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Lv X, Li Y, Cai B, He W, Wang R, Chen M, Pan J, Hou D. Utility of Machine Learning and Radiomics Based on Cavity for Predicting the Therapeutic Response of MDR-TB. Infect Drug Resist 2023; 16:6893-6904. [PMID: 37920476 PMCID: PMC10619461 DOI: 10.2147/idr.s435984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Background Sputum culture result at the sixth month is essential for predicting therapeutic response to longer multidrug-resistant tuberculosis (MDR-TB) regimens. This study aimed to construct a predictive model using cavity-based radiomics to predict sputum status at the sixth month for MDR-TB patients treated with longer regimens. Methods This retrospective study recruited 315 MDR-TB patients treated with longer regimens from two centers (250 patients from center 1 and 65 patients from center 2), who were divided into persistently positive and conversion to negative sputum culture groups according to sputum results. Radiomics features were extracted based on the cavity, and a radiomics model was selected and established using a random forest classifier. The clinical characteristics and primary CT signs with significant differences were integrated to build a clinical model. A combined model was generated using the radiomics and clinical model. ROC curves, F1-score and DCA curves were used to assess the predictive performance of the models. Results Twenty-eight radiomics features were selected to build a radiomics model for predicting the sputum status. The radiomics model achieved good performance, with AUCs of 0.892 and 0.839 in the training and testing cohort, respectively, which was similar to the performance of the combined model (0.913 and 0.815) and much higher than that of the clinical model (0.688 and 0.525) in the two cohorts. Conclusion The cavity-based radiomics model has the potential to predict sputum culture status for MDR-TB patients receiving longer regimens, which could guide follow-up treatment effectively.
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Affiliation(s)
- Xinna Lv
- Department of Radiology, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Ye Li
- Department of Radiology, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Botao Cai
- Department of Radiology, Harbin Chest Hospital, Harbin, 150000, People’s Republic of China
| | - Wei He
- Department of Radiology, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Ren Wang
- Department of Radiology, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Minghui Chen
- Department of Radiology, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Junhua Pan
- Department of Radiology, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Dailun Hou
- Department of Radiology, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
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Rossini NDO, Dias MVB. Mutations and insights into the molecular mechanisms of resistance of Mycobacterium tuberculosis to first-line. Genet Mol Biol 2023; 46:e20220261. [PMID: 36718771 PMCID: PMC9887390 DOI: 10.1590/1678-4685-gmb-2022-0261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/18/2022] [Indexed: 01/28/2023] Open
Abstract
Genetically antimicrobial resistance in Mycobacterium tuberculosis is currently one of the most important aspects of tuberculosis, considering that there are emerging resistant strains for almost every known drug used for its treatment. There are multiple antimicrobials used for tuberculosis treatment, and the most effective ones are the first-line drugs, which include isoniazid, pyrazinamide, rifampicin, and ethambutol. In this context, understanding the mechanisms of action and resistance of these molecules is essential for proposing new therapies and strategies of treatment. Additionally, understanding how and where mutations arise conferring a resistance profile to the bacteria and their effect on bacterial metabolism is an important requisite to be taken in producing safer and less susceptible drugs to the emergence of resistance. In this review, we summarize the most recent literature regarding novel mutations reported between 2017 and 2022 and the advances in the molecular mechanisms of action and resistance against first-line drugs used in tuberculosis treatment, highlighting recent findings in pyrazinamide resistance involving PanD and, additionally, resistance-conferring mutations for novel drugs such as bedaquiline, pretomanid, delamanid and linezolid.
