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Lung adenocarcinoma (LUAD) is a heterogeneous disease. Our study aimed to understand the unique molecular features of preinvasive to invasive LUAD subtypes. We retrospectively analyzed the clinical, histopathological, and molecular data of 3,254 Chinese patients with preinvasive lesions (n = 252), minimally invasive adenocarcinomas (n = 479), and invasive LUAD (n = 2,523). Molecular data were elucidated using a targeted 68-gene next-generation sequencing panel. Our findings revealed four preinvasive lesion-predominant gene mutations, including MAP2K1 insertion-deletions (indels), BRAF non-V600E kinase mutations, and exon 20 insertions (20ins) in both EGFR and ERBB2, which we referred to as mutations enriched in AIS (MEA). The detection rate of MEA in invasive tumors was relatively lower. MAP2K1 missense mutations, which were likely passenger mutations, co-occurred with oncogenic driver mutations, while small indels were mutually exclusive from other genes regardless of the invasion level. BRAF non-V600E kinase-mutant invasive adenocarcinomas (IAC) had significantly higher mutation rates in tumor suppressor genes but lower frequency of co-occurring oncogenic driver mutations than non-kinase-mutant IAC, suggesting the potential oncogenic activity of BRAF non-V600E kinase mutations albeit weaker than BRAF V600E. Moreover, similar to the extremely low frequency of MAP2K1 indels in IAC, BRAF non-V600E kinase domain mutations co-occurring with TSC1 mutations were exclusively found in preinvasive lesions. Compared with EGFR L858R and exon 19 deletion, patients with preinvasive lesions harboring 20ins in either EGFR or ERBB2 were significantly younger, while those with IAC had similar age. Furthermore, our study demonstrated distinct mutational features for subtypes of oncogene mutations favored by different invasion patterns in adenocarcinomas. In conclusion, our data demonstrate distinct mutational features between preinvasive lesions and invasive tumors with MEA, suggesting the involvement of MEA in the early stages of tumorigenesis. Further pre-clinical studies are required to establish the role of these genes in the malignant transformation of LUAD.

Non-alcoholic fatty liver disease (NAFLD), characterized by excessive lipid accumulation in hepatocytes, is an increasing global healthcare burden. Sirtuin 2 (SIRT2) functions as a preventive molecule for NAFLD with incompletely clarified regulatory mechanisms. Metabolic changes and gut microbiota imbalance are critical to the pathogenesis of NAFLD. However, their association with SIRT2 in NAFLD progression is still unknown. Here, we report that SIRT2 knockout (KO) mice are susceptible to HFCS (high-fat/high-cholesterol/high-sucrose)-induced obesity and hepatic steatosis accompanied with an aggravated metabolic profile, which indicates SIRT2 deficiency promotes NAFLD-NASH (nonalcoholic steatohepatitis) progression. Under palmitic acid (PA), cholesterol (CHO), and high glucose (Glu) conditions, SIRT2 deficiency promotes lipid deposition and inflammation in cultured cells. Mechanically, SIRT2 deficiency induces serum metabolites alteration including upregulation of L-proline and downregulation of phosphatidylcholines (PC), lysophosphatidylcholine (LPC), and epinephrine. Furthermore, SIRT2 deficiency promotes gut microbiota dysbiosis. The microbiota composition clustered distinctly in SIRT2 KO mice with decreased Bacteroides and Eubacterium, and increased Acetatifactor. In clinical patients, SIRT2 is downregulated in the NALFD patients compared with healthy controls, and is associated with exacerbated progression of normal liver status to NAFLD to NASH in clinical patients. In conclusion, SIRT2 deficiency accelerates HFCS-induced NAFLD-NASH progression by inducing alteration of gut microbiota and changes of metabolites.

Radiotherapy has shown measurable efficacy with objective response rate and prolonged progression-free survival (PFS) in patients with breast cancer (BC). However, radioresistance is still a major challenge in BC radiotherapy, leading to limited clinical application and treatment failure. Therefore, elucidating the underlying mechanisms and developing effective strategies to enhance the radiosensitivity is of clinical importance. In the present study, we demonstratedCCAAT enhancer-binding protein alpha (CEBPA) as a specific marker for predicting the efficacy of radiotherapy in BC patients. CEBPA enhanced radiotherapeutic sensitivity of BC by increasing the apoptosis both in vitro and in vivo. Mechanistically, CEBPA executed radio-sensitizing function in BC by promoting ferroptosis through negatively regulating the nuclear factor E2-related factor 2 (Nrf2) pathway genes. Furthermore, high expression of CEBPA was positively correlated with the infiltration of cytotoxic immune cells in BC microenvironment. In summary, our work revealed CEBPA as a critical regulator to enhance radiosensitivity, induce ferroptosis, as well as modulate tumor immune microenvironment in BC. Induction of CEBPA or ferroptosis with specific inducers or modulation of tumor immune microenvironment would be potential sensitizing therapeutic strategies in BC.

