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Bhat-Nakshatri P, Gao H, Khatpe AS, Adebayo AK, McGuire PC, Erdogan C, Chen D, Jiang G, New F, German R, Emmert L, Sandusky G, Storniolo AM, Liu Y, Nakshatri H. Single-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry. Nat Med 2024:10.1038/s41591-024-03011-9. [PMID: 39122969 DOI: 10.1038/s41591-024-03011-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 04/22/2024] [Indexed: 08/12/2024]
Abstract
Single-nucleus analysis allows robust cell-type classification and helps to establish relationships between chromatin accessibility and cell-type-specific gene expression. Here, using samples from 92 women of several genetic ancestries, we developed a comprehensive chromatin accessibility and gene expression atlas of the breast tissue. Integrated analysis revealed ten distinct cell types, including three major epithelial subtypes (luminal hormone sensing, luminal adaptive secretory precursor (LASP) and basal-myoepithelial), two endothelial and adipocyte subtypes, fibroblasts, T cells, and macrophages. In addition to the known cell identity genes FOXA1 (luminal hormone sensing), EHF and ELF5 (LASP), TP63 and KRT14 (basal-myoepithelial), epithelial subtypes displayed several uncharacterized markers and inferred gene regulatory networks. By integrating breast epithelial cell gene expression signatures with spatial transcriptomics, we identified gene expression and signaling differences between lobular and ductal epithelial cells and age-associated changes in signaling networks. LASP cells and fibroblasts showed genetic ancestry-dependent variability. An estrogen receptor-positive subpopulation of LASP cells with alveolar progenitor cell state was enriched in women of Indigenous American ancestry. Fibroblasts from breast tissues of women of African and European ancestry clustered differently, with accompanying gene expression differences. Collectively, these data provide a vital resource for further exploring genetic ancestry-dependent variability in healthy breast biology.
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Affiliation(s)
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aditi S Khatpe
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Adedeji K Adebayo
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Patrick C McGuire
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cihat Erdogan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Duojiao Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Guanglong Jiang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Felicia New
- NanoString Technology Inc., Seattle, WA, USA
| | - Rana German
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lydia Emmert
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - George Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anna Maria Storniolo
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA.
- VA Roudebush Medical Center, Indianapolis, IN, USA.
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2
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Zhu Y, Lin J, Li Y, Luo Z. Prognostic value and immune infiltration of the NEK family in clear cell renal cell carcinoma. Medicine (Baltimore) 2024; 103:e38961. [PMID: 39029088 PMCID: PMC11398795 DOI: 10.1097/md.0000000000038961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/21/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a fatal urological malignancy. Members of the never-in mitosis gene A (NIMA)-related kinase (NEK) family have been found to participate in the progression of several cancers and could be used as target genes to treat corresponding diseases. Nonetheless, the prognostic value and immune infiltration levels of NEK family genes in ccRCC remain unknown. The GSCA, TIMER, and GEPIA databases were utilized to examine the differential expression of NEK family members in ccRCC, and the Kaplan-Meier plotter was utilized to analyze the prognosis. The STRING database was used to construct a protein-protein interaction network. Analysis of function was performed by the Sangerbox tool. In addition, the relationship between NEK family genes and immune cells was explored using the TIMER and TISIDB databases. Finally, we used quantitative real-time PCR (qPCR) and immunohistochemistry (IHC) for experimental verification. Transcriptional levels of NEK2, NEK3, NEK5, NEK6, and NEK11 significantly differed between ccRCC and normal tissues. Moreover, there was a significant correlation between NEK1, NEK2, NEK4, NEK8, NEK9, and NEK10 and their clinicopathological stages in patients with ccRCC. Based on survival analysis, ccRCC patients with high transcriptional levels of NEK2, NEK3, NEK8, and NEK10 and low transcriptional levels of NEK1, NEK4, NEK5, NEK6, NEK7, NEK9, NEK11 had shorter survival times. Additionally, a significant relationship was observed between NEK family members and immune cell infiltration, immune cell markers, and immune subtypes. These results indicate that NEK family members are significantly differentially expressed in ccRCC, and a significant correlation exists between the NEK family and prognosis and immune infiltration. NEK family members may act as therapeutic targets and prognostic indicators in ccRCC.
