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An L, Gong H, Yu X, Zhang W, Liu X, Yang X, Shu L, Liu J, Yang L. Downregulation of MAL2 inhibits breast cancer progression through regulating β-catenin/c-Myc axis. Cancer Cell Int 2023; 23:144. [PMID: 37480012 PMCID: PMC10362617 DOI: 10.1186/s12935-023-02993-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
PURPOSE Myelin and lymphocyte protein 2 (MAL2) is mainly involved in endocytosis under physiological conditions and mediates the transport of materials across the membranes of cell and organelle. It has been reported that MAL2 is significantly upregulated in diverse cancers. This study aimed to investigate the role of MAL2 in breast cancer (BC). METHODS Bioinformatics analysis and Immunohistochemical assay were applied to detect the correlation between MAL2 expression in breast cancer tissues and the prognosis of breast cancer patients. Functional experiments were carried out to investigate the role of MAL2 in vitro and in vivo. The molecular mechanisms involved in MAL2-induced β-catenin and c-Myc expression and β-catenin/c-Myc-mediated enhancement of BC progression were confirmed by western blot, β-catenin inhibitor and agonist, Co-IP and immunofluorescence colocalization assays. RESULTS Results from the cancer genome atlas (TCGA) and clinical samples confirmed a significant upregulation of MAL2 in BC tissues than in adjacent non-tumor tissues. High expression of MAL2 was associated with worse prognosis. Functional experiments demonstrated that MAL2 knockdown reduced the migration and invasion associating with EMT, increased the apoptosis of BC cells in vitro and reduced the metastatic capacity in vivo. Mechanistically, MAL2 interacts with β-catenin in BC cells. MAL2 silencing reduced the expression of β-catenin and c-Myc, while the β-catenin agonist SKL2001 partially rescued the downregulation of c-Myc and inhibition of migration and invasion caused by MAL2 knockdown in BC cells. CONCLUSION These observations provided evidence that MAL2 acted as a potential tumor promoter by regulating EMT and β-catenin/c-Myc axis, suggesting potential implications for anti-metastatic therapy for BC.
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Affiliation(s)
- Lijun An
- Department of Immunology, Basic Medical College, Guizhou Medical University, Dongqing Road, Guian New District, Guiyang, Guizhou, 550004, China
| | - Huiyuan Gong
- Department of Immunology, Basic Medical College, Guizhou Medical University, Dongqing Road, Guian New District, Guiyang, Guizhou, 550004, China
| | - Xiaojing Yu
- Department of Immunology, Basic Medical College, Guizhou Medical University, Dongqing Road, Guian New District, Guiyang, Guizhou, 550004, China
| | - Wangming Zhang
- Department of Immunology, Basic Medical College, Guizhou Medical University, Dongqing Road, Guian New District, Guiyang, Guizhou, 550004, China
| | - Xiaohua Liu
- Department of Immunology, Basic Medical College, Guizhou Medical University, Dongqing Road, Guian New District, Guiyang, Guizhou, 550004, China
| | - Xiaomin Yang
- Department of Immunology, Basic Medical College, Guizhou Medical University, Dongqing Road, Guian New District, Guiyang, Guizhou, 550004, China
| | - Liping Shu
- Department of Immunology, Basic Medical College, Guizhou Medical University, Dongqing Road, Guian New District, Guiyang, Guizhou, 550004, China
| | - Jielin Liu
- Department of Immunology, Basic Medical College, Guizhou Medical University, Dongqing Road, Guian New District, Guiyang, Guizhou, 550004, China
| | - Liuqi Yang
- Department of Immunology, Basic Medical College, Guizhou Medical University, Dongqing Road, Guian New District, Guiyang, Guizhou, 550004, China.
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2
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Applications of mass spectroscopy in understanding cancer proteomics. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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3
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Wani S, Humaira, Farooq I, Ali S, Rehman MU, Arafah A. Proteomic profiling and its applications in cancer research. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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4
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Zhou X, Zhang Q, Liang G, Liang X, Luo B. Overexpression of HMGB3 and its prognostic value in breast cancer. Front Oncol 2022; 12:1048921. [PMID: 36620553 PMCID: PMC9815698 DOI: 10.3389/fonc.2022.1048921] [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: 09/20/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Background High mobility group protein B3 (HMGB3) is abundantly expressed in a number of malignancies, contributing to tumor cell growth and predicting poor outcomes. More research on the connection between HMGB3 and breast cancer is needed. The prognostic significance of HMGB3 in breast cancer was examined and validated in this study. Methods Using The Cancer Genome Atlas (TCGA) database RNA sequencing and clinical data, we investigated the associations between HMGB3 expression and tumor mutations, prognosis, and immune infiltration in breast cancer. The Gene Expression Profiling Interactive Analysis (GEPIA), Tumor Immune Estimation Resource (TIMER), breast cancer gene-expression miner (bc-GenExMiner), UALCAN, OncoLnc, cBio Cancer Genomics Portal (cBioPortal), and LinkedOmics databases were applied to examine the levels of expression, mutation, coexpression, and immune correlation of HMGB3 in breast cancer. cBioPortal and the Database for Annotation, Visualization, and Integrated Discovery (DAVID) were used for coexpression and enrichment analyses, respectively. Experimental tests and a separate cohort of breast cancer patients in our center were used for validation. To determine independent risk factors affecting breast carcinoma prognosis, multivariate Cox regression analysis was performed. The Kaplan-Meier method was applied to analyze the connection between HMGB3 expression and overall survival time in breast cancer. Results Pan-cancer investigation using the GEPIA and UALCAN databases revealed a high level of HMGB3 expression in different malignancies, including breast cancer. HMGB3 might be a potential diagnostic biomarker, according to the receiver operating characteristic (ROC) curve (AUC=0.932). And immunohistochemistry confirmed higher HMGB3 protein expression in breast cancer tissues in clinical samples. Experimental tests also showed that breast cancer cells have higher expression of HMGB3, and knockdown of HMGB3 can promote the proliferation of breast cancer cells and increase sensitivity to chemotherapy. Human epidermal growth factor receptor 2 (HER2), Nottingham Prognostic Index (NPI), basal-like status, nodal status (N+), triple-negative status, and Scarff-Bloom-Richardson (SBR) grade all showed positive correlations with HMGB3 expression. Conversely, HMGB3 expression was negatively associated with the expression of estrogen receptor (ER) and progesterone receptor (PR) in breast cancer. Breast cancer patients with high HMGB3 expression had poor overall survival, which was validated by an analysis of a separate cohort of breast cancer patients in our center. Cox regression analysis identified high HMGB3 expression as an independently associated risk factor for breast carcinoma. The amount of immunological infiltration was substantially linked with the high expression of HMGB3. The chromosome centromeric region, ATPase activity, and the cell cycle are critical areas where HMGB3 is involved, according to enrichment analysis. Therefore, we suspected that HMGB3 might be a potential biomarker for detecting and treating breast carcinoma. Conclusion Breast cancer tissues had higher HMGB3 expression than normal breast tissues. HMGB3 overexpression may serve as an indicator for poor breast cancer outcomes.
