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Lin H, Cui Z, E T, Xu H, Wang D, Wang P, Ruan X, Liu L, Xue Y. M6A-methylated circPOLR2B forms an R-loop and regulates the biological behavior of glioma stem cells through positive feedback loops. Cell Death Dis 2024; 15:554. [PMID: 39090090 PMCID: PMC11294345 DOI: 10.1038/s41419-024-06946-6] [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: 02/29/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Glioma is the most common primary brain tumor, and targeting glioma stem cells (GSCs) has become a key aspect of glioma treatment. In this study, we discovered a molecular network in which circRNA forms an R-loop structure with its parental gene to regulate the biological behavior of GSCs. Genes with abnormal expression in GSCs were screened using RNA-seq and circRNA microarray analyses. The study results showed that high expression of YTHDC1 in GSCs promoted the transportation of N6-methyladenosine (m6A)-modified circPOLR2B from the nucleus to the cytoplasm. Decreased circPOLR2B levels in the nucleus resulted in fewer R-loop structures formed with its parental gene POLR2B. This reduction in R-loop structures relieved the inhibitory effect on POLR2B transcription and upregulated PBX1 expression through alternative polyadenylation (APA) action, thereby promoting the malignant biological behavior of GSCs. Knockdown of YTHDC1, POLR2B, and PBX1 reduced xenograft tumor volume and prolonged the survival of nude mice. The YTHDC1/circPOLR2B/POLR2B/PBX1 axis plays a regulatory role in the biological behavior of GSCs, offering potential targets and novel strategies for the treatment of glioma.
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Affiliation(s)
- Hongda Lin
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Zheng Cui
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Tiange E
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Hailing Xu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Ping Wang
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Xuelei Ruan
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Libo Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Yixue Xue
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China.
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China.
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Safari M, Scotto L, Basseville A, Litman T, Xue H, Petrukhin L, Zhou P, Morales DV, Damoci C, Zhu M, Hull K, Olive KP, Fojo T, Romo D, Bates SE. Combined HDAC and eIF4A inhibition: A novel epigenetic therapy for pancreatic adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.30.600495. [PMID: 39005268 PMCID: PMC11244854 DOI: 10.1101/2024.06.30.600495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Pancreatic ductal adenocarcinoma-(PDAC) needs innovative approaches due to its 12% 5-year survival despite current therapies. We show marked sensitivity of pancreatic cancer cells to the combination of a novel eIF4A inhibitor, des-methyl pateamine A (DMPatA), and a histone deacetylase inhibitor, romidepsin, inducing epigenetic reprogramming as an innovative therapeutic strategy. Exploring the mechanistic activity of this combination showed that with a short duration of romidepsin at low doses, robust acetylation persisted up to 48h with the combination, while histone acetylation rapidly faded with monotherapy. This represents an unexpected mechanism of action against PDAC cells that triggers transcriptional overload, metabolic stress, and augmented DNA damage. Structurally different class I HDAC inhibitors exhibit the same hyperacetylation patterns when co-administered with DMPatA, suggesting a class effect. We show efficacy of this combination regimen against tumor growth in a MIA PaCa-2 xenograft model of PDAC with persistent hyperacetylation confirmed in tumor samples. STATEMENT OF SIGNIFICANCE Pancreatic ductal adenocarcinoma, a significant clinical challenge, could benefit from the latent potential of epigenetic therapies like HDAC inhibitors-(HDIs), typically limited to hematological malignancies. Our study shows that a synergistic low dose combination of HDIs with an eIF4A-inhibitor in pancreatic cancer models results in marked pre-clinical efficacy, offering a promising new treatment strategy.
