1
|
Zhou Z, Fan B, Qiu Q, Cheng H, Wang L, Wu Y, Xie J, Ni C, Li N. Pan-cancer analysis and experimental validation reveal FAM72D as a potential novel biomarker and therapeutic target in lung adenocarcinoma. Gene 2024; 928:148764. [PMID: 39013484 DOI: 10.1016/j.gene.2024.148764] [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: 03/25/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Cancers, particularly lung adenocarcinoma (LUAD), represent a major global health concern. However, the role of FAM72D in various cancers, including LUAD, remains poorly understood. METHODS We utilized databases such as The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx) and online tools to investigate the correlation between FAM72D expression and its prognostic, diagnostic, and mutational significance, as well as its impact on immune cell infiltration across multiple cancers. Additionally, we developed LUAD cell lines overexpressing FAM72D to confirm its oncogenic role. RESULTS FAM72D expression was elevated in cancerous tissues compared to noncancerous tissues, with diagnostic and prognostic implications in many cancers, including LUAD. Moreover, associations were identified between FAM72D expression and diverse immune subtypes, alongside factors such as microsatellite instability, neoantigens, and tumour mutational burden across pan-cancers. Additionally, FAM72D was associated with immune infiltration and various immune checkpoint-related genes in LUAD. In vitro experiments demonstrated that FAM72D promoted cell proliferation, colony formation, and migration, while inhibiting apoptosis in LUAD cells. CONCLUSIONS Our study establishes associations between FAM72D expression and diagnosis, prognosis, and tumour immunity across multiple cancers, as well as its oncogenic effects in LUAD. FAM72D shows promise as a biomarker and therapeutic target in LUAD.
Collapse
Affiliation(s)
- Zonglang Zhou
- Department of Respiratory and Critical Care Medicine, Center for Respiratory Medicine, The Fourth Affiliated Hospital, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Bingfu Fan
- Graduate School of Bengbu Medical College, Bengbu, Anhui, China
| | - Qinming Qiu
- Department of Psychiatry, Huzhou Third Municipal Hospital, Huzhou, China
| | - Hongrong Cheng
- Department of Neurology, The Fourth Affiliated Hospital, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Li Wang
- The Fourth Affiliated Hospital, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Yibo Wu
- Department of Orthopedics, Xixi Hospital of Hangzhou, Hangzhou, China
| | - Jun Xie
- Department of Nephrology, Center for Regeneration and Aging Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.
| | - Cheng Ni
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Ning Li
- Department of Respiratory and Critical Care Medicine, Center for Respiratory Medicine, The Fourth Affiliated Hospital, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.
| |
Collapse
|
2
|
Gou H, Chen P, Wu W. FAM72 family proteins as poor prognostic markers in clear cell renal carcinoma. Biochem Biophys Rep 2023; 35:101506. [PMID: 37457361 PMCID: PMC10344709 DOI: 10.1016/j.bbrep.2023.101506] [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: 04/22/2023] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023] Open
Abstract
Purpose This study aimed to investigate the prognostic significance of the Family with Sequence Similarity 72 member (FAM72) gene family in clear cell renal carcinoma (ccRCC) using a bioinformatic approach. Patients and methods To investigate the association between FAM72 and ccRCC, we utilized various databases and analysis tools, including TCGA, GEPIA, Metscape, cBioPortal, and MethSurv. We conducted an analysis of FAM72 expression levels in ccRCC tissues compared to normal kidney tissues and performed univariate and multivariate Cox analysis to determine the relationship between FAM72 expression and patient prognosis. Furthermore, we carried out Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) to identify enriched biological processes associated with FAM72 expression. Additionally, we analyzed immune cell infiltration and the level of methylation in ccRCC patients. Our bioinformatic analysis revealed that FAM72 expression levels were significantly higher in ccRCC tissues than in normal kidney tissues. High expression of FAM72 was associated with poor prognosis in ccRCC patients and was found to be an independent prognostic factor for ccRCC. GO and GSEA analyses indicated that FAM72 was enriched in biological processes related to mitosis, cell cycle, and DNA metabolism. Moreover, we found a significant correlation between FAM72 and immune cell infiltration and the level of methylation in ccRCC patients. Conclusion Our findings suggest that FAM72 could serve as an unfavorable prognostic molecular marker for ccRCC. A comprehensive understanding of FAM72 could provide crucial insights into tumor progression and prognosis.
