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Sonnemann HM, Pazdrak B, Nassif B, Sun Y, Elzohary L, Talukder AH, Katailiha AS, Bhat K, Lizée G. Placental co-transcriptional activator Vestigial-like 1 (VGLL1) drives tumorigenesis via increasing transcription of proliferation and invasion genes. Front Oncol 2024; 14:1403052. [PMID: 38912065 PMCID: PMC11190739 DOI: 10.3389/fonc.2024.1403052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
Introduction Vestigial-like 1 (VGLL1) is a co-transcriptional activator that binds to TEA domain-containing transcription factors (TEADs). Its expression is upregulated in a variety of aggressive cancer types, including pancreatic and basal-like breast cancer, and increased transcription of VGLL1 is strongly correlated with poor prognosis and decreased overall patient survival. In normal tissues, VGLL1 is most highly expressed within placental trophoblast cells, which share the common attributes of rapid cellular proliferation and invasion with tumor cells. The impact of VGLL1 in cancer has not been fully elucidated and no VGLL1-targeted therapy currently exists. Methods The aim of this study was to evaluate the cellular function and downstream genomic targets of VGLL1 in placental, pancreatic, and breast cancer cells. Functional assays were employed to assess the role of VGLL1 in cellular invasion and proliferation, and ChIP-seq and RNAseq assays were performed to identify VGLL1 target genes and potential impact using pathway analysis. Results ChIP-seq analysis identified eight transcription factors with a VGLL1-binding motif that were common between all three cell types, including TEAD1-4, AP-1, and GATA6, and revealed ~3,000 shared genes with which VGLL1 interacts. Furthermore, increased VGLL1 expression led to an enhancement of cell invasion and proliferation, which was supported by RNAseq analysis showing transcriptional changes in several genes known to be involved in these processes. Discussion This work expands our mechanistic understanding of VGLL1 function in tumor cells and provides a strong rationale for developing VGLL1-targeted therapies for treating cancer patients.
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Affiliation(s)
- Heather M. Sonnemann
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Barbara Pazdrak
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Barbara Nassif
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Yimo Sun
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Lama Elzohary
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Amjad H. Talukder
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Arjun S. Katailiha
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Krishna Bhat
- Department of Translational Molecular Pathology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, United States
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Parimita S, Das A, Samanta S. VGLL1 stabilization of cytoplasmic TAZ promotes EGFR expression and maintains tumor initiating cells in breast cancer independent of TEAD. Cell Signal 2024; 118:111120. [PMID: 38417636 DOI: 10.1016/j.cellsig.2024.111120] [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: 10/17/2023] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Vestigial-like family member 1 (VGLL1) is one of the X-linked genes whose expression is elevated in basal-like breast cancer (BLBC) because of X-chromosome isodisomy. As an approach towards understanding its function, we performed correlation study using transcript data of breast cancer patients from cBioPortal for Cancer Genomics. Our analysis identified EGFR as the most correlated transcript with VGLL1. We demonstrate that VGLL1 promotes EGFR expression and increases the frequency of breast tumor initiating cells (CD44high/+CD24low/-). These findings are crucial because an elevated EGFR expression and high frequency of CD44high/+CD24low/- cells are defining features of BLBC, and we provide a new mechanistic insight into how their expressions are controlled. Importantly, VGLL1 regulation of EGFR and CD44high/+CD24low/- population is mediated by the hippo-transducer TAZ which exerts its oncogenic roles by binding and activating TEAD transcription factors. A crucial finding is that TEAD-binding domain of TAZ is dispensable for its regulation of EGFR and CD44high/+CD24low/- cells. Instead, VGLL1 stabilization of cytoplasmic TAZ is essential for these functions. Also, we show that VGLL1/TAZ restricts the surface expression of CD24 which contributes to the increased number of CD44high/+CD24low/- cells. In addition, we observed that VGLL1 represses AXL expression and suppresses claudin-low phenotype, and that is caused by the VGLL1 mediated nuclear expulsion of TAZ. Therefore, EGFR and AXL seem to represent two different breast tumor subtypes, and their differential expressions is controlled by VGLL1.
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Affiliation(s)
- Shubhashree Parimita
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Uppal Road, Tarnaka, Hyderabad, TS 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amitava Das
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Uppal Road, Tarnaka, Hyderabad, TS 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sanjoy Samanta
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Uppal Road, Tarnaka, Hyderabad, TS 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Parrish AG, Arora S, Thirimanne HN, Rudoy D, Schmid S, Sievers P, Sahm F, Holland EC, Szulzewsky F. Aggressive high-grade NF2 mutant meningiomas downregulate oncogenic YAP signaling via the upregulation of VGLL4 and FAT3/4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596719. [PMID: 38854109 PMCID: PMC11160807 DOI: 10.1101/2024.05.30.596719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Meningiomas are the most common primary brain tumors in adults. Although generally benign, a subset of meningiomas is of higher grade, shows aggressive growth behavior and recurs even after multiple surgeries. Around half of all meningiomas harbor inactivating mutations in NF2. While benign low-grade NF2 mutant meningiomas exhibit few genetic events in addition to NF2 inactivation, aggressive high-grade NF2 mutant meningiomas frequently harbor a highly aberrant genome. We and others have previously shown that NF2 inactivation leads to YAP1 activation and that YAP1 acts as the pivotal oncogenic driver in benign NF2 mutant meningiomas. Using bulk and single-cell RNA-Seq data from a large cohort of human meningiomas, we show that aggressive NF2 mutant meningiomas harbor decreased levels YAP1 activity compared to their benign counterparts. Decreased expression levels of YAP target genes are significantly associated with an increased risk of recurrence. We then identify the increased expression of the YAP1 competitor VGLL4 as well as the YAP1 upstream regulators FAT3/4 as a potential mechanism for the downregulation of YAP activity in aggressive NF2 mutant meningiomas. High expression of these genes is significantly associated with an increased risk of recurrence. In vitro, overexpression of VGLL4 resulted in the downregulation of YAP activity in benign NF2 mutant meningioma cells, confirming the direct link between VGLL4 expression and decreased levels of YAP activity observed in aggressive NF2 mutant meningiomas. Our results shed new insight on the biology of benign and aggressive NF2 mutant meningiomas and may have important implications for the efficacy of therapies targeting oncogenic YAP1 activity in NF2 mutant meningiomas.
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Affiliation(s)
- Abigail G Parrish
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Dmytro Rudoy
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sebastian Schmid
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Seattle Translational Tumor Research Center, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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Li H, Cai L, Pan Q, Jiang X, Zhao J, Xiang T, Tang Y, Wang Q, He J, Weng D, Zhang Y, Liu Z, Xia J. N 6-methyladenosine-modified VGLL1 promotes ovarian cancer metastasis through high-mobility group AT-hook 1/Wnt/β-catenin signaling. iScience 2024; 27:109245. [PMID: 38439973 PMCID: PMC10910247 DOI: 10.1016/j.isci.2024.109245] [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: 07/17/2023] [Revised: 11/30/2023] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
The main causes of death in patients with ovarian cancer (OC) are invasive lesions and the spread of metastasis. The present study aimed to explore the mechanisms that might promote OC metastasis. Here, we identified that VGLL1 expression was remarkably increased in metastatic OC samples. The role of VGLL1 in OC metastasis and tumor growth was examined by cell function assays and mouse models. Mechanistically level, METTL3-mediated N6-methyladenosine (m6A) modification contributed to VGLL1 upregulation in an IGF2BP2 recognition-dependent manner. Furthermore, VGLL1 directly interacts with TEAD4 and co-transcriptionally activates HMGA1. HMGA1 further activates Wnt/β-catenin signaling to enhance OC metastasis by promoting the epithelial-mesenchyme transition traits. Rescue assays indicated that the upregulation of HMGA1 was essential for VGLL1-induced metastasis. Collectively, these findings showed that the m6A-induced VGLL1/HMGA1/β-catenin axis might play a vital role in OC metastasis and tumor growth. VGLL1 might serve as a prognostic marker and therapeutic target against the metastasis of OC.
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Affiliation(s)
- Han Li
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Gynecology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Liming Cai
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong, China
| | - Qiuzhong Pan
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Xingyu Jiang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jingjing Zhao
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Tong Xiang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yan Tang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Qijing Wang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jia He
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Desheng Weng
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yanna Zhang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong, China
| | - Jianchuan Xia
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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Chamandi G, El-Hajjar L, El Kurdi A, Le Bras M, Nasr R, Lehmann-Che J. ER Negative Breast Cancer and miRNA: There Is More to Decipher Than What the Pathologist Can See! Biomedicines 2023; 11:2300. [PMID: 37626796 PMCID: PMC10452617 DOI: 10.3390/biomedicines11082300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Breast cancer (BC), the most prevalent cancer in women, is a heterogenous disease. Despite advancements in BC diagnosis, prognosis, and therapeutics, survival rates have drastically decreased in the metastatic setting. Therefore, BC still remains a medical challenge. The evolution of high-throughput technology has highlighted gaps in the classification system of BCs. Of particular interest is the notorious triple negative BC, which was recounted as being heterogenous itself and it overlaps with distinct subtypes, namely molecular apocrine (MA) and luminal androgen (LAR) BCs. These subtypes are, even today, still misdiagnosed and poorly treated. As such, researchers and clinicians have been looking for ways through which to refine BC classification in order to properly understand the initiation, development, progression, and the responses to the treatment of BCs. One tool is biomarkers and, specifically, microRNA (miRNA), which are highly reported as associated with BC carcinogenesis. In this review, the diverse roles of miRNA in estrogen receptor negative (ER-) and androgen receptor positive (AR+) BC are depicted. While highlighting their oncogenic and tumor suppressor functions in tumor progression, we will discuss their diagnostic, prognostic, and predictive biomarker potentials, as well as their drug sensitivity/resistance activity. The association of several miRNAs in the KEGG-reported pathways that are related to ER-BC carcinogenesis is presented. The identification and verification of accurate miRNA panels is a cornerstone for tackling BC classification setbacks, as is also the deciphering of the carcinogenesis regulators of ER - AR + BC.
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Affiliation(s)
- Ghada Chamandi
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, 11-0236 Beirut, Lebanon; (G.C.); (L.E.-H.)
- Pathophysiology of Breast Cancer Team, INSERM U976, Immunologie Humaine, Pathophysiologie, Immunothérapie (HIPI), Université Paris Cité, 75010 Paris, France;
| | - Layal El-Hajjar
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, 11-0236 Beirut, Lebanon; (G.C.); (L.E.-H.)
- Office of Basic/Translational Research and Graduate Studies, Faculty of Medicine, American University of Beirut, 11-0236 Beirut, Lebanon
| | - Abdallah El Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, 11-0236 Beirut, Lebanon;
| | - Morgane Le Bras
- Pathophysiology of Breast Cancer Team, INSERM U976, Immunologie Humaine, Pathophysiologie, Immunothérapie (HIPI), Université Paris Cité, 75010 Paris, France;
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, 11-0236 Beirut, Lebanon; (G.C.); (L.E.-H.)
| | - Jacqueline Lehmann-Che
- Pathophysiology of Breast Cancer Team, INSERM U976, Immunologie Humaine, Pathophysiologie, Immunothérapie (HIPI), Université Paris Cité, 75010 Paris, France;
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Local augmented graph neural network for multi-omics cancer prognosis prediction and analysis. Methods 2023; 213:1-9. [PMID: 36933628 DOI: 10.1016/j.ymeth.2023.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/30/2022] [Accepted: 02/25/2023] [Indexed: 03/17/2023] Open
Abstract
Cancer prognosis prediction and analysis can help patients understand expected life and help clinicians provide correct therapeutic guidance. Thanks to the development of sequencing technology, multi-omics data, and biological networks have been used for cancer prognosis prediction. Besides, graph neural networks can simultaneously consider multi-omics features and molecular interactions in biological networks, becoming mainstream in cancer prognosis prediction and analysis. However, the limited number of neighboring genes in biological networks restricts the accuracy of graph neural networks. To solve this problem, a local augmented graph convolutional network named LAGProg is proposed in this paper for cancer prognosis prediction and analysis. The process follows: first, given a patient's multi-omics data features and biological network, the corresponding augmented conditional variational autoencoder generates features. Then, the generated augmented features and the original features are fed into a cancer prognosis prediction model to complete the cancer prognosis prediction task. The conditional variational autoencoder consists of two parts: encoder-decoder. In the encoding phase, an encoder learns the conditional distribution of the multi-omics data. As a generative model, a decoder takes the conditional distribution and the original feature as inputs to generate the enhanced features. The cancer prognosis prediction model consists of a two-layer graph convolutional neural network and a Cox proportional risk network. The Cox proportional risk network consists of fully connected layers. Extensive experiments on 15 real-world datasets from TCGA demonstrated the effectiveness and efficiency of the proposed method in predicting cancer prognosis. LAGProg improved the C-index values by an average of 8.5% over the state-of-the-art graph neural network method. Moreover, we confirmed that the local augmentation technique could enhance the model's ability to represent multi-omics features, improve the model's robustness to missing multi-omics features, and prevent the model's over-smoothing during training. Finally, based on genes identified through differential expression analysis, we discovered 13 prognostic markers highly associated with breast cancer, among which ten genes have been proved by literature review.
