1
|
Liu C, Han X, Zhang S, Huang M, Guo B, Zhao Z, Yang S, Jin J, Pu W, Yu H. The role of NCAPH in cancer treatment. Cell Signal 2024; 121:111262. [PMID: 38901722 DOI: 10.1016/j.cellsig.2024.111262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Many solid tumors frequently overexpress Non-SMC Condensin I Complex Subunit H (NCAPH), and new studies suggest that NCAPH may be a target gene for clinical cancer therapy. Numerous investigations have shown that a variety of transcription factors, including as MYBL2, FOXP3, GATA3, and OTC1, can stimulate the transcription of NCAPH. Additionally, NCAPH stimulates many oncogenic signaling pathways, such as β-Catenin/PD-L1, PI3K/AKT/SGK3, MEK/ERK, AURKB/AKT/mTOR, PI3K/PDK1/AKT, and Chk1/Chk2. Tumor immune microenvironment modification and tumor growth, apoptosis, metastasis, stemness, and treatment resistance all depend on these signals. NCAPH has the ability to form complexes with other proteins that are involved in glycolysis, DNA damage repair, and chromatin remodeling. This review indicates that NCAPH expression in most malignant tumors is associated with poor prognosis and low recurrence-free survival.
Collapse
Affiliation(s)
- Caiyan Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiao Han
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Siqi Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Manru Huang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Bin Guo
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zixuan Zhao
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shenshen Yang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jun Jin
- International Education College, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Weiling Pu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Haiyang Yu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| |
Collapse
|
2
|
Zhou X, Ying H, Sun Y, Zhang W, Luo P, Zhu S, Zhang J. Homologous recombination deficiency (HRD) is associated with better prognosis and possibly causes a non-inflamed tumour microenvironment in nasopharyngeal carcinoma. J Pathol Clin Res 2024; 10:e12391. [PMID: 39104056 DOI: 10.1002/2056-4538.12391] [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: 01/09/2024] [Revised: 06/18/2024] [Accepted: 06/30/2024] [Indexed: 08/07/2024]
Abstract
Homologous recombination deficiency (HRD) score is a reliable indicator of genomic instability. The significance of HRD in nasopharyngeal carcinoma (NPC), particularly its influence on prognosis and the immune microenvironment, has yet to be adequately explored. Understanding HRD status comprehensively can offer valuable insights for guiding precision treatment. We utilised three cohorts to investigate HRD status in NPC: the Zhujiang cohort from local collection and the Hong Kong (SRA288429) and Singapore (SRP035573) cohorts from public datasets. The GATK (genome analysis toolkit) best practice process was employed to investigate germline and somatic BRCA1/2 mutations and various bioinformatics tools and algorithms to examine the association between HRD status and clinical molecular characteristics. We found that individuals with a negative HRD status (no-HRD) exhibited a higher risk of recurrence [hazard ratio (HR), 1.43; 95% confidence interval (CI), 2.03-333.76; p = 0.012] in the Zhujiang cohort, whereas, in the Singapore cohort, they experienced a higher risk of mortality (HR, 26.04; 95% CI, 1.43-34.21; p = 0.016) compared with those in the HRD group. In vitro experiments demonstrated that NPC cells with BRCA1 knockdown exhibit heightened sensitivity to chemoradiotherapy. Furthermore, the HRD group showed significantly higher tumour mutational burden and tumour neoantigen burden levels than the no-HRD group. Immune infiltration analysis indicated that HRD tissues tend to have a non-inflamed tumour microenvironment. In conclusion, patients with HRD exhibit a comparatively favourable prognosis in NPC, possibly associated with a non-inflammatory immune microenvironment. These findings have positive implications for treatment stratification, enabling the selection of more precise and effective therapeutic approaches and aiding in the prediction of treatment response and prognosis to a certain extent.
Collapse
Affiliation(s)
- Xinyi Zhou
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Haoxuan Ying
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Yujie Sun
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Wenda Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Shuhan Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| |
Collapse
|
3
|
Santos JAV, Silva D, Marques MPM, Batista de Carvalho LAE. Platinum-based chemotherapy: trends in organic nanodelivery systems. NANOSCALE 2024; 16:14640-14686. [PMID: 39037425 DOI: 10.1039/d4nr01483a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Despite the investment in platinum drugs research, cisplatin, carboplatin and oxaliplatin are still the only Pt-based compounds used as first line treatments for several cancers, with a few other compounds being approved for administration in some Asian countries. However, due to the severe and worldwide impact of oncological diseases, there is an urge for improved chemotherapeutic approaches. Furthermore, the pharmaceutical application of platinum complexes is hindered by their inherent toxicity and acquired resistance. Nanodelivery systems rose as a key strategy to overcome these challenges, with recognized versatility and ability towards improving the safety, bioavailability and efficacy of the available drugs. Among the known nanocarriers, organic systems have been widely applied, taking advantage of their potential as drug vehicles. Researchers have mainly focused on the development of lipidic and polymeric carriers, including supramolecular structures, with an overall improvement of encapsulated platinum complexes. Herein, an overview of recent trends and strategies is presented, with the main focus on the encapsulation of platinum compounds into organic nanocarriers, showcasing the evolution in the design and development of these promising systems. This comprehensive review highlights formulation methods as well as characterization procedures, providing insights that may be helpful for the development of novel platinum nanocarriers aiming at future pharmaceutical applications.
Collapse
Affiliation(s)
- João A V Santos
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
| | - Daniela Silva
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
| | - Maria Paula M Marques
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
- Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Luís A E Batista de Carvalho
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
| |
Collapse
|
4
|
Uboveja A, Aird KM. Interplay between altered metabolism and DNA damage and repair in ovarian cancer. Bioessays 2024; 46:e2300166. [PMID: 38873912 DOI: 10.1002/bies.202300166] [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: 08/31/2023] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/15/2024]
Abstract
Ovarian cancer is the most lethal gynecological malignancy and is often associated with both DNA repair deficiency and extensive metabolic reprogramming. While still emerging, the interplay between these pathways can affect ovarian cancer phenotypes, including therapeutic resistance to the DNA damaging agents that are standard-of-care for this tumor type. In this review, we will discuss what is currently known about cellular metabolic rewiring in ovarian cancer that may impact DNA damage and repair in addition to highlighting how specific DNA repair proteins also promote metabolic changes. We will also discuss relevant data from other cancers that could be used to inform ovarian cancer therapeutic strategies. Changes in the choice of DNA repair mechanism adopted by ovarian cancer are a major factor in promoting therapeutic resistance. Therefore, the impact of metabolic reprogramming on DNA repair mechanisms in ovarian cancer has major clinical implications for targeted combination therapies for the treatment of this devastating disease.
Collapse
Affiliation(s)
- Apoorva Uboveja
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Katherine M Aird
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
5
|
Kulkarni S, Gajjar K, Madhusudan S. Poly (ADP-ribose) polymerase inhibitor therapy and mechanisms of resistance in epithelial ovarian cancer. Front Oncol 2024; 14:1414112. [PMID: 39135999 PMCID: PMC11317305 DOI: 10.3389/fonc.2024.1414112] [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: 04/08/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
Advanced epithelial ovarian cancer is the commonest cause of gynaecological cancer deaths. First-line treatment for advanced disease includes a combination of platinum-taxane chemotherapy (post-operatively or peri-operatively) and maximal debulking surgery whenever feasible. Initial response rate to chemotherapy is high (up to 80%) but most patients will develop recurrence (approximately 70-90%) and succumb to the disease. Recently, poly-ADP-ribose polymerase (PARP) inhibition (by drugs such as Olaparib, Niraparib or Rucaparib) directed synthetic lethality approach in BRCA germline mutant or platinum sensitive disease has generated real hope for patients. PARP inhibitor (PARPi) maintenance therapy can prolong survival but therapeutic response is not sustained due to intrinsic or acquired secondary resistance to PARPi therapy. Reversion of BRCA1/2 mutation can lead to clinical PARPi resistance in BRCA-germline mutated ovarian cancer. However, in the more common platinum sensitive sporadic HGSOC, the clinical mechanisms of development of PARPi resistance remains to be defined. Here we provide a comprehensive review of the current status of PARPi and the mechanisms of resistance to therapy.
Collapse
Affiliation(s)
- Sanat Kulkarni
- Department of Medicine, Sandwell and West Birmingham NHS Trust, West Bromwich, United Kingdom
| | - Ketankumar Gajjar
- Department of Gynaecological Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Srinivasan Madhusudan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| |
Collapse
|
6
|
Xiong J, Deng C, Fu Y, Tang J, Xie J, Chen Y. Prognostic and Potential Therapeutic Roles of PRKDC Expression in Lung Cancer. Mol Biotechnol 2024:10.1007/s12033-024-01209-3. [PMID: 39044064 DOI: 10.1007/s12033-024-01209-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/06/2024] [Indexed: 07/25/2024]
Abstract
PRKDC is a key factor involved in the ligation step of the non-homologous end joining pathway. Its dysfunction has proven to be a biomarker for radiosensitivity of cancer cells. However, the prognostic value of PRKDC and its underlying mechanisms have not been clarified yet. In this study, we found that PRKDC overexpressed in lung adenocarcinoma (LUAD) and is significantly related to unfavorable survival, while downregulation of PRKDC is link to inflamed tumor immune signature. Our further in vitro results also showed a potent antitumor efficacy of PRKDC inhibitors alone or combined with cisplatin in human lung cancer cells. This study demonstrated that PRKDC is a potential prognostic biomarker, immunotherapy target, and promising combination candidate for chemotherapy for lung cancer, and highlighted the potential of PRKDC-targeted inhibitors for the treatment of lung cancer.
Collapse
Affiliation(s)
- Jiani Xiong
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
- Cancer Bio-immunotherapy Center, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Cuimin Deng
- Department of Pharmacy, QuanZhou Women's and Children's Hospital, Quanzhou, Fujian Province, People's Republic of China
| | - YunRong Fu
- Department of Pharmacology, College of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China
| | - Jingji Tang
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
- Cancer Bio-immunotherapy Center, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Jieming Xie
- Department of Pharmacology, College of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China.
| | - Yu Chen
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China.
- Cancer Bio-immunotherapy Center, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China.
| |
Collapse
|
7
|
Lee JJ, Kang HJ, Kim D, Lim SO, Kim SS, Kim G, Kim S, Lee JK, Kim J. expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer. BMC Bioinformatics 2024; 25:236. [PMID: 38997639 PMCID: PMC11241885 DOI: 10.1186/s12859-024-05854-y] [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: 11/10/2023] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Homologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy and poly ADP-ribose polymerase (PARP) inhibitors. One of the conventional approaches to HRD prognostication has generally centered on identifying deleterious mutations within the BRCA1/2 genes, along with quantifying the genomic scars, such as Genomic Instability Score (GIS) estimation with scarHRD. However, the scarHRD method has limitations in scenarios involving tumors bereft of corresponding germline data. Although several RNA-seq-based HRD prediction algorithms have been developed, they mainly support cohort-wise classification, thereby yielding HRD status without furnishing an analogous quantitative metric akin to scarHRD. This study introduces the expHRD method, which operates as a novel transcriptome-based framework tailored to n-of-1-style HRD scoring. RESULTS The prediction model has been established using the elastic net regression method in the Cancer Genome Atlas (TCGA) pan-cancer training set. The bootstrap technique derived the HRD geneset for applying the expHRD calculation. The expHRD demonstrated a notable correlation with scarHRD and superior performance in predicting HRD-high samples. We also performed intra- and extra-cohort evaluations for clinical feasibility in the TCGA-OV and the Genomic Data Commons (GDC) ovarian cancer cohort, respectively. The innovative web service designed for ease of use is poised to extend the realms of HRD prediction across diverse malignancies, with ovarian cancer standing as an emblematic example. CONCLUSIONS Our novel approach leverages the transcriptome data, enabling the prediction of HRD status with remarkable precision. This innovative method addresses the challenges associated with limited available data, opening new avenues for utilizing transcriptomics to inform clinical decisions.
Collapse
Affiliation(s)
- Jae Jun Lee
- Computational Cancer Genomics Groups, Spanish Cancer Research Center (CNIO), Madrid, Spain
| | - Hyun Ju Kang
- Genomic Medicine Institute, Medical Research Center, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea
| | - Donghyo Kim
- Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Si On Lim
- Department of Biomedical Sciences, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea
| | - Stephanie S Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital (SNUBH), Seongnam, Gyeonggi-do, 13620, Republic of Korea
| | - Gahyun Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital (SNUBH), Seongnam, Gyeonggi-do, 13620, Republic of Korea
| | - Sanguk Kim
- Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea.
| | - Jin-Ku Lee
- Genomic Medicine Institute, Medical Research Center, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea.
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea.
| | - Jinho Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital (SNUBH), Seongnam, Gyeonggi-do, 13620, Republic of Korea.
- Department of Genomic Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, 13620, Republic of Korea.
