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Dagar G, Gupta A, Shankar A, Chauhan R, Macha MA, Bhat AA, Das D, Goyal R, Bhoriwal S, Pandita RK, Prasad CP, Sarkar PS, Pandita TK, Singh M. The future of cancer treatment: combining radiotherapy with immunotherapy. Front Mol Biosci 2024; 11:1409300. [PMID: 39044839 PMCID: PMC11263218 DOI: 10.3389/fmolb.2024.1409300] [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: 03/29/2024] [Accepted: 06/12/2024] [Indexed: 07/25/2024] Open
Abstract
Radiotherapy (RT) and immunotherapy (IT) are the powerful tools for cancer treatment which act through the stimulation of immune response, and evidence suggest that combinatorial actions of these therapies may augment each other's beneficial effect through complex synergistic mechanisms. These molecular strategies are designed to target rapidly dividing cancer cells by either directly or indirectly inducing DNA damage. However, when cells detect DNA damage, they activate a range of signalling pathways known as the DNA damage response (DDR) to repair. Strategies are being developed to interfere with the DDR pathways in cancer cells to ensure their damage-induced degeneration. The stability of a cell's genetic material is largely dependent on the efficacy of DNA repair and therefore, an in-depth understanding of DNA damages and repair mechanism(s) in cancer cells is important to develop a promising therapeutic strategies for ensuring the efficacy of damage-induced tumor cell death. In recent years, a wide range of small molecule drugs have been developed which are currently being employed to combat the DNA repair deficiencies associated with tumor cells. Sequential or concurrent use of these two modalities significantly enhances the anti-tumor response, however with a concurrent probability of increased incidence of symptomatic adverse effects. With advent of newer IT agents, and administration of higher doses of radiation per fraction, such effects are more difficult to predict owing to the paucity of randomized trial data. It is well established that anti cytotoxic-T-lymphocyte-associated antigen 4 (CTLA-4), anti- Programmed cell death protein 1(PD-1), anti-Programmed cell death one ligand 1 (PD-L1) can be safely administered with RT and many studies have demonstrated survival benefit with such combination for patients with metastatic malignancy. However, the biology of radioimmunotherapy (RT/IT) is still an open area where research need to be focused to determine optimum dosage specially the interaction of the RT/IT pathways to determine optimum dosing schedule. In the current article we have summarised the possible intracellular immunological events that might be triggered when RT and IT modalities are combined with the DDR antagonists and highlighted present clinical practices, outcome, and toxicity profile of this novel treatment strategy.
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Affiliation(s)
- Gunjan Dagar
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Ashna Gupta
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Abhishek Shankar
- Department of Radiation Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Ravi Chauhan
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Muzafar A. Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Pulwama, Jammu And Kashmir, India
| | - Ajaz A. Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Dayasagar Das
- Department of Medicine, NYU Langone Health, New York City, NY, United States
| | - Rajeev Goyal
- Department of Biochemistry, Lady Harding Medical College, New Delhi, India
| | - Sandeep Bhoriwal
- Department of Surgical Oncology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Raj K. Pandita
- Center for Genomics and Precision Medicine, Texas A and M College of Medicine, Houston, TX, United States
| | - Chandra Prakash Prasad
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Partha S. Sarkar
- Department of Neurobiology and Department of Neurology, University of Texas Medical Branch, Galveston, TX, United States
| | - Tej K. Pandita
- Center for Genomics and Precision Medicine, Texas A and M College of Medicine, Houston, TX, United States
| | - Mayank Singh
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
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2
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Papp O, Jordán V, Hetey S, Balázs R, Kaszás V, Bartha Á, Ordasi NN, Kamp S, Farkas B, Mettetal J, Dry JR, Young D, Sidders B, Bulusu KC, Veres DV. Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors. NPJ Syst Biol Appl 2024; 10:68. [PMID: 38906870 PMCID: PMC11192759 DOI: 10.1038/s41540-024-00394-w] [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: 08/22/2022] [Accepted: 06/14/2024] [Indexed: 06/23/2024] Open
Abstract
Combination therapy is well established as a key intervention strategy for cancer treatment, with the potential to overcome monotherapy resistance and deliver a more durable efficacy. However, given the scale of unexplored potential target space and the resulting combinatorial explosion, identifying efficacious drug combinations is a critical unmet need that is still evolving. In this paper, we demonstrate a network biology-driven, simulation-based solution, the Simulated Cell™. Integration of omics data with a curated signaling network enables the accurate and interpretable prediction of 66,348 combination-cell line pairs obtained from a large-scale combinatorial drug sensitivity screen of 684 combinations across 97 cancer cell lines (BAC = 0.62, AUC = 0.7). We highlight drug combination pairs that interact with DNA Damage Response pathways and are predicted to be synergistic, and deep network insight to identify biomarkers driving combination synergy. We demonstrate that the cancer cell 'avatars' capture the biological complexity of their in vitro counterparts, enabling the identification of pathway-level mechanisms of combination benefit to guide clinical translatability.
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Affiliation(s)
- Orsolya Papp
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | | | | | - Róbert Balázs
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | - Valér Kaszás
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | - Árpád Bartha
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | - Nóra N Ordasi
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | | | - Bálint Farkas
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | - Jay Mettetal
- Oncology Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, MA, USA
| | - Jonathan R Dry
- Early Data Science, Oncology Data Science, Oncology R&D, AstraZeneca, Waltham, MA, USA
| | - Duncan Young
- Search and Evaluation, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Ben Sidders
- Early Data Science, Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Krishna C Bulusu
- Early Data Science, Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
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3
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Bachus S, Akkerman N, Fulham L, Graves D, Helwer R, Rempel J, Pelka P. ARGLU1 enhances promoter-proximal pausing of RNA polymerase II and stimulates DNA damage repair. Nucleic Acids Res 2024; 52:5658-5675. [PMID: 38520408 PMCID: PMC11162773 DOI: 10.1093/nar/gkae208] [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: 10/25/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
Arginine and glutamate rich 1 (ARGLU1) is a poorly understood cellular protein with functions in RNA splicing and transcription. Computational prediction suggests that ARGLU1 contains intrinsically disordered regions and lacks any known structural or functional domains. We used adenovirus Early protein 1A (E1A) to probe for critical regulators of important cellular pathways and identified ARGLU1 as a significant player in transcription and the DNA damage response pathway. Transcriptional effects induced by ARGLU1 occur via enhancement of promoter-proximal RNA polymerase II pausing, likely by inhibiting the interaction between JMJD6 and BRD4. When overexpressed, ARGLU1 increases the growth rate of cancer cells, while its knockdown leads to growth arrest. Significantly, overexpression of ARGLU1 increased cancer cell resistance to genotoxic drugs and promoted DNA damage repair. These results identify new roles for ARGLU1 in cancer cell survival and the DNA damage repair pathway, with potential clinical implications for chemotherapy resistance.
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Affiliation(s)
- Scott Bachus
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Nikolas Akkerman
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Lauren Fulham
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Drayson Graves
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Rafe Helwer
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Jordan Rempel
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Peter Pelka
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
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4
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Oka Y, Nakazawa Y, Shimada M, Ogi T. Endogenous aldehyde-induced DNA-protein crosslinks are resolved by transcription-coupled repair. Nat Cell Biol 2024; 26:784-796. [PMID: 38600234 PMCID: PMC11098742 DOI: 10.1038/s41556-024-01401-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
DNA-protein crosslinks (DPCs) induced by aldehydes interfere with replication and transcription. Hereditary deficiencies in DPC repair and aldehyde clearance processes cause progeria, including Ruijs-Aalfs syndrome (RJALS) and AMeD syndrome (AMeDS) in humans. Although the elimination of DPC during replication has been well established, how cells overcome DPC lesions in transcription remains elusive. Here we show that endogenous aldehyde-induced DPC roadblocks are efficiently resolved by transcription-coupled repair (TCR). We develop a high-throughput sequencing technique to measure the genome-wide distribution of DPCs (DPC-seq). Using proteomics and DPC-seq, we demonstrate that the conventional TCR complex as well as VCP/p97 and the proteasome are required for the removal of formaldehyde-induced DPCs. TFIIS-dependent cleavage of RNAPII transcripts protects against transcription obstacles. Finally, a mouse model lacking both aldehyde clearance and TCR confirms endogenous DPC accumulation in actively transcribed regions. Collectively, our data provide evidence that transcription-coupled DPC repair (TC-DPCR) as well as aldehyde clearance are crucial for protecting against metabolic genotoxin, thus explaining the molecular pathogenesis of AMeDS and other disorders associated with defects in TCR, such as Cockayne syndrome.
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Affiliation(s)
- Yasuyoshi Oka
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mayuko Shimada
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan.
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Division of Animal Medical Science, Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Japan.
- Division of Molecular Physiology and Dynamics, Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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5
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Hoag A, Duan M, Mao P. The role of Transcription Factor IIH complex in nucleotide excision repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:72-81. [PMID: 37545038 PMCID: PMC10903506 DOI: 10.1002/em.22568] [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: 04/15/2023] [Revised: 07/05/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
DNA damage occurs throughout life from a variety of sources, and it is imperative to repair damage in a timely manner to maintain genome stability. Thus, DNA repair mechanisms are a fundamental part of life. Nucleotide excision repair (NER) plays an important role in the removal of bulky DNA adducts, such as cyclobutane pyrimidine dimers from ultraviolet light or DNA crosslinking damage from platinum-based chemotherapeutics, such as cisplatin. A main component for the NER pathway is transcription factor IIH (TFIIH), a multifunctional, 10-subunit protein complex with crucial roles in both transcription and NER. In transcription, TFIIH is a component of the pre-initiation complex and is important for promoter opening and the phosphorylation of RNA Polymerase II (RNA Pol II). During repair, TFIIH is important for DNA unwinding, recruitment of downstream repair factors, and verification of the bulky lesion. Several different disease states can arise from mutations within subunits of the TFIIH complex. Most strikingly are xeroderma pigmentosum (XP), XP combined with Cockayne syndrome (CS), and trichothiodystrophy (TTD). Here, we summarize the recruitment and functions of TFIIH in the two NER subpathways, global genomic (GG-NER) and transcription-coupled NER (TC-NER). We will also discuss how TFIIH's roles in the two subpathways lead to different genetic disorders.
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Affiliation(s)
- Allyson Hoag
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - Mingrui Duan
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States
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6
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Shen Y, Shi K, Li D, Wang Q, Wu K, Feng C. Prognostic analysis of mutated genes and insight into effects of DNA damage and repair on mutational strand asymmetries in gastric cancer. Biochem Biophys Rep 2024; 37:101597. [PMID: 38371526 PMCID: PMC10873876 DOI: 10.1016/j.bbrep.2023.101597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 02/20/2024] Open
Abstract
Gastric cancer (GACA) is a complex and multifaceted disease influenced by a variety of environmental and genetic factors. Somatic mutations play a major role in its development, and their characteristics, including the asymmetry between two DNA strands, are of great interest and appear as a signal of information and guidance, revealing mechanisms of DNA damage and repair. Here, we analyzed the impact of High-frequency mutated genes on patient prognosis and found that the effect of expression levels of tumor protein p53 (TP53) and lysine methyltransferase 2C (KMT2C) genes remained high throughout the development of GACA, with similar expression patterns. After investigating mutation asymmetry across mutagenic processes, we found that transcriptional asymmetry was dominated by T > G mutations under the influence of transcription couples repair and damage. The apolipoprotein B mRNA editing enzyme catalytic polypeptide like (APOBEC) enzyme that induces mutations during DNA replication has been identified here and we identified a replicative asymmetry, which was dominated by C > A mutations in left-replicating. Strand bias in different mutation classes at transcription factor binding sites and enhancer regions were also confirmed, which implies the important role of non-coding regulatory elements in the occurrence of mutations. This work systematically describes mutational strand asymmetries in specific genomic regions, shedding light on the DNA damage and repair mechanisms underlying somatic mutations in cohorts of GACA patients with gastric cancer.
