Review
Pharmacology & Pharmacy
Qi Xiao, Fangfei Zhang, Luang Xu, Liang Yue, Oi Lian Kon, Yi Zhu, Tiannan Guo
Summary: This paper summarizes the advances and limitations of biomarkers in cancer research, as well as the important applications of mass spectrometry technology in proteomics. The article emphasizes the role of artificial intelligence technology in clinical studies, as well as the importance of combining computational and statistical methods in biomarker research.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Review
Oncology
Yoshimi Haga, Yuriko Minegishi, Koji Ueda
Summary: Proteomic analysis has become an important tool in understanding the molecular characteristics of cancer. The use of mass spectrometry allows for direct examination of protein variants and modifications. Integrating proteomic data with genomic, epigenomic, and transcriptomic data has led to new knowledge in the field of proteogenomics. Deep proteomic profiling has potential clinical applications in cancer research and personalized medicine.
Review
Microbiology
Jiubiao Guo, Ximeng Zhang, Xinchun Chen, Yi Cai
Summary: Researchers are utilizing proteomics technology to discover new biomarkers for tuberculosis diagnosis, and while some progress has been made, challenges and uncertainties still remain.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Spectroscopy
Chad J. Creighton
Summary: Recent technological advancements in mass spectrometry (MS)-based proteomics have allowed for greater study of human tumor specimens and the generation of large-scale proteomic profiling data combined with multiomics data. These datasets can be revisited by researchers for different purposes than the original studies. This review examines the increasing role of proteomics in cancer research and the potential of previous studies and associated data to improve cancer diagnosis and treatment. It also explores publicly available proteomics and multi-omics data on cancer cell line models and how this information can contribute to the identification of therapeutic strategies for specific cancer subsets.
MASS SPECTROMETRY REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Sungtaek Oh, Yura Jang, Chan Hyun Na
Summary: This study used discovery-based approaches and quantitative comparative analyses to identify differential proteins in the cerebrospinal fluid (CSF) of patients with ALS. They found 15 proteins that showed significant differences between ALS and the control group, providing a foundation for biomarker research in ALS.
Review
Biochemistry & Molecular Biology
Joohyun Ryu, Stefani N. Thomas
Summary: Ovarian cancer is a deadly gynecologic malignancy with the need for new and more effective treatment strategies, while early detection and protein biomarkers play crucial roles. Targeted proteomics methods, including mass spectrometry, offer robust solutions for the development of ovarian cancer biomarkers.
Review
Biochemical Research Methods
Suruchi Aggarwal, Anurag Raj, Dhirendra Kumar, Debasis Dash, Amit Kumar Yadav
Summary: Proteogenomics integrates genome and proteome analysis to improve genome annotation and discover new insights by controlling error rates. However, challenges arise due to database size inflation, leading to reduced sensitivity and specificity in proteogenomic studies. Understanding key factors and applying modified strategies can enhance interpretation of mass spectrometry data and effectively manage false positives and negatives.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Muneeza Zafar, Imran Riaz Malik, Munazza Raza Mirza, Fazli Rabbi Awan, Arkadiusz Nawrocki, Misbah Hussain, Haq Nawaz Khan, Shahid Abbas, Muhammad Iqbal Choudhary, Martin R. R. Larsen
Summary: This study investigated the genetic influence of APOB rs1042031 (G/T) genotype on serum proteome in Pakistani subjects with Coronary Artery Disease (CAD). The genotypic frequencies were significantly different between CAD patients and healthy individuals, with the GG genotype showing a strong association with CAD. Proteomic analysis revealed altered expression of several proteins involved in pathways related to lipid metabolism in carriers of the GG genotype.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemical Research Methods
Caleb M. Lindgren, David W. Adams, Benjamin Kimball, Hannah Boekweg, Sadie Tayler, Samuel L. Pugh, Samuel H. Payne
Summary: Comprehensive cancer data sets generated by CPTAC offer potential for advancing cancer research. They have created an API for distributing processed data, facilitating data reuse and integration for analysis.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Sumaiya Nazli, Kip D. Zimmerman, Angelica M. Riojas, Laura A. Cox, Michael Olivier
Summary: The proteomic analysis of plasma has great potential for precision medicine and biomarker identification. However, detecting and quantifying low abundance proteins in plasma is challenging. This study developed a mass spectrometry approach using tandem mass tags (TMT) and a tissue reference sample, which successfully identified and quantified numerous proteins in nonhuman primate plasma samples. The methodology promises to increase the number of putative disease biomarkers by efficiently quantifying plasma proteins released from specific tissues.
