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Wu J, An K, Fang DD, Lu J, Hu L, Wang J, Zhang K, Xia Y, Ding C, Chen S, Wei S. Abstract 474: Preclinical development of an oral selective estrogen receptor degrader (SERD) TFX06 for the treatment of ER+HER2− breast cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Breast cancer (BC) has recently surpassed lung cancer to become the most commonly diagnosed cancer in women worldwide. Approximately 70% of BC was ER+, in which estrogen receptor α (ERα, encoded by ESR1 gene) drives dysregulated cell proliferation. In clinic, ER+ BC has been effectively treated by endocrine therapy targeting estrogen or ER. As the first approved ERα degrader, fulvestrant has proven to be effective for locally advanced or metastatic BC. However, its clinical utilization is hampered by inconvenience of intramuscular injection, as well as its poor PK/PD profile and limited efficacy, especially in the patient population that developed ESR1 mutation-conferring drug resistance after the earlier line of treatment with an aromatase inhibitor. Thus, developing an oral and more effective therapy for ER+ BC remains an unmet medical need. We report herein discovery and preclinical investigation of a novel orally bioavailable SERD TFX06. TFX06 demonstrated potent binding affinity to ERα with a Ki of 0.10 nM and preferably antagonized ERα to ERβ with an IC50 value of 0.086 nM and 2.83 nM, respectively. TFX06 potently induced ERα degradation in ER+ BC cells and substantially inhibited cell proliferation in BC cell lines with ER wild type (WT), and MCF-7 cells expressing Y537S or D538G mutants. Oral administration of TFX06 demonstrated impressive antitumor efficacy in ER WT (TGI = 101%) and ER D538G-expressing (TGI = 99%) MCF-7 cell line-derived xenograft (CDX) models in mice. Similarly, in an ER+ BC patient-derived xenograft (PDX) model (HCI-013) with ER Y537S mutation, TFX06 also exerted excellent antitumor activity (TGI = 99%). Furthermore, TFX06 in combination with palbociclib achieved synergistic activity in MCF-7 CDX model. Moreover, TFX06 exhibited an excellent correlation between systemic/local drug exposure, pharmacodynamic modulation (i.e., ERα downregulation) and antitumor activity. Collectively, these findings demonstrate that TFX06 is a novel, orally bioavailable SERD. TFX06 demonstrates substantial antitumor activity in both in vitro and in vivo preclinical tumor models, including those expressing ESR1 mutations, through downregulation of ERα. The preclinical data warranted the clinical evaluation of TFX06 in human with an IND application submitted to the China NPMA.
Citation Format: Jinping Wu, Ke An, Douglas D. Fang, Jianyu Lu, Lihong Hu, Jing Wang, Kaili Zhang, Yuanfeng Xia, Charles Ding, Shuhui Chen, Sha Wei. Preclinical development of an oral selective estrogen receptor degrader (SERD) TFX06 for the treatment of ER+HER2− breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 474.
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Venkatakrishnan S, Fancher CM, Ziatdinov M, Vasudevan RK, Saleeby K, Haley J, Yu D, An K, Plotkowski A. Adaptive Sampling for Accelerating Neutron Diffraction-Based Strain Mapping. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2023. [DOI: 10.1088/2632-2153/acc512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Abstract
Neutron diffraction is a useful technique for mapping residual strains in dense metal objects. The technique works by placing an object in the path of a neutron beam, measuring the diffracted signals and inferring the local lattice strain values from the measurement. In order to map the strains across the entire object, the object is stepped one position at a time in the path of the neutron beam, typically in raster order, and at each position a strain value is estimated. Typical dwell times at neutron diffraction instruments result in an overall measurement that can take several hours to map an object that is several tens of centimeters in each dimension at a resolution of a few millimeters, during which the end users do not have an estimate of the global strain features and are at risk of incomplete information in case of instruments outages. In this paper, we propose an object adaptive sampling strategy to measure the significant points first. We start with a small initial uniform set of measurement points across the object to be mapped, compute the strain in those positions and use a machine learning technique to predict the next position to measure in the object. Specifically,we use a Bayesian optimization based on a Gaussian process regression method to infer the underlying strain field from a sparse set of measurements and predict the next most informative positions to measure based on estimates of the mean and variance in the strain fields estimated from the previously measured points. We demonstrate our real-time measure-infer-predict workflow on additively manufactured steel parts- demonstrating that we can get an accurate strain estimate even with 30-40% of the typical number of measurements - leading the path to faster strain mapping with useful real-time feedback. We emphasize that the proposed method is general and can be used for fast mapping of other material properties such as phase fractions from time-consuming point-wise neutron measurements.