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Affiliation(s)
- Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Institute of Animal Science, Jiangsu Academy of Agriculture Science, Nanjing, China
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Dongfeng Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qiang Wang
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Kangkang Wu
- Department of Infectious Disease, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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7
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Sabharwal A, Gupta V, Kv S, Kumar Manokaran R, Verma A, Mishra A, Bhoyar RC, Jain A, Sivadas A, Rawat S, Jolly B, Mohanty S, Gulati S, Gupta N, Kabra M, Scaria V, Sivasubbu S. Whole genome sequencing followed by functional analysis of genomic deletion encompassing ERCC8 and NDUFAF2 genes in a non-consanguineous Indian family reveals dysfunctional mitochondrial bioenergetics leading to infant mortality. Mitochondrion 2024; 75:101844. [PMID: 38237647 DOI: 10.1016/j.mito.2024.101844] [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: 02/04/2023] [Revised: 12/07/2023] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
Genomic investigations on an infant who presented with a putative mitochondrial disorder led to identification of compound heterozygous deletion with an overlapping region of ∼142 kb encompassing two nuclear encoded genes namely ERCC8 and NDUFAF2. Investigations on fetal-derived fibroblast culture demonstrated impaired bioenergetics and mitochondrial dysfunction, which explains the phenotype and observed infant mortality in the present study. The genetic findings from this study extended the utility of whole-genome sequencing as it led to development of a MLPA-based assay for carrier screening in the extended family and the prenatal testing aiding in the birth of two healthy children.
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Affiliation(s)
- Ankit Sabharwal
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, Texas, United States.
| | - Vishu Gupta
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shamsudheen Kv
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Ankit Verma
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Anushree Mishra
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ambily Sivadas
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sonali Rawat
- Stem Cell Facility, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sujata Mohanty
- Stem Cell Facility, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Sheffali Gulati
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Neerja Gupta
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), Delhi, India.
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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8
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Bai B, Wan C, Xiao Z, Li D, Liu L, Zhang K, Zhang T, Zhang Q. High Homocysteine-Thiolactone Leads to Reduced MENIN Protein Expression and an Impaired DNA Damage Response: Implications for Neural Tube Defects. Mol Neurobiol 2024:10.1007/s12035-024-04033-7. [PMID: 38386135 DOI: 10.1007/s12035-024-04033-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/10/2024] [Indexed: 02/23/2024]
Abstract
DNA damage is associated with hyperhomocysteinemia (HHcy) and neural tube defects (NTDs). Additionally, HHcy is a risk factor for NTDs. Therefore, this study examined whether DNA damage is involved in HHcy-induced NTDs and investigated the underlying pathological mechanisms involved. Embryonic day 9 (E9) mouse neuroectoderm cells (NE4C) and homocysteine-thiolactone (HTL, active metabolite of Hcy)-induced NTD chicken embryos were studied by Western blotting, immunofluorescence. RNA interference or gene overexpression techniques were employed to investigate the impact of Menin expression changes on the DNA damage. Chromatin immunoprecipitation-quantitative polymerase chain reaction was used to investigate the epigenetic regulation of histone modifications. An increase in γH2AX (a DNA damage indicator) was detected in HTL-induced NTD chicken embryos and HTL-treated NE4C, accompanied by dysregulation of phospho-Atr-Chk1-nucleotide excision repair (NER) pathway. Further investigation, based on previous research, revealed that disruption of NER was subject to the epigenetic regulation of low-expressed Menin-H3K4me3. Overexpression of Menin or supplementation with folic acid in HTL-treated NE4C reversed the adverse effects caused by high HTL. Additionally, by overexpressing the Mars gene, we tentatively propose a mechanism whereby HTL regulates Menin expression through H3K79hcy, which subsequently influences H3K4me3 modifications, reflecting an interaction between histone modifications. Finally, in 10 human fetal NTDs with HHcy, we detected a decrease in the expression of Menin-H3K4me3 and disorder in the NER pathway, which to some extent validated our proposed mechanism. The present study demonstrated that the decreased expression of Menin in high HTL downregulated H3K4me3 modifications, further weakening the Atr-Chk1-NER pathway, resulting in the occurrence of NTDs.
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Affiliation(s)
- Baoling Bai
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Yabao Road 2, Beijing, 100020, China
| | - Chunlei Wan
- Department of Pediatrics, Tongzhou Maternal and Child Health Care Hospital, Beijing, 101101, China
| | - Zonghui Xiao
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Yabao Road 2, Beijing, 100020, China
| | - Dan Li
- Department of Pediatrics, Tongzhou Maternal and Child Health Care Hospital, Beijing, 101101, China
| | - Lingyun Liu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Yabao Road 2, Beijing, 100020, China
| | - Kexin Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Yabao Road 2, Beijing, 100020, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Yabao Road 2, Beijing, 100020, China.
| | - Qin Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Yabao Road 2, Beijing, 100020, China.
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Li Y, Gong Y, Zhou Y, Xiao Y, Huang W, Zhou Q, Tu Y, Zhao Y, Zhang S, Dai L, Sun Q. STK19 is a DNA/RNA-binding protein critical for DNA damage repair and cell proliferation. J Cell Biol 2024; 223:e202301090. [PMID: 38252411 PMCID: PMC10806857 DOI: 10.1083/jcb.202301090] [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: 01/20/2023] [Revised: 08/15/2023] [Accepted: 11/10/2023] [Indexed: 01/23/2024] Open
Abstract
STK19 was originally identified as a manganese-dependent serine/threonine-specific protein kinase, but its function has been highly debated. Here, the crystal structure of STK19 revealed that it does not contain a kinase domain, but three intimately packed winged helix (WH) domains. The third WH domain mediated homodimerization and double-stranded DNA binding, both being important for its nuclear localization. STK19 participated in the nucleotide excision repair (NER) and mismatch repair (MMR) pathways by recruiting damage repair factors such as RPA2 and PCNA. STK19 also bound double-stranded RNA through the DNA-binding interface and regulated the expression levels of many mRNAs. Furthermore, STK19 knockdown cells exhibited very slow cell proliferation, which cannot be rescued by dimerization or DNA-binding mutants. Therefore, this work concludes that STK19 is highly unlikely to be a kinase but a DNA/RNA-binding protein critical for DNA damage repair (DDR) and cell proliferation. To prevent further confusions, we renamed this protein as TWH19 (Tandem Winged Helix protein formerly known as STK19).
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Affiliation(s)
- Yuling Li
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yue Zhou
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yuzhou Xiao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Wenxin Huang
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Qiao Zhou
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yingfeng Tu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yinglan Zhao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shuyu Zhang
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Qingxiang Sun
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
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10
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Adav SS, Ng KW. Recent omics advances in hair aging biology and hair biomarkers analysis. Ageing Res Rev 2023; 91:102041. [PMID: 37634889 DOI: 10.1016/j.arr.2023.102041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/27/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Aging is a complex natural process that leads to a decline in physiological functions, which is visible in signs such as hair graying, thinning, and loss. Although hair graying is characterized by a loss of pigment in the hair shaft, the underlying mechanism of age-associated hair graying is not fully understood. Hair graying and loss can have a significant impact on an individual's self-esteem and self-confidence, potentially leading to mental health problems such as depression and anxiety. Omics technologies, which have applications beyond clinical medicine, have led to the discovery of candidate hair biomarkers and may provide insight into the complex biology of hair aging and identify targets for effective therapies. This review provides an up-to-date overview of recent omics discoveries, including age-associated alterations of proteins and metabolites in the hair shaft and follicle, and highlights the significance of hair aging and graying biomarker discoveries. The decline in hair follicle stem cell activity with aging decreased the regeneration capacity of hair follicles. Cellular senescence, oxidative damage and altered extracellular matrix of hair follicle constituents characterized hair follicle and hair shaft aging and graying. The review attempts to correlate the impact of endogenous and exogenous factors on hair aging. We close by discussing the main challenges and limitations of the field, defining major open questions and offering an outlook for future research.
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Affiliation(s)
- Sunil S Adav
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Kee Woei Ng
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, 637141, Singapore.
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11
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Huang Y, Gu L, Li GM. Heat shock protein DNAJA2 regulates transcription-coupled repair by triggering CSB degradation via chaperone-mediated autophagy. Cell Discov 2023; 9:107. [PMID: 37907457 PMCID: PMC10618452 DOI: 10.1038/s41421-023-00601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/01/2023] [Indexed: 11/02/2023] Open
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is an important genome maintenance system that preferentially removes DNA lesions on the transcribed strand of actively transcribed genes, including non-coding genes. TC-NER involves lesion recognition by the initiation complex consisting of RNA polymerase II (Pol II) and Cockayne syndrome group B (CSB), followed by NER-catalyzed lesion removal. However, the efficient lesion removal requires the initiation complex to yield the right of way to the excision machinery, and how this occurs in a timely manner is unknown. Here we show that heat shock protein DNAJA2 facilitates the HSC70 chaperone-mediated autophagy (CMA) to degrade CSB during TC-NER. DNAJA2 interacts with and enables HSC70 to recognize sumoylated CSB. This triggers the removal of both CSB and Pol II from the lesion site in a manner dependent on lysosome receptor LAMP2A. Defects in DNAJA2, HSC70 or LAMP2A abolish CSB degradation and block TC-NER. Our findings discover DNAJA2-mediated CMA as a critical regulator of TC-NER, implicating the DNAJA2-HSC70-CMA axis factors in genome maintenance.
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Affiliation(s)
- Yaping Huang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Liya Gu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Chinese Institutes for Medical Research, Beijing, China.
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12
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Mistry H, Kumari S, Aswal VK, Gupta GD. Structural characterization of transcription-coupled repair protein UVSSA and its interaction with TFIIH protein. Int J Biol Macromol 2023; 247:125792. [PMID: 37442507 DOI: 10.1016/j.ijbiomac.2023.125792] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Accepted: 07/09/2023] [Indexed: 07/15/2023]
Abstract
UV-stimulated scaffold protein A (UVSSA) is a key protein in the Transcription-Coupled Nucleotide Excision Repair (TC-NER) pathway. UVSSA, an intrinsically disordered protein, interacts with multiple members of the pathway, tethering them into the complex. Several studies have reported that UVSSA recruits Transcription Factor IIH (TFIIH) via direct interaction, following which CSB is degraded and the lesion recognition TC-NER complex dissociates from the damage site to facilitate the DNA repair. Structural insights into these events remain largely unknown. Herein, we have investigated the interaction of human UVSSA with the Pleckstrin-Homology-domain of p62 subunit of TFIIH (p62-PHD) using biophysical techniques. We observed that UVSSA forms a stable complex with the p62-PHD in vitro. Small-angle scattering measurements using X-rays and neutrons revealed a significant change in pair-distance distribution function for UVSSA662/p62-PHD complex compared to UVSSA alone. Additionally, a significant decrease was observed in the radius of gyration of the complex. Our findings suggest that TFIIH binding to UVSSA causes significant conformational changes in UVSSA. We hypothesize that these conformational changes play an important role in the dissociation of the lesion recognition TC-NER complex.
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Affiliation(s)
- Hiral Mistry
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Shweta Kumari
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Gagan D Gupta
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India.
