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Podgrajsek R, Hodzic A, Stimpfel M, Kunej T, Peterlin B. Insight into the complexity of male infertility: a multi-omics review. Syst Biol Reprod Med 2024; 70:73-90. [PMID: 38517373 DOI: 10.1080/19396368.2024.2317804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024]
Abstract
Male infertility is a reproductive disorder, accounting for 40-50% of infertility. Currently, in about 70% of infertile men, the cause remains unknown. With the introduction of novel omics and advancement in high-throughput technology, potential biomarkers are emerging. The main purpose of our work was to overview different aspects of omics approaches in association with idiopathic male infertility and highlight potential genes, transcripts, non-coding RNA, proteins, and metabolites worth further exploring. Using the Gene Ontology (GO) analysis, we aimed to compare enriched GO terms from each omics approach and determine their overlapping. A PubMed database screening for the literature published between February 2014 and June 2022 was performed using the keywords: male infertility in association with different omics approaches: genomics, epigenomics, transcriptomics, ncRNAomics, proteomics, and metabolomics. A GO enrichment analysis was performed using the Enrichr tool. We retrieved 281 global studies: 171 genomics (DNA level), 21 epigenomics (19 of methylation and two histone residue modifications), 15 transcriptomics, 31 non-coding RNA, 29 proteomics, two protein posttranslational modification, and 19 metabolomics studies. Gene ontology comparison showed that different omics approaches lead to the identification of different molecular factors and that the corresponding GO terms, obtained from different omics approaches, do not overlap to a larger extent. With the integration of novel omics levels into the research of idiopathic causes of male infertility, using multi-omic systems biology approaches, we will be closer to finding the potential biomarkers and consequently becoming aware of the entire spectrum of male infertility, their cause, prognosis, and potential treatment.
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Affiliation(s)
- Rebeka Podgrajsek
- Department of Human Reproduction, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Alenka Hodzic
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Faculty of Health Sciences, University of Novo mesto, Novo Mesto, Slovenia
| | - Martin Stimpfel
- Department of Human Reproduction, University Medical Center Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
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2
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Aumer T, Däther M, Bergmayr L, Kartika S, Zeng T, Ge Q, Giorgio G, Hess AJ, Michalakis S, Traube FR. The type of DNA damage response after decitabine treatment depends on the level of DNMT activity. Life Sci Alliance 2024; 7:e202302437. [PMID: 38906675 PMCID: PMC11192838 DOI: 10.26508/lsa.202302437] [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: 10/15/2023] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Decitabine and azacytidine are considered as epigenetic drugs that induce DNA methyltransferase (DNMT)-DNA crosslinks, resulting in DNA hypomethylation and damage. Although they are already applied against myeloid cancers, important aspects of their mode of action remain unknown, highly limiting their clinical potential. Using a combinatorial approach, we reveal that the efficacy profile of both compounds primarily depends on the level of induced DNA damage. Under low DNMT activity, only decitabine has a substantial impact. Conversely, when DNMT activity is high, toxicity and cellular response to both compounds are dramatically increased, but do not primarily depend on DNA hypomethylation or RNA-associated processes. By investigating proteome dynamics on chromatin, we show that decitabine induces a strictly DNMT-dependent multifaceted DNA damage response based on chromatin recruitment, but not expression-level changes of repair-associated proteins. The choice of DNA repair pathway hereby depends on the severity of decitabine-induced DNA lesions. Although under moderate DNMT activity, mismatch (MMR), base excision (BER), and Fanconi anaemia-dependent DNA repair combined with homologous recombination are activated in response to decitabine, high DNMT activity and therefore immense replication stress induce activation of MMR and BER followed by non-homologous end joining.
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Affiliation(s)
- Tina Aumer
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Maike Däther
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Linda Bergmayr
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Stephanie Kartika
- Department of Biochemistry, University of Munich (LMU), München, Germany
| | - Theodor Zeng
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Qingyi Ge
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Grazia Giorgio
- Department of Ophthalmology, University Hospital LMU Munich, München, Germany
| | - Alexander J Hess
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | | | - Franziska R Traube
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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3
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Dzhemileva LU, D'yakonov VA, Egorova KS, Ananikov VP. Mechanisms of Cytotoxicity in Six Classes of Ionic Liquids: Evaluating Cell Cycle Impact and Genotoxic and Apoptotic Effects. CHEMOSPHERE 2024:142964. [PMID: 39074667 DOI: 10.1016/j.chemosphere.2024.142964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/03/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024]
Abstract
Ionic liquids (ILs), earlier praised for their eco-friendliness, have emerged as key chemicals in advancing green chemistry, catalysis, solvent development, and more. However, the discovery of their notable toxicity has led to a controversial reputation of ILs and has shifted the research landscape towards understanding their biological impacts. The present study examines the mechanism of cytotoxicity of 32 ILs across six classes, highlighting their effects on the cell cycle of the Jurkat cell line. Focusing on five ILs with pronounced cytotoxicity, we uncover their genotoxic effects and their role in inducing apoptosis. Our findings suggest intricate interplay between the extrinsic and intrinsic apoptotic pathways at different time points after exposure to ILs. Moreover, the ILs studied displayed marked genotoxicity, likely stemming from the accumulation of double-strand DNA breaks in the Jurkat cells. This investigation offers a comprehensive view on interactions of ILs with eukaryotic cells, thereby providing new guidelines for developing safer pharmaceutical and industrial applications of these chemicals. The results not only broaden and enhance the previous perceptions but also open new avenues in research, emphasizing the dual potential of ILs in innovation and safety, and marking a significant step towards integrating chemical innovations with biological safety.
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Affiliation(s)
- Lilya U Dzhemileva
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Vladimir A D'yakonov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Ksenia S Egorova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia.
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4
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Mao C, Li S, Che J, Liu D, Mao X, Rao H. The ubiquitin ligase UBR4 and the deubiquitylase USP5 modulate the stability of DNA mismatch repair protein MLH1. J Biol Chem 2024:107592. [PMID: 39032648 DOI: 10.1016/j.jbc.2024.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/29/2024] [Accepted: 07/10/2024] [Indexed: 07/23/2024] Open
Abstract
MLH1 plays a critical role in DNA mismatch repair and genome maintenance. MLH1 deficiency promotes cancer development and progression, but the mechanism underlying MLH1 regulation remains enigmatic. In this study, we demonstrate that MLH1 protein is degraded by the ubiquitin-proteasome system and have identified vital cis-elements and trans-factors involved in MLH1 turnover. We found that the region encompassing the amino acids 516-650 is crucial for MLH1 degradation. The mismatch repair protein PMS2 may shield MLH1 from degradation as it bind to the MLH1 segment key to its turnover. Furthermore, we have identified the E3 ubiquitin ligase UBR4 and the deubiquitylase USP5, which oppositely modulate MLH1 stability. In consistence, UBR4 or USP5 deficiency affects the cellular response to nucleotide analog 6-TG, supporting their roles in regulating mismatch repair. Our study has revealed important insights into the regulatory mechanisms underlying MLH1 proteolysis, critical to DNA mismatch repair related diseases.
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Affiliation(s)
- Chenyu Mao
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China, 518055
| | - Siqi Li
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China, 518055
| | - Jun Che
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China, 518055
| | - Dongzhou Liu
- Department of Rheumatology and Immunology, Shenzhen People's Hospital; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, China, 518055
| | - Xinliang Mao
- Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China, 511436.
| | - Hai Rao
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China, 518055; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China, 518055.
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Ha GW, Lee MR, Ahn AR, Chung MJ, Kim KM. Attenuated adenomatous polyposis with MSH6 variation: Two case reports. Medicine (Baltimore) 2024; 103:e38791. [PMID: 38968511 PMCID: PMC11224831 DOI: 10.1097/md.0000000000038791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/12/2024] [Indexed: 07/07/2024] Open
Abstract
RATIONALE Adenomatous polyposis (AP) is a genetic disorder characterized by the occurrence of numerous adenomatous polyps in the colon and rectum and can be classified into classical AP and attenuated AP (AAP). AAP is diagnosed when the number of observed adenomas is between 10 and 99. The detection of AAP is significantly increasing mainly due to the improvement of the imaging technique and application of the screening program for colorectal cancer detection. Currently, the germline variations of the APC and MUTYH genes are reported as the main cause of classical AP. However, the underlying genetic basis of AAP is not well understood. In this study, we report 2 cases of AAP with MSH6 variations. PATIENT CONCERNS Both patients visited the hospital after multiple polyps were detected during colonoscopies conducted as part of their health checkups. DIAGNOSES The 2 patients were diagnosed with AAP through colonoscopic examination at our hospital. INTERVENTIONS The 2 received genetic consultation; and, for follow-up purposes, both patients agreed to be tested for an underlying genetic condition through next generation sequencing. And germline MSH6 variations were detected in both AAP patients. OUTCOMES There was no recurrence for both patients for 3 years follow-up. LESSONS Minor portion of AAP can cause by genetic mutation in MSH6, and further research is needed.
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Affiliation(s)
- Gi Won Ha
- Department of Surgery, Jeonbuk National University Medical School, Research Institute of Clinical Medicine of Jeonbuk National University, and Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
| | - Min Ro Lee
- Department of Surgery, Jeonbuk National University Medical School, Research Institute of Clinical Medicine of Jeonbuk National University, and Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
| | - Ae Ri Ahn
- Departments of Pathology, Jeonbuk National University Medical School, Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, and Research Institute for Endocrine Sciences, Jeonju, Republic of Korea
| | - Myoung Ja Chung
- Departments of Pathology, Jeonbuk National University Medical School, Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, and Research Institute for Endocrine Sciences, Jeonju, Republic of Korea
| | - Kyoung Min Kim
- Departments of Pathology, Jeonbuk National University Medical School, Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, and Research Institute for Endocrine Sciences, Jeonju, Republic of Korea
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6
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Miao H, Wang L, Gong F, Duan L, Wang L, Yao Y, Feng M, Deng K, Wang R, Xiao Y, Ling Q, Zhu H, Lu L. A long-term prognosis study of human USP8-mutated ACTH-secreting pituitary neuroendocrine tumours. Clin Endocrinol (Oxf) 2024; 101:32-41. [PMID: 38691659 DOI: 10.1111/cen.15065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 03/29/2024] [Accepted: 04/21/2024] [Indexed: 05/03/2024]
Abstract
OBJECTIVE Somatic variants in the ubiquitin-specific protease 8 (USP8) gene are the most common genetic cause of Cushing disease. We aimed to explore the relationship between clinical outcomes and USP8 status in a single centre. DESIGN, PATIENTS AND MEASUREMENTS We investigated the USP8 status in 48 patients with pituitary corticotroph tumours. A median of 62 months of follow-up was conducted after surgery from November 2013 to January 2015. The clinical, biochemical and imaging features were collected and analysed. RESULTS Seven USP8 variants (p.Ser718Pro, p.Ser719del, p.Pro720Arg, p.Pro720Gln, p.Ser718del, p.Ser718Phe, p.Lys713Arg) were identified in 24 patients (50%). USP8 variants showed a female predominance (100% vs. 75% in wild type [WT], p = .022). Patients with p.Ser719del showed an older age at surgery compared to patients with the p.Pro720Arg variant (47- vs. 24-year-olds, p = .033). Patients with p.Pro720Arg showed a higher rate of macroadenoma compared to patients harbouring the p.Ser718Pro variant (60% vs. 0%, p = .037). No significant differences were observed in serum and urinary cortisol and adrenocorticotropin hormone (ACTH) levels. Immediate surgical remission (79% vs. 75%) and long-term hormone remission (79% vs. 67%) were not significantly different between the two groups. The recurrence rate was 21% (4/19) in patients harbouring USP8 variants and 13% (2/16) in WT patients. Recurrence-free survival presented a tendency to be shorter in USP8-mutated individuals (76.7 vs. 109.2 months, p = .068). CONCLUSIONS Somatic USP8 variants accounted for 50% of the genetic causes in this cohort with a significant female frequency. A long-term follow-up revealed a tendency toward shorter recurrence-free survival in USP8-mutant patients.
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Affiliation(s)
- Hui Miao
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Luo Wang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Translational Medicine Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Fengying Gong
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Translational Medicine Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Lian Duan
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Translational Medicine Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Linjie Wang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Translational Medicine Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yong Yao
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ming Feng
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kan Deng
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Renzhi Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Xiao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qing Ling
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huijuan Zhu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Translational Medicine Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Lin Lu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Translational Medicine Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Gutierrez R, Chan AYS, Lai SWT, Itoh S, Lee DH, Sun K, Battad A, Chen S, O'Connor TR, Shuck SC. Lack of mismatch repair enhances resistance to methylating agents for cells deficient in oxidative demethylation. J Biol Chem 2024; 300:107492. [PMID: 38925328 DOI: 10.1016/j.jbc.2024.107492] [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: 12/21/2023] [Revised: 05/21/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The human alkylation B (AlkB) homologs, ALKBH2 and ALKBH3, respond to methylation damage to maintain genomic integrity and cellular viability. Both ALKBH2 and ALKBH3 are direct reversal repair enzymes that remove 1-methyladenine (1meA) and 3-methylcytosine (3meC) lesions commonly generated by alkylating chemotherapeutic agents. Thus, the existence of deficiencies in ALKBH proteins can be exploited in synergy with chemotherapy. In this study, we investigated possible interactions between ALKBH2 and ALKBH3 with other proteins that could alter damage response and discovered an interaction with the mismatch repair (MMR) system. To test whether the lack of active MMR impacts ALKBH2 and/or ALKBH3 response to methylating agents, we generated cells deficient in ALKBH2, ALKBH3, or both in addition to Mlh homolog 1 (MLH1), another MMR protein. We found that MLH1koALKBH3ko cells showed enhanced resistance toward SN1- and SN2-type methylating agents, whereas MLH1koALKBH2ko cells were only resistant to SN1-type methylating agents. Concomitant loss of ALKBH2 and ALKBH3 (ALKBH2ko3ko) rendered cells sensitive to SN1- and SN2-agents, but the additional loss of MLH1 enhanced resistance to both types of damage. We also showed that ALKBH2ko3ko cells have an ATR-dependent arrest at the G2/M checkpoint, increased apoptotic signaling, and replication fork stress in response to methylation. However, these responses were not observed with the loss of functional MLH1 in MLH1koALKBH2ko3ko cells. Finally, in MLH1koALKBH2ko3ko cells, we observed elevated mutant frequency in untreated and temozolomide treated cells. These results suggest that obtaining a more accurate prognosis of chemotherapeutic outcome requires information on the functionality of ALKBH2, ALKBH3, and MLH1.
