Clinical proteomics最新文献

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Proteomic analysis of breast cancer based on immune subtypes. 基于免疫亚型的乳腺癌蛋白质组分析。
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-29 DOI: 10.1186/s12014-024-09463-y
Yeonjin Jeon, GunHee Lee, Hwangkyo Jeong, Gyungyub Gong, JiSun Kim, Kyunggon Kim, Jae Ho Jeong, Hee Jin Lee
{"title":"Proteomic analysis of breast cancer based on immune subtypes.","authors":"Yeonjin Jeon, GunHee Lee, Hwangkyo Jeong, Gyungyub Gong, JiSun Kim, Kyunggon Kim, Jae Ho Jeong, Hee Jin Lee","doi":"10.1186/s12014-024-09463-y","DOIUrl":"10.1186/s12014-024-09463-y","url":null,"abstract":"<p><strong>Background: </strong>Immunotherapy is applied to breast cancer to resolve the limitations of survival gain in existing treatment modalities. With immunotherapy, a tumor can be classified into immune-inflamed, excluded and desert based on the distribution of immune cells. We assessed the clinicopathological features, each subtype's prognostic value and differentially expressed proteins between immune subtypes.</p><p><strong>Methods: </strong>Immune subtyping and proteomic analysis were performed on 56 breast cancer cases with neoadjuvant chemotherapy. The immune subtyping was based on the level of tumor-infiltrating lymphocytes (TILs) and Klintrup criteria. If the level of TILs was ≥ 10%, it was classified as immune-inflamed type without consideration of the Klintrup criteria. In cases of 1-9% TIL, Klintrup criteria 1-3 were classified as the immune-excluded subtype and Klintrup criteria not available (NA) was classified as NA. Cases of 1% TILs and Klintrup 0 were classified as the immune-desert subtype. Mass spectrometry was used to identify differentially expressed proteins in formalin-fixed paraffin-embedded biopsy tissues.</p><p><strong>Results: </strong>Of the 56 cases, 31 (55%) were immune-inflamed, 21 (38%) were immune-excluded, 2 (4%) were immune-desert and 2 (4%) were NA. Welch's t-test revealed two differentially expressed proteins between immune-inflamed and immune-excluded/desert subtypes. Coronin-1A was upregulated in immune-inflamed tumors (adjusted p = 0.008) and α-1-antitrypsin was upregulated in immune-excluded/desert tumors (adjusted p = 0.008). Titin was upregulated in pathologic complete response (pCR) than non-pCR among immune-inflamed tumors (adjusted p = 0.036).</p><p><strong>Conclusions: </strong>Coronin-1A and α-1-antitrypsin were upregulated in immune-inflamed and immune-excluded/desert subtypes, respectively. Titin's elevated expression in pCR within the immune-inflamed subtype may indicate a favorable prognosis. Further studies involving large representative cohorts are necessary to validate these findings.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10905797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Highly sensitive therapeutic drug monitoring of infliximab in serum by targeted mass spectrometry in comparison to ELISA data. 通过靶向质谱法对血清中的英夫利昔单抗进行高灵敏度治疗药物监测,并与酶联免疫吸附试验数据进行比较。
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-29 DOI: 10.1186/s12014-024-09464-x
Andreas Hentschel, Gina Piontek, Rob Dahlmann, Peter Findeisen, Roman Sakson, Phil Carbow, Thomas Renné, Yvonne Reinders, Albert Sickmann
{"title":"Highly sensitive therapeutic drug monitoring of infliximab in serum by targeted mass spectrometry in comparison to ELISA data.","authors":"Andreas Hentschel, Gina Piontek, Rob Dahlmann, Peter Findeisen, Roman Sakson, Phil Carbow, Thomas Renné, Yvonne Reinders, Albert Sickmann","doi":"10.1186/s12014-024-09464-x","DOIUrl":"10.1186/s12014-024-09464-x","url":null,"abstract":"<p><strong>Background: </strong>Presently, antibody concentration measurements for patients undergoing treatment are predominantly determined by ELISA, which still comes with known disadvantages. Therefore, our aim was to establish a targeted mass-spectrometric assay enabling the reproducible absolute quantification of peptides from the hypervariable and interaction regions of infliximab.</p><p><strong>Methods: </strong>Peptides of infliximab were measured post-trypsin digestion and subsequent separation on a Vanquish Horizon UHPLC coupled to a TSQ Altis Triple-Quad mass spectrometer. Normalization and absolute quantification were conducted using stable isotope-synthesized peptides. Calibration curves covering a range of 0.25-50 µg/ml were employed for quantitation.</p><p><strong>Results: </strong>We demonstrated the substantial influence of peptide selection, choice of hydrolase for digestion, and digestion time on absolute peptide yield (28-44% for peptide 1 and 64-97% for peptide 2). Furthermore, we showed that the generated calibration curves for absolute quantification were highly reproducible and robust (LLOQ1 0.72 µg/ml and LLOQ2 1.00 µg/ml) over several months. In comparison to ELISA values, the absolute values obtained by mass spectrometry often yielded lower results for both targeted peptides.