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Wang S, Hao X, Dai L, Lou N, Fan G, Gao R, Yang M, Xing P, Liu Y, Wang L, Zhang Z, Yao J, Tang L, Shi Y, Han X. Longitudinal plasma proteomic profiling of EML4-ALK positive lung cancer receiving ALK-TKIs therapy. Lung Cancer 2024; 189:107503. [PMID: 38359741 DOI: 10.1016/j.lungcan.2024.107503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Anaplastic lymphoma kinase-tyrosine kinase inhibitors (ALK-TKIs) has demonstrated remarkable therapeutic effects in ALK-positive non-small cell lung cancer (NSCLC) patients. Identifying prognostic biomarkers can enhance the clinical efficacy of relapsed or refractory patients. METHODS We profiled 737 plasma proteins from 159 pre-treatment and on-treatment plasma samples of 63 ALK-positive NSCLC patients using data-independent acquisition-mass spectrometry (DIA-MS). The consensus clustering algorithm was used to identify subtypes with distinct biological features. A plasma-based prognostic model was constructed using the LASSO-Cox method. We performed the Mfuzz analysis to classify the patterns of longitudinal changes in plasma proteins during treatment. 52 baseline plasma samples from another independent ALK-TKI treatment cohort were collected to validate the potential prognostic markers using ELISA. RESULTS We identified three subtypes of ALK-positive NSCLC with distinct biological features and clinical efficacy. Patients in subgroup 1 exhibited activated humoral immunity and inflammatory responses, increased expression of positive acute-phase response proteins, and the worst prognosis. Then we constructed and verified a prognostic model that predicts the efficacy of ALK-TKI therapy using the expression levels of five plasma proteins (SERPINA4, ATRN, APOA4, TF, and MYOC) at baseline. Next, we explored the longitudinal changes in plasma protein expression during treatment and identified four distinct change patterns (Clusters 1-4). The longitudinal changes of acute-phase proteins during treatment can reflect the treatment status and tumor progression of patients. Finally, we validated the prognostic efficacy of baseline plasma CRP, SAA1, AHSG, SERPINA4, and TF in another independent NSCLC cohort undergoing ALK-TKI treatment. CONCLUSIONS This study contributes to the search for prognostic and drug-resistance biomarkers in plasma samples for ALK-TKI therapy and provides new insights into the mechanism of drug resistance and the selection of follow-up treatment.
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Affiliation(s)
- Shasha Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Xuezhi Hao
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Liyuan Dai
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Ning Lou
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Guangyu Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Ruyun Gao
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Mengwei Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Puyuan Xing
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Yutao Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Lin Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Zhishang Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Jiarui Yao
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Le Tang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China.
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China.
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Miyagi T, Ueda K, Sugimoto M, Yagi T, Ito D, Yamazaki R, Narumi S, Hayamizu Y, Uji-i H, Kuroda M, Kanekura K. Differential toxicity and localization of arginine-rich C9ORF72 dipeptide repeat proteins depend on de-clustering of positive charges. iScience 2023; 26:106957. [PMID: 37332605 PMCID: PMC10275993 DOI: 10.1016/j.isci.2023.106957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Arginine-rich dipeptide repeat proteins (R-DPRs), poly(PR) and poly(GR), translated from the hexanucleotide repeat expansion in the amyotrophic lateral sclerosis (ALS)-causative C9ORF72 gene, contribute significantly to pathogenesis of ALS. Although both R-DPRs share many similarities, there are critical differences in their subcellular localization, phase separation, and toxicity mechanisms. We analyzed localization, protein-protein interactions, and phase separation of R-DPR variants and found that sufficient segregation of arginine charges is necessary for nucleolar distribution. Proline not only efficiently separated the charges, but also allowed for weak, but highly multivalent binding. In contrast, because of its high flexibility, glycine cannot fully separate the charges, and poly(GR) behaves similarly to the contiguous arginines, being trapped in the cytoplasm. We conclude that the amino acid that spaces the arginine charges determines the strength and multivalency of the binding, leading to differences in localization and toxicity mechanisms.
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Affiliation(s)
- Tamami Miyagi
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Department of Pharmacology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Institute for Advanced Biosciences, KEIO University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Takuya Yagi
- Department of Neurology, KEIO University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Daisuke Ito
- Department of Physiology, KEIO University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Rio Yamazaki
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Department of Pharmacology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroshi Uji-i
- Department of Nanomaterials and Nanoscopy, Research Institute for Electronic Science, Hokkaido University, Kita 10 Nishi 20, North Ward, Sapporo, Hokkaido 001-0020, Japan
- Department of Chemistry, KU Leuven Celestijnenlaan 200F, Heverlee, 3001 Leuven, Belgium
| | - Masahiko Kuroda
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Kohsuke Kanekura
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Department of Pharmacology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
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Li WH, Zhang L, Li YY, Wang XY, Li JL, Zhao SN, Ni MQ, Li Q, Sun H. Apolipoprotein A-IV Has Bi-Functional Actions in Alcoholic Hepatitis by Regulating Hepatocyte Injury and Immune Cell Infiltration. Int J Mol Sci 2022; 24:ijms24010670. [PMID: 36614113 PMCID: PMC9820766 DOI: 10.3390/ijms24010670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
Alcohol abuse can lead to alcoholic hepatitis (AH), a worldwide public health issue with high morbidity and mortality. Here, we identified apolipoprotein A-IV (APOA4) as a biomarker and potential therapeutic target for AH. APOA4 expression was detected by Gene Expression Omnibus (GEO) databases, Immunohistochemistry, and qRT-PCR in AH. Bioinformatics Methods (protein-protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Set Enrichment Analysis (GSEA) were used to show down-stream gene and pathways of APOA4 in AH. AML-12 cells were used to evaluate the biological function of APOA4 using an ELISA kit (AST, ALT, and IL-1β) and flow cytometry (ROS activity). Both in vivo and in vitro, APOA4 expression was significantly elevated in the AH model induced by alcohol (ETOH). AML-12 cell damage was specifically repaired by APOA4 deficiency, while AST, ALT, and IL-1β activity that was increased by ETOH (200 µmol, 12 h) were suppressed. APOA4 inhibition increased intracellular ROS induced by ETOH, which was detected by flow cytometry. Functional and PPI network analyses showed Fcgamma receptor (FCGR) and platelet activation signaling were potential downstream pathways. We identified CIDEC as a downstream gene of APOA4. The CIDEC AUC values for the ROC curves were 0.861. At the same time, APOA4 silencing downregulated the expression of CIDEC, whereas the knockdown of CIDEC did not influence the expression of APOA4 in AML-12 cells. Collectively, APOA4 regulates CIDEC expression and immune cell infiltration and may hold great potential as a biomarker and therapeutic target for AH.