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13
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Baker BH, Zhang S, Simon JM, McLarnan SM, Chung WK, Pearson BL. Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders. Front Neurosci 2023; 17:1106573. [PMID: 37599994 PMCID: PMC10435087 DOI: 10.3389/fnins.2023.1106573] [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: 11/23/2022] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction De novo mutations contribute to a large proportion of sporadic psychiatric and developmental disorders, yet the potential role of environmental carcinogens as drivers of causal de novo mutations in neurodevelopmental disorders is poorly studied. Methods To explore environmental mutation vulnerability of disease-associated gene sets, we analyzed publicly available whole genome sequencing datasets of mutations in human induced pluripotent stem cell clonal lines exposed to 12 classes of environmental carcinogens, and human lung cancers from individuals living in highly polluted regions. We compared observed rates of exposure-induced mutations in disease-related gene sets with the expected rates of mutations based on control genes randomly sampled from the genome using exact binomial tests. To explore the role of sequence characteristics in mutation vulnerability, we modeled the effects of sequence length, gene expression, and percent GC content on mutation rates of entire genes and gene coding sequences using multivariate Quasi-Poisson regressions. Results We demonstrate that several mutagens, including radiation and polycyclic aromatic hydrocarbons, disproportionately mutate genes related to neurodevelopmental disorders including autism spectrum disorders, schizophrenia, and attention deficit hyperactivity disorder. Other disease genes including amyotrophic lateral sclerosis, Alzheimer's disease, congenital heart disease, orofacial clefts, and coronary artery disease were generally not mutated more than expected. Longer sequence length was more strongly associated with elevated mutations in entire genes compared with mutations in coding sequences. Increased expression was associated with decreased coding sequence mutation rate, but not with the mutability of entire genes. Increased GC content was associated with increased coding sequence mutation rates but decreased mutation rates in entire genes. Discussion Our findings support the possibility that neurodevelopmental disorder genetic etiology is partially driven by a contribution of environment-induced germ line and somatic mutations.
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Affiliation(s)
- Brennan H. Baker
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shaoyi Zhang
- Master of Public Health Program, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jeremy M. Simon
- Department of Genetics and Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah M. McLarnan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Wendy K. Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Brandon L. Pearson
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
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14
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Wang S, Kang Y, Qi F, Jin H. Genetics of hair graying with age. Ageing Res Rev 2023; 89:101977. [PMID: 37276979 DOI: 10.1016/j.arr.2023.101977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 03/17/2023] [Accepted: 06/01/2023] [Indexed: 06/07/2023]
Abstract
Hair graying is an early and obvious phenotypic and physiological trait with age in humans. Several recent advances in molecular biology and genetics have increased our understanding of the mechanisms of hair graying, which elucidate genes related to the synthesis, transport, and distribution of melanin in hair follicles, as well as genes regulating these processes above. Therefore, we review these advances and examine the trends in the genetic aspects of hair graying from enrichment theory, Genome-Wide association studies, whole exome sequencing, gene expression studies, and animal models for hair graying with age, aiming to overview the changes in hair graying at the genetic level and establish the foundation for future research. Meanwhile, by summarizing the genetics, it's of great value to explore the possible mechanism, treatment, or even prevention of hair graying with age.
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Affiliation(s)
- Sifan Wang
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing 100730, China
| | - Yuanbo Kang
- Department of Plastic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Shuaifuyuan1#, Dongcheng District, Beijing 100730, P.R.China
| | - Fei Qi
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing 100730, China
| | - Hongzhong Jin
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing 100730, China.
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15
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Le J, Min JH. Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein. J Biomol Struct Dyn 2023; 41:13535-13562. [PMID: 36890638 PMCID: PMC10485178 DOI: 10.1080/07391102.2023.2177349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023]
Abstract
Xeroderma pigmentosum C (XPC) is a key initiator in the global genome nucleotide excision repair pathway in mammalian cells. Inherited mutations in the XPC gene can cause xeroderma pigmentosum (XP) cancer predisposition syndrome that dramatically increases the susceptibility to sunlight-induced cancers. Various genetic variants and mutations of the protein have been reported in cancer databases and literature. The current lack of a high-resolution 3-D structure of human XPC makes it difficult to assess the structural impact of the mutations/genetic variations. Using the available high-resolution crystal structure of its yeast ortholog, Rad4, we built a homology model of human XPC protein and compared it with a model generated by AlphaFold. The two models are largely consistent with each other in the structured domains. We have also assessed the degree of conservation for each residue using 966 sequences of XPC orthologs. Our structure- and sequence conservation-based assessments largely agree with the variant's impact on the protein's structural stability, computed by FoldX and SDM. Known XP missense mutations such as Y585C, W690S, and C771Y are consistently predicted to destabilize the protein's structure. Our analyses also reveal several highly conserved hydrophobic regions that are surface-exposed, which may indicate novel intermolecular interfaces that are yet to be characterized.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jennifer Le
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
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16
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Maguina M, Kang PB, Tsai AC, Pacak CA. Peripheral neuropathies associated with DNA repair disorders. Muscle Nerve 2023; 67:101-110. [PMID: 36190439 PMCID: PMC10075233 DOI: 10.1002/mus.27721] [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: 12/13/2021] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 01/25/2023]
Abstract
Repair of genomic DNA is a fundamental housekeeping process that quietly maintains the health of our genomes. The consequences of a genetic defect affecting a component of this delicate mechanism are quite harmful, characterized by a cascade of premature aging that injures a variety of organs, including the nervous system. One part of the nervous system that is impaired in certain DNA repair disorders is the peripheral nerve. Chronic motor, sensory, and sensorimotor polyneuropathies have all been observed in affected individuals, with specific physiologies associated with different categories of DNA repair disorders. Cockayne syndrome has classically been linked to demyelinating polyneuropathies, whereas xeroderma pigmentosum has long been associated with axonal polyneuropathies. Three additional recessive DNA repair disorders are associated with neuropathies, including trichothiodystrophy, Werner syndrome, and ataxia-telangiectasia. Although plausible biological explanations exist for why the peripheral nerves are specifically vulnerable to impairments of DNA repair, specific mechanisms such as oxidative stress remain largely unexplored in this context, and bear further study. It is also unclear why different DNA repair disorders manifest with different types of neuropathy, and why neuropathy is not universally present in those diseases. Longitudinal physiological monitoring of these neuropathies with serial electrodiagnostic studies may provide valuable noninvasive outcome data in the context of future natural history studies, and thus the responses of these neuropathies may become sentinel outcome measures for future clinical trials of treatments currently in development such as adeno-associated virus gene replacement therapies.
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Affiliation(s)
- Melissa Maguina
- Medical Education Program, Nova Southeastern University, Fort Lauderdale, Florida
| | - Peter B Kang
- Department of Neurology, Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, Minnesota.,Institute for Translational Neuroscience, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Ang-Chen Tsai
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida
| | - Christina A Pacak
- Department of Neurology, Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, Minnesota
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17
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Casimir L, Zimmer S, Racine-Brassard F, Jacques PÉ, Maréchal A. The mutational impact of Illudin S on human cells. DNA Repair (Amst) 2023; 122:103433. [PMID: 36566616 DOI: 10.1016/j.dnarep.2022.103433] [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: 08/09/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Illudin S (ILS) is a fungal sesquiterpene secondary metabolite with potent genotoxic and cytotoxic properties. Early genetic studies and more recent genome-wide CRISPR screens showed that Illudin-induced lesions are preferentially repaired by transcription-coupled nucleotide excision repair (TC-NER) with some contribution from post-replication repair pathways. In line with these results, Irofulven, a semi-synthetic ILS analog was recently shown to be particularly effective on cell lines and patient-derived xenografts with impaired NER (e.g. ERCC2/3 mutations), raising hope that ILS-derived molecules may soon enter the clinic. Despite the therapeutic potential of ILS and its analogs, we still lack a global understanding of their mutagenic potential. Here, we characterize the mutational signatures associated with chronic exposure to ILS in human cells. ILS treatment rapidly stalls DNA replication and transcription, leading to the activation of the replication stress response and the accumulation of DNA damage. Novel single and double base substitution signatures as well as a characteristic indel signature indicate that ILS treatment preferentially alkylates purine residues and induces oxidative stress, confirming prior in vitro data. Many mutation contexts exhibit a strong transcriptional strand bias, highlighting the contribution of TC-NER to the repair of ILS lesions. Finally, collateral mutations are also observed in response to ILS, suggesting a contribution of translesion synthesis pathways to ILS tolerance. Accordingly, ILS treatment led to the rapid recruitment of the Y-family DNA polymerase kappa onto chromatin, supporting its preferential use for ILS lesion bypass. Altogether, our work provides the first global assessment of the genomic impact of ILS, demonstrating the contribution of multiple DNA repair pathways to ILS resistance and mutagenicity.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
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18
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Sandoz J, Cigrang M, Zachayus A, Catez P, Donnio LM, Elly C, Nieminuszczy J, Berico P, Braun C, Alekseev S, Egly JM, Niedzwiedz W, Giglia-Mari G, Compe E, Coin F. Active mRNA degradation by EXD2 nuclease elicits recovery of transcription after genotoxic stress. Nat Commun 2023; 14:341. [PMID: 36670096 PMCID: PMC9859823 DOI: 10.1038/s41467-023-35922-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/06/2023] [Indexed: 01/22/2023] Open
Abstract
The transcriptional response to genotoxic stress involves gene expression arrest, followed by recovery of mRNA synthesis (RRS) after DNA repair. We find that the lack of the EXD2 nuclease impairs RRS and decreases cell survival after UV irradiation, without affecting DNA repair. Overexpression of wild-type, but not nuclease-dead EXD2, restores RRS and cell survival. We observe that UV irradiation triggers the relocation of EXD2 from mitochondria to the nucleus. There, EXD2 is recruited to chromatin where it transiently interacts with RNA Polymerase II (RNAPII) to promote the degradation of nascent mRNAs synthesized at the time of genotoxic attack. Reconstitution of the EXD2-RNAPII partnership on a transcribed DNA template in vitro shows that EXD2 primarily interacts with an elongation-blocked RNAPII and efficiently digests mRNA. Overall, our data highlight a crucial step in the transcriptional response to genotoxic attack in which EXD2 interacts with elongation-stalled RNAPII on chromatin to potentially degrade the associated nascent mRNA, allowing transcription restart after DNA repair.
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Affiliation(s)
- Jérémy Sandoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Max Cigrang
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Amélie Zachayus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Philippe Catez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Lise-Marie Donnio
- Institut NeuroMyogène (INMG) - Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, Lyon, France
| | - Clèmence Elly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | | | - Pietro Berico
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Sergey Alekseev
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | | | - Giuseppina Giglia-Mari
- Institut NeuroMyogène (INMG) - Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, Lyon, France
| | - Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Strasbourg, France.
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19
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Kalegari P, Leme DM, Disner GR, Cestari MM, de Lima Bellan D, Meira WV, Mazepa E, Martinez GR. High Melanin Content in Melanoma Cells Contributes to Enhanced DNA Damage after Rose Bengal Photosensitization. Photochem Photobiol 2022; 98:1355-1364. [PMID: 35398885 DOI: 10.1111/php.13632] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/30/2022]
Abstract
Melanoma is a type of tumor that originates from melanocytes. Irradiation of melanin with UVA and visible light can produce reactive oxygen species (ROS) such as singlet molecular oxygen (1 O2 ). The objective of this study was to examine DNA damage in melanoma cells (B16-F10) with different melanin contents, subjected to 1 O2 generation. To this end, we used the photosensitizer Rose Bengal acetate (RBAc) and irradiation with visible light (526 nm) (RBAc-PDT). We used the modified comet assay with the repair enzymes hOGG1 and T4 endonuclease V to detect the DNA damage associated with 8-oxo-7,8-dihydro-2'-deoxyguanosine and cyclobutane pyrimidine dimers lesions, respectively. We observed increased formation of hOGG1- and T4endoV-sensitive DNA lesions after light exposure (with or without RBAc). Furthermore, 18 h after irradiation, hOGG1-sensitive DNA lesions increased compared to that at the initial time point (0 h), which shows that a high melanin content contributes to post-irradiation formation of them, mainly via sustained oxidative stress, as confirmed by the measurement of ROS levels and activity of antioxidant enzymes. Contrastingly, the number of T4endoV-sensitive DNA lesions decreased over time (18 h). Our data indicate that in melanoma cells, a higher amount of melanin may affect DNA damage levels when subjected to RBAc-PDT.