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Contreras-Rodríguez JA, Puente-Rivera J, Córdova-Esparza DM, Nuñez-Olvera SI, Silva-Cázares MB. Bioinformatic miRNA-mRNAs Analysis Revels to miR-934 as a Potential Regulator of the Epithelial-Mesenchymal Transition in Triple-Negative Breast Cancer. Cells 2023; 12:cells12060834. [PMID: 36980175 PMCID: PMC10047237 DOI: 10.3390/cells12060834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/10/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer and has the worst prognosis. In patients with TNBC tumors, the tumor cells have been reported to have mesenchymal features, which help them migrate and invade. Various studies on cancer have revealed the importance of microRNAs (miRNAs) in different biological processes of the cell in that aberrations, in their expression, lead to alterations and deregulations in said processes, giving rise to tumor progression and aggression. In the present work, we determined the miRNAs that are deregulated in the epithelial-mesenchymal transition process in breast cancer. We discovered that 25 miRNAs that regulate mesenchymal genes are overexpressed in patients with TNBC. We found that miRNA targets modulate different processes and pathways, such as apoptosis, FoxO signaling pathways, and Hippo. We also found that the expression level of miR-934 is specific to the molecular subtype of the triple-negative breast cancer and modulates a set of related epithelial-mesenchymal genes. We determined that miR-934 inhibition in TNBC cell lines inhibits the migratory abilities of tumor cells.
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Affiliation(s)
| | | | | | - Stephanie I Nuñez-Olvera
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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Sonnemann HM, Pazdrak B, Antunes DA, Roszik J, Lizée G. Vestigial-like 1 (VGLL1): An ancient co-transcriptional activator linking wing, placenta, and tumor development. Biochim Biophys Acta Rev Cancer 2023; 1878:188892. [PMID: 37004960 DOI: 10.1016/j.bbcan.2023.188892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Vestigial-like 1 (VGLL1) is a recently discovered driver of proliferation and invasion that is expressed in many aggressive human malignancies and is strongly associated with poor prognosis. The VGLL1 gene encodes for a co-transcriptional activator that shows intriguing structural similarity to key activators in the hippo pathway, providing important clues to its functional role. VGLL1 binds to TEADs in an analogous fashion to YAP1 but appears to activate a distinct set of downstream gene targets. In mammals, VGLL1 expression is found almost exclusively in placental trophoblasts, cells that share many hallmarks of cancer. Due to its role as a driver of tumor progression, VGLL1 has become a target of interest for potential anticancer therapies. In this review, we discuss VGLL1 from an evolutionary perspective, contrast its role in placental and tumor development, summarize the current knowledge of how signaling pathways can modulate VGLL1 function, and discuss potential approaches for targeting VGLL1 therapeutically.
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Ni L, Tang C, Wang Y, Wan J, Charles MG, Zhang Z, Li C, Zeng R, Jin Y, Song P, Wei M, Li B, Zhang J, Wu Z. Construction of a miRNA-Based Nomogram Model to Predict the Prognosis of Endometrial Cancer. J Pers Med 2022; 12:jpm12071154. [PMID: 35887651 PMCID: PMC9318842 DOI: 10.3390/jpm12071154] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 12/11/2022] Open
Abstract
Objective: To investigate the differential expression of microRNA (miRNA) in patients with endometrial cancer and its relationship with prognosis and survival. Method: We used The Cancer Genome Atlas (TCGA) database to analyze differentially expressed miRNAs in endometrial cancer tissues and adjacent normal tissues. In addition, we successfully screened out key microRNAs to build nomogram models for predicting prognosis and we performed survival analysis on the key miRNAs as well. Result: We identified 187 differentially expressed miRNAs, which includes 134 up-regulated miRNAs and 53 down-regulated miRNAs. Further univariate Cox regression analysis screened out 47 significantly differentially expressed miRNAs and selected 12 miRNAs from which the prognostic nomogram model for ECA patients by LASSO analysis was constructed. Survival analysis showed that high expression of hsa-mir-138-2, hsa-mir-548f-1, hsa-mir-934, hsa-mir-940, and hsa-mir-4758 as well as low-expression of hsa-mir-146a, hsa-mir-3170, hsa-mir-3614, hsa-mir-3616, and hsa-mir-4687 are associated with poor prognosis in EC patients. However, significant correlations between the expressions levels of has-mir-876 and hsa-mir-1269a and patients' prognosis are not found. Conclusion: Our study found that 12 significantly differentially expressed miRNAs might promote the proliferation, invasion, and metastasis of cancer cells by regulating the expression of upstream target genes, thereby affecting the prognosis of patients with endometrial cancer.
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Affiliation(s)
- Leyi Ni
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Chengyun Tang
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Yuning Wang
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Jiaming Wan
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Morgan G. Charles
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Zilong Zhang
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, 14195 Berlin, Germany;
| | - Ruijie Zeng
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Yiyao Jin
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Penghao Song
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Ming Wei
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Bocen Li
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
| | - Jin Zhang
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Correspondence: (J.Z.); (Z.W.)
| | - Zhenghao Wu
- School of Medicine, I.M. Sechenov First Moscow State Medical University, Ministry of Health, Russian Federation, 8/2 Trubetskaya Street, 119991 Moscow, Russia; (L.N.); (C.T.); (Y.W.); (J.W.); (M.G.C.); (Z.Z.); (R.Z.); (Y.J.); (P.S.); (M.W.); (B.L.)
- Correspondence: (J.Z.); (Z.W.)
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10
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Sun X, Liswaniso S, Shan X, Zhao J, Chimbaka IM, Xu R, Qin N. The opposite effects of VGLL1 and VGLL4 genes on granulosa cell proliferation and apoptosis of hen ovarian prehierarchical follicles. Theriogenology 2022; 181:95-104. [PMID: 35074718 DOI: 10.1016/j.theriogenology.2022.01.017] [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: 08/20/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 11/26/2022]
Abstract
Transcription cofactors Vestigial like family (VGLL) members consisting of four homologs (VGLL1-4) are associated with cell growth and metastasis in mammals, among which VGLL1 gene has been documented to possess tumorigenic functions in various types of tumor, and VGLL4 acts as a new tumor suppressor; likewise several studies indicated that they potentially play a role in the regulation of ovary growth and function. However, the biological effects of chicken VGLL1 and VGLL4 on the proliferation, apoptosis, and steroidogenesis of the granulosa cells (GCs) during ovarian follicle development remain unknown now. This study found that VGLL1 and VGLL4 genes present divergent expression patterns of the transcripts in the GCs of various sized prehierarchical follicles (PFs) before follicle selection. Specific small interfering RNA (siRNA) was employed to elucidate the exact roles of VGLL1 and VGLL4 in regulating the PF development of the hen ovary. The results demonstrated that the mRNA expression levels of the steroidogenic-related enzyme steroidogenic acute regulatory protein (STAR) gene and the cell proliferation-related factors B-cell lymphoma-2 (BCL2), and cyclin D1 (CCND1) genes were significantly down-regulated in the cells with VGLL1 silence but remarkably up-regulated in the cells lacking VGLL4. Whereas the expression level of the cell apoptosis biomarker caspase-3 (CASP3) transcript was noticeably enhanced in the GCs without VGLL1 but significantly decreased in the GCs deprived of VGLL4. Further results showed that the siRNA-mediated silence of VGLL1 caused a significant increase in apoptosis with a reduction in the proliferation of GCs. Nevertheless, knockdown of VGLL4 resulted in a remarkable decrement in apoptosis but a memorable augment in proliferation of the GCs. Taken together, this study proved that VGLL1 promotes cell proliferation and steroidogenesis but inhibits apoptosis. In contrast, VGLL4 stimulates GC apoptosis while suppressing the GC proliferation and steroidogenesis in the hen ovarian follicles. We conluded that VGLL1 and VGLL4 affect oppositely the ovarian prehierarchical follicle development by the different regulatory manner in the GC proliferation and apoptosis of chicken ovary.
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Affiliation(s)
- Xue Sun
- Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Simushi Liswaniso
- Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Xuesong Shan
- Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jinghua Zhao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Ignatius Musenge Chimbaka
- Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Rifu Xu
- Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
| | - Ning Qin
- Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
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11
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An Efficient Algorithm for the Detection of Outliers in Mislabeled Omics Data. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2021:9436582. [PMID: 34976114 PMCID: PMC8716222 DOI: 10.1155/2021/9436582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/30/2021] [Indexed: 11/18/2022]
Abstract
High dimensionality and noise have made it difficult to detect related biomarkers in omics data. Through previous study, penalized maximum trimmed likelihood estimation is effective in identifying mislabeled samples in high-dimensional data with mislabeled error. However, the algorithm commonly used in these studies is the concentration step (C-step), and the C-step algorithm that is applied to robust penalized regression does not ensure that the criterion function is gradually optimized iteratively, because the regularized parameters change during the iteration. This makes the C-step algorithm runs very slowly, especially when dealing with high-dimensional omics data. The AR-Cstep (C-step combined with an acceptance-rejection scheme) algorithm is proposed. In simulation experiments, the AR-Cstep algorithm converged faster (the average computation time was only 2% of that of the C-step algorithm) and was more accurate in terms of variable selection and outlier identification than the C-step algorithm. The two algorithms were further compared on triple negative breast cancer (TNBC) RNA-seq data. AR-Cstep can solve the problem of the C-step not converging and ensures that the iterative process is in the direction that improves criterion function. As an improvement of the C-step algorithm, the AR-Cstep algorithm can be extended to other robust models with regularized parameters.
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12
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Discovery of a cryptic site at the interface 2 of TEAD - Towards a new family of YAP/TAZ-TEAD inhibitors. Eur J Med Chem 2021; 226:113835. [PMID: 34509860 DOI: 10.1016/j.ejmech.2021.113835] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022]
Abstract
The Hippo pathway is involved in organ size control and tissue homeostasis by regulating cell growth, proliferation and apoptosis. It controls the phosphorylation of the transcription co-activator YAP (Yes associated protein) and TAZ (Transcriptional coactivator with PDZ-binding motif) in order to control their nuclear import and their interaction with TEAD (Transcriptional Enhanced Associated Domain). YAP, TAZ and TEADs are dysregulated in several cancers making YAP/TAZ-TEAD interaction a new emerging anti-cancer target. We report the synthesis of a set of trisubstituted pyrazoles which bind to hTEAD2 at the interface 2 revealing for the first time a cryptic pocket created by the movement of the phenol ring of Y382. Compound 6 disrupts YAP/TAZ-TEAD interaction in HEK293T cells and inhibits TEAD target genes and cell proliferation in MDA-MB-231 cells. Compound 6 is therefore the first inhibitor of YAP/TAZ-TEAD targeting interface 2. This molecule could serve with other pan-TEAD inhibitors such as interface 3 ligands, for the delineation of the relative importance of VGLL vs YAP/TAZ in a given cellular model.