RET fusion has emerged as a targetable driver in non-small-cell lung cancer. A comparative analysis on RET fusions at DNA [DNA sequencing (DNA-seq)] and RNA [RNA sequencing (RNA-seq)] levels was performed in this study. Archived tumor samples from 54 non-small-cell lung cancer patients with DNA-level noncanonical RET fusions were selected for RNA-seq. RNA-seq identified RET fusion transcripts in 41 of 44 samples passing quality control. In the subset of cases harboring RET 3'-end fusions and predicted to produce in-frame proteins (group A; n = 33), RNA-seq identified the same 3'-end fusions in 32 (96.9%). A total of 26 of 32 also had a reciprocal RET 5'-end fusion detected by DNA-seq that was not transcribed. In the subset with DNA-level out-of-frame RET fusions (group B; n = 9), RNA-seq identified in-frame RET fusion transcripts in 8 cases (88.9%). In the subset only identified with a RET 5'-end fusion by DNA-seq (group C; n = 2), RNA-seq detected the corresponding 3'-end fusion in one case. The discordant DNA- and RNA-level fusions observed in group B may be mediated by complex genomic rearrangement events and transcriptional or post-transcriptional processes. In conclusion, DNA-seq demonstrates a high concordance of 96.9% on detecting in-frame RET fusion, but shows a low concordance on detecting out-of-frame RET fusion and RET 5'-end fusion compared with RNA-seq.

Over the past decades, the incidence of thyroid cancer (TC) rapidly increased all over the world, with the papillary thyroid cancer (PTC) accounting for the vast majority of TC cases. It is crucial to investigate novel diagnostic and therapeutic targets for PTC and explore more detailed molecular mechanisms in the carcinogenesis and progression of PTC. Based on the TCGA and GEO databases, FAM111B is downregulated in PTC tissues and predicts better prognosis in PTC patients. FAM111B suppresses the growth, migration, invasion and glycolysis of PTC both

RET-rearranged fusions have been considered as oncogenic drivers in 1% to 2% of non-small cell lung cancers (NSCLC). ARROW study has demonstrated a new selective RET tyrosine kinase inhibitors (TKIs) shows remarkable and durable responses in RET-rearranged NCSLC. In this study mainly recruited patients with common fusion partners KIF5B and CCDC6. There is still a lack of definitive conclusions about effective of rare RET fusion variants to anti-RET therapies.A Chinese 58-year-old female renal insufficient patient with no history of smoking was diagnosed as stage IIIA (T2N2M0) lung adenocarcinoma. Next-generation sequencing targeting 520 cancer-related genes was performed on the pleural effusion samples and revealed 2 novel RET fusions LINCO1264-RET and SEMA5A-RET, concomitant with a common CCDC6-RET.The patient was first treated with multiple lines of chemotherapy and switched to lenvatinib but failed to respond. Due to renal insufficiency, she subsequently received pralsetinib with gradually reduced dosages (400 mg-300 mg-200 mg-100 mg qd) and achieved a partial response (PR) lasting for more than 10 months, accompanied by the declined allele frequencies of all 3 RET fusions.We reported the first case of the pralsetinib efficacy in NSCLC with 3 concurrent RET fusions. Our case also indicates the sensitivity of the newly identified RET fusions to this RET selective inhibitor pralsetinib, and highlights the low-dose treatment option for patients with renal insufficient background.

This paper is concerned with the event-triggered control (ETC) problem for switched systems in networked environments, which are suffered from denial-of-service (DoS) attack and deception attack. Considering that the packet in networked switched systems contains the sampled state and switching signal, DoS attack prevents the packet transmission to cause the zero input, while deception attack falsifies the packet to cause the asynchronous control input with nonlinear disturbance. First, the probabilistic characterization of invalid packet transmissions caused by two different attack models is constructed, namely the ratio of the number of packet transmissions suffering from network attacks to the total number of packet transmissions. Second, a suitable ETC scheme is designed to determine the next triggering instant, which guarantees that the value of Lyapunov function cannot exceed a given restriction and updates the control input at switching instant. After that, the average dwell time and control gains are designed to guarantee the almost sure asymptotic stability of such systems. Finally, a numerical simulation is given to verify the effectiveness of the theoretical results.