Collapse
Affiliation(s)
- Hui Gou
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Ping Chen
- Department of Pharmacy, Suining Central Hospital, Suining, 629000, China
| | - Wenbing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| |
Collapse
|
3
|
Liu H, Huang Y, Chen Y, Tang Z, Huang M, Ming Y, Wang M, Chen W, Huang Z, Qing L, Wang Q, Jia B. Family with Sequence Similarity 72 (FAM72) - A prospective biomarker for poor prognosis in patients with oral squamous cell carcinoma. Arch Oral Biol 2023; 151:105695. [PMID: 37086493 DOI: 10.1016/j.archoralbio.2023.105695] [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: 02/19/2023] [Revised: 03/20/2023] [Accepted: 04/06/2023] [Indexed: 04/24/2023]
Abstract
OBJECTIVE To study the effect of FAM72 on the prognosis of patients with oral squamous cell carcinoma (OSCC) and to explore the relationship between FAM72 and OSCC. DESIGN We used a vast array of databases and analytical vehicles to assess the relation between FAM72 and OSCC, including The Cancer Genome Atlas (TCGA), Metascape, and MethSurv. We made a preliminary verification of OSCC lines and tissues by real time quantitative polymerase chain reaction (RT-qPCR). RESULTS FAM72 was higher in OSCC than in normal tissues. Analysis of univariate COX data indicated that elevated expression of FAM72A, FAM72B, and FAM72C in OSCC was related to poor overall survival. Moreover, FAM72B and FAM72C were independent of overall survival in multiple COX regression. FAM72A-D and its coexpressed genes in Metascape were analyzed by Gene Ontology (GO), they were enriched in cellular cycle, mitotic and DNA metabolism. Gene set enrichment analysis (GSEA) demonstrated an enrichment in pathways related to cell metabolism. Additionally, high FAM72 expression related to a worse prognosis in OSCC patients. FAM72A-D linked to the infiltration of tumor immune cell in OSCC patients. We found that methylation levels are likely linked to prognosis in OSCC patients. We used RT-qPCR to ascertain the differential FAM72B and FAM72C expression levels in cancer and paracancerous tissues of OSCC, human normal oral keratinocytes (HOK), and human tongue squamous cell carcinoma (Cal-33). CONCLUSION Our findings indicate that FAM72B and FAM72C are potential molecular markers of poor prognosis in OSCC and may act as novel targets for OSCC treatment strategies.
Collapse
Affiliation(s)
- Hongyu Liu
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Yisheng Huang
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Yuanxin Chen
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Zhengming Tang
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Mingshu Huang
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Yue Ming
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Min Wang
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Weixing Chen
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Zhijie Huang
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Ling Qing
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Qin Wang
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Bo Jia
- Department of Oral Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China.
| |
Collapse
|
4
|
Zhou Q, Chen L, Yang L, Zhou H, Chen Y, Guo Y. Integrated systemic analysis of FAM72A to identify its clinical relevance, biological function, and relationship to drug sensitivity in hepatocellular carcinoma. Front Oncol 2022; 12:1046473. [DOI: 10.3389/fonc.2022.1046473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
BackgroundThe family with sequence similarity 72 member A (FAM72A) protein has been identified as an effector of multiple pathological processes in many cancers. The value of FAM72A in HCC remains largely unknown.MethodsData from TCGA-LIHC, ICGC-LIRI-JP, IMvigor210, cBioPortal, GeneMANIA, and TIMER were processed and visualized to explore the association between FAM72A and the prognosis, stemness phenotype, mutational burden, immune cell infiltration, and drug sensitivity in HCC patients. Potential pathways were also revealed. Furthermore, we experimentally verified the results in vivo and in vitro using immunohistochemistry, western blotting, and CCK-8 assays.ResultsFirst, FAM72A mRNA expression was significantly upregulated in HCC. High FAM72A expression was independently associated with a poor prognosis. Experimental validation confirmed that FAM72A was remarkably overexpressed in HCC patients and mice. Moreover, FAM72A knockdown suppressed HCC cell proliferation. In addition, the frequency of TP53 mutations was significantly higher in the high FAM72A expression group. Subsequently, the enrichment analysis revealed that FAM72A was closely related to immune processes and mTOR pathways. Silencing FAM72A increased the expression levels of mTOR in HCC cell lines. The FAM72A-mTOR pathway was strongly associated with a poor prognosis for patients with HCC. Patients with high FAM72A expression levels might be more resistant to sorafenib. Furthermore, the expression of FAM72A and mTOR was significantly associated with the abundance of some tumor-infiltrating immune cells, especially CD4+ T cells. Finally, patients with high levels of FAM72A and mTOR were more sensitive to immunotherapy.ConclusionsFAM72A, a member of the FAM72 family, might be a prognostic and immunotherapeutic target for HCC patients.
