical hallmark of solid tumors, exhibits an essential role in the progression of colorectal cancer (CRC), in which the dysregulation of long non-coding RNAs (lncRNAs) is frequently observed. However, the underlying mechanisms are not clearly defined. Methods The TCGA database was analyzed to identify differential lncRNA expression involved in hypoxia-induced CRC progression. qRT-PCR was conducted to validate the upregulation of lncRNA STEAP3-AS1 in CRC cell lines and tumor-bearing mouse and zebrafish models under hypoxia. ChIP-qRT-PCR was used to detect the transcriptional activation of STEAP3-AS1 mediated by HIF-1α. RNA-seq, fluorescent in situ hybridization, RNA pulldown, RNA immunoprecipitation, co-immunoprecipitation, immunofluorescence and immunoblot experiments were used to ascertain the involved mechanisms. Functional assays were performed in both in vitro and in vivo models to investigate the regulatory role of STEAP3-AS1/STEAP3/Wnt/β-catenin axis in CRC proliferation and metastasis. Results Here, we identified a hypoxia-induced antisense lncRNA STEAP3-AS1 that was highly expressed in clinical CRC tissues and positively correlated with poor prognosis of CRC patients. Upregulation of lncRNA STEAP3-AS1, which was induced by HIF-1α-mediated transcriptional activation, facilitated the proliferation and metastasis of CRC cells both in vitro and in vivo. Mechanistically, STEAP3-AS1 interacted competitively with the YTH domain-containing family protein 2 (YTHDF2), a N6-methyladenosine (m6A) reader, leading to the disassociation of YTHDF2 with STEAP3 mRNA. This effect protected STEAP3 mRNA from m6A-mediated degradation, enabling the high expression of STEAP3 protein and subsequent production of cellular ferrous iron (Fe2+). Increased Fe2+ levels elevated Ser 9 phosphorylation of glycogen synthase kinase 3 beta (GSK3β) and inhibited its kinase activity, thus releasing β-catenin for nuclear translocation and subsequent activation of Wnt signaling to support CRC progression. Conclusions Taken together, our study highlights the mechanisms of lncRNA STEAP3-AS1 in facilitating CRC progression involving the STEAP3-AS1/STEAP3/Wnt/β-catenin axis, which may provide novel diagnostic biomarkers or therapeutic targets to benefit CRC treatment. Graphical abstract Hypoxia-induced HIF-1α transcriptionally upregulates the expression of lncRNA STEAP3-AS1, which interacts competitively with YTHDF2, thus upregulating mRNA stability of STEAP3 and consequent STEAP3 protein expression. The enhanced STEAP3 expression results in production of cellular ferrous iron (Fe2+), which induces the Ser 9 phosphorylation and inactivation of GSK3β, releasing β-catenin for nuclear translocation and contributing to subsequent activation of Wnt signaling to promote CRC progression.![]() Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01638-1.
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Chen M, Chen Z, Lin Z, Ding X, Liang T. Utilization of hypoxia-derived gene signatures to predict clinical outcomes and immune checkpoint blockade therapy responses in prostate cancer. Front Genet 2022; 13:922074. [PMID: 36035150 PMCID: PMC9412200 DOI: 10.3389/fgene.2022.922074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Increasing evidences show a clinical significance in the interaction between hypoxia and prostate cancer. However, reliable prognostic signatures based on hypoxia have not been established yet.Methods: We screened hypoxia-related gene modules by weighted gene co-expression network analysis (WGCNA) and established a hypoxia-related prognostic risk score (HPRS) model by univariate Cox and LASSO-Cox analyses. In addition, enriched pathways, genomic mutations, and tumor-infiltrating immune cells in HPRS subgroups were analyzed and compared. HPRS was also estimated to predict immune checkpoint blockade (ICB) therapy response.Results: A hypoxia-related 22-gene prognostic model was established. Furthermore, three independent validation cohorts showed moderate performance in predicting biochemical recurrence-free (BCR-free) survival. HPRS could be a useful tool in selecting patients who can benefit from ICB therapy. The CIBERSORT results in our study demonstrated that hypoxia might act on multiple T cells, activated NK cells, and macrophages M1 in various ways, suggesting that hypoxia might exert its anti-tumor effects by suppressing T cells and NK cells.Conclusion: Hypoxia plays an important role in the progression of prostate cancer. The hypoxia-derived signatures are promising biomarkers to predict biochemical recurrence-free survival and ICB therapy responses in patients with prostate cancer.
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Affiliation(s)
- Minhua Chen
- Emergency & Intensive Care Unit Center, Department of Intensive Care Unit, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Zhang Chen
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zongbin Lin
- Emergency & Intensive Care Unit Center, Department of Intensive Care Unit, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xiang Ding
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Tianyu Liang
- Emergency & Intensive Care Unit Center, Department of Intensive Care Unit, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Tianyu Liang,
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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Jinna N, Rida P, Smart M, LaBarge M, Jovanovic-Talisman T, Natarajan R, Seewaldt V. Adaptation to Hypoxia May Promote Therapeutic Resistance to Androgen Receptor Inhibition in Triple-Negative Breast Cancer. Int J Mol Sci 2022; 23:ijms23168844. [PMID: 36012111 PMCID: PMC9408190 DOI: 10.3390/ijms23168844] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/03/2022] [Accepted: 08/06/2022] [Indexed: 12/27/2022] Open
Abstract
Triple-negative breast cancer (TNBC) surpasses other BC subtypes as the most challenging to treat due to its lack of traditional BC biomarkers. Nearly 30% of TNBC patients express the androgen receptor (AR), and the blockade of androgen production and AR signaling have been the cornerstones of therapies for AR-positive TNBC. However, the majority of women are resistant to AR-targeted therapy, which is a major impediment to improving outcomes for the AR-positive TNBC subpopulation. The hypoxia signaling cascade is frequently activated in the tumor microenvironment in response to low oxygen levels; activation of the hypoxia signaling cascade allows tumors to survive despite hypoxia-mediated interference with cellular metabolism. The activation of hypoxia signaling networks in TNBC promotes resistance to most anticancer drugs including AR inhibitors. The activation of hypoxia network signaling occurs more frequently in TNBC compared to other BC subtypes. Herein, we examine the (1) interplay between hypoxia signaling networks and AR and (2) whether hypoxia and hypoxic stress adaptive pathways promote the emergence of resistance to therapies that target AR. We also pose the well-supported question, “Can the efficacy of androgen-/AR-targeted treatments be enhanced by co-targeting hypoxia?” By critically examining the evidence and the complex entwinement of these two oncogenic pathways, we argue that the simultaneous targeting of androgen biosynthesis/AR signaling and hypoxia may enhance the sensitivity of AR-positive TNBCs to AR-targeted treatments, derail the emergence of therapy resistance, and improve patient outcomes.