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Affiliation(s)
- Roberto Gutierrez
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Annie Yin S Chan
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Seigmund Wai Tsuen Lai
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Shunsuke Itoh
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Dong-Hyun Lee
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, South Korea
| | - Kelani Sun
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Alana Battad
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Shiuan Chen
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Timothy R O'Connor
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA.
| | - Sarah C Shuck
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute at the City of Hope, Duarte, California, USA.
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Suwakulsiri W, Xu R, Rai A, Shafiq A, Chen M, Greening DW, Simpson RJ. Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants. Proteomics 2024; 24:e2300057. [PMID: 37507836 DOI: 10.1002/pmic.202300057] [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: 05/02/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023]
Abstract
Cell-derived extracellular vesicles (EVs) are evolutionary-conserved secretory organelles that, based on their molecular composition, are important intercellular signaling regulators. At least three classes of circulating EVs are known based on mechanism of biogenesis: exosomes (sEVs/Exos), microparticles (lEVs/MPs), and shed midbody remnants (lEVs/sMB-Rs). sEVs/Exos are of endosomal pathway origin, microparticles (lEVs/MPs) from plasma membrane blebbing and shed midbody remnants (lEVs/sMB-Rs) arise from symmetric cytokinetic abscission. Here, we isolate sEVs/Exos, lEVs/MPs, and lEVs/sMB-Rs secreted from human isogenic primary (SW480) and metastatic (SW620) colorectal cancer (CRC) cell lines in milligram quantities for label-free MS/MS-based proteomic profiling. Purified EVs revealed selective composition packaging of exosomal protein markers in SW480/SW620-sEVs/Exos, metabolic enzymes in SW480/SW620-lEVs/MPs, while centralspindlin complex proteins, nucleoproteins, splicing factors, RNA granule proteins, translation-initiation factors, and mitochondrial proteins selectively traffic to SW480/SW620- lEVs/sMB-Rs. Collectively, we identify 39 human cancer-associated genes in EVs; 17 associated with SW480-EVs, 22 with SW620-EVs. We highlight oncogenic receptors/transporters selectively enriched in sEVs/Exos (EGFR/FAS in SW480-sEVs/Exos and MET, TGFBR2, ABCB1 in SW620-sEVs/Exos). Interestingly, MDK, STAT1, and TGM2 are selectively enriched in SW480-lEVs/sMB-Rs, and ADAM15 to SW620-lEVs/sMB-Rs. Our study reveals sEVs/Exos, lEVs/MPs, and lEVs/sMB-Rs have distinct protein signatures that open potential diagnostic avenues of distinct types of EVs for clinical utility.
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Affiliation(s)
- Wittaya Suwakulsiri
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science (LIMS), School of Agriculture, Biomedicine and Environment (SABE), La Trobe University, Melbourne, Victoria, Australia
- Department of Psychiatry, School of Clinical Sciences at Monash Health, Monash Medical Centre, Monash University, Clayton, Victoria, Australia
| | - Rong Xu
- Nanobiotechnology Laboratory, Centre Clinical, Australia Centre for Blood Diseases, School, Monash University, Melbourne, Victoria, Australia
| | - Alin Rai
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Adnan Shafiq
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science (LIMS), School of Agriculture, Biomedicine and Environment (SABE), La Trobe University, Melbourne, Victoria, Australia
| | - Maoshan Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - David W Greening
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard J Simpson
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science (LIMS), School of Agriculture, Biomedicine and Environment (SABE), La Trobe University, Melbourne, Victoria, Australia
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9
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Yudkina AV, Kim DV, Zharkov TD, Zharkov DO, Endutkin AV. Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides. Int J Mol Sci 2024; 25:6006. [PMID: 38892193 PMCID: PMC11172447 DOI: 10.3390/ijms25116006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The DNA building blocks 2'-deoxynucleotides are enantiomeric, with their natural β-D-configuration dictated by the sugar moiety. Their synthetic β-L-enantiomers (βLdNs) can be used to obtain L-DNA, which, when fully substituted, is resistant to nucleases and is finding use in many biosensing and nanotechnology applications. However, much less is known about the enzymatic recognition and processing of individual βLdNs embedded in D-DNA. Here, we address the template properties of βLdNs for several DNA polymerases and the ability of base excision repair enzymes to remove these modifications from DNA. The Klenow fragment was fully blocked by βLdNs, whereas DNA polymerase κ bypassed them in an error-free manner. Phage RB69 DNA polymerase and DNA polymerase β treated βLdNs as non-instructive but the latter enzyme shifted towards error-free incorporation on a gapped DNA substrate. DNA glycosylases and AP endonucleases did not process βLdNs. DNA glycosylases sensitive to the base opposite their cognate lesions also did not recognize βLdNs as a correct pairing partner. Nevertheless, when placed in a reporter plasmid, pyrimidine βLdNs were resistant to repair in human cells, whereas purine βLdNs appear to be partly repaired. Overall, βLdNs are unique modifications that are mostly non-instructive but have dual non-instructive/instructive properties in special cases.
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Affiliation(s)
- Anna V. Yudkina
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Daria V. Kim
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
| | - Timofey D. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
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10
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Quiroz D, Oya S, Lopez-Mateos D, Zhao K, Pierce A, Ortega L, Ali A, Carbonell-Bejerano P, Yarov-Yarovoy V, Suzuki S, Hayashi G, Osakabe A, Monroe G. H3K4me1 recruits DNA repair proteins in plants. THE PLANT CELL 2024; 36:2410-2426. [PMID: 38531669 PMCID: PMC11132887 DOI: 10.1093/plcell/koae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/28/2024]
Abstract
DNA repair proteins can be recruited by their histone reader domains to specific epigenomic features, with consequences on intragenomic mutation rate variation. Here, we investigated H3K4me1-associated hypomutation in plants. We first examined 2 proteins which, in plants, contain Tudor histone reader domains: PRECOCIOUS DISSOCIATION OF SISTERS 5 (PDS5C), involved in homology-directed repair, and MUTS HOMOLOG 6 (MSH6), a mismatch repair protein. The MSH6 Tudor domain of Arabidopsis (Arabidopsis thaliana) binds to H3K4me1 as previously demonstrated for PDS5C, which localizes to H3K4me1-rich gene bodies and essential genes. Mutations revealed by ultradeep sequencing of wild-type and msh6 knockout lines in Arabidopsis show that functional MSH6 is critical for the reduced rate of single-base substitution (SBS) mutations in gene bodies and H3K4me1-rich regions. We explored the breadth of these mechanisms among plants by examining a large rice (Oryza sativa) mutation data set. H3K4me1-associated hypomutation is conserved in rice as are the H3K4me1-binding residues of MSH6 and PDS5C Tudor domains. Recruitment of DNA repair proteins by H3K4me1 in plants reveals convergent, but distinct, epigenome-recruited DNA repair mechanisms from those well described in humans. The emergent model of H3K4me1-recruited repair in plants is consistent with evolutionary theory regarding mutation modifier systems and offers mechanistic insight into intragenomic mutation rate variation in plants.
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Affiliation(s)
- Daniela Quiroz
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Integrative Genetics and Genomics, University of California Davis, Davis, CA 95616, USA
| | - Satoyo Oya
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Diego Lopez-Mateos
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
- Biophysics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Kehan Zhao
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Alice Pierce
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Lissandro Ortega
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | - Alissza Ali
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | | | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
- Biophysics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Sae Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-0814, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-0814, Japan
| | - Akihisa Osakabe
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Integrative Genetics and Genomics, University of California Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, CA 95616, USA
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11
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Provasek VE, Bacolla A, Rangaswamy S, Mitra J, Kodavati M, Yusuf IO, Malojirao VH, Vasquez V, Britz GW, Li GM, Xu Z, Mitra S, Garruto RM, Tainer JA, Hegde ML. RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594552. [PMID: 38798341 PMCID: PMC11118483 DOI: 10.1101/2024.05.16.594552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
TDP43 is an RNA/DNA binding protein increasingly recognized for its role in neurodegenerative conditions including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). As characterized by its aberrant nuclear export and cytoplasmic aggregation, TDP43 proteinopathy is a hallmark feature in over 95% of ALS/FTD cases, leading to the formation of detrimental cytosolic aggregates and a reduction in nuclear functionality within neurons. Building on our prior work linking TDP43 proteinopathy to the accumulation of DNA double-strand breaks (DSBs) in neurons, the present investigation uncovers a novel regulatory relationship between TDP43 and DNA mismatch repair (MMR) gene expressions. Here, we show that TDP43 depletion or overexpression directly affects the expression of key MMR genes. Alterations include MLH1, MSH2, MSH3, MSH6, and PMS2 levels across various primary cell lines, independent of their proliferative status. Our results specifically establish that TDP43 selectively influences the expression of MLH1 and MSH6 by influencing their alternative transcript splicing patterns and stability. We furthermore find aberrant MMR gene expression is linked to TDP43 proteinopathy in two distinct ALS mouse models and post-mortem brain and spinal cord tissues of ALS patients. Notably, MMR depletion resulted in the partial rescue of TDP43 proteinopathy-induced DNA damage and signaling. Moreover, bioinformatics analysis of the TCGA cancer database reveals significant associations between TDP43 expression, MMR gene expression, and mutational burden across multiple cancers. Collectively, our findings implicate TDP43 as a critical regulator of the MMR pathway and unveil its broad impact on the etiology of both neurodegenerative and neoplastic pathologies.
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Affiliation(s)
- Vincent E Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Suganya Rangaswamy
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Joy Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Issa O Yusuf
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Vikas H Malojirao
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Velmarini Vasquez
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Gavin W Britz
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Neurosurgery and Department of Neuroscience, Weill Cornell Medical College, New York, NY 10065, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zuoshang Xu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Sankar Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Ralph M Garruto
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902
| | - John A Tainer
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Muralidhar L Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Neuroscience, Weill Cornell Medical College, New York, NY 10065, USA
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12
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Abdelmaksoud-Dammak R, Ammous-Boukhris N, BenAyed-Guerfali D, Gdoura Y, Boujelben I, Guidara S, Charfi S, Boudabbous W, Ammar S, Rhaiem W, Boudawara MZ, Kamoun H, Sallemi-Boudawara T, Mhiri R, Mokdad-Gargouri R. Strategies for diagnosis and management of CMMRD in low-resource countries: report of a Tunisian family. Fam Cancer 2024:10.1007/s10689-024-00386-z. [PMID: 38687438 DOI: 10.1007/s10689-024-00386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/30/2024] [Indexed: 05/02/2024]
Abstract
Constitutional Mismatch Repair Deficiency (CMMRD) is a rare childhood cancer predisposition syndrome, caused by biallelic pathogenic germline variants in the mismatch repair genes. Diagnosis and management of this syndrome is challenging, especially in low-resource settings. This study describes a patient diagnosed with colorectal cancer and grade 3 astrocytoma at the age of 11 and 12 respectively. Immunohistochemistry analysis showed a loss of MSH2 and MSH6 protein expression in CRC tissues of the patient. We identified by Targeted Exome Sequencing a homozygous pathogenic germline variant in exon 9 of the MSH6 gene (c.3991 C > T; p.Ala1268Glyfs*6). Genetic investigation of the family showed that the father was heterozygous for the identified pathogenic variant while the brother was wild type for this variant. Our study highlights the importance of a correct and timely diagnosis of CMMRD which can have implications for treatment. It also underlines the imperative need to enhance awareness, diagnostic standards, and surveillance that are crucial for patients and their families.
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Affiliation(s)
- Rania Abdelmaksoud-Dammak
- Department of Cancer Genetics, Laboratory of Molecular Biotechnology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax BPK 1177, Sfax, 3018, Tunisia
| | - Nihel Ammous-Boukhris
- Department of Cancer Genetics, Laboratory of Molecular Biotechnology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax BPK 1177, Sfax, 3018, Tunisia
| | - Dorra BenAyed-Guerfali
- Department of Cancer Genetics, Laboratory of Molecular Biotechnology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax BPK 1177, Sfax, 3018, Tunisia
| | - Yassine Gdoura
- Department of Neurosurgery, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Imen Boujelben
- Department of Human Genetics, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | - Souhir Guidara
- Department of Human Genetics, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | - Slim Charfi
- Department of Anatomopathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Wiem Boudabbous
- Department of Neurosurgery, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Saloua Ammar
- Department of Pediatric Surgery, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | - Wiem Rhaiem
- Department of Pediatric Surgery, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | | | - Hassen Kamoun
- Department of Human Genetics, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | | | - Riadh Mhiri
- Department of Pediatric Surgery, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | - Raja Mokdad-Gargouri
- Department of Cancer Genetics, Laboratory of Molecular Biotechnology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax BPK 1177, Sfax, 3018, Tunisia.
