1
|
Kumar N, Kaur K, Kaur N, Singh E, Bedi PMS. Pathology, target discovery, and the evolution of XO inhibitors from the first discovery to recent advances (2020-2023). Bioorg Chem 2024; 143:107042. [PMID: 38118298 DOI: 10.1016/j.bioorg.2023.107042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/11/2023] [Accepted: 12/15/2023] [Indexed: 12/22/2023]
Abstract
Hyperuricemia, a disease characterized by elevation of serum uric acid level beyond 6 mg/dL. This elevation led to appearance of symptoms from joint pain to gout and from gout to difficulty in mobility of the patient. So, in this review, we have summarized the pathology of hyperuricemia, discovery of target and discovery of first XO inhibitor. At last, this review provides in-sights about the recently discovered as natural XO inhibitors, followed by design, structure activity relationship and biological activity of synthetic compounds as XO inhibitors discovered between 2020 and 2023 years. At last, the pharmacophores generated in this study will guide new researchers to design and modify the structure of novel XO inhibitors.
Collapse
Affiliation(s)
- Nitish Kumar
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Komalpreet Kaur
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Navjot Kaur
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Ekampreet Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | | |
Collapse
|
2
|
Singh V, Katiyar A, Malik P, Kumar S, Mohan A, Singh H, Jain D. Identification of molecular biomarkers associated with non-small-cell lung carcinoma (NSCLC) using whole-exome sequencing. Cancer Biomark 2023:CBM220211. [PMID: 37694353 DOI: 10.3233/cbm-220211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
OBJECTIVES Significant progress has been made in the treatment of patients with pulmonary adenocarcinoma (ADCA) based on molecular profiling. However, no such molecular target exists for squamous cell carcinoma (SQCC). An exome sequence may provide new markers for personalized medicine for lung cancer patients of all subtypes. The current study aims to discover new genetic markers that can be used as universal biomarkers for non-small cell lung cancer (NSCLC). METHODS WES of 19 advanced NSCLC patients (10 ADCA and 9 SQCC) was performed using Illumina HiSeq 2000. Variant calling was performed using GATK HaplotypeCaller and then the impacts of variants on protein structure or function were predicted using SnpEff and ANNOVAR. The clinical impact of somatic variants in cancer was assessed using cancer archives. Somatic variants were further prioritized using a knowledge-driven variant interpretation approach. Sanger sequencing was used to validate functionally important variants. RESULTS We identified 24 rare single-nucleotide variants (SNVs) including 17 non-synonymous SNVs, and 7 INDELs in 18 genes possibly linked to lung carcinoma. Variants were classified as known somatic (n= 10), deleterious (n= 8), and variant of uncertain significance (n= 6). We found TBP and MPRIP genes exclusively associated with ADCA subtypes, FBOX6 with SQCC subtypes and GPRIN2, KCNJ18 and TEKT4 genes mutated in all the patients. The Sanger sequencing of 10 high-confidence somatic SNVs showed 100% concordance in 7 genes, and 80% concordance in the remaining 3 genes. CONCLUSIONS Our bioinformatics analysis identified KCNJ18, GPRIN2, TEKT4, HRNR, FOLR3, ESSRA, CTBP2, MPRIP, TBP, and FBXO6 may contribute to progression in NSCLC and could be used as new biomarkers for the treatment. The mechanism by which GPRIN2, KCNJ12, and TEKT4 contribute to tumorigenesis is unclear, but our results suggest they may play an important role in NSCLC and it is worth investigating in future.
Collapse
Affiliation(s)
- Varsha Singh
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Amit Katiyar
- Bioinformatics Facility, Centralized Core Research Facility, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Prabhat Malik
- Department of Medical Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Sunil Kumar
- Department of Surgical Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Anant Mohan
- Department of Pulmonary Critical Care & Sleep Medicine, All India Institute of Medical Sciences, New Delhi, Ansari Nagar, India
| | - Harpreet Singh
- ICMR-AIIMS Computational Genomics Center, Division of Biomedical Informatics, Indian Council of Medical Research, Ansari Nagar, New Delhi, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| |
Collapse
|
3
|
Meng Y, Sun J, Qu N, Zhang G, Yu T, Piao H. Application of Radiomics for Personalized Treatment of Cancer Patients. Cancer Manag Res 2019; 11:10851-10858. [PMID: 31920394 PMCID: PMC6941598 DOI: 10.2147/cmar.s232473] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/16/2019] [Indexed: 12/14/2022] Open
Abstract
Radiomics is a novel concept that relies on obtaining image data from examinations such as computed tomography (CT), magnetic resonance imaging (MRI), or positron emission tomography (PET). With the appropriate algorithm, the extracted results have broad applicability and potential for a massive positive impact in radiology. For example, clinicians can verify treatment efficiency, predict the location of tumor metastasis, correlate results with a histopathological examination, or more accurately define the type of cancer. Combining radiomics with other testing techniques allows every patient to have a personalized treatment plan that is essential for advanced examination and treatment. This article explains the process of radiomics, including data collection mechanisms, combined use with genomics, and artificial intelligence and immunology techniques, which may solve many of the challenges faced by doctors in diagnosing and treating their patients.
