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Cai Y, Chang C, Liao R. Overcoming the detrimental O-acylation in TMTpro labeling improves the proteome depth and quantification precision. Anal Chim Acta 2024; 1304:342538. [PMID: 38637049 DOI: 10.1016/j.aca.2024.342538] [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: 12/25/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND With the advent of proline-based reporter isobaric Tandem Mass Tag (TMTpro) reagents, the sample multiplexing capacity of tandem mass tags (TMTs) has been expanded, and up to 18 samples can be quantified in a multiplexed manner. Like classic TMT reagents, TMTpro reagents contain a tertiary amine group, which markedly enhances their reactivity toward hydroxyl groups and results in O-acylation of serine, threonine and tyrosine residues. This overlabeling significantly compromises proteome analysis in terms of depth and precision. In particular, the reactivity of hydroxyl-containing residues can be dramatically enhanced when coexisting with a histidine in the same peptides, leading to a severe systematic bias against the analysis of these peptides. Although some protocols using a reduced molar excess of TMT under alkaline conditions can alleviate overlabeling of histidine-free peptides to some extent, they have a limited effect on histidyl- and hydroxyl-containing peptides. RESULTS Here, we report a novel TMTpro labeling method that overcomes detrimental overlabeling while providing high labeling efficiency of amines. Additionally, our method is cost-effective, as it requires only half the amount of TMTpro reagents recommended by the reagent manufacturer. In a deep-scale analysis of a yeast/human two-proteome model sample, we compared our method with a typical alkaline labeling method using a reduced molar excess of TMTpro. Even at a depth of over 10,000 proteins, our method detected 23.7% more unique peptides and 8.7% more protein groups compared to the alkaline labeling method. Moreover, our method significantly improved the quantitative precision due to the reduced variability in labeling and increased protein sequence coverage. This substantially enhanced the statistical power of our method for detecting differentially abundant proteins, providing an average of 13% more yeast proteins that reached statistical significance. SIGNIFCANCE We presented a novel TMTpro labeling method that overcomes the detrimental O-acylation and thus significantly improves the depth and quantitative precision for proteome analysis.
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Affiliation(s)
- Yan Cai
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Chenchen Chang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Rijing Liao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.
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Zeng C, Xiao K, Shi Q, Zhan X, Li C. TMT-Based Quantitative Proteomic Analysis Reveals the Key Role of Cell Proliferation and Apoptosis in Intestine Regeneration of Apostichopus japonicus. Int J Mol Sci 2024; 25:4250. [PMID: 38673840 DOI: 10.3390/ijms25084250] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Sea cucumbers are widely known for their powerful regenerative abilities, which allow them to regenerate a complete digestive tract within a relatively short time following injury or autotomy. Recently, even though the histological changes and cellular events in the processes of intestinal regeneration have been extensively studied, the molecular machinery behind this faculty remains unclear. In this study, tandem mass tag (TMT)-based quantitation was utilized to investigate protein abundance changes during the process of intestine regeneration. Approximately 538, 445, 397, 1012, and 966 differential proteins (DEPs) were detected (p < 0.05) between the normal and 2, 7, 12, 20, and 28 dpe stages, respectively. These DEPs also mainly focus on pathways of cell proliferation and apoptosis, which were further validated by 5-Ethynyl-2'-deoxyuridine (EdU) or Tunel-based flow cytometry assay. These findings provide a reference for a comprehensive understanding of the regulatory mechanisms of various stages of intestinal regeneration and provide a foundation for subsequent research on changes in cell fate in echinoderms.
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Affiliation(s)
- Chuili Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
| | - Ke Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
| | - Qilin Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
| | - Xu Zhan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
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Hu S, Lin S, Xu H, He X, Chen L, Feng Q, Sun N. Molecular Mechanisms of Iron Transport and Homeostasis Regulated by Antarctic Krill-Derived Heptapeptide-Iron Complex. J Agric Food Chem 2024; 72:7517-7532. [PMID: 38527166 DOI: 10.1021/acs.jafc.3c05812] [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] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
In this study, the molecular mechanisms of iron transport and homeostasis regulated by the Antarctic krill-derived heptapeptide-iron (LVDDHFL-iron) complex were explored. LVDDHFL-iron significantly increased the hemoglobin, serum iron, total iron binding capacity levels, and iron contents in the liver and spleen to normal levels, regulated the gene expressions of iron homeostasis, and enhanced in vivo antioxidant capacity in iron-deficiency anemia mice (P < 0.05). The results revealed that iron ions within LVDDHFL-iron can be transported via the heme transporter and divalent metal transporter-1, and the absorption of LVDDHFL-iron involved receptor-mediated endocytosis. We also found that the transport of LVDDHFL-iron across cells via phagocytosis was facilitated by the up-regulation of the high mobility group protein, heat shock protein β, and V-type proton ATPase subunit, accompanied by the regulatory mechanism of autophagy. These findings provided deeper understandings of the mechanism of LVDDHFL-iron facilitating iron absorption.
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Affiliation(s)
- Shengjie Hu
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, P. R. China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Songyi Lin
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, P. R. China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China
- Engineering Research Center of Special Dietary Food, Education Department of Liaoning Province, Dalian 116034, P. R. China
| | - Haowei Xu
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Xueqing He
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Lei Chen
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Qi Feng
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Na Sun
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, P. R. China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China
- Engineering Research Center of Special Dietary Food, Education Department of Liaoning Province, Dalian 116034, P. R. China
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de Angelis M, Baudo A, Siech C, Jannello LMI, Di Bello F, Goyal JA, Tian Z, Longo N, de Cobelli O, Chun FKH, Saad F, Shariat SF, Carmignani L, Gandaglia G, Moschini M, Montorsi F, Briganti A, Karakiewicz PI. Non-Surgical Bladder-Sparing Multimodal Management in Organ-Confined Urothelial Carcinoma of the Urinary Bladder: A Population-Based Analysis. Cancers (Basel) 2024; 16:1292. [PMID: 38610970 PMCID: PMC11010909 DOI: 10.3390/cancers16071292] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Trimodal therapy is considered the most validated bladder-sparing treatment in patients with organ-confined urothelial carcinoma of the urinary bladder (T2N0M0). However, scarce evidence exists regarding cancer-specific mortality (CSM) differences between trimodal therapy and other non-extirpative multimodal treatment options such as radiotherapy alone after transurethral resection (TURBT + RT) or chemotherapy alone after transurethral resection (TURBT + CT). METHODS Within the Surveillance, Epidemiology, and End Results database (2004-2020), we identified T2N0M0 patients treated with either trimodal therapy, TURBT + CT, or TURBT + RT. Temporal trends described trimodal therapy vs. TUBRT + CT vs. TURBT + RT use over time. Survival analyses consisting of Kaplan-Meier plots and multivariable Cox regression (MCR) models addressed CSM according to each treatment modality. RESULTS 3729 (40%) patients underwent TMT vs. 4030 (43%) TURBT + CT vs. 1599 (17%) TURBT + RT. Over time, trimodal therapy use (Estimating annual percent change, EAPC: +1.2%, p = 0.01) and TURBT + CT use increased (EAPC: +1.5%, p = 0.01). In MCR models, relative to trimodal therapy, TURBT + CT exhibited 1-14-fold higher CSM and TURBT + RT 1.68-fold higher CSM. In a subgroup analysis, TURBT + RT was associated with 1.42-fold higher CSM than TURBT + CT (p < 0.001). CONCLUSIONS Strict trimodal therapy that includes both CT and RT after TURBT offers the best cancer control. When strict trimodal therapy cannot be delivered, cancer-specific survival outcomes appear to be superior with TURBT + chemotherapy compared to TURBT + RT.
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Affiliation(s)
- Mario de Angelis
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montreal Health Center, Montreal, QC H2X 3E4, Canada; (M.d.A.); (A.B.); (C.S.); (F.D.B.); (J.A.G.); (Z.T.); (F.S.)
- Division of Experimental Oncology, Unit of Urology, URI—Urological Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (G.G.); (M.M.); (F.M.); (A.B.)
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Andrea Baudo
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montreal Health Center, Montreal, QC H2X 3E4, Canada; (M.d.A.); (A.B.); (C.S.); (F.D.B.); (J.A.G.); (Z.T.); (F.S.)
- Department of Urology, IRCCS Policlinico San Donato, 20097 Milan, Italy;
| | - Carolin Siech
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montreal Health Center, Montreal, QC H2X 3E4, Canada; (M.d.A.); (A.B.); (C.S.); (F.D.B.); (J.A.G.); (Z.T.); (F.S.)
- Department of Urology, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany;
| | - Letizia Maria Ippolita Jannello
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montreal Health Center, Montreal, QC H2X 3E4, Canada; (M.d.A.); (A.B.); (C.S.); (F.D.B.); (J.A.G.); (Z.T.); (F.S.)
- Department of Urology, IEO European Institute of Oncology, IRCCS, Via Ripamonti 435, 20141 Milan, Italy;
| | - Francesco Di Bello
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montreal Health Center, Montreal, QC H2X 3E4, Canada; (M.d.A.); (A.B.); (C.S.); (F.D.B.); (J.A.G.); (Z.T.); (F.S.)
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy;
| | - Jordan A. Goyal
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montreal Health Center, Montreal, QC H2X 3E4, Canada; (M.d.A.); (A.B.); (C.S.); (F.D.B.); (J.A.G.); (Z.T.); (F.S.)
| | - Zhe Tian
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montreal Health Center, Montreal, QC H2X 3E4, Canada; (M.d.A.); (A.B.); (C.S.); (F.D.B.); (J.A.G.); (Z.T.); (F.S.)
| | - Nicola Longo
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy;
| | - Ottavio de Cobelli
- Department of Urology, IEO European Institute of Oncology, IRCCS, Via Ripamonti 435, 20141 Milan, Italy;
| | - Felix K. H. Chun
- Department of Urology, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany;
| | - Fred Saad
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montreal Health Center, Montreal, QC H2X 3E4, Canada; (M.d.A.); (A.B.); (C.S.); (F.D.B.); (J.A.G.); (Z.T.); (F.S.)
| | - Shahrokh F. Shariat
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria;
- Department of Urology, Weill Cornell Medical College, New York, NY 10065, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hourani Center of Applied Scientific Research, Al-Ahliyya Amman University, Amman 19328, Jordan
| | - Luca Carmignani
- Department of Urology, IRCCS Policlinico San Donato, 20097 Milan, Italy;
| | - Giorgio Gandaglia
- Division of Experimental Oncology, Unit of Urology, URI—Urological Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (G.G.); (M.M.); (F.M.); (A.B.)
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Marco Moschini
- Division of Experimental Oncology, Unit of Urology, URI—Urological Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (G.G.); (M.M.); (F.M.); (A.B.)
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Francesco Montorsi
- Division of Experimental Oncology, Unit of Urology, URI—Urological Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (G.G.); (M.M.); (F.M.); (A.B.)
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Alberto Briganti
- Division of Experimental Oncology, Unit of Urology, URI—Urological Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (G.G.); (M.M.); (F.M.); (A.B.)
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Pierre I. Karakiewicz
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montreal Health Center, Montreal, QC H2X 3E4, Canada; (M.d.A.); (A.B.); (C.S.); (F.D.B.); (J.A.G.); (Z.T.); (F.S.)
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Fu Y, Huang XQ, Qu HB, Ge YZ, Ru XL. Tandem Mass Tag-Based Proteomic Analysis of Normal and Degenerated Human Intervertebral Discs. J Pain Res 2024; 17:1313-1326. [PMID: 38563035 PMCID: PMC10982071 DOI: 10.2147/jpr.s449044] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Background Intervertebral disc degeneration (IVDD) is the main cause of low back pain (LBP), but the specific regulatory factors, pathways and specific molecular mechanisms remain unclear. Methods We identified and quantitatively analyzed Pfirrmann Grade II (n=3) and Pfirrmann Grade IV (n=3) pulposus samples via MRI. The differential abundance of proteins in the samples was determined and quantitatively analyzed by relative and absolute quantitative analysis of the isotope marker levels combined with the liquid chromatography-tandem mass spectrometry (LC‒MSMS/MS). Results A total of 70 proteins (30 significantly increased proteins (> 1.2-fold change) and 40 significantly decreased proteins (< 0.8-fold change)) showed different levels among the groups. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology (GO) enrichment analyses and Western blot analysis showed that CYCS, RAC1, and PSMD14 may play important roles in IVDD and that Epstein‒Barr virus infection, viral myocarditis, colorectal cancer, nonalcoholic fatty liver disease (NAFLD) and amyotrophic lateral sclerosis (ALS) are the main pathways involved in IVDD. Conclusion CYCS, RAC1 and PSMD14 may play important roles in IVDD, and Epstein‒Barr virus infection, viral myocarditis, colorectal cancer, NAFLD and ALS may be the main pathways involved in IVDD.
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Affiliation(s)
- Yang Fu
- Department of Orthopedics, Zhejiang Hospital, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Xiao-Qin Huang
- Department of Orthopedics, Zhejiang Hospital, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Hang-Bo Qu
- Department of Orthopedics, Zhejiang Hospital, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Yan Zhi Ge
- Department of Orthopedics, Zhejiang Hospital, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Xuan-Liang Ru
- Department of Orthopedics, Zhejiang Hospital, Hangzhou, Zhejiang Province, People’s Republic of China
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Forrester MT, Egol JR, Tata A, Tata PR, Foster MW. Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap). bioRxiv 2024:2024.03.23.586403. [PMID: 38585928 PMCID: PMC10996552 DOI: 10.1101/2024.03.23.586403] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Protein cysteine thiols undergo reversible S-acylation via a thioester linkage in vivo. S-palmitoylation, modification by C16:0 fatty acid, is a common S-acylation that mediates protein-membrane and protein-protein interactions critical to an array of biological processes, from homeostatic lung surfactant function to cellular transformation. The most widely used S-acylation assays, including acyl-biotin exchange (ABE) and acyl resin-assisted capture (Acyl-RAC), utilize blocking of free Cys thiols, hydroxylamine-dependent cleavage of the thioester and subsequent labeling of nascent thiol. ABE and Acyl-RAC have enabled both the proteome-wide identification of S-palmitoylation sites and basic biochemical studies. Yet, these assays generally utilize hundreds of micrograms to milligrams of input material and require numerous reagent removal and washing steps, making them laborious and ill-suited for high throughput and low input applications. To overcome this, we devised "Acyl-Trap", a suspension trap-based assay that utilizes a thiol-reactive quartz to enable buffer exchange and hydroxylamine-mediated S-acyl enrichment from 20-50 micrograms of input protein. The method is compatible with protein-level detection of Sacylated proteins as well as S-acyl site-based identification and quantification using on-quartz isobaric (tandem mass tag) labeling and LC-MS/MS. Also described are conditions for long-term hydroxylamine storage, which further expedites the assay and minimizes waste. More generally, Acyl-Trap serves as a proof-of-concept for PTM-tailored suspension traps suitable for both traditional intact protein detection and chemoproteomic workflows.