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13
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Turkistani S, Sugita BM, Fadda P, Marchi R, Afsari A, Naab T, Apprey V, Copeland RL, Campbell MC, Cavalli LR, Kanaan Y. A panel of miRNAs as prognostic markers for African-American patients with triple negative breast cancer. BMC Cancer 2021; 21:861. [PMID: 34315420 PMCID: PMC8317413 DOI: 10.1186/s12885-021-08573-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND To investigate the global expression profile of miRNAs, their impact on cellular signaling pathways, and their association with poor prognostic parameters in African-American (AA) patients with triple negative breast cancer (TNBC). METHODS Twenty-five samples of AA TNBC patients were profiled for global miRNA expression and stratified considering three clinical-pathological parameters: tumor size, lymph node (LN), and recurrence (REC) status. Differential miRNA expression analysis was performed for each parameter, and their discriminatory power was determined by Receiver Operating Characteristic (ROC) curve analysis. KMplotter was assessed to determine the association of the miRNAs with survival, and functional enrichment analysis to determine the main affected pathways and miRNA/mRNA target interactions. RESULTS A panel of eight, 23 and 27 miRNAs were associated with tumor size, LN, and REC status, respectively. Combined ROC analysis of two (miR-2117, and miR-378c), seven (let-7f-5p, miR-1255b-5p, miR-1268b, miR-200c-3p, miR-520d, miR-527, and miR-518a-5p), and three (miR-1200, miR-1249-3p, and miR-1271-3p) miRNAs showed a robust discriminatory power based on tumor size (AUC = 0.917), LN (AUC = 0.945) and REC (AUC = 0.981) status, respectively. Enrichment pathway analysis revealed their involvement in proteoglycans and glycan and cancer-associated pathways. Eight miRNAs with deregulated expressions in patients with large tumor size, positive LN metastasis, and recurrence were significantly associated with lower survival rates. Finally, the construction of miRNA/mRNA networks based in experimentally validated mRNA targets, revealed nodes of critical cancer genes, such as AKT1, BCL2, CDKN1A, EZR and PTEN. CONCLUSIONS Altogether, our data indicate that miRNA deregulated expression is a relevant biological factor that can be associated with the poor prognosis in TNBC of AA patients, by conferring to their TNBC cells aggressive phenotypes that are reflected in the clinical characteristics evaluated in this study.
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Affiliation(s)
- Safaa Turkistani
- Department of Microbiology, Howard University Cancer Center, Howard University, Washington DC, USA
| | - Bruna M Sugita
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Paolo Fadda
- Genomics Shared Resource, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rafael Marchi
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Ali Afsari
- Department of Pathology, Howard University Hospital, Washington DC, USA
| | - Tammey Naab
- Department of Pathology, Howard University Hospital, Washington DC, USA
| | - Victor Apprey
- Department of Community and Family Medicine, Howard University, Washington DC, USA
| | - Robert L Copeland
- Department of Pharmacology, College of Medicine and Cancer Center, Howard University, Washington DC, USA
| | | | - Luciane R Cavalli
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil.
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA.
| | - Yasmine Kanaan
- Department of Microbiology, Howard University Cancer Center, Howard University, Washington DC, USA
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14
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Yang L, Li X, Luo Y, Yang T, Wang H, Shi L, Feng M, Xie W. Weighted gene co-expression network analysis of the association between upregulated AMD1, EN1 and VGLL1 and the progression and poor prognosis of breast cancer. Exp Ther Med 2021; 22:1030. [PMID: 34373716 PMCID: PMC8343771 DOI: 10.3892/etm.2021.10462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most prevalent malignancy among females, but the molecular mechanisms involved in its pathogenesis and progression have remained to be fully elucidated. The aim of the present study was to identify novel potential therapeutic targets for breast cancer. The dataset GSE76275 was downloaded from the Gene Expression Omnibus database and weighted gene co-expression network analysis (WGCNA) was performed to identify hub genes. Furthermore, the dataset GSE25055, containing gene expression data and clinical information, was downloaded to validate the expression and survival association of these hub genes. In addition, the datasets GSE25065 and GSE42568 were used to validate the association between hub gene expression levels and clinical features. Immunohistochemistry (IHC), reverse transcription-quantitative PCR, as well as proliferation, migration, invasion and apoptosis assays, were used to verify gene expression and function. A total of 4,052 genes were selected for WGCNA and 18 modules were established; the red module was identified as the key module, as it had a strong positive correlation with the tumor grade. Survival analyses of hub genes [S-adenosylmethionine decarboxylase proenzyme (AMD1), homeobox protein engrailed-1 (EN1) and vestigial-like protein (VGLL1)] indicated that higher levels of gene expression were associated with poor prognosis of patients with breast cancer. This association was based on survival analysis of GSE25055 using the Kaplan-Meier plotter tool. Expression validation revealed that the upregulation of hub genes was associated with advanced tumor grade and malignant molecular subtype (basal-like). IHC results from the Human Protein Atlas also demonstrated that protein expression levels of the hub genes were higher in tumor tissues compared with those in adjacent normal tissues. Furthermore, the expression levels of AMD1, EN1 and VGLL1 were strongly correlated with each other. These results demonstrated that AMD1 is highly expressed in breast cancer tissues and cells and AMD1 knockdown decreased the proliferation and metastatic potential, while increasing apoptosis of breast cancer cells. These results suggested that AMD1, EN1 and VGLL1 are likely to contribute to breast cancer progression and unfavorable prognosis.
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Affiliation(s)
- Lijie Yang
- Department of Gastrointestinal Surgery, Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Clinical Cancer Study Center of Hubei Province, Key Laboratory of Tumor Biological Behavior of Hubei, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xuanfei Li
- Department of Gastrointestinal Surgery, Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Clinical Cancer Study Center of Hubei Province, Key Laboratory of Tumor Biological Behavior of Hubei, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yixing Luo
- Department of Emergency, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Tiecheng Yang
- Department of Gastrointestinal Surgery, Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Clinical Cancer Study Center of Hubei Province, Key Laboratory of Tumor Biological Behavior of Hubei, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Huaqiao Wang
- Department of Gastrointestinal Surgery, Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Clinical Cancer Study Center of Hubei Province, Key Laboratory of Tumor Biological Behavior of Hubei, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Liwen Shi
- Department of Gastrointestinal Surgery, Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Clinical Cancer Study Center of Hubei Province, Key Laboratory of Tumor Biological Behavior of Hubei, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Maohui Feng
- Department of Gastrointestinal Surgery, Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Clinical Cancer Study Center of Hubei Province, Key Laboratory of Tumor Biological Behavior of Hubei, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Wei Xie
- Department of Gastrointestinal Surgery, Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Clinical Cancer Study Center of Hubei Province, Key Laboratory of Tumor Biological Behavior of Hubei, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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15
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Guo M, Wang SM. Genome Instability-Derived Genes Are Novel Prognostic Biomarkers for Triple-Negative Breast Cancer. Front Cell Dev Biol 2021; 9:701073. [PMID: 34322487 PMCID: PMC8312551 DOI: 10.3389/fcell.2021.701073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/10/2021] [Indexed: 12/31/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is an aggressive disease. Recent studies have identified genome instability-derived genes for patient outcomes. However, most of the studies mainly focused on only one or a few genome instability-related genes. Prognostic potential and clinical significance of genome instability-associated genes in TNBC have not been well explored. Methods In this study, we developed a computational approach to identify TNBC prognostic signature. It consisted of (1) using somatic mutations and copy number variations (CNVs) in TNBC to build a binary matrix and identifying the top and bottom 25% mutated samples, (2) comparing the gene expression between the top and bottom 25% samples to identify genome instability-related genes, and (3) performing univariate Cox proportional hazards regression analysis to identify survival-associated gene signature, and Kaplan–Meier, log-rank test, and multivariate Cox regression analyses to obtain overall survival (OS) information for TNBC outcome prediction. Results From the identified 111 genome instability-related genes, we extracted a genome instability-derived gene signature (GIGenSig) of 11 genes. Through survival analysis, we were able to classify TNBC cases into high- and low-risk groups by the signature in the training dataset (log-rank test p = 2.66e−04), validated its prognostic performance in the testing (log-rank test p = 2.45e−02) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (log-rank test p = 2.57e−05) datasets, and further validated the predictive power of the signature in five independent datasets. Conclusion The identified novel signature provides a better understanding of genome instability in TNBC and can be applied as prognostic markers for clinical TNBC management.
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Affiliation(s)
- Maoni Guo
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
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16
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miR-934 promotes breast cancer metastasis by regulation of PTEN and epithelial-mesenchymal transition. Tissue Cell 2021; 71:101581. [PMID: 34147851 DOI: 10.1016/j.tice.2021.101581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 12/25/2022]
Abstract
Breast cancer (BC) is the most commonly diagnosed malignancy and the leading cause of cancer-related mortality among females. Over 90 % of the cases of death in BC patients are attributed to tumor cell metastasis. Therefore, it is urgently needed to investigate the molecular mechanisms of BC metastasis. The expression of miRNA in BC was evaluated by qRT-PCR and bioinformatics analysis. Clone formation, EdU assays, and subcutaneous xenograft model were used to test the growth of BC cells. Wound healing, transwell assays, and lung-metastasis model were used to explore the effect of miR-934 knockdown on cell metastasis. The miR-934 targets in BC were identified through bioinformatics analysis and luciferase reporter assays. The expression of protein was tested by western blot. The binding of mRNA and RNA-binding-protein was verified using RIP assays. miR-934 expression was significantly elevated in BC tissues, especially in those with lymph node metastasis and associated with poor patient prognosis. Experiments in vitro and in vivo showed that that upregulated miR-934 was not necessarily required for the growth of BC cells. However, miR-934 knockdown significantly inhibited the migration and invasion abilities of BC cells. Moreover, PTEN as identified as the direct target of miR-934 in BC, and miR-934 could promote BC cell metastasis by regulation of PTEN and epithelial-mesenchymal transition (EMT). Our results suggested that targeting miR-934 may be a practical treatment for BC cell metastasis.
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17
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Fan WM, Luo D, Zhang JZ, Wang D, Shen J. Vestigial suppresses apoptosis and cell migration in a manner dependent on the level of JNK-Caspase signaling in the Drosophila wing disc. INSECT SCIENCE 2021; 28:63-76. [PMID: 32037698 DOI: 10.1111/1744-7917.12762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/02/2020] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
The Decapentaplegic (Dpp) and Wingless (Wg) signal pathways play important roles in numerous biological processes in Drosophila. The Drosophila vestigial (vg) gene is selectively required for wing imaginal disc cell proliferation, which is essential for the formation of the adult wing and halter structures, and is regulated by Dpp and Wg signaling. Using a Drosophila invasion model of wing epithelium, we showed herein that inhibition of Dpp or Wg signaling promoted cells to migrate across the cell lineage restrictive anterior/posterior (A/P) compartment boundary. Being downstream of both Dpp and Wg signaling, vg can block cell migration induced by loss of either pathway. In addition, suppression of vg is sufficient to induce cell migration across the A/P boundary. Transcriptomic analysis revealed potential downstream genes involved in the cell migration after suppressing vg in the wing disc. We further demonstrated that the c-Jun N-terminal kinase (JNK) signaling promoted cell migration induced by vg suppression by upregulating Caspase activity. Taken together, our results revealed the requirement of Vg for suppressing cell migration and clarified how developmental signals collaborate to stabilize cells along the compartment boundary.