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Affiliation(s)
- Xiaomei Zhou
- Department of Radiotherapy Center, Hubei Cancer Hospital, The Seventh Clinical School Affiliated of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qu Zhang
- Department of Radiotherapy Center, Hubei Cancer Hospital, The Seventh Clinical School Affiliated of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gai Liang
- Department of Radiotherapy Center, Hubei Cancer Hospital, The Seventh Clinical School Affiliated of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinjun Liang
- Department of Abdominal Oncology, Hubei Cancer Hospital, The Seventh Clinical School Affiliated of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Luo
- Department of Radiotherapy Center, Hubei Cancer Hospital, The Seventh Clinical School Affiliated of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,*Correspondence: Bo Luo,
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5
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Tuli HS, Garg VK, Bhushan S, Uttam V, Sharma U, Jain A, Sak K, Yadav V, Lorenzo JM, Dhama K, Behl T, Sethi G. Natural flavonoids exhibit potent anticancer activity by targeting microRNAs in cancer: A signature step hinting towards clinical perfection. Transl Oncol 2022; 27:101596. [PMID: 36473401 PMCID: PMC9727168 DOI: 10.1016/j.tranon.2022.101596] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/15/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer prevalence and its rate of incidence are constantly rising since the past few decades. Owing to the toxicity of present-day antineoplastic drugs, it is imperative to explore safer and more effective molecules to combat and/or prevent this dreaded disease. Flavonoids, a class of polyphenols, have exhibited multifaceted implications against several diseases including cancer, without showing significant toxicity towards the normal cells. Shredded pieces of evidence suggest that flavonoids can enhance drug sensitivity and suppress proliferation, metastasis, and angiogenesis of cancer cells by modulating several oncogenic or oncosuppressor microRNAs (miRNAs, miRs). They play pivotal roles in regulation of various biological and pathological processes, including various cancers. In the present review, the structure, chemistry and miR targeting efficacy of quercetin, luteolin, silibinin, genistein, epigallocatechin gallate, and cyanidin against several cancer types are comprehensively discussed. miRs are considered as next-generation medicine of recent times, and their targeting by naturally occurring flavonoids in cancer cells could be deemed as a signature step. We anticipate that our compilations related to miRNA-mediated regulation of cancer cells by flavonoids might catapult the clinical investigations and affirmation in the future.
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Affiliation(s)
- Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Vivek Kumar Garg
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Sakshi Bhushan
- Department of Botany, Central University Jammu, Jammu and Kashmir 181143, India
| | - Vivek Uttam
- Department of Zoology, Central University of Punjab, Village-Ghudda, Punjab 151401, India
| | - Uttam Sharma
- Department of Zoology, Central University of Punjab, Village-Ghudda, Punjab 151401, India
| | - Aklank Jain
- Department of Zoology, Central University of Punjab, Village-Ghudda, Punjab 151401, India
| | | | - Vikas Yadav
- Department of Translational Medicine, Clinical Research Centre, Skåne University Hospital, Lund University, SE-20213 Malmö, Sweden
| | - Jose M. Lorenzo
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, Ourense 32900, Spain,Universidade de Vigo, Área de Tecnología de los Alimentos, Facultad de Ciencias de Ourense, 32004 Ourense, Spain
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh 243122, India
| | - Tapan Behl
- Department of Pharmacology, School of Health Sciences & Technology (SoHST), University of Petroleum and Energy Studies, Bidholi, Dehradun, Uttarakhand 248007, India,Corresponding authors.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore,Corresponding authors.
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Chen C, Wang K, Luo L. AuNPs and 2D functional nanomaterial-assisted SPR development for the cancer detection: a critical review. Cancer Nanotechnol 2022. [DOI: 10.1186/s12645-022-00138-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractCancer ranks as a leading cause of death and a huge obstacle to rising life expectancy. If cancers are spotted early there's a high chance of survival. The conventional methods relying on the phenotypic features of the tumor are not powerful to the early screening of cancer. Cancer biomarkers are capable of indicating specific cancer states. Current biochemical assay suffers from time and reagents consuming and discontinuous monitoring. Surface plasmon resonance (SPR) technology, a refractive index-based optical biosensor, has significant promise in biomarker detection because of its outstanding features of label-free, sensitivity, and reliability. The nanomaterial features exotic physical and chemical property work on the process of transferring biorecognition event into SPR signal and hence is functioned as signal enhancer. In this review, we mainly discussed the mechanism of gold nanoparticles (AuNPs) and two-dimensional (2D) functional nanomaterial for improving the SPR signal. We also introduced AuNPs and 2D nanomaterial assisted SPR technology in determining cancer biomarker. Last but not least, we discussed the challenges and outlooks of the aforementioned reformative SPR technology for cancer biomarker determination in the clinical trial.
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7
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Jiang Q, Tan XP, Zhang CH, Li ZY, Li D, Xu Y, Liu YX, Wang L, Ma Z. Non-Coding RNAs of Extracellular Vesicles: Key Players in Organ-Specific Metastasis and Clinical Implications. Cancers (Basel) 2022; 14:cancers14225693. [PMID: 36428785 PMCID: PMC9688215 DOI: 10.3390/cancers14225693] [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: 10/21/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Extracellular vesicles (EVs) are heterogeneous membrane-encapsulated vesicles released by most cells. They act as multifunctional regulators of intercellular communication by delivering bioactive molecules, including non-coding RNAs (ncRNAs). Metastasis is a major cause of cancer-related death. Most cancer cells disseminate and colonize a specific target organ via EVs, a process known as "organ-specific metastasis". Mounting evidence has shown that EVs are enriched with ncRNAs, and various EV-ncRNAs derived from tumor cells influence organ-specific metastasis via different mechanisms. Due to the tissue-specific expression of EV-ncRNAs, they could be used as potential biomarkers and therapeutic targets for the treatment of tumor metastasis in various types of cancer. In this review, we have discussed the underlying mechanisms of EV-delivered ncRNAs in the most common organ-specific metastases of liver, bone, lung, brain, and lymph nodes. Moreover, we summarize the potential clinical applications of EV-ncRNAs in organ-specific metastasis to fill the gap between benches and bedsides.
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Affiliation(s)
- Qian Jiang
- Department of Gastroenterology, First Affiliated Hospital of Yangtze University, Health Science Center, Yangtze University, Jingzhou 434023, China
- Digestive Disease Research Institution of Yangtze University, Yangtze University, Jingzhou 434023, China
- Department of Cardiovascular Medicine, Honghu Hospital of Traditional Chinese Medicine, Honghu 433200, China
| | - Xiao-Ping Tan
- Department of Gastroenterology, First Affiliated Hospital of Yangtze University, Health Science Center, Yangtze University, Jingzhou 434023, China
- Digestive Disease Research Institution of Yangtze University, Yangtze University, Jingzhou 434023, China
| | - Cai-Hua Zhang
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou 434023, China
| | - Zhi-Yuan Li
- Department of Cardiovascular Medicine, Honghu Hospital of Traditional Chinese Medicine, Honghu 433200, China
| | - Du Li
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou 434023, China
| | - Yan Xu
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou 434023, China
| | - Yu Xuan Liu
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Lingzhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore
- Correspondence: (Z.M.); (L.W.)
| | - Zhaowu Ma
- Department of Gastroenterology, First Affiliated Hospital of Yangtze University, Health Science Center, Yangtze University, Jingzhou 434023, China
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou 434023, China
- Correspondence: (Z.M.); (L.W.)
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8
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Shansky Y, Bespyatykh J. Bile Acids: Physiological Activity and Perspectives of Using in Clinical and Laboratory Diagnostics. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227830. [PMID: 36431930 PMCID: PMC9692537 DOI: 10.3390/molecules27227830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Bile acids play a significant role in the digestion of nutrients. In addition, bile acids perform a signaling function through their blood-circulating fraction. They regulate the activity of nuclear and membrane receptors, located in many tissues. The gut microbiota is an important factor influencing the effects of bile acids via enzymatic modification. Depending on the rate of healthy and pathogenic microbiota, a number of bile acids may support lipid and glucose homeostasis as well as shift to more toxic compounds participating in many pathological conditions. Thus, bile acids can be possible biomarkers of human pathology. However, the chemical structure of bile acids is similar and their analysis requires sensitive and specific methods of analysis. In this review, we provide information on the chemical structure and the biosynthesis of bile acids, their regulation, and their physiological role. In addition, the review describes the involvement of bile acids in various diseases of the digestive system, the approaches and challenges in the analysis of bile acids, and the prospects of their use in omics technologies.