Collapse
|
5
|
Renganathan S, Pramanik S, Ekambaram R, Kutzner A, Kim PS, Heese K. Identification of a Chemotherapeutic Lead Molecule for the Potential Disruption of the FAM72A-UNG2 Interaction to Interfere with Genome Stability, Centromere Formation, and Genome Editing. Cancers (Basel) 2021; 13:5870. [PMID: 34831023 PMCID: PMC8616359 DOI: 10.3390/cancers13225870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/15/2021] [Accepted: 11/20/2021] [Indexed: 01/05/2023] Open
Abstract
Family with sequence similarity 72 A (FAM72A) is a pivotal mitosis-promoting factor that is highly expressed in various types of cancer. FAM72A interacts with the uracil-DNA glycosylase UNG2 to prevent mutagenesis by eliminating uracil from DNA molecules through cleaving the N-glycosylic bond and initiating the base excision repair pathway, thus maintaining genome integrity. In the present study, we determined a specific FAM72A-UNG2 heterodimer protein interaction using molecular docking and dynamics. In addition, through in silico screening, we identified withaferin B as a molecule that can specifically prevent the FAM72A-UNG2 interaction by blocking its cell signaling pathways. Our results provide an excellent basis for possible therapeutic approaches in the clinical treatment of cancer.
Collapse
Affiliation(s)
- Senthil Renganathan
- Department of Bioinformatics, Marudupandiyar College, Thanjavur 613403, India;
| | - Subrata Pramanik
- Department of Biology, Life Science Centre, School of Science and Technology, Örebro University, 701-82 Örebro, Sweden;
| | | | - Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University, Seoul 133-791, Korea;
| | - Pok-Son Kim
- Department of Information Security, Cryptology, and Mathematics, Kookmin University, Seoul 136-702, Korea;
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Korea
| |
Collapse
|
6
|
Heide M, Huttner WB. Human-Specific Genes, Cortical Progenitor Cells, and Microcephaly. Cells 2021; 10:1209. [PMID: 34063381 PMCID: PMC8156310 DOI: 10.3390/cells10051209] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Over the past few years, human-specific genes have received increasing attention as potential major contributors responsible for the 3-fold difference in brain size between human and chimpanzee. Accordingly, mutations affecting these genes may lead to a reduction in human brain size and therefore, may cause or contribute to microcephaly. In this review, we will concentrate, within the brain, on the cerebral cortex, the seat of our higher cognitive abilities, and focus on the human-specific gene ARHGAP11B and on the gene family comprising the three human-specific genes NOTCH2NLA, -B, and -C. These genes are thought to have significantly contributed to the expansion of the cerebral cortex during human evolution. We will summarize the evolution of these genes, as well as their expression and functional role during human cortical development, and discuss their potential relevance for microcephaly. Furthermore, we will give an overview of other human-specific genes that are expressed during fetal human cortical development. We will discuss the potential involvement of these genes in microcephaly and how these genes could be studied functionally to identify a possible role in microcephaly.
Collapse
Affiliation(s)
- Michael Heide
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Wieland B. Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, D-01307 Dresden, Germany
| |
Collapse
|
7
|
FAM72 serves as a biomarker of poor prognosis in human lung adenocarcinoma. Aging (Albany NY) 2021; 13:8155-8176. [PMID: 33686947 PMCID: PMC8034972 DOI: 10.18632/aging.202625] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022]
Abstract
FAM72A-D promote the self-renewal of neural progenitor cells. There is accumulating evidence that FAM72 promotes tumorigenicity. However, its effects in lung adenocarcinoma (LUAD) have not been determined. Thus, we evaluated the prognostic value of FAM72A-D in LUAD using bioinformatics approaches. In particular, we evaluated the relationship between FAM72 and LUAD using a wide range of databases and analysis tools, including TCGA, GEO, GEPIA, Metascape, cBioPortal, and MethSurv. Compared with its expression in normal lung tissues, FAM72 expression was significantly increased in LUAD tissues. A univariate Cox analysis showed that high FAM72 expression levels were correlated with a poor OS in LUAD. Additionally, FAM72 expression was independently associated with OS through a multivariate Cox analysis. GO and GSEA revealed enrichment in mitotic nuclear division and cell cycle. Moreover, high FAM72 expression was associated with poor survival. An analysis of immune infiltration showed that FAM72 is correlated with immune cell infiltration. Finally, we found that the methylation level was associated with prognosis in patients with LUAD. In summary, these results indicate that FAM72 is a potential molecular marker for poor prognosis in LUAD and provide additional insight for the development of therapies and prognostic markers.