This brief deals with the event-triggered control problem for networked Markovian jump systems subject to deception attack. When deception attack is activated, it causes the asynchronous switching and falsifies the sampled state as the nonlinear disturbance. Then, based on the variation between two consecutive sampled states and the signals of switching and deception attack, a switching-like event-triggered scheme is proposed to adjust the threshold. Sufficient conditions are derived to ensure the mean-square exponential input-to-state practical stability for such systems. After that, the homotopy method is employed to obtain the state-feedback matrix with constrained structure. Finally, a model about connected vehicle systems is given to demonstrate the effectiveness of the design techniques.

Metagenomic screening is a widely applied biotechnological approach for screening of novel industrial enzymes. The traditional method of metagenomic screening is based on the functional analyses of heterologously expressed environmental genes in a suitable host, which is the bottleneck of this method. To avoid limitation from the clone-dependent system, an in vitro expression technology has been developed in combination with next-generation sequencing and bioinformatics. First, the sequence profile of a target enzyme, e.g., poly(ethylene terephthalate) esterase in this protocol, is constructed according to the sequences of well-characterized enzymes. Then, the sequence screening is performed with this computationally generated profile among all available metagenomic databases. Afterwards, the candidate genes are synthesized and expressed in vitro with RNA polymerase and translation machinery from special cell extract. Finally, such in vitro produced enzymes are directly applied for the functional analyses. Comparing to the traditional screening methods, this in vitro screening technology can not only save time and materials, but also be easily developed for high-throughput screening with an automatic pipetting robot.

The mining of genomes from non-cultivated microorganisms using metagenomics is a powerful tool to discover novel proteins and other valuable biomolecules. However, function-based metagenome searches are often limited by the time-consuming expression of the active proteins in various heterologous host systems. We here report the initial characterization of novel single-subunit bacteriophage RNA polymerase, RNAP_E, identified from a metagenome data set obtained from an elephant dung microbiome. RNAP_E and its promoter sequence are distantly related to T7 RNA polymerase. Using RNAP_E and a translation-competent Escherichia coli extract, we have developed an efficient medium throughput pipeline and protocol allowing the expression of metagenome-derived genes and the production of proteins in cell-free system is sufficient for the initial testing of the predicted activities. Here, we have successfully identified and verified 12 enzymes acting on bis(2-hydroxyethyl) terephthalate (BHET) in a completely clone-free approach and proposed an in vitro high-throughput metagenomic screening method with RNAP_E.

Unique properties of graphene open new opportunities for preparing composites with favorable functional capabilities. Herein, an ingenious synthesis route via re-pyrolysis process of ball-milling-induced SiC(rGO, Gx)p fillers/polycarbosilane-vinyltriethoxysilane-graphene oxide (PCS-VTES-GO, PVG) precursors blends is proposed to obtain structural-functional integrated SiC(rGO, Gx) bulk polymer-derived ceramics (PDCs). The introduction of SiC(rGO, Gx)p provides favorable moldability, ceramic yield and linear shrinkage. Attractively, graphene networks with more free-moving electrical-charge carriers and wider phonon-channel prominently enhance electrical and thermal conductivities of products. Particularly, SiC(rGO, G20%) bulk PDCs generated at 1300 °C own satisfactory ceramic yield (90.74%), linear shrinkage (5.00%), fracture toughness (2.07 MPa m1/2), bending strength (35.37 MPa), electrical conductivity (25.72 S cm−1) and thermal conductivity (6.72 W m−1·K−1), realizing outstanding values to the best of our knowledge. This fabrication method favors mass production of larger-sized PDCs and possess potential emerging uses.

AimsAn increasing number of small pulmonary nodules are being screened by CT, and an intraoperative diagnosis is necessary for preventing excessive treatment. However, there is limited literature on the frozen diagnosis of small sclerosing pneumocytomas (SPs). In particular, tumours smaller than 1 cm are challenging for pathologists performing intraoperative frozen diagnosis.MethodsIn total, 230 cases of SP were surgically resected between January 2015 and March 2019 at Shanghai Chest Hospital, and of them, 76 cases were smaller than 1 cm. The histology and clinical information of these 76 cases (33.0%, 76/230) were reviewed retrospectively, 54 cases of which were diagnosed intraoperatively, and the pitfalls were summarised. All diagnoses were confirmed on permanent sections and immunohistochemical sections.ResultsHistologically, 78.9% (60/76) of the small SP was dominated by one growth pattern, and solid and papillary growth pattern were the most commonly misdiagnosed circumstances. The rate of intraoperative misdiagnosis of these SP smaller than 1 cm was 11.1% (6/54).ConclusionsThe main reason for misdiagnosis was failure to recognise the dual cell populations and the cellular atypia. Diagnostic clues include the gross morphology, the presence of dual-cell populations and a hypercellular papillary core, foam cell accumulation in glandular spaces and haemorrhage and haemosiderin on the periphery. In spite of awareness of pitfalls some cases may still be essentially impossible to diagnose on frozen section.