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Affiliation(s)
- Wen-Min Fan
- Department of Entomology and MOA Lab for Pest Monitoring and Green Control, China Agricultural University, Beijing, China
| | - Dan Luo
- Department of Entomology and MOA Lab for Pest Monitoring and Green Control, China Agricultural University, Beijing, China
| | - Jun-Zheng Zhang
- Department of Entomology and MOA Lab for Pest Monitoring and Green Control, China Agricultural University, Beijing, China
| | - Dan Wang
- Department of Entomology and MOA Lab for Pest Monitoring and Green Control, China Agricultural University, Beijing, China
| | - Jie Shen
- Department of Entomology and MOA Lab for Pest Monitoring and Green Control, China Agricultural University, Beijing, China
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18
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Angius A, Cossu-Rocca P, Arru C, Muroni MR, Rallo V, Carru C, Uva P, Pira G, Orrù S, De Miglio MR. Modulatory Role of microRNAs in Triple Negative Breast Cancer with Basal-Like Phenotype. Cancers (Basel) 2020; 12:E3298. [PMID: 33171872 PMCID: PMC7695196 DOI: 10.3390/cancers12113298] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022] Open
Abstract
Development of new research, classification, and therapeutic options are urgently required due to the fact that TNBC is a heterogeneous malignancy. The expression of high molecular weight cytokeratins identifies a biologically and clinically distinct subgroup of TNBCs with a basal-like phenotype, representing about 75% of TNBCs, while the remaining 25% includes all other intrinsic subtypes. The triple negative phenotype in basal-like breast cancer (BLBC) makes it unresponsive to endocrine therapy, i.e., tamoxifen, aromatase inhibitors, and/or anti-HER2-targeted therapies; for this reason, only chemotherapy can be considered an approach available for systemic treatment even if it shows poor prognosis. Therefore, treatment for these subgroups of patients is a strong challenge for oncologists due to disease heterogeneity and the absence of unambiguous molecular targets. Dysregulation of the cellular miRNAome has been related to huge cellular process deregulations underlying human malignancy. Consequently, epigenetics is a field of great promise in cancer research. Increasing evidence suggests that specific miRNA clusters/signatures might be of clinical utility in TNBCs with basal-like phenotype. The epigenetic mechanisms behind tumorigenesis enable progress in the treatment, diagnosis, and prevention of cancer. This review intends to summarize the epigenetic findings related to miRNAome in TNBCs with basal-like phenotype.
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Affiliation(s)
- Andrea Angius
- Institute of Genetic and Biomedical Research (IRGB), CNR, Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy;
| | - Paolo Cossu-Rocca
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (P.C.-R.); (M.R.M.)
- Department of Diagnostic Services, “Giovanni Paolo II” Hospital, ASSL Olbia-ATS Sardegna, 07026 Olbia, Italy
| | - Caterina Arru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.); (G.P.)
| | - Maria Rosaria Muroni
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (P.C.-R.); (M.R.M.)
| | - Vincenzo Rallo
- Institute of Genetic and Biomedical Research (IRGB), CNR, Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy;
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.); (G.P.)
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.); (G.P.)
| | - Paolo Uva
- CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula, CA, Italy;
| | - Giovanna Pira
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.); (G.P.)
| | - Sandra Orrù
- Department of Pathology, “A. Businco” Oncologic Hospital, ASL Cagliari, 09121 Cagliari, Italy;
| | - Maria Rosaria De Miglio
- Institute of Genetic and Biomedical Research (IRGB), CNR, Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy;
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19
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Bradley SD, Talukder AH, Lai I, Davis R, Alvarez H, Tiriac H, Zhang M, Chiu Y, Melendez B, Jackson KR, Katailiha A, Sonnemann HM, Li F, Kang Y, Qiao N, Pan BF, Lorenzi PL, Hurd M, Mittendorf EA, Peterson CB, Javle M, Bristow C, Kim M, Tuveson DA, Hawke D, Kopetz S, Wolff RA, Hwu P, Maitra A, Roszik J, Yee C, Lizée G. Vestigial-like 1 is a shared targetable cancer-placenta antigen expressed by pancreatic and basal-like breast cancers. Nat Commun 2020; 11:5332. [PMID: 33087697 PMCID: PMC7577998 DOI: 10.1038/s41467-020-19141-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 09/24/2020] [Indexed: 12/13/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL)-based cancer immunotherapies have shown great promise for inducing clinical regressions by targeting tumor-associated antigens (TAA). To expand the TAA landscape of pancreatic ductal adenocarcinoma (PDAC), we performed tandem mass spectrometry analysis of HLA class I-bound peptides from 35 PDAC patient tumors. This identified a shared HLA-A*0101 restricted peptide derived from co-transcriptional activator Vestigial-like 1 (VGLL1) as a putative TAA demonstrating overexpression in multiple tumor types and low or absent expression in essential normal tissues. Here we show that VGLL1-specific CTLs expanded from the blood of a PDAC patient could recognize and kill in an antigen-specific manner a majority of HLA-A*0101 allogeneic tumor cell lines derived not only from PDAC, but also bladder, ovarian, gastric, lung, and basal-like breast cancers. Gene expression profiling reveals VGLL1 as a member of a unique group of cancer-placenta antigens (CPA) that may constitute immunotherapeutic targets for patients with multiple cancer types.
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MESH Headings
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Breast Neoplasms/genetics
- Breast Neoplasms/immunology
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/immunology
- Carcinoma, Pancreatic Ductal/therapy
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/immunology
- Female
- Gene Expression Profiling
- HLA-A1 Antigen/immunology
- Humans
- Immunotherapy, Adoptive
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/immunology
- Pancreatic Neoplasms/therapy
- Placenta/immunology
- Pregnancy
- Prognosis
- T-Lymphocytes, Cytotoxic/immunology
- Transcription Factors/genetics
- Transcription Factors/immunology
- Pancreatic Neoplasms
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Affiliation(s)
- Sherille D Bradley
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Amjad H Talukder
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ivy Lai
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Rebecca Davis
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Hector Alvarez
- Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Herve Tiriac
- Cold Spring Harbor Laboratory Cancer Center, Cold Spring Harbor, NY, USA
| | - Minying Zhang
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yulun Chiu
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Brenda Melendez
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Kyle R Jackson
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Arjun Katailiha
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Heather M Sonnemann
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Fenge Li
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yaan Kang
- Department of Surgical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Na Qiao
- Department of Breast Surgery Research, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Bih-Fang Pan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Mark Hurd
- Ahmed Center for Pancreatic Cancer Research, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Milind Javle
- Department of Gastrointestinal Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Bristow
- Center for Co-clinical Trials, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Kim
- Department of Surgical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - David A Tuveson
- Cold Spring Harbor Laboratory Cancer Center, Cold Spring Harbor, NY, USA
| | - David Hawke
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Pathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA.
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA.
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA.
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA.
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20
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Yoon G, Carroll RJ, Gaynanova I. Sparse semiparametric canonical correlation analysis for data of mixed types. Biometrika 2020; 107:609-625. [PMID: 34621080 PMCID: PMC8494134 DOI: 10.1093/biomet/asaa007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Canonical correlation analysis investigates linear relationships between two sets of variables, but often works poorly on modern datasets due to high-dimensionality and mixed data types (continuous/binary/zero-inflated). We propose a new approach for sparse canonical correlation analysis of mixed data types that does not require explicit parametric assumptions. Our main contribution is the use of truncated latent Gaussian copula to model the data with excess zeroes, which allows us to derive a rank-based estimator of latent correlation matrix without the estimation of marginal transformation functions. The resulting semiparametric sparse canonical correlation analysis method works well in high-dimensional settings as demonstrated via numerical studies, and application to the analysis of association between gene expression and micro RNA data of breast cancer patients.
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Affiliation(s)
- Grace Yoon
- Department of Statistics, Texas A&M University, College Station, Texas 77843, U.S.A
| | - Raymond J Carroll
- Department of Statistics, Texas A&M University, College Station, Texas 77843, U.S.A
| | - Irina Gaynanova
- Department of Statistics, Texas A&M University, College Station, Texas 77843, U.S.A
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21
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Screening and identification of potential prognostic biomarkers in bladder urothelial carcinoma: Evidence from bioinformatics analysis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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22
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Shiiba M, Yamagami H, Sudo T, Tomokuni Y, Kashiwabara D, Kirita T, Kusukawa J, Komiya M, Tei K, Kitagawa Y, Imai Y, Kawamata H, Bukawa H, Satomura K, Oki H, Shinozuka K, Sugihara K, Sugiura T, Sekine J, Yokoe H, Saito K, Tanzawa H. Development of prediction models for the sensitivity of oral squamous cell carcinomas to preoperative S-1 administration. Heliyon 2020; 6:e04601. [PMID: 32793829 PMCID: PMC7408317 DOI: 10.1016/j.heliyon.2020.e04601] [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: 07/02/2020] [Revised: 07/18/2020] [Accepted: 07/28/2020] [Indexed: 11/29/2022] Open
Abstract
S-1 is an anticancer agent that is comprised of tegafur, gimeracil, and oteracil potassium, and is widely used in various carcinomas including oral squamous cell carcinoma (OSCC). Although an established prediction tool is not available, we aimed to develop prediction models for the sensitivity of primary OSCC cases to the preoperative administration of S-1. We performed DNA microarray analysis of 95 cases with OSCC. Using global gene expression data and the clinical data, we developed two different prediction models, namely, model 1 that comprised the complete response (CR) + the partial response (PR) versus stable disease (SD) + progressive disease (PD), and model 2 that comprised responders versus non-responders. Twelve and 18 genes were designated as feature genes (FGs) in models 1 and 2, respectively, and, of these, six genes were common to both models. The sensitivity was 96.3%, the specificity was 91.2%, and the accuracy was 92.6% for model 1, and the sensitivity was 95.6%, the specificity was 85.2%, and the accuracy was 92.6% for model 2. These models were validated using receiver operating characteristic analysis, and the areas under the curves were 0.967 and 0.949 in models 1 and 2, respectively. The data led to the development of models that can reliably predict the sensitivity of patients with OSCC to the preoperative administration of S-1. The mechanism that regulates S-1 sensitivity remains unclear; however, the prediction models developed provide hope that further functional investigations into the FGs will lead to a greater understanding of drug resistance.
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Affiliation(s)
- Masashi Shiiba
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Japan.,Department of Oral Science, Graduate School of Medicine, Chiba University, Japan.,Division of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Japan
| | | | | | | | | | - Tadaaki Kirita
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Japan
| | - Jingo Kusukawa
- Department of Dental and Oral Medical Center, Kurume University School of Medicine, Japan
| | - Masamichi Komiya
- Department of Oral Surgery, Nihon University School of Dentistry at Matsudo, Japan.,Division of Dental and Oral Surgery, Nihon University Itabashi Hospital, Japan
| | - Kanchu Tei
- Department of Oral and Maxillofacial Surgery, Graduate School of Dental Medicine, Hokkaido University, Japan
| | - Yoshimasa Kitagawa
- Department of Oral Diagnosis and Medicine, Graduate School of Dental Medicine, Hokkaido University, Japan
| | - Yutaka Imai
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Japan
| | - Hitoshi Kawamata
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Japan
| | - Hiroki Bukawa
- Department of Oral and Maxillofacial Surgery, University of Tsukuba, Japan
| | - Kazuhito Satomura
- Department of Oral Medicine and Stomatology, School of Dental Medicine, Tsurumi University, Japan
| | - Hidero Oki
- Department of Maxillofacial Surgery, Nihon University School of Dentistry, Japan
| | - Keiji Shinozuka
- Department of Maxillofacial Surgery, Nihon University School of Dentistry, Japan
| | - Kazumasa Sugihara
- Maxillofacial Diagnostic and Surgical Sciences, Department of Oral and Maxillofacial Rehabilitation, Course of Developmental Therapeutics, Kagoshima University Graduate School of Medical and Dental Sciences, Japan
| | - Tsuyoshi Sugiura
- Maxillofacial Diagnostic and Surgical Sciences, Department of Oral and Maxillofacial Rehabilitation, Course of Developmental Therapeutics, Kagoshima University Graduate School of Medical and Dental Sciences, Japan
| | - Joji Sekine
- Department of Oral and Maxillofacial Surgery, Shimane University Faculty of Medicine, Japan
| | - Hidetaka Yokoe
- Department of Dentistry and Oral Surgery, National Defense Medical College, Japan
| | - Kengo Saito
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Japan
| | - Hideki Tanzawa
- Department of Oral Science, Graduate School of Medicine, Chiba University, Japan.,Division of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Japan
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23
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Sun H, Cui Y, Wang H, Liu H, Wang T. Comparison of methods for the detection of outliers and associated biomarkers in mislabeled omics data. BMC Bioinformatics 2020; 21:357. [PMID: 32795265 PMCID: PMC7646480 DOI: 10.1186/s12859-020-03653-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 07/10/2020] [Indexed: 02/08/2023] Open
Abstract
Background Previous studies have reported that labeling errors are not uncommon in omics data. Potential outliers may severely undermine the correct classification of patients and the identification of reliable biomarkers for a particular disease. Three methods have been proposed to address the problem: sparse label-noise-robust logistic regression (Rlogreg), robust elastic net based on the least trimmed square (enetLTS), and Ensemble. Ensemble is an ensembled classification based on distinct feature selection and modeling strategies. The accuracy of biomarker selection and outlier detection of these methods needs to be evaluated and compared so that the appropriate method can be chosen. Results The accuracy of variable selection, outlier identification, and prediction of three methods (Ensemble, enetLTS, Rlogreg) were compared for simulated and an RNA-seq dataset. On simulated datasets, Ensemble had the highest variable selection accuracy, as measured by a comprehensive index, and lowest false discovery rate among the three methods. When the sample size was large and the proportion of outliers was ≤5%, the positive selection rate of Ensemble was similar to that of enetLTS. However, when the proportion of outliers was 10% or 15%, Ensemble missed some variables that affected the response variables. Overall, enetLTS had the best outlier detection accuracy with false positive rates < 0.05 and high sensitivity, and enetLTS still performed well when the proportion of outliers was relatively large. With 1% or 2% outliers, Ensemble showed high outlier detection accuracy, but with higher proportions of outliers Ensemble missed many mislabeled samples. Rlogreg and Ensemble were less accurate in identifying outliers than enetLTS. The prediction accuracy of enetLTS was better than that of Rlogreg. Running Ensemble on a subset of data after removing the outliers identified by enetLTS improved the variable selection accuracy of Ensemble. Conclusions When the proportion of outliers is ≤5%, Ensemble can be used for variable selection. When the proportion of outliers is > 5%, Ensemble can be used for variable selection on a subset after removing outliers identified by enetLTS. For outlier identification, enetLTS is the recommended method. In practice, the proportion of outliers can be estimated according to the inaccuracy of the diagnostic methods used.