Collapse
|
8
|
Ho NTT, Rahane CS, Pramanik S, Kim PS, Kutzner A, Heese K. FAM72, Glioblastoma Multiforme (GBM) and Beyond. Cancers (Basel) 2021; 13:cancers13051025. [PMID: 33804473 PMCID: PMC7957592 DOI: 10.3390/cancers13051025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Glioblastoma multiforme (GBM) is a serious and aggressive cancer disease that has not allowed scientists to rest for decades. In this review, we consider the new gene pair |-SRGAP2–FAM72-| and discuss its role in the cell cycle and the possibility of defining new therapeutic approaches for the treatment of GBM and other cancers via this gene pair |-SRGAP2–FAM72-|. Abstract Neural stem cells (NSCs) offer great potential for regenerative medicine due to their excellent ability to differentiate into various specialized cell types of the brain. In the central nervous system (CNS), NSC renewal and differentiation are under strict control by the regulation of the pivotal SLIT-ROBO Rho GTPase activating protein 2 (SRGAP2)—Family with sequence similarity 72 (FAM72) master gene (i.e., |-SRGAP2–FAM72-|) via a divergent gene transcription activation mechanism. If the gene transcription control unit (i.e., the intergenic region of the two sub-gene units, SRGAP2 and FAM72) gets out of control, NSCs may transform into cancer stem cells and generate brain tumor cells responsible for brain cancer such as glioblastoma multiforme (GBM). Here, we discuss the surveillance of this |-SRGAP2–FAM72-| master gene and its role in GBM, and also in light of FAM72 for diagnosing various types of cancers outside of the CNS.
Collapse
Affiliation(s)
- Nguyen Thi Thanh Ho
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea;
| | - Chinmay Satish Rahane
- Maharashtra Institute of Medical Education and Research, Talegaon Dabhade, Maharashtra 410507, India;
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany;
| | - Pok-Son Kim
- Department of Mathematics, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 136-702, Korea;
| | - Arne Kutzner
- Department of Information Systems, College of Computer Science, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea;
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea;
- Correspondence:
| |
Collapse
|
9
|
Chatonnet F, Pignarre A, Sérandour AA, Caron G, Avner S, Robert N, Kassambara A, Laurent A, Bizot M, Agirre X, Prosper F, Martin-Subero JI, Moreaux J, Fest T, Salbert G. The hydroxymethylome of multiple myeloma identifies FAM72D as a 1q21 marker linked to proliferation. Haematologica 2020; 105:774-783. [PMID: 31221779 PMCID: PMC7049362 DOI: 10.3324/haematol.2019.222133] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/19/2019] [Indexed: 01/16/2023] Open
Abstract
Cell identity relies on the cross-talk between genetics and epigenetics and their impact on gene expression. Oxidation of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) is the first step of an active DNA demethylation process occurring mainly at enhancers and gene bodies and, as such, participates in processes governing cell identity in normal and pathological conditions. Although genetic alterations are well documented in multiple myeloma (MM), epigenetic alterations associated with this disease have not yet been thoroughly analyzed. To gain insight into the biology of MM, genome-wide 5hmC profiles were obtained and showed that regions enriched in this modified base overlap with MM enhancers and super enhancers and are close to highly expressed genes. Through the definition of a MM-specific 5hmC signature, we identified FAM72D as a poor prognostic gene located on 1q21, a region amplified in high risk myeloma. We further uncovered that FAM72D functions as part of the FOXM1 transcription factor network controlling cell proliferation and survival and we evidenced an increased sensitivity of cells expressing high levels of FOXM1 and FAM72 to epigenetic drugs targeting histone deacetylases and DNA methyltransferases.
