Simultaneous Detection of Gene Fusions and Base Mutations in Cancer Tissue Biopsies by Sequencing Dual Nucleic Acid Templates in Unified Reaction

BACKGROUND

Targeted next-generation sequencing is a powerful method to comprehensively identify biomarkers for cancer. Starting material is currently either DNA or RNA for different variations, but splitting to 2 assays is burdensome and sometimes unpractical, causing delay or complete lack of detection of critical events, in particular, potent and targetable fusion events. An assay that analyzes both templates in a streamlined process is eagerly needed.

METHODS

We developed a single-tube, dual-template assay and an integrated bioinformatics pipeline for relevant variant calling. RNA was used for fusion detection, whereas DNA was used for single-nucleotide variations (SNVs) and insertion and deletions (indels). The reaction chemistry featured barcoded adaptor ligation, multiplexed linear amplification, and multiplexed PCR for noise reduction and novel fusion detection. An auxiliary quality control assay was also developed.

RESULTS

In a 1000-sample lung tumor cohort, we identified all major SNV/indel hotspots and fusions, as well as MET exon 14 skipping and several novel or rare fusions. The occurrence frequencies were in line with previous reports and were verified by Sanger sequencing. One noteworthy fusion event was HLA-DRB1-MET that constituted the second intergenic MET fusion ever detected in lung cancer.

CONCLUSIONS

This method should benefit not only a majority of patients carrying core actionable targets but also those with rare variations. Future extension of this assay to RNA expression and DNA copy number profiling of target genes such as programmed death-ligand 1 may provide additional biomarkers for immune checkpoint therapies.

Screening and application of inducible promoters in Ruminiclostridium papyrosolvens

Ruminiclostridium papyrosolvens is a promising candidate for producing renewable green chemicals from cellulose due to its cellulolytic and ethanologenic capabilities. It is of significance to screen effective, and convenient-to-use inducible promoters that can be used for regulating the gene expression in R. papyrosolvens. We characterized two endogenous inducible promoters and investigated another two exogenous ones on the adaptability in R. papyrosolvens. Both of the endogenous xylan-inducible promoter Pxyl and exogenous lactose-inducible promoter Plac are found of high specificity and stringency. Pxyl has a short time to be induced while Plac has a low concentration of inducer. With these findings, a mazF-based counter selectable system has been constructed for promoting the efficiency of mutant screening via plasmid curing. The inducible gene expression systems provided novel tools for enhancing the capability of genetic manipulation in engineering R. papyrosolvens. SIGNIFICANCE AND IMPACT OF THE STUDY: Four inducible promoters from Clostridia were characterized in R. papyrosolvens. Xylan-inducible promoter Pxyl was found of a short time while lactose-inducible promoter Plac needs a low concentration of inducer to induce. Employing them, we successfully construct a mazF-based counter selectable system, which would be used to increase the mutant screening efficiency via induction of plasmid curing. The inducible gene expression systems provided novel tools for enhancing the capability of genetic manipulation in engineering R. papyrosolvens.

[Analysis of drug - resistant gene polymorphisms in Plasmodium falciparum imported from Equatorial Guinea to Shandong Province in 2015 and 2016]

OBJECTIVE

To investigate the drug-resistant gene polymorphisms in Plasmodium falciparum imported from Equatorial Guinea to Shandong Province.

METHODS

From 2015 to 2016, blood samples were collected from imported P. falciparum malaria patients returning from Equatorial Guinea to Shandong Province, and genome DNA of the malaria parasite was extracted. The drug-resistant Pfcrt, Pfmdr1, Pfdhfr, Pfdhps, and K13 genes of P. falciparum were amplified using a PCR assay, followed by DNA sequencing, and the sequences were aligned.

