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Shagufta, Ahmad I, Nasar NA, Zerin S. Designing molecular hybrids as novel breast cancer therapeutics. Future Med Chem 2025; 17:857-859. [PMID: 40099891 DOI: 10.1080/17568919.2025.2479418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Accepted: 03/10/2025] [Indexed: 03/20/2025] Open
Affiliation(s)
- Shagufta
- Department of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab Emirates
| | - Irshad Ahmad
- Department of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab Emirates
| | - Noora Ali Nasar
- Department of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab Emirates
| | - Sayma Zerin
- Department of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab Emirates
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2
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Wang J, Li Z, He Y, Chu Y. Targeting Siglec-15 mediates mitochondrial retrograde regulation of cervical cancer development. Tissue Cell 2025; 93:102713. [PMID: 39756115 DOI: 10.1016/j.tice.2024.102713] [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: 11/18/2024] [Revised: 12/26/2024] [Accepted: 12/27/2024] [Indexed: 01/07/2025]
Abstract
Cervical cancer (CCA) is the predominant cause of fatalities from gynecologic malignancies, with metastasis responsible for 80 % of cancer-related mortalities. This study preliminarily examined the involvement of Sialic Acid Binding Ig Like Lectin 15 (Siglec-15) in the development of CCA and its probable mechanisms. We assessed the capacity of Siglec-15 to modulate CCA progression by establishing knockdown and overexpression Siglec-15 cell lines, supplemented with animal models, using both in vivo and in vitro dual investigations. Our findings indicate that Siglec-15 is significantly expressed in CCA cell lines and is intimately associated with the proliferation, migration, and invasion capabilities of CCA cells, as well as mitochondrial ROS homeostasis. The suppression of Siglec-15 expression markedly reduced tumor growth in mice, potentially due to Siglec-15's role in regulating the Mitogen-Activated Protein Kinase (MAPK) signaling pathway, which mediates the retrograde regulation of mitochondrial ROS homeostasis. Siglec-15 may emerge as a novel therapeutic target and prognostic marker for patients with CCA.
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Affiliation(s)
- Jing Wang
- Department of Gynecology, Yantai Yuhuangding Hospital, Shandong University, Yantai, Shandong 264000, China
| | - Zenghui Li
- Department of Gynecology, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, China
| | - Yifan He
- Department of Radiology, Yantaishan Hospital, Yantai, Shandong 264000, China
| | - Yongli Chu
- Department of Gynecology, Yantai Yuhuangding Hospital, Shandong University, Yantai, Shandong 264000, China.
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3
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Xiang Z, Lin T, Ling J, Xu Z, Huang R, Hu H. MiRNA expression profiling and clinical implications in prostate cancer across various stages. Sci Rep 2025; 15:7771. [PMID: 40044915 PMCID: PMC11882840 DOI: 10.1038/s41598-025-92091-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 02/25/2025] [Indexed: 03/09/2025] Open
Abstract
This study aims to screen and identify microRNA (miRNA) expression profiles across different stages of prostate cancer (PCa) and benign prostatic hyperplasia (BPH) using high-throughput sequencing. The study seeks to determine whether specific miRNAs show consistent differential expression across various stages of PCa, with the goal of identifying potential biomarkers relevant to disease progression. In this study, a total of 12 specimens of PCa and BPH were collected from September 2021 to June 2022 in the Second Affiliated Hospital of Nanchang University, 330,006, P.R. China (including 3 specimens of early localized tumor, local invasion, and distant metastasis tumor and 3 specimens of BPH). The expression profile of miRNA was screened by high-throughput sequencing technology, and the differentially expressed miRNA between each group was screened by relevant bioinformatics analysis. Further targeted miRNA site analysis GO enrichment analysis and KEGG enrichment analysis of miRNA-derived genes were performed on the above differentially expressed miRNAs. Finally, the expression of hsa-miR-6715b-3p in PCa tissues was verified using qRT-PCR assay. A total of 1526 miRNAs were identified through high-throughput sequencing. By comparing groups, 228 differentially expressed miRNAs were identified, with 100 upregulated and 128 downregulated. Additionally, 69 novel miRNAs were predicted. qRT-PCR results showed that hsa-miR-6715b-3p was highly expressed in PCa tissues compared to BPH tissues. This study presents a preliminary investigation of the miRNA expression profiles in PCa and identifies hsa-miR-6715b-3p as a promising biomarker for disease progression. Our findings validate the high expression of hsa-miR-6715b-3p in PCa tissues and highlight its potential role in critical oncogenic pathways. These results provide a theoretical foundation for further functional studies to explore its clinical utility and its role in therapy resistance and disease progression, contributing to the growing knowledge of miRNA-based biomarkers in PCa.