Background: MET amplification (METamp) occurs in 1-5% of treatment-naïve or 5-20% of epidermal growth factor receptor tyrosine kinase inhibitors-treated lung cancers (LC). It is a promising therapeutic target in LC. Although fluorescence in situ hybridization (FISH), next-generation sequencing (NGS), and immunohistochemical staining (IHC) are available for METamp detection, but the most appropriate detection method and criteria for defining METamp are uncertain. Here, we explored the concordance of these three methods in informing METamp status and identified patients likely to benefit from MET inhibitors. Methods: Tissue samples from LC patients who underwent MET detection by FISH, NGS, and IHC tests at Shanghai Chest Hospital were retrospectively collected. MET focal amplification and polysomy by FISH were determined as MET/CEP7 ratio ≥ 2, and < 2 with the average MET signals per cell ≥ 5, respectively. NGS-based MET focal amplification and polysomy were determined with in-house scripts (Burning Rock Biotech). Focal amplification and polysomy were defined as METamp-positive. IHC-based MET positive was determined with H-score ≥ 200. FISH was used as a reference. Results: A total of 231 patients with a median age of 65 years were enrolled. With FISH as reference testing, NGS detection for METamp showed 66.9% (87/130) sensitivity and 95.1% sensitivity (96/101), and IHC had 71.5% (93/130) sensitivity and 91.1% (92/101) specificity. Furthermore, NGS detection for MET focal amplification achieved 87.2% (75/86) sensitivity and 96.6% (140/145) specificity, while MET polysomy detection showed 20.5% (9/44) sensitivity and 98.4% (184/187) specificity. Of 153 treatment-naïve patients, patients with focal amplification (FISH: 16.7%; NGS: 16.3%) had a significantly lower frequency of classic LC oncogene alterations than those with polysomy (FISH: 51.6%, p = 0.001; NGS: 58.3%, p = 0.006) and METamp-negative patients (METneg; FISH: 72.1%, p < 0.001; NGS: 64.1%, p < 0.001). A total of 27 patients had follow-up data. The disease control rate (DCR) to MET inhibitors was 73.1% (19/26) for overall METamp, 81.0% (17/21) for focal amplification, and 40.0% (2/5) for polysomy using FISH results. In contrast, corresponding DCRs using NGS results were 84.2% (16/19), 88.9% (16/18), and 0% (0/1), respectively. Moreover, patients with NGS-based focal amplification had a significantly longer progression-free survival (PFS) than those with polysomy or METneg. Of note, 1 patient with METneg by FISH was determined to harbor focal amplification by NGS and achieved partial response to crizotinib with a PFS of 314 days. Conclusion: Our results suggest that MET focal amplification leads to oncogenic MET addiction and is associated with promising efficacy of MET inhibitors. MET focal amplification by NGS tests might be a feasible and powerful biomarker to identify LC patients who benefit from MET inhibitors. Citation Format: Chan Xiang, Lianying Guo, Ruiying Zhao, Haohua Teng, Zhou Zhang, Ting Kuang, Xinze Lv, Ting Hou, Chenglin Liu, Wenjie Sun, Haiwei Du, Yuchen Han. Next-generation sequencing-based MET focal amplification can predict treatment efficacy of MET inhibitors in lung 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 2133.

Topology-linked binary degrees of freedom of guided waves have been used to expand the channel capacity of and to ensure robust transmission through photonic waveguides. However, selectively exciting optical modes associated with the desired degree of freedom is challenging and typically requires spatially extended sources or filters. Both approaches are incompatible with the ultimate objective of developing compact mode-selective sources powered by single emitters. In addition, the implementation of highly desirable functionalities, such as controllable distribution of guided modes between multiple detectors, becomes challenging in highly-compact devices due to photon loss to reflections. Here, we demonstrate that a linearly-polarized dipole-like source can selectively excite a topologically robust edge mode with the desired valley degree of freedom. Reflection-free routing of valley-polarized edge modes into two spatially-separated detectors with reconfigurable splitting ratios is also presented. An optical implementation of such a source will have the potential to broaden the applications of topological photonic devices., Comment: The following article has been submitted to Applied Physics Letters