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Hua D, Zhou XX, Wang Q, Sun CY, Shi CJ, Luo WJ, Jiang ZD, Yu SZ. [SRSF2 promotes glioblastoma cell proliferation by inducing alternative splicing of FSP1 and inhibiting ferroptosis]. Zhonghua Bing Li Xue Za Zhi 2024; 53:430-438. [PMID: 38678322 DOI: 10.3760/cma.j.cn112151-20240223-00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
Objective: To investigate the effect of serine/arginine-rich splicing factor 2 (SRSF2) on ferroptosis and its possible mechanism in glioblastoma cells. Methods: The online database of gene expression profiling interactive analysis 2 (GEPIA 2) and Chinese Glioma Genome Atlas were used to analyze the expression of SRSF2 in glioblastoma tissue and its association with patients prognosis. To validate the findings of the online databases, the pathological sections of glioblastoma and non-tumor brain tissues from Tianjin Medical University General Hospital, Tianjin, China were collected and analyzed by using immunohistochemistry. Silencing SRSF2 gene expression in glioblastoma cells by siRNA was analyzed with Western blot. The proliferation index was detected by using CCK8 assay. The rescued experiment was conducted by using expression plasmid of pcDNA3.1(+)-SRSF2. The activity of ferroptosis was assessed by using the levels of iron ions and malondialdehyde in glioblastoma cells and the changes in the ratio of glutathione to oxidized glutathione. The changes of gene expression and differential pre-mRNA alternative splicing (PMAS) induced by SRSF2 were monitored by using the third-generation sequencing technology analysis, namely Oxford nanopore technologies (ONT) sequencing analysis. Results: SRSF2 expression was higher in glioblastoma tissues than non-tumor brain tissues. Immunohistochemistry also showed a positive rate of 88.48%±4.60% in glioblastoma tissue which was much higher than the 9.97%±4.57% in non-tumor brain tissue. The expression of SRSF2 was inversely correlated with overall and disease-free disease survivals (P<0.01). The proliferation index of glioblastoma cells was significantly reduced by silencing with SRSF2 siRNA (P<0.01) and could be reversed with transfection of exogenous SRSF2. The levels of intracellulariron ions and malondialdehyde increased (P<0.05), but the glutathione/oxidized glutathione ratio and the expression of key proteins in the glutathione pathway remained unchanged (P>0.05). ONT sequencing results showed that silencing SRSF2 in glioblastoma cells could induce a significant alternative 3' splice site change on ferroptosis suppressor protein 1 (FSP1). Conclusion: SRSF2 inhibits the ferroptosis in glioblastoma cells and promotes their proliferation, which may be achieved by regulating FSP1 PMAS.
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Affiliation(s)
- D Hua
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - X X Zhou
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Q Wang
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - C Y Sun
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - C J Shi
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - W J Luo
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Z D Jiang
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - S Z Yu
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
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Hua D, Petrina N, Young N, Cho JG, Poon SK. Understanding the factors influencing acceptability of AI in medical imaging domains among healthcare professionals: A scoping review. Artif Intell Med 2024; 147:102698. [PMID: 38184343 DOI: 10.1016/j.artmed.2023.102698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 09/29/2023] [Accepted: 10/29/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Artificial intelligence (AI) technology has the potential to transform medical practice within the medical imaging industry and materially improve productivity and patient outcomes. However, low acceptability of AI as a digital healthcare intervention among medical professionals threatens to undermine user uptake levels, hinder meaningful and optimal value-added engagement, and ultimately prevent these promising benefits from being realised. Understanding the factors underpinning AI acceptability will be vital for medical institutions to pinpoint areas of deficiency and improvement within their AI implementation strategies. This scoping review aims to survey the literature to provide a comprehensive summary of the key factors influencing AI acceptability among healthcare professionals in medical imaging domains and the different approaches which have been taken to investigate them. METHODS A systematic literature search was performed across five academic databases including Medline, Cochrane Library, Web of Science, Compendex, and Scopus from January 2013 to September 2023. This was done in adherence to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) guidelines. Overall, 31 articles were deemed appropriate for inclusion in the scoping review. RESULTS The literature has converged towards three overarching categories of factors underpinning AI acceptability including: user factors involving trust, system understanding, AI literacy, and technology receptiveness; system usage factors entailing value proposition, self-efficacy, burden, and workflow integration; and socio-organisational-cultural factors encompassing social influence, organisational readiness, ethicality, and perceived threat to professional identity. Yet, numerous studies have overlooked a meaningful subset of these factors that are integral to the use of medical AI systems such as the impact on clinical workflow practices, trust based on perceived risk and safety, and compatibility with the norms of medical professions. This is attributable to reliance on theoretical frameworks or ad-hoc approaches which do not explicitly account for healthcare-specific factors, the novelties of AI as software as a medical device (SaMD), and the nuances of human-AI interaction from the perspective of medical professionals rather than lay consumer or business end users. CONCLUSION This is the first scoping review to survey the health informatics literature around the key factors influencing the acceptability of AI as a digital healthcare intervention in medical imaging contexts. The factors identified in this review suggest that existing theoretical frameworks used to study AI acceptability need to be modified to better capture the nuances of AI deployment in healthcare contexts where the user is a healthcare professional influenced by expert knowledge and disciplinary norms. Increasing AI acceptability among medical professionals will critically require designing human-centred AI systems which go beyond high algorithmic performance to consider accessibility to users with varying degrees of AI literacy, clinical workflow practices, the institutional and deployment context, and the cultural, ethical, and safety norms of healthcare professions. As investment into AI for healthcare increases, it would be valuable to conduct a systematic review and meta-analysis of the causal contribution of these factors to achieving high levels of AI acceptability among medical professionals.
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Affiliation(s)
- David Hua
- School of Computer Science, The University of Sydney, Australia; Sydney Law School, The University of Sydney, Australia
| | - Neysa Petrina
- School of Computer Science, The University of Sydney, Australia
| | - Noel Young
- Sydney Medical School, The University of Sydney, Australia; Lumus Imaging, Australia
| | - Jin-Gun Cho
- Sydney Medical School, The University of Sydney, Australia; Western Sydney Local Health District, Australia; Lumus Imaging, Australia
| | - Simon K Poon
- School of Computer Science, The University of Sydney, Australia; Western Sydney Local Health District, Australia.
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Abstract
Large language models like ChatGPT can generate authentic-seeming text at lightning speed, but many journal publishers reject language models as authors on manuscripts. Thus, a means to accurately distinguish human-generated from artificial intelligence (AI)-generated text is immediately needed. We recently developed an accurate AI text detector for scientific journals and, herein, test its ability in a variety of challenging situations, including on human text from a wide variety of chemistry journals, on AI text from the most advanced publicly available language model (GPT-4), and, most important, on AI text generated using prompts designed to obfuscate AI use. In all cases, AI and human text was assigned with high accuracy. ChatGPT-generated text can be readily detected in chemistry journals; this advance is a fundamental prerequisite for understanding how automated text generation will impact scientific publishing from now into the future.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
- Lead contact
| | - Aleesa E. Chua
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Min-Gyu Kim
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - David Hua
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
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Hua D, Nguyen K, Petrina N, Young N, Cho JG, Yap A, Poon SK. Benchmarking the diagnostic test accuracy of certified AI products for screening pulmonary tuberculosis in digital chest radiographs: Preliminary evidence from a rapid review and meta-analysis. Int J Med Inform 2023; 177:105159. [PMID: 37549498 DOI: 10.1016/j.ijmedinf.2023.105159] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/16/2023] [Accepted: 07/19/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND AND OBJECTIVE The global market for AI systems used in lung tuberculosis (TB) detection has expanded significantly in recent years. Verifying their performance across diverse settings is crucial before medical organisations can invest in them and pursue safe, wide-scale deployment. The goal of this research was to synthesise the clinical evidence for the diagnostic accuracy of certified AI products designed for screening TB in chest X-rays (CXRs) compared to a microbiological reference standard. METHODS Four databases were searched between June to September 2022. Data concerning study methodology, system characteristics, and diagnostic accuracy metrics was extracted and summarised. Study bias was evaluated using QUADAS-2 and by examining sources of funding. Forest plots for diagnostic odds ratio (DOR) and summary receiver operating characteristic (SROC) curves were constructed for the AI products individually and collectively. RESULTS 10 out of 3642 studies satisfied the review criteria however only 8 were subject to meta-analysis following bias assessment. Three AI products were evaluated with a 95 % confidence interval producing the following pooled estimates for accuracy rankings: qXR v2 (sensitivity of 0.944 [0.887-0.973], specificity of 0.692 [0.549-0.805], DOR of 3.63 [3.17-4.09], Lunit INSIGHT CXR v3.1 (sensitivity of 0.853 [0.787-0.901], specificity of 0.646 [0.627-0.665], DOR of 2.37 [1.96-2.78]), and CAD4TB v3.07 (sensitivity of 0.917 [0.848-0.956], specificity of 0.371 [0.336-0.408], DOR of 1.91 [1.4-2.47]). Overall, the products had a sensitivity of 0.903 (0.859-0.934), specificity of 0.526 (0.409-0.641), and DOR of 2.31 (1.78-2.84). CONCLUSION Current publicly available evidence indicates considerable variability in the diagnostic accuracy of available AI products although overall they have high sensitivity and modest specificity which is improving with time. These preliminary results are limited by the small number of studies and poor coverage for low TB burden settings. More research is needed to expand the clinical evidence base for the performance of AI products.