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13
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Begg KAG, Braun H, Ghaddar N, Wu L, Downs JA. Defects in DNA damage responses in SWI/SNF mutant cells and their impact on immune responses. DNA Repair (Amst) 2024; 133:103609. [PMID: 38101147 DOI: 10.1016/j.dnarep.2023.103609] [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: 09/15/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023]
Abstract
The mammalian SWI/SNF chromatin remodelling complexes are commonly dysregulated in cancer. These complexes contribute to maintaining genome stability through a variety of pathways. Recent research has highlighted an important interplay between genome instability and immune signalling, and evidence suggests that this interplay can modulate the response to immunotherapy. Here, we review emerging studies where direct evidence of this relationship has been uncovered in SWI/SNF deficient cells. We also highlight genome maintenance activities of SWI/SNF that could potentially shape immune responses and discuss potential therapeutic implications.
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Affiliation(s)
- Katheryn A G Begg
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Hanna Braun
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Nagham Ghaddar
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Lillian Wu
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Jessica A Downs
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.
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14
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Wang L, Yang S, Xue Y, Bo T, Xu J, Wang W. Mismatch Repair Protein Msh6 Tt Is Necessary for Nuclear Division and Gametogenesis in Tetrahymena thermophila. Int J Mol Sci 2023; 24:17619. [PMID: 38139447 PMCID: PMC10743813 DOI: 10.3390/ijms242417619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023] Open
Abstract
DNA mismatch repair (MMR) improves replication accuracy by up to three orders of magnitude. The MutS protein in E. coli or its eukaryotic homolog, the MutSα (Msh2-Msh6) complex, recognizes base mismatches and initiates the mismatch repair mechanism. Msh6 is an essential protein for assembling the heterodimeric complex. However, the function of the Msh6 subunit remains elusive. Tetrahymena undergoes multiple DNA replication and nuclear division processes, including mitosis, amitosis, and meiosis. Here, we found that Msh6Tt localized in the macronucleus (MAC) and the micronucleus (MIC) during the vegetative growth stage and starvation. During the conjugation stage, Msh6Tt only localized in MICs and newly developing MACs. MSH6Tt knockout led to aberrant nuclear division during vegetative growth. The MSH6TtKO mutants were resistant to treatment with the DNA alkylating agent methyl methanesulfonate (MMS) compared to wild type cells. MSH6Tt knockout affected micronuclear meiosis and gametogenesis during the conjugation stage. Furthermore, Msh6Tt interacted with Msh2Tt and MMR-independent factors. Downregulation of MSH2Tt expression affected the stability of Msh6Tt. In addition, MSH6Tt knockout led to the upregulated expression of several MSH6Tt homologs at different developmental stages. Msh6Tt is involved in macronuclear amitosis, micronuclear mitosis, micronuclear meiosis, and gametogenesis in Tetrahymena.
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Affiliation(s)
- Lin Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
| | - Sitong Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
| | - Yuhuan Xue
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
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15
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Sun Z, Chung D, Neelon B, Millar-Wilson A, Ethier SP, Xiao F, Zheng Y, Wallace K, Hardiman G. A Bayesian framework for pathway-guided identification of cancer subgroups by integrating multiple types of genomic data. Stat Med 2023; 42:5266-5284. [PMID: 37715500 DOI: 10.1002/sim.9911] [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: 03/19/2021] [Revised: 07/15/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
In recent years, comprehensive cancer genomics platforms, such as The Cancer Genome Atlas (TCGA), provide access to an enormous amount of high throughput genomic datasets for each patient, including gene expression, DNA copy number alterations, DNA methylation, and somatic mutation. While the integration of these multi-omics datasets has the potential to provide novel insights that can lead to personalized medicine, most existing approaches only focus on gene-level analysis and lack the ability to facilitate biological findings at the pathway-level. In this article, we propose Bayes-InGRiD (Bayesian Integrative Genomics Robust iDentification of cancer subgroups), a novel pathway-guided Bayesian sparse latent factor model for the simultaneous identification of cancer patient subgroups (clustering) and key molecular features (variable selection) within a unified framework, based on the joint analysis of continuous, binary, and count data. By utilizing pathway (gene set) information, Bayes-InGRiD does not only enhance the accuracy and robustness of cancer patient subgroup and key molecular feature identification, but also promotes biological understanding and interpretation. Finally, to facilitate an efficient posterior sampling, an alternative Gibbs sampler for logistic and negative binomial models is proposed using Pólya-Gamma mixtures of normal to represent latent variables for binary and count data, which yields a conditionally Gaussian representation of the posterior. The R package "INGRID" implementing the proposed approach is currently available in our research group GitHub webpage (https://dongjunchung.github.io/INGRID/).
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Affiliation(s)
- Zequn Sun
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Brian Neelon
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | | | - Stephen P Ethier
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Feifei Xiao
- Department of Biostatistics, University of Florida, Gainesville, Florida
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Kristin Wallace
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Gary Hardiman
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences and Institute for Global Food Security, Queen's University Belfast, Belfast, UK
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16
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Bratei AA, Stefan-van Staden RI. Correlations between MSH2 and MSH6 Concentrations in Different Biological Fluids and Clinicopathological Features in Colorectal Adenocarcinoma Patients and Their Contribution to Fast and Early Diagnosis of Colorectal Adenocarcinoma. Biomedicines 2023; 11:3213. [PMID: 38137434 PMCID: PMC10741075 DOI: 10.3390/biomedicines11123213] [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: 10/26/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
(1) Background: The human MutS homolog, hMSH2, is known to be involved in DNA mismatch repair and is responsible for maintaining the stability of the genome. When DNA damage occurs, MSH2 promotes cell apoptosis via the regulation of ATR/Chk2/p53 signal transduction, and MSH2 deficiency is also related to accelerated telomere shortening in humans. MSH2 missense mutations are involved in a defective DNA reparation process, and it can be implied in carcinogenesis, as it is already involved in well-known cancer-related syndromes such as Lynch syndrome. Human MSH6, which stands for mutS homolog 6, is a member of the MMR family that is responsible for the repair of post-replicative mismatched DNA bases. It is also one of the proteins with gene mutations that are associated with a high risk of developing Lynch syndrome, leading to a large series of tumors. (2) Methods: Patients and their clinical and pathological features were selected from the database of the project GRAPHSENSGASTROINTES and used accordingly, with ethics committee approval no. 32647/2018 awarded by the County Emergency Hospital from Targu-Mures. Analyses were conducted on whole blood, saliva, urine, and tumoral tissue samples using a stochastic method with stochastic microsensors. (3) Results: The results obtained using stochastic sensors were correlated with a series of macroscopic and microscopic pathological features for each sample type. Criteria or relationships were established for tumor location, vascular and perineural invasions, lymph node metastases, the presence of tumor deposits, and the presence of a mucus compound in the tumor mass. (4) Conclusions: The correlation between the concentrations of MSH2 in the four types of samples and the pathological features allowed for the fast characterization of a tumor, which can help surgeons and oncologists choose personalized treatments. Also, the colorectal tumor location was correlated with the concentration of MSH2 in whole blood, urine, and saliva. MSH6, which stands for mutS homolog 6, is not only useful in immunohistochemistry but in pathology practice as well. In this paper, the relationships between MSH6 levels in four biological fluids-whole blood, saliva, urine, and tissues-and tumor locations among the colorectal area, gross features, presence of a mucinous compound, molecular subtype, stroma features, and vascular invasions are presented.
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Affiliation(s)
- Alexandru Adrian Bratei
- Faculty of Chemical Engineering and Biotechnologies, University Politehnica of Bucharest, 060042 Bucharest, Romania;
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, 060021 Bucharest, Romania
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu-Mures, 540139 Targu-Mures, Romania
| | - Raluca-Ioana Stefan-van Staden
- Faculty of Chemical Engineering and Biotechnologies, University Politehnica of Bucharest, 060042 Bucharest, Romania;
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, 060021 Bucharest, Romania
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17
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Wei Y, Huang D, Ye Z, Jiang Z, Ge L, Ren Y, Wang J, Xu X, Yang J, Wang T. Comparative transcriptome analysis reveals key genes and pathways related to gonad development in the sea cucumber Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101144. [PMID: 37769382 DOI: 10.1016/j.cbd.2023.101144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023]
Abstract
The sea cucumber Apostichopus japonicus is an economically important marine species in China, and understanding the mechanisms underlying its gonad development is crucial for successful reproduction and breeding. In this study, we performed transcriptome comparisons and analyses of A. japonicus gonadal and non-gonadal tissues to identify genes and molecular pathways associated with gonadal development. We also supplemented the annotation of the A. japonicus genome. Collectively, results revealed a total of 941 ovary-specific genes and 2499 testis-specific genes through different expression analysis and WGCNA analysis. The most enriched pathways in ovary and testis were "DNA replication" and "purine metabolism", respectively. Additionally, we identified key candidate gene modules that control gonad development and germ cell maturation, with CDT1 and DYNC2LI1 serving as hub genes. Our findings provide important insights into the gonadal development system of A. japonicus and offer valuable references for further research on reproductive biology in this marine invertebrate species.
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Affiliation(s)
- Ying Wei
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Dexiang Huang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Zhiqing Ye
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Zhijing Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Lifei Ge
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Yucheng Ren
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Jixiu Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Xiuwen Xu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Jingwen Yang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Tianming Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China.
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18
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Wang J, Mi Y, Sun X, Xue X, Zhao H, Zhang M, Hu B, Bukhari I, Zheng P. Lnc-PTCHD4-AS inhibits gastric cancer through MSH2-MSH6 dimerization and ATM-p53-p21 activation. Aging (Albany NY) 2023; 15:13558-13578. [PMID: 38016120 DOI: 10.18632/aging.205329] [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: 08/25/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023]
Abstract
Conserved long non-coding RNAs (lncRNAs) have not thoroughly been studied in many cancers, including gastric cancer (GC). We have identified a novel lncRNA PTCHD4-AS which was highly conserved between humans and mice and naturally downregulated in GC cell lines and tissues. Notably, PTCHD4-AS was found to be transcriptionally induced by DNA damage agents and its upregulation led to cell cycle arrest at the G2/M phase, in parallel, it facilitated the cell apoptosis induced by cisplatin (CDDP) in GC. Mechanistically, PTCHD4-AS directly bound to the DNA mismatch repair protein MSH2-MSH6 dimer, and facilitated the binding of dimer to ATM, thereby promoting the expression of phosphorylated ATM, p53 and p21. Here we conclude that the upregulation of PTCHD4-AS inhibits proliferation and increases CDDP sensitivity of GC cells via binding with MSH2-MSH6 dimer, activating the ATM-p53-p21 pathway.
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Affiliation(s)
- Jingyun Wang
- Henan Key Laboratory for Helicobacter pylori and Microbiota and GI Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Yang Mi
- Henan Key Laboratory for Helicobacter pylori and Microbiota and GI Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Xiangdong Sun
- Henan Key Laboratory for Helicobacter pylori and Microbiota and GI Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Xia Xue
- Henan Key Laboratory for Helicobacter pylori and Microbiota and GI Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Huanjie Zhao
- Henan Key Laboratory for Helicobacter pylori and Microbiota and GI Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Mengfei Zhang
- Henan Key Laboratory for Helicobacter pylori and Microbiota and GI Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Baitong Hu
- Henan Key Laboratory for Helicobacter pylori and Microbiota and GI Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Ihtisham Bukhari
- Henan Key Laboratory for Helicobacter pylori and Microbiota and GI Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Pengyuan Zheng
- Henan Key Laboratory for Helicobacter pylori and Microbiota and GI Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
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19
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Yang X, Smirnov A, Buonomo OC, Mauriello A, Shi Y, Bischof J, Woodsmith J, Melino G, Candi E, Bernassola F. A primary luminal/HER2 negative breast cancer patient with mismatch repair deficiency. Cell Death Discov 2023; 9:365. [PMID: 37783677 PMCID: PMC10545677 DOI: 10.1038/s41420-023-01650-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/23/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023] Open
Abstract
Here, we present the case of a 47-year-old woman diagnosed with luminal B breast cancer subtype and provide an in-depth analysis of her gene mutations, chromosomal alterations, mRNA and protein expression changes. We found a point mutation in the FGFR2 gene, which is potentially hyper-activating the receptor function, along with over-expression of its ligand FGF20 due to genomic amplification. The patient also harbors somatic and germline mutations in some mismatch repair (MMR) genes, with a strong MMR mutational signature. The patient displays high microsatellite instability (MSI) and tumor mutational burden (TMB) status and increased levels of CTLA-4 and PD-1 expression. Altogether, these data strongly implicate that aberrant FGFR signaling, and defective MMR system might be involved in the development of this breast tumor. In addition, high MSI and TMB in the context of CTLA-4 and PD-L1 positivity, suggest the potential benefit of immune checkpoint inhibitors. Accurate characterization of molecular subtypes, based on gene mutational and expression profiling analyses, will be certainly helpful for individualized treatment and targeted therapy of breast cancer patients, especially for those subtypes with adverse outcome.
