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Yang A, Botsi S, Kumar S, Pal SB, Lam MM, Čepaitė I, Laugharn A, Dieckmann K. Singlet Pathway to the Ground State of Ultracold Polar Molecules. PHYSICAL REVIEW LETTERS 2020; 124:133203. [PMID: 32302184 DOI: 10.1103/physrevlett.124.133203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/09/2020] [Indexed: 06/11/2023]
Abstract
Starting from weakly bound Feshbach molecules, we demonstrate a two-photon pathway to the dipolar ground state of bi-alkali molecules that involves only singlet-to-singlet optical transitions. This pathway eliminates the search for a suitable intermediate state with sufficient singlet-triplet mixing and the exploration of its hyperfine structure, as is typical for pathways starting from triplet dominated Feshbach molecules. By selecting a Feshbach state with a stretched singlet hyperfine component and controlling the laser polarizations, we assure coupling to only single hyperfine components of the A^{1}Σ^{+} excited potential and the X^{1}Σ^{+} rovibrational ground state. In this way an ideal three level system is established, even if the hyperfine structure is not resolved. We demonstrate this pathway with ^{6}Li^{40}K molecules, and discuss its application to other important molecular species.
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Yang A, Xuan R, Melbourne W, Tran K, Murrell DF. Validation of the BIOCHIP test for the diagnosis of bullous pemphigoid, pemphigus vulgaris and pemphigus foliaceus. J Eur Acad Dermatol Venereol 2020; 34:153-160. [PMID: 31260565 DOI: 10.1111/jdv.15770] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 05/28/2019] [Indexed: 12/17/2023]
Abstract
BACKGROUND The BIOCHIP is a novel multiplex indirect immunofluorescence technique used in the serological diagnosis of bullous pemphigoid and pemphigus. The BIOCHIP method combines the screening of autoantibodies and target antigen-specific substrates in a single miniature incubation field. OBJECTIVE To evaluate the diagnostic accuracy of the new immunofluorescence BIOCHIP multiplex tool in pemphigus and bullous pemphigoid. METHODS For the validation of the BIOCHIP, sera from patients with BP (n = 38), PF (n = 8) and pemphigus vulgaris (PV) (n = 23) were used. In addition, sera from disease control patients (n = 63) and healthy volunteers (n = 39) were used. The multiplex BIOCHIP and direct immunofluorescence (DIF) were performed for all BP, PF and PV patients. Additional indirect immunofluorescence (IIF) was performed on patients with BP, and ELISA was performed on patients with pemphigus. RESULTS The BIOCHIP mosaic showed a sensitivity of 86.8% and specificity of 85% for BP180 or BP230 being positive in BP. It demonstrated a sensitivity of 75% and specificity of 97.7% for Dsg1 in PF. The BIOCHIP was found to have a sensitivity of 60.9% and specificity of 73.6% for Dsg3 in PV. CONCLUSION The BIOCHIP mosaic-based immunofluorescence test is potentially a simple, time and effort saving test that can aid in the diagnosis and screening of BP, PV and PF. However, there is potential for interpretation bias and a learning curve that needs to be taken into consideration.
