Search for exotic decays of the Higgs boson to a pair of pseudoscalars in the μμbb and ττbb final states

A search for exotic decays of the Higgs boson (H ) with a mass of 125Ge V to a pair of light pseudoscalars a 1 is performed in final states where one pseudoscalar decays to two b quarks and the other to a pair of muons or τ leptons. A data sample of proton-proton collisions at s = 13 Te V corresponding to an integrated luminosity of 138fb - 1 recorded with the CMS detector is analyzed. No statistically significant excess is observed over the standard model backgrounds. Upper limits are set at 95% confidence level (CL ) on the Higgs boson branching fraction to μ μ b b and to τ τ b b , via a pair of a 1 s. The limits depend on the pseudoscalar mass m a 1 and are observed to be in the range (0.17-3.3) × 10 - 4 and (1.7-7.7) × 10 - 2 in the μ μ b b and τ τ b b final states, respectively. In the framework of models with two Higgs doublets and a complex scalar singlet (2HDM+S), the results of the two final states are combined to determine upper limits on the branching fraction B ( H → a 1 a 1 → ℓ ℓ b b ) at 95% CL , with ℓ being a muon or a τ lepton. For different types of 2HDM+S, upper bounds on the branching fraction B ( H → a 1 a 1 ) are extracted from the combination of the two channels. In most of the Type II 2HDM+S parameter space, B ( H → a 1 a 1 ) values above 0.23 are excluded at 95% CL for m a 1 values between 15 and 60Ge V .

Observation of WWγ Production and Search for Hγ Production in Proton-Proton Collisions at sqrt[s]=13 TeV

The observation of WWγ production in proton-proton collisions at a center-of-mass energy of 13 TeV with an integrated luminosity of 138  fb^{-1} is presented. The observed (expected) significance is 5.6 (5.1) standard deviations. Events are selected by requiring exactly two leptons (one electron and one muon) of opposite charge, moderate missing transverse momentum, and a photon. The measured fiducial cross section for WWγ is 5.9±0.8(stat)±0.8(syst)±0.7(modeling)  fb, in agreement with the next-to-leading order quantum chromodynamics prediction. The analysis is extended with a search for the associated production of the Higgs boson and a photon, which is generated by a coupling of the Higgs boson to light quarks. The result is used to constrain the Higgs boson couplings to light quarks.

New Structures in the J/ψJ/ψ Mass Spectrum in Proton-Proton Collisions at sqrt[s]=13 TeV

A search is reported for near-threshold structures in the J/ψJ/ψ invariant mass spectrum produced in proton-proton collisions at sqrt[s]=13  TeV from data collected by the CMS experiment, corresponding to an integrated luminosity of 135  fb^{-1}. Three structures are found, and a model with quantum interference among these structures provides a good description of the data. A new structure is observed with a local significance above 5 standard deviations at a mass of 6638_{-38}^{+43}(stat)_{-31}^{+16}(syst)  MeV. Another structure with even higher significance is found at a mass of 6847_{-28}^{+44}(stat)_{-20}^{+48}(syst)  MeV, which is consistent with the X(6900) resonance reported by the LHCb experiment and confirmed by the ATLAS experiment. Evidence for another new structure, with a local significance of 4.7 standard deviations, is found at a mass of 7134_{-25}^{+48}(stat)_{-15}^{+41}(syst)  MeV. Results are also reported for a model without interference, which does not fit the data as well and shows mass shifts up to 150 MeV relative to the model with interference.

Search for Scalar Leptoquarks Produced via τ-Lepton-Quark Scattering in pp Collisions at sqrt[s]=13 TeV

The first search for scalar leptoquarks produced in τ-lepton-quark collisions is presented. It is based on a set of proton-proton collision data recorded with the CMS detector at the LHC at a center-of-mass energy of 13 TeV corresponding to an integrated luminosity of 138  fb^{-1}. The reconstructed final state consists of a jet, significant missing transverse momentum, and a τ lepton reconstructed through its hadronic or leptonic decays. Limits are set on the product of the leptoquark production cross section and branching fraction and interpreted as exclusions in the plane of the leptoquark mass and the leptoquark-τ-quark coupling strength.

ELABELA-APJ Axis Enhances Mesenchymal Stem Cell Proliferation and Migration via the METTL3/PI3K/AKT Pathway

Mesenchymal stem cells (MSCs) possess a strong therapeutic potential in regenerative medicine. ELABELA (ELA) is a 32 amino acid peptide that binds to the apelin peptide jejunum receptor (APJ) to regulate cell proliferation and migration. The aim of this study was to investigate the function of ELA vis-a-vis the MSC proliferation and migration, and further explore the underlying mechanism. We demonstrated that the exogenous supplement of ELA boosts the proliferation and migration ability of MSCs, alongside improved in vitro cell viability. These capabilities were rendered moot upon APJ knockdown. In addition, ELA (5-20 μM) was shown to upregulate the expression of METTL3 in a concentrationdependent pattern, a capacity which was suppressed by APJ reduction, whereas the downregulation of METTL3 expression blocked the beneficial effects induced by ELA. ELA was also observed to upregulate the phosphorylation level of AKT. This ELA-induced activation of the PI3K/AKT pathway, however, is inhibited with knockdown of METTL3. Our data indicate that ELA could act as a promoter of MSC proliferation and migration in vitro through the APJ receptor, something which might be attributed to the activation of the METTL3/PI3K/AKT signaling pathway. Therefore, ELA is a candidate for optimizing MSC-based cell therapy, while METTL3 is a potential target for its promoting action on MSCs.

Impact of Cucurbita moschata Resistant Rootstocks on Cucumis sativus Fruit and Meloidogyne incognita Development

Plant grafting can provide resistance to nematodes. There is a distinct need to determine the role of Meloidogyne incognita-resistant rootstocks on the growth and quality of grafted cucumber plants. Cucumber (Cucumis sativus L.) cultivar Jinchun No. 4 (J) was hole grafted onto the pumpkin (Cucurbita moschata) cultivars Xiuli (X), Banzhen No. 3 (B), and its root to generate JX, JB, and JJ plants. The histopathology and M. incognita development associated with JX, JB, and JJ were analyzed under incubator and high plastic tunnel conditions. Under incubator conditions, M. incognita root galls and egg mass indices associated with the JX and JB resistant rootstocks were significantly (P < 0.05) lower than those associated with JJ susceptible rootstocks. In addition, the number of eggs were 73.3 ± 8.8% and 85.3 ± 7.7% less, respectively. The number of second-stage juveniles (J2s) in JX roots decreased by 57.1 ± 9.2% compared with that in JJ, and the giant cell and J2 development were poor in JX and JB roots. In pot experiments under a high plastic tunnel, plant height, stem diameter, leaf area, and yield of M. incognita-infected JX plants were not significantly different from those of noninoculated control. There was no significant difference in fruit weight, length, firmness, soluble solids, and color among the three grafted plants. The yield per JB plant was increased compared with that of JJ, irrespective of nematode presence. In the M. incognita-infested soil experiment in a high plastic tunnel, the yield per JX and JB plant were significantly higher than JJ (P < 0.05). Thus, the pumpkin rootstock Xiuli and Banzhen No. 3 are promising rootstocks for managing M. incognita without affecting cucumber fruit quality. Grafting provides a good basis for studying the defense mechanism of rootstocks against M. incognita.

Observation of Single-Top-Quark Production in Association with a Photon Using the ATLAS Detector

This Letter reports the observation of single top quarks produced together with a photon, which directly probes the electroweak coupling of the top quark. The analysis uses 139  fb^{-1} of 13 TeV proton-proton collision data collected with the ATLAS detector at the Large Hadron Collider. Requiring a photon with transverse momentum larger than 20 GeV and within the detector acceptance, the fiducial cross section is measured to be 688±23(stat) _{-71}^{+75}(syst)  fb, to be compared with the standard model prediction of 515_{-42}^{+36}  fb at next-to-leading order in QCD.