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Affiliation(s)
- Xue Yang
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
- The Third Affiliated Hospital of Soochow University, Institutes for Translational Medicine, Soochow University, Suzhou, 215000, China
| | - Artem Smirnov
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
- Istituto Dermopatico Immacolata (IDI-IRCCS), 00100, Rome, Italy
| | - Oreste Claudio Buonomo
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Alessandro Mauriello
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University, Institutes for Translational Medicine, Soochow University, Suzhou, 215000, China
| | - Julia Bischof
- Indivumed GmbH, Falkenried, Germany Biochemistry Laboratory, 88 Building D, 20251, Hamburg, Germany
| | - Jonathan Woodsmith
- Indivumed GmbH, Falkenried, Germany Biochemistry Laboratory, 88 Building D, 20251, Hamburg, Germany
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
| | - Eleonora Candi
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
- Istituto Dermopatico Immacolata (IDI-IRCCS), 00100, Rome, Italy.
| | - Francesca Bernassola
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
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20
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Firnau MB, Plotz G, Zeuzem S, Brieger A. Key role of phosphorylation sites in ATPase domain and Linker region of MLH1 for DNA binding and functionality of MutLα. Sci Rep 2023; 13:12503. [PMID: 37532794 PMCID: PMC10397344 DOI: 10.1038/s41598-023-39750-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023] Open
Abstract
MutLα is essential for human DNA mismatch repair (MMR). It harbors a latent endonuclease, is responsible for recruitment of process associated proteins and is relevant for strand discrimination. Recently, we demonstrated that the MMR function of MutLα is regulated by phosphorylation of MLH1 at serine (S) 477. In the current study, we focused on S87 located in the ATPase domain of MLH1 and on S446, S456 and S477 located in its linker region. We analysed the phosphorylation-dependent impact of these amino acids on DNA binding, MMR ability and thermal stability of MutLα. We were able to demonstrate that phosphorylation at S87 of MLH1 inhibits DNA binding of MutLα. In addition, we detected that its MMR function seems to be regulated predominantly via phosphorylation of serines in the linker domain, which are also partially involved in the regulation of DNA binding. Furthermore, we found that the thermal stability of MutLα decreased in relation to its phosphorylation status implying that complete phosphorylation might lead to instability and degradation of MLH1. In summary, we showed here, for the first time, a phosphorylation-dependent regulation of DNA binding of MutLα and hypothesized that this might significantly impact its functional regulation during MMR in vivo.
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Affiliation(s)
- May-Britt Firnau
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Biomedical Research Laboratory, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Guido Plotz
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Biomedical Research Laboratory, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Stefan Zeuzem
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Biomedical Research Laboratory, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Angela Brieger
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Biomedical Research Laboratory, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
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21
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Ashraf S, Deshpande N, Vasanth S, Melangath G, Wong RJ, Zhao Y, Price MO, Price FW, Jurkunas UV. Dysregulation of DNA repair genes in Fuchs endothelial corneal dystrophy. Exp Eye Res 2023; 231:109499. [PMID: 37169279 PMCID: PMC10246500 DOI: 10.1016/j.exer.2023.109499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/27/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
Fuchs Endothelial Corneal Dystrophy (FECD), a late-onset oxidative stress disorder, is the most common cause of corneal endothelial degeneration and is genetically associated with CTG repeat expansion in Transcription Factor 4 (TCF4). We previously reported accumulation of nuclear (nDNA) and mitochondrial (mtDNA) damage in FECD. Specifically, mtDNA damage was a prominent finding in development of disease in the ultraviolet-A (UVA) induced FECD mouse model. We hypothesize that an aberrant DNA repair may contribute to the increased DNA damage seen in FECD. We analyzed differential expression profiles of 84 DNA repair genes by real-time PCR arrays using Human DNA Repair RT-Profiler plates using cDNA extracted from Descemet's membrane-corneal endothelium (DM-CE) obtained from FECD patients with expanded (>40) or non-expanded (<40) intronic CTG repeats in TCF4 gene and from age-matched normal donors. Change in mRNA expression of <0.5- or >2.0-fold in FECD relative to normal was set as cutoff for down- or upregulation. Downregulated mitochondrial genes were further validated using the UVA-based mouse model of FECD. FECD specimens exhibited downregulation of 9 genes and upregulation of 8 genes belonging to the four major DNA repair pathways, namely, base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), and double strand break (DSB) repair, compared to normal donors. MMR gene MSH2 and BER gene POLB were preferentially upregulated in expanded FECD. BER genes LIG3 and NEIL2, DSB repair genes PARP3 and TOP3A, NER gene XPC, and unclassified pathway gene TREX1, were downregulated in both expanded and non-expanded FECD. MtDNA repair genes, Lig3, Neil2, and Top3a, were also downregulated in the UVA-based mouse model of FECD. Our findings identify impaired DNA repair pathways that may play an important role in DNA damage due to oxidative stress as well as genetic predisposition noted in FECD.
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Affiliation(s)
- Shazia Ashraf
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Neha Deshpande
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Shivakumar Vasanth
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Geetha Melangath
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Raymond J Wong
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Yan Zhao
- Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Marianne O Price
- Price Vision Group and Cornea Research Foundation of America, Indianapolis, IN, 46260, United States
| | - Francis W Price
- Price Vision Group and Cornea Research Foundation of America, Indianapolis, IN, 46260, United States
| | - Ula V Jurkunas
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States.
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22
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Daniels HG, Knicely BG, Miller AK, Thompson A, Plattner R, Goellner EM. Inhibition of ABL1 by tyrosine kinase inhibitors leads to a downregulation of MLH1 by Hsp70-mediated lysosomal protein degradation. Front Genet 2022; 13:940073. [PMID: 36338985 PMCID: PMC9631443 DOI: 10.3389/fgene.2022.940073] [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: 05/09/2022] [Accepted: 10/03/2022] [Indexed: 01/07/2023] Open
Abstract
The DNA mismatch repair (MMR) pathway and its regulation are critical for genomic stability. Mismatch repair (MMR) follows replication and repairs misincorporated bases and small insertions or deletions that are not recognized and removed by the proofreading polymerase. Cells deficient in MMR exhibit an increased overall mutation rate and increased expansion and contraction of short repeat sequences in the genome termed microsatellite instability (MSI). MSI is often a clinical measure of genome stability in tumors and is used to determine the course of treatment. MMR is also critical for inducing apoptosis after alkylation damage from environmental agents or DNA-damaging chemotherapy. MLH1 is essential for MMR, and loss or mutation of MLH1 leads to defective MMR, increased mutation frequency, and MSI. In this study, we report that tyrosine kinase inhibitors, imatinib and nilotinib, lead to decreased MLH1 protein expression but not decreased MLH1 mRNA levels. Of the seven cellular targets of Imatinib and nilotinib, we show that silencing of ABL1 also reduces MLH1 protein expression. Treatment with tyrosine kinase inhibitors or silencing of ABL1 results in decreased apoptosis after treatment with alkylating agents, suggesting the level of MLH1 reduction is sufficient to disrupt MMR function. We also report MLH1 is tyrosine phosphorylated by ABL1. We demonstrate that MLH1 downregulation by ABL1 knockdown or inhibition requires chaperone protein Hsp70 and that MLH1 degradation can be abolished with the lysosomal inhibitor bafilomycin. Taken together, we propose that ABL1 prevents MLH1 from being targeted for degradation by the chaperone Hsp70 and that in the absence of ABL1 activity at least a portion of MLH1 is degraded through the lysosome. This study represents an advance in understanding MMR pathway regulation and has important clinical implications as MMR status is used in the clinic to inform patient treatment, including the use of immunotherapy.
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Affiliation(s)
- Hannah G. Daniels
- University of Kentucky, College of Medicine Department of Toxicology and Cancer Biology, Lexington, KY, United States
| | - Breanna G. Knicely
- University of Kentucky, College of Medicine Department of Toxicology and Cancer Biology, Lexington, KY, United States
| | - Anna Kristin Miller
- University of Kentucky, College of Medicine Department of Toxicology and Cancer Biology, Lexington, KY, United States
| | - Ana Thompson
- Berea College, Berea, KY, United States,University of Kentucky Markey Cancer Center, Lexington, KY, United States
| | - Rina Plattner
- University of Kentucky Markey Cancer Center, Lexington, KY, United States,University of Kentucky, College of Medicine Department of Pharmacology and Nutritional Sciences, Lexington, KY, United States
| | - Eva M. Goellner
- University of Kentucky, College of Medicine Department of Toxicology and Cancer Biology, Lexington, KY, United States,University of Kentucky Markey Cancer Center, Lexington, KY, United States,*Correspondence: Eva M. Goellner,
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23
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Amar-Schwartz A, Ben Hur V, Jbara A, Cohen Y, Barnabas GD, Arbib E, Siegfried Z, Mashahreh B, Hassouna F, Shilo A, Abu-Odeh M, Berger M, Wiener R, Aqeilan R, Geiger T, Karni R. S6K1 phosphorylates Cdk1 and MSH6 to regulate DNA repair. eLife 2022; 11:79128. [PMID: 36189922 PMCID: PMC9529248 DOI: 10.7554/elife.79128] [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: 04/08/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022] Open
Abstract
The mTORC1 substrate, S6 Kinase 1 (S6K1), is involved in the regulation of cell growth, ribosome biogenesis, glucose homeostasis, and adipogenesis. Accumulating evidence has suggested a role for mTORC1 signaling in the DNA damage response. This is mostly based on the findings that mTORC1 inhibitors sensitized cells to DNA damage. However, a direct role of the mTORC1-S6K1 signaling pathway in DNA repair and the mechanism by which this signaling pathway regulates DNA repair is unknown. In this study, we discovered a novel role for S6K1 in regulating DNA repair through the coordinated regulation of the cell cycle, homologous recombination (HR) DNA repair (HRR) and mismatch DNA repair (MMR) mechanisms. Here, we show that S6K1 orchestrates DNA repair by phosphorylation of Cdk1 at serine 39, causing G2/M cell cycle arrest enabling homologous recombination and by phosphorylation of MSH6 at serine 309, enhancing MMR. Moreover, breast cancer cells harboring RPS6KB1 gene amplification show increased resistance to several DNA damaging agents and S6K1 expression is associated with poor survival of breast cancer patients treated with chemotherapy. Our findings reveal an unexpected function of S6K1 in the DNA repair pathway, serving as a tumorigenic barrier by safeguarding genomic stability. Damage to the DNA in our cells can cause harmful changes that, if unchecked, can lead to the development of cancer. To help prevent this, cellular mechanisms are in place to repair defects in the DNA. A particular process, known as the mTORC1-S6K1 pathway is suspected to be important for repair because when this pathway is blocked, cells become more sensitive to DNA damage. It is still unknown how the various proteins involved in the mTORC1-S6K1 pathway contribute to repairing DNA. One of these proteins, S6K1, is an enzyme involved in coordinating cell growth and survival. The tumor cells in some forms of breast cancer produce more of this protein than normal, suggesting that S6K1 benefits these cells’ survival. However, it is unclear exactly how the enzyme does this. Amar-Schwartz, Ben-Hur, Jbara et al. studied the role of S6K1 using genetically manipulated mouse cells and human cancer cells. These experiments showed that the protein interacts with two other proteins involved in DNA repair and activates them, regulating two different repair mechanisms and protecting cells against damage. These results might explain why some breast cancer tumors are resistant to radiotherapy and chemotherapy treatments, which aim to kill tumor cells by damaging their DNA. If this is the case, these findings could help clinicians choose more effective treatment options for people with cancers that produce additional S6K1. In the future, drugs that block the activity of the enzyme could make cancer cells more susceptible to chemotherapy.
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Affiliation(s)
- Adi Amar-Schwartz
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Vered Ben Hur
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Amina Jbara
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yuval Cohen
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Georgina D Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eliran Arbib
- Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Bayan Mashahreh
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Fouad Hassouna
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Asaf Shilo
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Mohammad Abu-Odeh
- Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Michael Berger
- Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Rami Aqeilan
- Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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24
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Meulemans L, Baert Desurmont S, Waill MC, Castelain G, Killian A, Hauchard J, Frebourg T, Coulet F, Martins A, Muleris M, Gaildrat P. Comprehensive RNA and protein functional assessments contribute to the clinical interpretation of MSH2 variants causing in-frame splicing alterations. J Med Genet 2022; 60:450-459. [PMID: 36113988 DOI: 10.1136/jmg-2022-108576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/26/2022] [Indexed: 11/04/2022]
Abstract
BackgroundSpliceogenic variants in disease-causing genes are often presumed pathogenic since most induce frameshifts resulting in loss of function. However, it was recently shown in cancer predisposition genes that some may trigger in-frame anomalies that preserve function. Here, we addressed this question by using MSH2, a DNA mismatch repair gene implicated in Lynch syndrome, as a model system.MethodsEighteen MSH2 variants, mostly localised within canonical splice sites, were analysed by using minigene splicing assays. The impact of the resulting protein alterations was assessed in a methylation tolerance-based assay. Clinicopathological characteristics of variant carriers were collected.ResultsThree in-frame RNA biotypes were identified based on variant-induced spliceogenic outcomes: exon skipping (E3, E4, E5 and E12), segmental exonic deletions (E7 and E15) and intronic retentions (I3, I6, I12 and I13). The 10 corresponding protein isoforms exhibit either large deletions (49–93 amino acids (aa)), small deletions (12 or 16 aa) or insertions (3–10 aa) within different functional domains. We showed that all these modifications abrogate MSH2 function, in agreement with the clinicopathological features of variant carriers.ConclusionAltogether, these data demonstrate that MSH2 function is intolerant to in-frame indels caused by the spliceogenic variants analysed in this study, supporting their pathogenic nature. This work stresses the importance of combining complementary RNA and protein approaches to ensure accurate clinical interpretation of in-frame spliceogenic variants.
