1
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Zhou L, Liu S, Li C, Zhou W, Dai F, Tong X. BmE2F1 regulates endoreplication of silk gland cells in silkworm, Bombyx mori. Int J Biol Macromol 2024:138916. [PMID: 39706412 DOI: 10.1016/j.ijbiomac.2024.138916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 12/04/2024] [Accepted: 12/16/2024] [Indexed: 12/23/2024]
Abstract
Endoreplication is particularly important in the context of silk protein synthesis within the silk gland cells of silkworms. Our previous research indicated that the BmE2F1 enhances the silk yield of silkworm cocoons, but the underlying molecular mechanism remains elusive. In this study, we employed RNA-sequencing to dissect the transcriptional profiles of silk glands in the wild-type Dazao silkworm strain and the overexpression (OE) silkworm strain with specific overexpression of the BmE2F1 gene in silk glands. Among the 1126 differentially expressed genes (DEGs), many related to DNA replication (endoreplication in silk glands of silkworm larvae) were significantly enriched. Quantitative real-time PCR confirmed that overexpression of BmE2F1 led to a substantial increase in the expression of 13 genes involved in the DNA replication pathway. Additionally, BmE2F1 upregulated the expression of BmCyclin E, a pivotal gene in the G/S phase transition. Moreover, BmE2F1 overexpression in silk glands significantly boosted DNA replication and concurrently increased the DNA content within silk glands. In conclusion, BmE2F1 regulates endoreplication in silk gland cells of silkworms through dual mechanisms: firstly, by enhancing the formation of the DNA replication complex; and secondly, by facilitating the cells' entry into the S phase.
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Affiliation(s)
- Linli Zhou
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Shuo Liu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Chunlin Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Wei Zhou
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Fangyin Dai
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China; Yibin Academy of Southwest University, Southwest University, Chongqing 400715, China
| | - Xiaoling Tong
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China; Yibin Academy of Southwest University, Southwest University, Chongqing 400715, China.
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2
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Arza-Apalategi S, Heuts BMH, Bergevoet SM, Meering R, Gilissen D, Jansen PWTC, Krippner-Heidenreich A, Valk PJM, Vermeulen M, Heidenreich O, Haferlach T, Jansen JH, Martens JHA, van der Reijden BA. HMX3 is a critical vulnerability in MECOM-negative KMT2A::MLLT3 acute myelomonocytic leukemia. Leukemia 2024:10.1038/s41375-024-02485-3. [PMID: 39633068 DOI: 10.1038/s41375-024-02485-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/27/2024] [Accepted: 11/22/2024] [Indexed: 12/07/2024]
Abstract
KMT2A::MLLT3 acute myelomonocytic leukemia (AML) comes in two clinically and biologically different subtypes. One is characterized by inferior outcome, older age, and MECOM oncogene expression. The other is mainly observed in children and young adults, associates with better clinical outcome, but lacks MECOM. To identify cell fate determining transcription factors downstream of KMT2A::MLLT3, we applied a bioinformatic algorithm that integrates gene and enhancer expression from primary MECOM-positive and -negative KMT2A::MLLT3 AML samples. This identified MECOM to be most influential in the MECOM-positive group, while neuronal transcription factor HMX3 was most influential in the MECOM-negative group. In large AML cohorts, HMX3 expression associated with a unique gene expression profile, younger age (p < 0.002) and KMT2A-rearranged and KAT6A-CREBBP leukemia (p < 0.00001). HMX3 was not expressed in other major genetic risk groups and healthy blood cells. RNA-sequencing analyses following forced HMX3 expression in healthy CD34+ cells and its silencing in KMT2A::MLT3 cells showed that HMX3 drives cancer-associated E2F and MYC gene programs (p < 0.001). HMX3 expression in healthy CD34+ cells blocked monocytic but not granulocytic colony formation. Strikingly, HMX3 silencing in KMT2A::MLLT3 patient cells resulted in cell cycle arrest, monocytic differentiation and apoptosis. Thus, the neuronal transcription factor HMX3 is a leukemia-specific vulnerability in KMT2A::MLLT3 AML.
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Affiliation(s)
- Saioa Arza-Apalategi
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Branco M H Heuts
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, The Netherlands
| | - Saskia M Bergevoet
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Roos Meering
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daan Gilissen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, The Netherlands
| | | | - Peter J M Valk
- Department Hematology, Erasmus MC, Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, The Netherlands
| | - Olaf Heidenreich
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, The Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands.
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3
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Woo MS, Khalil AAK, Gonzalez FJ, Kim JH. E2F3a activates Gadd45b gene expression through PPARα-mediated transcriptional regulation in hepatic cells. Mol Cells 2024; 47:100148. [PMID: 39537030 DOI: 10.1016/j.mocell.2024.100148] [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: 09/18/2024] [Revised: 10/29/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024] Open
Abstract
Growth arrest and DNA damage-inducible beta (GADD45b) plays a critical role in intracellular events such as cell growth and apoptosis. Although the functional study of GADD45b has been conducted, the mechanism for the transcriptional regulation of GADD45b is largely unknown. Due to the drastic induction of hepatic GADD45b mRNA by peroxisome proliferator-activated receptor alpha activation in wild-type mice, we investigated a key factor that affects the upregulation of GADD45b mRNA. Interestingly, we found that GADD45b-promoter luciferase activity was dramatically increased as the 5'-flanking regions were closer to the transcription start site in Hepa1c1c7 cells. Additionally, we found 2 E2F (E2F-myc activator/cell cycle regulator) binding motifs in the region (-150/-1) of the GADD45b promoter. Notably, E2F3 mRNA was significantly increased only in wild-type mice treated with WY-14643, a peroxisome proliferator-activated receptor alpha agonist, followed by the induction of GADD45b mRNA. Furthermore, gene functional studies and Chromatin Immunoprecipitation assays revealed that E2F3 could regulate the GADD45b gene via the E2F binding motif. Thus, we suggest that E2F3 may play a key role in regulating the GADD45b gene as a positive transcription factor.
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Affiliation(s)
- Min Seok Woo
- Department of Pharmacology, School of Medicine, Institute of Medical Sciences, Gyeongsang National University, Jinju 52727, Republic of Korea.
| | - Atif Ali Khan Khalil
- Department of Pharmacology, School of Medicine, Institute of Medical Sciences, Gyeongsang National University, Jinju 52727, Republic of Korea.
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Jung-Hwan Kim
- Department of Pharmacology, School of Medicine, Institute of Medical Sciences, Gyeongsang National University, Jinju 52727, Republic of Korea.
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4
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Zhou Z, Sicairos B, Zhou J, Du Y. Proteomic Analysis Reveals Major Proteins and Pathways That Mediate the Effect of 17-β-Estradiol in Cell Division and Apoptosis in Breast Cancer MCF7 Cells. J Proteome Res 2024; 23:4835-4848. [PMID: 39392593 PMCID: PMC11536429 DOI: 10.1021/acs.jproteome.4c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 09/28/2024] [Accepted: 10/01/2024] [Indexed: 10/12/2024]
Abstract
Despite extensive research, the genes/proteins and pathways responsible for the physiological effects of estrogen remain elusive. In this study, we determined the effect of estrogen on global protein expression in breast cancer MCF7 cells using a proteomic method. The expression of 77 cytosolic, 74 nuclear, and 81 membrane/organelle proteins was significantly altered by 17-β-estradiol (E2). Protein enrichment analyses suggest that E2 may stimulate cell division primarily by promoting the G1 to S phase transition and advancing the G2/M checkpoint. The effect of E2 on cell survival was complex, as it could simultaneously enhance and inhibit apoptosis. Bioinformatics analysis suggests that E2 may enhance apoptosis by promoting the accumulation of the pore-forming protein Bax in the mitochondria and inhibit apoptosis by activating the PI3K/AKT/mTOR signaling pathway. We verified the activation of the PI3K signaling and the accumulation of Bax in the membrane/organelle fraction in E2-treated cells using immunoblotting. Treatment of MCF7 cells with E2 and the PI3K inhibitor Ly294002 significantly enhanced apoptosis compared to those treated with E2 alone, suggesting that combining estrogen with a PI3K inhibitor could be a promising strategy for treating ERα-positive breast cancer. Interestingly, many of the E2-upregulated proteins contained the HEAT, KH, and RRM domains.
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Affiliation(s)
| | | | | | - Yuchun Du
- Department of Biological
Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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5
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Spitschak A, Dhar P, Singh KP, Garduño RC, Gupta SK, Vera J, Musella L, Murr N, Stoll A, Pützer BM. E2F1-induced autocrine IL-6 inflammatory loop mediates cancer-immune crosstalk that predicts T cell phenotype switching and therapeutic responsiveness. Front Immunol 2024; 15:1470368. [PMID: 39544930 PMCID: PMC11560763 DOI: 10.3389/fimmu.2024.1470368] [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: 07/25/2024] [Accepted: 10/14/2024] [Indexed: 11/17/2024] Open
Abstract
Melanoma is a metastatic, drug-refractory cancer with the ability to evade immunosurveillance. Cancer immune evasion involves interaction between tumor intrinsic properties and the microenvironment. The transcription factor E2F1 is a key driver of tumor evolution and metastasis. To explore E2F1's role in immune regulation in presence of aggressive melanoma cells, we established a coculture system and utilized transcriptome and cytokine arrays combined with bioinformatics and structural modeling. We identified an E2F1-dependent gene regulatory network with IL6 as a central hub. E2F1-induced IL-6 secretion unleashes an autocrine inflammatory feedback loop driving invasiveness and epithelial-to-mesenchymal transition. IL-6-activated STAT3 physically interacts with E2F1 and cooperatively enhances IL-6 expression by binding to an E2F1-STAT3-responsive promoter element. The E2F1-STAT3/IL-6 axis strongly modulates the immune niche and generates a crosstalk with CD4+ cells resulting in transcriptional changes of immunoregulatory genes in melanoma and immune cells that is indicative of an inflammatory and immunosuppressive environment. Clinical data from TCGA demonstrated that elevated E2F1, STAT3, and IL-6 correlate with infiltration of Th2, while simultaneously blocking Th1 in primary and metastatic melanomas. Strikingly, E2F1 depletion reduces the secretion of typical type-2 cytokines thereby launching a Th2-to-Th1 phenotype shift towards an antitumor immune response. The impact of activated E2F1-STAT3/IL-6 axis on melanoma-immune cell communication and its prognostic/therapeutic value was validated by mathematical modeling. This study addresses important molecular aspects of the tumor-associated microenvironment in modulating immune responses, and will contribute significantly to the improvement of future cancer therapies.
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Affiliation(s)
- Alf Spitschak
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Prabir Dhar
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Krishna P. Singh
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Rosaely Casalegno Garduño
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Shailendra K. Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Department of Biomedical Engineering & Bioinformatics, Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh, India
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Uniklinikum Erlangen and Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Luca Musella
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Uniklinikum Erlangen and Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Nico Murr
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Anja Stoll
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Brigitte M. Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
- Department Life, Light & Matter, University of Rostock, Rostock, Germany
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6
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Wang H, Wang Y, Tan P, Liu Y, Zhou S, Ma W. Prognostic value and anti-tumor immunity role of TMED9 in pan-cancer: a bioinformatics study. Transl Cancer Res 2024; 13:5429-5445. [PMID: 39525003 PMCID: PMC11543038 DOI: 10.21037/tcr-24-258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 07/07/2024] [Indexed: 11/16/2024]
Abstract
Background Transmembrane p24 trafficking protein 9 (TMED9) belongs to the TMED family, and its overexpression frequently induces cancer. Studies have demonstrated the association between the overexpression of TMED9 and cancer development and proliferative migration in cancers such as ovarian cancer, hepatocellular carcinoma, and breast cancer. However, there has been no study investigating the clinical value, biological function, and anti-tumor immune effects of TMED9 from a pan-cancer perspective. The aim of this study is to evaluate the prognostic value and anti-tumor immunity role of TMED9 across pan-cancers. Methods We utilized R language along with The Cancer Genome Atlas (TCGA), UCSC Xena (University of California, Santa Cruz Xena Browser), Human Protein Atlas (HPA), and other datasets to investigate TMED9 expression in various tumors. The association between high TMED9 expression and clinical prognosis and patient survival was examined using the Kaplan-Meier method, log-rank test, as well as univariate and multivariate Cox regression analyses. Tumor Immune Estimation Resource 2.0 (TIMER2.0) and various algorithms were employed to explore the relationship between TMED9 and the tumor microenvironment (TME). Additionally, the biological function of TMED9 in cancer was investigated through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) analyses. Results TMED9 was over-expressed in the majority of cancers. Patients exhibiting elevated TMED9 expression typically experienced diminished survival rates and unfavorable clinical outcomes. TMED9 played a role as a mediator in the aggressive phenotype of numerous tumors, actively engaging in various biological and signaling pathways linked to cancer development. TMED9 demonstrated the capacity to modulate the anti-tumor immune response in pan-cancer patients, exerting its influence on the infiltration levels of immune cells and cancer-associated fibroblasts (CAFs). Conclusions TMED9 serves as a novel "cancer indicator" and "clinical prognostic marker", capable of reshaping the TME, impacting the immunotherapeutic response, and guiding precise treatments for cancers to a certain extent.
