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Kawata D, Iwai H, Oba S, Komiya Y, Koike R, Miyamoto S, Kanno T, Ainai A, Suzuki T, Hosoya T, Yasuda S. Diverse pro-inflammatory ability of mutated spike protein derived from variant strains of SARS-CoV-2. Cytokine 2024; 178:156592. [PMID: 38574505 DOI: 10.1016/j.cyto.2024.156592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/09/2024] [Accepted: 03/29/2024] [Indexed: 04/06/2024]
Abstract
The severity of COVID-19 has been reported to differ among SARS-CoV-2 mutant variants. The overactivation of macrophages is involved in severe COVID-19, yet the effects of SARS-CoV-2 mutations on macrophages remain poorly understood. To clarify the effects, we examined whether mutations of spike proteins (S-proteins) affect macrophage activation. CD14+ monocyte-derived macrophages were stimulated with the recombinant S-protein of the wild-type, Delta, and Omicron strains or live viral particles of individual strains. Regarding IL-6 and TNF-α, Delta or Omicron S-protein had stronger or weaker pro‑inflammatory ability, respectively, than the wild-type. Similar trends were observed between S-proteins and viral particles. S-protein mutations could be related to the diversity in macrophage activation and severity rates in COVID-19 caused by various SARS-CoV-2 strains.
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Affiliation(s)
- Daisuke Kawata
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hideyuki Iwai
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Seiya Oba
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yoji Komiya
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ryuji Koike
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Sho Miyamoto
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Kanno
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadashi Hosoya
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Shinsuke Yasuda
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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2
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Sharma S, Gupta S, Yadav PK. Sex and blood group determination from hair using ATR-FTIR spectroscopy and chemometrics. Int J Legal Med 2024; 138:801-814. [PMID: 37980281 DOI: 10.1007/s00414-023-03123-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/06/2023] [Indexed: 11/20/2023]
Abstract
Examination of hair with its intact root is commonly used for DNA profiling of the donor. However, its use for gathering other types of information is less explored. Using attenuated total reflectance-Fourier transform infrared spectroscopy, the present study aims to explore other relevant aspects in a non-destructive manner for forensics. Determining the sex and blood group of human hair samples were the major goals of the study. Sex determination was accomplished by analyzing the differential vibrational intensities and stretching of various chemical groups associated with hair and its proteins. Statistical inference of spectral data was performed using chemometric algorithms such as PCA and PLS-DA. The PLS-DA model determined sex with 100% accuracy and blood grouping with an average accuracy of 95%. The present study is the first of its kind to determine sex and blood grouping from human scalp hair shafts, as far as the author knows. By acting as a preliminary screening test, this study could have significant implications for forensic analysis of crime scene samples. Human and synthetic hair were used in validation studies, resulting in 100% accuracy, specificity, and sensitivity, with 0% false positives and false negatives. The technique ATR FTIR spectroscopy could complement the currently used methods of hair analysis such as physical examination and mitochondrial or genomic DNA analysis.
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Affiliation(s)
- Sweety Sharma
- LNJN NICFS, School of Forensic Sciences, National Forensic Science University, An Institute of National Importance, Ministry of Home Affairs, Govt. of India, Delhi Campus, Delhi, 110085, India.
| | - Srishti Gupta
- LNJN NICFS, School of Forensic Sciences, National Forensic Science University, An Institute of National Importance, Ministry of Home Affairs, Govt. of India, Delhi Campus, Delhi, 110085, India
| | - Praveen Kumar Yadav
- Department of Forensic Science, Sandip University, Nashik, Maharastra, India
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Zhang X, Xiao J, Yang F, Qu H, Ye C, Chen S, Guo Y. Identification of sudden cardiac death from human blood using ATR-FTIR spectroscopy and machine learning. Int J Legal Med 2024; 138:1139-1148. [PMID: 38047927 DOI: 10.1007/s00414-023-03118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/25/2023] [Indexed: 12/05/2023]
Abstract
OBJECTIVE The aim of this study is to identify a rapid, sensitive, and non-destructive auxiliary approach for postmortem diagnosis of SCD, addressing the challenges faced in forensic practice. METHODS ATR-FTIR spectroscopy was employed to collect spectral features of blood samples from different cases, combined with pathological changes. Mixed datasets were analyzed using ANN, KNN, RF, and SVM algorithms. Evaluation metrics such as accuracy, precision, recall, F1-score and confusion matrix were used to select the optimal algorithm and construct the postmortem diagnosis model for SCD. RESULTS A total of 77 cases were collected, including 43 cases in the SCD group and 34 cases in the non-SCD group. A total of 693 spectrogram were obtained. Compared to other algorithms, the SVM algorithm demonstrated the highest accuracy, reaching 95.83% based on spectral biomarkers. Furthermore, by combing spectral biomarkers with age, gender, and cardiac histopathological changes, the accuracy of the SVM model could get 100%. CONCLUSION Integrating artificial intelligence technology, pathology, and physical chemistry analysis of blood components can serve as an effective auxiliary method for postmortem diagnosis of SCD.
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Affiliation(s)
- Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Jiao Xiao
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Fengqin Yang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Hongke Qu
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Chengxin Ye
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Sile Chen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China.
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4
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Mateus Pereira de Souza N, Kimberli Abeg da Rosa D, de Moraes C, Caeran M, Bordin Hoffmann M, Pozzobon Aita E, Prochnow L, Lya Assmann da Motta A, Antonio Corbellini V, Rieger A. Structural characterization of DNA amplicons by ATR-FTIR spectroscopy as a guide for screening metainflammatory disorders in blood plasma. Spectrochim Acta A Mol Biomol Spectrosc 2024; 310:123897. [PMID: 38266599 DOI: 10.1016/j.saa.2024.123897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
Attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy is a promising rapid, reagent-free, and low-cost technique considered for clinical translation. It allows to characterize biofluids proteome, lipidome, and metabolome at once. Metainflammatory disorders share a constellation of chronic systemic inflammation, oxidative stress, aberrant adipogenesis, and hypoxia, that significantly increased cardiovascular and cancer risk. As a result, these patients have elevated concentration of cfDNA in the bloodstream. Considering this, DNA amplicons were analyzed by ATR-FTIR at 3 concentrations with 1:100 dilution: (IU/mL): 718, 7.18, and 0.0718. The generated IR spectrum was used as a guide for variable selection. The main peaks in the biofingerprint (1800-900 cm-1) give important information about the base, base-sugar, phosphate, and sugar-phosphate transitions of DNA. To validate our method of selecting variables in blood plasma, 38 control subjects and 12 with metabolic syndrome were used. Using the wavenumbers of the peaks in the biofingerprint of the DNA amplicons, was generated a discriminant analysis model with Mahalanobis distance in blood plasma, and 100 % discrimination accuracy was obtained. In addition, the interval 1475-1188 cm-1 showed the greatest sensitivity to variation in the concentration of DNA amplicons, so curve fitting with Gaussian funcion was performed, obtaining adjusted-R2 of 0.993. PCA with Mahalanobis distance in the interval 1475-1188 cm-1 obtained an accuracy of 96 % and PLS-DA modeling in the interval 1475-1088 cm-1 obtained AUC = 0.991 with sensitivity of 95 % and specificity of 100 %. Therefore, ATR-FTIR spectroscopy with variable selection guided by DNA IR peaks is a promising and efficient method to be applied in metainflammatory disorders.
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Affiliation(s)
| | - Dhuli Kimberli Abeg da Rosa
- Bioprocess Engineering and Biotechnology, State University of Rio Grande do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Caroline de Moraes
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Mariana Caeran
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Mairim Bordin Hoffmann
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Eduardo Pozzobon Aita
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Laura Prochnow
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Anna Lya Assmann da Motta
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Valeriano Antonio Corbellini
- Department of Sciences, Humanities, and Education, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Alexandre Rieger
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, Rio Grande do Sul, Brazil.
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5
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Hsieh MJ, Lin CC, Lo YS, Chuang YC, Ho HY, Chen MK. Semilicoisoflavone B induces oral cancer cell apoptosis by targeting claspin and ATR-Chk1 signaling pathways. Environ Toxicol 2024; 39:2417-2428. [PMID: 38197544 DOI: 10.1002/tox.24107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/10/2023] [Indexed: 01/11/2024]
Abstract
The prevalence of oral squamous cell carcinoma (OSCC) is increasing worldwide mainly due to poor oral hygiene and unrestricted lifestyle. Advanced-stage OSCC is associated with poor prognosis and a 5-year survival rate of only 30%-50%. The present study was designed to investigate the anticancer effect and mode of action of Glycyrrhiza-derived semilicoisoflavone B (SFB) in 5-fluorourasil (5FU)-resistant human OSCC cell lines. The study findings revealed that SFB significantly reduces OSCC cell viability and colony formation ability by arresting cell cycle at the G2/M and S phases and reducing the expressions of key cell cycle regulators including cyclin A, cyclin B, CDC2, and CDK2. The compound caused a significant induction in the percentage of nuclear condensation and apoptotic cells in OSCC. Regarding pro-apoptotic mode of action, SFB was found to increase Fas-associated death domain and death receptor 5 expressions and reduce decoy receptor 2 expression, indicating involvement of extrinsic pathway. Moreover, SFB was found to increase pro-apoptotic Bim expression and reduce anti-apoptotic Bcl-2 and Bcl-xL expressions, indicating involvement of intrinsic pathway. Moreover, SFB-mediated induction in cleaved caspases 3, 8, and 9 and cleaved poly(ADP-ribose) polymerase confirmed the induction of caspase-mediated apoptotic pathways. Regarding upstream signaling pathway, SFB was found to reduce extracellular signal regulated kinase 1/2 (ERK) phosphorylation to execute its pro-apoptotic activity. The Human Apoptotic Array findings revealed that SFB suppresses claspin expression, which in turn caused reduced phosphorylation of ATR, checkpoint kinase 1 (Chk1), Wee1, and CDC25C, indicating disruption of ATR-Chk1 signaling pathway by SFB. Taken together, these findings indicate that SFB acts as a potent anticancer compound against 5FU-resistant OSCC by modulating mitogen-activated protein kinase (MAPK) and ATR-Chk1 signaling pathways.
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Affiliation(s)
- Ming-Ju Hsieh
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, Taiwan
- Doctoral Program in Tissue Engineering and Regenerative Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Chia-Chieh Lin
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, Taiwan
| | - Yu-Sheng Lo
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Ching Chuang
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, Taiwan
| | - Hsin-Yu Ho
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, Taiwan
| | - Mu-Kuan Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, Changhua Christian Hospital, Changhua, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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6
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Woodward ER, Lalloo F, Forde C, Pugh S, Burghel GJ, Schlecht H, Harkness EF, Howell A, Howell SJ, Gandhi A, Evans DG. Germline testing of BRCA1, BRCA2, PALB2 and CHEK2 c.1100delC in 1514 triple negative familial and isolated breast cancers from a single centre, with extended testing of ATM, RAD51C and RAD51D in over 400. J Med Genet 2024; 61:385-391. [PMID: 38123987 DOI: 10.1136/jmg-2023-109671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The identification of germline pathogenic gene variants (PGVs) in triple negative breast cancer (TNBC) is important to inform further primary cancer risk reduction and TNBC treatment strategies. We therefore investigated the contribution of breast cancer associated PGVs to familial and isolated invasive TNBC. METHODS Outcomes of germline BRCA1, BRCA2 and CHEK2_c.1100delC testing were recorded in 1514 women (743-isolated, 771-familial), and for PALB2 in 846 women (541-isolated, 305-familial), with TNBC and smaller numbers for additional genes. Breast cancer free controls were identified from Predicting Risk Of Cancer At Screening and BRIDGES (Breast cancer RIsk after Diagnostic GEne Sequencing) studies. RESULTS BRCA1_PGVs were detected in 52 isolated (7.0%) and 195 (25.3%) familial cases (isolated-OR=58.9, 95% CI: 16.6 to 247.0), BRCA2_PGVs in 21 (2.8%) isolated and 67 (8.7%) familial cases (isolated-OR=5.0, 95% CI: 2.3 to 11.2), PALB2_PGVs in 9 (1.7%) isolated and 12 (3.9%) familial cases (isolated-OR=8.8, 95% CI: 2.5 to 30.4) and CHEK2_c.1100delC in 0 isolated and 3 (0.45%) familial cases (isolated-OR=0.0, 95% CI: 0.00 to 2.11). BRCA1_PGV detection rate was >10% for all familial TNBC age groups and significantly higher for younger diagnoses (familial: <50 years, n=165/538 (30.7%); ≥50 years, n=30/233 (12.9%); p<0.0001). Women with a G3_TNBC were more likely to have a BRCA1_PGV as compared with a BRCA2 or PALB2_PGV (p<0.0001). 0/743 isolated TNBC had the CHEK2_c.1100delC PGV and 0/305 any ATM_PGV, but 2/240 (0.83%) had a RAD51D_PGV. CONCLUSION PGVs in BRCA1 are associated with G3_TNBCs. Familial TNBCs and isolated TNBCs <30 years have a >10% likelihood of a PGV in BRCA1. BRCA1_PGVs are associated with younger age of familial TNBC. There was no evidence for any increased risk of TNBC with CHEK2 or ATM PGVs.
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Affiliation(s)
- Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Claire Forde
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Sarah Pugh
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Elaine F Harkness
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Anthony Howell
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
- Prevent Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Sacha J Howell
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
- Prevent Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Ashu Gandhi
- Prevent Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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van Haaren C, Byrne B, Kazarian SG. Study of Monoclonal Antibody Aggregation at the Air-Liquid Interface under Flow by ATR-FTIR Spectroscopic Imaging. Langmuir 2024; 40:5858-5868. [PMID: 38445553 PMCID: PMC10956494 DOI: 10.1021/acs.langmuir.3c03730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/07/2024]
Abstract
Throughout bioprocessing, transportation, and storage, therapeutic monoclonal antibodies (mAbs) experience stress conditions that may cause protein unfolding and/or chemical modifications. Such structural changes may lead to the formation of aggregates, which reduce mAb potency and may cause harmful immunogenic responses in patients. Therefore, aggregates need to be detected and removed or ideally prevented from forming. Air-liquid interfaces, which arise during various stages of bioprocessing, are one of the stress factors causing mAb aggregation. In this study, the behavior of an immunoglobulin G (IgG) at the air-liquid interface was investigated under flow using macro attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic imaging. This chemically specific imaging technique allows observation of adsorption of IgG to the air-liquid interface and detection of associated secondary structural changes. Chemical images revealed that IgG rapidly accumulated around an injected air bubble under flow at 45 °C; however, no such increase was observed at 25 °C. Analysis of the second derivative spectra of IgG at the air-liquid interface revealed changes in the protein secondary structure associated with increased intermolecular β-sheet content, indicative of aggregated IgG. The addition of 0.01% w/v polysorbate 80 (PS80) reduced the amount of IgG at the air-liquid interface in a static setup at 30 °C; however, this protective effect was lost at 45 °C. These results suggest that the presence of air-liquid interfaces under flow may be detrimental to mAb stability at elevated temperatures and demonstrate the power of ATR-FTIR spectroscopic imaging for studying the structural integrity of mAbs under bioprocessing conditions.