Observation of the γγ→ττ Process in Pb+Pb Collisions and Constraints on the τ-Lepton Anomalous Magnetic Moment with the ATLAS Detector

This Letter reports the observation of τ-lepton-pair production in ultraperipheral lead-lead collisions Pb+Pb→Pb(γγ→ττ)Pb and constraints on the τ-lepton anomalous magnetic moment a_{τ}. The dataset corresponds to an integrated luminosity of 1.44  nb^{-1} of LHC Pb+Pb collisions at sqrt[s_{NN}]=5.02  TeV recorded by the ATLAS experiment in 2018. Selected events contain one muon from a τ-lepton decay, an electron or charged-particle track(s) from the other τ-lepton decay, little additional central-detector activity, and no forward neutrons. The γγ→ττ process is observed in Pb+Pb collisions with a significance exceeding 5 standard deviations and a signal strength of μ_{ττ}=1.03_{-0.05}^{+0.06} assuming the standard model value for a_{τ}. To measure a_{τ}, a template fit to the muon transverse-momentum distribution from τ-lepton candidates is performed, using a dimuon (γγ→μμ) control sample to constrain systematic uncertainties. The observed 95% confidence-level interval for a_{τ} is -0.057 Collapse

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Exploring the Efficacy and Molecular Mechanism of Systemic Therapy-Based Split-Course Stereotactic Body Radiation Therapy for Solid Tumors

PURPOSE/OBJECTIVE(S)

Considering the therapeutic toxicity, the question of how to administer adequate chemotherapy to synchronize Stereotactic body radiation therapy (SBRT) treatment strategy for maximizing the benefits of neoadjuvant therapy to improve prognosis is a challenging and debatable issue. This study explores the feasibility and theoretical advantages of the simultaneous implementation of split-course SBRT with systemic treatment.

MATERIALS/METHODS

We evaluated the effect of three irradiation regimens (conventional radiotherapy (C-R, 15×2 Gy, (D1-5, D8-12, D15-19)), continuous SBRT (C-S, 3×7 Gy, (D1-3)), split SBRT (S-S, 3×7 Gy, (D1, D10, D19)) in combination with systemic therapy (chemotherapy (gemcitabine), PD-1 inhibitor (Anti-mouse PD-1 antibody) and angiogenesis-targeting agent (Anlotinib)) on tumor growth and survival by using the immunologically active C57BL/6 bilateral subcutaneous model with different cancer cells. At different time points after treatment, we monitored changes in the tumor microenvironment and explored the possible mechanisms.

RESULTS

In the case of radiotherapy alone, we found similar tumor control in all groups but the best survival in the S-S group. When combined with systemic therapy, the S-S group has shown advantages in tumor control and survival. And the S-S combination group induced more CD4+ and CD8+ T lymphocyte infiltration in the tumor, which had the highest number of tumor vessels and the smallest area of hypoxia. Tumor cell PD-L1 expression was increased after radiotherapy in all but the most elevated and persistent S-S combination treatment group. CD3+ T cells, CD4+ T cells and CD8+ T cells peaked at weeks 2-3 after treatment, and all remained at the highest level for 6 weeks in the S-S combination group. Meanwhile, PD-L1 expression was significantly higher in all tumors in the third week than in other groups. The most significant reduction in the hypoxic area and increase in perfusion level was observed in the S-S group in the third week. RNA sequencing analysis revealed that immune response-related pathways were upregulated on the irradiated and non-irradiated side, tumor proliferation and invasion on the non-irradiated side, and angiogenesis-related pathways were down-regulated in the fractionated SBRT combination treatment group. In both irradiated side and non-irradiated side tumor tissues where the abscopal effect was observed, immune response-related pathways were upregulated in the S-S group relative to the C-R group, and tumor proliferation and invasion and angiogenesis-related pathways were found to be downregulated in the non-irradiated side.

CONCLUSION

In preclinical models, the combination of split SBRT with systemic therapy has been shown to be more advantageous than conventional segmentation, possibly by affecting immune cell infiltration in the tumor microenvironment and reducing tumor hypoxia.

Multimodal analysis of cell-free DNA whole-methylome sequencing for cancer detection and localization

Multimodal epigenetic characterization of cell-free DNA (cfDNA) could improve the performance of blood-based early cancer detection. However, integrative profiling of cfDNA methylome and fragmentome has been technologically challenging. Here, we adapt an enzyme-mediated methylation sequencing method for comprehensive analysis of genome-wide cfDNA methylation, fragmentation, and copy number alteration (CNA) characteristics for enhanced cancer detection. We apply this method to plasma samples of 497 healthy controls and 780 patients of seven cancer types and develop an ensemble classifier by incorporating methylation, fragmentation, and CNA features. In the test cohort, our approach achieves an area under the curve value of 0.966 for overall cancer detection. Detection sensitivity for early-stage patients achieves 73% at 99% specificity. Finally, we demonstrate the feasibility to accurately localize the origin of cancer signals with combined methylation and fragmentation profiling of tissue-specific accessible chromatin regions. Overall, this proof-of-concept study provides a technical platform to utilize multimodal cfDNA features for improved cancer detection.

Erratum: Global Polarization of Ξ and Ω Hyperons in Au+Au Collisions at sqrt[s_{NN}]=200 GeV [Phys. Rev. Lett. 126, 162301 (2021)]

This corrects the article DOI: 10.1103/PhysRevLett.126.162301.

Strong Constraints on Jet Quenching in Centrality-Dependent p+Pb Collisions at 5.02 TeV from ATLAS

Jet quenching is the process of color-charged partons losing energy via interactions with quark-gluon plasma droplets created in heavy-ion collisions. The collective expansion of such droplets is well described by viscous hydrodynamics. Similar evidence of collectivity is consistently observed in smaller collision systems, including pp and p+Pb collisions. In contrast, while jet quenching is observed in Pb+Pb collisions, no evidence has been found in these small systems to date, raising fundamental questions about the nature of the system created in these collisions. The ATLAS experiment at the Large Hadron Collider has measured the yield of charged hadrons correlated with reconstructed jets in 0.36  nb^{-1} of p+Pb and 3.6  pb^{-1} of pp collisions at 5.02 TeV. The yields of charged hadrons with p_{T}^{ch}>0.5  GeV near and opposite in azimuth to jets with p_{T}^{jet}>30 or 60 GeV, and the ratios of these yields between p+Pb and pp collisions, I_{pPb}, are reported. The collision centrality of p+Pb events is categorized by the energy deposited by forward neutrons from the struck nucleus. The I_{pPb} values are consistent with unity within a few percent for hadrons with p_{T}^{ch}>4  GeV at all centralities. These data provide new, strong constraints that preclude almost any parton energy loss in central p+Pb collisions.