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Affiliation(s)
- Yingli Zhu
- Department of Endocrinology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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3
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Dutt P, Haider N, Mouaaz S, Podmore L, Stambolic V. β-catenin turnover is regulated by Nek10-mediated tyrosine phosphorylation in A549 lung adenocarcinoma cells. Proc Natl Acad Sci U S A 2024; 121:e2300606121. [PMID: 38683979 PMCID: PMC11087748 DOI: 10.1073/pnas.2300606121] [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: 01/13/2023] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
β-catenin has influential roles affecting embryonic development, tissue homeostasis, and human diseases including cancer. Cellular β-catenin levels are exquisitely controlled by a variety of regulatory mechanisms. In the course of exploring the functions of the Nek10 tyrosine kinase, we observed that deletion of Nek10 in lung adenocarcinoma cells resulted in dramatic stabilization of β-catenin, suggestive of a Nek10 role in the control of β-catenin turnover. Nek10-deficient cells exhibited diminished ability to form tumorspheres in suspension, grow in soft agar, and colonize mouse lung tissue following tail vein injection. Mechanistically, Nek10 associates with the Axin complex, responsible for β-catenin degradation, where it phosphorylates β-catenin at Tyr30, located within the regulatory region governing β-catenin turnover. In the absence of Nek10 phosphorylation, GSK3-mediated phosphorylation of β-catenin, a prerequisite for its turnover, is impaired. This represents a divergent function within the Nek family, whose other members are serine-threonine kinases involved in different elements of the centrosomal cycle, primary cilia function, and DNA damage responses.
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Affiliation(s)
- Previn Dutt
- Princess Margaret Cancer Centre, University Health Network, Princess Margaret Cancer Research Tower, Toronto, ONM5G 1L7, Canada
| | - Nasir Haider
- Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower, Toronto, ONM5G 1L7, Canada
| | - Samar Mouaaz
- Princess Margaret Cancer Centre, University Health Network, Princess Margaret Cancer Research Tower, Toronto, ONM5G 1L7, Canada
| | - Lauren Podmore
- Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower, Toronto, ONM5G 1L7, Canada
| | - Vuk Stambolic
- Princess Margaret Cancer Centre, University Health Network, Princess Margaret Cancer Research Tower, Toronto, ONM5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower, Toronto, ONM5G 1L7, Canada
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4
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Basei FL, E Silva IR, Dias PRF, Ferezin CC, Peres de Oliveira A, Issayama LK, Moura LAR, da Silva FR, Kobarg J. The Mitochondrial Connection: The Nek Kinases' New Functional Axis in Mitochondrial Homeostasis. Cells 2024; 13:473. [PMID: 38534317 DOI: 10.3390/cells13060473] [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: 01/24/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
Mitochondria provide energy for all cellular processes, including reactions associated with cell cycle progression, DNA damage repair, and cilia formation. Moreover, mitochondria participate in cell fate decisions between death and survival. Nek family members have already been implicated in DNA damage response, cilia formation, cell death, and cell cycle control. Here, we discuss the role of several Nek family members, namely Nek1, Nek4, Nek5, Nek6, and Nek10, which are not exclusively dedicated to cell cycle-related functions, in controlling mitochondrial functions. Specifically, we review the function of these Neks in mitochondrial respiration and dynamics, mtDNA maintenance, stress response, and cell death. Finally, we discuss the interplay of other cell cycle kinases in mitochondrial function and vice versa. Nek1, Nek5, and Nek6 are connected to the stress response, including ROS control, mtDNA repair, autophagy, and apoptosis. Nek4, in turn, seems to be related to mitochondrial dynamics, while Nek10 is involved with mitochondrial metabolism. Here, we propose that the participation of Neks in mitochondrial roles is a new functional axis for the Nek family.
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Affiliation(s)
- Fernanda L Basei
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Ivan Rosa E Silva
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Pedro R Firmino Dias
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Camila C Ferezin
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | | | - Luidy K Issayama
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Livia A R Moura
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | | | - Jörg Kobarg
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
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5
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Nguyen K, Boehling J, Tran MN, Cheng T, Rivera A, Collins-Burow BM, Lee SB, Drewry DH, Burow ME. NEK Family Review and Correlations with Patient Survival Outcomes in Various Cancer Types. Cancers (Basel) 2023; 15:cancers15072067. [PMID: 37046733 PMCID: PMC10093199 DOI: 10.3390/cancers15072067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
The Never in Mitosis Gene A (NIMA)–related kinases (NEKs) are a group of serine/threonine kinases that are involved in a wide array of cellular processes including cell cycle regulation, DNA damage repair response (DDR), apoptosis, and microtubule organization. Recent studies have identified the involvement of NEK family members in various diseases such as autoimmune disorders, malignancies, and developmental defects. Despite the existing literature exemplifying the importance of the NEK family of kinases, this family of protein kinases remains understudied. This report seeks to provide a foundation for investigating the role of different NEKs in malignancies. We do this by evaluating the 11 NEK family kinase gene expression associations with patients’ overall survival (OS) from various cancers using the Kaplan–Meier Online Tool (KMPlotter) to correlate the relationship between mRNA expression of NEK1-11 in various cancers and patient survival. Furthermore, we use the Catalog of Somatic Mutations in Cancer (COSMIC) database to identify NEK family mutations in cancers of different tissues. Overall, the data suggest that the NEK family has varying associations with patient survival in different cancers with tumor-suppressive and tumor-promoting effects being tissue-dependent.