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Affiliation(s)
- Céline van Haaren
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
| | - Bernadette Byrne
- Department
of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K.
| | - Sergei G. Kazarian
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
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8
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Li YP, Lu TY, Huang FR, Zhang WM, Chen ZQ, Guang PW, Deng LY, Yang XH. Differential diagnosis of Crohn's disease and intestinal tuberculosis based on ATR-FTIR spectroscopy combined with machine learning. World J Gastroenterol 2024; 30:1377-1392. [PMID: 38596500 PMCID: PMC11000079 DOI: 10.3748/wjg.v30.i10.1377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/02/2024] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Crohn's disease (CD) is often misdiagnosed as intestinal tuberculosis (ITB). However, the treatment and prognosis of these two diseases are dramatically different. Therefore, it is important to develop a method to identify CD and ITB with high accuracy, specificity, and speed. AIM To develop a method to identify CD and ITB with high accuracy, specificity, and speed. METHODS A total of 72 paraffin wax-embedded tissue sections were pathologically and clinically diagnosed as CD or ITB. Paraffin wax-embedded tissue sections were attached to a metal coating and measured using attenuated total reflectance fourier transform infrared spectroscopy at mid-infrared wavelengths combined with XGBoost for differential diagnosis. RESULTS The results showed that the paraffin wax-embedded specimens of CD and ITB were significantly different in their spectral signals at 1074 cm-1 and 1234 cm-1 bands, and the differential diagnosis model based on spectral characteristics combined with machine learning showed accuracy, specificity, and sensitivity of 91.84%, 92.59%, and 90.90%, respectively, for the differential diagnosis of CD and ITB. CONCLUSION Information on the mid-infrared region can reveal the different histological components of CD and ITB at the molecular level, and spectral analysis combined with machine learning to establish a diagnostic model is expected to become a new method for the differential diagnosis of CD and ITB.
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Affiliation(s)
- Yuan-Peng Li
- College of Physical Science and Technology, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Tian-Yu Lu
- Department of Gastroenterology, The Affiliated Hospital of South University of Science and Technology, Shenzhen 518000, Guangdong Province, China
| | - Fu-Rong Huang
- Department of Optoelectronic Engineering, Jinan University, Guangzhou 510632, Guangdong Province, China
| | - Wei-Min Zhang
- Department of Gastroenterology, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510632, Guangdong Province, China
| | - Zhen-Qiang Chen
- Department of Optoelectronic Engineering, Jinan University, Guangzhou 510632, Guangdong Province, China
| | - Pei-Wen Guang
- Department of Optoelectronic Engineering, Jinan University, Guangzhou 510632, Guangdong Province, China
| | - Liang-Yu Deng
- Department of Optoelectronic Engineering, Jinan University, Guangzhou 510632, Guangdong Province, China
| | - Xin-Hao Yang
- Department of Optoelectronic Engineering, Jinan University, Guangzhou 510632, Guangdong Province, China
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Wei CT, You JL, Weng SK, Jian SY, Lee JCL, Chiang TL. Enhancing forensic investigations: Identifying bloodstains on various substrates through ATR-FTIR spectroscopy combined with machine learning algorithms. Spectrochim Acta A Mol Biomol Spectrosc 2024; 308:123755. [PMID: 38101254 DOI: 10.1016/j.saa.2023.123755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/16/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
The forensic analysis of bloodstains on various substrates plays a crucial role in criminal investigations. This study presents a novel approach for analyzing bloodstains using Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FTIR) in combination with machine learning. ATR-FTIR offers non-destructive and non-invasive advantages, requiring minimal sample preparation. By detecting specific chemical bonds in blood components, it enables the differentiation of various body fluids. However, the subjective interpretation of the spectra poses challenges in distinguishing different fluids. To address this, we employ machine learning techniques. Machine learning is extensively used in chemometrics to analyze chemical data, build models, and extract useful information. This includes both unsupervised learning and supervised learning methods, which provide objective characterization and differentiation. The focus of this study was to identify human and porcine blood on substrates using ATR-FTIR spectroscopy. The substrates included paper, plastic, cloth, and wood. Data preprocessing was performed using Principal Component Analysis (PCA) to reduce dimensionality and analyze latent variables. Subsequently, six machine learning algorithms were used to build classification models and compare their performance. These algorithms comprise Partial Least Squares Discriminant Analysis (PLS-DA), Decision Trees (DT), Logistic Regression (LR), Naive Bayes Classifier (NBC), Support Vector Machine (SVM), and Neural Network (NN). The results indicate that the PCA-NN model provides the optimal solution on most substrates. Although ATR-FTIR spectroscopy combined with machine learning effectively identifies bloodstains on substrates, the performance of different identification models still varies based on the type of substrate. The integration of these disciplines enables researchers to harness the power of data-driven approaches for solving complex forensic problems. The objective differentiation of bloodstains using machine learning holds significant implications for criminal investigations. This technique offers a non-destructive, simple, selective, and rapid approach for forensic analysis, thereby assisting forensic scientists and investigators in determining crucial evidence related to bloodstains.
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Affiliation(s)
- Chun-Ta Wei
- School of Defense Science, Chung Cheng Institute of Technology, National Defense University, Taoyuan 335009, Taiwan
| | - Jhu-Lin You
- Department of Chemical and Materials Engineering, Chung Cheng Institute of Technology, National Defense University, Taoyuan 335009, Taiwan; System Engineering and Technology Program, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Shiuh-Ku Weng
- Department of Electronic Engineering, Chien Hsin University of Science and Technology, Taoyuan 320678, Taiwan.
| | - Shun-Yi Jian
- Department of Material Engineering, Ming Chi University of Technology, New Taipei 243303, Taiwan; Center for Plasma and Thin Film Technologies, Ming Chi University of Technology, New Taipei 243303, Taiwan.
| | - Jeff Cheng-Lung Lee
- Department of Criminal Investigation, Taiwan Police College, Taipei 116078, Taiwan
| | - Tang-Lun Chiang
- School of Defense Science, Chung Cheng Institute of Technology, National Defense University, Taoyuan 335009, Taiwan
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10
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Zhang X, Yang F, Xiao J, Qu H, Jocelin NF, Ren L, Guo Y. Analysis and comparison of machine learning methods for species identification utilizing ATR-FTIR spectroscopy. Spectrochim Acta A Mol Biomol Spectrosc 2024; 308:123713. [PMID: 38056185 DOI: 10.1016/j.saa.2023.123713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/26/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Accurate identification of insect species holds paramount significance in diverse fields as it facilitates a comprehensive understanding of their ecological habits, distribution range, and impact on both the environment and humans. While morphological characteristics have traditionally been employed for species identification, the utilization of empty pupariums for this purpose remains relatively limited. In this study, ATR-FTIR was employed to acquire spectral information from empty pupariums of five fly species, subjecting the data to spectral pre-processing to obtain average spectra for preliminary analysis. Subsequently, PCA and OPLS-DA were utilized for clustering and classification. Notably, two wavebands (3000-2800 cm-1 and 1800-1300 cm-1) were found to be significant in distinguishing A. grahami. Further, we established three machine learning models, including SVM, KNN, and RF, to analyze spectra from different waveband groups. The biological fingerprint region (1800-1300 cm-1) demonstrated a substantial advantage in identifying empty puparium species. Remarkably, the SVM model exhibited an impressive accuracy of 100 % in identifying all five fly species. This study represents the first instance of employing infrared spectroscopy and machine learning methods for identifying insect species using empty pupariums, providing a robust research foundation for future investigations in this area.
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Affiliation(s)
- Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, Hunan, China
| | - Fengqin Yang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, Hunan, China
| | - Jiao Xiao
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, Hunan, China
| | - Hongke Qu
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Ngando Fernand Jocelin
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, Hunan, China
| | - Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, Hunan, China.
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11
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Podralska M, Sajek MP, Bielicka A, Żurawek M, Ziółkowska-Suchanek I, Iżykowska K, Kolenda T, Kazimierska M, Kasprzyk ME, Sura W, Pietrucha B, Cukrowska B, Rozwadowska N, Dzikiewicz-Krawczyk A. Identification of ATM-dependent long non-coding RNAs induced in response to DNA damage. DNA Repair (Amst) 2024; 135:103648. [PMID: 38382170 DOI: 10.1016/j.dnarep.2024.103648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/23/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
DNA damage response (DDR) is a complex process, essential for cell survival. Especially deleterious type of DNA damage are DNA double-strand breaks (DSB), which can lead to genomic instability and malignant transformation if not repaired correctly. The central player in DSB detection and repair is the ATM kinase which orchestrates the action of several downstream factors. Recent studies have suggested that long non-coding RNAs (lncRNAs) are involved in DDR. Here, we aimed to identify lncRNAs induced upon DNA damage in an ATM-dependent manner. DNA damage was induced by ionizing radiation (IR) in immortalized lymphoblastoid cell lines derived from 4 patients with ataxia-telangiectasia (AT) and 4 healthy donors. RNA-seq revealed 10 lncRNAs significantly induced 1 h after IR in healthy donors, whereas none in AT patients. 149 lncRNAs were induced 8 h after IR in the control group, while only three in AT patients. Among IR-induced mRNAs, we found several genes with well-known functions in DDR. Gene Set Enrichment Analysis and Gene Ontology revealed delayed induction of key DDR pathways in AT patients compared to controls. The induction and dynamics of selected 9 lncRNAs were confirmed by RT-qPCR. Moreover, using a specific ATM inhibitor we proved that the induction of those lncRNAs is dependent on ATM. Some of the detected lncRNA genes are localized next to protein-coding genes involved in DDR. We observed that induction of lncRNAs after IR preceded changes in expression of adjacent genes. This indicates that IR-induced lncRNAs may regulate the transcription of nearby genes. Subcellular fractionation into chromatin, nuclear, and cytoplasmic fractions revealed that the majority of studied lncRNAs are localized in chromatin. In summary, our study revealed several lncRNAs induced by IR in an ATM-dependent manner. Their genomic co-localization and co-expression with genes involved in DDR suggest that those lncRNAs may be important players in cellular response to DNA damage.
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Affiliation(s)
- Marta Podralska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Marcin Piotr Sajek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Antonina Bielicka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Żurawek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Marta Kazimierska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Weronika Sura
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Pietrucha
- Children's Memorial Health Institute, Department of Immunology, Warsaw, Poland
| | - Bożena Cukrowska
- Children's Memorial Health Institute, Department of Pathomorphology, Immunology Laboratorium, Warsaw, Poland
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12
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Brun BF, Nascimento MHC, Dias PAC, Marcarini WD, Singh MN, Filgueiras PR, Vassallo PF, Romão W, Mill JG, Martin FL, Barauna VG. Fast screening using attenuated total reflectance- fourier transform infrared (ATR-FTIR) spectroscopy of patients based on D-dimer threshold value. Talanta 2024; 269:125482. [PMID: 38042146 DOI: 10.1016/j.talanta.2023.125482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/04/2023]
Abstract
Attenuated Total Reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is an emerging technology in the medical field. Blood D-dimer was initially studied as a marker of the activation of coagulation and fibrinolysis. It is mainly used as a potential diagnosis screening test for pulmonary embolism or deep vein thrombosis but was recently associated with COVID-19 severity. This study aimed to evaluate the use of ATR-FTIR spectroscopy with machine learning to classify plasma D-dimer concentrations. The plasma ATR-FTIR spectra from 100 patients were studied through principal component analysis (PCA) and two supervised approaches: genetic algorithm with linear discriminant analysis (GA-LDA) and partial least squares with linear discriminant (PLS-DA). The spectra were truncated to the fingerprint region (1800-1000 cm-1). The GA-LDA method effectively classified patients according to D-dimer cutoff (≤0.5 μg/mL and >0.5 μg/mL) with 87.5 % specificity and 100 % sensitivity on the training set, and 85.7 % specificity, and 95.6 % sensitivity on the test set. Thus, we demonstrate that ATR-FTIR spectroscopy might be an important additional tool for classifying patients according to D-dimer values. ATR-FTIR spectral analyses associated with clinical evidence can contribute to a faster and more accurate medical diagnosis, reduce patient morbidity, and save resources and demand for professionals.
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Affiliation(s)
- Bruna F Brun
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Marcia H C Nascimento
- Exact Sciences Center, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Pedro A C Dias
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Wena D Marcarini
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil; Centro Universitário Vale do CRICARÉ, São Matheus, Espírito Santo, Brazil
| | - Maneesh N Singh
- Biocel UK Ltd, Hull, HU10 6TS, UK; Chesterfield Royal Hospital, Chesterfield Road, Calow, Chesterfield, S44 5BL, UK
| | - Paulo R Filgueiras
- Exact Sciences Center, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Paula F Vassallo
- Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Wanderson Romão
- Exact Sciences Center, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil; Federal Institute of Education Science and Technology of Espírito Santo, Vila Velha, Espírito Santo, Brazil
| | - José G Mill
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Francis L Martin
- Biocel UK Ltd, Hull, HU10 6TS, UK; Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool, FY3 8NR, UK
| | - Valerio G Barauna
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil.
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13
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Hardaker EL, Sanseviero E, Karmokar A, Taylor D, Milo M, Michaloglou C, Hughes A, Mai M, King M, Solanki A, Magiera L, Miragaia R, Kar G, Standifer N, Surace M, Gill S, Peter A, Talbot S, Tohumeken S, Fryer H, Mostafa A, Mulgrew K, Lam C, Hoffmann S, Sutton D, Carnevalli L, Calero-Nieto FJ, Jones GN, Pierce AJ, Wilson Z, Campbell D, Nyoni L, Martins CP, Baker T, Serrano de Almeida G, Ramlaoui Z, Bidar A, Phillips B, Boland J, Iyer S, Barrett JC, Loembé AB, Fuchs SY, Duvvuri U, Lou PJ, Nance MA, Gomez Roca CA, Cadogan E, Critichlow SE, Fawell S, Cobbold M, Dean E, Valge-Archer V, Lau A, Gabrilovich DI, Barry ST. The ATR inhibitor ceralasertib potentiates cancer checkpoint immunotherapy by regulating the tumor microenvironment. Nat Commun 2024; 15:1700. [PMID: 38402224 PMCID: PMC10894296 DOI: 10.1038/s41467-024-45996-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/09/2024] [Indexed: 02/26/2024] Open
Abstract
The Ataxia telangiectasia and Rad3-related (ATR) inhibitor ceralasertib in combination with the PD-L1 antibody durvalumab demonstrated encouraging clinical benefit in melanoma and lung cancer patients who progressed on immunotherapy. Here we show that modelling of intermittent ceralasertib treatment in mouse tumor models reveals CD8+ T-cell dependent antitumor activity, which is separate from the effects on tumor cells. Ceralasertib suppresses proliferating CD8+ T-cells on treatment which is rapidly reversed off-treatment. Ceralasertib causes up-regulation of type I interferon (IFNI) pathway in cancer patients and in tumor-bearing mice. IFNI is experimentally found to be a major mediator of antitumor activity of ceralasertib in combination with PD-L1 antibody. Improvement of T-cell function after ceralasertib treatment is linked to changes in myeloid cells in the tumor microenvironment. IFNI also promotes anti-proliferative effects of ceralasertib on tumor cells. Here, we report that broad immunomodulatory changes following intermittent ATR inhibition underpins the clinical therapeutic benefit and indicates its wider impact on antitumor immunity.