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Gao Z, Huang D, Chen H, Yang Y, An K, Ding C, Yuan Z, Zhai Z, Niu P, Gao Q, Cai J, Zeng Q, Wang Y, Hong Y, Rong W, Huang W, Lei F, Wang X, Chen S, Zhao X, Bai Y, Gu J. Development and validation of postoperative circulating tumor DNA combined with clinicopathological risk factors for recurrence prediction in patients with stage I-III colorectal cancer. J Transl Med 2023; 21:63. [PMID: 36717891 PMCID: PMC9887832 DOI: 10.1186/s12967-023-03884-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/10/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) detection following curative-intent surgery could directly reflect the presence of minimal residual disease, the ultimate cause of clinical recurrence. However, ctDNA is not postoperatively detected in ≥ 50% of patients with stage I-III colorectal cancer (CRC) who ultimately recur. Herein we sought to improve recurrence risk prediction by combining ctDNA with clinicopathological risk factors in stage I-III CRC. METHODS Two independent cohorts, both consisting of early-stage CRC patients who underwent curative surgery, were included: (i) the discovery cohort (N = 124) with tumor tissues and postoperative plasmas for ctDNA determination; and (ii) the external validation cohort (N = 125) with available ctDNA results. In the discovery cohort, somatic variations in tumor tissues and plasmas were determined via a 733-gene and 127-gene next-generation sequencing panel, respectively. RESULTS In the discovery cohort, 17 of 108 (15.7%) patients had detectable ctDNA. ctDNA-positive patients had a significantly high recurrence rate (76.5% vs. 16.5%, P < 0.001) and short recurrence-free survival (RFS; P < 0.001) versus ctDNA-negative patients. In addition to ctDNA status, the univariate Cox model identified pathologic stage, lymphovascular invasion, nerve invasion, and preoperative carcinoembryonic antigen level associated with RFS. We combined the ctDNA and clinicopathological risk factors (CTCP) to construct a model for recurrence prediction. A significantly higher recurrence rate (64.7% vs. 8.1%, P < 0.001) and worse RFS (P < 0.001) were seen in the high-risk patients classified by the CTCP model versus those in the low-risk patients. Receiver operating characteristic analysis demonstrated that the CTCP model outperformed ctDNA alone at recurrence prediction, which increased the sensitivity of 2 year RFS from 49.6% by ctDNA alone to 87.5%. Harrell's concordance index, calibration curve, and decision curve analysis also suggested that the CTCP model had good discrimination, consistency, and clinical utility. These results were reproduced in the validation cohort. CONCLUSION Combining postoperative ctDNA and clinical risk may better predict recurrence than ctDNA alone for developing a personalized postoperative management strategy for CRC.
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Tan R, You Q, Cui J, Wang M, Song N, An K, Lin L, Adu-Amankwaah J, Yuan J, Sun H. Sodium houttuyfonate against cardiac fibrosis attenuates isoproterenol-induced heart failure by binding to MMP2 and p38. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 109:154590. [PMID: 36610170 DOI: 10.1016/j.phymed.2022.154590] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/17/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Heart failure (HF), caused by stress cardiomyopathy, is a major cause of mortality. Cardiac fibrosis is an essential structural remodeling associated with HF; therefore, preventing cardiac fibrosis is crucial to decelerating the progression of HF. Sodium houttuyfonate (SH), an extract of Houttuynia cordata, has a potent therapeutic effect on hypoxic cardiomyocytes in a myocardial infarction model. PURPOSE To investigate the preventative and therapeutic effects of SH during isoproterenol (ISO)-induced HF and explore the pharmacological mechanism of SH in alleviating HF. METHODS We analyzed the overlapping target genes between SH and cardiac fibrosis or HF using a network pharmacology analytical method. We verified the suppressive effect of SH on ISO-induced proliferation and activation of cardiac fibroblasts by immunohistochemical staining and histological analysis in an isoproterenol-induced HF mouse model. Additionally, we investigated the effect of SH by evaluating fibrosis and cardiac remodeling markers. To further decipher the pharmacological mechanism of SH against cardiac fibrosis and HF, we performed a molecular docking analysis between SH and hub common target genes. RESULTS There were 20 overlapping target genes between SH and cardiac fibrosis and 32 overlapping target genes between SH and HF. The 16 common target genes of SH against cardiac fibrosis and HF included MMP2 (matrix metalloproteinase 2), and p38. SH significantly inhibited the ISO- or TGF-β-induced expression of Col1α (collagen 1), α-SMA (smooth muscle actin), MMP2, TIMP2 (tissue inhibitor of metalloproteinase 2), TGF-β (transforming growth factor), and Smad2 phosphorylation. Moreover, both ISO- and TGF-β-induced p38 phosphorylation was inhibited. Molecular docking analysis showed that SH forms a stable complex with MMP2 and p38. CONCLUSIONS In addition to protecting cardiomyocytes, SH directly inhibits cardiac fibroblast activation and proliferation by binding to MMP2 and p38, subsequently delaying cardiac fibrosis and HF progression. Our prevention- and intervention-based approaches in this study showed that SH inhibited the development of stress cardiomyopathy-mediated cardiac fibrosis and HF when SH was administered before or after the initiation of cardiac stress.