RESULTS

The target fragments of all 5 drug-resistant genes of P. falciparum were successfully amplified and sequenced. There were 72.8%, 18.6%, and 8.6% of P. falciparum parasites carrying the wild-, mutant-, and mixed-type Pfcrt gene, respectively, and all mutant haplotypes were CVIET (the underline indicates the mutation site). There were 20.0%, 61.4% and 18.6% of P. falciparum parasites carrying the wild-, mutant-, and mixed-type Pfmdr1 gene, respectively, and the mutant haplotypes mainly included YF and NF (the underlines indicate the mutation sites). There were 1.4%, 98.6%, and 0 of P. falciparum parasites carrying the wild-, mutant-, and mixed-type Pfdhfr gene, respectively, and AIRNI was the predominant mutant haplotype (the underline indicates the mutation site). There were 1.4%, 94.3%, and 4.3% of P. falciparum parasites carrying the wild-, mutant-, and mixed-type Pfdhps gene, respectively, and SGKAA was the predominant mutant haplotype (the underline indicates the mutation site). The complete drug-resistant IRNGE genotype consisted of 8.6% of the Pfdhfr and Pfdhps genes, and the K13 gene A578S mutation occurred in 1.4% of the parasite samples.

CONCLUSIONS

There are mutations in the Pfcrt, Pfmdr1, Pfdhfr, Pfdhps, and K13 genes of P. falciparum imported from Equatorial Guinea to Shandong Province, with a low frequency in the Pfcrt gene mutation and a high frequency in the Pfmdr1, Pfdhfr, and Pfdhps gene mutations, and the K13 gene A578S mutation is detected in the parasite samples.

Risk factors for disease progression in patients with mild to moderate coronavirus disease 2019-a multi-centre observational study

Objectives

Since December 2019, the novel coronavirus disease 2019 (COVID-19) that emerged in Wuhan city has spread rapidly around the world. The risk for poor outcome dramatically increases once a patient progresses to the severe or critical stage. The present study aims to investigate the risk factors for disease progression in individuals with mild to moderate COVID-19.

Methods

We conducted a cohort study that included 1007 individuals with mild to moderate COVID-19 from three hospitals in Wuhan. Clinical characteristics and baseline laboratory findings were collected. Patients were followed up for 28 days for observation of disease progression. The end point was the progression to a more severe disease stage.

Results

During a follow up of 28 days, 720 patients (71.50%) had recovered or were symptomatically stable, 222 patients (22.05%) had progressed to severe disease, 22 patients (2.18%) had progressed to the critically ill stage and 43 patients (4.27%) had died. Multivariate Cox proportional hazards models identified that increased age (hazard ratio (HR) 2.56, 95% CI 1.97–3.33), male sex (HR 1.79, 95% CI 1.41–2.28), presence of hypertension (HR 1.44, 95% CI 1.11–1.88), diabetes (HR 1.82, 95% CI 1.35–2.44), chronic obstructive pulmonary disease (HR 2.01, 95% CI 1.38–2.93) and coronary artery disease (HR 1.83, 95% CI 1.26–2.66) were risk factors for disease progression. History of smoking was protective against disease progression (HR 0.56, 95% CI 0.34–0.91). Elevated procalcitonin (HR 1.72, 95% CI 1.02–2.90), urea nitrogen (HR 1.72, 95% CI 1.21–2.43), α-hydroxybutyrate dehydrogenase (HR 3.02, 95% CI 1.26–7.21) and D-dimer (HR 2.01, 95% CI 1.12–3.58) at baseline were also associated with risk for disease progression.

Conclusions

This study identified a panel of risk factors for disease progression in individuals with mild to moderate COVID-19.

Non-invasive prediction of fetal growth restriction by whole-genome promoter profiling of maternal plasma DNA: a nested case-control study

Objective

To predict fetal growth restriction (FGR) by whole‐genome promoter profiling of maternal plasma.

Design

Nested case–control study.

Setting

Hospital‐based.

Population or Sample

810 pregnancies: 162 FGR cases and 648 controls.

Methods

We identified gene promoters with a nucleosome footprint that differed between FGR cases and controls based on maternal plasma cell‐free DNA (cfDNA) nucleosome profiling. Optimal classifiers were developed using support vector machine (SVM) and logistic regression (LR) models.

Main outcome measures

Genes with differential coverages in promoter regions through the low‐coverage whole‐genome sequencing data analysis among FGR cases and controls. Receiver operating characteristic (ROC) analysis (area under the curve [AUC], accuracy, sensitivity and specificity) was used to evaluate the performance of classifiers.