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Affiliation(s)
- Yaroslav Shansky
- Department of Molecular Medicine, Center of Molecular Medicine and Diagnostics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str., 1a, 119435 Moscow, Russia
- Correspondence:
| | - Julia Bespyatykh
- Department of Molecular Medicine, Center of Molecular Medicine and Diagnostics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str., 1a, 119435 Moscow, Russia
- Department of Expertise in Doping and Drug Control, Mendeleev University of Chemical Technology of Russia, Miusskaya Square, 9, 125047 Moscow, Russia
- Department of Public Health and Health Care, Federal Scientific State Budgetary Institution «N.A. Semashko National Research Institute of Public Health», Vorontsovo Pole Str., 12-1, 105064 Moscow, Russia
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Schoffman H, Levin Y, Itzhaki-Alfia A, Tselekovits L, Gonen L, Vainer GW, Hout-Siloni G, Barshack I, Cohen ZR, Margalit N, Shahar T. Comparison of matched formalin-fixed paraffin embedded and fresh frozen meningioma tissue reveals bias in proteomic profiles. Proteomics 2022; 22:e2200085. [PMID: 36098096 DOI: 10.1002/pmic.202200085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/29/2022]
Abstract
Tissue biopsies are most commonly archived in a paraffin block following tissue fixation with formaldehyde (FFPE) or as fresh frozen tissue (FFT). While both methods preserve biological samples, little is known about how they affect the quantifiable proteome. We performed a 'bottom-up' proteomic analysis (N = 20) of short and long-term archived FFPE surgical samples of human meningiomas and compared them to matched FFT specimens. FFT facilitated a similar number of proteins assigned by MetaMorpheus compared with matched FFPE specimens (5378 vs. 5338 proteins, respectively (p = 0.053), regardless of archival time. However, marked differences in the proteome composition were apparent between FFPE and FFT specimens. Twenty-three percent of FFPE-derived peptides and 8% of FFT-derived peptides contained at least one chemical modification. Methylation and formylation were most prominent in FFPE-derived peptides (36% and 17% of modified FFPE peptides, respectively) while, most of phosphorylation and iron modifications appeared in FFT-derived peptides (p < 0.001). A mean 14% (± 2.9) of peptides identified in FFPE contained at least one modified Lysine residue. Importantly, larger proteins were significantly overrepresented in FFT specimens, while FFPE specimens were enriched with smaller proteins.
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Affiliation(s)
- Hanan Schoffman
- Laboratory of Molecular Neuro Oncology, Neurosurgery Department, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | | | - Lea Tselekovits
- Laboratory of Molecular Neuro Oncology, Neurosurgery Department, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Lior Gonen
- Neurosurgery Department, Shaare Zedek Medical Center, Hebrew University Medical School, Jerusalem, Israel
| | - Gilad Wolf Vainer
- Department of Pathology, Hadassah Hebrew University Medical School, Jerusalem, Israel
| | - Goni Hout-Siloni
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zvi R Cohen
- Department of Neurosurgery, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nevo Margalit
- Neurosurgery Department, Shaare Zedek Medical Center, Hebrew University Medical School, Jerusalem, Israel
| | - Tal Shahar
- Laboratory of Molecular Neuro Oncology, Neurosurgery Department, Shaare Zedek Medical Center, Jerusalem, Israel.,Neurosurgery Department, Shaare Zedek Medical Center, Hebrew University Medical School, Jerusalem, Israel
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10
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Guo Y, Li Q, Ren W, Wu H, Wang C, Li X, Xue B, Qiu Y, Zhang J, Chen J, Fang L. Quantitative Proteomics Reveals Down-Regulated Glycolysis/Gluconeogenesis in the Large-Duct Type Intrahepatic Cholangiocarcinoma. J Proteome Res 2022; 21:2504-2514. [PMID: 36066509 DOI: 10.1021/acs.jproteome.2c00472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a lethal hepatobiliary malignancy that arises from the epithelial cells of the intrahepatic bile ducts, accounting for approximately 10% of cholangiocarcinoma (CCA). According to the 2019 World Health Organization (WHO) classification of tumors of the digestive system, iCCA is divided into small-duct type (SD-type) and large-duct type (LD-type). However, it remains unknown which molecular events contribute to the disparity. To explore the proteomic characteristics of iCCA, we used an isobaric tag for relative and absolute quantitation (iTRAQ) based quantitative proteomics strategy to investigate stably dysregulated proteins in the SD-type and LD-type of iCCA tissues. Importantly, we found three glycolysis/gluconeogenesis-related enzymes, triosephosphate isomerize 1 (TPI1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and phosphoglycerate kinase 1 (PGK1), were significantly down-regulated in the LD-type iCCA, which were further confirmed by immunohistochemistry using tissue microarray. Moreover, we demonstrated that the knockdown of these three candidate proteins by siRNAs notably increased the ability of proliferation in two CCA cell lines (HuH28 and RBE), suggesting that effective down-regulation of the glycolysis/gluconeogenesis pathway might be an underlying novel mechanism contributing to the LD-type iCCA.
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Affiliation(s)
- Yan Guo
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Qi Li
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Wei Ren
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing 210008, China
| | - Hongyan Wu
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Chengzhi Wang
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Xinyu Li
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Bin Xue
- Core Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Yudong Qiu
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Jingzi Zhang
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Jun Chen
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Lei Fang
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
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11
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Luo H, Ge H. Application of Proteomics in the Discovery of Radiosensitive Cancer Biomarkers. Front Oncol 2022; 12:852791. [PMID: 35280744 PMCID: PMC8904368 DOI: 10.3389/fonc.2022.852791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/04/2022] [Indexed: 12/21/2022] Open
Abstract
Radiation therapy remains an important component of cancer treatment. Gene-encoded proteins were the actual executors of cellular functions. Proteomic was a novel technology that can systematically analysis protein composition and measure their levels of change, this was a high throughput method, and were the import tools in the post genomic era. In recent years, rapid progress of proteomic have been made in the study of cancer mechanism, diagnosis, and treatment. This article elaborates current advances and future directions of proteomics in the discovery of radiosensitive cancer biomarkers.
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Affiliation(s)
- Hui Luo
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong Ge
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
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12
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Wu Y, Chen H, Chen Y, Sun N, Deng C. Metal organic frameworks as advanced extraction adsorbents for separation and analysis in proteomics and environmental research. Sci China Chem 2022. [DOI: 10.1007/s11426-021-1195-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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13
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Wei S, Liu W, Xu M, Qin H, Liu C, Zhang R, Zhou S, Li E, Liu Z, Wang Q. Cathepsin F and Fibulin-1 as novel diagnostic biomarkers for brain metastasis of non-small cell lung cancer. Br J Cancer 2022; 126:1795-1805. [PMID: 35217799 PMCID: PMC9174239 DOI: 10.1038/s41416-022-01744-3] [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: 03/14/2021] [Revised: 01/14/2022] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
Background The lack of non-invasive methods for detection of early micro-metastasis is a major cause of the poor prognosis of non-small cell lung cancer (NSCLC) brain metastasis (BM) patients. Herein, we aimed to identify circulating biomarkers based on proteomics for the early diagnosis and monitoring of patients with NSCLC BM. Methods Upregulated proteins were detected by secretory proteomics in the animal-derived high brain metastatic lung cancer cell line. A well-designed study composed of three independent cohorts was then performed to verify these blood-based protein biomarkers: the serum discovery and verification cohorts (n = 80; n = 459), and the tissue verification cohort (n = 76). Logistic regression was used to develop a diagnostic biomarker panel. Model validation cohort (n = 160) was used to verify the stability of the constructed predictive model. Changes in serum Cathepsin F (CTSF) levels of patients were tracked to monitor the treatment response. Progression-free survival (PFS) and overall survival (OS) were analysed to assess their prognostic relevance. Results CTSF and Fibulin-1 (FBLN1) levels were specifically upregulated in sera and tissues of patients with NSCLC BM compared with NSCLC without BM and primary brain tumour. The combined diagnostic performance of CTSF and FBLN1 was superior to their individual ones. CTSF serum changes were found to reflect the therapeutic response of patients with NSCLC BM and the trends of progression were detected earlier than the magnetic resonance imaging changes. Elevated expression of CTSF in NSCLC BM tissues was associated with poor PFS, and was found to be an independent prognostic factor. Conclusions We report a novel blood-based biomarker panel for early diagnosis, monitoring of therapeutic response, and prognostic evaluation of patients with NSCLC BM.
