1
|
Luo T, Chen X, Pan W, Zhang S, Huang J. The sorafenib resistance-related gene signature predicts prognosis and indicates immune activity in hepatocellular carcinoma. Cell Cycle 2024; 23:150-168. [PMID: 38444181 PMCID: PMC11037289 DOI: 10.1080/15384101.2024.2309020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 12/15/2023] [Indexed: 03/07/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death worldwide. Most patients with advanced HCC acquire sorafenib resistance. Drug resistance reflects the heterogeneity of tumors and is the main cause of tumor recurrence and death.We identified and validated sorafenib resistance related-genes (SRGs) as prognostic biomarkers for HCC. We obtained SRGs from the Gene Expression Omnibus and selected four key SRGs using the least absolute shrinkage and selection operator, random forest, and Support Vector Machine-Recursive feature elimination machine learning algorithms. Samples from the The Cancer Genome Atlas (TCGA)-HCC were segregated into two groups by consensus clustering. Following difference analysis, 19 SRGs were obtained through univariate Cox regression analysis, and a sorafenib resistance model was constructed for risk stratification and prognosis prediction. In multivariate Cox regression analysis, the risk score was an independent predictor of overall survival (OS). Patients classified as high-risk were more sensitive to other chemotherapy drugs and showed a higher expression of the common immune checkpoints. Additionally, the expression of drug-resistance genes was verified in the International Cancer Genome Consortium cohort. A nomogram model with a risk score was established, and its prediction performance was verified by calibration chart analysis of the TCGA-HCC cohort. We conclude that there is a significant correlation between sorafenib resistance and the tumor immune microenvironment in HCC. The risk score could be used to identify a reliable prognostic biomarker to optimize the therapeutic benefits of chemotherapy and immunotherapy, which can be helpful in the clinical decision-making for HCC patients.
Collapse
Affiliation(s)
- Tianxin Luo
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, China
| | - Xiaomei Chen
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, China
| | - Wei Pan
- Prenatal Diagnosis Center, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shu Zhang
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, China
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jian Huang
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| |
Collapse
|
2
|
Kumari S, Kumar P. Identification and characterization of putative biomarkers and therapeutic axis in Glioblastoma multiforme microenvironment. Front Cell Dev Biol 2023; 11:1236271. [PMID: 37538397 PMCID: PMC10395518 DOI: 10.3389/fcell.2023.1236271] [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: 06/07/2023] [Accepted: 06/23/2023] [Indexed: 08/05/2023] Open
Abstract
Non-cellular secretory components, including chemokines, cytokines, and growth factors in the tumor microenvironment, are often dysregulated, impacting tumorigenesis in Glioblastoma multiforme (GBM) microenvironment, where the prognostic significance of the current treatment remains unsatisfactory. Recent studies have demonstrated the potential of post-translational modifications (PTM) and their respective enzymes, such as acetylation and ubiquitination in GBM etiology through modulating signaling events. However, the relationship between non-cellular secretory components and post-translational modifications will create a research void in GBM therapeutics. Therefore, we aim to bridge the gap between non-cellular secretory components and PTM modifications through machine learning and computational biology approaches. Herein, we highlighted the importance of BMP1, CTSB, LOX, LOXL1, PLOD1, MMP9, SERPINE1, and SERPING1 in GBM etiology. Further, we demonstrated the positive relationship between the E2 conjugating enzymes (Ube2E1, Ube2H, Ube2J2, Ube2C, Ube2J2, and Ube2S), E3 ligases (VHL and GNB2L1) and substrate (HIF1A). Additionally, we reported the novel HAT1-induced acetylation sites of Ube2S (K211) and Ube2H (K8, K52). Structural and functional characterization of Ube2S (8) and Ube2H (1) have identified their association with protein kinases. Lastly, our results found a putative therapeutic axis HAT1-Ube2S(K211)-GNB2L1-HIF1A and potential predictive biomarkers (CTSB, HAT1, Ube2H, VHL, and GNB2L1) that play a critical role in GBM pathogenesis.