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Affiliation(s)
- Zhengjie Xiang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Tao Lin
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Jian Ling
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Zuhuan Xu
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Ruizhen Huang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Honglin Hu
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China.
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4
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Cozac-Szőke AR, Cozac DA, Negovan A, Tinca AC, Vilaia A, Cocuz IG, Sabău AH, Niculescu R, Chiorean DM, Tomuț AN, Cotoi OS. Immune Cell Interactions and Immune Checkpoints in the Tumor Microenvironment of Gastric Cancer. Int J Mol Sci 2025; 26:1156. [PMID: 39940924 PMCID: PMC11818890 DOI: 10.3390/ijms26031156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 01/26/2025] [Accepted: 01/27/2025] [Indexed: 02/16/2025] Open
Abstract
Gastric cancer (GC) ranks as the fifth most prevalent malignant neoplasm globally, with an increased death rate despite recent advancements in research and therapeutic options. Different molecular subtypes of GC have distinct interactions with the immune system, impacting the tumor microenvironment (TME), prognosis, and reaction to immunotherapy. Tumor-infiltrating lymphocytes (TILs) in the TME are crucial for preventing tumor growth and metastasis, as evidenced by research showing that patients with GC who have a significant density of TILs have better survival rates. But cancer cells have evolved a variety of mechanisms to evade immune surveillance, both sialic acid-binding immunoglobulin-like lectin 15 (Siglec-15) and Programmed Death-Ligand 1 (PD-L1) playing a pivotal role in the development of an immunosuppressive TME. They prevent T cell activation and proliferation resulting in a decrease in the immune system's capacity to recognize and eliminate malignant cells. These immune checkpoint molecules function via different but complementary mechanisms, the expression of Siglec-15 being mutually exclusive with PD-L1 and, therefore, providing a different therapeutic approach. The review explores how TILs affect tumor growth and patient outcomes in GC, with particular emphasis on their interactions within the TME and potential targeting of the PD-L1 and Siglec-15 pathways for immunotherapy.
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Affiliation(s)
- Andreea-Raluca Cozac-Szőke
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.-R.C.-S.); (A.H.S.); (R.N.); (D.M.C.)
- Pathophysiology Department, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.C.T.); (I.-G.C.); (O.S.C.)
- Pathology Department, Mures Clinical County Hospital, 540011 Targu Mures, Romania
| | - Dan Alexandru Cozac
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.-R.C.-S.); (A.H.S.); (R.N.); (D.M.C.)
- Emergency Institute for Cardiovascular Diseases and Transplantation Targu Mures, 540142 Targu Mures, Romania
| | - Anca Negovan
- Department of Clinical Science-Internal Medicine, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania;
| | - Andreea Cătălina Tinca
- Pathophysiology Department, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.C.T.); (I.-G.C.); (O.S.C.)
- Pathology Department, Mures Clinical County Hospital, 540011 Targu Mures, Romania
| | - Alexandra Vilaia
- Department of Infectious Diseases I, Doctoral School of Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Iuliu-Gabriel Cocuz
- Pathophysiology Department, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.C.T.); (I.-G.C.); (O.S.C.)
- Pathology Department, Mures Clinical County Hospital, 540011 Targu Mures, Romania
| | - Adrian Horațiu Sabău
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.-R.C.-S.); (A.H.S.); (R.N.); (D.M.C.)
- Pathophysiology Department, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.C.T.); (I.-G.C.); (O.S.C.)
- Pathology Department, Mures Clinical County Hospital, 540011 Targu Mures, Romania
| | - Raluca Niculescu
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.-R.C.-S.); (A.H.S.); (R.N.); (D.M.C.)