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Affiliation(s)
- Song Wei
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China.,Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Wenwen Liu
- Cancer Translational Medicine Research Center, The Second Hospital, Dalian Medical University, Dalian, China
| | - Mingxin Xu
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
| | - Huamin Qin
- Department of Pathology, The Second Hospital, Dalian Medical University, Dalian, China
| | - Chang Liu
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
| | - Rui Zhang
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
| | - Sihai Zhou
- Department of Urology Surgery, The Second Hospital, Dalian Medical University, Dalian, China
| | - Encheng Li
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China.
| | - Zhiyu Liu
- Department of Urology Surgery, The Second Hospital, Dalian Medical University, Dalian, China.
| | - Qi Wang
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China. .,Cancer Translational Medicine Research Center, The Second Hospital, Dalian Medical University, Dalian, China.
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14
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Guo Z, Jin B, Fang Y, Deng Y, Chen Z, Chen H, Li S, Leung P, Wang H, Cai L, He N. Selected aptamer specially combing 5-8F cells based on automatic screening instrument. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.01.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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An electrochemical aptasensor for highly sensitive detection of CEA based on exonuclease III and hybrid chain reaction dual signal amplification. Bioelectrochemistry 2021; 143:107986. [PMID: 34735912 DOI: 10.1016/j.bioelechem.2021.107986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 12/11/2022]
Abstract
At present, carcinoembryonic antigen (CEA) is considered a broad-spectrum cancer biomarker, and its accurate analysis in clinical samples can assist early cancer diagnosis and treatment. Herein, a novel electrochemical aptasensor has been proposed for CEA detection based on exonuclease III and hybrid chain reaction. The target CEA specifically binds to the aptamer region in hairpin probe 1 (defined as H1) by strong attraction, which leads the rest of the H1 triggering catalytic hairpin assembly to form a high quantity of H1 and hairpin probe 2 (defined as H2) double chain complex (denoted as H1@H2). Subsequently, the exonuclease III digests the complex of H1@H2 and liberates H1 to induce the first signal amplification. Simultaneously, a large number of generated trigger chains initiate a hybrid chain reaction and produce a second signal amplification. This proposed sensor exhibited excellent analytical performance for the detection of CEA, with wide linear range from 10 pg.mL-1 to 100 ng.mL-1 and low limit of detection of 0.84 pg.mL-1. Additionally, the biosensing strategy was successfully verified for direct measurement of CEA in human serum. Therefore, this elaborated sensor provides a new simple method for detecting CEA and exhibits great promise in the early screening of cancer.
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16
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Overexpression of MAL2 Correlates with Immune Infiltration and Poor Prognosis in Breast Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:5557873. [PMID: 34567213 PMCID: PMC8457941 DOI: 10.1155/2021/5557873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/07/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022]
Abstract
Background Myelin and lymphocyte, T cell differentiation protein 2 (MAL2) is highly expressed in various cancers and associated with the development and prognosis of cancer. However, the relationship between MAL2 and breast cancer requires further investigation. This study aimed to explore the prognostic significance of MAL2 in breast cancer. Methods MAL2 expression was initially assessed using the Oncomine database and The Cancer Genome Atlas (TCGA) database and verified by quantitative real-time polymerase chain reaction (RT-qPCR). The chi-square test or Fisher's exact test was used to explore the association between clinical characteristics and MAL2 expression. The prognostic value of MAL2 in breast cancer was assessed by the Kaplan–Meier method and Cox regression analysis. Gene set enrichment analysis (GSEA) was performed to identify the biological pathways correlated with MAL2 expression in breast cancer. Besides, a single-sample GSEA (ssGSEA) was used to assess the relationship between the level of immune infiltration and MAL2 in breast cancer. Results Both bioinformatics and RT-qPCR results showed that MAL2 was expressed at high levels in breast cancer tissues compared with the adjacent tissues. The chi-square test or Fisher's exact test indicated that MAL2 expression was related to stage, M classification, and vital status. Kaplan–Meier curves implicated that high MAL2 expression was significantly associated with the poor prognosis. Cox regression models showed that high MAL2 expression could be an independent risk factor for breast cancer. GSEA showed that 14 signaling pathways were enriched in the high-MAL2-expression group. Besides, the MAL2 expression level negatively correlated with infiltrating levels of eosinophils and plasmacytoid dendritic cells in breast cancer. Conclusion Overexpression of MAL2 correlates with poor prognosis and lower immune infiltrating levels of eosinophils and plasmacytoid dendritic cells in breast cancer and may become a biomarker for breast cancer prognosis.
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17
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Erozenci LA, Piersma SR, Pham TV, Bijnsdorp IV, Jimenez CR. Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals. Sci Rep 2021; 11:15629. [PMID: 34341426 PMCID: PMC8329217 DOI: 10.1038/s41598-021-95082-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The protein content of urinary extracellular vesicles (EVs) is considered to be an attractive non-invasive biomarker source. However, little is known about the consistency and variability of urinary EV proteins within and between individuals over a longer time-period. Here, we evaluated the stability of the urinary EV proteomes of 8 healthy individuals at 9 timepoints over 6 months using data-independent-acquisition mass spectrometry. The 1802 identified proteins had a high correlation amongst all samples, with 40% of the proteome detected in every sample and 90% detected in more than 1 individual at all timepoints. Unsupervised analysis of top 10% most variable proteins yielded person-specific profiles. The core EV-protein-interaction network of 516 proteins detected in all measured samples revealed sub-clusters involved in the biological processes of G-protein signaling, cytoskeletal transport, cellular energy metabolism and immunity. Furthermore, gender-specific expression patterns were detected in the urinary EV proteome. Our findings indicate that the urinary EV proteome is stable in longitudinal samples of healthy subjects over a prolonged time-period, further underscoring its potential for reliable non-invasive diagnostic/prognostic biomarkers.
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Affiliation(s)
- Leyla A. Erozenci
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands ,grid.509540.d0000 0004 6880 3010Department of Urology, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Sander R. Piersma
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Thang V. Pham
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Irene V. Bijnsdorp
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands ,grid.509540.d0000 0004 6880 3010Department of Urology, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Connie R. Jimenez
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
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18
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Bickner AN, Champion MM, Hummon AB, Bruening ML. Electroblotting through a tryptic membrane for LC-MS/MS analysis of proteins separated in electrophoretic gels. Analyst 2021; 145:7724-7735. [PMID: 33000802 DOI: 10.1039/d0an01380c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Digestion of proteins separated via sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) remains a popular method for protein identification using mass-spectrometry based proteomics. Although robust and routine, the in-gel digestion procedure is laborious and time-consuming. Electroblotting to a capture membrane prior to digestion reduces preparation steps but requires on-membrane digestion that yields fewer peptides than in-gel digestion. This paper develops direct electroblotting through a trypsin-containing membrane to a capture membrane to simplify extraction and digestion of proteins separated by SDS-PAGE. Subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) identifies the extracted peptides. Analysis of peptides from different capture membrane pieces shows that electrodigestion does not greatly disturb the spatial resolution of a standard protein mixture separated by SDS-PAGE. Electrodigestion of an Escherichia coli (E. coli) cell lysate requires four hours of total sample preparation and results in only 13% fewer protein identifications than in-gel digestion, which can take 24 h. Compared to simple electroblotting and protein digestion on a poly(vinylidene difluoride) (PVDF) capture membrane, adding a trypsin membrane to the electroblot increases the number of protein identifications by 22%. Additionally, electrodigestion experiments using capture membranes coated with polyelectrolyte layers identify a higher fraction of small proteolytic peptides than capture on PVDF or in-gel digestion.