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Affiliation(s)
| | | | | | - Devon Taylor
- Oncology R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Marta Milo
- Oncology R&D, AstraZeneca, Cambridge, UK
| | | | | | - Mimi Mai
- Oncology R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | | | | | | | | | - Gozde Kar
- Oncology R&D, AstraZeneca, Cambridge, UK
| | - Nathan Standifer
- Oncology R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
- Tempest Therapeutics, Brisbane, CA, USA
| | | | - Shaan Gill
- Oncology R&D, AstraZeneca, Cambridge, UK
| | | | | | | | | | - Ali Mostafa
- Oncology R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Kathy Mulgrew
- Oncology R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | | | | | - Daniel Sutton
- Imaging and Data Analytics, AstraZeneca, Cambridge, UK
| | | | | | | | - Andrew J Pierce
- Oncology R&D, AstraZeneca, Cambridge, UK
- Crescendo Biologics Limited, Cambridge, UK
| | | | | | | | | | | | | | | | - Abdel Bidar
- CPSS, Imaging, AstraZeneca, Gothenburg, Sweden
| | - Benjamin Phillips
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Joseph Boland
- Oncology R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Sonia Iyer
- Oncology R&D, AstraZeneca, Boston, MA, USA
| | | | | | - Serge Y Fuchs
- Department of Biomedical Sciences, School of Veterinary Medicine University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Umamaheswar Duvvuri
- UPMC Department of Otolaryngology and UPMC Hillman Cancer Center, 200 Lothrop St. Suite 500, Pittsburg, PA, 15213, USA
| | - Pei-Jen Lou
- National Taiwan University Hospital, No. 7, Chung Shan S. Rd. (Zhongshan S. Rd.), Zhongzheng Dist., Taipei City, 10002, Taiwan
| | - Melonie A Nance
- VA Pittsburgh Healthcare System, University Drive C, Pittsburg, PA, 15240, USA
| | - Carlos Alberto Gomez Roca
- Institut Claudius Regaud-Cancer Comprehensive Center, 1 Avenue Irene Joliot-Curie, IUCT-O, Toulouse, 31059 Cedex 9, France
| | | | | | | | - Mark Cobbold
- Oncology R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Emma Dean
- Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Alan Lau
- Oncology R&D, AstraZeneca, Cambridge, UK
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14
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Pike KG, Hunt TA, Barlaam B, Benstead D, Cadogan E, Chen K, Cook CR, Colclough N, Deng C, Durant ST, Eatherton A, Goldberg K, Johnström P, Liu L, Liu Z, Nissink JWM, Pang C, Pass M, Robb GR, Roberts C, Schou M, Steward O, Sykes A, Yan Y, Zhai B, Zheng L. Identification of Novel, Selective Ataxia-Telangiectasia Mutated Kinase Inhibitors with the Ability to Penetrate the Blood-Brain Barrier: The Discovery of AZD1390. J Med Chem 2024; 67:3090-3111. [PMID: 38306388 DOI: 10.1021/acs.jmedchem.3c02277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
The inhibition of ataxia-telangiectasia mutated (ATM) has been shown to chemo- and radio-sensitize human glioma cells in vitro and therefore might provide an exciting new paradigm in the treatment of glioblastoma multiforme (GBM). The effective treatment of GBM will likely require a compound with the potential to efficiently cross the blood-brain barrier (BBB). Starting from clinical candidate AZD0156, 4, we investigated the imidazoquinolin-2-one scaffold with the goal of improving likely CNS exposure in humans. Strategies aimed at reducing hydrogen bonding, basicity, and flexibility of the molecule were explored alongside modulating lipophilicity. These studies identified compound 24 (AZD1390) as an exceptionally potent and selective inhibitor of ATM with a good preclinical pharmacokinetic profile. 24 showed an absence of human transporter efflux in MDCKII-MDR1-BCRP studies (efflux ratio <2), significant BBB penetrance in nonhuman primate PET studies (Kp,uu 0.33) and was deemed suitable for development as a clinical candidate to explore the radiosensitizing effects of ATM in intracranial malignancies.
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Affiliation(s)
- Kurt G Pike
- Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | | | - David Benstead
- Pharmaceutical Sciences, AstraZeneca, Silk Road Business Park, Macclesfield SK10 2NA, U.K
| | | | - Kan Chen
- Innovation Center China, Asia & Emerging Markets iMED, 199 Liangjing Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Calum R Cook
- Pharmaceutical Sciences, AstraZeneca, Silk Road Business Park, Macclesfield SK10 2NA, U.K
| | | | - Chao Deng
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | | | | | | | - Peter Johnström
- PET Science Centre, Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Karolinska Institutet, Stockholm SE-171 76, Sweden
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm SE-171 76, Sweden
| | - Libin Liu
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Zhaoqun Liu
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | | | - Chengling Pang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Martin Pass
- Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | | | - Magnus Schou
- PET Science Centre, Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Karolinska Institutet, Stockholm SE-171 76, Sweden
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm SE-171 76, Sweden
| | | | - Andy Sykes
- Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Yumei Yan
- Innovation Center China, Asia & Emerging Markets iMED, 199 Liangjing Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Baochang Zhai
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Li Zheng
- Innovation Center China, Asia & Emerging Markets iMED, 199 Liangjing Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
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15
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Black WC, Abdoli A, An X, Auger A, Beaulieu P, Bernatchez M, Caron C, Chefson A, Crane S, Diallo M, Dorich S, Fader LD, Ferraro GB, Fournier S, Gao Q, Ginzburg Y, Hamel M, Han Y, Jones P, Lanoix S, Lacbay CM, Leclaire ME, Levy M, Mamane Y, Mulani A, Papp R, Pellerin C, Picard A, Skeldon A, Skorey K, Stocco R, St-Onge M, Truchon JF, Truong VL, Zimmermann M, Zinda M, Roulston A. Discovery of the Potent and Selective ATR Inhibitor Camonsertib (RP-3500). J Med Chem 2024; 67:2349-2368. [PMID: 38299539 DOI: 10.1021/acs.jmedchem.3c01917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
ATR is a key kinase in the DNA-damage response (DDR) that is synthetic lethal with several other DDR proteins, making it an attractive target for the treatment of genetically selected solid tumors. Herein we describe the discovery of a novel ATR inhibitor guided by a pharmacophore model to position a key hydrogen bond. Optimization was driven by potency and selectivity over the related kinase mTOR, resulting in the identification of camonsertib (RP-3500) with high potency and excellent ADME properties. Preclinical evaluation focused on the impact of camonsertib on myelosuppression, and an exploration of intermittent dosing schedules to allow recovery of the erythroid compartment and mitigate anemia. Camonsertib is currently undergoing clinical evaluation both as a single agent and in combination with talazoparib, olaparib, niraparib, lunresertib, or gemcitabine (NCT04497116, NCT04972110, NCT04855656). A preliminary recommended phase 2 dose for monotherapy was identified as 160 mg QD given 3 days/week.
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Affiliation(s)
- W Cameron Black
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Abbas Abdoli
- Nuchem Sciences, Inc., 2350 Rue Cohen, Suite 201, Saint-Laurent, Quebec H4R 2N6, Canada
| | - Xiuli An
- New York Blood Center Enterprises, New York, New York 10065, United States
| | - Anick Auger
- Ventus Therapeutics, Inc., 7150 Frederick-Banting, Saint-Laurent, Quebec H4S 2A1, Canada
| | | | | | - Cathy Caron
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Amandine Chefson
- Ventus Therapeutics, Inc., 7150 Frederick-Banting, Saint-Laurent, Quebec H4S 2A1, Canada
| | - Sheldon Crane
- Nuchem Sciences, Inc., 2350 Rue Cohen, Suite 201, Saint-Laurent, Quebec H4R 2N6, Canada
| | - Mohamed Diallo
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Stéphane Dorich
- Ventus Therapeutics, Inc., 7150 Frederick-Banting, Saint-Laurent, Quebec H4S 2A1, Canada
| | - Lee D Fader
- Ventus Therapeutics, Inc., 7150 Frederick-Banting, Saint-Laurent, Quebec H4S 2A1, Canada
| | - Gino B Ferraro
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Sara Fournier
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Qi Gao
- J-Star Research, Inc., 3001 Hadley Road, Suites 1-5A, South Plainfield, New Jersey 07080, United States
| | - Yelena Ginzburg
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Martine Hamel
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Yongshuai Han
- New York Blood Center Enterprises, New York, New York 10065, United States
| | - Paul Jones
- Nuchem Sciences, Inc., 2350 Rue Cohen, Suite 201, Saint-Laurent, Quebec H4R 2N6, Canada
| | - Stéphanie Lanoix
- Nuchem Sciences, Inc., 2350 Rue Cohen, Suite 201, Saint-Laurent, Quebec H4R 2N6, Canada
| | - Cyrus M Lacbay
- Nuchem Sciences, Inc., 2350 Rue Cohen, Suite 201, Saint-Laurent, Quebec H4R 2N6, Canada
| | - Marie-Eve Leclaire
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Maayan Levy
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Yael Mamane
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Amina Mulani
- Nuchem Sciences, Inc., 2350 Rue Cohen, Suite 201, Saint-Laurent, Quebec H4R 2N6, Canada
| | - Robert Papp
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Charles Pellerin
- Ventus Therapeutics, Inc., 7150 Frederick-Banting, Saint-Laurent, Quebec H4S 2A1, Canada
| | - Audrey Picard
- Ventus Therapeutics, Inc., 7150 Frederick-Banting, Saint-Laurent, Quebec H4S 2A1, Canada
| | - Alexander Skeldon
- Ventus Therapeutics, Inc., 7150 Frederick-Banting, Saint-Laurent, Quebec H4S 2A1, Canada
| | - Kathryn Skorey
- Nuchem Sciences, Inc., 2350 Rue Cohen, Suite 201, Saint-Laurent, Quebec H4R 2N6, Canada
| | - Rino Stocco
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Miguel St-Onge
- Ventus Therapeutics, Inc., 7150 Frederick-Banting, Saint-Laurent, Quebec H4S 2A1, Canada
| | - Jean-François Truchon
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Vouy Linh Truong
- Nuchem Sciences, Inc., 2350 Rue Cohen, Suite 201, Saint-Laurent, Quebec H4R 2N6, Canada
| | - Michal Zimmermann
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Michael Zinda
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
| | - Anne Roulston
- Repare Therapeutics, Inc., 7171 Frederick-Banting, Building 2, Saint-Laurent, Quebec H4S 1Z9, Canada
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16
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Rosen E, Yap TA, Lee EK, Højgaard M, Mettu NB, Lheureux S, Carneiro BA, Plummer R, Fretland AJ, Ulanet D, Xu Y, McDougall R, Koehler M, Fontana E. Development of a Practical Nomogram for Personalized Anemia Management in Patients Treated with Ataxia Telangiectasia and Rad3-related Inhibitor Camonsertib. Clin Cancer Res 2024; 30:687-694. [PMID: 38078898 PMCID: PMC10870112 DOI: 10.1158/1078-0432.ccr-23-2080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/04/2023] [Accepted: 12/06/2023] [Indexed: 02/17/2024]
Abstract
PURPOSE Camonsertib is a highly selective and potent inhibitor of ataxia telangiectasia and Rad3-related (ATR) kinase. Dose-dependent anemia is a class-related on-target adverse event often requiring dose modifications. Individual patient risk factors for the development of significant anemia complicate the selection of a "one-size-fits-all" ATR inhibitor (ATRi) dose and schedule, possibly leading to suboptimal therapeutic doses in patients at low risk of anemia. We evaluated whether early predictors of anemia could be identified to ultimately inform a personalized dose-modification approach. PATIENTS AND METHODS On the basis of preclinical observations and a mechanistic understanding of ATRi-related anemia, we identified several potential factors to explore in a multivariable linear regression modeling tool for predicting hemoglobin level ahead of day 22 (cycle 2) of treatment. RESULTS In patients treated with camonsertib monotherapy (NCT04497116), we observed that hemoglobin decline is consistently preceded by reticulocytopenia, and dose- and exposure-dependent decreases in monocytes. We developed a nomogram incorporating baseline and day 8 hemoglobin and reticulocyte values that predicted the day 22 hemoglobin values of patients with clinically valuable concordance (within 7.5% of observations) 80% of the time in a cross-validation performance test of data from 60 patients. CONCLUSIONS The prediction of future hemoglobin decrease, after a week of treatment, may enable a personalized, early dose modification to prevent development of clinically significant anemia and resulting unscheduled dose holds or transfusions.
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Affiliation(s)
- Ezra Rosen
- Early Drug Development and Breast Medicine Services, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy A. Yap
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth K. Lee
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | | | - Benedito A. Carneiro
- Legorreta Cancer Center at Brown University, and Lifespan Cancer Institute, Division of Hematology/Oncology, Department of Medicine, The Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Ruth Plummer
- Newcastle University and Newcastle Hospitals NHS Foundation Trust, Northern Centre for Cancer Care, Newcastle-upon-Tyne, United Kingdom
| | | | | | - Yi Xu
- Repare Therapeutics, Cambridge, Massachusetts
| | | | | | - Elisa Fontana
- Sarah Cannon Research Institute UK, London, United Kingdom
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17
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Novais Â, Gonçalves AB, Ribeiro TG, Freitas AR, Méndez G, Mancera L, Read A, Alves V, López-Cerero L, Rodríguez-Baño J, Pascual Á, Peixe L. Development and validation of a quick, automated, and reproducible ATR FT-IR spectroscopy machine-learning model for Klebsiella pneumoniae typing. J Clin Microbiol 2024; 62:e0121123. [PMID: 38284762 PMCID: PMC10865814 DOI: 10.1128/jcm.01211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
The reliability of Fourier-transform infrared (FT-IR) spectroscopy for Klebsiella pneumoniae typing and outbreak control has been previously assessed, but issues remain in standardization and reproducibility. We developed and validated a reproducible FT-IR with attenuated total reflectance (ATR) workflow for the identification of K. pneumoniae lineages. We used 293 isolates representing multidrug-resistant K. pneumoniae lineages causing outbreaks worldwide (2002-2021) to train a random forest classification (RF) model based on capsular (KL)-type discrimination. This model was validated with 280 contemporaneous isolates (2021-2022), using wzi sequencing and whole-genome sequencing as references. Repeatability and reproducibility were tested in different culture media and instruments throughout time. Our RF model allowed the classification of 33 capsular (KL)-types and up to 36 clinically relevant K. pneumoniae lineages based on the discrimination of specific KL- and O-type combinations. We obtained high rates of accuracy (89%), sensitivity (88%), and specificity (92%), including from cultures obtained directly from the clinical sample, allowing to obtain typing information the same day bacteria are identified. The workflow was reproducible in different instruments throughout time (>98% correct predictions). Direct colony application, spectral acquisition, and automated KL prediction through Clover MS Data analysis software allow a short time-to-result (5 min/isolate). We demonstrated that FT-IR ATR spectroscopy provides meaningful, reproducible, and accurate information at a very early stage (as soon as bacterial identification) to support infection control and public health surveillance. The high robustness together with automated and flexible workflows for data analysis provide opportunities to consolidate real-time applications at a global level. IMPORTANCE We created and validated an automated and simple workflow for the identification of clinically relevant Klebsiella pneumoniae lineages by FT-IR spectroscopy and machine-learning, a method that can be extremely useful to provide quick and reliable typing information to support real-time decisions of outbreak management and infection control. This method and workflow is of interest to support clinical microbiology diagnostics and to aid public health surveillance.