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6
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Lin W, Lu X, Yang H, Huang L, Huang W, Tang Y, Liu S, Wang H, Zhang Y. Metabolic heterogeneity protects metastatic mucosal melanomas cells from ferroptosis. Int J Mol Med 2022; 50:124. [PMID: 36004461 PMCID: PMC9448297 DOI: 10.3892/ijmm.2022.5180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/18/2022] [Indexed: 11/08/2022] Open
Abstract
Cancer heterogeneity has been proposed to be one of the main causes of metastatic dissemination and therapy failure. However, the underlying mechanisms of this phenomenon remain poorly understood. Melanoma is an aggressive malignancy with a high heterogeneity and metastatic potential. Therefore, the present study investigated the possible association between cancer heterogeneity and metastasis in melanoma. In total, two novel Chinese oral mucosal melanoma (COMM) cell lines, namely COMM-1 and COMM-2, were established for exploring methods into preventing the loss of cellular heterogeneity caused by long-term cell culture. Each cell line was grown under two different models of culture, which yielded two subtypes, one exhibited an adhesive morphology (COMM-AD), whereas the other was grown in suspension (COMM-SUS). Compared with the COMM-AD cells, the COMM-SUS cells exhibited higher metastatic capacities and autofluorescence. Further investigations indicated that the COMM-SUS cells exhibited metabolic reprogramming by taking up lactate produced by COMM-AD cells at increased levels to accumulate NADH through monocarboxylate transporter 1, whilst also increasing NADPH levels through the pentose phosphate pathway (PPP). Additionally, increased NADH and NADPH levels in the COMM-SUS cells, coupled with the upregulation of the anti-ferroptotic proteins, glutathione peroxidase 4 and ferroptosis suppressor protein 1, enabled them to resist ferroptotic cell death induced by oxidative stress during hematogenous dissemination. The inhibition of ferroptosis was found to substantially increase the metastatic capacity of COMM-AD cells. Furthermore, suppressing lactate uptake and impairing PPP activation significantly decreased the metastatic potential of the COMM-SUS cells. Thus, the present study on metabolic heterogeneity in COMM cells potentially provides a novel perspective for exploring this mechanism underlying cancer metastasis.
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Affiliation(s)
- Weifan Lin
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Xiangwan Lu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Hang Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Linxuan Huang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Wuheng Huang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Yuluan Tang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Situn Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Hua Wang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Guanghua Hospital of Stomatology, Sun Yat‑sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Yan Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
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7
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In Mitosis You Are Not: The NIMA Family of Kinases in Aspergillus, Yeast, and Mammals. Int J Mol Sci 2022; 23:ijms23074041. [PMID: 35409400 PMCID: PMC8999480 DOI: 10.3390/ijms23074041] [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: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
The Never in mitosis gene A (NIMA) family of serine/threonine kinases is a diverse group of protein kinases implicated in a wide variety of cellular processes, including cilia regulation, microtubule dynamics, mitotic processes, cell growth, and DNA damage response. The founding member of this family was initially identified in Aspergillus and was found to play important roles in mitosis and cell division. The yeast family has one member each, Fin1p in fission yeast and Kin3p in budding yeast, also with functions in mitotic processes, but, overall, these are poorly studied kinases. The mammalian family, the main focus of this review, consists of 11 members named Nek1 to Nek11. With the exception of a few members, the functions of the mammalian Neks are poorly understood but appear to be quite diverse. Like the prototypical NIMA, many members appear to play important roles in mitosis and meiosis, but their functions in the cell go well beyond these well-established activities. In this review, we explore the roles of fungal and mammalian NIMA kinases and highlight the most recent findings in the field.