Collapse
|
3
|
Voinsky I, Zoabi Y, Shomron N, Harel M, Cassuto H, Tam J, Rose S, Scheck AC, Karim MA, Frye RE, Aran A, Gurwitz D. Blood RNA Sequencing Indicates Upregulated BATF2 and LY6E and Downregulated ISG15 and MT2A Expression in Children with Autism Spectrum Disorder. Int J Mol Sci 2022; 23:ijms23179843. [PMID: 36077244 PMCID: PMC9456089 DOI: 10.3390/ijms23179843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
Mutations in over 100 genes are implicated in autism spectrum disorder (ASD). DNA SNPs, CNVs, and epigenomic modifications also contribute to ASD. Transcriptomics analysis of blood samples may offer clues for pathways dysregulated in ASD. To expand and validate published findings of RNA-sequencing (RNA-seq) studies, we performed RNA-seq of whole blood samples from an Israeli discovery cohort of eight children with ASD compared with nine age- and sex-matched neurotypical children. This revealed 10 genes with differential expression. Using quantitative real-time PCR, we compared RNAs from whole blood samples of 73 Israeli and American children with ASD and 26 matched neurotypical children for the 10 dysregulated genes detected by RNA-seq. This revealed higher expression levels of the pro-inflammatory transcripts BATF2 and LY6E and lower expression levels of the anti-inflammatory transcripts ISG15 and MT2A in the ASD compared to neurotypical children. BATF2 was recently reported as upregulated in blood samples of Japanese adults with ASD. Our findings support an involvement of these genes in ASD phenotypes, independent of age and ethnicity. Upregulation of BATF2 and downregulation of ISG15 and MT2A were reported to reduce cancer risk. Implications of the dysregulated genes for pro-inflammatory phenotypes, immunity, and cancer risk in ASD are discussed.
Collapse
Affiliation(s)
- Irena Voinsky
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yazeed Zoabi
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moria Harel
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
| | | | - Joseph Tam
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Shannon Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR 72205, USA
| | - Adrienne C. Scheck
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Mohammad A. Karim
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Richard E. Frye
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
- Rossignol Medical Center, Phoenix, AZ 85050, USA
| | - Adi Aran
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
- Correspondence: (A.A.); (D.G.)
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (A.A.); (D.G.)
| |
Collapse
|
4
|
Bombyx batryticatus Cocoonase Inhibitor Separation, Purification, and Inhibitory Effect on the Proliferation of SMCC-7721 HeLa-Derived Cells. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4064829. [PMID: 35747381 PMCID: PMC9213135 DOI: 10.1155/2022/4064829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022]
Abstract
The present study was to isolate and purify Bombyx batryticatus cocoonase inhibitor (BBCI) and to evaluate its inhibitory effect on the proliferation of SMCC-7721 cells. BBCI was purified from the crude proteins of Bombyx batryticatus using affinity chromatography with cocoonase as the ligand, its N-terminal amino acid sequence was determined using the Edman degradation method, and its inhibiting activity on SMCC-7721 cell proliferation was detected in vitro using the MTT method and in vivo in tumor-bearing nude mice. The purified BBCI presented as a single band in SDS-PAGE, the molecular weight determined by time-of-flight mass spectrometry was 13,973.63 Da, and its N-terminal amino acid sequence was VRNKRQSNDD. BBCI was a noncompetitive cocoonase inhibitor with an average Michaelis constant of 76.50, and it inhibited cocoonase activity with an inhibition ratio of 1 : 1 (molar). BBCI could inhibit the proliferation of SMCC-7721 cells in vitro with the IC50 being about 260.52 μg/ml within 36 h of treatment and inhibit the SMCC-7721 tumor growth in nude mice by subcutaneous injection of BBCI around the tumor, where the tumor inhibitory effect was dose dependent. BBCI did not significantly influence the spleen coefficient of the mice. In conclusion, to the best of our knowledge, the present study is the first to report that BBCI, which was purified from Bombyx batryticatus, was a serine proteinase inhibitor with antitumor activity.