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Johnson M, Spira A, Carbone D, Drake C, Henick B, Ingham M, Caldwell K, Chan S, Hart M, Malloy A, Maloney E, Palmer C, Yang A, Zhong M, Basciano P, Bournazou E, Ferguson A, Catenacci D. First Results of Phase I/II Studies Evaluating Viral Vector-Based Heterologous Prime/Boost Immunotherapy Against Predicted HLA Class I Neoantigens Demonstrate CD8 T Cell Responses In Patients with Advanced Cancers. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz451.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Yoon I, Nam M, Kim HK, Moon HS, Kim S, Jang J, Song JA, Jeong SJ, Kim SB, Cho S, Kim Y, Lee J, Yang WS, Yoo HC, Kim K, Kim MS, Yang A, Cho K, Park HS, Hwang GS, Hwang KY, Han JM, Kim JH, Kim S. Glucose-dependent control of leucine metabolism by leucyl-tRNA synthetase 1. Science 2019; 367:205-210. [PMID: 31780625 DOI: 10.1126/science.aau2753] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 03/20/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022]
Abstract
Despite the importance of glucose and amino acids for energy metabolism, interactions between the two nutrients are not well understood. We provide evidence for a role of leucyl-tRNA synthetase 1 (LARS1) in glucose-dependent control of leucine usage. Upon glucose starvation, LARS1 was phosphorylated by Unc-51 like autophagy activating kinase 1 (ULK1) at the residues crucial for leucine binding. The phosphorylated LARS1 showed decreased leucine binding, which may inhibit protein synthesis and help save energy. Leucine that is not used for anabolic processes may be available for catabolic pathway energy generation. The LARS1-mediated changes in leucine utilization might help support cell survival under glucose deprivation. Thus, depending on glucose availability, LARS1 may help regulate whether leucine is used for protein synthesis or energy production.
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Skinner H, Hu C, Tsakiridis T, Santana-Davila R, Lu B, Erasmus J, Doemer A, Videtic G, Coster J, Yang A, Lee R, Wasik MW, Schaner P, Mccormack S, Esparaz B, Mcgarry R, Bazan J, Stuve T, Bradley J. OA12.03 Initial Reporting of NRG-LU001, Randomized Phase II Trial of Concurrent Chemoradiotherapy +/- Metformin HCL in Locally Advanced NSCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yang A, Xuan R, Melbourne W, Hashimoto T, Uzun S, Daneshpazhooh M, Yamagami J, Di Zenzo G, Mascaro J, Mahmoudi H, Patsatsi A, Drenovska K, Vassileva S, Murrell D. Inter‐rater reliability of the BIOCHIP indirect immunofluorescence dermatology mosaic in bullous pemphigoid and pemphigus patients. J Eur Acad Dermatol Venereol 2019; 33:2327-2333. [DOI: 10.1111/jdv.15817] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 07/03/2019] [Indexed: 01/10/2023]
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Yang A, Xin X, Yang W, Li M, Yang W, Li L, Liu X. Etanercept reduces anxiety and depression in psoriasis patients, and sustained depression correlates with reduced therapeutic response to etanercept. Ann Dermatol Venereol 2019; 146:363-371. [PMID: 31047699 DOI: 10.1016/j.annder.2019.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 01/01/2019] [Accepted: 03/06/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND The purpose of this study was to explore the correlation of anxiety and depression with therapeutic response to etanercept in psoriasis patients. PATIENTS AND METHODS One hundred and thirty-three patients with moderate-to-severe plaque psoriasis undergoing etanercept treatment were consecutively enrolled in this prospective cohort study, with all patients receiving etanercept treatment for 6 months. Psoriasis Area and Severity Index (PASI) score was evaluated at baseline (M0) and at month 1 (M1), M3 and M6 after treatment, and PASI 75/90 responses were calculated. The Hospital Anxiety and Depression Scale-Anxiety (HADS-A) score and the HADS-Depression (HADS-D) score were used to evaluate patients' anxiety and depression at M0, M1, M3 and M6. Sustained anxiety/depression were defined as HADS-A/D score≥8points both at M0 and M1. RESULTS Female gender and higher PASI score were associated with high risk of anxiety, while female gender, higher PASI score and longer disease duration were correlated with increased depression risk. After 6 months of etanercept treatment, 65.4% and 36.1% patients achieved PASI 75 and PASI 90 responses respectively, and both HADS-A and HADS-D scores were decreased. Most importantly, no correlation of baseline anxiety and depression with PASI 75 or PASI 90 response after 6 months of treatment was noted, while sustained depression, though not sustained anxiety, was observed to be correlated with decreased PASI 75 and PASI 90 responses. CONCLUSIONS Etanercept reduces anxiety and depression in psoriasis patients, and sustained depression correlates with reduced therapeutic response to etanercept.