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Affiliation(s)
- Nicolas de Oliveira Rossini
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil. Universidade de São PauloInstituto de Ciências BiomédicasDepartamento de MicrobiologiaSão PauloSPBrazil
| | - Marcio Vinicius Bertacine Dias
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil. Universidade de São PauloInstituto de Ciências BiomédicasDepartamento de MicrobiologiaSão PauloSPBrazil,University of Warwick, Department of Chemistry, Coventry, United Kingdom. University of WarwickDepartment of ChemistryCoventryUnited Kingdom
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Kabahita JM, Kabugo J, Kakooza F, Adam I, Guido O, Byabajungu H, Namutebi J, Namaganda MM, Lutaaya P, Otim J, Kakembo FE, Kanyerezi S, Nabisubi P, Sserwadda I, Kasule GW, Nakato H, Musisi K, Oola D, Joloba ML, Mboowa G. First report of whole-genome analysis of an extensively drug-resistant Mycobacterium tuberculosis clinical isolate with bedaquiline, linezolid and clofazimine resistance from Uganda. Antimicrob Resist Infect Control 2022; 11:68. [PMID: 35550202 PMCID: PMC9102340 DOI: 10.1186/s13756-022-01101-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Background Uganda remains one of the countries with the highest burden of TB/HIV. Drug-resistant TB remains a substantial challenge to TB control globally and requires new strategic effective control approaches. Drug resistance usually develops due to inadequate management of TB patients including improper treatment regimens and failure to complete the treatment course which may be due to an unstable supply or a lack of access to treatment, as well as patient noncompliance. Methods Two sputa samples were collected from Xpert MTB/RIF® assay-diagnosed multi-drug resistant tuberculosis (MDR-TB) patient at Lira regional referral hospital in northern Uganda between 2020 and 2021 for comprehensive routine mycobacterial species identification and drug susceptibility testing using culture-based methods. Detection of drug resistance-conferring genes was subsequently performed using whole-genome sequencing with Illumina MiSeq platform at the TB Supranational Reference Laboratory in Uganda. Results In both isolates, extensively drug-resistant TB (XDR-TB) was identified including resistance to Isoniazid (katG p.Ser315Thr), Rifampicin (rpoB p.Ser450Leu), Moxifloxacin (gyrA p.Asp94Gly), Bedaquiline (Rv0678 Glu49fs), Clofazimine (Rv0678 Glu49fs), Linezolid (rplC Cys154Arg), and Ethionamide (ethA c.477del). Further analysis of these two high quality genomes revealed that this 32 years-old patient was infected with the Latin American Mediterranean TB strain (LAM). Conclusions This is the first identification of extensively drug-resistant Mycobacterium tuberculosis clinical isolates with bedaquiline, linezolid and clofazimine resistance from Uganda. These acquired resistances were because of non-adherence as seen in the patient’s clinical history. Our study also strongly highlights the importance of combating DR-TB in Africa through implementing next generation sequencing that can test resistance to all drugs while providing a faster turnaround time. This can facilitate timely clinical decisions in managing MDR-TB patients with non-adherence or lost to follow-up. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01101-2.
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Verma N, Arora V, Awasthi R, Chan Y, Jha NK, Thapa K, Jawaid T, Kamal M, Gupta G, Liu G, Paudel KR, Hansbro PM, George Oliver BG, Singh SK, Chellappan DK, Dureja H, Dua K. Recent developments, challenges and future prospects in advanced drug delivery systems in the management of tuberculosis. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Chen K, Lu P, Beeraka NM, Sukocheva OA, Madhunapantula SV, Liu J, Sinelnikov MY, Nikolenko VN, Bulygin KV, Mikhaleva LM, Reshetov IV, Gu Y, Zhang J, Cao Y, Somasundaram SG, Kirkland CE, Fan R, Aliev G. Mitochondrial mutations and mitoepigenetics: Focus on regulation of oxidative stress-induced responses in breast cancers. Semin Cancer Biol 2022; 83:556-569. [PMID: 33035656 DOI: 10.1016/j.semcancer.2020.09.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/08/2023]
Abstract
Epigenetic regulation of mitochondrial DNA (mtDNA) is an emerging and fast-developing field of research. Compared to regulation of nucler DNA, mechanisms of mtDNA epigenetic regulation (mitoepigenetics) remain less investigated. However, mitochondrial signaling directs various vital intracellular processes including aerobic respiration, apoptosis, cell proliferation and survival, nucleic acid synthesis, and oxidative stress. The later process and associated mismanagement of reactive oxygen species (ROS) cascade were associated with cancer progression. It has been demonstrated that cancer cells contain ROS/oxidative stress-mediated defects in mtDNA repair system and mitochondrial nucleoid protection. Furthermore, mtDNA is vulnerable to damage caused by somatic mutations, resulting in the dysfunction of the mitochondrial respiratory chain and energy production, which fosters further generation of ROS and promotes oncogenicity. Mitochondrial proteins are encoded by the collective mitochondrial genome that comprises both nuclear and mitochondrial genomes coupled by crosstalk. Recent reports determined the defects in the collective mitochondrial genome that are conducive to breast cancer initiation and progression. Mutational damage to mtDNA, as well as its overproliferation and deletions, were reported to alter the nuclear epigenetic landscape. Unbalanced mitoepigenetics and adverse regulation of oxidative phosphorylation (OXPHOS) can efficiently facilitate cancer cell survival. Accordingly, several mitochondria-targeting therapeutic agents (biguanides, OXPHOS inhibitors, vitamin-E analogues, and antibiotic bedaquiline) were suggested for future clinical trials in breast cancer patients. However, crosstalk mechanisms between altered mitoepigenetics and cancer-associated mtDNA mutations remain largely unclear. Hence, mtDNA mutations and epigenetic modifications could be considered as potential molecular markers for early diagnosis and targeted therapy of breast cancer. This review discusses the role of mitoepigenetic regulation in cancer cells and potential employment of mtDNA modifications as novel anti-cancer targets.