Collapse
|
5
|
MCM6 Promotes Hepatocellular Carcinoma Progression via the Notch Pathway: Clinical, Functional, and Genomic Insights. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3116303. [PMID: 35720029 PMCID: PMC9203181 DOI: 10.1155/2022/3116303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/21/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022]
Abstract
Objective To evaluate the expression profile of MCM6 in HCC and the relationship between MCM6 level and clinicopathological parameters through bioinformatics analysis of several databases. Methods MCM expression level, clinical parameters, survival data, and gene set enrichment analysis were analyzed by bioinformatics database, including Oncomine™, UALCAN, HCCDB, TCGA, cBioPortal, and LinkedOmics. Real-time PCR, western blotting, and IHC staining were conducted to identify the expression of MCM6 in HCC compared to normal liver tissues. Results Bioinformatics analysis indicated that the mRNA of MCM6 was obviously increased in multiple cancer types, especially in HCC. MCM6 level was positively associated with multiple clinical parameters (stage 3 and grades 3 and 4) and negatively associated with patient outcomes (overall survival). Moreover, enrichment of functions and signaling pathways analysis of MCM6 suggested that MCM6 might mediate DNA replication and cellular metabolism to promote the development and progression of HCC. Furthermore, IHC staining and western blotting indicated that the MCM6 was enhanced in HCC tissue, and MCM6 could promote HCC proliferation in activating Notch pathway via WB and bioinformatic analysis. Conclusion This study actually revealed the expression and related functions of MCM6 in HCC. Furthermore, MCM6 is a carcinogenic role in activating Notch pathway to promote HCC cell proliferation, which may be a new prognostic biomarker and therapeutic target for HCC patients.
Collapse
|
6
|
Liu J, Lan Y, Tian G, Yang J. A Systematic Framework for Identifying Prognostic Genes in the Tumor Microenvironment of Colon Cancer. Front Oncol 2022; 12:899156. [PMID: 35664768 PMCID: PMC9161737 DOI: 10.3389/fonc.2022.899156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/19/2022] [Indexed: 12/23/2022] Open
Abstract
As one of the most common cancers of the digestive system, colon cancer is a predominant cause of cancer-related deaths worldwide. To investigate prognostic genes in the tumor microenvironment of colon cancer, we collected 461 colon adenocarcinoma (COAD) and 172 rectal adenocarcinoma (READ) samples from The Cancer Genome Atlas (TCGA) database, and calculated the stromal and immune scores of each sample. We demonstrated that stromal and immune scores were significantly associated with colon cancer stages. By analyzing differentially expressed genes (DEGs) between two stromal and immune score groups, we identified 952 common DEGs. The significantly enriched Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms for these DEGs were associated with T-cell activation, immune receptor activity, and cytokine–cytokine receptor interaction. Through univariate Cox regression analysis, we identified 22 prognostic genes. Furthermore, nine key prognostic genes, namely, HOXC8, SRPX, CCL22, CD72, IGLON5, SERPING1, PCOLCE2, FABP4, and ARL4C, were identified using the LASSO Cox regression analysis. The risk score of each sample was calculated using the gene expression of the nine genes. Patients with high-risk scores had a poorer prognosis than those with low-risk scores. The prognostic model established with the nine-gene signature was able to effectively predict the outcome of colon cancer patients. Our findings may help in the clinical decisions and improve the prognosis for colon cancer.