- Pathophysiology Department, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.C.T.); (I.-G.C.); (O.S.C.)
- Pathology Department, Mures Clinical County Hospital, 540011 Targu Mures, Romania
| | - Diana Maria Chiorean
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.-R.C.-S.); (A.H.S.); (R.N.); (D.M.C.)
- Pathophysiology Department, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.C.T.); (I.-G.C.); (O.S.C.)
- Pathology Department, Mures Clinical County Hospital, 540011 Targu Mures, Romania
| | - Alexandru Nicușor Tomuț
- Faculty of Medicine, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania;
| | - Ovidiu Simion Cotoi
- Pathophysiology Department, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.C.T.); (I.-G.C.); (O.S.C.)
- Pathology Department, Mures Clinical County Hospital, 540011 Targu Mures, Romania
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5
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Ahmad MS, Braoudaki M, Siddiqui SS. Differential expression of ST6GALNAC1 and ST6GALNAC2 and their clinical relevance to colorectal cancer progression. PLoS One 2024; 19:e0311212. [PMID: 39348343 PMCID: PMC11441655 DOI: 10.1371/journal.pone.0311212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 09/13/2024] [Indexed: 10/02/2024] Open
Abstract
Colorectal cancer (CRC) has become a significant global health concern and ranks among the leading causes of morbidity and mortality worldwide. Due to its malignant nature, current immunotherapeutic treatments are used to tackle this issue. However, not all patients respond positively to treatment, thereby limiting clinical effectiveness and requiring the identification of novel therapeutic targets to optimise current strategies. The putative ligand of Siglec-15, Sialyl-Tn (STn), is associated with tumour progression and is synthesised by the sialyltransferases ST6GALNAC1 and ST6GALNAC2. However, the deregulation of both sialyltransferases within the literature remain limited, and the involvement of microRNAs (miRNAs) in STn production require further elucidation. Here, we identified miRNAs involved in the regulation of ST6GALNAC1 via a computational approach and further analysis of miRNA binding sites were determined. In silico tools predicted miR-21, miR-30e and miR-26b to regulate the ST6GALNAC1 gene, all of which had shown significant upregulated expression in the tumour cohort. Moreover, each miRNA displayed a high binding affinity towards the seed region of ST6GALNAC1. Additionally, enrichment analysis outlined pathways associated with several cancer hallmarks, including epithelial to mesenchymal transition (EMT) and MYC targets associated with tumour progression. Furthermore, our in silico findings demonstrated that the ST6GALNAC1 expression profile was significantly downregulated in CRC tumours, and its low expression correlated with poor survival outcomes when compared with patient survival data. In comparison to its counterpart, there were no significant differences in the expression of ST6GALNAC2 between normal and malignant tissues, which was further evidenced in our immunohistochemistry analysis. Immunohistochemistry staining highlighted significantly higher expression was more prevalent in normal human tissues with regard to ST6GALNAC1. In conclusion, the integrated in silico analysis highlighted that STn production is not reliant on deregulated sialyltransferase expression in CRC, and ST6GALNAC1 expression is regulated by several oncomirs. We proposed the involvement of other sialyltransferases in the production of the STn antigen and CRC progression via the Siglec-15/Sia axis.
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Affiliation(s)
- Mohammed Saqif Ahmad
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Maria Braoudaki
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Shoib Sarwar Siddiqui
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
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6
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Mustafov D, Ahmad MS, Serrano A, Braoudaki M, Siddiqui SS. MicroRNA:Siglec crosstalk in cancer progression. Curr Opin Chem Biol 2024; 81:102502. [PMID: 39029379 DOI: 10.1016/j.cbpa.2024.102502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/21/2024]
Abstract
Aberrant Siglec expression in the tumour microenvironment has been implicated in tumour malignancies and can impact tumour behaviour and patient survival. Further to this, engagement with sialoglycans induces masked antigen recognition and promotes immune evasion, highlighting deregulated immune function. This necessitates the elucidation of their expression profiles in tumour progression. MicroRNAs (miRNAs) mediated targeting represents a novel approach to further elucidate Siglec potential and clinical relevance. Although miRNA activity in Siglec expression remains limited, we highlight current literature detailing miRNA:Siglec interactions within the tumour landscape and provide insights for possible diagnostic and therapeutic strategies in targeting the Siglec/sialic acid axis.