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Affiliation(s)
- Nikita Jinna
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Max Smart
- Rowland Hall, Salt Lake City, UT 84102, USA
| | - Mark LaBarge
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Victoria Seewaldt
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
- Correspondence:
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Lv Y, Lv Y, Wang Z, Yuan K, Zeng Y. Noncoding RNAs as sensors of tumor microenvironmental stress. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:224. [PMID: 35842651 PMCID: PMC9288030 DOI: 10.1186/s13046-022-02433-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/06/2022] [Indexed: 12/19/2022]
Abstract
The tumor microenvironment (TME) has been demonstrated to modulate the biological behavior of tumors intensively. Multiple stress conditions are widely observed in the TME of many cancer types, such as hypoxia, inflammation, and nutrient deprivation. Recently, accumulating evidence demonstrates that the expression levels of noncoding RNAs (ncRNAs) are dramatically altered by TME stress, and the dysregulated ncRNAs can in turn regulate tumor cell proliferation, metastasis, and drug resistance. In this review, we elaborate on the signal transduction pathways or epigenetic pathways by which hypoxia-inducible factors (HIFs), inflammatory factors, and nutrient deprivation in TME regulate ncRNAs, and highlight the pivotal roles of TME stress-related ncRNAs in tumors. This helps to clarify the molecular regulatory networks between TME and ncRNAs, which may provide potential targets for cancer therapy.
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Affiliation(s)
- Yue Lv
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yinghao Lv
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Zhen Wang
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.,Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Kefei Yuan
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China. .,Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yong Zeng
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China. .,Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Guadagni S, Masedu F, Fiorentini G, Sarti D, Fiorentini C, Guadagni V, Apostolou P, Papasotiriou I, Parsonidis P, Valenti M, Ricevuto E, Bruera G, Farina AR, Mackay AR, Clementi M. Circulating tumour cell gene expression and chemosensitivity analyses: predictive accuracy for response to multidisciplinary treatment of patients with unresectable refractory recurrent rectal cancer or unresectable refractory colorectal cancer liver metastases. BMC Cancer 2022; 22:660. [PMID: 35710393 PMCID: PMC9202660 DOI: 10.1186/s12885-022-09770-3] [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: 02/07/2022] [Accepted: 06/08/2022] [Indexed: 01/19/2023] Open
Abstract
Background Patients with unresectable recurrent rectal cancer (RRC) or colorectal cancer (CRC) with liver metastases, refractory to at least two lines of traditional systemic therapy, may receive third line intraarterial chemotherapy (IC) and targeted therapy (TT) using drugs selected by chemosensitivity and tumor gene expression analyses of liquid biopsy-derived circulating tumor cells (CTCs). Methods In this retrospective study, 36 patients with refractory unresectable RRC or refractory unresectable CRC liver metastases were submitted for IC and TT with agents selected by precision oncotherapy chemosensitivity assays performed on liquid biopsy-derived CTCs, transiently cultured in vitro, and by tumor gene expression in the same CTC population, as a ratio to tumor gene expression in peripheral mononuclear blood cells (PMBCs) from the same individual. The endpoint was to evaluate the predictive accuracy of a specific liquid biopsy precision oncotherapy CTC purification and in vitro culture methodology for a positive RECIST 1.1 response to the therapy selected. Results Our analyses resulted in evaluations of 94.12% (95% CI 0.71–0.99) for sensitivity, 5.26% (95% CI 0.01–0.26) for specificity, a predictive value of 47.06% (95% CI 0.29–0.65) for a positive response, a predictive value of 50% (95% CI 0.01–0.98) for a negative response, with an overall calculated predictive accuracy of 47.22% (95% CI 0.30–0.64). Conclusions This is the first reported estimation of predictive accuracy derived from combining chemosensitivity and tumor gene expression analyses on liquid biopsy-derived CTCs, transiently cultured in vitro which, despite limitations, represents a baseline and benchmark which we envisage will be improve upon by methodological and technological advances and future clinical trials.
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Affiliation(s)
- Stefano Guadagni
- Department of Applied Clinical and Biotechnological Sciences, University of L'Aquila, 67100, L'Aquila, Italy.