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Affiliation(s)
- Paloma Kalegari
- Departamento de Bioquímica e Biologia Molecular, Programa de Pós-graduação em Ciências (Bioquímica), Setor de Ciências Biológicas, UFPR, Curitiba, Brazil
| | - Daniela Morais Leme
- Departamento de Genética, Setor de Ciências Biológicas, UFPR, Curitiba, Brazil
| | | | | | - Daniel de Lima Bellan
- Departamento de Biologia Celular, Setor de Ciências Biológicas, UFPR, Curitiba, Brazil
| | - Willian Vanderlei Meira
- Departamento de Bioquímica e Biologia Molecular, Programa de Pós-graduação em Ciências (Bioquímica), Setor de Ciências Biológicas, UFPR, Curitiba, Brazil
| | - Ester Mazepa
- Departamento de Bioquímica e Biologia Molecular, Programa de Pós-graduação em Ciências (Bioquímica), Setor de Ciências Biológicas, UFPR, Curitiba, Brazil
| | - Glaucia Regina Martinez
- Departamento de Bioquímica e Biologia Molecular, Programa de Pós-graduação em Ciências (Bioquímica), Setor de Ciências Biológicas, UFPR, Curitiba, Brazil
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20
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Guh CY, Shen HJ, Chen LW, Chiu PC, Liao IH, Lo CC, Chen Y, Hsieh YH, Chang TC, Yen CP, Chen YY, Chen TWW, Chen LY, Wu CS, Egly JM, Chu HPC. XPF activates break-induced telomere synthesis. Nat Commun 2022; 13:5781. [PMID: 36184605 PMCID: PMC9527253 DOI: 10.1038/s41467-022-33428-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
Alternative Lengthening of Telomeres (ALT) utilizes a recombination mechanism and break-induced DNA synthesis to maintain telomere length without telomerase, but it is unclear how cells initiate ALT. TERRA, telomeric repeat-containing RNA, forms RNA:DNA hybrids (R-loops) at ALT telomeres. We show that depleting TERRA using an RNA-targeting Cas9 system reduces ALT-associated PML bodies, telomere clustering, and telomere lengthening. TERRA interactome reveals that TERRA interacts with an extensive subset of DNA repair proteins in ALT cells. One of TERRA interacting proteins, the endonuclease XPF, is highly enriched at ALT telomeres and recruited by telomeric R-loops to induce DNA damage response (DDR) independent of CSB and SLX4, and thus triggers break-induced telomere synthesis and lengthening. The attraction of BRCA1 and RAD51 at telomeres requires XPF in FANCM-deficient cells that accumulate telomeric R-loops. Our results suggest that telomeric R-loops activate DDR via XPF to promote homologous recombination and telomere replication to drive ALT.
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Affiliation(s)
- Chia-Yu Guh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Hong-Jhih Shen
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Liv WeiChien Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Pei-Chen Chiu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - I-Hsin Liao
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Chen-Chia Lo
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Yunfei Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Yu-Hung Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Ting-Chia Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Chien-Ping Yen
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Yi-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tom Wei-Wu Chen
- Department of Oncology, National Taiwan University Hospital and Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Liuh-Yow Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Ching-Shyi Wu
- Department of Pharmacology, National Taiwan University, Taipei, Taiwan
| | - Jean-Marc Egly
- Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Strasbourg, France.,College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsueh-Ping Catherine Chu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan.
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21
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Naumenko NV, Petruseva IO, Lavrik OI. Bulky Adducts in Clustered DNA Lesions: Causes of Resistance to the NER System. Acta Naturae 2022; 14:38-49. [PMID: 36694906 PMCID: PMC9844087 DOI: 10.32607/actanaturae.11741] [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: 05/31/2022] [Accepted: 10/18/2022] [Indexed: 01/22/2023] Open
Abstract
The nucleotide excision repair (NER) system removes a wide range of bulky DNA lesions that cause significant distortions of the regular double helix structure. These lesions, mainly bulky covalent DNA adducts, are induced by ultraviolet and ionizing radiation or the interaction between exogenous/endogenous chemically active substances and nitrogenous DNA bases. As the number of DNA lesions increases, e.g., due to intensive chemotherapy and combination therapy of various diseases or DNA repair impairment, clustered lesions containing bulky adducts may occur. Clustered lesions are two or more lesions located within one or two turns of the DNA helix. Despite the fact that repair of single DNA lesions by the NER system in eukaryotic cells has been studied quite thoroughly, the repair mechanism of these lesions in clusters remains obscure. Identification of the structural features of the DNA regions containing irreparable clustered lesions is of considerable interest, in particular due to a relationship between the efficiency of some antitumor drugs and the activity of cellular repair systems. In this review, we analyzed data on the induction of clustered lesions containing bulky adducts, the potential biological significance of these lesions, and methods for quantification of DNA lesions and considered the causes for the inhibition of NER-catalyzed excision of clustered bulky lesions.
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Affiliation(s)
- N. V. Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - I. O. Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - O. I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
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22
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A Novel Missense Mutation in ERCC8 Co-Segregates with Cerebellar Ataxia in a Consanguineous Pakistani Family. Cells 2022; 11:cells11193090. [PMID: 36231052 PMCID: PMC9564319 DOI: 10.3390/cells11193090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
Autosomal-recessive cerebellar ataxias (ARCAs) are heterogeneous rare disorders mainly affecting the cerebellum and manifest as movement disorders in children and young adults. To date, ARCA causing mutations have been identified in nearly 100 genes; however, they account for less than 50% of all cases. We studied a multiplex, consanguineous Pakistani family presenting with a slowly progressive gait ataxia, body imbalance, and dysarthria. Cerebellar atrophy was identified by magnetic resonance imaging of brain. Using whole exome sequencing, a novel homozygous missense mutation ERCC8:c.176T>C (p.M59T) was identified that co-segregated with the disease. Previous studies have identified homozygous mutations in ERCC8 as causal for Cockayne Syndrome type A (CSA), a UV light-sensitive syndrome, and several ARCAs. ERCC8 plays critical roles in the nucleotide excision repair complex. The p.M59T, a substitution mutation, is located in a highly conserved WD1 beta-transducin repeat motif. In silico modeling showed that the structure of this protein is significantly affected by the p.M59T mutation, likely impairing complex formation and protein-protein interactions. In cultured cells, the p.M59T mutation significantly lowered protein stability compared to wildtype ERCC8 protein. These findings expand the role of ERCC8 mutations in ARCAs and indicate that ERCC8-related mutations should be considered in the differential diagnosis of ARCAs.
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23
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Carraro C, Bonaguro L, Schulte-Schrepping J, Horne A, Oestreich M, Warnat-Herresthal S, Helbing T, De Franco M, Haendler K, Mukherjee S, Ulas T, Gandin V, Goettlich R, Aschenbrenner AC, Schultze JL, Gatto B. Decoding mechanism of action and sensitivity to drug candidates from integrated transcriptome and chromatin state. eLife 2022; 11:e78012. [PMID: 36043458 PMCID: PMC9433094 DOI: 10.7554/elife.78012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Omics-based technologies are driving major advances in precision medicine, but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development of 3-chloropiperidines, a new class of candidate anticancer agents. Combined analyses of transcriptome and chromatin accessibility elucidated the mechanisms underlying sensitivity to test agents. Furthermore, we implemented a new versatile strategy for the integration of RNA- and ATAC-seq (Assay for Transposase-Accessible Chromatin) data, able to accelerate and extend the standalone analyses of distinct omic layers. This platform guided the construction of a perturbation-informed basal signature predicting cancer cell lines' sensitivity and to further direct compound development against specific tumor types. Overall, this approach offers a scalable pipeline to support the early phases of drug discovery, understanding of mechanisms, and potentially inform the positioning of therapeutics in the clinic.
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Affiliation(s)
- Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Arik Horne
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Marie Oestreich
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
| | - Stefanie Warnat-Herresthal
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Tim Helbing
- Institute of Organic Chemistry, Justus Liebig University GiessenGiessenGermany
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Kristian Haendler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
- Institute of Human Genetics, University of LübeckLübeckGermany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- MRC Biostatistics Unit, University of CambridgeCambridgeUnited Kingdom
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Richard Goettlich
- Institute of Organic Chemistry, Justus Liebig University GiessenGiessenGermany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical CenterNijmegenNetherlands
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
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24
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Evolution of intra-tumoral heterogeneity across different pathological stages in papillary thyroid carcinoma. Cancer Cell Int 2022; 22:263. [PMID: 35996174 PMCID: PMC9394008 DOI: 10.1186/s12935-022-02680-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Intra-tumor heterogeneity (ITH) results from the continuous accumulation of mutations during disease progression, thus impacting patients' clinical outcome. How the ITH evolves across papillary thyroid carcinoma (PTC) different tumor stages is lacking. METHODS We used the whole-exome sequencing data from The Cancer Genome Atlas Thyroid Cancer (TCGA-THCA) cohort to track the ITH and assessed its relationship with clinical features through different stages of the PTC progression. We further assayed the expression levels of the specific genes in papillary thyroid cancer cell lines compared to an immortalized normal thyroid epithelial cell line by qRT-PCR. RESULTS We revealed the timing of mutational processes and the dynamics of the temporal acquisition of somatic events during the lifetime of the PTC. ITH significantly influences the PTC patient's survival rate and, as genetic heterogeneity increases, the prognosis gets worse in advanced tumor stages. ITH also affects the mutational architecture of each clinical stage which is subject to periodic fluctuations. Different mutational processes may cooperate to shape a stage-specific mutational spectrum during the progression from early to advanced tumor stages. Moreover, different evolutionary paths characterize PTC progression across pathological stages due to both mutations recurrently occurring in all stages in hotspot positions and distinct codon changes dominating in different stages. A different expression level of specific genes also exists in different thyroid cancer cell lines. CONCLUSIONS Our findings suggest ITH as a potential unfavorable prognostic factor in PTC and highlight the dynamic changes in different clinical stages of PTC, providing some clues for the precision medicine and suggesting different diagnostic decisions depending on the clinical stages of patients. Finally, complete clear guidelines to define risk stratification of PTC patients are lacking; thus, this work could contribute to defining patients who need more aggressive treatments and, in turn, could reduce the social burden of this cancer.
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25
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Kolacsek O, Wachtl G, Fóthi Á, Schamberger A, Sándor S, Pergel E, Varga N, Raskó T, Izsvák Z, Apáti Á, Orbán TI. Functional indications for transposase domestications - Characterization of the human piggyBac transposase derived (PGBD) activities. Gene 2022; 834:146609. [PMID: 35609796 DOI: 10.1016/j.gene.2022.146609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022]
Abstract
Transposable elements are widespread in all living organisms. In addition to self-reproduction, they are a major source of genetic variation that drives genome evolution but our knowledge of the functions of human genes derived from transposases is limited. There are examples of transposon-derived, domesticated human genes that lost (SETMAR) or retained (THAP9) their transposase activity, however, several remnants in the human genome have not been thoroughly investigated yet. These include the five human piggyBac-derived sequences (PGBD1-5) which share ancestry with the Trichoplusia ni originated piggyBac (PB) transposase. Since PB is widely used in gene delivery applications, the potential activities of endogenous PGBDs are important to address. However, previous data is controversial, especially with the claimed transposition activity of PGBD5, it awaits further investigations. Here, we aimed to systematically analyze all five human PGBD proteins from several aspects, including phylogenetic conservation, potential transposase activity, expression pattern and their regulation in different stress conditions. Among PGBDs, PGBD5 is under the highest purifying selection, and exhibits the most cell type specific expression pattern. In a two-component vector system, none of the human PGBDs could mobilize either the insect PB transposon or the endogenous human PB-like MER75 and MER85 elements with intact terminal sequences. When cells were exposed to various stress conditions, including hypoxia, oxidative or UV stress, the expression profiles of all PGBDs showed different, often cell type specific responses; however, the pattern of PGBD5 in most cases had the opposite tendency than that of the other piggyBac-derived elements. Taken together, our results indicate that human PGBD elements did not retain their mobilizing activity, but their cell type specific, and cellular stress related expression profiles point toward distinct domesticated functions that require further characterization.