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Affiliation(s)
- Laëtitia Meulemans
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Stéphanie Baert Desurmont
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, and CHU Rouen, Department of Genetics, F-76000 Rouen, France
| | - Marie-Christine Waill
- Department of Genetics, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Gaia Castelain
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Audrey Killian
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Julie Hauchard
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, and CHU Rouen, Department of Genetics, F-76000 Rouen, France
| | - Florence Coulet
- Department of Genetics, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Inserm UMR-S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Alexandra Martins
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Martine Muleris
- Department of Genetics, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Inserm UMR-S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Pascaline Gaildrat
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
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25
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Firnau MB, Brieger A. CK2 and the Hallmarks of Cancer. Biomedicines 2022; 10:biomedicines10081987. [PMID: 36009534 PMCID: PMC9405757 DOI: 10.3390/biomedicines10081987] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Cancer is a leading cause of death worldwide. Casein kinase 2 (CK2) is commonly dysregulated in cancer, impacting diverse molecular pathways. CK2 is a highly conserved serine/threonine kinase, constitutively active and ubiquitously expressed in eukaryotes. With over 500 known substrates and being estimated to be responsible for up to 10% of the human phosphoproteome, it is of significant importance. A broad spectrum of diverse types of cancer cells has been already shown to rely on disturbed CK2 levels for their survival. The hallmarks of cancer provide a rationale for understanding cancer’s common traits. They constitute the maintenance of proliferative signaling, evasion of growth suppressors, resisting cell death, enabling of replicative immortality, induction of angiogenesis, the activation of invasion and metastasis, as well as avoidance of immune destruction and dysregulation of cellular energetics. In this work, we have compiled evidence from the literature suggesting that CK2 modulates all hallmarks of cancer, thereby promoting oncogenesis and operating as a cancer driver by creating a cellular environment favorable to neoplasia.
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26
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Suganuma T, Workman JL. MPTAC links alkylation damage signaling to sterol biosynthesis. Redox Biol 2022; 51:102270. [PMID: 35189552 PMCID: PMC8866156 DOI: 10.1016/j.redox.2022.102270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 12/19/2022] Open
Abstract
Overproduction of reactive oxygen species (ROS) drives inflammation and mutagenesis. However, the role of the DNA damage response in immune responses remains largely unknown. Here we found that stabilization of the mismatch repair (MMR) protein MSH6 in response to alkylation damage requires interactions with the molybdopterin synthase associating complex (MPTAC) and Ada2a-containing histone acetyltransferase complex (ATAC). Furthermore, MSH6 promotes sterol biosynthesis via the mevalonate pathway in a MPTAC- and ATAC-dependent manner. MPTAC reduces the source of alkylating agents (ROS). Therefore, the association between MMR proteins, MPTAC, and ATAC promotes anti-inflammation response and reduces alkylating agents. The inflammatory responses measured by xanthine oxidase activity are elevated in Lymphoblastoid Cell Lines (LCLs) from some Fragile X-associated disorders (FXD) patients, suggesting that alkylating agents are increased in these FXD patients. However, MPTAC is disrupted in LCLs from some FXD patients. In LCLs from other FXD patients, interaction between MSH6 and ATAC was lost, destabilizing MSH6. Thus, impairment of MPTAC and ATAC may cause alkylation damage resistance in some FXD patients.
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Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA.
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA.
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Katayama N, Koi S, Sassa A, Kurata T, Imaichi R, Kato M, Nishiyama T. Elevated mutation rates underlie the evolution of the aquatic plant family Podostemaceae. Commun Biol 2022; 5:75. [PMID: 35058542 PMCID: PMC8776956 DOI: 10.1038/s42003-022-03003-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/23/2021] [Indexed: 12/18/2022] Open
Abstract
Molecular evolutionary rates vary among lineages and influence the evolutionary process. Here, we report elevated genome-wide mutation rates in Podostemaceae, a family of aquatic plants with a unique body plan that allows members to live on submerged rocks in fast-flowing rivers. Molecular evolutionary analyses using 1640 orthologous gene groups revealed two historical increases in evolutionary rates: the first at the emergence of the family and the second at the emergence of Podostemoideae, which is the most diversified subfamily. In both branches, synonymous substitution rates were elevated, indicating higher mutation rates. On early branches, mutations were biased in favour of AT content, which is consistent with a role for ultraviolet light-induced mutation and habitat shift. In ancestors of Podostemoideae, DNA-repair genes were enriched in genes under positive selection, which may have responded to the meristem architectural changes.
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Affiliation(s)
- Natsu Katayama
- Graduate School of Science, Chiba University, Chiba, 263-8522, Japan.
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, 102-0083, Japan.
| | - Satoshi Koi
- Botanical Gardens, Osaka City University, Osaka, 575-0004, Japan
| | - Akira Sassa
- Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
| | - Tetsuya Kurata
- Division of Biological Science, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Ryoko Imaichi
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Masahiro Kato
- Department of Botany, National Museum of Nature and Science, Tsukuba, 305-0005, Japan
| | - Tomoaki Nishiyama
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-0934, Japan.
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An integrative pan-cancer analysis reveals the oncogenic role of mutS homolog 6 (MSH6) in human tumors. Aging (Albany NY) 2021; 13:25271-25290. [PMID: 34941572 PMCID: PMC8714153 DOI: 10.18632/aging.203745] [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: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 11/25/2022]
Abstract
There are three most important mismatch repair genes in the mismatch repair system, MSH6 is one of them and it plays an essential role in DNA mismatch repair. Several emerging cell- or animal-based studies have verified that MSH6 mutations are closely linked to the occurrence, progression or metastasis of cancer, but there is still no practicable pan-cancer analysis. On account of the available datasets of the cancer genome atlas (TCGA) and Gene expression omnibus (GEO), a comprehensive analysis of the potential carcinogenic effects of the MSH6 gene was conducted in 33 human cancers. MSH6 was highly expressed in most cancers, and the high expression of MSH6 was associated with poor overall survival prognosis of patients with multiple cancers, such as adrenocortical carcinoma. MSH6 mutations occurred in most cancers and were closely related to the prognosis of cancer patients. Increased phosphorylation levels of S227 and S830 were noted in several tumors, including breast cancer and colon cancer. MSH6 expression was also observed to be correlated with cancer-associated fibroblasts and CD8+ T-cells infiltration levels in various cancer types, e. g. pancreatic adenocarcinoma or testicular germ cell tumors. Furthermore, pathway enrichment analysis demonstrated that the main biological activities of MSH6 were related to ATPase activity, mismatch repair, and DNA metabolism-related functions. Altogether, our pan-cancer research has suggested that the MSH6 expression level was closely related to the carcinogenesis and prognosis of certain tumors, which helps to know the effect of MSH6 in tumorigenesis from the point of view of clinical tumor samples.
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Liu S, Chen X, Lin T. Emerging strategies for the improvement of chemotherapy in bladder cancer: Current knowledge and future perspectives. J Adv Res 2021; 39:187-202. [PMID: 35777908 PMCID: PMC9263750 DOI: 10.1016/j.jare.2021.11.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/01/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022] Open
Abstract
The response of chemotherapy and prognosis in bladder cancer is unsatisfied. Immunotherapy, targeted therapy, and ADC improve the efficacy of chemotherapy. Emerging targets in cancer cells and TME spawned novel preclinical agents. Novel drug delivery, such as nanotechnology, enhances effects of chemotherapeutics. The organoid and PDX model are promising to screen and evaluate the target therapy.
Background Chemotherapy is a first-line treatment for advanced and metastatic bladder cancer, but the unsatisfactory objective response rate to this treatment yields poor 5-year patient survival. Only PD-1/PD-L1-based immune checkpoint inhibitors, FGFR3 inhibitors and antibody-drug conjugates are approved by the FDA to be used in bladder cancer, mainly for platinum-refractory or platinum-ineligible locally advanced or metastatic urothelial carcinoma. Emerging studies indicate that the combination of targeted therapy and chemotherapy shows better efficacy than targeted therapy or chemotherapy alone. Newly identified targets in cancer cells and various functions of the tumour microenvironment have spawned novel agents and regimens, which give impetus to sensitizing chemotherapy in the bladder cancer setting. Aim of Review This review aims to present the current evidence for potentiating the efficacy of chemotherapy in bladder cancer. We focus on combining chemotherapy with other treatments as follows: targeted therapy, including immunotherapy and antibody-drug conjugates in clinic; novel targeted drugs and nanoparticles in preclinical models and potential targets that may contribute to chemosensitivity in future clinical practice. The prospect of precision therapy is also discussed in bladder cancer. Key Scientific Concepts of Review Combining chemotherapy drugs with immune checkpoint inhibitors, antibody-drug conjugates and VEGF inhibitors potentially elevates the response rate and survival. Novel targets, including cancer stem cells, DNA damage repair, antiapoptosis, drug metabolism and the tumour microenvironment, contribute to chemosensitization. Gene alteration-based drug selection and patient-derived xenograft- and organoid-based drug validation are the future for precision therapy.
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30
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Packard JE, Dembowski JA. HSV-1 DNA Replication-Coordinated Regulation by Viral and Cellular Factors. Viruses 2021; 13:v13102015. [PMID: 34696446 PMCID: PMC8539067 DOI: 10.3390/v13102015] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
DNA replication is an integral step in the herpes simplex virus type 1 (HSV-1) life cycle that is coordinated with the cellular DNA damage response, repair and recombination of the viral genome, and viral gene transcription. HSV-1 encodes its own DNA replication machinery, including an origin binding protein (UL9), single-stranded DNA binding protein (ICP8), DNA polymerase (UL30), processivity factor (UL42), and a helicase/primase complex (UL5/UL8/UL52). In addition, HSV-1 utilizes a combination of accessory viral and cellular factors to coordinate viral DNA replication with other viral and cellular processes. The purpose of this review is to outline the roles of viral and cellular proteins in HSV-1 DNA replication and replication-coupled processes, and to highlight how HSV-1 may modify and adapt cellular proteins to facilitate productive infection.
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31
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Zhang Y, Han K, Dong X, Hou Q, Li T, Li L, Zhou G, Liu X, Zhao G, Li W. Case Report and Literature Review: Primary Pulmonary NUT-Midline Carcinoma. Front Oncol 2021; 11:700781. [PMID: 34527578 PMCID: PMC8435908 DOI: 10.3389/fonc.2021.700781] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/06/2021] [Indexed: 12/22/2022] Open
Abstract
Nuclear protein of the testis (NUT) carcinoma is a very rare and aggressive carcinoma characterized by chromosomal rearrangement. NUT-midline carcinoma (NMC) can occur anywhere in the body, but most of the tumors are found in the midline anatomic structure or mediastinum. Pulmonary-originated NMC is extremely rare and often difficult to be distinguished from other poorly differentiated tumors, making the diagnosis awfully challenged in clinical practice. There are less than 100 cases of NUT carcinoma reported so far. In this study, the diagnosis and molecular mechanisms of reported NUT carcinoma cases were reviewed. Furthermore, a case of primary pulmonary NUT-midline carcinoma and its pathological features was reported. The process of pathological identification and genomic analysis for establishing the diagnosis was discussed. We found that NUT carcinoma could be identified by combining CT, H&E staining, immunohistochemistry (IHC), and molecular tests. The development of NUT carcinoma might be associated with mutation of MYC, p63, and MED24 genes and the Wnt, MAPK, and PI3K signaling pathways. Our study provided a detailed molecular mechanistic review on NMC and established a procedure to identify pulmonary NMC.
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Affiliation(s)
- Yunxiang Zhang
- Pathology Department, Weifang People’s Hospital, Weifang, China
| | - Kai Han
- Pathology Department, Weifang People’s Hospital, Weifang, China
| | - Xiaotong Dong
- Pathology Department, Weifang People’s Hospital, Weifang, China
| | - Qian Hou
- Pathology Department, Weifang People’s Hospital, Weifang, China
| | - Tianbao Li
- Scientific Research Department, Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Li Li
- Pathology Department, Qilu Hospital of Shandong University, Jinan, China
| | - Gengyin Zhou
- Pathology Department, Qilu Hospital of Shandong University, Jinan, China
| | - Xia Liu
- Ophthalmology Department, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Guifeng Zhao
- Prenatal Diagnosis Department, Weifang People’s Hospital, Weifang, China
| | - Wei Li
- Thoracic Surgery Department, Weifang People’s Hospital, Weifang, China
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32
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Huang B, Seefelder M, Buck E, Engler T, Lindenberg KS, Klein F, Landwehrmeyer GB, Kochanek S. HAP40 protein levels are huntingtin-dependent and decrease in Huntington disease. Neurobiol Dis 2021; 158:105476. [PMID: 34390835 DOI: 10.1016/j.nbd.2021.105476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/08/2021] [Accepted: 08/09/2021] [Indexed: 12/01/2022] Open
Abstract
The huntingtin-associated protein 40 (HAP40) is an abundant interactor of huntingtin (HTT). In complexes of these proteins, HAP40 tightly binds to HTT in a cleft formed by two larger domains rich in HEAT repeats, and a smaller bridge domain connecting the two. We show that HAP40 steady-state protein levels are directly dependent on HTT (both normal and mutant HTT) and that HAP40 is strongly stabilized by the interaction with HTT resulting in an at least 5-fold increase in HAP40's half-life when bound to HTT. Cellular HAP40 protein levels were reduced in primary fibroblasts and lymphoblasts of Huntington Disease (HD) patients and in brain tissue of a full-length HTT mouse model of HD, concomitant with decreased soluble HTT levels in these cell types. This data and our previous demonstration of coevolution between HTT and HAP40 and evolutionary conservation of their interaction suggest that HAP40 is an obligate interaction partner of HTT. Our observation of reduced HAP40 levels in HD invites further studies, whether HAP40 loss-of-function contributes to the pathophysiology of HD.