</p><p><strong>Conclusions: </strong>In this study, a semi-automated workflow was employed and tested with 8 patients and corresponding replicates (n = 3-4). We demonstrated the robust implementation of calibration curves for the absolute quantification of infliximab in patient samples, with coefficients of variation ranging from 0.5 to 9%. Taken together, we have developed a platform enabling the rapid (2 days of sample preparation and 30 min of measurement time per sample) and robust quantification of Infliximab antibody concentration in patients. The use of mass spectrometry also facilitates the straightforward expansion of the method to include additional antibody peptides.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10905900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Proteomic insights into the pathophysiology of hypertension-associated albuminuria: Pilot study in a South African cohort. 蛋白质组学对高血压相关性白蛋白尿病理生理学的启示:南非队列试点研究。
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-24 DOI: 10.1186/s12014-024-09458-9
Melanie A Govender, Stoyan H Stoychev, Jean-Tristan Brandenburg, Michèle Ramsay, June Fabian, Ireshyn S Govender
{"title":"Proteomic insights into the pathophysiology of hypertension-associated albuminuria: Pilot study in a South African cohort.","authors":"Melanie A Govender, Stoyan H Stoychev, Jean-Tristan Brandenburg, Michèle Ramsay, June Fabian, Ireshyn S Govender","doi":"10.1186/s12014-024-09458-9","DOIUrl":"10.1186/s12014-024-09458-9","url":null,"abstract":"<p><strong>Background: </strong>Hypertension is an important public health priority with a high prevalence in Africa. It is also an independent risk factor for kidney outcomes. We aimed to identify potential proteins and pathways involved in hypertension-associated albuminuria by assessing urinary proteomic profiles in black South African participants with combined hypertension and albuminuria compared to those who have neither condition.</p><p><strong>Methods: </strong>The study included 24 South African cases with both hypertension and albuminuria and 49 control participants who had neither condition. Protein was extracted from urine samples and analysed using ultra-high-performance liquid chromatography coupled with mass spectrometry. Data were generated using data-independent acquisition (DIA) and processed using Spectronaut™ 15. Statistical and functional data annotation were performed on Perseus and Cytoscape to identify and annotate differentially abundant proteins. Machine learning was applied to the dataset using the OmicLearn platform.</p><p><strong>Results: </strong>Overall, a mean of 1,225 and 915 proteins were quantified in the control and case groups, respectively. Three hundred and thirty-two differentially abundant proteins were constructed into a network. Pathways associated with these differentially abundant proteins included the immune system (q-value [false discovery rate] = 1.4 × 10<sup>- 45</sup>), innate immune system (q = 1.1 × 10<sup>- 32</sup>), extracellular matrix (ECM) organisation (q = 0.03) and activation of matrix metalloproteinases (q = 0.04). Proteins with high disease scores (76-100% confidence) for both hypertension and chronic kidney disease included angiotensinogen (AGT), albumin (ALB), apolipoprotein L1 (APOL1), and uromodulin (UMOD). A machine learning approach was able to identify a set of 20 proteins, differentiating between cases and controls.</p><p><strong>Conclusions: </strong>The urinary proteomic data combined with the machine learning approach was able to classify disease status and identify proteins and pathways associated with hypertension-associated albuminuria.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10893729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139943978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recent progress in mass spectrometry-based urinary proteomics. 基于质谱的尿液蛋白质组学的最新进展。
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-22 DOI: 10.1186/s12014-024-09462-z
Neha Joshi, Kishore Garapati, Vivek Ghose, Richard K Kandasamy, Akhilesh Pandey
{"title":"Recent progress in mass spectrometry-based urinary proteomics.","authors":"Neha Joshi, Kishore Garapati, Vivek Ghose, Richard K Kandasamy, Akhilesh Pandey","doi":"10.1186/s12014-024-09462-z","DOIUrl":"10.1186/s12014-024-09462-z","url":null,"abstract":"<p><p>Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10885485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139930345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Lessons learned: establishing a CLIA-equivalent laboratory for targeted mass spectrometry assays – navigating the transition from research to clinical practice 经验教训:为目标质谱测定建立 CLIA 同等实验室 - 从研究到临床实践的过渡导航