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Affiliation(s)
- Hongwei Sun
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan City, 030001, Shanxi, China.,Department of Health Statistics, School of Public Health and Management, Binzhou Medical University, City, Yantai, 264003, Shandong, China
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, 48824, USA
| | - Hui Wang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan City, 030001, Shanxi, China
| | - Haixia Liu
- Department of Health Statistics, School of Public Health and Management, Binzhou Medical University, City, Yantai, 264003, Shandong, China
| | - Tong Wang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan City, 030001, Shanxi, China.
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24
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Yamaguchi N. Multiple Roles of Vestigial-Like Family Members in Tumor Development. Front Oncol 2020; 10:1266. [PMID: 32793503 PMCID: PMC7393262 DOI: 10.3389/fonc.2020.01266] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022] Open
Abstract
Vestigial-like family (VGLL) members are mammalian orthologs of vestigial gene in Drosophila, and they consist of four homologs (VGLL1–4). VGLL members have TDU motifs that are binding regions to TEA/ATSS-DNA-binding domain transcription factor (TEAD). Through TDU motifs, VGLL members act as transcriptional cofactors for TEAD. VGLL1-3 have single TDU motif, whereas VGLL4 has two tandem TDU motifs, suggesting that VGLL4 has distinct molecular functions among this family. Although molecular and physiological functions of VGLL members are still obscure, emerging evidence has shown that these members are involved in tumor development. Gene alterations and elevated expression of VGLL1-3 were observed in various types of tumors, and VGLL1-3 have been shown to possess tumorigenic functions. In contrast, down-regulation of VGLL4 was detected in various tumors, and the tumor-suppressing role of VGLL4 has been demonstrated. In this review, we summarize the recently identified multiple roles of VGLL members in tumor development and provide important and novel insights regarding tumorigenesis.
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Affiliation(s)
- Noritaka Yamaguchi
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.,Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
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25
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The Transcriptional Cofactor VGLL1 Drives Transcription of Human Papillomavirus Early Genes via TEAD1. J Virol 2020; 94:JVI.01945-19. [PMID: 32132238 DOI: 10.1128/jvi.01945-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/26/2020] [Indexed: 12/31/2022] Open
Abstract
The TEAD family of transcription factors requires associating cofactors to induce gene expression. TEAD1 is known to activate the early promoter of human papillomavirus (HPV), but the precise mechanisms of TEAD1-mediated transactivation of the HPV promoter, including its relevant cofactors, remain unexplored. Here, we reveal that VGLL1, a TEAD-interacting cofactor, contributes to HPV early gene expression. Knockdown of VGLL1 and/or TEAD1 led to a decrease in viral early gene expression in human cervical keratinocytes and cervical cancer cell lines. We identified 11 TEAD1 target sites in the HPV16 long control region (LCR) by in vitro DNA pulldown assays; 8 of these sites contributed to the transcriptional activation of the early promoter in luciferase reporter assays. VGLL1 bound to the HPV16 LCR via its interaction with TEAD1 both in vitro and in vivo Furthermore, introducing HPV16 and HPV18 whole genomes into primary human keratinocytes led to increased levels of VGLL1, due in part to the upregulation of TEADs. These results suggest that multiple VGLL1/TEAD1 complexes are recruited to the LCR to support the efficient transcription of HPV early genes.IMPORTANCE Although a number of transcription factors have been reported to be involved in HPV gene expression, little is known about the cofactors that support HPV transcription. In this study, we demonstrate that the transcriptional cofactor VGLL1 plays a prominent role in HPV early gene expression, dependent on its association with the transcription factor TEAD1. Whereas TEAD1 is ubiquitously expressed in a variety of tissues, VGLL1 displays tissue-specific expression and is implicated in the development and differentiation of epithelial lineage tissues, where HPV gene expression occurs. Our results suggest that VGLL1 may contribute to the epithelial specificity of HPV gene expression, providing new insights into the mechanisms that regulate HPV infection. Further, VGLL1 is also critical for the growth of cervical cancer cells and may represent a novel therapeutic target for HPV-associated cancers.
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26
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Jin Y, Weng Y, Wang Y, Lin J, Deng X, Shen B, Zhan Q, Lu X. miR-934 as a Prognostic Marker Facilitates Cell Proliferation and Migration of Pancreatic Tumor by Targeting PROX1. Onco Targets Ther 2020; 13:3389-3399. [PMID: 32368095 PMCID: PMC7183785 DOI: 10.2147/ott.s249662] [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: 02/13/2020] [Accepted: 04/06/2020] [Indexed: 01/09/2023] Open
Abstract
Background Pancreatic cancer is an extremely lethal digestive cancer with late diagnosis and poor prognosis. miR-934 has been reported to serve as an oncogene in multiple cancers, such as ovarian cancer and bladder cancer. However, its role in pancreatic cancer remains undiscovered. Materials and Methods The expression data of miR-934 were obtained from the Gene Expression Omnibus database and from our own patient samples. The clinicopathological data and corresponding follow-up data were retrieved from The Cancer Genome Atlas database. CCK8 and colony formation assays were conducted to measure cell proliferation capacity in vitro. Wound healing and transwell assays were performed to detect the migration ability of pancreatic cancer cell. Results We found that miR-934 was significantly upregulated in pancreatic tumor samples and cell lines. The expression of miR-934 was related to pathological stages. Upregulated miR-934 was associated with poor prognosis in patients with pancreatic cancer. Mir-934 inhibition reduced, while overexpression promoted, cell proliferation and migration. Mechanically, we found miR-934 could directly bind to 3'-UTR of PROX1 leading to mRNA derogation. Furthermore, increased cell proliferation and migration caused by miR-934 overexpression could be reversed by forced PROX1 expression. Conclusion miR-934 is an oncogene in pancreatic cancer and could serve as a prognosis indicator for patients with pancreatic cancer, suggesting that miR-934 is a promising therapeutic target for pancreatic cancer.
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Affiliation(s)
- Yangbing Jin
- Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China.,Research Institute of Pancreatic Disease, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Yuanchi Weng
- Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China.,Research Institute of Pancreatic Disease, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Yue Wang
- Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China.,Research Institute of Pancreatic Disease, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Jiewei Lin
- Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China.,Research Institute of Pancreatic Disease, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Xiaxing Deng
- Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China.,Research Institute of Pancreatic Disease, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Baiyong Shen
- Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China.,Research Institute of Pancreatic Disease, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Qian Zhan
- Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China.,Research Institute of Pancreatic Disease, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Xiongxiong Lu
- Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China.,Research Institute of Pancreatic Disease, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
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27
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Wei G, Zhang T, Li Z, Yu N, Xue X, Zhou D, Chen Y, Zhang L, Yao X, Ji G. USF1-mediated upregulation of lncRNA GAS6-AS2 facilitates osteosarcoma progression through miR-934/BCAT1 axis. Aging (Albany NY) 2020; 12:6172-6190. [PMID: 32269179 PMCID: PMC7185141 DOI: 10.18632/aging.103015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/22/2020] [Indexed: 12/11/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been certified as important regulators in tumorigenesis. LncRNA GAS6-AS2 (GAS6-AS2) was a newly identified tumor-related lncRNA, and its dysregulation and oncogenic effects in melanoma and bladder cancer had been reported in previous studies. However, the expression pattern and potential function of GAS6-AS2 in osteosarcoma (OS) have not been investigated. In this study, we identified a novel OS-related lncRNA GAS6-AS2. We found that GAS6-AS2 was distinctly upregulated in both OS specimens and cell lines. Distinct up-regulation of GAS6-AS2 in OS was correlated with advanced clinical stages and shorter survivals. In addition, USF1 could directly bind to the GAS6-AS2 promoter and contribute to its overexpression. Furthermore, GAS6-AS2 knockdown caused tumor suppressive effects via reducing cellular proliferation, migration and invasion, and promoting OS cell apoptosis. Besides, GAS6-AS2 directly bound to miR-934 and downregulated its expression. Mechanistically, GAS6-AS2 positively regulated the expression of BCAT1 through sponging miR-934. Taken together, our data illustrated how GAS6-AS2 played an oncogenic role in OS and might offer a potential therapeutic target for treating OS.
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Affiliation(s)
- Guojun Wei
- Department of Orthopaedics, The Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, Fujian, China
| | - Tianwei Zhang
- Department of Anesthesiology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Zongguang Li
- Department of Orthopaedics, The Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, Fujian, China
| | - Naichun Yu
- Department of Orthopaedics, The Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, Fujian, China
| | - Xiang Xue
- Department of Orthopaedics, The Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, Fujian, China
| | - Daguo Zhou
- Department of Orthopaedics, The Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, Fujian, China
| | - Yongjie Chen
- Department of Orthopaedics, The Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, Fujian, China
| | - Linlin Zhang
- Department of Orthopaedics, The Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, Fujian, China
| | - Xiaoli Yao
- Department of Gastroenterology, The Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, Fujian, China
| | - Guangrong Ji
- Department of Orthopaedics, The Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, Fujian, China
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28
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PI3K/AKT/β-Catenin Signaling Regulates Vestigial-Like 1 Which Predicts Poor Prognosis and Enhances Malignant Phenotype in Gastric Cancer. Cancers (Basel) 2019; 11:cancers11121923. [PMID: 31816819 PMCID: PMC6966677 DOI: 10.3390/cancers11121923] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 01/05/2023] Open
Abstract
Although gastric cancer is a common cause of cancer mortality worldwide, its biological heterogeneity limits the available therapeutic options. Therefore, identifying novel therapeutic targets for developing effective targeted therapy of gastric cancer is a pressing need. Here, we investigate molecular function and regulatory mechanisms of Vestigial-like 1 (VGLL1) in gastric cancer. Microarray analysis of 556 gastric cancer tissues revealed that VGLL1 was a prognostic biomarker that correlated with PI3KCA and PI3KCB. VGLL1 regulates the proliferation of gastric cancer cells, as shown in live cell imaging, sphere formation, and in vivo xenograft model. Tail vein injection of NUGC3 cells expressing shVGLL1 resulted in less lung metastasis occurring when compared to the control. In contrast, larger metastatic lesions in lung and liver were detected in the VGLL1-overexpressing NUGC3 cell xenograft excision mouse model. Importantly, VGLL1 expression is transcriptionally regulated by the PI3K-AKT-β-catenin pathway. Subsequently, MMP9, a key molecule in gastric cancer, was explored as one of target genes that were transcribed by VGLL1-TEAD4 complex, a component of the transcription factor. Taken together, PI3K/AKT/β-catenin signaling regulates the transcription of VGLL1, which promotes the proliferation and metastasis in gastric cancer. This finding suggests VGLL1 as a novel prognostic biomarker and a potential therapeutic target.
