Review
Medicine, Research & Experimental
Weihua Zhan, Song Zhang
Summary: TRIM proteins play key roles in various biological processes and are closely related to tumor development; Alterations in TRIM gene and protein levels frequently emerge in tumors and affect tumor progression; TRIM proteins maintain the balance between tumor suppressive and tumor promoting genes through ubiquitylation events.
Article
Biochemistry & Molecular Biology
Claudia Musial, Narcyz Knap, Renata Zaucha, Paulina Bastian, Giampaolo Barone, Giosue Lo Bosco, Fabrizio Lo-Celso, Lucyna Konieczna, Mariusz Belka, Tomasz Baczek, Antonella Marino Gammazza, Alicja Kuban-Jankowska, Francesco Cappello, Stephan Nussberger, Magdalena Gorska-Ponikowska
Summary: 2-Methoxyestradiol (2-ME) as an inhibitor for non-small cell lung cancer cells may serve as a potential therapeutic approach, reducing cell viability, promoting protein palmitoylation and oxidative stress, and showing relative safety in healthy human cells compared to other estrogen metabolism intermediates.
Article
Biochemistry & Molecular Biology
Claudia Musial, Narcyz Knap, Renata Zaucha, Paulina Bastian, Giampaolo Barone, Giosue Lo Bosco, Fabrizio Lo-Celso, Lucyna Konieczna, Mariusz Belka, Tomasz Baczek, Antonella Marino Gammazza, Alicja Kuban-Jankowska, Francesco Cappello, Stephan Nussberger, Magdalena Gorska-Ponikowska
Summary: Research shows that 2-ME can inhibit the growth of lung cancer cells and increase protein palmitoylation and oxidative stress phenomena. Through metabolomics analysis of blood serum, 2-ME can be used as a selective tumor biomarker in specific types of lung cancer. In addition, computational analysis suggests that 2-ME has relatively safe bioactivity in healthy human cells.
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Young-Ki Paik, Ileana M. Cristea, Fernando J. Corrales, Cecilia Lindskog, Susan Weintraub, Michael H. A. Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yu-Ju Chen, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: The 2021 Metrics of the HUPO Human Proteome Project (HPP) reveal significant progress in detecting protein expression in the human genome. The number of missing proteins has decreased, and the utilization of proteomics in biological and clinical research continues to expand and integrate effectively with other omics platforms. This represents a promising advancement in understanding the human proteome and its potential applications in healthcare.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Cardiac & Cardiovascular Systems
Hannah N. Marmor, Michael N. Kammer, Stephen A. Deppen, Maren Shipe, Valerie F. Welty, Khushbu Patel, Caroline Godfrey, Ehab Billatos, James G. Herman, David O. Wilson, Amanda K. Kussrow, Darryl J. Bornhop, Fabien Maldonado, Heidi Chen, Eric L. Grogan
Summary: The study aimed to compare different methods in diagnosing indeterminate pulmonary nodules, and the results showed that the integrated biomarker model had higher diagnostic accuracy.
JOURNAL OF THORACIC AND CARDIOVASCULAR SURGERY
(2023)
Article
Biochemistry & Molecular Biology
Wei-Sheng Wu, Hsin-Yi Wu, Pin-Hsuan Wang, Ting-Yu Chen, Kuan-Ru Chen, Chih-Wei Chang, Dong-En Lee, Bo-Heng Lin, William Chih-Wei Chang, Pao-Chi Liao
Summary: Lung cancer is a major cause of cancer-related death worldwide, and research is needed to dissect its pathogenic mechanisms and discover specific biomarkers. LCMD is the first database to provide information on lung cancer-related metabolites, aiming to promote the discovery of biomarkers for lung cancer.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Oncology
Jingwei Li, Qiran Zhang, Decheng Jiang, Jun Shao, Weimin Li, Chengdi Wang
Summary: Lung cancer has the highest mortality rate among malignancies worldwide. Circular RNAs (circRNAs), a type of covalently closed molecules, show potential clinical application prospects in lung cancer. This review explains the biogenesis, biological functions, and pathophysiology of circRNAs, and highlights their forefront in the diagnosis, prognosis, and therapy of lung cancer.