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Affiliation(s)
- David Hua
- School of Computer Science, The University of Sydney, Australia; Sydney Law School, The University of Sydney, Australia
| | - Khang Nguyen
- School of Computer Science, The University of Sydney, Australia
| | - Neysa Petrina
- School of Computer Science, The University of Sydney, Australia
| | - Noel Young
- Lumus Imaging, Australia; Western Sydney Local Health District, Australia
| | - Jin-Gun Cho
- Sydney Medical School, The University of Sydney, Australia; Lumus Imaging, Australia; Western Sydney Local Health District, Australia
| | - Adeline Yap
- School of Computer Science, The University of Sydney, Australia
| | - Simon K Poon
- School of Computer Science, The University of Sydney, Australia; Western Sydney Local Health District, Australia.
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Desaire H, Chua AE, Isom M, Jarosova R, Hua D. Distinguishing academic science writing from humans or ChatGPT with over 99% accuracy using off-the-shelf machine learning tools. Cell Rep Phys Sci 2023; 4:101426. [PMID: 37426542 PMCID: PMC10328544 DOI: 10.1016/j.xcrp.2023.101426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
ChatGPT has enabled access to artificial intelligence (AI)-generated writing for the masses, initiating a culture shift in the way people work, learn, and write. The need to discriminate human writing from AI is now both critical and urgent. Addressing this need, we report a method for discriminating text generated by ChatGPT from (human) academic scientists, relying on prevalent and accessible supervised classification methods. The approach uses new features for discriminating (these) humans from AI; as examples, scientists write long paragraphs and have a penchant for equivocal language, frequently using words like "but," "however," and "although." With a set of 20 features, we built a model that assigns the author, as human or AI, at over 99% accuracy. This strategy could be further adapted and developed by others with basic skills in supervised classification, enabling access to many highly accurate and targeted models for detecting AI usage in academic writing and beyond.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
- Lead contact
| | - Aleesa E. Chua
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Madeline Isom
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Romana Jarosova
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - David Hua
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
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Guo YH, He ZL, Ji QL, Zhou HJ, Meng FL, Hu XF, Wei XY, Ma JC, Yang YH, Zhao W, Long LJ, Wang X, Fan JM, Yu XJ, Zhang JZ, Hua D, Yan XM, Wang HB. [Population structure of food-borne Staphylococcus aureus in China]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:982-989. [PMID: 37380423 DOI: 10.3760/cma.j.cn112338-20221206-01043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Objective: To understand the population structure of food-borne Staphylococcus (S.) aureus in China. Methods: Whole genome sequencing was used to analyze 763 food-borne S. aureus strains from 16 provinces in China from 2006 to 2020. Multilocus sequence typing (MLST), staphylococcal protein A gene (spa) typing, and staphylococcal chromosome cassettemec (SCCmec) typing were conducted, and minimum spanning tree based on ST types (STs) was constructed by BioNumerics 7.5 software. Thirty-one S. aureus strains isolated from imported food products were also included in constructing the genome phylogenetic tree. Results: A total of 90 STs (20 novel types) and 160 spa types were detected in the 763 S. aureus isolates. The 72 STs (72/90, 80.0%) were related to 22 clone complexes. The predominant clone complexes were CC7, CC1, CC5, CC398, CC188, CC59, CC6, CC88, CC15, and CC25, accounting for 82.44% (629/763) of the total. The STs and spa types in the predominant clone complexes changed over the years. The methicillin-resistant S. aureus (MRSA) detection rate was 7.60%, and 7 SCCmec types were identified. The ST59-t437-Ⅳa (17.24%, 10/58), ST239-t030-Ⅲ (12.07%, 7/58), ST59-t437-Ⅴb (8.62%, 5/58), ST338-t437-Ⅴb (6.90%, 4/58) and ST338-t441-Ⅴb (6.90%, 4/58) were the main types in MRSA strains. The genome phylogenetic tree had two clades, and the strains with the same CC, ST, and spa types clustered together. All CC7 methicillin sensitive S. aureus strains were included in Clade1, while 21 clone complexes and all MRSA strains were in Clade2. The MRSA strains clustered according to the SCCmec and STs. The strains from imported food products in CC398, CC7, CC30, CC12, and CC188 had far distances from Chinese strains in the tree. Conclusions: In this study, the predominant clone complexes of food-borne strains were CC7, CC1, CC5, CC398, CC188, CC59, CC6, CC88, CC15, and CC25, which overlapped with the previously reported clone complexes of hospital and community-associated strains in China, suggesting that close attention needs to be paid to food, a vehicle of pathogen transmission in community and food poisoning.
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Affiliation(s)
- Y H Guo
- Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou 014040, China State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Z L He
- Beijing Advanced Innovation Center for Big Data-based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beijing University of Aeronautics and Astronautics, Beijing 100191, China
| | - Q L Ji
- Chinese Academy of Inspection and Quarantine, Beijing 100020, China
| | - H J Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - F L Meng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X F Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100032, China
| | - X Y Wei
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - J C Ma
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Y H Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - W Zhao
- Institute of Microbiology, Jilin Provincial Center for Disease Control and Prevention, Changchun 130051, China
| | - L J Long
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X Wang
- College of Food Science and Engineering, Northwest Agriculture & Forestry University, Xi'an 712100, China
| | - J M Fan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X J Yu
- Hainan Center for Disease Control and Prevention, Haikou 570203, China
| | - J Z Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - D Hua
- Hainan Center for Disease Control and Prevention, Haikou 570203, China
| | - X M Yan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - H B Wang
- Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou 014040, China Chaoyang District Center for Disease Control and Prevention, Beijing 100020, China
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Fan YF, Li ZP, Yu XJ, Li Z, Zhou HJ, Zhang YL, Gan XT, Hua D, Lu X, Kan B. [Study of the urban-impact on microbial communities and their virulence factors and antibiotic resistance genomes in the Nandu River, Haikou]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:974-981. [PMID: 37380422 DOI: 10.3760/cma.j.cn112338-20221229-01090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Objective: To explore the changes in bacterial community structure, antibiotic resistance genome, and pathogen virulence genome in river water before and after the river flowing through Haikou City and their transmission and dispersal patterns and to reveal anthropogenic disturbance's effects on microorganisms and resistance genes in the aquatic environment. Methods: The Nandu River was divided into three study areas: the front, middle and rear sections from the upstream before it flowed through Haikou City to the estuary. Three sampling sites were selected in each area, and six copies of the sample were collected in parallel at each site and mixed for 3 L per sample. Microbial community structure, antibiotic resistance, virulence factors, and mobile genetic elements were analyzed through bioinformatic data obtained by metagenomic sequencing and full-length sequencing of 16S rRNA genes. Variations in the distribution of bacterial communities between samples and correlation of transmission patterns were analyzed by principal co-ordinates analysis, procrustes analysis, and Mantel test. Results: As the river flowed through Haikou City, microbes' alpha diversity gradually decreased. Among them, Proteobacteria dominates in the bacterial community in the front, middle, and rear sections, and the relative abundance of Proteobacteria in the middle and rear sections was higher than that in the front segment. The diversity and abundance of antibiotic resistance genes, virulence factors, and mobile genetic elements were all at low levels in the front section and all increased significantly after flow through Haikou City. At the same time, horizontal transmission mediated by mobile genetic elements played a more significant role in the spread of antibiotic-resistance genes and virulence factors. Conclusions: Urbanization significantly impacts river bacteria and the resistance genes, virulence factors, and mobile genetic elements they carry. The Nandu River in Haikou flows through the city, receiving antibiotic-resistant and pathogen-associated bacteria excreted by the population. In contrast, antibiotic-resistant genes and virulence factors are enriched in bacteria, which indicates a threat to environmental health and public health. Comparison of river microbiomes and antibiotic resistance genomes before and after flow through cities is a valuable early warning indicator for monitoring the spread of antibiotic resistance.
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Affiliation(s)
- Y F Fan
- Department of Diarrheal Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Z P Li
- Department of Diarrheal Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X J Yu
- Inspection and Testing Institute, Hainan Center for Disease Control and Prevention, Haikou 570203, China
| | - Z Li
- Department of Diarrheal Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - H J Zhou
- Department of Diarrheal Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y L Zhang
- Inspection and Testing Institute, Hainan Center for Disease Control and Prevention, Haikou 570203, China
| | - X T Gan
- Inspection and Testing Institute, Hainan Center for Disease Control and Prevention, Haikou 570203, China
| | - D Hua
- Inspection and Testing Institute, Hainan Center for Disease Control and Prevention, Haikou 570203, China
| | - X Lu
- Department of Diarrheal Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - B Kan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
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Abstract
The fields of proteomics and machine learning are both large disciplines, each producing well over 5,000 publications per year. However, studies combining both fields are still relatively rare, with only about 2% of recent proteomics papers including machine learning. This review, which focuses on the intersection of the fields, is intended to inspire proteomics researchers to develop skills and knowledge in the application of machine learning. A brief tutorial introduction to machine learning is provided, and research advances that rely on both fields, particularly as they relate to proteomics tools development and biomarker discovery, are highlighted. Key knowledge gaps and opportunities for scientific advancement are also enumerated.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - David Hua
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
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9
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Suleman M, Ma M, Ge G, Hua D, Li H. The role of alternative oxidase in plant hypersensitive response. Plant Biol (Stuttg) 2021; 23:415-419. [PMID: 33480175 DOI: 10.1111/plb.13237] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
The innate immune system of plants is crucial in defining the fate of a plant cell during plant-pathogen interactions. This response is often accompanied by a hypersensitive reaction leading to the death of a plant cell and restricted pathogen growth. Plant mitochondria, in this case, play a key role by maintaining a balance between cell respiration and reactive oxygen species formation. One of the key features of the hypersensitive response is the shift of the normal plant respiratory pathway to a special 'alternative' pathway. Plants contain an enzyme, alternative oxidase, for maintaining metabolic homeostasis of the cell. This energy dissipating respiration provides a branch in normal respiration by using ubiquinone to form water and heat, thus maintaining the energy status of the cell. Alternative oxidase is thought to minimize production of reactive oxygen species and can also function in 'anti-apoptotic' machinery in plant cells. In this mini review, we briefly describe the alternative respiratory pathway and explain the role of alternative oxidase in important cellular processes, such as programmed cell death and the hypersensitive response.