Results

Through the low‐coverage whole‐genome sequencing data analysis of FGR cases and controls, genes with significantly differential DNA coverage at promoter regions (−1000 to +1000 bp of transcription start sites) were identified. The non‐invasive ‘FGR classifier 1’ (C_FGR1) had the highest classification performance (AUC, 0.803; 95% CI 0.767–0.839; accuracy, 83.2%) was developed based on 14 genes with differential promoter coverage using a support vector machine.

Conclusions

A promising FGR prediction method was successfully developed for assessing the risk of FGR at an early gestational age based on maternal plasma cfDNA nucleosome profiling.

Tweetable abstract

A promising FGR prediction method was successfully developed, based on maternal plasma cfDNA nucleosome profiling.

A promising FGR prediction method was successfully developed, based on maternal plasma cfDNA nucleosome profiling.

SAT0017 METABOLIC CHANGES INDUCED BY ANTI-MALONDIALDEHYDE/MALINDIALDEHYDE-ACETALDEHYDE ANTIBODIES PROMOTE OSTEOCLAST DEVELOPMENT

Background:

Malondialdehyde (MDA) is a highly reactive compound produced by lipid-peroxidation in situations associated with oxidative stress. MDA can irreversibly modify proteins residues such as lysine, arginine and histidine. In addition, MDA adducts can further react with acetaldehyde to generate malondialdehyde-acetaldehyde (MAA) modifications. Such modifications can give rise to immunogenic neo-epitopes that are recognized by autoantibodies. In fact, anti-MDA/MAA IgG antibodies are significantly increased in the serum of patients with autoimmune diseases, such as rheumatoid arthritis (RA) (1) and systemic lupus erythematosus (2). Recently, we have shown that anti-MDA/MAA IgG antibodies are able to promote osteoclast (OC) differentiationin vitro(1).

Objectives:

To investigate the molecular mechanisms triggered by anti-MDA/MAA autoantibodies during osteoclastogenesis.

Methods:

OCs were generated from monocyte-derived macrophages in the presence of the cytokines RANK-L and M-CSF. The development of OCs was monitored by light microscopy following tartrate-resistant acid phosphatase (TRAP) staining and erosion area on synthetic calcium phosphate-coated plates. Three different recombinant human monoclonal anti-MDA/MAA antibodies, cloned from single synovial B cells of RA patients, control antibodies and Fab fragments of the antibodies were added to OC cultures. Glycolysis was inhibited by 2-deoxyglucose, and Fc-gamma receptor I or II by anti-CD64 or anti-CD16 neutralizing antibodies. IL-8 levels were measured by enzyme linked immunosorbent assay. Cellular metabolism was monitored using Seahorse XF Analyzer (extracellular acidification rate and oxygen consumption) and a colorimetric L-Lactate assay.

Results:

Lactic acid production correlated with the osteoclastogenetic effect of some but not all anti-MDA/MAA antibodies on OCs (R=0.4758, p=0.0252) suggesting an antibody-mediated regulation of glycolysis. Further, extracellular acidification (ECAR) and oxygen consumption (OCR) rate of the developing OCs were increased by the osteoclastogenic anti-MDA/MAA clones (maximum increase of 54% for the ECAR and 78% for the OCR by clone 146+:01G07, and maximum increase of 28% for the ECAR and 39% for the OCR by clone 1103:01H05), but not by the non-osteoclastogenetic anti-MDA/MAA clones or control antibodies. The glycolysis inhibitor 2-deoxyglucose completely abolished the osteoclastogenetic effect of the anti-MDA/MAA clones at drug concentrations that did not influenced baseline OC development. Fab2 fragments of the osteocalstogenetic anti-MDA/MAA clones had no effect on OC development and metabolism. In accordance with this, Fc-gamma receptor I neutralizing antibodies completely abolished the osteocalstogenetic effect of the anti-MDA/MAA clones. The osteoclastogenetic effect of the anti-MDA/MAA antibodies was independent of IL-8 production. In contrast to anti MDA/MAA antibodies, ACPA-mediated osteoclastogenesis was independent of glycolysis and Fc-gamma receptors but dependent on IL-8.

Conclusion:

Our results describe a novel glycolysis-dependent mechanism by which anti-MDA/MAA antibodies promote osteoclast development that is different from the one previously described for ACPA.