Article
Biochemistry & Molecular Biology
Hyebin Lee, Han Suk Ryu, Hee Chul Park, Jeong Il Yu, Gyu Sang Yoo, Changhoon Choi, Heerim Nam, Jason Joon Bock Lee, In-Gu Do, Dohyun Han, Sang Yun Ha
Summary: This study utilized mass spectrometry to analyze the proteomic profile of rectal cancer patients and validated the predictive capacity of protein biomarkers through immunohistochemical staining. The results revealed significantly differentially expressed proteins between different response groups, with biological processes related to cytoskeletal organization and immune response enriched in the complete responder group, and biosynthesis and transcription associated processes enriched in the non-complete responder group. Using machine learning algorithms, dual oxidase 2 (DUOX2) was identified as a potential biomarker for predicting treatment response. Overall, the study highlights the impact of pre-treatment tumor microenvironment on treatment response and suggests DUOX2 as an early predictor for non-complete response after chemoradiation therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Yanhong Liu, Lan Gao, Yanru Fan, Rufei Ma, Yunxia An, Guanghui Chen, Yan Xie
Summary: Potential protein biomarkers and mechanism of venous thromboembolism (VTE) in non-small cell lung cancer (NSCLC) patients were identified through proteomics research. A total of 280 differentially expressed proteins were found, and 5 proteins (SAA1, S100A8, LBP, HP and LDHB) showed significant changes between VTE and non-VTE patients. These results suggest that these proteins may be used for diagnosing VTE in NSCLC patients.
FRONTIERS IN ONCOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Natalia A. Shnayder, Victoria B. Sharavii, Marina M. Petrova, Polina Moskaleva, Elena A. Pozhilenkova, Darya S. Kaskaeva, Olga Tutynina, Tatiana E. Popova, Natalia P. Garganeeva, Regina F. Nasyrova
Summary: The research analyzed potential proteomic biomarkers in the serum and urine of chronic headache patients, identified several proteins related to MOH, and discussed their potential roles in identifying patients with MOH development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medical Laboratory Technology
Ximeng Chen, Jianan Wang, Jinyang Wang, Jingyun Ye, Ping Di, Chang Dong, Hong Lei, Chengbin Wang
Summary: This study utilized proteomics to analyze serum proteins and identify potential biomarkers for the diagnosis of osteoarticular tuberculosis. ITIH2, CFHR2, CFHR3, and CFHR5 were found to be potential biomarkers, with CFHR2 and CFHR3 showing good diagnostic efficacy when combined in a diagnostic model.
CLINICA CHIMICA ACTA
(2023)
Review
Biochemistry & Molecular Biology
Gengjun Zhu, Lifang Jin, Wanchun Sun, Shuang Wang, Ning Liu
Summary: This review highlights the importance of post-translational modifications (PTMs) in colorectal cancer (CRC) and discusses their role in diagnosis, prognosis, and treatment. The review summarizes the proteomic profiling strategies for key PTMs and describes the methods used to delineate the global landscapes of each PTM. The review also discusses the current status of PTM research in CRC and provides future perspectives on the role of PTM regulation in translational medicine for CRC.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Article
Biochemical Research Methods
Matthew Waas, Thomas Kislinger
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Biochemical Research Methods
Joseph J. Otto, Vanessa L. Correll, Hampus A. Engstroem, Naomi L. Hitefield, Brian P. Main, Brenna Albracht, Teresa Johnson-Pais, Li Fang Yang, Michael Liss, Paul C. Boutros, Thomas Kislinger, Robin J. Leach, Oliver J. Semmes, Julius O. Nyalwidhe
PROTEOMICS CLINICAL APPLICATIONS
(2020)
Article
Multidisciplinary Sciences
Deborah Wenk, Vladimir Ignatchenko, Andrew Macklin, Harald Huebner, Peter Gmeiner, Dorothee Weikert, Monika Pischetsrieder, Thomas Kislinger
Summary: The study found that biased and balanced dopamine D-2 receptor agonists and antagonists can impact the global protein expression in cells, with antagonists affecting exocytosis and peroxisome function, while balanced agonists leading to downregulation of proteins involved in synaptic signaling.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Andres Di Paolo, Joaquina Farias, Joaquin Garat, Andrew Macklin, Vladimir Ignatchenko, Thomas Kislinger, Jose Sotelo Silveira
