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1.
Opt Express ; 32(11): 19088-19104, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38859052

ABSTRACT

Compared with traditional electrical logic gates, optical or terahertz (THz) computing logic gates have faster computing speeds and lower power consumption, and can better meet the huge data computing needs. However, there are limitations inherent in existing optical logic gates, such as single input/output channels and susceptibility to interference. Here, we proposed a new approach utilizing polarization-sensitive graphene-vanadium dioxide metasurface THz logic gates. Benefitting from two actively tunable materials, the proposed controlled-NOT logic gate(CNOT LG) enables versatile functionality through a dual-parameter control system. This system allows for the realization of multiple output states under diverse polarized illuminating conditions, aligning with the expected input-output logic relationship of the CNOT LG. Furthermore, to demonstrate the robustness of the designed THz CNOT LG metasurface, we designed an imaging array harnessing the dynamic control capabilities of tunable meta-atoms, facilitating clear near-field imaging. This research is promising for advancing CNOT LG applications in the THz spectrum. It has potential applications in telecommunications, sensing, and imaging.

2.
Sensors (Basel) ; 24(7)2024 Mar 22.
Article in English | MEDLINE | ID: mdl-38610242

ABSTRACT

Current real-time direction judgment systems are inaccurate and insensitive, as well as limited by the sampling rate of analog-to-digital converters. To address this problem, we propose a dynamic real-time direction judgment system based on an integral dual-frequency laser interferometer and field-programmable gate array technology. The optoelectronic signals resulting from the introduction of a phase subdivision method based on the amplitude resolution of the laser interferometer when measuring displacement are analyzed. The proposed system integrates the optoelectronic signals to increase the accuracy of its direction judgments and ensures these direction judgments are made in real time by dynamically controlling the integration time. Several experiments were conducted to verify the performance of the proposed system. The results show that, compared with current real-time direction judgment systems, the proposed system makes accurate judgements during low-speed motions and can update directions within 0.125 cycles of the phase difference change at different speeds. Moreover, a sweep frequency experiment confirmed the system's ability to effectively judge dynamic directions. The proposed system is capable of accurate and real-time directional judgment during low-speed movements of a table in motion.

3.
Opt Express ; 31(18): 29255-29270, 2023 Aug 28.
Article in English | MEDLINE | ID: mdl-37710730

ABSTRACT

To improve the measurement accuracy of interferometer displacement measurement systems, this study analyzes the characteristics of the interference signal to identify sources of nonlinear errors and develops compensation strategies. Specifically, a model is established for the nonlinear errors of the interferometer, which can be attributed to a laser and polarizing beam splitter (PBS). Following that, the dual orthogonal lock-in amplification algorithm is used to separate and compensate for the frequency uncertainty and amplitude errors. Additionally, a real-time compensation algorithm based on ellipse fitting is proposed to compensate for errors caused by the PBS and the uncertainty of amplitude caused by the light source. Experimental results demonstrate that the peak-to-peak value of the compensated nonlinear error is reduced from 11.62 nm to 5.37 nm.

4.
Org Biomol Chem ; 21(14): 2910-2916, 2023 Apr 05.
Article in English | MEDLINE | ID: mdl-36942676

ABSTRACT

The reactions of direct Csp2-H chalcogenylation and halogenation of N-arylpyrrolidone under the action of PIFA without a directing group and under metal-free conditions were reported in this paper. Diphenyl selenide/sulfur and selenium phenyl halides were used as reaction reagents to obtain chalcogenylated and halogenated N-arylpyrrolidone products, respectively. The mechanistic studies indicated that a radical pathway was likely involved in these reactions. Preliminary antitumor tests showed that these compounds have moderate to potent activities against human acute leukemia cells K562 in vitro, which may be used as lead compounds for subsequent research.