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Gyeonggi-do, 13620, Republic of Korea.
| |
Collapse
|
8
|
Feng LL, Bie SY, Deng ZH, Bai SM, Shi J, Qin CL, Liu HL, Li JX, Chen WY, Zhou JY, Jiao CM, Ma Y, Qiu MB, Ai HS, Zheng J, Hung MC, Wang YL, Wan XB, Fan XJ. Ubiquitin-induced RNF168 condensation promotes DNA double-strand break repair. Proc Natl Acad Sci U S A 2024; 121:e2322972121. [PMID: 38968116 PMCID: PMC11252754 DOI: 10.1073/pnas.2322972121] [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: 01/01/2024] [Accepted: 05/22/2024] [Indexed: 07/07/2024] Open
Abstract
Rapid accumulation of repair factors at DNA double-strand breaks (DSBs) is essential for DSB repair. Several factors involved in DSB repair have been found undergoing liquid-liquid phase separation (LLPS) at DSB sites to facilitate DNA repair. RNF168, a RING-type E3 ubiquitin ligase, catalyzes H2A.X ubiquitination for recruiting DNA repair factors. Yet, whether RNF168 undergoes LLPS at DSB sites remains unclear. Here, we identified K63-linked polyubiquitin-triggered RNF168 condensation which further promoted RNF168-mediated DSB repair. RNF168 formed liquid-like condensates upon irradiation in the nucleus while purified RNF168 protein also condensed in vitro. An intrinsically disordered region containing amino acids 460-550 was identified as the essential domain for RNF168 condensation. Interestingly, LLPS of RNF168 was significantly enhanced by K63-linked polyubiquitin chains, and LLPS largely enhanced the RNF168-mediated H2A.X ubiquitination, suggesting a positive feedback loop to facilitate RNF168 rapid accumulation and its catalytic activity. Functionally, LLPS deficiency of RNF168 resulted in delayed recruitment of 53BP1 and BRCA1 and subsequent impairment in DSB repair. Taken together, our finding demonstrates the pivotal effect of LLPS in RNF168-mediated DSB repair.
Collapse
Affiliation(s)
- Li-Li Feng
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong510060, China
- Department of Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong510060, China
| | - Shu-Ying Bie
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong510655, China
| | - Zhi-Heng Deng
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing100084, China
| | - Shao-Mei Bai
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong510655, China
| | - Jie Shi
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong510655, China
- Department of Radiation Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong510655, China
| | - Cao-Litao Qin
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong510655, China
- Department of Radiation Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong510655, China
| | - Huan-Lei Liu
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Jia-Xu Li
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Wan-Ying Chen
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Jin-Ying Zhou
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Chun-Mei Jiao
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Yi Ma
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong510655, China
| | - Meng-Bo Qiu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Hua-Song Ai
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing100084, China
| | - Jian Zheng
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong510655, China
- Department of Radiation Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong510655, China
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, Institute of Biochemistry and Molecular Biology, Research Center for Cancer Biology, Cancer Biology and Precision Therapeutics Center, and Center for Molecular Medicine, China Medical University, Taichung406, Taiwan (Republic of China)
| | - Yun-Long Wang
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Xiang-Bo Wan
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Xin-Juan Fan
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| |
Collapse
|
9
|
Zhao Y, Li R, Wang W, Zhang H, Zhang Q, Jiang J, Wang Y, Li Y, Guan F, Nie Y. O-GlcNAc signaling: Implications for stress-induced adaptive response pathway in the tumor microenvironment. Cancer Lett 2024; 598:217101. [PMID: 38969156 DOI: 10.1016/j.canlet.2024.217101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/19/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
The tumor microenvironment (TME) consists of tumor cells, non-tumor cells, extracellular matrix, and signaling molecules, which can contribute to tumor initiation, progression, and therapy resistance. In response to starvation, hypoxia, and drug treatments, tumor cells undergo a variety of deleterious endogenous stresses, such as hypoxia, DNA damage, and oxidative stress. In this context, to survive the difficult situation, tumor cells evolve multiple conserved adaptive responses, including metabolic reprogramming, DNA damage checkpoints, homologous recombination, up-regulated antioxidant pathways, and activated unfolded protein responses. In the last decades, the protein O-GlcNAcylation has emerged as a crucial causative link between glucose metabolism and tumor progression. Here, we discuss the relevant pathways that regulate the above responses. These pathways are adaptive adjustments induced by endogenous stresses in cells. In addition, we systematically discuss the role of O-GlcNAcylation-regulated stress-induced adaptive response pathways (SARPs) in TME remodeling, tumor progression, and treatment resistance. We also emphasize targeting O-GlcNAcylation through compounds that modulate OGT or OGA activity to inhibit tumor progression. It seems that targeting O-GlcNAcylated proteins to intervene in TME may be a novel approach to improve tumor prognosis.
Collapse
Affiliation(s)
- Yu Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Renlong Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, 710032, China
| | - Weizhen Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, 710032, China
| | - Haohao Zhang
- Department of Digestive Surgery, Honghui Hospital, Xi'an Jiaotong University, 710054, Xi'an, Shaanxi, China
| | - Qiujin Zhang
- Second Clinical Medicine College, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
| | - Jialu Jiang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, 710032, China
| | - Ying Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yan Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, 710032, China
| | - Feng Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China.
| | - Yongzhan Nie
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China; State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, 710032, China.
| |
Collapse
|
10
|
Zuckerman JT, Jackson AS, Minko IG, Kant M, Jaruga P, Stone MP, Dizdaroglu M, McCullough AK, Lloyd RS. Functional characterization of single nucleotide polymorphic variants of DNA repair enzyme NEIL1 in South Asian populations. DNA Repair (Amst) 2024; 139:103695. [PMID: 38795603 PMCID: PMC11218669 DOI: 10.1016/j.dnarep.2024.103695] [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: 02/13/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/28/2024]
Abstract
The base excision repair (BER) pathway is a precise and versatile mechanism of DNA repair that is initiated by DNA glycosylases. Endonuclease VIII-like 1 (NEIL1) is a bifunctional glycosylase/abasic site (AP) lyase that excises a damaged base and subsequently cleaves the phosphodiester backbone. NEIL1 is able to recognize and hydrolyze a broad range of oxidatively-induced base lesions and substituted ring-fragmented guanines, including aflatoxin-induced 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua). Due to NEIL1's protective role against these and other pro-mutagenic lesions, it was hypothesized that naturally occurring single nucleotide polymorphic (SNP) variants of NEIL1 could increase human risk for aflatoxin-induced hepatocellular carcinoma (HCC). Given that populations in South Asia experience high levels of dietary aflatoxin exposures and hepatitis B viral infections that induce oxidative stress, investigations on SNP variants of NEIL1 that occur in this region may have clinical implications. In this study, the most common South Asian variants of NEIL1 were expressed, purified, and functionally characterized. All tested variants exhibited activities and substrate specificities similar to wild type (wt)-NEIL1 on high-molecular weight DNA containing an array of oxidatively-induced base lesions. On short oligodeoxynucleotides (17-mers) containing either a site-specific apurinic/apyrimidinic (AP) site, thymine glycol (ThyGly), or AFB1-FapyGua, P206L-NEIL1 was catalytically comparable to wt-NEIL1, while the activities of NEIL1 variants Q67K and T278I on these substrates were ≈2-fold reduced. Variant T103A had a greatly diminished ability to bind to 17-mer DNAs, limiting the subsequent glycosylase and lyase reactions. Consistent with this observation, the rate of excision by T103A on 17-mer oligodeoxynucleotides containing ThyGly or AFB1-FapyGua could not be measured. However, the ability of T103A to excise ThyGly was improved on longer oligodeoxynucleotides (51-mers), with ≈7-fold reduced activity compared to wt-NEIL1. Our studies suggest that NEIL1 variant T103A may present a pathogenic phenotype that is limited in damage recognition, potentially increasing human risk for HCC.
Collapse
Affiliation(s)
- Jamie T Zuckerman
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Asia Sage Jackson
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Math & Sciences, Corban University, Salem, OR 97317, United States
| | - Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Melis Kant
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Pawel Jaruga
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Michael P Stone
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240, United States
| | - Miral Dizdaroglu
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, United States.
| |
Collapse
|
11
|
Zheng S, Li M, Xu W, Zhang J, Li G, Xiao H, Liu X, Shi J, Xia F, Tian C, Kamei KI. Dual-targeted nanoparticulate drug delivery systems for enhancing triple-negative breast cancer treatment. J Control Release 2024; 371:371-385. [PMID: 38849089 DOI: 10.1016/j.jconrel.2024.06.012] [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: 01/23/2024] [Revised: 05/22/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
The efficacy of DNA-damaging agents, such as the topoisomerase I inhibitor SN38, is often compromised by the robust DNA repair mechanisms in tumor cells, notably homologous recombination (HR) repair. Addressing this challenge, we introduce a novel nano-strategy utilizing binary tumor-killing mechanisms to enhance the therapeutic impact of DNA damage and mitochondrial dysfunction in cancer treatment. Our approach employs a synergistic drug pair comprising SN38 and the BET inhibitor JQ-1. We synthesized two prodrugs by conjugating linoleic acid (LA) to SN38 and JQ-1 via a cinnamaldehyde thioacetal (CT) bond, facilitating co-delivery. These prodrugs co-assemble into a nanostructure, referred to as SJNP, in an optimal synergistic ratio. SJNP was validated for its efficacy at both the cellular and tissue levels, where it primarily disrupts the transcription factor protein BRD4. This disruption leads to downregulation of BRCA1 and RAD51, impairing the HR process and exacerbating DNA damage. Additionally, SJNP releases cinnamaldehyde (CA) upon CT linkage cleavage, elevating intracellular ROS levels in a self-amplifying manner and inducing ROS-mediated mitochondrial dysfunction. Our results indicate that SJNP effectively targets murine triple-negative breast cancer (TNBC) with minimal adverse toxicity, showcasing its potential as a formidable opponent in the fight against cancer.
Collapse
Affiliation(s)
- Shunzhe Zheng
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Meng Li
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Wenqian Xu
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jiaxin Zhang
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Guanting Li
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hongying Xiao
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xinying Liu
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jianbin Shi
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Fengli Xia
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chutong Tian
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China; Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, Shenyang 110016, China; Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, Hangzhou 310058, China.
| | - Ken-Ichiro Kamei
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China; Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, Shenyang 110016, China; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan; Program of Biology, Division of Science, New York University Abu Dhabi, Abu Dhabi, The United Arab Emirates; Program of Bioengineering, Division of Engineering, New York University Abu Dhabi, Abu Dhabi, The United Arab Emirates; Department of Biomedical Engineering, Tandon School of Engineering, New York University, MetroTech, Brooklyn, NY 11201, United States of America.
| |
Collapse
|
12
|
Leu YL, Cheng SF, Wang TH, Feng CH, Chen YJ, Hsieh YC, Lan YH, Chen CC. Increasing DNA damage sensitivity through corylin-mediated inhibition of homologous recombination. Biomed Pharmacother 2024; 176:116864. [PMID: 38865847 DOI: 10.1016/j.biopha.2024.116864] [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: 03/24/2024] [Revised: 05/23/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND DNA repair allows the survival of cancer cells. Therefore, the development of DNA repair inhibitors is a critical need for sensitizing cancers to chemoradiation. Sae2CtIP has specific functions in initiating DNA end resection, as well as coordinating cell cycle checkpoints, and it also greatly interacts with the DDR at different levels. RESULTS In this study, we demonstrated that corylin, a potential sensitizer, causes deficiencies in DNA repair and DNA damage checkpoints in yeast cells. More specifically, corylin increases DNA damage sensitivity through the Sae2-dependent pathway and impairs the activation of Mec1-Ddc2, Rad53-p and γ-H2A. In breast cancer cells, corylin increases apoptosis and reduces proliferation following Dox treatment by inhibiting CtIP. Xenograft assays showed that treatment with corylin combined with Dox significantly reduced tumor growth in vivo. CONCLUSIONS Our findings herein delineate the mechanisms of action of corylin in regulating DNA repair and indicate that corylin has potential long-term clinical utility as a DDR inhibitor.
Collapse
Affiliation(s)
- Yann-Lii Leu
- Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Biobank, Chang Gung Memorial Hospital, No. 5, Fuxing St., Guishan Dist., Taoyuan City 33305, Taiwan, ROC
| | - Shu-Fang Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City, Taiwan, ROC; Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC
| | - Tong-Hong Wang
- Biobank, Chang Gung Memorial Hospital, No. 5, Fuxing St., Guishan Dist., Taoyuan City 33305, Taiwan, ROC
| | - Chun-Hao Feng
- Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC
| | - Yu-Ju Chen
- Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC
| | - Yi-Cheng Hsieh
- Office of the Texas State Chemist, Texas A&M AgriLife Research, Texas A&M University System, College Station, TX 77843, USA
| | - Yu-Hsuan Lan
- Department of Pharmacy, College of Pharmacy, China Medical University, No.100, Section 1, Jingmao Rd., Beitun Dist., Taichung City 406040, Taiwan, ROC.
| | - Chin-Chuan Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City, Taiwan, ROC; Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Healthy Aging Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Biobank, Chang Gung Memorial Hospital, No. 5, Fuxing St., Guishan Dist., Taoyuan City 33305, Taiwan, ROC.
| |
Collapse
|
13
|
Zhao X, Luo T, Qiu Y, Yang Z, Wang D, Wang Z, Zeng J, Bi Z. Mechanisms of traditional Chinese medicine overcoming of radiotherapy resistance in breast cancer. Front Oncol 2024; 14:1388750. [PMID: 38993643 PMCID: PMC11237312 DOI: 10.3389/fonc.2024.1388750] [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: 02/20/2024] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Breast cancer stands as the most prevalent malignancy among women, with radiotherapy serving as a primary treatment modality. Despite radiotherapy, a subset of breast cancer patients experiences local recurrence, attributed to the intrinsic resistance of tumors to radiation. Therefore, there is a compelling need to explore novel approaches that can enhance cytotoxic effects through alternative mechanisms. Traditional Chinese Medicine (TCM) and its active constituents exhibit diverse pharmacological actions, including anti-tumor effects, offering extensive possibilities to identify effective components capable of overcoming radiotherapy resistance. This review delineates the mechanisms underlying radiotherapy resistance in breast cancer, along with potential candidate Chinese herbal medicines that may sensitize breast cancer cells to radiotherapy. The exploration of such herbal interventions holds promise for improving therapeutic outcomes in the context of breast cancer radiotherapy resistance.
