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Bao Q, Li D, Yang X, Ren S, Ding H, Guo C, Wan J, Xiong Y, Zhu M, Wang Y. Comprehensive analysis and experimental verification of the mechanism of anoikis related genes in pancreatic cancer. Heliyon 2024; 10:e36234. [PMID: 39253230 PMCID: PMC11381735 DOI: 10.1016/j.heliyon.2024.e36234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 07/30/2024] [Accepted: 08/12/2024] [Indexed: 09/11/2024] Open
Abstract
Background Pancreatic cancer (PC), characterized by its aggressive nature and low patient survival rate, remains a challenging malignancy. Anoikis, a process inhibiting the spread of metastatic cancer cells, is closely linked to cancer progression and metastasis through anoikis-related genes. Nonetheless, the precise mechanism of action of these genes in PC remains unclear. Methods Study data were acquired from the Cancer Genome Atlas (TCGA) database, with validation data accessed at the Gene Expression Omnibus (GEO) database. Differential expression analysis and univariate Cox analysis were performed to determine prognostically relevant differentially expressed genes (DEGs) associated with anoikis. Unsupervised cluster analysis was then employed to categorize cancer samples. Subsequently, a least absolute shrinkage and selection operator (LASSO) Cox regression analysis was conducted on the identified DEGs to establish a clinical prognostic gene signature. Using risk scores derived from this signature, patients with cancer were stratified into high-risk and low-risk groups, with further assessment conducted via survival analysis, immune infiltration analysis, and mutation analysis. External validation data were employed to confirm the findings, and Western blot and immunohistochemistry were utilized to validate risk genes for the clinical prognostic gene signature. Results A total of 20 prognostic-related DEGs associated with anoikis were obtained. The TCGA dataset revealed two distinct subgroups: cluster 1 and cluster 2. Utilizing the 20 DEGs, a clinical prognostic gene signature comprising two risk genes (CDKN3 and LAMA3) was constructed. Patients with pancreatic adenocarcinoma (PAAD) were classified into high-risk and low-risk groups per their risk scores, with the latter exhibiting a superior survival rate. Statistically significant variation was noted across immune infiltration and mutation levels between the two groups. Validation cohort results were consistent with the initial findings. Additionally, experimental verification confirmed the high expression of CDKN3 and LAMA3 in tumor samples. Conclusion Our study addresses the gap in understanding the involvement of genes linked to anoikis in PAAD. The clinical prognostic gene signature developed herein accurately stratifies patients with PAAD, contributing to the advancement of precision medicine for these patients.
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Affiliation(s)
- Qian Bao
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, 226001, China
- Nantong University Medical School, Nantong, Jiangsu, 226001, China
| | - Dongqian Li
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, 226001, China
- Nantong University Medical School, Nantong, Jiangsu, 226001, China
| | - Xinyu Yang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Shiqi Ren
- Nantong University Medical School, Nantong, Jiangsu, 226001, China
| | - Haoxiang Ding
- Nantong University Medical School, Nantong, Jiangsu, 226001, China
| | - Chengfeng Guo
- Nantong University Medical School, Nantong, Jiangsu, 226001, China
| | - Jian Wan
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, 226001, China
| | - Yicheng Xiong
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, 226001, China
| | - MingYan Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, 226001, China
| | - Yao Wang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, 226001, China
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de Araújo NS, Moreira ADS, Abreu RDS, Junior VV, Antunes D, Mendonça JB, Sassaro TF, Jurberg AD, Ferreira-Reis R, Bastos NC, Fernandes PV, Guimarães ACR, Degrave WMS, Tilli TM, Waghabi MC. Aptamer-Based Recognition of Breast Tumor Cells: A New Era for Breast Cancer Diagnosis. Int J Mol Sci 2024; 25:840. [PMID: 38255914 PMCID: PMC10815801 DOI: 10.3390/ijms25020840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 01/24/2024] Open
Abstract
Breast cancer is one of the leading causes of death among women worldwide and can be classified into four major distinct molecular subtypes based on the expression of specific receptors. Despite significant advances, the lack of biomarkers for detailed diagnosis and prognosis remains a major challenge in the field of oncology. This study aimed to identify short single-stranded oligonucleotides known as aptamers to improve breast cancer diagnosis. The Cell-SELEX technique was used to select aptamers specific to the MDA-MB-231 tumor cell line. After selection, five aptamers demonstrated specific recognition for tumor breast cell lines and no binding to non-tumor breast cells. Validation of aptamer specificity revealed recognition of primary and metastatic tumors of all subtypes. In particular, AptaB4 and AptaB5 showed greater recognition of primary tumors and metastatic tissue, respectively. Finally, a computational biology approach was used to identify potential aptamer targets, which indicated that CSKP could interact with AptaB4. These results suggest that aptamers are promising in breast cancer diagnosis and treatment due to their specificity and selectivity.