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Affiliation(s)
- Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana Beatriz Gonçalves
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa G. Ribeiro
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Gema Méndez
- CLOVER Bioanalytical Software, Granada, Spain
| | | | - Antónia Read
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Valquíria Alves
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
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18
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Karakostis K, Malbert-Colas L, Thermou A, Vojtesek B, Fåhraeus R. The DNA damage sensor ATM kinase interacts with the p53 mRNA and guides the DNA damage response pathway. Mol Cancer 2024; 23:21. [PMID: 38263180 PMCID: PMC10804554 DOI: 10.1186/s12943-024-01933-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND The ATM kinase constitutes a master regulatory hub of DNA damage and activates the p53 response pathway by phosphorylating the MDM2 protein, which develops an affinity for the p53 mRNA secondary structure. Disruption of this interaction prevents the activation of the nascent p53. The link of the MDM2 protein-p53 mRNA interaction with the upstream DNA damage sensor ATM kinase and the role of the p53 mRNA in the DNA damage sensing mechanism, are still highly anticipated. METHODS The proximity ligation assay (PLA) has been extensively used to reveal the sub-cellular localisation of the protein-mRNA and protein-protein interactions. ELISA and co-immunoprecipitation confirmed the interactions in vitro and in cells. RESULTS This study provides a novel mechanism whereby the p53 mRNA interacts with the ATM kinase enzyme and shows that the L22L synonymous mutant, known to alter the secondary structure of the p53 mRNA, prevents the interaction. The relevant mechanistic roles in the DNA Damage Sensing pathway, which is linked to downstream DNA damage response, are explored. Following DNA damage (double-stranded DNA breaks activating ATM), activated MDMX protein competes the ATM-p53 mRNA interaction and prevents the association of the p53 mRNA with NBS1 (MRN complex). These data also reveal the binding domains and the phosphorylation events on ATM that regulate the interaction and the trafficking of the complex to the cytoplasm. CONCLUSION The presented model shows a novel interaction of ATM with the p53 mRNA and describes the link between DNA Damage Sensing with the downstream p53 activation pathways; supporting the rising functional implications of synonymous mutations altering secondary mRNA structures.
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Affiliation(s)
- Konstantinos Karakostis
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France.
- Institut de Biotecnologia I de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
| | - Laurence Malbert-Colas
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France
| | - Aikaterini Thermou
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Robin Fåhraeus
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France.
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic.
- Department of Medical Biosciences, Umeå University, Umeå, 90185, Sweden.
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19
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Pang W, Xing Y, Morais CLM, Lao Q, Li S, Qiao Z, Li Y, Singh MN, Barauna VG, Martin FL, Zhang Z. Serum-based ATR-FTIR spectroscopy combined with multivariate analysis for the diagnosis of pre-diabetes and diabetes. Analyst 2024; 149:497-506. [PMID: 38063458 DOI: 10.1039/d3an01519j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Diabetes mellitus (DM) is a metabolic disease with an increasing prevalence that is causing worldwide concern. The pre-diabetes stage is the only reversible stage in the patho-physiological process towards DM. Due to the limitations of traditional methods, the diagnosis and detection of DM and pre-diabetes are complicated, expensive, and time-consuming. Therefore, it would be of great benefit to develop a simple, rapid and inexpensive diagnostic test. Herein, the infrared (IR) spectra of serum samples from 111 DM patients, 111 pre-diabetes patients and 333 healthy volunteers were collected using attenuated total reflection Fourier-transform IR (ATR-FTIR) spectroscopy and this was combined with the multivariate analysis of principal component analysis linear discriminant analysis (PCA-LDA) to develop a discriminant model to verify the diagnostic potential of this approach. The study found that the accuracy of the test model established by ATR-FTIR spectroscopy combined with PCA-LDA was 97%, and the sensitivity and specificity were 100% and 100% in the control group, 94% and 98% in the pre-diabetes group, and 91% and 98% in the DM group, respectively. This indicates that this method can effectively diagnose DM and pre-diabetes, which has far-reaching clinical significance.
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Affiliation(s)
- Weiyi Pang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, 541199, Guangxi, China.
- School of Public Health, Guilin Medical University, Guilin, 541199, Guangxi, China
- School of Humanities and Management, Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Yu Xing
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, 541199, Guangxi, China.
- School of Public Health, Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Camilo L M Morais
- Center for Education, Science and Technology of the Inhamuns Region, State University of Ceará, Tauá 63660-000, Brazil
| | - Qiufeng Lao
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, 541199, Guangxi, China.
- School of Public Health, Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Shengle Li
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, 541199, Guangxi, China.
- School of Public Health, Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Zipeng Qiao
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, 541199, Guangxi, China.
- School of Public Health, Guilin Medical University, Guilin, 541199, Guangxi, China
| | - You Li
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, 541199, Guangxi, China.
- School of Public Health, Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Maneesh N Singh
- Biocel UK Ltd, Hull HU10 6TS, UK.
- Chesterfield Royal Hospital, Chesterfield Road, Calow, Chesterfield S44 5BL, UK
| | - Valério G Barauna
- Department of Physiological Sciences, Federal University of Espírito Santo, Vitoria, Brazil
| | - Francis L Martin
- Biocel UK Ltd, Hull HU10 6TS, UK.
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| | - Zhiyong Zhang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, 541199, Guangxi, China.
- School of Public Health, Guilin Medical University, Guilin, 541199, Guangxi, China
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20
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Tran HL, Lai KH, Chang HS, Chen YS, Wang HC, Yang SS, Chang HW, Hsu CM, Yen CH, Hsiao HH. Indigofera suffruticosa aerial parts extract induce G2/M arrest and ATR/CHK1 pathway in Jurkat cells. BMC Complement Med Ther 2024; 24:28. [PMID: 38195460 PMCID: PMC10775588 DOI: 10.1186/s12906-023-04325-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Indigofera suffruticosa Mill. is used as a folk medicine for treating patients with leukemia, however very little is known regarding the molecular mechanism of its anti-leukemic activity and the chemical profile of the active extract. The present study aimed to reveal the molecular effect of I. suffruticosa aerial parts extract (ISAE) on leukemia cells and its chemical constituents. METHODS Cytotoxicity of ISAE were determined by resazurin viability assay, multitox - Glo multiplex cytotoxicity assay, and Annexin V staining assay. Cell cycle profiles were revealed by propidium iodide staining assay. The effects of ISAE on G2/M arrest signaling and DNA damage were evaluated by Western blot assay and phospho-H2A.X staining assay. The chemical profile of ISAE were determined by tandem mass spectroscopy and molecular networking approach. RESULTS We showed that the acute lymphoblastic leukemia cell line Jurkat cell was more responsive to ISAE treatment than other leukemia cell lines. In contrast, ISAE did not induce cytotoxic effects in normal fibroblast cells. Cell cycle analysis revealed that ISAE triggered G2/M arrest in Jurkat cells in dose- and time-dependent manners. Elevation of annexin V-stained cells and caspase 3/7 activity suggested ISAE-induced apoptosis. Furthermore, ISAE alone could increase the phosphorylation of CDK1 at Y15 and activate the ATR/CHK1/Wee1/CDC25C signaling pathway. However, the addition of caffeine, a widely used ATR inhibitor to ISAE, reduced the phosphorylation of ATR, CHK1, and CDK1, as well as G2/M arrest in Jurkat cells. Moreover, increased phospho-H2A.X stained cells indicated the involvement of DNA damage in the anti-leukemic effect of ISAE. Finally, qualitative analysis using UPLC-tandem mass spectroscopy and molecular networking revealed that tryptanthrin was the most abundant organoheterocyclic metabolite in ISAE. At equivalent concentrations to ISAE, tryptanthrin induced G2/M arrest of Jurkat cells, which can be prevented by caffeine. CONCLUSIONS ISAE causes G2/M arrest via activating ATR/CHK1/CDK1 pathway and tryptanthrin is one of the active components of ISAE. Our findings provide subtle support to the traditional use of I. suffruitcosa in leukemia management in folk medicine.
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Affiliation(s)
- Hong-Loan Tran
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Kuei-Hung Lai
- PhD Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan
| | - Hsun-Shuo Chang
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Yi-Siao Chen
- Ph.D. Program in Environmental and Occupational Medicine, College of Medicine, Kaohsiung Medical University and National Health Research Institutes, Kaohsiung, 80708, Taiwan
| | - Hui-Chun Wang
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Shuen-Shin Yang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Hsueh-Wei Chang
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Chin-Mu Hsu
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, 80708, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, 80708, Taiwan
| | - Chia-Hung Yen
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, 80708, Taiwan.
| | - Hui-Hua Hsiao
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, 80708, Taiwan.
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, 80708, Taiwan.
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
- Faculty of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, 80708, Taiwan.
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21
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Tugrul F, Akin Geyik G, Yalinbaş Kaya B, Peker Cengiz B, Karuk Elmas SN, Yilmaz I, Arslan FN. A biospectroscopic approach toward colorectal cancer diagnosis from bodily fluid samples via ATR-MIR spectroscopy combined with multivariate data analysis. Spectrochim Acta A Mol Biomol Spectrosc 2024; 304:123342. [PMID: 37688884 DOI: 10.1016/j.saa.2023.123342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023]
Abstract
In this study, a biospectroscopic approach was reported for the detection of spectral changes and biomarkers for the diagnosis of colorectal cancer (CC) cases from different bodily fluids (blood plasma, blood serum, saliva and colonoscopy disinfection/wash fluids) by using attenuated total reflection-mid infrared (ATR-MIR) spectroscopy. To recognize the molecular level changes in the spectral characteristics of CC and their healthy/control (CH) groups, different multivariate data analyses (HCA, LDA, PCA and SIMCA) were successfully performed over the data of ATR-MIR spectroscopy. Two hundred specimens were characterized in detail over the data of spectral regions (4000-650 cm-1 and regions V-XXII). The findings revealed that significant changes were clearly observed in the concentrations of lipid, protein, nucleic acid and carbohydrate biomolecules for cancer cases based upon their necessity to overcome energy requirements. Supervised multivariate data methodology SIMCA, presented an excellent classification for the studied groups; similarly 100% of the specimens from different bodily fluids were correctly classified by supervised methodology LDA. As a result, the developed ATR-MIR methodology for the classification of CC and their healthy groups highlighted a rapid cancer diagnosis approach from different bodily fluids; therefore, it could be guide to make well decision before histopathological assessment and to screen CC populations existing in society.
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Affiliation(s)
- Fuzuli Tugrul
- Eskişehir City Hospital, Clinic of Radiation Oncology, 26080 Eskisehir, Turkey
| | - Gonul Akin Geyik
- Karamanoglu Mehmetbey University, K.O. Science Faculty, Department of Chemistry, 70100 Karaman, Turkey
| | | | - Betul Peker Cengiz
- Eskişehir Yunus Emre State Hospital, Clinic of Medical Pathology, 26190 Eskisehir, Turkey
| | - Sukriye Nihan Karuk Elmas
- Karamanoglu Mehmetbey University, K.O. Science Faculty, Department of Chemistry, 70100 Karaman, Turkey; Istanbul University-Cerrahpaşa, Pharmacy Faculty, Department of Analytical Chemistry, 34500 Istanbul, Turkey
| | - Ibrahim Yilmaz
- Karamanoglu Mehmetbey University, K.O. Science Faculty, Department of Chemistry, 70100 Karaman, Turkey.
| | - Fatma Nur Arslan
- Karamanoglu Mehmetbey University, K.O. Science Faculty, Department of Chemistry, 70100 Karaman, Turkey.
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22
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Sokolenko AP, Bakaeva EK, Venina AR, Kuligina ES, Romanko AA, Aleksakhina SN, Belysheva YV, Belogubova EV, Stepanov IA, Zaitseva OA, Yatsuk OS, Togo AV, Khamgokov ZM, Kadyrova AO, Pirmagomedov AS, Bolieva MB, Epkhiev AA, Tsutsaev AK, Chakhieva MD, Khabrieva KM, Khabriev IM, Murachuev MA, Buttaeva BN, Baboshkina LS, Bayramkulova FI, Katchiev IR, Alieva LK, Raskin GA, Orlov SV, Khachmamuk ZK, Levonyan KR, Gichko DM, Kirtbaya DV, Degtyariov AM, Sultanova LV, Musayeva HS, Belyaev AM, Imyanitov EN. Ethnicity-specific BRCA1, BRCA2, PALB2, and ATM pathogenic alleles in breast and ovarian cancer patients from the North Caucasus. Breast Cancer Res Treat 2024; 203:307-315. [PMID: 37851290 DOI: 10.1007/s10549-023-07135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Mountain areas of the North Caucasus host several large ethnic communities that have preserved their national identity over the centuries. METHODS This study involved high-grade serous ovarian cancer (HGSOC) and breast cancer (BC) patients from Dagestan (HGSOC: 37; BC: 198), Kabardino-Balkaria (HGSOC: 68; BC: 155), North Ossetia (HGSOC: 51; BC: 104), Chechnya (HGSOC: 68; BC: 79), Ingushetia (HGSOC: 19; BC: 103), Karachay-Cherkessia (HGSOC: 13; BC: 47), and several Armenian settlements (HGSOC: 16; BC: 101). The group of BC patients was enriched by young-onset and/or family history-positive and/or bilateral and/or receptor triple-negative cases. The entire coding region of BRCA1, BRCA2, PALB2, and ATM genes was analyzed by next-generation sequencing. RESULTS A significant contribution of BRCA1/2 pathogenic variants (PVs) to HGSOC and BC development was observed across all North Caucasus regions (HGSOC: 19-39%; BC: 6-13%). Founder alleles were identified in all ethnic groups studied, e.g., BRCA1 c.3629_3630delAG in Chechens, BRCA2 c.6341delC in North Ossetians, BRCA2 c.5351dupA in Ingush, and BRCA1 c.2907_2910delTAAA in Karachays. Some BRCA1/2 alleles, particularly BRCA2 c.9895C > T, were shared by several nationalities. ATM PVs were detected in 14 patients, with c.1673delG and c.8876_8879delACTG alleles occurring twice each. PALB2 heterozygosity was observed in 5 subjects, with one variant seen in 2 unrelated women. CONCLUSION This study adds to the evidence for the global-wide contribution of BRCA1/2 genes to HGSOC and BC morbidity, although the spectrum of their PVs is a subject of ethnicity-specific variations. The data on founder BRCA1/2 alleles may be considered when adjusting the BRCA1/2 testing procedure to the ethnic origin of patients.
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Affiliation(s)
- Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758.