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Affiliation(s)
- Orsolya Kolacsek
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gerda Wachtl
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ábel Fóthi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Anita Schamberger
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sára Sándor
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Enikő Pergel
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nóra Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Raskó
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Ágota Apáti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
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26
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Paccosi E, Balajee AS, Proietti-De-Santis L. A matter of delicate balance: Loss and gain of Cockayne syndrome proteins in premature aging and cancer. FRONTIERS IN AGING 2022; 3:960662. [PMID: 35935726 PMCID: PMC9351357 DOI: 10.3389/fragi.2022.960662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 12/26/2022]
Abstract
DNA repair genes are critical for preserving genomic stability and it is well established that mutations in DNA repair genes give rise to progeroid diseases due to perturbations in different DNA metabolic activities. Cockayne Syndrome (CS) is an autosomal recessive inheritance caused by inactivating mutations in CSA and CSB genes. This review will primarily focus on the two Cockayne Syndrome proteins, CSA and CSB, primarily known to be involved in Transcription Coupled Repair (TCR). Curiously, dysregulated expression of CS proteins has been shown to exhibit differential health outcomes: lack of CS proteins due to gene mutations invariably leads to complex premature aging phenotypes, while excess of CS proteins is associated with carcinogenesis. Thus it appears that CS genes act as a double-edged sword whose loss or gain of expression leads to premature aging and cancer. Future mechanistic studies on cell and animal models of CS can lead to potential biological targets for interventions in both aging and cancer development processes. Some of these exciting possibilities will be discussed in this review in light of the current literature.
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Affiliation(s)
- Elena Paccosi
- Unit of Molecular Genetics of Aging, Department of Ecology and Biology, University of Tuscia, Viterbo, Italy
- *Correspondence: Elena Paccosi, ; Adayabalam S. Balajee, ; Luca Proietti-De-Santis,
| | - Adayabalam S. Balajee
- Cytogenetic Biodosimetry Laboratory, Radiation Emergency Assistance Center/Training Site, Oak Ridge Institute of Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN, United States
- *Correspondence: Elena Paccosi, ; Adayabalam S. Balajee, ; Luca Proietti-De-Santis,
| | - Luca Proietti-De-Santis
- Unit of Molecular Genetics of Aging, Department of Ecology and Biology, University of Tuscia, Viterbo, Italy
- *Correspondence: Elena Paccosi, ; Adayabalam S. Balajee, ; Luca Proietti-De-Santis,
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27
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Gopaul D, Denby Wilkes C, Goldar A, Giordanengo Aiach N, Barrault MB, Novikova E, Soutourina J. Genomic analysis of Rad26 and Rad1-Rad10 reveals differences in their dependence on Mediator and RNA polymerase II. Genome Res 2022; 32:gr.276371.121. [PMID: 35738899 PMCID: PMC9435749 DOI: 10.1101/gr.276371.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 06/16/2022] [Indexed: 02/03/2023]
Abstract
Mediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and nucleotide excision repair (NER) via a direct contact with Rad2/ERCC5(XPG) endonuclease. In this work, we analyzed the genome-wide distribution of Rad26/ERCC6(CSB) and Rad1-Rad10/ERCC4(XPF)-ERCC1, addressing the question of a potential link of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae Our genomic analyses reveal that Rad1-Rad10 and Rad26 are present on the yeast genome in the absence of genotoxic stress, especially at highly transcribed regions, with Rad26 binding strongly correlating with that of Pol II. Moreover, we show that Rad1-Rad10 and Rad26 colocalize with Mediator at intergenic regions and physically interact with this complex. Using kin28 TFIIH mutant, we found that Mediator stabilization on core promoters leads to an increase in Rad1-Rad10 chromatin binding, whereas Rad26 occupancy follows mainly a decrease in Pol II transcription. Combined with multivariate analyses, our results show the relationships between Rad1-Rad10, Rad26, Mediator, and Pol II, modulated by the changes in binding dynamics of Mediator and Pol II transcription. In conclusion, we extend the Mediator link to Rad1-Rad10 and Rad26 NER proteins and reveal important differences in their dependence on Mediator and Pol II. Rad2 is the most dependent on Mediator, followed by Rad1-Rad10, whereas Rad26 is the most closely related to Pol II. Our work thus contributes to new concepts of the functional interplay between transcription and DNA repair machineries, which are relevant for human diseases including cancer and XP/CS syndromes.
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Affiliation(s)
- Diyavarshini Gopaul
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Nathalie Giordanengo Aiach
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie-Bénédicte Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Elizaveta Novikova
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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28
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Moretton A, Slyskova J, Simaan ME, Arasa-Verge EA, Meyenberg M, Cerrón-Infantes DA, Unterlass MM, Loizou JI. Clickable Cisplatin Derivatives as Versatile Tools to Probe the DNA Damage Response to Chemotherapy. Front Oncol 2022; 12:874201. [PMID: 35719993 PMCID: PMC9202558 DOI: 10.3389/fonc.2022.874201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 12/04/2022] Open
Abstract
Cisplatin induces DNA crosslinks that are highly cytotoxic. Hence, platinum complexes are frequently used in the treatment of a broad range of cancers. Efficiency of cisplatin treatment is limited by the tumor-specific DNA damage response to the generated lesions. We reasoned that better tools to investigate the repair of DNA crosslinks induced by cisplatin would therefore be highly useful in addressing drug limitations. Here, we synthesized a series of cisplatin derivatives that are compatible with click chemistry, thus allowing visualization and isolation of DNA-platinum crosslinks from cells to study cellular responses. We prioritized one alkyne and one azide Pt(II) derivative, Pt-alkyne-53 and Pt-azide-64, for further biological characterization. We demonstrate that both compounds bind DNA and generate DNA lesions and that the viability of treated cells depends on the active DNA repair machinery. We also show that the compounds are clickable with both a fluorescent probe as well as biotin, thus they can be visualized in cells, and their ability to induce crosslinks in genomic DNA can be quantified. Finally, we show that Pt-alkyne-53 can be used to identify DNA repair proteins that bind within its proximity to facilitate its removal from DNA. The compounds we report here can be used as valuable experimental tools to investigate the DNA damage response to platinum complexes and hence might shed light on mechanisms of chemoresistance.
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Affiliation(s)
- Amandine Moretton
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jana Slyskova
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marwan E Simaan
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Materials Chemistry, Technische Universität Wien, Vienna, Austria.,Institute of Applied Synthetic Chemistry, Technische Universität Wien, Vienna, Austria
| | - Emili A Arasa-Verge
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Mathilde Meyenberg
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - D Alonso Cerrón-Infantes
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Materials Chemistry, Technische Universität Wien, Vienna, Austria.,Institute of Applied Synthetic Chemistry, Technische Universität Wien, Vienna, Austria.,Department of Chemistry, Solid State Chemistry, Universität Konstanz, Konstanz, Germany
| | - Miriam M Unterlass
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Materials Chemistry, Technische Universität Wien, Vienna, Austria.,Institute of Applied Synthetic Chemistry, Technische Universität Wien, Vienna, Austria.,Department of Chemistry, Solid State Chemistry, Universität Konstanz, Konstanz, Germany
| | - Joanna I Loizou
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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29
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Zhang X, Yin M, Hu J. Nucleotide excision repair: a versatile and smart toolkit. Acta Biochim Biophys Sin (Shanghai) 2022; 54:807-819. [PMID: 35975604 PMCID: PMC9828404 DOI: 10.3724/abbs.2022054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nucleotide excision repair (NER) is a major pathway to deal with bulky adducts induced by various environmental toxins in all cellular organisms. The two sub-pathways of NER, global genome repair (GGR) and transcription-coupled repair (TCR), differ in the damage recognition modes. In this review, we describe the molecular mechanism of NER in mammalian cells, especially the details of damage recognition steps in both sub-pathways. We also introduce new sequencing methods for genome-wide mapping of NER, as well as recent advances about NER in chromatin by these methods. Finally, the roles of NER factors in repairing oxidative damages and resolving R-loops are discussed.
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Affiliation(s)
| | | | - Jinchuan Hu
- Correspondence address. Tel: +86-21-54237702; E-mail:
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30
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Cannataro VL, Mandell JD, Townsend JP. Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes. Mol Biol Evol 2022; 39:msac084. [PMID: 35580068 PMCID: PMC9113445 DOI: 10.1093/molbev/msac084] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Mutational processes in tumors create distinctive patterns of mutations, composed of neutral "passenger" mutations and oncogenic drivers that have quantifiable effects on the proliferation and survival of cancer cell lineages. Increases in proliferation and survival are mediated by natural selection, which can be quantified by comparing the frequency at which we detect substitutions to the frequency at which we expect to detect substitutions assuming neutrality. Most of the variants detectable with whole-exome sequencing in tumors are neutral or nearly neutral in effect, and thus the processes generating the majority of mutations may not be the primary sources of the tumorigenic mutations. Across 24 cancer types, we identify the contributions of mutational processes to each oncogenic variant and quantify the degree to which each process contributes to tumorigenesis. We demonstrate that the origination of variants driving melanomas and lung cancers is predominantly attributable to the preventable, exogenous mutational processes associated with ultraviolet light and tobacco exposure, respectively, whereas the origination of selected variants in gliomas and prostate adenocarcinomas is largely attributable to endogenous processes associated with aging. Preventable mutations associated with pathogen exposure and apolipoprotein B mRNA-editing enzyme activity account for a large proportion of the cancer effect within head-and-neck, bladder, cervical, and breast cancers. These attributions complement epidemiological approaches-revealing the burden of cancer driven by single-nucleotide variants caused by either endogenous or exogenous, nonpreventable, or preventable processes, and crucially inform public health strategies.
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Affiliation(s)
| | - Jeffrey D. Mandell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Jeffrey P. Townsend
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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31
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Nasrallah NA, Wiese BM, Sears CR. Xeroderma Pigmentosum Complementation Group C (XPC): Emerging Roles in Non-Dermatologic Malignancies. Front Oncol 2022; 12:846965. [PMID: 35530314 PMCID: PMC9069926 DOI: 10.3389/fonc.2022.846965] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Xeroderma pigmentosum complementation group C (XPC) is a DNA damage recognition protein essential for initiation of global-genomic nucleotide excision repair (GG-NER). Humans carrying germline mutations in the XPC gene exhibit strong susceptibility to skin cancer due to defective removal via GG-NER of genotoxic, solar UV-induced dipyrimidine photoproducts. However, XPC is increasingly recognized as important for protection against non-dermatologic cancers, not only through its role in GG-NER, but also by participating in other DNA repair pathways, in the DNA damage response and in transcriptional regulation. Additionally, XPC expression levels and polymorphisms likely impact development and may serve as predictive and therapeutic biomarkers in a number of these non-dermatologic cancers. Here we review the existing literature, focusing on the role of XPC in non-dermatologic cancer development, progression, and treatment response, and highlight possible future applications of XPC as a prognostic and therapeutic biomarker.