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Affiliation(s)
- Michael T Forrester
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jacob R Egol
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Purushothama Rao Tata
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Matthew W Foster
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, 27710, USA
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Yang K, Whitehouse RL, Dawson SL, Zhang L, Martin JG, Johnson DS, Paulo JA, Gygi SP, Yu Q. Accelerating multiplexed profiling of protein-ligand interactions: High-throughput plate-based reactive cysteine profiling with minimal input. Cell Chem Biol 2024; 31:565-576.e4. [PMID: 38118439 PMCID: PMC10960705 DOI: 10.1016/j.chembiol.2023.11.015] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/07/2023] [Accepted: 11/28/2023] [Indexed: 12/22/2023]
Abstract
Chemoproteomics has made significant progress in investigating small-molecule-protein interactions. However, the proteome-wide profiling of cysteine ligandability remains challenging to adapt for high-throughput applications, primarily due to a lack of platforms capable of achieving the desired depth using low input in 96- or 384-well plates. Here, we introduce a revamped, plate-based platform which enables routine interrogation of either ∼18,000 or ∼24,000 reactive cysteines based on starting amounts of 10 or 20 μg, respectively. This represents a 5-10X reduction in input and 2-3X improved coverage. We applied the platform to screen 192 electrophiles in the native HEK293T proteome, mapping the ligandability of 38,450 reactive cysteines from 8,274 human proteins. We further applied the platform to characterize new cellular targets of established drugs, uncovering that ARS-1620, a KRASG12C inhibitor, binds to and inhibits an off-target adenosine kinase ADK. The platform represents a major step forward to high-throughput proteome-wide evaluation of reactive cysteines.
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Affiliation(s)
- Ka Yang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Shane L Dawson
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lu Zhang
- Biogen, Cambridge, MA 02142, USA
| | | | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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de Angelis M, Baudo A, Siech C, Jannello LMI, Di Bello F, Goyal JA, Tian Z, Longo N, de Cobelli O, Chun FKH, Saad F, Shariat SF, Carmignani L, Gandaglia G, Moschini M, Montorsi F, Briganti A, Karakiewicz PI. The effect of race/ethnicity on cancer-specific mortality after trimodal therapy. J Racial Ethn Health Disparities 2024:10.1007/s40615-024-01973-7. [PMID: 38509444 DOI: 10.1007/s40615-024-01973-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Trimodal therapy (TMT) is the most validated bladder-sparing treatment for organ-confined urothelial carcinoma of the urinary bladder (OC UCUB, namely cT2N0M0). However, it is unknown if barriers to the use of TMT or cancer-specific mortality (CSM) differences exist according to race/ethnicity. We addressed this knowledge gap. MATERIAL AND METHODS Within the Surveillance, Epidemiology, and End Results database (2004-2020), we identified OC UCUB patients aged from 18 to 85 treated with radical cystectomy (RC) or TMT. Temporal trends described TMT versus RC use over time. Subsequently, in the subgroup of TMT-treated patients, survival analyses consisting of Kaplan-Meier plots and multivariable Cox regression (MCR) models addressed CSM according to race/ethnicity. RESULTS Among 19,501 assessable patients, 15,336 (79%) underwent RC versus 4165 TMT (21%). Overall, of all races/ethnicities, 16,245 (83.3%) were White Americans, 1215 (6.3%) Hispanics, 1160 (5.9%) African Americans, and 881 (4.5%) Asian/Pacific Islanders. Among TMT-treated patients, 3460 (83.1%) were White Americans, 298 (7.1%) African Americans, 218 (5.3%) Hispanics, and 189 (4.5%) Asian/Pacific Islanders. The lowest rate of TMT use relative to RC and TMT patients was recorded in Hispanics (17.9%). Over time, TMT use increased in White Americans (EAPC: + 4.5%, p = 0.001) and Asians/Pacific Islanders (EAPC: + 5.2%, p = 0.003), but not in others. Kaplan-Meier analyses showed median CSM of 49 months, 41 months, and 34 months and not reached in White Americans, Hispanics, African Americans, and Asian/Pacific Islanders, respectively (p = 0.02). In MCR models, two race/ethnicity subgroups independently predicted either worse (African Americans, HR: 1.20, p = 0.02) or better CSM (Asian/Pacific Islanders, HR: 0.75, p = 0.02). CONCLUSION Race/ethnicity affects both access to TMT (lower access in Hispanics) as well as survival after TMT (better in Asians/Pacific Islanders and worse in African Americans).
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Affiliation(s)
- Mario de Angelis
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Québec, Canada.
- Division of Experimental Oncology/Unit of Urology, URI, IRCCS Ospedale San Raffaele, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
| | - Andrea Baudo
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Québec, Canada
- Department of Urology, IRCCS Policlinico San Donato, Milan, Italy
| | - Carolin Siech
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Québec, Canada
- Goethe University Frankfurt Am Main, Frankfurt Am Main, Germany
| | - Letizia Maria Ippolita Jannello
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Québec, Canada
- Department of Urology, IEO European Institute of Oncology, IRCCS, Via Ripamonti 435, Milan, Italy
| | - Francesco Di Bello
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Québec, Canada
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131, Naples, Italy
| | - Jordan A Goyal
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Québec, Canada
| | - Zhe Tian
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Québec, Canada
| | - Nicola Longo
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131, Naples, Italy
| | - Ottavio de Cobelli
- Department of Urology, IEO European Institute of Oncology, IRCCS, Via Ripamonti 435, Milan, Italy
| | - Felix K H Chun
- Goethe University Frankfurt Am Main, Frankfurt Am Main, Germany
| | - Fred Saad
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Québec, Canada
| | - Shahrokh F Shariat
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hourani Center of Applied Scientific Research, Al-Ahliyya Amman University, Amman, Jordan
| | - Luca Carmignani
- Department of Urology, IRCCS Policlinico San Donato, Milan, Italy
| | - Giorgio Gandaglia
- Division of Experimental Oncology/Unit of Urology, URI, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Marco Moschini
- Division of Experimental Oncology/Unit of Urology, URI, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Francesco Montorsi
- Division of Experimental Oncology/Unit of Urology, URI, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Alberto Briganti
- Division of Experimental Oncology/Unit of Urology, URI, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Pierre I Karakiewicz
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Québec, Canada
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Hamza GM, Raghunathan R, Ashenden S, Zhang B, Miele E, Jarnuczak AF. Proteomics of prostate cancer serum and plasma using low and high throughput approaches. Clin Proteomics 2024; 21:21. [PMID: 38475692 DOI: 10.1186/s12014-024-09461-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Despite progress, MS-based proteomics in biofluids, especially blood, faces challenges such as dynamic range and throughput limitations in biomarker and disease studies. In this work, we used cutting-edge proteomics technologies to construct label-based and label-free workflows, capable of quantifying approximately 2,000 proteins in biofluids. With 70µL of blood and a single depletion strategy, we conducted an analysis of a homogenous cohort (n = 32), comparing medium-grade prostate cancer patients (Gleason score: 7(3 + 4); TNM stage: T2cN0M0, stage IIB) to healthy donors. The results revealed dozens of differentially expressed proteins in both plasma and serum. We identified the upregulation of Prostate Specific Antigen (PSA), a well-known biomarker for prostate cancer, in the serum of cancer cohort. Further bioinformatics analysis highlighted noteworthy proteins which appear to be differentially secreted into the bloodstream, making them good candidates for further exploration.
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Affiliation(s)
| | - Rekha Raghunathan
- Bioanalytical and Biomarker, Prevail Therapeutics, Wholly Owned Subsidiary of Eli Lilly and Company, New York, NY, 10016, USA
| | | | - Bairu Zhang
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Eric Miele
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.
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10
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Peng H, Huang Y, Wei G, Pang Y, Yuan H, Zou X, Xie Y, Chen W. Testicular Toxicity in Rats Exposed to AlCl 3: a Proteomics Study. Biol Trace Elem Res 2024; 202:1084-1102. [PMID: 37382810 DOI: 10.1007/s12011-023-03745-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023]
Abstract
Aluminum contamination is a growing environmental and public health concern, and aluminum testicular toxicity has been reported in male rats; however, the underlying mechanisms of this toxicity are unclear. The objective of this study was to investigate the effects of exposure to aluminum chloride (AlCl3) on alterations in the levels of sex hormones (testosterone [T], luteinizing hormone [LH], and follicle-stimulating hormone [FSH]) and testicular damage. Additionally, the mechanisms of toxicity in the testes of AlCl3-exposed rats were analyzed by proteomics. Three different concentrations of AlCl3 were administered to rats. The results demonstrated a decrease in T, LH, and FSH levels with increasing concentrations of AlCl3 exposure. HE staining results revealed that the spermatogenic cells in the AlCl3-exposed rats were widened, disorganized, or absent, with increased severe tissue destruction at higher concentrations of AlCl3 exposure. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses revealed that differentially expressed proteins (DEPs) after AlCl3 exposure were primarily associated with various metabolic processes, sperm fibrous sheath, calcium-dependent protein binding, oxidative phosphorylation, and ribosomes. Subsequently, DEPs from each group were subjected to protein-protein interaction (PPI) analysis followed by the screening of interactional key DEPs. Western blot experiments validated the proteomics data, revealing the downregulation of sperm-related DEPs (AKAP4, ODF1, and OAZ3) and upregulation of regulatory ribosome-associated protein (UBA52) and mitochondrial ribosomal protein (MRPL32). These findings provide a basis for studying the mechanism of testicular toxicity due to AlCl3 exposure.
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Affiliation(s)
- Huixin Peng
- The Affiliated Hospital of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
- Graduate School of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Yanxin Huang
- The Affiliated Hospital of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
- Graduate School of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Guangji Wei
- The Affiliated Hospital of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
- Graduate School of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Yanfang Pang
- The Affiliated Hospital of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
- Graduate School of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Huixiong Yuan
- The Affiliated Hospital of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
- Graduate School of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Xiong Zou
- Guangxi Key Laboratory of reproductive health and birth defect prevention, Nanning, 530000, Guangxi, China
| | - Yu'an Xie
- Guangxi Key Laboratory of reproductive health and birth defect prevention, Nanning, 530000, Guangxi, China.
| | - Wencheng Chen
- The Affiliated Hospital of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China.
- Graduate School of You jiang Medical University for Nationalities, Baise, 533000, Guangxi, China.
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11
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Hao P, Han L, Wu Y, Wang Y, Ruan S, Liu Z, Zhang W, Ding J. TMT-based proteomics analysis of sea urchin (Strongylocentrotus intermedius) under high temperature stress. Comp Biochem Physiol Part D Genomics Proteomics 2024; 49:101186. [PMID: 38159402 DOI: 10.1016/j.cbd.2023.101186] [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] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
In the context of global warming and continuous high temperatures in the northern part of China in summer, the mortality rate of Strongylocentrotus intermedius through the summer reaches 70-80 %. The protein regulatory mechanism of S. intermedius in response to high temperature stress is still unclear. In order to investigate the protein expression of S. intermedius under high temperature stress, the study was conducted with the high-temperature resistant strain of S. intermedius and the control group of S. intermedius. Tandem Mass Tag (TMT) tagging technique was applied to resolve the protein expression profile of S. intermedius in response to high temperature stress. The results showed that, compared to 15 °C,136 DEPs were screened in high-temperature resistant strain groups of S. intermedius under high temperature stress and 87 DEPs were screened in the control group of S. intermedius. There were 33 common differential proteins in the two groups, such as APOLP, HSP 70, CDC37 and CALM. Further Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses revealed that the up-regulated proteins CALM and HSP70 are significantly enriched in the "Phosphatidylinositol signaling system" and "Protein processing in endoplasmic reticulum" in heat-tolerant S. intermedius strains under high temperature stress. The control group of S. intermedius DEPs were significantly enriched in protein processing in the endoplasmic reticulum. These results provide a theoretical basis for the molecular mechanism of sea urchin heat tolerance and fundamental data for sea urchin selection and breeding for high temperature tolerance.
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Affiliation(s)
- Pengfei Hao
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Lingshu Han
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, PR China
| | - Yanglei Wu
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yongjie Wang
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Shuchao Ruan
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Ziyu Liu
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Weijie Zhang
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Jun Ding
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
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12
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Qu Y, Chen L, Ren X, Shari A, Yuan Y, Yu M, Xiao H, Li G. Milk proteomic analysis reveals differentially expressed proteins in high-yielding and low-yielding Guanzhong dairy goats at peak lactation. J DAIRY RES 2024:1-7. [PMID: 38415394 DOI: 10.1017/s0022029924000013] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The aim of this experiment was to investigate the differential proteomic characteristics of milk from high- and low-yielding Guanzhong dairy goats during the peak lactation period under the same feeding conditions. Nine Guanzhong dairy goats with high yield (H: 3.5 ± 0.17 kg/d) and nine with low yield (L:1.2 ± 0.25 kg/d) were selected for milk proteomic analysis using tandem mass tag technology. A total of 78 differentially expressed proteins were identified. Compared with L, 50 proteins including HK3, HSPB1 and ANXA2 were significantly upregulated in H milk, while 28 proteins including LALBA and XDH were significantly downregulated. Bioinformatics analysis of the differentially expressed proteins showed that galactose metabolism, purine metabolism, glycolysis/gluconeogenesis, MAPK signaling pathway, regulation of actin cytoskeleton and other pathways were closely related to milk yield. HK3, HSPB1, ANXA2, LALBA and XDH were important candidate proteins associated with the milk production characteristics of Guanzhong dairy goats. Our data provide relevant biomarkers and a theoretical basis for improving milk production in Guanzhong dairy goats.