Collapse
Affiliation(s)
- Xiaohui Zhao
- Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oncology, Shenshan Medical Centre, Memorial Hospital of Sun Yat-Sen University, Shanwei, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ting Luo
- Department of Oncology, Shenshan Medical Centre, Memorial Hospital of Sun Yat-Sen University, Shanwei, China
| | - Yuting Qiu
- Department of Oncology, Shenshan Medical Centre, Memorial Hospital of Sun Yat-Sen University, Shanwei, China
| | - Zhiwei Yang
- Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Danni Wang
- Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zairui Wang
- Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiale Zeng
- Department of Radiology, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhuofei Bi
- Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
14
|
Yang Q, Madueke-Laveaux OS, Cun H, Wlodarczyk M, Garcia N, Carvalho KC, Al-Hendy A. Comprehensive Review of Uterine Leiomyosarcoma: Pathogenesis, Diagnosis, Prognosis, and Targeted Therapy. Cells 2024; 13:1106. [PMID: 38994959 PMCID: PMC11240800 DOI: 10.3390/cells13131106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
Uterine leiomyosarcoma (uLMS) is the most common subtype of uterine sarcomas. They have a poor prognosis with high rates of recurrence and metastasis. The five-year survival for uLMS patients is between 25 and 76%, with survival rates approaching 10-15% for patients with metastatic disease at the initial diagnosis. Accumulating evidence suggests that several biological pathways are involved in uLMS pathogenesis. Notably, drugs that block abnormal functions of these pathways remarkably improve survival in uLMS patients. However, due to chemotherapy resistance, there remains a need for novel drugs that can target these pathways effectively. In this review article, we provide an overview of the recent progress in ascertaining the biological functions and regulatory mechanisms in uLMS from the perspective of aberrant biological pathways, including DNA repair, immune checkpoint blockade, protein kinase and intracellular signaling pathways, and the hedgehog pathway. We review the emerging role of epigenetics and epitranscriptome in the pathogenesis of uLMS. In addition, we discuss serum markers, artificial intelligence (AI) combined with machine learning, shear wave elastography, current management and medical treatment options, and ongoing clinical trials for patients with uLMS. Comprehensive, integrated, and deeper insights into the pathobiology and underlying molecular mechanisms of uLMS will help develop novel strategies to treat patients with this aggressive tumor.
Collapse
Affiliation(s)
- Qiwei Yang
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
| | | | - Han Cun
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
| | - Marta Wlodarczyk
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
| | - Natalia Garcia
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Katia Candido Carvalho
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento deObstetricia e Ginecologia, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 05403-010, Brazil
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
15
|
Patel V, Casimiro S, Abreu C, Barroso T, de Sousa RT, Torres S, Ribeiro LA, Nogueira-Costa G, Pais HL, Pinto C, Costa L, Costa L. DNA damage targeted therapy for advanced breast cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:678-698. [PMID: 38966174 PMCID: PMC11220312 DOI: 10.37349/etat.2024.00241] [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: 08/30/2023] [Accepted: 01/04/2024] [Indexed: 07/06/2024] Open
Abstract
Breast cancer (BC) is the most prevalent malignancy affecting women worldwide, including Portugal. While the majority of BC cases are sporadic, hereditary forms account for 5-10% of cases. The most common inherited mutations associated with BC are germline mutations in the BReast CAncer (BRCA) 1/2 gene (gBRCA1/2). They are found in approximately 5-6% of BC patients and are inherited in an autosomal dominant manner, primarily affecting younger women. Pathogenic variants within BRCA1/2 genes elevate the risk of both breast and ovarian cancers and give rise to distinct clinical phenotypes. BRCA proteins play a key role in maintaining genome integrity by facilitating the repair of double-strand breaks through the homologous recombination (HR) pathway. Therefore, any mutation that impairs the function of BRCA proteins can result in the accumulation of DNA damage, genomic instability, and potentially contribute to cancer development and progression. Testing for gBRCA1/2 status is relevant for treatment planning, as it can provide insights into the likely response to therapy involving platinum-based chemotherapy and poly[adenosine diphosphate (ADP)-ribose] polymerase inhibitors (PARPi). The aim of this review was to investigate the impact of HR deficiency in BC, focusing on BRCA mutations and their impact on the modulation of responses to platinum and PARPi therapy, and to share the experience of Unidade Local de Saúde Santa Maria in the management of metastatic BC patients with DNA damage targeted therapy, including those with the Portuguese c.156_157insAlu BRCA2 founder mutation.
Collapse
Affiliation(s)
- Vanessa Patel
- Oncology Division, Unidade Local de Saúde Santa Maria, 1649-028 Lisboa, Portugal
| | - Sandra Casimiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Lisboa, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Catarina Abreu
- Oncology Division, Unidade Local de Saúde Santa Maria, 1649-028 Lisboa, Portugal
| | - Tiago Barroso
- Oncology Division, Unidade Local de Saúde Santa Maria, 1649-028 Lisboa, Portugal
| | | | - Sofia Torres
- Oncology Division, Unidade Local de Saúde Santa Maria, 1649-028 Lisboa, Portugal
| | - Leonor Abreu Ribeiro
- Oncology Division, Unidade Local de Saúde Santa Maria, 1649-028 Lisboa, Portugal
| | | | - Helena Luna Pais
- Oncology Division, Unidade Local de Saúde Santa Maria, 1649-028 Lisboa, Portugal
| | - Conceição Pinto
- Oncology Division, Unidade Local de Saúde Santa Maria, 1649-028 Lisboa, Portugal
| | - Leila Costa
- Pharmacy Department, Unidade Local de Saúde Santa Maria, 1649-028 Lisboa, Portugal
| | - Luís Costa
- Oncology Division, Unidade Local de Saúde Santa Maria, 1649-028 Lisboa, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Lisboa, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| |
Collapse
|
16
|
Meyer D, Ceballos SJ, Gore S, Liu J, Reginato G, Cano-Linares MI, Maslowska KH, Villafañez F, Ede C, Pagès V, Prado F, Cejka P, Heyer WD. Rad51 determines pathway usage in post-replication repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599120. [PMID: 38915629 PMCID: PMC11195247 DOI: 10.1101/2024.06.14.599120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Stalled replication forks can be processed by several distinct mechanisms collectively called post-replication repair which includes homologous recombination, fork regression, and translesion DNA synthesis. However, the regulation of the usage between these pathways is not fully understood. The Rad51 protein plays a pivotal role in maintaining genomic stability through its roles in HR and in protecting stalled replication forks from degradation. We report the isolation of separation-of-function mutations in Saccharomyces cerevisiae Rad51 that retain their recombination function but display a defect in fork protection leading to a shift in post-replication repair pathway usage from HR to alternate pathways including mutagenic translesion synthesis. Rad51-E135D and Rad51-K305N show normal in vivo and in vitro recombination despite changes in their DNA binding profiles, in particular to dsDNA, with a resulting effect on their ATPase activities. The mutants lead to a defect in Rad51 recruitment to stalled forks in vivo as well as a defect in the protection of dsDNA from degradation by Dna2-Sgs1 and Exo1 in vitro . A high-resolution cryo-electron microscopy structure of the Rad51-ssDNA filament at 2.4 Å resolution provides a structural basis for a mechanistic understanding of the mutant phenotypes. Together, the evidence suggests a model in which Rad51 binding to duplex DNA is critical to control pathway usage at stalled replication forks.
Collapse
|
17
|
Xu Y, Chen YJA, Wu Y, Saverimuthu A, Jadhav A, Bhuiyan R, Sandler J, Yio J, Kumar V. The prognostic and predictive value of homologous recombination deficiency status in patients with advanced stage epithelial ovarian carcinoma after first-line platinum-based chemotherapy. Front Oncol 2024; 14:1372482. [PMID: 38915363 PMCID: PMC11194312 DOI: 10.3389/fonc.2024.1372482] [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: 01/18/2024] [Accepted: 04/23/2024] [Indexed: 06/26/2024] Open
Abstract
Objective Homologous recombination (HR) comprises series of interrelated pathways that repair double-stranded DNA breaks and inter-strand crosslinks. It provides support for DNA replication to recover stalled or broken replication forks. Compared with homologous recombination proficiency (HRP), cancers with homologous recombination deficiency (HRD) are more likely to undergo cell death when treated with DNA-damaging agents, such as platinum agents, and have better disease control. Methods Patients diagnosed with stage III/IV ovarian cancer, early stages with recurrence, who received adjuvant chemotherapy after debulking surgery, and who also had known HR status were eligible. Results Forty-four patients were included, with 21 in the HRD group (including 8 with germline mutations) and 23 in the HRP group. The HRD group was composed predominantly of serous carcinoma (95.2%), while mucinous (n=3) and clear cell (n=1) cases were all found in the HRP group. Stage III/IV disease was 66.7% and 91.3% in HRD and HRP groups, respectively (p=0.064). Patients who were optimally debulked to no residual disease was 90.0% and 72.7% (p=0.243), respectively. Late line use of PARP inhibitors was 33.3% and 17.4% (p=0.303). Median PFS was 22.5 months (95% CI, 18.5 - 66.6) and 21.5 months (95% CI, 18.3-39.5) (p=0.49) in HRD and HRP respectively. Median platinum free interval (PFI) was 15.8 months (95% CI 12.4-60.4) and 15.9 months (95% CI 8.3-34.1) (p=0.24), respectively. Median OS was 88.2 months (95% CI 71.2-NA) and 49.7 months (95% CI 35.1-NA) (p=0.21). The PFS of the patients with germline BRCA mutations (n=5) was 54.3 months (95% CI 23.1-NA) and 21.5 months (95% CI 18.3-39.5) in the HRP group (p=0.095); the PFI difference was 47.7 months (95% CI 17.6-NA) in the BRCA mutation group, and 15.9 months (95% CI 12.4-60.4) in HRP, showing statistical significance (p=0.039); while the median OS was NA and 49.7 months (95% CI 35.1-NA) respectively (p=0.051). When adding two additional patients with somatic BRCA mutations to the germline BRCA mutation carriers, the median OS is NA (95% CI 73, NA) versus 49.7 months (95% CI 35.1, NA) for HRP (p=0.045). Conclusions HRD status was not associated with longer PFS or PFI in advanced ovarian cancer who received first line adjuvant platinum-based chemotherapy. Its role as a prognostic marker for overall survival is suggested, particularly in the subgroup with germline and somatic BRCA mutations.
Collapse
Affiliation(s)
- Yiqing Xu
- Division of Hematologic Oncology, Department of Internal Medicine, Maimonides Medical Center, Brooklyn, NY, United States
| | - Yi-Ju Amy Chen
- Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, Weill Cornell Medical College and New York Presbyterian/Queens Hospital, Flushing, NY, United States
| | - Yunhong Wu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Angela Saverimuthu
- Division of Hematologic Oncology, Department of Internal Medicine, Maimonides Medical Center, Brooklyn, NY, United States
| | - Archana Jadhav
- Division of Hematologic Oncology, Department of Internal Medicine, Maimonides Medical Center, Brooklyn, NY, United States
| | - Rehana Bhuiyan
- Division of Hematologic Oncology, Department of Internal Medicine, Maimonides Medical Center, Brooklyn, NY, United States
| | - Jason Sandler
- Division of Hematologic Oncology, Department of Internal Medicine, Maimonides Medical Center, Brooklyn, NY, United States
| | - Jiang Yio
- Division of Hematologic Oncology, Department of Internal Medicine, Maimonides Medical Center, Brooklyn, NY, United States
| | - Vivek Kumar
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| |
Collapse
|
18
|
Xiao H, Chen H, Zhang L, Duolikun M, Zhen B, Kuerban S, Li X, Wang Y, Chen L, Lin J. Cytoskeletal gene alterations linked to sorafenib resistance in hepatocellular carcinoma. World J Surg Oncol 2024; 22:152. [PMID: 38849867 PMCID: PMC11157844 DOI: 10.1186/s12957-024-03417-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/20/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Although sorafenib has been consistently used as a first-line treatment for advanced hepatocellular carcinoma (HCC), most patients will develop resistance, and the mechanism of resistance to sorafenib needs further study. METHODS Using KAS-seq technology, we obtained the ssDNA profiles within the whole genome range of SMMC-7721 cells treated with sorafenib for differential analysis. We then intersected the differential genes obtained from the analysis of hepatocellular carcinoma patients in GSE109211 who were ineffective and effective with sorafenib treatment, constructed a PPI network, and obtained hub genes. We then analyzed the relationship between the expression of these genes and the prognosis of hepatocellular carcinoma patients. RESULTS In this study, we identified 7 hub ERGs (ACTB, CFL1, ACTG1, ACTN1, WDR1, TAGLN2, HSPA8) related to drug resistance, and these genes are associated with the cytoskeleton. CONCLUSIONS The cytoskeleton is associated with sorafenib resistance in hepatocellular carcinoma. Using KAS-seq to analyze the early changes in tumor cells treated with drugs is feasible for studying the drug resistance of tumors, which provides reference significance for future research.