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29
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Komatsu M, Kawamoto T, Kanzawa M, Kawakami Y, Hara H, Akisue T, Kuroda R, Nakamura H, Hokka D, Jimbo N, Itoh T, Hirose T. A novel
EWSR1
‐
VGLL1
gene fusion in a soft tissue malignant myoepithelial tumor. Genes Chromosomes Cancer 2019; 59:249-254. [DOI: 10.1002/gcc.22823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 01/06/2023] Open
Affiliation(s)
- Masato Komatsu
- Department of Diagnostic Pathology Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
| | - Teruya Kawamoto
- Department of Orthopedic Surgery Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
- Division of Orthopedic Surgery Kobe University International Clinical Cancer Research Center Kobe Hyogo Prefecture Japan
| | - Maki Kanzawa
- Department of Diagnostic Pathology Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
| | - Yohei Kawakami
- Department of Orthopedic Surgery Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
| | - Hitomi Hara
- Department of Orthopedic Surgery Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
| | - Toshihiro Akisue
- Department of Rehabilitation Science Kobe University Graduate School of Health Sciences Kobe Hyogo Prefecture Japan
| | - Ryosuke Kuroda
- Department of Orthopedic Surgery Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
| | - Hayate Nakamura
- Division of Thoracic Surgery, Department of Surgery Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
| | - Daisuke Hokka
- Division of Thoracic Surgery, Department of Surgery Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
| | - Naoe Jimbo
- Department of Diagnostic Pathology Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
| | - Tomoo Itoh
- Department of Diagnostic Pathology Kobe University Graduate School of Medicine Kobe Hyogo Prefecture Japan
| | - Takanori Hirose
- Department of Diagnostic Pathology Hyogo Cancer Center Akashi Hyogo Prefecture Japan
- Division of Pathology for Regional Communication Kobe University School of Medicine Kobe Hyogo Prefecture Japan
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30
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Xue C, Liu X, Wen B, Yang R, Gao S, Tao J, Zhou J. Zebrafish Vestigial Like Family Member 4b Is Required for Valvulogenesis Through Sequestration of Transcription Factor Myocyte Enhancer Factor 2c. Front Cell Dev Biol 2019; 7:277. [PMID: 31799250 PMCID: PMC6874126 DOI: 10.3389/fcell.2019.00277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
A variety of cardiac transcription factors/cofactors, signaling pathways, and downstream structural genes integrate to form the regulatory hierarchies to ensure proper cardiogenesis in vertebrate. Major interaction proteins of the transcription cofactor vestigial like family member 4 (VGLL4) include myocyte enhancer factor 2 (MEF2) and TEA domain transcription factors (TEAD), both of which play important roles in embryonic cardiac development and in adulthood. In this study, we identified that the deficiency of zebrafish vgll4b paralog, a unique family member expressed in developing heart, led to an impaired valve development. Mechanistically, in vgll4b mutant embryos the disruption of Vgll4b-Mef2c complex, rather than that of Vgll4b-Tead complex, resulted in an aberrant expression of krüppel-like factor 2a (klf2a) in endocardium. Such misexpression of klf2a eventually evoked the valvulogenesis defects. Our findings suggest that zebrafish Vgll4b plays an important role in modulating the transcription activity of Mef2c on klf2a during valve development in a blood-flow-independent manner.
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Affiliation(s)
- Chang Xue
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohui Liu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin Wen
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruimeng Yang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuo Gao
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiong Tao
- Prenatal Diagnosis Center, Shanghai Jiao Tong University Affiliated First People's Hospital, Shanghai, China
| | - Jun Zhou
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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31
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Gong Z, Wang J, Wang D, Buas MF, Ren X, Freudenheim JL, Belinsky SA, Liu S, Ambrosone CB, Higgins MJ. Differences in microRNA expression in breast cancer between women of African and European ancestry. Carcinogenesis 2019; 40:61-69. [PMID: 30321299 DOI: 10.1093/carcin/bgy134] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/21/2018] [Accepted: 10/09/2018] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is a heterogeneous disease, characterized by molecularly and phenotypically distinct tumor subtypes, linked to disparate clinical outcomes. American women of African ancestry (AA) are more likely than those of European ancestry (EA) to be diagnosed with aggressive, estrogen receptor negative (ER-) or triple negative breast cancer, and to die of this disease. However, the underlying causes of AA predisposition to ER-/triple negative breast cancer are still largely unknown. In this study, we performed high-throughput whole-genome miRNA expression profiling in breast tissue samples from both AA and EA women. A number of differentially expressed miRNAs, i.e., DEmiRs defined as >2-fold change in expression and false discovery rate <0.05, were identified as up- or downregulated by tumor ER status or by ancestry. We found that among 102 ER-subtype-related DEmiRs identified in breast tumors, the majority of these DEmiRs were race specific, with only 23 DEmiRs shared in tumors from both AAs and EAs; this finding indicates that there are unique subsets of miRNAs differentially expressed between ER- and ER positive tumors within AAs versus EAs. Our overall results support the notion that miRNA expression patterns may differ not only by tumor subtype but by ancestry, indicating differences in tumor biology and heterogeneity of breast cancer between AAs and EAs. These results will provide the basis for further functional analysis to elucidate biological differences between AAs and EAs and to help develop targeted treatment strategies to reduce disparities in breast cancer.
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Affiliation(s)
- Zhihong Gong
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jie Wang
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA.,Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Dan Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Matthew F Buas
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xuefeng Ren
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY, USA
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Michael J Higgins
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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Guo M, Sinha S, Wang SM. Coupled Genome-Wide DNA Methylation and Transcription Analysis Identified Rich Biomarkers and Drug Targets in Triple-Negative Breast Cancer. Cancers (Basel) 2019; 11:E1724. [PMID: 31690011 PMCID: PMC6896154 DOI: 10.3390/cancers11111724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 02/02/2023] Open
Abstract
Triple-negative breast cancer (TNBC) has poor clinical prognosis. Lack of TNBC-specific biomarkers prevents active clinical intervention. We reasoned that TNBC must have its specific signature due to the lack of three key receptors to distinguish TNBC from other types of breast cancer. We also reasoned that coupling methylation and gene expression as a single unit may increase the specificity for the detected TNBC signatures. We further reasoned that choosing the proper controls may be critical to increasing the sensitivity to identify TNBC-specific signatures. Furthermore, we also considered that specific drugs could target the detected TNBC-specific signatures. We developed a system to identify potential TNBC signatures. It consisted of (1) coupling methylation and expression changes in TNBC to identify the methylation-regulated signature genes for TNBC; (2) using TPBC (triple-positive breast cancer) as the control to detect TNBC-specific signature genes; (3) searching in the drug database to identify those targeting TNBC signature genes. Using this system, we identified 114 genes with both altered methylation and expression, and 356 existing drugs targeting 10 of the 114 genes. Through docking and molecular dynamics simulation, we determined the structural basis between sapropterin, a drug used in the treatment of tetrahydrobiopterin deficiency, and PTGS2, a TNBC signature gene involved in the conversion of arachidonic acid to prostaglandins. Our study reveals the existence of rich TNBC-specific signatures, and many can be drug target and biomarker candidates for clinical applications.
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Affiliation(s)
- Maoni Guo
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China.
| | - Siddharth Sinha
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China.
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China.
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33
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Yan H, Ren S, Lin Q, Yu Y, Chen C, Hua X, Jin H, Lu Y, Zhang H, Xie Q, Huang C, Huang H. Inhibition of UBE2N-dependent CDK6 protein degradation by miR-934 promotes human bladder cancer cell growth. FASEB J 2019; 33:12112-12123. [PMID: 31373842 DOI: 10.1096/fj.201900499rr] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Because bladder cancer (BC) is one of the most common malignant cancers of the urinary system, identification of BC cell growth-associated effectors is of great significance. Cyclin-dependent kinase (CDK)6 is a member of the CDK family of cell cycle-related proteins and plays an important role in cancer cell growth. This is borne out by the fact that a CDK6 inhibitor had been approved to treat several types of cancers. Nevertheless, underlying molecular mechanisms concerning how to regulate CDK6 expression in BC remains unclear. In the present study, it was observed that miR-934 was much higher in human BCs and human BC cell lines as well. The results also revealed that miR-934 inhibition dramatically decreased human BC cell monolayer growth in vitro and xenograft tumor growth in vivo; the outcomes were accompanied by CDK6 protein down-regulation and G0-G1 cell cycle arrest. Moreover, overexpression of CDK6 reversed the inhibition of BC cell growth induced by miR-934. Further studies showed that miR-934 binds to a 3'-UTR of ubiquitin-conjugating enzyme 2N (ube2n) mRNA, down-regulated UBE2N protein expression; this, in turn, attenuated CDK6 protein degradation and led to CDK6 protein accumulation as well as the promotion of BC tumor growth. Collectively, this study not only establishes a novel regulatory axis of miR-934/UBE2N of CDK6 but also provides data suggesting that miR-934 and UBE2N may be potentially promising targets for therapeutic strategies against BC.-Yan, H., Ren, S., Lin, Q., Yu, Y., Chen, C., Hua, X., Jin, H., Lu, Y., Zhang, H., Xie, Q., Huang, C., Huang, H. Inhibition of UBE2N-dependent CDK6 protein degradation by miR-934 promotes human bladder cancer cell growth.
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Affiliation(s)
- Huiying Yan
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shuwei Ren
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qi Lin
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuan Yu
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Caiyi Chen
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaohui Hua
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Honglei Jin
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yongyong Lu
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huxiang Zhang
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qipeng Xie
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chuanshu Huang
- Department of Environmental Medicine, New York University School of Medicine, New York, New York, USA
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
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34
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Gong Y, Zou B, Chen J, Ding L, Li P, Chen J, Chen J, Zhang B, Li J. Potential Five-MicroRNA Signature Model for the Prediction of Prognosis in Patients with Wilms Tumor. Med Sci Monit 2019; 25:5435-5444. [PMID: 31328722 PMCID: PMC6668497 DOI: 10.12659/msm.916230] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Wilms tumor (WT) is the most common type of pediatric renal malignancy, and is associated with poor prognosis. The aim of the present study was to identify microRNA (miRNA) signatures which might predict prognosis and categorize WTs into high- and low-risk subgroups. Material/Methods The miRNA expression profiles of WT patients and normal samples were obtained from the Therapeutically Applicable Research to Generate Effective Treatment database. Differentially expressed miRNAs between WT patients and normal samples were identified using the EdgeR package. Subsequently, correlations between differentially expressed miRNAs and the prognosis of overall survival were analyzed. Enrichment analyses for the targeted mRNAs were conducted via the Database for Annotation, Visualization, and Integration Discovery. Results A total of 154 miRNAs were identified as differentially expressed in WT. Of those, 18 miRNAs were associated with overall survival (P<0.05). A prognostic signature of 5 differentially expressed miRNAs (i.e., has-mir-149, has-mir-7112, has-mir-940, has-mir-1248, and has-mir-490) was constructed to classify the patients into high- and low-risk subgroups. The targeted mRNAs of these prognostic miRNAs were primarily enriched in Gene Ontology terms (i.e., protein autophosphorylation, protein dephosphorylation, and stress-activated MAPK cascade) and the Kyoto Encyclopedia of Genes and Genomes signaling pathways (i.e., MAPK, AMPK, and PI3K-Akt). Conclusions The 5-miRNA signature model might be useful in determining the prognosis of WT patients. As a promising prediction tool, this prognosis signature might serve as a potential biomarker for WT patients.