Search for Heavy Neutral Leptons in Decays of W Bosons Using a Dilepton Displaced Vertex in sqrt[s]=13 TeV pp Collisions with the ATLAS Detector

A search for a long-lived, heavy neutral lepton (N) in 139  fb^{-1} of sqrt[s]=13  TeV pp collision data collected by the ATLAS detector at the Large Hadron Collider is reported. The N is produced via W→Nμ or W→Ne and decays into two charged leptons and a neutrino, forming a displaced vertex. The N mass is used to discriminate between signal and background. No signal is observed, and limits are set on the squared mixing parameters of the N with the left-handed neutrino states for the N mass range 3  GeV Collapse

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Test of CP Invariance in Higgs Boson Vector-Boson-Fusion Production Using the H→γγ Channel with the ATLAS Detector

A test of CP invariance in Higgs boson production via vector-boson fusion has been performed in the H→γγ channel using 139  fb^{-1} of proton-proton collision data at sqrt[s]=13  TeV collected by the ATLAS detector at the LHC. The optimal observable method is used to probe the CP structure of interactions between the Higgs boson and electroweak gauge bosons, as described by an effective field theory. No sign of CP violation is observed in the data. Constraints are set on the parameters describing the strength of the CP-odd component in the coupling between the Higgs boson and the electroweak gauge bosons in two effective field theory bases: d[over ˜] in the HISZ basis and c_{HW[over ˜]} in the Warsaw basis. The results presented are the most stringent constraints on CP violation in the coupling between Higgs and weak bosons. The 95% C.L. constraint on d[over ˜] is derived for the first time and the 95% C.L. constraint on c_{HW[over ˜]} has been improved by a factor of 5 compared to the previous measurement.

[Diagnostic and prognostic values of flow cytometry in diffuse large B-cell lymphoma with bone marrow involvement]

Objective: To analyze the diagnostic and prognostic values of flow cytometry (FC) in diffuse large B cell lymphoma (DLBCL) with bone marrow involvement (BMI). Methods: The clinical data of 412 patients with newly diagnosed DLBCL, including 243 males and 169 females, aged 64 (28-92) years old, in the Department of Hematology at Peking University Third Hospital from December 2012 to June 2022 were retrospectively analyzed. All patients underwent bone marrow biopsy (BMB) and bone marrow FC. The patients with BMI by FC were further detected by fluorescence in situ hybridization (FISH) for gene analysis. The positive rates and consistency of BMI detected by BMB and FC were evaluated. According to the results of BMB and FC examinations, all patients were divided into four groups: the BMB+FC+group (115 cases), the BMB-FC+group (50 cases), the BMB+FC-group (8 cases, the results did not include in statistical analysis because of small sample size), and the BMB-FC-group (239 cases). The clinical features, treatment response rates, 5-year survival rates, and immunophenotype characteristics by FC in different groups were analyzed. Results: Among the 412 patients with DLBCL, the positivity rates of BMB and FC for BMI detection were 29.9% (123/412) and 40.0% (165/412), respectively. Good consistency between BMB and FC was found (Kappa=0.841, P=0.001). The numbers of extranodal involvement≥2, splenomegaly, huge mass, higher Ki-67 score, higher international prognostic index (IPI) score, thrombocytopenia, and elevated lactate dehydrogenase level were more prevalent in the BMB+FC+group than those in the BMB-FC+group and the BMB-FC-group (all P<0.05). The treatment response rate in BMB+FC+group was 63.5% (73/115), which was lower than those in BMB-FC+group (88.0%, 44/50, P=0.048) and BMB-FC-group (90.0%, 215/239, P=0.032), respectively. The 5-year overall survival rates in three groups were (53.6±9.7) %, (72.5±8.6) %, and (75.2±7.6) %, respectively, with a statistically significant difference (P=0.037). According to the FISH results of bone marrow, 102 cases were diagnosed as not otherwise specified (NOS), 48 cases were diagnosed as double hit lymphoma (DHL), and 15 cases were diagnosed as triple hit lymphoma (THL). Compared with NOS subtypes, the tumor cells in DHL or THL subtypes had higher proportion of increased side scatter (SSC), higher positive rates of CD10 expression, CD38 strong expression and CD56 expression, and lower proportion of surface immunoglobulin light chain restriction (all P<0.05). Conclusions: FC is well consistent with BMB in diagnosing DLBCL with BMI. Combined with FISH detection, FC can contribute to the auxiliary diagnosis and risk stratification for DHL and THL, and provide reference for the prognostic evaluation in DLBCL with BMI.

Screening and Identification of Garlic Leaf Blight (Pleospora herbarum)-Resistant Mutants Induced by Ethyl Methane Sulphonate

Garlic (Allium sativum L.) is a popular condiment used as both medicine and food. Garlic production in China is severely affected by continuous cropping and is especially affected by leaf blight disease. Garlic is sterile, so it is very important to develop specialized genotypes, such as those for disease resistance, nutritional quality, and plant architecture, through genetic modification and innovation. In this experiment, we applied the induction method using EMS to mutate garlic cloves of cultivar G024. From the mutations, 5000 M₀ mutants were generated and planted in the field. Then, 199 M₁ mutant lines were screened according to growth potential and resistance to leaf blight. From M₂ to M₃, 169 generational lines were selected that grew well and were resistant to leaf blight in the field. Thereafter, their resistance to leaf blight was further analyzed in the lab; 21 lines resistant to leaf blight that had good growth potential were identified, among which 3 mutants were significantly different, and these were further screened. Also, transcriptome analysis of two mutants infected with Pleospora herbarum, A150 and G024, was performed, and the results revealed 2026 and 4678 differentially expressed genes (DEGs), respectively. These DEGs were highly enriched in hormone signaling pathway, plant-pathogen interaction, and MAPK signaling pathway. Therefore, the results provide a theoretical and technical basis for the creation of garlic germplasm resistant to leaf blight.

[LRG1 inhibits hepatic macrophage activation by enhancing TGF-β1 signaling to alleviate MAFLD in mice]

OBJECTIVE

To explore the effect of leucine-rich α-2-glycoprotein (LRG1) derived from hepatocytes on activation of hepatic M1 Kupffer cells.

METHODS

A metabolic dysfunction-associated fatty liver disease (MAFLD) model was established in BALB/c mice by high-fat diet (HFD) feeding for 16 weeks. Oleic acid was used to induce steatosis in primary cultures of mouse hepatocytes. The mRNA and protein expressions of LRG1 in mouse liver tissues and hepatocytes were detected by real-time PCR and Western blotting. Primary hepatic macrophages were stimulated with the conditioned medium (CM) from steatotic hepatocyte along with LRG1 or transforming growth factor-β1 (TGF-β1), or both for 24 h, and the expression levels of inducible nitric oxide synthase (iNOS) was detected with Western botting, and the mRNA expressions of iNOS, chemokine ligand 1 (CXCL-1) and interleukin-1β (IL-1β) were measured by RT-PCR. The MAFLD mice were injected with LRG1 (n=6), TGF-β1 (n=6), or both (n=6) through the caudal vein, and the live tissues were collected for HE staining and immumohistochemical detection of F4/80 expression; the mRNA expressions of iNOS, CXCL-1 and IL-1β in liver tissues were detected using RT-PCR.

RESULTS

The mRNA and protein expression levels of LRG1 were significantly downregulated in the liver tissues of MAFLD mice and steatotic hepatocytes (P < 0.05). Treatment of the hepatic macrophages with CM from steatosis hepatocytes significantly enhanced the mRNA expression levels of iNOS, CXCL-1 and IL-1β, and these changes were significantly inhibited by the combined treatment with TGF-β1 and LRG1 (P < 0.05). In MAFLD mice, injections with either LRG1 or TGF-β1 alone reduced hepatic lipid deposition and intrahepatic macrophage infiltration, and these effects were significantly enhanced by their combined treatment, which also more strongly inhibited the mRNA expression levels of iNOS, CXCL-1 and IL-1β (P < 0.05).

CONCLUSION

LRG1 inhibits hepatic macrophage infiltration by enhancing TGF-β1 signaling to alleviate fatty liver inflammation in MAFLD mice.

Is endometrial sampler SAP-1 a good way to diagnose the common intrauterine occupying lesions?-A diagnostic study

Background

Intrauterine occupying lesion is clinically common in the female reproductive organs. Endometrial cancer is the most critical one among intrauterine occupying lesions, which accordingly is considered as the main indication for endometrial cancer screening, for which endometrial sampler SAP-1 was recommended as an effective sampling tool.