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Jamison JK, Zhou M, Gelmann EP, Luk L, Bates SE, Califano A, Fojo T. Entinostat in patients with relapsed or refractory abdominal neuroendocrine tumors. Oncologist 2024:oyae118. [PMID: 38886159 DOI: 10.1093/oncolo/oyae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 04/19/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare neoplasms with an increasing annual incidence and prevalence. Many are metastatic at presentation or recur following surgical resection and require systemic therapy, for which somatostatin analogs such as octreotide or lanreotide comprise typical first-line therapies. Nonetheless, treatment options remain limited. Epigenetic processes such as histone modifications have been implicated in malignant transformation and progression. In this study, we evaluated the anti-proliferative effects of a histone deacetylase (HDAC) inhibitor, entinostat, which was computationally predicted to show anti-cancer activity, as confirmed in in vitro and in vivo models of GEP-NETs. METHODS This was a phase II study to evaluate the efficacy and safety of entinostat in patients with relapsed or refractory abdominal NETs. The primary objective was to estimate the objective response rate to entinostat. Additionally, with each patient as his/her own control we estimated the rates of tumor growth prior to enrollment on study and while receiving entinostat. Patients received 5 mg entinostat weekly until disease progression or intolerable toxicity. The dose could be changed to 10 mg biweekly for patients who did not experience grade ≥ 2 treatment-related adverse events (AEs) in cycle 1, but was primarily administered at the starting 5 mg weekly dose. RESULTS The study enrolled only 5 patients due to early termination by the drug sponsor. The first patient that enrolled had advanced disease and died within days of enrollment before follow-up imaging due to a grade 5 AE unrelated to study treatment and was considered non-evaluable. Best RECIST response for the remaining 4 patients was stable disease (SD) with time on study of 154+, 243, 574, and 741 days. With each patient as his/her own control, rates of tumor growth on entinostat were markedly reduced with rates 20%, 33%, 54%, and 68% of the rates prior to enrollment on study. Toxicities possibly or definitely related to entinostat included grade 2/3 neutrophil count decrease [2/4 (50%)/ 2/4 (50%)], grade 3 hypophosphatemia [1/4, (25%)], grade 1/2 fatigue [1/4 (25%)/ 2/4 (50%)], and other self-limiting grade 1/2 AEs. CONCLUSION In the treatment of relapsed or refractory abdominal NETs, entinostat 5 mg weekly led to prolonged SD and reduced the rate of tumor growth by 32% to 80% with an acceptable safety profile (ClinicalTrials.gov Identifier: NCT03211988).
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Affiliation(s)
| | - Mengxi Zhou
- Department of Medicine, Division of Hematology Oncology, Columbia University Irving Medical Center, New York, NY, United States
| | | | - Lyndon Luk
- Department of Radiology, Columbia University Irving Medical Center, New York, NY, United States
| | - Susan E Bates
- Department of Medicine, Division of Hematology Oncology, Columbia University Irving Medical Center, New York, NY, United States
| | - Andrea Califano
- Department of Medicine, Division of Hematology Oncology, Columbia University Irving Medical Center, New York, NY, United States
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, United States
- Chan Zuckerberg Biohub New York, New York, NY, United States
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, United States
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, United States
| | - Tito Fojo
- Department of Medicine, Division of Hematology Oncology, Columbia University Irving Medical Center, New York, NY, United States
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Ashry R, Mustafa AHM, Hausmann K, Linnebacher M, Strand S, Sippl W, Wirth M, Krämer OH. NOXA Accentuates Apoptosis Induction by a Novel Histone Deacetylase Inhibitor. Cancers (Basel) 2023; 15:3650. [PMID: 37509312 PMCID: PMC10377841 DOI: 10.3390/cancers15143650] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/17/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Epigenetic modifiers of the histone deacetylase (HDAC) family are often dysregulated in cancer cells. Experiments with small molecule HDAC inhibitors (HDACi) have proven that HDACs are a vulnerability of transformed cells. We evaluated a novel hydroxamic acid-based HDACi (KH16; termed yanostat) in human pancreatic ductal adenocarcinoma (PDAC) cells, short- and long-term cultured colorectal cancer (CRC) cells, and retinal pigment epithelial cells. We show that KH16 induces cell cycle arrest and apoptosis, both time and dose dependently in PDAC and CRC cells. This is associated with altered expression of BCL2 family members controlling intrinsic apoptosis. Recent data illustrate that PDAC cells frequently have an altered expression of the pro-apoptotic BH3-only protein NOXA and that HDACi induce an accumulation of NOXA. Using PDAC cells with a deletion of NOXA by CRISPR-Cas9, we found that a lack of NOXA delayed apoptosis induction by KH16. These results suggest that KH16 is a new chemotype of hydroxamic acid HDACi with superior activity against solid tumor-derived cells. Thus, KH16 is a scaffold for future research on compounds with nanomolar activity against HDACs.