Collapse
Affiliation(s)
- Jinyang Liu
- Department of Sciences, Geneis Beijing Co., Ltd., Beijing, China
- Department of Data Mining,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Yu Lan
- Department of Sciences, Geneis Beijing Co., Ltd., Beijing, China
- Department of Data Mining,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Geng Tian
- Department of Sciences, Geneis Beijing Co., Ltd., Beijing, China
- Department of Data Mining,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Jialiang Yang
- Department of Sciences, Geneis Beijing Co., Ltd., Beijing, China
- Department of Data Mining,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
- PhD Workstation, Chifeng Municipal Hospital, Chifeng, China
- *Correspondence: Jialiang Yang,
| |
Collapse
|
7
|
Clanchy FIL, Huang YS, Ogbechi J, Darlington LG, Williams RO, Stone TW. Induction of IDO1 and Kynurenine by Serine Proteases Subtilisin, Prostate Specific Antigen, CD26 and HtrA: A New Form of Immunosuppression? Front Immunol 2022; 13:832989. [PMID: 35371018 PMCID: PMC8964980 DOI: 10.3389/fimmu.2022.832989] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/23/2022] [Indexed: 11/18/2022] Open
Abstract
Several serine proteases have been linked to autoimmune disorders and tumour initiation although the mechanisms are not fully understood. Activation of the kynurenine pathway enzyme indoleamine-2,3-dioxygenase (IDO1) modulates cellular activity in the brain, tolerogenesis in the immune system and is a major checkpoint in cancer development. We now report that IDO1 mRNA and IDO1 protein expression (generating kynurenine) are induced in human monocyte-derived macrophages by several chymotryptic serine proteases with direct links to tumorigenesis, including Prostate Specific Antigen (PSA), CD26 (Dipeptidyl-peptidase-4, CD26/DPP-4), High Temperature Requirement protein-A (HtrA), and the bacterial virulence factor subtilisin. These proteases also induce expression of the pro-inflammatory cytokine genes IL1B and IL6. Other serine proteases tested: bacterial glu-C endopeptidase and mammalian Pro-protein Convertase Subtilase-Kexin-3 (PCSK3, furin), urokinase plasminogen activator (uPA), cathepsin G or neutrophil elastase, did not induce IDO1, indicating that the reported effects are not a general property of all serine proteases. The results represent a novel mechanism of activating immunosuppressive IDO1 and inducing kynurenine generation which, together with the production of inflammatory cytokines, would contribute to tumour initiation and progression, providing a new target for drug development. In addition, the proteasomal S20 serine protease inhibitor carfilzomib, used in the treatment of myeloma, prevented the induction of IDO1 and cytokine gene expression, potentially contributing to its clinical anti-cancer activity.
Collapse
Affiliation(s)
- Felix I. L. Clanchy
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Yi-Shu Huang
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Joy Ogbechi
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - L. Gail Darlington
- Department of Medicine and Rheumatology, Ashtead Hospital, Ashtead, United Kingdom
| | - Richard O. Williams
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Trevor W. Stone
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| |
Collapse
|
8
|
Identification of Autophagy-Related Prognostic Signature and Analysis of Immune Cell Infiltration in Low-Grade Gliomas. BIOMED RESEARCH INTERNATIONAL 2021; 2021:7918693. [PMID: 34790823 PMCID: PMC8592714 DOI: 10.1155/2021/7918693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/15/2021] [Accepted: 10/21/2021] [Indexed: 12/21/2022]
Abstract
Autophagy plays an important role in cancer. Many studies have demonstrated that autophagy-related genes (ARGs) can act as a prognostic signature for some cancers, but little has been known in low-grade gliomas (LGG). In our study, we aimed to establish a prognostical model based on ARGs and find prognostic risk-related key genes in LGG. In the present study, a prognostic signature was constructed based on a total of 8 ARGs (MAPK8IP1, EEF2, GRID2, BIRC5, DLC1, NAMPT, GRID1, and TP73). It was revealed that the higher the risk score, the worse was the prognosis. Time-dependent ROC analysis showed that the risk score could precisely predict the prognosis of LGG patients. Additionally, four key genes (TGFβ2, SERPING1, SERPINE1, and TIMP1) were identified and found significantly associated with OS of LGG patients. Besides, they were also discovered to be strongly related to six types of immune cells which infiltrated in LGG tumor. Taken together, the present study demonstrated the promising potential of the ARG risk score formula as an independent factor for LGG prediction. It also provided the autophagy-related signature of prognosis and potential therapeutic targets for the treatment of LGG.