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Affiliation(s)
- A N Bickner
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, Indiana 46556, USA.
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Bian J, Sze YH, Tse DYY, To CH, McFadden SA, Lam CSY, Li KK, Lam TC. SWATH Based Quantitative Proteomics Reveals Significant Lipid Metabolism in Early Myopic Guinea Pig Retina. Int J Mol Sci 2021; 22:4721. [PMID: 33946922 PMCID: PMC8124159 DOI: 10.3390/ijms22094721] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
Most of the previous myopic animal studies employed a single-candidate approach and lower resolution proteomics approaches that were difficult to detect minor changes, and generated limited systems-wide biological information. Hence, a complete picture of molecular events in the retina involving myopic development is lacking. Here, to investigate comprehensive retinal protein alternations and underlying molecular events in the early myopic stage, we performed a data-independent Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) based proteomic analysis coupled with different bioinformatics tools in pigmented guinea pigs after 4-day lens-induced myopia (LIM). Myopic eyes compared to untreated contralateral control eyes caused significant changes in refractive error and choroid thickness (p < 0.05, n = 5). Relative elongation of axial length and the vitreous chamber depth were also observed. Using pooled samples from all individuals (n = 10) to build a species-specific retinal ion library for SWATH analysis, 3202 non-redundant proteins (with 24,616 peptides) were identified at 1% global FDR. For quantitative analysis, the 10 individual retinal samples (5 pairs) were analyzed using a high resolution Triple-TOF 6600 mass spectrometry (MS) with technical replicates. In total, 37 up-regulated and 21 down-regulated proteins were found significantly changed after LIM treatment (log2 ratio (T/C) > 0.26 or < -0.26; p ≤ 0.05). Data are accepted via ProteomeXchange with identifier PXD025003. Through Ingenuity Pathways Analysis (IPA), "lipid metabolism" was found as the top function associated with the differentially expressed proteins. Based on the protein abundance and peptide sequences, expression patterns of two regulated proteins (SLC6A6 and PTGES2) identified in this pathway were further successfully validated with high confidence (p < 0.05) using a novel Multiple Reaction Monitoring (MRM) assay on a QTRAP 6500+ MS. In summary, through an integrated discovery and targeted proteomic approach, this study serves as the first report to detect and confirm novel retinal protein changes and significant biological functions in the early LIM mammalian guinea pigs. The study provides new workflow and insights for further research to myopia control.
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Affiliation(s)
- Jingfang Bian
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Ying-Hon Sze
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Dennis Yan-Yin Tse
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Chi-Ho To
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Sally A. McFadden
- School of Psychology, College of Engineering, Science and the Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Carly Siu-Yin Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - King-Kit Li
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Thomas Chuen Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen 518052, China
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Chen CJ, Chou CY, Shu KH, Chen HC, Wang MC, Chang CC, Hsu BG, Wu MS, Yang YL, Liao WL, Yang C, Hsiao YT, Huang CC. Discovery of Novel Protein Biomarkers in Urine for Diagnosis of Urothelial Cancer Using iTRAQ Proteomics. J Proteome Res 2021; 20:2953-2963. [PMID: 33780252 DOI: 10.1021/acs.jproteome.1c00164] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Urothelial carcinoma (UC) is the ninth most prevalent malignancy worldwide. Noninvasive and efficient biomarkers with high accuracy are imperative for the surveillance and diagnosis of UC. CKD patients were enrolled as a control group in this study for the discovery of highly specific urinary protein markers of UC. An iTRAQ-labeled quantitative proteomic approach was used to discover novel potential markers. These markers were further validated with 501 samples by ELISA assay, and their diagnostic accuracies were compared to those of other reported UC markers. BRDT, CYBP, GARS, and HDGF were identified as novel urinary UC biomarkers with a high discrimination ability in a population comprising CKD and healthy subjects. The diagnostic values of the four novel UC markers were better than that of a panel of well-known or FDA-approved urinary protein markers CYFR21.1, Midkine, and NUMA1. Three of our discovered markers (BRDT, HDGF, GARS) and one well-known marker (CYFR21.1) were finally selected and combined as a marker panel having AUC values of 0.962 (95% CI, 0.94-0.98) and 0.860 (95% CI, 0.83-0.89) for the discrimination between UC and normal groups and UC and control (healthy + CKD) groups, respectively.
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Affiliation(s)
- Chao-Jung Chen
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 404333, Taiwan.,Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404332, Taiwan
| | - Che-Yi Chou
- Department of Internal Medicine, Asia University Hospital, Taichung 41354, Taiwan.,Department of Post-baccalaureate Veterinary Medicine, Asia University, Taichung, Taiwan.,Division of Nephrology, China Medical University Hospital, Taichung 404332, Taiwan
| | - Kuo-Hsiung Shu
- Division of Nephrology, Lin Shin Hospital, Taichung 40867, Taiwan
| | - Hung-Chun Chen
- Division of Nephrology, Kaohsiung Medical University and Hospitals, Kaohsiung 80708, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Cheng Kung University Hospital, Tainan 70403, Taiwan
| | - Chia-Chu Chang
- Department of Internal Medicine, Kuang Tien General Hospital, Taichung 43303, Taiwan
| | - Bang-Gee Hsu
- Division of Nephrology, Buddhist Tzu Chi General Hospital, Hualien 43303, Taiwan
| | - Mai-Szu Wu
- Division of Nephrology, Taipei Medical University and Hospitals, Taipei 110, Taiwan
| | - Yuan-Lung Yang
- Division of Urology, St. Mary's Hospital, Yilan 26546, Taiwan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 404333, Taiwan.,Center for Personalized Medicine, China Medical University Hospital, Taichung 404332, Taiwan
| | - Chieh Yang
- Division of Nephrology and the Kidney Institute, Department of Internal Medicine, China Medical University and Hospitals, Taichung 404332, Taiwan
| | - Yu-Tien Hsiao
- Division of Nephrology and the Kidney Institute, Department of Internal Medicine, China Medical University and Hospitals, Taichung 404332, Taiwan
| | - Chiu-Ching Huang
- Division of Nephrology and the Kidney Institute, Department of Internal Medicine, China Medical University and Hospitals, Taichung 404332, Taiwan
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Orfanou IM, Argyros O, Papapetropoulos A, Tseleni-Balafouta S, Vougas K, Tamvakopoulos C. Discovery and Pharmacological Evaluation of STEAP4 as a Novel Target for HER2 Overexpressing Breast Cancer. Front Oncol 2021; 11:608201. [PMID: 33842315 PMCID: PMC8034292 DOI: 10.3389/fonc.2021.608201] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 03/08/2021] [Indexed: 01/11/2023] Open
Abstract
Breast cancer (BC) is a highly heterogeneous disease encompassing multiple subtypes with different molecular and histopathological features, disease prognosis, and therapeutic responses. Among these, the Triple Negative BC form (TNBC) is an aggressive subtype with poor prognosis and therapeutic outcome. With respect to HER2 overexpressing BC, although advanced targeted therapies have improved the survival of patients, disease relapse and metastasis remains a challenge for therapeutic efficacy. In this study the aim was to identify key membrane-associated proteins which are overexpressed in these aggressive BC subtypes and can serve as potential biomarkers or drug targets. We leveraged on the development of a membrane enrichment protocol in combination with the global profiling GeLC-MS/MS technique, and compared the proteomic profiles of a HER2 overexpressing (HCC-1954) and a TNBC (MDA-MB-231) cell line with that of a benign control breast cell line (MCF-10A). An average of 2300 proteins were identified from each cell line, of which approximately 600 were membrane-associated proteins. Our global proteomic methodology in tandem with invigoration by Western blot and Immunofluorescence analysis, readily detected several previously-established BC receptors like HER2 and EPHA2, but importantly STEAP4 and CD97 emerged as novel potential candidate markers. This is the first time that the mitochondrial iron reductase STEAP4 protein up-regulation is linked to BC (HER2+ subtype), while for CD97, its role in BC has been previously described, but never before by a global proteomic technology in TNBC. STEAP4 was selected for further detailed evaluation by the employment of Immunohistochemical analysis of BC xenografts and clinical tissue microarray studies. Results showed that STEAP4 expression was evident only in malignant breast tissues whereas all the benign breast cases had no detectable levels. A functional role of STEAP4 intervention was established in HER2 overexpressing BC by pharmacological studies, where blockage of the STEAP4 pathway with an iron chelator (Deferiprone) in combination with the HER2 inhibitor Lapatinib led to a significant reduction in cell growth in vitro. Furthermore, siRNA mediated knockdown of STEAP4 also suppressed cell proliferation and enhanced the inhibition of Lapatinib in HER2 overexpressing BC, confirming its potential oncogenic role in BC. In conclusion, STEAP4 may represent a novel BC related biomarker and a potential pharmacological target for the treatment of HER2 overexpressing BC.