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Affiliation(s)
- Kuo Chen
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China; Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Pengwei Lu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Narasimha M Beeraka
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Olga A Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - SubbaRao V Madhunapantula
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Junqi Liu
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Str., Zhengzhou, 450052, China
| | - Mikhail Y Sinelnikov
- Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Vladimir N Nikolenko
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Kirill V Bulygin
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Liudmila M Mikhaleva
- Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation
| | - Igor V Reshetov
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yuanting Gu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Jin Zhang
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yu Cao
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Siva G Somasundaram
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Cecil E Kirkland
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Ruitai Fan
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China.
| | - Gjumrakch Aliev
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation; Institute of Physiologically Active Compounds of Russian Academy of Sciences, Severny pr. 1, Chernogolovka, Moscow Region, 142432, Russia; GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA
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Natural products from Brazilian biodiversity identified as potential inhibitors of PknA and PknB of M. tuberculosis using molecular modeling tools. Comput Biol Med 2021; 136:104694. [PMID: 34365277 DOI: 10.1016/j.compbiomed.2021.104694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/07/2021] [Accepted: 07/23/2021] [Indexed: 11/21/2022]
Abstract
Mycobacterium tuberculosis was discovered in 1882 by Robert Koch but, since its discovery, the tuberculosis (TB) epidemic has endured, being one of the top 10 causes of death worldwide. Drug-resistant TB continues to be a public health threat and bioactive compounds with a new mode of action (MoA) are needed to overcome this. Since natural products are described as important sources for the development of new drugs, the objective of this work was to identify potential ligands from Brazilian natural products (NPs) for M. tuberculosis targets using molecular modeling tools. Using chemogenomics we identified the Serine/Threonine Protein Kinase PknB as a putative target for 13 NPs from a database from Brazilian biodiversity (NuBBE). Literature data supported further investigation of NuBBE105, NuBBE598, NuBBE936, NuBBE964, NuBBE1045, and NuBBE1180 by molecular docking and dynamics. Key interactions were observed with PknB and simulations confirmed stability and favorable binding energies. Considering structural similarity with PknB, we further explored binding of the NPs to PknA, critical for M. tuberculosis survival, and all of them resembled important interactions with the enzyme, showing stable and favorable binding energies, whilst van der Waals interactions seem to play a key role for binding to PknA and PknB. NuBBE936 and NuBBE1180 have already had their antimycobacterial activity reported and our results can provide a basis for their MoA. Finally, the other NPs which have not been tested against M. tuberculosis deserve further investigation, aiming at the discovery of antimycobacterial drug candidates with innovative MoA.
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Guglielmetti L, Varaine F. The coming-of-age of bedaquiline: a tale with an open ending. Eur Respir J 2021; 57:57/6/2100066. [PMID: 34112716 DOI: 10.1183/13993003.00066-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 01/18/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Lorenzo Guglielmetti
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, équipe 13, Paris, France .,APHP, Groupe Hospitalier Universitaire Sorbonne Université, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France.,Médecins Sans Frontières, Paris, France
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Raphoko LA, Lekgau K, Lebepe CM, Leboho TC, Matsebatlela TM, Nxumalo W. Synthesis of novel quinoxaline-alkynyl derivatives and their anti-Mycobacterium tuberculosis activity. Bioorg Med Chem Lett 2021; 35:127784. [PMID: 33422606 DOI: 10.1016/j.bmcl.2021.127784] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/29/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022]
Abstract
The study report on the synthesis of a series of novel quinoxaline-alkynyl derivatives that were evaluated for their activity against Mycobacterium tuberculosis (Mtb) H37RV strain. A total of 19 compounds bearing an alcohol, aldehyde, mesylate and ester groups on the alkynly group, and also containing a chloro and nitro groups at the 6-position, were prepared. Seven compounds (3c, 4a-b, 5a, 5c, 6c and 6i), were found to have MIC90 < 10 µM, while five compounds (3b, 6a, 6b, 6d and 6h) had MIC90 in the range 10-20 µM. Compounds bearing a nitro substituent in the 6-position were generally more active and demonstrated a better safety profile, when compared to the unsubstituted and 6-chloro derivatives. Of the seven most active compounds, four contained nitro group at the 6-position.
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Affiliation(s)
- Lerato A Raphoko
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Karabo Lekgau
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Charity M Lebepe
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Tlabo C Leboho
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Thabe M Matsebatlela
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Winston Nxumalo
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa.
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