Collapse
Affiliation(s)
- Hong Xiao
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Hainan, China
| | - Hangyu Chen
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China
| | - Lei Zhang
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China
| | - Maimaitiyasen Duolikun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Hainan, China
| | - Baixin Zhen
- Department of Pharmacology, Xinjiang Medical University, Urumqi, China
| | - Subinuer Kuerban
- Department of Pharmacology, Xinjiang Medical University, Urumqi, China
| | - Xuehui Li
- Department of Pharmacology, Xinjiang Medical University, Urumqi, China
| | - Yuxi Wang
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China
| | - Long Chen
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
- Peking University, Third Hospital Cancer Center, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
| | - Jian Lin
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Hainan, China.
- Department of Pharmacy, Peking University Third Hospital, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Peking University, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
- Peking University, Third Hospital Cancer Center, 49 Huayuan North Rd, Haidian District, Beijing, 100191, China.
| |
Collapse
|
19
|
Zhang S, Zhou N, Chen J, Li Q, Wang Y, Sun W, Lv C. DNA Polymerase-Endonuclease Efficiently Synthesizes DNA to Prepare DNA Materials and Develop Novel Signal Amplification System. Anal Chem 2024; 96:9285-9293. [PMID: 38768388 DOI: 10.1021/acs.analchem.4c01964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
DNA biosynthesis, a focus of fundamental and applied research, typically involves DNA polymerases by using templates, primers, and dNTPs. Some polymerases can polymerize dNTPs for DNA de novo synthesis, although this is generally to occur randomly. This novel synthesis method has garnered our attention and practical use. Herein, we observed that the addition of endonuclease significantly enhances the efficiency of the de novo synthesis reaction catalyzed by the DNA polymerase. We further investigated the reaction conditions that influence this efficiency. Building on the optimal reaction conditions, we developed a rapid and efficient strategy for preparing DNA hydrogel. Further, coupled with the CRISPR-Cas system, we developed a nucleic acid signal amplification system characterized by versatility, sensitivity, specificity, and no risk of aerosol contamination. We successfully detected viral nucleic acids in clinical samples. In summary, our study demonstrates the significant potential of DNA polymerase- and endonuclease-catalyzed DNA de novo synthesis in diverse applications.
Collapse
Affiliation(s)
- Shun Zhang
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Ning Zhou
- Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong 524045, P. R. China
| | - Jiao Chen
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Quan Li
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Yang Wang
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Wen Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610000, P. R. China
| | - ChuanZhu Lv
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| |
Collapse
|
20
|
Chauvin SD, Ando S, Holley JA, Sugie A, Zhao FR, Poddar S, Kato R, Miner CA, Nitta Y, Krishnamurthy SR, Saito R, Ning Y, Hatano Y, Kitahara S, Koide S, Stinson WA, Fu J, Surve N, Kumble L, Qian W, Polishchuk O, Andhey PS, Chiang C, Liu G, Colombeau L, Rodriguez R, Manel N, Kakita A, Artyomov MN, Schultz DC, Coates PT, Roberson EDO, Belkaid Y, Greenberg RA, Cherry S, Gack MU, Hardy T, Onodera O, Kato T, Miner JJ. Inherited C-terminal TREX1 variants disrupt homology-directed repair to cause senescence and DNA damage phenotypes in Drosophila, mice, and humans. Nat Commun 2024; 15:4696. [PMID: 38824133 PMCID: PMC11144269 DOI: 10.1038/s41467-024-49066-7] [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: 11/03/2023] [Accepted: 05/22/2024] [Indexed: 06/03/2024] Open
Abstract
Age-related microangiopathy, also known as small vessel disease (SVD), causes damage to the brain, retina, liver, and kidney. Based on the DNA damage theory of aging, we reasoned that genomic instability may underlie an SVD caused by dominant C-terminal variants in TREX1, the most abundant 3'-5' DNA exonuclease in mammals. C-terminal TREX1 variants cause an adult-onset SVD known as retinal vasculopathy with cerebral leukoencephalopathy (RVCL or RVCL-S). In RVCL, an aberrant, C-terminally truncated TREX1 mislocalizes to the nucleus due to deletion of its ER-anchoring domain. Since RVCL pathology mimics that of radiation injury, we reasoned that nuclear TREX1 would cause DNA damage. Here, we show that RVCL-associated TREX1 variants trigger DNA damage in humans, mice, and Drosophila, and that cells expressing RVCL mutant TREX1 are more vulnerable to DNA damage induced by chemotherapy and cytokines that up-regulate TREX1, leading to depletion of TREX1-high cells in RVCL mice. RVCL-associated TREX1 mutants inhibit homology-directed repair (HDR), causing DNA deletions and vulnerablility to PARP inhibitors. In women with RVCL, we observe early-onset breast cancer, similar to patients with BRCA1/2 variants. Our results provide a mechanistic basis linking aberrant TREX1 activity to the DNA damage theory of aging, premature senescence, and microvascular disease.
Collapse
Affiliation(s)
- Samuel D Chauvin
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shoichiro Ando
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Joe A Holley
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Atsushi Sugie
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | - Fang R Zhao
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Subhajit Poddar
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rei Kato
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Cathrine A Miner
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yohei Nitta
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rie Saito
- Department of Pathology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yue Ning
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yuya Hatano
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Sho Kitahara
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Shin Koide
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - W Alexander Stinson
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Jiayuan Fu
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nehalee Surve
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lindsay Kumble
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wei Qian
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Oleksiy Polishchuk
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Prabhakar S Andhey
- Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Cindy Chiang
- Department of Microbiology, The University of Chicago, Chicago, IL, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Guanqun Liu
- Department of Microbiology, The University of Chicago, Chicago, IL, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Ludovic Colombeau
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Raphaël Rodriguez
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Nicolas Manel
- INSERM U932, Institut Curie, PSL Research University, Paris, France
| | - Akiyoshi Kakita
- Department of Pathology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO, USA
| | - David C Schultz
- High-throughput Screening Core, University of Pennsylvania, Philadelphia, PA, USA
| | - P Toby Coates
- Central and Northern Adelaide Renal and Transplantation Service (CNARTS), The Royal Adelaide Hospital, Adelaide, South Australia, Australia
- School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Elisha D O Roberson
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institut Pasteur, Paris, France
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sara Cherry
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Tristan Hardy
- Genetics, Repromed, Monash IVF, Dulwich, South Australia, Australia
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Osamu Onodera
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
- Department of Molecular Neuroscience, Brain Science Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Taisuke Kato
- Department of Molecular Neuroscience, Brain Science Branch, Brain Research Institute, Niigata University, Niigata, Japan.
| | - Jonathan J Miner
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Penn Colton Center for Autoimmunity, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
21
|
Yilmaz I, Ozbek T. Genome editing in Acinetobacter baumannii through enhanced natural transformation. J Basic Microbiol 2024; 64:e2300644. [PMID: 38412427 DOI: 10.1002/jobm.202300644] [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: 10/28/2023] [Revised: 01/29/2024] [Accepted: 02/03/2024] [Indexed: 02/29/2024]
Abstract
Acinetobacter baumannii, a multidrug-resistant bacterium has become a significant cause of life-threatening infections acquired in hospitals worldwide. The existing drugs used to treat A. baumannii infections are rapidly losing efficacy, and the increasing antimicrobial resistance, which is expected to turn into a global health crisis, underscores the urgency to develop novel prevention and treatment strategies. We reasoned that the discovery of novel virulence targets for vaccine and therapy interventions requires a more enhanced method for the introduction of multiple elements of foreign DNA for genome editing than the current methods of natural transformation techniques. Herein, we employed a novel and a much-improved enhanced technique for the natural transformation of elements of the genome editing system CRISPR-Cas9 to suppress specific genomic regions linked to selectively suppress bacterial virulence. We modified the genome of the laboratory-adapted strain of A. baumannii BAA-747 by targeting the AmpC, as a marker gene, for disruption by three different genomic manipulation strategies, and created mutant strains of A. baumannii that are, at least, fourfold susceptible to ampicillin. This work has established an optimized enhanced natural transformation system that enables efficient genome editing of pathogenic bacteria in a laboratory setting, providing a valuable future tool for exploring the function of unidentified virulence genes in bacterial genomes.
Collapse
Affiliation(s)
- Ilknur Yilmaz
- Department of Molecular Biology and Genetics, Graduate School of Science & Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Tulin Ozbek
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| |
Collapse
|
22
|
Han Y, Zhao H, Li G, Jia J, Guo H, Tan J, Sun X, Li S, Ran Q, Bai C, Gu Y, Li Z, Guan H, Gao S, Zhou PK. GCN5 mediates DNA-PKcs crotonylation for DNA double-strand break repair and determining cancer radiosensitivity. Br J Cancer 2024; 130:1621-1634. [PMID: 38575732 PMCID: PMC11091118 DOI: 10.1038/s41416-024-02636-4] [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: 12/12/2023] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND DNA double-strand break (DSB) induction and repair are important events for determining cell survival and the outcome of cancer radiotherapy. The DNA-dependent protein kinase (DNA-PK) complex functions at the apex of DSBs repair, and its assembly and activity are strictly regulated by post-translation modifications (PTMs)-associated interactions. However, the PTMs of the catalytic subunit DNA-PKcs and how they affect DNA-PKcs's functions are not fully understood. METHODS Mass spectrometry analyses were performed to identify the crotonylation sites of DNA-PKcs in response to γ-ray irradiation. Co-immunoprecipitation (Co-IP), western blotting, in vitro crotonylation assays, laser microirradiation assays, in vitro DNA binding assays, in vitro DNA-PK assembly assays and IF assays were employed to confirm the crotonylation, identify the crotonylase and decrotonylase, and elucidate how crotonylation regulates the activity and function of DNA-PKcs. Subcutaneous xenografts of human HeLa GCN5 WT or HeLa GCN5 siRNA cells in BALB/c nude mice were generated and utilized to assess tumor proliferation in vivo after radiotherapy. RESULTS Here, we reveal that K525 is an important site of DNA-PKcs for crotonylation, and whose level is sharply increased by irradiation. The histone acetyltransferase GCN5 functions as the crotonylase for K525-Kcr, while HDAC3 serves as its dedicated decrotonylase. K525 crotonylation enhances DNA binding activity of DNA-PKcs, and facilitates assembly of the DNA-PK complex. Furthermore, GCN5-mediated K525 crotonylation is indispensable for DNA-PKcs autophosphorylation and the repair of double-strand breaks in the NHEJ pathway. GCN5 suppression significantly sensitizes xenograft tumors of mice to radiotherapy. CONCLUSIONS Our study defines K525 crotonylation of DNA-PKcs is important for the DNA-PK complex assembly and DSBs repair activity via NHEJ pathway. Targeting GCN5-mediated K525 Kcr of DNA-PKcs may be a promising therapeutic strategy for improving the outcome of cancer radiotherapy.
Collapse
Affiliation(s)
- Yang Han
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Hongling Zhao
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Gang Li
- School of Public Health, Institute for Environmental Medicine and Radiation Hygiene, University of South China, Hengyang, China
- Department of Hospital Infection Control, Shenzhen Luohu Peoples Hospital, Shenzhen, China
| | - Jin Jia
- School of Medicine, University of South China, Hengyang, China
| | - Hejiang Guo
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jinpeng Tan
- School of Medicine, University of South China, Hengyang, China
| | - Xingyao Sun
- School of Medicine, University of South China, Hengyang, China
| | - Saiyu Li
- School of life Sciences, Hebei University, Baoding, China
| | - Qian Ran
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Chenjun Bai
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yongqing Gu
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - ZhongJun Li
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China.
| | - Hua Guan
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Shanshan Gao
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
- School of Public Health, Institute for Environmental Medicine and Radiation Hygiene, University of South China, Hengyang, China.
| |
Collapse
|
23
|
Yedla P, Bhamidipati P, Syed R, Amanchy R. Working title: Molecular involvement of p53-MDM2 interactome in gastrointestinal cancers. Cell Biochem Funct 2024; 42:e4075. [PMID: 38924101 DOI: 10.1002/cbf.4075] [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: 02/16/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
The interaction between murine double minute 2 (MDM2) and p53, marked by transcriptional induction and feedback inhibition, orchestrates a functional loop dictating cellular fate. The functional loop comprising p53-MDM2 axis is made up of an interactome consisting of approximately 81 proteins, which are spatio-temporally regulated and involved in DNA repair mechanisms. Biochemical and genetic alterations of the interactome result in dysregulation of the p53-mdm2 axis that leads to gastrointestinal (GI) cancers. A large subset of interactome is well known and it consists of proteins that either stabilize p53 or MDM2 and proteins that target the p53-MDM2 complex for ubiquitin-mediated destruction. Upstream signaling events brought about by growth factors and chemical messengers invoke a wide variety of posttranslational modifications in p53-MDM2 axis. Biochemical changes in the transactivation domain of p53 impact the energy landscape, induce conformational switching, alter interaction potential and could change solubility of p53 to redefine its co-localization, translocation and activity. A diverse set of chemical compounds mimic physiological effectors and simulate biochemical modifications of the p53-MDM2 interactome. p53-MDM2 interactome plays a crucial role in DNA damage and repair process. Genetic aberrations in the interactome, have resulted in cancers of GI tract (pancreas, liver, colorectal, gastric, biliary, and esophageal). We present in this article a review of the overall changes in the p53-MDM2 interactors and the effectors that form an epicenter for the development of next-generation molecules for understanding and targeting GI cancers.