Collapse
|
9
|
Chen P, Wu S, Yu J, Tang X, Dai C, Qi H, Zhu J, Li W, Chen B, Zhu J, Wang H, Zhao S, Liu H, Kuang P, He Y. mRNA Network: Solution for Tracking Chemotherapy Insensitivity in Small-Cell Lung Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:2105176. [PMID: 34621500 PMCID: PMC8492269 DOI: 10.1155/2021/2105176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/14/2021] [Accepted: 08/05/2021] [Indexed: 12/25/2022]
Abstract
Background Small-cell lung cancer (SCLC) has poor prognosis and is prone to drug resistance. It is necessary to search for possible influencing factors for SCLC chemotherapy insensitivity. Therefore, we proposed an mRNA network to track the chemotherapy insensitivity in SCLC. Methods Six samples of patients with SCLC were recruited for RNA sequencing. TopHat2 and Cufflinks were used to make differential analysis. Functional analysis was applied as well. Finally, multidimensional validation was applied for verifying the results we obtained by experiment. Results This study was a trial of drug resistance in 6 SCLC patients after first-line chemotherapy. The top 10 downregulated genes differentially expressed in the chemo-insensitive group were SERPING1, DRD5, PARVG, PRAME, NKX1-1, MCTP2, PID1, PLEKHA4, SPP1, and SLN. Cell-cell signaling by Wnt (p=6.98E - 21) was the most significantly enriched GO term in biological process, while systemic lupus erythematosus (p=6.97E - 10), alcoholism (p=1.01E - 09), and transcriptional misregulation in cancer (p=0.00227988) were the top three ones of KEGG pathways. In multiple public databases, we also highlighted and verified the vital role of glycolysis/gluconeogenesis pathway and corresponding genes in chemo-insensitivity in SCLC. Conclusion Our study confirmed some SCLC chemotherapy insensitivity-related genes, biological processes, and pathways, thus constructing the chemotherapy-insensitive network for SCLC.
Collapse
Affiliation(s)
- Peixin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Shengyu Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Jia Yu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Xuzhen Tang
- Oncology and Immunology BU, Research Service Division, WuXi Apptec, Shanghai, China
| | - Chunlei Dai
- Oncology and Immunology BU, Research Service Division, WuXi Apptec, Shanghai, China
| | - Hui Qi
- Oncology and Immunology BU, Research Service Division, WuXi Apptec, Shanghai, China
| | - Junjie Zhu
- Department of Surgery, Shanghai Pulmonary Hospital, Tongji University, Tongji University School of Medicine, Shanghai 200433, China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Bin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Jun Zhu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Hao Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Sha Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Hongcheng Liu
- Department of Surgery, Shanghai Pulmonary Hospital, Tongji University, Tongji University School of Medicine, Shanghai 200433, China
| | - Peng Kuang
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| |
Collapse
|
10
|
Wang S, Qin H, Mao J, Fang Z, Chen Y, Zhang X, Hu L, Ye M. Profiling of Endogenously Intact N-Linked and O-Linked Glycopeptides from Human Serum Using an Integrated Platform. J Proteome Res 2020; 19:1423-1434. [PMID: 32090575 DOI: 10.1021/acs.jproteome.9b00592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Endogenous glycopeptides in serum are an invaluable resource for biomarker discovery. Due to the low abundance and the poor fragmentation in tandem mass spectrometry, the identification of endogenously intact glycopeptides still faces many challenges. Herein, an integrated platform is fabricated for the identification of N-linked and O-linked endogenously intact glycopeptides. In this platform, the high-temperature acid denaturation, ultrafiltration, and hydrophilic interaction chromatography steps are combined together for the highly efficient extraction of the endogenously intact glycopeptides from a small amount of serum. Additionally, the twin-spectra scheme and in silico deglycosylation strategy were applied for the identification of N-linked and O-linked endogenous glycopeptides, respectively. In total, 223 intact N-glycopeptides and 51 intact O-glycopeptides are identified from only 40 μL of the human serum sample. This is the first study reporting the identification of endogenously intact N-linked and O-linked glycopeptide and is also the largest data set of endogenously intact glycopeptides reported so far. The distributions of glycans among peptides and proteins and cleavage sites on peptides are further analyzed to seek the regulation of endogenous glycosylation for disease mechanism. The developed strategy provides a novel platform for the disease biomarker discovery.