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Wong MYW, Wang B, Yang A, Khor A, Xuan W, Rajendra S. Human papillomavirus exposure and sexual behavior are significant risk factors for Barrett's dysplasia/esophageal adenocarcinoma. Dis Esophagus 2018; 31:5042155. [PMID: 29931323 DOI: 10.1093/dote/doy051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Given the comparable strains of high-risk human papillomavirus (HPV) present in a subset of Barrett's dysplasia and esophageal adenocarcinoma as in head and neck squamous cell carcinomas and the anatomical proximity of both lesions, we hypothesized that oral sex may increase the risk of Barrett's dysplasia/esophageal adenocarcinoma. Therefore, we compared the sexual behavior of patients with Barrett's dysplasia/esophageal adenocarcinoma and controls (hospital, reflux, and Barrett's metaplasia) to explore a plausible mechanism of viral transmission to the lower esophagus. A hospital-based case-control study involving 36 Barrett's dysplasia/esophageal adenocarcinoma subjects and 55 controls with known HPV DNA status and markers of transcriptional activity i.e p16INK4A and E6/E7 mRNA of the esophageal epithelium was conducted to evaluate differences in sexual history (if any). Barrett's dysplasia/esophageal adenocarcinoma patients were more likely than controls to be positive for HPV DNA (18 of 36, 50% vs. 6/55, 11%, p for trend <0.0001), be male (P = 0.001) and in a relationship (P = 0.02). Viral genotypes identified were HPV 16 (n = 14), 18 (n = 2), 11 (n = 1) and 6 (n = 1). HPV exposure conferred a significantly higher risk for Barrett's dysplasia/esophageal adenocarcinoma as compared with hospital/reflux/Barrett's metaplasia controls (OR = 6.8, 95% CI: 2.1-23.1, adjusted P = 0.002). On univariate analysis, ≥6 lifetime oral sex partners were significantly associated with dysplastic Barrett's esophagus and adenocarcinoma (OR, 4.0; 95% CI: 1.2-13.7, P = 0.046). After adjustment for confounders, HPV exposure and men with ≥2 lifetime sexual partners were at significant risk for Barrett's dysplasia/esophageal adenocarcinoma. If these initial findings can be confirmed in larger studies, it could lead to effective prevention strategies in combating some of the exponential increase in the incidence of esophageal adenocarcinoma in the West.
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Ahn J, Lee JG, Chin C, In S, Yang A, Park HS, Kim J, Park JH. MSK1 functions as a transcriptional coactivator of p53 in the regulation of p21 gene expression. Exp Mol Med 2018; 50:1-12. [PMID: 30305627 PMCID: PMC6180136 DOI: 10.1038/s12276-018-0160-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 12/20/2022] Open
Abstract
Mitogen- and stress-activated kinase 1 (MSK1) is a chromatin kinase that facilitates activator-dependent transcription by altering chromatin structure through histone H3 phosphorylation. The kinase activity of MSK1 is activated by intramolecular autophosphorylation, which is initially triggered by the activation of upstream mitogen-activated protein kinases (MAPKs), such as p38 and ERK1/2. MSK1 has been implicated in the expression of p21, a p53 target gene; however, the precise connection between MSK1 and p53 has not been clearly elucidated. Here, using in vitro and cell-based transcription assays, we show that MSK1 functions as a transcriptional coactivator of p53 in p21 expression, an action associated with MAPK-dependent phosphorylation of MSK1 and elevated kinase activity. Of special significance, we show that MSK1 directly interacts with p53 and is recruited to the p21 promoter, where it phosphorylates histone H3 in a p53-dependent manner. In addition, phosphomimetic mutant analysis demonstrated that negative charges in the hydrophobic motif are critical for serine 212 phosphorylation in the N-terminal kinase domain, which renders MSK1 competent for histone kinase activity. These studies suggest that MSK1 acts through a direct interaction with p53 to function as a transcriptional coactivator and that MSK1 activation by upstream MAPK signaling is important for efficient p21 gene expression.