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8
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Yang M, Guo Y, Guo X, Mao Y, Zhu S, Wang N, Lu D. Analysis of the effect of NEKs on the prognosis of patients with non-small-cell lung carcinoma based on bioinformatics. Sci Rep 2022; 12:1705. [PMID: 35105934 PMCID: PMC8807624 DOI: 10.1038/s41598-022-05728-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/14/2022] [Indexed: 12/14/2022] Open
Abstract
NEKs are proteins that are involved in various cell processes and play important roles in the formation and development of cancer. However, few studies have examined the role of NEKs in the development of non-small-cell lung carcinoma (NSCLC). To address this problem, the Oncomine, UALCAN, and the Human Protein Atlas databases were used to analyze differential NEK expression and its clinicopathological parameters, while the Kaplan-Meier, cBioPortal, GEPIA, and DAVID databases were used to analyze survival, gene mutations, similar genes, and biological enrichments. The rate of NEK family gene mutation was high (> 50%) in patients with NSCLC, in which NEK2/4/6/8/ was overexpressed and significantly correlated with tumor stage and nodal metastasis status. In addition, the high expression of NEK2/3mRNA was significantly associated with poor prognosis in patients with NSCLC, while high expression of NEK1/4/6/7/8/9/10/11mRNA was associated with good prognosis. In summary, these results suggest that NEK2/4/6/8 may be a potential prognostic biomarker for the survival of patients with NSCLC.
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Affiliation(s)
- Mengxia Yang
- Graduate School, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China.,Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Yikun Guo
- Graduate School, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Xiaofei Guo
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Yun Mao
- Department of Oncology, The Second Hospital of Hunan University of Chinese Medicine, Changsha, 410005, People's Republic of China
| | - Shijie Zhu
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Ningjun Wang
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China.
| | - Dianrong Lu
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China.
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Anuraga G, Wang WJ, Phan NN, An Ton NT, Ta HDK, Berenice Prayugo F, Minh Xuan DT, Ku SC, Wu YF, Andriani V, Athoillah M, Lee KH, Wang CY. Potential Prognostic Biomarkers of NIMA (Never in Mitosis, Gene A)-Related Kinase (NEK) Family Members in Breast Cancer. J Pers Med 2021; 11:1089. [PMID: 34834441 PMCID: PMC8625415 DOI: 10.3390/jpm11111089] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Breast cancer remains the most common malignant cancer in women, with a staggering incidence of two million cases annually worldwide; therefore, it is crucial to explore novel biomarkers to assess the diagnosis and prognosis of breast cancer patients. NIMA-related kinase (NEK) protein kinase contains 11 family members named NEK1-NEK11, which were discovered from Aspergillus Nidulans; however, the role of NEK family genes for tumor development remains unclear and requires additional study. In the present study, we investigate the prognosis relationships of NEK family genes for breast cancer development, as well as the gene expression signature via the bioinformatics approach. The results of several integrative analyses revealed that most of the NEK family genes are overexpressed in breast cancer. Among these family genes, NEK2/6/8 overexpression had poor prognostic significance in distant metastasis-free survival (DMFS) in breast cancer patients. Meanwhile, NEK2/6 had the highest level of DNA methylation, and the functional enrichment analysis from MetaCore and Gene Set Enrichment Analysis (GSEA) suggested that NEK2 was associated with the cell cycle, G2M checkpoint, DNA repair, E2F, MYC, MTORC1, and interferon-related signaling. Moreover, Tumor Immune Estimation Resource (TIMER) results showed that the transcriptional levels of NEK2 were positively correlated with immune infiltration of B cells and CD4+ T Cell. Collectively, the current study indicated that NEK family genes, especially NEK2 which is involved in immune infiltration, and may serve as prognosis biomarkers for breast cancer progression.