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-22 DOI: 10.1186/s12014-024-09455-y
Chia-Li Han, Chi-Ting Lai, Aaron James Reyes, Hao-Chin Yang, Jin-Ying Lu, Shyang-Rong Shih, Kuen-Yuan Chen, Andrew N. Hoofnagle, Sung-Liang Yu, William Bocik, Tara Hiltke, Huan-Chi Chiu, Ching-Yi Wan, Henry Rodriguez, Victoria Zhang, Yu-Ju Chen
{"title":"Lessons learned: establishing a CLIA-equivalent laboratory for targeted mass spectrometry assays – navigating the transition from research to clinical practice","authors":"Chia-Li Han, Chi-Ting Lai, Aaron James Reyes, Hao-Chin Yang, Jin-Ying Lu, Shyang-Rong Shih, Kuen-Yuan Chen, Andrew N. Hoofnagle, Sung-Liang Yu, William Bocik, Tara Hiltke, Huan-Chi Chiu, Ching-Yi Wan, Henry Rodriguez, Victoria Zhang, Yu-Ju Chen","doi":"10.1186/s12014-024-09455-y","DOIUrl":"https://doi.org/10.1186/s12014-024-09455-y","url":null,"abstract":"Mass spectrometry (MS) assays offer exceptional capabilities in high multiplexity, specificity, and throughput. As proteomics technologies continue advancements to identify new disease biomarkers, transition of these innovations from research settings to clinical applications becomes imperative. To meet the rigorous regulatory standards of clinical laboratories, development of a clinical protein MS assay necessitates adherence to stringent criteria. To illustrate the process, this project focused on using thyroglobulin (Tg) as a biomarker and an immuno-multiple reaction monitoring (iMRM) MS-based assay as a model for establishing a Clinical Laboratory Improvement Amendments (CLIA) compliant laboratory within the Centers of Genomic and Precision Medicine, National Taiwan University. The chosen example also illustrates the clinical utility of MS assays to complement conventional immunoassay-based methods, particularly in cases where the presence of autoantibodies in 10–30% of patients hinders accuracy. The laboratory design entails a comprehensive coordination in spatial layout, workflow organization, equipment selection, ventilation systems, plumbing, electrical infrastructure, documentation procedures, and communication protocols. Practical aspects of the transformation process, including preparing laboratory facilities, testing environments, instrument validation, assay development and validation, quality management, sample testing, and personnel competency, are discussed. Finally, concordant results in proficiency testing demonstrate the harmonization with the University of Washington Medical Center and the quality assurance of the CLIA-equivalent Tg-iMRM MS assay established in Taiwan. The realization of this model protein MS assay in Taiwan highlights the feasibility of international joint development and provides a detailed reference map to expedite the implementation of more MS-based protein assays in clinical laboratories for patient care.","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139925524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Kinome and phosphoproteome reprogramming underlies the aberrant immune responses in critically ill COVID-19 patients COVID-19重症患者异常免疫反应的基因组和磷酸蛋白组重编程基础
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-22 DOI: 10.1186/s12014-024-09457-w
Tomonori Kaneko, Sally Ezra, Rober Abdo, Courtney Voss, Shanshan Zhong, Xuguang Liu, Owen Hovey, Marat Slessarev, Logan Robert Van Nynatten, Mingliang Ye, Douglas Fraser, Shawn Shun-Cheng Li
{"title":"Kinome and phosphoproteome reprogramming underlies the aberrant immune responses in critically ill COVID-19 patients","authors":"Tomonori Kaneko, Sally Ezra, Rober Abdo, Courtney Voss, Shanshan Zhong, Xuguang Liu, Owen Hovey, Marat Slessarev, Logan Robert Van Nynatten, Mingliang Ye, Douglas Fraser, Shawn Shun-Cheng Li","doi":"10.1186/s12014-024-09457-w","DOIUrl":"https://doi.org/10.1186/s12014-024-09457-w","url":null,"abstract":"SARS-CoV-2 infection triggers extensive host immune reactions, leading to severe diseases in certain individuals. However, the molecular basis underlying the excessive yet non-productive immune responses in severe COVID-19 remains incompletely understood. In this study, we conducted a comprehensive analysis of the peripheral blood mononuclear cell (PBMC) proteome and phosphoproteome in sepsis patients positive or negative for SARS-CoV-2 infection, as well as healthy subjects, using quantitative mass spectrometry. Our findings demonstrate dynamic changes in the COVID-19 PBMC proteome and phosphoproteome during disease progression, with