Collapse
Affiliation(s)
- Shuyue Wang
- Key Laboratory Molecular Enzymology and Engineering, The Ministry of Education, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130023, China.,CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jiawei Mao
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Zheng Fang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Chen
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolei Zhang
- Key Laboratory Molecular Enzymology and Engineering, The Ministry of Education, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130023, China.,CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Lianghai Hu
- Key Laboratory Molecular Enzymology and Engineering, The Ministry of Education, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130023, China
| | - Mingliang Ye
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| |
Collapse
|
11
|
Furuya H, Hayashi K, Shimizu Y, Kim N, Tsukikawa Y, Chen R, Sun Y, Chan OTM, Pagano I, Peres R, Hokutan K, Igari F, Chan KS, Rosser CJ. Plasminogen activator inhibitor-2 (PAI-2) overexpression supports bladder cancer development in PAI-1 knockout mice in N-butyl-N- (4-hydroxybutyl)-nitrosamine- induced bladder cancer mouse model. J Transl Med 2020; 18:57. [PMID: 32024545 PMCID: PMC7003426 DOI: 10.1186/s12967-020-02239-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/24/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Accumulating evidence suggests that plasminogen activator inhibitor-1 (PAI-1) plays an important role in bladder tumorigenesis by regulating cell cycle. However, it remains unclear whether and how inhibition of PAI-1 suppresses bladder tumorigenesis. METHODS To elucidate the therapeutic effect of PAI-1 inhibition, we tested its tumorigenicity in PAI-1 knockout (KO) mice exposed to a known bladder carcinogen. RESULTS PAI-1 deficiency did not inhibit carcinogen-induced bladder cancer in mice although carcinogen-exposed wild type mice significantly increased PAI-1 levels in bladder tissue, plasma and urine. We found that PAI-1 KO mice exposed to carcinogen tended to upregulate protein C inhibitor (PAI-3), urokinase-type plasminogen activator (uPA) and tissue-type PA (tPA), and significantly increased PAI-2, suggesting a potential compensatory function of these molecules when PAI-1 is abrogated. Subsequent studies employing gene expression microarray using mouse bladder tissues followed by post hoc bioinformatics analysis and validation experiments by qPCR and IHC demonstrated that SERPING1 is further downregulated in PAI-1 KO mice exposed to BBN, suggesting that SERPING1 as a potential missing factor that regulate PAI-2 overexpression (compensation pathway). CONCLUSIONS These results indicate that serpin compensation pathway, specifically PAI-2 overexpression in this model, supports bladder cancer development when oncoprotein PAI-1 is deleted. Further investigations into PAI-1 are necessary in order to identify true potential targets for bladder cancer therapy.
Collapse
Affiliation(s)
- Hideki Furuya
- Clinical & Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA.
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Davis Research Building, 110 N. George Burns Road, Los Angeles, CA, 90048, USA.
| | - Kazukuni Hayashi
- Clinical & Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
- Department of Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Yoshiko Shimizu
- Clinical & Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Nari Kim
- Clinical & Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Yutaro Tsukikawa
- Clinical & Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Runpu Chen
- Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Yijun Sun
- Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, NY, 14203, USA
- Department of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Owen T M Chan
- Clinical & Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Ian Pagano
- Cancer Prevention in Pacific Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Rafael Peres
- Clinical & Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Kanani Hokutan
- Clinical & Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Fumie Igari
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Davis Research Building, 110 N. George Burns Road, Los Angeles, CA, 90048, USA
| | - Keith S Chan
- Department of Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Charles J Rosser
- Clinical & Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Davis Research Building, 110 N. George Burns Road, Los Angeles, CA, 90048, USA
| |
Collapse
|
12
|
Eggener SE, Rumble RB, Armstrong AJ, Morgan TM, Crispino T, Cornford P, van der Kwast T, Grignon DJ, Rai AJ, Agarwal N, Klein EA, Den RB, Beltran H. Molecular Biomarkers in Localized Prostate Cancer: ASCO Guideline. J Clin Oncol 2019; 38:1474-1494. [PMID: 31829902 DOI: 10.1200/jco.19.02768] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