| | - Francesco Masedu
- Department of Applied Clinical and Biotechnological Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Giammaria Fiorentini
- Department of Oncology and Hematology, Azienda Ospedaliera "Ospedali Riuniti Marche Nord", Pesaro, Italy
| | - Donatella Sarti
- Department of Oncology and Hematology, Azienda Ospedaliera "Ospedali Riuniti Marche Nord", Pesaro, Italy
| | - Caterina Fiorentini
- Department of Prevention and Sports Medicine, University Hospital Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Veronica Guadagni
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | | | | | - Marco Valenti
- Department of Applied Clinical and Biotechnological Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Enrico Ricevuto
- Department of Applied Clinical and Biotechnological Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Gemma Bruera
- Department of Applied Clinical and Biotechnological Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Antonietta R Farina
- Department of Applied Clinical and Biotechnological Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Andrew R Mackay
- Department of Applied Clinical and Biotechnological Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Marco Clementi
- Department of Applied Clinical and Biotechnological Sciences, University of L'Aquila, 67100, L'Aquila, Italy
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Schumacher A, Roumans N, Rademakers T, Joris V, Eischen-Loges MJ, van Griensven M, LaPointe VL. Enhanced Microvasculature Formation and Patterning in iPSC–Derived Kidney Organoids Cultured in Physiological Hypoxia. Front Bioeng Biotechnol 2022; 10:860138. [PMID: 35782512 PMCID: PMC9240933 DOI: 10.3389/fbioe.2022.860138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/05/2022] [Indexed: 01/10/2023] Open
Abstract
Stem cell–derived kidney organoids have been shown to self-organize from induced pluripotent stem cells into most important renal structures. However, the structures remain immature in culture and contain endothelial networks with low connectivity and limited organoid invasion. Furthermore, the nephrons lose their phenotype after approximately 25 days. To become applicable for future transplantation, further maturation in vitro is essential. Since kidneys in vivo develop in hypoxia, we studied the modulation of oxygen availability in culture. We hypothesized that introducing long-term culture at physiological hypoxia, rather than the normally applied non-physiological, hyperoxic 21% O2, could initiate angiogenesis, lead to enhanced growth factor expression and improve the endothelial patterning. We therefore cultured the kidney organoids at 7% O2 instead of 21% O2 for up to 25 days and evaluated nephrogenesis, growth factor expression such as VEGF-A and vascularization. Whole mount imaging revealed a homogenous morphology of the endothelial network with enhanced sprouting and interconnectivity when the kidney organoids were cultured in hypoxia. Three-dimensional vessel quantification confirmed that the hypoxic culture led to an increased average vessel length, likely due to the observed upregulation of VEGFA-189 and VEGFA-121, and downregulation of the antiangiogenic protein VEGF-A165b measured in hypoxia. This research indicates the importance of optimization of oxygen availability in organoid systems and the potential of hypoxic culture conditions in improving the vascularization of organoids.
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Affiliation(s)
- Anika Schumacher
- Department of Cell Biology–Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
| | - Nadia Roumans
- Department of Cell Biology–Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
| | - Timo Rademakers
- Department of Cell Biology–Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
| | - Virginie Joris
- Department of Cell Biology–Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
| | - Maria José Eischen-Loges
- Department of Cell Biology–Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
| | - Martijn van Griensven
- Department of Cell Biology–Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
| | - Vanessa L.S. LaPointe
- Department of Cell Biology–Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
- *Correspondence: Vanessa L.S. LaPointe,
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A Novel Hypoxia-Related Gene Signature with Strong Predicting Ability in Non-Small-Cell Lung Cancer Identified by Comprehensive Profiling. Int J Genomics 2022; 2022:8594658. [PMID: 35634481 PMCID: PMC9135579 DOI: 10.1155/2022/8594658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 12/10/2021] [Accepted: 04/16/2022] [Indexed: 12/24/2022] Open
Abstract
Background Non-small-cell lung cancer (NSCLC) is the most common malignant tumor among males and females worldwide. Hypoxia is a typical feature of the tumor microenvironment, and it affects cancer development. Circular RNAs (circRNAs) have been reported to sponge miRNAs to regulate target gene expression and play an essential role in tumorigenesis and progression. This study is aimed at identifying whether circRNAs could be used as the diagnostic biomarkers for NSCLC. Methods The heterogeneity of samples in this study was assessed by principal component analysis (PCA). Furthermore, the Gene Expression Omnibus (GEO) database was normalized by the affy R package. We further screened the differentially expressed genes (DEGs) and differentially expressed circular RNAs (DEcircRNAs) using the DEseq2 R package. Moreover, we analyzed the Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of DEGs using the cluster profile R package. Besides, the Gene Set Enrichment Analysis (GSEA) was used to identify the biological function of DEGs. The interaction between DEGs and the competing endogenous RNAs (ceRNA) network was detected using STRING and visualized using Cytoscape. Starbase predicted the miRNAs of target hub genes, and miRanda predicted the target miRNAs of circRNAs. The RNA-seq profiler and clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. Then, the variables were assessed by the univariate and multivariate Cox proportional hazard regression models. Significant variables in the univariate Cox proportional hazard regression model were included in the multivariate Cox proportional hazard regression model to analyze the association between the variables of clinical features. Furthermore, the overall survival of variables was determined by the Kaplan-Meier survival curve, and the time-dependent receiver operating characteristic (ROC) curve analysis was used to calculate and validate the risk score in NSCLC patients. Moreover, predictive nomograms were constructed and used to predict the prognostic features between the high-risk and low-risk score groups. Results We screened a total of 2039 DEGs, including 1293 upregulated DEGs and 746 downregulated DEGs in hypoxia-treated A549 cells. A549 cells treated with hypoxia had a total of 70 DEcircRNAs, including 21 upregulated and 49 downregulated DEcircRNAs, compared to A549 cells treated with normoxia. The upregulated genes were significantly enriched in 284 GO terms and 42 KEGG pathways, while the downregulated genes were significantly enriched in 184 GO terms and 25 KEGG pathways. Moreover, the function analysis by GSEA showed enrichment in the enzyme-linked receptor protein signaling pathway, hypoxia-inducible factor- (HIF-) 1 signaling pathway, and G protein-coupled receptor (GPCR) downstream signaling. Furthermore, six hub modules and 10 hub genes, CDC45, EXO1, PLK1, RFC4, CCNB1, CDC6, MCM10, DLGAP5, AURKA, and POLE2, were identified. The ceRNA network was constructed, and it consisted of 4 circRNAs, 14 miRNAs, and 38 mRNAs. The ROC curve was constructed and calculated. The area under the curve (AUC) value was 0.62, and the optimal threshold was 0.28. Based on the optimal threshold, the patients were divided into the high-risk score and low-risk score groups. The survival rate in the high-risk score group was lower than that in the low-risk score group. The expression of SERPINE1, STC2, and LPCAT1; clinical stage; and age of the patient were significantly correlated with the high-risk score. Moreover, nomograms were established based on the risk factors in multivariate analysis, and the median survival time, 3-year survival probability, and 5-year survival were possibly predicted according to nomograms. Conclusion The ceRNA network associated with NSCLC was identified, and the hub genes, circRNAs, might act as the potential biomarkers for NSCLC.