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Affiliation(s)
- Wan-Hong Li
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Li Zhang
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Yue-Ying Li
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Xin-Yue Wang
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Jin-Liang Li
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Shu-Ning Zhao
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Ming-Qi Ni
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Qian Li
- Pharmaceutical Analysis and Analytical Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
- Correspondence: (Q.L.); (H.S.); Tel./Fax: +86-451-86699347 (Q.L.)
| | - Hui Sun
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
- Correspondence: (Q.L.); (H.S.); Tel./Fax: +86-451-86699347 (Q.L.)
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Zhai G, Yang L, Luo Q, Wu K, Zhao Y, Wang F. Serum phosphopeptide profiling for colorectal cancer diagnosis using liquid chromatography-mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9316. [PMID: 35416361 DOI: 10.1002/rcm.9316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
RATIONALE The identification and evaluation of novel biomarkers are essential to clinical diagnosis and prognosis of colorectal cancer (CRC). Serum phosphopeptides have been recognized as a potential signature pool for cancers; therefore, we aim to profile the expression of serum phosphopeptides and to evaluate their feasibility in CRC diagnosis. METHODS We conducted the characterization and absolute quantification of endogenous phosphopeptides in sera using liquid chromatography-mass spectrometry analysis in combination with enrichment of phosphopeptides by ZrAs-Fe3 O4 @SiO2 nanoparticles and use of deuterium-labeled standards. Differentially expressed analysis of four phosphopeptides was performed, generating a two-phosphopeptide-based biomarker, LF3-4 , by logistic regression analysis, where LF3-4 is equal to (5.85 - 5.13 × [F3] - 3.57 × [F4]), and [F3] and [F4] are the concentration of phosphopeptides DpSGEGDFLAEGGGVR and ADpSGEGDFLAEGGGVR in sera, respectively. RESULTS The LF3-4 values showed significant difference in CRC cases compared with controls, and yielded a specificity of 100%, leading to correct classification of 56 (93%) out of 60 CRC patients, including 12 (92.3%) of 13 CRC cases in stage I. Double-blind validation showed that 97.5% of CRC cases were discriminated accurately. CONCLUSIONS The LF3-4 value was firstly verified to be a potential biomarker for CRC diagnosis, and may expand our view in underlying mechanisms for CRC.
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Affiliation(s)
- Guijin Zhai
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- Department of Biochemistry and Molecular Biology; Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Liping Yang
- Cancer Research Centre, Tumour Hospital Affiliated to Nantong University, Nantong, Jiangsu, China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Kui Wu
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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A Circulating Risk Score, Based on Combined Expression of Exo-miR-130a-3p and Fibrinopeptide A, as Predictive Biomarker of Relapse in Resectable Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2022; 14:cancers14143412. [PMID: 35884472 PMCID: PMC9317031 DOI: 10.3390/cancers14143412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary To date, the five-year survival rate of early stages of non-small cell lung cancer (NSCLC) is still disappointing and reliable prognostic factors are mandatory. Here, we performed in-depth high-throughput analyses of plasma circulating markers, including exosomal microRNAs and peptidome to identify a prognostic score. The miRnome profile selected the Exo-miR-130a-3p as the most overexpressed in relapsed patients. Peptidome analysis identified four progressively more degraded forms of fibrinopeptide A (FpA), which were depleted in relapse patients. Notably, a stepwise algorithm selected Exo-miR-130a-3p and the greatest FpA (2–16) to build a prognostic score, where high-risk patients had 18 months of median disease-free survival. Overexpression of miR-130a-3p cells led to a deregulation of pathways such as angiogenesis as well as the coagulation and metalloprotease, which might be linked to FpA reduction. The risk score integrating circulating markers may help clinicians predict early-stage NSCLC patients who are more likely to relapse after surgery. Abstract To date, the 5-year overall survival rate of 60% for early-stage non-small cell lung cancer (NSCLC) is still unsatisfactory. Therefore, reliable prognostic factors are needed. Growing evidence shows that cancer progression may depend on an interconnection between cancer cells and the surrounding tumor microenvironment; hence, circulating molecules may represent promising markers of cancer recurrence. In order to identify a prognostic score, we performed in-depth high-throughput analyses of plasma circulating markers, including exosomal microRNAs (Exo-miR) and peptides, in 67 radically resected NSCLCs. The miRnome profile selected the Exo-miR-130a-3p as the most overexpressed in relapsed patients. Peptidome analysis identified four progressively more degraded forms of fibrinopeptide A (FpA), which were depleted in progressing patients. Notably, stepwise Cox regression analysis selected Exo-miR-130a-3p and the greatest FpA (2-16) to build a score predictive of recurrence, where high-risk patients had 18 months of median disease-free survival. Moreover, in vitro transfections showed that higher levels of miR-130a-3p lead to a deregulation of pathways involved in metastasis and angiogenesis, including the coagulation process and metalloprotease increase which might be linked to FpA reduction. In conclusion, by integrating circulating markers, the identified risk score may help clinicians predict early-stage NSCLC patients who are more likely to relapse after primary surgery.