5.
Opt Express ; 30(26): 46259-46279, 2022 Dec 19.
Article in English | MEDLINE | ID: mdl-36558584

ABSTRACT

In this paper, to separate and compensate the nonlinear error in the grating interferometer, we analyze the source and generation mechanism of this error, deduce the nonlinear error model of the measured signal and the calculated phase signal, and study the characteristics of the established nonlinear error model. The reason why the frequency multiples of ideal phase signals and higher-order nonlinear errors caused by ghost reflections and angular errors of the laser's z-axis are not integers is explained. Then, a nonlinear error separation and compensation method based on cross-correlation coefficient is proposed. Experiments show that the frequency multiplier relationship between the high-order nonlinear error and the ideal interference signal is close to but not equal to 3-fold. The peak-to-peak value of the compensated nonlinear error is reduced from 17.40 nm to 7.05 nm.

6.
Sensors (Basel) ; 22(14)2022 Jul 20.
Article in English | MEDLINE | ID: mdl-35891103

ABSTRACT

In this study, a subnanometer heterodyne interference signal processing algorithm with a dynamic filter is proposed. The algorithm can effectively reduce the measurement error caused by the noise introduced in the optical path and circuit. Because of the low signal-to-noise ratio of the measurement signal, a dynamic filter with variable coefficients is designed. The role of the bi-quadrature lock-in amplifier algorithm in the problem of different amplitudes among the measurement signal, reference signal, and uncertainty of the frequency difference of the dual-frequency laser is analyzed. With the aid of the heterodyne interferometry platform, the error in the solution results of the proposed algorithm and the conventional algorithm is compared. The results indicate that the maximum deviation of the phase increment of the algorithm does not exceed 6 mrad, the single-cycle phase difference can be subdivided by 1024, and the system resolution reaches 0.15 nm.

7.
Oncology ; 98(8): 583-588, 2020.
Article in English | MEDLINE | ID: mdl-32521533

ABSTRACT

BACKGROUND: Gastric cancer (GC) is one of the leading causes of cancer death in China, while the nature of genetic factors related to GC has not been well-studied. OBJECTIVES: To assess the inherited genetic factors regarding pathogenic germline mutations in Chinese GC population. METHODS: Genomic profiling of DNA was performed through next-generation sequencing with 381 cancer-related genes on tissue from patients with GC between January 1, 2017, and May 7, 2019. RESULTS: 470 GC patients were included for analysis. A total of 28 (6.0%) patients were identified to harbor 25 different pathogenic or very likely pathogenic germline mutations in 15 genes. The variants fell most frequently in BRCA2 (n = 6, 1.28%), CHEK2 (n = 5, 1.06%), MUTYH (n = 3, 0.64%), CDH1 (n = 2, 0.43%), and ATM (n = 2, 0.43%). Of all the germline-mutated genes, 66.7% (n = 10) lay in the DNA damage repair pathways. Seven patients were identified to have a high TMB status, among whom two were also identified as MSI-H. Overall, 20 out of the 28 patients (71.4%) carried clinically actionable mutations. CONCLUSIONS: Our study has depicted the spectrum of pathogenic germline mutations in Chinese GC patients, which may provide valuable clues for the assessment of the genetic susceptibility and clinical management in GC.


Subject(s)
Germ-Line Mutation , High-Throughput Nucleotide Sequencing/methods , Stomach Neoplasms/epidemiology , Stomach Neoplasms/genetics , Aged , BRCA2 Protein/genetics , Checkpoint Kinase 2/genetics , China/epidemiology , DNA Damage/genetics , DNA Glycosylases/genetics , Female , Genetic Predisposition to Disease , Humans , Male , Microsatellite Instability , Middle Aged , Stomach Neoplasms/pathology
8.
Small ; 13(1)2017 Jan.
Article in English | MEDLINE | ID: mdl-27709780