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An K, Zhu X, Yan J, Xu P, Hu L, Bai C. A systematic study on the binding affinity of SARS-CoV-2 spike protein to antibodies. AIMS Microbiol 2022; 8:595-611. [PMID: 36694585 PMCID: PMC9834082 DOI: 10.3934/microbiol.2022038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
The COVID-19 pandemic has caused a worldwide health crisis and economic recession. Effective prevention and treatment methods are urgently required to control the pandemic. However, the emergence of novel SARS-CoV-2 variants challenges the effectiveness of currently available vaccines and therapeutic antibodies. In this study, through the assessment of binding free energies, we analyzed the mutational effects on the binding affinity of the coronavirus spike protein to neutralizing antibodies, patient-derived antibodies, and artificially designed antibody mimics. We designed a scoring method to assess the immune evasion ability of viral variants. We also evaluated the differences between several targeting sites on the spike protein of antibodies. The results presented herein might prove helpful in the development of more effective therapies in the future.
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An K, Zhu X, Bai C. The Nature of Functional Features of Different Classes of G-Protein-Coupled Receptors. BIOLOGY 2022; 11:biology11121839. [PMID: 36552350 PMCID: PMC9775959 DOI: 10.3390/biology11121839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
G-protein-coupled receptors (GPCRs) are a critical family in the human proteome and are involved in various physiological processes. They are also the most important drug target, with approximately 30% of approved drugs acting on such receptors. The members of the family are divided into six classes based on their structural and functional characteristics. Understanding their structural-functional relationships will benefit us in future drug development. In this article, we investigate the features of protein function, structure, and energy that describe the dynamics of the GPCR activation process between different families. GPCRs straddle the cell membrane and transduce signals from outside the membrane into the cell. During the process, the conformational change in GPCRs that is activated by the binding of signal molecules is essential. During the binding process, different types of signal molecules result in different signal transfer efficiencies. Therefore, the GPCR classes show a variety of structures and activation processes. Based on the experimental crystal structures, we modeled the activation process of the β2 adrenergic receptor (β2AR), glucagon receptor (GCGR), and metabotropic glutamate receptor 2 (mGluR2), which represent class A, B, and C GPCRs, respectively. We calculated their activation free-energy landscapes and analyzed the structure-energy-function relationship. The results show a consistent picture of the activation mechanisms between different types of GPCRs. This could also provide us a way to understand other signal transduction proteins.
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Peterson NE, Fancher CM, Frontzek M, Bunn J, Payzant A, An K, Agnew S. Quantitative texture analysis at the WAND 2 and HIDRA diffractometers. J Appl Crystallogr 2022. [DOI: 10.1107/s1600576722009013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Data collection and analysis strategies have been developed for efficient and reliable crystallographic texture measurements at two recently upgraded neutron diffractometers: the Wide Angle Neutron Diffractometer Squared (WAND2) and the High Intensity Diffractometer for Residual Stress Analysis (HIDRA) at the High Flux Isotope Reactor located at Oak Ridge National Laboratory. These methods are demonstrated using measurements on a variety of textured samples, including multi-phase steel composites and polycrystalline calcite (CaCO3). Reference measurements were also made at VULCAN, the engineering diffractometer located at the Spallation Neutron Source. The texture data obtained on the different instruments are in agreement, and WAND2 is more time efficient than HIDRA. Two analysis methods were investigated, single-peak fitting to obtain individual pole figures for inversion and Rietveld texture analysis using MAUD. The impact of the differences between the various textures obtained was evaluated through the calculation of diffraction elastic constants, which is one application of the texture data collected. Both instruments were found to provide texture data that are suitable for complementing other analyses, such as residual stress mapping.
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Xu W, Li Y, Li N, Sun Y, Wang C, An K. Combination of thoracic epidural analgesia with patient-controlled intravenous analgesia versus traditional thoracic epidural analgesia for postoperative analgesia and early recovery of laparotomy: a prospective single-centre, randomized controlled trial. BMC Anesthesiol 2022; 22:341. [PMID: 36344910 PMCID: PMC9639277 DOI: 10.1186/s12871-022-01891-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022] Open
Abstract
Background Thoracic epidural analgesia (TEA) has always been the first choice for postoperative pain treatment, but associated complications and contraindications may limit its use. Our study put forward a new analgesic strategy that combines TEA with patient controlled intravenous analgesia (PCIA) to optimize TEA. Methods Patients undergoing laparotomy were enrolled in this prospective randomized study. Patients were randomized to one of two groups: TEA/PCIA group and TEA group. Patients in TEA/PCIA group received TEA in the day of surgery and the first postoperative day and PCIA continued to use until the third postoperative day. Patients in TEA group received TEA for three days postoperatively. Visual analogue scale (VSA) pain scores at rest and on movement at 6, 24,48,72 h after surgery were recorded. In addition, the incidence of inadequate analgesia, adverse events, time to first mobilization, time to pass first flatus, time of oral intake recovery, time of urinary catheter removal, postoperative length of hospital stay, cumulative opioid consumption, and the overall cost were compared between the two groups. We examined VAS pain scores using repeated measures analysis of variance; P < 0.05 was considered as statistically significant. Results Eighty-six patients were analysed (TEA/PCIA = 44, TEA = 42). The mean VAS pain scores at rest and on movement in TEA/PCIA group were lower than TEA group, with a significant difference on movement and 48 h postoperatively (P < 0.05). The time to first mobilization and pass first flatus were shorter in TEA/PCIA group (P < 0.05). Other measurement showed no statistically significant differences. Conclusions The combination of TEA with PCIA for patients undergoing laparotomy, can enhance postoperative pain control and facilitate early recovery without increasing the incidence of adverse effects and overall cost of hospitalization. Trial registration Chinese Clinical Trial Registry(www.chictr.org.cn), ChiCTR 1,800,020,308, 13 December 2018.