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The Patterning and Proportion of Charged Residues in the Arginine-Rich Mixed-Charge Domain Determine the Membrane-Less Organelle Targeted by the Protein. Int J Mol Sci 2022; 23:ijms23147658. [PMID: 35887012 PMCID: PMC9324279 DOI: 10.3390/ijms23147658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022] Open
Abstract
Membrane-less organelles (MLOs) are formed by biomolecular liquid–liquid phase separation (LLPS). Proteins with charged low-complexity domains (LCDs) are prone to phase separation and localize to MLOs, but the mechanism underlying the distributions of such proteins to specific MLOs remains poorly understood. Recently, proteins with Arg-enriched mixed-charge domains (R-MCDs), primarily composed of R and Asp (D), were found to accumulate in nuclear speckles via LLPS. However, the process by which R-MCDs selectively incorporate into nuclear speckles is unknown. Here, we demonstrate that the patterning of charged amino acids and net charge determines the targeting of specific MLOs, including nuclear speckles and the nucleolus, by proteins. The redistribution of R and D residues from an alternately sequenced pattern to uneven blocky sequences caused a shift in R-MCD distribution from nuclear speckles to the nucleolus. In addition, the incorporation of basic residues in the R-MCDs promoted their localization to the MLOs and their apparent accumulation in the nucleolus. The R-MCD peptide with alternating amino acids did not undergo LLPS, whereas the blocky R-MCD peptide underwent LLPS with affinity to RNA, acidic poly-Glu, and the acidic nucleolar protein nucleophosmin, suggesting that the clustering of R residues helps avoid their neutralization by D residues and eventually induces R-MCD migration to the nucleolus. Therefore, the distribution of proteins to nuclear speckles requires the proximal positioning of D and R for the mutual neutralization of their charges.
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Shan L, Jones B. Nano liquid chromatography, an updated review. Biomed Chromatogr 2022; 36:e5317. [PMID: 34981550 DOI: 10.1002/bmc.5317] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 11/11/2022]
Abstract
Low flow chromatography has a rich history of innovation but has yet to reach widespread implementation in bioanalytical applications. Improvements in pump technology, microfluidic connections, and nano-electrospray sources for mass spectrometry have laid the groundwork for broader application, and innovation in this space has accelerated in recent years. This article reviews the instrumentation used for nano-flow liquid chromatography , the types of columns employed, and strategies for multi-dimensionality of separations, which is key to the future state of the technique to the high-throughput needs of modern bioanalysis. An update of the current applications where nano-LC is widely used, such as proteomics and metabolomics, is discussed. But the trend towards biopharmaceutical development of increasingly complex, targeted, and potent therapeutics for the safe treatment of disease drives the need for ultimate selectivity and sensitivity of our analytical platforms for targeted quantitation in a regulated space. The selectivity needs are best addressed by mass spectrometric detection, especially at high resolutions, and exquisite sensitivity is provided by nano-electrospray ionization as the technology continues to evolve into an accessible, robust, and easy to use platform.
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Kanekura K, Hayamizu Y, Kuroda M. Order controls disordered droplets: structure-function relationships in C9orf72-derived poly(PR). Am J Physiol Cell Physiol 2021; 322:C197-C204. [PMID: 34910602 DOI: 10.1152/ajpcell.00372.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) have been thought as two distinct neurodegenerative diseases. However, recent genetic screening and careful investigations found the genetic and pathological overlap among these disorders. Hexanucleotide expansions in intron 1 of C9orf72 are a leading cause of familial ALS and familial FTD. These expansions facilitate the repeat-associated non-ATG initiated translation (RAN translation), producing five dipeptide repeat proteins (DRPs), including Arg-rich poly(PR: Pro-Arg) and poly-(GR: Gly-Arg) peptides. Arg is a positively charged, highly polar amino acid that facilitates interactions with anionic molecules such as nucleic acids and acidic amino acids via electrostatic forces and aromatic amino acids via cation-pi interaction, suggesting that Arg-rich DRPs underlie the pathophysiology of ALS via Arg-mediated molecular interactions. Arg-rich DRPs have also been reported to induce neurodegeneration in cellular and animal models via multiple mechanisms; however, it remains unclear why the Arg-rich DRPs exhibit such diverse toxic properties, because not all Arg-rich peptides are toxic. In this mini-review, we discuss the current understanding of the pathophysiology of Arg-rich C9orf72 DRPs and introduce recent findings on the role of Arg distribution as a determinant of the toxicity and its contribution to the pathogenesis of ALS.
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Affiliation(s)
- Kohsuke Kanekura
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Tokyo, Japan
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Masahiko Kuroda
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Tokyo, Japan
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Chen C, Yamanaka Y, Ueda K, Li P, Miyagi T, Harada Y, Tezuka S, Narumi S, Sugimoto M, Kuroda M, Hayamizu Y, Kanekura K. Phase separation and toxicity of C9orf72 poly(PR) depends on alternate distribution of arginine. J Cell Biol 2021; 220:212626. [PMID: 34499080 PMCID: PMC8438627 DOI: 10.1083/jcb.202103160] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022] Open
Abstract
Arg (R)-rich dipeptide repeat proteins (DPRs; poly(PR): Pro-Arg and poly(GR): Gly-Arg), encoded by a hexanucleotide expansion in the C9ORF72 gene, induce neurodegeneration in amyotrophic lateral sclerosis (ALS). Although R-rich DPRs undergo liquid-liquid phase separation (LLPS), which affects multiple biological processes, mechanisms underlying LLPS of DPRs remain elusive. Here, using in silico, in vitro, and in cellulo methods, we determined that the distribution of charged Arg residues regulates the complex coacervation with anionic peptides and nucleic acids. Proteomic analyses revealed that alternate Arg distribution in poly(PR) facilitates entrapment of proteins with acidic motifs via LLPS. Transcription, translation, and diffusion of nucleolar nucleophosmin (NPM1) were impaired by poly(PR) with an alternate charge distribution but not by poly(PR) variants with a consecutive charge distribution. We propose that the pathogenicity of R-rich DPRs is mediated by disturbance of proteins through entrapment in the phase-separated droplets via sequence-controlled multivalent protein-protein interactions.