Collapse
Affiliation(s)
- Fabrice Chatonnet
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Amandine Pignarre
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Aurélien A Sérandour
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Nantes, France
- Institut de Cancérologie de l'Ouest, Site René-Gauducheau, Saint-Herblain, France
| | - Gersende Caron
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Stéphane Avner
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| | - Nicolas Robert
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
| | | | - Audrey Laurent
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| | - Maud Bizot
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| | - Xabier Agirre
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | - Felipe Prosper
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | | | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- IGH, CNRS, Univ Montpellier, France
| | - Thierry Fest
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Gilles Salbert
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| |
Collapse
|
10
|
Cheng B, He Q, Cheng Y, Yang H, Pei L, Deng Q, Long H, Zhu L, Jiang R. A Three-Gene Classifier Associated With MicroRNA-Mediated Regulation Predicts Prostate Cancer Recurrence After Radical Prostatectomy. Front Genet 2020; 10:1402. [PMID: 32117427 PMCID: PMC7011265 DOI: 10.3389/fgene.2019.01402] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/23/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND AND OBJECTIVE After radical prostatectomy (RP), prostate cancer (PCa) patients may experience biochemical recurrence (BCR) and clinical recurrence, which remains a dominant issue in PCa treatment. The purpose of this study was to identify a protein-coding gene classifier associated with microRNA (miRNA)-mediated regulation to provide a comprehensive prognostic index to predict PCa recurrence after RP. METHODS Candidate classifiers were constructed using two machine-learning algorithms (a least absolute shrinkage and selector operation [LASSO]-based classifier and a decision tree-based classifier) based on a discovery cohort (n = 156) from The Cancer Genome Atlas (TCGA) database. After selecting the LASSO-based classifier based on the prediction accuracy, both an internal validation cohort (n = 333) and an external validation cohort (n = 100) were used to examined the classifier using survival analysis, time-dependent receiver operating characteristic (ROC) curve analysis, and univariate and multivariate Cox proportional hazards regression analyses. Functional enrichment analysis of co-expressed genes was carried out to explore the underlying moleculer mechanisms of the genes included in the classifier. RESULTS We constructed a three-gene classifier that included FAM72B, GNE, and TRIM46, and we identified four upstream prognostic miRNAs (hsa-miR-133a-3p, hsa-miR-222-3p, hsa-miR-1301-3p, and hsa-miR-30c-2-3p). The classifier exhibited a remarkable ability (area under the curve [AUC] = 0.927) to distinguish PCa patients with high and low Gleason scores in the discovery cohort. Furthermore, it was significantly associated with clinical recurrence (p < 0.0001, log rank statistic = 20.7, AUC = 0.733) and could serve as an independent prognostic factor of recurrence-free survival (hazard ratio: 1.708, 95% CI: 1.180-2.472, p < 0.001). Additionally, it was a predictor of BCR according to BCR-free survival analysis (p = 0.0338, log rank statistic = 4.51). CONCLUSIONS The three-gene classifier associated with miRNA-mediated regulation may serve as a novel prognostic biomarker for PCa patients after RP.
Collapse
Affiliation(s)
- Bo Cheng
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qidan He
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yong Cheng
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Haifan Yang
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lijun Pei
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qingfu Deng
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Hao Long
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Likun Zhu
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Rui Jiang
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| |
Collapse
|
11
|
A Bayesian gene network reveals insight into the JAK-STAT pathway in systemic lupus erythematosus. PLoS One 2019; 14:e0225651. [PMID: 31790472 PMCID: PMC6886858 DOI: 10.1371/journal.pone.0225651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/08/2019] [Indexed: 12/22/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic, remitting, and relapsing, inflammatory disease involving multiple organs, which exhibits abnormalities of both the innate and adaptive immune responses. A limited number of transcriptomic studies have characterized the gene pathways involved in SLE in an attempt to identify the key pathogenic drivers of the disease. In order to further advance our understanding of the pathogenesis of SLE, we used a novel Bayesian network algorithm to hybridize knowledge- and data-driven methods, and then applied the algorithm to build an SLE gene network using transcriptomic data from 1,760 SLE patients’ RNA from the two tabalumab Phase III trials (ILLUMINATE-I & -II), the largest SLE RNA dataset to date. Further, based on the gene network, we carried out hub- and key driver-gene analyses for gene prioritization. Our analyses identified that the JAK-STAT pathway genes, including JAK2, STAT1, and STAT2, played essential roles in SLE pathogenesis, and reaffirmed the recent discovery of pathogenic relevance of JAK-STAT signaling in SLE. Additionally, we showed that other genes, such as IRF1, IRF7, PDIA4, FAM72C, TNFSF10, DHX58, SIGLEC1, and PML, may be also important in SLE and serve as potential therapeutic targets for SLE. In summary, using a hybridized network construction approach, we systematically investigated gene-gene interactions based on their transcriptomic profiles, prioritized genes based on their importance in the network structure, and revealed new insights into SLE activity.