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Affiliation(s)
- Ioanna-Maria Orfanou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Orestis Argyros
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Andreas Papapetropoulos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Sofia Tseleni-Balafouta
- Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Vougas
- Proteomics Laboratory, Division of Biotechnology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Constantin Tamvakopoulos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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22
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Sarbu M, Clemmer DE, Zamfir AD. Ion mobility mass spectrometry of human melanoma gangliosides. Biochimie 2020; 177:226-237. [DOI: 10.1016/j.biochi.2020.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/05/2020] [Accepted: 08/18/2020] [Indexed: 02/09/2023]
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Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer. Cancers (Basel) 2020; 12:cancers12092428. [PMID: 32867043 PMCID: PMC7564506 DOI: 10.3390/cancers12092428] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The traditional approach in identifying cancer related protein biomarkers has focused on evaluation of a single peptide/protein in tissue or circulation. At best, this approach has had limited success for clinical applications, since multiple pathological tumor pathways may be involved during initiation or progression of cancer which diminishes the significance of a single candidate protein/peptide. Emerging sensitive proteomic based technologies like liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics can provide a platform for evaluating serial serum or plasma samples to interrogate secreted products of tumor–host interactions, thereby revealing a more “complete” repertoire of biological variables encompassing heterogeneous tumor biology. However, several challenges need to be met for successful application of serum/plasma based proteomics. These include uniform pre-analyte processing of specimens, sensitive and specific proteomic analytical platforms and adequate attention to study design during discovery phase followed by validation of discovery-level signatures for prognostic, predictive, and diagnostic cancer biomarker applications. Abstract Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding disease mechanisms, although several challenges will have to be met. Serum/plasma proteome biomarkers are present in very low abundance, and there is high complexity involved due to the heterogeneity of cancers, for which there is a compelling need to develop sensitive and specific proteomic technologies and analytical platforms. To date, liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics has been a dominant analytical workflow to discover new potential cancer biomarkers in serum/plasma. This review will summarize the opportunities of serum proteomics for clinical applications; the challenges in the discovery of novel biomarkers in serum/plasma; and current proteomic strategies in cancer research for the application of serum/plasma proteomics for clinical prognostic, predictive, and diagnostic applications, as well as for monitoring minimal residual disease after treatments. We will highlight some of the recent advances in MS-based proteomics technologies with appropriate sample collection, processing uniformity, study design, and data analysis, focusing on how these integrated workflows can identify novel potential cancer biomarkers for clinical applications.
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Bai Y, Zhang H, Zhao L, Wang Y, Chen X, Zhai H, Tian M, Zhao R, Wang T, Xu H, Feng F. A novel aptasensor based on HCR and G-quadruplex DNAzyme for fluorescence detection of Carcinoembryonic Antigen. Talanta 2020; 221:121451. [PMID: 33076074 DOI: 10.1016/j.talanta.2020.121451] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/15/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022]
Abstract
In this paper, a rationally designed aptasensing platform based on Hybridization Chain Reaction (HCR) and G-quadruplex DNAzyme for the fluorescence detection of Carcinoembryonic Antigen (CEA) has been developed. In the presence of target CEA, the aptamer sequence in Aptamer Probe (AP) specifically bound to CEA, resulting in the AP conformation change and thus releasing initiator, which triggered the autonomous cross-opening of Hairpin 1 (H1) and Hairpin 2 (H2) that yielded extended nicked double-stranded DNA via HCR. Upon the addition of hemin, G-rich segments at the end of H1 and H2 self-assembled into the peroxidase-mimicking hemin/G-quadruplex DNAzymes, which catalyzed the hydrogen peroxide-mediated oxidation of thiamine to achieve fluorescence detection of CEA. The HCR product, and the formation and catalytic performance of DNAzyme were characterized by agarose gel electrophoresis, UV-vis spectroscopy and fluorescence spectroscopy, respectively. Under optimal conditions, the fluorescent aptasensor showed a linear relationship ranging from 0.25 to 1.5 nM toward CEA with a detection limit of 0.2 nM. In addition, this aptasensor exhibited high selectivity for CEA without being affected by other interfering proteins, such as IgG, AFP and PSA. Furthermore, this proposed aptasensor was successfully applied to CEA analysis in diluted human serum samples. It is believed that this strategy has a promising potential in biochemical analysis and clinic application.
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Affiliation(s)
- Yunfeng Bai
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China.
| | - Huilin Zhang
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China; College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
| | - Lu Zhao
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Yuzhen Wang
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Xiaoliang Chen
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Hong Zhai
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Maozhong Tian
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Ruirui Zhao
- College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
| | - Tao Wang
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Hui Xu
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Feng Feng
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China; College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China.
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Sun J, Sun X. Recent advances in the construction of DNA nanostructure with signal amplification and ratiometric response for miRNA sensing and imaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115900] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Salerno C, Berardi G, Laera G, Pollice A. Functional Response of MBR Microbial Consortia to Substrate Stress as Revealed by Metaproteomics. MICROBIAL ECOLOGY 2019; 78:873-884. [PMID: 30976843 DOI: 10.1007/s00248-019-01360-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Bacterial consortia have a primary role in the biological degradations occurring in activated sludge for wastewater treatment, for their capacities to metabolize the polluting matter. Therefore, the knowledge of the main metabolic pathways for the degradation of pollutants becomes critical for a correct design and operation of wastewater treatment plants. The metabolic activity of the different bacterial groups in activated sludge is commonly investigated through respirometry. Furthermore, in the last years, the development of "omic" approaches has offered more opportunities to integrate or substitute the conventional microbiological assays and to deeply understand the taxonomy and dynamics of complex microbial consortia. In the present work, an experimental membrane bioreactor (MBR) was set up and operated for the treatment of municipal wastewater, and the effects of a sudden decrease of the organic supply on the activated sludge were investigated. Both respirometric and metaproteomic approaches revealed a resistance of autotrophic bacteria to the substrate stress, and particularly of nitrifying bacteria. Furthermore, metaproteomics allowed the identification of the taxonomy of the microbial consortium based on its protein expression, unveiling the prevalence of Sorangium and Nitrosomonas genera both before and after the organic load decrease. Moreover, it confirmed the results obtained through respirometry and revealed a general expression of proteins involved in metabolism and transport of nitrogen, or belonging to nitrifying species like Nitrosomonas europeae, Nitrosomonas sp. AL212, or Nitrospira defluvii.