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Affiliation(s)
- Haodi Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yue Wang
- College of Future Education, Beijing Normal University at Zhuhai, Zhuhai, China
| | - Pengyu Tan
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yichi Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Sa Zhou
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wenjian Ma
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, China
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7
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Zhao L, Nakajima R, Zhou Y, Shirasawa M, Fikriyanti M, Kamiya Y, Toh H, Komori H, Iwanaga R, Bradford AP, Nishitani H, Kurayoshi K, Araki K, Ohtani K. The N-Terminal Region of the Transcription Factor E2F1 Contains a Novel Transactivation Domain and Recruits General Transcription Factor GTF2H2. Biomolecules 2024; 14:1357. [PMID: 39595534 PMCID: PMC11592155 DOI: 10.3390/biom14111357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 10/18/2024] [Accepted: 10/21/2024] [Indexed: 11/28/2024] Open
Abstract
The transcription factor E2F1 is the principal target of the tumor suppressor pRB. E2F1 promotes cell proliferation by activating growth-promoting genes upon growth stimulation. In contrast, E2F1 contributes to tumor suppression by activating tumor suppressor genes, such as ARF, upon loss of pRB function, a major oncogenic change. The transactivation domain of E2F1 has previously been mapped to the C-terminal region. We show here that the N-terminal region of E2F1 is critical for the activation of tumor suppressor genes. Deletion of the N-terminal region dramatically compromised E2F1 activation of tumor suppressor genes. The N-terminal region showed transactivation ability when fused to the DNA-binding domain of GAL4. A search for novel interacting factors with the N-terminal region, using a yeast two-hybrid system, identified the general transcription factor GTF2H2. Overexpression of GTF2H2 enhanced E2F1 activation of tumor suppressor genes and induction of cell death. Conversely, the knockdown of GTF2H2 compromised both. E2F1 binding enhanced the binding of GTF2H2 to target promoters depending on the integrity of the N-terminal region. Taken together, these results suggest that the N-terminal region of E2F1 contains a novel transactivation domain that mediates the activation of tumor suppressor genes, at least in part, by recruiting GTF2H2.
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Affiliation(s)
- Lin Zhao
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda 669-1330, Hyogo, Japan; (L.Z.); (R.N.); (Y.Z.); (M.S.); (M.F.); (Y.K.); (H.T.)
| | - Rinka Nakajima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda 669-1330, Hyogo, Japan; (L.Z.); (R.N.); (Y.Z.); (M.S.); (M.F.); (Y.K.); (H.T.)
| | - Yaxuan Zhou
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda 669-1330, Hyogo, Japan; (L.Z.); (R.N.); (Y.Z.); (M.S.); (M.F.); (Y.K.); (H.T.)
| | - Mashiro Shirasawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda 669-1330, Hyogo, Japan; (L.Z.); (R.N.); (Y.Z.); (M.S.); (M.F.); (Y.K.); (H.T.)
| | - Mariana Fikriyanti
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda 669-1330, Hyogo, Japan; (L.Z.); (R.N.); (Y.Z.); (M.S.); (M.F.); (Y.K.); (H.T.)
| | - Yuki Kamiya
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda 669-1330, Hyogo, Japan; (L.Z.); (R.N.); (Y.Z.); (M.S.); (M.F.); (Y.K.); (H.T.)
| | - Hiroyuki Toh
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda 669-1330, Hyogo, Japan; (L.Z.); (R.N.); (Y.Z.); (M.S.); (M.F.); (Y.K.); (H.T.)
| | - Hideyuki Komori
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA;
| | - Ritsuko Iwanaga
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12700 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Andrew P. Bradford
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12700 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Hideo Nishitani
- Graduate School of Life Science, University of Hyogo, Kamigori, Ako-gun 678-1297, Hyogo, Japan;
| | - Kenta Kurayoshi
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa, Japan;
| | - Keigo Araki
- Department of Morphological Biology, Ohu University School of Dentistry, 31-1 Misumido Tomitamachi, Koriyama 963-8611, Fukushima, Japan;
| | - Kiyoshi Ohtani
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda 669-1330, Hyogo, Japan; (L.Z.); (R.N.); (Y.Z.); (M.S.); (M.F.); (Y.K.); (H.T.)
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8
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Meyers S, Gielen O, Cools J, Demeyer S. Single-cell CRISPR screening characterizes transcriptional deregulation in T-cell acute lymphoblastic leukemia. Haematologica 2024; 109:3167-3181. [PMID: 38813729 PMCID: PMC11443379 DOI: 10.3324/haematol.2023.284901] [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: 12/27/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of leukemia caused by accumulation of multiple genetic alterations in T-cell progenitors. However, for many genes it remains unknown how their mutations contribute to disease development. We therefore performed two single-cell CRISPR screens in primary pro-T cells ex vivo to study the transcriptional impact of loss-of-function alterations in T-ALL and correlate this with effects on cell fitness. The various perturbations were clustered based on their effects on E2F/MYC or STAT/NOTCH signatures, which play a defining role in driving T-cell proliferation. Many of the perturbations resulted in positive effects on the STAT and NOTCH signatures and were predicted to behave as haploinsufficient tumor suppressors in T-ALL. Additionally, Spi1 was identified as an essential gene for pro-T-cell survival, associated with deregulation of the MYC signature and epigenetic consequences. In contrast, Bcl11b was identified as a strong tumor suppressor gene in immature T lymphocytes, associated with deregulation of NF-kB and JAK/STAT signaling. We found a correlation between BCL11B expression level and JAK/STAT pathway mutations in T-ALL patients and demonstrated oncogenic cooperation between Bcl11b inactivation and JAK3 hyperactivation in pro-T cells. Altogether, these single-cell CRISPR screens in pro-T cells provide fundamental insights into the mechanisms of transcriptional deregulation caused by genetic alterations in T-ALL.
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Affiliation(s)
- Sarah Meyers
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven
| | - Olga Gielen
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven.
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven.
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9
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Li HJ, Qiu ZB, Wang MM, Zhang C, Hong HZ, Fu R, Peng LS, Huang C, Cui Q, Zhang JT, Ren JY, Jiang L, Wu YL, Zhong WZ. Radiomics-Based Support Vector Machine Distinguishes Molecular Events Driving the Progression of Lung Adenocarcinoma. J Thorac Oncol 2024:S1556-0864(24)02330-X. [PMID: 39306192 DOI: 10.1016/j.jtho.2024.09.1431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/08/2024] [Accepted: 09/15/2024] [Indexed: 11/16/2024]
Abstract
INTRODUCTION An increasing number of early-stage lung adenocarcinomas (LUAD) are detected as lung nodules. The radiological features related to LUAD progression warrant further investigation. Exploration is required to bridge the gap between radiomics-based features and molecular characteristics of lung nodules. METHODS Consensus clustering was applied to the radiomic features of 1212 patients to establish stable clustering. Clusters were illustrated using clinicopathological and next-generation sequencing. A classifier was constructed to further investigate the molecular characteristics in patients with paired computed tomography and RNA sequencing data. RESULTS Patients were clustered into four clusters. Cluster 1 was associated with a low consolidation-to-tumor ratio, preinvasion, grade I disease, and good prognosis. Clusters 2 and 3 reported increasing malignancy with a higher consolidation-to-tumor ratio, higher pathologic grade, and poor prognosis. Cluster 2 possessed more spread through air spaces and cluster 3 reported a higher proportion of pleural invasion. Cluster 4 had similar clinicopathological features as cluster 1 except but a proportion of grade II disease. RNA sequencing indicated that cluster 1 represented nodules with indolent growth and good differentiation, whereas cluster 4 reported progression in cell development but still had low proliferative activity. Nodules with high proliferation were classified into clusters 2 and 3. In addition, the radiomics classifier distinguished cluster 2 as nodules harboring an activated immune environment, whereas cluster 3 represented nodules with a suppressive immune environment. Furthermore, signatures associated with the prognosis of early-stage LUAD were validated in external datasets. CONCLUSIONS Radiomics features can manifest molecular events driving the progression of LUAD. Our study provides molecular insight into radiomics features and assists in the diagnosis and treatment of early-stage LUAD.
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Affiliation(s)
- Hong-Ji Li
- School of Medicine, South China University of Technology, Guangzhou, People's Republic of China; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Zhen-Bin Qiu
- School of Medicine, South China University of Technology, Guangzhou, People's Republic of China; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Meng-Min Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Chao Zhang
- School of Medicine, South China University of Technology, Guangzhou, People's Republic of China; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Hui-Zhao Hong
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Rui Fu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Li-Shan Peng
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Chen Huang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Qian Cui
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Jia-Tao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Jing-Yun Ren
- Department of Nuclear Medicine, WeiLun PET Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Lei Jiang
- Department of Nuclear Medicine, WeiLun PET Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Wen-Zhao Zhong
- School of Medicine, South China University of Technology, Guangzhou, People's Republic of China; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China.
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10
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Cao L, Lu X, Wang X, Wu H, Miao X. From single-cell to spatial transcriptomics: decoding the glioma stem cell niche and its clinical implications. Front Immunol 2024; 15:1475235. [PMID: 39355251 PMCID: PMC11443156 DOI: 10.3389/fimmu.2024.1475235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Accepted: 08/28/2024] [Indexed: 10/03/2024] Open
Abstract
Background Gliomas are aggressive brain tumors associated with a poor prognosis. Cancer stem cells (CSCs) play a significant role in tumor recurrence and resistance to therapy. This study aimed to identify and characterize glioma stem cells (GSCs), analyze their interactions with various cell types, and develop a prognostic signature. Methods Single-cell RNA sequencing data from 44 primary glioma samples were analyzed to identify GSC populations. Spatial transcriptomics and gene regulatory network analyses were performed to investigate GSC localization and transcription factor activity. CellChat analysis was conducted to infer cell-cell communication patterns. A GSC signature (GSCS) was developed using machine learning algorithms applied to bulk RNA sequencing data from multiple cohorts. In vitro and in vivo experiments were conducted to validate the role of TUBA1C, a key gene within the signature. Results A distinct GSC population was identified, characterized by high proliferative potential and an enrichment of E2F1, E2F2, E2F7, and BRCA1 regulons. GSCs exhibited spatial proximity to myeloid-derived suppressor cells (MDSCs). CellChat analysis revealed an active MIF signaling pathway between GSCs and MDSCs. A 26-gene GSCS demonstrated superior performance compared to existing prognostic models. Knockdown of TUBA1C significantly inhibited glioma cell migration, and invasion in vitro, and reduced tumor growth in vivo. Conclusion This study offers a comprehensive characterization of GSCs and their interactions with MDSCs, while presenting a robust GSCS. The findings offer new insights into glioma biology and identify potential therapeutic targets, particularly TUBA1C, aimed at improving patient outcomes.
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Affiliation(s)
- Lei Cao
- Department of Oncology, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Xu Lu
- Department of Oncology, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Xia Wang
- Department of Oncology, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Hao Wu
- Department of Oncology, The Affiliated Huai’an Hospital of Xuzhou Medical University and the Second People’s Hospital of Huai’an, Huai'an, China
| | - Xiaye Miao
- Department of Laboratory Medicine, Northern Jiang su People's Hospital, Yangzhou, Jiangsu, China
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11
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Guo Q, Qiu P, Pan K, Liang H, Liu Z, Lin J. Integrated machine learning algorithms identify KIF15 as a potential prognostic biomarker and correlated with stemness in triple-negative breast cancer. Sci Rep 2024; 14:21449. [PMID: 39271768 PMCID: PMC11399402 DOI: 10.1038/s41598-024-72406-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 09/06/2024] [Indexed: 09/15/2024] Open
Abstract
Cancer stem cells (CSCs) have the potential to self-renew and induce cancer, which may contribute to a poor prognosis by enabling metastasis, recurrence, and therapy resistance. Hence, this study was performed to identify the association between CSC-related genes and triple-negative breast cancer (TNBC) development. Stemness gene sets were downloaded from StemChecker. Based on the online databases, a consensus clustering algorithm was conducted for unsupervised classification of TNBC samples. The variations between subtypes were assessed with regard to prognosis, tumor immune microenvironment (TIME), and chemotherapeutic sensitivity. The stemness-related gene signature was established and random survival forest analysis was employed to identify the core gene for validation experiments and tumor sphere formation assays. 499 patients with TNBC were classified into three subgroups and the Cluster 1 had a better OS than others. After that, WGCNA study was performed to identify genes important for Cluster 1 subtype. Out of all 8 modules, the subtype of Cluster 1 and the yellow module with 103 genes demonstrated the largest positive association. After that, a four-gene stemness-related signature was established. Based on the yellow module, the 39 potential pivotal genes were subjected to the random forest survival analysis to find out the gene that was relatively important for OS. KIF15 was confirmed as the targeted gene by LASSO and random survival forest analyses. In vitro experiments, the downregulation of KIF15 promoted the stemness of TNBC cells. The expression levels of stem cell markers Nanog, SOX2, and OCT4 were found to be elevated in TNBC cell lines after KIF15 inhibition. A stemness-associated risk model was constructed to forecast the clinical outcomes of TNBC patients. The downregulation of KIF15 expression in a subpopulation of TNBC stem cells may promote stemness and possibly TNBC progression.