Collapse
|
12
|
Ho NTT, Kutzner A, Heese K. A Novel Divergent Gene Transcription Paradigm-the Decisive, Brain-Specific, Neural |-Srgap2-Fam72a-| Master Gene Paradigm. Mol Neurobiol 2019; 56:5891-5899. [PMID: 30685845 DOI: 10.1007/s12035-019-1486-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/10/2019] [Indexed: 01/22/2023]
Abstract
Brain development and repair largely depend on neural stem cells (NSCs). Here, we suggest that two genes, i.e., Srgap2 (SLIT-ROBO Rho GTPase-activating protein 2) and Fam72a (family with sequence similarity to 72, member A), constitute a single, NSC-specific, |-Srgap2-Fam72a-| master gene pair co-existing in reciprocal functional dependency. This gene pair has a dual, commonly used, intergenic region (IGR) promotor, which is a prerequisite in controlling human brain plasticity. We applied fluorescence cellular microscopy and fluorescence-activated cell sorting (FACS) to assess rat |-Srgap2-Fam72a-| master gene IGR promotor activity upon stimulation with two contrary growth factors: nerve growth factor (Ngf, a differentiation growth factor) and epidermal growth factor (Egf, a mitotic growth factor). We found that Ngf and Egf acted on the same IGR gene promotor element of the |-Srgap2-Fam72a-| master gene to mediate cell differentiation and proliferation, respectively. Ngf mediated Srgap2 expression and neuronal survival and differentiation while Egf activated Fam72a transcription and cell proliferation. Our data provide new insights into the specific regulation of the |-Srgap2-Fam72a-| master gene with its dual IGR promotor that controls two reverse-oriented functional-dependent genes located on opposite DNA strands. This structure represents a novel paradigm for controlling transcription of divergent genes in regulating NSC gene expression. This paradigm may allow for novel therapeutic approaches to restore or improve higher cognitive functions and cure cancers.
Collapse
Affiliation(s)
- Nguyen Thi Thanh Ho
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
| | - Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea.
| |
Collapse
|
13
|
Rahane CS, Kutzner A, Heese K. Establishing a human adrenocortical carcinoma (ACC)-specific gene mutation signature. Cancer Genet 2019; 230:1-12. [DOI: 10.1016/j.cancergen.2018.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 02/05/2023]
|
14
|
Rahane CS, Kutzner A, Heese K. A cancer tissue-specific FAM72 expression profile defines a novel glioblastoma multiform (GBM) gene-mutation signature. J Neurooncol 2018; 141:57-70. [PMID: 30414097 DOI: 10.1007/s11060-018-03029-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/09/2018] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Glioblastoma multiform (GBM) is a neural stem cell (NSC)-derived malignant brain tumor with complex genetic alterations challenging clinical treatments. FAM72 is a NSC-specific protein comprised of four paralogous genes (FAM72 A-D) in the human genome, but its functional tumorigenic significance is unclear. METHODS We conducted an in-depth expression and somatic mutation data analysis of FAM72 (A-D) in GBM using the comprehensive human clinical cancer study database cBioPortal [including The Cancer Genome Atlas (TCGA)]. RESULTS We established a FAM72 transcription profile across TCGA correlated with the expression of the proliferative marker MKI67 and a tissue-specific gene-mutation signature represented by pivotal genes involved in driving the cell cycle. FAM72 paralogs are overexpressed in cancer cells, specifically correlating with the mitotic cell cycle genes ASPM, KIF14, KIF23, CENPE, CENPE, CEP55, SGO1, and BUB1, thereby contributing to centrosome and mitotic spindle formation. FAM72 expression correlation identifies a novel GBM-specific gene set (SCN9A, MXRA5, ADAM29, KDR, LRP1B, and PIK3C2G) in the de novo pathway of primary GBM predestined as viable targets for therapeutics. CONCLUSION Our newly identified primary GBM-specific gene-mutation signature, along with FAM72, could thus provide a new basis for prognostic biomarkers for diagnostics of GBM and could serve as potential therapeutic targets.