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Affiliation(s)
- Ramy Ashry
- Institute of Toxicology, University Medical Centre Mainz, 55131 Mainz, Germany
- Department of Oral Pathology, Faculty of Dentistry, Mansoura University, Mansoura 35516, Egypt
| | - Al-Hassan M Mustafa
- Institute of Toxicology, University Medical Centre Mainz, 55131 Mainz, Germany
- Department of Zoology, Faculty of Science, Aswan University, Aswan 81528, Egypt
| | - Kristin Hausmann
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Michael Linnebacher
- Clinic of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, 18057 Rostock, Germany
| | - Susanne Strand
- Department of Internal Medicine I, Molecular Hepatology, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Centre Mainz, 55131 Mainz, Germany
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5
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Elsakrmy N, Cui H. R-Loops and R-Loop-Binding Proteins in Cancer Progression and Drug Resistance. Int J Mol Sci 2023; 24:ijms24087064. [PMID: 37108225 PMCID: PMC10138518 DOI: 10.3390/ijms24087064] [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: 02/26/2023] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
R-loops are three-stranded DNA/RNA hybrids that form by the annealing of the mRNA transcript to its coding template while displacing the non-coding strand. While R-loop formation regulates physiological genomic and mitochondrial transcription and DNA damage response, imbalanced R-loop formation can be a threat to the genomic integrity of the cell. As such, R-loop formation is a double-edged sword in cancer progression, and perturbed R-loop homeostasis is observed across various malignancies. Here, we discuss the interplay between R-loops and tumor suppressors and oncogenes, with a focus on BRCA1/2 and ATR. R-loop imbalances contribute to cancer propagation and the development of chemotherapy drug resistance. We explore how R-loop formation can cause cancer cell death in response to chemotherapeutics and be used to circumvent drug resistance. As R-loop formation is tightly linked to mRNA transcription, their formation is unavoidable in cancer cells and can thus be explored in novel cancer therapeutics.
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Affiliation(s)
- Noha Elsakrmy
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
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6
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Lin C, Liu P, Shi C, Qiu L, Shang D, Lu Z, Tu Z, Liu H. Therapeutic targeting of DNA damage repair pathways guided by homologous recombination deficiency scoring in ovarian cancers. Fundam Clin Pharmacol 2023; 37:194-214. [PMID: 36130021 DOI: 10.1111/fcp.12834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/23/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
The susceptibility of cells to DNA damage and their DNA repair ability are crucial for cancer therapy. Homologous recombination is one of the major repairing mechanisms for DNA double-strand breaks. Approximately half of ovarian cancer (OvCa) cells harbor homologous recombination deficiency (HRD). Considering that HRD is a major hallmark of OvCas, scholars proposed HRD scoring to evaluate the HRD degree and guide the choice of therapeutic strategies for OvCas. In the last decade, synthetic lethal strategy by targeting poly (ADP-ribose) polymerase (PARP) in HR-deficient OvCas has attracted considerable attention in view of its favorable clinical effort. We therefore suggested that the uses of other DNA damage/repair-targeted drugs in HR-deficient OvCas might also offer better clinical outcome. Here, we reviewed the current small molecule compounds that targeted DNA damage/repair pathways and discussed the HRD scoring system to guide their clinical uses.
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Affiliation(s)
- Chunxiu Lin
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Chaowen Shi
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Lipeng Qiu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Dongsheng Shang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ziwen Lu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhigang Tu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hanqing Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
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7
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Saha S, Pommier Y. R-loops, type I topoisomerases and cancer. NAR Cancer 2023; 5:zcad013. [PMID: 37600974 PMCID: PMC9984992 DOI: 10.1093/narcan/zcad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
R-loops are abundant and dynamic structures ubiquitously present in human cells both in the nuclear and mitochondrial genomes. They form in cis in the wake of transcription complexes and in trans apart from transcription complexes. In this review, we focus on the relationship between R-loops and topoisomerases, and cancer genomics and therapies. We summarize the topological parameters associated with the formation and resolution of R-loops, which absorb and release high levels of genomic negative supercoiling (Sc-). We review the deleterious consequences of excessive R-loops and rationalize how human type IA (TOP3B) and type IB (TOP1) topoisomerases regulate and resolve R-loops in coordination with helicase and RNase H enzymes. We also review the drugs (topoisomerase inhibitors, splicing inhibitors, G4 stabilizing ligands) and cancer predisposing genes (BRCA1/2, transcription, and splicing genes) known to induce R-loops, and whether stabilizing R-loops and thereby inducing genomic damage can be viewed as a strategy for cancer treatment.