Objective

This study aimed to evaluate the diagnostic efficacy of SAP-1 for endometrial polyp and uterine submucous myoma.

Materials and Methods

From August 2018 to June 2022, patients who were hospitalized for undergoing hysteroscopy examination were enrolled in this study. Before the procedure, endometrial samples were collected by the method of SAP-1. The histological results were compared with those by hysteroscopy sampling to analyze the diagnostic efficacy of SAP-1.

Results

The qualified rate for the SAP-1 sampling was 92.1%, which is a bit lower than that by method of hysteroscopy (95.3%). And the difference was not statistically significant (P > 0.05). Endometrial polyp (47.5%) and uterine submucous myoma (7.1%) accounted for the majority of endometrial lesions, while only 11.3% endometrial polyps (17/151) and 0% submucous myomas (0/23) were detected by SAP-1 sampling.

Conclusion

Endometrial sampler SAP-1 is not effective in detection of solid intrauterine lesions indicated by the imaging examination. Hysteroscopy is recommended for definite diagnosis.

Detection of multiple types of cancer driver mutations using targeted RNA sequencing in nonsmall cell lung cancer

BACKGROUND

DNA-based next-generation sequencing has been widely used in the selection of target therapies for patients with nonsmall cell lung cancer (NSCLC). RNA-based next-generation sequencing has been proven to be valuable in detecting fusion and exon-skipping mutations and is recommended by National Comprehensive Cancer Network guidelines for these mutation types.

METHODS

The authors developed an RNA-based hybridization panel targeting actionable driver oncogenes in solid tumors. Experimental and bioinformatics pipelines were optimized for the detection of fusions, single-nucleotide variants (SNVs), and insertion/deletion (indels). In total, 1253 formalin-fixed, paraffin-embedded samples from patients with NSCLC were analyzed by DNA and RNA panel sequencing in parallel to assess the performance of the RNA panel in detecting multiple types of mutations.

RESULTS

In analytical validation, the RNA panel achieved a limit of detection of 1.45-3.15 copies per nanogram for SNVs and 0.21-6.48 copies per nanogram for fusions. In 1253 formalin-fixed, paraffin-embedded NSCLC samples, the RNA panel identified a total of 124 fusion events and 26 MET exon 14-skipping events, in which 14 fusions and six MET exon 14-skipping mutations were missed by DNA panel sequencing. By using the DNA panel as the reference, the positive percent agreement and the positive predictive value of the RNA panel were 98.08% and 98.62%, respectively, for detecting targetable SNVs and 98.15% and 99.38%, respectively, for detecting targetable indels.

CONCLUSIONS

Parallel DNA and RNA sequencing analyses demonstrated the accuracy and robustness of the RNA sequencing panel in detecting multiple types of clinically actionable mutations. The simplified experimental workflow and low sample consumption will make RNA panel sequencing a potentially effective method in clinical testing.

Identification of genetic and immune signatures for the recurrence of HER2-positive breast cancer after trastuzumab-based treatment

PURPOSE

To determine the genetic and immune features associated with the recurrence of human epidermal growth factor receptor2-positive (HER2 +) breast cancer (BC) after trastuzumab-based treatment.

METHODS

A retrospective cohort study of 48 patients who received trastuzumab-based treatment was divided into recurrent and non-recurrent groups according to clinical follow-up. Baseline samples from all 48 patients were analyzed for genetic variation, HLA allele type, gene expression, and immune features, which were linked to HER2 + BC recurrence. Statistics included logistic regression models, Kaplan-Meier plots, and Univariate Cox proportional hazards models.

RESULTS

Compared with the non-recurrent group, the extracellular matrix-related pathway and 3 Hallmark gene sets were enriched in the recurrent group. The infiltration levels of immature B cells and activated B cells were significantly increased in the non-recurrent group, which correlated remarkably with improved overall survival (OS) in two other published gene expression datasets, including TCGA and METABRIC. In the TCGA cohort (n = 275), activated B cells (HR 0.23, 95%CI 0.13-0.43, p < 0.0001), and immature B cells (HR 0.26, 95%CI 0.12-0.59, p < 0.0001). In the METABRIC cohort (n = 236), activated B cells (HR 0.60, 95%CI 0.43-0.83, p = 0.002), and immature B cells (HR 0.65, 95%CI 0.47-0.91, p = 0.011). Cox regression suggested that immature B cells and activated B cells were protective factors for outcome OS.

CONCLUSIONS

Aberrant activation of multiple pathways and low baseline tumor-infiltrating B cells are related to HER2 + BC trastuzumab-based recurrence, which primarily affects the antitumor activity of trastuzumab.

Early Release Science of the exoplanet WASP-39b with JWST NIRSpec PRISM

Transmission spectroscopy1-3 of exoplanets has revealed signatures of water vapour, aerosols and alkali metals in a few dozen exoplanet atmospheres4,5. However, these previous inferences with the Hubble and Spitzer Space Telescopes were hindered by the observations' relatively narrow wavelength range and spectral resolving power, which precluded the unambiguous identification of other chemical species-in particular the primary carbon-bearing molecules6,7. Here we report a broad-wavelength 0.5-5.5 µm atmospheric transmission spectrum of WASP-39b8, a 1,200 K, roughly Saturn-mass, Jupiter-radius exoplanet, measured with the JWST NIRSpec's PRISM mode9 as part of the JWST Transiting Exoplanet Community Early Release Science Team Program10-12. We robustly detect several chemical species at high significance, including Na (19σ), H2O (33σ), CO2 (28σ) and CO (7σ). The non-detection of CH4, combined with a strong CO2 feature, favours atmospheric models with a super-solar atmospheric metallicity. An unanticipated absorption feature at 4 µm is best explained by SO2 (2.7σ), which could be a tracer of atmospheric photochemistry. These observations demonstrate JWST's sensitivity to a rich diversity of exoplanet compositions and chemical processes.

Identification and characterization of CsSRP43, a major gene controlling leaf yellowing in cucumber

Mutants are crucial to extending our understanding of genes and their functions in higher plants. In this study a spontaneous cucumber mutant, yf, showed yellow color leaves, had significant decreases in related physiological indexes of photosynthesis characteristics, and had more abnormal chloroplasts and thylakoids. Inheritance analysis indicated that the yellow color of the leaf was controlled by a recessive nuclear locus, yf. A candidate gene, CsSRP43, encoding a chloroplast signal recognition particle 43 protein, was identified through map-based cloning and whole-genome sequence analysis. Alignment of the CsSRP43 gene homologs between both parental lines revealed a 7-kb deletion mutation including the promoter region and the coding sequence in the yf mutant. In order to determine if the CsSRP43 gene was involved in the formation of leaf color, the CRISPR/Cas9-mediate system was used to modify CsSRP43 in the 9930 background; two independent transgenic lines, srp43-1 and srp43-2, were generated, and they showed yellow leaves with abnormal chloroplasts and thylakoids. Transcriptomic analysis revealed that differentially expressed genes associated with the photosynthesis-related pathway were highly enriched between srp43-1 and wild type, most of which were significantly downregulated in line srp43-1. Furthermore, yeast two-hybrid and biomolecular fluorescence complementation assays were used to confirm that CsSRP43 directly interacted with LHCP and cpSRP54 proteins. A model was established to explain the molecular mechanisms by which CsSRP43 participates in the leaf color and photosynthesis pathway, and it provides a valuable basis for understanding the molecular and genetic mechanisms of leaf color in cucumber.