References:

[1] C. Grönwall et al. Journal of Autoimmunity 84 (2017) 29-45.

[2] C. Wang et al. Arthritis and Rheumatism 62 (2010) 2064-2072

Disclosure of Interests:

Koji Sakuraba: None declared, Akilan Krishnamurthy: None declared, Alexandra Circiumaru: None declared, Meng Sun: None declared, Vijay Joshua: None declared, Marianne Engström: None declared, Xiaowei Zheng: None declared, Cheng Xu: None declared, Khaled Amara: None declared, Vivianne Malmström Grant/research support from: VM has had research grants from Janssen Pharmaceutica, Sergiu-Bogdan Catrina: None declared, Caroline Grönwall: None declared, Bence Réthi: None declared, Anca Catrina: None declared

AB0270 THE IMPACT OF DIABETES MELLITUS ON OUTCOMES OF RHEUMATOID ARTHRITIS AT 5-YEAR FOLLOW-UP: RESULTS FROM A MULTI-ETHNIC ASIAN COHORT IN SINGAPORE

Background:

Both diabetes mellitus (DM) and rheumatoid arthritis (RA) are prevalent diseases and represent the leading causes of disability and mortality worldwide. Systemic chronic inflammation is recognized as the underlying etiology of a variety of diseases, including DM and RA [1]. Additionally, cardiovascular and musculoskeletal complications from DM may influence the outcomes of RA patients.

Objectives:

To investigate the impact of DM on outcomes of RA patients.

Methods:

This is a cross-sectional study including 583 RA patients with 5 years’ history after diagnosis in Tan Tock Seng Hospital RA registry, Singapore from 2001 to 2013. Information related to demographics, serologies, clinical features, comorbidities, and outcomes was collected. Independent t-test or Mann-Whitney U test was used to compare continuous quantitative data, while Pearson Chi-square or Fisher Exact test for categorical data. With adjustment for age, gender, ethnicity, smoking and comorbidities, multivariate regressions were performed to analyze the impact of DM on outcomes of RA patients.

Results:

DM is more prevalent in Malay and Indian patients than Chinese patients with RA (26%, 24% and 11% respectively,p= 0.005). There is no difference of disease activity between DM and non DM patients. There is a tendency that non diabetic RA patients use more methotrexate (p= 0.052) and leflunomide (p= 0.058). Diabetic RA patients are in higher risk of poor American College of Rheumatology (ACR) functional status (p= 0.009), knee arthroplasty (p< 0.001) and admissions (p= 0.006). Adjusted for age, gender, ethnicity, smoking and comorbidities, multivariate regression analyses showed a trend of poor function status for diabetic RA patients, i.e. ACR functional status (adjusted odds ratio [aOR]: 1.802, 95% confidence interval [CI]: 0.968 – 3.353,p= 0.063) and median Health Assessment Questionnaire (HAQ) (β coefficient value: 0.129, 95% CI: -0.010 – 0.267,p= 0.068), and higher risk for knee arthroplasty for diabetic RA patients (aOR: 3.480, 95% CI: 1.016 – 11.920,p= 0.047).

Conclusion:

This is the first report on the impact of DM on RA outcomes in a long term follow-up RA registry in a multiethnic Asian society.

References:

[1]Furman, D., Campisi, J., Verdin, E.et al.Chronic inflammation in the etiology of disease across the life span.Nat Med25,1822–1832 (2019).

Acknowledgments:

TTSH Rheumatoid Arthritis Study Group

Disclosure of Interests:

None declared

Label-free sensing of exosomal MCT1 and CD147 for tracking metabolic reprogramming and malignant progression in glioma

Malignant glioma is a fatal brain tumor whose pathological progression is closely associated with glycolytic reprogramming, leading to the high expression of monocarboxylate transporter 1 (MCT1) and its ancillary protein, cluster of differentiation 147 (CD147) for enhancing lactate efflux. In particular, malignant glioma cells (GMs) release tremendous number of exosomes, nanovesicles of 30 to 200 nm in size, promoting tumor progression by the transport of pro-oncogenic molecules to neighboring cells. In the present study, we found that hypoxia-induced malignant GMs strongly enhanced MCT1 and CD147 expression, playing a crucial role in promoting calcium-dependent exosome release. Furthermore, it was first identified that hypoxic GMs-derived exosomes contained significantly high levels of MCT1 and CD147, which could be quantitatively detected by noninvasive localized surface plasmon resonance and atomic force microscopy biosensors, demonstrating that they could be precise surrogate biomarkers for tracking parent GMs' metabolic reprogramming and malignant progression as liquid biopsies.