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Affiliation(s)
- Nawar Al Nasrallah
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Benjamin M. Wiese
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Catherine R. Sears
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
- Division of Pulmonary Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN, United States
- *Correspondence: Catherine R. Sears,
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32
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Palazzo AF, Kejiou NS. Non-Darwinian Molecular Biology. Front Genet 2022; 13:831068. [PMID: 35251134 PMCID: PMC8888898 DOI: 10.3389/fgene.2022.831068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper “Non-Darwinian Evolution”, where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura’s new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.
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33
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Campos JTADM, Oliveira MSD, Soares LP, Medeiros KAD, Campos LRDS, Lima JG. DNA repair-related genes and adipogenesis: Lessons from congenital lipodystrophies. Genet Mol Biol 2022; 45:e20220086. [DOI: 10.1590/1678-4685-gmb-2022-0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
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34
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Kneubil M, Goulart K, Brollo J, Coelho G, Mandelli J, Orlandin B, Corso L, Roesch-Ely M, Henriques J. Predictive value of DNA repair gene expression for response to neoadjuvant chemotherapy in breast cancer. Braz J Med Biol Res 2022; 55:e11857. [PMID: 35293552 PMCID: PMC8922549 DOI: 10.1590/1414-431x2021e11857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/17/2021] [Indexed: 11/22/2022] Open
Abstract
Genome-wide analysis using microarrays has revolutionized breast cancer (BC)
research. A substantial body of evidence supports the clinical utility of the
21-gene assay (Oncotype DX) and 70-gene assay (MammaPrint) to predict BC
recurrence and the magnitude of benefit from chemotherapy. However, there is
currently no genetic tool able to predict chemosensitivity and chemoresistance
to neoadjuvant chemotherapy (NACT) during BC treatment. In this study, we
explored the predictive value of DNA repair gene expression in the neoadjuvant
setting. We selected 98 patients with BC treated with NACT. We assessed DNA
repair expression in 98 formalin-fixed, paraffin-embedded core biopsy fragments
used at diagnosis and in 32 formalin-fixed, paraffin-embedded post-NACT residual
tumors using quantitative reverse transcription-polymerase chain reaction. The
following genes were selected: BRCA1, PALB2,
RAD51C, BRCA2, ATM,
FANCA, MSH2, XPA,
ERCC1, PARP1, and SNM1.
Of 98 patients, 33 (33.7%) achieved pathologic complete response (pCR). The DNA
expression of 2 genes assessed in pre-NACT biopsies (PALB2 and
ERCC1) was lower in pCR than in non-pCR patients (P=0.005
and P=0.009, respectively). There was no correlation between molecular subtype
and expression of DNA repair genes. The genes BRCA2 (P=0.009),
ATM (P=0.004), FANCA (P=0.001), and
PARP1 (P=0.011) showed a lower expression in post-NACT
residual tumor samples (n=32) than in pre-NACT biopsy samples (n=98). The
expression of 2 genes (PALB2 and ERCC1) was
lower in pCR patients. These alterations in DNA repair could be considered
suitable targets for cancer therapy.
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Affiliation(s)
- M.C. Kneubil
- Universidade de Caxias do Sul, Brasil; Universidade de Caxias do Sul, Brasil
| | | | - J. Brollo
- Universidade de Caxias do Sul, Brasil
| | | | | | | | - L.L. Corso
- Universidade de Caxias do Sul, Brasil; Instituto Hercílio Randon, Brasil
| | | | - J.A.P. Henriques
- Universidade de Caxias do Sul, Brasil; Universidade do Vale do Taquari - UNIVATES, Brasil
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35
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Jiang L, Jiang H, Dai S, Chen Y, Song Y, Tang CSM, Pang SYY, Ho SL, Wang B, Garcia-Barcelo MM, Tam PKH, Cherny SS, Li MJ, Sham PC, Li M. Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases. Nucleic Acids Res 2021; 50:e34. [PMID: 34931221 PMCID: PMC8989543 DOI: 10.1093/nar/gkab1234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 02/07/2023] Open
Abstract
Identifying rare variants that contribute to complex diseases is challenging because of the low statistical power in current tests comparing cases with controls. Here, we propose a novel and powerful rare variants association test based on the deviation of the observed mutation burden of a gene in cases from a baseline predicted by a weighted recursive truncated negative-binomial regression (RUNNER) on genomic features available from public data. Simulation studies show that RUNNER is substantially more powerful than state-of-the-art rare variant association tests and has reasonable type 1 error rates even for stratified populations or in small samples. Applied to real case-control data, RUNNER recapitulates known genes of Hirschsprung disease and Alzheimer's disease missed by current methods and detects promising new candidate genes for both disorders. In a case-only study, RUNNER successfully detected a known causal gene of amyotrophic lateral sclerosis. The present study provides a powerful and robust method to identify susceptibility genes with rare risk variants for complex diseases.
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Affiliation(s)
- Lin Jiang
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hui Jiang
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
| | - Sheng Dai
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ying Chen
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
| | - Youqiang Song
- School of Biomedical Sciences, the University of Hong Kong, Hong Kong, SAR China.,State Key Laboratory of Brain and Cognitive Sciences, the University of Hong Kong, Hong Kong, SAR China
| | - Clara Sze-Man Tang
- Department of Surgery, the University of Hong Kong, Hong Kong, SAR China.,Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, SAR China
| | - Shirley Yin-Yu Pang
- Division of Neurology, Department of Medicine, the University of Hong Kong, Hong Kong, SAR China
| | - Shu-Leong Ho
- Division of Neurology, Department of Medicine, the University of Hong Kong, Hong Kong, SAR China
| | - Binbin Wang
- Department of Genetics, National Research Institute for Family Planning, Beijing, China
| | | | - Paul Kwong-Hang Tam
- Department of Surgery, the University of Hong Kong, Hong Kong, SAR China.,Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, SAR China.,Faculty of Medicine, Macau University of Science and Technology, Macau, SAR China
| | | | - Mulin Jun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Pak Chung Sham
- The Centre for PanorOmic Sciences, the University of Hong Kong, Hong Kong, SAR China.,State Key Laboratory of Brain and Cognitive Sciences, the University of Hong Kong, Hong Kong, SAR China.,Department of Psychiatry, the University of Hong Kong, Hong Kong, SAR China
| | - Miaoxin Li
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China.,The Centre for PanorOmic Sciences, the University of Hong Kong, Hong Kong, SAR China.,Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
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36
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Rose E, Moraes A, Shiroma T, Nitz N, Rosa ADC, Pratesi R, Hagström L, de Carvalho JL, Hecht M. Host DNA repair response to oxidative damage is modulated by Trypanosoma cruzi in a strain-dependent manner. Acta Trop 2021; 224:106127. [PMID: 34509459 DOI: 10.1016/j.actatropica.2021.106127] [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: 04/19/2021] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022]
Abstract
The conservation of genomic integrity and stability is essential for cell survival. DNA Damage Responses (DDRs) are considered of paramount importance for all living beings and involve mechanisms of cell cycle regulation and damage-specific DNA repair pathways. Hydrogen peroxide (H2O2) is a compound that, in supraphysiological concentrations, damages biomolecules including the DNA, causing base modifications and strand breaks. There is evidence that Trypanosoma cruzi, the protozoan that causes Chagas disease, interferes in the host cell's DNA metabolism. In order to investigate the influence of T. cruzi infection over the host cell capacity to withstand and repair DNA damage, we analyzed L6 cells infected with Berenice, and Colombiana T. cruzi strains according to their viability, proliferation, morphology, DNA degradation, expression of DNA repair, and cell cycle genes following H2O2 treatment. It was noted that T. cruzi infection might act as either a stressor or a protective element of host DNA, depending on the strain and H2O2 concentration. Cells infected with Berenice strain and treated with 0.8 mM H2O2 presented a reduced DNA damage response intensity (e.g., BER and HR). Infection with T. cruzi Colombiana prevented the activation of DNA repair pathways in response to 0.8mM and 1.6mM H2O2 (NER and MMR). Nevertheless, since cellular viability was not significantly compromised in Colombiana-infected cells following the oxidative insult, it is possible that the parasite directly influenced the host DNA repair machinery. Our results support the notion that T. cruzi is able to modulate the host cell DNA metabolism in a strain-dependent manner, an event which can be explored in future drug development strategies.
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Affiliation(s)
- Ester Rose
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasilia, Brasilia, Brazil.
| | - Aline Moraes
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | - Tatiana Shiroma
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | - Nadjar Nitz
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | - Ana de Cássia Rosa
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | - Riccardo Pratesi
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | - Luciana Hagström
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | - Juliana Lott de Carvalho
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | - Mariana Hecht
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
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Targeting the DNA damage response: PARP inhibitors and new perspectives in the landscape of cancer treatment. Crit Rev Oncol Hematol 2021; 168:103539. [PMID: 34800653 DOI: 10.1016/j.critrevonc.2021.103539] [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: 05/07/2021] [Revised: 09/26/2021] [Accepted: 11/15/2021] [Indexed: 12/27/2022] Open
Abstract
Cancer derives from alterations of pathways responsible for cell survival, differentiation and proliferation. Dysfunctions of mechanisms protecting genome integrity can promote oncogenesis but can also be exploited as therapeutic target. Poly-ADP-Ribose-Polymerase (PARP)-inhibitors, the first approved targeted agents able to tackle DNA damage response (DDR), have demonstrated antitumor activity, particularly when homologous recombination impairment is present. Despite the relevant results achieved, a large proportion of patients fail to obtain durable responses. The development of innovative treatments, able to overcome resistance and ensure long-lasting benefit for a wider population is still an unmet need. Moreover, improvement in biomarker assays is necessary to properly identify patients who can benefit from DDR targeting agents. Here we summarize the main DDR pathways, explain the current role of PARP inhibitors in cancer therapy and illustrate new therapeutic strategies targeting the DDR, focusing on the combinations of PARP inhibitors with other agents and on cell-cycle checkpoint inhibitors.
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38
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Erber L, Goodman S, Jokipii Krueger CC, Rusyn I, Tretyakova N. Quantitative NanoLC/NSI +-HRMS Method for 1,3-Butadiene Induced bis-N7-guanine DNA-DNA Cross-Links in Urine. TOXICS 2021; 9:247. [PMID: 34678943 PMCID: PMC8540193 DOI: 10.3390/toxics9100247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/13/2021] [Accepted: 09/28/2021] [Indexed: 01/16/2023]
Abstract
1,3-Butadiene (BD) is a common environmental and industrial chemical widely used in plastic and rubber manufacturing and also present in cigarette smoke and automobile exhaust. BD is classified as a known human carcinogen based on evidence of carcinogenicity in laboratory animals treated with BD by inhalation and epidemiological studies revealing an increased risk of leukemia and lymphohematopoietic cancers in workers occupationally exposed to BD. Upon exposure via inhalation, BD is bioactivated to several toxic epoxides including 3,4-epoxy-1-butene (EB), 3,4-epoxy-1,2-butanediol (EBD), and 1,2,3,4-diepoxybutane (DEB); these are conjugated with glutathione and excreted as 2-(N-acetyl-L-cystein-S-yl)-1-hydroxybut-3-ene/1-(N-acetyl-L-cystein-S-yl)-2-hydroxybut-3-ene (MHBMA), 4-(N-acetyl-L-cystein-S-yl)-1,2-dihydroxybutane (DHBMA), and 1,4-bis-(N-acetyl-L-cystein-S-yl)butane-2,3-diol (bis-BDMA). Exposure to DEB generates monoalkylated DNA adducts, DNA-DNA crosslinks, and DNA-protein crosslinks, which can cause base substitutions, genomic rearrangements, and large genomic deletions. In this study, we developed a quantitative nanoLC/NSI+-HRMS methodology for 1,4-bis-(gua-7-yl)-2,3-butanediol (bis-N7G-BD) adducts in urine (LOD: 0.1 fmol/mL urine, LOQ: 1.0 fmol/mL urine). This novel method was used to quantify bis-N7G-BD in urine of mice treated with 590 ± 150 ppm BD for 2 weeks (6 h/day, 5 days/week). Bis-N7G-BD was detected in urine of male and female BD-exposed mice (574.6 ± 206.0 and 571.1 ± 163.4 pg/mg of creatinine, respectively). In addition, major urinary metabolites of BD, bis-BDMA, MHBMA and DHBMA, were measured in the same samples. Urinary bis-N7G-BD adduct levels correlated with DEB-derived metabolite bis-BDMA (r = 0.80, Pearson correlation), but not with the EB-derived DNA adducts (EB-GII) or EB-derived metabolites MHBMA and DHBMA (r = 0.24, r = 0.14, r = 0.18, respectively, Pearson correlations). Urinary bis-N7G-BD could be employed as a novel non-invasive biomarker of exposure to BD and bioactivation to its most mutagenic metabolite, DEB. This method will be useful for future studies of 1,3-butadiene exposure and metabolism.