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Affiliation(s)
- D Mustafov
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK; College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - M S Ahmad
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - A Serrano
- Francisco de Vitoria University, Ctra. M-515 Pozuelo-Majadahonda, Km. 1,800, Pozuelo de Alarcón, 28223, Madrid, Spain. https://twitter.com/Antonation2002
| | - M Braoudaki
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK.
| | - S S Siddiqui
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK.
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7
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Mustafov D, Siddiqui SS, Kukol A, Lambrou GI, Shagufta, Ahmad I, Braoudaki M. MicroRNA-Dependent Mechanisms Underlying the Function of a β-Amino Carbonyl Compound in Glioblastoma Cells. ACS OMEGA 2024; 9:31789-31802. [PMID: 39072119 PMCID: PMC11270567 DOI: 10.1021/acsomega.4c02991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 07/30/2024]
Abstract
Glioblastoma (GB) is an aggressive brain malignancy characterized by its invasive nature. Current treatment has limited effectiveness, resulting in poor patients' prognoses. β-Amino carbonyl (β-AC) compounds have gained attention due to their potential anticancerous properties. In vitro assays were performed to evaluate the effects of an in-house synthesized β-AC compound, named SHG-8, upon GB cells. Small RNA sequencing (sRNA-seq) and biocomputational analyses investigated the effects of SHG-8 upon the miRNome and its bioavailability within the human body. SHG-8 exhibited significant cytotoxicity and inhibition of cell migration and proliferation in U87MG and U251MG GB cells. GB cells treated with the compound released significant amounts of reactive oxygen species (ROS). Annexin V and acridine orange/ethidium bromide staining also demonstrated that the compound led to apoptosis. sRNA-seq revealed a shift in microRNA (miRNA) expression profiles upon SHG-8 treatment and significant upregulation of miR-3648 and downregulation of miR-7973. Real-time polymerase chain reaction (RT-qPCR) demonstrated a significant downregulation of CORO1C, an oncogene and a player in the Wnt/β-catenin pathway. In silico analysis indicated SHG-8's potential to cross the blood-brain barrier. We concluded that SHG-8's inhibitory effects on GB cells may involve the deregulation of various miRNAs and the inhibition of CORO1C.
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Affiliation(s)
- Denis Mustafov
- School
of Life and Medical Sciences, University
of Hertfordshire, Hatfield, AL10 9AB, United
Kingdom
- College
of Health, Medicine and Life Sciences, Brunel
University London, Uxbridge UB8 3PH, United
Kingdom
| | - Shoib S. Siddiqui
- School
of Life and Medical Sciences, University
of Hertfordshire, Hatfield, AL10 9AB, United
Kingdom
| | - Andreas Kukol
- School
of Life and Medical Sciences, University
of Hertfordshire, Hatfield, AL10 9AB, United
Kingdom
| | - George I. Lambrou
- Choremeio
Research Laboratory, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Athens,
Greece, Thivon and Levadeias
8, Goudi, 11527 Athens, Greece
- University
Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, Thivon and Levadeias 8, 11527 Athens, Greece
| | - Shagufta
- Department
of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab
Emirates
| | - Irshad Ahmad
- Department
of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab
Emirates
| | - Maria Braoudaki
- School
of Life and Medical Sciences, University
of Hertfordshire, Hatfield, AL10 9AB, United
Kingdom
- University
Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, Thivon and Levadeias 8, 11527 Athens, Greece
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Shagufta, Ahmad I, Nelson DJ, Hussain MI, Nasar NA. Potential of covalently linked tamoxifen hybrids for cancer treatment: recent update. RSC Med Chem 2024; 15:1877-1898. [PMID: 38911170 PMCID: PMC11187546 DOI: 10.1039/d3md00632h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/14/2024] [Indexed: 06/25/2024] Open
Abstract
Cancer is a complex disease and the second leading cause of death globally, and breast cancer is still a leading cause of cancer death in women. Tamoxifen is the most commonly used drug for breast cancer (ER-positive) treatment and chemoprevention, saving the lives of millions of patients every year. In addition, the tamoxifen template has been explored extensively for the development of selective estrogen receptor modulators (SERMs) applicable in breast cancer, osteoporosis, and postmenopausal symptom treatment. Numerous anticancer drugs, including tamoxifen, are in use, but the complexity and heterogeneous nature of cancer complicate the effect of conventional targeted drugs, leading to adverse reactions and resistance. One of the significant approaches to overcome these shortcomings is drug hybrids, generated by covalently linking two or more active pharmacophores. These drug hybrids are remarkably effective in acting on multiple drug targets with higher selectivity and specificity. In recent years, several tamoxifen hybrids have been discovered as potential candidates for cancer treatment. The review highlights the recent progress in developing anticancer hybrids, including organometallic, fluorescent, photocaged, and novel ligand-based tamoxifen hybrids. It also demonstrates the significance of merging various pharmacophores with tamoxifen to produce more potent, precise, and effective anticancer agents. The study offers valuable knowledge to researchers working on cancer research with the hope of enhancing drug potency and reducing drug toxicity to improve cancer patients' lives.