ABSTRACT

The significance of bionanomotors in nanotechnology is analogous to mechanical motors in daily life. Here the principle and approach for designing and constructing biomimetic nanomotors with continuous single-directional motion are reported. This bionanomotor is composed of a dodecameric protein channel, a six-pRNA ring, and an ATPase hexamer. Based on recent elucidations of the one-way revolving mechanisms of the phi29 double-stranded DNA (dsDNA) motor, various RNA and protein elements are designed and tested by single-molecule imaging and biochemical assays, with which the motor with active components has been constructed. The motor motion direction is controlled by three operation elements: (1) Asymmetrical ATPase with ATP-interacting domains for alternative DNA binding/pushing regulated by an arginine finger in a sequential action manner. The arginine finger bridges two adjacent ATPase subunits into a non-covalent dimer, resulting in an asymmetrical hexameric complex containing one dimer and four monomers. (2) The dsDNA translocation channel as a one-way valve. (3) The hexameric pRNA ring geared with left-/right-handed loops. Assessments of these constructs reveal that one inactive subunit of pRNA/ATPase is sufficient to completely block motor function (defined as K = 1), implying that these components work sequentially based on the principle of binomial distribution and Yang Hui's triangle.


Subject(s)
Biomimetics , Molecular Motor Proteins/chemistry , Motion , Adenosine Triphosphate/chemistry , Bacteriophages , Base Sequence , Computer Systems , DNA/chemistry , DNA, Viral/chemistry , Entropy , Hydrolysis , Models, Molecular , Protein Conformation , Protein Subunits/chemistry , RNA, Viral/chemistry , Virus Assembly
9.
J Virol ; 90(18): 8036-46, 2016 09 15.
Article in English | MEDLINE | ID: mdl-27356896

ABSTRACT

The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially.


Subject(s)
Antiviral Agents/isolation & purification , Antiviral Agents/pharmacology , DNA Packaging/drug effects , Drug Discovery , Virus Assembly/drug effects , DNA Viruses/drug effects , DNA Viruses/enzymology , Molecular Motor Proteins/chemistry , Molecular Motor Proteins/metabolism , Viral Proteins/chemistry , Viral Proteins/metabolism
10.
Small ; 12(33): 4572-8, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27435806

ABSTRACT

Nanopore technology has become a highly sensitive and powerful tool for single molecule sensing of chemicals and biopolymers. Protein pores have the advantages of size amenability, channel homogeneity, and fabrication reproducibility. But most well-studied protein pores for sensing are too small for passage of peptide analytes that are typically a few nanometers in dimension. The funnel-shaped channel of bacteriophage phi29 DNA packaging motor has previously been inserted into a lipid membrane to serve as a larger pore with a narrowest N-terminal constriction of 3.6 nm and a wider C-terminal end of 6 nm. Here, the utility of phi29 motor channel for fingerprinting of various peptides using single molecule electrophysiological assays is reported. The translocation of peptides is proved unequivocally by single molecule fluorescence imaging. Current blockage percentage and distinctive current signatures are used to distinguish peptides with high confidence. Each peptide generated one or two distinct current blockage peaks, serving as typical fingerprint for each peptide. The oligomeric states of peptides can also be studied in real time at single molecule level. The results demonstrate the potential for further development of phi29 motor channel for detection of disease-associated peptide biomarkers.


Subject(s)
Bacteriophages/chemistry , DNA Packaging , Peptide Mapping/methods , Peptides/chemistry , Fluorescence , Lipid Bilayers/chemistry , Reproducibility of Results , Time Factors
11.
Nanomedicine ; 10(7): 1433-40, 2014 Oct.
Article in English | MEDLINE | ID: mdl-24650885

ABSTRACT

Living systems produce ordered structures and nanomachines that inspire the development of biomimetic nanodevices such as chips, MEMS, actuators, sensors, sorters, and apparatuses for single-pore DNA sequencing, disease diagnosis, drug or therapeutic RNA delivery. Determination of the copy numbers of subunits that build these machines is challenging due to small size. Here we report a simple mathematical method to determine the stoichiometry, using phi29 DNA-packaging nanomotor as a model to elucidate the application of a formula ∑M=0(Z)((Z)M)p(Z-M)q(M), where p and q are the percentage of wild-type and inactive mutant in the empirical assay; M is the copy numbers of mutant and Z is the stoichiometry in question. Variable ratios of mutants and wild-type were mixed to inhibit motor function. Empirical data were plotted over the theoretical curves to determine the stoichiometry and the value of K, which is the number of mutant needed in each machine to block the function, all based on the condition that wild-type and mutant are equal in binding affinity. Both Z and K from 1-12 were investigated. The data precisely confirmed that phi29 motor contains six copies (Z) of the motor ATPase gp16, and K=1. From the clinical editor: To determine copy numbers of subunits that form nanomachines in living organisms is a daunting task due to the complexities and the inherently small sizes associated with such systems. In this paper, a simple mathematical method is described how to determine the stoichiometry of copies in biomimetic nanodevices, using phi29 DNA-packaging nanomotor as a model.