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Affiliation(s)
- Luke Erber
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (L.E.); (C.C.J.K.)
| | - Samantha Goodman
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Caitlin C. Jokipii Krueger
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (L.E.); (C.C.J.K.)
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (L.E.); (C.C.J.K.)
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Chen J, Li L, Sun L, Yuan Y, Jing J. Associations of individual and joint expressions of ERCC6 and ERCC8 with clinicopathological parameters and prognosis of gastric cancer. PeerJ 2021; 9:e11791. [PMID: 34316408 PMCID: PMC8286707 DOI: 10.7717/peerj.11791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/25/2021] [Indexed: 11/20/2022] Open
Abstract
Background Excision repair cross-complementing group 6 and 8 (ERCC6 and ERCC8) have been implicated in ailments such as genetic diseases and cancers. However, the relationship between individual and joint expressions of ERCC6/ERCC8 and clinicopathological parameters as well as prognosis of gastric cancer (GC) still remains unclear. Methods In this study, protein expressions of ERCC6, ERCC8 and ERCC6-ERCC8 were detected by immunohistochemistry (IHC) in 109 paired GC and para-cancerous normal tissue samples. The mRNA expression was detected in 36 pairs of tissue samples. IHC results and RNA-seq data extracted from The Cancer Genome Atlas (TCGA) were used to explore the clinical value of ERCC6 and ERCC8 expression in GC. We further conducted protein-protein interaction analysis, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment analysis, and gene-gene interaction analysis to explore the function and regulation networks of ERCC6 and ERCC8 in GC. Results Individual and joint ERCC6/ERCC8 expression were significantly higher in adjacent normal mucosa compared with GC tissues. ERCC6 mRNA expression showed no difference in GC and paired tissues, while ERCC8 mRNA was significantly decreased in GC tissues. Protein expression of ERCC6, ERCC8, double negative ERCC6-ERCC8 and double positive ERCC6-ERCC8 and overexpressed ERCC6 mRNA were related to better clinicopathologic parameters, while overexpressed ERCC8 mRNA suggested worse parameters. Univariate survival analysis indicated that the OS was longer when ERCC6 protein expression and ERCC8 mRNA expression increased, and double negative ERCC6-ERCC8 expression was associated with a short OS. Bioinformatics analyses showed ERCC6 and ERCC8 were associated with nucleotide excision repair (NER) pathway, and six and ten gene sets were figured out to be related with ERCC6 and ERCC8, respectively. KEGG pathway showed that ERCC6/ERCC8 related gene sets were mainly involved in the regulation of PI3K/AKT/mTOR pathway. Direct physical interactions were found between ERCC6 and ERCC8. Conclusions Individual and joint expressions of ERCC6/ERCC8 were associated with clinical features of GC. Protein expression of ERCC6, ERCC6-ERCC8, and mRNA expression of ERCC8 were related to prognosis of GC. ERCC6 and ERCC8 primarily function in the NER pathway, and may regulate GC progression through the regulation of PI3K/AKT/mTOR pathway.
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Affiliation(s)
- Jing Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Liang Li
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Liping Sun
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, Liaoning, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, Liaoning, China
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Chervova A, Fatykhov B, Koblov A, Shvarov E, Preobrazhenskaya J, Vinogradov D, Ponomarev GV, Gelfand MS, Kazanov MD. Analysis of gene expression and mutation data points on contribution of transcription to the mutagenesis by APOBEC enzymes. NAR Cancer 2021; 3:zcab025. [PMID: 34316712 PMCID: PMC8253550 DOI: 10.1093/narcan/zcab025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 11/30/2022] Open
Abstract
Since the discovery of the role of the APOBEC enzymes in human cancers, the mechanisms of this type of mutagenesis remain little understood. Theoretically, targeting of single-stranded DNA by the APOBEC enzymes could occur during cellular processes leading to the unwinding of DNA double-stranded structure. Some evidence points to the importance of replication in the APOBEC mutagenesis, while the role of transcription is still underexplored. Here, we analyzed gene expression and whole genome sequencing data from five types of human cancers with substantial APOBEC activity to estimate the involvement of transcription in the APOBEC mutagenesis and compare its impact with that of replication. Using the TCN motif as the mutation signature of the APOBEC enzymes, we observed a correlation of active APOBEC mutagenesis with gene expression, confirmed the increase of APOBEC-induced mutations in early-replicating regions and estimated the relative impact of transcription and replication on the APOBEC mutagenesis. We also found that the known effect of higher density of APOBEC-induced mutations on the lagging strand was highest in middle-replicating regions and observed higher APOBEC mutation density on the sense strand, the latter bias positively correlated with the gene expression level.
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Affiliation(s)
- Almira Chervova
- Institute of Oncology, Radiology and Nuclear Medicine, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - Bulat Fatykhov
- Department of Control and Applied Mathematics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | | | | | - Julia Preobrazhenskaya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Dmitry Vinogradov
- Research and Training Center of Bioinformatics, Institute for Information Transmission Problems (the Kharkevich Institute, RAS), Moscow, 127051, Russia
| | - Gennady V Ponomarev
- Research and Training Center of Bioinformatics, Institute for Information Transmission Problems (the Kharkevich Institute, RAS), Moscow, 127051, Russia
| | - Mikhail S Gelfand
- Research and Training Center of Bioinformatics, Institute for Information Transmission Problems (the Kharkevich Institute, RAS), Moscow, 127051, Russia
| | - Marat D Kazanov
- Research and Training Center of Bioinformatics, Institute for Information Transmission Problems (the Kharkevich Institute, RAS), Moscow, 127051, Russia
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He Y, Shi M, Wu X, Ma J, Ng KTP, Xia Q, Zhu L, Fu PPC, Man K, Tsui SKW, Lin G. Mutational Signature Analysis Reveals Widespread Contribution of Pyrrolizidine Alkaloid Exposure to Human Liver Cancer. Hepatology 2021; 74:264-280. [PMID: 33462832 DOI: 10.1002/hep.31723] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/06/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Mutational signature analyses are an effective tool in identifying cancer etiology. Humans are frequently exposed to pyrrolizidine alkaloids (PAs), the most common carcinogenic phytotoxins widely distributed in herbal remedies and foods. However, due to the lack of human epidemiological data, PAs are classified as group II hepatocarcinogens by the World Health Organization. This study identified a PA mutational signature as the biomarker to investigate the association of PA exposure with human liver cancer. APPROACH AND RESULTS Pyrrole-protein adducts (PPAs), the PA exposure biomarker, were measured and found in 32% of surgically resected specimens from 34 patients with liver cancer in Hong Kong. Next, we delineated the mode of mutagenic and tumorigenic actions of retrorsine, a representative PA, in mice and human hepatocytes (HepaRG). Retrorsine induced DNA adduction, DNA damage, and activation of tumorigenic hepatic progenitor cells, which initiated hepatocarcinogenesis. PA mutational signature, as the unique molecular fingerprint of PA-induced mutation, was derived from exome mutations in retrorsine-exposed mice and HepaRG cells. Notably, PA mutational signature was validated in genomes of patients with PPA-positive liver cancer but not patients with PPA-negative liver cancer, confirming the specificity of this biomarker in revealing PA-associated liver cancers. Furthermore, we examined the established PA mutational signature in 1,513 liver cancer genomes and found that PA-associated liver cancers were potentially prevalent in Asia (Mainland China [48%], Hong Kong [44%], Japan [22%], South Korea [6%], Southeast Asia [25%]) but minor in Western countries (North America [3%] and Europe [5%]). CONCLUSIONS This study provides a clinical indication of PA-associated liver cancer. We discovered an unexpectedly extensive implication of PA exposure in patients with liver cancer, laying the scientific basis for precautionary approaches and prevention of PA-associated human liver cancers.
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Affiliation(s)
- Yisheng He
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mai Shi
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xu Wu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jiang Ma
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kevin Tak-Pan Ng
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Qingsu Xia
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR
| | - Lin Zhu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peter Pi-Cheng Fu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR
| | - Kwan Man
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ge Lin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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42
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Wang H, Lautrup S, Caponio D, Zhang J, Fang EF. DNA Damage-Induced Neurodegeneration in Accelerated Ageing and Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms22136748. [PMID: 34201700 PMCID: PMC8268089 DOI: 10.3390/ijms22136748] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/18/2022] Open
Abstract
DNA repair ensures genomic stability to achieve healthy ageing, including cognitive maintenance. Mutations on genes encoding key DNA repair proteins can lead to diseases with accelerated ageing phenotypes. Some of these diseases are xeroderma pigmentosum group A (XPA, caused by mutation of XPA), Cockayne syndrome group A and group B (CSA, CSB, and are caused by mutations of CSA and CSB, respectively), ataxia-telangiectasia (A-T, caused by mutation of ATM), and Werner syndrome (WS, with most cases caused by mutations in WRN). Except for WS, a common trait of the aforementioned progerias is neurodegeneration. Evidence from studies using animal models and patient tissues suggests that the associated DNA repair deficiencies lead to depletion of cellular nicotinamide adenine dinucleotide (NAD+), resulting in impaired mitophagy, accumulation of damaged mitochondria, metabolic derailment, energy deprivation, and finally leading to neuronal dysfunction and loss. Intriguingly, these features are also observed in Alzheimer’s disease (AD), the most common type of dementia affecting more than 50 million individuals worldwide. Further studies on the mechanisms of the DNA repair deficient premature ageing diseases will help to unveil the mystery of ageing and may provide novel therapeutic strategies for AD.
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Affiliation(s)
- Heling Wang
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
| | - Sofie Lautrup
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
| | - Domenica Caponio
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
| | - Jianying Zhang
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
- Xiangya School of Stomatology, Central South University, Changsha 410083, China
| | - Evandro F. Fang
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
- The Norwegian Centre on Healthy Ageing (NO-Age), 0010 Oslo, Norway
- Correspondence:
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43
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Mohanan G, Das A, Rajyaguru PI. Genotoxic stress response: What is the role of cytoplasmic mRNA fate? Bioessays 2021; 43:e2000311. [PMID: 34096096 DOI: 10.1002/bies.202000311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 12/18/2022]
Abstract
Genotoxic stress leads to DNA damage which can be detrimental to the cell. A well-orchestrated cellular response is mounted to manage and repair the genotoxic stress-induced DNA damage. Our understanding of genotoxic stress response is derived mainly from studies focused on transcription, mRNA splicing, and protein turnover. Surprisingly not as much is understood about the role of mRNA translation and decay in genotoxic stress response. This is despite the fact that regulation of gene expression at the level of mRNA translation and decay plays a critical role in a myriad of cellular processes. This review aims to summarize some of the known findings of the role of mRNA translation and decay by focusing on two categories of examples. We discuss examples of mRNA whose fates are regulated in the cytoplasm and RNA-binding proteins that regulate mRNA fates in response to genotoxic stress.