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Affiliation(s)
- Yingxin Qu
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Lu Chen
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xinyang Ren
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Akang Shari
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Yuxin Yuan
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Mengqi Yu
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Haoqi Xiao
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Guang Li
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
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13
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Geng H, Chen L, Lv S, Li M, Huang X, Li M, Liu C, Liu C. Photochemically Controlled Release of the Glucose Transporter 1 Inhibitor for Glucose Deprivation Responses and Cancer Suppression Research. J Proteome Res 2024; 23:653-662. [PMID: 38170682 DOI: 10.1021/acs.jproteome.3c00469] [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] [Indexed: 01/05/2024]
Abstract
Cancer cells need a greater supply of glucose mainly due to their aerobic glycolysis, known as the Warburg effect. Glucose transport by glucose transporter 1 (GLUT1) is the rate-limiting step for glucose uptake, making it a potential cancer therapeutic target. However, GLUT1 is widely expressed and performs crucial functions in a variety of cells, and its indiscriminate inhibition will cause serious side effects. In this study, we designed and synthesized a photocaged GLUT1 inhibitor WZB117-PPG to suppress the growth of cancer cells in a spatiotemporally controllable manner. WZB117-PPG exhibited remarkable photolysis efficiency and substantial cytotoxicity toward cancer cells under visible light illumination with minimal side effects, ensuring its safety as a potential cancer therapy. Furthermore, our quantitative proteomics data delineated a comprehensive portrait of responses in cancer cells under glucose deprivation, underlining the mechanism of cell death via necrosis rather than apoptosis. We reason that our study provides a potentially reliable cancer treatment strategy and can be used as a spatiotemporally controllable trigger for studying nutrient deprivation-related stress responses.
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Affiliation(s)
- Hongen Geng
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Linfeng Chen
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - ShuWen Lv
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Mengzhao Li
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xiaoping Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Man Li
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Changlin Liu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Chunrong Liu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
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14
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Yang G, Dai R, Ma X, Huang C, Ma X, Li X, La Y, Dingkao R, Renqing J, Guo X, Zhaxi T, Liang C. Proteomic Analysis Reveals the Effects of Different Dietary Protein Levels on Growth and Development of Jersey-Yak. Animals (Basel) 2024; 14:406. [PMID: 38338049 PMCID: PMC10854544 DOI: 10.3390/ani14030406] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Jersey-yak is a hybrid offspring of Jersey cattle and yak (Bos grunniens). Changing the feeding system of Jersey-yak can significantly improve its growth performance. In this study, tandem mass tag (TMT) proteomics technology was used to determine the differentially expressed proteins (DEPs) of the longissimus lumborum (LL) muscle of Jersey-yak fed different protein levels of diet. The results showed that compared with the traditional grazing feeding, the growth performance of Jersey-yaks was significantly improved by crude protein supplementation after grazing. A total of 3368 proteins were detected in these muscle samples, of which 3365 were quantified. A total of 434 DEPs were identified. Through analyses, it was found that some pathways related to muscle growth and development were significantly enriched, such as Rap1 signaling pathway, mTOR signaling pathway, and TGF-beta signaling pathway. A number of DEPs enriched in these pathways are related to muscle cell development, differentiation, and muscle development, including integrin subunit alpha 7 (ITGA7), myosin heavy chain 8 (MYH8), and collagen type XII alpha 1 chain (COL12A1). In conclusion, the results of this study provide insights into the proteomics of different feeding patterns of Jersey-yak, providing a stronger basis for further understanding the biological mechanism of hybrid varieties.
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Affiliation(s)
- Guowu Yang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (G.Y.); (R.D.); (X.M.); (C.H.); (X.M.); (X.L.); (Y.L.); (X.G.)
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou 730106, China
| | - Rongfeng Dai
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (G.Y.); (R.D.); (X.M.); (C.H.); (X.M.); (X.L.); (Y.L.); (X.G.)
| | - Xiaoming Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (G.Y.); (R.D.); (X.M.); (C.H.); (X.M.); (X.L.); (Y.L.); (X.G.)
| | - Chun Huang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (G.Y.); (R.D.); (X.M.); (C.H.); (X.M.); (X.L.); (Y.L.); (X.G.)
| | - Xiaoyong Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (G.Y.); (R.D.); (X.M.); (C.H.); (X.M.); (X.L.); (Y.L.); (X.G.)
| | - Xinyi Li
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (G.Y.); (R.D.); (X.M.); (C.H.); (X.M.); (X.L.); (Y.L.); (X.G.)
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou 730106, China
| | - Yongfu La
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (G.Y.); (R.D.); (X.M.); (C.H.); (X.M.); (X.L.); (Y.L.); (X.G.)
| | - Renqing Dingkao
- Animal Husbandry Station, Gannan Tibetan Autonomous Prefecture, Hezuo 747099, China;
| | - Ji Renqing
- Zogemanma Town Animal Husbandry and Veterinary Station, Hezuo 747003, China;
| | - Xian Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (G.Y.); (R.D.); (X.M.); (C.H.); (X.M.); (X.L.); (Y.L.); (X.G.)
| | - Ta Zhaxi
- Qilian County Animal Husbandry Veterinary Workstation, Haibei Prefecture, Qilian 810400, China
| | - Chunnian Liang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (G.Y.); (R.D.); (X.M.); (C.H.); (X.M.); (X.L.); (Y.L.); (X.G.)
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15
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Wei L, Gao J, Wang L, Tao Q, Tu C. Multi-omics analysis reveals the potential pathogenesis and therapeutic targets of diabetic kidney disease. Hum Mol Genet 2024; 33:122-137. [PMID: 37774345 DOI: 10.1093/hmg/ddad166] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/29/2023] [Accepted: 09/27/2023] [Indexed: 10/01/2023] Open
Abstract
Clinicians have long been interested in understanding the molecular basis of diabetic kidney disease (DKD)and its potential treatment targets. Its pathophysiology involves protein phosphorylation, one of the most recognizable post-transcriptional modifications, that can take part in many cellular functions and control different metabolic processes. In order to recognize the molecular and protein changes of DKD kidney, this study applied Tandem liquid chromatography-mass spectrometry (LC-MS/MS) and Next-Generation Sequencing, along with Tandem Mass Tags (TMT) labeling techniques to evaluate the mRNA, protein and modified phosphorylation sites between DKD mice and model ones. Based on Gene Ontology (GO) and KEGG pathway analyses of transcriptome and proteome, The molecular changes of DKD include accumulation of extracellular matrix, abnormally activated inflammatory microenvironment, oxidative stress and lipid metabolism disorders, leading to glomerulosclerosis and tubulointerstitial fibrosis. Oxidative stress has been emphasized as an important factor in DKD and progression to ESKD, which is directly related to podocyte injury, albuminuria and renal tubulointerstitial fibrosis. A histological study of phosphorylation further revealed that kinases were crucial. Three groups of studies have found that RAS signaling pathway, RAP1 signaling pathway, AMPK signaling pathway, PPAR signaling pathway and HIF-1 signaling pathway were crucial for the pathogenesis of DKD. Through this approach, it was discovered that targeting specific molecules, proteins, kinases and critical pathways could be a promising approach for treating DKD.
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Affiliation(s)
- Lan Wei
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
| | - Jingjing Gao
- Zhonglou District Center for Disease Control and Prevention, Changzhou, Jiangsu 213000, China
| | - Liangzhi Wang
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
| | - Qianru Tao
- Department of Nephrology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
| | - Chao Tu
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
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16
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Dong KD, Schmid EW, Bomgarden RD, Choi JH, Gygi SP, Yu Q, Paulo JA. Adapting an Isobaric Tag-Labeled Yeast Peptide Standard to Develop Targeted Proteomics Assays. J Proteome Res 2024; 23:142-148. [PMID: 38009700 PMCID: PMC10777125 DOI: 10.1021/acs.jproteome.3c00493] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Targeted proteomics strategies present a streamlined hypothesis-driven approach to analyze specific sets of pathways or disease related proteins. goDig is a quantitative, targeted tandem mass tag (TMT)-based assay that can measure the relative abundance differences for hundreds of proteins directly from unfractionated mixtures. Specific protein groups or entire pathways of up to 200 proteins can be selected for quantitative profiling, while leveraging sample multiplexing permits the simultaneous analysis of up to 18 samples. Despite these benefits, implementing goDig is not without challenges, as it requires access to an instrument application programming interface (iAPI), an elution order and spectral library, a web-based method builder, and dedicated companion software. In addition, the absence of an example test assay may dissuade researchers from testing or implementing goDig. Here, we repurpose the TKO11 standard─which is commercially available but may also be assembled in-lab─and establish it as a de facto test assay for goDig. We build a proteome-wide goDig yeast library, quantify protein expression across several gene ontology (GO) categories, and compare these results to a fully fractionated yeast gold-standard data set. Essentially, we provide a guide detailing the goDig-based quantification of TKO11, which can also be used as a template for user-defined assays in other species.
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Affiliation(s)
- Kevin D Dong
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ernst W Schmid
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ryan D Bomgarden
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Jae H Choi
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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17
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Lv Y, Shao Y, Jiang C, Wang Y, Li Y, Li Y, Duan X, Dong S, Lin J, Zhang H, Shan H. Quantitative proteomics based on TMT revealed the response of PK15 cells infected PEDV wild strain. Microb Pathog 2024; 186:106503. [PMID: 38142905 DOI: 10.1016/j.micpath.2023.106503] [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: 08/12/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023]
Abstract
Porcine epidemic diarrhea (PED), caused by porcine epidemic diarrhea virus (PEDV), is an acute and highly contagious enteric disease with a high mortality rate in suckling piglets. Identification of proteins associated with PEDV infection may provide insights into the pathogenesis of this viral disease. In this study, we employed tandem mass tag (TMT) quantitative protein analysis to investigate proteomic changes in PK15 cells following PEDV infection, and differential protein expression profiles were obtained at 0 h, 24 h, and 48 h post-infection. Overall, a total of 6330 proteins were identified. Applying criteria for fold change >1.5 < 0.67 and p-values <0.05 resulted in the identification of 59 up-regulated proteins and 103 down-regulated proteins that exhibited significant alterations in the H24 group compared to the H0 group. The H48 group demonstrated significant upregulation of 110 proteins and downregulation of 144 proteins compared to the H0 group; additionally, there were also 10 upregulated and 30 downregulated proteins in the H48 group when compared to the H24 group. These differentially expressed proteins (DEPs) were involved in immune response regulation, signal transduction, lipid transport and metabolism processes as well as cell apoptosis pathways. Based on these DEPs, we propose that PEDV may disrupt signal transduction pathways along with lipid transport and metabolism processes leading to maximal viral replication, it may also trigger inflammatory cascades accordingly. These findings could provide valuable information for elucidating specific pathogenesis related to PEDV infection while contributing towards developing new antiviral strategies.
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Affiliation(s)
- Yuting Lv
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yu Shao
- Gansu Agricultural University, Lanzhou, Gansu, China
| | - Chengyuan Jiang
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yongming Wang
- Shandong Huahong Biological Engineering Co., LTD, Binzhou, Shandong, China
| | - Yingguang Li
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yan Li
- Qingdao Animal Disease Prevention and Control Center, Qingdao, Shandong, China
| | - Xiaoxiao Duan
- Qingdao Animal Disease Prevention and Control Center, Qingdao, Shandong, China
| | - Shaoming Dong
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Jiaxu Lin
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hongliang Zhang
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
| | - Hu Shan
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
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Madern M, Reiter W, Stanek F, Hartl N, Mechtler K, Hartl M. A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics. Mol Cell Proteomics 2024; 23:100694. [PMID: 38097181 PMCID: PMC10828822 DOI: 10.1016/j.mcpro.2023.100694] [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: 07/05/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 01/29/2024] Open
Abstract
Multiplex proteomics using isobaric labeling tags has emerged as a powerful tool for the simultaneous relative quantification of peptides and proteins across multiple experimental conditions. However, the quantitative accuracy of the approach is largely compromised by ion interference, a phenomenon that causes fold changes to appear compressed. The degree of compression is generally unknown, and the contributing factors are poorly understood. In this study, we thoroughly characterized ion interference at the MS2 level using a defined two-proteome experimental system with known ground-truth. We discovered remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2 scans-a discrepancy that we found resolved by considering cofragmentation of peptide ions hidden within the spectral "noise" of the MS1 isolation window. To address this issue, we developed a regression modeling strategy to accurately predict reporter ion interference in any dataset. Finally, we demonstrate the utility of our procedure for improved fold change estimation and unbiased PTM site-to-protein normalization. All computational tools and code required to apply this method to any MS2 TMT dataset are documented and freely available.
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Affiliation(s)
- Moritz Madern
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria; Department for Biochemistry and Cell Biology, Center for Molecular Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Wolfgang Reiter
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria; Department for Biochemistry and Cell Biology, Center for Molecular Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Florian Stanek
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Natascha Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Markus Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria; Department for Biochemistry and Cell Biology, Center for Molecular Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria.
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Ornelas LC, Besheer J. Predator Odor Stressor, 2,3,5-Trimethyl-3-Thiazoline ( TMT): Assessment of Stress Reactive Behaviors During an Animal Model of Traumatic Stress in Rats. Curr Protoc 2024; 4:e967. [PMID: 38193654 PMCID: PMC10783820 DOI: 10.1002/cpz1.967] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Animal models utilizing predator odor stress are important in understanding implications for post-traumatic stress disorder. 2,5-dihydro-2,4,5-trimethylthiazoline (TMT) has been used to measure stress reactive behaviors during TMT exposure, indicative of stress coping behaviors. In addition, long-term consequences of stress including contextual-induced stress memory, anxiety-like and hyperarousal behaviors, and subsequent increases in alcohol self-administration can also be examined after TMT exposure. In this article, we describe the TMT exposure protocol used in our lab and how we measure different stress-reactive behaviors that rats engage in during the TMT exposure. Rats are placed in Plexiglass chambers that contain white bedding on the bottom of the chamber and a metal basket in the top right corner containing a filter paper that 10 µl of TMT is pipetted onto. During the 10 min exposure, rats can move around the chamber freely. Exposures are recorded by a video camera for later analysis. During TMT exposure, rats engage in a variety of stress-reactive behaviors, including digging and immobility behavior. These are two distinctly different types of stress-induced behavioral coping strategies to measure individual differences in stress responsivity. To examine individual differences, we group rats into TMT-subgroups based on time spent engaging in digging or immobility behavior. We calculate a digging/immobility ratio score in which we divide the total time spent digging by the total time spent immobile. A cut-off strategy is used such that rats with a criterion ratio score <1.0 are classified as TMT-1 (i.e., low digging/high immobility; greater passive coping) and rats with a ratio score >1.0 are classified as TMT-2 (i.e., high digging/low immobility; greater active coping). Here, we provide a detailed description of the TMT exposure protocol and step-by-step process in evaluation of stress-reactive behaviors. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Predator odor stressor exposure using TMT Basic Protocol 2: Description of stress-reactive behaviors during TMT exposure and formation of TMT-subgroups.