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Sin P, Yang A, Pon Q, Lavoie A, Crawford J, Harenberg S, Zimmermann R, Booker J, Kelly S, Lavi S, Cantor W, Mehta S, Bagai A, Goodman S, Cheema A, Dehghani P. EFFECTS OF BASELINE PLATELET REACTIVITY IN FIBRINOLYSIS-TREATED ST ELEVATION MYOCARDIAL INFARCTION PATIENTS UNDERGOING EARLY PERCUTANEOUS CORONARY INTERVENTION. Can J Cardiol 2018. [DOI: 10.1016/j.cjca.2018.07.393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Yang A, Tan C, Daneman N, Hansen MS, Habib G, Salaun E, Lavoute C, Hubert S, Adhikari NKJ. Clinical and echocardiographic predictors of embolism in infective endocarditis: systematic review and meta-analysis. Clin Microbiol Infect 2018; 25:178-187. [PMID: 30145401 DOI: 10.1016/j.cmi.2018.08.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 07/30/2018] [Accepted: 08/11/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Prediction of embolic events (EEs) in infective endocarditis (IE) could inform clinical decisions, such as surgical timing. We conducted a systematic review to more precisely define associations between risk factors and EEs. METHODS We searched two bibliographic databases (1994-2018) for observational studies that reported EEs in IE patients and considered clinical, microbiological or echocardiographic risk factors. Studies that did not use Duke criteria or only investigated a subset of IE patients were excluded. Study quality was assessed using the Newcastle-Ottawa scale. A pooled risk ratio (RR) for each risk factor was estimated using random-effects models; statistical heterogeneity was estimated using I2. RESULTS Of 3862 unique citations, 47 cohort studies (11 215 IE cases) were included; 54 risk factors were analysed in at least two studies, with nine studies reporting other individual factors. Most studies were of high methodological quality. Major predictors of EEs were intravenous drug use (RR 1.69, 95% CI 1.32-2.17; I2 = 46%), Staphylococcus aureus infection (RR 1.64, 95% CI 1.45-1.86, I2 = 32%), mitral valve vegetation (RR 1.24, 95% CI 1.11-1.37, I2 = 30%), and vegetation size >10 mm (RR 1.87, 95% CI 1.57-2.21, I2 = 48%). EE risk was also higher with human immunodeficiency virus, chronic liver disease, elevated C-reactive protein, Staphylococcus spp. infection, vegetation presence, and multiple, mobile or prosthetic mechanical valve vegetation, and lower with Streptococcus spp. infection. Most findings were unchanged in sensitivity analyses that removed studies with pulmonary EEs from the outcome. CONCLUSIONS Given the serious consequences of embolism, surgical evaluation may be considered in patients with these risk factors.