[Direct intraoperative two-step distraction and reduction for basilar invagination with atlantoaxial dislocation]

Objective: To assess the clinical impact of direct two-step distraction reduction (TSDR) for basilar invagination (BI) with atlantoaxial dislocation (AAD). Methods: Retrospective analysis was conducted on the clinical data of patients who underwent TSDR and occipitocervical fusion in West China Hospital between October 2013 and March 2021. Depending on whether the preoperative decrease was greater than 50% on preoperative hyperextension X-rays, the patients were split into two groups. The neurological function [Japanese Orthopedic Association (JOA) score], atlantodens interval (ADI), the distance of odontoid process beyond McRae Line (ML) and Wackenheim Line (WL), cervicomedullary angle (CMA), O-C₂ angle (OC2A), and complications incidence were compared between two groups preoperatively and postoperatively. Results: There were 12 men and 23 women among the 35 patients with BI and AAD, and the age ranged from 28 to 71 years, with an mean age of (52.0±13.4) years. In the preoperative reduction ≥50% group, there were 4 males and 9 females with an average age of (54.0±13.8) years; in the preoperative reduction <50% group, there were 8 males and 14 females with a mean age of (50.9±13.4) years. All the patients were followed-up for a mean time of (23.3±13.4) months. There was no significant difference in age, gender, bleeding, length of hospital stay and follow-up time between the two groups (all P>0.05). The JOA score, ADI, WL, ML and CMA of 35 patients were significantly improved when compared with those before operation (all P<0.05). The reduction degree of ADI, ML and WL was more than 80% in 31 cases (88.57%), 30 cases (85.71%) and 31 cases (88.57%), respectively. There was no significant difference in postoperative ADI, ML and WL between the two groups (all P>0.05). All patients had no incision infection, no loosening or breakage of the internal fixators. Dysphagia occurred in 3 patients, non-fusion happened in 1 patient, but no instability in X-ray of cervical dynamic position was found, no loosening or displacement occurred in internal fixators, and partial spontaneous fusion occurred between atlantoaxial lateral mass joints. Conclusions: For BI with AAD without atlantoaxial bony connection or serious atlantoaxial facet joint inclination, TSDR could obtain satisfactory reduction degree. The reduction degree on preoperative hyperextension X-ray doesn't affect the degree of intraoperative reduction.

Relationship between Key Environmental Factors and the Architecture of Fruit Shape and Size in Near-Isogenic Lines of Cucumber (Cucumis sativus L.)

Fruit shape and size are complex traits influenced by numerous factors, especially genetics and environment factors. To explore the mechanism of fruit shape and size development in cucumber, a pair of near-isogenic lines (NIL) Ln35 and Ln37 were used. The fruit length and diameter, cell length and diameter, and related gene expression were measured. Both the fruit length, diameter, and cell length and diameter showed sigmate curves in the two lines. The cell length and diameter were significantly positively correlated with fruit length and diameter both in two lines. The expression of CsACS2 and CsLNG showed significant positive correlations with fruit length and diameter increment in Ln35, and there was no correlation in Ln37. Furthermore, there were significant positive correlations between fruit size and thermal effectiveness (TE), as well as between fruit size and photosynthetic active radiation (PAR), both in two lines. Two models using logistic regression were formulated to assess the relationships among fruit length and diameter in Ln35 and Ln37, respectively, based on thermal effectiveness and photosynthetic active radiation (TEP). The coefficient R² values of the models were 0.977 and 0.976 in Ln35, and 0.987 and 0.981 in Ln37, respectively. The root mean square error (RMSE) was 12.012 mm and 4.338 mm in Ln35, and 5.17 mm and 7.082 mm in Ln37, respectively, which illustrated the accurate and efficient of these models. These biologically interpreted parameters will provide precision management for monitoring fruit growth and forecasting the time of harvesting under different temperatures and light conditions.

Can Digital Finance Promote Peak Carbon Dioxide Emissions? Evidence from China

This paper uses Chinese provincial panel data from 2011 to 2019, measures CO₂ emissions of provinces in China using the IPCC method, and explores the impact of digital finance on CO₂ emissions through the SAR model and SDM. Empirical study shows that digital finance significantly reduces CO₂ emissions. Digital finance reduces CO₂ emissions by promoting energy industrial structure transformation and spreads to surrounding areas through spillover effects, contributes to increasing green patents granted and thus reduces regional CO₂ emissions, advances the green technological progress and therefore inhibits CO₂ emissions, but reduces the green technological progress in surrounding areas and increases CO₂ emissions due to the siphon effect. With the development of digital finance itself, the higher the level of financial regulation, green development and the green finance index, the better the effect of digital finance on CO₂ emission reduction. Additionally, digital finance significantly reduces CO₂ emissions in the south of China.

Heat Equilibration of Integer and Fractional Quantum Hall Edge Modes in Graphene

Hole-conjugate states of the fractional quantum Hall effect host counterpropagating edge channels which are thought to exchange charge and energy. These exchanges have been the subject of extensive theoretical and experimental works; in particular, it is yet unclear if the presence of integer quantum Hall edge channels stemming from fully filled Landau levels affects heat equilibration along the edge. In this Letter, we present heat transport measurements in quantum Hall states of graphene demonstrating that the integer channels can strongly equilibrate with the fractional ones, leading to markedly different regimes of quantized heat transport that depend on edge electrostatics. Our results allow for a better comprehension of the complex edge physics in the fractional quantum Hall regime.

[Epidemic trend and control progress of taeniasis and cysticercosis in Henan Province]

Henan Province is one of the provinces where taeniasis and cysticercosis were historically highly prevalent, and Taenia solium is the dominant species of tapeworm. Following the concerted efforts since 1970s, the prevalence of human taeniasis and cysticercosis has been maintained at a low level in Henan Province, which facilitates the national taeniasis and cysticercosis elimination program in China. Following the implementation of the policy of aeniasis and cysticercosis elimination and classified guidance, a great success has been achieved in aeniasis and cysticercosis control in Henan Province. With continuous promotion of the opening-up policy and the Belt and Road Initiative, there are still challenges in taeniasis and cysticercosis control. This review summarizes the control progress of taeniasis and cysticercosis and proposes the challenges of taeniasis and cysticercosis control in Henan Province.

Observation of WWW Production in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

This Letter reports the observation of WWW production and a measurement of its cross section using 139  fb^{-1} of proton-proton collision data recorded at a center-of-mass energy of 13 TeV by the ATLAS detector at the Large Hadron Collider. Events with two same-sign leptons (electrons or muons) and at least two jets, as well as events with three charged leptons, are selected. A multivariate technique is then used to discriminate between signal and background events. Events from WWW production are observed with a significance of 8.0 standard deviations, where the expectation is 5.4 standard deviations. The inclusive WWW production cross section is measured to be 820±100 (stat)±80 (syst)  fb, approximately 2.6 standard deviations from the predicted cross section of 511±18  fb calculated at next-to-leading-order QCD and leading-order electroweak accuracy.

A detailed map of Higgs boson interactions by the ATLAS experiment ten years after the discovery

The standard model of particle physics1-4 describes the known fundamental particles and forces that make up our Universe, with the exception of gravity. One of the central features of the standard model is a field that permeates all of space and interacts with fundamental particles5-9. The quantum excitation of this field, known as the Higgs field, manifests itself as the Higgs boson, the only fundamental particle with no spin. In 2012, a particle with properties consistent with the Higgs boson of the standard model was observed by the ATLAS and CMS experiments at the Large Hadron Collider at CERN10,11. Since then, more than 30 times as many Higgs bosons have been recorded by the ATLAS experiment, enabling much more precise measurements and new tests of the theory. Here, on the basis of this larger dataset, we combine an unprecedented number of production and decay processes of the Higgs boson to scrutinize its interactions with elementary particles. Interactions with gluons, photons, and W and Z bosons-the carriers of the strong, electromagnetic and weak forces-are studied in detail. Interactions with three third-generation matter particles (bottom (b) and top (t) quarks, and tau leptons (τ)) are well measured and indications of interactions with a second-generation particle (muons, μ) are emerging. These tests reveal that the Higgs boson discovered ten years ago is remarkably consistent with the predictions of the theory and provide stringent constraints on many models of new phenomena beyond the standard model.