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Affiliation(s)
- Yihang Gong
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Baojia Zou
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jianxu Chen
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Lei Ding
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Peiping Li
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jiafan Chen
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jiandi Chen
- Department of Endocrinology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Baimeng Zhang
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jian Li
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
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35
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Zhang P, Zheng P, Liu Y. Amplification of the CD24 Gene Is an Independent Predictor for Poor Prognosis of Breast Cancer. Front Genet 2019; 10:560. [PMID: 31244889 PMCID: PMC6581687 DOI: 10.3389/fgene.2019.00560] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/29/2019] [Indexed: 12/25/2022] Open
Abstract
CD24 is a glycosyl-phosphatidyl-inositol linked glycoprotein expressed in a broad range of cell types including cancer cells. Although it is overexpressed in nearly 70% of human cancers, copy number variation of the CD24 locus has not been reported for any cancer. Here, we analyzed the genomics, transcriptomics, and clinical data of 1082 breast cancer (BRCA) samples and other cancer samples from the clinically annotated genomic database, The Cancer Genome Atlas (TCGA). The GISTIC2 method was applied to stratify the CD24 copy number, and Cox regression was performed to compare hazard ratio (HR) of CD24 overexpression, amplification and other traditional prognosis features for overall survival (OS). Our data demonstrated that CD24 amplification strongly correlated with its mRNA overexpression as well as TP53 mutant, cancer proliferation and metastasis features. In particular, CD24 amplification was enriched in basal-like subtype samples and associated with poor clinical outcome. Surprisingly, based on the univariate Cox regression analysis, CD24 overexpression (HR = 1.62, P = 0.010) and copy number amplification (HR = 1.79, P = 0.022) was more relevant to OS than TP53 mutant, mutation counts, diagnosis age, and BRCA subtypes. And based on multivariate survival analysis, CD24 amplification remained the most significant and independent predictor for worse OS (HR = 1.88, P = 0.015).
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Affiliation(s)
- Peng Zhang
- Division of Immunotherapy, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Pan Zheng
- Division of Immunotherapy, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States.,OncoImmune, Inc., Rockville, MD, United States
| | - Yang Liu
- Division of Immunotherapy, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States.,OncoImmune, Inc., Rockville, MD, United States
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36
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Naorem LD, Muthaiyan M, Venkatesan A. Identification of dysregulated miRNAs in triple negative breast cancer: A meta‐analysis approach. J Cell Physiol 2018; 234:11768-11779. [DOI: 10.1002/jcp.27839] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Leimarembi Devi Naorem
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University Pondicherry India
| | - Mathavan Muthaiyan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University Pondicherry India
| | - Amouda Venkatesan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University Pondicherry India
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37
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Segaert P, Lopes MB, Casimiro S, Vinga S, Rousseeuw PJ. Robust identification of target genes and outliers in triple-negative breast cancer data. Stat Methods Med Res 2018; 28:3042-3056. [PMID: 30146936 PMCID: PMC6745616 DOI: 10.1177/0962280218794722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Correct classification of breast cancer subtypes is of high importance as it directly affects the therapeutic options. We focus on triple-negative breast cancer which has the worst prognosis among breast cancer types. Using cutting edge methods from the field of robust statistics, we analyze Breast Invasive Carcinoma transcriptomic data publicly available from The Cancer Genome Atlas data portal. Our analysis identifies statistical outliers that may correspond to misdiagnosed patients. Furthermore, it is illustrated that classical statistical methods may fail to identify outliers due to their heavy influence, prompting the need for robust statistics. Using robust sparse logistic regression we obtain 36 relevant genes, of which ca. 60% have been previously reported as biologically relevant to triple-negative breast cancer, reinforcing the validity of the method. The remaining 14 genes identified are new potential biomarkers for triple-negative breast cancer. Out of these, JAM3, SFT2D2, and PAPSS1 were previously associated to breast tumors or other types of cancer. The relevance of these genes is confirmed by the new DetectDeviatingCells outlier detection technique. A comparison of gene networks on the selected genes showed significant differences between triple-negative breast cancer and non-triple-negative breast cancer data. The individual role of FOXA1 in triple-negative breast cancer and non-triple-negative breast cancer, and the strong FOXA1-AGR2 connection in triple-negative breast cancer stand out. The goal of our paper is to contribute to the breast cancer/triple-negative breast cancer understanding and management. At the same time it demonstrates that robust regression and outlier detection constitute key strategies to cope with high-dimensional clinical data such as omics data.
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Affiliation(s)
| | - Marta B Lopes
- IDMEC, Instituto de Engenharia Mecânica, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Sandra Casimiro
- Luís Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Susana Vinga
- IDMEC, Instituto de Engenharia Mecânica, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,INESC-ID, Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento, Lisboa, Portugal
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38
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Frisch SM, Farris JC, Pifer PM. Roles of Grainyhead-like transcription factors in cancer. Oncogene 2017; 36:6067-6073. [PMID: 28714958 DOI: 10.1038/onc.2017.178] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/12/2017] [Accepted: 05/04/2017] [Indexed: 12/18/2022]
Abstract
The mammalian homologs of the D. melanogaster Grainyhead gene, Grainyhead-like 1-3 (GRHL1, GRHL2 and GRHL3), are transcription factors implicated in wound healing, tubulogenesis and cancer. Their induced target genes encode diverse epithelial cell adhesion molecules, while mesenchymal genes involved in cell migration and invasion are repressed. Moreover, GRHL2 suppresses the oncogenic epithelial-mesencyhmal transition, thereby acting as a tumor suppressor. Mechanisms, some involving established cancer-related signaling/transcription factor pathways (for example, Wnt, TGF-β, mir200, ZEB1, OVOL2, p63 and p300) and translational implications of the Grainyhead proteins in cancer are discussed in this review article.
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Affiliation(s)
- S M Frisch
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - J C Farris
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - P M Pifer
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA
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39
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Ju L, Han M, Li X, Zhao C. MicroRNA Signature of Lung Adenocarcinoma with EGFR Exon 19 Deletion. J Cancer 2017; 8:1311-1318. [PMID: 28607607 PMCID: PMC5463447 DOI: 10.7150/jca.17817] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/06/2017] [Indexed: 12/16/2022] Open
Abstract
The findings of EGFR mutations and the development of targeted therapies have significantly improved the overall survival of lung cancer patients. Still, the prognosis remains poor, so we need to know more about the genetic alterations in lung cancer. MicroRNAs are dysregulated in lung cancer, and some of them can regulate EGFR. So it is very important to predict the candidate microRNAs that target mutated EGFR and to investigate the role of these candidate microRNAs in lung cancer. In this study, we investigated the difference of microRNAs expression between lung adenocarcinoma cell lines with EGFR exon 19 deletion (H1650 and PC9) and wild-type (H1299 and A549) using the Phalanx Human Whole Genome Microarray. Then the expression of individual microRNAs was validated by qRT-PCR assays. Moreover, we detected the microRNAs expression in plasma of lung adenocarcinoma patients with EGFR exon 19 deletion and wild-type. Lastly, we explored the function of the positive microRNA in EGFR tyrosine kinase inhibitors (EGFR-TKIs ) resistance using MTT and Annexin V-APC assays. The expression of 1,732 microRNAs was evaluated, and we found that microRNAs expression was different between these two groups. Hsa-miR-141-3p, hsa-miR-200c-3p, hsa-miR-203, hsa-miR-3182, hsa-miR-934 were up-regulated and hsa-miR-3196 was down-regulated in the EGFR exon 19 deletion group compared with wild-type group. The detection of circulating microRNAs showed that miR-3196 was down-regulated in lung adenocarcinoma patients with EGFR exon 19 deletion compared with wild-type. And then the MTT assay results showed that miR-3196 had no effect on the sensitivity of erlotinib. The results of apoptosis analysis showed that inhibition of miR-3196 and erlotinib induced more apoptosis in H1299 cells than erlotinib alone, and overexpressed miR-3196 and erlotinib induced less apoptosis in PC9 cells than erlotinib alone (P<0.05). It is suggested that microRNAs associate with EGFR exon 19 deletion and miR-3196 may be further explored as a potential predictor and targeted biomarker when it is difficult to get the tumors.
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Affiliation(s)
- Lixia Ju
- Department of Integrative Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Mingquan Han
- Department of Integrative Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Xuefei Li
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University, Shanghai, People's Republic of China
| | - Chao Zhao
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University, Shanghai, People's Republic of China
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40
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Pimmett VL, Deng H, Haskins JA, Mercier RJ, LaPointe P, Simmonds AJ. The activity of the Drosophila Vestigial protein is modified by Scalloped-dependent phosphorylation. Dev Biol 2017; 425:58-69. [PMID: 28322734 DOI: 10.1016/j.ydbio.2017.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 12/18/2022]
Abstract
The Drosophila vestigial gene is required for proliferation and differentiation of the adult wing and for differentiation of larval and adult muscle identity. Vestigial is part of a multi-protein transcription factor complex, which includes Scalloped, a TEAD-class DNA binding protein. Binding Scalloped is necessary for translocation of Vestigial into the nucleus. We show that Vestigial is extensively post-translationally modified and at least one of these modifications is required for proper function during development. We have shown that there is p38-dependent phosphorylation of Serine 215 in the carboxyl-terminal region of Vestigial. Phosphorylation of Serine 215 occurs in the nucleus and requires the presence of Scalloped. Comparison of a phosphomimetic and non-phosphorylatable mutant forms of Vestigial shows differences in the ability to rescue the wing and muscle phenotypes associated with a null vestigial allele.
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Affiliation(s)
- Virginia L Pimmett
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Hua Deng
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7; Howard Hughes Medical Institute, Dept. of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Julie A Haskins
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Rebecca J Mercier
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
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Panaccione A, Guo Y, Yarbrough WG, Ivanov SV. Expression Profiling of Clinical Specimens Supports the Existence of Neural Progenitor-Like Stem Cells in Basal Breast Cancers. Clin Breast Cancer 2017; 17:298-306.e7. [PMID: 28216417 DOI: 10.1016/j.clbc.2017.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/09/2017] [Accepted: 01/20/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND We previously characterized in salivary adenoid cystic carcinoma (ACC) a novel population of cancer stem cells (CSCs) marked by coexpression of 2 stemness genes, sex-determining region Y (SRY)-related HMG box-containing factor 10 (SOX10) and CD133. We also reported that in ACC and basal-like breast carcinoma (BBC), a triple-negative breast cancer subtype, expression of SOX10 similarly demarcates a highly conserved gene signature enriched with neural stem cell genes. On the basis of these findings, we hypothesized that BBC might be likewise driven by SOX10-positive (SOX10+)/CD133+ cells with neural stem cell properties. MATERIALS AND METHODS To validate our hypothesis on clinical data, we used a novel approach to meta-analysis that merges gene expression data from independent breast cancer studies and ranks genes according to statistical significance of their coexpression with the gene of interest. Genes that showed strong association with CD133/PROM1 as well as SOX10 were validated across different platforms and data sets and analyzed for enrichment with genes involved in neurogenesis. RESULTS We identified in clinical breast cancer data sets a highly conserved SOX10/PROM1 gene signature that contains neural stem cell markers common for Schwann cells, ACC, BBC, and melanoma. Identification of tripartite motif-containing 2 (TRIM2), TRIM29, MPZL2, potassium calcium-activated channel subfamily N member 4 (KCNN4), and V-set domain containing T cell activation inhibitor 1 (VTCN1)/B7 homolog 4 (B7H4) within this signature provides insight into molecular mechanisms of CSC maintenance. CONCLUSION Our results suggest that BBC is driven by SOX10+/CD133+ cells that express neural stem cell-specific markers and share molecular similarities with CSCs of neural crest origin. Our study provides clinically relevant information on possible drivers of these cells that might facilitate development of CSC-targeting therapies against this cancer distinguished with poor prognosis and resistance to conventional therapies.