Subject(s)
DNA Packaging , Nanostructures , Proteins/chemistry , Models, Theoretical
12.
Pathol Oncol Res ; 28: 1610360, 2022.
Article in English | MEDLINE | ID: mdl-35911441

ABSTRACT

ERBB2 abnormalities frequently occur and serve as rationale therapeutic targets in cancer. In this study, clinical and next-generation sequencing data from 14,956 patients across more than 20 tumor types were collected. A total of 406 (2.7%) patients were identified with ERBB2 amplifications, and 303 (2.0%) patients with pathogenic somatic ERBB2 mutations. ERBB2 amplifications fell most frequently in breast (15.9%) and stomach (8.3%) cancers. Somatic ERBB2 SNVs/indels occurred most common in bladder/urinary tract (7.3%) and intestine (6.1%) cancers. The top mutated ERBB2 SNVs/indels were p.Y772_A775dup (25.5%) and p.S310F/Y (19.9%). Significantly higher rates of ERBB2 SNV/indels were found in women compared to men (2.8% vs. 1.5%, p < 0.0001). CDK12 was the most common co-amplification gene with ERBB2 in cancers with a high frequency of ERBB2 amplifications. Patients with ERBB2 amplifications or mutations had higher TMB compared with patients with non-ERBB2 alterations. The study provided the landscape of ERBB2 alterations across a variety of solid tumors that may benefit from anti-HER2 agents.


Subject(s)
Neoplasms , Receptor, ErbB-2 , Female , High-Throughput Nucleotide Sequencing , Humans , Male , Mutation , Neoplasms/genetics , Receptor, ErbB-2/genetics
13.
Adv Mater ; 34(20): e2200115, 2022 May.
Article in English | MEDLINE | ID: mdl-35128734

ABSTRACT

Due to the wet and dynamic environment of the oral cavity, the healing of intraoral wounds, such as tooth extraction wounds, requires stable and firm wound dressings. In clinical practice, cotton balls and gauzes, sponge plugs, or sutures are used to treat extraction wounds, but none of these means can continuously isolate the wound from the intraoral environment and facilitate ideal healing conditions. Herein, inspired by the natural extracellular matrix, a family of wound dressings is developed for intraoral wound repair. Infiltrating a ductile long-chain hydrogel network into a prefabricated, sturdy macromolecular meshwork and in situ crosslinking endowed the composite hydrogel with controllable swelling behaviors and robust mechanical properties. The macromolecular meshwork functioned as the backbone to support the composite and restricts the swelling of the long-chain hydrogel network. In vitro tests verified that this wound dressing can provide durable protection for intraoral wounds against complex irritations. Furthermore, accelerated wound healing occurred when the wound dressing is applied in vivo on a canine tooth extraction model, due to the effective reduction of acute inflammation. These results suggest that this family of bioinspired hydrogels has great potential for application as intraoral wound dressing.


Subject(s)
Bandages , Hydrogels , Extracellular Matrix , Wound Healing
14.
Front Oncol ; 11: 761110, 2021.
Article in English | MEDLINE | ID: mdl-34858840