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Yang Y, Yuan H, Yang Q, Cai Y, Ren Y, Li Y, Gao C, Zhao S. Post-transcriptional regulation through alternative splicing in the lungs of Tibetan pigs under hypoxia. Gene 2022; 819:146268. [PMID: 35124151 DOI: 10.1016/j.gene.2022.146268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/22/2022] [Accepted: 01/28/2022] [Indexed: 11/15/2022]
Abstract
In multicellular organisms, alternative splicing (AS) is central to the regulation of multiple biological processes. To further elucidate the adaptive strategy of AS in the lungs of Tibetan pigs in response to hypoxia, we identified and analyzed five basic AS types and 59,930 AS events in 18,179 genes. We found that approximately 65.10% of the total expressed genes underwent AS in the lungs of Tibetan pigs at a high altitude (TH). The frequencies of AS events were similar among the different groups (5.06-5.30 events in each gene on average). Skipped exons (SEs) were the predominant type of AS event, followed by mutually exclusive exons (MXEs), alternative 3' splice sites (A3SSs) and alternative 5' splice sites (A5SSs). Retained introns (RIs), the remaining type of AS event, showed lower frequencies. Further comparison analysis of differentially expressed genes (DEGs) and differentially spliced genes (DSGs) identified 2,209 differential splicing events in the above 18,000 expressed genes, including 918 increased and 1,291 decreased splicing events between the TH and Tibetan pigs at a low altitude (TL) groups. We identified 227 hypoxia-related genes involved in lung development that were differentially regulated through AS. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis clearly identified many DEGs and DSGs at high or low altitude. Seven pathways in the top 20 enriched KEGG terms overlapped for the DEGs and DSGs, including the chemokine signaling pathway, B cell receptor signaling pathway, and cytokine-cytokine receptor interaction, which exert many immunoregulatory and inflammatory actions critical to the lung under hypoxia. Twelve pathways overlapped in hypoxic DEGs and DSGs and included antigen processing, presentation and biosynthesis. GO analysis of the DEGs and DSGs among the four groups showed that numerous GO terms were enriched in the biological category, and the proportion of genes with downregulated expression was greater among 227 hypoxic genes than that of all genes. The results suggest that AS plays an essential role in the regulation of gene expression during hypoxia and that numerous genes involved in lung development are differentially regulated through AS.
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Affiliation(s)
- Yanan Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Haonan Yuan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Qiaoli Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuan Cai
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yue Ren
- Academy of Agriculture and Animal Husbandry Sciences, Institute of Animal Husbandry and Veterinary Medicine, Lhasa, Xizang, China
| | - Yongqing Li
- Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China.
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YTHDF1 upregulation mediates hypoxia-dependent breast cancer growth and metastasis through regulating PKM2 to affect glycolysis. Cell Death Dis 2022; 13:258. [PMID: 35319018 PMCID: PMC8940925 DOI: 10.1038/s41419-022-04711-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/15/2022] [Accepted: 03/03/2022] [Indexed: 02/05/2023]
Abstract
N6-methyladenosine modification is the most common RNA modification mechanism in mammals. YTHDF1, a m6A reader, can recognize the m6A of mRNAs to facilitate the interaction with the mRNA ribosome assembly and recruitment of translation initiators to promote translation. From a clinical perspective, YTHDF1 upregulation is frequently observed in breast cancer, but its involvement in those cancer-related events is still unclear. Here we report that YTHDF1 is a cancer driver capable of facilitating the proliferation and invasion of breast cancer cells as well as enhancing tumorigenicity and metastasis through promoting glycolysis. We found that tumor hypoxia can transcriptionally induce HIF1α and post-transcriptionally inhibit the expression of miR-16-5p to promote YTHDF1 expression, which could sequentially enhance tumor glycolysis by upregulating PKM2 and eventually increase the tumorigenesis and metastasis potential of breast cancer cells. Inhibiting YTHDF1 via gene knockdown or miR-16-5p would significantly abolish YTHDF1-dependent tumor growth and metastasis. In summary, we identified the role of the YTHDF1-PKM2 signal axis in the occurrence and development of breast cancer, which can be used as a potential target for breast cancer treatment.
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Lei Y, Xiao J, Zhao W, Liu F, Sui Y, Wang K, Liu Y. Myc pathway-guided alternative splicing events predict the overall survival of lung squamous cell carcinoma. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2043449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Youming Lei
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Jian Xiao
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, People’s Republic of China
| | - Wei Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Fanghao Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Yi Sui
- Department of IVD Medical Marketing, 3D Medicine Inc., Shanghai, People’s Republic of China
| | - Kun Wang
- Department of Thoracic Surgery, Anning First People’s Hospital (Kunming Fourth People’s Hospital), Seventh Affiliated Hospital of Dali University, Kunming, People’s Republic of China
| | - Yinqiang Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
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Peng Q, Zhou Y, Oyang L, Wu N, Tang Y, Su M, Luo X, Wang Y, Sheng X, Ma J, Liao Q. Impacts and mechanisms of alternative mRNA splicing in cancer metabolism, immune response, and therapeutics. Mol Ther 2022; 30:1018-1035. [PMID: 34793975 PMCID: PMC8899522 DOI: 10.1016/j.ymthe.2021.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/11/2021] [Indexed: 02/08/2023] Open
Abstract
Alternative pre-mRNA splicing (AS) provides the potential to produce diversity at RNA and protein levels. Disruptions in the regulation of pre-mRNA splicing can lead to diseases. With the development of transcriptome and genome sequencing technology, increasing diseases have been identified to be associated with abnormal splicing of mRNAs. In tumors, abnormal alternative splicing frequently plays critical roles in cancer pathogenesis and may be considered as new biomarkers and therapeutic targets for cancer intervention. Metabolic abnormalities and immune disorders are important hallmarks of cancer. AS produces multiple different isoforms and diversifies protein expression, which is utilized by the immune and metabolic reprogramming systems to expand gene functions. The abnormal splicing events contributed to tumor progression, partially due to effects on immune response and metabolic reprogramming. Herein, we reviewed the vital role of alternative splicing in regulating cancer metabolism and immune response. We discussed how alternative splicing regulates metabolic reprogramming of cancer cells and antitumor immune response, and the possible strategies to targeting alternative splicing pathways or splicing-regulated metabolic pathway in the context of anticancer immunotherapy. Further, we highlighted the challenges and discuss the perspectives for RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Jian Ma
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China.