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Affiliation(s)
- Laura C. Ornelas
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Joyce Besheer
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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Ji J, Zhu X, Zhang Y, Shui L, Bai S, Huang L, Wang H, Fan S, Zhang Z, Luo L, Xu B. A Proteomic Analysis of Human Follicular Fluid: Proteomic Profile Associated with Embryo Quality. Reprod Sci 2024; 31:199-211. [PMID: 37607985 DOI: 10.1007/s43032-023-01293-x] [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: 04/09/2023] [Accepted: 06/30/2023] [Indexed: 08/24/2023]
Abstract
Embryo selection is a key point of in vitro fertilization (IVF). The most commonly used method for embryo selection is morphological assessment. However, it is sometimes inaccurate. Follicular fluid (FF) contains a complex mixture of proteins that are essential for follicle development and oocyte maturation. Analyzing human FF proteomic profiles and identifying predictive biomarkers might be helpful for evaluating embryo quality. A total of 22 human FF samples were collected from 19 infertile women who underwent IVF/intracytoplasmic sperm injection (ICSI) treatment between October 2021 and November 2021. FFs were grouped into two categories on the basis of the day 3 embryo quality, grade I or II in the hqFF group and grade III in the nhqFF group. FF was analyzed by liquid chromatography-tandem mass spectrometry (LC/MS/MS). The key differentially expressed proteins (DEPs) were validated by parallel reaction monitoring (PRM) and enzyme-linked immunosorbent assay (ELISA). Differentially expressed proteins were further analyzed using DAVID software. A total of 558 proteins were identified, of which 50 proteins were differentially expressed in the hqFF versus nhqFF group, including 32 upregulated proteins (> 1.20-fold, P < 0.05) and 18 downregulated proteins (< 0.67-fold, P < 0.05). Bioinformatics analyses showed that the upregulated DEPs were enriched in components of the coagulation and complement systems and negative regulation of peptidase activity, while the downregulated DEPs were enriched in molecular function of extracellular matrix structural and constituent collagen binding. Our results suggested that a number of protein biomarkers in FF were associated with embryo quality. It may help develop an effective and noninvasive method for embryo selection.
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Affiliation(s)
- Jingjuan Ji
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Xinyi Zhu
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Yan Zhang
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Lijun Shui
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Shun Bai
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Lingli Huang
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Haoyu Wang
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Shiwei Fan
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Zelin Zhang
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Lihua Luo
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Bo Xu
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China.
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21
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Lai Z, Huang W, Lin W, Weng X, Mao Y, Xu G. A single 1,500 m freestyle at maximal speed decreases cognitive function in athletes. Front Psychol 2023; 14:1283585. [PMID: 38125859 PMCID: PMC10731674 DOI: 10.3389/fpsyg.2023.1283585] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction Physical exercise can improve cognitive function, and the degree of impact on cognitive function is related to exercise modality, intensity, and duration. However, few studies have been conducted on the effects of competitive sports on cognitive function. The 1,500 m freestyle is the longest pool-based swimming event in the Olympic Games. This study explores the effects of 1,500 m freestyle at maximal speed on athletes' cognitive function and analyzes the potential mechanism of cognitive function reduction in freestyle at maximal speed from the perspective of hemoglobin oxygenation difference (Hbdiff). Methods A total of 13 male university swimmers were required to take part in a 1,500 m freestyle competition, swimming at maximal speed. The relevant indicators, including cognitive function and freestyle at maximal speed, before and after the competition were tested and analyzed. Cognitive function was assessed using the Schulte grid test (SGT), the trail-making test (TMT), and the digit span test (DST). The neurobiological characteristics of cognitive function, such as the prefrontal cortex (PFC), response time (RT), and accuracy rate (ACC), were tested using functional near-infrared spectroscopy (fNIRS). Results A significant decrease in scores for SGT, TMT, and digit span test-backward (DST-B) (p < 0.01). Oxygenated hemoglobin (Oxy-Hb) concentrations in the right frontopolar area (R-FPA) of brain channels 8 (p < 0.01) and 9 (CH8, 9) (p < 0.05), the right dorsolateral prefrontal cortex (R-DLPFC) CH10 (p < 0.05), and the middle dorsolateral prefrontal cortex (M-DLPFC) CH18 (p < 0.01) were significantly altered, and the right area of the brain was activated. The total Oxy-Hb concentrations in the regions of interest (ROIs) of R-FPA, R-DLFPC, and M-DLFPC were changed significantly (p < 0.01). Discussion The exhaustive performance of a 1,500 m freestyle event resulted in both physical fatigue and a decline in cognitive function. This decline may be attributed to the activation of specific regions of interest, namely the FPA, DLPFC, and M-DLPFC, within the prefrontal cortex (PFC), as well as alterations in functional connectivity.
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Affiliation(s)
- Zhijie Lai
- Department of Graduation, Guangzhou Sport University, Guangzhou, China
- Department of School of Physical Education, Guangzhou College of Commerce, Guangzhou, China
| | - Weiwei Huang
- Department of Physical Education, Guangzhou Sport University, Guangzhou, China
| | - Wentao Lin
- Department of School of Physical Education, Zhuhai College of Science and Technology, Zhuhai, China
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
| | - Xiquan Weng
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
| | - Yuheng Mao
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
| | - Guoqin Xu
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
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22
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Zhao X, Jia W, Wang J, Wang S, Zheng Q, Shan T. Identification of a Candidate Gene Regulating Intramuscular Fat Content in Pigs through the Integrative Analysis of Transcriptomics and Proteomics Data. J Agric Food Chem 2023; 71:19154-19164. [PMID: 37987700 DOI: 10.1021/acs.jafc.3c05806] [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] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Pork is a widely consumed source of animal protein worldwide, and the intramuscular fat (IMF) content in pork plays a crucial role in determining its quality. In this study, we sought to identify candidate genes that regulate IMF deposition in pigs. We performed tandem mass tags (TMT)-based quantitative proteomics analysis using Longissimus dorsi (LD) muscle samples obtained from eight pigs with extremely high and low IMF content among a group of 28 Duroc pigs and identified 50 differentially abundant proteins (DAPs). Additionally, we compared the proteomics data with RNA-sequencing data obtained in our previous study and identified TUSC5 as a differentially expressed gene corresponding to the relevant DAP. To investigate the potential role of TUSC5 in adipogenesis, we suppressed TUSC5 expression in mouse 3T3-L1 preadipocytes using short hairpin RNA (shRNA) and observed a significant reduction in the differentiation of 3T3-L1 cells into adipocytes, as indicated by Oil Red O staining and triglyceride content. Moreover, we observed a reduction in the expression of genes associated with adipogenesis (PPARG, CEBPA, FABP4, and FASN) following TUSC5 suppression. Through an integrative analysis of transcriptomics and proteomics data, our study identified TUSC5 as a crucial candidate gene associated with the regulation of IMF content in pigs.
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Affiliation(s)
- Xueyan Zhao
- Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
- DELISI GROUP Co. Ltd., Weifang, Shandong 262200, China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Wanli Jia
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Jiying Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Shouwei Wang
- DELISI GROUP Co. Ltd., Weifang, Shandong 262200, China
| | - Qiankun Zheng
- DELISI GROUP Co. Ltd., Weifang, Shandong 262200, China
| | - Tizhong Shan
- Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
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23
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Wang C, Hou J, Zhang M, Zheng Y, Ye H, Qi Y, Guo L, Hu Y. Effects of HSYA on serum and brain cholesterol levels in AD rats based on quantitative proteomics. Int J Neurosci 2023; 133:1411-1423. [PMID: 35633062 DOI: 10.1080/00207454.2022.2082964] [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: 11/30/2021] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
Backgroud: Hydroxysafflor yellow A (HSYA) has a certain improvement effect on Alzheimer's disease (AD) rats, but its specific mechanism is still unclear. The purpose of this study was to observe the regulatory effect of HSYA on learning and memory ability of AD rats induced by Aβ1-42.Materials and methods: Morris water maze test was used to evaluate the effect of HSYA on the learning and memory ability of AD model rats. To explore the effective targets and potential molecular mechanisms of HSYA in AD treatment based on quantitative proteomics.Results: Through the Morris water maze experiment, we found that after HSYA treatment, the learning ability of rats in the model group has been significantly improved. Quantitative proteomics results showed that among the 11 common differential proteins between the "model/sham operation" comparison group and the "HSYA treatment/model" comparison group, the cholesterol synthesis rate-limiting enzyme mevalonate decarboxylase (Mvd) Western Blot results are consistent with the results of quantitative proteomics analysis. We found that HSYA can inhibit the expression of BACE protein in hippocampus of AD rats and decrease the level of Aβ1-42. Besides, HSYA could also reduce cholesterol levels in serum and hippocampus.Conclusion: In summary, HSYA can effectively improve learning and memory disorders in AD rats, and exert neuroprotective effects by effectively controlling serum and brain cholesterol to down-regulate the expression of BACE and thus reduce the content of Aβ1-42.
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Affiliation(s)
- Chunhui Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, P.R. China
| | - Jiawei Hou
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, P.R. China
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Mengyu Zhang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, P.R. China
| | - Yanjie Zheng
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, P.R. China
| | - Hongxia Ye
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, P.R. China
| | - Yanqiang Qi
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, P.R. China
| | - Li Guo
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Sciences and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yanli Hu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, P.R. China
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Dey KK, Yarbro JM, Liu D, Han X, Wang Z, Jiao Y, Wu Z, Yang S, Lee D, Dasgupta A, Yuan ZF, Wang X, Zhu L, Peng J. Identifying Sex-Specific Serum Patterns of Alzheimer's Mice through Deep TMT Profiling and a Concentration-Dependent Concatenation Strategy. J Proteome Res 2023; 22:3843-3853. [PMID: 37910662 PMCID: PMC10872962 DOI: 10.1021/acs.jproteome.3c00496] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia, disproportionately affecting women in disease prevalence and progression. Comprehensive analysis of the serum proteome in a common AD mouse model offers potential in identifying possible AD pathology- and gender-associated biomarkers. Here, we introduce a multiplexed, nondepleted mouse serum proteome profiling via tandem mass-tag (TMTpro) labeling. The labeled sample was separated into 475 fractions using basic reversed-phase liquid chromatography (RPLC), which were categorized into low-, medium-, and high-concentration fractions for concatenation. This concentration-dependent concatenation strategy resulted in 128 fractions for acidic RPLC-tandem mass spectrometry (MS/MS) analysis, collecting ∼5 million MS/MS scans and identifying 3972 unique proteins (3413 genes) that cover a dynamic range spanning at least 6 orders of magnitude. The differential expression analysis between wild type and the commonly used AD model (5xFAD) mice exhibited minimal significant protein alterations. However, we detected 60 statistically significant (FDR < 0.05), sex-specific proteins, including complement components, serpins, carboxylesterases, major urinary proteins, cysteine-rich secretory protein 1, pregnancy-associated murine protein 1, prolactin, amyloid P component, epidermal growth factor receptor, fibrinogen-like protein 1, and hepcidin. The results suggest that our platform possesses the sensitivity and reproducibility required to detect sex-specific differentially expressed proteins in mouse serum samples.
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Affiliation(s)
- Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jay M. Yarbro
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee, TN 38163, USA
| | - Danting Liu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xian Han
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yun Jiao
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Shu Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - DongGeun Lee
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Abhijit Dasgupta
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zuo-Fei Yuan
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xusheng Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Liqin Zhu
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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Qian L, Gu Y, Zhai Q, Xue Z, Liu Y, Li S, Zeng Y, Sun R, Zhang Q, Cai X, Ge W, Dong Z, Gao H, Zhou Y, Zhu Y, Xu Y, Guo T. Multitissue Circadian Proteome Atlas of WT and Per1 -/-/Per2 -/- Mice. Mol Cell Proteomics 2023; 22:100675. [PMID: 37940002 PMCID: PMC10750102 DOI: 10.1016/j.mcpro.2023.100675] [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: 04/27/2023] [Revised: 10/22/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
The molecular basis of circadian rhythm, driven by core clock genes such as Per1/2, has been investigated on the transcriptome level, but not comprehensively on the proteome level. Here we quantified over 11,000 proteins expressed in eight types of tissues over 46 h with an interval of 2 h, using WT and Per1/Per2 double knockout mouse models. The multitissue circadian proteome landscape of WT mice shows tissue-specific patterns and reflects circadian anticipatory phenomena, which are less obvious on the transcript level. In most peripheral tissues of double knockout mice, reduced protein cyclers are identified when compared with those in WT mice. In addition, PER1/2 contributes to controlling the anticipation of the circadian rhythm, modulating tissue-specific cyclers as well as key pathways including nucleotide excision repair. Severe intertissue temporal dissonance of circadian proteome has been observed in the absence of Per1 and Per2. The γ-aminobutyric acid might modulate some of these temporally correlated cyclers in WT mice. Our study deepens our understanding of rhythmic proteins across multiple tissues and provides valuable insights into chronochemotherapy. The data are accessible at https://prot-rhythm.prottalks.com/.
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Affiliation(s)
- Liujia Qian
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Yue Gu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China
| | - Qiaocheng Zhai
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China
| | - Zhangzhi Xue
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Youqi Liu
- Westlake Omics (Hangzhou) Biotechnology Co, Ltd, Hangzhou, Zhejiang Province, China
| | - Sainan Li
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Yizhun Zeng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China
| | - Rui Sun
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Qiushi Zhang
- Westlake Omics (Hangzhou) Biotechnology Co, Ltd, Hangzhou, Zhejiang Province, China
| | - Xue Cai
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co, Ltd, Hangzhou, Zhejiang Province, China
| | - Zhen Dong
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Huanhuan Gao
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Yan Zhou
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Yi Zhu
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China.