distinctive protein or phosphoprotein signatures capable of distinguishing longitudinal disease states. Furthermore, SARS-CoV-2 infection induces a global reprogramming of the kinome and phosphoproteome, resulting in defective adaptive immune response mediated by the B and T lymphocytes, compromised innate immune responses involving the SIGLEC and SLAM family of immunoreceptors, and excessive cytokine-JAK-STAT signaling. In addition to uncovering host proteome and phosphoproteome aberrations caused by SARS-CoV-2, our work recapitulates several reported therapeutic targets for COVID-19 and identified numerous new candidates, including the kinases PKG1, CK2, ROCK1/2, GRK2, SYK, JAK2/3, TYK2, DNA-PK, PKCδ, and the cytokine IL-12.","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139925591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparison of early changes in tear film protein profiles after small incision lenticule extraction (SMILE) and femtosecond LASIK (FS-LASIK) surgery 小切口皮瓣摘除术(SMILE)和飞秒激光角膜切割术(FS-LASIK)术后泪膜蛋白图谱早期变化的比较
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-17 DOI: 10.1186/s12014-024-09460-1
Petri Mäkinen, Janika Nättinen, Ulla Aapola, Juhani Pietilä, Hannu Uusitalo
{"title":"Comparison of early changes in tear film protein profiles after small incision lenticule extraction (SMILE) and femtosecond LASIK (FS-LASIK) surgery","authors":"Petri Mäkinen, Janika Nättinen, Ulla Aapola, Juhani Pietilä, Hannu Uusitalo","doi":"10.1186/s12014-024-09460-1","DOIUrl":"https://doi.org/10.1186/s12014-024-09460-1","url":null,"abstract":"Small incision lenticule extraction (SMILE) and femtosecond laser-assisted in situ keratomileusis (LASIK) are widely used surgical methods to correct myopia with comparable efficacy, predictability, and safety. We examined and compared the early changes of tear protein profiles after SMILE and FS-LASIK surgery in order to find possible differences in the initial corneal healing process. SMILE operations for 26 eyes were made with Visumax femtosecond laser. In FS-LASIK surgery for 30 eyes, the flaps were made with Ziemer FEMTO LDV Z6 femtosecond laser and stromal ablation with Wavelight EX500 excimer laser. Tear samples were collected preoperatively, and 1.5 h and 1 month postoperatively using glass microcapillary tubes. Tear protein identification and quantification were performed with sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS). Immediately (1.5 h) after we found differences in 89 proteins after SMILE and in 123 after FS-LASIK operation compared to preoperative protein levels. Of these differentially expressed proteins, 48 proteins were common for both surgery types. There were, however, quantitative differences between SMILE and FS-LASIK. Upregulated proteins were mostly connected to inflammatory response and migration of the cells connected to immune system. One month after the operation protein expressions levels were returned to baseline levels with both surgical methods. Our study showed that immediate changes in protein profiles after SMILE and FS-LASIK surgeries and differences between the methods are connected to inflammatory process, and the protein levels quickly return to the baseline within 1 month. The differences in protein profiles between the methods are probably associated with the different size of the epithelial wound induced.","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the novel duo of Reticulocalbin, and Sideroflexin as future biomarker candidates for Exacerbated Chronic Obstructive Pulmonary Disease. 探索网状钙化素和苷元钙化素的新型二重奏,作为未来慢性阻塞性肺疾病恶化的候选生物标记物。
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-14 DOI: 10.1186/s12014-024-09459-8
Sonu Das, Supriya Adiody, Jinsu Varghese, M Vanditha, Evelyn Maria, Mathew John
{"title":"Exploring the novel duo of Reticulocalbin, and Sideroflexin as future biomarker candidates for Exacerbated Chronic Obstructive Pulmonary Disease.","authors":"Sonu Das, Supriya Adiody, Jinsu Varghese, M Vanditha, Evelyn Maria, Mathew John","doi":"10.1186/s12014-024-09459-8","DOIUrl":"10.1186/s12014-024-09459-8","url":null,"abstract":"<p><strong>Background: </strong>COPD is a complex respiratory disorder with high morbidity and mortality rates. Even with the current conventional diagnostic methods, including circulating inflammatory biomarkers, underdiagnosis rates in COPD remain as high as 70%. Our study was a comparative cross-sectional study that aimed to address the diagnostic challenges by identifying future biomarker candidates in COPD variants.