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Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Tang J, Wang X, Xiao D, Liu S, Tao Y. The chromatin-associated RNAs in gene regulation and cancer. Mol Cancer 2023; 22:27. [PMID: 36750826 PMCID: PMC9903551 DOI: 10.1186/s12943-023-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Eukaryotic genomes are prevalently transcribed into many types of RNAs that translate into proteins or execute gene regulatory functions. Many RNAs associate with chromatin directly or indirectly and are called chromatin-associated RNAs (caRNAs). To date, caRNAs have been found to be involved in gene and transcriptional regulation through multiple mechanisms and have important roles in different types of cancers. In this review, we first present different categories of caRNAs and the modes of interaction between caRNAs and chromatin. We then detail the mechanisms of chromatin-associated nascent RNAs, chromatin-associated noncoding RNAs and emerging m6A on caRNAs in transcription and gene regulation. Finally, we discuss the roles of caRNAs in cancer as well as epigenetic and epitranscriptomic mechanisms contributing to cancer, which could provide insights into the relationship between different caRNAs and cancer, as well as tumor treatment and intervention.
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Affiliation(s)
- Jun Tang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078 Hunan China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078 Hunan China
| | - Xiang Wang
- grid.216417.70000 0001 0379 7164Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China. .,Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China. .,Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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9
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Valdez BC, Nieto Y, Yuan B, Murray D, Andersson BS. HDAC inhibitors suppress protein poly(ADP-ribosyl)ation and DNA repair protein levels and phosphorylation status in hematologic cancer cells: implications for their use in combination with PARP inhibitors and chemotherapeutic drugs. Oncotarget 2022; 13:1122-1135. [PMID: 36243940 PMCID: PMC9564514 DOI: 10.18632/oncotarget.28278] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/22/2022] [Indexed: 11/25/2022] Open
Abstract
The therapeutic efficacy of histone deacetylase inhibitors (HDACi) for hematologic malignancies and solid tumors is attributed to their ability to remodel chromatin, normalize dysregulated gene expression, and inhibit repair of damaged DNA. Studies on the interactions of HDACi with PARP inhibitors in hematologic cancers are limited, especially when combined with chemotherapeutic agents. Exposure of hematologic cancer cell lines and patient-derived cell samples to various HDACi resulted in a significant caspase-independent inhibition of protein PARylation, mainly catalyzed by PARP1. HDACi affected the expression of PARP1 at the transcription and/or post-translation levels in a cell line-dependent manner. HDACi-mediated inhibition of PARylation correlated with decreased levels and phosphorylation of major proteins involved in DNA repair. Combination of HDAC and PARP1 inhibitors provided synergistic cytotoxicity, which was further enhanced when combined with a chemotherapeutic regimen containing gemcitabine, busulfan and melphalan as observed in lymphoma cell lines. Our results indicate that the anti-tumor efficacy of HDACi is partly due to down-regulation of PARylation, which negatively affects the status of DNA repair proteins. This repair inhibition, combined with the high levels of oxidative and DNA replication stress characteristic of cancer cells, could have conferred these hematologic cancer cells not only with a high sensitivity to HDACi but also with a heightened dependence on PARP and therefore with extreme sensitivity to combined HDACi/PARPi treatment and, by extension, to their combination with conventional DNA-damaging chemotherapeutic agents. The observed synergism of these drugs could have a major significance in improving treatment of these cancers.
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Affiliation(s)
- Benigno C. Valdez
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yago Nieto
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Yuan
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Murray
- Department of Experimental Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Borje S. Andersson
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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10
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Petermann E, Lan L, Zou L. Sources, resolution and physiological relevance of R-loops and RNA-DNA hybrids. Nat Rev Mol Cell Biol 2022; 23:521-540. [PMID: 35459910 DOI: 10.1038/s41580-022-00474-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
RNA-DNA hybrids are generated during transcription, DNA replication and DNA repair and are crucial intermediates in these processes. When RNA-DNA hybrids are stably formed in double-stranded DNA, they displace one of the DNA strands and give rise to a three-stranded structure called an R-loop. R-loops are widespread in the genome and are enriched at active genes. R-loops have important roles in regulating gene expression and chromatin structure, but they also pose a threat to genomic stability, especially during DNA replication. To keep the genome stable, cells have evolved a slew of mechanisms to prevent aberrant R-loop accumulation. Although R-loops can cause DNA damage, they are also induced by DNA damage and act as key intermediates in DNA repair such as in transcription-coupled repair and RNA-templated DNA break repair. When the regulation of R-loops goes awry, pathological R-loops accumulate, which contributes to diseases such as neurodegeneration and cancer. In this Review, we discuss the current understanding of the sources of R-loops and RNA-DNA hybrids, mechanisms that suppress and resolve these structures, the impact of these structures on DNA repair and genome stability, and opportunities to therapeutically target pathological R-loops.