Collapse
Affiliation(s)
- Poornachandra Yedla
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
- Department of Pharmacogenomics, Institute of Translational Research, Asian Healthcare Foundation, Hyderabad, Telangana, India
| | - Pranav Bhamidipati
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
- Department of Life Sciences, Imperial College London, London, UK
| | - Riyaz Syed
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
| | - Ramars Amanchy
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
| |
Collapse
|
24
|
Zhang H, Jiang L, Du X, Qian Z, Wu G, Jiang Y, Mao Z. The cGAS-Ku80 complex regulates the balance between two end joining subpathways. Cell Death Differ 2024; 31:792-803. [PMID: 38664591 PMCID: PMC11164703 DOI: 10.1038/s41418-024-01296-4] [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: 10/26/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 06/12/2024] Open
Abstract
As the major DNA sensor that activates the STING-TBK1 signaling cascade, cGAS is mainly present in the cytosol. A number of recent reports have indicated that cGAS also plays critical roles in the nucleus. Our previous work demonstrated for the first time that cGAS is translocated to the nucleus upon the occurrence of DNA damage and inhibits homologous recombination (HR), one of the two major pathways of DNA double strand break (DSB) repair. However, whether nuclear cGAS regulates the other DSB repair pathway, nonhomologous end joining (NHEJ), which can be further divided into the less error-prone canonical NHEJ (c-NHEJ) and more mutagenic alternative NHEJ (alt-NHEJ) subpathways, has not been characterized. Here, we demonstrated that cGAS tipped the balance of the two NHEJ subpathways toward c-NHEJ. Mechanistically, the cGAS-Ku80 complex enhanced the interaction between DNA-PKcs and the deubiquitinase USP7 to improve DNA-PKcs protein stability, thereby promoting c-NHEJ. In contrast, the cGAS-Ku80 complex suppressed alt-NHEJ by directly binding to the promoter of Polθ to suppress its transcription. Together, these findings reveal a novel function of nuclear cGAS in regulating DSB repair, suggesting that the presence of cGAS in the nucleus is also important in the maintenance of genome integrity.
Collapse
Affiliation(s)
- Haiping Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lijun Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xinyi Du
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhen Qian
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guizhu Wu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Ying Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| |
Collapse
|
25
|
Mahapatra K, Roy S. SOG1 and BRCA1 Interdependently Regulate RAD54 Expression for Repairing Salinity-Induced DNA Double-Strand Breaks in Arabidopsis. PLANT & CELL PHYSIOLOGY 2024; 65:708-728. [PMID: 38242160 DOI: 10.1093/pcp/pcae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
As sessile organisms, land plants experience various forms of environmental stresses throughout their life span. Therefore, plants have developed extensive and complicated defense mechanisms, including a robust DNA damage response (DDR) and DNA repair systems for maintaining genome integrity. In Arabidopsis, the NAC [NO APICAL MERISTEM (NAM), ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR (ATAF), CUP-SHAPED COTYLEDON (CUC)] domain family transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) plays an important role in regulating DDR. Here, we show that SOG1 plays a key role in regulating the repair of salinity-induced DNA double-strand breaks (DSBs) via the homologous recombination (HR) pathway in Arabidopsis. The sog1-1 mutant seedlings display a considerably slower rate of repair of salinity-induced DSBs. Accumulation of SOG1 protein increases in wild-type Arabidopsis under salinity stress, and it enhances the expression of HR pathway-related genes, including RAD51, RAD54 and BReast CAncer gene 1 (BRCA1), respectively, as found in SOG1 overexpression lines. SOG1 binds specifically to the AtRAD54 promoter at the 5'-(N)4GTCAA(N)3C-3' consensus sequence and positively regulates its expression under salinity stress. The phenotypic responses of sog1-1/atrad54 double mutants suggest that SOG1 functions upstream of RAD54, and both these genes are essential in regulating DDR under salinity stress. Furthermore, SOG1 interacts directly with BRCA1, an important component of the HR-mediated DSB repair pathway in plants, where BRCA1 appears to facilitate the binding of SOG1 to the RAD54 promoter. At the genetic level, SOG1 and BRCA1 function interdependently in modulating RAD54 expression under salinity-induced DNA damage. Together, our results suggest that SOG1 regulates the repair of salinity-induced DSBs via the HR-mediated pathway through genetic interactions with RAD54 and BRCA1 in Arabidopsis.
Collapse
Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104 West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104 West Bengal, India
| |
Collapse
|
26
|
Sanese P, De Marco K, Lepore Signorile M, La Rocca F, Forte G, Latrofa M, Fasano C, Disciglio V, Di Nicola E, Pantaleo A, Bianco G, Spilotro V, Ferroni C, Tubertini M, Labarile N, De Marinis L, Armentano R, Gigante G, Lantone V, Lantone G, Naldi M, Bartolini M, Varchi G, Del Rio A, Grossi V, Simone C. The novel SMYD3 inhibitor EM127 impairs DNA repair response to chemotherapy-induced DNA damage and reverses cancer chemoresistance. J Exp Clin Cancer Res 2024; 43:151. [PMID: 38812026 PMCID: PMC11137994 DOI: 10.1186/s13046-024-03078-9] [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: 02/13/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND SMYD3 has been found implicated in cancer progression. Its overexpression correlates with cancer growth and invasion, especially in gastrointestinal tumors. SMYD3 transactivates multiple oncogenic mechanisms, favoring cancer development. Moreover, it was recently shown that SMYD3 is required for DNA restoration by promoting homologous recombination (HR) repair. METHODS In cellulo and in vivo models were employed to investigate the role of SMYD3 in cancer chemoresistance. Analyses of SMYD3-KO cells, drug-resistant cancer cell lines, patients' residual gastric or rectal tumors that were resected after neoadjuvant therapy and mice models were performed. In addition, the novel SMYD3 covalent inhibitor EM127 was used to evaluate the impact of manipulating SMYD3 activity on the sensitization of cancer cell lines, tumorspheres and cancer murine models to chemotherapeutics (CHTs). RESULTS Here we report that SMYD3 mediates cancer cell sensitivity to CHTs. Indeed, cancer cells lacking SMYD3 functions showed increased responsiveness to CHTs, while restoring its expression promoted chemoresistance. Specifically, SMYD3 is essential for the repair of CHT-induced double-strand breaks as it methylates the upstream sensor ATM and allows HR cascade propagation through CHK2 and p53 phosphorylation, thereby promoting cancer cell survival. SMYD3 inhibition with the novel compound EM127 showed a synergistic effect with CHTs in colorectal, gastric, and breast cancer cells, tumorspheres, and preclinical colorectal cancer models. CONCLUSIONS Overall, our results show that targeting SMYD3 may be an effective therapeutic strategy to overcome chemoresistance.
Collapse
Affiliation(s)
- Paola Sanese
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Francesca La Rocca
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Marialaura Latrofa
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Elisabetta Di Nicola
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Antonino Pantaleo
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Giusy Bianco
- Animal Facility, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Vito Spilotro
- Animal Facility, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Claudia Ferroni
- Institute of Organic Synthesis and Photoreactivity - National Research Council, Bologna, 40129, Italy
| | - Matilde Tubertini
- Institute of Organic Synthesis and Photoreactivity - National Research Council, Bologna, 40129, Italy
- Department of Chemical and Environmental Sciences, University of Insubria, Como, 22100, Italy
| | - Nicoletta Labarile
- Histopathology Unit, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Lucia De Marinis
- Histopathology Unit, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Raffaele Armentano
- Histopathology Unit, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Gianluigi Gigante
- General Surgery Unit, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Valerio Lantone
- General Surgery Unit, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
- General Surgery Unit, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, Bari, 70124, Italy
| | | | - Marina Naldi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, 40126, Italy
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, 40126, Italy
| | - Greta Varchi
- Institute of Organic Synthesis and Photoreactivity - National Research Council, Bologna, 40129, Italy
| | - Alberto Del Rio
- Institute of Organic Synthesis and Photoreactivity - National Research Council, Bologna, 40129, Italy
- Innovamol Consulting Srl, Modena, 41126, Italy
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy.
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy.
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, Bari, 70124, Italy.
| |
Collapse
|
27
|
Jian P, Liu J, Li L, Song Q, Zhang D, Zhang S, Chai C, Zhao H, Zhao G, Zhu H, Qiao J. AcrR1, a novel TetR/AcrR family repressor, mediates acid and antibiotic resistance and nisin biosynthesis in Lactococcus lactis F44. J Dairy Sci 2024:S0022-0302(24)00806-3. [PMID: 38762103 DOI: 10.3168/jds.2024-24754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/31/2024] [Indexed: 05/20/2024]
Abstract
Lactococcus lactis, widely used in the manufacture of dairy products, encounters various environmental stresses both in natural habitats and during industrial processes. It has evolved intricate machinery of stress sensing and defense to survive harsh stress conditions. Here, we identified a novel TetR/AcrR family transcription regulator, designated AcrR1, to be a repressor for acid and antibiotic tolerance that was derepressed in the presence of vancomycin or under acid stress. The survival rates of acrR1 deletion strain ΔAcrR1 under acid and vancomycin stresses were about 28.7-fold (pH 3.0, HCl), 8.57-fold (pH 4.0, lactic acid) and 2.73-fold (300 ng/mL vancomycin) as that of original strain F44. We also demonstrated that ΔAcrR1 was better able to maintain intracellular pH homeostasis and had a lower affinity to vancomycin. No evident effects of AcrR1 deletion on the growth and morphology of strain F44 were observed. Subsequently, we characterized that the transcription level of genes associated with amino acids biosynthesis, carbohydrate transport and metabolism, multiple drug resistance and DNA repair proteins significantly upregulated in ΔAcrR1 using transcriptome analysis and quantitative reverse transcription-PCR (qRT-PCR) assays. Additionally, AcrR1 could repress the transcription of nisin post-translational modification gene, nisC, leading to a 16.3% increase in nisin yield after AcrR1 deletion. Our results not only refined the knowledge of the regulatory mechanism of TetR/AcrR family regulator in L. lactis, but presented a potential strategy to enhance industrial production of nisin.
Collapse
Affiliation(s)
- Pingqiu Jian
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Jiaheng Liu
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China.
| | - Li Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Qianqian Song
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Di Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Shenyi Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Chaofan Chai
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Hui Zhao
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hongji Zhu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| |
Collapse
|
28
|
Kulkarni A, Zhou J, Biyani N, Kathad U, Banerjee PP, Srivastava S, Prucsi Z, Solarczyk K, Bhatia K, Ewesuedo RB, Sharma P. LP-184, a Novel Acylfulvene Molecule, Exhibits Anticancer Activity against Diverse Solid Tumors with Homologous Recombination Deficiency. CANCER RESEARCH COMMUNICATIONS 2024; 4:1199-1210. [PMID: 38630886 PMCID: PMC11072798 DOI: 10.1158/2767-9764.crc-23-0554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/11/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Homologous recombination (HR)-related gene alterations are present in a significant subset of prostate, breast, ovarian, pancreatic, lung, and colon cancers rendering these tumors as potential responders to specific DNA damaging agents. A small molecule acylfulvene prodrug, LP-184, metabolizes to an active compound by the oxidoreductase activity of enzyme prostaglandin reductase 1 (PTGR1), which is frequently elevated in multiple solid tumor types. Prior work demonstrated that cancer cell lines deficient in a spectrum of DNA damage repair (DDR) pathway genes show increased susceptibility to LP-184. Here, we investigated the potential of LP-184 in targeting multiple tumors with impaired HR function and its mechanism of action as a DNA damaging agent. LP-184 induced elevated DNA double-strand breaks in HR deficient (HRD) cancer cells. Depletion of key HR components BRCA2 or ataxia telangiectasia mutated (ATM) in cancer cells conferred up to 12-fold increased sensitivity to the LP-184. LP-184 showed nanomolar potency in a diverse range of HRD cancer models, including prostate cancer organoids, leiomyosarcoma cell lines, and patient-derived tumor graft models of lung, pancreatic, and prostate cancers. LP-184 demonstrated complete, durable tumor regression in 10 patient-derived xenograft (PDX) models of HRD triple-negative breast cancer (TNBC) including those resistant to PARP inhibitors (PARPi). LP-184 further displayed strong synergy with PARPi in ovarian and prostate cancer cell lines as well as in TNBC PDX models. These preclinical findings illustrate the potential of LP-184 as a pan-HRD cancer therapeutic. Taken together, our results support continued clinical evaluation of LP-184 in a large subset of HRD solid tumors. SIGNIFICANCE New agents with activity against DDR-deficient solid tumors refractory to standard-of-care therapies are needed. We report multiple findings supporting the potential for LP-184, a novel alkylating agent with three FDA orphan drug designations, to fill this void clinically: strong nanomolar potency; sustained, durable regression of solid tumor xenografts; synthetic lethality with HR defects. LP-184 adult phase IA trial to assess safety in advanced solid tumors is ongoing.