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Affiliation(s)
- Natassia Silva de Araújo
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Aline dos Santos Moreira
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Rayane da Silva Abreu
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Valdemir Vargas Junior
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Deborah Antunes
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Julia Badaró Mendonça
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Tayanne Felippe Sassaro
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Arnon Dias Jurberg
- Laboratório de Pesquisas sobre o Timo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (A.D.J.); (R.F.-R.)
- Laboratório de Animais Transgênicos, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, RJ, Brazil
- Instituto de Educação Médica (IDOMED), Universidade Estácio de Sá (UNESA)—Campus Vista Carioca, Rio de Janeiro 20071-004, RJ, Brazil
| | - Rafaella Ferreira-Reis
- Laboratório de Pesquisas sobre o Timo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (A.D.J.); (R.F.-R.)
| | - Nina Carrossini Bastos
- Divisão de Patologia (DIPAT), Instituto Nacional do Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil; (N.C.B.); (P.V.F.)
| | - Priscila Valverde Fernandes
- Divisão de Patologia (DIPAT), Instituto Nacional do Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil; (N.C.B.); (P.V.F.)
| | - Ana Carolina Ramos Guimarães
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Wim Maurits Sylvain Degrave
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Tatiana Martins Tilli
- Laboratório de Fisiopatologia Clínica e Experimental, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil;
- Plataforma de Oncologia Translacional, Centro de Desenvolvimento Tecnológico em Saúde, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Mariana Caldas Waghabi
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
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Tello JA, Jiang L, Zohar Y, Restifo LL. Drosophila CASK regulates brain size and neuronal morphogenesis, providing a genetic model of postnatal microcephaly suitable for drug discovery. Neural Dev 2023; 18:6. [PMID: 37805506 PMCID: PMC10559581 DOI: 10.1186/s13064-023-00174-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND CASK-related neurodevelopmental disorders are untreatable. Affected children show variable severity, with microcephaly, intellectual disability (ID), and short stature as common features. X-linked human CASK shows dosage sensitivity with haploinsufficiency in females. CASK protein has multiple domains, binding partners, and proposed functions at synapses and in the nucleus. Human and Drosophila CASK show high amino-acid-sequence similarity in all functional domains. Flies homozygous for a hypomorphic CASK mutation (∆18) have motor and cognitive deficits. A Drosophila genetic model of CASK-related disorders could have great scientific and translational value. METHODS We assessed the effects of CASK loss of function on morphological phenotypes in Drosophila using established genetic, histological, and primary neuronal culture approaches. NeuronMetrics software was used to quantify neurite-arbor morphology. Standard nonparametric statistics methods were supplemented by linear mixed effects modeling in some cases. Microfluidic devices of varied dimensions were fabricated and numerous fluid-flow parameters were used to induce oscillatory stress fields on CNS tissue. Dissociation into viable neurons and neurite outgrowth in vitro were assessed. RESULTS We demonstrated that ∆18 homozygous flies have small brains, small heads, and short bodies. When neurons from developing CASK-mutant CNS were cultured in vitro, they grew small neurite arbors with a distinctive, quantifiable "bushy" morphology that was significantly rescued by transgenic CASK+. As in humans, the bushy phenotype showed dosage-sensitive severity. To overcome the limitations of manual tissue trituration for neuronal culture, we optimized the design and operation of a microfluidic system for standardized, automated dissociation of CNS tissue into individual viable neurons. Neurons from CASK-mutant CNS dissociated in the microfluidic system recapitulate the bushy morphology. Moreover, for any given genotype, device-dissociated neurons grew larger arbors than did manually dissociated neurons. This automated dissociation method is also effective for rodent CNS. CONCLUSIONS These biological and engineering advances set the stage for drug discovery using the Drosophila model of CASK-related disorders. The bushy phenotype provides a cell-based assay for compound screening. Nearly a dozen genes encoding CASK-binding proteins or transcriptional targets also have brain-development mutant phenotypes, including ID. Hence, drugs that improve CASK phenotypes might also benefit children with disorders due to mutant CASK partners.