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Ji W, An K, Wang C, Wang S. Bioinformatics analysis of diagnostic biomarkers for Alzheimer's disease in peripheral blood based on sex differences and support vector machine algorithm. Hereditas 2022; 159:38. [PMID: 36195955 PMCID: PMC9531459 DOI: 10.1186/s41065-022-00252-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022] Open
Abstract
Background The prevalence of Alzheimer's disease (AD) varies based on gender. Due to the lack of early stage biomarkers, most of them are diagnosed at the terminal stage. This study aimed to explore sex-specific signaling pathways and identify diagnostic biomarkers of AD. Methods Microarray dataset for blood was obtained from the Gene Expression Omnibus (GEO) database of GSE63060 to conduct differentially expressed genes (DEGs) analysis by R software limma. Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene set enrichment analysis (GSEA) were conducted. Immune checkpoint gene expression was compared between females and males. Using CytoHubba, we identified hub genes in a protein–protein interaction network (PPI). Then, we evaluated their distinct effectiveness using unsupervised hierarchical clustering. Support vector machine (SVM) and ten-fold cross-validation were used to further verify these biomarkers. Lastly, we confirmed our findings by using another independent dataset. Results A total of 37 female-specific DEGs and 27 male-specific DEGs were identified from GSE63060 datasets. Analyses of enrichment showed that female-specific DEGs primarily focused on energy metabolism, while male-specific DEGs mostly involved in immune regulation. Three immune-checkpoint-relevant genes dysregulated in males. In females, however, these eight genes were not differentially expressed. SNRPG, RPS27A, COX7A2, ATP5PO, LSM3, COX7C, PFDN5, HINT1, PSMA6, RPS3A and RPL31 were regarded as hub genes for females, while SNRPG, RPL31, COX7C, RPS27A, RPL35A, RPS3A, RPS20 and PFDN5 were regarded as hub genes for males. Thirteen hub genes mentioned above was significantly lower in both AD and mild cognitive impairment (MCI). The diagnostic model of 15-marker panel (13 hub genes with sex and age) was developed. Both the training dataset and the independent validation dataset have area under the curve (AUC) with a high value (0.919, 95%CI 0.901–0.929 and 0.803, 95%CI 0.789–0.826). Based on GSEA for hub genes, they were associated with some aspects of AD pathogenesis. Conclusion DEGs in males and females contribute differently to AD pathogenesis. Algorithms combining blood-based biomarkers may improve AD diagnostic accuracy, but large validation studies are needed. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00252-x.
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Park KW, Kim J, Seo J, Moon S, Jeong K, An K. Entropic comparison of Landau-Zener and Demkov interactions in the phase space of a quadrupole billiard. CHAOS (WOODBURY, N.Y.) 2022; 32:103101. [PMID: 36319274 DOI: 10.1063/5.0101495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
We investigate two types of avoided crossings in a chaotic billiard within the framework of information theory. The Shannon entropy in the phase space for the Landau-Zener interaction increases as the center of the avoided crossing is approached, whereas for the Demkov interaction, the Shannon entropy decreases as the center of avoided crossing is passed by with an increase in the deformation parameter. This feature can provide a new indicator for scar formation. In addition, it is found that the Fisher information of the Landau-Zener interaction is significantly larger than that of the Demkov interaction.