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Affiliation(s)
- Gangga Anuraga
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Wei-Jan Wang
- Research Center for Cancer Biology, Department of Biological Science and Technology, China Medical University, Taichung 40604, Taiwan;
| | - Nam Nhut Phan
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Nu Thuy An Ton
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Hoang Dang Khoa Ta
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Fidelia Berenice Prayugo
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Yung-Fu Wu
- Department of Medical Research, Tri-Service General Hospital, School of Medicine, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Vivin Andriani
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Muhammad Athoillah
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Kuen-Haur Lee
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
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Uddin MA, Akhter MS, Kubra KT, Barabutis N. Induction of the NEK family of kinases in the lungs of mice subjected to cecal ligation and puncture model of sepsis. Tissue Barriers 2021; 9:1929787. [PMID: 34151722 DOI: 10.1080/21688370.2021.1929787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Endothelial barrier dysfunction (EBD) is the hallmark of Acute Respiratory Distress Syndrome (ARDS), a potentially lethal respiratory disorder associated with the COVID-19 - related deaths. Herein, we employed a cecal ligation and puncture (CLP) murine model of sepsis, to evaluate the effects of sepsis-induced EBD in the expression of the never in mitosis A (NIMA)-related kinases (NEKs). Members of that family of kinases regulate the activity and expression of the tumor suppressor P53, previously shown to modulate the actin cytoskeleton remodeling. Our results introduce the induction of NEK2, NEK3, NEK4, NEK7, and NEK9 in a CLP model of sepsis. Hence, we suggest that NEKs are involved in inflammatory processes and are holding the potential to serve as novel therapeutic targets for pathologies related to EBD, including ARDS and sepsis. Further studies will delineate the underlying molecular events and their interrelations with P53.
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Affiliation(s)
- Mohammad A Uddin
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana USA
| | - Mohammad S Akhter
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana USA
| | - Khadeja-Tul Kubra
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana USA
| | - Nektarios Barabutis
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana USA
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11
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Xiao M, Du C, Zhang C, Zhang X, Li S, Zhang D, Jia W. Bioinformatics analysis of the prognostic value of NEK8 and its effects on immune cell infiltration in glioma. J Cell Mol Med 2021; 25:8748-8763. [PMID: 34374193 PMCID: PMC8435421 DOI: 10.1111/jcmm.16831] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/28/2021] [Accepted: 07/15/2021] [Indexed: 12/26/2022] Open
Abstract
Glioma is the most common malignancy of the nervous system with high rates of recurrence and mortality, even after surgery. The 5‐year survival rate is only about 5%. NEK8 is involved in multiple biological processes in a variety of cancers; however, its role in glioma is still not clear. In the current study, we evaluated the prognostic value of NEK8, as well as its role in the pathogenesis of glioma. Using a bioinformatics approach and RNA‐seq data from public databases, we found that NEK8 expression is elevated in glioma tissues; we further verified this result by RT‐PCR, Western blotting and immunochemistry using clinical samples. Functional enrichment analyses of genes with correlated expression indicated that elevated NEK8 expression is associated with increased immune cell infiltration in glioma and may affect the tumour microenvironment via the regulation of DNA damage/repair. Survival analyses revealed that high levels of NEK8 are associated with a poorer prognosis; higher WHO grade, IDH status, 1p/19q codeletion, age and NEK8 were identified as an independent prognostic factor. These findings support the crucial role of NEK8 in the progression of glioma via effects on immune cell infiltration and suggest that it is a new prognostic biomarker.
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Affiliation(s)
- Meng Xiao
- Henan Key Laboratory of Neurorestoratology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Chaoyang Du
- Henan Key Laboratory of Neurorestoratology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Chuanbo Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Xinzhong Zhang
- Henan Key Laboratory of Neurorestoratology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Shaomin Li
- Henan Key Laboratory of Neurorestoratology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China.,Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dainan Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wang Jia
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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12
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Pavan ICB, Peres de Oliveira A, Dias PRF, Basei FL, Issayama LK, Ferezin CDC, Silva FR, Rodrigues de Oliveira AL, Alves dos Reis Moura L, Martins MB, Simabuco FM, Kobarg J. On Broken Ne(c)ks and Broken DNA: The Role of Human NEKs in the DNA Damage Response. Cells 2021; 10:507. [PMID: 33673578 PMCID: PMC7997185 DOI: 10.3390/cells10030507] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
NIMA-related kinases, or NEKs, are a family of Ser/Thr protein kinases involved in cell cycle and mitosis, centrosome disjunction, primary cilia functions, and DNA damage responses among other biological functional contexts in vertebrate cells. In human cells, there are 11 members, termed NEK1 to 11, and the research has mainly focused on exploring the more predominant roles of NEKs in mitosis regulation and cell cycle. A possible important role of NEKs in DNA damage response (DDR) first emerged for NEK1, but recent studies for most NEKs showed participation in DDR. A detailed analysis of the protein interactions, phosphorylation events, and studies of functional aspects of NEKs from the literature led us to propose a more general role of NEKs in DDR. In this review, we express that NEK1 is an activator of ataxia telangiectasia and Rad3-related (ATR), and its activation results in cell cycle arrest, guaranteeing DNA repair while activating specific repair pathways such as homology repair (HR) and DNA double-strand break (DSB) repair. For NEK2, 6, 8, 9, and 11, we found a role downstream of ATR and ataxia telangiectasia mutated (ATM) that results in cell cycle arrest, but details of possible activated repair pathways are still being investigated. NEK4 shows a connection to the regulation of the nonhomologous end-joining (NHEJ) repair of DNA DSBs, through recruitment of DNA-PK to DNA damage foci. NEK5 interacts with topoisomerase IIβ, and its knockdown results in the accumulation of damaged DNA. NEK7 has a regulatory role in the detection of oxidative damage to telomeric DNA. Finally, NEK10 has recently been shown to phosphorylate p53 at Y327, promoting cell cycle arrest after exposure to DNA damaging agents. In summary, this review highlights important discoveries of the ever-growing involvement of NEK kinases in the DDR pathways. A better understanding of these roles may open new diagnostic possibilities or pharmaceutical interventions regarding the chemo-sensitizing inhibition of NEKs in various forms of cancer and other diseases.