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Affiliation(s)
- Bin Huang
- Department of Gene Therapy, Ulm University, 89081 Ulm, Germany
| | | | - Eva Buck
- Department of Neurology, Ulm University, 89081 Ulm, Germany
| | - Tatjana Engler
- Department of Gene Therapy, Ulm University, 89081 Ulm, Germany
| | | | - Fabrice Klein
- Department of Neurology, Ulm University, 89081 Ulm, Germany
| | | | - Stefan Kochanek
- Department of Gene Therapy, Ulm University, 89081 Ulm, Germany.
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33
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Ollodart AR, Yeh CLC, Miller AW, Shirts BH, Gordon AS, Dunham MJ. Multiplexing mutation rate assessment: determining pathogenicity of Msh2 variants in Saccharomyces cerevisiae. Genetics 2021; 218:iyab058. [PMID: 33848333 PMCID: PMC8225350 DOI: 10.1093/genetics/iyab058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/02/2021] [Indexed: 01/01/2023] Open
Abstract
Despite the fundamental importance of mutation rate as a driving force in evolution and disease risk, common methods to assay mutation rate are time-consuming and tedious. Established methods such as fluctuation tests and mutation accumulation experiments are low-throughput and often require significant optimization to ensure accuracy. We established a new method to determine the mutation rate of many strains simultaneously by tracking mutation events in a chemostat continuous culture device and applying deep sequencing to link mutations to alleles of a DNA-repair gene. We applied this method to assay the mutation rate of hundreds of Saccharomyces cerevisiae strains carrying mutations in the gene encoding Msh2, a DNA repair enzyme in the mismatch repair pathway. Loss-of-function mutations in MSH2 are associated with hereditary nonpolyposis colorectal cancer, an inherited disorder that increases risk for many different cancers. However, the vast majority of MSH2 variants found in human populations have insufficient evidence to be classified as either pathogenic or benign. We first benchmarked our method against Luria-Delbrück fluctuation tests using a collection of published MSH2 missense variants. Our pooled screen successfully identified previously characterized nonfunctional alleles as high mutators. We then created an additional 185 human missense variants in the yeast ortholog, including both characterized and uncharacterized alleles curated from ClinVar and other clinical testing data. In a set of alleles of known pathogenicity, our assay recapitulated ClinVar's classification; we then estimated pathogenicity for 157 variants classified as uncertain or conflicting reports of significance. This method is capable of studying the mutation rate of many microbial species and can be applied to problems ranging from the generation of high-fidelity polymerases to measuring the frequency of antibiotic resistance emergence.
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Affiliation(s)
- Anja R Ollodart
- Molecular Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Chiann-Ling C Yeh
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Aaron W Miller
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Adam S Gordon
- Department of Pharmacology, Northwestern University, Chicago, IL 60208, USA
| | - Maitreya J Dunham
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
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34
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Whitley MJ, Suwanpradid J, Lai C, Jiang SW, Cook JL, Zelac DE, Rudolph R, Corcoran DL, Degan S, Spasojevic I, Levinson H, Erdmann D, Reid C, Zhang JY, Robson SC, Healy E, Havran WL, MacLeod AS. ENTPD1 (CD39) Expression Inhibits UVR-Induced DNA Damage Repair through Purinergic Signaling and Is Associated with Metastasis in Human Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2021; 141:2509-2520. [PMID: 33848530 DOI: 10.1016/j.jid.2021.02.753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/21/2021] [Accepted: 02/07/2021] [Indexed: 12/24/2022]
Abstract
UVR and immunosuppression are major risk factors for cutaneous squamous cell carcinoma (cSCC). Regulatory T cells promote cSCC carcinogenesis, and in other solid tumors, infiltrating regulatory T cells and CD8+ T cells express ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1) (also known as CD39), an ectoenzyme that catalyzes the rate-limiting step in converting extracellular adenosine triphosphate (ATP) to extracellular adenosine (ADO). We previously showed that extracellular purine nucleotides influence DNA damage repair. In this study, we investigate whether DNA damage repair is modulated through purinergic signaling in cSCC. We found increased ENTPD1 expression on T cells within cSCCs when compared with the expression on T cells from blood or nonlesional skin, and accordingly, concentrations of derivative extracellular adenosine diphosphate (ADP), adenosine monophosphate (AMP), and ADO are increased in tumors compared with those in normal skin. Importantly, ENTPD1 expression is significantly higher in human cSCCs that metastasize than in those that are nonmetastatic. We also identify in a mouse model that ENTPD1 expression is induced by UVR in an IL-27-dependent manner. Finally, increased extracellular ADO is shown to downregulate the expression of NAP1L2, a nucleosome assembly protein we show to be important for DNA damage repair secondary to UVR. Together, these data suggest a role for ENTPD1 expression on skin-resident T cells to regulate DNA damage repair through purinergic signaling to promote skin carcinogenesis and metastasis.
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Affiliation(s)
- Melodi Javid Whitley
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jutamas Suwanpradid
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Chester Lai
- Dermatopharmacology, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Department of Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Simon W Jiang
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jonathan L Cook
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Daniel E Zelac
- Department of Dermatology and Mohs Surgery, Scripps Clinic, La Jolla, California, USA
| | - Ross Rudolph
- Division of Plastic Surgery, Scripps Clinic, San Diego, California, USA; Division of Plastic Surgery, University of California San Diego, San Diego, California, USA
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Simone Degan
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ivan Spasojevic
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA; PK/PD Core Lab, Duke Cancer Institute, Durham, North Carolina, USA
| | - Howard Levinson
- Division of Plastic, Maxillofacial, and Oral Surgery, Duke Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Detlev Erdmann
- Division of Plastic, Maxillofacial, and Oral Surgery, Duke Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Claire Reid
- Dermatopharmacology, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Department of Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Jennifer Y Zhang
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA; Pinnell Center for Investigative Dermatology, Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Simon C Robson
- Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Harvard University, Boston, Massachusetts, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts, USA
| | - Eugene Healy
- Dermatopharmacology, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Department of Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Wendy L Havran
- Department of Immunology and Microbiology, The Scripps Research Institute, San Diego, California, USA
| | - Amanda S MacLeod
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA; Pinnell Center for Investigative Dermatology, Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, USA; Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA.
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35
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Luo H, Cui L, Shen K, Li R, Wang Z, Xie Z. HER2 Overexpression and Mismatch Repair Deficiency are Correlated with Malignancy in Colorectal Cancer. Cancer Manag Res 2021; 13:3443-3454. [PMID: 33907467 PMCID: PMC8068489 DOI: 10.2147/cmar.s297596] [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: 12/16/2020] [Accepted: 03/23/2021] [Indexed: 12/02/2022] Open
Abstract
PURPOSE This study was designed to investigate the correlation between the expression of human epidermal growth factor receptor 2 (HER2), mismatch repair (MMR), and clinicopathological parameters and serum tumor markers in a total of 522 resection samples materials from colorectal cancer (CRC) patients. These data were also used to determine the links between HER2 and MMR expression and prognosis. METHODS We conducted a retrospective analysis of the clinical data from 522 CRC patients. Immunohistochemistry (IHC) was used to detect HER2 overexpression and MMR deficiency (dMMR) in tumor specimens which were then correlated with various clinicopathological parameters. Prognostic value for HER2 and MMR expression was then evaluated using the data from 105 CRC patients. RESULTS HER2 overexpression was identified in 35.63% of the samples evaluated in this study, while the total dMMR rate was 12.64%. Expression of HER2 and several, MMR proteins (MLH1, MSH-2, MSH-6, and PMS-2) were then correlated with tumor location. HER2 overexpression is significantly associated with increased depth of tumor invasion, lymph node metastasis, distant metastases, pTNM staging, vascular invasion, nerve infiltration, and serum carcinoembryonic antigen (CEA) levels. HER2 overexpression and dMMR increased with advancing clinical stage. In addition, deficiencies in MLH1 and PMS2 correlated with HER2 overexpression. Finally, the prognostic evaluations revealed that HER2 overexpression was closely associated with poorer clinical outcomes. CONCLUSION HER2 overexpression is significantly correlated with multiple clinicopathological parameters resulting in a poorer prognosis. Moreover, the prognosis of patients with HER2 overexpression was worse, confirming its significance during disease assessment. In clinical practice, clinicians should pay close attention to the HER2 profile of patients as they may require more extensive clinical intervention. In addition, deficiencies in MLH1, MSH-2, MSH-6, or PMS-2 correlate with tumor location, and MLH1 and PMS2 expression is associated with lymph node metastasis and pTNM stage, suggesting that these may be additional markers in CRC risk assessments.
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Affiliation(s)
- Hai Luo
- Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Lingzhi Cui
- General Surgery, The Second Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, People’s Republic of China
| | - Kexin Shen
- Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Ruiqi Li
- Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Zeming Wang
- Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Zhongshi Xie
- Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
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36
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Zhang H, Xiao X, Wei W, Huang C, Wang M, Wang L, He Y, Sun J, Jiang Y, Jiang G, Zhang X. CircLIFR synergizes with MSH2 to attenuate chemoresistance via MutSα/ATM-p73 axis in bladder cancer. Mol Cancer 2021; 20:70. [PMID: 33874956 PMCID: PMC8054397 DOI: 10.1186/s12943-021-01360-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Background Cisplatin (CDDP) has become a standard-of-care treatment for muscle-invasive bladder cancer (MIBC), while chemoresistance remains a major challenge. Accumulating evidence indicates that circular RNAs (circRNAs) are discrete functional entities. However, the regulatory functions as well as complexities of circRNAs in modulating CDDP-based chemotherapy in bladder cancer are yet to be well revealed. Methods Through analyzing the expression profile of circRNAs in bladder cancer tissues, RNA FISH, circRNA pull-down assay, mass spectrometry analysis and RIP, circLIFR was identified and its interaction with MSH2 was confirmed. The effects of circLIFR and MSH2 on CDDP-based chemotherapy were explored by flow cytometry and rescue experiments. Co-IP and Western blot were used to investigate the molecular mechanisms underlying the functions of circLIFR and MSH2. Biological implications of circLIFR and MSH2 in bladder cancer were implemented in tumor xenograft models and PDX models. Results CircLIFR was downregulated in bladder cancer and expression was positively correlated with favorable prognosis. Moreover, circLIFR synergizing with MSH2, which was a mediator of CDDP sensitivity in bladder cancer cells, positively modulated sensitivity to CDDP in vitro and in vivo. Mechanistically, circLIFR augmented the interaction between MutSα and ATM, ultimately contributing to stabilize p73, which triggered to apoptosis. Importantly, MIBC with high expression of circLIFR and MSH2 was more sensitive to CDDP-based chemotherapy in tumor xenograft models and PDX models. Conclusions CircLIFR could interact with MSH2 to positively modulate CDDP-sensitivity through MutSα/ATM-p73 axis in bladder cancer. CircLIFR and MSH2 might be act as promising therapeutic targets for CDDP-resistant bladder cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01360-4.
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Affiliation(s)
- Hui Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xingyuan Xiao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wenjie Wei
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chao Huang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Miao Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yuanqiao He
- Department of Laboratory Animal Science, Nanchang University, Nanchang, 330006, China
| | - Jiayin Sun
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yangkai Jiang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Guosong Jiang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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37
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Toy HI, Karakülah G, Kontou PI, Alotaibi H, Georgakilas AG, Pavlopoulou A. Investigating Molecular Determinants of Cancer Cell Resistance to Ionizing Radiation Through an Integrative Bioinformatics Approach. Front Cell Dev Biol 2021; 9:620248. [PMID: 33898418 PMCID: PMC8058375 DOI: 10.3389/fcell.2021.620248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Eradication of cancer cells through exposure to high doses of ionizing radiation (IR) is a widely used therapeutic strategy in the clinical setting. However, in many cases, cancer cells can develop remarkable resistance to radiation. Radioresistance represents a prominent obstacle in the effective treatment of cancer. Therefore, elucidation of the molecular mechanisms and pathways related to radioresistance in cancer cells is of paramount importance. In the present study, an integrative bioinformatics approach was applied to three publicly available RNA sequencing and microarray transcriptome datasets of human cancer cells of different tissue origins treated with ionizing radiation. These data were investigated in order to identify genes with a significantly altered expression between radioresistant and corresponding radiosensitive cancer cells. Through rigorous statistical and biological analyses, 36 genes were identified as potential biomarkers of radioresistance. These genes, which are primarily implicated in DNA damage repair, oxidative stress, cell pro-survival, and apoptotic pathways, could serve as potential diagnostic/prognostic markers cancer cell resistance to radiation treatment, as well as for therapy outcome and cancer patient survival. In addition, our findings could be potentially utilized in the laboratory and clinical setting for enhancing cancer cell susceptibility to radiation therapy protocols.