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Affiliation(s)
- Gayatri Mohanan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Amiyaranjan Das
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Barve A, Galande AA, Ghaskadbi SS, Ghaskadbi S. DNA Repair Repertoire of the Enigmatic Hydra. Front Genet 2021; 12:670695. [PMID: 33995496 PMCID: PMC8117345 DOI: 10.3389/fgene.2021.670695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/12/2021] [Indexed: 12/20/2022] Open
Abstract
Since its discovery by Abraham Trembley in 1744, hydra has been a popular research organism. Features like spectacular regeneration capacity, peculiar tissue dynamics, continuous pattern formation, unique evolutionary position, and an apparent lack of organismal senescence make hydra an intriguing animal to study. While a large body of work has taken place, particularly in the domain of evolutionary developmental biology of hydra, in recent years, the focus has shifted to molecular mechanisms underlying various phenomena. DNA repair is a fundamental cellular process that helps to maintain integrity of the genome through multiple repair pathways found across taxa, from archaea to higher animals. DNA repair capacity and senescence are known to be closely associated, with mutations in several repair pathways leading to premature ageing phenotypes. Analysis of DNA repair in an animal like hydra could offer clues into several aspects including hydra’s purported lack of organismal ageing, evolution of DNA repair systems in metazoa, and alternative functions of repair proteins. We review here the different DNA repair mechanisms known so far in hydra. Hydra genes from various DNA repair pathways show very high similarity with their vertebrate orthologues, indicating conservation at the level of sequence, structure, and function. Notably, most hydra repair genes are more similar to deuterostome counterparts than to common model invertebrates, hinting at ancient evolutionary origins of repair pathways and further highlighting the relevance of organisms like hydra as model systems. It appears that hydra has the full repertoire of DNA repair pathways, which are employed in stress as well as normal physiological conditions and may have a link with its observed lack of senescence. The close correspondence of hydra repair genes with higher vertebrates further demonstrates the need for deeper studies of various repair components, their interconnections, and functions in this early metazoan.
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Affiliation(s)
- Apurva Barve
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India.,Centre of Excellence in Science and Mathematics Education, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Alisha A Galande
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Surendra Ghaskadbi
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India
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45
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Kara A, Özgür A, Nalbantoğlu S, Karadağ A. DNA repair pathways and their roles in drug resistance for lung adenocarcinoma. Mol Biol Rep 2021; 48:3813-3825. [PMID: 33856604 DOI: 10.1007/s11033-021-06314-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/24/2021] [Indexed: 01/24/2023]
Abstract
Lung cancer is the leading cancer type of death rate. The lung adenocarcinoma subtype is responsible for almost half of the total lung cancer deaths. Despite the improvements in cancer treatment in recent years, lung adenocarcinoma patients' overall survival rate remains poor. Immunetherapy and chemotherapy are two of the most widely used options for the treatment of cancer. Although many cancer types initially respond to these treatments, the development of resistance is inevitable. The rapid development of drug resistance mainly characterizes lung adenocarcinoma. Despite being the subject of many studies in recent years, the resistance initiation and progression mechanism is still unclear. In this review, we have examined the role of the primary DNA repair pathways (non-homologous end joining (NHEJ) pathway, homologous-recombinant repair (HR) pathway, base excision repair (BER) pathway, and nucleotide excision repair (NER) pathway and transactivation mechanisms of tumor protein 53 (TP53) in drug resistance development. This review suggests that mentioned pathways have essential roles in developing the resistance against chemotherapy and immunotherapy in lung adenocarcinoma patients.
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Affiliation(s)
- Altan Kara
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey.
| | - Aykut Özgür
- Laboratory and Veterinary Health Program, Department of Veterinary Medicine, Artova Vocational School, Tokat Gaziosmanpaşa University, Tokat, Turkey
| | - Sinem Nalbantoğlu
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey
| | - Abdullah Karadağ
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey
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46
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Douki T. Wavelengths and temporal effects on the response of mammalian cells to UV radiation: Limitations of action spectra illustrated by genotoxicity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 217:112169. [PMID: 33713895 DOI: 10.1016/j.jphotobiol.2021.112169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 01/17/2023]
Abstract
All photobiological events depend on the wavelength of the incident radiation. In real-life situations and in the vast majority of laboratory experiments, exposure always involves sources with various emission spectra spreading over a wide wavelength range. Action spectra are often used to describe the efficiency of a process at different wavelengths and to predict the effects of a given light source by summation of the individual effects at each wavelength. However, a full understanding of the biological effects of complex sources requires more than considering these concomitant events at each specific wavelength. Indeed, photons of different energies may not have additive but synergistic or inhibitory effects on photochemical processes and cellular responses. The evolution of a photobiological response with post-irradiation time must also be considered. These two aspects may represent some limitations to the use of action spectra. The present review, focused on mammalian cells, illustrates the concept of action spectrum and discusses its drawbacks using theoretical considerations and examples taken from the literature. Emphasis is placed on genotoxicity for which wavelength effects have been extensively studied. Other effects of UV exposure are also mentioned.
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Affiliation(s)
- Thierry Douki
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France.
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47
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Rechkunova NI, Krasikova YS, Lavrik OI. Interactome of Base and Nucleotide Excision DNA Repair Systems. Mol Biol 2021. [DOI: 10.1134/s0026893321020126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Xie Y, Yu Y, Wu H, Gao H, Yang Z, Zhang Y, Zhang X. XAB2 TagSNP Is Associated with the Risk of Gastric Cancer in Chinese Population: A Case-Control Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041494. [PMID: 33557438 PMCID: PMC7914850 DOI: 10.3390/ijerph18041494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 11/26/2022]
Abstract
XAB2 protein (xeroderma pigmentosum group A-binding protein 2) plays a significant role in the nucleotide excision repair pathway. Polymorphisms in the XAB2 gene may have an effect on the capability of DNA repair and further contribute to the risk of developing various cancers. In order to investigate the relationship between XAB2 genetic variants and the risk of gastric cancer, we performed a hospital-based case–control study. XAB2 tagSNPs were selected and then genotyped by iPlex Gold Genotyping Assay and Sequenom MassArray. By performing logistic regression analysis, odds ratio (OR) and 95% confidence interval (CI) were used to estimate the association of XAB2 tagSNPs with the risk of gastric cancer. Our results showed that XAB2 rs794078AA genotype was associated with a significantly lower risk of gastric cancer compared with GG genotype with OR (95% CI) of 0.33 (0.12–0.91). Stratified analysis indicated a significantly decreased risk for gastric cancer among smokers with rs794078AA genotype compared with nonsmokers with GG genotype (OR = 0.11, 95% CI = 0.01–0.91, p = 0.040). The gene–gene interactions by multifactor dimensionality reduction (MDR) showed that tagSNP rs794078 was the best predictive element for gastric cancers (Testing Bal. Acc = 51.68%, p = 0.055, cross-validation consistency = 9). Therefore, the XAB2 tagSNP rs794078 may play an important role in the development of gastric cancer.
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Affiliation(s)
- Yuning Xie
- School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (Y.X.); (H.W.); (H.G.)
- College of Life Science, North China University of Science and Technology, Tangshan 063210, China;
| | - Yuan Yu
- College of Life Science, North China University of Science and Technology, Tangshan 063210, China;
| | - Hongjiao Wu
- School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (Y.X.); (H.W.); (H.G.)
| | - Hui Gao
- School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (Y.X.); (H.W.); (H.G.)
| | - Zhenbang Yang
- School of Basic Medical Sciences, North China University of Science and Technology, Tangshan 063210, China; (Z.Y.); (Y.Z.)
| | - Yi Zhang
- School of Basic Medical Sciences, North China University of Science and Technology, Tangshan 063210, China; (Z.Y.); (Y.Z.)
| | - Xuemei Zhang
- School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (Y.X.); (H.W.); (H.G.)
- College of Life Science, North China University of Science and Technology, Tangshan 063210, China;
- Correspondence: ; Tel.: +86-3158805603
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49
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Bordin DL, Lirussi L, Nilsen H. Cellular response to endogenous DNA damage: DNA base modifications in gene expression regulation. DNA Repair (Amst) 2021; 99:103051. [PMID: 33540225 DOI: 10.1016/j.dnarep.2021.103051] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022]
Abstract
The integrity of the genetic information is continuously challenged by numerous genotoxic insults, most frequently in the form of oxidation, alkylation or deamination of the bases that result in DNA damage. These damages compromise the fidelity of the replication, and interfere with the progression and function of the transcription machineries. The DNA damage response (DDR) comprises a series of strategies to deal with DNA damage, including transient transcriptional inhibition, activation of DNA repair pathways and chromatin remodeling. Coordinated control of transcription and DNA repair is required to safeguardi cellular functions and identities. Here, we address the cellular responses to endogenous DNA damage, with a particular focus on the role of DNA glycosylases and the Base Excision Repair (BER) pathway, in conjunction with the DDR factors, in responding to DNA damage during the transcription process. We will also discuss functions of newly identified epigenetic and regulatory marks, such as 5-hydroxymethylcytosine and its oxidative products and 8-oxoguanine, that were previously considered only as DNA damages. In light of these resultsthe classical perception of DNA damage as detrimental for cellular processes are changing. and a picture emerges whereDNA glycosylases act as dynamic regulators of transcription, placing them at the intersection of DNA repair and gene expression modulation.
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Affiliation(s)
- Diana L Bordin
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway
| | - Lisa Lirussi
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway.
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50
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Shen X, Wang R, Kim MJ, Hu Q, Hsu CC, Yao J, Klages-Mundt N, Tian Y, Lynn E, Brewer TF, Zhang Y, Arun B, Gan B, Andreeff M, Takeda S, Chen J, Park JI, Shi X, Chang CJ, Jung SY, Qin J, Li L. A Surge of DNA Damage Links Transcriptional Reprogramming and Hematopoietic Deficit in Fanconi Anemia. Mol Cell 2021; 80:1013-1024.e6. [PMID: 33338401 DOI: 10.1016/j.molcel.2020.11.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 07/26/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022]
Abstract
Impaired DNA crosslink repair leads to Fanconi anemia (FA), characterized by a unique manifestation of bone marrow failure and pancytopenia among diseases caused by DNA damage response defects. As a germline disorder, why the hematopoietic hierarchy is specifically affected is not fully understood. We find that reprogramming transcription during hematopoietic differentiation results in an overload of genotoxic stress, which causes aborted differentiation and depletion of FA mutant progenitor cells. DNA damage onset most likely arises from formaldehyde, an obligate by-product of oxidative protein demethylation during transcription regulation. Our results demonstrate that rapid and extensive transcription reprogramming associated with hematopoietic differentiation poses a major threat to genome stability and cell viability in the absence of the FA pathway. The connection between differentiation and DNA damage accumulation reveals a novel mechanism of genome scarring and is critical to exploring therapies to counteract the aplastic anemia for the treatment of FA patients.
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Affiliation(s)
- Xi Shen
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Rui Wang
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Moon Jong Kim
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Qianghua Hu
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Chih-Chao Hsu
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Jun Yao
- Department of Molecular Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Naeh Klages-Mundt
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Yanyan Tian
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Erica Lynn
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Thomas F Brewer
- Department of Chemistry, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yilei Zhang
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Banu Arun
- Department of Breast Medical Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Boyi Gan
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Michael Andreeff
- Department of Leukemia, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Shunichi Takeda
- Department of Radiation Biology, Kyoto University, 606-8501 Kyoto, Japan
| | - Junjie Chen
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Jae-Il Park
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Christopher J Chang
- Department of Chemistry, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sung Yun Jung
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Qin
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA; Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.
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