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Affiliation(s)
- Chen Chen
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yoshiaki Yamanaka
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Peiying Li
- Center for Biosystems Dynamics Research, RIKEN, Kanagawa, Japan
| | - Tamami Miyagi
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Yuichiro Harada
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Sayaka Tezuka
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies, Tokyo Medical University, Tokyo, Japan
| | - Masahiko Kuroda
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kohsuke Kanekura
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
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Pathophysiological Implications of Urinary Peptides in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13153786. [PMID: 34359689 PMCID: PMC8345155 DOI: 10.3390/cancers13153786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 11/23/2022] Open
Abstract
Simple Summary In this study, the application of capillary electrophoresis mass spectrometry enabled identification of 31 urinary peptides significantly associated with hepatocellular carcinoma diagnosis and prognosis. Further assessment of these peptides lead to prediction of cellular proteases involved in their development namely Meprin A subunit α and Kallikrein-6. Subsequent identification of the proteases was verified by immunohistochemistry in normal liver, cirrhosis and hepatocellular carcinoma. Histopathological assessment of the proteases revealed numerical gradient staining signifying their involvement in liver fibrosis and hepatocellular carcinoma formation. The discovered urinary peptides offered a potential noninvasive tool for diagnosis and prognosis of hepatocellular carcinoma. Abstract Hepatocellular carcinoma (HCC) is known to be associated with protein alterations and extracellular fibrous deposition. We investigated the urinary proteomic profiles of HCC patients in this prospective cross sectional multicentre study. 195 patients were recruited from the UK (Coventry) and Germany (Hannover) between 1 January 2013 and 30 June 2019. Out of these, 57 were HCC patients with a background of liver cirrhosis (LC) and 138 were non-HCC controls; 72 patients with LC, 57 with non-cirrhotic liver disease and 9 with normal liver function. Analysis of the urine samples was performed by capillary electrophoresis (CE) coupled to mass spectrometry (MS). Peptide sequences were obtained and 31 specific peptide markers for HCC were identified and further integrated into a multivariate classification model. The peptide model demonstrated 79.5% sensitivity and 85.1% specificity (95% CI: 0.81–0.93, p < 0.0001) for HCC and 4.1-fold increased risk of death (95% CI: 1.7–9.8, p = 0.0005). Proteases potentially involved in HCC progression were mapped to the N- and C-terminal sequence motifs of the CE-MS peptide markers. In silico protease prediction revealed that kallikrein-6 (KLK6) elicits increased activity, whilst Meprin A subunit α (MEP1A) has reduced activity in HCC compared to the controls. Tissue expression of KLK6 and MEP1A was subsequently verified by immunohistochemistry.
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Hypertensive disorders of pregnancy: Strategy to develop clinical peptide biomarkers for more accurate evaluation of the pathophysiological status of this syndrome. Adv Clin Chem 2019; 94:1-30. [PMID: 31952570 DOI: 10.1016/bs.acc.2019.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hypertensive disorders of pregnancy (HDP) is the most common and widely known as serious complication of pregnancy. As this syndrome is a major leading cause of maternal, fetal, and neonatal morbidity/mortality worldwide, many studies have sought to identify candidate molecules as potential disease biomarkers (DBMs) for use in clinical examinations. Accumulating evidence over the past 2 decades that the many proteolytic peptides appear in human humoral fluids, including peripheral blood, in association with an individual's health condition. This review provides the potential utility of peptidomic analysis for monitoring for pathophysiological status in HDP, and presents an overview of current status of peptide quantification technology. Especially, the technical limitations of the methods used for DBM discovery in the blood are discussed.
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12
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Iwamoto N, Shimada T. Recent advances in mass spectrometry-based approaches for proteomics and biologics: Great contribution for developing therapeutic antibodies. Pharmacol Ther 2017; 185:147-154. [PMID: 29274706 DOI: 10.1016/j.pharmthera.2017.12.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Since the turn of the century, mass spectrometry (MS) technologies have continued to improve dramatically, and advanced strategies that were impossible a decade ago are increasingly becoming available. The basic characteristics behind these advancements are MS resolution, quantitative accuracy, and information science for appropriate data processing. The spectral data from MS contain various types of information. The benefits of improving the resolution of MS data include accurate molecular structural-derived information, and as a result, we can obtain a refined biomolecular structure determination in a sequential and large-scale manner. Moreover, in MS data, not only accurate structural information but also the generated ion amount plays an important rule. This progress has greatly contributed a research field that captures biological events as a system by comprehensively tracing the various changes in biomolecular dynamics. The sequential changes of proteome expression in biological pathways are very essential, and the amounts of the changes often directly become the targets of drug discovery or indicators of clinical efficacy. To take this proteomic approach, it is necessary to separate the individual MS spectra derived from each biomolecule in the complexed biological samples. MS itself is not so infinite to perform the all peak separation, and we should consider improving the methods for sample processing and purification to make them suitable for injection into MS. The above-described characteristics can only be achieved using MS with any analytical instrument. Moreover, MS is expected to be applied and expand into many fields, not only basic life sciences but also forensic medicine, plant sciences, materials, and natural products. In this review, we focus on the technical fundamentals and future aspects of the strategies for accurate structural identification, structure-indicated quantitation, and on the challenges for pharmacokinetics of high-molecular-weight protein biopharmaceuticals.
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Affiliation(s)
- Noriko Iwamoto
- Leading Technology of Bioanalysis and Protein Chemistry, SHIMADZU Corporation, Kyoto, Japan
| | - Takashi Shimada
- Leading Technology of Bioanalysis and Protein Chemistry, SHIMADZU Corporation, Kyoto, Japan.