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Ferrucci L, Wilson DM, Donegà S, Gorospe M. The energy-splicing resilience axis hypothesis of aging. NATURE AGING 2022; 2:182-185. [PMID: 37118371 DOI: 10.1038/s43587-022-00189-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- Luigi Ferrucci
- Biomedical Research Center, National Institute on Aging, National Institute of Health, Baltimore, MD, USA.
| | - David M Wilson
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Stefano Donegà
- Biomedical Research Center, National Institute on Aging, National Institute of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Biomedical Research Center, National Institute on Aging, National Institute of Health, Baltimore, MD, USA
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Establishment and External Validation of a Hypoxia-Derived Gene Signature for Robustly Predicting Prognosis and Therapeutic Responses in Glioblastoma Multiforme. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7858477. [PMID: 35155681 PMCID: PMC8837434 DOI: 10.1155/2022/7858477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/04/2022] [Indexed: 12/11/2022]
Abstract
Objective Hypoxia presents a salient feature investigated in most solid tumors that holds key roles in cancer progression, including glioblastoma multiforme (GBM). Here, we aimed to construct a hypoxia-derived gene signature for identifying the high-risk GBM patients to guide adjuvant therapy and precision nursing based on signs of hypoxia. Methods We retrospectively analyzed the transcriptome profiling and clinicopathological characteristics of GBM from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) cohorts. A series of bioinformatic and machine learning methods were comprehensively applied for establishing a hypoxia-derived gene signature in prediction of overall survival, disease-free survival, disease-specific survival, and progression-free survival. The predictive efficacy of this model was assessed with receiver operator characteristic (ROC) and uni- and multivariate cox regression analysis. The associations of this signature with tumor microenvironment and immunotherapeutic response predictors were evaluated across GBM. RT-qPCR and western blotting were presented for validating the expression of ALDH3B1 and CTSZ in human glioma cell lines (U251, SHG-44, and U87) and normal glial cell line HEB. Results Among hallmarks of cancer, hypoxia acted as a prominent risk factor of GBM prognosis. A hypoxia-derived gene signature displayed efficient ability in predicting clinical outcomes. High risk score indicated undesirable prognosis, recurrence, and progression of GBM. Moreover, this risk score displayed positive correlations to immunity and stromal activation. Combining immunotherapeutic response predictors, high-risk patients more benefited from immunotherapy. ALDH3B1 and CTSZ expression had prominent upregulation in glioma cells than normal glial cells. Conclusion Collectively, this hypoxia-derived gene signature could become a reliable biomarker for predicting prognosis and therapeutic response and providing theoretical support for hypoxia treatment and precision nursing of GBM patients.
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A Novel Nomogram Combining Alternative Splicing Events and Clinical Factors for Prognosis Prediction in Head and Neck Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:4552445. [PMID: 35103061 PMCID: PMC8800633 DOI: 10.1155/2022/4552445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/18/2022]
Abstract
Due to limitations of sensitive biomarkers, the clinical prognosis of patients with head and neck squamous cell carcinoma (HNSCC) remains poor. Alternative splicing (AS) is the basis of both transcriptome and proteome richness, so more and more evidence indicates an important relationship between AS and tumor progression. The aim of this study was to offer a comprehensive analysis on AS events and then investigate its potentials as a new biomarker for patients with squamous cell carcinoma of the head and neck. In this study, univariate assays were conducted to examine the prognosis-associated AS events, and we screened 4068 survival-related AS events in 2573 genes. Then, the AS events related to survival were further determined and analyzed using LASSO regression and multivariate assays, and an eleven-AS signature was developed. Kaplan–Meier assays indicated patients with high-risk scores exhibited a shorter OS than those with low-risk scores. Multivariate assays further demonstrated that the signature’s risk score was independent of HNSCC survivals. Meanwhile, we analyzed the clinical association of AS-based prognostic signature in HNSCC patients and observed that tumor specimens with advanced stages and grades exhibited a high risk score. In addition, the results of survival nomogram revealed that predicted outcomes and actual outcomes were highly consistent. Overall, our group showed an eleven-AS signature of HNSCC, which could be regarded as a separate prognostic factor.
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Zhang H, He C, Guo X, Fang Y, Lai Q, Wang X, Pan X, Li H, Qin K, Li A, Liu S, Li Q. DDX39B contributes to the proliferation of colorectal cancer through direct binding to CDK6/CCND1. Cell Death Dis 2022; 8:30. [PMID: 35046400 PMCID: PMC8770491 DOI: 10.1038/s41420-022-00827-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 12/01/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022]
Abstract
DDX39B (also called UAP56 or BAT1) which is a kind of DEAD-box family helicase plays pivotal roles in mRNA binding, splicing, and export. It has been found upregulated in many kinds of tumors as an oncogene. Nevertheless, the underlying molecular mechanisms of DDX39B in the proliferation of human colorectal cancer (CRC) remain fairly elusive. In our study, function experiments including the CCK8 and colony formation assay revealed that DDX39B facilitates CRC proliferation in vitro. DDX39B knockdown cells were administered for the orthotopic CRC tumor xenograft mouse model, after which tumor growth was monitored and immunohistochemistry (IHC) was performed to prove that DDX39B can also facilitates CRC proliferation in vivo. Flow cytometry demonstrated that DDX39B promotes the proliferation of CRC cells by driving the cell cycle from G0/G1 phase to the S phase. Mechanistically, RNA-binding protein immunoprecipitation-sequencing (RIP-seq) confirmed that DDX39B binds directly to the first exon of the CDK6/CCND1 pre-mRNA and upregulates their expression. Splicing experiments in vitro using a RT-PCR and gel electrophoresis assay confirmed that DDX39B promotes CDK6/CCND1 pre-mRNA splicing. Rescue experiments indicated that CDK6/CCND1 is a downstream effector of DDX39B-mediated CRC cell proliferation. Collectively, our results demonstrated that DDX39B and CDK6/CCND1 direct interactions serve as a CRC proliferation promoter, which can accelerate the G1/S phase transition to enhance CRC proliferation, and can offer novel and emerging treatment strategies targeting this cell proliferation-promoting gene.