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Affiliation(s)
- M Suleman
- Institute of Microbiology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - M Ma
- Institute of Microbiology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - G Ge
- Institute of Microbiology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - D Hua
- Institute of Microbiology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - H Li
- Institute of Microbiology, School of Life Sciences, Lanzhou University, Lanzhou, China
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10
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Abstract
Mass spectrometry data sets from omics studies are an optimal information source for discriminating patients with disease and identifying biomarkers. Thousands of proteins or endogenous metabolites can be queried in each analysis, spanning several orders of magnitude in abundance. Machine learning tools that effectively leverage these data to accurately identify disease states are in high demand. While mass spectrometry data sets are rich with potentially useful information, using the data effectively can be challenging because of missing entries in the data sets and because the number of samples is typically much smaller than the number of features, two challenges that make machine learning difficult. To address this problem, we have modified a new supervised classification tool, the Aristotle Classifier, so that omics data sets can be better leveraged for identifying disease states. The optimized classifier, AC.2021, is benchmarked on multiple data sets against its predecessor and two leading supervised classification tools, Support Vector Machine (SVM) and XGBoost. The new classifier, AC.2021, outperformed existing tools on multiple tests using proteomics data. The underlying code for the classifier, provided herein, would be useful for researchers who desire improved classification accuracy when using their omics data sets to identify disease states.
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Affiliation(s)
- David Hua
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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11
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Desaire H, Patabandige MW, Hua D. The local-balanced model for improved machine learning outcomes on mass spectrometry data sets and other instrumental data. Anal Bioanal Chem 2021; 413:1583-1593. [PMID: 33580828 PMCID: PMC8516084 DOI: 10.1007/s00216-020-03117-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/17/2020] [Accepted: 12/08/2020] [Indexed: 11/25/2022]
Abstract
One unifying challenge when classifying biological samples with mass spectrometry data is overcoming the obstacle of sample-to-sample variability so that differences between groups, such as between a healthy set and a disease set, can be identified. Similarly, when the same sample is re-analyzed under identical conditions, instrument signals can fluctuate by more than 10%. This signal inconsistency imposes difficulties in identifying subtle differences across a set of samples, and it weakens the mass spectrometrist’s ability to effectively leverage data in domains as diverse as proteomics, metabolomics, glycomics, and imaging. We selected challenging data sets in the fields of glycomics, mass spectrometry imaging, and bacterial typing to study the problem of within-group signal variability and adapted a 30 year old statistical approach to address the problem. The solution, “local-balanced model,” relies on using balanced subsets of training data to classify test samples. This analysis strategy was assessed on ESI-MS data of IgG-based glycopeptides and MALDI-MS imaging data of endogenous lipids, and MALDI-MS data of bacterial proteins. Two preliminary examples on non-mass spectrometry data sets are also included to show the potential generality of the method outside the field of MS analysis. We demonstrate that this approach is superior to simple normalization methods, generalizable to multiple mass spectrometry domains, and potentially appropriate in fields as diverse as physics and satellite imaging. In some cases, improvements in classification can be dramatic, with accuracy escalating from 60% with normalization alone to over 90% with the additional development described herein.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS, 66045, USA.
| | | | - David Hua
- Department of Chemistry, University of Kansas, Lawrence, KS, 66045, USA
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12
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Hua D, Zhao Y, Nan X, Xue F, Wang Y, Jiang L, Xiong B. Effect of different glucogenic to lipogenic nutrient ratios on rumen fermentation and bacterial community in vitro. J Appl Microbiol 2020; 130:1868-1882. [PMID: 32998176 PMCID: PMC8247007 DOI: 10.1111/jam.14873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022]
Abstract
Aims This study was to investigate the effect of different ratios of glucogenic to lipogenic nutrients on rumen fermentation and the corresponding ruminal bacterial communities. Methods and Results Four diets, including glucogenic diet (G), lipogenic diet (L), two mixed diets: GL1 (G: L = 2 : 1) and GL2 (G:L = 1 : 2), served as substrates and were incubated with rumen fluid in vitro. The results revealed that the gas production, dry matter digestibility and propionate proportion were significantly increased by the G diet than others. The G diet increased the bacterial genera of Succinivibrionaceae_UCG_002, Succinivibrio, Selenomonas_1 and Ruminobacter but decreased some cellulolytic bacteria including the Eubacterium and several genera in family Ruminococcaceae than others. Conclusions When the glucogenic nutrient was above 1/3 of the dietary energy source among the four diets, the in vitro incubation had a higher feed digestibility and lower acetate to propionate ratio. Bacterial genera, including Selenomonas, Succinivibrio, Ruminobacter, certain genera in Ruminococcaceae, Christensenellaceae_R‐7_group and Eubacterium, were more sensitive to the glucogenic to lipogenic nutrients ratio. Significance and Impact of the Study The present study provides a new perspective about the effect of dietary glucogenic to lipogenic ingredient ratios on rumen metabolism by comparing end‐products, gas production and bacterial composition via an in vitro technique.
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Affiliation(s)
- D Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Y Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - F Xue
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Y Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L Jiang
- Beijing Key Laboratory for Dairy Cattle Nutrition, Beijing Agricultural College, Beijing, China
| | - B Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhang LH, Wang Z, Fan QQ, Yin ZJ, Jin LF, Mao Y, Hua D. AK5, a novel prognosis marker, inhibits apoptosis and promotes autophagy as well as proliferation in human gastric cancer. Eur Rev Med Pharmacol Sci 2020; 23:9900-9906. [PMID: 31799658 DOI: 10.26355/eurrev_201911_19555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To explore the relationship between AK5 and gastric cancer. MATERIALS AND METHODS The in situ levels of AK5 in the GC tissues from 255 patients were detected by immunohistochemistry (IHC). The correlation between AK5 expression and the clinicopathological parameters was analyzed by Pearson correlation, and the prognostic factors were identified by Cox regression analysis. The transcriptome data of 14 human GC cell lines deposited in the CCLE database were analyzed, and two lines were selected for functional studies. AK5 was knocked down in the AZ521 and MKN74 cells using siRNA, and their proliferation and apoptosis were evaluated by Cell Counting Kit-8 (CCK-8) assay and Annexin-V staining, respectively. In addition, the apoptosis and autophagy of the markers were detected by Western blotting. RESULTS Patients expressing high AK5 levels in the tumor tissues had significantly shorter survival compared to low-expressing group. In addition, AK5 expression was associated with T stage and N stage and was an independent prognostic factor. AK5 knockdown in the AZ521 and MKN74 cells significantly inhibited proliferation and autophagy, and increased apoptosis. CONCLUSIONS AK5 is a potential prognostic marker and therapeutic target for GC.
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Affiliation(s)
- L-H Zhang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China.
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14
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Hua D, Liu X, Go EP, Wang Y, Hummon AB, Desaire H. How to Apply Supervised Machine Learning Tools to MS Imaging Files: Case Study with Cancer Spheroids Undergoing Treatment with the Monoclonal Antibody Cetuximab. J Am Soc Mass Spectrom 2020; 31:1350-1357. [PMID: 32469221 PMCID: PMC7685566 DOI: 10.1021/jasms.0c00010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
As the field of mass spectrometry imaging continues to grow, so too do its needs for optimal methods of data analysis. One general need in image analysis is the ability to classify the underlying regions within an image, as healthy or diseased, for example. Classification, as a general problem, is often best accomplished by supervised machine learning strategies; unfortunately, conducting supervised machine learning on MS imaging files is not typically done by mass spectrometrists because a high degree of specialized knowledge is needed. To address this problem, we developed a fully open-source approach that facilitates supervised machine learning on MS imaging files, and we demonstrated its implementation on sets of cancer spheroids that either had or had not undergone chemotherapy treatment. These supervised machine learning studies demonstrated that metabolic changes induced by the monoclonal antibody, Cetuximab, are detectable but modest at 24 h, and by 72 h, the drug induces a larger and more diverse metabolic response.