ABSTRACT

OBJECTIVE: Emerging evidence showed that immune checkpoint inhibitors (ICIs) lead to hyperprogressive disease (HPD) in a small proportion of patients. There is no well-recognized standard for the evaluation of HPD. Comprehensive exploration of HPD definition system in gastrointestinal cancer treated with ICI is lacking to date. METHODS: A total of 126 patients with advanced or metastatic gastrointestinal cancer treated with ICI monotherapy were analyzed. Seven definitions of HPD were defined with tumor growth kinetics (TGK) or tumor growth rate (TGR) by including new lesions or not, and with different cutoffs. Incidence and performance of different criteria were compared. Clinicopathologic characteristics and baseline genomic variations associated with HPD were also explored. RESULTS: Tumor growth kinetics ratio of more than two fold that incorporated new lesions into calculation of HPD outperformed other definitions by successfully stratifying 14 patients (11.1%) with both accelerated disease progression (median PFS, 1.62 versus 1.93 months; hazard ratio, 1.85; 95% CI, 0.98 to 3.48; P = 0.059) and worse overall survival (median OS, 3.97 versus 10.23 months; hazard ratio, 2.30; 95% CI, 1.11 to 4.78; P = 0.021). Baseline genomic alterations in circulating tumor DNA, including SMARCA2, MSH6, APC signaling pathway, and Wnt signaling pathway, might be associated with the risk of HPD. CONCLUSION: Incorporating new lesions emerging during the treatment was shown to be reliable for the assessment of TGK. TGK serves as a more convenient way to reflect tumor growth acceleration compared with TGR. Genomic alterations were suggested to be associated with the occurrence of HPD.

15.
Ann Transl Med ; 9(22): 1660, 2021 Nov.
Article in English | MEDLINE | ID: mdl-34988169

ABSTRACT

BACKGROUND: Depending on the context, the transforming growth factor beta (TGF-ß) signaling pathway is involved in opposing cell processes of tumor suppression and tumor promotion. However, the effects of TGF-ß pathway on immunotherapy efficacy have not yet been systematically investigated. METHODS: In this study, we have extracted the available data of whole-exome sequencing, messenger RNA (mRNA) expression, baseline characterization, and prognosis information of 10,912 pan-cancer patients from The Cancer Genome Atlas to explore the role of TGF-ß pathway in immune regulation. Formalin-fixed, paraffin-embedded tissue samples from 6,717 Chinese cancer patients assayed by next-generation sequencing (NGS) were used as a validation cohort (3DMed cohort). Data sets from the public MSK (Memorial Sloan Kettering Cancer Center) cohort (N=1,610) were used to explore the association of TGF-ß pathway with immunotherapy effects. RESULTS: The results showed that TGF-ß pathway alteration was significantly correlated with high microsatellite instability (MSI), high tumor mutational burden, and high neoantigen burden (TNB) (P<0.001 for each). Consistently, the pathway mutations were associated with distinct patterns of immune-related gene expression and tumor-infiltrating immune cells. Patients with TGF-ß pathway mutations exhibited significantly worse prognosis than did the wild-type patients regardless of the interventions [overall survival (OS): hazard ratio (HR) 1.20; 95% confidence interval (CI): 1.08-1.33; P=0.001]. However, when treated with immune checkpoint inhibitors (ICIs), superior survival benefit was observed in patients from the mutation group versus the wild-type group (OS: HR 0.73; 95% CI: 0.61-0.88; P=0.001). CONCLUSIONS: Collectively, our study suggested that mutations in TGF-ß pathway may be associated with positive immune regulation and better efficacy of immunotherapy.

16.
Mol Genet Genomic Med ; 9(8): e1697, 2021 08.
Article in English | MEDLINE | ID: mdl-34145795

ABSTRACT

BACKGROUND: Isocitrate dehydrogenase (IDH) is an enzyme family involved in cell aerobic metabolism of tricarboxylic acid cycle. However, the landscape of IDH mutations in pan-cancer has not been fully characterized. METHODS: Tissue or blood samples were subjected to next-generation sequencing (NGS) for detection the IDH mutation. RESULTS: A total of 28.868 patients from more than 20 solid tumor species were analyzed. A total of 374 cases (1.30%) with IDH mutations were identified. Among all the IDH mutations cases, 80 (21.4%) were biliary tract cancer (BTC), 80 (21.4%) were lung cancer, 57 (15.2%) were liver cancer, and 42 (11.2%) were colorectal cancer. The most common IDH variant were IDH1 and IDH2 which were discovered in 0.81% cases and 0.47% cases, respectively. However, there were significant differences in IDH1 and IDH2 mutation frequency among different tumor species (p = 0.0003). Of the patients with IDH1 mutations, about 53.0% of these mutations occur in codons 132. Codons 172 (25.4%) was high-frequency mutation subtypes in IDH2 mutation. TP53, PBRM1, and BAP1 were the most significantly mutated genes in BTC which were different from others cancer. Moreover, TMB were significantly higher in lung cancer, colorectal cancer, and gastric cancer than BTC (p = 0.0164, p < 0.0001, p = 0.0067, respectively) and BTC patients with IDH mutation had lower TMB compared with wild-type IDH. CONCLUSION: Somatic IDH mutation was found in multiple solid tumors and IDH would be a driver gene in BTC.