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Affiliation(s)
- Judith A Tello
- Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, 85721, USA
- Department of Neurology, University of Arizona Health Sciences, 1501 N. Campbell Ave, Tucson, AZ, 85724-5023, USA
- Present address: Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, 10010, USA
| | - Linan Jiang
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - Yitshak Zohar
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, 85721, USA
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, 85721, USA
- BIO5 Interdisciplinary Research Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Linda L Restifo
- Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, 85721, USA.
- Department of Neurology, University of Arizona Health Sciences, 1501 N. Campbell Ave, Tucson, AZ, 85724-5023, USA.
- BIO5 Interdisciplinary Research Institute, University of Arizona, Tucson, AZ, 85721, USA.
- Department of Cellular & Molecular Medicine, University of Arizona Health Sciences, Tucson, AZ, 85724, USA.
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4
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Mori T, Zhou M, Tabuchi K. Diverse Clinical Phenotypes of CASK-Related Disorders and Multiple Functional Domains of CASK Protein. Genes (Basel) 2023; 14:1656. [PMID: 37628707 PMCID: PMC10454856 DOI: 10.3390/genes14081656] [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: 08/07/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
CASK-related disorders are a form of rare X-linked neurological diseases and most of the patients are females. They are characterized by several symptoms, including microcephaly with pontine and cerebellar hypoplasia (MICPCH), epilepsy, congenital nystagmus, and neurodevelopmental disorders. Whole-genome sequencing has identified various mutations, including nonsense and missense mutations, from patients with CASK-related disorders, revealing correlations between specific mutations and clinical phenotypes. Notably, missense mutations associated with epilepsy and intellectual disability were found throughout the whole region of the CASK protein, while missense mutations related to microcephaly and MICPCH were restricted in certain domains. To investigate the pathophysiology of CASK-related disorders, research groups have employed diverse methods, including the generation of CASK knockout mice and the supplementation of CASK to rescue the phenotypes. These approaches have yielded valuable insights into the identification of functional domains of the CASK protein associated with a specific phenotype. Additionally, recent advancements in the AI-based prediction of protein structure, such as AlphaFold2, and the application of genome-editing techniques to generate CASK mutant mice carrying missense mutations from patients with CASK-related disorders, allow us to understand the pathophysiology of CASK-related disorders in more depth and to develop novel therapeutic methods for the fundamental treatment of CASK-related disorders.
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Affiliation(s)
- Takuma Mori
- Department of Neuroinnovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto 390-8621, Japan;
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
| | - Mengyun Zhou
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
| | - Katsuhiko Tabuchi
- Department of Neuroinnovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto 390-8621, Japan;
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
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Chen S, Cai K, Zheng D, Liu Y, Li L, He Z, Sun C, Yu C. RHBDL2 promotes the proliferation, migration, and invasion of pancreatic cancer by stabilizing the N1ICD via the OTUD7B and activating the Notch signaling pathway. Cell Death Dis 2022; 13:945. [PMID: 36351890 PMCID: PMC9646733 DOI: 10.1038/s41419-022-05379-3] [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: 07/15/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Pancreatic cancer (PC) is one of the most malignant types of cancer, and is characterized by early metastasis, limited response to chemotherapeutics, and poor prognosis. Therefore, there is an urgent need to explore new therapeutic strategies for PC treatment. Human rhomboid-like 2 (RHBDL2) is differentially expressed in cervical and breast cancer. However, the correlation between RHBDL2 and PC remains unclear. We found that RHBDL2 is highly expressed in human PC cells and tissues and is significantly associated with distant metastasis and poor survival of patients with PC. Gain- and loss-of-function assays indicated that RHBDL2 could accelerate PC cell proliferation and mobility in vitro and in vivo. The RNA-Seq results suggest that RHBDL2 may be involved in the activation of Notch signaling pathway. IMR-1 could restore the proliferation and metastatic capacity of PC cells mediated by RHBDL2. RHBDL2 interacted with and cleaved Notch1, resulting in the release of N1ICD. RHBDL2 decreased the ubiquitination level of N1ICD and collaborated with Ovarian tumor domain-containing 7B (OTUD7B) to stabilize N1ICD via the ubiquitin-proteasome pathway. RHBDL2 facilitated PC cell proliferation and mobility by stabilizing the N1ICD via the OTUD7B and activating the Notch signaling pathway. Thus, targeting this novel pathway may be a potential therapeutic strategy for PC.