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Affiliation(s)
- Alex Panaccione
- Department of Surgery, Section of Otolaryngology, Yale School of Medicine, New Haven, CT
| | - Yan Guo
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Wendell G Yarbrough
- Department of Surgery, Section of Otolaryngology, Yale School of Medicine, New Haven, CT; Head and Neck Disease Center, Smilow Cancer Hospital, New Haven, CT; Molecular Virology Program, Yale Cancer Center, New Haven, CT
| | - Sergey V Ivanov
- Department of Surgery, Section of Otolaryngology, Yale School of Medicine, New Haven, CT.
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Luo J, Xiang G, Pan C. Discovery of microRNAs and Transcription Factors Co-Regulatory Modules by Integrating Multiple Types of Genomic Data. IEEE Trans Nanobioscience 2017; 16:51-59. [DOI: 10.1109/tnb.2017.2649560] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Exploring the intrinsic differences among breast tumor subtypes defined using immunohistochemistry markers based on the decision tree. Sci Rep 2016; 6:35773. [PMID: 27786176 PMCID: PMC5082366 DOI: 10.1038/srep35773] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023] Open
Abstract
Exploring the intrinsic differences among breast cancer subtypes is of crucial importance for precise diagnosis and therapeutic decision-making in diseases of high heterogeneity. The subtypes defined with several layers of information are related but not consistent, especially using immunohistochemistry markers and gene expression profiling. Here, we explored the intrinsic differences among the subtypes defined by the estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 based on the decision tree. We identified 30 mRNAs and 7 miRNAs differentially expressed along the tree's branches. The final signature panel contained 30 mRNAs, whose performance was validated using two public datasets based on 3 well-known classifiers. The network and pathway analysis were explored for feature genes, from which key molecules including FOXQ1 and SFRP1 were revealed to be densely connected with other molecules and participate in the validated metabolic pathways. Our study uncovered the differences among the four IHC-defined breast tumor subtypes at the mRNA and miRNA levels, presented a novel signature for breast tumor subtyping, and identified several key molecules potentially driving the heterogeneity of such tumors. The results help us further understand breast tumor heterogeneity, which could be availed in clinics.
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Peritoneal tumor spread in serous ovarian cancer-epithelial mesenchymal status and outcome. Oncotarget 2016; 6:17261-75. [PMID: 25991672 PMCID: PMC4627306 DOI: 10.18632/oncotarget.3746] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/28/2015] [Indexed: 01/03/2023] Open
Abstract
In this study we aimed to analyze the biological mechanisms underlying apparently different modes of peritoneal tumor spread in serous ovarian cancer: miliary (widespread, millet-like lesions) versus non-miliary (bigger, exophytically growing implants). Tumor tissues and ascites from 23 chemotherapy naive patients were analyzed by RNA-sequencing and flow cytometry. On the basis of differential gene expression between miliary and non-miliary, gene signatures were developed. A calculated tumor spread factor revealed a significant independent negative impact of miliary spread on overall survival (HR 3.77; CI95 1.14–12.39; p = 0.029) in an independent cohort of 165 serous ovarian cancer patients. Comparing previously published epithelial-mesenchymal transition (EMT) gene signatures, non-miliary spread correlated significantly with a reduced epithelial status. We conclude that serous ovarian cancer is a heterogeneous disease with distinct modes of peritoneal tumor spread, differing not only in clinical appearance, but also in molecular characteristics and outcome.. EMT, peritoneal inflammation status, and therapeutic options are discussed.
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From vestigial to vestigial-like: the Drosophila gene that has taken wing. Dev Genes Evol 2016; 226:297-315. [DOI: 10.1007/s00427-016-0546-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/10/2016] [Indexed: 12/16/2022]
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Yin Y, Shen C, Xie P, Cheng Z, Zhu Q. Construction of an initial microRNA regulation network in breast invasive carcinoma by bioinformatics analysis. Breast 2016; 26:1-10. [PMID: 27017236 DOI: 10.1016/j.breast.2015.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/03/2015] [Accepted: 11/23/2015] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION microRNAs (miRNA) are involved in many biological processes. They repress target gene expression and play a vital role in breast invasive carcinoma (BRCA). Although many miRNAs are identified to be aberrantly expressed in BRCA and deemed as tumor markers, only sporadic individual studies report their target genes and the pathways involved. METHODS miRNA and mRNA expression data were collected from the Cancer Genome Atlas (TCGA) pilot project. Aberrantly expressed miRNAs and mRNAs in BRCA were identified by comparing tumor samples with normal adjacent tissues. Differentially expressed miRNAs and mRNAs in different breast cancer subtypes were also analyzed. miRNA/target correlations were predicted by calculating the spearman correlation coefficients between miRNA and mRNA, and validated by luciferase assay. RESULTS 31 up-regulated miRNAs, 37 down-regulated miRNAs, 1105 up-regulated mRNAs and 1222 down-regulated mRNAs were identified in BRCA; 125 miRNA/target correlations were predicted, 6 of them were validated. In addition, we also found 9 miRNAs and 143 mRNAs differently expressed between estrogen receptor positive and negative breast cancers, and 4 miRNAs and 46 mRNAs differently expressed between progesterone receptor positive and negative breast cancers. Twelve miRNA/target correlations determined the breast cancer subtypes. CONCLUSION We developed a new systematic analytic method for analyzing TCGA database, which took into account both miRNA and mRNA data to dissect the miRNA regulation network in BRCA.
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Affiliation(s)
- Yongjia Yin
- The School of Pharmaceutical Science in Central South University, Changsha 410013, Hunan, China.
| | - Cheng Shen
- The School of Pharmaceutical Science in Central South University, Changsha 410013, Hunan, China.
| | - Pan Xie
- The School of Pharmaceutical Science in Central South University, Changsha 410013, Hunan, China.
| | - Zeneng Cheng
- The School of Pharmaceutical Science in Central South University, Changsha 410013, Hunan, China.
| | - Qubo Zhu
- The School of Pharmaceutical Science in Central South University, Changsha 410013, Hunan, China.
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Sandhu GK, Milevskiy MJG, Wilson W, Shewan AM, Brown MA. Non-coding RNAs in Mammary Gland Development and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 886:121-153. [PMID: 26659490 DOI: 10.1007/978-94-017-7417-8_7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs (ncRNAs) are untranslated RNA molecules that function to regulate the expression of numerous genes and associated biochemical pathways and cellular functions. NcRNAs include small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs). They participate in the regulation of all developmental processes and are frequently aberrantly expressed or functionally defective in disease. This Chapter will focus on the role of ncRNAs, in particular miRNAs and lncRNAs, in mammary gland development and disease.
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Affiliation(s)
- Gurveen K Sandhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Michael J G Milevskiy
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Wesley Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Annette M Shewan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia.
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Saad MA, Kuo SZ, Rahimy E, Zou AE, Korrapati A, Rahimy M, Kim E, Zheng H, Yu MA, Wang-Rodriguez J, Ongkeko WM. Alcohol-dysregulated miR-30a and miR-934 in head and neck squamous cell carcinoma. Mol Cancer 2015; 14:181. [PMID: 26472042 PMCID: PMC4608114 DOI: 10.1186/s12943-015-0452-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 10/06/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Alcohol consumption is a well-established risk factor for head and neck squamous cell carcinoma (HNSCC); however, the molecular mechanisms by which alcohol promotes HNSCC pathogenesis and progression remain poorly understood. Our study sought to identify microRNAs that are dysregulated in alcohol-associated HNSCC and investigate their contribution to the malignant phenotype. METHOD Using RNA-sequencing data from 136 HNSCC patients, we compared the expression levels of 1,046 microRNAs between drinking and non-drinking cohorts. Dysregulated microRNAs were verified by qRT-PCR in normal oral keratinocytes treated with biologically relevant doses of ethanol and acetaldehyde. The most promising microRNA candidates were investigated for their effects on cellular proliferation and invasion, sensitivity to cisplatin, and expression of cancer stem cell genes. Finally, putative target genes were identified and evaluated in vitro to further establish roles for these miRNAs in alcohol-associated HNSCC. RESULTS From RNA-sequencing analysis we identified 8 miRNAs to be significantly upregulated in alcohol-associated HNSCCs. qRT-PCR experiments determined that among these candidates, miR-30a and miR-934 were the most highly upregulated in vitro by alcohol and acetaldehyde. Overexpression of miR-30a and miR-934 in normal and HNSCC cell lines produced up to a 2-fold increase in cellular proliferation, as well as induction of the anti-apoptotic gene BCL-2. Upon inhibition of these miRNAs, HNSCC cell lines exhibited increased sensitivity to cisplatin and reduced matrigel invasion. miRNA knockdown also indicated direct targeting of several tumor suppressor genes by miR-30a and miR-934. CONCLUSIONS Alcohol induces the dysregulation of miR-30a and miR-934, which may play crucial roles in HNSCC pathogenesis and progression. Future investigation of the alcohol-mediated pathways effecting these transformations will prove valuable for furthering the understanding and treatment of alcohol-associated HNSCC.
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Affiliation(s)
- Maarouf A Saad
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
| | - Selena Z Kuo
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
| | - Elham Rahimy
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
| | - Angela E Zou
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
| | - Avinaash Korrapati
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
| | - Mehran Rahimy
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
| | - Elizabeth Kim
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
| | - Hao Zheng
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
| | - Michael Andrew Yu
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
| | - Jessica Wang-Rodriguez
- Department of Pathology, Veterans Administration Health Care System, San Diego, CA, USA. .,Department of Pathology, University of California, San Diego, CA, USA.
| | - Weg M Ongkeko
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, La Jolla, San Diego, CA, USA.
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Díaz-Martín J, López-García MÁ, Romero-Pérez L, Atienza-Amores MR, Pecero ML, Castilla MÁ, Biscuola M, Santón A, Palacios J. Nuclear TAZ expression associates with the triple-negative phenotype in breast cancer. Endocr Relat Cancer 2015; 22:443-54. [PMID: 25870251 DOI: 10.1530/erc-14-0456] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/01/2015] [Indexed: 12/31/2022]
Abstract
The Hippo signaling pathway, a conserved regulator of organ size, has emerged as an important regulatory pathway in cancer. The final transducer effectors of this pathway in mammals are the oncoproteins TAZ and YAP1, which are transcriptional coactivators of target genes involved in cell proliferation and survival. TAZ has been previously reported to play a role in tumorigenesis in breast cancer, but detailed analyses of the different breast cancer phenotypes have not been conducted thus far. We analyzed TAZ expression by immunohistochemistry in a retrospective series of 640 invasive breast carcinomas, comprising estrogen/progesterone receptor-positive (ER+/PR+), HER2-positive, and triple-negative (TN) tumors. We found a strong association of TAZ nuclear expression with the TN phenotype (60.5% TAZ-positive, P<0.001), which was strengthened when stratified into the basal-like subtype (70.8% TAZ-positive, P<0.001). Moreover, 90% of metaplastic breast carcinomas with morphological epithelial-mesenchymal transition features were TAZ-positive. We also investigated whether amplification or differential DNA methylation of the TAZ-encoding locus could account for the observed enhanced TAZ protein expression in the TN/basal phenotype. Amplification of the TAZ locus was analyzed by fluorescence in situ hybridization in 30 TN tumors, and we found gene amplification in some cases (6.45%). DNA methylation analysis was performed using the Sequenom MassArray MALDI-TOF platform, and we observed similar low methylation levels both in TN (n=25) and ER+/PR+ (n=26) tumors. These results were further confirmed using a panel of breast cancer cell lines and using the TCGA dataset. Finally, patients with strong TAZ expression showed poorer clinical outcomes with respect to both recurrence and overall survival.
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Affiliation(s)
- Juan Díaz-Martín
- Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - María Ángeles López-García
- Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - Laura Romero-Pérez
- Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - María Reina Atienza-Amores
- Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - María Luisa Pecero
- Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - María Ángeles Castilla
- Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - Michele Biscuola
- Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - Almudena Santón
- Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - José Palacios
- Department of Pathology Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Avenida Manuel Siurot S/N, 41013 Seville, Spain Red Temática de Investigación Cooperativa en Cáncer (RETICC RD012/0036/0017), Madrid, Spain Department of Pathology Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
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