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
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Bou Khalil R, Haddad F, Cordahi CC, Fiani D, Moukarzel JM, Chamoun Y, Kourie HR, Richa S, Kattan J. Cognitive functions of patients treated with chemotherapy: A comparative study. Encephale 2023:S0013-7006(23)00205-1. [PMID: 38040507 DOI: 10.1016/j.encep.2023.10.001] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 09/26/2023] [Accepted: 10/27/2023] [Indexed: 12/03/2023]
Abstract
OBJECTIVES Chemobrain is a well-established clinical syndrome that has become an increasing concern because of the growing number of long-term cancer survivors. It refers to the post-chemotherapy related cognitive dysfunction. The aim of this study was to objectively assess the impact of cancer treatment on the cognition of cancer patients. METHODS This was a convenience sample comparative study conducted at the Hematology and Oncology Department of Hôtel Dieu de France University Hospital in Beirut, Lebanon. It included cancer patients (G1) aged under 65 years who had already been treated for cancer compared to two control groups. The first control group (G2) consisted of treatment-naïve cancer patients aged under 65, and the second group (G3) was recruited from a pool of healthy controls aged between 40 and 65 years. All participants were asked to complete the part B of the trail making test (TMT) and the digital symbolic substitution test (DSST). RESULTS In the bivariate analysis, patients in G1 had significantly higher scores than patients in G2 (P=0.017) and G3 (P<0.001) on the TMT-B. However, patients in G1 only had lower scores on DSST when compared with G3 (P=0.017). In the logistic regression taking different groups two-by-two as the dependent variable, the only significant difference was found in the comparison between G2 and G3 with higher TMT-B scores more in favor of belonging to G2 (OR=0.946; P=0.003). CONCLUSIONS Our results suggest that, after controlling for anxiety and depression symptoms, patients treated with chemotherapy have significantly poorer outcomes on the DSST and TMT-B than treatment-naïve cancer patients and healthy controls. However, when taking confounding factors into account, the difference only persisted between patients undergoing chemotherapy and healthy controls. These findings are in favor of a multifactor cognitive impairment in patients with cancer partially related to chemotherapeutic treatment.
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Affiliation(s)
- Rami Bou Khalil
- Department of Psychiatry, Hôtel Dieu de France, A. Naccache boulevard, P.O. box: 166830, Achrafieh-Beirut, Lebanon; Department of Psychiatry, Saint-Joseph University, Beirut, Lebanon.
| | - Fady Haddad
- Department of Oncology, Hôtel Dieu de France, Beirut, Lebanon; Department of Oncology, Saint-Joseph University, Beirut, Lebanon
| | - Colin Charbel Cordahi
- Department of Psychiatry, Hôtel Dieu de France, A. Naccache boulevard, P.O. box: 166830, Achrafieh-Beirut, Lebanon; Department of Psychiatry, Saint-Joseph University, Beirut, Lebanon
| | - Dimitri Fiani
- Department of Oncology, Hôtel Dieu de France, Beirut, Lebanon; Department of Oncology, Saint-Joseph University, Beirut, Lebanon
| | - Jean-Marie Moukarzel
- Department of Oncology, Hôtel Dieu de France, Beirut, Lebanon; Department of Oncology, Saint-Joseph University, Beirut, Lebanon
| | - Yara Chamoun
- Department of Psychiatry, Hôtel Dieu de France, A. Naccache boulevard, P.O. box: 166830, Achrafieh-Beirut, Lebanon; Department of Psychiatry, Saint-Joseph University, Beirut, Lebanon
| | - Hampig Raphael Kourie
- Department of Oncology, Hôtel Dieu de France, Beirut, Lebanon; Department of Oncology, Saint-Joseph University, Beirut, Lebanon
| | - Sami Richa
- Department of Psychiatry, Hôtel Dieu de France, A. Naccache boulevard, P.O. box: 166830, Achrafieh-Beirut, Lebanon; Department of Psychiatry, Saint-Joseph University, Beirut, Lebanon
| | - Joseph Kattan
- Department of Oncology, Hôtel Dieu de France, Beirut, Lebanon; Department of Oncology, Saint-Joseph University, Beirut, Lebanon
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魏 敏, 陈 乃, 李 璟, 刘 丹, 沈 双, 王 丰, 吴 润, 陈 沁. [Quantitative analysis of differential proteins in renal tissues of rats with chronic intermittent hypoxic exposure based on TMT and PRM technology]. Nan Fang Yi Ke Da Xue Xue Bao 2023; 43:1857-1864. [PMID: 38081602 PMCID: PMC10713465 DOI: 10.12122/j.issn.1673-4254.2023.11.04] [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] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Indexed: 12/18/2023]
Abstract
OBJECTIVE To screen the differentially expressed proteins in the kidneys of rats exposed to chronic intermittent hypoxia (CIH) based on TMT-PRM technology to identify the potential biomarkers of renal injuries induced by CIH. METHODS Twenty SD rats were randomized into two groups (n=10) and exposed to CIH or normoxia. After 12 weeks of exposure, the kidneys of the rats were collected for observing pathological changes. The renal proteins were extracted, enzymatically digested and labelled with TMT, and LC-MS/MS was used to identify the proteins. The data were processed using Proteome Discoverer2.4 for bioinformatic analysis of the differentially expressed proteins. PRM technology was used to verify the expression of the candidate proteins. RESULTS CIH induced obvious renal injury in the rats, manifested by irregular glomerulus and swelling of the epithelial cells of the renal tubules. A total of 31 differentially expressed proteins were identified in CIH rats, including 22 up-regulated and 9 down-regulated proteins. Enrichment analysis of GO function and KEGG pathway analysis showed that the differentially expressed proteins participated mainly in the biological processes of cell adhesion, hypoxic stress, and calcium ions and were involved in the PPAR, AMPK, and metabolic pathways. In PRM quantitative analysis, 3 proteins, namely P07379 (PCK1), P19132 (Fth1) and Q5XI79 (Ndufaf7), showed results consistent with those of TMT-quantitative proteomic analysis. CONCLUSION Thirty-one differentially expressed proteins were identified in the renal tissues of rats with CIH exposure, and among them P07379 (PCK1), P19132 (Fth1), and Q5XI79 (Ndufaf7) may be the key proteins closely related to the renal injury in induced by CIH.
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Affiliation(s)
- 敏 魏
- 福建中医药大学中西医结合学院,福建 福州 350122College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - 乃洁 陈
- 福建中医药大学中西医结合学院,福建 福州 350122College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - 璟怡 李
- 福建中医药大学中西医结合学院,福建 福州 350122College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - 丹 刘
- 福建中医药大学中西医结合学院,福建 福州 350122College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - 双宏 沈
- 福建中医药大学中西医结合学院,福建 福州 350122College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - 丰 王
- 福建中医药大学中西医结合学院,福建 福州 350122College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - 润华 吴
- 福建中医药大学中西医结合学院,福建 福州 350122College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - 沁 陈
- 福建中医药大学临床技能教学中心,福建 福州 350122Clinical Skills Teaching Center, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
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Xu W, Liang Y, Zhu Y, Sun T, Yuan Z, Han X. Proteomic study of aqueous humour in diabetic patients with cataracts by TMT combined with HPLC-MS/MS. BMC Ophthalmol 2023; 23:435. [PMID: 37884923 PMCID: PMC10604804 DOI: 10.1186/s12886-023-03162-2] [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: 01/08/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND The purpose of this study is to identify the proteomic differences between the aqueous humour of diabetes patients with cataracts and that of non-diabetic sufferers of cataracts in a clinical setting. METHODS Patients were divided into the diabetic experimental group and the non-diabetic control group. Aqueous humour specimens were obtained via cataract surgery. Sample proteins were treated with a TMT reagent, separated using a cation chromatography column, and analysed using a C18 desalting column. Proteins were identified using HPLC-MS/MS. The differential proteins were identified using both a p value of < 0.05 and a fold change of > 1.2. GO classification enrichment analysis, KEGG pathway enrichment analysis, protein interaction network analysis, and ingenuity pathway analysis were all carried out. The expression level of four differential proteins were verified by Western blot, and GC and TTR expressions were further examined using an expanded sample pool. RESULTS The postprandial glucose levels between the experimental group (9.40 ± 1.35 mmol/L) and the control group (6.56 ± 0.81 mmol/L) were significantly different, with a p value of 1.16E-06. It is important to note, however, that the baseline levels of the parameters showed no statistical differences. In total, 397 aqueous humour proteins were identified; of these, 137 showed significant differences, with 63 upregulated ones and 74 down-regulated ones. The differential proteins play important roles in numerous biological processes and pathways, such as complement and coagulation cascades (p = 1.71E-09). Some of these differential proteins are associated with diabetic retinal degeneration and other diabetic complications. Differential proteins, such as HP, GC, and TTR, have high node degree in the protein interaction network. Western blot results further confirmed that GC were down-regulated while TTR was up-regulated in aqueous humour under diabetic condition. CONCLUSION A list of differential proteins in the human aqueous humour of diabetic patients was established. Proteins with high interaction scores as per protein interaction analysis, such as GC and TTR, were further verified and could potentially be used as early diagnostic markers for diabetic eye complications in clinical practice.
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Affiliation(s)
- Weihai Xu
- Department of Ophthalmology, Binhai county people's hospital, Yancheng, Jiangsu, China
- Department of Ophthalmology, the First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ya Liang
- Department of Ophthalmology, the First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunxia Zhu
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Jiangsu Diabetes Center, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Tong Sun
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Jiangsu Diabetes Center, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Zhilan Yuan
- Department of Ophthalmology, the First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Xiao Han
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Jiangsu Diabetes Center, Nanjing Medical University, Nanjing, Jiangsu, China.
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29
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Cooper CD, Hiller N. Leader humor across levels. Curr Opin Psychol 2023; 53:101688. [PMID: 37708609 DOI: 10.1016/j.copsyc.2023.101688] [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: 07/25/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Leaders use humor. This humor has real effects and has been a topic of scholarly interest. We review and interpret this literature though the lens of leader hierarchical level (front-line managers versus senior executives), enumerating intriguing research possibilities and practical implications. We know much more about the humor of front-line leaders than executives, and much more about benefits than risks of leader humor. Not only are the risks and benefits likely to be amplified for executives, but they are qualitatively different due to the differential reach of executive leadership. In terms of enacting humor, the more diverse set of observers and stakeholders for executive leaders versus front-line managers creates additional challenges and a narrower window for successful use of humor.
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Affiliation(s)
| | - Nathan Hiller
- Department of Global Leadership and Management, Florida International University, United States
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30
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Wang H, Dai C, Pfeuffer J, Sachsenberg T, Sanchez A, Bai M, Perez-Riverol Y. Tissue-based absolute quantification using large-scale TMT and LFQ experiments. Proteomics 2023; 23:e2300188. [PMID: 37488995 DOI: 10.1002/pmic.202300188] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
Relative and absolute intensity-based protein quantification across cell lines, tissue atlases and tumour datasets is increasingly available in public datasets. These atlases enable researchers to explore fundamental biological questions, such as protein existence, expression location, quantity and correlation with RNA expression. Most studies provide MS1 feature-based label-free quantitative (LFQ) datasets; however, growing numbers of isobaric tandem mass tags (TMT) datasets remain unexplored. Here, we compare traditional intensity-based absolute quantification (iBAQ) proteome abundance ranking to an analogous method using reporter ion proteome abundance ranking with data from an experiment where LFQ and TMT were measured on the same samples. This new TMT method substitutes reporter ion intensities for MS1 feature intensities in the iBAQ framework. Additionally, we compared LFQ-iBAQ values to TMT-iBAQ values from two independent large-scale tissue atlas datasets (one LFQ and one TMT) using robust bottom-up proteomic identification, normalisation and quantitation workflows.
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Affiliation(s)
- Hong Wang
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Chengxin Dai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Julianus Pfeuffer
- Algorithmic Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Timo Sachsenberg
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen, Germany
- Institute for Biological and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Mingze Bai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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Li J, Yang X, Liu F, Liu X, Zhao T, Yan X, Pang Q. Redox Regulation of Salt Tolerance in Eutrema salsugineum by Proteomics. Int J Mol Sci 2023; 24:14518. [PMID: 37833966 PMCID: PMC10572166 DOI: 10.3390/ijms241914518] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Salt stress severely restricts plant growth and crop production, which is accompanied by accumulation of reactive oxygen species (ROS) that disturb cell redox homeostasis and oxidize redox-sensitive proteins. Eutrema salsugineum, a halophytic species closely related to Arabidopsis, shows a high level of tolerance to salinity and is increasingly used as a model plant in abiotic stress biology. To understand redox modifications and signaling pathways under salt stress, we used tandem mass tag (TMT)-based proteomics to quantify the salt-induced changes in protein redox modifications in E. salsugineum. Salt stress led to increased oxidative modification levels of 159 cysteine sites in 107 proteins, which play roles in carbohydrate and energy metabolism, transport, ROS homeostasis, cellular structure modulation, and folding and assembly. These lists of unknown redox reactive proteins in salt mustard lay the foundation for future research to understand the molecular mechanism of plant salt response. However, glutathione peroxidase (GPX) is one of the most important antioxidant enzymes in plants. Our research indicates that EsGPX may be involved in regulating ROS levels and that plants with overexpressed EsGPX have much improved salt tolerance.
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Affiliation(s)
- Jiawen Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Xiaomin Yang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Fuqing Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Xinxin Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Tong Zhao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Xiufeng Yan
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Qiuying Pang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
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Olanrewaju GO, Kruse CPS, Wyatt SE. Functional Meta-Analysis of the Proteomic Responses of Arabidopsis Seedlings to the Spaceflight Environment Reveals Multi-Dimensional Sources of Variability across Spaceflight Experiments. Int J Mol Sci 2023; 24:14425. [PMID: 37833871 PMCID: PMC10573023 DOI: 10.3390/ijms241914425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The human quest for sustainable habitation of extraterrestrial environments necessitates a robust understanding of life's adaptability to the unique conditions of spaceflight. This study provides a comprehensive proteomic dissection of the Arabidopsis plant's responses to the spaceflight environment through a meta-analysis of proteomics data from four separate spaceflight experiments conducted on the International Space Station (ISS) in different hardware configurations. Raw proteomics LC/MS spectra were analyzed for differential expression in MaxQuant and Perseus software. The analysis of dissimilarities among the datasets reveals the multidimensional nature of plant proteomic responses to spaceflight, impacted by variables such as spaceflight hardware, seedling age, lighting conditions, and proteomic quantification techniques. By contrasting datasets that varied in light exposure, we elucidated proteins involved in photomorphogenesis and skotomorphogenesis in plant spaceflight responses. Additionally, with data from an onboard 1 g control experiment, we isolated proteins that specifically respond to the microgravity environment and those that respond to other spaceflight conditions. This study identified proteins and associated metabolic pathways that are consistently impacted across the datasets. Notably, these shared proteins were associated with critical metabolic functions, including carbon metabolism, glycolysis, gluconeogenesis, and amino acid biosynthesis, underscoring their potential significance in Arabidopsis' spaceflight adaptation mechanisms and informing strategies for successful space farming.