Article
Biochemistry & Molecular Biology
Junwen Ou, Qiulin Liao, Yanping Du, Wentao Xi, Qiong Meng, Kexin Li, Qichun Cai, Clifford L. K. Pang
Summary: This study explored the effect of high-dose intravenous vitamin C (IVC) treatment on gene expression in non-small cell lung cancer (NSCLC) cells and identified SERPINE1 and SERPINB7 as downregulated genes following IVC treatment. These genes were found to be related to patient prognosis in NSCLC, with high expression correlated with favorable prognosis in patients receiving IVC treatment.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Review
Pharmacology & Pharmacy
Adlina Roslan, Nurshahira Sulaiman, Khairul Asri Mohd Ghani, Armania Nurdin
Summary: This review discusses the studies on membrane proteins as potential biomarkers for personalized medicine, describing their types and significant functions as potential biomarkers for future medicine.
Article
Medicine, Research & Experimental
Soudeh Ghafouri-Fard, Marcel E. Dinger, Parichehr Maleki, Mohammad Taheri, Mohammadreza Hajiesmaeili
Summary: circRNAs have been proposed as molecular markers for lung cancer due to their stability in blood, showing potential value in disease detection. Dysregulation of circRNAs in lung cancer tissues suggests their potential involvement in carcinogenesis.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Review
Oncology
Median Zhao, Jianguo Feng, Liling Tang
Summary: CeRNAs can regulate biological processes through complex networks, potentially leading to cancer when imbalanced; Dysregulated RNAs in lung cancer may serve as ceRNAs to regulate various biological functions; CeRNAs are also being explored as potential prognostic and diagnostic biomarkers in lung cancer.
CANCER BIOLOGY & MEDICINE
(2021)
Article
Oncology
Hong Huang, Yongfeng Yang, Yihan Zhu, Hongyu Chen, Ying Yang, Li Zhang, Weimin Li
Summary: Lung cancer is the leading cause of cancer-related mortality, often diagnosed at advanced stages. Early detection and intervention are crucial to reducing mortality, and circulating biomarkers offer noninvasive and cost-effective real-time information. This review focuses on the research progress of three common types of blood protein biomarkers in lung cancer for potential clinical translation.
Article
Medicine, General & Internal
Roberto Gasparri, Giulia Sedda, Valentina Caminiti, Patrick Maisonneuve, Elena Prisciandaro, Lorenzo Spaggiari
Summary: Lung cancer is the leading cause of cancer deaths worldwide, and early detection is crucial for reducing the burden of the disease. Current diagnostic techniques have limitations, highlighting the need for reliable biomarkers for early identification. Urine could be a non-invasive alternative matrix, with potential for discovering diagnostic biomarkers.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Alina Frey, Daniel Martin, Louisa D'Cruz, Emmanouil Fokas, Claus Rodel, Maximilian Fleischmann
Summary: The study assessed the C-reactive protein (CRP) to albumin ratio (CAR) as a prognostic score in locally advanced non-small-cell lung cancer (NSCLC) patients treated with CRT. The findings showed that elevated CAR was associated with worse outcomes, including poorer local control and shorter survival.
Article
Biochemistry & Molecular Biology
Yihong Ren, Yuxin Zhao, Yanan Shan, Sixuan Li, Nan Su, Zhigang Cui, Zhihua Yin
Summary: This study found that hsa_circ_0049657, a circular RNA derived from the NFIX gene, was down-regulated in NSCLC tissues and cells. In addition, we could suppress the proliferation and invasion abilities and promote apoptosis of NSCLC cells by up-regulating hsa_circ_0049657.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Wooyoung Eric Jang, Ji Hwan Park, Gaeun Park, Geul Bang, Chan Hyun Na, Jin Young Kim, Kwang-Youl Kim, Kwang Pyo Kim, Chan Young Shin, Joon-Yong An, Yong-Seok Lee, Min-Sik Kim
Summary: This study revealed the Cntnap2-dependent molecular networks in ASD through multi-omics analysis. The findings showed that ASD cellular processes were mainly linked to excitatory neurons and exhibited mitochondrial dysfunction, axonal impairment, and synaptic activity.
MOLECULAR PSYCHIATRY
(2023)
Article
Materials Science, Multidisciplinary
R. Raman, Akhilesh Pandey, Sandeep Dalal, Subodh Tyagi, Shiv Kumar
Summary: Polarized Raman spectroscopy is used to determine and validate the crystallographic orientations of Zinc blend crystals. Two crystals of GaAs and ZnTe oriented along (112) are used in the study. Different angles of in-plane rotation and polarization are achieved by fixing the excitation laser polarization and rotating the sample. Raman spectroscopy is used to study crystallographic plane identification by measuring the Raman scattered intensity and fitting it with a transformation matrix relation.