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Affiliation(s)
- Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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11
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Huang Q, Kemnade J, Cornwell L, Kheradmand F, Sabichi AL, Das D. Non-small cell lung cancer in the era of immunotherapy. Semin Oncol 2022; 49:S0093-7754(22)00049-5. [PMID: 35879123 DOI: 10.1053/j.seminoncol.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 11/11/2022]
Abstract
Immunotherapy for non-small cell lung cancer (NSCLC) has revolutionized treatment for those with advanced disease, and recent data have emerged providing evidence for its benefits in earlier stages of the disease. Several pivotal clinical trials provide compelling data that adaptive immune cells may be highly effective and possibly even curative for NSCLC. Immune checkpoint inhibitors (ICIs) can unleash highly reactive memory immune responses to tumor antigens with durable effects against advanced or recurrent disease. Despite these encouraging results, many critical questions remain in the field including, for example, how to identify the subsets of NSCLC patients who most benefit from ICI treatment, and how ICI efficacy might be enhanced by utilizing combinations or sequencing of agents. A deeper understanding of biological mechanisms involved in lung cancer offers a unique opportunity to further explore the interaction between the adaptive immune landscape and NSCLC. Given the high incidence of lung cancer in Veterans and many Veterans being treated with immunotherapy for this disease, it is timely to have their adequate representation in future clinical trials. New clinical trials focused on Veterans can assist in exploring ways to mitigate resistant mechanisms as well as to investigate predictive and prognostic biomarkers for response to ICIs and other treatments. This paper will review current data and indications for immunotherapy in NSCLC, introduce new areas of research within immunotherapy, and discuss its applicability to the Veteran population.
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Affiliation(s)
- Quillan Huang
- Department of Medicine, Baylor College of Medicine, Houston, TX; Medical Care Line, Section of Hematology Oncology, Michael E DeBakey VA, Houston, TX
| | - Jan Kemnade
- Department of Medicine, Baylor College of Medicine, Houston, TX; Medical Care Line, Section of Hematology Oncology, Michael E DeBakey VA, Houston, TX
| | - Loraine Cornwell
- Surgical Care Line, Section of Thoracic Surgery Michael E DeBakey VAMC, Houston, TX
| | - Farrah Kheradmand
- Department of Medicine, Baylor College of Medicine, Houston, TX; Medical Care Line, Section of Pulmonary & Critical Care Michael E DeBakey VA, Houston, TX.
| | - Anita L Sabichi
- Department of Medicine, Baylor College of Medicine, Houston, TX; Medical Care Line, Section of Hematology Oncology, Michael E DeBakey VA, Houston, TX.
| | - Devika Das
- Hematology and Oncology, Birmingham VA Medical Center, Birmingham, AL; Department of Medicine, Division of Hematology and Oncology, UAB, Birmingham, AL.
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Basseville A, Violet PC, Safari M, Sourbier C, Linehan WM, Robey RW, Levine M, Sackett DL, Bates SE. A Histone Deacetylase Inhibitor Induces Acetyl-CoA Depletion Leading to Lethal Metabolic Stress in RAS-Pathway Activated Cells. Cancers (Basel) 2022; 14:2643. [PMID: 35681624 PMCID: PMC9179484 DOI: 10.3390/cancers14112643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The mechanism of action of romidepsin and other histone deacetylase inhibitors is still not fully explained. Our goal was to gain a mechanistic understanding of the RAS-linked phenotype associated with romidepsin sensitivity. METHODS The NCI60 dataset was screened for molecular clues to romidepsin sensitivity. Histone acetylation, DNA damage, ROS production, metabolic state (real-time measurement and metabolomics), and gene expression alterations (transcriptomics) were determined in KRAS-WT versus KRAS-mutant cell groups. The search for biomarkers in response to HDACi was implemented by supervised machine learning analysis on a 608-cell transcriptomic dataset and validated in a clinical dataset. RESULTS Romidepsin treatment induced depletion in acetyl-CoA in all tested cell lines, which led to oxidative stress, metabolic stress, and increased death-particularly in KRAS-mutant cell lines. Romidepsin-induced stresses and death were rescued by acetyl-CoA replenishment. Two acetyl-CoA gene expression signatures associated with HDACi sensitivity were derived from machine learning analysis in the CCLE (Cancer Cell Line Encyclopedia) cell panel. Signatures were then validated in the training cohort for seven HDACi, and in an independent 13-patient cohort treated with belinostat. CONCLUSIONS Our study reveals the importance of acetyl-CoA metabolism in HDAC sensitivity, and it highlights acetyl-CoA generation pathways as potential targets to combine with HDACi.