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Affiliation(s)
- Carlo Salerno
- IRSA CNR, Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy.
| | - Giovanni Berardi
- IRSA CNR, Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy
| | - Giuseppe Laera
- IRSA CNR, Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy
| | - Alfieri Pollice
- IRSA CNR, Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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Diurnal variation of inflammatory plasma proteins involved in pain. Pain Rep 2019; 4:e776. [PMID: 31875183 PMCID: PMC6882578 DOI: 10.1097/pr9.0000000000000776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/19/2022] Open
Abstract
Supplemental Digital Content is Available in the Text. Introduction: Proteomics is a powerful approach for biochemical research because it directly studies the main functional components of biochemical systems. The understanding of the normal fluctuations of the proteome in health is essential to identify pain-specific biomarkers. Objective: To investigate fluctuations of the plasma proteome in healthy pain-free individuals. Methods: Blood samples were structurally collected in the early morning and evening from 10 clinically healthy individuals (26.3 ± 3.3 years). High abundant proteins were removed from plasma, and proteins were then analysed by nanoliquid chromatography combined with mass spectrometry. In addition, an assay of 71 cytokines/chemokines/growth factors was analysed. Results: Multivariate statistical analysis displayed that there were up to 64 proteins whose expression levels were significantly altered between the plasma samples collected during the morning and evening; no changes existed for the assay. The levels of 34 proteins were increased and 30 proteins were decreased during the evening compared with the morning sample. The increased proteins were involved in the biological processes such as protein activation cascade, complement activation, and stress response. The decreased proteins were involved in regulation of endopeptidase activity, inflammatory response, and protein metabolic processes. Conclusion: The circadian variations in the plasma proteome stress the need to collect blood samples of both patients and controls at a fixed time of the day. The results in this study might be useful for better understanding of the complexity of individual variation in the human plasma proteome over time and provide a baseline for improved pain biomarker discovery.
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Erozenci LA, Böttger F, Bijnsdorp IV, Jimenez CR. Urinary exosomal proteins as (pan‐)cancer biomarkers: insights from the proteome. FEBS Lett 2019; 593:1580-1597. [DOI: 10.1002/1873-3468.13487] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/31/2019] [Accepted: 06/05/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Leyla Ayse Erozenci
- Department of Medical Oncology Cancer Center Amsterdam Amsterdam UMC Vrije Universiteit Amsterdam The Netherlands
- OncoProteomics Laboratory Cancer Center Amsterdam Amsterdam UMC Vrije Universiteit Amsterdam The Netherlands
| | - Franziska Böttger
- Department of Medical Oncology Cancer Center Amsterdam Amsterdam UMC Vrije Universiteit Amsterdam The Netherlands
- OncoProteomics Laboratory Cancer Center Amsterdam Amsterdam UMC Vrije Universiteit Amsterdam The Netherlands
| | - Irene V. Bijnsdorp
- OncoProteomics Laboratory Cancer Center Amsterdam Amsterdam UMC Vrije Universiteit Amsterdam The Netherlands
- Department of Urology Amsterdam UMC Vrije Universiteit Amsterdam The Netherlands
| | - Connie R. Jimenez
- Department of Medical Oncology Cancer Center Amsterdam Amsterdam UMC Vrije Universiteit Amsterdam The Netherlands
- OncoProteomics Laboratory Cancer Center Amsterdam Amsterdam UMC Vrije Universiteit Amsterdam The Netherlands
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Umaña-Pérez YA, Calderón Rodriguez SI. Estudio proteómico 2DE-DIGE en plasma sanguíneo de pacientes en etapa infantil con leucemia linfoblástica aguda. REVISTA COLOMBIANA DE QUÍMICA 2019. [DOI: 10.15446/rev.colomb.quim.v48n1.75170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
En Colombia, durante la última década la leucemia linfoblástica aguda (LLA) ha sido el cáncer con mayor incidencia, siendo más del 40% de las muertes por cáncer en menores de edad atribuidas a esta enfermedad. Entre los factores que influyen en estas cifras, el diagnóstico tardío es tal vez el factor más sensible que afecta de manera negativa el éxito del tratamiento. Esta investigación se centró en el estudio del proteoma plasmático de niños colombianos diagnosticados con LLA tipo B, dada su alta incidencia, en comparación con controles en la búsqueda de proteínas que podrían tener potencialidad a ser clasificadas como biomarcadores de diagnóstico. Ahora bien, en vista de los avances en las herramientas proteómicas y de espectrometría de masas y sabiendo que son una alternativa para abordar la complejidad molecular de enfermedades como el cáncer, utilizamos una aproximación proteómica basada en una separación por electroforesis bidimensional diferencial (2DE-DIGE) con posterior separación por cromatografía líquida acoplada a espectrometría de masas en tándem. Se encontraron 8 proteínas con expresión diferencial en plasma de pacientes con LLA-B, entre las cuales resaltan la serotransferrina, la Alfa-1-antitripsina, la haptoglobina, la α2-glicoproteína de zinc y la complemento C3.
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Lin H, He QY, Shi L, Sleeman M, Baker MS, Nice EC. Proteomics and the microbiome: pitfalls and potential. Expert Rev Proteomics 2018; 16:501-511. [PMID: 30223687 DOI: 10.1080/14789450.2018.1523724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Human symbiotic microbiota are now known to play important roles in human health and disease. Significant progress in our understanding of the human microbiome has been driven by recent technological advances in the fields of genomics, transcriptomics, and proteomics. As a complementary method to metagenomics, proteomics is enabling detailed protein profiling of the microbiome to decipher its structure and function and to analyze its relationship with the human body. Fecal proteomics is being increasingly applied to discover and validate potential health and disease biomarkers, and Therapeutic Goods Administration (TGA)-approved instrumentation and a range of clinical assays are being developed that will collectively play key roles in advancing personalized medicine. Areas covered: This review will introduce the complexity of the microbiome and its role in health and disease (in particular the gastrointestinal tract or gut microbiome), discuss current genomic and proteomic methods for studying this system, including the discovery of potential biomarkers, and outline the development of clinically accepted protocols leading to personalized medicine. Expert commentary: Recognition of the important role the microbiome plays in both health and disease is driving current research in this key area. A proteogenomics approach will be essential to unravel the biologies underlying this complex network.
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Affiliation(s)
- Huafeng Lin
- a Department of Biotechnology , College of Life Science and Technology, Jinan University , Guangzhou , Guangdong , China.,b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Qing-Yu He
- c Institute of Life and Health Engineering, College of Life Science and Technology , Jinan University , Guangzhou , China
| | - Lei Shi
- b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Mark Sleeman
- d Biomedicine Discovery Institute , Monash University , Melbourne , Australia
| | - Mark S Baker
- e Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , Australia
| | - Edouard C Nice
- f Department of Biochemistry and Molecular Biology , Monash University , Melbourne , Victoria , Australia
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Gu Z, Li Y, Yang X, Yu M, Chen Z, Zhao C, Chen L, Wang L. Overexpression of CLC-3 is regulated by XRCC5 and is a poor prognostic biomarker for gastric cancer. J Hematol Oncol 2018; 11:115. [PMID: 30217218 PMCID: PMC6137920 DOI: 10.1186/s13045-018-0660-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/31/2018] [Indexed: 02/07/2023] Open
Abstract
Background Recently, many potential prognostic biomarkers for gastric cancer (GC) have been identified, but the prognosis of advanced GC patients remains poor. Chloride channels are promising cancer biomarkers, and their family member chloride channel-3 (CLC-3) is involved in multiple biological behaviors. However, whether CLC-3 is a prognostic biomarker for GC patients is rarely reported. The molecular mechanisms by which CLC-3 is regulated in GC are unclear. Methods The expression of CLC-3 and XRCC5 in human specimens was analyzed using immunohistochemistry. The primary biological functions and pathways related to CLC-3 were enriched by RNA sequencing. A 5′-biotin-labeled DNA probe with a promoter region between − 248 and + 226 was synthesized to pull down CLC-3 promoter-binding proteins. Functional studies were detected by MTS, clone formation, wound scratch, transwell, and xenograft mice model. Mechanistic studies were investigated by streptavidin-agarose-mediated DNA pull-down, mass spectrometry, ChIP, dual-luciferase reporter assay system, Co-IP, and immunofluorescence. Results The results showed that CLC-3 was overexpressed in human GC tissues and that overexpression of CLC-3 was a poor prognostic biomarker for GC patients (P = 0.012). Furthermore, higher expression of CLC-3 was correlated with deeper tumor invasion (P = 0.006) and increased lymph node metastasis (P = 0.016), and knockdown of CLC-3 inhibited cell proliferation and migration in vitro. In addition, X-ray repair cross-complementing 5 (XRCC5) was identified as a CLC-3 promoter-binding protein, and both CLC-3 (HR 1.671; 95% CI 1.012–2.758; P = 0.045) and XRCC5 (HR 1.795; 95% CI 1.076–2.994; P = 0.025) were prognostic factors of overall survival in GC patients. The in vitro and in vivo results showed that the expression and function of CLC-3 were inhibited after XRCC5 knockdown, and the inhibition effects were rescued by CLC-3 overexpression. Meanwhile, the expression and function of CLC-3 were promoted after XRCC5 overexpression, and the promotion effects were reversed by the CLC-3 knockdown. The mechanistic study revealed that knockdown of XRCC5 suppressed the binding of XRCC5 to the CLC-3 promoter and subsequent promoter activity, thus regulating CLC-3 expression at the transcriptional level by interacting with PARP1. Conclusions Our findings indicate that overexpression of CLC-3 is regulated by XRCC5 and is a poor prognostic biomarker for gastric cancer. Double targeting CLC-3 and XRCC5 may provide the promising therapeutic potential for GC treatment. Electronic supplementary material The online version of this article (10.1186/s13045-018-0660-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhuoyu Gu
- Department of Pharmacology, Medical College, Jinan University, Guangzhou, 510632, China.,Department of Pathophysiology, Medical College, Jinan University, Guangzhou, China
| | - Yixin Li
- Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xiaoya Yang
- Department of Pathophysiology, Medical College, Jinan University, Guangzhou, China.,Department of Physiology, Medical College, Jinan University, Guangzhou, 510632, China
| | - Meisheng Yu
- Department of Pharmacology, Medical College, Jinan University, Guangzhou, 510632, China.,Department of Pathophysiology, Medical College, Jinan University, Guangzhou, China
| | - Zhanru Chen
- Department of Physiology, Medical College, Jinan University, Guangzhou, 510632, China
| | - Chan Zhao
- Department of Physiology, Medical College, Jinan University, Guangzhou, 510632, China
| | - Lixin Chen
- Department of Pharmacology, Medical College, Jinan University, Guangzhou, 510632, China.