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Wang W, Xin X, An K, Chen Y, Zhao Z, Tan J, Yang D, Jiang Z. Bioinspired construction of g-C3N4 isotype heterojunction on carbonized poly(tannic acid) nanorod surface with multistep electron transfer path. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sihota T, Chen Y, Nagelberg A, Chow J, Shi R, An K, Lockwood W. EP16.03-039 Characterizing SHPRH as a Novel Tumor Suppressor Gene in Lung Adenocarcinoma. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.1100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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An K, Gu J. [Concept of lateral lymph nodes in rectal cancer and controversy over lateral lymph node dissection]. ZHONGHUA WEI CHANG WAI KE ZA ZHI = CHINESE JOURNAL OF GASTROINTESTINAL SURGERY 2022; 25:694-698. [PMID: 35970803 DOI: 10.3760/cma.j.cn441530-20220725-00326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lateral lymph node (LLN) metastasis in locally advanced rectal cancer (LARC) is associated with patient prognosis. However, the role of lateral lymph node dissection (LLND) remains controversial. The concept of LLN and the exact definition of LLND have been inconsistently reported in the literatures. The treatment strategy for LARC has differed between the East and the West. The Japanese doctors advocates total mesorectal excision (TME) with LLND for LARC, but less neoadjuvant radiochemotherapy (NARC). European and Americans prefer NARC plus TME, and do not recommend LLND. So far, only the Japanese Statute of Colorectal Cancer has a clear definition of the concept of LLN and LLND. The use of TME plus LLND for LARC is not supported by high level evidences. In today's high-speed development of minimally invasive surgery, the proper selection of standardized surgical methods for LARC requires the joint efforts of scholars from the East and the West to conduct multicenter high-grade clinical trials to select the best treatment option for patients with LARC.
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Gao Y, Zhao H, An K, Liu Z, Hai L, Li R, Zhou Y, Zhao W, Jia Y, Wu N, Li L, Ying J, Wang J, Xu B, Wu Z, Tong Z, He J, Sun Y. Whole-genome bisulfite sequencing analysis of circulating tumour DNA for the detection and molecular classification of cancer. Clin Transl Med 2022; 12:e1014. [PMID: 35998020 PMCID: PMC9398227 DOI: 10.1002/ctm2.1014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Background Cancer cell–specific variation and circulating tumour DNA (ctDNA) methylation are promising biomarkers for non‐invasive cancer detection and molecular classification. Nevertheless, the applications of ctDNA to the early detection and screening of cancer remain highly challenging due to the scarcity of cancer cell–specific ctDNA, the low signal‐to‐noise ratio of DNA variation, and the lack of non‐locus‐specific DNA methylation technologies. Methods We enrolled three cohorts of breast cancer (BC) patients from two hospitals in China (BC: n = 123; healthy controls: n = 40). We developed a ctDNA whole‐genome bisulfite sequencing technology employing robust trace ctDNA capture from up to 200 μL plasma, mini‐input (1 ng) library preparation, unbiased genome‐wide coverage and comprehensive computational methods. Results A diagnostic signature comprising 15 ctDNA methylation markers exhibited high accuracy in the early (area under the curve [AUC] of 0.967) and advanced (AUC of 0.971) BC stages in multicentre patient cohorts. Furthermore, we revealed a ctDNA methylation signature that discriminates estrogen receptor status (Training set: AUC of 0.984 and Test set: AUC of 0.780). Different cancer types, including hepatocellular carcinoma and lung cancer, could also be well distinguished. Conclusions Our study provides a toolset to generate unbiased whole‐genome ctDNA methylomes with a minimal amount of plasma to develop highly specific and sensitive biomarkers for the early diagnosis and molecular subtyping of cancer.
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Li W, Lin K, Yan Y, Yu C, Cao Y, Chen X, Wang CW, Kato K, Chen Y, An K, Zhang Q, Gu L, Li Q, Deng J, Xing X. A Seawater-Corrosion-Resistant and Isotropic Zero Thermal Expansion (Zr,Ta)(Fe,Co) 2 Alloy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2109592. [PMID: 35772730 DOI: 10.1002/adma.202109592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Zero thermal expansion (ZTE) alloys as dimensionally stable materials are usually challenged by harsh environmental erosion, since ZTE and corrosion resistance are generally mutually exclusive. Here, a high-performance alloy, Zr0.8 Ta0.2 Fe1.7 Co0.3 , is reported, that shows isotropic ZTE behavior (αl = 0.21(2) × 10-6 K-1 ) in a wide temperature range of 5-360 K, high corrosion resistance in a seawater-like solution compared with classic Invar and stainless Invar, and excellent cyclic thermal and structural stabilities. Such stabilities are attributed to the cubic symmetry, the controllable magnetic order, and the spontaneously formed passive film with Ta and Zr chemical modifications. The results are evidenced by X-ray/neutron diffraction, microscopy, spectroscopy, and electrochemistry investigations. Such multiple stabilities have the potential to broaden the robust applications of ZTE alloys, especially in marine services.