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Affiliation(s)
- Shagufta
- Department of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah Ras Al Khaimah United Arab Emirates
| | - Irshad Ahmad
- Department of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah Ras Al Khaimah United Arab Emirates
| | - Donna J Nelson
- Department of Chemistry and Biochemistry, The University of Oklahoma Norman Oklahoma USA
| | - Maheen Imtiaz Hussain
- Department of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah Ras Al Khaimah United Arab Emirates
| | - Noora Ali Nasar
- Department of Biotechnology, School of Arts and Sciences, American University of Ras Al Khaimah Ras Al Khaimah United Arab Emirates
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Li T, Yao J. Unveiling the hub genes in the SIGLECs family in colon adenocarcinoma with machine learning. Front Genet 2024; 15:1375100. [PMID: 38650859 PMCID: PMC11033367 DOI: 10.3389/fgene.2024.1375100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Background Despite the recognized roles of Sialic acid-binding Ig-like lectins (SIGLECs) in endocytosis and immune regulation across cancers, their molecular intricacies in colon adenocarcinoma (COAD) are underexplored. Meanwhile, the complicated interactions between different SIGLECs are also crucial but open questions. Methods We investigate the correlation between SIGLECs and various properties, including cancer status, prognosis, clinical features, functional enrichment, immune cell abundances, immune checkpoints, pathways, etc. To fully understand the behavior of multiple SIGLECs' co-evolution and subtract its leading effect, we additionally apply three unsupervised machine learning algorithms, namely, Principal Component Analysis (PCA), Self-Organizing Maps (SOM), K-means, and two supervised learning algorithms, Least Absolute Shrinkage and Selection Operator (LASSO) and neural network (NN). Results We find significantly lower expression levels in COAD samples, together with a systematic enhancement in the correlations between distinct SIGLECs. We demonstrate SIGLEC14 significantly affects the Overall Survival (OS) according to the Hazzard ratio, while using PCA further enhances the sensitivity to both OS and Disease Free Interval (DFI). We find any single SIGLEC is uncorrelated to the cancer stages, which can be significantly improved by using PCA. We further identify SIGLEC-1,15 and CD22 as hub genes in COAD through Differentially Expressed Genes (DEGs), which is consistent with our PCA-identified key components PC-1,2,5 considering both the correlation with cancer status and immune cell abundance. As an extension, we use SOM for the visualization of the SIGLECs and show the similarities and differences between COAD patients. SOM can also help us define subsamples according to the SIGLECs status, with corresponding changes in both immune cells and cancer T-stage, for instance. Conclusion We conclude SIGLEC-1,15 and CD22 as the most promising hub genes in the SIGLECs family in treating COAD. PCA offers significant enhancement in the prognosis and clinical analyses, while using SOM further unveils the transition phases or potential subtypes of COAD.
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Affiliation(s)
- Tiantian Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Yao
- Department of Astronomy, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Astronomical Observatory, Shanghai, China
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