APPLIED PHYSICS A-MATERIALS SCIENCE & PROCESSING
(2023)
Article
Neurosciences
Stefan Nicolau, Aneesha Dasgupta, Surendra Dasari, M. Cristine Charlesworth, Kenneth L. Johnson, Akhilesh Pandey, Jason D. Doles, Margherita Milone
Summary: Acquired sporadic late onset nemaline myopathy (SLONM) and inherited nemaline myopathy (iNM) both involve the accumulation of nemaline rods in muscle fibers. However, SLONM can be treated while iNM cannot. The distinction between these disorders is crucial for accurate diagnosis and the development of effective treatments. Through histological, proteomic, and transcriptomic analysis, we identified unique pathological and molecular signatures associated with SLONM and iNM, suggesting different underlying mechanisms. These findings provide valuable insights for enhancing diagnostic tools and developing treatments for SLONM.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Sudeep Verma, Akhilesh Pandey, Sandeep Dalal, Meenakshi Srivastava, R. Raman
Summary: This paper presents the growth of ZnTe crystal by the temperature gradient solvent method and the use of X-ray pole figure analysis to precisely orient the crystal along the (110) direction. The effect of orientation on Raman scattering and the terahertz response of (110) ZnTe substrates are studied. The results show enhanced multiphonon peaks in the resonant Raman spectra and high transmittance in the terahertz region for the (110) oriented ZnTe crystals.
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS
(2023)
Article
Biochemical Research Methods
Nicholas A. Shortreed, Anjali J. Panicker, Kiran K. Mangalaparthi, Jun Zhong, Akhilesh Pandey, Leigh G. Griffiths
Summary: This study optimized a shotgun immunoproteomics approach to improve the quantitative and reproducible identification of antigens, with the potential to facilitate novel antigen identification studies and innovations in various fields.
JOURNAL OF PROTEOMICS
(2023)
Article
Biochemical Research Methods
Ganesh P. Pujari, Kiran K. Mangalaparthi, Benjamin J. Madden, Firdous A. Bhat, M. Cristine Charlesworth, Amy J. French, Gunveen Sachdeva, Eugenio Daviso, Ulrich Thomann, Patrick McCarthy, Sameer Vasantgadkar, Debadeep Bhattacharyya, Akhilesh Pandey
Summary: Lasercapture microdissection (LCM) is essential for proteomic analysis of specific regions from FFPE tissue samples. Automation of sample preparation workflows is still under development. This study presents a simplified and rapid workflow using adaptive focused acoustics (AFA) technology for high-throughput FFPE-based proteomics.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Correction
Neurosciences
Wenhui Qiao, Yixing Chen, Jun Zhong, Benjamin J. Madden, Cristine M. Charlesworth, Yuka A. Martens, Chia-Chen Liu, Joshua Knight, Tadafumi C. Ikezu, Kurti Aishe, Yiyang Zhu, Axel Meneses, Cassandra L. Rosenberg, Lindsey A. Kuchenbecker, Lucy K. Vanmaele, Fuyao Li, Kai Chen, Francis Shue, Maxwell V. Dacquel, John Fryer, Akhilesh Pandey, Na Zhao, Guojun Bu
MOLECULAR NEURODEGENERATION
(2023)
Article
Biochemistry & Molecular Biology
Mithila Sawant, Audrey Wilson, Dhivya Sridaran, Kiran Mahajan, Christopher J. O'Conor, Ian S. Hagemann, Jingqin Luo, Cody Weimholt, Tiandao Li, Juan Carlos Roa, Akhilesh Pandey, Xinyan Wu, Nupam P. Mahajan
Summary: Hormone receptor-positive, HER2-negative advanced breast cancers, which are sensitive to CDK4/6 inhibitors, often develop resistance. However, a study found that the non-receptor tyrosine kinase ACK1 is activated in breast cancer subtypes independent of hormone receptor status. Inhibition of ACK1 resulted in the suppression of cell cycle genes, leading to G2/M arrest and regression of palbociclib-resistant breast tumor growth. ACK1 inhibition also impaired the metastasis of breast cancer cells to the lung.