Collapse
Affiliation(s)
| | | | | | | | - Partha P. Banerjee
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Shiv Srivastava
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | | | | | | | | | | |
Collapse
|
29
|
Trajano-Silva LAM, Mule SN, Palmisano G. Molecular tools to regulate gene expression in Trypanosoma cruzi. Adv Clin Chem 2024; 120:169-190. [PMID: 38762241 DOI: 10.1016/bs.acc.2024.04.008] [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] [Indexed: 05/20/2024]
Abstract
Developing molecular strategies to manipulate gene expression in trypanosomatids is challenging, particularly with respect to the unique gene expression mechanisms adopted by these unicellular parasites, such as polycistronic mRNA transcription and multi-gene families. In the case of Trypanosoma cruzi (T. cruzi), the causative agent of Chagas Disease, the lack of RNA interference machinery further complicated functional genetic studies important for understanding parasitic biology and developing biomarkers and potential therapeutic targets. Therefore, alternative methods of performing knockout and/or endogenous labelling experiments were developed to identify and understand the function of proteins for survival and interaction with the host. In this review, we present the main tools for the genetic manipulation of T. cruzi, focusing on the Clustered Regularly Interspaced Short Palindromic Repeats Cas9-associated system technique widely used in this organism. Moreover, we highlight the importance of using these tools to elucidate the function of uncharacterized and glycosylated proteins. Further developments of these technologies will allow the identification of new biomarkers, therapeutic targets and potential vaccines against Chagas disease with greater efficiency and speed.
Collapse
Affiliation(s)
- Lays Adrianne M Trajano-Silva
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Simon Ngao Mule
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Giuseppe Palmisano
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil; School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
| |
Collapse
|
30
|
Slootbeek PHJ, Tolmeijer SH, Mehra N, Schalken JA. Therapeutic biomarkers in metastatic castration-resistant prostate cancer: does the state matter? Crit Rev Clin Lab Sci 2024; 61:178-204. [PMID: 37882463 DOI: 10.1080/10408363.2023.2266482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
The treatment of metastatic castration-resistant prostate cancer (mCRPC) has been fundamentally transformed by our greater understanding of its complex biological mechanisms and its entrance into the era of precision oncology. A broad aim is to use the extreme heterogeneity of mCRPC by matching already approved or new targeted therapies to the correct tumor genotype. To achieve this, tumor DNA must be obtained, sequenced, and correctly interpreted, with individual aberrations explored for their druggability, taking into account the hierarchy of driving molecular pathways. Although tumor tissue sequencing is the gold standard, tumor tissue can be challenging to obtain, and a biopsy from one metastatic site or primary tumor may not provide an accurate representation of the current genetic underpinning. Sequencing of circulating tumor DNA (ctDNA) might catalyze precision oncology in mCRPC, as it enables real-time observation of genomic changes in tumors and allows for monitoring of treatment response and identification of resistance mechanisms. Moreover, ctDNA can be used to identify mutations that may not be detected in solitary metastatic lesions and can provide a more in-depth understanding of inter- and intra-tumor heterogeneity. Finally, ctDNA abundance can serve as a prognostic biomarker in patients with mCRPC.The androgen receptor (AR)-axis is a well-established therapeutical target for prostate cancer, and through ctDNA sequencing, insights have been obtained in (temporal) resistance mechanisms that develop through castration resistance. New third-generation AR-axis inhibitors are being developed to overcome some of these resistance mechanisms. The druggability of defects in the DNA damage repair machinery has impacted the treatment landscape of mCRPC in recent years. For patients with deleterious gene aberrations in genes linked to homologous recombination, particularly BRCA1 or BRCA2, PARP inhibitors have shown efficacy compared to the standard of care armamentarium, but platinum-based chemotherapy may be equally effective. A hierarchy exists in genes associated with homologous recombination, where, besides the canonical genes in this pathway, not every other gene aberration predicts the same likelihood of response. Moreover, evidence is emerging on cross-resistance between therapies such as PARP inhibitors, platinum-based chemotherapy and even radioligand therapy that target this genotype. Mismatch repair-deficient patients can experience a beneficial response to immune checkpoint inhibitors. Activation of other cellular signaling pathways such as PI3K, cell cycle, and MAPK have shown limited success with monotherapy, but there is potential in co-targeting these pathways with combination therapy, either already witnessed or anticipated. This review outlines precision medicine in mCRPC, zooming in on the role of ctDNA, to identify genomic biomarkers that may be used to tailor molecularly targeted therapies. The most common druggable pathways and outcomes of therapies matched to these pathways are discussed.
Collapse
Affiliation(s)
- Peter H J Slootbeek
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherland
| | - Sofie H Tolmeijer
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherland
| | - Niven Mehra
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherland
| | - Jack A Schalken
- Department of Experimental Urology, Research Institute of Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
| |
Collapse
|
31
|
Meschichi A, Rosa S. Plant chromatin on the move: an overview of chromatin mobility during transcription and DNA repair. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:953-962. [PMID: 36811211 DOI: 10.1111/tpj.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
It has become increasingly clear in recent years that chromosomes are highly dynamic entities. Chromatin mobility and re-arrangement are involved in many biological processes, including gene regulation and the maintenance of genome stability. Despite extensive studies on chromatin mobility in yeast and animal systems, up until recently, not much had been investigated at this level in plants. For plants to achieve proper growth and development, they need to respond rapidly and appropriately to environmental stimuli. Therefore, understanding how chromatin mobility can support plant responses may offer profound insights into the functioning of plant genomes. In this review, we discuss the state of the art related to chromatin mobility in plants, including the available technologies for their role in various cellular processes.
Collapse
Affiliation(s)
- Anis Meschichi
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
| |
Collapse
|
32
|
Qu H, Wang Y, Yan Q, Fan C, Zhang X, Wang D, Guo C, Chen P, Shi L, Liao Q, Zhou M, Wang F, Zeng Z, Xiang B, Xiong W. CircCDYL2 bolsters radiotherapy resistance in nasopharyngeal carcinoma by promoting RAD51 translation initiation for enhanced homologous recombination repair. J Exp Clin Cancer Res 2024; 43:122. [PMID: 38654320 PMCID: PMC11036759 DOI: 10.1186/s13046-024-03049-0] [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: 01/11/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Radiation therapy stands to be one of the primary approaches in the clinical treatment of malignant tumors. Nasopharyngeal Carcinoma, a malignancy predominantly treated with radiation therapy, provides an invaluable model for investigating the mechanisms underlying radiation therapy resistance in cancer. While some reports have suggested the involvement of circRNAs in modulating resistance to radiation therapy, the underpinning mechanisms remain unclear. METHODS RT-qPCR and in situ hybridization were used to detect the expression level of circCDYL2 in nasopharyngeal carcinoma tissue samples. The effect of circCDYL2 on radiotherapy resistance in nasopharyngeal carcinoma was demonstrated by in vitro and in vivo functional experiments. The HR-GFP reporter assay determined that circCDYL2 affected homologous recombination repair. RNA pull down, RIP, western blotting, IF, and polysome profiling assays were used to verify that circCDYL2 promoted the translation of RAD51 by binding to EIF3D protein. RESULTS We have identified circCDYL2 as highly expressed in nasopharyngeal carcinoma tissues, and it was closely associated with poor prognosis. In vitro and in vivo experiments demonstrate that circCDYL2 plays a pivotal role in promoting radiotherapy resistance in nasopharyngeal carcinoma. Our investigation unveils a specific mechanism by which circCDYL2, acting as a scaffold molecule, recruits eukaryotic translation initiation factor 3 subunit D protein (EIF3D) to the 5'-UTR of RAD51 mRNA, a crucial component of the DNA damage repair pathway to facilitate the initiation of RAD51 translation and enhance homologous recombination repair capability, and ultimately leads to radiotherapy resistance in nasopharyngeal carcinoma. CONCLUSIONS These findings establish a novel role of the circCDYL2/EIF3D/RAD51 axis in nasopharyngeal carcinoma radiotherapy resistance. Our work not only sheds light on the underlying molecular mechanism but also highlights the potential of circCDYL2 as a therapeutic sensitization target and a promising prognostic molecular marker for nasopharyngeal carcinoma.
Collapse
Affiliation(s)
- Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
| | - Qijia Yan
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Xiangyan Zhang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Dan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Pan Chen
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Lei Shi
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
| |
Collapse
|
33
|
Wang J, Takyi NA, Hsiao YC, Tang Q, Chen YT, Liu CW, Ma J, Qi R, Bian K, Peng Z, Essigmann JM, Lu K, Wetmore SD, Li D. Stable Interstrand Cross-Links Generated from the Repair of 1, N6-Ethenoadenine in DNA by α-Ketoglutarate/Fe(II)-Dependent Dioxygenase ALKBH2. J Am Chem Soc 2024; 146:10381-10392. [PMID: 38573229 PMCID: PMC11060877 DOI: 10.1021/jacs.3c12890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA cross-links severely challenge replication and transcription in cells, promoting senescence and cell death. In this paper, we report a novel type of DNA interstrand cross-link (ICL) produced as a side product during the attempted repair of 1,N6-ethenoadenine (εA) by human α-ketoglutarate/Fe(II)-dependent enzyme ALKBH2. This stable/nonreversible ICL was characterized by denaturing polyacrylamide gel electrophoresis analysis and quantified by high-resolution LC-MS in well-matched and mismatched DNA duplexes, yielding 5.7% as the highest level for cross-link formation. The binary lesion is proposed to be generated through covalent bond formation between the epoxide intermediate of εA repair and the exocyclic N6-amino group of adenine or the N4-amino group of cytosine residues in the complementary strand under physiological conditions. The cross-links occur in diverse sequence contexts, and molecular dynamics simulations rationalize the context specificity of cross-link formation. In addition, the cross-link generated from attempted εA repair was detected in cells by highly sensitive LC-MS techniques, giving biological relevance to the cross-link adducts. Overall, a combination of biochemical, computational, and mass spectrometric methods was used to discover and characterize this new type of stable cross-link both in vitro and in human cells, thereby uniquely demonstrating the existence of a potentially harmful ICL during DNA repair by human ALKBH2.
Collapse
Affiliation(s)
- Jie Wang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Nathania A Takyi
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Yi-Tzai Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jian Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Rui Qi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Zhiyuan Peng
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - John M Essigmann
- Departments of Biological Engineering, Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| |
Collapse
|
34
|
Xu M, Qian Y, Li X, Gu B, He S, Lu X, Song S. Janus ACSP Nanoparticle for Synergistic Chemodynamic Therapy and Radiosensitization. ACS APPLIED MATERIALS & INTERFACES 2024; 16:17242-17252. [PMID: 38556729 DOI: 10.1021/acsami.4c00499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Protective autophagy and DNA damage repair lead to tumor radio-resistance. Some hypoxic tumors exhibit a low radiation energy absorption coefficient in radiation therapy. High doses of X-rays may lead to side effects in the surrounding normal tissues. In order to overcome the radio-resistance and improve the efficacy of radiotherapy based on the characteristics of the tumor microenvironment, the development of radiosensitizers has attracted much attention. In this study, a Janus ACSP nanoparticle (NP) was developed for chemodynamic therapy and radiosensitization. The reactive oxygen species generated by the Fenton-like reaction regulated the distribution of cell cycles from a radioresistant phase to a radio-sensitive phase. The high-Z element, Au, enhanced the production of hydroxyl radicals (•OH) under X-ray radiation, promoting DNA damage and cell apoptosis. The NP delayed DNA damage repair by interfering with certain proteins involved in the DNA repair signaling pathway. In vivo experiments demonstrated that the combination of the copper-ion-based Fenton-like reaction and low-dose X-ray radiation enhanced the effectiveness of radiotherapy, providing a novel approach for synergistic chemodynamic and radiosensitization therapy. This study provides valuable insights and strategies for the development and application of NPs in cancer treatment.
Collapse
Affiliation(s)
- Mingzhen Xu
- Department of Nuclear Medicine, Shanghai Proton and Heavy Ion Center, Fudan University Shanghai Cancer Center, Shanghai 201315, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 201315, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai 201315, China
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Xuhui District, No. 270 Dong'an Road, Shanghai 200032, China
| | - Yuyi Qian
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Xuhui District, No. 270 Dong'an Road, Shanghai 200032, China
| | - Xinyi Li
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Xuhui District, No. 270 Dong'an Road, Shanghai 200032, China
| | - Bingxin Gu
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Xuhui District, No. 270 Dong'an Road, Shanghai 200032, China
| | - Simin He
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Xuhui District, No. 270 Dong'an Road, Shanghai 200032, China
| | - Xin Lu
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Xuhui District, No. 270 Dong'an Road, Shanghai 200032, China
| | - Shaoli Song
- Department of Nuclear Medicine, Shanghai Proton and Heavy Ion Center, Fudan University Shanghai Cancer Center, Shanghai 201315, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 201315, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai 201315, China
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Xuhui District, No. 270 Dong'an Road, Shanghai 200032, China
| |
Collapse
|
35
|
Alanazi AFR, Parkinson GN, Haider S. Structural Motifs at the Telomeres and Their Role in Regulatory Pathways. Biochemistry 2024; 63:827-842. [PMID: 38481135 PMCID: PMC10993422 DOI: 10.1021/acs.biochem.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand. While many essential proteins at telomeres have been identified, the intricacies of their interactions and structural details are still not fully understood. This Perspective highlights recent advancements in comprehending the structures associated with human telomeres. It emphasizes the significance of telomeres, explores various telomeric structural motifs, and delves into the structural biology surrounding telomeres and telomerase. Furthermore, telomeric loops, their topologies, and the associated proteins that contribute to the safeguarding of telomeres are discussed.