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He G, Peng X, Wei S, Yang S, Li X, Huang M, Tang S, Jin H, Liu J, Zhang S, Zheng H, Fan Q, Liu J, Yang L, Li H. Exosomes in the hypoxic TME: from release, uptake and biofunctions to clinical applications. Mol Cancer 2022; 21:19. [PMID: 35039054 PMCID: PMC8762953 DOI: 10.1186/s12943-021-01440-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 10/02/2021] [Indexed: 02/06/2023] Open
Abstract
Hypoxia is a remarkable trait of the tumor microenvironment (TME). When facing selective pressure, tumor cells show various adaptive characteristics, such as changes in the expression of cancer hallmarks (increased proliferation, suppressed apoptosis, immune evasion, and so on) and more frequent cell communication. Because of the adaptation of cancer cells to hypoxia, exploring the association between cell communication mediators and hypoxia has become increasingly important. Exosomes are important information carriers in cell-to-cell communication. Abundant evidence has proven that hypoxia effects in the TME are mediated by exosomes, with the occasional formation of feedback loops. In this review, we equally focus on the biogenesis and heterogeneity of cancer-derived exosomes and their functions under hypoxia and describe the known and potential mechanism ascribed to exosomes and hypoxia. Notably, we call attention to the size change of hypoxic cancer cell-derived exosomes, a characteristic long neglected, and propose some possible effects of this size change. Finally, jointly considering recent developments in the understanding of exosomes and tumors, we describe noteworthy problems in this field that urgently need to be solved for better research and clinical application.
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Affiliation(s)
- Guangpeng He
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xueqiang Peng
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Shibo Wei
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Shuo Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xinyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Mingyao Huang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Shilei Tang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Hongyuan Jin
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Jiaxing Liu
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Sheng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Hongyu Zheng
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Qing Fan
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Jingang Liu
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Liang Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
| | - Hangyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
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Khurshid S, Montes M, Comiskey DF, Shane B, Matsa E, Jung F, Brown C, Bid HK, Wang R, Houghton PJ, Roberts R, Rigo F, Chandler D. Splice-switching of the insulin receptor pre-mRNA alleviates tumorigenic hallmarks in rhabdomyosarcoma. NPJ Precis Oncol 2022; 6:1. [PMID: 35017650 PMCID: PMC8752779 DOI: 10.1038/s41698-021-00245-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/16/2021] [Indexed: 01/07/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is an aggressive pediatric tumor with a poor prognosis for metastasis and recurrent disease. Large-scale sequencing endeavors demonstrate that Rhabdomyosarcomas have a dearth of precisely targetable driver mutations. However, IGF-2 signaling is known to be grossly altered in RMS. The insulin receptor (IR) exists in two alternatively spliced isoforms, IR-A and IR-B. The IGF-2 signaling molecule binds both its innate IGF-1 receptor as well as the insulin receptor variant A (IR-A) with high affinity. Mitogenic and proliferative signaling via the canonical IGF-2 pathway is, therefore, augmented by IR-A. This study shows that RMS patients express increased IR-A levels compared to control tissues that predominantly express the IR-B isoform. We also found that Hif-1α is significantly increased in RMS tumors, portraying their hypoxic phenotype. Concordantly, the alternative splicing of IR adapts to produce more IR-A in response to hypoxic stress. Upon examining the pre-mRNA structure of the gene, we identified a potential hypoxia-responsive element, which is also the binding site for the RNA-binding protein CUG-BP1 (CELF1). We designed Splice Switching Oligonucleotides (SSO) against this binding site to decrease IR-A levels in RMS cell lines and, consequently, rescue the IR-B expression levels. SSO treatment resulted in a significant reduction in cell proliferation, migration, and angiogenesis. Our data shows promising insight into how impeding the IGF-2 pathway by reducing IR-A expression mitigates tumor growth. It is evident that Rhabdomyosarcomas use IR alternative splicing as yet another survival strategy that can be exploited as a therapeutic intervention in conjunction with already established anti-IGF-1 receptor therapies.
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Affiliation(s)
- Safiya Khurshid
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Matias Montes
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Daniel F Comiskey
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Brianne Shane
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Eleftheria Matsa
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Francesca Jung
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Chelsea Brown
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | | | - Ruoning Wang
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Peter J Houghton
- Greenhey Children's Cancer Research Institute, UT Health, San Antonio, TX, 78229, USA
| | - Ryan Roberts
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, 92010, USA
| | - Dawn Chandler
- Department of Pediatrics and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA.