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13
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Current and Prospective Protein Biomarkers of Lung Cancer. Cancers (Basel) 2017; 9:cancers9110155. [PMID: 29137182 PMCID: PMC5704173 DOI: 10.3390/cancers9110155] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/02/2017] [Accepted: 11/06/2017] [Indexed: 12/23/2022] Open
Abstract
Lung cancer is a malignant lung tumor with various histological variants that arise from different cell types, such as bronchial epithelium, bronchioles, alveoli, or bronchial mucous glands. The clinical course and treatment efficacy of lung cancer depends on the histological variant of the tumor. Therefore, accurate identification of the histological type of cancer and respective protein biomarkers is crucial for adequate therapy. Due to the great diversity in the molecular-biological features of lung cancer histological types, detection is impossible without knowledge of the nature and origin of malignant cells, which release certain protein biomarkers into the bloodstream. To date, different panels of biomarkers are used for screening. Unfortunately, a uniform serum biomarker composition capable of distinguishing lung cancer types is yet to be discovered. As such, histological analyses of tumor biopsies and immunohistochemistry are the most frequently used methods for establishing correct diagnoses. Here, we discuss the recent advances in conventional and prospective aptamer based strategies for biomarker discovery. Aptamers like artificial antibodies can serve as molecular recognition elements for isolation detection and search of novel tumor-associated markers. Here we will describe how these small synthetic single stranded oligonucleotides can be used for lung cancer biomarker discovery and utilized for accurate diagnosis and targeted therapy. Furthermore, we describe the most frequently used in-clinic and novel lung cancer biomarkers, which suggest to have the ability of differentiating between histological types of lung cancer and defining metastasis rate.
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Zakharova NV, Shornikova AY, Bugrova AE, Baybakova VV, Indeykina MI, Kononikhin AS, Popov IA, Kechko OI, Makarov AA, Nikolaev EN. Evaluation of plasma peptides extraction methods by high-resolution mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:209-212. [PMID: 29028405 DOI: 10.1177/1469066717720907] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Monitoring of peptides offers a promising approach for the discovery of novel biomarkers, which might be valuable for detection, treatment and prevention of large variety of diseases. Development of highly effective methods for plasma peptide extraction remains an important task. In the current study, we applied different types of plasma peptide extraction approaches to reveal efficient methods which would provide the highest peptide yield. We used different combinations of plasma treatment with acetonitrile and/or urea/guanidine, protein precipitation by acetone, gel-filtration, ultrafiltration, and two types of solid phase extraction. The extracted peptides were analyzed by LC-MS/MS. The obtained results suggest that several methods, including differential solubilization, organic precipitation, as well as some variants of ultrafiltration and solid phase extraction, provide effective plasma peptide enrichment convenient for further LC-MS/MS analysis. Alas, most of the identified peptides were extracted by only one of the applied methods. Hence, it seems reasonable to consider several methods to increase the possibility of novel biomarker discovery.
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Affiliation(s)
- N V Zakharova
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - A Y Shornikova
- 3 School of chemistry, Department of analytical chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A E Bugrova
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - V V Baybakova
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - M I Indeykina
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - A S Kononikhin
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- 4 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - I A Popov
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- 4 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - O I Kechko
- 5 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A A Makarov
- 5 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E N Nikolaev
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- 4 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 6 Skolkovo Institute of Science and Technology, Moscow, Russia
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15
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Liu Y, Xun XH, Yi JM, Xiang Y, Hua J. Discovery of lung squamous carcinoma biomarkers by profiling the plasma peptide with LC/MS/MS. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2016.11.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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16
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Zhai G, Yang L, Luo Q, Wu K, Zhao Y, Liu J, Xiong S, Wang F. Evaluation of serum phosphopeptides as potential biomarkers of gastric cancer. RSC Adv 2017. [DOI: 10.1039/c7ra00827a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A serum phosphopeptide (DpSGEGDFLAEGGGVR) was demonstrated to be a potential biomarker for gastric cancer diagnosis, particularly for early stage cases.
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Affiliation(s)
- Guijin Zhai
- Beijing National Laboratory for Molecular Sciences
- National Centre for Mass Spectrometry in Beijing
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
| | - Liping Yang
- Cancer Research Centre
- Tumour Hospital Affiliated to Nantong University
- Nantong 226361
- PR China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences
- National Centre for Mass Spectrometry in Beijing
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
| | - Kui Wu
- Beijing National Laboratory for Molecular Sciences
- National Centre for Mass Spectrometry in Beijing
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences
- National Centre for Mass Spectrometry in Beijing
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
| | - Jianan Liu
- Beijing National Laboratory for Molecular Sciences
- National Centre for Mass Spectrometry in Beijing
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
| | - Shaoxiang Xiong
- Beijing National Laboratory for Molecular Sciences
- National Centre for Mass Spectrometry in Beijing
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences
- National Centre for Mass Spectrometry in Beijing
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
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Holton TA, Dillon ET, Robinson A, Wynne K, Cagney G, Shields DC. Optimal computational comparison of mass spectrometric peptide profiles of alternative hydrolysates from the same starting material. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Admoni-Elisha L, Nakdimon I, Shteinfer A, Prezma T, Arif T, Arbel N, Melkov A, Zelichov O, Levi I, Shoshan-Barmatz V. Novel Biomarker Proteins in Chronic Lymphocytic Leukemia: Impact on Diagnosis, Prognosis and Treatment. PLoS One 2016; 11:e0148500. [PMID: 27078856 PMCID: PMC4831809 DOI: 10.1371/journal.pone.0148500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 01/19/2016] [Indexed: 12/31/2022] Open
Abstract
In many cancers, cells undergo re-programming of metabolism, cell survival and anti-apoptotic defense strategies, with the proteins mediating this reprogramming representing potential biomarkers. Here, we searched for novel biomarker proteins in chronic lymphocytic leukemia (CLL) that can impact diagnosis, treatment and prognosis by comparing the protein expression profiles of peripheral blood mononuclear cells from CLL patients and healthy donors using specific antibodies, mass spectrometry and binary logistic regression analyses and other bioinformatics tools. Mass spectrometry (LC-HR-MS/MS) analysis identified 1,360 proteins whose expression levels were modified in CLL-derived lymphocytes. Some of these proteins were previously connected to different cancer types, including CLL, while four other highly expressed proteins were not previously reported to be associated with cancer, and here, for the first time, DDX46 and AK3 are linked to CLL. Down-regulation expression of two of these proteins resulted in cell growth inhibition. High DDX46 expression levels were associated with shorter survival of CLL patients and thus can serve as a prognosis marker. The proteins with modified expression include proteins involved in RNA splicing and translation and particularly mitochondrial proteins involved in apoptosis and metabolism. Thus, we focused on several metabolism- and apoptosis-modulating proteins, particularly on the voltage-dependent anion channel 1 (VDAC1), regulating both metabolism and apoptosis. Expression levels of Bcl-2, VDAC1, MAVS, AIF and SMAC/Diablo were markedly increased in CLL-derived lymphocytes. VDAC1 levels were highly correlated with the amount of CLL-cancerous CD19+/CD5+ cells and with the levels of all other apoptosis-modulating proteins tested. Binary logistic regression analysis demonstrated the ability to predict probability of disease with over 90% accuracy. Finally, based on the changes in the levels of several proteins in CLL patients, as revealed from LC-HR-MS/MS, we could distinguish between patients in a stable disease state and those who would be later transferred to anti-cancer treatments. The over-expressed proteins can thus serve as potential biomarkers for early diagnosis, prognosis, new targets for CLL therapy, and treatment guidance of CLL, forming the basis for personalized therapy.