Article
Clinical Neurology
Neeharika Sriram, Vikram V. Holla, Riyanka Kumari, Nitish Kamble, Jitender Saini, Rohan Mahale, Manjunath Netravathi, Hansashree Padmanabha, Vykuntaraju K. Gowda, Rajani Battu, Akhilesh Pandey, Ravi Yadav, Babylakshmi Muthusamy, Pramod Kumar Pal
Summary: This study aimed to investigate the clinical, radiological, and genetic features of PKAN. The study found that most patients had symptoms before the age of 10, with difficulty walking and dystonia being the most common symptoms. MRI showed hypo intensity signals in the brain. Genetic testing revealed mutations in the PANK2 gene, with 10 novel variants identified.
PARKINSONISM & RELATED DISORDERS
(2023)
Article
Biochemical Research Methods
Hung M. M. Vu, Hazara Begum Mohammad, Thy N. C. Nguyen, Jun Hyung Lee, Yeji Do, Ji-Youn Sung, Seung Hyeun Lee, Min-Sik Kim
Summary: In this study, potential biomarkers for small cell lung cancer (SCLC) were identified through quantitative proteomic analysis of bronchoalveolar lavage fluid (BALF). BALF is an emerging source of biomarkers for lung cancer. CNDP2 and RNPEP were found to be potential markers for SCLC subtypes, and CNDP2 was positively correlated with drug responses. These biomarkers could contribute to the diagnosis and treatment of SCLC.
PROTEOMICS CLINICAL APPLICATIONS
(2023)
Review
Biology
Siheun Lee, Hung M. M. Vu, Jung-Hyun Lee, Heejin Lim, Min-Sik Kim
Summary: Cell-to-cell variation in a population of the same cell type is influenced by stochastic gene and protein expression as well as environmental factors. Understanding this cellular heterogeneity is crucial for studying fundamental biology and complex diseases, and it requires advanced technologies for single-cell molecular profiling. Recent advances in mass spectrometry (MS)-based methods have greatly contributed to this field by enabling the analysis of proteins and metabolites at the single-cell level. This review provides an overview of the latest developments in MS-based single-cell analysis and their applications in biology and medicine.
Article
Biochemical Research Methods
Dong-Gi Mun, Neha S. Joshi, Rohit Budhraja, Gunveen S. Sachdeva, Taewook Kang, Firdous A. Bhat, Husheng Ding, Benjamin J. Madden, Jun Zhong, Akhilesh Pandey
Summary: This study compared the performance of an automated platform, AccelerOme, with manual sample processing. The results demonstrated that the automated platform performs at a level similar to a manual process performed by an expert for TMT-based proteomics. It has the potential to replace manual pipelines and be applied to large-scale TMT-based studies, providing robust results and high sample throughput.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Public, Environmental & Occupational Health
Varsha Nair, Sneha D. Mallya, Akhilesh Kumar Pandey, Prashant Kumar Singh, Amit Yadav, Muralidhar M. Kulkarni
Summary: The objective of this study was to identify the factors associated with quit attempts among tobacco users in India. The study found significant differences in quit attempt rates across different states, suggesting the need for tailored tobacco control policies for specific groups to increase the utilization of cessation services.
CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH
(2023)
Article
Biotechnology & Applied Microbiology
Neha Joshi, Firdous Bhat, Anikha Bellad, Gajanan Sathe, Anu Jain, Sandip Chavan, Ravi Sirdeshmukh, Akhilesh Pandey
Summary: For precision in clinical oncology practice, the detection of tumor-derived peptides and proteins in urine can provide a noninvasive alternative for diagnosis or screening. In this study, comparative quantitative proteomic profiling of urine samples from gastric cancer patients and healthy controls identified differentially expressed proteins, including known and novel candidates related to gastric cancer progression. Targeted proteomics validation confirmed the abundance changes of selected proteins. Overall, this study provides molecular candidates for biomarker development in gastric cancer and supports the potential of urinary proteomics for noninvasive diagnostics and personalized/precision medicine.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jae Hun Jung, Da-Qing Yang, Hongming Song, Xiangyu Wang, Xinyan Wu, Kwang Pyo Kim, Akhilesh Pandey, Seul Kee Byeon
Summary: Lipids play important roles in health and disease, including cancer. Mutations in the PIK3CA gene, which codes for the PI3K catalytic subunit p110α, are frequently found in cancer cells. We used untargeted lipidomics to analyze changes in lipid profiles in breast cancer cells with these mutations. Our results reveal a potential link between altered lipid profile and carcinogenesis caused by PIK3CA mutations.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)