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Affiliation(s)
- David Hua
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Xin Liu
- Department of Chemistry and Biochemistry and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Yijia Wang
- Department of Chemistry and Biochemistry and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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15
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Hua D, Ma M, Ge G, Suleman M, Li H. The role of cyanide-resistant respiration in Solanum tuberosum L. against high light stress. Plant Biol (Stuttg) 2020; 22:425-432. [PMID: 32052535 DOI: 10.1111/plb.13098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/21/2020] [Indexed: 05/23/2023]
Abstract
Cyanide-resistant respiration in potato mitochondria is an important pathway for energy dissipation. It can be activated by high light; however, it is unclear what roles cyanide-resistant respiration plays in the response to high light stress in potato. We designed a CRISPR vector for the functional gene StAOX of the potato cyanide-resistant respiratory pathway. Agrobacterium tumefaciens GV3101 was transformed into potato. Hydrogen peroxide level, MDA content, antioxidant activity and cyanide-resistant respiratory capacity of potato leaves under high light stress were determined. Photosynthetic efficiency and chlorophyll content were determined. In addition, the operation of the malate-oxaloacetate shuttle route and transcription level of photorespiration-related enzymes were also examined. The results showed that two base substitutions occurred at the sequencing target site on leaves of the transformed potato. Accumulation of ROS and increased membrane lipid peroxidation were detected in the transformed potato leaves and lower photosynthetic efficiency was observed. The transcription level of the malate-oxaloacetate shuttle route and photorespiration-related enzymes also significantly increased. These results indicate that the cyanide-resistant respiration is an important physiological pathway in potato in response to high light stress. It also suggests that plant cyanide-resistant respiration is closely related to photosynthesis. This implies the unexplored importance of plant cyanide-resistant respiration in plant photosynthesis, energy conversion and carbon skeleton formation.
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Affiliation(s)
- D Hua
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - M Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - G Ge
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - M Suleman
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - H Li
- School of Life Sciences, Lanzhou University, Lanzhou, China
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Abstract
MALDI-TOF MS has shown great utility for rapidly identifying microbial species. It can be used to successfully type bacteria and fungi from a variety of sources more rapidly and cost-effectively than traditional methods. One area where improvements are necessary is in the typing of highly similar samples, such as those samples from the same genus but different species or samples from within a single species but from different strains. One promising way to address this current limitation is by using advanced machine learning techniques. In this work, we adapt a newly developed machine learning tool, the Aristotle Classifier, to bacterial classification of MALDI-TOF MS data. This tool was originally developed for classifying glycomics and glycoproteomics data, so we modified it to be well-suited for assigning mass spectral data from bacterial proteins. The classifier exceeds existing benchmarks in classifying bacteria, and it shows particularly strong performance when the samples to be identified are highly similar. The combination of mass spectrometry data and tools like the Aristotle Classifier could ameliorate the ambiguities associated with challenging bacterial classification problems.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
| | - David Hua
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
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17
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Hua D, Liu Q, Xu J, Xu Y, Chen M, Deng L, Wu J, Zhou T, Zhang L, Tan J, Pu X, Shang Y, Hua J, Li Y, Cai W, Gu Y, Peng X. OA03.01 A Non-Randomized, Open-Label, Prospective, Multicenter Study of Apatinib as Second-Line and Later-Line Therapy in Patients with ES-SCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
"The totality is not, as it were, a mere heap, but the whole is something besides the parts."-Aristotle. We built a classifier that uses the totality of the glycomic profile, not restricted to a few glycoforms, to differentiate samples from two different sources. This approach, which relies on using thousands of features, is a radical departure from current strategies, where most of the glycomic profile is ignored in favor of selecting a few features, or even a single feature, meant to capture the differences in sample types. The classifier can be used to differentiate the source of the material; applicable sources may be different species of animals, different protein production methods, or, most importantly, different biological states (disease vs healthy). The classifier can be used on glycomic data in any form, including derivatized monosaccharides, intact glycans, or glycopeptides. It takes advantage of the fact that changing the source material can cause a change in the glycomic profile in many subtle ways: some glycoforms can be upregulated, some downregulated, some may appear unchanged, yet their proportion-with respect to other forms present-can be altered to a detectable degree. By classifying samples using the entirety of their glycan abundances, along with the glycans' relative proportions to each other, the "Aristotle Classifier" is more effective at capturing the underlying trends than standard classification procedures used in glycomics, including PCA (principal components analysis). It also outperforms workflows where a single, representative glycomic-based biomarker is used to classify samples. We describe the Aristotle Classifier and provide several examples of its utility for biomarker studies and other classification problems using glycomic data from several sources.
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Affiliation(s)
- David Hua
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
| | | | - Eden P Go
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
| | - Heather Desaire
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
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19
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Abstract
Glycopeptide analysis is a growing field that is struggling to adopt effective, automated tools. Many creative workflows and software apps have emerged recently that offer promising capabilities for assigning glycopeptides to MS data in an automated fashion. The effectiveness of these tools is best measured and improved by determining how often they would select a glycopeptide decoy as a spectral match, instead of its correct assignment; yet generating the appropriate number and type of glycopeptide decoys can be challenging. To address this need, we have designed DecoyDeveloper, an on-demand decoy glycopeptide generator that can produce a high volume of decoys with low mass differences. DecoyDeveloper has a simple user interface and is capable of producing large sets of decoys containing complete, biologically relevant glycan and peptide sequences. We demonstrate the tool's efficiency by applying it to a set of 80 glycopeptide targets. This tool is freely available and can be found at http://glycopro.chem.ku.edu/J1.php .
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Affiliation(s)
- Joshua T Shipman
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
| | - Xiaomeng Su
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
| | - David Hua
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
| | - Heather Desaire
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
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Turner SWD, Voisin N, Fazio J, Hua D, Jourabchi M. Compound climate events transform electrical power shortfall risk in the Pacific Northwest. Nat Commun 2019; 10:8. [PMID: 30602781 PMCID: PMC6315041 DOI: 10.1038/s41467-018-07894-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/27/2018] [Indexed: 11/09/2022] Open
Abstract
Power system reliability is sensitive to climate-driven variations in both energy demand and water availability, yet the combined effect of these impacts is rarely evaluated. Here we show that combined climate change impacts on loads and hydropower generation may have a transformative effect on the nature and seasonality of power shortfall risk in the U.S. Pacific Northwest. Under climate change, potential shortfall events occur more readily, but are significantly less severe in nature. A seasonal reversal in shortfall risk occurs: winter shortfalls are eradicated due to reduced building heating demands, while summer shortfalls multiply as increased peak loads for day-time cooling coincide with impaired hydropower generation. Many of these summer shortfalls go unregistered when climate change impacts on loads and hydropower dispatch are analyzed in isolation-highlighting an important role of compound events.
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Affiliation(s)
- S W D Turner
- Pacific Northwest National Laboratory, Seattle Research Center, 1100 Dexter Ave N., Suite 500, Seattle, WA, 98109, USA
| | - N Voisin
- Pacific Northwest National Laboratory, Seattle Research Center, 1100 Dexter Ave N., Suite 500, Seattle, WA, 98109, USA. .,Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA.
| | - J Fazio
- Northwest Power and Conservation Council, 851 S.W. Sixth Avenue, Suite 1100, Portland, OR, 97204, USA
| | - D Hua
- Northwest Power and Conservation Council, 851 S.W. Sixth Avenue, Suite 1100, Portland, OR, 97204, USA
| | - M Jourabchi
- Northwest Power and Conservation Council, 851 S.W. Sixth Avenue, Suite 1100, Portland, OR, 97204, USA
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Feng J, Shen B, Jiang H, Wang L, Qian J, Shu Y, Chen P, Mao G, Liu B, Zhang X, Liu C, Wu J, Li X, Cai W, Shen W, Wang Q, He J, Hua D, Zhang Z, Zhang Y. Identification of patients who benefit from apatinib in advanced gastric cancer: Data derived from a real-world study. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy282.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Lakbub JC, Su X, Hua D, Go EP, Desaire H. Dissecting the Dissociation Patterns of Fucosylated Glycopeptides Undergoing CID: A Case Study in Improving Automated Glycopeptide Analysis Scoring Algorithms. Anal Methods 2017; 10:256-262. [PMID: 29662551 PMCID: PMC5898446 DOI: 10.1039/c7ay02687k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The need to investigate the fragmentation of fucosylated glycopeptides is driven by recent work showing that at least one, and perhaps many, glycopeptide analysis scoring algorithms are less effective at identifying fucosylated glycopeptides than non-fucosylated glycopeptides. Herein, we study the CID fragmentation characteristics of fucosylated glycopeptides and the scoring rules of the glycopeptide analysis software, GlycoPep Grader, in an effort to improve automated assignments of these important glycopeptides. We identified some prominent product ions from a common fragmentation pathway of fucosylated glycopeptides that were not accounted for in the scoring rules. Based on this finding, we propose new scoring rules for fucosylated glycopeptides that can be incorporated into GlycoPep Grader and other similar analysis software tools to more accurately identify these species. The approach used here, to improve one particular scoring algorithm, could henceforth be used to improve any other algorithm that assigns glycopeptides based on their MS/MS data.