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MESH Headings
- Aged
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Blotting, Western
- Chromatography, Liquid
- Female
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukocytes, Mononuclear/metabolism
- Male
- Prognosis
- Proteome/analysis
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Tandem Mass Spectrometry/methods
- Tumor Cells, Cultured
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Affiliation(s)
- Lee Admoni-Elisha
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Itay Nakdimon
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anna Shteinfer
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tal Prezma
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tasleem Arif
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Nir Arbel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anna Melkov
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ori Zelichov
- Department of Hematology, Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Itai Levi
- Department of Hematology, Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Varda Shoshan-Barmatz
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
- * E-mail:
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Liu Z, Gao Y, Hao F, Lou X, Zhang X, Li Y, Wu D, Xiao T, Yang L, Li Q, Qiu X, Wang E. Secretomes are a potential source of molecular targets for cancer therapies and indicate that APOE is a candidate biomarker for lung adenocarcinoma metastasis. Mol Biol Rep 2014; 41:7507-23. [PMID: 25098600 DOI: 10.1007/s11033-014-3641-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 07/23/2014] [Indexed: 12/20/2022]
Abstract
Identifying patients at high risk of metastasis is a major challenge in lung adenocarcinoma (ADC) therapy, therefore discovery of noninvasive biomarkers and therapeutic targets is urgent. We found significant differences between the secretomes of differentially expressed proteins in lung ADC cell lines, clinical tissue samples and serum plasma samples with high and low metastatic potential. In particular, Apolipoprotein E (APOE) levels were three-times greater in cells with lymph node metastases (LNM) than those without. Our study indicates that APOE is a potential indicator of metastatic lung ADC and that secretomes may offer a valuable resource for biomarkers of lung ADC with LNM.
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Affiliation(s)
- Zan Liu
- Department of Pathology, The First Affiliated Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, 110001, China
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Viglio S, Stolk J, Iadarola P, Giuliano S, Luisetti M, Salvini R, Fumagalli M, Bardoni A. Respiratory Proteomics Today: Are Technological Advances for the Identification of Biomarker Signatures Catching up with Their Promise? A Critical Review of the Literature in the Decade 2004-2013. Proteomes 2014; 2:18-52. [PMID: 28250368 PMCID: PMC5302730 DOI: 10.3390/proteomes2010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/08/2014] [Accepted: 01/10/2014] [Indexed: 01/14/2023] Open
Abstract
To improve the knowledge on a variety of severe disorders, research has moved from the analysis of individual proteins to the investigation of all proteins expressed by a tissue/organism. This global proteomic approach could prove very useful: (i) for investigating the biochemical pathways involved in disease; (ii) for generating hypotheses; or (iii) as a tool for the identification of proteins differentially expressed in response to the disease state. Proteomics has not been used yet in the field of respiratory research as extensively as in other fields, only a few reproducible and clinically applicable molecular markers, which can assist in diagnosis, having been currently identified. The continuous advances in both instrumentation and methodology, which enable sensitive and quantitative proteomic analyses in much smaller amounts of biological material than before, will hopefully promote the identification of new candidate biomarkers in this area. The aim of this report is to critically review the application over the decade 2004-2013 of very sophisticated technologies to the study of respiratory disorders. The observed changes in protein expression profiles from tissues/fluids of patients affected by pulmonary disorders opens the route for the identification of novel pathological mediators of these disorders.
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Affiliation(s)
- Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Jan Stolk
- Department of Pulmonology, Leiden University Medical Center, Leiden 2333, The Netherlands.
| | - Paolo Iadarola
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Serena Giuliano
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
- Faculty of Science "Parc Valrose", University of Nice "Sophia Antipolis", FRE 3472 CNRS, LP2M Nice, France.
| | - Maurizio Luisetti
- Department of Molecular Medicine, Division of Pneumology, University of Pavia & IRCCS Policlinico San Matteo, Via Taramelli 5, Pavia 27100, Italy.