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Affiliation(s)
- Qiaonan Guo
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Pengjun Qiu
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Kelun Pan
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Huikai Liang
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Zundong Liu
- Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
| | - Jianqing Lin
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
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12
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Glaviano A, Wander SA, Baird RD, Yap KCH, Lam HY, Toi M, Carbone D, Geoerger B, Serra V, Jones RH, Ngeow J, Toska E, Stebbing J, Crasta K, Finn RS, Diana P, Vuina K, de Bruin RAM, Surana U, Bardia A, Kumar AP. Mechanisms of sensitivity and resistance to CDK4/CDK6 inhibitors in hormone receptor-positive breast cancer treatment. Drug Resist Updat 2024; 76:101103. [PMID: 38943828 DOI: 10.1016/j.drup.2024.101103] [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: 02/28/2024] [Revised: 05/17/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
Cell cycle dysregulation is a hallmark of cancer that promotes eccessive cell division. Cyclin-dependent kinase 4 (CDK4) and cyclin-dependent kinase 6 (CDK6) are key molecules in the G1-to-S phase cell cycle transition and are crucial for the onset, survival, and progression of breast cancer (BC). Small-molecule CDK4/CDK6 inhibitors (CDK4/6i) block phosphorylation of tumor suppressor Rb and thus restrain susceptible BC cells in G1 phase. Three CDK4/6i are approved for the first-line treatment of patients with advanced/metastatic hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2-) BC in combination with endocrine therapy (ET). Though this has improved the clinical outcomes for survival of BC patients, there is no established standard next-line treatment to tackle drug resistance. Recent studies suggest that CDK4/6i can modulate other distinct effects in both BC and breast stromal compartments, which may provide new insights into aspects of their clinical activity. This review describes the biochemistry of the CDK4/6-Rb-E2F pathway in HR+ BC, then discusses how CDK4/6i can trigger other effects in BC/breast stromal compartments, and finally outlines the mechanisms of CDK4/6i resistance that have emerged in recent preclinical studies and clinical cohorts, emphasizing the impact of these findings on novel therapeutic opportunities in BC.
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Affiliation(s)
- Antonino Glaviano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo 90123, Italy
| | - Seth A Wander
- Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Richard D Baird
- Cancer Research UK Cambridge Centre, Hills Road, Cambridge CB2 0QQ, UK
| | - Kenneth C-H Yap
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Hiu Yan Lam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Masakazu Toi
- School of Medicine, Kyoto University, Kyoto, Japan
| | - Daniela Carbone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo 90123, Italy
| | - Birgit Geoerger
- Gustave Roussy Cancer Center, Department of Pediatric and Adolescent Oncology, Inserm U1015, Université Paris-Saclay, Villejuif, France
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Robert H Jones
- Cardiff University and Velindre Cancer Centre, Museum Avenue, Cardiff CF10 3AX, UK
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Experimental Medicine Building, 636921, Singapore; Cancer Genetics Service (CGS), National Cancer Centre Singapore, 168583, Singapore
| | - Eneda Toska
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Justin Stebbing
- School of Life Sciences, Anglia Ruskin University, Cambridge, UK; Division of Cancer, Imperial College London, Hammersmith Campus, London, UK
| | - Karen Crasta
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593, Singapore; Healthy Longetivity Translational Program, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
| | - Richard S Finn
- Department of Oncology, Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Patrizia Diana
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo 90123, Italy
| | - Karla Vuina
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Robertus A M de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Uttam Surana
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; SiNOPSEE Therapeutics Pte Ltd, A⁎STARTCentral, 139955, Singapore
| | - Aditya Bardia
- Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.
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13
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Kreis NN, Moon HH, Wordeman L, Louwen F, Solbach C, Yuan J, Ritter A. KIF2C/MCAK a prognostic biomarker and its oncogenic potential in malignant progression, and prognosis of cancer patients: a systematic review and meta-analysis as biomarker. Crit Rev Clin Lab Sci 2024; 61:404-434. [PMID: 38344808 DOI: 10.1080/10408363.2024.2309933] [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: 10/31/2023] [Revised: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 03/24/2024]
Abstract
KIF2C/MCAK (KIF2C) is the most well-characterized member of the kinesin-13 family, which is critical in the regulation of microtubule (MT) dynamics during mitosis, as well as interphase. This systematic review briefly describes the important structural elements of KIF2C, its regulation by multiple molecular mechanisms, and its broad cellular functions. Furthermore, it systematically summarizes its oncogenic potential in malignant progression and performs a meta-analysis of its prognostic value in cancer patients. KIF2C was shown to be involved in multiple crucial cellular processes including cell migration and invasion, DNA repair, senescence induction and immune modulation, which are all known to be critical during the development of malignant tumors. Indeed, an increasing number of publications indicate that KIF2C is aberrantly expressed in multiple cancer entities. Consequently, we have highlighted its involvement in at least five hallmarks of cancer, namely: genome instability, resisting cell death, activating invasion and metastasis, avoiding immune destruction and cellular senescence. This was followed by a systematic search of KIF2C/MCAK's expression in various malignant tumor entities and its correlation with clinicopathologic features. Available data were pooled into multiple weighted meta-analyses for the correlation between KIF2Chigh protein or gene expression and the overall survival in breast cancer, non-small cell lung cancer and hepatocellular carcinoma patients. Furthermore, high expression of KIF2C was correlated to disease-free survival of hepatocellular carcinoma. All meta-analyses showed poor prognosis for cancer patients with KIF2Chigh expression, associated with a decreased overall survival and reduced disease-free survival, indicating KIF2C's oncogenic potential in malignant progression and as a prognostic marker. This work delineated the promising research perspective of KIF2C with modern in vivo and in vitro technologies to further decipher the function of KIF2C in malignant tumor development and progression. This might help to establish KIF2C as a biomarker for the diagnosis or evaluation of at least three cancer entities.
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Affiliation(s)
- Nina-Naomi Kreis
- Obstetrics and Prenatal Medicine, Gynaecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University, Frankfurt, Germany
| | - Ha Hyung Moon
- Obstetrics and Prenatal Medicine, Gynaecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University, Frankfurt, Germany
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA, USA
| | - Frank Louwen
- Obstetrics and Prenatal Medicine, Gynaecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University, Frankfurt, Germany
| | - Christine Solbach
- Obstetrics and Prenatal Medicine, Gynaecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University, Frankfurt, Germany
| | - Juping Yuan
- Obstetrics and Prenatal Medicine, Gynaecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University, Frankfurt, Germany
| | - Andreas Ritter
- Obstetrics and Prenatal Medicine, Gynaecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University, Frankfurt, Germany
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14
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Mahboobnia K, Beveridge DJ, Yeoh GC, Kabir TD, Leedman PJ. MicroRNAs in Hepatocellular Carcinoma Pathogenesis: Insights into Mechanisms and Therapeutic Opportunities. Int J Mol Sci 2024; 25:9393. [PMID: 39273339 PMCID: PMC11395074 DOI: 10.3390/ijms25179393] [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: 07/21/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024] Open
Abstract
Hepatocellular carcinoma (HCC) presents a significant global health burden, with alarming statistics revealing its rising incidence and high mortality rates. Despite advances in medical care, HCC treatment remains challenging due to late-stage diagnosis, limited effective therapeutic options, tumor heterogeneity, and drug resistance. MicroRNAs (miRNAs) have attracted substantial attention as key regulators of HCC pathogenesis. These small non-coding RNA molecules play pivotal roles in modulating gene expression, implicated in various cellular processes relevant to cancer development. Understanding the intricate network of miRNA-mediated molecular pathways in HCC is essential for unraveling the complex mechanisms underlying hepatocarcinogenesis and developing novel therapeutic approaches. This manuscript aims to provide a comprehensive review of recent experimental and clinical discoveries regarding the complex role of miRNAs in influencing the key hallmarks of HCC, as well as their promising clinical utility as potential therapeutic targets.
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Affiliation(s)
- Khadijeh Mahboobnia
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, Perth, WA 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Dianne J Beveridge
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, Perth, WA 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - George C Yeoh
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, Perth, WA 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Tasnuva D Kabir
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, Perth, WA 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Peter J Leedman
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, Perth, WA 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
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15
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Brislinger-Engelhardt MM, Walentek P. Multiciliogenesis: Tricking the cell-cycle machinery to build hundreds of cilia. Curr Biol 2024; 34:R786-R788. [PMID: 39163842 DOI: 10.1016/j.cub.2024.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Multiciliated cells produce over a hundred motile cilia anchored to the membrane by modified centrioles. Recent work has characterized an alternative cell cycle used by this post-mitotic cell type to generate additional centrioles without undergoing cell division.
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Affiliation(s)
- Magdalena Maria Brislinger-Engelhardt
- Internal Medicine IV, Medical Center - University of Freiburg, CIBSS Centre for Integrative Biological Signalling Studies, and SGBM Spemann Graduate School for Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Walentek
- Internal Medicine IV, Medical Center - University of Freiburg, CIBSS Centre for Integrative Biological Signalling Studies, and SGBM Spemann Graduate School for Biology and Medicine, University of Freiburg, Freiburg, Germany.
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16
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Abulihaiti Z, Li W, Yang L, Zhang H, Du A, Tang N, Lu Y, Zeng J. Hypoxia-driven lncRNA CTD-2510F5.4: a potential player in hepatocellular carcinoma's prognostic stratification, cellular behavior, tumor microenvironment, and therapeutic response. Mol Biol Rep 2024; 51:905. [PMID: 39133347 DOI: 10.1007/s11033-024-09826-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a highly aggressive cancer with limited therapeutic options. Hypoxia is a common feature of the tumor microenvironment that reportedly promotes tumorigenesis. Long non-coding RNAs (lncRNAs) are a class of regulatory molecules with diverse functions in cancer biology. This study aimed to identify hypoxia-induced lncRNAs associated with HCC and evaluate their potential as prognostic and therapeutic biomarkers. METHODS We employed microarray and The Cancer Genome Atlas (TCGA) data to identify hypoxia-induced lncRNAs in HCC. Subsequently, we focused on CTD-2510F5.4, a candidate lncRNA, and predicted its functional roles in HCC using Gene Ontology (GO) and Guilt-by-Association (GBA) analyses. We validated its expression under hypoxia in Huh7 and HepG2 cells using RT-PCR. Functional assays, including CCK8, wound-healing, and transwell assays, were performed to assess the effects of CTD-2510F5.4 overexpression on HCC cell proliferation, invasion, and metastasis potential. Furthermore, we investigated the association between CTD-2510F5.4 expression and patient prognosis, tumor mutation signature, immune microenvironment characteristics, and therapeutic response to different treatment modalities. RESULTS Our data demonstrated a significant upregulation of CTD-2510F5.4 expression in response to hypoxia. Functional enrichment analyses revealed the involvement of CTD-2510F5.4 in cell cycle regulation, E2F targets, G2M checkpoint control, and MYC signaling pathways. Functionally, CTD-2510F5.4 overexpression promoted HCC cell proliferation, invasion, and metastasis. Patients with high CTD-2510F5.4 expression exhibited a worse prognosis, a higher prevalence of TP53 mutations, increased infiltration by immunosuppressive regulatory T cells, elevated expression of immune checkpoint molecules, and higher TIDE scores indicative of immune dysfunction and exclusion. Notably, patients with low CTD-2510F5.4 expression displayed greater sensitivity to immunotherapy and antiangiogenic therapy, while those with high expression responded better to chemotherapy. CONCLUSION Our findings suggest that CTD-2510F5.4 plays a critical role in HCC progression and immune modulation. Its potential as a prognostic biomarker and a predictor of therapeutic response warrants further investigation for personalized treatment strategies in HCC patients.
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Affiliation(s)
- Zulipiya Abulihaiti
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, China
| | - Weihong Li
- Department of Radiology, Wenzhou Central Hospital, The Second Affiliated Hospital of Shanghai University, Wenzhou, 325000, China
| | - Liangyu Yang
- Department of Gastrointestinal Oncology Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, China
| | - Haihang Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, China
| | - Ainong Du
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, China
| | - Ni Tang
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, China
| | - Yanda Lu
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, China.
| | - Jiangzheng Zeng
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, China.
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17
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Shi J. Early 2-Factor Transcription Factors Associated with Progression and Recurrence in Bevacizumab-Responsive Subtypes of Glioblastoma. Cancers (Basel) 2024; 16:2536. [PMID: 39061176 PMCID: PMC11275000 DOI: 10.3390/cancers16142536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The early 2-factor (E2F) family of transcription factors, including E2F1 through 8, plays a critical role in apoptosis, metabolism, proliferation, and angiogenesis within glioblastoma (GBM). However, the specific functions of E2F transcription factors (E2Fs) and their impact on the malignancy of Bevacizumab (BVZ)-responsive GBM subtypes remain unclear. This study used data from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), and Gene Expression Omnibus (GEO) to explore the impact of eight E2F family members on the clinical characteristics of BVZ-responsive GBM subtypes and possible mechanisms of recurrence after BVZ treatment. Using machine learning algorithms, including TreeBagger and deep neural networks, we systematically predicted and validated GBM patient survival terms based on the expression profiles of E2Fs across BVZ-responsive GBM subtypes. Our bioinformatics analyses suggested that a significant increase in E2F8 post-BVZ treatment may enhance the function of angiogenesis and stem cell proliferation, implicating this factor as a candidate mechanism of GBM recurrence after treatment. In addition, BVZ treatment in unresponsive GBM patients may potentially worsen disease progression. These insights underscore that E2F family members play important roles in GBM malignancy and BVZ treatment response, highlighting their potential as prognostic biomarkers, therapeutic targets, and recommending precision BVZ treatment to individual GBM patients.