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Affiliation(s)
- Jude C. Lakbub
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
| | - Xiaomeng Su
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
| | - David Hua
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
| | - Eden P. Go
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
| | - Heather Desaire
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
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Shi YK, Zhang L, Zhang S, Shi M, Qin S, Wu C, Zhuang Z, Mao G, Hua D, Zhou X, Qu Y, Wang Y, Shi X, Hu C, Li W, Ouyang M, Chen L, Sun Y, Wu G, Sun Y. Humanized recombinant endostatin combined with vinorelbine plus cisplatin followed by maintenance therapy with humanized recombinant endostatin in advanced non-small cell lung cancer: A multicentre, double-blind, randomised phase 3 trial. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Post RF, Fowler TK, Bulmer R, Byers J, Hua D, Tung L. Axisymmetric Tandem Mirrors: Stabilization and Confinement Studies. Fusion Science and Technology 2017. [DOI: 10.13182/fst05-a607] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- R. F. Post
- Lawrence Livermore National Laboratory: 7000 East Ave, L-644, Livermore, CA 94551,
| | - T. K. Fowler
- Lawrence Livermore National Laboratory: 7000 East Ave, L-644, Livermore, CA 94551,
| | - R. Bulmer
- Lawrence Livermore National Laboratory: 7000 East Ave, L-644, Livermore, CA 94551,
| | - J. Byers
- Lawrence Livermore National Laboratory: 7000 East Ave, L-644, Livermore, CA 94551,
| | - D. Hua
- Lawrence Livermore National Laboratory: 7000 East Ave, L-644, Livermore, CA 94551,
| | - L. Tung
- Lawrence Livermore National Laboratory: 7000 East Ave, L-644, Livermore, CA 94551,
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Lakbub JC, Su X, Zhu Z, Patabandige MW, Hua D, Go EP, Desaire H. Two New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptides. J Proteome Res 2017; 16:3002-3008. [PMID: 28691494 DOI: 10.1021/acs.jproteome.7b00289] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The glycopeptide analysis field is tightly constrained by a lack of effective tools that translate mass spectrometry data into meaningful chemical information, and perhaps the most challenging aspect of building effective glycopeptide analysis software is designing an accurate scoring algorithm for MS/MS data. We provide the glycoproteomics community with two tools to address this challenge. The first tool, a curated set of 100 expert-assigned CID spectra of glycopeptides, contains a diverse set of spectra from a variety of glycan types; the second tool, Glycopeptide Decoy Generator, is a new software application that generates glycopeptide decoys de novo. We developed these tools so that emerging methods of assigning glycopeptides' CID spectra could be rigorously tested. Software developers or those interested in developing skills in expert (manual) analysis can use these tools to facilitate their work. We demonstrate the tools' utility in assessing the quality of one particular glycopeptide software package, GlycoPep Grader, which assigns glycopeptides to CID spectra. We first acquired the set of 100 expert assigned CID spectra; then, we used the Decoy Generator (described herein) to generate 20 decoys per target glycopeptide. The assigned spectra and decoys were used to test the accuracy of GlycoPep Grader's scoring algorithm; new strengths and weaknesses were identified in the algorithm using this approach. Both newly developed tools are freely available. The software can be downloaded at http://glycopro.chem.ku.edu/GPJ.jar.
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Affiliation(s)
- Jude C Lakbub
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
| | - Xiaomeng Su
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
| | - Zhikai Zhu
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
| | - Milani W Patabandige
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
| | - David Hua
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
| | - Eden P Go
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
| | - Heather Desaire
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
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Qi QH, Wang T, Mao Y, Hua D. [Prognostic significance of tumor deposits in patients with stage Ⅲ colon cancer]. Zhonghua Zhong Liu Za Zhi 2017; 38:784-789. [PMID: 27784466 DOI: 10.3760/cma.j.issn.0253-3766.2016.10.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the prognostic significance of tumor deposits (TD) in patients with stage Ⅲ colorectal cancer who underwent radical resection. Methods: We retrospectively analyzed the clinicopathological data, and the impact of tumor deposits on the disease free survival (DFS) and overall survival (OS) in 206 patients with stage Ⅲ colorectal cancer using Kaplan-Meier and Cox regression analyses. Results: Among the 206 patients with stage Ⅲ colorectal cancer, there were 112 (54.4%) tumor deposit-positive (TD+ ) cases and 94 (45.6%) tumor deposit-negative (TD-) cases. The TD- and TD+ cases accounted for 10.6% and 21.4% of patients aged <50 years, 22.3% and 36.6% of patients with poorly differentiated carcinoma, and 16% and 29.5% of patients with neural invasion, respectively (P<0.05 for all). In addition, the neural invasion was more often found along with the increasing number of TD. However, multivariate analysis showed that TD was not significantly associated with DFS and OS of the patients. Among the patients with N1 stage cancer, the 3-year DFS rates of TD+ and TD- groups were 23.0% and 58.8%, and the median disease-free survival durations were 26 months and 43 months, respectively (P=0.002). Meanwhile, in the TD- group, the 3-year DFS rates in the patients with stage N1a~1b without tumor deposit and N1c cancer were 63.5% and 21.2%, and the median disease-free survival durations were 41 and 25 months, respectively (P=0.004). Conclusions: Tumor deposit is an independent unfavorable prognostic factor affecting the DFS. The number of tumor deposits may be an important factor affecting prognosis in stage Ⅲ colorectal cancer patients. Tumor deposits after radical resection are associated with neural invasion, and can be used as an independent factor of poor prognostic evaluation in patients with stage N1 colorectal cancer.
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Affiliation(s)
- Q H Qi
- Department of Oncology, The Fourth People's Hospital of Wuxi, Wuxi 214062, China
| | - T Wang
- Department of Oncology, The Fourth People's Hospital of Wuxi, Wuxi 214062, China
| | - Y Mao
- Department of Oncology, The Fourth People's Hospital of Wuxi, Wuxi 214062, China
| | - D Hua
- Department of Oncology, The Fourth People's Hospital of Wuxi, Wuxi 214062, China
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Hua D, Jiao Y, Neves R, Jones J. Periodic growth and growth cessations in the federally endangered freshwater mussel Cumberlandian combshell using a hierarchical Bayesian approach. ENDANGER SPECIES RES 2016. [DOI: 10.3354/esr00773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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28
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Trushina E, Zhang L, Zhang S, Trushin S, Hua D. Mitochondria-targeted therapeutics for Alzheimer's disease. J Neurol Sci 2015. [DOI: 10.1016/j.jns.2015.08.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Go EP, Hua D, Desaire H. Glycosylation and disulfide bond analysis of transiently and stably expressed clade C HIV-1 gp140 trimers in 293T cells identifies disulfide heterogeneity present in both proteins and differences in O-linked glycosylation. J Proteome Res 2014; 13:4012-27. [PMID: 25026075 PMCID: PMC4156237 DOI: 10.1021/pr5003643] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The HIV-1 envelope protein (Env) mediates viral entry into host cells to initiate infection and is the sole target of antibody-based vaccine development. Significant efforts have been made toward the design, engineering, and expression of various soluble forms of HIV Env immunogen, yet a highly effective immunogen remains elusive. One of the key challenges in the development of an effective HIV vaccine is the presence of the complex set of post-translational modifications (PTMs) on Env, namely, glycosylation and disulfide bonds, that affect protein folding, epitope accessibility, and immunogenecity. Although these PTMs vary with expression systems, variations in Env's PTMs due to changes in the expression method are not yet well established. In this study, we compared the disulfide bond network and glycosylation profiles of clade C recombinant HIV-1 Env trimers, C97ZA012 gp140, expressed by stable and transient transfections using an integrated mass mapping workflow that combines collision induced dissociation (CID) and electron transfer dissociation (ETD). Site-specific analysis of the N- and O-glycosylation profiles revealed that C97ZA012 gp140 produced by both transfection methods displayed a high degree of similarity in N-glycosylation profiles and site occupancy except for one site. By contrast, different O-glycosylation profiles were detected. Analysis of the disulfide bond networks of the Env revealed that both transfection methods yielded C97ZA012 gp140 adopting the expected disulfide bond pattern identified for the monomeric gp120 and gp41 as well as alternative disulfide bond patterns in the C1, V1/V2, and C2 regions. The finding that disulfide bonding is consistently heterogeneous in these proteins is perhaps the most significant outcome of these studies; this disulfide heterogeneity has been reported for multiple other recombinant gp140s, and it is likely present in most recombinantly expressed Env immunogens.
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Affiliation(s)
- Eden P Go
- Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
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Qi XW, Xia SH, Yin Y, Jin LF, Pu Y, Hua D, Wu HR. Expression features of CXCR5 and its ligand, CXCL13 associated with poor prognosis of advanced colorectal cancer. Eur Rev Med Pharmacol Sci 2014; 18:1916-1924. [PMID: 25010623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
OBJECTIVE CXCL13 plays a unique role in the trafficking and homing of B1 cells associated with its cognate receptor, CXCR5. The CXCR5-CXCL13 axis has been previously demonstrated to be a poor prognosis factor in malignancies. However, the clinical significance of the CXCR5-CXCL13 expression in colorectal cancer carcinoma (CRC) remains unclear. The aim of this study was to investigate the CXCR5-CXCL13 expression in CRC and determine its correlation with the progression and prognosis of the tumor. PATIENTS AND METHODS A total of 144 paraffin-embedded specimens with advanced colon cancer were assessed for CXCR5 and CXCL13 by immunohistochemistry. Patients' long-term survival was also monitored. There were significant differences in lymph node metastasis (p = 0.0066), neural invasion (p = 0.0061) and neural invasion (p = 0.0001) between high and low expression of CXCR5. RESULTS There were significant differences in distant metastasis (p = 0.0261), TNM stage (p = 0.0409), differentiation (p < 0.0001) and neural invasion of the CXCL13. Both CXCR5 and CXCL13 was associated with poor correlation with the overall survival (OS) and relapse-free survival (RFS). CONCLUSIONS Our data suggest that the CXCR5 and CXCL13 may play a crucial role in the development, metastasis and relapse of advanced colon cancer. They can be used as prognostic markers of colon cancer in clinical practice.
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Affiliation(s)
- X-W Qi
- Department of General Surgery, the Second Affiliated Hospital of Soochow University, Suzhou, China.