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Affiliation(s)
- Gbolaga O. Olanrewaju
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Colin P. S. Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA;
| | - Sarah E. Wyatt
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
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33
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McGann CD, Barshop WD, Canterbury JD, Lin C, Gabriel W, Huang J, Bergen D, Zabrouskov V, Melani RD, Wilhelm M, McAlister GC, Schweppe DK. Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics. J Proteome Res 2023; 22:2836-2846. [PMID: 37557900 DOI: 10.1021/acs.jproteome.3c00085] [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] [Indexed: 08/11/2023]
Abstract
Sample multiplexed quantitative proteomics assays have proved to be a highly versatile means to assay molecular phenotypes. Yet, stochastic precursor selection and precursor coisolation can dramatically reduce the efficiency of data acquisition and quantitative accuracy. To address this, intelligent data acquisition (IDA) strategies have recently been developed to improve instrument efficiency and quantitative accuracy for both discovery and targeted methods. Toward this end, we sought to develop and implement a new real-time spectral library searching (RTLS) workflow that could enable intelligent scan triggering and peak selection within milliseconds of scan acquisition. To ensure ease of use and general applicability, we built an application to read in diverse spectral libraries and file types from both empirical and predicted spectral libraries. We demonstrate that RTLS methods enable improved quantitation of multiplexed samples, particularly with consideration for quantitation from chimeric fragment spectra. We used RTLS to profile proteome responses to small molecule perturbations and were able to quantify up to 15% more significantly regulated proteins in half the gradient time compared to traditional methods. Taken together, the development of RTLS expands the IDA toolbox to improve instrument efficiency and quantitative accuracy for sample multiplexed analyses.
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Affiliation(s)
- Chris D McGann
- University of Washington, Seattle, Washington 98105, United States
| | | | | | - Chuwei Lin
- University of Washington, Seattle, Washington 98105, United States
| | | | - Jingjing Huang
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - David Bergen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Rafael D Melani
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | | | - Devin K Schweppe
- University of Washington, Seattle, Washington 98105, United States
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Xu C, Liu X, Yu L, Fang X, Yao L, Lau H, Vyas P, Pryke L, Xu B, Tang L, Jiang J, Chen X. CD147 monoclonal antibody attenuates abdominal aortic aneurysm formation in angiotensin II-Infused apoE -/- mice. Int Immunopharmacol 2023; 122:110526. [PMID: 37393837 DOI: 10.1016/j.intimp.2023.110526] [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: 04/16/2023] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Abdominal aortic aneurysm (AAA) is a life threatening vascular disease. Our previous study reported the upregulation of CD147 expression in human aortic aneurysms. OBJECTIVE In this study, we injected apoE-/- mice intraperitoneally with CD147 monoclonal antibody or IgG control antibody to observe its effect on Angiotensin II (AngII) induced AAA formation. METHODS ApoE-/- mice were randomly divided into an AngⅡ+CD147 antibody group (n = 20) and an AngⅡ+IgG antibody group (n = 20). The Alzet osmotic minipump was implanted subcutaneously into the backs of mice to infuse AngII (1000 ng/kg/min) for 28 days and subsequently treated with CD147 monoclonal antibody or control IgG mAb (10 μg/mouse/day) beginning one day after surgery. Body weight, food intake, drinking volume and blood pressure were measured weekly throughout the study. After 4 weeks of injection, routine bloodwork measuring liver function, kidney function and lipid levels were recorded. Hematoxylin and eosin (H&E), Masson's trichrome, and Elastic van Gieson (EVG) staining were used to evaluate the pathological changes in blood vessels. In addition, Immunohistochemical assay was used to detect infiltration of inflammatory cells. Tandem mass tag (TMT)-based proteomic analysis was used to define differentially expressed proteins (DEPs) using a p-value < 0.05 and fold change > 1.2 or < 0.83 as the threshold. Subsequently, we conducted protein-protein interaction (PPI) network and GO enrichment analysis to determine the core biological function altered after CD147 antibody injection. RESULTS The CD147 monoclonal antibody suppresses Ang II-induced AAA formation in apoE-/- mice and reduced aortic expansion, elastic lamina degradation, and inflammatory cells accumulation. Bioinformatics analysis showed that Ptk6, Itch, Casp3, and Oas1a were the hub DEPs. These DEPs in the two group were mainly involved in collagen fibril organization, extracellular matrix organization, and muscle contraction. These data robustly demonstrated that CD147 monoclonal antibody suppresses Ang II-induced AAA formation through reduction of inflammatory response and regulation of the above defined hub proteins and biological processes. Thus, the CD147 monoclonal antibody might be a promising target in the treatment of abdominal aortic aneurysm.
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Affiliation(s)
- Cheng Xu
- Department of Cardiology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, PR China
| | - Xiaowei Liu
- Department of Cardiology, Zhejiang Hospital, Hangzhou 310013, PR China
| | - Lei Yu
- Department of Cardiology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, PR China
| | - Xiaoxin Fang
- Department of Cardiology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, PR China
| | - Lei Yao
- Department of Cardiology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, PR China
| | - HuiChong Lau
- Department of Medicine, Crozer-Chester Medical Center, Upland, PA 19013, USA
| | - Punit Vyas
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Luke Pryke
- Internal medicine, Indiana University, Indianapolis, IN 46202
| | - Baohui Xu
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Lijiang Tang
- Department of Cardiology, Zhejiang Hospital, Hangzhou 310013, PR China
| | - Jianjun Jiang
- Department of Cardiology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, PR China
| | - Xiaofeng Chen
- Department of Cardiology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, PR China; Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
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Huang Y, Jonsson NN, McLaughlin M, Burchmore R, Johnson PCD, Jones RO, McGill S, Brady N, Weidt S, Eckersall PD. Quantitative TMT-based proteomics revealing host, dietary and microbial proteins in bovine faeces including barley serpin Z4, a prominent component in the head of beer. J Proteomics 2023; 285:104941. [PMID: 37285906 DOI: 10.1016/j.jprot.2023.104941] [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: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023]
Abstract
There has been little information about the proteome of bovine faeces or about the contribution to the faecal proteome of proteins from the host, the feed or the intestinal microbiome. Here, the bovine faecal proteome and the origin of its component proteins was assessed, while also determining the effect of treating barley, the major carbohydrate in the feed, with either ammonia (ATB) or sodium propionate (PTB) preservative. Healthy continental crossbreed steers were allocated to two groups and fed on either of the barley-based diets. Five faecal samples from each group were collected on Day 81 of the trial and analysed by quantitative proteomics using nLC-ESI-MS/MS after tandem mass tag labelling. In total, 281 bovine proteins, 199 barley proteins, 176 bacterial proteins and 190 archaeal proteins were identified in the faeces. Mucosal pentraxin, albumin and digestive enzymes were among bovine proteins identified. Serpin Z4 a protease inhibitor was the most abundant barley protein identified which is also found in barley-based beer, while numerous microbial proteins were identified, many originating bacteria from Clostridium, while Methanobrevibacter was the dominant archaeal genus. Thirty-nine proteins were differentially abundant between groups, the majority being more abundant in the PTB group compared to the ATB group. SIGNIFICANCE: Proteomic examination of faeces is becoming a valuable means to assess the health of the gastro-intestinal tract in several species, but knowledge on the proteins present in bovine faeces is limited. This investigation aimed to characterise the proteome of bovine faecal extracts in order to evaluate the potential for investigations of the proteome as a means to assess the health, disease and welfare of cattle in the future. The investigation was able to identify proteins in bovine faeces that had been (i) produced by the individual cattle, (ii) present in the barley-based feed eaten by the cattle or (iii) produced by bacteria and other microbes in the rumen or intestines. Bovine proteins identified included mucosal pentraxin, serum albumin and a variety of digestive enzymes. Barley proteins found in the faeces included serpin Z4, a protease inhibitor that is also found in beer having survived the brewing process. Bacterial and archaeal proteins in the faecal extracts were related to several pathways related to the metabolism of carbohydrates. The recognition of the range of proteins that can be identified in bovine faeces raises the possibility that non-invasive sample collection of this material could provide a novel diagnostic approach to cattle health and welfare.
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Affiliation(s)
- Y Huang
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - N N Jonsson
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - M McLaughlin
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - R Burchmore
- Institute of Infection, Immunity & Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | - P C D Johnson
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - R O Jones
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - S McGill
- Institute of Infection, Immunity & Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | - N Brady
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - S Weidt
- Institute of Infection, Immunity & Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | - P D Eckersall
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK; Interdisciplinary Laboratory of Clinical Analysis of the University of Murcia (Interlab-UMU), Department of Animal Medicine and Surgery, Veterinary School, University of Murcia, Murcia 30100, Spain.
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Gräwe C, Hernandez-Quiles M, Jansen PWTC, Brimmers A, Vermeulen M. Determining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/ TMT Labeling Strategy. J Proteome Res 2023; 22:2683-2693. [PMID: 37466164 PMCID: PMC10407929 DOI: 10.1021/acs.jproteome.3c00248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 07/20/2023]
Abstract
In recent years, quantitative mass spectrometry-based interaction proteomics technology has proven very useful in identifying specific DNA-protein interactions using single pull-downs from crude lysates. Here, we applied a SILAC/TMT-based higher-order multiplexing approach to develop an interaction proteomics workflow called Protein-nucleic acid Affinity and Specificity quantification by MAss spectrometry in Nuclear extracts or PASMAN. In PASMAN, DNA pull-downs using a concentration range of specific and control DNA baits are performed in SILAC-labeled nuclear extracts. MS1-based quantification to determine specific DNA-protein interactions is then combined with sequential TMT-based quantification of fragmented SILAC peptides, allowing the generation of Hill-like curves and determination of apparent binding affinities. We benchmarked PASMAN using the SP/KLF motif and further applied it to gain insights into two CGCG-containing consensus DNA motifs. These motifs are recognized by two BEN domain-containing proteins, BANP and BEND3, which we find to interact with these motifs with distinct affinities. Finally, we profiled the BEND3 proximal proteome, revealing the NuRD complex as the major BEND3 proximal protein complex in vivo. In summary, PASMAN represents, to our knowledge, the first higher-order multiplexing-based interaction proteomics method that can be used to decipher specific DNA-protein interactions and their apparent affinities in various biological and pathological contexts.
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Affiliation(s)
- Cathrin Gräwe
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Miguel Hernandez-Quiles
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
| | - Pascal W. T. C. Jansen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Annika Brimmers
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
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Bowser BL, Patterson KL, Robinson RA. Evaluating cPILOT Data toward Quality Control Implementation. J Am Soc Mass Spectrom 2023; 34:1741-1752. [PMID: 37459602 DOI: 10.1021/jasms.3c00179] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Multiplexing enables the monitoring of hundreds to thousands of proteins in quantitative proteomics analyses and increases sample throughput. In most mass-spectrometry-based proteomics workflows, multiplexing is achieved by labeling biological samples with heavy isotopes via precursor isotopic labeling or isobaric tagging. Enhanced multiplexing strategies, such as combined precursor isotopic labeling and isobaric tagging (cPILOT), combine multiple technologies to afford an even higher sample throughput. Critical to enhanced multiplexing analyses is ensuring that analytical performance is optimal and that missingness of sample channels is minimized. Automation of sample preparation steps and use of quality control (QC) metrics can be incorporated into multiplexing analyses and reduce the likelihood of missing information, thus maximizing the amount of usable quantitative data. Here, we implemented QC metrics previously developed in our laboratory to evaluate a 36-plex cPILOT experiment that encompassed 144 mouse samples of various tissue types, time points, genotypes, and biological replicates. The evaluation focuses on the use of a sample pool generated from all samples in the experiment to monitor the daily instrument performance and to provide a means for data normalization across sample batches. Our results show that tracking QC metrics enabled the quantification of ∼7000 proteins in each sample batch, of which ∼70% had minimal missing values across up to 36 sample channels. Implementation of QC metrics for future cPILOT studies as well as other enhanced multiplexing strategies will help yield high-quality data sets.
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Affiliation(s)
- Bailey L Bowser
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Khiry L Patterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã As Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Memory & Alzheimer's Center, Nashville, Tennessee 37212, United States
- Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Nashville, Tennessee 37232, United States
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Chen Y, Ning Q, Wu Z, Zhou H, Liao J, Sun X, Lin J, Pang J. Use of Tandem Mass Spectrometry Quantitative Proteomics to Identify Potential Biomarkers to Follow the Effects of Cold and Frozen Storage of Muscle Tissue of Litopenaeus vannamei. Foods 2023; 12:2920. [PMID: 37569188 PMCID: PMC10418843 DOI: 10.3390/foods12152920] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
L. vannamei has become one of the most productive species. However, it is susceptible to microbial contamination during fishing, transportation, and storage, which can lead to spoilage and quality deterioration. This study investigates the relationship between changes in the proteome of Litopenaeus vannamei (L. vannamei) muscle and quality characteristics during low-temperature storage using the tandem mass spectrometry technology of quantitative proteomics strategy. The differential expression of proteins under cold storage (4 °C, CS), partial slight freezing (-3 °C, PFS), and frozen storage (-18 °C, FS) conditions was compared with the fresh group (CK), resulting in 1572 proteins identified as differentially expressed. The purpose of this research is to identify potential biochemical markers by analyzing quality changes and relative differential proteins through searches in the UniProt database, Gene Ontology database, and Genome Encyclopedia. Correlation analysis revealed that seven DEPs were significantly related to physical and chemical indicators. Bioinformatics analysis demonstrated that most DEPs are involved in binding proteins, metabolic enzymes, and protein turnover. Additionally, some DEPs were identified as potential biomarkers for muscle decline. These findings contribute to understanding the mechanism of freshness decline in L. vannamei under low-temperature storage and the changes in muscle proteome.