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Affiliation(s)
- Jian Shi
- Department of Neurology, San Francisco Veterans Affairs Health Care System and University of California, San Francisco, CA 94121, USA
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18
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Wang S, Xia Y, Sun Y, Wang W, Shan L, Zhang Z, Zhao C. E2F8-CENPL pathway contributes to homologous recombination repair and chemoresistance in breast cancer. Cell Signal 2024; 118:111151. [PMID: 38522807 DOI: 10.1016/j.cellsig.2024.111151] [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: 01/08/2024] [Revised: 03/06/2024] [Accepted: 03/22/2024] [Indexed: 03/26/2024]
Abstract
Chemoresistance poses a significant obstacle to the treatment of breast cancer patients. The increased capacity of DNA damage repair is one of the mechanisms underlying chemoresistance. Bioinformatic analyses showed that E2F8 was associated with cell cycle progression and homologous recombination (HR) repair of DNA double-strand breaks (DSBs) in breast cancer. E2F8 knockdown suppressed cell growth and attenuated HR repair. Accordingly, E2F8 knockdown sensitized cancer cells to Adriamycin and Cisplatin. Centromere protein L (CENPL) is a transcriptional target by E2F8. CENPL overexpression in E2F8-knockdowned cells recovered at least in part the effect of E2F8 on DNA damage repair and chemotherapy sensitivity. Consistently, CENPL knockdown impaired DNA damage repair and sensitized cancer cells to DNA-damaging drugs. These findings demonstrate that targeting E2F8-CENPL pathway is a potential approach to overcoming chemoresistance.
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Affiliation(s)
- Shan Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning Province, PR China
| | - Yuhong Xia
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning Province, PR China
| | - Yu Sun
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning Province, PR China
| | - Wei Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning Province, PR China
| | - Lianfeng Shan
- Department of Intelligent Computation, School of Intelligent Medicine, China Medical University, Shenyang 110122, Liaoning Province, PR China.
| | - Zhongbo Zhang
- Department of Pancreatic and Biliary Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, PR China.
| | - Chenghai Zhao
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning Province, PR China.
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19
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Daks A, Parfenyev S, Shuvalov O, Fedorova O, Nazarov A, Melino G, Barlev NA. Lysine-specific methyltransferase Set7/9 in stemness, differentiation, and development. Biol Direct 2024; 19:41. [PMID: 38812048 PMCID: PMC11137904 DOI: 10.1186/s13062-024-00484-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024] Open
Abstract
The enzymes performing protein post-translational modifications (PTMs) form a critical post-translational regulatory circuitry that orchestrates literally all cellular processes in the organism. In particular, the balance between cellular stemness and differentiation is crucial for the development of multicellular organisms. Importantly, the fine-tuning of this balance on the genetic level is largely mediated by specific PTMs of histones including lysine methylation. Lysine methylation is carried out by special enzymes (lysine methyltransferases) that transfer the methyl group from S-adenosyl-L-methionine to the lysine residues of protein substrates. Set7/9 is one of the exemplary protein methyltransferases that however, has not been fully studied yet. It was originally discovered as histone H3 lysine 4-specific methyltransferase, which later was shown to methylate a number of non-histone proteins that are crucial regulators of stemness and differentiation, including p53, pRb, YAP, DNMT1, SOX2, FOXO3, and others. In this review we summarize the information available to date on the role of Set7/9 in cellular differentiation and tissue development during embryogenesis and in adult organisms. Finally, we highlight and discuss the role of Set7/9 in pathological processes associated with aberrant cellular differentiation and self-renewal, including the formation of cancer stem cells.
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Affiliation(s)
- Alexandra Daks
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064.
| | - Sergey Parfenyev
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064
| | - Oleg Shuvalov
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064
| | - Olga Fedorova
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064
| | - Alexander Nazarov
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Nickolai A Barlev
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064.
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, 001000, Astana, Kazakhstan.
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20
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Wu J, Li W, Su J, Zheng J, Liang Y, Lin J, Xu B, Liu Y. Integration of single-cell sequencing and bulk RNA-seq to identify and develop a prognostic signature related to colorectal cancer stem cells. Sci Rep 2024; 14:12270. [PMID: 38806611 PMCID: PMC11133358 DOI: 10.1038/s41598-024-62913-3] [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: 01/08/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
The prognosis for patients with colorectal cancer (CRC) remains worse than expected due to metastasis, recurrence, and resistance to chemotherapy. Colorectal cancer stem cells (CRCSCs) play a vital role in tumor metastasis, recurrence, and chemotherapy resistance. However, there are currently no prognostic markers based on CRCSCs-related genes available for clinical use. In this study, single-cell transcriptome sequencing was employed to distinguish cancer stem cells (CSCs) in the CRC microenvironment and analyze their properties at the single-cell level. Subsequently, data from TCGA and GEO databases were utilized to develop a prognostic risk model for CRCSCs-related genes and validate its diagnostic performance. Additionally, functional enrichment, immune response, and chemotherapeutic drug sensitivity of the relevant genes in the risk model were investigated. Lastly, the key gene RPS17 in the risk model was identified as a potential prognostic marker and therapeutic target for further comprehensive studies. Our findings provide new insights into the prognostic treatment of CRC and offer novel perspectives for a systematic and comprehensive understanding of CRC development.
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Affiliation(s)
- Jiale Wu
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Wanyu Li
- Well Lead Medical Co., Ltd., Guangzhou, 511434, Guangdong, China
| | - Junyu Su
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Jiamin Zheng
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Yanwen Liang
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Jiansuo Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Bilian Xu
- School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China.
| | - Yi Liu
- School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China.
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21
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Li GX, Chen L, Hsiao Y, Mannan R, Zhang Y, Luo J, Petralia F, Cho H, Hosseini N, Leprevost FDV, Calinawan A, Li Y, Anand S, Dagar A, Geffen Y, Kumar-Sinha C, Chugh S, Le A, Ponce S, Guo S, Zhang C, Schnaubelt M, Al Deen NN, Chen F, Caravan W, Houston A, Hopkins A, Newton CJ, Wang X, Polasky DA, Haynes S, Yu F, Jing X, Chen S, Robles AI, Mesri M, Thiagarajan M, An E, Getz GA, Linehan WM, Hostetter G, Jewell SD, Chan DW, Wang P, Omenn GS, Mehra R, Ricketts CJ, Ding L, Chinnaiyan AM, Cieslik MP, Dhanasekaran SM, Zhang H, Nesvizhskii AI. Comprehensive proteogenomic characterization of rare kidney tumors. Cell Rep Med 2024; 5:101547. [PMID: 38703764 PMCID: PMC11148773 DOI: 10.1016/j.xcrm.2024.101547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.
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Affiliation(s)
- Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Yi Hsiao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Luo
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanbyul Cho
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Aniket Dagar
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seema Chugh
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne Le
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Shenghao Guo
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Cissy Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Alex Hopkins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Xiaoming Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaojun Jing
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | | | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Gad A Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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22
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Raj-Kumar PK, Lin X, Liu T, Sturtz LA, Gritsenko MA, Petyuk VA, Sagendorf TJ, Deyarmin B, Liu J, Praveen-Kumar A, Wang G, McDermott JE, Shukla AK, Moore RJ, Monroe ME, Webb-Robertson BJM, Hooke JA, Fantacone-Campbell L, Mostoller B, Kvecher L, Kane J, Melley J, Somiari S, Soon-Shiong P, Smith RD, Mural RJ, Rodland KD, Shriver CD, Kovatich AJ, Hu H. Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection. Breast Cancer Res 2024; 26:76. [PMID: 38745208 PMCID: PMC11094977 DOI: 10.1186/s13058-024-01835-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. METHODS We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. RESULTS We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations in TP53, PLXNB3, Zinc finger genes, and fewer mutations in SDC2, CDH1, PIK3CA, SVIL, and PTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA-protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, including KIAA1522, DCK, FOXO3, MYO9B, ARID1A, EPRS, ZC3HAV1, and RBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. CONCLUSIONS This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.
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Affiliation(s)
- Praveen-Kumar Raj-Kumar
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Xiaoying Lin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lori A Sturtz
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | | | - Brenda Deyarmin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Guisong Wang
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | | | - Anil K Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Jeffrey A Hooke
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Leigh Fantacone-Campbell
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Brad Mostoller
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Leonid Kvecher
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Kane
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jennifer Melley
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Stella Somiari
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | | | - Richard J Mural
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- Department of Surgery, Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Albert J Kovatich
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA.
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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23
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Gao Z, Su Y, Xia J, Cao RF, Ding Y, Zheng CH, Wei PJ. DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding. Brief Bioinform 2024; 25:bbae143. [PMID: 38581416 PMCID: PMC10998536 DOI: 10.1093/bib/bbae143] [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: 01/17/2024] [Revised: 03/02/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024] Open
Abstract
The inference of gene regulatory networks (GRNs) from gene expression profiles has been a key issue in systems biology, prompting many researchers to develop diverse computational methods. However, most of these methods do not reconstruct directed GRNs with regulatory types because of the lack of benchmark datasets or defects in the computational methods. Here, we collect benchmark datasets and propose a deep learning-based model, DeepFGRN, for reconstructing fine gene regulatory networks (FGRNs) with both regulation types and directions. In addition, the GRNs of real species are always large graphs with direction and high sparsity, which impede the advancement of GRN inference. Therefore, DeepFGRN builds a node bidirectional representation module to capture the directed graph embedding representation of the GRN. Specifically, the source and target generators are designed to learn the low-dimensional dense embedding of the source and target neighbors of a gene, respectively. An adversarial learning strategy is applied to iteratively learn the real neighbors of each gene. In addition, because the expression profiles of genes with regulatory associations are correlative, a correlation analysis module is designed. Specifically, this module not only fully extracts gene expression features, but also captures the correlation between regulators and target genes. Experimental results show that DeepFGRN has a competitive capability for both GRN and FGRN inference. Potential biomarkers and therapeutic drugs for breast cancer, liver cancer, lung cancer and coronavirus disease 2019 are identified based on the candidate FGRNs, providing a possible opportunity to advance our knowledge of disease treatments.
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Affiliation(s)
- Zhen Gao
- The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Yansen Su
- The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Junfeng Xia
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Rui-Fen Cao
- The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Yun Ding
- The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Chun-Hou Zheng
- The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Pi-Jing Wei
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
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24
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Meng J, Qian W, Yang Z, Gong L, Xu D, Huang H, Jiang X, Pu Z, Yin Y, Zou J. p53/E2F7 axis promotes temozolomide chemoresistance in glioblastoma multiforme. BMC Cancer 2024; 24:317. [PMID: 38454344 PMCID: PMC10921682 DOI: 10.1186/s12885-024-12017-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is the most aggressive form of brain cancer, and chemoresistance poses a significant challenge to the survival and prognosis of GBM. Although numerous regulatory mechanisms that contribute to chemoresistance have been identified, many questions remain unanswered. This study aims to identify the mechanism of temozolomide (TMZ) resistance in GBM. METHODS Bioinformatics and antibody-based protein detection were used to examine the expression of E2F7 in gliomas and its correlation with prognosis. Additionally, IC50, cell viability, colony formation, apoptosis, doxorubicin (Dox) uptake, and intracranial transplantation were used to confirm the role of E2F7 in TMZ resistance, using our established TMZ-resistance (TMZ-R) model. Western blot and ChIP experiments provided confirmation of p53-driven regulation of E2F7. RESULTS Elevated levels of E2F7 were detected in GBM tissue and were correlated with a poor prognosis for patients. E2F7 was found to be upregulated in TMZ-R tumors, and its high levels were linked to increased chemotherapy resistance by limiting drug uptake and decreasing DNA damage. The expression of E2F7 was also found to be regulated by the activation of p53. CONCLUSIONS The high expression of E2F7, regulated by activated p53, confers chemoresistance to GBM cells by inhibiting drug uptake and DNA damage. These findings highlight the significant connection between sustained p53 activation and GBM chemoresistance, offering the potential for new strategies to overcome this resistance.
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Affiliation(s)
- Jiao Meng
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Wei Qian
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Department of Clinical Laborator, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, 215300, Suzhou, Jiangsu, China
| | - Zhenkun Yang
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Lingli Gong
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Daxing Xu
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Hongbo Huang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, 214063, Wuxi, China
| | - Xinyi Jiang
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Zhening Pu
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
| | - Ying Yin
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
| | - Jian Zou
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
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25
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Deng J, Lai G, Zhang C, Li K, Zhu W, Xie B, Zhong X. A robust primary liver cancer subtype related to prognosis and drug response based on a multiple combined classifying strategy. Heliyon 2024; 10:e25570. [PMID: 38352751 PMCID: PMC10861988 DOI: 10.1016/j.heliyon.2024.e25570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
The recurrence or resistance to treatment of primary liver cancer (PLL) is significantly related to the heterogeneity present within the tumor. In this study, we integrated prognosis risk score, mRNAsi index, and immune characteristics clustering to classify patients. The four subtypes obtained from the combined classification are associated with PLC's prognosis and drug response. In these subtypes, we observed mRNAsiH_ICCA subtype, the intersection between high mRNAsi and immune characteristics clustering A, had the worst prognosis. Specifically, immune characteristics clustering B (ICC_B) had high drug sensitivity in most drugs regardless of the value of mRNAsi. On the other hand, patients with low mRNAsi responded better to ten drugs including KU-55933 and NU7441, while patients with high mRNAsi might benefit from drugs like Leflunomide. By matching the specific characteristics of each combined subtype with the drug-induced cell line expression profile, we identified a group of potential therapeutic drugs that might regulate the expression of disease signature genes. We developed a feasible multiple combined typing strategy, hoping to guide therapeutic selection and promote the development of precision medicine.