Abstract 5150: Multimodal analysis of plasma cell-free DNA methylome for sensitive multi-cancer detection

Introduction: Genomic scale copy number, methylation, and fragmentation aberrations are proven genetic and epigenetic biomarkers of circulating tumor DNA (ctDNA). We developed a novel cell-free DNA (cfDNA) methylome sequencing assay that allows for integrative analysis of these genomic features for sensitive detection of multiple types of cancer.

Methods: Whole methylome sequencing (WMS) libraries were generated from enzymatically converted cfDNA. Low-pass (~2X) paired-end NGS sequencing was performed on WMS libraries and paired whole genome sequencing (WGS) libraries of unconverted cfDNA for technical comparison and analytical validation. For development of cancer detection models, we profiled the genome-wide methylation density (MD), fragment size index (FSI), fragment end motif (motif) and chromosome instability (CIN) based on WMS data from a discovery cohort of 352 healthy controls and 559 newly diagnosed cancer patients (45 breast, 105 colorectal, 44 esophageal, 79 gastric, 79 liver, 110 lung, 83 pancreatic, and 14 others), 34.5% of which were at stage I or II. Machine learning models, including KNN, SVM, LR, GBDT, and random forest were trained and tested for individual biomarker types, with a final ensemble classifier to integrate all biomarkers. Performance of the predictive model was confirmed on an independent validation cohort consisting of 145 healthy controls and 236 cancer patients (21 breast, 45 colorectal, 18 esophageal, 35 gastric, 34 liver, 47 lung, and 36 pancreatic), among which 31.8% were at early stages (I or II).

Results: WMS and WGS data from 512 cfDNA samples showed high concordance in CIN (R=0.988, 95% CI: 0.986-0.990) and FSI (R=0.961, 0.954-0.967) profiles. On the independent validation cohort, the optimal model selected for each of individual genomic features achieved following area under the ROC curve (AUC) values for cancer detection: MD-KNN, 0.830 (0.789-0.870); FSI-SVM, 0.904 (0.874-0.933); motif-SVM, 0.943 (0.920-0.966); and CIN-PAscore, 0.812 (0.770-0.854). The ensemble classifier based on linear SVM outperformed individual biomarkers, with an AUC value of 0.952 (0.934-0.971), which translated to, at 95% specificity, detection sensitivity of 66.7% for breast, 77.8% for colorectal, 83.3% for esophageal, 62.9% for gastric, 82.4% for liver, 66.0% for lung, and 77.8% for pancreatic cancers. Noteworthily, the overall sensitivity on early-stage cancer was 74.7%.

Conclusions: These results demonstrate the first proof of principle on the feasibility of integrating multiple genomic cancer markers on the same WMS technical platform. Low-pass WMS on plasma cfDNA from 10ml of blood with integrative multimodal analysis of methylation, fragmentation, and CNV profiles yields in satisfactory sensitivity and specificity for detection of multiple types of cancer, warranting a forthcoming prospective study to further assess its clinical performance in a larger cohort.

Citation Format: Yulong Li, Fenglong Bie, Fengwei Tan, Tiancheng Han, Shunli Yang, Fang Lv, Peiyao Nie, Qi Zhang, Yuanyuan Hong, Zhijie Wang, Ji He, Weizhi Chen, Liang Zhao, Shugeng Gao. Multimodal analysis of plasma cell-free DNA methylome for sensitive multi-cancer detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5150.

Early detection of colorectal adenocarcinoma by decoding epigenetic and DNA fragmentation fingerprints of plasma cell-free DNA

3550

Background: Cell-free DNA (cfDNA) methylation, fragmentation patterns, chromosome instability, and chromatin accessiblity have been previously shown to be valid plasma biomarkers for non-invasive cancer detection. However, conventional whole-genome bisulfite sequencing (WGBS) is unable to simultaneously profile all these biomarkers due to bisulfite-induced DNA damages. Here we developed a machine learning approach to comprehensively integrate multiple types of cancer genomic markers from enzyme-conversion-based low-pass whole-methylome sequencing (WMS) of plasma cfDNA to non-invasively detect colorectal adenocarcinoma. Methods: Plasma cfDNA sampels from 215 colorectal adenocarcinoma patients and 568 healthy individuals were collected and were split into the discovery and independent testing cohort. The discovery cohort includes 150 cancer patients and 398 healthy individuals and the independent testing cohort includes 65 cancer patients and 170 healthy individuals. Whole methylome sequencing (WMS) libraries were generated from enzymatically converted cfDNA and were subsequently paired-end sequenced at ̃2X coverage. The genome-wide methylation density, fragmentation fingerprints, chromosome instability, and chromatin accessibility were extracted from the WMS data and individually modelled via machine learning methods such as SVM, LR, GBDT, random forest. The final predictive model is an ensemble model integrating all uni-modal models. All models were trained and fitted on the discovery cohort. Results: Data of different modalities provide complementary information in separating the cancer patients from the healthy individuals. Unsupervised clustering of the individuals showed clear separation between cancer patients and healthy individuals. The final predictive model achieved AUC =0.982 in the discovery cohort and AUC =0.9664 in the independent testing cohort. Under a specificity of 94.71% (CI: 90% - 98.82%), sensitivity was 78.46% (CI: 60% - 92.31%) in the independent testing cohort. Separating the cancer patients into different stages, we found that the detection power is usuaul lower for early-stage cancer patients. Conclusions: These results demonstrate the first proof of principle on the feasibility of integrating multiple genomic cancer markers to non-invasively detect colorectal adenocarcinoma from WMS plasma cell-free DNA. A large prospective cohort study is planned to further validate its clinical performance.

An ultrasensitive approach for cancer screening and tissue of origin prediction based on targeted methylation sequencing of cell-free DNA

10553

Background: Cancer-specific therapy requires the identification of the tumor origin. Detecting cancer and identifying the tumor origin in early stage can improve the survival and prognosis of cancer patients. However, early diagnosis of cancer is challenging as the early symptoms of cancer are mild or even absent. In order to improve the diagnostic efficacy and the patient compliance, we developed a two-stage model for cancer diagnosis and tissue of origin (TOO) classification, using DNA methylation profile evaluated through non-invasive blood-based testing as biomarker. Methods: cfDNA samples from 302 healthy and 598 cancer patients of 8 cancer types (colorectal, lung, liver, pancreatic, gastric, esophagus, breast and ovarian) were sequenced by our in-house-designed DNA methylation panel and randomly split into a training dataset (213:426) and a testing dataset (89:172). The testing dataset was reserved to evaluate the performance of models and would not be used during the feature selection and model development process. Methylation levels of cfDNA samples were measured by the methylated fragment ratios (MFRs) in methylated-correlated blocks (MCBs). We first selected pan-cancer markers by comparing the MFR values of MCBs between the healthy and the diseased individuals and developed a binary classifier (hyper-methylation score). Sample correctly predicted by the hyper-methylation score in the cancer group were then used for TOO marker selection and model fitting. TOO biomarkers were obtained by a series of pairwise comparisons of MFR values between any two cancer types. A deconvolution model was built to estimate the composition of ctDNA, which implied the tumor origin. Results: The hyper-methylation score model based on 135 MCB biomarkers achieved an area under the curve (AUC) of 0.89 in the training dataset and 0.85 in the testing dataset. Under a specificity of 94.8%, sensitivity was 66.2% in the training dataset. Using the 282 cases successfully being predicted, 583 TOO markers were selected to build the deconvolution model. In the testing dataset, the specificity was 95.5%, and the overall sensitivity was 66.3%. With increasing stage, sensitivity increased in all cancer types: 34.6%, 57.1%, 62.5% and 84.8% in stage I, II, III and IV respectively. In stage I-III, sensitivity was 52.3%. TOO classes were predicted in the 114 true positives from the hyper-methylation score model, producing a top 1 accuracy (true class matched the most probable class) of 75.4% and a top 2 accuracy (true class matched the first or the second most probable class) of 84.2%. Top 1 accuracy was 71.1% in stage I-III, vs. 84.0% in stage IV. Top 2 accuracy was 82.2% in stage I-III, vs. 90.0% in stage IV. Conclusions: Our cfDNA-based epigenetic method achieved outstanding performance either in pan-cancer detection or in TOO classification, and is a promising tool for early-stage cancer diagnosis.