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Yang J, Hao M, Yang A, Wang Z, Wang W, Wang Z, Wang Y, Wang J, Zhao W. Serum folate, human papillomavirus, and risk of cervical intraepithelial neoplasia: A Chinese population-based cohort study. Gynecol Oncol 2018. [DOI: 10.1016/j.ygyno.2018.04.269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Xuan R, Yang A, Melbourne W, Hashimoto T, Uzun S, Daneshpazhooh M, Yamagami J, Di Zenzo G, Mascaro J, Murrell D. 059 Reliability of the BIOCHIP in pemphigus and pemphigoid patients the evaluations of blistering disease experts. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Werbel WA, Ison MG, Angarone MP, Yang A, Stosor V. Lymphopenia is associated with late onset Pneumocystis jirovecii pneumonia in solid organ transplantation. Transpl Infect Dis 2018. [PMID: 29512868 DOI: 10.1111/tid.12876] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Pneumocystis jirovecii pneumonia (PJP) affected 5%-15% of solid organ transplant (SOT) recipients prior to universal prophylaxis, classically with trimethoprim-sulfamethoxazole (TMP-SMX). Guidelines generally recommend 6-12 months of prophylaxis post-SOT, yet optimal duration and robust PJP risk stratification have not been established. METHODS A retrospective, single-center, case-control study of PJP among SOT recipients from January 1998 to December 2013 was conducted. Cases had positive PJ direct fluorescent antibody assay of respiratory specimens. Controls were matched 4:1 by nearest date of SOT. Univariate testing and multivariate logistic regressions were performed. RESULTS Fifteen cases were identified among 5505 SOT recipients (0.27% rate) and analyzed vs 60 controls. PJP occurred on average 6.1 years (range 0.9-13.8) post-SOT; no case was receiving PJP prophylaxis at diagnosis. Most were treated with reduced immunosuppression and TMP-SMX plus steroids (80%). Six patients (40%) required critical care; 3 (20%) died. There were no significant demographic differences, though cases tended to be older at SOT (54 vs 48 years, P = .1). In univariate analysis, prior viral infection was more common among cases (67% vs 37%, P = .08). Lower absolute lymphocyte count (ALC) at diagnosis date was strongly associated with PJP (400 vs 1230 × 106 cells/μL, P < .001); odds of infection were high with ALC ≤ 500 × 106 cells (OR 18.7, P < .01). CONCLUSION Pneumocystis jirovecii pneumonia is a rare, late complication of SOT with significant morbidity and mortality. Severe lymphopenia may be useful in identifying SOT recipients who warrant continued or reinstated PJP prophylaxis.
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Kornaga EN, Gratton K, Shi Q, Yang A, Nixon NA, Roldan Urgoiti G, Morris DG. Abstract P3-07-08: Temozolomide as a targeted therapy strategy for triple negative breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p3-07-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND:
Approximately 15% of newly diagnosed breast cancers are classified as triple negative (TNBC). TNBCs are considered more aggressive and have a worse prognosis as no targeted therapies are currently available. These tumors are routinely treated with chemotherapy agents with only modest proven efficacy.
Temozolomide (TMZ) is an oral chemotherapy agent commonly used for the treatment of brain tumors and melanoma. TMZ is an alkylating agent, and its therapeutic benefit depends on its ability to alkylate/methylate DNA, most commonly at the N-7 or O-6 positions of guanine residues. This process leads to DNA damage and subsequently triggers cell death. Cells that express the enzyme O6-Methylguanine-DNA Methyltransferase (MGMT) are able to repair damage caused by TMZ. Tumors that lack expression of MGMT, owing to methylation of the gene promoter, demonstrate a better response to TMZ treatment as a result of synthetic lethality.
It was first reported in 2012 that TNBCs were more likely to be MGMT methylated, which was confirmed by another group that reported up to 64% of wild-type BRCA1 TNBC exhibited MGMT gene methylation. In 2013 it was found that basal-like breast cancers were more likely to be MGMT methylated and linked to larger tumor size. Together these findings suggest that a sub-population of TNBCs lack MGMT expression, due to promoter methylation.
Currently, TMZ is not a treatment option for breast cancers given the modest efficacy of TMZ noted in breast cancer clinical trials; however, most of these trials have focused on using this agent to either treat or prevent brain metastases, due to TMZs ability to cross the blood-brain barrier. Importantly, none of these trials investigated MGMT expression or specifically TNBC populations.
We hypothesize that TMZ may be a viable and efficacious treatment option for TNBCs that lack MGMT expression, due to promoter methylation.
METHODS:
We analyzed 12 archival specimens and 4 TNBC cell lines (HTB132, HTB26, HTB126 and HCC1806) for MGMT expression using a qRT-PCR clinical assay available from Calgary Laboratory Services. Additionally, we also looked at MGMT protein expression in the cell lines using Western Blot analysis to confirm the qRT-PCR results. Finally, we performed an in vitro assay with TNBC cell lines to determine cytotoxicity of TMZ.