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Zhang W, Hua D, Ma S, Chen Z, Wang Y, Zhang F, Len F, Pu X. Preliminary Study for Vascular Tissue Engineering by Electrospinning Angelica Polysaccharide (ASP)/PLA Microfibrous Scaffolds. INT J POLYM MATER PO 2014. [DOI: 10.1080/00914037.2013.854241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Zhu Z, Hua D, Clark DF, Go EP, Desaire H. GlycoPep Detector: a tool for assigning mass spectrometry data of N-linked glycopeptides on the basis of their electron transfer dissociation spectra. Anal Chem 2013; 85:5023-32. [PMID: 23510108 DOI: 10.1021/ac400287n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Electron transfer dissociation (ETD) is commonly used in fragmenting N-linked glycopeptides in their mass spectral analyses to complement collision-induced dissociation (CID) experiments. The glycan remains intact through ETD, while the peptide backbone is cleaved, providing the sequence of amino acids for a glycopeptide. Nonetheless, data analysis is a major bottleneck to high-throughput glycopeptide identification based on ETD data, due to the complexity and diversity of ETD mass spectra compared to CID counterparts. GlycoPep Detector (GPD) is a web-based tool to address this challenge. It filters out noise peaks that interfere with glycopeptide sequencing, correlates input glycopeptide compositions with the ETD spectra, and assigns a score for each candidate. By considering multiple ion series (c-, z-, and y-ions) and scoring them separately, the software gives more weighting to the ion series that matches peaks of high intensity in the spectra. This feature enables the correct glycopeptide to receive a high score while keeping scores of incorrect compositions low. GPD has been utilized to interpret data collected on six model glycoproteins (RNase B, avidin, fetuin, asialofetuin, transferrin, and AGP) as well as a clade C HIV envelope glycoprotein, C.97ZA012 gp140ΔCFI. In every assignment made by GPD, the correct glycopeptide composition earns a score that is about 2-fold higher than other incorrect glycopeptide candidates (decoys). The software can be accessed at http://glycopro.chem.ku.edu/ZZKHome.php .
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Affiliation(s)
- Zhikai Zhu
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
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Go EP, Liao HX, Alam SM, Hua D, Haynes BF, Desaire H. Characterization of host-cell line specific glycosylation profiles of early transmitted/founder HIV-1 gp120 envelope proteins. J Proteome Res 2013; 12:1223-34. [PMID: 23339644 PMCID: PMC3674872 DOI: 10.1021/pr300870t] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Glycosylation plays an essential role in regulating protein function by modulating biological, structural, and therapeutic properties. However, due to its inherent heterogeneity and diversity, the comprehensive analysis of protein glycosylation remains a challenge. As part of our continuing effort in the analysis of glycosylation profiles of recombinant HIV-1 envelope-based immunogens, we evaluated and compared the host-cell specific glycosylation pattern of recombinant HIV-1 surface glycoprotein, gp120, derived from clade C transmitted/founder virus 1086.C expressed in Chinese hamster ovary (CHO) and human embryonic kidney containing T antigen (293T) cell lines. We used an integrated glycopeptide-based mass mapping workflow that includes a partial deglycosylation step described in our previous study with the inclusion of a fragmentation technique, electron transfer dissociation (ETD), to complement collision-induced dissociation. The inclusion of ETD facilitated the analysis by providing additional validation for glycopeptide identification and expanding the identified glycopeptides to include coverage of O-linked glycosylation. The site-specific glycosylation analysis shows that the transmitted/founder 1086.C gp120 expressed in CHO and 293T displayed distinct similarities and differences. For N-linked glycosylation, two sites (N386 and N392) in the V4 region were populated with high mannose glycans in the CHO cell-derived 1086.C gp120, while these sites had a mixture of high mannose and processed glycans in the 293T cell-derived 1086.C gp120. Compositional analysis of O-linked glycans revealed that 293T cell-derived 1086.C gp120 consisted of core 1, 2, and 4 type O-linked glycans, while CHO cell-derived 1086.C exclusively consisted of core 1 type O-linked glycans. Overall, glycosylation site occupancy of the CHO and 293T cell-derived 1086.C gp120 showed a high degree of similarity except for one site at N88 in the C1 region. This site was partially occupied in 293T-gp120 but fully occupied in CHO-gp120. Site-specific glycopeptide analysis of transmitted/founder 1086.C gp120 expressed in CHO cells revealed the presence of phosphorylated glycans, while 293T cell-produced 1086.C gp120 glycans were not phosphorylated. While the influence of phosphorylated glycans on immunogenicity is unclear, distinguishing host-cell specific variations in glycosylation profiles provide insights into the similarity (or difference) in recombinant vaccine products. While these differences had minimal effect on envelope antigenicity, they may be important in considering immunogenicity and functional capacities of recombinant envelope proteins produced in different expression systems.
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Affiliation(s)
- Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, KS
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, NC
| | - S. Munir Alam
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, NC
| | - David Hua
- Department of Chemistry, University of Kansas, Lawrence, KS
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, NC
- Department of Immunology, Duke University Medical Center, Durham, NC
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Gao J, He Q, Hua D, Mao Y, Li Y, Shen L. Polymorphism of TS 3′-UTR predicts survival of Chinese advanced gastric cancer patients receiving first-line capecitabine plus paclitaxel. Clin Transl Oncol 2012; 15:619-25. [DOI: 10.1007/s12094-012-0979-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 11/20/2012] [Indexed: 01/27/2023]
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Woodin CL, Hua D, Maxon M, Rebecchi KR, Go EP, Desaire H. GlycoPep grader: a web-based utility for assigning the composition of N-linked glycopeptides. Anal Chem 2012; 84:4821-9. [PMID: 22540370 DOI: 10.1021/ac300393t] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
GlycoPep grader (GPG) is a freely available software tool designed to accelerate the process of accurately determining glycopeptide composition from tandem mass spectrometric data. GPG relies on the identification of unique dissociation patterns shown for high mannose, hybrid, and complex N-linked glycoprotein types, including patterns specific to those structures containing fucose or sialic acid residues. The novel GPG scoring algorithm scores potential candidate compositions of the same nominal mass against MS/MS data through evaluation of the Y(1) ion and other peptide-containing product ions, across multiple charge states, when applicable. In addition to evaluating the peptide portion of a given glycopeptide, the GPG algorithm predicts and scores product ions that result from unique neutral losses of terminal glycans. GPG has been applied to a variety of glycoproteins, including RNase B, asialofetuin, and transferrin, and the HIV envelope glycoprotein, CON-S gp140ΔCFI. The GPG software is implemented predominantly in PostgreSQL, with PHP as the presentation tier, and is publicly accessible online. Thus far, the algorithm has identified the correct compositional assignment from multiple candidate N-glycopeptides in all tests performed.
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Affiliation(s)
- Carrie L Woodin
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
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Hua D, Lau W, Mumtaz F, Mikhailidis D, Thompson C. 1131 IN-VITRO STUDIES INVESTIGATING THE ROLE OF PERIPHERAL SEROTONERGIC PATHWAY ON THE NORMAL AND DIABETIC HUMAN ERECTILE PROCESS. J Urol 2011. [DOI: 10.1016/j.juro.2011.02.728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Xinning W, Mingsheng L, Liying C, Yuzhou G, Benhong L, Hua D. P12-26 Neurophysiological characteristics of Hirayama disease. Clin Neurophysiol 2010. [DOI: 10.1016/s1388-2457(10)60730-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tian Y, Hua D, Ji Y, Li X, Liu J, Wang B, Yu D. The patterns of care studies for operable breast cancer in China. J Clin Oncol 2009. [DOI: 10.1200/jco.2009.27.15_suppl.e11607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e11607 Background: To present the results of clinical practices for operable breast cancer (BC) in the developed areas of China during the past decade. Methods: Four academic levels of radiotherapy (RT) departments, located in the Southeast coast of China, were selected. A pattern of care study, about women with operated BC and post-operative RT during 1999 and 2006, was conducted. The recruited samples were evaluated for their medical files completeness at first. For qualified documentations, data collected included patient characteristics, clinical and pathologic features, and treatment course received. Frequencies and corresponding percentages were calculated and analyzed for comparisons between 1999 and 2006. Results: 97 in 1999 and 271 in 2006 were identified as qualified files. Patient's diagnosis median age were 48 (1996) and 46 (2006) years. The clinical staging with I, II, and III (UICC 1997) were in 11%, 69%, 13% of 1999 patients and 15%, 74%, 7% of the 2006. The pathological characteristics were clearly defined in 78% (1999) and 84% (2006), but hormonal receptors and Her2neu were performed in 59% and 0% in the 1999 vs. 73% (p < 0.05) and 1% in 2006 survey. As type and extent of surgery and RT, the percentage of conservative treatment was increased from 4% in 1999 to 12% in 2006 (p< 0.05), postmastectomy RT was done for all the others. The time interval from operation to initiation of RT were longer in 2006, the mean was delayed from 23.8 to 43.4 days. The axillary operation pattern including lymph node dissection, level I/II dissection, and sentinel lymph node biopsy (SLNB), were documented in 61%, 24%, and 8% of patients in 2006. For patients of 1999, no SLNB was performed and 16% with level I/II operation (p< 0.05). Systemic chemotherapy (CT) and/or hormonal therapy were used in 74% (1999) and 98% (2006) of patients respectively (p< 0.05). Anthracyclines and paclitaxel-based CT regimens use significantly increased between 1999 and 2006 (31% vs. 52% and 12% vs. 36%). Conclusions: The practice patterns established in this study provide a baseline data. The present results demonstrate a low level of compliance with Western guidelines of clinical practices with current BC standards and continued improvement in many categories. Establishment and widespread use of international guidelines in China are desirable. No significant financial relationships to disclose.