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Yu Z, Lv Y, Huang F, Zhang F, Shi Q, An K, Fan T, Li G, Wang J. Photoatalytic Degradation of Organic Pollutants in Water Under Visible Light by NH
2
‐MIL‐125(Ti‐Zr)@BiOCl
x
I
1‐
x
Composite Photocatalyst. ChemistrySelect 2022. [DOI: 10.1002/slct.202201958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Tam A, Kulkarni J, An K, Li L, Dorscheid DR, Singhera GK, Bernatchez P, Reid G, Chan K, Witzigmann D, Cullis PR, Sin DD, Lim CJ. Lipid nanoparticle formulations for optimal RNA-based topical delivery to murine airways. Eur J Pharm Sci 2022; 176:106234. [PMID: 35688311 DOI: 10.1016/j.ejps.2022.106234] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Lipid nanoparticles (LNP) have been successfully used as a platform technology for delivering nucleic acids to the liver. To broaden the application of LNPs in targeting non-hepatic tissues, we developed LNP-based RNA therapies (siRNA or mRNA) for the respiratory tract. Such optimized LNP systems could offer an early treatment strategy for viral respiratory tract infections such as COVID-19. METHODS We generated a small library of six LNP formulations with varying helper lipid compositions and characterized their hydrodynamic diameter, size distribution and cargo entrapment properties. Next, we screened these LNP formulations for particle uptake and evaluated their potential for transfecting mRNA encoding green fluorescence protein (GFP) or SARS-CoV2 nucleocapsid-GFP fusion reporter gene in a human airway epithelial cell line in vitro. Following LNP-siGFP delivery, GFP protein knockdown efficiency was assessed by flow cytometry to determine %GFP+ cells and median fluorescence intensity (MFI) for GFP. Finally, lead LNP candidates were validated in Friend leukemia virus B (FVB) male mice via intranasal delivery of an mRNA encoding luciferase, using in vivo bioluminescence imaging. RESULTS Dynamic light scattering revealed that all LNP formulations contained particles with an average diameter of <100 nm and a polydispersity index of <0.2. Human airway epithelial cell lines in culture internalized LNPs with differential GFP transfection efficiencies (73-97%). The lead formulation LNP6 entrapping GFP or Nuc-GFP mRNA demonstrated the highest transfection efficiency (97%). Administration of LNP-GFP siRNA resulted in a significant reduction of GFP protein expression. For in vivo studies, intranasal delivery of LNPs containing helper lipids (DSPC, DOPC, ESM or DOPS) with luciferase mRNA showed significant increase in luminescence expression in nasal cavity and lungs by at least 10 times above baseline control. CONCLUSION LNP formulations enable the delivery of RNA payloads into human airway epithelial cells, and in the murine respiratory system; they can be delivered to nasal mucosa and lower respiratory tract via intranasal delivery. The composition of helper lipids in LNPs crucially modulates transfection efficiencies in airway epithelia, highlighting their importance in effective delivery of therapeutic products for airways diseases.
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Gu J, Lei F, Wang X, Chen H, Huang W, He X, Hong Y, Zeng Q, Wang Y, Gao Q, Yuan Z, Niu P, Huang D, Gao Z, Ding C, Zhai Z, An K, Chen S, Zhao X, Bai Y. Recurrence risk stratification model for patients with stage I-III colorectal cancer based on clinicopathological and postoperative ctDNA predictors. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e15511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15511 Background: The aim of this study was to propose a new kind of recurrence risk classification and further establish a prognostic model for resected stage I-III colorectal cancer (CRC). Methods: From 2017 to 2020, 142 patients diagnosed with stage I-III CRC at Peking University Shougang Hospital were recruited for this study. Tissues and paired white blood cells were analyzed with a 733-gene NGS panel, and peripheral plasma obtained 7-10 days after surgery was analyzed with a 127-gene ultra-deep target panel in a CLIA-certified laboratory. The relationship between the postoperative ctDNA status, clinicopathological features and recurrence-free survival (RFS) was identified by log-rank test and Cox regression analysis. Results: In total, 108 patients successfully completed both tissue and postoperative plasma NGS tests, of which 17 patients were postoperatively positive for ctDNA (tumor-informed, ≥1 somatic mutation). Postoperative ctDNA positivity was independently associated with poorer RFS (HR = 8.4, P < 0.0001). Postoperative recurrence rates were significantly higher in ctDNA-positive patients than ctDNA-negative patients (76.5% vs 16.5%, P < 0.0001). Univariate analysis showed that, in addition to ctDNA status, stage, vascular invasion, neural invasion, and preoperative CEA were all significantly associated with worse RFS (P < 0.05). Furthermore, in a COX regression model, the contribution of these clinicopathological factors to RFS has been adjusted. The model showed good discrimination [the concordance index (c-index): 0.811] of recurrence. Clinically high-risk groups according to clinicopathological risk model had significantly poorer RFS than low-risk groups (HR = 10.6, P < 0.001). In the clinicopathological high-risk group, ctDNA-positive patients can still further differentiate the higher risk of recurrence (HR = 3.7, P = 0.0012). There were similar trends in the clinicopathological low-risk group (HR = 6.1, P = 0.066). Combining the clinicopathological model and ctDNA, patients with either clinicopathological high-risk or ctDNA-positive had a significantly poorer RFS, compared with both clinicopathological low-risk and ctDNA-negative (HR = 12.9, P < 0.0001). Conclusions: Postoperative ctDNA can independently predict the risk of recurrence in stage I-III CRC. Combining clinicopathological factors and ctDNA showed superiority for recurrence risk stratification over either alone. This recurrence risk stratification model may serve as a useful clinical tool to help clinicians determine individualized treatment plans for stage I-III CRC patients. However, the model still needs further external cohort validation.