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Liu Q, Zhang H, Yang X, Liu X, Yin F, Guo P, Yin Y, Zheng K, Yang Z, Han Y. Systemic characterization of alternative splicing related to prognosis, immune infiltration, and drug sensitivity analysis in ovarian cancer. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:126. [PMID: 35282039 PMCID: PMC8848412 DOI: 10.21037/atm-21-6422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022]
Abstract
Background Alternative splicing (AS) plays an essential role in tumorigenesis and progression. This study intended to construct an innovative prognostic model based on AS events to gain more precise survival prediction and search for potential therapeutic targets in ovarian cancer. Methods Seven types of AS events in ovarian serous cystadenocarcinoma (OV) patients with RNA-seq were obtained using The Cancer Genome Atlas (TCGA) SpliceSeq tool and database. Cox and Kaplan-Meier curve analyses were employed to establish the prognostic models. Relying on drug sensitivity data from the CellMiner database, Genomics of Drug Sensitivity (GDS) was adopted to estimate the platinum-sensitive analysis. Furthermore, a prognostic splicing factor (SF)-AS network was constructed using Cytoscape. Finally, in order to explore the influence of the tumor microenvironment on the prognosis of OV patients, we first combined a similar network fusion and consensus clustering (SNF-CC) algorithm to identify three OV subtypes based on survival-related AS events and then utilized single-sample Gene Set Enrichment Analysis (ssGSEA) method to perform immune cell infiltration analysis. Results A total of 48,049 AS events and 21,841 related genes were selected from 318 OV samples, and 2,206 AS events associated with disease-free survival (DFS) were identified. Multivariate Cox and Kaplan-Meier curve analyses were then employed to establish the prognostic models. Receiver operating characteristic (ROC) analysis from 0.59 to 0.75 showed that these models were highly efficient in distinguishing patient survival. GDS was adopted with the CellMiner database to provide some insights for platinum-sensitive analysis of OV. Furthermore, a prognostic SF-AS network, which discovered a significant connection between SFs and prognostic AS genes, was constructed using Cytoscape. The combined SNF-CC algorithm revealed three distinct OV subtypes based on the prognostic AS events, and the associations between this novel molecular classification and immune cell infiltration were further explored. Conclusions We developed a powerful prognostic AS signature for OV and provided a deeper understanding of SF-AS network regulatory mechanisms, as well as platinum-sensitive and cancer immune microenvironments. These results revealed various candidate biomarkers and potential targets for OV treatment strategies.
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Affiliation(s)
- Qingyang Liu
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Hao Zhang
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Xiaocheng Yang
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Xuesong Liu
- School of Health Professions, Yingkou Vocational and Technical College, Yingkou, China
| | - Fanxing Yin
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Panpan Guo
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Yuhan Yin
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Kaijiang Zheng
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Zhuo Yang
- Department of Gynecology, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital & Institute), Shenyang, China
| | - Yanshuo Han
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
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Parker KA, Robinson NJ, Schiemann WP. The role of RNA processing and regulation in metastatic dormancy. Semin Cancer Biol 2022; 78:23-34. [PMID: 33775829 PMCID: PMC8464634 DOI: 10.1016/j.semcancer.2021.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023]
Abstract
Tumor dormancy is a major contributor to the lethality of metastatic disease, especially for cancer patients who develop metastases years-to-decades after initial diagnosis. Indeed, tumor cells can disseminate during early disease stages and persist in new microenvironments at distal sites for months, years, or even decades before initiating metastatic outgrowth. This delay between primary tumor remission and metastatic relapse is known as "dormancy," during which disseminated tumor cells (DTCs) acquire quiescent states in response to intrinsic (i.e., cellular) and extrinsic (i.e., microenvironmental) signals. Maintaining dormancy-associated phenotypes requires DTCs to activate transcriptional, translational, and post-translational mechanisms that engender cellular plasticity. RNA processing is emerging as an essential facet of cellular plasticity, particularly with respect to the initiation, maintenance, and reversal of dormancy-associated phenotypes. Moreover, dysregulated RNA processing, particularly that associated with alternative RNA splicing and expression of noncoding RNAs (ncRNAs), can occur in DTCs to mediate intrinsic and extrinsic metastatic dormancy. Here we review the pathophysiological impact of alternative RNA splicing and ncRNAs in promoting metastatic dormancy and disease recurrence in human cancers.
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Affiliation(s)
- Kimberly A. Parker
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nathaniel J. Robinson
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - William P. Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA,Corresponding Author: William P. Schiemann, Case Comprehensive Cancer Center, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH 44106 Phone: 216-368-5763.
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Chen J, Wang G, Zhang D, Luo X, Zhang D, Zhang Y. Construction of novel hypoxia-related gene model for prognosis and tumor microenvironment in endometrial carcinoma. Front Endocrinol (Lausanne) 2022; 13:1075431. [PMID: 36589842 PMCID: PMC9797861 DOI: 10.3389/fendo.2022.1075431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Endometrial cancer is currently one of the three most common female reproductive cancers, which seriously threatens women's lives and health. Hypoxia disrupts the tumor microenvironment, thereby affecting tumor progression and drug resistance. METHODS We established hypoxia-related gene model to predict patient prognosis and 1-, 3-, and 5-year overall survival rates. Then, the expression level of hypoxia-related genes and survival data were extracted for comprehensive analysis by Cox regression analysis, and the model was established. RESULTS We analyzed the survival and prognosis of patients in the high and low-risk groups. The Kaplan-Meier curve showed that the low-risk group is associated with a better survival rate. The 1-, 3-, and 5-year AUC values of the model were 0.680, 0.698, and 0.687, respectively. Finally, we found that LAG3 may be a potential immune checkpoint for endometrial cancer. CONCLUSION We found four hypoxia-related genes (ANXA2, AKAP12, NR3C1, and GPI) associated with prognosis. The hypoxia-related gene model can also predict prognosis and tumor microenvironment in endometrial cancer.