Summary: In this study, proteomic analysis was used to investigate axons in adult rat sciatic nerves, revealing an increase in ribosomal proteins after injury and newly synthesized axonal proteins. The results suggest that proteomics profiling is an effective method for interrogating axons, and that ribosomal proteins may play an important role during injury.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Farshad Nassiri, Jeff Liu, Vikas Patil, Yasin Mamatjan, Justin Z. Wang, Rupert Hugh-White, Andrew M. Macklin, Shahbaz Khan, Olivia Singh, Shirin Karimi, Rosario I. Corona, Lydia Y. Liu, Caroline Y. Chen, Ankur Chakravarthy, Qingxia Wei, Bharati Mehani, Suganth Suppiah, Andrew Gao, Adriana M. Workewych, Ghazaleh Tabatabai, Paul C. Boutros, Gary D. Bader, Daniel D. de Carvalho, Thomas Kislinger, Kenneth Aldape, Gelareh Zadeh
Summary: Meningiomas, the most common primary intracranial tumor in adults, often require surgery due to lack of effective medical therapies. This study introduced four consensus molecular groups of meningioma, which accurately predicted clinical outcomes and informed therapeutic options. Single-cell RNA sequencing revealed inter-individual variations in meningioma biology, highlighting the importance of molecular classification in guiding treatment strategies.
Review
Urology & Nephrology
Amanda Khoo, Lydia Y. Liu, Julius O. Nyalwidhe, O. John Semmes, Danny Vesprini, Michelle R. Downes, Paul C. Boutros, Stanley K. Liu, Thomas Kislinger
Summary: Prostate cancer patients urgently need biomarkers to improve risk stratification, as current clinical prognostic tools are not accurate enough. Mass spectrometry technologies enable systematic discovery and validation of protein-based biomarkers in relevant fluids. Existing protein biomarkers for diagnosis, prognosis, and relapse-monitoring in localized prostate cancer are predominantly centered around PSA and its variants.
NATURE REVIEWS UROLOGY
(2021)
Article
Biochemical Research Methods
Natalie Kurganovs, Hanzhi Wang, Xiaoyong Huang, Vladimir Ignatchenko, Andrew Macklin, Shahbaz Khan, Michelle R. Downes, Paul C. Boutros, Stanley K. Liu, Thomas Kislinger
Summary: Proteomic analysis of DU145 prostate cancer cells revealed over 400 differentially expressed proteins in radiation resistant cell lines, with enrichment in pathways such as epithelial to mesenchymal transition, glycolysis, and hypoxia. The cell surface protein CD44 was identified as a potential therapeutic target in the glycolysis and epithelial to mesenchymal transition pathways among the radiation resistant protein candidates.
PROTEOMICS CLINICAL APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Barbara T. Grunwald, Antoine Devisme, Geoffroy Andrieux, Foram Vyas, Kazeera Aliar, Curtis W. McCloskey, Andrew Macklin, Gun Ho Jang, Robert Denroche, Joan Miguel Romero, Prashant Bavi, Peter Bronsert, Faiyaz Notta, Grainne O'Kane, Julie Wilson, Jennifer Knox, Laura Tamblyn, Molly Udaskin, Nikolina Radulovich, Sandra E. Fischer, Melanie Boerries, Steven Gallinger, Thomas Kislinger, Rama Khokha
Summary: Through large-scale integration of histology-guided regional multiOMICs with clinical data and patient-derived preclinical models, we identified distinct subTMEs in the human pancreatic tumor microenvironment (TME) that are linked to tumor immunity, subtypes, differentiation, and treatment response. Reactive subTMEs rich in coordinated fibroblast communities were immune hot, while matrix-rich deserted subTMEs harbored fewer activated fibroblasts but showed chemoprotective features. These subTMEs originated in fibroblast differentiation trajectories and produced patient-specific heterogeneity tightly linked to malignant biology.
Article
Oncology
Jeffrey A. Zuccato, Vikas Patil, Sheila Mansouri, Jeffrey C. Liu, Farshad Nassiri, Yasin Mamatjan, Ankur Chakravarthy, Shirin Karimi, Joao Paulo Almeida, Anne-Laure Bernat, Mohammed Hasen, Olivia Singh, Shahbaz Khan, Thomas Kislinger, Namita Sinha, Sebastien Froelich, Homa Adle-Biassette, Kenneth D. Aldape, Daniel D. De Carvalho, Gelareh Zadeh
Summary: This study identifies prognostic epigenetic chordoma subtypes using plasma methylomes and may transform patient management by balancing treatment aggressiveness with patient risk according to prognosis. Plasma methylomes can distinguish chordomas from other clinical diagnoses and accurately classify tumors based on plasma methylation data.