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Li Z, Guan B, Xia F, Nie J, Li W, Ma L, Li W, Zhou L, Wang Y, Tian H, Luo J, Chen Y, Frost M, An K, Liu X. High-Entropy Perovskite as a High-Performing Chromium-Tolerant Cathode for Solid Oxide Fuel Cells. ACS APPLIED MATERIALS & INTERFACES 2022; 14:24363-24373. [PMID: 35576580 DOI: 10.1021/acsami.2c03657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To achieve chromium tolerance and high performance, a new series of high-entropy perovskites (HEPs) are investigated as cathode materials for solid oxide fuel cells (SOFCs). Multiple rare-earth, alkaline-earth, and high-order transition metal elements are used for the A-site of this ABO3 structure. A pure phase is achieved through the designed combination of different elements in seven out of eight candidates. Due to the retaining of alkaline-earth elements Sr and/or Ba, the electrical conductivities of these HEPs are in the order of 100 S/cm at 550-700 °C, a value that can practically eliminate the electronic resistance of the porous cathode. Three out of eight candidates show similar or better performance than the (La0.6Sr0.4)(Co0.2Fe0.8)O3-δ (LSCF) benchmark. It is found that A-site elements can cast a substantial influence on the overall performance even with a change as small as 10% of the total cations. It seems that each element has its individual "phenomenal activity" that can be transferred from one candidate to the other in the general setting of the perovskite structure, leading to the best candidate by using the three most active elements simultaneously at the A-site. Excellent Cr tolerance has been observed on the (La0.2Sr0.2Pr0.2Y0.2Ba0.2)Co0.2Fe0.8O3-δ sample, showing degradation of only 0.25%/kh during a 41 day operation in the presence of Cr, while LSCF increases by 100% within the first day in the same condition. X-ray photoelectron spectroscopy discovers no Sr segregation as LSCF is found in this HEP; rather, the active element Y takes more A-sites on the outermost layer after long-term operation.
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An K, Stoica AD, Huegle T, Lin JYY, Graves V. MENUS-Materials engineering by neutron scattering. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:053911. [PMID: 35649786 DOI: 10.1063/5.0089783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Materials engineering by neutron scattering (MENUS) at the second target station will be a transformational high-flux, versatile, multiscale materials engineering diffraction beamline with unprecedented new capabilities for the study of complex materials and structures. It will support both fundamental and applied materials research in a broad range of fields. MENUS will combine unprecedented long-wavelength neutron flux and unique detector coverage to enable real-time studies of complex structural and functional materials under external stimuli. The incorporated small angle neutron scattering and transmission/imaging capabilities will extend its sensitivity to larger length scales and higher spatial resolution. Multimodal MENUS will provide crystallographic and microstructure data to the materials science and engineering community to understand lattice strain/phase transition/microstructure/texture evolution in three orthogonal directions in complex material systems under combined extreme applied conditions. The capabilities of MENUS will open new scientific opportunities and meet the research needs for science challenges to enable studies of a range of phenomena and answer the key questions in material design/exploration, advanced material processing, transformative manufacturing, and material operations of national impacts in our daily life.
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Shi D, An K, Zhang H, Xu P, Bai C. Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines. ENTROPY 2022; 24:e24050620. [PMID: 35626506 PMCID: PMC9140642 DOI: 10.3390/e24050620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 12/14/2022]
Abstract
Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but also related to the conformational transition dynamics and the corresponding energy profiles. With the rapid development of crystallographic techniques, the spatial scale of resolved structures is reaching up to thousands of residues, and the concomitant conformational changes become more and more complicated, posing a great challenge for computational biology research. Previously, a coarse-grained (CG) model aiming at conformational free energy evaluation was developed and showed excellent ability to reproduce the energy profiles by accurate electrostatic interaction calculations. In this study, we extended the application of the CG model to a series of large-scale protein machine systems. The spike protein trimer of SARS-CoV-2, ATP citrate lyase (ACLY) tetramer, and P4-ATPases systems were carefully studied and discussed as examples. It is indicated that the CG model is effective to depict the energy profiles of the conformational pathway between two endpoint structures, especially for large-scale systems. Both the energy change and energy barrier between endpoint structures provide reasonable mechanism explanations for the associated biological processes, including the opening of receptor binding domain (RBD) of spike protein, the phospholipid transportation of P4-ATPase, and the loop translocation of ACLY. Taken together, the CG model provides a suitable alternative in mechanistic studies related to conformational change in large-scale protein machines.