PURPOSE This guideline provides recommendations for available tissue-based prostate cancer biomarkers geared toward patient selection for active surveillance, identification of clinically significant disease, choice of postprostatectomy adjuvant versus salvage radiotherapy, and to address emerging questions such as the relative value of tissue biomarkers compared with magnetic resonance imaging. METHODS An ASCO multidisciplinary Expert Panel, with representatives from the European Association of Urology, American Urological Association, and the College of American Pathologists, conducted a systematic literature review of localized prostate cancer biomarker studies between January 2013 and January 2019. Numerous tissue-based molecular biomarkers were evaluated for their prognostic capabilities and potential for improving management decisions. Here, the Panel makes recommendations regarding the clinical use and indications of these biomarkers. RESULTS Of 555 studies identified, 77 were selected for inclusion plus 32 additional references selected by the Expert Panel. Few biomarkers had rigorous testing involving multiple cohorts and only 5 of these tests are commercially available currently: Oncotype Dx Prostate, Prolaris, Decipher, Decipher PORTOS, and ProMark. With various degrees of value and validation, multiple biomarkers have been shown to refine risk stratification and can be considered for select men to improve management decisions. There is a paucity of prospective studies assessing short- and long-term outcomes of patients when these markers are integrated into clinical decision making. RECOMMENDATIONS Tissue-based molecular biomarkers (evaluating the sample with the highest volume of the highest Gleason pattern) may improve risk stratification when added to standard clinical parameters, but the Expert Panel endorses their use only in situations in which the assay results, when considered as a whole with routine clinical factors, are likely to affect a clinical decision. These assays are not recommended for routine use as they have not been prospectively tested or shown to improve long-term outcomes-for example, quality of life, need for treatment, or survival. Additional information is available at www.asco.org/genitourinary-cancer-guidelines.
Collapse
Affiliation(s)
| | | | | | - Todd M Morgan
- University of Michigan School of Medicine, Ann Arbor, MI
| | | | - Philip Cornford
- Royal Liverpool University Hospital, Liverpool, United Kingdom
| | | | | | - Alex J Rai
- Columbia University Irving Medical Center, New York, NY
| | | | | | | | | |
Collapse
|
13
|
Yi Y, Liu Y, Wu K, Wu W, Zhang W. The core genes involved in the promotion of depression in patients with ovarian cancer. Oncol Lett 2019; 18:5995-6007. [PMID: 31788074 PMCID: PMC6865084 DOI: 10.3892/ol.2019.10934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 08/08/2019] [Indexed: 12/09/2022] Open
Abstract
The present study aimed to identify the core genes and pathways involved in depression in patients with ovarian cancer (OC) who suffer from high or low-grade depression. The dataset GSE9116 from Gene Expression Omnibus database was analyzed to identify differentially expressed genes (DEGs) in these patients. To elucidate how certain genes could promote depression in patients with OC, pathway crosstalk, protein-protein interaction (PPI) and comprehensive gene-pathway analyses were determined using WebGestalt, ToppGene and Search Tool for the Retrieval of Interacting Genes and gene ontology analysis. Key genes and pathways were extracted from the gene-pathway network, and gene expression and survival analysis were evaluated. A total of 93 DEGs were identified from GSE9116 dataset, including 84 upregulated genes and nine downregulated genes. The PPI, pathway crosstalk and comprehensive gene-pathway analyses highlighted C-C motif chemokine ligand 2 (CCL2), Fos proto-oncogene, AP-1 transcription factor subunit (FOS), serpin family E member 1 (SERPINE1) and serpin family G member 1 (SERPING1) as core genes involved in the promotion of depression in patients with OC. These core genes were involved in the following four pathways 'Ensemble of genes encoding ECM-associated proteins including ECM-affiliated proteins', 'ECM regulators and secreted factors', 'Ensemble of genes encoding extracellular matrix and extracellular matrix-associated proteins' and 'MAPK signaling pathway and IL-17 signaling pathway'. The results from gene expression and survival analysis demonstrated that these four key genes were upregulated in patients with OC and high-grade depression and could worsen patients' survival. These results suggested that CCL2, FOS, SERPINE1 and SERPING1 may serve a crucial role in the promotion of depression in patients with OC. This finding may provide novel markers for predicting and treating depression in patients with OC; however, the underlying mechanisms remain unknown and require further investigation.
Collapse
Affiliation(s)
- Yuexiong Yi
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yanyan Liu
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Kejia Wu
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Wanrong Wu
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| |
Collapse
|