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Affiliation(s)
- Yu Chen
- College of Food Scientific, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (Z.W.); (H.Z.); (J.L.); (X.S.); (J.L.)
| | - Qian Ning
- Jinshan College of Fujian Agriculture and Forestry University, Fuzhou 350001, China;
| | - Zhenzhen Wu
- College of Food Scientific, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (Z.W.); (H.Z.); (J.L.); (X.S.); (J.L.)
| | - Hanlin Zhou
- College of Food Scientific, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (Z.W.); (H.Z.); (J.L.); (X.S.); (J.L.)
| | - Jun Liao
- College of Food Scientific, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (Z.W.); (H.Z.); (J.L.); (X.S.); (J.L.)
| | - Xiangyun Sun
- College of Food Scientific, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (Z.W.); (H.Z.); (J.L.); (X.S.); (J.L.)
| | - Jing Lin
- College of Food Scientific, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (Z.W.); (H.Z.); (J.L.); (X.S.); (J.L.)
| | - Jie Pang
- College of Food Scientific, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (Z.W.); (H.Z.); (J.L.); (X.S.); (J.L.)
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Keele GR, Zhang JG, Szpyt J, Korstanje R, Gygi SP, Churchill GA, Schweppe DK. Global and tissue-specific aging effects on murine proteomes. Cell Rep 2023; 42:112715. [PMID: 37405913 PMCID: PMC10588767 DOI: 10.1016/j.celrep.2023.112715] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/06/2023] [Accepted: 06/13/2023] [Indexed: 07/07/2023] Open
Abstract
Maintenance of protein homeostasis degrades with age, contributing to aging-related decline and disease. Previous studies have primarily surveyed transcriptional aging changes. To define the effects of age directly at the protein level, we perform discovery-based proteomics in 10 tissues from 20 C57BL/6J mice, representing both sexes at adult and late midlife ages (8 and 18 months). Consistent with previous studies, age-related changes in protein abundance often have no corresponding transcriptional change. Aging results in increases in immune proteins across all tissues, consistent with a global pattern of immune infiltration with age. Our protein-centric data reveal tissue-specific aging changes with functional consequences, including altered endoplasmic reticulum and protein trafficking in the spleen. We further observe changes in the stoichiometry of protein complexes with important roles in protein homeostasis, including the CCT/TriC complex and large ribosomal subunit. These data provide a foundation for understanding how proteins contribute to systemic aging across tissues.
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Affiliation(s)
| | | | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA.
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Sweatt AJ, Griffiths CD, Paudel BB, Janes KA. Proteome-wide copy-number estimation from transcriptomics. bioRxiv 2023:2023.07.10.548432. [PMID: 37503057 PMCID: PMC10369941 DOI: 10.1101/2023.07.10.548432] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein copy numbers constrain systems-level properties of regulatory networks, but absolute proteomic data remain scarce compared to transcriptomics obtained by RNA sequencing. We addressed this persistent gap by relating mRNA to protein statistically using best-available data from quantitative proteomics-transcriptomics for 4366 genes in 369 cell lines. The approach starts with a central estimate of protein copy number and hierarchically appends mRNA-protein and mRNA-mRNA dependencies to define an optimal gene-specific model that links mRNAs to protein. For dozens of independent cell lines and primary prostate samples, these protein inferences from mRNA outmatch stringent null models, a count-based protein-abundance repository, and empirical protein-to-mRNA ratios. The optimal mRNA-to-protein relationships capture biological processes along with hundreds of known protein-protein interaction complexes, suggesting mechanistic relationships are embedded. We use the method to estimate viral-receptor abundances of CD55-CXADR from human heart transcriptomes and build 1489 systems-biology models of coxsackievirus B3 infection susceptibility. When applied to 796 RNA sequencing profiles of breast cancer from The Cancer Genome Atlas, inferred copy-number estimates collectively reclassify 26% of Luminal A and 29% of Luminal B tumors. Protein-based reassignments strongly involve a pharmacologic target for luminal breast cancer (CDK4) and an α-catenin that is often undetectable at the mRNA level (CTTNA2). Thus, by adopting a gene-centered perspective of mRNA-protein covariation across different biological contexts, we achieve accuracies comparable to the technical reproducibility limits of contemporary proteomics. The collection of gene-specific models is assembled as a web tool for users seeking mRNA-guided predictions of absolute protein abundance (http://janeslab.shinyapps.io/Pinferna).
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Affiliation(s)
- Andrew J. Sweatt
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908
| | - Cameron D. Griffiths
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908
| | - B. Bishal Paudel
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, 22908
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Xu L, Liu H, Zhu S, Meng Y, Wang Y, Li J, Zhang F, Huang L. VmPacC-mediated pH regulation of Valsa mali confers to host acidification identified by comparative proteomics analysis. Stress Biol 2023; 3:18. [PMID: 37676527 PMCID: PMC10441875 DOI: 10.1007/s44154-023-00097-y] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/24/2023] [Indexed: 09/06/2023]
Abstract
Apple valsa canker caused by the Ascomycete fungus Valsa mali is one of the most serious diseases of apple, resulting in huge economic losses in the apple-growing area of China. Previous study found that the pathogen could acidify the infected tissues to make lower ambient pH (from 6.0 to 3.5) for their successfully colonization. The pH signaling transcription factor VmPacC is required for acidification of its environment and for full virulence in V. mali. It is known that the functional cooperation of proteins secreted by V. mali plays pivotal role in its successful colonization of host plants. In this study, we used tandem mass tag (TMT) labeling coupled with LC-MS/MS-based quantitative proteomics to analyze the VmPacC-mediated pH regulation in V. mali, focusing on differentially expressed proteins (DEPs). We identified 222 DEPs specific to VmPacC deletion, and 921 DEPs specific to different pH conditions (pH 6.0 and 3.4). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these DEPs were mainly involved in pathways associated with carbon metabolism, biosynthesis of antibiotics, citrate cycle (TCA cycle), glycolysis/gluconeogenesis, glutathione metabolism, ribosomes, and pentose phosphate pathways. Additionally, we identified 119 DEPs that were shared among the VmPacC deletion mutant and different pH conditions, which were mainly related to energy metabolism pathways, providing the energy required for the hyphal growth and responses to environmental stresses. A protein-protein interaction (PPI) network analysis indicated that most of the shared proteins were mapped to an interaction network with a medium confidence score of 0.4. Notably, one uncharacterized protein (KUI69106.1), and two known proteins (heat shock protein 60 (KUI73579.1), aspartate aminotransferase (KUI73864.1)) located in the core of the network were highly connected (with ≥ 38 directed edges) with the other shared DEPs. Our results suggest that VmPacC participates in the pathogen's regulation to ambient pH through the regulation of energy metabolism pathways such as the glycolysis/gluconeogenesis pathway and TCA cycle. Finally, we proposed a sophisticated molecular regulatory network to explain pH decrease in V. mali. Our study, by providing insights into V. mali regulating pH, helps to elucidate the mechanisms of host acidification during pathogen infection.
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Affiliation(s)
- Liangsheng Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Hailong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shan Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yangguang Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yinghao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jianyu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Feiran Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Pérez-Cervera L, De Santis S, Marcos E, Ghorbanzad-Ghaziany Z, Trouvé-Carpena A, Selim MK, Pérez-Ramírez Ú, Pfarr S, Bach P, Halli P, Kiefer F, Moratal D, Kirsch P, Sommer WH, Canals S. Alcohol-induced damage to the fimbria/fornix reduces hippocampal-prefrontal cortex connection during early abstinence. Acta Neuropathol Commun 2023; 11:101. [PMID: 37344865 PMCID: PMC10286362 DOI: 10.1186/s40478-023-01597-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023] Open
Abstract
INTRODUCTION Alcohol dependence is characterized by a gradual reduction in cognitive control and inflexibility to contingency changes. The neuroadaptations underlying this aberrant behavior are poorly understood. Using an animal model of alcohol use disorders (AUD) and complementing diffusion-weighted (dw)-MRI with quantitative immunohistochemistry and electrophysiological recordings, we provide causal evidence that chronic intermittent alcohol exposure affects the microstructural integrity of the fimbria/fornix, decreasing myelin basic protein content, and reducing the effective communication from the hippocampus (HC) to the prefrontal cortex (PFC). Using a simple quantitative neural network model, we show how disturbed HC-PFC communication may impede the extinction of maladaptive memories, decreasing flexibility. Finally, combining dw-MRI and psychometric data in AUD patients, we discovered an association between the magnitude of microstructural alteration in the fimbria/fornix and the reduction in cognitive flexibility. Overall, these findings highlight the vulnerability of the fimbria/fornix microstructure in AUD and its potential contribution to alcohol pathophysiology. Fimbria vulnerability to alcohol underlies hippocampal-prefrontal cortex dysfunction and correlates with cognitive impairment.
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Affiliation(s)
- Laura Pérez-Cervera
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Alicante, Spain
| | - Silvia De Santis
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Alicante, Spain
| | - Encarni Marcos
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Alicante, Spain
| | - Zahra Ghorbanzad-Ghaziany
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Alicante, Spain
- Radiation Science and Biomedical Imaging, University of Sherbrooke, Sherbrooke, Québec, Canada
| | - Alejandro Trouvé-Carpena
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Alicante, Spain
| | - Mohamed Kotb Selim
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Alicante, Spain
| | - Úrsula Pérez-Ramírez
- Center for Biomaterials and Tissue Engineering, Universitat Politècnica de València, Valencia, Spain
| | - Simone Pfarr
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Patrick Bach
- Department of Addiction Medicine, Department of Clinical Psychology, Medical Faculty Mannheim, Central Institute of Mental Health, University of Heidelberg, Mannheim, Germany
| | - Patrick Halli
- Department of Psychology, University of Heidelberg, Heidelberg, Germany
| | - Falk Kiefer
- Department of Addiction Medicine, Department of Clinical Psychology, Medical Faculty Mannheim, Central Institute of Mental Health, University of Heidelberg, Mannheim, Germany
| | - David Moratal
- Center for Biomaterials and Tissue Engineering, Universitat Politècnica de València, Valencia, Spain
| | - Peter Kirsch
- Department of Psychology, University of Heidelberg, Heidelberg, Germany
| | - Wolfgang H Sommer
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical faculty Mannheim, University of Heidelberg, Mannheim, Germany.
- Department of Addiction Medicine, Department of Clinical Psychology, Medical Faculty Mannheim, Central Institute of Mental Health, University of Heidelberg, Mannheim, Germany.
| | - Santiago Canals
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Alicante, Spain.
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Ma TP, Izrael-Tomasevic A, Mroue R, Budayeva H, Malhotra S, Raisner R, Evangelista M, Rose CM, Kirkpatrick DS, Yu K. Azido TMT Enables Direct Enrichment and Highly Multiplexed Quantitation of Proteome-Wide Functional Residues. J Proteome Res 2023. [PMID: 37285454 DOI: 10.1021/acs.jproteome.2c00703] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances in targeted covalent inhibitors have aroused significant interest for their potential in drug development for difficult therapeutic targets. Proteome-wide profiling of functional residues is an integral step of covalent drug discovery aimed at defining actionable sites and evaluating compound selectivity in cells. A classical workflow for this purpose is called IsoTOP-ABPP, which employs an activity-based probe and two isotopically labeled azide-TEV-biotin tags to mark, enrich, and quantify proteome from two samples. Here we report a novel isobaric 11plex-AzidoTMT reagent and a new workflow, named AT-MAPP, that significantly expands multiplexing power as compared to the original isoTOP-ABPP. We demonstrate its application in identifying cysteine on- and off-targets using a KRAS G12C covalent inhibitor ARS-1620. However, changes in some of these hits can be explained by modulation at the protein and post-translational levels. Thus, it would be crucial to interrogate site-level bona fide changes in concurrence to proteome-level changes for corroboration. In addition, we perform a multiplexed covalent fragment screening using four acrylamide-based compounds as a proof-of-concept. This study identifies a diverse set of liganded cysteine residues in a compound-dependent manner with an average hit rate of 0.07% in intact cell. Lastly, we screened 20 sulfonyl fluoride-based compounds to demonstrate that the AT-MAPP assay is flexible for noncysteine functional residues such as tyrosine and lysine. Overall, we envision that 11plex-AzidoTMT will be a useful addition to the current toolbox for activity-based protein profiling and covalent drug development.
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Affiliation(s)
- Taylur P Ma
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Rana Mroue
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Hanna Budayeva
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Ryan Raisner
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Marie Evangelista
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher M Rose
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Donald S Kirkpatrick
- Interline Therapeutics, Inc., South San Francisco, California 94080, United States
| | - Kebing Yu
- Fuhong Biopharma, Inc., Shanghai 201206, China
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Chen Y, Gong H, Tang D, Yu L, Long S, Zheng B, Luo D, Cai A. Liver proteomic analysis reveals the key proteins involved in host immune response to sepsis. PeerJ 2023; 11:e15294. [PMID: 37255592 PMCID: PMC10226476 DOI: 10.7717/peerj.15294] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/04/2023] [Indexed: 06/01/2023] Open
Abstract
Background Sepsis is a serious infection-induced response in the host, which can result in life-threatening organ dysfunction. It is of great importance to unravel the relationship between sepsis and host immune response and its mechanisms of action. Liver is one of the most vulnerable organs in sepsis, however, the specific pathogenesis of septic liver injury has not been well understood at the protein level. Methods A total of 12 healthy Sprague-Dawley (SD) male rats aged from 6 to 8 weeks were adaptively housed in individual cages in the specific pathogen free animal room. These lab rats were grouped into two groups: treatment (N = 9) and control (N = 3) groups; only three mice from the treatment group survived and were used for subsequent experiments. A TMT-based proteomic analysis for liver tissue was performed in the septic rat model. Results A total of 37,012 unique peptides were identified, and then 6,166 proteins were determined, among which 5,701 were quantifiable. Compared to the healthy control group, the septic rat group exhibited 162 upregulated and 103 downregulated differentially expressed proteins (DEPs). The upregulated and downregulated DEPs were the most significantly enriched into the complement and coagulation cascades and metabolic pathways. Protein-protein interaction (PPI) analysis further revealed that the upregulated and downregulated DEPs each clustered in a PPI network. Several highly connected upregulated and downregulated DEPs were also enriched into the complement and coagulation cascades pathways and metabolic pathways, respectively. The parallel reaction monitoring (PRM) results of the selected DEPs were consistent with the results of the TMT analysis, supporting the proteomic data. Conclusion Our findings highlight the roles of complement and coagulation cascades and metabolic pathways that may play vital roles in the host immune response. The DEPs may serve as clinically potential treatment targets for septic liver injury.