</p><p><strong>Methods: </strong>This study used a label-free plasma proteomics approach that combined mass spectrometric data with bioinformatics to shed light on the functional roles of differentially expressed proteins in the COPD lung microenvironment. The predictive capacity of the screened proteins was assessed using Receiver Operating Characteristic (ROC) curves, with Western blot analysis validating protein expression patterns in an independent cohort.</p><p><strong>Results: </strong>Our study identified three DEPs-reticulocalbin-1, sideroflexin-4, and liprinα-3 that consistently exhibited altered expression in COPD exacerbation. ROC analysis indicated strong predictive potential, with AUC values of 0.908, 0.715, and 0.856 for RCN1, SFXN4, and LIPα-3, respectively. Validation through Western blot analysis confirmed their expression patterns in an independent validation cohort.</p><p><strong>Conclusions: </strong>Our study discovered a novel duo of proteins reticulocalbin-1, and sideroflexin-4 that showed potential as valuable future biomarkers for the diagnosis and clinical management of COPD exacerbations.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10865594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction: Glial cell proteome using targeted quantitative methods for potential multi-diagnostic biomarkers. 更正:胶质细胞蛋白质组使用靶向定量方法寻找潜在的多种诊断生物标记物。
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-10 DOI: 10.1186/s12014-024-09456-x
Narae Kang, Hyun Jeong Oh, Ji Hye Hong, Hyo Eun Moon, Yona Kim, Hyeon-Jeong Lee, Hophil Min, Hyeonji Park, Sang Hun Lee, Sun Ha Paek, Jonghwa Jin
{"title":"Correction: Glial cell proteome using targeted quantitative methods for potential multi-diagnostic biomarkers.","authors":"Narae Kang, Hyun Jeong Oh, Ji Hye Hong, Hyo Eun Moon, Yona Kim, Hyeon-Jeong Lee, Hophil Min, Hyeonji Park, Sang Hun Lee, Sun Ha Paek, Jonghwa Jin","doi":"10.1186/s12014-024-09456-x","DOIUrl":"10.1186/s12014-024-09456-x","url":null,"abstract":"","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10858455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139715892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Absolute quantitation of human wild-type DNAI1 protein in lung tissue using a nanoLC-PRM-MS-based targeted proteomics approach coupled with immunoprecipitation. 利用基于纳米液相色谱-PRM-MS 的靶向蛋白质组学方法和免疫沉淀技术,对肺组织中的人类野生型 DNAI1 蛋白进行绝对定量。
IF 3.8 3区 医学
Clinical proteomics Pub Date : 2024-02-04 DOI: 10.1186/s12014-024-09453-0
Hui Wang, Xiaoyan Ni, Nicholas Clark, Kristen Randall, Lianne Boeglin, Sudha Chivukula, Caroline Woo, Frank DeRosa, Gang Sun
{"title":"Absolute quantitation of human wild-type DNAI1 protein in lung tissue using a nanoLC-PRM-MS-based targeted proteomics approach coupled with immunoprecipitation.","authors":"Hui Wang, Xiaoyan Ni, Nicholas Clark, Kristen Randall, Lianne Boeglin, Sudha Chivukula, Caroline Woo, Frank DeRosa, Gang Sun","doi":"10.1186/s12014-024-09453-0","DOIUrl":"10.1186/s12014-024-09453-0","url":null,"abstract":"<p><strong>Background: </strong>Dynein axonemal intermediate chain 1 protein (DNAI1) plays an essential role in cilia structure and function, while its mutations lead to primary ciliary dyskinesia (PCD). Accurate quantitation of DNAI1 in lung tissue is crucial for comprehensive understanding of its involvement in PCD, as well as for developing the potential PCD therapies. However, the current protein quantitation method is not sensitive enough to detect the endogenous level of DNAI1 in complex biological matrix such as lung tissue.</p><p><strong>Methods: </strong>In this study, a quantitative method combining immunoprecipitation with nanoLC-MS/MS was developed to measure the expression level of human wild-type (WT) DNAI1 protein in lung tissue. To our understanding, it is the first immunoprecipitation (IP)-MS based method for absolute quantitation of DNAI1 protein in lung tissue. The DNAI1 quantitation was achieved through constructing a standard curve with recombinant human WT DNAI1 protein spiked into lung tissue matrix.</p><p><strong>Results: </strong>This method was qualified with high sensitivity and accuracy. The lower limit of quantitation of human DNAI1 was 4 pg/mg tissue. This assay was successfully applied to determine the endogenous level of WT DNAI1 in human lung tissue.</p><p><strong>Conclusions: </strong>The results clearly demonstrate that the developed assay can accurately quantitate low-abundance WT DNAI1 protein in human lung tissue with high sensitivity, indicating its high potential use in the drug development for DNAI1 mutation-caused PCD therapy.</p>","PeriodicalId":10468,"journal":{"name":"Clinical proteomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10840268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139680807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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