Collapse
Affiliation(s)
- Abeer F R Alanazi
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, United Kingdom
| |
Collapse
|
36
|
Lin L, Hu P, Luo M, Chen X, Xiao M, Zhong Z, Peng S, Chen G, Yang G, Zhang F, Zhang Y. CircNOP14 increases the radiosensitivity of hepatocellular carcinoma via inhibition of Ku70-dependent DNA damage repair. Int J Biol Macromol 2024; 264:130541. [PMID: 38460628 DOI: 10.1016/j.ijbiomac.2024.130541] [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: 11/05/2023] [Revised: 02/13/2024] [Accepted: 02/27/2024] [Indexed: 03/11/2024]
Abstract
Circular RNAs (circRNAs) are profoundly affected in hepatocellular carcinoma (HCC) through various pathways. However, the role of circRNAs in the radiosensitivity of HCC cells is yet to be explored. In this study, we identified a circRNA-hsa_circ_0006737 (circNOP14) involved in the radiosensitivity of HCC. We found that circNOP14 increased the radiosensitivity of HCC cells both in vitro and in vivo. Notably, using a circRNA pulldown assay and RNA-binding protein immunoprecipitation, we identified Ku70 as a novel and robust interacting protein of circNOP14. Mechanistically, circNOP14 interacts with Ku70 and prevents its nuclear translocation, thereby increasing irradiation-induced DNA damage. Therefore, our findings may provide a predictive indicator and intervention option for 125I brachytherapy or external radiotherapy in HCC.
Collapse
Affiliation(s)
- Letao Lin
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Pan Hu
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Ma Luo
- Department of Medical Imaging, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Xi Chen
- Department of Oncology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518000, PR China
| | - Meigui Xiao
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Zhihui Zhong
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Sheng Peng
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Guanyu Chen
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Guang Yang
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Fujun Zhang
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China.
| | - Yanling Zhang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, PR China.
| |
Collapse
|
37
|
Chen W, Mi C, Zhang Y, Yang Y, Huang W, Xu Z, Zhao J, Wang R, Wang M, Wan S, Wang X, Zhang H. Defective Homologous Recombination Repair By Up-Regulating Lnc-HZ10/Ahr Loop in Human Trophoblast Cells Induced Miscarriage. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2207435. [PMID: 38286681 PMCID: PMC10987163 DOI: 10.1002/advs.202207435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/27/2023] [Indexed: 01/31/2024]
Abstract
Human trophoblast cells are crucial for healthy pregnancy. However, whether the defective homologous recombination (HR) repair of dsDNA break (DSB) in trophoblast cells may induce miscarriage is completely unknown. Moreover, the abundance of BRCA1 (a crucial protein for HR repair), its recruitment to DSB foci, and its epigenetic regulatory mechanisms, are also fully unexplored. In this work, it is identified that a novel lnc-HZ10, which is highly experssed in villous tissues of recurrent miscarriage (RM) vs their healthy control group, suppresses HR repair of DSB in trophoblast cell. Lnc-HZ10 and AhR (aryl hydrocarbon receptor) form a positive feedback loop. AhR acts as a transcription factor to promote lnc-HZ10 transcription. Meanwhile, lnc-HZ10 also increases AhR levels by suppressing its CUL4B-mediated ubiquitination degradation. Subsequently, AhR suppresses BRCA1 transcription; and lnc-HZ10 (mainly 1-447 nt) interacts with γ-H2AX; and thus, impairs its interactions with BRCA1. BPDE exposure may trigger this loop to suppress HR repair in trophoblast cells, possibly inducing miscarriage. Knockdown of murine Ahr efficiently recovers HR repair in placental tissues and alleviates miscarriage in a mouse miscarriage model. Therefore, it is suggested that AhR/lnc-HZ10/BRCA1 axis may be a promising target for alleviation of unexplained miscarriage.
Collapse
Affiliation(s)
- Weina Chen
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
- Key Laboratory of Environment and Female Reproductive HealthWest China School of Public Health & West China Fourth HospitalSichuan UniversityChengdu610041China
| | - Chenyang Mi
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Ying Zhang
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Yang Yang
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Wenxin Huang
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Zhongyan Xu
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Jingsong Zhao
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Rong Wang
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Manli Wang
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Shukun Wan
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Xiaoqing Wang
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Huidong Zhang
- Research Center for Environment and Female Reproductive HealthThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| |
Collapse
|
38
|
Edsjö A, Gisselsson D, Staaf J, Holmquist L, Fioretos T, Cavelier L, Rosenquist R. Current and emerging sequencing-based tools for precision cancer medicine. Mol Aspects Med 2024; 96:101250. [PMID: 38330674 DOI: 10.1016/j.mam.2024.101250] [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: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024]
Abstract
Current precision cancer medicine is dependent on the analyses of a plethora of clinically relevant genomic aberrations. During the last decade, next-generation sequencing (NGS) has gradually replaced most other methods for precision cancer diagnostics, spanning from targeted tumor-informed assays and gene panel sequencing to global whole-genome and whole-transcriptome sequencing analyses. The shift has been impelled by a clinical need to assess an increasing number of genomic alterations with diagnostic, prognostic and predictive impact, including more complex biomarkers (e.g. microsatellite instability, MSI, and homologous recombination deficiency, HRD), driven by the parallel development of novel targeted therapies and enabled by the rapid reduction in sequencing costs. This review focuses on these sequencing-based methods, puts their emergence in a historic perspective, highlights their clinical utility in diagnostics and decision-making in pediatric and adult cancer, as well as raises challenges for their clinical implementation. Finally, the importance of applying sensitive tools for longitudinal monitoring of treatment response and detection of measurable residual disease, as well as future avenues in the rapidly evolving field of sequencing-based methods are discussed.
Collapse
Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.
| | - David Gisselsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, Sweden
| | - Louise Holmquist
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Lucia Cavelier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden; Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
39
|
Rojas-Barón L, Hermosilla C, Taubert A, Velásquez ZD. Toxoplasma gondii infection-induced host cellular DNA damage is strain-dependent and leads to the activation of the ATM-dependent homologous recombination pathway. Front Cell Infect Microbiol 2024; 14:1374659. [PMID: 38524184 PMCID: PMC10957594 DOI: 10.3389/fcimb.2024.1374659] [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: 01/22/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Toxoplasma gondii is a globally occurring apicomplexan parasite that infects humans and animals. Globally, different typical and atypical haplotypes of T. gondii induce varying pathologies in hosts. As an obligate intracellular protozoon, T. gondii was shown to interfere with host cell cycle progression, leading to mitotic spindle alteration, chromosome segregation errors and cytokinesis failure which all may reflect chromosomal instability. Referring to strain-dependent virulence, we here studied the potential of different T. gondii strains (RH, Me49 and NED) to drive DNA damage in primary endothelial host cells. Utilizing microscopic analyses, comet assays and γ-H2AX quantification, we demonstrated a strain-dependent induction of binucleated host cells, DNA damage and DNA double strand breaks, respectively, in T. gondii-infected cells with the RH strain driving the most prominent effects. Interestingly, only the NED strain significantly triggered micronuclei formation in T. gondii-infected cells. Focusing on the RH strain, we furthermore demonstrated that T. gondii-infected primary host cells showed a DNA damage response by activating the ATM-dependent homologous recombination (HR) pathway. In contrast, key molecules of the nonhomologous DNA end joining (NHEJ) pathway were either not affected or downregulated in RH-infected host cells, suggesting that this pathway is not activated by infection. In conclusion, current finding suggests that T. gondii infection affects the host cell genome integrity in a strain-dependent manner by causing DNA damage and chromosomal instability.
Collapse
Affiliation(s)
| | | | | | - Zahady D. Velásquez
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| |
Collapse
|
40
|
Arizala D, Arif M. Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri. Genome Biol Evol 2024; 16:evae032. [PMID: 38385549 PMCID: PMC10946231 DOI: 10.1093/gbe/evae032] [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: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43 bp to 119 kb and 36 bp to 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.
Collapse
Affiliation(s)
- Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| |
Collapse
|
41
|
Casadei C, Scarpi E, Conteduca V, Gurioli G, Cursano MC, Brighi N, Lolli C, Schepisi G, Basso U, Fornarini G, Bleve S, Farolfi A, Altavilla A, Burgio SL, Giunta EF, Gianni C, Filograna A, Ulivi P, Olmos D, Castro E, De Giorgi U. Inherited Mutations in DNA Damage Repair Genes in Italian Men with Metastatic Prostate Cancer: Results from the Meet-URO 10 Study. EUR UROL SUPPL 2024; 61:44-51. [PMID: 38384439 PMCID: PMC10879937 DOI: 10.1016/j.euros.2024.01.015] [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] [Accepted: 01/25/2024] [Indexed: 02/23/2024] Open
Abstract
Background The prevalence of pathogenic germline mutations in DNA damage repair (gDDR) genes in the Italian population is unknown. Objective In this prospective multicenter cohort study, we evaluated the prevalence of gDDR alterations in the Italian population affected by metastatic prostate cancer (mPCa) and analyzed the impact on response to therapy, survival, and time to castration resistance. Design setting and participants In an observational prospective trial, 300 consecutive Italian mPCa patients, enrolled in the Meet-Uro-10 trial from three academic Italian centers, were recruited between 2017 and 2019 and were screened for gDDR mutations in 107 genes. Outcome measurements and statistical analysis The primary endpoint was to assess the prevalence of gDDR mutations in the Italian population of patients with mPCa. The secondary endpoints included the association of gDDR subgroups with metastatic onset, Gleason score, and time to castration resistance. Results and limitations We identified 297 valuable patients. Forty-six patients had a pathogenic/likely pathogenic variant (15.5%, 95% confidence interval: 11.4-19.6): the more frequent was gBRCA2 found in nine cases (3%), followed by gATM in five cases (1.7%). In patients without mutations, longer median overall survival was observed with the sequence docetaxel-androgen receptor signaling inhibitor (ARSI) than with the sequence ARSI-docetaxel (87.9 vs 42 mo, p = 0.0001). In a univariate analysis, the median time to castration resistance in gDDR mutated patients was 19.8 mo, versus 23.7 mo in no mutated patients (p = 0.024). There were no associations of gDDR subgroups with metastatic onset and Gleason score ≥8. In our cohort, variants of unknown significance in gDDR genes were found in 80 patients and might have a prognostic relevance. Conclusions The study reported the prevalence of gDDR in the Italian population. The presence of gBRCA2 mutations correlates with a shorter time to the onset of castration resistance disease. Patient summary The prevalence of gBRCA2 in the Italian population is 3%, which is similar to that in the Spanish population, identifying similarities between people of the Western Mediterranean area.
Collapse
Affiliation(s)
- Chiara Casadei
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Emanuela Scarpi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | | | - Giorgia Gurioli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | | | - Nicole Brighi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Cristian Lolli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Giuseppe Schepisi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | | | | | - Sara Bleve
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Alberto Farolfi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Amelia Altavilla
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Salvatore Luca Burgio
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | | | - Caterina Gianni
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Alessia Filograna
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Paola Ulivi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - David Olmos
- Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Elena Castro
- Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain
| | - Ugo De Giorgi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| |
Collapse
|
42
|
Akhoundova D, Francica P, Rottenberg S, Rubin MA. DNA Damage Response and Mismatch Repair Gene Defects in Advanced and Metastatic Prostate Cancer. Adv Anat Pathol 2024; 31:61-69. [PMID: 38008971 PMCID: PMC10846598 DOI: 10.1097/pap.0000000000000422] [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] [Indexed: 11/28/2023]
Abstract
Alterations in DNA damage response (DDR) and related genes are present in up to 25% of advanced prostate cancers (PCa). Most frequently altered genes are involved in the homologous recombination repair, the Fanconi anemia, and the mismatch repair pathways, and their deficiencies lead to a highly heterogeneous spectrum of DDR-deficient phenotypes. More than half of these alterations concern non- BRCA DDR genes. From a therapeutic perspective, poly-ADP-ribose polymerase inhibitors have demonstrated robust clinical efficacy in tumors with BRCA2 and BRCA1 alterations. Mismatch repair-deficient PCa, and a subset of CDK12-deficient PCa, are vulnerable to immune checkpoint inhibitors. Emerging data point to the efficacy of ATR inhibitors in PCa with ATM deficiencies. Still, therapeutic implications are insufficiently clarified for most of the non- BRCA DDR alterations, and no successful targeted treatment options have been established.