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Affiliation(s)
- Agnes Basseville
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
- Omics Data Science Unit, Institut de Cancérologie de l’Ouest, 49055 Angers, France
| | - Pierre-Christian Violet
- Molecular and Clinical Nutrition Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (P.-C.V.); (M.L.)
| | - Maryam Safari
- Division of Hematology/Oncology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA;
| | - Carole Sourbier
- Urology Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.S.); (W.M.L.)
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA
| | - W. Marston Linehan
- Urology Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.S.); (W.M.L.)
| | - Robert W. Robey
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Levine
- Molecular and Clinical Nutrition Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (P.-C.V.); (M.L.)
| | - Dan L. Sackett
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Susan E. Bates
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
- Division of Hematology/Oncology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA;
- Hematology/Oncology Research Department, James J. Peters Department of Veterans Affairs Medical Center, New York, NY 10468, USA
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The role of chromatin at transcription-replication conflicts as a genome safeguard. Biochem Soc Trans 2021; 49:2727-2736. [PMID: 34821364 DOI: 10.1042/bst20210691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022]
Abstract
DNA replication ensures the correct copying of the genome and the faithful transfer of the genetic information to the offspring. However, obstacles to replication fork (RF) progression cause RF stalling and compromise efficient genome duplication. Since replication uses the same DNA template as transcription, both transcription and replication must be coordinated to prevent Transcription-Replication Conflicts (TRCs) that could stall RF progression. Several factors contribute to limit the occurrence of such conflicts and their harmful impact on genome integrity. Increasing evidence indicates that chromatin homeostasis plays a key role in the cellular response to TRCs as well as in the preservation of genome integrity. Indeed, chromatin regulating enzymes are frequently mutated in cancer cells, a common characteristic of which is genome instability. Therefore, understanding the role of chromatin in TRC occurrence and resolution may help identify the molecular mechanism by which chromatin protects genome integrity, and the causes and physiological relevance of the high mutation rates of chromatin regulating factors in cancer. Here we review the current knowledge in the field, as well as the perspectives and future applications.
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Fernandez A, O’Leary C, O’Byrne KJ, Burgess J, Richard DJ, Suraweera A. Epigenetic Mechanisms in DNA Double Strand Break Repair: A Clinical Review. Front Mol Biosci 2021; 8:685440. [PMID: 34307454 PMCID: PMC8292790 DOI: 10.3389/fmolb.2021.685440] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Upon the induction of DNA damage, the chromatin structure unwinds to allow access to enzymes to catalyse the repair. The regulation of the winding and unwinding of chromatin occurs via epigenetic modifications, which can alter gene expression without changing the DNA sequence. Epigenetic mechanisms such as histone acetylation and DNA methylation are known to be reversible and have been indicated to play different roles in the repair of DNA. More importantly, the inhibition of such mechanisms has been reported to play a role in the repair of double strand breaks, the most detrimental type of DNA damage. This occurs by manipulating the chromatin structure and the expression of essential proteins that are critical for homologous recombination and non-homologous end joining repair pathways. Inhibitors of histone deacetylases and DNA methyltransferases have demonstrated efficacy in the clinic and represent a promising approach for cancer therapy. The aims of this review are to summarise the role of histone deacetylase and DNA methyltransferase inhibitors involved in DNA double strand break repair and explore their current and future independent use in combination with other DNA repair inhibitors or pre-existing therapies in the clinic.
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Affiliation(s)
- Alejandra Fernandez
- Centre for Genomics and Personalised Health, School of Biomedical Sciences and Translational Research Institute, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Connor O’Leary
- Centre for Genomics and Personalised Health, School of Biomedical Sciences and Translational Research Institute, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Kenneth J O’Byrne
- Centre for Genomics and Personalised Health, School of Biomedical Sciences and Translational Research Institute, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Joshua Burgess
- Centre for Genomics and Personalised Health, School of Biomedical Sciences and Translational Research Institute, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Derek J Richard
- Centre for Genomics and Personalised Health, School of Biomedical Sciences and Translational Research Institute, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Amila Suraweera
- Centre for Genomics and Personalised Health, School of Biomedical Sciences and Translational Research Institute, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
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