RESULTS:
Analysis of the archival specimens found that 33% of samples analyzed had MGMT promoter methylation by qRT-PCR. Additionally, we found that HTB26 and HTB126 cell lines showed MGMT promoter methylation by qRT-pCR analysis. Western Blot analysis confirmed lack of MGMT expression in these two cell lines, and also identified another cell line (HCC1806) lacking MGMT protein that was classified as unmethylated by the qRT-PCR clinical assay. Moreover, our in vitro assay found that two cell lines (HTB26 and HCC1806) showed a noticeable response to treatment with TMZ. Interestingly, HTB126 did not show response to TMZ, suggesting that there may be another putative resistance pathway.
CONCLUSIONS:
Preliminary findings suggest that TMZ may be a viable targeted treatment option for TNBCs. Currently, we are investigating drug response using in vivo mouse models, as well as investigating synergistic combination therapy options.
Citation Format: Kornaga EN, Gratton K, Shi Q, Yang A, Nixon NA, Roldan Urgoiti G, Morris DG. Temozolomide as a targeted therapy strategy for triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-07-08.
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Yang A, Cho K, Park HS. Chemical biology approaches for studying posttranslational modifications. RNA Biol 2017; 15:427-440. [PMID: 28901832 DOI: 10.1080/15476286.2017.1360468] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Posttranslational modification (PTM) is a key mechanism for regulating diverse protein functions, and thus critically affects many essential biological processes. Critical for systematic study of the effects of PTMs is the ability to obtain recombinant proteins with defined and homogenous modifications. To this end, various synthetic and chemical biology approaches, including genetic code expansion and protein chemical modification methods, have been developed. These methods have proven effective for generating site-specific authentic modifications or structural mimics, and have demonstrated their value for in vitro and in vivo functional studies of diverse PTMs. This review will discuss recent advances in chemical biology strategies and their application to various PTM studies.
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Dong B, Yang A, Hao Q. THE ESTABLISHMENT OF COMPREHENSIVE EVALUATION PERIOPERATIVE EVALUATION SYSTEM AMONG ELDERLY PATIENTS. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.2804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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Yang A, Cheng N, Pu H, Liu S, Dai M, Zheng T, Bai Y. Occupational metal exposures, smoking and risk of diabetes and prediabetes. Occup Med (Lond) 2017; 67:217-223. [PMID: 27418044 PMCID: PMC5927150 DOI: 10.1093/occmed/kqw078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Metal exposure and tobacco smoking have been independently associated with diabetes, but no study has been conducted to investigate the interaction between them on the risk of diabetes. AIMS To investigate the effect of occupational exposure to metals, and potential effect modification by smoking, on the risk of diabetes and prediabetes in a cohort of Chinese male workers. METHODS We assessed metal exposure and tobacco smoking at baseline in the Jinchang Cohort of male workers. We used Poisson regression analyses to estimate the interaction between smoking and metal exposures based on occupations, which we grouped according to the measured urinary metal levels. RESULTS Among the 26008 study subjects, compared with non-smokers, the adjusted prevalence ratio (PR) for diabetes was 1.8 [95% confidence interval (CI) 1.3-2.4] for smokers of >40 pack-years. The adjusted PRs were 1.2 (95% CI 1.1-1.4) among mining/production workers and 2.7 (95% CI 2.4-3.0) among smelting/refining workers, both compared with office workers. There was significant effect modification under the additive model between smoking and metal exposure on the prevalence of diabetes (Pinteraction = 0.001), with an adjusted PR of 3.6 (95% CI 2.4-5.4) for those with >40 pack-years of smoking who had the highest metal exposures, whereas no significant interaction was observed for prediabetes. CONCLUSIONS Both exposure to metals and heavy smoking were associated with an increased prevalence of diabetes in this large cohort of male workers. There was also strong interaction between these two exposures in affecting diabetes risk that should be confirmed in future studies.