- St. Petersburg Pediatric Medical University, St. Petersburg, Russia.
| | - Elvina Kh Bakaeva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Aigul R Venina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Ekaterina Sh Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Alexandr A Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Svetlana N Aleksakhina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Yana V Belysheva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Evgeniya V Belogubova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Ilya A Stepanov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Olga A Zaitseva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Olga S Yatsuk
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Alexandr V Togo
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Zaur M Khamgokov
- Republican Cancer Center, The Kabardino-Balkarian Republic, Nalchik, Russia
| | - Azinat O Kadyrova
- Republican Cancer Center, The Kabardino-Balkarian Republic, Nalchik, Russia
| | | | - Marina B Bolieva
- Republican Cancer Center, The Republic of North Ossetia-Alania, Vladikavkaz, Russia
| | - Alexandr A Epkhiev
- Republican Cancer Center, The Republic of North Ossetia-Alania, Vladikavkaz, Russia
| | - Aslan K Tsutsaev
- Republican Cancer Center, The Republic of North Ossetia-Alania, Vladikavkaz, Russia
| | | | | | - Idris M Khabriev
- Republican Cancer Center, The Republic of Ingushetia, Pliyevo, Russia
| | - Mirza A Murachuev
- Republican Cancer Center, The Republic of Dagestan, Makhachkala, Russia
| | - Bella N Buttaeva
- Republican Bureau of Pathology, The Republic of Dagestan, Makhachkala, Russia
| | - Liliya S Baboshkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | | | - Islam R Katchiev
- Republican Cancer Center, The Karachay-Cherkess Republic, Cherkessk, Russia
| | - Lina Kh Alieva
- Republican Cancer Center, The Karachay-Cherkess Republic, Cherkessk, Russia
| | - Grigory A Raskin
- Dr. Sergey Berezin Medical Institute of Biological Systems, St. Petersburg, Russia
| | - Sergey V Orlov
- I.P. Pavlov St.-Petersburg State Medical University, St. Petersburg, Russia
| | | | | | | | | | | | | | - Hedi S Musayeva
- Republican Cancer Center, Grozny, The Chechen Republic, Russia
| | - Alexey M Belyaev
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
- St. Petersburg Pediatric Medical University, St. Petersburg, Russia
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Pfeiffer C, Grandits AM, Asnagli H, Schneller A, Huber J, Zojer N, Schreder M, Parker AE, Bolomsky A, Beer PA, Ludwig H. CTPS1 is a novel therapeutic target in multiple myeloma which synergizes with inhibition of CHEK1, ATR or WEE1. Leukemia 2024; 38:181-192. [PMID: 37898670 DOI: 10.1038/s41375-023-02071-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023]
Abstract
Targeting nucleotide biosynthesis is a proven strategy for the treatment of cancer but is limited by toxicity, reflecting the fundamental nucleotide requirement of dividing cells. The rate limiting step in de novo pyrimidine synthesis is of interest, being catalyzed by two homologous enzymes, CTP synthase 1 (CTPS1) and CTPS2, that could be differentially targeted. Herein, analyses of publicly available datasets identified an essential role for CTPS1 in multiple myeloma (MM), linking high expression of CTPS1 (but not CTPS2) with advanced disease and poor outcomes. In cellular experiments, CTPS1 knockout induced apoptosis of MM cell lines. Exposure of MM cells to STP-B, a novel and highly selective pharmacological inhibitor of CTPS1, inhibited proliferation, induced S phase arrest and led to cell death by apoptosis. Mechanistically, CTPS1 inhibition by STP-B activated DNA damage response (DDR) pathways and induced double-strand DNA breaks which accumulated in early S phase. Combination of STP-B with pharmacological inhibitors of key components of the DDR pathway (ATR, CHEK1 or WEE1) resulted in synergistic growth inhibition and early apoptosis. Taken together, these findings identify CTPS1 as a promising new target in MM, either alone or in combination with DDR pathway inhibition.
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Affiliation(s)
- Christina Pfeiffer
- Department of Medicine I, Klinik Ottakring, Wilhelminen Cancer Research Institute, Vienna, Austria
| | - Alexander M Grandits
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | | | - Anja Schneller
- Department of Medicine I, Klinik Ottakring, Wilhelminen Cancer Research Institute, Vienna, Austria
| | - Julia Huber
- Department of Medicine I, Klinik Ottakring, Wilhelminen Cancer Research Institute, Vienna, Austria
| | - Niklas Zojer
- Department of Medicine I, Klinik Ottakring, Wilhelminen Cancer Research Institute, Vienna, Austria
- Department of Medicine I, Center for Oncology and Hematology, Klinik Ottakring, Vienna, Austria
| | - Martin Schreder
- Department of Medicine I, Center for Oncology and Hematology, Klinik Ottakring, Vienna, Austria
| | | | - Arnold Bolomsky
- Department of Medicine I, Klinik Ottakring, Wilhelminen Cancer Research Institute, Vienna, Austria
| | | | - Heinz Ludwig
- Department of Medicine I, Klinik Ottakring, Wilhelminen Cancer Research Institute, Vienna, Austria.
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24
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Whitehouse W. Peripheral neuropathy in ataxia-telangiectasia: Newly characterized, has potential as a biomarker. Eur J Neurol 2023; 30:3643. [PMID: 37553836 DOI: 10.1111/ene.16032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/10/2023]
Affiliation(s)
- William Whitehouse
- University of Nottingham-School of Medicine, E Floor East Block Queen's Medical Centre, Nottingham, UK
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25
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Lin SF, Lee YY, Wu MH, Lu YL, Yeh CN, Chen WY, Chou TC, Wong RJ. Therapeutic inhibition of ATR in differentiated thyroid cancer. Endocr Relat Cancer 2023; 30:e230142. [PMID: 37902083 DOI: 10.1530/erc-23-0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/28/2023] [Indexed: 10/01/2023]
Abstract
Ataxia telangiectasia and Rad3-related protein (ATR) is a critical component of the DNA damage response and a potential target in the treatment of cancers. An ATR inhibitor, BAY 1895344, was evaluated for its use in differentiated thyroid cancer (DTC) therapy. BAY 1895344 inhibited cell viability in four DTC cell lines (TPC1, K1, FTC-133, and FTC-238) in a dose-dependent manner. BAY 1895344 treatment arrested DTC cells in the G2/M phase, increased caspase-3 activity, and caused apoptosis. BAY 1895344 in combination with either sorafenib or lenvatinib showed mainly synergistic effects in four DTC cell lines. The combination of BAY 1895344 with dabrafenib plus trametinib revealed synergistic effects in K1 cells that harbor BRAFV600E. BAY 1895344 monotherapy retarded the growth of K1 and FTC-133 tumors in xenograft models. The combinations of BAY 1895344 plus lenvatinib and BAY 1895344 with dabrafenib plus trametinib were more effective than any single therapy in a K1 xenograft model. No appreciable toxicity appeared in animals treated with either a single therapy or a combination treatment. Our findings provide the rationale for the development of clinical trials of BAY 1895344 in the treatment of DTC.
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Affiliation(s)
- Shu-Fu Lin
- Department of Internal Medicine, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Yin Lee
- Department of Internal Medicine, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| | - Ming-Hsien Wu
- Department of Internal Medicine, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| | - Yu-Ling Lu
- Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chun-Nan Yeh
- Department of Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ting-Chao Chou
- Laboratory of Preclinical Pharmacology Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- PD Science, Inc., Mill Run, Paramus, New Jersey, USA
| | - Richard J Wong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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26
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Kitamura H, Morizane C, Tanabe N, Go I, Maruki Y, Ohba A, Nagashio Y, Kondo S, Hijioka S, Ueno H, Yoshida T, Okusaka T. Clinical features of germline BRCA1/2 or ATM pathogenic variant positive pancreatic cancer in Japan. Pancreatology 2023; 23:964-969. [PMID: 37914629 DOI: 10.1016/j.pan.2023.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/08/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND There has been increasing interest into the role of germline BRCA1/2 pathogenic variants (gBRCA PV) and gATM PV and likely PV (PV and LPV; PV + LPV) in the carcinogenesis and treatment of pancreatic cancer (PC), but the clinical features have not been well described. METHODS Patients with confirmed gBRCA PV and gATM PV + LPV PC treated at our hospital between April 2016 and December 2021, were retrospectively evaluated for clinical characteristics and outcomes. RESULTS Twenty-two patients harbored gBRCA PV and three patients harbored gATM PV + LPV. Of the gBRCA PV patients, 81.8 % received platinum-based chemotherapy with favorable treatment outcomes with an objective response rate of 50.0 % (95 % CI: 23.0-77.0), median progression free survival (PFS) of 334 days, and median overall survival (OS) of 926 days from the initiation of first-line chemotherapy. The annual number of patients with gBRCA PV was two patients per year before January 2021 (when BRACAnalysis became available in Japan), and ten patients during the 10 months thereafter. Four patients (20 %) with gBRCA PV developed soft-tissue metastasis with progression. Two patients with gATM PV + LPV received platinum-based chemotherapy and the best response of those patients was partial response and stable disease and their OS from the initiation of first-line chemotherapy was 1192 and 989 days, and PFS was 579 and 140 days, respectively. CONCLUSION The diagnosis of gBRCA PV-positive PC has increased revealed in recent years. These tumors appear to be sensitive to platinum-based chemotherapy, with long term survival observed in gATM PV + LPV-positive patients.
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Affiliation(s)
- Hidetoshi Kitamura
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan
| | - Chigusa Morizane
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan.
| | - Noriko Tanabe
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Japan
| | - Ikeda Go
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan
| | - Yuta Maruki
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan
| | - Akihiro Ohba
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan
| | - Yoshikuni Nagashio
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan
| | - Shunsuke Kondo
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan
| | - Susumu Hijioka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan
| | - Hideki Ueno
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan
| | - Teruhiko Yoshida
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Japan
| | - Takuji Okusaka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Japan
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Barbora A, Karri S, Firer MA, Minnes R. Multifractal analysis of cellular ATR-FTIR spectrum as a method for identifying and quantifying cancer cell metastatic levels. Sci Rep 2023; 13:18935. [PMID: 37919384 PMCID: PMC10622493 DOI: 10.1038/s41598-023-46014-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023] Open
Abstract
Cancer is a leading cause of mortality today. Sooner a cancer is detected, the more effective is the treatment. Histopathological diagnosis continues to be the gold standard worldwide for cancer diagnosis, but the methods used are invasive, time-consuming, insensitive, and still rely to some degree on the subjective judgment of pathologists. Recent research demonstrated that Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopy can be used to determine the metastatic potential of cancer cells by evaluating their membrane hydration. In the current study, we demonstrate that the conversion of ATR-FTIR spectra using multifractal transformation generates a unique number for each cell line's metastatic potential. Applying this technique to murine and human cancer cells revealed a correlation between the metastatic capacity of cancer cells within the same lineage and higher multifractal value. The multifractal spectrum value was found to be independent of the cell concentration used in the assay and unique to the tested lineage. Healthy cells exhibited a smaller multifractal spectrum value than cancer cells. Further, the technique demonstrated the ability to detect cancer progression by being sensitive to the proportional change between healthy and cancerous cells in the sample. This enables precise determination of cancer metastasis and disease progression independent of cell concentration by comparing the measured spectroscopy derived multifractal spectrum value. This quick and simple technique devoid of observer bias can transform cancer diagnosis to a great extent improving public health prognosis worldwide.
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Affiliation(s)
- Ayan Barbora
- Department of Physics, Ariel University, 40700, Ariel, Israel
| | - Sirish Karri
- Department of Chemical Engineering, Ariel University, 40700, Ariel, Israel
| | - Michael A Firer
- Department of Chemical Engineering, Ariel University, 40700, Ariel, Israel
- Adelson School of Medicine, Ariel University, 40700, Ariel, Israel
- Ariel Center for Applied Cancer Research, Ariel University, 40700, Ariel, Israel
| | - Refael Minnes
- Department of Physics, Ariel University, 40700, Ariel, Israel.
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28
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Weitering TJ, Willemsen MAAP, Taylor AMR, Weemaes CMR, van der Burg M, Berghuis D. Early Diagnosis of Ataxia Telangiectasia Through Newborn Screening for SCID: a Case Report Highlighting the Dilemma of Pre-emptive HSCT. J Clin Immunol 2023; 43:1770-1773. [PMID: 37624468 DOI: 10.1007/s10875-023-01571-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Affiliation(s)
- T J Weitering
- Willem-Alexander Children's Hospital, Laboratory for Pediatric Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - M A A P Willemsen
- Department of Neurology - Pediatric Neurology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - A M R Taylor
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - C M R Weemaes
- Department of Pediatrics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - M van der Burg
- Willem-Alexander Children's Hospital, Laboratory for Pediatric Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dagmar Berghuis
- Willem-Alexander Children's Hospital, Department of Pediatrics, Division of Pediatric Immunology and Stem Cell Transplantation, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands.
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29
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Zhang S, Vasudevan S, Tan SPH, Olivo M. Fiber optic probe-based ATR-FTIR spectroscopy for rapid breast cancer detection: A pilot study. J Biophotonics 2023; 16:e202300199. [PMID: 37496212 DOI: 10.1002/jbio.202300199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/11/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
Breast cancer diagnosis is crucial for timely treatment and improved outcomes. This paper proposes a novel approach for rapid breast cancer diagnosis using optical fiber probe-based attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy from 750 to 4000 cm-1 . The technique enables direct analysis of tissue samples, eliminating the need for microtome sectioning and staining, thus saving time and resources. By capturing molecular fingerprint information, various machine-learning models were used to analyze the spectroscopic data to classify cancerous and non-cancerous tissues accurately. Comparing deparaffinized and paraffinized samples reveals the impact of sample preparation and experimental methods. The study demonstrates a strong correlation between the cancerous nature of a sample and its ATR-FTIR spectrum, suggesting its potential for breast cancer diagnosis (sensitivity of 74.2% and specificity of 78.3%). The proposed approach holds promise for integration into clinical operations, providing a rapid method for preliminary breast cancer diagnosis.