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Affiliation(s)
- Yingying Chen
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Hui Gong
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Lan Yu
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Shoubin Long
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Bao Zheng
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Dixian Luo
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Anji Cai
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
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Carbonell AU, Freire-Cobo C, Deyneko IV, Dobariya S, Erdjument-Bromage H, Clipperton-Allen AE, Page DT, Neubert TA, Jordan BA. Comparing synaptic proteomes across five mouse models for autism reveals converging molecular similarities including deficits in oxidative phosphorylation and Rho GTPase signaling. Front Aging Neurosci 2023; 15:1152562. [PMID: 37255534 PMCID: PMC10225639 DOI: 10.3389/fnagi.2023.1152562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023] Open
Abstract
Specific and effective treatments for autism spectrum disorder (ASD) are lacking due to a poor understanding of disease mechanisms. Here we test the idea that similarities between diverse ASD mouse models are caused by deficits in common molecular pathways at neuronal synapses. To do this, we leverage the availability of multiple genetic models of ASD that exhibit shared synaptic and behavioral deficits and use quantitative mass spectrometry with isobaric tandem mass tagging (TMT) to compare their hippocampal synaptic proteomes. Comparative analyses of mouse models for Fragile X syndrome (Fmr1 knockout), cortical dysplasia focal epilepsy syndrome (Cntnap2 knockout), PTEN hamartoma tumor syndrome (Pten haploinsufficiency), ANKS1B syndrome (Anks1b haploinsufficiency), and idiopathic autism (BTBR+) revealed several common altered cellular and molecular pathways at the synapse, including changes in oxidative phosphorylation, and Rho family small GTPase signaling. Functional validation of one of these aberrant pathways, Rac1 signaling, confirms that the ANKS1B model displays altered Rac1 activity counter to that observed in other models, as predicted by the bioinformatic analyses. Overall similarity analyses reveal clusters of synaptic profiles, which may form the basis for molecular subtypes that explain genetic heterogeneity in ASD despite a common clinical diagnosis. Our results suggest that ASD-linked susceptibility genes ultimately converge on common signaling pathways regulating synaptic function and propose that these points of convergence are key to understanding the pathogenesis of this disorder.
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Affiliation(s)
- Abigail U. Carbonell
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Carmen Freire-Cobo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ilana V. Deyneko
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Saunil Dobariya
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Hediye Erdjument-Bromage
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Amy E. Clipperton-Allen
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, United States
| | - Damon T. Page
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, United States
| | - Thomas A. Neubert
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Bryen A. Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, United States
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Xu S, Xu X, Wu R. Deciphering the Properties and Functions of Glycoproteins Using Quantitative Proteomics. J Proteome Res 2023. [PMID: 37010087 DOI: 10.1021/acs.jproteome.3c00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Glycosylation is one of the most common and important protein modifications, and it regulates the properties and functions of a wide range of proteins. Aberrant glycosylation is directly related to human diseases. Recently, with the advancement of mass spectrometry (MS) instrumentation and MS-based glycoproteomic methods, global characterization of glycoproteins in complex biological samples has become possible. Using quantitative proteomics, the abundance of glycoproteins in different samples can be quantified, which provides a wealth of information to further our understanding of protein functions, cellular activities, and the molecular mechanisms of diseases. In this review, we discuss quantitative proteomic methods used for comprehensive analysis of protein glycosylation, and cover the applications of quantitative glycoproteomics to unveil the properties and functions of glycoproteins and their association with various diseases. It is expected that quantitative proteomic methods will be extensively applied to explore the role of protein glycosylation in complex biological systems, and to identify glycoproteins as biomarkers for disease detection and as therapeutic targets for disease treatment.
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Fan Y, Li X, Guo Y, He X, Wang Y, Zhao D, Ma Y, Feng X, Zhang J, Li J, Zi X, Xiong X, Fu W, Xiong Y. TMT-based quantitative proteomics analysis reveals the differential proteins between fresh and frozen-thawed sperm of yak (Bos grunniens). Theriogenology 2023; 200:60-69. [PMID: 36764186 DOI: 10.1016/j.theriogenology.2023.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/29/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Sperm cryopreservation is one of the most effective methods for the conservation of germplasm resources and used of superior sires widely. However, the motility of yak (Bos grunniens) sperm was low after thawing and the proteomics changes in sperm cryopreservation remain unknown. Therefore, the aim of this study was to explore the differences between fresh sperm and frozen sperm of yak through the proteomic analysis and thus improve the understanding of sperm cryodamage. The Tandem Mass Tags (TMT) technology was used to screen differentially expressed proteins (DEPs) before and after freezing. Then, GO and KEGG analysis were conducted to analyze the DEPs enriched signaling pathways. Finally, the DEPs, including superoxide dismutase 1 (SOD1) and NADH ubiquinone oxidoreductase core subunit S8 (NDUFS8) were verified by the immunofluorescence technique. The results showed that there were 229 DEPs between fresh and frozen-thawed yak sperm. Compared with the fresh sperm, 120 proteins were up-regulated and 109 proteins were down-regulated in frozen-thawed sperm. The GO annotation showed that the up-regulated proteins enriched in metabolic and cytoskeleton-related processes, including lipoprotein metabolic process, lipid transport, extracellular region and intermediate filament cytoskeleton organization. In contrast, the down-regulated proteins enriched in biological processes including single fertilization, sperm capacitation and response to unfolded protein. KEGG pathway analysis indicated that freezing and thawing affected the oxidative phosphorylation pathway, the fructose and mannose metabolic pathway and the glycerolipid metabolic pathway of yak sperm. Immunofluorescence results showed that the protein expression level of SOD1 protein in the frozen group was significantly lower than that in the fresh group (P < 0.01), and the protein expression level of NDUFS8 protein was significantly higher in frozen group (P < 0.01). This study revealed the DEPs between fresh and frozen-thawed sperm and provides a theoretical basis to further explore the exertion of normal biological functions of yak sperm after freezing and thawing.
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Affiliation(s)
- Yilin Fan
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization of Sichuan Province, Southwest Minzu University, Chengdu, 610041, China
| | - Xiaowei Li
- Longri Breeding Stock Farm of Sichuan Province, Dujiangyan, 611800, China
| | - Yu Guo
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization of Sichuan Province, Southwest Minzu University, Chengdu, 610041, China
| | - Xiaoqiang He
- Longri Breeding Stock Farm of Sichuan Province, Dujiangyan, 611800, China
| | - Yanwen Wang
- Longri Breeding Stock Farm of Sichuan Province, Dujiangyan, 611800, China
| | - Dan Zhao
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization of Sichuan Province, Southwest Minzu University, Chengdu, 610041, China
| | - Yan Ma
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Xinxin Feng
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Jiyue Zhang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Jian Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization of Sichuan Province, Southwest Minzu University, Chengdu, 610041, China.
| | - Xiangdong Zi
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization of Sichuan Province, Southwest Minzu University, Chengdu, 610041, China
| | - Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Utilization of Sichuan Province, Southwest Minzu University, Chengdu, 610041, China
| | - Wei Fu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu, 610041, China
| | - Yan Xiong
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu, 610041, China.
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Xu J, Gao S, Xin M, Chen W, Wang K, Liu W, Yan X, Peng S, Ren Y. Comparative Tandem Mass Tag-Based Quantitative Proteomics Analysis of Liver Against Chronic Hypoxia: Molecular Insights Into Metabolism in Rats. High Alt Med Biol 2023; 24:49-58. [PMID: 36706039 PMCID: PMC10027340 DOI: 10.1089/ham.2022.0003] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Xu, Jin, Shenhan Gao, Mingyuan Xin, Wenjie Chen, Kaikun Wang, Wenjing Liu, Xinzong Yan, Sinan Peng, and Yanming Ren. Comparative tandem mass tag-based quantitative proteomics analysis of liver against chronic hypoxia: molecular insights into metabolism in rats. High Alt Med Biol. 24:49-58, 2023. Objective: Using a metabolomic approach, we uncovered key regulators in metabolism from tandem mass tag (TMT)-based proteomic analysis in animals chronically exposed to hypoxia. Methods: Sixteen Sprague-Dawley rats (n = 8 per group) were exposed to chronic normoxia or hypoxia (380 mmHg corresponding to a simulated altitude of 5,500 m) for 35 consecutive days. Hypoxia-induced alterations in metabolic pathways were analyzed from TMT-based proteomic analysis, complemented by western blot validation of key regulators. Results: We profiled biochemical parameters and serum lipids, found that serum alanine aminotransferase and blood glucose were not significantly changed due to chronic hypoxia. However, serum triglycerides, total cholesterol, high-density lipoprotein, and low-density lipoprotein (LDL) were significantly affected by chronic hypoxia. And the levels of LDL nearly doubled (p < 0.05) after hypoxia exposure for 35 days. Through Kyoto Encyclopedia of Genes and Genomes classification, we found several metabolic pathways were enriched, including lipid metabolism, cofactor and vitamin metabolism, amino acids metabolism, carbohydrate metabolism, and energy metabolism. To explore the potential functions of proteins in metabolic pathways that become a coordinated shift under chronic hypoxic conditions, Gene Ontology and pathway analysis were carried out on differentially expressed proteins. As the co-expression network shown in Figure, we identified the most significant differentially expressed proteins after chronic hypoxic changes in the livers of rats. Furthermore, we validated the gene expression profiles at the protein level using western blot. Results of western blot were in accordance with our quantitative polymerase chain reaction findings. The levels of fatty acid synthase and aquaporin 1 were significantly downregulated after 35 days and the levels of ATP citrate lyase, 2'-5'-oligoadenylate synthetase 1A, aldehyde dehydrogenase 2, and Ras-related protein Rap-1A were significantly upregulated after 35 days. Conclusions: Although this study cannot completely account for all the molecular mechanisms in rats, we provide a good analysis of protein expression and profiling of rats under chronic hypoxia conditions.
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Affiliation(s)
- Jin Xu
- Department of Medicine, Qinghai University, Xining, China
| | - Shenhan Gao
- Department of Ecology, Qinghai University Plateau Biology Jing Ying Class, Grade 19, Xining, China
| | - Mingyuan Xin
- Department of Medicine, Qinghai University Clinical Medicine Class 1, Grade 19, Xining, China
| | - Wenjie Chen
- Department of Medicine, Qinghai University Clinical Medicine Class 6, Grade 20, Xining, China
| | - Kaikun Wang
- Department of Medicine, Qinghai University Clinical Medicine Class 3, Grade 20, Xining, China
| | - Wenjing Liu
- Department of Medicine, Qinghai University the Graduate Student of Foundation Medical of 2020, Xining, China
| | - Xinzong Yan
- Department of Medicine, Qinghai University the Graduate Student of Foundation Medical of 2021, Xining, China
| | - Sinan Peng
- Department of Mechanical Engineering, Qinghai University Material Forming and Control Engineering Class, Grade 20, Xining, China
| | - Yanming Ren
- Department of Medicine, Qinghai University, Xining, China
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Barpanda A, Halder A, Dhote A, Parihari S, Kantharia C, Srivastava S. Colon Adenocarcinoma Quantitative Proteomics Reveals Dysregulation in Key Cancer Signaling Pathways and a Candidate Protein Marker Panel. OMICS 2023; 27:75-85. [PMID: 36730729 DOI: 10.1089/omi.2022.0169] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Colorectal cancer (CRC) is reportedly the second leading cause of cancer death worldwide. By the end of the decade, there will likely be more than one million fatalities worldwide from this cancer, with an estimated 2.2 million additional cases. We need new ways of thinking about cancer research. One approach is to deploy systems science using quantitative proteomics to obtain postgenomic and functional insights into cancer. The present study compares the tissue proteome of CRC (n = 10) with the matched peritumoral controls (n = 10) in samples obtained from the Indian subcontinent. When compared with the controls, a list of 22 substantially altered protein candidates was identified, which were associated with the growth, survival, and metastasis of the tumor. A list of the unique peptides from top significant proteins, including olfactomedin-4, alanyl aminopeptidase, and grancalcin was further validated using a parallel reaction monitoring-based targeted proteomics approach. In addition, biological pathway analysis showed perturbation in key biological processes, including dysregulation in purine metabolism, MYC targets in cancer, DNA repair, and replication, and leukocyte transendothelial migration, among others. The protein panel reported herein is also shown to be dysregulated in CRC and warrants further research toward understanding pathobiology, diagnostics, and therapeutics development in CRC.
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Affiliation(s)
- Abhilash Barpanda
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.,Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ankit Halder
- Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ayushi Dhote
- Saint Francis de Sales College, Nagpur, Maharashtra, India
| | - Shashwati Parihari
- Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Chetan Kantharia
- Department of Surgical Gastroenterology, Seth G.S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.,Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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Griesser E, Gesell M, Veyel D, Lamla T, Geillinger-Kästle K, Rist W. Whole lung proteome of an acute epithelial injury mouse model in comparison to spatially resolved proteomes. Proteomics 2023; 23:e2100414. [PMID: 36641648 DOI: 10.1002/pmic.202100414] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/21/2022] [Accepted: 01/09/2023] [Indexed: 01/16/2023]
Abstract
Epithelial injury is one of the major drivers of acute pulmonary diseases. Recurring injury followed by aberrant repair is considered as the primary cause of chronic lung diseases, such as idiopathic pulmonary fibrosis (IPF). Preclinical in vivo models allow studying early disease-driving mechanisms like the recently established adeno-associated virus-diphtheria toxin receptor (AAV-DTR) mouse model of acute epithelial lung injury, which utilises AAV mediated expression of the human DTR. We performed quantitative proteomics of homogenised lung samples from this model and compared the results to spatially resolved proteomics data of epithelial cell regions from the same animals. In whole lung tissue proteins involved in cGAS-STING and interferon pathways, proliferation, DNA replication and the composition of the provisional extracellular matrix were upregulated upon injury. Besides epithelial cell markers SP-A, SP-C and Scgb1a1, proteins involved in cilium assembly, lipid metabolism and redox pathways were among downregulated proteins. Comparison of the bulk to spatially resolved proteomics data revealed a large overlap of protein changes and striking differences. Together our study underpins the broad usability of bulk proteomics and pinpoints to the benefit of sophisticated proteomic analyses of specific tissue regions or single cell types.
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Affiliation(s)
- Eva Griesser
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Martin Gesell
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Daniel Veyel
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Thorsten Lamla
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Kerstin Geillinger-Kästle
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Wolfgang Rist
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
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