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Affiliation(s)
- Y. Tian
- Second Affiliated Hospital of Suzhou University, Suzhou, Jiangsu, China; Fourth People's Hospital of Wuxi, Wuxi, Jiangsu, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China; Shenzhen People's Hospital, Shenzhen, Guangdong, China; Xiamen Sun Yat-sen Hospital, Xiamen, Fujian, China
| | - D. Hua
- Second Affiliated Hospital of Suzhou University, Suzhou, Jiangsu, China; Fourth People's Hospital of Wuxi, Wuxi, Jiangsu, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China; Shenzhen People's Hospital, Shenzhen, Guangdong, China; Xiamen Sun Yat-sen Hospital, Xiamen, Fujian, China
| | - Y. Ji
- Second Affiliated Hospital of Suzhou University, Suzhou, Jiangsu, China; Fourth People's Hospital of Wuxi, Wuxi, Jiangsu, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China; Shenzhen People's Hospital, Shenzhen, Guangdong, China; Xiamen Sun Yat-sen Hospital, Xiamen, Fujian, China
| | - X. Li
- Second Affiliated Hospital of Suzhou University, Suzhou, Jiangsu, China; Fourth People's Hospital of Wuxi, Wuxi, Jiangsu, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China; Shenzhen People's Hospital, Shenzhen, Guangdong, China; Xiamen Sun Yat-sen Hospital, Xiamen, Fujian, China
| | - J. Liu
- Second Affiliated Hospital of Suzhou University, Suzhou, Jiangsu, China; Fourth People's Hospital of Wuxi, Wuxi, Jiangsu, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China; Shenzhen People's Hospital, Shenzhen, Guangdong, China; Xiamen Sun Yat-sen Hospital, Xiamen, Fujian, China
| | - B. Wang
- Second Affiliated Hospital of Suzhou University, Suzhou, Jiangsu, China; Fourth People's Hospital of Wuxi, Wuxi, Jiangsu, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China; Shenzhen People's Hospital, Shenzhen, Guangdong, China; Xiamen Sun Yat-sen Hospital, Xiamen, Fujian, China
| | - D. Yu
- Second Affiliated Hospital of Suzhou University, Suzhou, Jiangsu, China; Fourth People's Hospital of Wuxi, Wuxi, Jiangsu, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China; Shenzhen People's Hospital, Shenzhen, Guangdong, China; Xiamen Sun Yat-sen Hospital, Xiamen, Fujian, China
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Liu J, Meng F, Hua D. [Epidemiological survey of malaria in Nangiao endemic area of Hunan Province using IFAT and PCR]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi 2003; 18:253-4. [PMID: 12567679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
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He J, Cai X, Zhang Y, Wang X, Hua D, Wang S. [Detection of Plasmodium vivax by polymerase chain reaction in Hainan]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi 2003; 17:356-8. [PMID: 12563734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
AIM To establish a modified polymerase chain reaction(PCR) method for the detection of Plasmodium vivax in the endemic areas of malaria and compare the method with the conventional light microscopy in the field. METHODS A PCR method was modified by improving the collection procedures of blood samples, template extraction, primer design and optimizing the reaction condition. The method was evaluated by examining blood samples from 310 patients with vivax malaria and compared with the conventional light microscopy in endemic areas of Hainan Province. RESULTS The positive rates of the modified PCR method and microscopic method were 34.2% and 31.9%, respectively. CONCLUSION The modified PCR method is simple, sensitive and specific for the detection of vivax malaria patients in endemic areas.
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Affiliation(s)
- J He
- Department of Clinical Laboratory of Changhai Hospital, Second Military Medical University, Shanghai 200433
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Lewis S, Karrer J, Saleh S, Chan X, Tan Z, Hua D, McGill J, Pang YP, Fenwick B, Brightman A, Takemoto D. Synthesis and evaluation of novel aldose reductase inhibitors: Effects on lens protein kinase Cgamma. Mol Vis 2001; 7:164-71. [PMID: 11483892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
PURPOSE To synthesize novel aldose reductase inhibitors (ARI) that will normalize losses in protein kinase Cgamma (PKCgamma) observed during diabetes and galactosemia. METHODS ARI were synthesized as tricyclic pyrones 1-6 (HAR-1 through HAR-6) from 3-methyl-1H,7H-5a,6,8,9-tetrahydro-1-oxopyrano[4,3-b][1]benzopyran and (5aS,7S)-7-isopropenyl-3-methyl-1H,7H-5a,6,8,9-tetrahydro-1-oxopyrano[4,3-b][1]benzopyran and were tested by inhibition of aldose reductase enzyme activity in vitro and by inhibition of polyol formation in lens epithelial cells in culture. Identified compounds were further tested in galactosemic rat lens in vivo for (a) normalized PKCgamma levels by Western blot, (b) reduction of phosphorylation of the gap junction protein Cx46 by analyses of co-immunoprecipitated proteins, and (c) by normalization of gap junction activity as measured by dye transfer. RESULTS HAR-1 (1H,7H-5a,6,8,9-tetrahydro-1-oxopyrano[4,3-b][1]benzopyran-3-acetic acid) was identified as an ARI with IC50 for aldose reductase inhibition at 2 nM. Polyol accumulation in lens epithelial cells was reduced by 80% at 10 microM. Rats fed 40% galactose for 9 days had an 80% reduction in PKCgamma levels which were normalized by HAR-1 at 100 mg/kg/day, fed orally. Phosphorylation of Cx46 was increased by 50% and this was normalized in HAR-1 treated rats (6 day treatment). Gap junction activity of galactosemic rats was reduced by 55% and this was normalized by HAR-1 in six day-treated rats. CONCLUSIONS HAR-1 is a novel ARI which normalized losses of PKCgamma, changes in Cx46 phosphorylation, and gap junction activity.
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Affiliation(s)
- S Lewis
- Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA
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Chompret A, Brugières L, Ronsin M, Gardes M, Dessarps-Freichey F, Abel A, Hua D, Ligot L, Dondon MG, Bressac-de Paillerets B, Frébourg T, Lemerle J, Bonaïti-Pellié C, Feunteun J. P53 germline mutations in childhood cancers and cancer risk for carrier individuals. Br J Cancer 2000; 82:1932-7. [PMID: 10864200 PMCID: PMC2363254 DOI: 10.1054/bjoc.2000.1167] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The family history of cancer in children treated for a solid malignant tumour in the Paediatric Oncology Department at Institute Gustave-Roussy, has been investigated. In order to determine the role of germline p53 mutations in genetic predisposition to childhood cancer, germline p53 mutations were sought in individuals with at least one relative (first- or second-degree relative or first cousin) affected by any cancer before 46 years of age, or affected by multiple cancers. Screening for germline p53 mutation was possible in 268 index cases among individuals fulfilling selection criteria. Seventeen (6.3%) mutations were identified, of which 13 were inherited and four were de novo. Using maximum likelihood methods that incorporate retrospective family data and correct for ascertainment bias, the lifetime risk of cancer for mutation carriers was estimated to be 73% for males and nearly 100% for females with a high risk of breast cancer accounting for the difference. The risk of cancer associated with such mutations is very high and no evidence of low penetrance mutation was found. These mutations are frequently inherited but de novo mutations are not rare.
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Affiliation(s)
- A Chompret
- Départment d'Oncologie Pédiatrique, Institute Gustave-Roussy, Villejuif, France
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Chen C, Liu J, Hua D, Ma L, Lai T, Fallon JT, Knibbs D, Gillam L, Mangion J, Knight DR, Waters D. Impact of delayed reperfusion of myocardial hibernation on myocardial ultrastructure and function and their recoveries after reperfusion in a pig model of myocardial hibernation. Cardiovasc Pathol 2000; 9:67-84. [PMID: 10867357 DOI: 10.1016/s1054-8807(00)00029-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
UNLABELLED This study examined the effect of delayed reperfusion of myocardial hibernation from 24 hours to 7 days on myocardial ultrastructural and functional changes and their recoveries after reperfusion. BACKGROUND We have previously shown in pigs that after reperfusion the functional and structural alterations in short-term myocardial hibernation which was reperfused in 24 hours can recover in 7 days. The effect of delayed reperfusion of hibernating myocardium on the extent and severity of cellular and extracellular structural changes of hibernating myocardium, and their recoveries after reperfusion is not known. METHODS AND RESULTS A severe LAD stenosis was created in 27 pigs, reducing resting flow by 30-40% immediately after placement of the stenosis and producing acute ischemia as evidenced by regional lactate production, a decrease in regional coronary venous pH, reduced regional wall thickening (from 38.5 +/- 5.1% to 10.4 +/- 8.0%) and a 33% reduction of regional oxygen consumption. The stenosis was maintained either for 24 hours in 9 pigs (group 1) with LAD flow of 0.65 +/- 0.13 ml/min/g (38% reduction), or for 7 days in 17 pigs (group 2) with LAD flow of 0.67 +/- 0.14 ml/min/g (36% reduction). There were no differences (p = NS) in the reduction of wall thickening, rate-pressure product, lactate production, or regional oxygen consumption between group 1 and group 2. Quantitative morphometric evaluation of the ultrastructure on electromicrographs revealed a greater decrease in sarcomere volume and a higher incidence of myocytes with reduced sarcomere volume in 7-day than in 24-hour hibernating regions (53 +/- 19% versus 33 +/- 14%, p < 0.05). Patchy myocardial necrosis with replacement fibrosis was common, but 6 of the 18 pigs had no myocardial necrosis or replacement fibrosis in the 7-day hibernating group, and 4 of 9 pigs had no patchy myocyte necrosis in the 24 hour hibernating group. In 6 pigs in group 1 in which the stenosis was then released and hibernating myocardium reperfused in 24 hours, regional wall thickening recovered to 30 +/- 6% (p = NS compared to baseline) after one week of reperfusion. In 12 pigs in group 2 in which the stenosis was released and hibernating myocardium reperfused in 7 days, regional wall thickening recovered slowly, from 10.1 +/- 7.2% to 18.1 +/- 8.3% at one week (n = 5) and to 28.0 +/- 3.6% at 3-4 weeks of reperfusion (n = 7, p < 0.05 compared to baseline). Similarly, the sarcomere volume or myofilament recovered significantly (p < 0.01) and was not different compared to the normal region (p = NS) in the 24-hour hibernating region of group 1, but the recovery was much slower and was incomplete at 4 weeks (p < 0.01) compared to baseline in the 7-day hibernating region of group 2. Recovery of regional wall thickening correlated with ultrstructural recovery (p < 0.01). By multivariate stepwise regression analysis, the degree of LAD flow reduction, the extent of fibrosis, and myofilament loss were independent predictors of the extent of functional recovery. CONCLUSIONS In a porcine model of myocardial hibernation with myocardial hypoperfusion, systolic dysfunction, and metabolic adaptations, a longer period of myocardial hibernation with delayed reperfusion was associated with more severe abnormalities of myocytes. an increasing interstitial fibrosis, and more protracted myofibrillar and functional recoveries after reperfusion. The extent of functional recovery is related to the degree of coronary flow reduction, the severity of the ultrastructural changes, and the extent of interstitial fibrosis.