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Affiliation(s)
- Shiyu Chen
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Translational Medicine, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Kun Cai
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Dijie Zheng
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Yanqing Liu
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Translational Medicine, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Lin Li
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Translational Medicine, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Zhiwei He
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Chengyi Sun
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Chao Yu
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
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Caggiano C, Pieraccioli M, Pitolli C, Babini G, Zheng D, Tian B, Bielli P, Sette C. The androgen receptor couples promoter recruitment of RNA processing factors to regulation of alternative polyadenylation at the 3' end of transcripts. Nucleic Acids Res 2022; 50:9780-9796. [PMID: 36043441 PMCID: PMC9508809 DOI: 10.1093/nar/gkac737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 07/20/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Prostate cancer (PC) relies on androgen receptor (AR) signaling. While hormonal therapy (HT) is efficacious, most patients evolve to an incurable castration-resistant stage (CRPC). To date, most proposed mechanisms of acquired resistance to HT have focused on AR transcriptional activity. Herein, we uncover a new role for the AR in alternative cleavage and polyadenylation (APA). Inhibition of the AR by Enzalutamide globally regulates APA in PC cells, with specific enrichment in genes related to transcription and DNA topology, suggesting their involvement in transcriptome reprogramming. AR inhibition selects promoter-distal polyadenylation sites (pAs) enriched in cis-elements recognized by the cleavage and polyadenylation specificity factor (CPSF) complex. Conversely, promoter-proximal intronic pAs relying on the cleavage stimulation factor (CSTF) complex are repressed. Mechanistically, Enzalutamide induces rearrangement of APA subcomplexes and impairs the interaction between CPSF and CSTF. AR inhibition also induces co-transcriptional CPSF recruitment to gene promoters, predisposing the selection of pAs depending on this complex. Importantly, the scaffold CPSF160 protein is up-regulated in CRPC cells and its depletion represses HT-induced APA patterns. These findings uncover an unexpected role for the AR in APA regulation and suggest that APA-mediated transcriptome reprogramming represents an adaptive response of PC cells to HT.
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Affiliation(s)
- Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome 00168, Italy.,IRCCS Fondazione Policlinico A. Gemelli, Rome 00168, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome 00168, Italy.,IRCCS Fondazione Policlinico A. Gemelli, Rome 00168, Italy
| | - Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome 00168, Italy.,IRCCS Fondazione Policlinico A. Gemelli, Rome 00168, Italy
| | | | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Bin Tian
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy.,IRCCS Fondazione Santa Lucia, Rome 00143, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome 00168, Italy.,IRCCS Fondazione Policlinico A. Gemelli, Rome 00168, Italy
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7
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Prediction of Response to Radiotherapy by Characterizing the Transcriptomic Features in Clinical Tumor Samples across 15 Cancer Types. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:5443709. [PMID: 35586092 PMCID: PMC9110128 DOI: 10.1155/2022/5443709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022]
Abstract
Purpose Radiotherapy (RT) is one of the major cancer treatments. However, the responses to RT vary among individual patients, partly due to the differences of the status of gene expression and mutation in tumors of patients. Identification of patients who will benefit from RT will improve the efficacy of RT. However, only a few clinical biomarkers were currently used to predict RT response. Our aim is to obtain gene signatures that can be used to predict RT response by analyzing the transcriptome differences between RT responder and nonresponder groups. Materials and Methods We obtained transcriptome data of 1664 patients treated with RT from the TCGA database across 15 cancer types. First, the genes with a significant difference between RT responder (R group) and nonresponder groups (PD group) were identified, and the top 100 genes were used to build the gene signatures. Then, we developed the predictive model based on binary logistic regression to predict patient response to RT. Results We identified a series of differentially expressed genes between the two groups, which are involved in cell proliferation, migration, invasion, EMT, and DNA damage repair pathway. Among them, MDC1, UCP2, and RBM45 have been demonstrated to be involved in DNA damage repair and radiosensitivity. Our analysis revealed that the predictive model was highly specific for distinguishing the R and PD patients in different cancer types with an area under the curve (AUC) ranging from 0.772 to 0.972. It also provided a more accurate prediction than that from a single-gene signature for the overall survival (OS) of patients. Conclusion The predictive model has a potential clinical application as a biomarker to help physicians create optimal treatment plans. Furthermore, some of the genes identified here may be directly involved in radioresistance, providing clues for further studies on the mechanism of radioresistance.