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Affiliation(s)
- Jielian Deng
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
- Medical Department, Yidu Cloud (Beijing) Technology Co., Beijing, China
| | - Guichuan Lai
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Cong Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Kangjie Li
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Wenyan Zhu
- Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Medical Department, Yidu Cloud (Beijing) Technology Co., Beijing, China
| | - Biao Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Xiaoni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
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26
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Ferrer-Diaz AI, Sinha G, Petryna A, Gonzalez-Bermejo R, Kenfack Y, Adetayo O, Patel SA, Hooda-Nehra A, Rameshwar P. Revealing role of epigenetic modifiers and DNA oxidation in cell-autonomous regulation of Cancer stem cells. Cell Commun Signal 2024; 22:119. [PMID: 38347590 PMCID: PMC10863086 DOI: 10.1186/s12964-024-01512-1] [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: 12/30/2023] [Accepted: 02/01/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Breast cancer cells (BCCs) can remain undetected for decades in dormancy. These quiescent cells are similar to cancer stem cells (CSCs); hence their ability to initiate tertiary metastasis. Dormancy can be regulated by components of the tissue microenvironment such as bone marrow mesenchymal stem cells (MSCs) that release exosomes to dedifferentiate BCCs into CSCs. The exosomes cargo includes histone 3, lysine 4 (H3K4) methyltransferases - KMT2B and KMT2D. A less studied mechanism of CSC maintenance is the process of cell-autonomous regulation, leading us to examine the roles for KMT2B and KMT2D in sustaining CSCs, and their potential as drug targets. METHODS Use of pharmacological inhibitor of H3K4 (WDR5-0103), knockdown (KD) of KMT2B or KMT2D in BCCs, real time PCR, western blot, response to chemotherapy, RNA-seq, and flow cytometry for circulating markers of CSCs and DNA hydroxylases in BC patients. In vivo studies using a dormancy model studied the effects of KMT2B/D to chemotherapy. RESULTS H3K4 methyltransferases sustain cell autonomous regulation of CSCs, impart chemoresistance, maintain cycling quiescence, and reduce migration and proliferation of BCCs. In vivo studies validated KMT2's role in dormancy and identified these genes as potential drug targets. DNA methylase (DNMT), predicted within a network with KMT2 to regulate CSCs, was determined to sustain circulating CSC-like in the blood of patients. CONCLUSION H3K4 methyltransferases and DNA methylation mediate cell autonomous regulation to sustain CSC. The findings provide crucial insights into epigenetic regulatory mechanisms underlying BC dormancy with KMT2B and KMT2D as potential therapeutic targets, along with standard care. Stem cell and epigenetic markers in circulating BCCs could monitor treatment response and this could be significant for long BC remission to partly address health disparity.
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Affiliation(s)
- Alejandra I Ferrer-Diaz
- Department of Medicine - Division of Hematology/Oncology, Rutgers, New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers School of Graduate Studies at New Jersey Medical School, Newark, NJ, USA
| | - Garima Sinha
- Department of Medicine - Division of Hematology/Oncology, Rutgers, New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers School of Graduate Studies at New Jersey Medical School, Newark, NJ, USA
| | - Andrew Petryna
- Department of Medicine - Division of Hematology/Oncology, Rutgers, New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers School of Graduate Studies at New Jersey Medical School, Newark, NJ, USA
| | | | - Yannick Kenfack
- Department of Medicine - Division of Hematology/Oncology, Rutgers, New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers School of Graduate Studies at New Jersey Medical School, Newark, NJ, USA
| | | | - Shyam A Patel
- Division of Hematology and Oncology, Department of Medicine, UMass Memorial Medical Center, UMass Chan Medical School, Worcester, MA, USA
| | - Anupama Hooda-Nehra
- Department of Medicine - Division of Hematology/Oncology, Rutgers, New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, USA
| | - Pranela Rameshwar
- Department of Medicine - Division of Hematology/Oncology, Rutgers, New Jersey Medical School, Newark, NJ, 07103, USA.
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27
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Sizer RE, Butterfield SP, Hancocks LA, Gato De Sousa L, White RJ. Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III. Cancers (Basel) 2024; 16:481. [PMID: 38339234 PMCID: PMC10854548 DOI: 10.3390/cancers16030481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
In all cases tested, TFIIIB is responsible for recruiting pol III to its genetic templates. In mammalian cells, RB binds TFIIIB and prevents its interactions with both promoter DNA and pol III, thereby suppressing transcription. As TFIIIB is not recruited to its target genes when bound by RB, the mechanism predicts that pol III-dependent templates will not be occupied by RB; this contrasts with the situation at most genes controlled by RB, where it can be tethered by promoter-bound sequence-specific DNA-binding factors such as E2F. Contrary to this prediction, however, ChIP-seq data reveal the presence of RB in multiple cell types and the related protein p130 at many loci that rely on pol III for their expression, including RMRP, RN7SL, and a variety of tRNA genes. The sets of genes targeted varies according to cell type and growth state. In such cases, recruitment of RB and p130 can be explained by binding of E2F1, E2F4 and/or E2F5. Genes transcribed by pol III had not previously been identified as common targets of E2F family members. The data provide evidence that E2F may allow for the selective regulation of specific non-coding RNAs by RB, in addition to its influence on overall pol III output through its interaction with TFIIIB.
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Affiliation(s)
| | | | | | | | - Robert J. White
- Department of Biology, University of York, York YO10 5DD, UK; (R.E.S.)
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28
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Ghafouri-Fard S, Askari A, Hussen BM, Taheri M, Akbari Dilmaghani N. Role of miR-424 in the carcinogenesis. Clin Transl Oncol 2024; 26:16-38. [PMID: 37178445 PMCID: PMC10761534 DOI: 10.1007/s12094-023-03209-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Recent studies have revealed the impact of microRNAs (miRNAs) in the carcinogenic process. miR-424 is a miRNA whose role in this process is being to be identified. Experiments in the ovarian cancer, cervical cancer, hepatocellular carcinoma, neuroblastoma, breast cancer, osteosarcoma, intrahepatic cholangiocarcinoma, prostate cancer, endometrial cancer, non-small cell lung cancer, hemangioma and gastric cancer have reported down-regulation of miR-424. On the other hand, this miRNA has been found to be up-regulated in melanoma, laryngeal and esophageal squamous cell carcinomas, glioma, multiple myeloma and thyroid cancer. Expression of this miRNA is regulated by methylation status of its promoter. Besides, LINC00641, CCAT2, PVT1, LIN00657, LINC00511 and NNT-AS1 are among lncRNAs that act as molecular sponges for miR-424, thus regulating its expression. Moreover, several members of SNHG family of lncRNAs have been found to regulate expression of miR-424. This miRNA is also involved in the regulation of E2F transcription factors. The current review aims at summarization of the role of miR-424 in the process of cancer evolution and its impact on clinical outcome of patients in order to find appropriate markers for malignancies.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arian Askari
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Nader Akbari Dilmaghani
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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29
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Zhou Y, Nakajima R, Shirasawa M, Fikriyanti M, Zhao L, Iwanaga R, Bradford AP, Kurayoshi K, Araki K, Ohtani K. Expanding Roles of the E2F-RB-p53 Pathway in Tumor Suppression. BIOLOGY 2023; 12:1511. [PMID: 38132337 PMCID: PMC10740672 DOI: 10.3390/biology12121511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
The transcription factor E2F links the RB pathway to the p53 pathway upon loss of function of pRB, thereby playing a pivotal role in the suppression of tumorigenesis. E2F fulfills a major role in cell proliferation by controlling a variety of growth-associated genes. The activity of E2F is controlled by the tumor suppressor pRB, which binds to E2F and actively suppresses target gene expression, thereby restraining cell proliferation. Signaling pathways originating from growth stimulative and growth suppressive signals converge on pRB (the RB pathway) to regulate E2F activity. In most cancers, the function of pRB is compromised by oncogenic mutations, and E2F activity is enhanced, thereby facilitating cell proliferation to promote tumorigenesis. Upon such events, E2F activates the Arf tumor suppressor gene, leading to activation of the tumor suppressor p53 to protect cells from tumorigenesis. ARF inactivates MDM2, which facilitates degradation of p53 through proteasome by ubiquitination (the p53 pathway). P53 suppresses tumorigenesis by inducing cellular senescence or apoptosis. Hence, in almost all cancers, the p53 pathway is also disabled. Here we will introduce the canonical functions of the RB-E2F-p53 pathway first and then the non-classical functions of each component, which may be relevant to cancer biology.
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Affiliation(s)
- Yaxuan Zhou
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Rinka Nakajima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mashiro Shirasawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mariana Fikriyanti
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Lin Zhao
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Ritsuko Iwanaga
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Andrew P. Bradford
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Kenta Kurayoshi
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan;
| | - Keigo Araki
- Department of Morphological Biology, Ohu University School of Dentistry, 31-1 Misumido Tomitamachi, Koriyama, Fukushima 963-8611, Japan;
| | - Kiyoshi Ohtani
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
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30
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Zhang W, Zhou R, Liu X, You L, Chen C, Ye X, Liu J, Liang Y. Key role of exosomes derived from M2 macrophages in maintaining cancer cell stemness (Review). Int J Oncol 2023; 63:126. [PMID: 37711063 PMCID: PMC10609468 DOI: 10.3892/ijo.2023.5574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023] Open
Abstract
Cancer stem cells (CSCs) constitute a specific subset of cells found within tumors that are responsible for initiating, advancing and resisting traditional cancer treatments. M2 macrophages, also known as alternatively activated macrophages, contribute to the development and progression of cancer through their involvement in promoting angiogenesis, suppressing the immune system, supporting tumor growth and facilitating metastasis. Exosomes, tiny vesicles released by cells, play a crucial role in intercellular communications and have been shown to be associated with cancer development and progression by influencing the immune response; thus, they may serve as markers for diagnosis and prognosis. Currently, investigating the impact of exosomes derived from M2 macrophages on the maintenance of CSCs is a crucial area of research with the aim of developing novel therapeutic strategies to target this process and improve outcomes for individuals with cancer. Understanding the biological functions of exosomes derived from M2 macrophages and their involvement in cancer may lead to the formulation of novel diagnostic tools and treatments for this disease. By targeting M2 macrophages and the exosomes they secrete, promising prospects emerge for cancer treatment, given their substantial contribution to cancer development and progression. Further research is required to fully grasp the intricate interactions between CSCs, M2 macrophages and exosomes in cancer, and to identify fresh targets for cancer therapy. The present review explores the pivotal roles played by exosomes derived from M2 cells in maintaining the stem‑like properties of cancer cells.
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Affiliation(s)
- Weiqiong Zhang
- Department of Orthopedics, The Fourth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Ruiping Zhou
- Department of Stomatology, Yantian District People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518081, P.R. China
| | - Xin Liu
- Department of Stomatology, Yantian District People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518081, P.R. China
| | - Lin You
- Department of Stomatology, Yantian District People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518081, P.R. China
| | - Chang Chen
- Department of Stomatology, Yantian District People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518081, P.R. China
| | - Xiaoling Ye
- Department of Stomatology, Yantian District People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518081, P.R. China
| | - Jie Liu
- Department of Stomatology, Yantian District People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518081, P.R. China
| | - Youde Liang
- Department of Stomatology, Yantian District People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518081, P.R. China
- Department of Stomatology, The People's Hospital of Baoan Shenzhen, Shenzhen, Guangdong 518081, P.R. China
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31
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Inthanon S, Dejkriengkraikul P, Yodkeeree S. Notopterol Suppresses IL-17-Induced Proliferation and Invasion of A549 Lung Adenocarcinoma Cells via Modulation of STAT3, NF-κB, and AP-1 Activation. Int J Mol Sci 2023; 24:15057. [PMID: 37894738 PMCID: PMC10606807 DOI: 10.3390/ijms242015057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Interleukine-17 is a proinflammatory cytokine that promotes lung cancer growth and progression though the activation of the STAT3, NF-κB, and AP-1 signaling pathways. Therefore, blocking the IL-17-induced oncogenic pathway is a new strategy for the treatment of lung cancer. Notopterol, a furanocoumarin, has demonstrated anti-tumor effects in several types of tumors. However, its molecular function in relation to the IL-17-induced proliferation and invasion of A549 lung adenocarcinoma cells remains unknown. Here, notopterol exhibited an inhibitory effect on IL-17-promoted A549 cell proliferation and induced G0/G1 cell cycle arrest. Western blot analysis revealed that notopterol inhibited the expression of cell-cycle-regulatory proteins, including cyclin D1, cyclin E, CDK4, and E2F. Moreover, notopterol blocked IL-17-induced A549 cell migration and invasion by regulating the epithelial-mesenchymal transition (EMT) and reducing the expression of extracellular degradation enzymes. At the molecular level, notopterol treatment significantly down-regulated the IL-17-activated phosphorylation of Akt, JNK, ERK1/2, and STAT3, leading to a reduced level of transcriptional activity of NF-κB and AP-1. Collectively, our results suggest that notopterol blocks IL-17-induced A549 cell proliferation and invasion through the suppression of the MAPK, Akt, STAT3, AP-1, and NF-κB signaling pathways, as well as modulating EMT.
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Affiliation(s)
- Sirinada Inthanon
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.I.); (P.D.)
| | - Pornngarm Dejkriengkraikul
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.I.); (P.D.)
- Anticarcinogenesis and Apoptosis Research Cluster, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supachai Yodkeeree
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.I.); (P.D.)