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Marco Fumagalli
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
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21
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Pham TV, Piersma SR, Oudgenoeg G, Jimenez CR. Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Rev Mol Diagn 2014; 12:343-59. [DOI: 10.1586/erm.12.31] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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22
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Ueda K, Tatsuguchi A, Saichi N, Toyama A, Tamura K, Furihata M, Takata R, Akamatsu S, Igarashi M, Nakayama M, Sato TA, Ogawa O, Fujioka T, Shuin T, Nakamura Y, Nakagawa H. Plasma Low-Molecular-Weight Proteome Profiling Identified Neuropeptide-Y as a Prostate Cancer Biomarker Polypeptide. J Proteome Res 2013; 12:4497-506. [DOI: 10.1021/pr400547s] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Koji Ueda
- Laboratory
for Biomarker Development, Center for Genomic Medicine, RIKEN, General
Research Building 6F, Institute of Medical Science, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Ayako Tatsuguchi
- Laboratory
for Biomarker Development, Center for Genomic Medicine, RIKEN, General
Research Building 6F, Institute of Medical Science, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Naomi Saichi
- Laboratory
for Biomarker Development, Center for Genomic Medicine, RIKEN, General
Research Building 6F, Institute of Medical Science, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Atsuhiko Toyama
- Life
Science Research Center, Shimadzu Corporation, 1-3, Nishikicho, Kanda, Chiyoda-ku, Tokyo 101-8448, Japan
| | - Kenji Tamura
- Department
of Urology, Kochi Medical School Hospital, Oko-cho Kohasu, Nankoku-shi, Kochi 783-8505, Japan
| | - Mutsuo Furihata
- Department
of Pathology, Kochi Medical School, Oko-cho Kohasu, Nankoku-shi, Kochi 783-8505, Japan
| | - Ryo Takata
- Department
of Urology, Iwate Medical University, 19-1 Uchimaru, Morioka, Iwate Prefecture 020-0023, Japan
| | - Shusuke Akamatsu
- Department
of Urology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiro Igarashi
- Endoscopy
Division, Gastrointestinal Center, Cancer Institute Hospital, 3-8-31, Ariake, Koto, Tokyo 135-8550, Japan
| | - Masato Nakayama
- Toppan Printing Co., Ltd., 1-5-1, Taito, Taito-ku, Tokyo 110-8560, Japan
| | - Taka-Aki Sato
- Life
Science Research Center, Shimadzu Corporation, 1-3, Nishikicho, Kanda, Chiyoda-ku, Tokyo 101-8448, Japan
| | - Osamu Ogawa
- Department
of Urology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoaki Fujioka
- Department
of Urology, Iwate Medical University, 19-1 Uchimaru, Morioka, Iwate Prefecture 020-0023, Japan
| | - Taro Shuin
- Department
of Urology, Kochi Medical School Hospital, Oko-cho Kohasu, Nankoku-shi, Kochi 783-8505, Japan
| | - Yusuke Nakamura
- Section
of Hematology/Oncology, Department of Medicine Faculty, The University of Chicago, 5841 South Maryland Avenue, Chicago, Illinois, United States
| | - Hidewaki Nakagawa
- Laboratory
for Biomarker Development, Center for Genomic Medicine, RIKEN, General
Research Building 6F, Institute of Medical Science, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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23
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Araki Y, Nonaka D, Hamamura K, Yanagida M, Ishikawa H, Banzai M, Maruyama M, Endo S, Tajima A, Lee LJ, Nojima M, Takamori K, Yoshida K, Takeda S, Tanaka K. Clinical peptidomic analysis by a one-step direct transfer technology: Its potential utility for monitoring of pathophysiological status in female reproductive system disorders. J Obstet Gynaecol Res 2013; 39:1440-8. [DOI: 10.1111/jog.12140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 04/04/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Yoshihiko Araki
- Institute for Environmental and Gender-specific Medicine; Juntendo University Graduate School of Medicine; Chiba Japan
- Department of Obstetrics and Gynecology; Juntendo University Graduate School of Medicine; Tokyo Japan
| | - Daisuke Nonaka
- Membrane Protein and Ligand Analysis Center; Protosera Inc; Hyogo Japan
| | - Kensuke Hamamura
- Institute for Environmental and Gender-specific Medicine; Juntendo University Graduate School of Medicine; Chiba Japan
- Department of Obstetrics and Gynecology; Juntendo University Graduate School of Medicine; Tokyo Japan
| | - Mitsuaki Yanagida
- Institute for Environmental and Gender-specific Medicine; Juntendo University Graduate School of Medicine; Chiba Japan
| | - Hitoshi Ishikawa
- Department of Health Information Management; Yamagata Saisei Hospital; Yamagata Japan
| | - Michio Banzai
- Department of Obstetrics and Gynecology; Yamagata Saisei Hospital; Yamagata Japan
| | - Mayuko Maruyama
- Department of Obstetrics and Gynecology; Juntendo University Graduate School of Medicine; Tokyo Japan
- Department of Obstetrics and Gynecology; Juntendo University Urayasu Hospital; Chiba Japan
| | - Shuichiro Endo
- Institute for Environmental and Gender-specific Medicine; Juntendo University Graduate School of Medicine; Chiba Japan
- Department of Obstetrics and Gynecology; Juntendo University Graduate School of Medicine; Tokyo Japan
| | - Atsushi Tajima
- Department of Obstetrics and Gynecology; Juntendo University Graduate School of Medicine; Tokyo Japan
- Department of Obstetrics and Gynecology; Juntendo University Urayasu Hospital; Chiba Japan
| | - Lyang-Ja Lee
- Membrane Protein and Ligand Analysis Center; Protosera Inc; Hyogo Japan
| | - Michio Nojima
- Department of Obstetrics and Gynecology; Juntendo University Graduate School of Medicine; Tokyo Japan
- Department of Obstetrics and Gynecology; Juntendo University Urayasu Hospital; Chiba Japan
| | - Kenji Takamori
- Institute for Environmental and Gender-specific Medicine; Juntendo University Graduate School of Medicine; Chiba Japan
| | - Koyo Yoshida
- Department of Obstetrics and Gynecology; Juntendo University Graduate School of Medicine; Tokyo Japan
- Department of Obstetrics and Gynecology; Juntendo University Urayasu Hospital; Chiba Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology; Juntendo University Graduate School of Medicine; Tokyo Japan
| | - Kenji Tanaka
- Membrane Protein and Ligand Analysis Center; Protosera Inc; Hyogo Japan
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Ueda K. Glycoproteomic strategies: From discovery to clinical application of cancer carbohydrate biomarkers. Proteomics Clin Appl 2013; 7:607-17. [PMID: 23640819 DOI: 10.1002/prca.201200123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Carbohydrate antigens are the most frequently and traditionally used biomarkers for cancer, such as CA19-9, CA125, DUPAN-II, AFP-L3, and many others. The diagnostic potential of them was simply based on the cancer-specific alterations of glycan structures on particular glycoproteins in serum/plasma. In spite of the facts that glycosylation disorders are feasible for cancer biomarkers and glycomic analysis technologies to explore them have been rapidly developed, it remains difficult to sensitively screen glycan structure changes on cancer-associated glycoproteins from clinical specimens. Moreover, a lot of additional issues should be appropriately addressed for the clinical application of newly identified glycosylation biomarkers, including analytical throughput, quantitative confirmation of structural changes, and biological explanation for the alterations. In the last decade, significant improvement of mass spectrometric techniques is being made in the aspects of both hardware spec and preanalytical purification procedures for glycoprotein analysis. Here we review potential approaches to perform comprehensive analysis of glycoproteomic biomarker screening from serum/plasma and to realize high-throughput validation of site-specific oligosaccharide variations. The power and problems of mass spectrometric applications on the clinical use of carbohydrate biomarkers are also discussed in this review.