Subject(s)
Gene Frequency , Isocitrate Dehydrogenase , Neoplasms , Female , Humans , Male , Middle Aged , China , Isocitrate Dehydrogenase/genetics , Mutation , Neoplasms/classification , Neoplasms/genetics
17.
J Cancer ; 11(22): 6695-6699, 2020.
Article in English | MEDLINE | ID: mdl-33046990

ABSTRACT

Purpose: The aberrant of fibroblast growth factors and their receptors (FGF/FGFR) is an emerging target in the treatment of solid tumors. This study aimed to explore the landscape of FGF/FGFR alterations in a large cohort of cancer patients. Material and Methods: The formalin-fixed paraffin-embedded specimens of cancer patients who have underwent next-generation sequencing (NGS) from 2017 to 2019 in 3DMed Clinical Laboratory Inc. were included in this study. Findings: Of 12,372 Chinese cancer patients with more than 20 tumor types (60% male, median age, 58.0 [IQR, 49.0-66.0]), genomic alterations in FGF, FGFR, and both were observed in 895 (7.2%), 862 (7.0%), and 186 (1.5%) patients, respectively. The highest prevalence of FGF/FGFR mutations fell in esophagus cancer (61.6%, 98/159) and urinary tract cancer (52.7%, 145/275). The most common pathway-level mutations were FGFR single nucleotide variants (635, 5.1%) and FGF amplifications (628, 5.1%). The microsatellite instability status was negatively associated with amplifications (p=0.0017). Conclusion: FGF/FGFR alterations were widely occurred in cancer patients, and the mutational landscape may contribute to the further study design and development of FGF/FGFR inhibitors.

18.
Pathol Oncol Res ; 26(1): 109-114, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31721094

ABSTRACT

Lung cancer is currently a leading cause of cancer-associated mortality worldwide. Despite the increasing evidences of variants that were associated with lung cancer risk, investigations of genetic factors and their roles in genetic susceptibility to lung cancer were limited. Here we systematically investigated the spectrum of pathogenic germline mutations in Chinese population with lung cancer. Genomic profiling of DNA was performed through next-generation sequencing (NGS) on tissue biopsy from 1764 Chinese lung cancer patients with a 381 cancer gene panel between January 01, 2017 and May 07, 2019. Patients with germline mutations were identified, and their clinical information were collected. Of 1764 patients with lung cancer, 67 (3.8%) patients were identified to carry pathogenic or likely pathogenic germline mutations in 25 cancer predisposition genes, with a frequency of 3.6% in lung adenocarcinoma (49/1349), 4.3% in squamous cell lung cancer (14/322), 5.6% in small cell lung cancer (4/72), and none in lung adenosquamous carcinoma (0/21), respectively. The highest pathogenic germline mutational prevalence were found in BRCA2 (0.79%), CHEK2 (0.40%), BRCA1 (0.34%), and TP53 (0.34%). Two splice mutations were reported for the first time in this study. Notably, a majority (85.5%) of the detected germline mutations fell in DNA damage repair pathways.