Collapse
Affiliation(s)
- Chinmay Satish Rahane
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
| | - Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea.
| |
Collapse
|
15
|
Ho NTT, Kutzner A, Heese K. Brain plasticity, cognitive functions and neural stem cells: a pivotal role for the brain-specific neural master gene |-SRGAP2-FAM72-|. Biol Chem 2017; 399:55-61. [PMID: 28822221 DOI: 10.1515/hsz-2017-0190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/11/2017] [Indexed: 12/12/2022]
Abstract
Due to an aging society with an increased dementia-induced threat to higher cognitive functions, it has become imperative to understand the molecular and cellular events controlling the memory and learning processes in the brain. Here, we suggest that the novel master gene pair |-SRGAP2-FAM72-| (SLIT-ROBO Rho GTPase activating the protein 2, family with sequence similarity to 72) reveals a new dogma for the regulation of neural stem cell (NSC) gene expression and is a distinctive player in the control of human brain plasticity. Insight into the specific regulation of the brain-specific neural master gene |-SRGAP2-FAM72-| may essentially contribute to novel therapeutic approaches to restore or improve higher cognitive functions.
Collapse
Affiliation(s)
- Nguyen Thi Thanh Ho
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Republic of Korea
| | - Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Republic of Korea
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Republic of Korea
| |
Collapse
|
16
|
Pramanik S, Kutzner A, Heese K. Livebearing or egg-laying mammals: 27 decisive nucleotides of FAM168. Biosci Trends 2017; 11:169-178. [PMID: 28381702 DOI: 10.5582/bst.2016.01252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In the present study, we determine comprehensive molecular phylogenetic relationships of the novel myelin-associated neurite-outgrowth inhibitor (MANI) gene across the entire eukaryotic lineage. Combined computational genomic and proteomic sequence analyses revealed MANI as one of the two members of the novel family with sequence similarity 168 member (FAM168) genes, consisting of FAM168A and FAM168B, having distinct genetic differences that illustrate diversification in its biological function and genetic taxonomy across the phylogenetic tree. Phylogenetic analyses based on coding sequences of these FAM168 genes revealed that they are paralogs and that the earliest emergence of these genes occurred in jawed vertebrates such as Callorhinchus milii. Surprisingly, these two genes are absent in other chordates that have a notochord at some stage in their lives, such as branchiostoma and tunicates. In the context of phylogenetic relationships among eukaryotic species, our results demonstrate the presence of FAM168 orthologs in vertebrates ranging from Callorhinchus milii to Homo sapiens, displaying distinct taxonomic clusters, comprised of fish, amphibians, reptiles, birds, and mammals. Analyses of individual FAM168 exons in our sample provide new insights into the molecular relationships between FAM168A and FAM168B (MANI) on the one hand and livebearing and egg-laying mammals on the other hand, demonstrating that a distinctive intermediate exon 4, comprised of 27 nucleotides, appears suddenly only in FAM168A and there in the livebearing mammals only but is absent from all other species including the egg-laying mammals.
Collapse
Affiliation(s)
- Subrata Pramanik
- Graduate School of Biomedical Science and Engineering, Hanyang University
| | - Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University
| |
Collapse
|
17
|
Cognitive Functions: Human vs. Animal - 4:1 Advantage |-FAM72-SRGAP2-|. J Mol Neurosci 2017; 61:603-606. [PMID: 28255958 DOI: 10.1007/s12031-017-0901-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/16/2017] [Indexed: 10/20/2022]
Abstract
With the advent of computational genomics, an intensive search is underway for unique biomarkers for Homo sapiens that could be used to differentiate taxa within the Hominoidea, in particular to distinguish Homo from the apes (Pan, Gorilla, Pongo, and Hylobates) and species or subspecies within the genus Homo (H. sapiens, H. heidelbergensis, H. neanderthalensis, H. erectus, and the Denisovans). Here, we suggest that the |-FAM72-SRGAP2-| (family with sequence similarity 72/SLIT-ROBO Rho GTPase activating protein 2) gene pair is a unique molecular biomarker for the genus Homo that could also help to place Australopithecus at its most appropriate place within the phylogenetic tree and may explain the distinctive higher brain cognitive functions of humans.
Collapse
|