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8
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Russ N, Schröder M, Berger BT, Mandel S, Aydogan Y, Mauer S, Pohl C, Drewry DH, Chaikuad A, Müller S, Knapp S. Design and Development of a Chemical Probe for Pseudokinase Ca 2+/calmodulin-Dependent Ser/Thr Kinase. J Med Chem 2021; 64:14358-14376. [PMID: 34543009 DOI: 10.1021/acs.jmedchem.1c00845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
CASK (Ca2+/calmodulin-dependent Ser/Thr kinase) is a member of the MAGUK (membrane-associated guanylate kinase) family that functions as neurexin kinases with roles implicated in neuronal synapses and trafficking. The lack of a canonical DFG motif, which is altered to GFG in CASK, led to the classification as a pseudokinase. However, functional studies revealed that CASK can still phosphorylate substrates in the absence of divalent metals. CASK dysfunction has been linked to many diseases, including colorectal cancer, Parkinson's disease, and X-linked mental retardation, suggesting CASK as a potential drug target. Here, we exploited structure-based design for the development of highly potent and selective CASK inhibitors based on 2,4-diaminopyrimidine-5-carboxamides targeting an unusual pocket created by the GFG motif. The presented inhibitor design offers a more general strategy for the development of pseudokinase ligands that harbor unusual sequence motifs. It also provides a first chemical probe for studying the biological roles of CASK.
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Affiliation(s)
- Nadine Russ
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Martin Schröder
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Benedict-Tilman Berger
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Sebastian Mandel
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Yagmur Aydogan
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Sandy Mauer
- Buchman Institute for Molecular Life Science and Institute of Biochemistry II, Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Christian Pohl
- Buchman Institute for Molecular Life Science and Institute of Biochemistry II, Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,UNC Lineberger Comprehensive Cancer Center, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Apirat Chaikuad
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Susanne Müller
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany.,German Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
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9
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Xu J, Xu W, Yang X, Liu Z, Sun Q. LncRNA HCG11/miR-579-3p/MDM2 axis modulates malignant biological properties in pancreatic carcinoma via Notch/Hes1 signaling pathway. Aging (Albany NY) 2021; 13:16471-16484. [PMID: 34230221 PMCID: PMC8266358 DOI: 10.18632/aging.203167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/14/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Increasing reports have revealed that dysregulated expression of long non-coding RNAs (lncRNAs) is involved in pancreatic carcinoma progression. This study intends to explore the function and molecular mechanism of lncRNA HLA complex group 11 (HCG11) in pancreatic carcinoma. METHODS The expression profiles of HCG11 in pancreatic carcinoma samples were detected by qPCR. Bioinformatics analysis was applied to detect the associations among HCG11/miR-579-3p/MDM2. The malignant properties of pancreatic carcinoma cells were measured by numerous biological assays. Xenograft model was exploited to detect the effect of HCG11 on tumor growth. RESULTS A significant increase of HCG11 was occurred in pancreatic carcinoma samples. Knockdown of HCG11 suppressed the progression of pancreatic carcinoma cells. Bioinformatics analysis revealed that HCG11 upregulated MDM2 expression by competitively targeting miR-579-3p. The rescue assays showed that miR-579-3p reversed cell behaviors caused by HCG11, and MDM2 reversed cell properties induced by miR-579-3p. The Notch1 intracellular domain (NICD) and Hes1 protein levels were increased by overexpression of HCG11/MDM2. The tumor growth was suppressed after depletion of HCG11, followed by suppressing Ki67, PCNA and Vimentin expression, increasing TUNEL-positive cells and E-cadherin expression. CONCLUSIONS Our observations highlighted that HCG11 contributed to the progression of pancreatic carcinoma by promoting growth and aggressiveness, and inhibiting apoptosis via miR-579-3p/MDM2/Notch/Hes1 axis.
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Affiliation(s)
- Jin Xu
- Department of Pancreatic and Thyroid Surgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - Weixue Xu
- Department of Pancreatic and Thyroid Surgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - Xuan Yang
- Department of Pancreatic and Thyroid Surgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - Zhen Liu
- Department of Pancreatic and Thyroid Surgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - Qinyun Sun
- Department of Pancreatic and Thyroid Surgery, Shengjing Hospital, China Medical University, Shenyang, China
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