TP53 fusions with next-generation sequencing (NGS) in Chinese non-small cell lung cancer (NSCLC): A multicenter study

e21742

Background: Currently, with the advances in detection techniques, such as next generation sequencing (NGS), more and more rare or atypical TP53 fusions had been identified. Such as TP53-PSMD14, the importance of EGFR signaling in the pathogenesis of lung cancer and the efficacy of EGFR-TKI treatment had been demonstrated. The aim of this study was to evaluate the prevalence of TP53 fusions in Chinese NSCLC populations, which had not been reported earlier, and to describe targeting potential in Chinese NSCLC populations. Methods: A multicenter study in China was initiated from February 2014, and NSCLC patients have been enrolled as of December 2018. A total of 2743 patients with NSCLC were screened by using next-generation sequencing (NGS)-based 381 genes panel assay for detecting TP53 fusions. Results: Of this entire cohort, just four (0.15%) patients were identified with a TP53 fusion, including DNAH2-TP53 (1), TP53-MPDU1 (1), TP53-FXR2 (1), TP53-VEZF1 (1). Of the TP53 fusion NSCLC patients, 50.00% were detected in female patients. Biopsies were obtained from primary lung tumor (25.00%) and metastatic sites (75.00%). Overall TMB in the TP53 fusion was high, which had more than 20 mut/Mb. Of the TP53 fusion NSCLC, two cases (50.00%) featured EGFR SV alterations. Conclusions: The frequency of TP53 fusions in Chinese populations with NSCLC is extremely rare (0.17%). TP53 fusions may reduce responsiveness to TKIs and worsen prognosis in EGFR-mutated NSCLC patients, mainly those carrying exon 19 deletions or exon 21 L858R.

Genomic origin and immune-related status of pulmonary sarcomatoid carcinoma

e13500

Background: Pulmonary sarcomatoid carcinoma (PSC), composed of sarcomatous component (SaC) and carcinomatous component (CaC), is a rare and generally aggressive subtype of non-small-cell lung cancer (NSCLC). Little is known about the genetic origin, TMB, and PD-L1 status of PSC. Methods: 31 immunohistochemically (IHC) confirmed PSCs were enrolled and tumor samples were subjected to microdissection to obtain SaC and CaC. Different components were subjected to targeted sequencing with a 1021-gene-panel. Somatic mutations were used to assess TMB and construct phylogenetic tree. PD-L1 expression level was determined by IHC. Independent cohorts of 90 lung adenocarcinomas (LUAD) from the Geneplus database and 167 sarcomas from TCGA were used for genomic comparison. Results: 87% of patients (pts) were male, with a median age of 57.0 years. 52% were smokers. The most recurrently mutated genes were TP53 (80%), MET (24%), NF1 (21%), EGFR (21%), and KRAS (21%) in CaC, while TP53 (76%), MAP3K1 (21%), NF1 (21%), MET (21%), and KRAS (21%) in SaC. 55.4% of the variations (SNV, small indels, SV, and CNV) were shared within SaC and CaC. TP53, MET, NF1, and EGFR were mostly frequently found in shared mutations. Overwhelming majority of PSCs (29/30) had common mutations between SaC and CaC implying a monoclonal origin. EGFR were mutated significantly less in adenocarcinoma components (AdC) than LUAD (Fisher Exact test, 4/24 vs 52/90, p < 0.001). High-frequency mutated driver genes in SaC, MET, EGFR, NF1, and ALK, were rarely detected in leiomyosarcomas and uterine sarcomas. The median of TMB in SaC and CaC were both 12.9 mutations/Mb (range, SaC 2.88-33.1, CaC 2.88-47.5), with high correlation between the two components (p < 0.001). PD-L1 expression levels in the two components also had high correlation (p < 0.001). More pts showed high PD-L1 expression ( > = 50%) in SaC rather than CaC (8 versus 3). Conclusions: A majority of PSCs share a monoclonal origin. PSCs with AdC exhibited lower mutated frequency of EGFR than LUAD. SaC and CaC had similar higher TMB status than LUAD. SaC and CaC had similar level of PD-L1expression.