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Affiliation(s)
- Shuyan Zhang
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Swetha Vasudevan
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | - Sonia Peng Hwee Tan
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | - Malini Olivo
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), Singapore
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30
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Liu XD, Zhang YT, McGrail DJ, Zhang X, Lam T, Hoang A, Hasanov E, Manyam G, Peterson CB, Zhu H, Kumar SV, Akbani R, Pilie PG, Tannir NM, Peng G, Jonasch E. SETD2 Loss and ATR Inhibition Synergize to Promote cGAS Signaling and Immunotherapy Response in Renal Cell Carcinoma. Clin Cancer Res 2023; 29:4002-4015. [PMID: 37527013 PMCID: PMC10592192 DOI: 10.1158/1078-0432.ccr-23-1003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/13/2023] [Accepted: 07/27/2023] [Indexed: 08/03/2023]
Abstract
PURPOSE Immune checkpoint blockade (ICB) demonstrates durable clinical benefits in a minority of patients with renal cell carcinoma (RCC). We aimed to identify the molecular features that determine the response and develop approaches to enhance it. EXPERIMENTAL DESIGN We investigated the effects of SET domain-containing protein 2 (SETD2) loss on the DNA damage response pathway, the cytosolic DNA-sensing pathway, the tumor immune microenvironment, and the response to ataxia telangiectasia and rad3-related (ATR) and checkpoint inhibition in RCC. RESULTS ATR inhibition activated the cyclic GMP-AMP synthase (cGAS)-interferon regulatory factor 3 (IRF3)-dependent cytosolic DNA-sensing pathway, resulting in the concurrent expression of inflammatory cytokines and immune checkpoints. Among the common RCC genotypes, SETD2 loss is associated with preferential ATR activation and sensitizes cells to ATR inhibition. SETD2 knockdown promoted the cytosolic DNA-sensing pathway in response to ATR inhibition. Treatment with the ATR inhibitor VE822 concurrently upregulated immune cell infiltration and immune checkpoint expression in Setd2 knockdown Renca tumors, providing a rationale for ATR inhibition plus ICB combination therapy. Setd2-deficient Renca tumors demonstrated greater vulnerability to ICB monotherapy or combination therapy with VE822 than Setd2-proficient tumors. Moreover, SETD2 mutations were associated with a higher response rate and prolonged overall survival in patients with ICB-treated RCC but not in patients with non-ICB-treated RCC. CONCLUSIONS SETD2 loss and ATR inhibition synergize to promote cGAS signaling and enhance immune cell infiltration, providing a mechanistic rationale for the combination of ATR and checkpoint inhibition in patients with RCC with SETD2 mutations.
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Affiliation(s)
- Xian-De Liu
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- These authors contributed equally
| | - Yan-Ting Zhang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- These authors contributed equally
| | - Daniel J. McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Xuesong Zhang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Truong Lam
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anh Hoang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elshad Hasanov
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ganiraju Manyam
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Haifeng Zhu
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shwetha V Kumar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick G. Pilie
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention at The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Lee J, Oubre B, Daneault JF, Lee SI, Gupta AS. Estimation of ataxia severity in children with ataxia-telangiectasia using ankle-worn sensors. J Neurol 2023; 270:5097-5101. [PMID: 37368132 PMCID: PMC10826283 DOI: 10.1007/s00415-023-11786-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Affiliation(s)
- Juhyeon Lee
- College of Information and Computer Sciences, University of Massachusetts Amherst, 140 Governors Dr, Amherst, MA, USA
| | - Brandon Oubre
- College of Information and Computer Sciences, University of Massachusetts Amherst, 140 Governors Dr, Amherst, MA, USA
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 100 Cambridge St, Boston, MA, USA
| | - Jean-Francois Daneault
- Department of Rehabilitation and Movement Sciences, Rutgers University, 65 Bergen St, Newark, NJ, USA
| | - Sunghoon Ivan Lee
- College of Information and Computer Sciences, University of Massachusetts Amherst, 140 Governors Dr, Amherst, MA, USA.
| | - Anoopum S Gupta
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 100 Cambridge St, Boston, MA, USA.
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32
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Geng Y, Long X, Zhang Y, Wang Y, You G, Guo W, Zhuang G, Zhang Y, Cheng X, Yuan Z, Zan J. FTO-targeted siRNA delivery by MSC-derived exosomes synergistically alleviates dopaminergic neuronal death in Parkinson's disease via m6A-dependent regulation of ATM mRNA. J Transl Med 2023; 21:652. [PMID: 37737187 PMCID: PMC10515429 DOI: 10.1186/s12967-023-04461-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD), characterized by the progressive loss of dopaminergic neurons in the substantia nigra and striatum of brain, seriously threatens human health, and is still lack of effective treatment. Dysregulation of N6-methyladenosine (m6A) modification has been implicated in PD pathogenesis. However, how m6A modification regulates dopaminergic neuronal death in PD remains elusive. Mesenchymal stem cell-derived exosomes (MSC-Exo) have been shown to be effective for treating central nervous disorders. We thus propose that the m6A demethylase FTO-targeted siRNAs (si-FTO) may be encapsulated in MSC-Exo (Exo-siFTO) as a synergistic therapy against dopaminergic neuronal death in PD. METHODS In this study, the effect of m6A demethylase FTO on dopaminergic neuronal death was evaluated both in vivo and in vitro using a MPTP-treated mice model and a MPP + -induced MN9D cellular model, respectively. The mechanism through which FTO influences dopaminergic neuronal death in PD was investigated with qRT-PCR, western blot, immumohistochemical staining, immunofluorescent staining and flow cytometry. The therapeutic roles of MSC-Exo containing si-FTO were examined in PD models in vivo and in vitro. RESULTS The total m6A level was significantly decreased and FTO expression was increased in PD models in vivo and in vitro. FTO was found to promote the expression of cellular death-related factor ataxia telangiectasia mutated (ATM) via m6A-dependent stabilization of ATM mRNA in dopaminergic neurons. Knockdown of FTO by si-FTO concomitantly suppressed upregulation of α-Synuclein (α-Syn) and downregulation of tyrosine hydroxylase (TH), and alleviated neuronal death in PD models. Moreover, MSC-Exo were utilized to successfully deliver si-FTO to the striatum of animal brain, resulting in the significant suppression of α-Syn expression and dopaminergic neuronal death, and recovery of TH expression in the brain of PD mice. CONCLUSIONS MSC-Exo delivery of si-FTO synergistically alleviates dopaminergic neuronal death in PD via m6A-dependent regulation of ATM mRNA.
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Affiliation(s)
- Yan Geng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Xinyi Long
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yuting Zhang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yupeng Wang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Guoxing You
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Wenjie Guo
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Gaoming Zhuang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, 511400, China
| | - Yuanyuan Zhang
- The affiliated TCM Hospital of Guangzhou Medical University, Guangzhou, 510130, China.
| | - Xiao Cheng
- State Key Laboratory of Dampness, Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China.
- Department of Neurology, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, 510120, China.
| | - Zhengqiang Yuan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Jie Zan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China.
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Leskovar T, Inkret J, Zupanič Pajnič I, Jerman I. Comparison of DNA preservation and ATR-FTIR spectroscopy indices of cortical and trabecular bone of metacarpals and metatarsals. Sci Rep 2023; 13:15498. [PMID: 37726341 PMCID: PMC10509243 DOI: 10.1038/s41598-023-41259-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Shape, size, composition, and function of the bones in the human body vary on the macro, micro and nanoscale. This can influence changes caused by taphonomy and post-mortem preservation, including DNA. Highly mineralised compact bone is less susceptible to taphonomic factors than porous trabecular bone. Some studies imply that DNA can be better preserved in trabecular bone, due to remnants of the soft tissue or bacteria better digesting organic matter while not digesting DNA. The aim of this study was to understand the differences between compact (diaphyses) and trabecular (epiphyses) bone on a molecular level and thus the reasons for the better preservation of the DNA in the trabecular bone. The powder obtained from epiphyses and diaphyses of metacarpals and metatarsals was analysed using ATR-FTIR spectroscopy and compared. Samples with poorest DNA preservation originated from diaphyses, predominantly of metatarsals. They were characterised by higher concentrations of phosphates and crystallinity, while lower collagen quality in comparison to samples with the best DNA preservation. Epiphyses presented higher concentrations of better-preserved collagen while diaphyses had higher concentrations of carbonates and phosphates and higher crystallinity. Due to better-preserved collagen in the epiphyses, the soft tissue remnants hypothesis seems more likely than the bacteria hypothesis.
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Affiliation(s)
- Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000, Ljubljana, Slovenia
| | - Jezerka Inkret
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Ivan Jerman
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
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Majewski M, Pérez A, Thölke P, Doerr S, Charron NE, Giorgino T, Husic BE, Clementi C, Noé F, De Fabritiis G. Machine learning coarse-grained potentials of protein thermodynamics. Nat Commun 2023; 14:5739. [PMID: 37714883 PMCID: PMC10504246 DOI: 10.1038/s41467-023-41343-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/29/2023] [Indexed: 09/17/2023] Open
Abstract
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics.
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Affiliation(s)
- Maciej Majewski
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
- Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain
| | - Adrià Pérez
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
- Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain
| | - Philipp Thölke
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Stefan Doerr
- Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain
| | - Nicholas E Charron
- Department of Physics, Rice University, Houston, TX, 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
- Department of Physics, FU Berlin, Arnimallee 12, 14195, Berlin, Germany
| | - Toni Giorgino
- Biophysics Institute, National Research Council (CNR-IBF), 20133, Milan, Italy
| | - Brooke E Husic
- Department of Mathematics and Computer Science, FU Berlin, Arnimallee 12, 14195, Berlin, Germany
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
- Princeton Center for Theoretical Science, Princeton University, Princeton, NJ, 08540, USA
- Center for the Physics of Biological Function, Princeton University, Princeton, NJ, 08540, USA
| | - Cecilia Clementi
- Department of Physics, Rice University, Houston, TX, 77005, USA.
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA.
- Department of Physics, FU Berlin, Arnimallee 12, 14195, Berlin, Germany.
- Department of Chemistry, Rice University, Houston, TX, 77005, USA.
| | - Frank Noé
- Department of Physics, FU Berlin, Arnimallee 12, 14195, Berlin, Germany.
- Department of Mathematics and Computer Science, FU Berlin, Arnimallee 12, 14195, Berlin, Germany.
- Department of Chemistry, Rice University, Houston, TX, 77005, USA.
- Microsoft Research AI4Science, Karl-Liebknecht Str. 32, 10178, Berlin, Germany.
| | - Gianni De Fabritiis
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain.
- Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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Jiang F, Huang X, Ling L, Tang S, Zhou H, Cai X, Wang Y. Long Noncoding RNA ZBED5-AS1 Facilitates Tumor Progression and Metastasis in Lung Adenocarcinoma via ZNF146/ATR/Chk1 Axis. Int J Mol Sci 2023; 24:13925. [PMID: 37762228 PMCID: PMC10530271 DOI: 10.3390/ijms241813925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in tumorigenesis, including lung adenocarcinoma (LUAD). However, the functional and regulatory mechanisms of lncRNAs in LUAD remain poorly understood. In this study, we investigated the role of lncRNA ZBED5-AS1 in LUAD. We found that ZBED5-AS1 was upregulated in LUAD specimens and overexpressed in LUAD cell lines. ZBED5-AS1 promoted LUAD cell proliferation, migration, and invasion in vitro and promoted LUAD cell growth in vivo. ZBED5-AS1 promoted ZNF146 expression, activating the ATR/Chk1 pathway and leading to LUAD progression. We observed that exosomes from LUAD cells have a higher expression of ZBED5-AS1 compared with exosomes from the normal cell line BEAS-2B. Coculture experiments with exosomes showed that ZBED5-AS1 expression was downregulated after coculture with Si-ZBED5-AS1 exosomes, and coculture with exosomes with low ZBED5-AS1 expression inhibited proliferation and invasion of LUAD cells. Our results indicate that ZBED5-AS1 functions as an oncogenic factor in LUAD cells by targeting the ZNF146/ATR/Chk1 axis.
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Affiliation(s)
- Feng Jiang
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China; (F.J.)
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325015, China
| | - Xiaolu Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China; (F.J.)
| | - Liqun Ling
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China; (F.J.)
| | - Shiyi Tang
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China; (F.J.)
| | - Huixin Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China; (F.J.)
| | - Xueding Cai
- Department of Respiration, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China
| | - Yumin Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China; (F.J.)
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325015, China
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Takata M, Harada H. Meeting report: AT workshop 2023-A platform for discussing cutting-edge science in DNA damage signaling, repair, and human disorders. Genes Cells 2023; 28:642-645. [PMID: 37341149 DOI: 10.1111/gtc.13054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/03/2023] [Indexed: 06/22/2023]
Abstract
Ataxia-telangiectasia (A-T) is a rare devastating hereditary condition, which affects multiple organ systems including cerebellar motor function as well as DNA repair, resulting in a higher incidence of cancer and immunodeficiency. The genetic defect in A-T lies in ATM kinase, which is activated by DNA damage and regulates a plethora of substrates including the p53 tumor suppressor. We have organized an international meeting "The 19th Ataxia-Telangiectasia Workshop 2023 (ATW2023)" with support from the Molecular Biology Society of Japan (MBSJ) and other funders. Here, we report that ATW2023 was successfully held in Kyoto from March 2nd to 5th, 2023 with more than 150 participants traveling from all over the world, despite the still smoldering COVID-19 pandemic. In this meeting report, we will briefly describe the highlights of the meeting and would like to express our gratitude to the MBSJ for the financial support.
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Affiliation(s)
- Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hiroshi Harada
- Laboratory of Cancer Cell Biology, Department of Genome Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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Hussain N, Alkhateeb MA, Bashir A, Iqbal R, Hussain T, Aziz T, Al-Abbas NS, Shaer NA, Alamri AS, Alhomrani M, Shakoori A, Labban S. Deletions of SMNI gene exon 7 and NAIP gene exon 5 in spinal muscular atrophy patients in selected population. Eur Rev Med Pharmacol Sci 2023; 27:7935-7945. [PMID: 37750622 DOI: 10.26355/eurrev_202309_33552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
OBJECTIVE Spinal muscular atrophy (SMA) is common among various populations because the genetic makeup is monogamous due to consanguineous marriages. Two genes, i.e., survival motor neuron (SMN1) and neuronal apoptosis inhibitory protein (NAIP) are mapped to the SMA vicinity of chromosome 5q13. The main objective of the study was to develop a solitary advanced genetic tool for the diagnosis of SMA by using SMN1 gene exon 7 and NAIP gene exon 5. PATIENTS AND METHODS This study involved SMA patients (n=84) belonging to different clinical features and socio-economic status. The identity of the intact NAIP gene is primarily based on the amplification of exon 5 only in those SMA patients that have a deletion of SMN1 gene exon 7. Healthy controls (n=84) were also included in this study. The mutational analysis was observed through the Sanger sequencing method, where chromatograms were observed by using Chromas version 2.6.0. RESULTS This study showed a higher prevalence of SMA in females than in males. NAIP gene is considered a phenotype modifier as most SMA patients (94.90%) have SMN1 exon 7 deletion along with a deletion in exon 5 of the NAIP gene. Single nucleotide conversion C-T in exon 7 of SMN1 gene leads to its complete deletion. Mutated proteins encoded by SMN1 and NAIP genes also result in degeneration and muscle weakness in SMA patients. CONCLUSIONS These SMA-associated gene deletions can be used as a molecular evaluation tool for pre- and postnatal diagnosis of SMA. This will be valuable when there is a need for precise and consistent results with a strong focus on quantification.
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Affiliation(s)
- N Hussain
- Institute of Microbiology and Molecular Genetics, New Campus, University of the Punjab, Lahore, Pakistan.