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Affiliation(s)
- Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Minato-ku, Tokyo, Japan.
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25
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Abstract
Adult T-cell leukemia (ATL) is one of the most aggressive hematologic malignancies caused by human T-lymphotropic virus type 1 (HTLV-1) infection. The prognosis of ATL is extremely poor; however, effective strategies for diagnosis and treatment have not been established. To identify novel therapeutic targets and diagnostic markers for ATL, we employed focused proteomic profiling of the CD4(+)CD25(+)CCR4(+) T-cell subpopulation in which HTLV-1-infected cells were enriched. Comprehensive quantification of 14 064 peptides and subsequent 2-step statistical analysis using 29 cases (6 uninfected controls, 5 asymptomatic carriers, 9 HTLV-1-associated myelopathy/tropical spastic paraparesis patients, 9 ATL patients) identified 91 peptide determinants that statistically classified 4 clinical groups with an accuracy rate of 92.2% by cross-validation test. Among the identified 17 classifier proteins, α-II spectrin was drastically accumulated in infected T cells derived from ATL patients, whereas its digestive protease calpain-2 (CAN2) was significantly downregulated. Further cell cycle analysis and cell growth assay revealed that rescue of CAN2 activity by overexpressing constitutively active CAN2 (Δ(19)CAN2) could induce remarkable cell death on ATL cells accompanied by reduction of α-II spectrin. These results support that proteomic profiling of HTLV-1-infected T cells could provide potential diagnostic biomarkers and an attractive resource of therapeutic targets for ATL.
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26
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Serum biomarkers identification by mass spectrometry in high-mortality tumors. INTERNATIONAL JOURNAL OF PROTEOMICS 2013; 2013:125858. [PMID: 23401773 PMCID: PMC3562576 DOI: 10.1155/2013/125858] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 11/16/2012] [Accepted: 12/11/2012] [Indexed: 02/08/2023]
Abstract
Cancer affects millions of people worldwide. Tumor mortality is substantially due to diagnosis at stages that are too late for therapies to be effective. Advances in screening methods have improved the early diagnosis, prognosis, and survival for some cancers. Several validated biomarkers are currently used to diagnose and monitor the progression of cancer, but none of them shows adequate specificity, sensitivity, and predictive value for population screening. So, there is an urgent need to isolate novel sensitive, specific biomarkers to detect the disease early and improve prognosis, especially in high-mortality tumors. Proteomic techniques are powerful tools to help in diagnosis and monitoring of treatment and progression of the disease. During the last decade, mass spectrometry has assumed a key role in most of the proteomic analyses that are focused on identifying cancer biomarkers in human serum, making it possible to identify and characterize at the molecular level many proteins or peptides differentially expressed. In this paper we summarize the results of mass spectrometry serum profiling and biomarker identification in high mortality tumors, such as ovarian, liver, lung, and pancreatic cancer.
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27
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Gianazza E, Chinello C, Mainini V, Cazzaniga M, Squeo V, Albo G, Signorini S, Di Pierro SS, Ferrero S, Nicolardi S, van der Burgt YE, Deelder AM, Magni F. Alterations of the serum peptidome in renal cell carcinoma discriminating benign and malignant kidney tumors. J Proteomics 2012; 76 Spec No.:125-40. [DOI: 10.1016/j.jprot.2012.07.032] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/16/2012] [Accepted: 07/19/2012] [Indexed: 01/21/2023]
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28
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Sample preparation techniques for the untargeted LC-MS-based discovery of peptides in complex biological matrices. J Biomed Biotechnol 2011; 2011:245291. [PMID: 22203783 PMCID: PMC3238806 DOI: 10.1155/2011/245291] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 09/01/2011] [Indexed: 12/31/2022] Open
Abstract
Although big progress has been made in sample pretreatment over the last years, there are still considerable limitations when it comes to overcoming complexity and dynamic range problems associated with peptide analyses from biological matrices. Being the little brother of proteomics, peptidomics is a relatively new field of research aiming at the direct analysis of the small proteins, called peptides, many of which are not amenable for typical trypsin-based analytics. In this paper, we present an overview of different techniques and methods currently used for reducing a sample's complexity and for concentrating low abundant compounds to enable successful peptidome analysis. We focus on techniques which can be employed prior to liquid chromatography coupled to mass spectrometry for peptide detection and identification and indicate their advantages as well as their shortcomings when it comes to the untargeted analysis of native peptides from complex biological matrices.
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29
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Abstract
Two frontline MS technologies, which have recently gained much attention, are discussed within the scope of this review. Besides a brief summary on the contemporary state of lung cancer and chronic obstructive pulmonary disease, the principles of multiple reaction monitoring and matrix assisted laser desorption ionization (MALDI) MS imaging are presented. A comprehensive overview of quantitative mass spectrometry applications is provided, covering multiple reaction monitoring assay developments for analysis of proteins (biomarkers) and low-molecular-weight compounds (drugs) with a special focus on the disease areas of lung cancer and chronic obstructive pulmonary disease. The MALDI-MS imaging applications are discussed similarly, providing references to studies conducted on lung tissues in order to localize drug compounds and protein biomarkers.
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