- Anticarcinogenesis and Apoptosis Research Cluster, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
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32
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Lamichhane A, Luker GD, Agarwal S, Tavana H. Inhibiting BRAF/EGFR/MEK suppresses cancer stemness and drug resistance of primary colorectal cancer cells. Oncotarget 2023; 14:879-889. [PMID: 37791907 PMCID: PMC10549774 DOI: 10.18632/oncotarget.28517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023] Open
Abstract
Drug resistance is a major barrier against successful treatments of cancer patients. Gain of stemness under drug pressure is a major mechanism that renders treatments ineffective. Identifying approaches to target cancer stem cells (CSCs) is expected to improve treatment outcomes for patients. To elucidate the role of cancer stemness in resistance of colorectal cancer cells to targeted therapies, we developed spheroid cultures of patient-derived BRAFmut and KRASmut tumor cells and studied resistance mechanisms to inhibition of MAPK pathway through phenotypic and gene and protein expression analysis. We found that treatments enriched the expression of CSC markers CD166, ALDH1A3, CD133, and LGR5 and activated PI3K/Akt pathway in cancer cells. We examined various combination treatments to block these activities and found that a triple combination against BRAF, EGFR, and MEK significantly reduced stemness and activities of oncogenic signaling pathways. This study demonstrates the feasibility of blocking stemness-mediated drug resistance and tumorigenic activities in colorectal cancer.
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Affiliation(s)
- Astha Lamichhane
- Department of Biomedical Engineering, The University of Akron, Akron, OH 44325, USA
| | - Gary D. Luker
- Department of Radiology, Microbiology and Immunology, Biomedical Engineering, University of Michigan, Ann Arbor, MI 48105, USA
| | - Seema Agarwal
- Department of Pathology, Biochemistry, Molecular and Cellular Biology, Georgetown University, Washington, DC 20007, USA
| | - Hossein Tavana
- Department of Biomedical Engineering, The University of Akron, Akron, OH 44325, USA
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Shahi N, Yadav PN, Chaudhary U, Saad M, Mahiya K, Khan A, Shafi S, Pokharel YR. 5-Methoxyisatin N(4)-Pyrrolidinyl Thiosemicarbazone (MeOIstPyrd) Restores Mutant p53 and Inhibits the Growth of Skin Cancer Cells, In Vitro. ACS OMEGA 2023; 8:31998-32016. [PMID: 37692215 PMCID: PMC10483675 DOI: 10.1021/acsomega.3c03824] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023]
Abstract
A series of novel thiosemicarbazone derivatives containing 5-methoxy isatin were designed and synthesized with modification on N(4) position. Derivatives considering structure-activity relationship have been designed and synthesized by condensing thiosemicarbazide with 5-methoxy isatin. The synthesized compounds were characterized by elemental analysis, FT-IR spectroscopy, UV-visible spectroscopy, NMR (1H, 13C) spectroscopy, mass spectrometry, and a single-crystal study. Biological evaluation of the synthesized compounds revealed that MeOIstPyrd is the most promising compound against skin cancer cell line, A431, with an IC50 value of 0.9 μM. In addition, MeOIstPyrd also exhibited low toxicity against the normal human fibroblast and the human embryonic kidney 293 cell line, HLF-1, and HEK293, respectively. Furthermore, the mechanistic study revealed that MeOIstPyrd efficiently inhibited cell proliferation, migration, and spheroid formation by activating the mitochondrial intrinsic apoptotic pathway. MeOIstPyrd also induces DNA damage and activates p53 irrespective of the p53 status. It increases the half-life of p53 and stabilizes p53 by phosphorylating it at ser15. Moreover, MeOIstPyrd was found to bind to MDM2 in the p53 sub-pocket and, therefore, block p53-MDM2 interaction. Our result exhibited potential anticancer activity of MeOIstPyrd in the A431 cell line and its ability in restoring mutant p53, which is an interesting and promising strategy for cancer therapeutics.
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Affiliation(s)
- Nerina Shahi
- Cancer
Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi 110068, India
| | - Paras Nath Yadav
- Central
Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu 700128, Nepal
| | - Upendra Chaudhary
- Central
Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu 700128, Nepal
| | - Mohd Saad
- Cancer
Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi 110068, India
| | - Kuldeep Mahiya
- Department
of Chemistry, F.G.M. Government College, Mandi Adampur, Hisar 125052, Haryana, India
| | - Arif Khan
- Department
of Chemistry, Jamia Hamdard University, Hamdard Nagar, New Delhi 110062, India
| | - Syed Shafi
- Department
of Chemistry, Jamia Hamdard University, Hamdard Nagar, New Delhi 110062, India
| | - Yuba Raj Pokharel
- Cancer
Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi 110068, India
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Yun R, Hong E, Kim J, Park B, Kim SJ, Lee B, Song YS, Kim SJ, Park S, Kang JM. N-linked glycosylation is essential for anti-tumor activities of KIAA1324 in gastric cancer. Cell Death Dis 2023; 14:546. [PMID: 37612293 PMCID: PMC10447535 DOI: 10.1038/s41419-023-06083-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/04/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023]
Abstract
KIAA1324 is a transmembrane protein largely reported as a tumor suppressor and favorable prognosis marker in various cancers, including gastric cancer. In this study, we report the role of N-linked glycosylation in KIAA1324 as a functional post-translational modification (PTM). Loss of N-linked glycosylation eliminated the potential of KIAA1324 to suppress cancer cell proliferation and migration. Furthermore, we demonstrated that KIAA1324 undergoes fucosylation, a modification of the N-glycan mediated by fucosyltransferase, and inhibition of fucosylation also significantly suppressed KIAA1324-induced cell growth inhibition and apoptosis of gastric cancer cells. In addition, KIAA1324-mediated apoptosis and tumor regression were inhibited by the loss of N-linked glycosylation. RNA sequencing (RNAseq) analysis revealed that genes most relevant to the apoptosis and cell cycle arrest pathways were modulated by KIAA1324 with the N-linked glycosylation, and Gene Regulatory Network (GRN) analysis suggested novel targets of KIAA1324 for anti-tumor effects in the transcription level. The N-linked glycosylation blockade decreased protein stability through rapid proteasomal degradation. The non-glycosylated mutant also showed altered localization and lost apoptotic activity that inhibits the interaction between GRP78 and caspase 7. These data demonstrate that N-linked glycosylation of KIAA1324 is essential for the suppressive role of KIAA1324 protein in gastric cancer progression and indicates that KIAA1324 may have anti-tumor effects by targeting cancer-related genes with N-linked glycosylation. In conclusion, our study suggests the PTM of KIAA1324 including N-linked glycosylation and fucosylation is a necessary factor to consider for cancer prognosis and therapy improvement.
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Affiliation(s)
- Rebecca Yun
- GILO Institute, GILO Foundation, Seoul, 06668, Republic of Korea
- Interdisciplinary Program in Cancer Biology, Seoul National University, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eunji Hong
- GILO Institute, GILO Foundation, Seoul, 06668, Republic of Korea
- Department of Biomedical Science, College of Life Science, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Bora Park
- WellSpan York Hospital Family Medicine Residency Program, York, PA, USA
| | - Staci Jakyong Kim
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan
| | - Bona Lee
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yong Sang Song
- Interdisciplinary Program in Cancer Biology, Seoul National University, Gwanak-gu, Seoul, 08826, Republic of Korea
- Department of Obstetrics and Gynecology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Seong-Jin Kim
- GILO Institute, GILO Foundation, Seoul, 06668, Republic of Korea
- Medpacto Inc., Seoul, 06668, Republic of Korea
| | - Sujin Park
- GILO Institute, GILO Foundation, Seoul, 06668, Republic of Korea.
| | - Jin Muk Kang
- Department of Pediatric Hematology & Oncology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
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Soltan MA, Alhanshani AA, Shati AA, Alqahtani YA, Alshaya DS, Alharthi J, Altalhi SA, Fayad E, Zaki MSA, Eid RA. Cyclin Dependent Kinase Inhibitor 2A Genetic and Epigenetic Alterations Interfere with Several Immune Components and Predict Poor Clinical Outcome. Biomedicines 2023; 11:2254. [PMID: 37626750 PMCID: PMC10452213 DOI: 10.3390/biomedicines11082254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Cyclin dependent kinase inhibitor 2A (CDKN2A) is a well-known tumor suppressor gene as it functions as a cell cycle regulator. While several reports correlate the malfunction of CDKN2A with the initiation and progression of several types of human tumors, there is a lack of a comprehensive study that analyzes the potential effect of CDKN2A genetic alterations on the human immune components and the consequences of that effect on tumor progression and patient survival in a pan-cancer model. The first stage of the current study was the analysis of CDKN2A differential expression in tumor tissues and the corresponding normal ones and correlating that with tumor stage, grade, metastasis, and clinical outcome. Next, a detailed profile of CDKN2A genetic alteration under tumor conditions was described and assessed for its effect on the status of different human immune components. CDKN2A was found to be upregulated in cancerous tissues versus normal ones and that predicted the progression of tumor stage, grade, and metastasis in addition to poor prognosis under different forms of tumors. Additionally, CDKN2A experienced different forms of genetic alteration under tumor conditions, a characteristic that influenced the infiltration and the status of CD8, the chemokine CCL4, and the chemokine receptor CCR6. Collectively, the current study demonstrates the potential employment of CDKN2A genetic alteration as a prognostic and immunological biomarker under several types of human cancers.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt
| | - Ahmad A. Alhanshani
- Department of Child Health, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia
| | - Ayed A. Shati
- Department of Child Health, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia
| | - Youssef A. Alqahtani
- Department of Child Health, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia
| | - Dalal Sulaiman Alshaya
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Jawaher Alharthi
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Sarah Awwadh Altalhi
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Mohamed Samir A. Zaki
- Anatomy Department, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia
| | - Refaat A. Eid
- Pathology Department, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia
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Zhang M, Xu Y, Zhang Y, Lou G. E2F8 knockdown suppresses cell proliferation and induces cell cycle arrest via Wnt/β-Catenin pathway in ovarian cancer. CHINESE J PHYSIOL 2023; 66:266-275. [PMID: 37635486 DOI: 10.4103/cjop.cjop-d-22-00142] [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] [Indexed: 08/29/2023] Open
Abstract
Ovarian cancer is one of the leading causes of death in female reproductive system cancers. However, the pathogenesis of ovarian cancer remains elusive. Our aim is to investigate the potential targets for ovarian cancer. Two microarray datasets were obtained from the Gene Expression Omnibus public database. Using R package limma, the differentially expressed genes (DEGs) were identified from the datasets. There were 95 overlapping DEGs in two microarray datasets. GO, KEGG pathway analysis, and protein-protein interaction (PPI) network analysis were carried out based on the DEGs. Wnt signaling pathway and cell cycle were enriched in the KEGG pathway analysis. Moreover, the top 10 hub genes with the most nodes were determined by PPI network analysis. E2F8, one of hub genes was positively linked to a bad outcome in ovarian cancer patients. Furthermore, E2F8 knockdown suppressed cell proliferation and induced cell cycle arrest in ovarian cancer. In addition, we found that silencing E2F8 inhibited the Wnt/β-catenin signaling pathway. In ovarian cancer cells with E2F8 knockdown, overexpressing β-catenin restored both the suppressed capacity of cell proliferation and cell cycle progression. Therefore, our results revealed that E2F8 had an involvement in the development of ovarian cancer which might act as a therapeutic target.
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Affiliation(s)
- Meiyin Zhang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Ye Xu
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yongjian Zhang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Ge Lou
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
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37
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Waseem A, Rashid S, Rashid K, Khan MA, Khan R, Haque R, Seth P, Raza SS. Insight into the transcription factors regulating Ischemic Stroke and Glioma in Response to Shared Stimuli. Semin Cancer Biol 2023; 92:102-127. [PMID: 37054904 DOI: 10.1016/j.semcancer.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/28/2023] [Accepted: 04/09/2023] [Indexed: 04/15/2023]
Abstract
Cerebral ischemic stroke and glioma are the two leading causes of patient mortality globally. Despite physiological variations, 1 in 10 people who have an ischemic stroke go on to develop brain cancer, most notably gliomas. In addition, glioma treatments have also been shown to increase the risk of ischemic strokes. Stroke occurs more frequently in cancer patients than in the general population, according to traditional literature. Unbelievably, these events share multiple pathways, but the precise mechanism underlying their co-occurrence remains unknown. Transcription factors (TFs), the main components of gene expression programmes, finally determine the fate of cells and homeostasis. Both ischemic stroke and glioma exhibit aberrant expression of a large number of TFs, which are strongly linked to the pathophysiology and progression of both diseases. The precise genomic binding locations of TFs and how TF binding ultimately relates to transcriptional regulation remain elusive despite a strong interest in understanding how TFs regulate gene expression in both stroke and glioma. As a result, the importance of continuing efforts to understand TF-mediated gene regulation is highlighted in this review, along with some of the primary shared events in stroke and glioma.