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Al-Choboq J, Mathis T, Restier-Verlet J, Sonzogni L, El Nachef L, Granzotto A, Bourguignon M, Foray N. The Radiobiological Characterization of Human and Porcine Lens Cells Suggests the Importance of the ATM Kinase in Radiation-Induced Cataractogenesis. Cells 2023; 12:2118. [PMID: 37626928 PMCID: PMC10453874 DOI: 10.3390/cells12162118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Studies about radiation-induced human cataractogenesis are generally limited by (1) the poor number of epithelial lens cell lines available (likely because of the difficulties of cell sampling and amplification) and (2) the lack of reliable biomarkers of the radiation-induced aging process. We have developed a mechanistic model of the individual response to radiation based on the nucleoshuttling of the ATM protein (RIANS). Recently, in the frame of the RIANS model, we have shown that, to respond to permanent endo- and exogenous stress, the ATM protein progressively agglutinates around the nucleus attracted by overexpressed perinuclear ATM-substrate protein. As a result, perinuclear ATM crowns appear to be an interesting biomarker of aging. The radiobiological characterization of the two human epithelial lens cell lines available and the four porcine epithelial lens cell lines that we have established showed delayed RIANS. The BFSP2 protein, found specifically overexpressed around the lens cell nucleus and interacting with ATM, may be a specific ATM-substrate protein facilitating the formation of perinuclear ATM crowns in lens cells. The perinuclear ATM crowns were observed inasmuch as the number of culture passages is high. Interestingly, 2 Gy X-rays lead to the transient disappearance of the perinuclear ATM crowns. Altogether, our findings suggest a strong influence of the ATM protein in radiation-induced cataractogenesis.
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Affiliation(s)
- Joëlle Al-Choboq
- INSERM U1296 Unit “Radiation: Defense, Health, Environment”, 28 Rue Laennec, 69008 Lyon, France; (J.A.-C.); (J.R.-V.); (L.S.); (L.E.N.); (A.G.); (M.B.)
| | - Thibaud Mathis
- Ophtalmology Department, Hospices Civils de Lyon, General University Hospital of Croix-Rousse, 103 Grande Rue Croix Rousse, 69004 Lyon, France;
- MATEIS Laboratory, CNRS UMR5510, INSA, Université Claude-Bernard Lyon 1, Campus de la Doua, 69100 Villeurbanne, France
| | - Juliette Restier-Verlet
- INSERM U1296 Unit “Radiation: Defense, Health, Environment”, 28 Rue Laennec, 69008 Lyon, France; (J.A.-C.); (J.R.-V.); (L.S.); (L.E.N.); (A.G.); (M.B.)
| | - Laurène Sonzogni
- INSERM U1296 Unit “Radiation: Defense, Health, Environment”, 28 Rue Laennec, 69008 Lyon, France; (J.A.-C.); (J.R.-V.); (L.S.); (L.E.N.); (A.G.); (M.B.)
| | - Laura El Nachef
- INSERM U1296 Unit “Radiation: Defense, Health, Environment”, 28 Rue Laennec, 69008 Lyon, France; (J.A.-C.); (J.R.-V.); (L.S.); (L.E.N.); (A.G.); (M.B.)
| | - Adeline Granzotto
- INSERM U1296 Unit “Radiation: Defense, Health, Environment”, 28 Rue Laennec, 69008 Lyon, France; (J.A.-C.); (J.R.-V.); (L.S.); (L.E.N.); (A.G.); (M.B.)
| | - Michel Bourguignon
- INSERM U1296 Unit “Radiation: Defense, Health, Environment”, 28 Rue Laennec, 69008 Lyon, France; (J.A.-C.); (J.R.-V.); (L.S.); (L.E.N.); (A.G.); (M.B.)
- Department of Biophysics and Nuclear Medicine, Université Paris Saclay Versailles St Quentin-en-Yvelines, 78035 Versailles, France
| | - Nicolas Foray
- INSERM U1296 Unit “Radiation: Defense, Health, Environment”, 28 Rue Laennec, 69008 Lyon, France; (J.A.-C.); (J.R.-V.); (L.S.); (L.E.N.); (A.G.); (M.B.)
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Zhang H, Chen Q, Zhang Q, Gan H, Li H, Chen S, Shan H, Pang P, He H. DDX24 Mutation Alters NPM1 Phase Behavior and Disrupts Nucleolar Homeostasis in Vascular Malformations. Int J Biol Sci 2023; 19:4123-4138. [PMID: 37705750 PMCID: PMC10496494 DOI: 10.7150/ijbs.84097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/25/2023] [Indexed: 09/15/2023] Open
Abstract
Point mutations in the DEAD-box helicase DDX24 are associated with vascular malformations such as multi-organ venous and lymphatic defect (MOVLD) syndrome and Budd-Chiari syndrome, with the pathogenesis largely uncharacterized. DDX24 is mainly located in the nucleolus, where nucleophosmin (NPM1) regulates nucleolar homeostasis via liquid-liquid phase separation (LLPS). However, the connection between DDX24 and NPM1 in vascular malformation remains elusive. Here we demonstrated that DDX24 formed biomolecular condensates in vitro and the mutated DDX24 protein, DDX24E271K, partitioned less into the nucleoli in tissues from patients with MOVLD syndrome and cultured endothelial cells (ECs), altering nucleolar morphology. Furthermore, DDX24 was directly associated with NPM1 to regulate its phase behavior as a client in the nucleolar granular component (GC). Functionally, we showed that DDX24 was essential in maintaining nucleolar homeostasis of ECs and that either mutation or knockdown of DDX24 led to the dysfunction of ribosome biogenesis and the elevated capability of cell migration and tube formation. Our findings illustrate how DDX24 mutation affects nucleolar structure and function by regulating the phase behavior of NPM1 in the setting of vascular malformation.
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Affiliation(s)
- Haopei Zhang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Department of Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
| | - Qiuyue Chen
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Department of Radiology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong Province, China 519000
| | - Qianqian Zhang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
| | - Hairun Gan
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Department of Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
| | - Hanjie Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Department of Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
| | - Shoudeng Chen
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
| | - Hong Shan
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Department of Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
| | - Pengfei Pang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Department of Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
| | - Huanhuan He
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China 519000
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Gleich J, Neuerburg C, Schoeneberg C, Knobe M, Böcker W, Rascher K, Fleischhacker E. Time to surgery after proximal femur fracture in geriatric patients depends on hospital size and provided level of care: analysis of the Registry for Geriatric Trauma (ATR-DGU). Eur J Trauma Emerg Surg 2023; 49:1827-1833. [PMID: 36929034 PMCID: PMC10449710 DOI: 10.1007/s00068-023-02246-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/08/2023] [Indexed: 03/18/2023]
Abstract
PURPOSE Proximal femur fractures predominantly affect older patients and can mark a drastic turning point in their lives. To avoid complications and reduce mortality, expert associations recommend surgical treatment within 24-48 h after admission. Due to the high incidence, treatment is provided at a wide range of hospitals with different size and level of care, which may affect time to surgery. METHODS Data from 19,712 patients included from 2016 to 2019 in the Registry for Geriatric Trauma (ATR-DGU) were analyzed in terms of time to surgery, in-house mortality, mobilization on the first postoperative day, ambulation status on the 7th day after surgery, and initiation of osteoporosis therapy. Participating hospitals were grouped according to their classification as level I, II or III trauma centers. Also presence of additional injuries, intake and type of anticoagulants were considered. Linear and logistic regression analysis was performed to evaluate the influence of hospitals level of care on each item. RESULTS 28.6% of patients were treated in level I, 37.7% in level II, and 33.7% in level III trauma centers. There was no significant difference in age, sex and ASA-score. Mean time to surgery was 19.2 h (IQR 9.0-29.8) in level I trauma centers and 16.8 h (IQR 6.5-24) in level II/III trauma centers (p < 0.001). Surgery in the first 24 h after admission was provided for 64.7% of level I and 75.0% of level II/III patients (p < 0.001). Treatment in hospitals with higher level of care and subsequent increased time to surgery showed no significant influence on in-house mortality (OR 0.90, 95%-CI 0.78-1.04), but negative effects on walking ability 7 days after surgery could be observed (OR 1.28, 95%-CI 1.18-1.38). CONCLUSION In hospitals of larger size and higher level of care the time to surgery for patients with a proximal femur fracture was significantly higher than in smaller hospitals. No negative effects regarding in-house mortality, but for ambulation status during in-hospital stay could be observed. As the number of these patients will constantly increase, specific treatment capacities should be established regardless of the hospitals size.
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Affiliation(s)
- Johannes Gleich
- Department of Orthopaedics and Trauma Surgery, Musculoskeletal University Center Munich (MUM), University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Carl Neuerburg
- Department of Orthopaedics and Trauma Surgery, Musculoskeletal University Center Munich (MUM), University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
| | - Carsten Schoeneberg
- Department of Orthopedic and Emergency Surgery, Alfried Krupp Klinikum, Essen, Germany
| | - Matthias Knobe
- Westmünsterland Hospital, Ahaus, Germany
- Medical Faculty, RWTH University Hospital Aachen, Aachen, Germany
- Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Wolfgang Böcker
- Department of Orthopaedics and Trauma Surgery, Musculoskeletal University Center Munich (MUM), University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | | | - Evi Fleischhacker
- Department of Orthopaedics and Trauma Surgery, Musculoskeletal University Center Munich (MUM), University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
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Fischer A, Fitzgerald M, Curtis K, Balogh ZJ. The Australian Trauma Registry (ATR): a leading clinical quality registry. Eur J Trauma Emerg Surg 2023; 49:1639-1645. [PMID: 37347297 PMCID: PMC10449940 DOI: 10.1007/s00068-023-02288-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023]
Abstract
Operating since 2012 under the auspices of the Australian Trauma Quality Improvement Program (AusTQIP), the Australian Trauma Registry (ATR) has established itself as a leading clinical quality registry (CQR). Initially developed as a national program for improved safety and quality trauma care across Australian trauma centers, it has since expanded to include New Zealand, becoming one of the few bi-national trauma registries. The registry has recorded close to 100,000 episodes of care for severely injured patients since its inception, with 10.7% growth in annual inclusions. The ATR, administered by the National Trauma Research Institute (NTRI), monitors the continuum of trauma care from pre-hospital settings, to discharge from definitive care. Collection and analysis of data about severely injured trauma patients, their injuries, management and outcomes, aims to inform future improvements to health service provision and reduce preventable morbidity and mortality.
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Affiliation(s)
- Angela Fischer
- Department of Traumatology, John Hunter Hospital, Newcastle, NSW, Australia
- Injury and Trauma Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia
- Discipline of Surgery, School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia
| | - Mark Fitzgerald
- Department of Surgery, Central Clinical School, Trauma Services, The Alfred, National Trauma Research Institute, Monash University, Melbourne, VIC, Australia
| | - Kate Curtis
- Susan Wakil School of Nursing and Midwifery, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Illawarra Shoalhaven Local Health District, Shoalhaven, NSW, Australia
| | - Zsolt J Balogh
- Department of Traumatology, John Hunter Hospital, Newcastle, NSW, Australia.
- Injury and Trauma Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia.
- Discipline of Surgery, School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia.
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Duan Y, Zhuang L, Xu Y, Cheng H, Xia J, Lu T, Chen Y. Design, synthesis, and biological evaluation of pyrido[3,2-d]pyrimidine derivatives as novel ATR inhibitors. Bioorg Chem 2023; 136:106535. [PMID: 37086581 DOI: 10.1016/j.bioorg.2023.106535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/24/2023]
Abstract
Targeting ataxia telangiectasia mutated and Rad3-related (ATR) kinase is being pursued as a new therapeutic strategy for the treatment of advanced solid tumor with specific DNA damage response deficiency. Herein, we report a series of pyrido[3,2-d]pyrimidine derivatives with potent ATR inhibitory activity through structure-based drug design. Among them, the representative compound 10q exhibited excellent potency against ATR in both biochemical and cellular assays. More importantly, 10q exhibited good liver microsomes stability in different species and also showed moderate inhibitory activity against HT-29 cells in combination treatment with the ATM inhibitor AZD1390. Thus, this work provides a promising lead compound against ATR for further study.
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Affiliation(s)
- Yunxin Duan
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Lili Zhuang
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yerong Xu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Haodong Cheng
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Jiawei Xia
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
| | - Yadong Chen
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China.
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Liang X, Wang G, Li Z, Chen R, Wu H, Li H, Shen C, Deng M, Hao Z, Wu S, Yu K, Wei X, Liu R, Zhang K, Sun Q, Wang Z. Accurate identification of traumatic lung injury (TLI) by ATR-FTIR spectroscopy combined with chemometrics. Spectrochim Acta A Mol Biomol Spectrosc 2023; 288:122186. [PMID: 36481535 DOI: 10.1016/j.saa.2022.122186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Traumatic lung injury (TLI), which is a common mechanical injury, is receiving increasing attention because of its serious hazards. In forensic practices, accurately identifying TLI is of great importance for investigations and case trials. The main goal of this research was to identify TLI utilizing attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy in combination with chemometrics. The macroscopic appearance of lung tissue showed that identifying TLI in lung tissue at the decomposition stage is not feasible by only visualization, and significant pulmonary hypostasis was observed in the lungs regardless of whether the lung tissue was injured. Average spectra and principal component analysis (PCA) suggested that the biochemical difference between injured lung tissue samples from the TLI group and noninjured lung tissue samples from the negative control group was mainly attributed to the different structures and contents of proteins. Partial least squares discriminant analysis (PLS-DA) was then utilized to identify TLI with an accuracy of 96.4% and 98.6% based on the training set and the test set, respectively. Next, we focused on samples that were misclassified in the model and proposed that the misclassification could be caused by the pulmonary hypostasis effect. Therefore, two additional PCA and PLS-DA models were created to identify the pulmonary hypostatic areas between the TLI group and the negative control group and the nonpulmonary hypostatic areas between the TLI group and the negative control group. The PCA results indicated that the biochemical difference between the two groups was still associated with proteins, and the two PLS-DA models achieved 100% accuracy based on both the training and test sets. This result indicated that when pulmonary hypostasis was considered and the lung tissue was divided into pulmonary hypostatic areas and nonpulmonary hypostatic areas for separate comparisons, TLI identification was achieved with a greater accuracy than that obtained when the two areas were combined. This research confirms that the combined application of ATR-FTIR spectroscopy and chemometrics can be utilized to accurately identify TLI.