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Yang A, Juzwik J. Use of Nested and Real-Time PCR for the Detection of Ceratocystis fagacearum in the Sapwood of Diseased Oak Species in Minnesota. PLANT DISEASE 2017; 101:480-486. [PMID: 30677343 DOI: 10.1094/pdis-07-16-0990-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Oak wilt caused by Ceratocystis fagacearum is a significant disease of Quercus spp. in the eastern United States. Early and accurate detection of the pathogen is particularly important when disease control is planned. Nested and real-time polymerase chain reaction (PCR) methods utilizing fungal DNA extracted from sapwood drill shavings of red, bur, and white oak at different stages of disease development were compared with culture-based detection from sapwood. The pathogen was detected in all (n = 3) actively wilting branches of each of nine red oak trees using all three methods. The lowest detection rate (33% of assayed branches; 6 of 8 trees) for actively wilting branches was found for white oak using isolation while nested PCR had a branch detection rate of 100% (8 of 8 trees) and real-time PCR of 87% (8 of 8 trees) for the same samples. For both bur and white oak, the pathogen was not detected by isolation in branches over 1 year after their death but was detected using both PCR methods. Only the PCR assays detected the fungus in sapwood samples underlying remnants of sporulation mats (n = 21; 90%, nested and 62%, real-time) on red oak. These PCR methods offer several significant improvements for laboratory-based detection methods of C. fagacearum.
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Han S, Yang A, Lee S, Lee HW, Park CB, Park HS. Expanding the genetic code of Mus musculus. Nat Commun 2017; 8:14568. [PMID: 28220771 PMCID: PMC5321798 DOI: 10.1038/ncomms14568] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/13/2017] [Indexed: 01/17/2023] Open
Abstract
Here we report the expansion of the genetic code of Mus musculus with various unnatural amino acids including Nɛ-acetyl-lysine. Stable integration of transgenes encoding an engineered Nɛ-acetyl-lysyl-tRNA synthetase (AcKRS)/tRNAPyl pair into the mouse genome enables site-specific incorporation of unnatural amino acids into a target protein in response to the amber codon. We demonstrate temporal and spatial control of protein acetylation in various organs of the transgenic mouse using a recombinant green fluorescent protein (GFPuv) as a model protein. This strategy will provide a powerful tool for systematic in vivo study of cellular proteins in the most commonly used mammalian model organism for human physiology and disease.
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Le L, Pickett H, Ho J, Thavapalachandran S, Farraha M, Yang A, Yang S, dos Remedios C, Kizana E, Chong J. Telomerase Reverse Transcriptase Over-Expression Enhances Human Cardiac Progenitor Cell Cardiac Regeneration after Myocardial Infarction. Heart Lung Circ 2017. [DOI: 10.1016/j.hlc.2017.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang X, Feng Y, Bajaj G, Gupta M, Agrawal S, Yang A, Park J, Lestini B, Roy A. Quantitative Characterization of the Exposure-Response Relationship for Cancer Immunotherapy: A Case Study of Nivolumab in Patients With Advanced Melanoma. CPT Pharmacometrics Syst Pharmacol 2017; 6:40-48. [PMID: 28019090 PMCID: PMC5270290 DOI: 10.1002/psp4.12133] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/02/2016] [Indexed: 12/14/2022] Open
Abstract
To inform the benefit-risk assessment of nivolumab in patients with advanced melanoma, analyses of efficacy and safety exposure-response (E-R) relationships were conducted with data from patients with advanced melanoma enrolled in two clinical studies (phase I and phase III) who received nivolumab 0.1-10.0 mg/kg every 2 weeks. E-R efficacy analyses were performed by relating the nivolumab time-averaged concentration after the first dose (Cavg1 ) to two endpoints: RECIST objective response (OR) and overall survival (OS). E-R safety analyses characterized the relationship between nivolumab Cavg1 and the hazard of all-causality adverse events leading to discontinuation or death (AE-DC/D). Nivolumab exposure represented by Cavg1 was not a significant predictor of OR, OS, or the hazard of AE-DC/D. E-R efficacy and safety relationships were relatively flat over the exposure range.