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Affiliation(s)
- C Chen
- Division of Cardiology, Hartford Hospital, Hartford, CT, USA.
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Hua D, Li J, Xia X. [Immunophenotype and P-glycoprotein expression in CD7 positive adult acute myeloid leukemia]. Zhonghua Xue Ye Xue Za Zhi 1999; 20:88-90. [PMID: 11601207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
OBJECTIVE To study the immunophenotype and P-glycoprotein expression in CD7 positive adult acute myeloid leukemia (CD7+ AML). METHODS Morphology, P-glycoprotein, cytogenetics and immunophenotype were examined in 30 previously untreated CD7+ AML patients. RESULTS The CD7 positive rate was 11.4% in 262 AML patients. CD7+ AML patients had a significantly higher incidence of peripheral leukocytosis and blasts and FAB M1 subtype and were associated with CD34 and P-glycoprotein expression. 42.3% of CD7+ AML achieved complete remission with a median remission duration of 4 months, and a median time to CR of 48 days. CONCLUSION Patients with CD7+ AML are usually CD34 and P-glycoprotein positive. These patients had a lower CR rate and a shorter remission duration.
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Affiliation(s)
- D Hua
- First Affiliated Hospital, Suzhou Medical College, Jiangsu Institute of Hematology, Suzhou 215006
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Hua D, Li J, Xia X. [The clinical and biological significance of megakaryocytic antigen expression in acute myeloid leukemia]. Zhonghua Xue Ye Xue Za Zhi 1999; 20:21-3. [PMID: 11498838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
OBJECTIVE To explore megakaryocytic (MK) antigen expression in previously untreated adult acute myeloid leukemia (AML) and its relation to the clinical and biological characteristics. METHODS Two hundred and eleven cases of AML were detected with flow cytometric immunofluorescence assay. RESULTS Twenty-seven cases (12.8%) were MK antigen positive with the higher positive rates in hybrid acute leukemia (45.5%) and acute monoblastic leukemia (24.1%). MK antigen expression was significantly correlated with CD34 antigen expression, high white cell count, high P-glycoprotein positivity and had no correlation with chromosome aberration. 33.3% of MK positive AML patients achieved complete remission which was significantly lower than that (71.9%) in MK negative cases. CONCLUSION MK antigen positive AML might derived from malignant transformation of hemotopoietic stem cell at earlier stage and the detection of MK expression was of values in predicting treatment effect and prognosis for adult AML.
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Affiliation(s)
- D Hua
- First Affiliated Hospital of Suzhou Medical College, Suzhou 215006
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Li J, Hua D, Xia X. [Prognostic significance of P-glycoprotein expression in acute leukemia in adults]. Zhonghua Zhong Liu Za Zhi 1998; 20:302-4. [PMID: 10920991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
OBJECTIVE To explore the prognostic significance of P-glycoprotein (P-gp) expression in previously untreated acute leukemia in adults. METHODS P-gp expression in 151 acute myeloblastic leukemia (AML) and 47 acute lymphoblastic leukemia (ALL) was determined by monoclonal antibody UIC2 and flow cytometry. RESULTS The rate of complete remission (CR) differed between P-gp+ and P-gp- AML (20.5% vs 78.5%, P < 0.001), but the CR rate did not significantly differ between P-gp+ and P-gp- ALL(66.7% vs 80%, P > 0.05). The six-month relapse rate was significantly higher in P-gp+ group than that of P-gp- group (AML: 66.7% vs 8.7%, P < 0.001; ALL: 50% vs 9.5%, P < 0.05). The median disease-free survival time was shorter in P-gp+ group than in P-gp- group (AML: 5 months vs 13 months; ALL: 4 months vs 13 months). CONCLUSION Overexpression of P-gp is a poor prognostic factor in adult acute leukemia and P-gp detection is useful for the prediction of treatment response and early relapse.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/biosynthesis
- Adolescent
- Adult
- Aged
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Disease-Free Survival
- Female
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Promyelocytic, Acute/drug therapy
- Leukemia, Promyelocytic, Acute/metabolism
- Male
- Middle Aged
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Recurrence
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Affiliation(s)
- J Li
- Jiangsu Institute of Hematology, First Affiliated Hospital, Suzhou Medical College, Suzhou
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Li J, Xia X, Hua D, Wang W, Chen Z, Ruan C. Clinical and biological relevance of flow cytometric determination of P-glycoprotein expression in acute non-lymphocytic leukemia. Chin Med J (Engl) 1997; 110:919-22. [PMID: 9772402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
OBJECTIVE To evaluate the characteristics of P-glycoprotein (P-gp) expression of acute non-lymphocytic leukemia (ANLL) at different status and the prognostic and biological features in ANLL at diagnosis. METHODS Monoclonal antibody UIC2 and indirect immunofluorescence assay by flow cytometry were used to determine P-gp expression of 169 patients with ANLL, including 152 previously untreated, 7 refractory and 10 at remission. RESULTS P-gp was expressed in 28.9% of the previously untreated ANLL cases and P-gp was lower than that in 71.4% of the refractory cases (P < 0.05). No P-gp expression was found in the patients at remission. For previously untreated AN-LL, P-gp was highly expressed in hybrid acute leukemia (66.7%) and acute monoblastic leukemia (47.4%). P-gp expression was highly associated with surface markers [cluster of differentiation (CD) 34, CD7, CD14, CD42b and CD61] and unfavorable cytogenetic abnormalities. About 23% of P-gp-ANLL obtained complete remission, which was significantly lower than that (76%) in P-gp-cases. CONCLUSIONS P-gp expression is higher in refractory ANLL cases than that in cases at diagnosis or at remission. P-gp is an index of poor prognosis in adults with ANLL. P-gp+ ANLL cases have unique clinical and biological characteristics.
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Affiliation(s)
- J Li
- Jiangsu Institute of Hematology, Affiliated First Hospital, Suzhou Medical College, China
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Li J, Xia X, Hua D. [The clinical and biological significance of P-glycoprotein expression in acute nonlymphocytic leukemia]. Zhonghua Nei Ke Za Zhi 1997; 36:304-7. [PMID: 10374270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
To evaluate the clinical and biological significance of P-glycoprotein (P-gp) expression in adult acute nonlymphocytic leukemia (ANLL), P-gp was detected in 169 patients including 152 previously untreated cases, 7 refractory cases, and 10 cases at remission by using monoclonal antibody UIC2 and flow cytometry. P-gp was expressed in 29% of previously untreated cases, being less than in 71% of the refractory cases. P-gp expression was not found in patients at remission. Morphologically, P-gp expression was high in hybrid acute leukemia (67%) and acute monoblastic leukemia (47%) subtypes. Immunologically, P-gp expression was significantly associated with CD34, CD7, CD14 or CD42b/CD61. Cytogenetically, P-gp expression was highly associated with poor prognosis abnormalities (54%), which was significantly higher than 7% of P-gp expression in good prognosis abnormalities. 23% of P-gp positive previously untreated ANLL (not including M3) achieved complete remission; this was significantly lower than 76% in P-gp negative cases. These suggested that P-gp expression is an index of poor prognosis in adult ANLL and P-gp positive ANLL has unique clinical and biological features.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/biosynthesis
- Adult
- Antigens, CD/metabolism
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Female
- Genes, MDR
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/metabolism
- Male
- Prognosis
- Remission Induction
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Affiliation(s)
- J Li
- First Affiliated Hospital of Suzhou Medical College
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Abstract
A cDNA encoding the Renilla reniformis luciferase was expressed in similan and murine cells in a transient and stable manner, respectively. Light emission catalyzed by luciferase was detected from transfected cells both in vitro and in vivo. This work establishes the Renilla luciferase gene as a new efficient marker of gene expression in mammalian cells.
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Affiliation(s)
- W W Lorenz
- Department of Biochemistry, University of Georgia, Athens 30602, USA
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