Non-invasive detection of esophageal carcinoma by integrative analysis of low-pass whole methylome sequencing of plasma cell-free DNA

4067

Background: Cell-free DNA (cfDNA) methylation, fragmentation patterns, chromosome instability, and chromatin accessiblity have been previously shown to be valid plasma biomarkers for non-invasive cancer detection. However, conventional whole-genome bisulfite sequencing (WGBS) is unable to simultaneously profile all these biomarkers due to bisulfite-induced DNA damages. Here we developed a machine learning approach to comprehensively integrate multiple types of cancer genomic markers from enzyme-conversion-based low-pass whole-methylome sequencing (WMS) of plasma cfDNA to non-invasively detect esophageal carcinoma. Methods: Plasma cfDNA sampels from 85 patients and 568 healthy individuals were collected and were split into the discovery and independent testing cohort. The discovery cohort includes 60 cancer patients and 398 healthy individuals and the independent testing cohort includes 25 cancer patients and 170 healthy individuals. Whole methylome sequencing (WMS) libraries were generated from enzymatically converted cfDNA and were subsequently paired-end sequenced at ̃2X coverage. The genome-wide methylation density, fragmentation fingerprints, chromosome instability, and chromatin accessibility were extracted from the WMS data and individually modelled via machine learning methods such as SVM, LR, GBDT, random forest. The final predictive model is an ensemble model integrating all uni-modal models. All models were trained and fitted on the discovery cohort. Results: Data of different modalities provide complementary information in separating the cancer patients from the healthy individuals. Unsupervised clustering of the individuals showed clear separation between cancer patients and healthy individuals. The final predictive model achieved AUC =96.25% in the discovery cohort and AUC =91.15% in the independent testing cohort. Under a specificity of 95.29% (CI: 87.64% - 100.00%), sensitivity was 72.00% (CI: 56.00% - 92.00%) in the independent testing cohort. Separating the cancer patients into different stages, we found that the detection power is usuaul lower for early-stage cancer patients. Conclusions: These results demonstrate the first proof of principle on the feasibility of integrating multiple genomic cancer markers to non-invasively detect esophageal carcinoma from WMS plasma cell-free DNA. A large prospective cohort study is planned to further validate its clinical performance.

Sensitive detection of pancreatic adenocarcinoma using plasma cell-free DNA methylomes

e16277

Background: Cell-free DNA (cfDNA) methylation, fragmentation patterns, chromosome instability, and chromatin accessiblity have been previously shown to be valid plasma biomarkers for non-invasive cancer detection. However, conventional whole-genome bisulfite sequencing (WGBS) is unable to simultaneously profile all these biomarkers due to bisulfite-induced DNA damages. Here we developed a machine learning approach to comprehensively integrate multiple types of cancer genomic markers from enzyme-conversion-based low-pass whole-methylome sequencing (WMS) of plasma cfDNA to non-invasively detect pancreatic adenocarcinoma. Methods: Plasma cfDNA sampels from 139 cancer patients and 568 healthy individuals were collected and were split into the discovery and independent testing cohort. The discovery cohort includes 99 cancer patients and 398 healthy individuals and the independent testing cohort includes 40 cancer patients and 170 healthy individuals. Whole methylome sequencing (WMS) libraries were generated from enzymatically converted cfDNA and were subsequently paired-end sequenced at ̃2X coverage. The genome-wide methylation density, fragmentation fingerprints, chromosome instability, and chromatin accessibility were extracted from the WMS data and individually modelled via machine learning methods such as SVM, LR, GBDT, random forest. The final predictive model is an ensemble model integrating all uni-modal models. All models were trained and fitted on the discovery cohort. Results: Data of different modalities provide complementary information in separating the cancer patients from the healthy individuals. Unsupervised clustering of the individuals showed clear separation between cancer patients and healthy individuals. The final predictive model achieved AUC =0.982 in the discovery cohort and AUC =0.986 in the independent testing cohort. Under a specificity of 96.23% (CI: 87% - 88%), sensitivity was 95% (CI: 93% - 96%) in the independent testing cohort. Separating the cancer patients into different stages, we found that the detection power is usuaul lower for early-stage cancer patients. Conclusions: These results demonstrate the first proof of principle on the feasibility of integrating multiple genomic cancer markers to non-invasively detect pancreatic adenocarcinoma from WMS plasma cell-free DNA. A large prospective cohort study is planned to further validate its clinical performance.

Detection of multiple types of cancer driver mutations using targeted RNA sequencing in NSCLC

e15043

Background: DNA NGS sequencing has been widely used as a companion diagnostic method for matching NSCLC patients with appropriate personalized target therapy. RNA-based NGS has been proved to be valuable in detecting fusion and exon skipping mutations and therefore recommended by NCCN guidelines for these mutation types. It would be helpful to have a diagnostic method that suits different types of clinically actionable mutations in a single tube. Methods: We developed an RNA-based hybridization panel targeting actionable driver oncogenes in solid tumors. Experimental and bioinformatics pipelines were optimized for detection of fusion, SNV and indel mutations, as well as gene expression quantification. Reference materials were used for analytical validation of the panel, and 1253 FFPE samples from NSCLC patients were analyzed by DNA panel sequencing and RNA panel sequencing in parallel to assess the performance of the RNA panel in detection of multiple types of clinically actionable mutations. Results: Analytical validation showed a detection specificity of 100.0% for SNVs and fusions. The targeted RNA panel achieved a 1.45-3.15 copies/ng limit of detection (LOD) for SNVs and a 0.21-6.48 copies/ng LOD for fusions. Gene expression analysis revealed a correlation greater than 0.9 between the RNA-seq and targeted RNA panel results. Among 1253 NSCLC FFPE samples, multiple mutation types were called at both DNA and RNA levels and compared between the two assays. Twenty-one fusion and six METex14 skipping events were only detected by the RNA panel. The positive percent agreement (PPA) and positive prediction value (PPV) were 98.08% and 98.62% for targetable SNVs and 98.15% and 99.38% for targetable Indels, respectively. We also explored the relationship of RNA expression with gene copy number and protein expression. The RPKM (reads per kilobase per million mapped reads) of EGFR transcripts exhibited a linear relationship with copy number, whereas MET gene expression seemed to be regulated in a more complexed manner. In IHC analysis, all MET IHC 3+ samples had significantly higher RPKM levels than samples with MET IHC level of 2+/1+. Conclusions: Parallel DNA and RNA systematic analysis demonstrated the accuracy and robustness of the RNA sequencing panel for detection of multiple types of clinically actionable mutations. The simplified experimental workflow, lowered cost and sample consumption, along with the superior performance in simultaneous detection of multiple types of mutations will make RNA panel sequencing an effective method in clinical testing for NSCLC.