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48
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Yang A, Ha S, Ahn J, Kim R, Kim S, Lee Y, Kim J, Söll D, Lee HY, Park HS. A chemical biology route to site-specific authentic protein modifications. Science 2016; 354:623-626. [PMID: 27708052 PMCID: PMC5135561 DOI: 10.1126/science.aah4428] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022]
Abstract
Many essential biological processes are controlled by posttranslational protein modifications. The inability to synthetically attain the diversity enabled by these modifications limits functional studies of many proteins. We designed a three-step approach for installing authentic posttranslational modifications in recombinant proteins. We first use the established O-phosphoserine (Sep) orthogonal translation system to create a Sep-containing recombinant protein. The Sep residue is then dephosphorylated to dehydroalanine (Dha). Last, conjugate addition of alkyl iodides to Dha, promoted by zinc and copper, enables chemoselective carbon-carbon bond formation. To validate our approach, we produced histone H3, ubiquitin, and green fluorescent protein variants with site-specific modifications, including different methylations of H3K79. The methylated histones stimulate transcription through histone acetylation. This approach offers a powerful tool to engineer diverse designer proteins.
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Yang A, Yu X, Zheng A, James AT. Rebalance between 7S and 11S globulins in soybean seeds of differing protein content and 11SA4. Food Chem 2016; 210:148-55. [PMID: 27211633 DOI: 10.1016/j.foodchem.2016.04.095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/31/2016] [Accepted: 04/20/2016] [Indexed: 11/22/2022]
Abstract
Protein content and globulin subunit composition of soybean seeds affect the quality of soy foods. In this proteomic study, the protein profile of soybean seeds with high (∼45.5%) or low (∼38.6%) protein content and with or without the glycinin (11S) subunit 11SA4 was examined. 44 unique proteins and their homologues were identified and showed that both protein content and 11SA4 influenced the abundance of a number of proteins. The absence of 11SA4 exerted a greater impact than the protein content, and led to a decreased abundance of glycinin G2/A2B1 and G5/A5A4B3 subunits, which resulted in lower total 11S with a concomitant higher total β-conglycinin (7S). Low protein content was associated with higher glycinin G3/A1aB1b and lower glycinin G4/A5A4B3. Using the proteomic approach, it was demonstrated that 11SA4 deficiency induced compensatory accumulation of 7S globulins and led to a similar total abundance for 7S+11S irrespective of protein content or 11SA4.
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Josefowicz SZ, Shimada M, Armache A, Li CH, Miller RM, Lin S, Yang A, Dill BD, Molina H, Park HS, Garcia BA, Taunton J, Roeder RG, Allis CD. Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription. Mol Cell 2016; 64:347-361. [PMID: 27768872 PMCID: PMC5081221 DOI: 10.1016/j.molcel.2016.09.026] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/12/2016] [Accepted: 09/20/2016] [Indexed: 02/05/2023]
Abstract
The inflammatory response requires coordinated activation of both transcription factors and chromatin to induce transcription for defense against pathogens and environmental insults. We sought to elucidate the connections between inflammatory signaling pathways and chromatin through genomic footprinting of kinase activity and unbiased identification of prominent histone phosphorylation events. We identified H3 serine 28 phosphorylation (H3S28ph) as the principal stimulation-dependent histone modification and observed its enrichment at induced genes in mouse macrophages stimulated with bacterial lipopolysaccharide. Using pharmacological and genetic approaches, we identified mitogen- and stress-activated protein kinases (MSKs) as primary mediators of H3S28ph in macrophages. Cell-free transcription assays demonstrated that H3S28ph directly promotes p300/CBP-dependent transcription. Further, MSKs can activate both signal-responsive transcription factors and the chromatin template with additive effects on transcription. Specific inhibition of MSKs in macrophages selectively reduced transcription of stimulation-induced genes. Our results suggest that MSKs incorporate upstream signaling inputs and control multiple downstream regulators of inducible transcription.
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