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Affiliation(s)
- Halil Ibrahim Toy
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Hani Alotaibi
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Department of Physics, School of Applied Mathematical and Physical Sciences, Zografou, National Technical University of Athens, Athens, Greece
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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38
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Neri S, Guidotti S, Bini C, Pelotti S, D'Adamo S, Minguzzi M, Platano D, Santi S, Mariani E, Cattini L, Borzì RM. Oxidative stress-induced DNA damage and repair in primary human osteoarthritis chondrocytes: focus on IKKα and the DNA Mismatch Repair System. Free Radic Biol Med 2021; 166:212-225. [PMID: 33636333 DOI: 10.1016/j.freeradbiomed.2021.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/15/2022]
Abstract
During osteoarthritis development, chondrocytes are subjected to a functional derangement. This increases their susceptibility to stressful conditions such as oxidative stress, a characteristic of the aging tissue, which can further provoke extrinsic senescence by DNA damage responses. It was previously observed that IκB kinase α knockdown increases the replicative potential of primary human OA chondrocytes cultured in monolayer and the survival of the same cells undergoing hypertrophic-like differentiation in 3-D. In this paper we investigated whether IKKα knockdown could modulate oxidative stress-induced senescence of OA chondrocytes undergoing a DDR and particularly the involvement in this process of the DNA mismatch repair system, the principal mechanism for repair of replicative and recombinational errors, devoted to genomic stability maintenance in actively replicating cells. This repair system is also implicated in oxidative stress-mediated DNA damage repair. We analyzed microsatellite instability and expression of the mismatch repair components in human osteoarthritis chondrocytes after IKKα knockdown and H2O2 exposure. Only low MSI levels and incidence were detected and exclusively in IKKα proficient cells. Moreover, we found that IKKα proficient and deficient chondrocytes differently regulated MMR proteins after oxidative stress, both at mRNA and protein level, suggesting a reduced susceptibility of IKKα deficient cells. Our data suggest an involvement of the MMR system in the response to oxidative stress that tends to be more efficient in IKKαKD cells. This argues for a partial contribution of the MMR system to the better ability to recover DNA damage already observed in these cells.
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Affiliation(s)
- Simona Neri
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Serena Guidotti
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Carla Bini
- Department of Medical and Surgical Sciences, (DIMEC), Unit of Legal Medicine, University of Bologna, Via Irnerio, 49, 40126, Bologna, Italy.
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, (DIMEC), Unit of Legal Medicine, University of Bologna, Via Irnerio, 49, 40126, Bologna, Italy.
| | - Stefania D'Adamo
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Manuela Minguzzi
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum-Università di Bologna, Bologna, Italy.
| | - Daniela Platano
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum-Università di Bologna, Bologna, Italy.
| | - Spartaco Santi
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna at IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Erminia Mariani
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum-Università di Bologna, Bologna, Italy.
| | - Luca Cattini
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Rosa Maria Borzì
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
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Alcalá-Vida R, Seguin J, Lotz C, Molitor AM, Irastorza-Azcarate I, Awada A, Karasu N, Bombardier A, Cosquer B, Skarmeta JLG, Cassel JC, Boutillier AL, Sexton T, Merienne K. Age-related and disease locus-specific mechanisms contribute to early remodelling of chromatin structure in Huntington's disease mice. Nat Commun 2021; 12:364. [PMID: 33441541 PMCID: PMC7807045 DOI: 10.1038/s41467-020-20605-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022] Open
Abstract
Temporal dynamics and mechanisms underlying epigenetic changes in Huntington's disease (HD), a neurodegenerative disease primarily affecting the striatum, remain unclear. Using a slowly progressing knockin mouse model, we profile the HD striatal chromatin landscape at two early disease stages. Data integration with cell type-specific striatal enhancer and transcriptomic databases demonstrates acceleration of age-related epigenetic remodelling and transcriptional changes at neuronal- and glial-specific genes from prodromal stage, before the onset of motor deficits. We also find that 3D chromatin architecture, while generally preserved at neuronal enhancers, is altered at the disease locus. Specifically, we find that the HD mutation, a CAG expansion in the Htt gene, locally impairs the spatial chromatin organization and proximal gene regulation. Thus, our data provide evidence for two early and distinct mechanisms underlying chromatin structure changes in the HD striatum, correlating with transcriptional changes: the HD mutation globally accelerates age-dependent epigenetic and transcriptional reprogramming of brain cell identities, and locally affects 3D chromatin organization.
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Affiliation(s)
- Rafael Alcalá-Vida
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Jonathan Seguin
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Caroline Lotz
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Anne M Molitor
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), 67404, Illkirch, France
- CNRS UMR7104, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- University of Strasbourg, 67000, Strasbourg, France
| | - Ibai Irastorza-Azcarate
- Berlin Institute of Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ali Awada
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Nezih Karasu
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), 67404, Illkirch, France
- CNRS UMR7104, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- University of Strasbourg, 67000, Strasbourg, France
| | - Aurélie Bombardier
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Brigitte Cosquer
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Jose Luis Gomez Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Jean-Christophe Cassel
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Anne-Laurence Boutillier
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Thomas Sexton
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), 67404, Illkirch, France
- CNRS UMR7104, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- University of Strasbourg, 67000, Strasbourg, France
| | - Karine Merienne
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France.
- CNRS UMR 7364, 67000, Strasbourg, France.
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40
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Pal A, Greenblatt HM, Levy Y. Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6. Biochemistry 2020; 59:4822-4832. [PMID: 33319999 PMCID: PMC7872316 DOI: 10.1021/acs.biochem.0c00669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
DNA
mismatch repair (MMR) is an important postreplication process
that eliminates mispaired or unpaired nucleotides to ensure genomic
replication fidelity. In humans, Msh2-Msh6 and Msh2-Msh3 are the two
mismatch repair initiation factors that recognize DNA lesions. While
X-ray crystal structures exist for these proteins in complex with
DNA lesions, little is known about their structures during the initial
search along nonspecific double-stranded DNA, because they are short-lived
and difficult to determine experimentally. In this study, various
computational approaches were used to sidestep these difficulties.
All-atom and coarse-grained simulations based on the crystal structures
of Msh2-Msh3 and Msh2-Msh6 showed no translation along the DNA, suggesting
that the initial search conformation differs from the lesion-bound
crystal structure. We modeled probable search-mode structures of MSH
proteins and showed, using coarse-grained molecular dynamics simulations,
that they can perform rotation-coupled diffusion on DNA, which is
a suitable and efficient search mechanism for their function and one
predicted earlier by fluorescence resonance energy transfer and fluorescence
microscopy studies. This search mechanism is implemented by electrostatic
interactions among the mismatch-binding domain (MBD), the clamp domains,
and the DNA backbone. During simulations, their diffusion rate did
not change significantly with an increasing salt concentration, which
is consistent with observations from experimental studies. When the
gap between their DNA-binding clamps was increased, Msh2-Msh3 diffused
mostly via the clamp domains while Msh2-Msh6 still diffused using
the MBD, reproducing the experimentally measured lower diffusion coefficient
of Msh2-Msh6. Interestingly, Msh2-Msh3 was capable of dissociating
from the DNA, whereas Msh2-Msh6 always diffused on the DNA duplex.
This is consistent with the experimental observation that Msh2-Msh3,
unlike Msh2-Msh6, can overcome obstacles such as nucleosomes. Our
models provide a molecular picture of the different mismatch search
mechanisms undertaken by Msh2-Msh6 and Msh2-Msh3, despite the similarity
of their structures.
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Affiliation(s)
- Arumay Pal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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41
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Bai L, Hirose T, Assi W, Wada S, Takeshima SN, Aida Y. Bovine Leukemia Virus Infection Affects Host Gene Expression Associated with DNA Mismatch Repair. Pathogens 2020; 9:pathogens9110909. [PMID: 33143351 PMCID: PMC7694100 DOI: 10.3390/pathogens9110909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/17/2023] Open
Abstract
Bovine leukemia virus (BLV) causes enzootic bovine leukosis, a malignant form of B-cell lymphoma, and is closely related to human T-cell leukemia viruses. We investigated whether BLV infection affects host genes associated with DNA mismatch repair (MMR). Next-generation sequencing of blood samples from five calves experimentally infected with BLV revealed the highest expression levels of seven MMR genes (EXO1, UNG, PCNA, MSH2, MSH3, MSH6, and PMS2) at the point of peak proviral loads (PVLs). Furthermore, MMR gene expression was only upregulated in cattle with higher PVLs. In particular, the expression levels of MSH2, MSH3, and UNG positively correlated with PVL in vivo. The expression levels of all seven MMR genes in pig kidney-15 cells and the levels of PMS2 and EXO1 in HeLa cells also increased tendencies after transient transfection with a BLV infectious clone. Moreover, MMR gene expression levels were significantly higher in BLV-expressing cell lines compared with those in the respective parental cell lines. Expression levels of MSH2 and EXO1 in BLV-infected cattle with lymphoma were significantly lower and higher, respectively, compared with those in infected cattle in vivo. These results reveal that BLV infection affects MMR gene expression, offering new candidate markers for lymphoma diagnosis.
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Affiliation(s)
- Lanlan Bai
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan; (L.B.); (W.A.); (S.W.); (S.-n.T.)
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
| | - Tomoya Hirose
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
- Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Wlaa Assi
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan; (L.B.); (W.A.); (S.W.); (S.-n.T.)
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
- Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Satoshi Wada
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan; (L.B.); (W.A.); (S.W.); (S.-n.T.)
| | - Shin-nosuke Takeshima
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan; (L.B.); (W.A.); (S.W.); (S.-n.T.)
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
- Department of Food and Nutrition, Faculty of Human Life, Jumonji University, Niiza 352-0017, Japan
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
- Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Tokyo 113-8657, Japan
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, Wako 351-0198, Japan
- Correspondence: ; Tel.: +81-48-462-4418
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42
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Lui GYL, Shaw R, Schaub FX, Stork IN, Gurley KE, Bridgwater C, Diaz RL, Rosati R, Swan HA, Ince TA, Harding TC, Gadi VK, Goff BA, Kemp CJ, Swisher EM, Grandori C. BET, SRC, and BCL2 family inhibitors are synergistic drug combinations with PARP inhibitors in ovarian cancer. EBioMedicine 2020; 60:102988. [PMID: 32927276 PMCID: PMC7494677 DOI: 10.1016/j.ebiom.2020.102988] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Homologous recombination deficiencies (HRD) are present in approximately half of epithelial ovarian cancers, for which PARP inhibitors (PARPi) are becoming a preferred treatment option. However, a considerable proportion of these carcinomas acquire resistance or harbour de novo resistance, posing a significant challenge to treatment. METHODS To identify new combinatorial therapeutics to overcome resistance to PARPi, we employed high-throughput conditional RNAi and drug screening of patient-derived ovarian cancer cells. To prioritise clinically relevant drug combinations, we integrated empirical validation with analysis of The Cancer Genome Atlas (TCGA) and Genomics of Drug Sensitivity in Cancer (GDSC) datasets to nominate candidate targets and drugs, reaching three main findings. FINDINGS Firstly, we found that the PARPi rucaparib enhanced the effect of BET inhibitors (CPI-203 & CPI-0610) irrespective of clinical subtype or HRD status. Additional drug combination screens identified that dasatinib, a non-receptor tyrosine kinase inhibitor, augmented the effects of rucaparib and BET inhibitors, proposing a potential broadly applicable triple-drug combination for high-grade serous and clear cell ovarian carcinomas. Secondly, rucaparib synergised with the BCL2 family inhibitor navitoclax, with preferential activity in ovarian carcinomas that harbour alterations in BRCA1/2, BARD1, or MSH2/6. Thirdly, we identified potentially antagonistic drug combinations between the PARPi rucaparib and vinca alkaloids, anthracyclines, and antimetabolites, cautioning their use in the clinic. INTERPRETATION These findings propose therapeutic strategies to address PARP inhibitor resistance using agents that are already approved or are in clinical development, with the potential for rapid translation to benefit a broad population of ovarian cancer patients.
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Affiliation(s)
- Goldie Y L Lui
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Reid Shaw
- SEngine Precision Medicine, Seattle, WA, USA; Cure First, Seattle, WA, USA
| | - Franz X Schaub
- SEngine Precision Medicine, Seattle, WA, USA; Cure First, Seattle, WA, USA
| | - Isabella N Stork
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kay E Gurley
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Rachele Rosati
- SEngine Precision Medicine, Seattle, WA, USA; Cure First, Seattle, WA, USA
| | | | - Tan A Ince
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA & New York Presbyterian-Brooklyn Methodist Hospital, Brooklyn, NY, USA
| | | | - Vijayakrishna K Gadi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Barbara A Goff
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Christopher J Kemp
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elizabeth M Swisher
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Carla Grandori
- SEngine Precision Medicine, Seattle, WA, USA; Cure First, Seattle, WA, USA.
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43
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Micronuclei Formation upon Radioiodine Therapy for Well-Differentiated Thyroid Cancer: The Influence of DNA Repair Genes Variants. Genes (Basel) 2020; 11:genes11091083. [PMID: 32957448 PMCID: PMC7565468 DOI: 10.3390/genes11091083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/07/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022] Open
Abstract
Radioiodine therapy with 131I remains the mainstay of standard treatment for well-differentiated thyroid cancer (DTC). Prognosis is good but concern exists that 131I-emitted ionizing radiation may induce double-strand breaks in extra-thyroidal tissues, increasing the risk of secondary malignancies. We, therefore, sought to evaluate the induction and 2-year persistence of micronuclei (MN) in lymphocytes from 26 131I-treated DTC patients and the potential impact of nine homologous recombination (HR), non-homologous end-joining (NHEJ), and mismatch repair (MMR) polymorphisms on MN levels. MN frequency was determined by the cytokinesis-blocked micronucleus assay while genotyping was performed through pre-designed TaqMan® Assays or conventional PCR-restriction fragment length polymorphism (RFLP). MN levels increased significantly one month after therapy and remained persistently higher than baseline for 2 years. A marked reduction in lymphocyte proliferation capacity was also apparent 2 years after therapy. MLH1 rs1799977 was associated with MN frequency (absolute or net variation) one month after therapy, in two independent groups. Significant associations were also observed for MSH3 rs26279, MSH4 rs5745325, NBN rs1805794, and tumor histotype. Overall, our results suggest that 131I therapy may pose a long-term challenge to cells other than thyrocytes and that the individual genetic profile may influence 131I sensitivity, hence its risk-benefit ratio. Further studies are warranted to confirm the potential utility of these single nucleotide polymorphisms (SNPs) as radiogenomic biomarkers in the personalization of radioiodine therapy.