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Affiliation(s)
- Junfeng Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guocheng Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Donghai Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaomei Luo
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Da Zhang
- Department of Gynecological Oncology, Changchun Center Hospital, Changchun, Jilin, China
- *Correspondence: Yongli Zhang, ; Da Zhang,
| | - Yongli Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yongli Zhang, ; Da Zhang,
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Junk D, Krämer S, Broschewitz J, Laura H, Massa C, Moulla Y, Hoang NA, Monecke A, Eichfeld U, Bechmann I, Lordick F, Seliger B, Kallendrusch S. Human tissue cultures of lung cancer predict patient susceptibility to immune-checkpoint inhibition. Cell Death Discov 2021; 7:264. [PMID: 34564709 PMCID: PMC8464600 DOI: 10.1038/s41420-021-00651-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/17/2021] [Accepted: 09/07/2021] [Indexed: 12/24/2022] Open
Abstract
Despite novel immunotherapies being approved and established for the treatment of non-small cell lung cancer (NSCLC), ex vivo models predicting individual patients' responses to immunotherapies are missing. Especially immune modulating therapies with moderate response rates urge for biomarkers and/or assays to determine individual prediction of treatment response and investigate resistance mechanisms. Here, we describe a standardized ex vivo tissue culture model to investigate individual tumor responses. NSCLC tissue cultures preserve morphological characteristics of the baseline tumor specimen for up to 12 days ex vivo and also maintain T-cell function for up to 10 days ex vivo. A semi-automated analysis of proliferating and apoptotic tumor cells was used to evaluate tissue responses to the PD-1 inhibitor nivolumab (n = 12), from which two cases could be successfully correlated to the clinical outcome. T-cell responses upon nivolumab treatment were investigated by flow cytometry and multispectral imaging. Alterations in the frequency of the Treg population and reorganization of tumor tissues could be correlated to nivolumab responsiveness ex vivo. Thus, our findings not only demonstrate the functionality of T cells in NSCLC slice cultures up to 10 days ex vivo, but also suggests this model for stratifying patients for treatment selection and to investigate in depth the tumor-associated T-cell regulation.
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Affiliation(s)
- David Junk
- Institute of Anatomy, University of Leipzig, Liebigstr. 13, 04103, Leipzig, Germany
| | - Sebastian Krämer
- Department of Visceral, Transplantation, Thoracic and Vascular Surgery, University Hospital Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
| | - Johannes Broschewitz
- Department of Visceral and Thoracic Surgery, University Hospital Brandenburg, Gehrbelliner Straße 38, 16816, Neuruppin, Germany
| | - Hennig Laura
- Institute of Anatomy, University of Leipzig, Liebigstr. 13, 04103, Leipzig, Germany
| | - Chiara Massa
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, 06112, Halle, Germany
| | - Yousef Moulla
- Department of Visceral, Transplantation, Thoracic and Vascular Surgery, University Hospital Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
| | - Ngoc Anh Hoang
- University Cancer Center Leipzig, University Hospital Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
| | - Astrid Monecke
- Institute of Pathology, University Hospital Leipzig, Liebigstraße 26, 04103, Leipzig, Germany
| | - Uwe Eichfeld
- Department of Visceral, Transplantation, Thoracic and Vascular Surgery, University Hospital Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
| | - Ingo Bechmann
- Institute of Anatomy, University of Leipzig, Liebigstr. 13, 04103, Leipzig, Germany
| | - Florian Lordick
- University Cancer Center Leipzig, University Hospital Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, 06112, Halle, Germany
| | - Sonja Kallendrusch
- Institute of Anatomy, University of Leipzig, Liebigstr. 13, 04103, Leipzig, Germany.
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Wang S, Xu G, Chao F, Zhang C, Han D, Chen G. HNRNPC Promotes Proliferation, Metastasis and Predicts Prognosis in Prostate Cancer. Cancer Manag Res 2021; 13:7263-7276. [PMID: 34584453 PMCID: PMC8464311 DOI: 10.2147/cmar.s330713] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/13/2021] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION The incidence of prostate cancer remains high worldwide, while exploring new therapeutic targets for prostate cancer is essential. Heterogeneous nuclear ribonucleoproteins have been proved to regulate tumorigeneses in various cancers. This study aimed to explore the role of HNRNPC in prostate cancer progression. METHODS HNRNPC expression and its correlation with clinical features and immune infiltration were analyzed by bioinformatics analysis. The effects of HNRNPC on prostate cell proliferation, migration, and invasion were accessed by EdU, colony formation, transwell, and wound-healing assays. RESULTS The expression level of HNRNPC was significantly increased in prostate cancer tissues and was correlated with the T stage, N stage, Gleason score, PSA level, residual tumors, overall survival, disease-specific survival, and progression-free interval of prostate cancer patients. Silencing HNRNPC inhibited the proliferation and metastasis of prostate cancer cells. The expression of HNRNPC was negatively correlated with the infiltration level of most immune cells in prostate cancer. Mechanistically, HNRNPC may function through regulating gene expression at the posttranscriptional level. CONCLUSION HNRNPC could be a potential marker for the treatment and prognosis prediction of prostate cancer.
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Affiliation(s)
- Shiyu Wang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Guoxiong Xu
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
| | - Fan Chao
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Cong Zhang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Dunsheng Han
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Gang Chen
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
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Functional Characteristics and Regulated Expression of Alternatively Spliced Tissue Factor: An Update. Cancers (Basel) 2021; 13:cancers13184652. [PMID: 34572880 PMCID: PMC8471299 DOI: 10.3390/cancers13184652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/11/2022] Open
Abstract
In human and mouse, alternative splicing of tissue factor's primary transcript yields two mRNA species: one features all six TF exons and encodes full-length tissue factor (flTF), and the other lacks exon 5 and encodes alternatively spliced tissue factor (asTF). flTF, which is oftentimes referred to as "TF", is an integral membrane glycoprotein due to the presence of an alpha-helical domain in its C-terminus, while asTF is soluble due to the frameshift resulting from the joining of exon 4 directly to exon 6. In this review, we focus on asTF-the more recently discovered isoform of TF that appears to significantly contribute to the pathobiology of several solid malignancies. There is currently a consensus in the field that asTF, while dispensable to normal hemostasis, can activate a subset of integrins on benign and malignant cells and promote outside-in signaling eliciting angiogenesis; cancer cell proliferation, migration, and invasion; and monocyte recruitment. We provide a general overview of the pioneering, as well as more recent, asTF research; discuss the current concepts of how asTF contributes to cancer progression; and open a conversation about the emerging utility of asTF as a biomarker and a therapeutic target.
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