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Affiliation(s)
- Arshi Waseem
- Laboratory for Stem Cell & Restorative Neurology, Department of Biotechnology, Era's Lucknow Medical College and Hospital, Era University, Sarfarazganj, Lucknow-226003, India
| | - Sumaiya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Khalid Rashid
- Department of Cancer Biology, Vontz Center for Molecular Studies, Cincinnati, OH 45267-0521
| | | | - Rehan Khan
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City,Mohali, Punjab 140306, India
| | - Rizwanul Haque
- Department of Biotechnology, Central University of South Bihar, Gaya -824236, India
| | - Pankaj Seth
- Molecular and Cellular Neuroscience, Neurovirology Section, National Brain Research Centre, Manesar, Haryana-122052, India
| | - Syed Shadab Raza
- Laboratory for Stem Cell & Restorative Neurology, Department of Biotechnology, Era's Lucknow Medical College and Hospital, Era University, Sarfarazganj, Lucknow-226003, India; Department of Stem Cell Biology and Regenerative Medicine, Era's Lucknow Medical College Hospital, Era University, Sarfarazganj, Lucknow-226003, India
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38
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Wang P, Zhu Y, Jia X, Ying X, Sun L, Ruan S. Clinical prognostic value of OSGIN2 in gastric cancer and its proliferative effect in vitro. Sci Rep 2023; 13:5775. [PMID: 37031243 PMCID: PMC10082810 DOI: 10.1038/s41598-023-32934-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/04/2023] [Indexed: 04/10/2023] Open
Abstract
This study explored the promoting effect of oxidative stress-induced growth inhibitor family member 2(OSGIN2) on gastric cancer (GC) through public databases and in vitro experiments. The potential relationship between OSGIN2 expression, prognosis, functional enrichment of associated differential genes, immune infiltration, and mutational information in gastric cancer were comprehensively investigated using bioinformatics analysis. OSGIN2 was knocked down using small interfering RNA (siRNA) transfection for subsequent cell function testing. The results showed that gastric carcinoma cells and tissues contained high levels of OSGIN2, which was associated with a poor prognosis for GC patients. It was important in the cell cycle, autophagy, etc., and was related to a variety of tumor-related signal pathways. Knockdown of OSGIN2 inhibited tumor cell proliferation and contributed to cell cycle arrest. It was also correlated with tumor immune infiltrating cells (TILs), affecting antitumor immune function. Our analysis highlights that OSING2, as a new biomarker, has diagnostic and prognostic value in gastric cancer and is a potentially effective target in GC treatment.
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Affiliation(s)
- Peipei Wang
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310006, China
- Zhejiang Key Lab of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Ying Zhu
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310006, China
| | - Xinru Jia
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xiangchang Ying
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Leitao Sun
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310006, China.
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Shanming Ruan
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310006, China.
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Kula A, Dawidowicz M, Mielcarska S, Kiczmer P, Skiba H, Krygier M, Chrabańska M, Piecuch J, Szrot M, Robotycka J, Ochman B, Strzałkowska B, Czuba Z, Świętochowska E, Waniczek D. Overexpression and Role of HHLA2, a Novel Immune Checkpoint, in Colorectal Cancer. Int J Mol Sci 2023; 24:ijms24065876. [PMID: 36982953 PMCID: PMC10057377 DOI: 10.3390/ijms24065876] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The study aimed to investigate correlations between HHLA2 levels and parameters, including microsatellite instability (MSI) status, CD8+ cells, and histopathological features: budding, tumor-infiltrating lymphocytes (TILs), TNM scale, grading, cytokines, chemokines, and cell signaling moleculesin colorectal cancer (CRC). Furthermore, the immune infiltration landscape and HHLA2-related pathways in colorectal cancer using available online datasets were analyzed. The study included 167 patients diagnosed with CRC. Expression of HHLA2 was detected by immunohistochemistry method (IHC) and enzyme-linked immunosorbent assay (ELISA). The IHC was used to evaluate the MSI and CD8+ status. The budding and TILs were measured using a light microscope. The concentrations of cytokines, chemokines, and cell signaling molecules were measured to analyze the data by the Bio-Plex Pro Human cytokine screening panel, 48 cytokine assay, and principal component analysis (PCA). Geneset enrichment analysis (GSEA) was conducted to identify HHLA2-related pathways. The biological function of HHLA2 was predicted by Gene Ontology (GO). Analysis of the immune infiltration landscape of HHLA2 in colorectal cancer was made by the web-based tool Camoip. High HHLA2 expression was detected in CRC tumor tissues compared to the adjacent noncancerous tissues. The percentage of HHLA2-positive tumors was 97%. GSEA and GO showed that HHLA2 upregulation correlated with cancer-related pathways and several biological functions. Tumor-infiltrating lymphocytes score correlated positively with IHC HHLA2 expression level percentage. There was a negative correlation between HHLA2, anti-tumor cytokines and pro-tumor growth factors. This study provides a valuable insight into the role of HHLA2 in CRC. We reveal the role of HHLA2 expression as well as a stimulatory and inhibitory immune checkpoint in colorectal cancer. Further research may verify the therapeutic values of the HHLA2-KIR3DL3/TMIGD2 pathway in colorectal cancer.
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Affiliation(s)
- Agnieszka Kula
- Department of Oncological Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
| | - Miriam Dawidowicz
- Department of Oncological Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
| | - Sylwia Mielcarska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Paweł Kiczmer
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 13-15 3 Maja, 41-800 Zabrze, Poland
| | - Hanna Skiba
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 13-15 3 Maja, 41-800 Zabrze, Poland
| | - Małgorzata Krygier
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 13-15 3 Maja, 41-800 Zabrze, Poland
| | - Magdalena Chrabańska
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 13-15 3 Maja, 41-800 Zabrze, Poland
| | - Jerzy Piecuch
- Department of General and Bariatric Surgery and Emergency Medicine, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
| | - Monika Szrot
- Department of General and Bariatric Surgery and Emergency Medicine, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
| | - Julia Robotycka
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Błażej Ochman
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Bogumiła Strzałkowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Zenon Czuba
- Department of Microbiology and Immunology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | - Elżbieta Świętochowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Dariusz Waniczek
- Department of Oncological Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland
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Deregulated E2F Activity as a Cancer-Cell Specific Therapeutic Tool. Genes (Basel) 2023; 14:genes14020393. [PMID: 36833320 PMCID: PMC9956157 DOI: 10.3390/genes14020393] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/24/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The transcription factor E2F, the principal target of the tumor suppressor pRB, plays crucial roles in cell proliferation and tumor suppression. In almost all cancers, pRB function is disabled, and E2F activity is enhanced. To specifically target cancer cells, trials have been undertaken to suppress enhanced E2F activity to restrain cell proliferation or selectively kill cancer cells, utilizing enhanced E2F activity. However, these approaches may also impact normal growing cells, since growth stimulation also inactivates pRB and enhances E2F activity. E2F activated upon the loss of pRB control (deregulated E2F) activates tumor suppressor genes, which are not activated by E2F induced by growth stimulation, inducing cellular senescence or apoptosis to protect cells from tumorigenesis. Deregulated E2F activity is tolerated in cancer cells due to inactivation of the ARF-p53 pathway, thus representing a feature unique to cancer cells. Deregulated E2F activity, which activates tumor suppressor genes, is distinct from enhanced E2F activity, which activates growth-related genes, in that deregulated E2F activity does not depend on the heterodimeric partner DP. Indeed, the ARF promoter, which is specifically activated by deregulated E2F, showed higher cancer-cell specific activity, compared to the E2F1 promoter, which is also activated by E2F induced by growth stimulation. Thus, deregulated E2F activity is an attractive potential therapeutic tool to specifically target cancer cells.
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Wang B, Zhang J, Wang X, Zhao L, Wang Y, Fan Z, Liu L, Gao W. Identification and clinical validation of key genes as the potential biomarkers in colorectal adenoma. BMC Cancer 2023; 23:39. [PMID: 36631756 PMCID: PMC9832797 DOI: 10.1186/s12885-022-10422-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 12/07/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC), ranking third in cancer prevalence and second in mortality worldwide, is mainly derived from colorectal adenoma (CRA). CRA is a common benign disease in the intestine with rapidly increasing incidence and malignant potential. Therefore, this study aimed to recognize significant biomarkers and original pathogenesis in CRA. METHODS Transcriptome data of GSE8671, GSE37364, and GSE15960 were downloaded from the Gene Expression Omnibus (GEO) datasets, and differentially expressed genes (DEGs) were screened. Functional pathways enrichment, protein-protein interaction (PPI) network, stem-correlation analysis, CIBERSORT, risk score and survival analyses were performed. RT-qPCR and immunohistochemical staining were applied to verify our results. RESULTS: Screening for significant DEGs in each dataset, we identified 230 robust DEGs, including 127 upregulated and 103 downregulated genes. Functional pathways enrichment showed that these DEGs were distinctly enriched in various tumor-associated pathways, such as growth factor activity, extracellular structure organization, neutrophil activation, and inflammatory response. We filtered out two hub genes via STRING and Modules analysis, including CA2 and HSD11B2. Stem-correlation analysis displayed that hub genes were negatively associated with stem-related genes (Olfm4, CD44, CCND1 and MYC). The CIBERSORT algorithm indicated that Macrophage2, activated mast cells, and Neutrophils promoted CRA progression through inflammation. Survival analysis showed that CA2 and HSD11B2 were positively associated with survival outcomes in CRC. CONCLUSION Our study has successfully identified the critical role of two core genes in the development and oncogenesis of CRA, which provides novel insight into the underlying pathogenesis, potential biomarkers and therapeutic targets.
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Affiliation(s)
- Bangting Wang
- grid.412676.00000 0004 1799 0784Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu China
| | - Jiting Zhang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Wang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Lili Zhao
- grid.412676.00000 0004 1799 0784Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu China
| | - Yan Wang
- grid.412676.00000 0004 1799 0784Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu China
| | - Zhining Fan
- grid.412676.00000 0004 1799 0784Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu China
| | - Li Liu
- Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China.
| | - Wenqing Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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Gattupalli M, Dey P, Poovizhi S, Patel RB, Mishra D, Banerjee S. The Prospects of RNAs and Common Significant Pathways in Cancer Therapy and Regenerative Medicine. Regen Med 2023. [DOI: 10.1007/978-981-19-6008-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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High Expression of E2F4 Is an Adverse Prognostic Factor and Related to Immune Infiltration in Oral Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4731364. [PMID: 36567912 PMCID: PMC9780755 DOI: 10.1155/2022/4731364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/01/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Background We aimed to evaluate the prognostic value of E2F4 expression in oral squamous cell carcinoma (OSCC) and clarify its influence on immune cell infiltration and biological functions. Methods The Cancer Genome Atlas (TCGA) database, the STRING database, and related online tools as well as single-sample gene set enrichment analysis (ssGSEA) were used for the analyses in our study. Results The E2F4 expression was elevated in OSCC tumor tissue compared with paracancerous tissues. The high expression of E2F4 was closely related to the poorer overall survival, disease-free survival, and progression-free interval of OSCC. In addition, pathway enrichment analyses revealed that the top 49 genes most closely related to E2F4 were strongly associated with the cell cycle. E2F4-related proteins were closely related to the following KEGG pathways: cell cycle, cellular senescence, PI3K-Akt signaling pathway, Wnt signaling pathway, and notch signaling pathway. It was also demonstrated that the E2F4 expression was negatively correlated with immune purity and strongly related to immune cell infiltration in OSCC. Conclusions E2F4 can be used as a novel biomarker for the diagnosis and prognosis of OSCC.
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Huang J, Cao Y, Li X, Yu F, Han X. E2F1 regulates miR-215-5p to aggravate paraquat-induced pulmonary fibrosis via repressing BMPR2 expression. Toxicol Res (Camb) 2022; 11:940-950. [PMID: 36569483 PMCID: PMC9773066 DOI: 10.1093/toxres/tfac071] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 02/01/2023] Open
Abstract
Background Pulmonary fibrosis is considered to be an irreversible lung injury, which can be caused by paraquat (PQ) poisoning. MiRNAs have been demonstrated crucial roles in pulmonary fibrosis caused by numerous approaches including PQ induction. The purpose of this study was to investigate the role and the underlying mechanism of miR-215 in PQ-induced pulmonary fibrosis. Methods The cell and animal models of pulmonary fibrosis were established through PQ intervention. Cell viability was performed to test by MTT assay. Immunofluorescence assay was used to detect COL1A1 expression and its location. The relationships among E2F1, miR-215-5p, and BMPR2 were validated by dual luciferase reporter gene assay, chromatin immunoprecipitation and RNA-binding protein immunoprecipitation. Lung morphology was evaluated by hematoxylin and eosin staining. Results MiR-215-5p was upregulated in PQ-induced pulmonary fibrosis in vitro and in vivo. MiR-215-5p silencing relieved PQ-induced pulmonary fibrosis progression by enhancing cell viability and reducing the expression of fibrosis-related markers (COL1A1, COL3A1, and α-SMA). Mechanistically, miR-215-5p directly targeted BMRP2. BMPR2 knockdown abolished the suppressive effects of miR-215-5p knockdown on PQ-induced pulmonary fibrosis. In addition, E2F1 interacted with miR-215-5p promoter and positively regulated miR-215-5p expression. E2F1 downregulation reduced miR-215-5p level and promoted BMPR2 level via regulating TGF-β/Smad3 pathway, and then suppressed PQ-induced pulmonary fibrosis, whereas these effects were compromised by miR-215-5p sufficiency. Conclusion MiR-215-5p was activated by E2F1 to repress BMPR2 expression and activate TGF-β/Smad3 pathway, which aggravated PQ-induced pulmonary fibrosis progression. Targeting the E2F1/miR-215-5p/BMPR2 axis might be a new approach to alleviate PQ-induced pulmonary fibrosis.