| | - Liwei Wang
- Department of Physiology, Medical College, Jinan University, Guangzhou, 510632, China.
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Latosinska A, Frantzi M, Merseburger AS, Mischak H. Promise and Implementation of Proteomic Prostate Cancer Biomarkers. Diagnostics (Basel) 2018; 8:diagnostics8030057. [PMID: 30158500 PMCID: PMC6174350 DOI: 10.3390/diagnostics8030057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/26/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022] Open
Abstract
Prostate cancer is one of the most commonly diagnosed malignancy and the fifth leading cause of cancer mortality in men. Despite the broad use of prostate-specific antigen test that resulted in an increase in number of diagnosed cases, disease management needs to be improved. Proteomic biomarkers alone and or in combination with clinical and pathological risk calculators are expected to improve on decreasing the unnecessary biopsies, stratify low risk patients, and predict response to treatment. To this end, significant efforts have been undertaken to identify novel biomarkers that can accurately discriminate between indolent and aggressive cancer forms and indicate those men at high risk for developing prostate cancer that require immediate treatment. In the era of “big data” and “personalized medicine” proteomics-based biomarkers hold great promise to provide clinically applicable tools, as proteins regulate all biological functions, and integrate genomic information with the environmental impact. In this review article, we aim to provide a critical assessment of the current proteomics-based biomarkers for prostate cancer and their actual clinical applicability. For that purpose, a systematic review of the literature published within the last 10 years was performed using the Web of Science Database. We specifically discuss the potential and prospects of use for diagnostic, prognostic and predictive proteomics-based biomarkers, including both body fluid- and tissue-based markers.
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Affiliation(s)
| | - Maria Frantzi
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany.
| | - Axel S Merseburger
- Department of Urology, University Clinic of Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany.
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Qu X, Xiao M, Li F, Lai W, Li L, Zhou Y, Lin C, Li Q, Ge Z, Wen Y, Pei H, Liu G. Framework Nucleic Acid-Mediated Pull-Down MicroRNA Detection with Hybridization Chain Reaction Amplification. ACS APPLIED BIO MATERIALS 2018; 1:859-864. [DOI: 10.1021/acsabm.8b00278] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xiangmeng Qu
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhangheng Road, Shanghai 201203, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Zhou
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu 611137, China
| | - Chenglie Lin
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu 611137, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanli Wen
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhangheng Road, Shanghai 201203, China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Gang Liu
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhangheng Road, Shanghai 201203, China
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Employing proteomics to understand the effects of nutritional intervention in cancer treatment. Anal Bioanal Chem 2018; 410:6371-6386. [PMID: 29974151 DOI: 10.1007/s00216-018-1219-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 12/22/2022]
Abstract
Lifestyle optimizations are implementable changes that can have an impact on health and disease. Nutrition is a lifestyle optimization that has been shown to be of great importance in cancer initiation, progression, and metastasis. Dozens of clinical trials are currently in progress that focus on the nutritional modifications that cancer patients can make prior to and during medical care that increase the efficacy of treatment. In this review, we discuss various nutritional inventions for cancer patients and the analytical approaches to characterize the downstream molecular effects. We first begin by briefly explaining the many different forms of nutritional intervention currently being used in cancer treatment as well as their motivating biology. The forms of nutrient modulation described in this review include calorie restriction, the different practices of fasting, and carbohydrate restriction. The review then shifts to explain how proteomics is used to determine biomarkers of cancer and how it can be utilized in the future to determine the metabolic phenotype of a tumor, and inform physicians if nutritional intervention should be recommended for a cancer patient. Nutrigenomics aims to understand the relationship of nutrients and gene expression and can be used to understand the downstream molecular effects of nutrition restriction, partially through proteomic analysis. Proteomics is just beginning to be used as cancer diagnostic and predictive tools. However, these approaches have not been used to their full potential to understand nutritional intervention in cancer. Graphical abstract ᅟ.
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Signal-Targeted Therapies and Resistance Mechanisms in Pancreatic Cancer: Future Developments Reside in Proteomics. Cancers (Basel) 2018; 10:cancers10060174. [PMID: 29865155 PMCID: PMC6025626 DOI: 10.3390/cancers10060174] [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] [Received: 05/09/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 12/18/2022] Open
Abstract
For patients with metastatic pancreatic cancer that are not eligible for surgery, signal-targeted therapies have so far failed to significantly improve survival. These therapeutic options have been tested in phase II/III clinical trials mostly in combination with the reference treatment gemcitabine. Innovative therapies aim to annihilate oncogenic dependency, or to normalize the tumoural stroma to allow immune cells to function and/or re-vascularisation to occur. Large scale transcriptomic and genomic analysis revealed that pancreatic cancers display great heterogeneity but failed to clearly delineate specific oncogene dependency, besides oncogenic Kras. Beyond these approaches, proteomics appears to be an appropriate approach to classify signal dependency and to identify specific alterations at the targetable level. However, due to difficulties in sampling, proteomic data for this pathology are scarce. In this review, we will discuss the current state of clinical trials for targeted therapies against pancreatic cancer. We will then highlight the most recent proteomic data for pancreatic tumours and their metastasis, which could help to identify major oncogenic signalling dependencies, as well as provide future leads to explain why pancreatic tumours are intrinsically resistant to signal-targeted therapies. We will finally discuss how studies on phosphatidylinositol-3-kinase (PI3K) signalling, as the paradigmatic pro-tumoural signal downstream of oncogenic Kras in pancreatic cancer, would benefit from exploratory proteomics to increase the efficiency of targeted therapies.
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Huang R, He N, Li Z. Recent progresses in DNA nanostructure-based biosensors for detection of tumor markers. Biosens Bioelectron 2018. [DOI: 10.1016/j.bios.2018.02.053] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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