Collapse
Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research
- Department of Medical Oncology
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Paola Francica
- Department for BioMedical Research
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Sven Rottenberg
- Department for BioMedical Research
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Mark A. Rubin
- Department for BioMedical Research
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| |
Collapse
|
43
|
Rezqallah A, Torres-Esquius S, Llop-Guevara A, Cruellas M, Martinez MT, Romey M, Denkert C, Serra V, Chirivella I, Balmaña J. Two Germline Pathogenic Variants in Cancer Susceptibility Genes and Their Null Implication in Breast Cancer Pathogenesis: The Importance of Tumoral Homologous Recombination Deficiency Testing. JCO Precis Oncol 2024; 8:e2300446. [PMID: 38513169 DOI: 10.1200/po.23.00446] [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: 08/17/2023] [Revised: 12/28/2023] [Accepted: 01/22/2024] [Indexed: 03/23/2024] Open
Abstract
Homologous recombination proficiency in patients with breast cancer despite germline PALB2/RAD51C pathogenic variants.
Collapse
Affiliation(s)
- Alejandra Rezqallah
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sara Torres-Esquius
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Mara Cruellas
- Medical Oncology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - María T Martinez
- Medical Oncology Department, INCLIVA Biomedical Research Institute, Hospital Clínico de València, University of Valencia, Valencia, Spain
| | - Marcel Romey
- Institute of Pathology, Universitätsklinikum Marburg, Marburg, Germany
| | - Carsten Denkert
- Institute of Pathology, Universitätsklinikum Marburg, Marburg, Germany
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Isabel Chirivella
- Medical Oncology Department, INCLIVA Biomedical Research Institute, Hospital Clínico de València, University of Valencia, Valencia, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| |
Collapse
|
44
|
Song B, Yang P, Zhang S. Cell fate regulation governed by p53: Friends or reversible foes in cancer therapy. Cancer Commun (Lond) 2024; 44:297-360. [PMID: 38311377 PMCID: PMC10958678 DOI: 10.1002/cac2.12520] [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: 07/26/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 02/10/2024] Open
Abstract
Cancer is a leading cause of death worldwide. Targeted therapies aimed at key oncogenic driver mutations in combination with chemotherapy and radiotherapy as well as immunotherapy have benefited cancer patients considerably. Tumor protein p53 (TP53), a crucial tumor suppressor gene encoding p53, regulates numerous downstream genes and cellular phenotypes in response to various stressors. The affected genes are involved in diverse processes, including cell cycle arrest, DNA repair, cellular senescence, metabolic homeostasis, apoptosis, and autophagy. However, accumulating recent studies have continued to reveal novel and unexpected functions of p53 in governing the fate of tumors, for example, functions in ferroptosis, immunity, the tumor microenvironment and microbiome metabolism. Among the possibilities, the evolutionary plasticity of p53 is the most controversial, partially due to the dizzying array of biological functions that have been attributed to different regulatory mechanisms of p53 signaling. Nearly 40 years after its discovery, this key tumor suppressor remains somewhat enigmatic. The intricate and diverse functions of p53 in regulating cell fate during cancer treatment are only the tip of the iceberg with respect to its equally complicated structural biology, which has been painstakingly revealed. Additionally, TP53 mutation is one of the most significant genetic alterations in cancer, contributing to rapid cancer cell growth and tumor progression. Here, we summarized recent advances that implicate altered p53 in modulating the response to various cancer therapies, including chemotherapy, radiotherapy, and immunotherapy. Furthermore, we also discussed potential strategies for targeting p53 as a therapeutic option for cancer.
Collapse
Affiliation(s)
- Bin Song
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengduSichuanP. R. China
| | - Ping Yang
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengduSichuanP. R. China
| | - Shuyu Zhang
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengduSichuanP. R. China
- The Second Affiliated Hospital of Chengdu Medical CollegeChina National Nuclear Corporation 416 HospitalChengduSichuanP. R. China
- Laboratory of Radiation MedicineNHC Key Laboratory of Nuclear Technology Medical TransformationWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengduSichuanP. R. China
| |
Collapse
|
45
|
Muhammad AA, Basto C, Peterlini T, Guirouilh-Barbat J, Thomas M, Veaute X, Busso D, Lopez B, Mazon G, Le Cam E, Masson JY, Dupaigne P. Human RAD52 stimulates the RAD51-mediated homology search. Life Sci Alliance 2024; 7:e202201751. [PMID: 38081641 PMCID: PMC10713436 DOI: 10.26508/lsa.202201751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Homologous recombination (HR) is a DNA repair mechanism of double-strand breaks and blocked replication forks, involving a process of homology search leading to the formation of synaptic intermediates that are regulated to ensure genome integrity. RAD51 recombinase plays a central role in this mechanism, supported by its RAD52 and BRCA2 partners. If the mediator function of BRCA2 to load RAD51 on RPA-ssDNA is well established, the role of RAD52 in HR is still far from understood. We used transmission electron microscopy combined with biochemistry to characterize the sequential participation of RPA, RAD52, and BRCA2 in the assembly of the RAD51 filament and its activity. Although our results confirm that RAD52 lacks a mediator activity, RAD52 can tightly bind to RPA-coated ssDNA, inhibit the mediator activity of BRCA2, and form shorter RAD51-RAD52 mixed filaments that are more efficient in the formation of synaptic complexes and D-loops, resulting in more frequent multi-invasions as well. We confirm the in situ interaction between RAD51 and RAD52 after double-strand break induction in vivo. This study provides new molecular insights into the formation and regulation of presynaptic and synaptic intermediates by BRCA2 and RAD52 during human HR.
Collapse
Affiliation(s)
- Ali Akbar Muhammad
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Clara Basto
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Thibaut Peterlini
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Quebec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Canada
| | - Josée Guirouilh-Barbat
- https://ror.org/02vjkv261 INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, Université de Paris, Paris, France
| | - Melissa Thomas
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Quebec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Canada
| | - Xavier Veaute
- https://ror.org/02vjkv261 CIGEx Platform, INSERM, IRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Didier Busso
- https://ror.org/02vjkv261 CIGEx Platform, INSERM, IRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Bernard Lopez
- https://ror.org/02vjkv261 INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, Université de Paris, Paris, France
| | - Gerard Mazon
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Eric Le Cam
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Quebec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Canada
| | - Pauline Dupaigne
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| |
Collapse
|
46
|
Kim J, Yu J, Lee S, Kim S, Lee IS, Lee W, Chun S. Reverse Transcription-PCR-based Sanger Sequencing-confirmed Exon-skipping Effect of a Novel GEN1 Intronic Variant (c.1408+4A>G). Ann Lab Med 2024; 44:188-191. [PMID: 37840312 PMCID: PMC10628752 DOI: 10.3343/alm.2023.0163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/22/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Affiliation(s)
- Jiyeon Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Joonsang Yu
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seunghoo Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sollip Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - In-Seob Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sail Chun
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| |
Collapse
|
47
|
Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
Collapse
Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| |
Collapse
|
48
|
Yu W, Liu J, Liu Y, Forlenza M, Chen H. Application of CRISPR/Cas9 for Rapid Genome Editing of Pseudorabies Virus and Bovine Herpesvirus-1. Viruses 2024; 16:311. [PMID: 38400086 PMCID: PMC10892916 DOI: 10.3390/v16020311] [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: 01/28/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The CRISPR/Cas9 system is widely used to manipulate viral genomes. Although Alphaherpesvirinae genomes are large and complicated to edit, in recent years several Pseudorabies virus (PRV) mutants have been successfully generated using the CRISPR/Cas9 system. However, the application of CRISPR/Cas9 editing on another member of alpha herpesviruses, bovine herpesvirus-1 (BHV-1), is rarely reported. This paper reports a rapid and straightforward approach to manipulating herpesviruses genome using CRISPR/Cas9. The recombinant plasmids contained the left and right arm of the thymidine kinase (TK) gene of PRV or of the glycoprotein I (gI) and glycoprotein E (gE) of BHV-1. Upon the cleavage of the TK or gIgE gene by Cas9 protein, this was replaced by the enhanced green fluorescence protein (eGFP) by homologous recombination. With this approach, we generated recombinant TK-/eGFP+ PRV and gIgE-/eGFP+ BHV-1 mutants and then proceeded to characterize their biological activities in vitro and in vivo. In conclusion, we showed that alpha herpesvirus, including PRV and BHV-1, can be rapidly edited using the CRISPR/Cas9 approach paving the way to the development of animal herpesvirus vaccines.
Collapse
Affiliation(s)
- Wanqi Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.Y.); (J.L.); (Y.L.)
- Institute of Animal Sciences, Wageningen University and Research, 6708 WD Wageningen, The Netherlands
| | - Jingyi Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.Y.); (J.L.); (Y.L.)
| | - Yingnan Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.Y.); (J.L.); (Y.L.)
| | - Maria Forlenza
- Institute of Animal Sciences, Wageningen University and Research, 6708 WD Wageningen, The Netherlands
| | - Hongjun Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.Y.); (J.L.); (Y.L.)
| |
Collapse
|
49
|
Kumar N, Taneja A, Ghosh M, Rothweiler U, Sundaresan N, Singh M. Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites. Nucleic Acids Res 2024; 52:1450-1470. [PMID: 38153196 PMCID: PMC10853778 DOI: 10.1093/nar/gkad1208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
The regulator of telomere elongation helicase 1 (RTEL1) plays roles in telomere DNA maintenance, DNA repair, and genome stability by dismantling D-loops and unwinding G-quadruplex structures. RTEL1 comprises a helicase domain, two tandem harmonin homology domains 1&2 (HHD1 and HHD2), and a Zn2+-binding RING domain. In vitro D-loop disassembly by RTEL1 is enhanced in the presence of replication protein A (RPA). However, the mechanism of RTEL1 recruitment at non-telomeric D-loops remains unknown. In this study, we have unravelled a direct physical interaction between RTEL1 and RPA. Under DNA damage conditions, we showed that RTEL1 and RPA colocalise in the cell. Coimmunoprecipitation showed that RTEL1 and RPA interact, and the deletion of HHDs of RTEL1 significantly reduced this interaction. NMR chemical shift perturbations (CSPs) showed that RPA uses its 32C domain to interact with the HHD2 of RTEL1. Interestingly, HHD2 also interacted with DNA in the in vitro experiments. HHD2 structure was determined using X-ray crystallography, and NMR CSPs mapping revealed that both RPA 32C and DNA competitively bind to HHD2 on an overlapping surface. These results establish novel roles of accessory HHDs in RTEL1's functions and provide mechanistic insights into the RPA-mediated recruitment of RTEL1 to DNA repair sites.
Collapse
Affiliation(s)
- Niranjan Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Arushi Taneja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Meenakshi Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Ulli Rothweiler
- The Norwegian Structural Biology Centre, Department of Chemistry, The Arctic University of Norway, N-9037, Tromsø, Norway
| | | | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| |
Collapse
|
50
|
Shao C, Ren Y, Zhou H, Lee LC, Chen C, Dettman EJ, Cristescu R, Gozman A, Jin F, Zhou W. Biomarker Testing Journey Among Patients with Advanced Solid Tumors and Treatment Patterns by Homologous Recombination Repair Status: A Clinico-Genomic Database Study. Adv Ther 2024; 41:759-776. [PMID: 38169059 DOI: 10.1007/s12325-023-02734-4] [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: 08/29/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
INTRODUCTION Defects in the homologous recombination repair (HRR) pathway can include mutations in BRCA1 and BRCA2 (BRCAm) and other HRR genes (HRRm). These mutations are associated with a homologous recombination deficiency (HRD) phenotype. We evaluated testing journey and treatment patterns by BRCAm, HRRm, and HRD status in a real-world dataset. METHODS Deidentified data for patients who had undergone comprehensive genomic profiling using FoundationOne®CDx were collected through December 31, 2020, from a real-world multi-tumor clinico-genomic database (CGDB) capturing data from clinics in the United States. Patients eligible for inclusion in this analysis had a confirmed diagnosis with advanced or metastatic disease between January 1, 2018, and December 31, 2019, for 1 of 15 solid tumor types. Objectives were to evaluate patient treatment patterns by BRCAm, HRRm, and HRD status and to describe the timing of when (throughout disease course) comprehensive genomic profiling was performed. RESULTS Among 9457 patients included in the overall population with evaluable biomarker status, 7856 (83.1%) received ≥ 1 systemic therapy. Among the 7856 patients who received systemic therapy, 2324 (30.0%) underwent testing before first-line therapy, 4114 (52.4%) were tested after receiving first-line therapy and before receiving subsequent therapy (if any), 970 (12.3%) were tested after second-line therapy and before receiving subsequent therapy (if any), and 447 (5.7%) patients underwent testing after receiving third-line therapy. A higher proportion of patients with BRCAm, HRRm, or HRD-positive status were treated with poly(ADP-ribose) polymerase (PARP) inhibitors across all lines of therapy. There was no evidence of a meaningful difference in the proportion of patients who received other treatment (including chemotherapy and immunotherapy) by BRCAm, HRRm, or HRD status. CONCLUSION The majority of patients from this real-world dataset underwent FoundationOne®CDx testing after initiation of first-line treatment. Testing appeared to influence treatment patterns, with a higher proportion of patients with BRCAm, HRRm, and HRD-positive disease receiving PARP inhibitors.
Collapse
Affiliation(s)
- Changxia Shao
- Merck & Co., Inc., Rahway, NJ, USA.
- , Mailstop WP37A-250, 770 Sumneytown Pike, West Point, PA, 19486, USA.
| | | | | | | | - Cai Chen
- Merck & Co., Inc., Rahway, NJ, USA
| | | | | | | | - Fan Jin
- Merck & Co., Inc., Rahway, NJ, USA
| | - Wei Zhou
- Merck & Co., Inc., Rahway, NJ, USA
| |
Collapse
|