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Affiliation(s)
- Jie Huang
- Emergency Department, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, No.61, Jiefang west Road, Furong District, Changsha, Hunan Province 410005, P. R. China
| | - Yan Cao
- Emergency Department, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, No.61, Jiefang west Road, Furong District, Changsha, Hunan Province 410005, P. R. China
| | - Xiang Li
- Emergency Department, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, No.61, Jiefang west Road, Furong District, Changsha, Hunan Province 410005, P. R. China
| | - Fang Yu
- Emergency Department, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, No.61, Jiefang west Road, Furong District, Changsha, Hunan Province 410005, P. R. China
| | - Xiaotong Han
- Emergency Department, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, No.61, Jiefang west Road, Furong District, Changsha, Hunan Province 410005, P. R. China
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Ghelichkhani F, Gonzalez FA, Kapitonova MA, Schaefer-Ramadan S, Liu J, Cheng R, Rozovsky S. Selenoprotein S: A versatile disordered protein. Arch Biochem Biophys 2022; 731:109427. [PMID: 36241082 PMCID: PMC10026367 DOI: 10.1016/j.abb.2022.109427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022]
Abstract
Selenoprotein S (selenos) is a small, intrinsically disordered membrane protein that is associated with various cellular functions, such as inflammatory processes, cellular stress response, protein quality control, and signaling pathways. It is primarily known for its contribution to the ER-associated degradation (ERAD) pathway, which governs the extraction of misfolded proteins or misassembled protein complexes from the ER to the cytosol for degradation by the proteasome. However, selenos's other cellular roles in signaling are equally vital, including the control of transcription factors and cytokine levels. Consequently, genetic polymorphisms of selenos are associated with increased risk for diabetes, dyslipidemia, and cardiovascular diseases, while high expression levels correlate with poor prognosis in several cancers. Its inhibitory role in cytokine secretion is also exploited by viruses. Since selenos binds multiple protein complexes, however, its specific contributions to various cellular pathways and diseases have been difficult to establish. Thus, the precise cellular functions of selenos and their interconnectivity have only recently begun to emerge. This review aims to summarize recent insights into the structure, interactome, and cellular roles of selenos.
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Affiliation(s)
- Farid Ghelichkhani
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Fabio A Gonzalez
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Mariia A Kapitonova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | | | - Jun Liu
- Enlaza Therapeutics, 11099 N. Torrey Pines Rd, suite 290, La Jolla, CA, 92037, USA
| | - Rujin Cheng
- NGM Biopharmaceuticals, Inc., 333 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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Jiang H, Li AM, Ye J. The magic bullet: Niclosamide. Front Oncol 2022; 12:1004978. [PMID: 36479072 PMCID: PMC9720275 DOI: 10.3389/fonc.2022.1004978] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/12/2022] [Indexed: 08/27/2023] Open
Abstract
The term 'magic bullet' is a scientific concept proposed by the German Nobel laureate Paul Ehrlich in 1907, describing a medicine that could specifically and efficiently target a disease without harming the body. Oncologists have been looking for a magic bullet for cancer therapy ever since. However, the current therapies for cancers-including chemotherapy, radiation therapy, hormone therapy, and targeted therapy-pose either pan-cytotoxicity or only single-target efficacy, precluding their ability to function as a magic bullet. Intriguingly, niclosamide, an FDA-approved drug for treating tapeworm infections with an excellent safety profile, displays broad anti-cancer activity in a variety of contexts. In particular, niclosamide inhibits multiple oncogenic pathways such as Wnt/β-catenin, Ras, Stat3, Notch, E2F-Myc, NF-κB, and mTOR and activates tumor suppressor signaling pathways such as p53, PP2A, and AMPK. Moreover, niclosamide potentially improves immunotherapy by modulating pathways such as PD-1/PDL-1. We recently discovered that niclosamide ethanolamine (NEN) reprograms cellular metabolism through its uncoupler function, consequently remodeling the cellular epigenetic landscape to promote differentiation. Inspired by the promising results from the pre-clinical studies, several clinical trials are ongoing to assess the therapeutic effect of niclosamide in cancer patients. This current review summarizes the functions, mechanism of action, and potential applications of niclosamide in cancer therapy as a magic bullet.
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Affiliation(s)
- Haowen Jiang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, United States
| | - Albert M. Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, United States
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, United States
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, United States
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, United States
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Russi S, Marano L, Laurino S, Calice G, Scala D, Marino G, Sgambato A, Mazzone P, Carbone L, Napolitano G, Roviello F, Falco G, Zoppoli P. Gene Regulatory Network Characterization of Gastric Cancer's Histological Subtypes: Distinctive Biological and Clinically Relevant Master Regulators. Cancers (Basel) 2022; 14:4961. [PMID: 36230884 PMCID: PMC9563962 DOI: 10.3390/cancers14194961] [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: 09/01/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
Gastric cancer (GC) molecular heterogeneity represents a major determinant for clinical outcomes, and although new molecular classifications have been introduced, they are not easy to translate from bench to bedside. We explored the data from GC public databases by performing differential gene expression analysis (DEGs) and gene network reconstruction to identify master regulators (MRs), as well as a gene set analysis (GSA) to reveal their biological features. Moreover, we evaluated the association of MRs with clinicopathological parameters. According to the GSA, the Diffuse group was characterized by an epithelial-mesenchymal transition (EMT) and inflammatory response, while the Intestinal group was associated with a cell cycle and drug resistance pathways. In particular, the regulons of Diffuse MRs, such as Vgll3 and Ciita, overlapped with the EMT and interferon-gamma response, while the regulons Top2a and Foxm1 were shared with the cell cycle pathways in the Intestinal group. We also found a strict association between MR activity and several clinicopathological features, such as survival. Our approach led to the identification of genes and pathways differentially regulated in the Intestinal and Diffuse GC histotypes, highlighting biologically interesting MRs and subnetworks associated with clinical features and prognosis, suggesting putative actionable candidates.
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Affiliation(s)
- Sabino Russi
- IRCCS-CROB Centro di Riferimento Oncologico della Basilica, 85028 Rionero in Vulture, Italy
| | - Luigi Marano
- Unit of General Surgery and Surgical Oncology, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy
| | - Simona Laurino
- IRCCS-CROB Centro di Riferimento Oncologico della Basilica, 85028 Rionero in Vulture, Italy
| | - Giovanni Calice
- IRCCS-CROB Centro di Riferimento Oncologico della Basilica, 85028 Rionero in Vulture, Italy
| | - Dario Scala
- IRCCS-CROB Centro di Riferimento Oncologico della Basilica, 85028 Rionero in Vulture, Italy
| | - Graziella Marino
- IRCCS-CROB Centro di Riferimento Oncologico della Basilica, 85028 Rionero in Vulture, Italy
| | - Alessandro Sgambato
- IRCCS-CROB Centro di Riferimento Oncologico della Basilica, 85028 Rionero in Vulture, Italy
| | - Pellegrino Mazzone
- Biogem, Istituto di Biologia e Genetica Molecolare, Via Camporeale, 83031 Ariano Irpino, Italy
| | - Ludovico Carbone
- Unit of General Surgery and Surgical Oncology, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy
| | - Giuliana Napolitano
- Department of Biology, University of Naples ‘Federico II’, 80126 Naples, Italy
| | - Franco Roviello
- Unit of General Surgery and Surgical Oncology, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy
| | - Geppino Falco
- Biogem, Istituto di Biologia e Genetica Molecolare, Via Camporeale, 83031 Ariano Irpino, Italy
- Department of Biology, University of Naples ‘Federico II’, 80126 Naples, Italy
| | - Pietro Zoppoli
- Department of Molecular Medicine and Health Biotechnolgy, Università di Napoli Federico II, 80131 Naples, Italy
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Ognibene M, Cangelosi D, Sorrentino S, Zanardi S, Zara F, Pezzolo A, Parodi S. E2F3 gene expression is a potential negative prognostic marker for localised and MYCN not-amplified neuroblastoma: Results of in silico analysis of 786 samples. Pediatr Blood Cancer 2022; 69:e29800. [PMID: 35652628 DOI: 10.1002/pbc.29800] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/13/2022] [Accepted: 05/09/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Neuroblastoma (NB) is an enigmatic childhood malignancy characterised by a wide range of clinical behaviour. Many potential oncogenes for NB have recently been identified. Among them, E2 transcription factor 3 (E2F3) expression was associated with a poor survival in 134 stage 4S patients, but evidence for other stage groups remains poorly investigated. METHODS We have analysed the expression of E2F3 gene from a database of 786 NB samples. Overall and event-free survivals (EFS) were assessed by the Kaplan-Meier method, splitting the data on the median and tertile expression values. The Cox model was applied to control for the confounding by stage, age and MYCN amplification. Validation was performed by an in silico analysis of an independent cohort of 283 NB patients. Furthermore, an immunofluorescence analysis on 48 formalin-fixed, paraffin-embedded NB specimens was also performed. RESULTS E2F3 overexpression was associated with a poor survival (EFS = 84%, 95% CI: 79%-95%, for low expression levels; EFS = 62%, 95% CI: 56%-68% for middle levels; EFS = 30%, 95% CI: 24%-36%, for high levels, p < .001). This association was confirmed in multivariable analysis and was more evident in patients with MYCN not-amplified and localised stages. Immunofluorescence results and the validation on an independent cohort of NB primary samples confirmed these findings. CONCLUSIONS E2F3 is a new potential prognostic marker in NB with favourable characteristics at diagnosis. Further studies are needed to elucidate the potential role of E2F3 in NB oncogenesis and progression, in order to identify new targets for therapeutic interventions.
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Affiliation(s)
- Marzia Ognibene
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Davide Cangelosi
- Unità di Bioinformatica Clinica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Stefania Sorrentino
- U.O.C. Divisione di Oncologia, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Sabrina Zanardi
- U.O.S.I.D. Epidemiologia e Biostatistica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Federico Zara
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | | | - Stefano Parodi
- Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genova, Italy
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Loren P, Saavedra N, Saavedra K, De Godoy Torso N, Visacri MB, Moriel P, Salazar LA. Contribution of MicroRNAs in Chemoresistance to Cisplatin in the Top Five Deadliest Cancer: An Updated Review. Front Pharmacol 2022; 13:831099. [PMID: 35444536 PMCID: PMC9015654 DOI: 10.3389/fphar.2022.831099] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/16/2022] [Indexed: 12/02/2022] Open
Abstract
Cisplatin (DDP) is a well-known anticancer drug used for the treatment of numerous human cancers in solid organs, including bladder, breast, cervical, head and neck squamous cell, ovarian, among others. Its most important mode of action is the DNA-platinum adducts formation, inducing DNA damage response, silencing or activating several genes to induce apoptosis; these mechanisms result in genetics and epigenetics modifications. The ability of DDP to induce tumor cell death is often challenged by the presence of anti-apoptotic regulators, leading to chemoresistance, wherein many patients who have or will develop DDP-resistance. Cancer cells resist the apoptotic effect of chemotherapy, being a problem that severely restricts the successful results of treatment for many human cancers. In the last 30 years, researchers have discovered there are several types of RNAs, and among the most important are non-coding RNAs (ncRNAs), a class of RNAs that are not involved in protein production, but they are implicated in gene expression regulation, and representing the 98% of the human genome non-translated. Some ncRNAs of great interest are long ncRNAs, circular RNAs, and microRNAs (miRs). Accumulating studies reveal that aberrant miRs expression can affect the development of chemotherapy drug resistance, by modulating the expression of relevant target proteins. Thus, identifying molecular mechanisms underlying chemoresistance development is fundamental for setting strategies to improve the prognosis of patients with different types of cancer. Therefore, this review aimed to identify and summarize miRs that modulate chemoresistance in DDP-resistant in the top five deadliest cancer, both in vitro and in vivo human models.
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Affiliation(s)
- Pía Loren
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Nicolás Saavedra
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Kathleen Saavedra
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | | | | | - Patricia Moriel
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, Brazil
| | - Luis A Salazar
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
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Xia H, Wang M, Su X, Lv Z, Yan Q, Guo X, Liu M. A Novel Gene Signature Associated With “E2F Target” Pathway for Predicting the Prognosis of Prostate Cancer. Front Mol Biosci 2022; 9:838654. [PMID: 35495629 PMCID: PMC9045651 DOI: 10.3389/fmolb.2022.838654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/15/2022] [Indexed: 01/24/2023] Open
Abstract
Background: The effect of the adenoviral early region 2 binding factors (E2Fs) target pathway on prostate cancer is not clear. It is necessary to establish an E2F target-related gene signature to predict prognosis and facilitate clinical decision-making.Methods: An E2F target-related gene signature was established by univariate and LASSO Cox regression analyses, and its predictive ability was verified in multiple cohorts. Moreover, the enrichment pathway, immune microenvironment, and drug sensitivity of the activated E2F target pathway were also explored.Results: The E2F target-related gene signature consisted of MXD3, PLK1, EPHA10, and KIF4A. The patients with high-risk scores showed poor prognosis, therapeutic resistance, and immunosuppression, along with abnormal growth characteristics of cells. Tinib drugs showed high sensitivity to the expression of MXD3 and EPHA10 genes.Conclusion: Our research established an E2F target-related signature for predicting the prognosis of prostate cancer. This study provides insights into formulating individualized detection and treatment as well as provides a theoretical basis for future research.
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Affiliation(s)
- Haoran Xia
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Miaomiao Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaonan Su
- Department of Urology, Zoucheng People’s Hospital, Zoucheng, China
| | - Zhengtong Lv
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qiuxia Yan
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Xiaoxiao Guo
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Xiaoxiao Guo, ; Ming Liu,
| | - Ming Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Xiaoxiao Guo, ; Ming Liu,
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