Collapse
Affiliation(s)
- Yiming Meng
- Central Laboratory, Cancer Hospital of China Medical University, Liaoning Province Cancer Hospital, Shenyang 110042, People's Republic of China
| | - Jing Sun
- Central Laboratory, Cancer Hospital of China Medical University, Liaoning Province Cancer Hospital, Shenyang 110042, People's Republic of China
| | - Na Qu
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Province Cancer Hospital, Shenyang 110042, People's Republic of China
| | - Guirong Zhang
- Central Laboratory, Cancer Hospital of China Medical University, Liaoning Province Cancer Hospital, Shenyang 110042, People's Republic of China
| | - Tao Yu
- Department of Medical Image, Cancer Hospital of China Medical University, Liaoning Province Cancer Hospital, Shenyang 110042, People's Republic of China
| | - Haozhe Piao
- Central Laboratory, Cancer Hospital of China Medical University, Liaoning Province Cancer Hospital, Shenyang 110042, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Province Cancer Hospital, Shenyang 110042, People's Republic of China
| |
Collapse
|
4
|
Maggi EC, Gravina S, Cheng H, Piperdi B, Yuan Z, Dong X, Libutti SK, Vijg J, Montagna C. Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model. Front Genet 2018; 9:6. [PMID: 29410677 PMCID: PMC5787102 DOI: 10.3389/fgene.2018.00006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 01/05/2018] [Indexed: 12/18/2022] Open
Abstract
The goal of this study was to develop a method for whole genome cell-free DNA (cfDNA) methylation analysis in humans and mice with the ultimate goal to facilitate the identification of tumor derived DNA methylation changes in the blood. Plasma or serum from patients with pancreatic neuroendocrine tumors or lung cancer, and plasma from a murine model of pancreatic adenocarcinoma was used to develop a protocol for cfDNA isolation, library preparation and whole-genome bisulfite sequencing of ultra low quantities of cfDNA, including tumor-specific DNA. The protocol developed produced high quality libraries consistently generating a conversion rate >98% that will be applicable for the analysis of human and mouse plasma or serum to detect tumor-derived changes in DNA methylation.
Collapse
Affiliation(s)
- Elaine C Maggi
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, United States
| | - Silvia Gravina
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, United States
| | - Haiying Cheng
- Department of Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Bilal Piperdi
- Department of Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ziqiang Yuan
- Department of Surgery, Albert Einstein College of Medicine, New York, NY, United States
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, United States
| | - Steven K Libutti
- Department of Surgery, Albert Einstein College of Medicine, New York, NY, United States
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, United States.,Department of Ophthalmology and Visual Science, Albert Einstein College of Medicine, New York, NY, United States.,Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, New York, NY, United States
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, United States.,Department of Pathology, Albert Einstein College of Medicine, New York, NY, United States
| |
Collapse
|
5
|
Abstract
Peripheral blood mononuclear cells (PBMCs) have been used as a surrogate model of immune function in studies of multiple medical areas, such as metabolic diseases and immune dysfunction. This chapter describes a standardized technique for blood draw and preparation of PBMCs from whole blood using density gradient centrifugation, followed by cell culture. The main focus is on collection of the PBMC culture media and extraction of cellular proteins in order to provide the materials for biomarker studies.
Collapse
Affiliation(s)
- Hassan Rahmoune
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| |
Collapse
|
6
|
Development and validation of a targeted next generation DNA sequencing panel outperforming whole exome sequencing for the identification of clinically relevant genetic variants. Oncotarget 2017; 8:102033-102045. [PMID: 29254223 PMCID: PMC5731933 DOI: 10.18632/oncotarget.22116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/08/2017] [Indexed: 02/07/2023] Open
Abstract
Next generation sequencing (NGS) technologies have revolutionized our approach to genomic research. The use of whole genome sequencing (WGS), whole exome sequencing (WES), transcriptome profiling, and targeted DNA sequencing has exponentially improved our understanding of the human genome and the genetic complexities underlying malignancy. Yet, WGS and WES clinical applications remain limited due to high costs and the large volume of data generated. When utilized to address biological questions in basic science studies, targeted sequencing panels have proven extremely valuable due to reduced costs and higher sequencing depth. However, the routine application of targeted sequencing to the clinical setting is limited to a few cancer subtypes. Some highly aggressive tumor types, like type 2 endometrial cancer (EC), could greatly benefit from routine genomic analysis using targeted sequencing. To explore the potential utility of a mid size panel (~150 genes) in the clinical setting, we developed and validated a custom panel against WGS, WES, and another commercially available targeted panel. Our results indicate that a mid size custom designed panel is as efficient as WGS and WES in mapping variants of biological and clinical relevance, rendering higher coverage, at a lower cost, with fewer variants of uncertain significance. Because of the much higher sequencing depth that could be achieved, our results demonstrate that targeted sequencing outperformed WGS and WES in the mapping of pathogenic variants in a breast cancer case, as well as a case of mixed serous and high-grade endometrioid EC, the most aggressive EC subtype.
Collapse
|