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44
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Sabino F, Madzharova E, Auf dem Keller U. Cell density-dependent proteolysis by HtrA1 induces translocation of zyxin to the nucleus and increased cell survival. Cell Death Dis 2020; 11:674. [PMID: 32826880 PMCID: PMC7442833 DOI: 10.1038/s41419-020-02883-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/01/2023]
Abstract
Proteases modulate critical processes in cutaneous tissue repair to orchestrate inflammation, cell proliferation and tissue remodeling. However, the functional consequences and implications in healing impairments of most cleavage events are not understood. Using iTRAQ-based Terminal Amine Isotopic Labeling of Substrates (TAILS) we had characterized proteolytic signatures in a porcine wound healing model and identified two neo-N termini derived from proteolytic cleavage of the focal adhesion protein and mechanotransducer zyxin. Here, we assign these proteolytic events to the activity of either caspase-1 or serine protease HtrA1 and analyze the biological relevance of the resultant zyxin truncations. By cellular expression of full-length and truncated zyxin proteins, we demonstrate nuclear translocation of a C-terminal zyxin fragment that could also be generated in vitro by HtrA1 cleavage and provide evidence for its anti-apoptotic activities, potentially by regulating the expression of modulators of cell proliferation, protein synthesis and genome stability. Targeted degradomics correlated endogenous generation of the same zyxin fragment with increased cell density in human primary dermal fibroblasts. Hence, this newly identified HtrA1-zyxin protease signaling axis might present a novel mechanism to transiently enhance cell survival in environments of increased cell density like in wound granulation tissue.
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Affiliation(s)
- Fabio Sabino
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Søltofts Plads, 2800, Kongens Lyngby, Denmark
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland
| | - Elizabeta Madzharova
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland
| | - Ulrich Auf dem Keller
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Søltofts Plads, 2800, Kongens Lyngby, Denmark.
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.
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45
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Liu JY, Zou T, Yin JY, Wang Z, Wang Y, Liu ZQ, Chen J, Chen ZW. Genetic Variants in DNA Mismatch Repair Pathway predict prognosis of Lung Cancer patients with receiving Platinum-Based Chemotherapy. J Cancer 2020; 11:5281-5288. [PMID: 32742474 PMCID: PMC7391198 DOI: 10.7150/jca.46150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/15/2020] [Indexed: 12/15/2022] Open
Abstract
Objective: To investigate the relationships between genetic variants in DNA mismatch repair pathway genes and the prognosis of platinum-based chemotherapy in lung cancer patients. Methods: 346 lung cancer patients who received at least two cycles of platinum-based chemotherapy were recruited in this study. A total of 35 single nucleotide polymorphisms in 7 DNA mismatch repair genes were genotyped to investigate their associations with platinum-based chemotherapy prognosis. Result: The results revealed that patients carried MSH2 rs4608577 TT genotype had a significantly shorter progression free survival than patients with GG or GT genotypes (Additive model: P=0.003, OR =0.94, 95% CI =0.33-1.57). Patients with SAPCD1 rs707937 TT genotype had a significantly longer overall survival than patients with GG or GT genotypes (Additive model: P=0.0003, OR=0.75, 95% CI =0.35-1.14). Eight SNPs and fourteen SNPs were related to progression free survival and overall survival in subgroup analyses, respectively. Conclusion: Our findings suggest that the MSH2 rs4608577 and SAPCD1 rs707937 may be potential clinical biomarkers for predicting platinum-based chemotherapy prognosis in lung cancer patients.
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Affiliation(s)
- Jun-Yan Liu
- Department of Orthopaedics, The First Affiliated Hospital of the University of South China, Hengyang 421001, China
| | - Ting Zou
- National Institution of Drug Clinical Trial, Xiangya Hospital, Central South University, Changsha, Hunan, P.R.China
| | - Ji-Ye Yin
- Departments of Clinical Pharmacology, Xinagya Hospital, Central South University, Changsha 410008, China.,Institute of Clinical Pharmacology and Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China
| | - Zhan Wang
- Department of Medical Oncology, Lung cancer and Gastrointestinal unit, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha 410013, China
| | - Ying Wang
- Hunan clinical research center in gynecologic cancer, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha 410013, China
| | - Zhao-Qian Liu
- National Institution of Drug Clinical Trial, Xiangya Hospital, Central South University, Changsha, Hunan, P.R.China.,Departments of Clinical Pharmacology, Xinagya Hospital, Central South University, Changsha 410008, China
| | - Juan Chen
- Department of Pharmacy, Xinagya Hospital, Central South University, Changsha 410008, China
| | - Zhi-Wei Chen
- Department of Orthopaedics, The First Affiliated Hospital of the University of South China, Hengyang 421001, China
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46
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Ryu SW, Stewart R, Pectol DC, Ender NA, Wimalarathne O, Lee JH, Zanini CP, Harvey A, Huibregtse JM, Mueller P, Paull TT. Proteome-wide identification of HSP70/HSC70 chaperone clients in human cells. PLoS Biol 2020; 18:e3000606. [PMID: 32687490 PMCID: PMC7392334 DOI: 10.1371/journal.pbio.3000606] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 07/30/2020] [Accepted: 06/29/2020] [Indexed: 12/25/2022] Open
Abstract
The 70 kDa heat shock protein (HSP70) family of chaperones are the front line of protection from stress-induced misfolding and aggregation of polypeptides in most organisms and are responsible for promoting the stability, folding, and degradation of clients to maintain cellular protein homeostasis. Here, we demonstrate quantitative identification of HSP70 and 71 kDa heat shock cognate (HSC70) clients using a ubiquitin-mediated proximity tagging strategy and show that, despite their high degree of similarity, these enzymes have largely nonoverlapping specificities. Both proteins show a preference for association with newly synthesized polypeptides, but each responds differently to changes in the stoichiometry of proteins in obligate multi-subunit complexes. In addition, expression of an amyotrophic lateral sclerosis (ALS)-associated superoxide dismutase 1 (SOD1) mutant protein induces changes in HSP70 and HSC70 client association and aggregation toward polypeptides with predicted disorder, indicating that there are global effects from a single misfolded protein that extend to many clients within chaperone networks. Together these findings show that the ubiquitin-activated interaction trap (UBAIT) fusion system can efficiently isolate the complex interactome of HSP chaperone family proteins under normal and stress conditions. Development of a ubiquitin-based system to comprehensively identify substrates of HSP70 enzymes in human cells reveals that constitutive HSC70 and stress-induced HSP70 have different binding preferences and respond dynamically to changes in misfolded protein levels.
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Affiliation(s)
- Seung W. Ryu
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Rose Stewart
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - D. Chase Pectol
- The Department of Chemistry, Texas A&M University, College Station, Texas, United States of America
| | - Nicolette A. Ender
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Oshadi Wimalarathne
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Ji-Hoon Lee
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Carlos P. Zanini
- Department of Statistics & Data Sciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Antony Harvey
- Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Jon M. Huibregtse
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Peter Mueller
- Department of Statistics & Data Sciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Tanya T. Paull
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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47
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Pećina-Šlaus N, Kafka A, Salamon I, Bukovac A. Mismatch Repair Pathway, Genome Stability and Cancer. Front Mol Biosci 2020; 7:122. [PMID: 32671096 PMCID: PMC7332687 DOI: 10.3389/fmolb.2020.00122] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/25/2020] [Indexed: 01/02/2023] Open
Abstract
The acquisition of genomic instability is one of the key characteristics of the cancer cell, and microsatellite instability (MSI) is an important segment of this phenomenon. This review aims to describe the mismatch DNA repair (MMR) system whose deficiency is responsible for MSI and discuss the cellular roles of MMR genes. Malfunctioning of the MMR repair pathway increases the mutational burden of specific cancers and is often involved in its etiology, sometimes as an influential bystander and sometimes as the main driving force. Detecting the presence of MSI has for a long time been an important part of clinical diagnostics, but has still not achieved its full potential. The MSI blueprints of specific tumors are useful for precize grading, evaluation of cancer chance and prognosis and to help us understand how and why therapy-resistant cancers arise. Furthermore, evidence indicates that MSI is an important predictive biomarker for the application of immunotherapy.
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Affiliation(s)
- Nives Pećina-Šlaus
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Zagreb, Croatia.,Department of Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Anja Kafka
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Zagreb, Croatia.,Department of Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Iva Salamon
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Anja Bukovac
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Zagreb, Croatia.,Department of Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
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48
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Abstract
Recent studies have suggested an increased risk of prostate cancer in men with Lynch syndrome driven by germline mutations in mismatch repair (MMR) genes. However, the incidence and clinical implication of MMR deficiency in sporadic prostate cancers remain poorly understood. We immunohistochemically stained for MLH1, MSH2, MSH6, and PMS2 in a set of tissue microarray consisting of 220 radical prostatectomy specimens and evaluated the relationship between loss of their expression and available clinicopathological features. MLH1, MSH2, MSH6, and PMS2 were lost in 2 (0.9%), 6 (2.7%), 37 (16.8%), and 27 (12.3%) prostate cancers, respectively. Loss of at least 1 MMR protein was identified in 50 (22.7%) cases. There were no statistically significant associations between MMR deficiency and patient age, family history of prostate cancer, Gleason score, or pT/pN stage. Nonetheless, the levels of preoperative prostate-specific antigen (PSA) were significantly (P = .015) higher in patients with MMR deficiency (mean ± SD: 9.12 ± 9.01 ng/mL) than in those without abnormal MMR (5.76 ± 3.17 ng/mL). There were 15 (6.8%) cases showing loss of at least 2 MMR proteins, which was not significantly associated with PSA level or tumor grade/stage. Additionally, 5 and 2 cases showed losses of at least 3 MMR proteins and all 4 proteins, respectively. Kaplan-Meier analysis revealed no significant associations between loss of MLH1 (P = .373), MSH2 (P = .348), MSH6 (P = .946), or PMS2 (P = .681), or at least 1 (P = .477), 2 (P = .486), or 3 (P = .352) MMR proteins and biochemical recurrence. Further analyses of the data on programmed death-ligand 1 (PD-L1) expression previously stained in the same set of tissue microarray demonstrated associations between loss of ≥2 MMR proteins and a higher rate of PD-L1 expression in cancer cells (17.2% vs 5.2%; P = .033) as well as between cases showing both loss of ≥1 MMR protein(s) and PD-L1 expression in tumor-infiltrating immune cells vs a higher risk of biochemical recurrence (P = .045). MMR protein loss was seen in a subset of prostate cancers. Interestingly, it was associated with significantly higher levels of PSA. Moreover, immunohistochemical detection of MMR proteins together with other proteins, such as PD-L1, might be helpful in predicting tumor recurrence following radical prostatectomy.
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Affiliation(s)
| | | | - Hiroshi Miyamoto
- Department of Pathology and Laboratory Medicine
- Department of Urology
- James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY
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49
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Grazielle-Silva V, Zeb TF, Burchmore R, Machado CR, McCulloch R, Teixeira SMR. Trypanosoma brucei and Trypanosoma cruzi DNA Mismatch Repair Proteins Act Differently in the Response to DNA Damage Caused by Oxidative Stress. Front Cell Infect Microbiol 2020; 10:154. [PMID: 32373549 PMCID: PMC7176904 DOI: 10.3389/fcimb.2020.00154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 03/23/2020] [Indexed: 01/05/2023] Open
Abstract
MSH2, associated with MSH3 or MSH6, is a central component of the eukaryotic DNA Mismatch Repair (MMR) pathway responsible for the recognition and correction of base mismatches that occur during DNA replication and recombination. Previous studies have shown that MSH2 plays an additional DNA repair role in response to oxidative damage in Trypanosoma cruzi and Trypanosoma brucei. By performing co-immunoprecipitation followed by mass spectrometry with parasites expressing tagged proteins, we confirmed that the parasites' MSH2 forms complexes with MSH3 and MSH6. To investigate the involvement of these two other MMR components in the oxidative stress response, we generated knockout mutants of MSH6 and MSH3 in T. brucei bloodstream forms and MSH6 mutants in T. cruzi epimastigotes. Differently from the phenotype observed with T. cruzi MSH2 knockout epimastigotes, loss of one or two alleles of T. cruzi msh6 resulted in increased susceptibility to H2O2 exposure, besides impaired MMR. In contrast, T. brucei msh6 or msh3 null mutants displayed increased tolerance to MNNG treatment, indicating that MMR is affected, but no difference in the response to H2O2 treatment when compared to wild type cells. Taken together, our results suggest that, while T. cruzi MSH6 and MSH2 are involved with the oxidative stress response in addition to their role as components of the MMR, the DNA repair pathway that deals with oxidative stress damage operates differently in T. brucei.
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Affiliation(s)
- Viviane Grazielle-Silva
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Tehseen Fatima Zeb
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Richard Burchmore
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Santuza M R Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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50
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Protein complexes including PGRMC1 and actin-associated proteins are disrupted by AG-205. Biochem Biophys Res Commun 2020; 524:64-69. [DOI: 10.1016/j.bbrc.2019.12.108] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/20/2019] [Indexed: 12/18/2022]
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