Article
Oncology
Mathieu Seyfrid, William Thomas Maich, Vaseem Muhammad Shaikh, Nazanin Tatari, Deepak Upreti, Deween Piyasena, Minomi Subapanditha, Neil Savage, Dillon McKenna, Nicholas Mikolajewicz, Hong Han, Chirayu Chokshi, Laura Kuhlmann, Amanda Khoo, Sabra Khalid Salim, Blessing Archibong-Bassey, William Gwynne, Kevin Brown, Nadeem Murtaza, David Bakhshinyan, Parvez Vora, Chitra Venugopal, Jason Moffat, Thomas Kislinger, Sheila Singh
Summary: This study identifies CD70 as a potential therapeutic target for recurrent glioblastoma stem cells (CSCs). Targeting CD70 with CAR-T therapy significantly improves prognosis in animal models and the CD70/CD27 axis may provide a viable polytherapeutic avenue for targeting both glioblastoma and its tumor immune microenvironment.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Cell Biology
Vanessa L. Correll, Joseph J. Otto, Cristina M. Risi, Brian P. Main, Paul C. Boutros, Thomas Kislinger, Vitold E. Galkin, Julius O. Nyalwidhe, O. John Semmes, Lifang Yang
Summary: Isolation and analysis of extracellular vesicles (EVs) from urine samples is a common strategy for studying vesicle biology and biomarker discovery. However, standard EV isolation methods often co-isolate protein contaminants and high levels of uromodulin (THP) in urine can reduce EV yield. In this study, a modified isolation method was developed to improve EV isolation and enrich prostate cancer-associated EV-resident proteins.
JOURNAL OF EXTRACELLULAR VESICLES
(2022)
Article
Biochemical Research Methods
Laura Kuhlmann, Meinusha Govindarajan, Salvador Mejia-Guerrero, Vladimir Ignatchenko, Lydia Y. Liu, Barbara T. Grunwald, Jennifer Cruickshank, Hal Berman, Rama Khokha, Thomas Kislinger
Summary: This study identified a previously undescribed TNBC-enriched cell surface protein, PLXNB3, through N-glycoproteome analysis, and demonstrated its crucial role in the growth, invasion, and migration of TNBC cells.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Meinusha Govindarajan, Vladimir Ignatchenko, Laurie Ailles, Thomas Kislinger
Summary: The tumor microenvironment, particularly cancer-associated fibroblasts (CAFs), plays a crucial role in the progression of high-grade serous ovarian cancer (HGSC). In this study, we used mass-spectrometry to analyze the proteomes of HGSC patient-derived CAFs and compared them with the epithelial component of HGSC, aiming to understand their tumor-promoting characteristics. By integrating our data with primary tissue data, we identified a proteomic signature of HGSC CAFs and discovered several novel CAF proteins that have prognostic value in an independent HGSC patient cohort. This study provides the first MS-based global proteomic characterization of CAFs in HGSC and emphasizes the clinical significance of HGSC CAFs.
Article
Endocrinology & Metabolism
Mathepan Jeya Mahendralingam, Hyeyeon Kim, Curtis William McCloskey, Kazeera Aliar, Alison Elisabeth Casey, Pirashaanthy Tharmapalan, Davide Pellacani, Vladimir Ignatchenko, Mar Garcia-Valero, Luis Palomero, Ankit Sinha, Jennifer Cruickshank, Ronak Shetty, Ravi N. Vellanki, Marianne Koritzinsky, Vid Stambolic, Mina Alam, Aaron David Schimmer, Hal Kenneth Berman, Connie J. Eaves, Miquel Angel Pujana, Thomas Kislinger, Rama Khokha
Summary: Cancer cells adapt their metabolic network from the tissue of origin. Normal mammary cells exhibit diverse metabolic programs, with basal cells enriched in glycolysis and luminal progenitors in oxidative phosphorylation. Targeting these metabolic vulnerabilities in mammary progenitors could potentially advance breast cancer therapy, as breast cancer subtypes retain metabolic features of their putative cell of origin.