Plasma cell-free DNA integrative analysis for early detection of hepatocellular carcinoma

e16173

Background: Cell-free DNA (cfDNA) methylation, fragmentation patterns, chromosome instability, and chromatin accessiblity have been previously shown to be valid plasma biomarkers for non-invasive cancer detection. However, conventional whole-genome bisulfite sequencing (WGBS) is unable to simultaneously profile all these biomarkers due to bisulfite-induced DNA damages. Here we developed a machine learning approach to comprehensively integrate multiple types of cancer genomic markers from enzyme-conversion-based low-pass whole-methylome sequencing (WMS) of plasma cfDNA to non-invasively detect hepatocellular carcinoma. Methods: Plasma cfDNA sampels from 127 cancer patients and 568 healthy individuals were collected and were split into the discovery and independent testing cohort. The discovery cohort includes 90 cancer patients and 398 healthy individuals and the independent testing cohort includes 37 cancer patients and 170 healthy individuals. Whole methylome sequencing (WMS) libraries were generated from enzymatically converted cfDNA and were subsequently paired-end sequenced at ̃2X coverage. The genome-wide methylation density, fragmentation fingerprints, chromosome instability, and chromatin accessibility were extracted from the WMS data and individually modelled via machine learning methods such as SVM, LR, GBDT, random forest. The final predictive model is an ensemble model integrating all uni-modal models. All models were trained and fitted on the discovery cohort. Results: Data of different modalities provide complementary information in separating the cancer patients from the healthy individuals. Unsupervised clustering of the individuals showed clear separation between cancer patients and healthy individuals. The final predictive model achieved AUC =0.979 in the discovery cohort and AUC =0.98 in the independent testing cohort. Under a specificity of 96.23%(CI: 86% - 87%), sensitivity was 86% (CI: 85% - 88%) in the independent testing cohort. Separating the cancer patients into different stages, we found that the detection power is usuaul lower for early-stage cancer patients. Conclusions: These results demonstrate the first proof of principle on the feasibility of integrating multiple genomic cancer markers to non-invasively detect hepatocellular carcinoma from WMS plasma cell-free DNA. A large prospective cohort study is planned to further validate its clinical performance.

Schisandrin A alleviates mycophenolic acid-induced intestinal toxicity by regulating cell apoptosis and oxidative damage

The gastrointestinal side effects of mycophenolic acid affect its efficacy in kidney transplant patients, which may be due to its toxicity to the intestinal epithelial mechanical barrier, including intestinal epithelial cell apoptosis and destruction of tight junctions. The toxicity mechanism of mycophenolic acid is related to oxidative stress-mediated the activation of mitogen-activated protein kinases (MAPK). Schisandrin A (Sch A), one of the main active components of the Schisandra chinensis, can protects intestinal epithelial cells from deoxynivalenol-induced cytotoxicity and oxidative damage by antioxidant effects. The aim of this study was to investigate the protective effect and potential mechanism of Sch A on mycophenolic acid-induced damage in intestinal epithelial cell. The results showed that Sch A significantly reversed the mycophenolic acid-induced cell viability reduction, restored the expression of tight junction protein ZO-1, occludin and reduced cell apoptosis. In addition, Sch A inhibited mycophenolic acid-mediated MAPK activation and reactive oxygen species (ROS) increase. Collectively, our study showed that Sch A protected intestinal epithelial cells from mycophenolic acid intestinal toxicity, at least in part, by reducing oxidative stress and inhibiting MAPK signaling pathway.

[Evaluation of efficiency of different anti-cysticercus antibody test kits for serodiagnosis of cysticercosis]

OBJECTIVE

To evaluate the diagnostic efficiency of four anti-cysticercus IgG, IgG4 or IgM antibody test kits (enzyme-linked immunosorbent assay, ELISA) by different manufacturers, so as to provide insights into the epidemiological investigation and clinical detection of cysticercosis.

METHODS

Forty serum samples from cerebral cysticercosis patients, 100 serum samples from healthy volunteers, 30 serum samples from paragonimiasis skrjabini patients, 17 serum samples from cystic echinococcosis and 19 serum samples from subcutaneous or cerebral sparganosis patients were collected and detected using anti-cysticercus IgG, IgG4 or IgM antibody test kits (brand A) and the anti-cysticercus IgG antibody test kit (brand B). The sensitivity, specificity and false negative rate of the four kits for detection of cysticercosis were estimated.

RESULTS

The anti-cysticercus IgG, IgG4 or IgM antibody test kits (brand A) showed 95.00% (38/40), 87.50% (35/40), 7.50% (3/40) sensitivities and 98.00% (98/100), 100.00% (100/100) and 100.00% (100/100) for detection of cysticercosis, while the anti-cysticercus IgG antibody test kit (brand B) presented a 75.00% (30/40) sensitivity and 100.00% (100/100) specificity for detection of cysticercosis. The sensitivity for detection of cysticercosis was significantly higher by the anti-cysticercus IgG antibody test kit (brand A) than by the anti-cysticercus IgG antibody test kit (brand B) (χ² = 6.28, P < 0.05); however, no significant difference was seen in the specificity by two kits (χ² = 2.01, P > 0.05). The four ELISA kits showed overall false positive rates of 37.88% (25/66), 22.73% (15/66), 62.12% (41/66) and 15.15% (10/66) for detection of paragonimiasis, echinococcosis and sparganosis (χ² = 37.61, P < 0.05), and the anti-cysticercus IgG antibody test kit (brand A) presented the highest overall false positive rate for detection of paragonimiasis, echinococcosis and sparganosis (χ² = 7.56, P' < 0.008), while a higher overall false positive rate was seen for detection of paragonimiasis, echinococcosis and sparganosis by the anti-cysticercus IgG antibody test kit (brand A) than by the anti-cysticercus IgG antibody test kit (brand B) (χ² = 8.75, P' < 0.008). The four ELISA kits showed false positive rates of 40.00% (12/30), 16.67% (5/30), 76.67% (23/30) and 13.33% (4/30) for detection of paragonimiasis (χ2 = 32.88, P < 0.05) and 21.05% (4/19), 26.32% (5/19), 73.68% (14/19) and 15.79% (3/19) for detection of sparganosis (χ² = 19.97, P < 0.05), and the highest false positive rates were found by the anti-cysticercus IgM antibody test kit (brand A) for detection of paragonimiasis and sparganosis (all P' < 0.008). However, the four ELISA kits showed comparable false positive rates of 52.94% (9/17), 29.41% (5/17), 23.53% (4/17) and 17.65% (3/17) for detection of echinococcosis (χ² = 8.24, P > 0.05). In addition, the anti-cysticercus IgM anti-body test kit (brand A) showed false positive rates of 76.67% (23/30), 23.53% (4/17) and 73.68% (14/19) for detection of paragonimiasis, echinococcosis and sparganosis (χ² = 14.537, P < 0.05), with the lowest false positive rate seen for detection of echinococcosis (χ² = 14.537, P' < 0.014), while no significant differences were seen in the false positive rate for detection of paragonimiasis, echinococcosis and sparganosis by other three ELISA kits (all P > 0.05).

CONCLUSIONS

The four anti-cysticercus IgG, IgG4 or IgM antibody test kits exhibit various efficiencies for serodiagnosis of cysticercosis. The anti-cysticercus IgG antibody test kit (brand A) has a high sensitivity for serodiagnosis of cysticercosis; however, it still needs to solve the problems of cross-reaction with other parasitic diseases and stability.