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Affiliation(s)
- Xinggong Liang
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Gongji Wang
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Zefeng Li
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Run Chen
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Hao Wu
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Huiyu Li
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Chen Shen
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Mingyan Deng
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Zeyi Hao
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Shuo Wu
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Kai Yu
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Xin Wei
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Ruina Liu
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Kai Zhang
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Qinru Sun
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
| | - Zhenyuan Wang
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
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Mateus Pereira de Souza N, Hunter Machado B, Koche A, Beatriz Fernandes da Silva Furtado L, Becker D, Antonio Corbellini V, Rieger A. Detection of metabolic syndrome with ATR-FTIR spectroscopy and chemometrics in blood plasma. Spectrochim Acta A Mol Biomol Spectrosc 2023; 288:122135. [PMID: 36442341 DOI: 10.1016/j.saa.2022.122135] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/02/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Metabolic Syndrome (MetS) is a constellation of 3 or more risk factor (abdominal obesity, high triglycerides, low HDL-c, high blood pressure, and elevated blood glucose) for atherosclerotic cardiovascular disease. Considering these systemic metabolic changes in the biochemical pathways of all biomolecules, Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopy is a rapid, low-cost, and reagent-free alternative technique capable of identifying spectral biomarkers that differentiate subjects with MetS from control. In this study, plasma samples from 74 subjects (14 MetS, 60 control) were analyzed on the ATR-FTIR spectrophotometer. The objective was to differentiate subjects with MetS from control with supervised chemometrics modeling (Orthogonal Partial Least Squares-Discriminant Analysis, OPLS-DA). Additionally, the inflammatory status of subjects with MetS and control (supervised by C-reactive protein - CRP, leptin, and cell-free DNA - cfDNA) was verified. The OPLS-DA model achieved 100% sensitivity and specificity in cross-validation. For 1 latent variable (93.4% of variance), RMSECV < 0.002, PRESS CV < 0.0001, and R2 > 0.9999 was obtained. Significant spectrochemical differences (p < 0.05) were found between MetS and control subjects in the following biomolecular regions (cm-1): 1717-1703 [ν(CO) and δ(NH)], 1166-1137 [ν(C-OH) + ν(CO) and ν(CC) + δ(OH) + ν(CO)], 1113-1040 [ν(PO2-) and ν(C-OH)], and 1027-1008 [ν(CO) and v(CH2OH)]. In the OPLS-DA model loadings, amide I [1720-1600 cm-1, ν(CO)] and amide II [1570-1480 cm-1, δ(NH) + ν(CH)] had significantly greater weight than all other regions. There was a significant difference in inflammatory status between MetS patient and control (p < 0.05 for CRP and leptin, and p < 0.01 for cfDNA).
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Affiliation(s)
| | - Brenda Hunter Machado
- International Affairs, International University Centre, Santa Cruz do Sul, RS, Brazil.
| | - Andreia Koche
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil.
| | | | - Débora Becker
- Bachelor of Biological Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Valeriano Antonio Corbellini
- Department of Sciences, Humanities and, Education, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, RS, Brazil.
| | - Alexandre Rieger
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, RS, Brazil.
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Li X, Chung CI, Yang J, Chaudhuri S, Munster PN, Shu X. ATM-SPARK: A GFP phase separation-based activity reporter of ATM. Sci Adv 2023; 9:eade3760. [PMID: 36857446 PMCID: PMC9977181 DOI: 10.1126/sciadv.ade3760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
The kinase ataxia telangiectasia mutated (ATM) plays a key role in the DNA damage response (DDR). It is thus essential to visualize spatiotemporal dynamics of ATM activity during DDR. Here, we designed a robust ATM activity reporter based on phosphorylation-inducible green fluorescent protein phase separation, dubbed ATM-SPARK (separation of phases-based activity reporter of kinase). Upon ATM activation, it undergoes phase separation via multivalent interactions, forming intensely bright droplets. The reporter visualizes spatiotemporal dynamics of endogenous ATM activity in living cells, and its signal is proportional to the amount of DNA damage. ATM-SPARK also enables high-throughput screening of biological and small-molecule regulators. We identified the protein phosphatase 4 that blocks ATM activity. We also identified BGT226 as a potent ATM inhibitor with a median inhibitory concentration of ~3.8 nanomolars. Furthermore, BGT226 sensitizes cancer cells to the radiomimetic drug neocarzinostatin, suggesting that BGT226 might be combined with radiotherapeutic treatment. ATM-SPARK achieves large dynamic range, bright fluorescence, and simple signal pattern.
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Affiliation(s)
- Xiaoquan Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Chan-I Chung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - JunJiao Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sibapriya Chaudhuri
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Pamela N. Munster
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
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Cloete KJ, Šmit Ž, Gianoncelli A. Multidimensional Profiling of Human Body Hairs Using Qualitative and Semi-Quantitative Approaches with SR-XRF, ATR-FTIR, DSC, and SEM-EDX. Int J Mol Sci 2023; 24:ijms24044166. [PMID: 36835578 PMCID: PMC9964782 DOI: 10.3390/ijms24044166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
This study aimed to assess the potential of a multidimensional approach to differentiate body hairs based on their physico-chemical properties and whether body hairs can replace the use of scalp hair in studies linked to forensic and systemic intoxication. This is the first case report controlling for confounding variables to explore the utility of multidimensional profiling of body hair using synchrotron synchrotron microbeam X-ray fluorescence (SR-XRF) for longitudinal and hair morphological region mapping) and benchtop methods, including attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) (complemented with chemometrics analysis), energy dispersive X-ray analysis (EDX) (complemented with heatmap analysis), differential scanning calorimetry (DSC), and scanning electron microscopy (SEM) analysis (complemented by descriptive statistics) to profile different body hairs in terms of their elemental, biochemical, thermal, and cuticle properties. This multidimensional approach provided supportive information to emphasize the intricate and rather complex interplay between the organization and levels of elements and biomolecules within the crystalline and amorphous matrix of different body hairs responsible for the differences in physico-chemical properties between body hairs that are predominantly affected by the growth rate, follicle or apocrine gland activity, and external factors such as cosmetic use and exposure to environmental xenobiotics. The data from this study may have important implications for forensic science, toxicology and systemic intoxication, or other studies involving hair as a research matrix.
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Affiliation(s)
- Karen J. Cloete
- UNESCO-UNISA Africa Chair in Nanosciences and Nanotechnology Laboratories, College of Graduate Studies, University of South Africa, Muckleneuk Ridge, P.O. Box 392, Pretoria 0003, South Africa
- Nanosciences African Network (NANOAFNET), iThemba LABS-National Research Foundation, P.O. Box 722, Somerset West 7129, South Africa
- Correspondence: or ; Tel.: +27-21-82-587-6720
| | - Žiga Šmit
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000 Ljubljana, Slovenia
- Jožef Stefan Institute, Jamova 39, SI-1001 Ljubljana, Slovenia
| | - Alessandra Gianoncelli
- Elettra Sincrotrone Trieste, Strada Statale 14, km 163.5 in Area Science Park, 34149 Basovizza, TS, Italy
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de Souza NMP, Machado BH, Koche A, da Silva Furtado LBF, Becker D, Corbellini VA, Rieger A. Discrimination of dyslipidemia types with ATR-FTIR spectroscopy and chemometrics associated with multivariate analysis of the lipid profile, anthropometric, and pro-inflammatory biomarkers. Clin Chim Acta 2023; 540:117231. [PMID: 36682440 DOI: 10.1016/j.cca.2023.117231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/20/2022] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
BACKGROUND Obesity, dyslipidemia, and low-grade inflammatory state form a triad of self-sustaining metabolic dysfunction. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy is a simple, rapid, and non-destructive technique that generates spectral fingerprints of biomolecules that can be correlated with metabolic changes. We verified the efficiency of ATR-FTIR spectroscopy in blood plasma (n = 74) to discriminate the types of dyslipidemias and suggest metabolic inflammatory changes. METHODS Principal Component Analysis (PCA) was performed on the biochemical and anthropometric data to verify whether the dyslipidemia types share a similar biochemical profile plausible of discrimination in chemometric modeling. To discriminate the types of dyslipidemias based on spectral data, Orthogonal Partial Least-Squares Discriminant Analysis (OPLS-DA) was used and validated with leave-one-out cross-validation. RESULTS Although no significant difference was obtained between the types of dyslipidemia and normal subjects by CRP, leptin, and cfDNA, there was a significant difference between normal subjects vs combined hyperlipidemia (CH) + hypercholesterolemia (HCL) + hypertriglyceridemia (HTG) (p < 0.05) by the 1245 cm-1 peak [νas(PO2-)] (possible indication of chronic inflammation by increased cfDNA). The area under the curve of the region between 1770 and 1720 cm-1 was significantly increased for CH in relation to other dyslipidemias and normal subjects. Furthermore, there were significant differences for the main representative peaks of lipids, proteins, carbohydrates, and nucleic acids between the types of dyslipidemias and between the types of dyslipidemias and normal subjects. The OPLS-DA model achieved 100 % accuracy with 1 latent variable and Standard Error of Cross-Validation (SECV) < 0.004 for all types of dyslipidemia and the control group. CONCLUSIONS Our results suggest that ATR-FTIR spectroscopy associated with chemometric modeling is a plausible applicant for screening the types of dyslipidemias. However, more extensive studies should be conducted to verify the real applicability in clinical analysis laboratories or medical clinics.
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Affiliation(s)
| | - Brenda Hunter Machado
- International Affairs, International University Centre, Santa Cruz do Sul, RS, Brazil
| | - Andreia Koche
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | | | - Débora Becker
- Bachelor of Biological Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Valeriano Antonio Corbellini
- Department of Sciences, Humanities and, Education, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, RS, Brazil
| | - Alexandre Rieger
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, RS, Brazil
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Lohberger B, Glänzer D, Eck N, Stasny K, Falkner A, Leithner A, Georg D. The ATR Inhibitor VE-821 Enhances the Radiosensitivity and Suppresses DNA Repair Mechanisms of Human Chondrosarcoma Cells. Int J Mol Sci 2023; 24:2315. [PMID: 36768638 PMCID: PMC9917087 DOI: 10.3390/ijms24032315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
To overcome the resistance to radiotherapy in chondrosarcomas, the prevention of efficient DNA repair with an additional treatment was explored for particle beams as well as reference X-ray irradiation. The combined treatment with DNA repair inhibitors-with a focus on ATRi VE-821-and proton or carbon ions irradiation was investigated regarding cell viability, proliferation, cell cycle distribution, MAPK phosphorylation, and the expression of key DNA repair genes in two human chondrosarcoma cell lines. Pre-treatment with the PARPis Olaparib or Veliparib, the ATMi Ku-55933, and the ATRi VE-821 resulted in a dose-dependent reduction in viability, whereas VE-821 has the most efficient response. Quantification of γH2AX phosphorylation and protein expression of the DNA repair pathways showed a reduced regenerative capacity after irradiation. Furthermore, combined treatment with VE-821 and particle irradiation increased MAPK phosphorylation and the expression of apoptosis markers. At the gene expression and at the protein expression/phosphorylation level, we were able to demonstrate the preservation of DNA damage after combined treatment. The present data showed that the combined treatment with ATMi VE-821 increases the radiosensitivity of human chondrosarcoma cells in vitro and significantly suppresses efficient DNA repair mechanisms, thus improving the efficiency of radiotherapy.
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Affiliation(s)
- Birgit Lohberger
- Department of Orthopedics and Trauma, Medical University of Graz, 8036 Graz, Austria
| | - Dietmar Glänzer
- Department of Orthopedics and Trauma, Medical University of Graz, 8036 Graz, Austria
| | - Nicole Eck
- Department of Orthopedics and Trauma, Medical University of Graz, 8036 Graz, Austria
| | | | - Anna Falkner
- MedAustron Ion Therapy Center, 2700 Wiener Neustadt, Austria
| | - Andreas Leithner
- Department of Orthopedics and Trauma, Medical University of Graz, 8036 Graz, Austria
| | - Dietmar Georg
- MedAustron Ion Therapy Center, 2700 Wiener Neustadt, Austria
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
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Hsu J, Eid AM, Randall C, Houache MSE, Abu-Lebdeh Y, Al-Abadleh HA. Mechanistic In Situ ATR-FTIR Studies on the Adsorption and Desorption of Major Intermediates in CO 2 Electrochemical Reduction on CuO Nanoparticles. Langmuir 2022; 38:14789-14798. [PMID: 36417502 DOI: 10.1021/acs.langmuir.2c02445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Increasing levels of carbon dioxide (CO2) from human activities is affecting the ecosystem and civilization as we know it. CO2 removal from the atmosphere and emission reduction by heavy industries through carbon capture, utilization, and storage (CCUS) technologies to store or convert CO2 to useful products or fuels is a popular approach to meet net zero targets by 2050. One promising process of CO2 removal and conversion is CO2 electrochemical reduction (CO2ER) using metal and metal oxide catalysts, particularly copper-based materials. However, the current limitations of CO2ER stem from the low product selectivity of copper electrocatalysts due to existing knowledge gaps of the reaction mechanisms using surfaces that normally have native oxide layers. Here, we report systematic control studies of the surface interactions of major intermediates in CO2ER, formate, bicarbonate, and acetate, with CuO nanoparticles in situ and in real time using attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR). Spectra were collected as a function of concentration, pH, and time in the dark and the in absence of added electrolytes. Isotopic exchange experiments were also performed to elucidate the type of surface complexes from H/D exchange. Our results show that the organics and bicarbonate form mostly outer-sphere complexes mediated by hydrogen bonding with CuO nanoparticles with Gibbs free energy of adsorption of about -25 kJ mol-1. The desorption kinetics of the surface species indicated relatively fast and slow regions reflective of the heterogeneity of sites that affect the strength of hydrogen bonding. These results suggest that hydrogen bonding, whether intermolecular or with surface sites on CuO nanoparticles, might be playing a more important role in the CO2ER reaction mechanism than previously thought, contributing to the lack of product selectivity.
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Affiliation(s)
- Jason Hsu
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ONN2L 3C5, Canada
| | - Ahmed M Eid
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ONN2L 3C5, Canada
| | - Connor Randall
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ONN2L 3C5, Canada
| | - Mohamed S E Houache
- National Research Council of Canada, Energy, Mining and EnvironmentOttawa, ONK1A 0R6, Canada
| | - Yaser Abu-Lebdeh
- National Research Council of Canada, Energy, Mining and EnvironmentOttawa, ONK1A 0R6, Canada
| | - Hind A Al-Abadleh
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ONN2L 3C5, Canada
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50
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Ahmed S, Alam W, Aschner M, Alsharif KF, Albrakati A, Saso L, Khan H. Natural products targeting the ATR-CHK1 signaling pathway in cancer therapy. Biomed Pharmacother 2022; 155:113797. [PMID: 36271573 PMCID: PMC9590097 DOI: 10.1016/j.biopha.2022.113797] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/19/2022] Open
Abstract
Cancer is one of the most severe medical conditions in the world, causing millions of deaths each year. Chemotherapy and radiotherapy are critical for treatment approaches, but both have numerous adverse health effects. Furthermore, the resistance of cancerous cells to anticancer medication leads to treatment failure. The rising burden of cancer requires novel efficacious treatment modalities. Natural remedies offer feasible alternative options against malignancy in contrast to available synthetic medication. Selective killing of cancer cells is privileged mainstream in cancer treatment, and targeted therapy represents the new tool with the potential to pursue this aim. The discovery of innovative therapies targeting essential components of DNA damage signaling and repair pathways such as ataxia telangiectasia mutated and Rad3 related Checkpoint kinase 1 (ATR-CHK1)has offered a possibility of significant therapeutic improvement in oncology. The activation and inhibition of this pathway account for chemopreventive and chemotherapeutic activity, respectively. Targeting this pathway can also aid to overcome the resistance of conventional chemo- or radiotherapy. This review enlightens the anticancer role of natural products by ATR-CHK1 activation and inhibition. Additionally, these compounds have been shown to have chemotherapeutic synergistic potential when used in combination with other anticancer drugs. Ideally, this review will trigger interest in natural products targeting ATR-CHK1 and their potential efficacy and safety as cancer lessening agents.
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Affiliation(s)
- Salman Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Waqas Alam
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Forchheimer 209, 1300 Morris Park Avenue Bronx, NY 10461, USA
| | - Khalaf F Alsharif
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer"Sapienza University, Rome 00185, Italy
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan.
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