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Liu D, Zhang G, Zhu Y, Liu X, Xu S, He M, Chen S, An K, Liang G, Zhu Z. Effectiveness of Ultrasound-Guided Retrolaminar Block and Erector Spinae Plane Block in Retroperitoneal Laparoscopic Surgery: A Randomized Controlled Trial. J Pain Res 2022; 15:815-826. [PMID: 35370419 PMCID: PMC8974250 DOI: 10.2147/jpr.s349028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/24/2022] [Indexed: 01/12/2023] Open
Abstract
Purpose Retrolaminar block (RLB) and erector spine plane block (ESPB) share a similar block site, but their analgesia principle may differ. This study compared the postoperative analgesic effects of ultrasound-guided RLB and ESPB for retroperitoneal laparoscopic surgery. Patients and Methods The study included patients who scheduled for laparoscopic nephrectomy from July 2020 to January 2021. Patients in RLB group received a three-point block at the posterior surface of T8-T10 lamina, and those in ESPB group received at the T9 level. The primary result was the score of visual analogue scale (VAS). Secondary results included information on intraoperative and postoperative analgesia consumption and rescue analgesia usage, skin temperature, serum interleukin (IL)-1β, prostaglandin E2 (PGE2) level and the occurrence of safety events. Results There was no significant difference between the two groups in the postoperative VAS scores at both the rest and cough state (All P>0.05). The skin surface temperature of the affected side and the healthy side in ESPB group was higher than that in the RLB group at the end of the surgery (P=0.002) and after surgery (P=0.016). The RLB group had a higher ephedrine usage than the ESPB group (P=0.027). Compared with the ESPB group, the RLB group had a shorter time to exhaust (P=0.045) and lower serum IL-1β level (P=0.049). Patients in neither group developed severe adverse event. Conclusion Ultrasound-guided RLB and ESPB can provide safe and effective postoperative analgesia for retroperitoneal laparoscopic surgery. ESPB has more stable intraoperative hemodynamics, while RLB has more potential research value for patients’ rapid recovery.
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Lam TN, Wu YH, Liu CJ, Chae H, Lee SY, Jain J, An K, Huang EW. Transient Phase-Driven Cyclic Deformation in Additively Manufactured 15-5 PH Steel. MATERIALS 2022; 15:ma15030777. [PMID: 35160723 PMCID: PMC8836881 DOI: 10.3390/ma15030777] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/19/2022]
Abstract
The present work extends the examination of selective laser melting (SLM)-fabricated 15-5 PH steel with the 8%-transient-austenite-phase towards fully-reversed strain-controlled low-cycle fatigue (LCF) test. The cyclic-deformation response and microstructural evolution were investigated via in-situ neutron-diffraction measurements. The transient-austenite-phase rapidly transformed into the martensite phase in the initial cyclic-hardening stage, followed by an almost complete martensitic transformation in the cyclic-softening and steady stage. The compressive stress was much greater than the tensile stress at the same strain amplitude. The enhanced martensitic transformation associated with lower dislocation densities under compression predominantly governed such a striking tension-compression asymmetry in the SLM-built 15-5 PH.
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An K, Tan J, Yang D, Ren H, Zhao Z, Chen Y, Wang W, Xin X, Shi Y, Jiang Z. Modular Assembly of Electron Transfer Pathway in Bimetallic MOF for Photocatalytic Ammonia Synthesis. Catal Sci Technol 2022. [DOI: 10.1039/d1cy02294f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is a long-term pursuit to implement the green and sustainable photocatalytic production of ammonia via the conversion of water and nitrogen under mild conditions. Due to the rapid recombination...
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An K, Cui Y, Zhong X, Li K, Zhang J, Liu H, Wen Z. Immortalized Bone Mesenchymal Stromal Cells With Inducible Galanin Expression Produce Controllable Pain Relief in Neuropathic Rats. Cell Transplant 2022; 31:9636897221103861. [PMID: 35726855 PMCID: PMC9218486 DOI: 10.1177/09636897221103861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Management of chronic pain is one of the most difficult problems in modern practice. Grafted human telomerase reverse transcriptase–immortalized bone marrow mesenchymal stromal cells (hTERT-BMSCs) with inducible galanin (GAL) expression have been considered to be a potentially safe and controllable approach for the alleviation of chronic pain. Therefore, in this study, we aimed to assess the feasibility of hTERT-BMSCs/Tet-on/GAL cells secreting GAL under the transcriptional control of doxycycline (Dox) for controllable pain relief. After transplanted into the subarachnoid space of neuropathic rats induced by spared nerve injury of sciatic nerve, their analgesic actions were investigated by behavioral tests. The results showed that the pain-related behaviors, mechanical allodynia, and thermal hyperalgesia were significantly alleviated during 1 to 7 weeks after grafts of hTERT-BMSCs/Tet-on/GAL cells without motor incoordination. Importantly, these effects could be reversed by GAL receptor antagonist M35 and regulated by Dox induction as compared with control. Moreover, the GAL level in cerebrospinal fluid and spinal GAL receptor 1 (GalR1) expression were correlated with Dox administration, but not GAL receptor 2 (GalR2). Meanwhile, spinal protein kinase Mζ (PKMζ) expression was also inhibited significantly. Taken together, these data suggest that inducible release of GAL from transplanted cells was able to produce controllable pain relief in neuropathic rats via inhibiting the PKMζ activation and activating its GalR1 rather than GalR2. This provides a promising step toward a novel stem cell–based strategy for pain therapy.
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