Subject(s)
Biomarkers, Tumor/genetics , Genetic Predisposition to Disease/genetics , Germ-Line Mutation , Lung Neoplasms/genetics , Aged , Asian People/genetics , Female , High-Throughput Nucleotide Sequencing , Humans , Lung Neoplasms/pathology , Male , Middle Aged , Mutation Rate
19.
Cancer Med ; 9(6): 2190-2200, 2020 03.
Article in English | MEDLINE | ID: mdl-31991061

ABSTRACT

BACKGROUND: Defects in DNA damage repair (DDR) system may lead to genomic instability and manifest as increased immunogenicity. DDR deficiency is prevalent in ovarian cancer (OvCa); however, the association of DDR mutation with immune profiles in OvCa remains largely unknown. This knowledge will provide an essential basis to the rational design of biomarker-guided immune combination therapy of OvCa in the future. METHODS: Whole-exome sequencing data of 587 OvCa from The Cancer Genome Atlas (TCGA) were used to determine the expression profiles of 47 immune-related genes and the abundance of tumor-infiltrating immune cells. A Chinese OvCa cohort (n = 220) tested by next-generation sequencing (NGS) was used to validate the association between DDR status and tumor mutation burden (TMB). RESULTS: A total of 19.3% in TCGA cohort and 25.9% in Chinese cohort harbored at least one DDR somatic mutation. DDR deficiency exhibited a distinct immune profile with significant higher expression levels of PTPRCAP, CCL5, IFI16, LAG3, IL15RA, and GBP1 in OvCa in the TCGA cohort. Different DDR pathway deficiency displayed various immune profiles. Increased levels of Th1 cells, TMB, and neoantigen were also observed in DDR-deficient tumors. CONCLUSIONS: DDR deficiency was associated with specific immune signatures in OvCa. Our findings emphasize the urgent need for biomarker-guided rational immune combination therapy to maximize the OvCa patients who could benefit from immunotherapy.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/pharmacology , Biomarkers, Tumor/genetics , DNA Repair/immunology , Gene Expression Regulation, Neoplastic/immunology , Ovarian Neoplasms/genetics , Adult , Aged , Aged, 80 and over , Antineoplastic Agents, Immunological/pharmacology , Antineoplastic Agents, Immunological/therapeutic use , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , B7-H1 Antigen/antagonists & inhibitors , B7-H1 Antigen/genetics , Biomarkers, Tumor/antagonists & inhibitors , Chemotherapy, Adjuvant/methods , Cohort Studies , DNA Repair/drug effects , Datasets as Topic , Female , Gene Expression Regulation, Neoplastic/drug effects , High-Throughput Nucleotide Sequencing , Humans , Middle Aged , Mutation , Ovarian Neoplasms/immunology , Ovarian Neoplasms/mortality , Ovarian Neoplasms/therapy , Ovariectomy , Progression-Free Survival , Exome Sequencing , Young Adult
20.
J Cancer ; 11(3): 741-749, 2020.
Article in English | MEDLINE | ID: mdl-31942197

ABSTRACT

Immune checkpoint inhibitor combination therapy exhibited outstanding efficacy in first line setting for advanced non-small cell lung cancer (aNSCLC) patients. However, whether PD-1 inhibitor combined treatment is effective in second line or later setting remains unknown. Therefore, we retrospectively evaluated the efficacy of combined therapy of PD-1 inhibitor with chemotherapy and/or bevacizumab compared to PD-1 inhibitor alone for aNSCLC patients in second line or later setting. Patients with aNSCLC who have received anti-PD-1 based therapy between 2015 and 2017 were screened, and 55 patients were ultimately included and divided into the monotherapy group (N=33) and the combination group (N=22). Patients treated with combination therapy exhibited superior PFS versus those treated with monotherapy (median PFS, 7.5 months vs 3.3 months; hazard ratio 0.28; 95% CI, 0.14-0.56; P<0.001). Objective response rate and disease control rate were 31.8% (7/22) and 95.5% (21/22) in the combination group and 10.0% (3/30) and 46.7% (14/30) in the monotherapy group, respectively (ORR, P=0.075; DCR, P<0.001). Five patients (22.7%) experienced grade 3-4 adverse events in the combination group and two patients (6.1%) in the monotherapy group. Taken together, our results indicated that for NSCLC patients who had failed on the first-line or later treatment, PD-1 inhibitor in combination with chemotherapy and/or bevacizumab might be a favorable treatment option. These findings warrant further validation in prospective studies.

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