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Affiliation(s)
- Isadora Carolina Betim Pavan
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Andressa Peres de Oliveira
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Pedro Rafael Firmino Dias
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Fernanda Luisa Basei
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Luidy Kazuo Issayama
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Camila de Castro Ferezin
- Graduate Program in “Biologia Funcional e Molecular”, Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas 13083-857, Brazil;
| | - Fernando Riback Silva
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Ana Luisa Rodrigues de Oliveira
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Lívia Alves dos Reis Moura
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Mariana Bonjiorno Martins
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
- Graduate Program in “Biologia Funcional e Molecular”, Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas 13083-857, Brazil;
| | | | - Jörg Kobarg
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
- Graduate Program in “Biologia Funcional e Molecular”, Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas 13083-857, Brazil;
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13
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Thom CS, Voight BF. Genetic colocalization atlas points to common regulatory sites and genes for hematopoietic traits and hematopoietic contributions to disease phenotypes. BMC Med Genomics 2020; 13:89. [PMID: 32600345 PMCID: PMC7325014 DOI: 10.1186/s12920-020-00742-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/17/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Genetic associations link hematopoietic traits and disease end-points, but most causal variants and genes underlying these relationships are unknown. Here, we used genetic colocalization to nominate loci and genes related to shared genetic signal for hematopoietic, cardiovascular, autoimmune, neuropsychiatric, and cancer phenotypes. METHODS Our aim was to identify colocalization sites for human traits among established genome-wide significant loci. Using genome-wide association study (GWAS) summary statistics, we determined loci where multiple traits colocalized at a false discovery rate < 5%. We then identified quantitative trait loci among colocalization sites to highlight related genes. In addition, we used Mendelian randomization analysis to further investigate certain trait relationships genome-wide. RESULTS Our findings recapitulated developmental hematopoietic lineage relationships, identified loci that linked traits with causal genetic relationships, and revealed novel trait associations. Out of 2706 loci with genome-wide significant signal for at least 1 blood trait, we identified 1779 unique sites (66%) with shared genetic signal for 2+ hematologic traits. We could assign some sites to specific developmental cell types during hematopoiesis based on affected traits, including those likely to impact hematopoietic progenitor cells and/or megakaryocyte-erythroid progenitor cells. Through an expanded analysis of 70 human traits, we defined 2+ colocalizing traits at 2123 loci from an analysis of 9852 sites (22%) containing genome-wide significant signal for at least 1 GWAS trait. In addition to variants and genes underlying shared genetic signal between blood traits and disease phenotypes that had been previously related through Mendelian randomization studies, we defined loci and related genes underlying shared signal between eosinophil percentage and eczema. We also identified colocalizing signals in a number of clinically relevant coding mutations, including sites linking PTPN22 with Crohn's disease, NIPA with coronary artery disease and platelet trait variation, and the hemochromatosis gene HFE with altered lipid levels. Finally, we anticipate potential off-target effects on blood traits related novel therapeutic targets, including TRAIL. CONCLUSIONS Our findings provide a road map for gene validation experiments and novel therapeutics related to hematopoietic development, and offer a rationale for pleiotropic interactions between hematopoietic loci and disease end-points.
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Affiliation(s)
- Christopher S Thom
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin F Voight
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA.
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA.
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