Community-based practice of early lung cancer screening with low-dose spiral computed tomography in Jiaxing city from Zhejiang Province

e13557

Background: As one of the most frequent malignant tumors in China, the morbidity and mortality of lung cancer remain high. Early diagnosis and normative treatment is the key to improve the prognosis of lung cancer. The aim of this study is to explore the practice of early lung cancer screening with low-dose spiral computed tomography (CT) based on the current situation in community health service, with integration of superior resources of medical institutions at all levels in Jiaxing City from Zhejiang Province. Methods: From Jan. 2017 to Dec. 2019, we screened 13491 (male 8783, female 4708) individuals high-risk population in selected communities of Nanhu District, Pinghu County and Haiyan County, Zhejiang Province, for early diagnosis of lung cancer with low-dose spiral CT combined with multidisciplinary comprehensive treatment models including minimally invasive surgery, exploring the medical service network covering prevention, diagnosis, treatment, rehabilitation and follow-up. Results: Screening resulted in a diagnosis of cancer in 27 participants. Of these participants, 24 cases of primary lung cancer, 1 case of lung metastasis, 1 case of breast cancer, 1 case of thyroid cancer. The morbidity of primary lung cancer is 224.53×10-5. There were 20 cases of Stage 0-Ⅰlung cancer accounting for 83.33% of all diagnosed primary lung cancer. Conclusions: Based on community health service, screening with LDCT could improve the early diagnosis rate of lung cancer in both smokers and nonsmokers with feasibility and validity, which could be applicable in qualified eligible medical centers and communities in China. It is not reasonable to exclude nonsmokers from screening with LDCT.

Real-world mutational profiling of Chinese non-small cell lung cancer patients with epidermal growth factor receptor (EGFR) uncommon mutations acquired resistant to icotinib using next generation sequencing: A multicenter study

e21557

Background: Just like classical EGFR mutations, EGFR uncommon mutations non-small cell lung cancer (NSCLC) will still have acquired resistant problem to icotinib. The mechanism of icotinib resistance in such uncommon EGFR mutant patients has also risen to be a difficult question in lung cancer research. In order to explore the resistance mechanism in EGFR uncommon mutant NSCLC patients treated by icotinib, it is necessary to first identify the resistant gene profiles and clinic-pathologic characteristics of those patients. As far as we know that there is no large cohort of EGFR uncommon mutant NSCLC study in evaluating the efficacy and resistant genomic profiling of icotinib. Methods: We screened 3279 patients with NSCLC for EGFR uncommon mutations. Among them, 106 patients received icotinib treatment, and a total of 69 patients with stage IIIb-IV EGFR uncommon mutations NSCLC were undergoing tumor biopsies or blood withdrawing by the time of primary or acquiring to icotinib, in including formalin-fixed paraffin-embedded (FFPE) samples, serum samples and serous effusions. We used targeted next-generation sequencing to detect genes status of patients. Results: Among 69 patients treated with icotinib, 69.57% (48/69) developed acquired resistance, and 30.43% (21/69) had primary resistance. Using the specimens at the baseline, there were 39(81.25%) patients with EGFR T790M (including 7 patients with EGFR T790M, 32 patients with EGFR T790M plus EGFR amplification), 3(36.25%) patients with EGFR amplification, 1(2.08%) patient with BRAF mutation, 1(2.08%) patient with PIK3CA mutation, 1(2.08%) patient with CTNNB1 mutation, 1(2.08%) patient with ALK fusion, 1(2.08%) patient with ROS1 fusion, and 1(2.08%) patient with unknown status. Conclusions: EGFR T790M, EGFR amplification, BRAF mutation, PI3K-AKT-mTOR signaling pathway (PIK3CA mutations), CTNNB1 mutation, ALK fusion or ROS1 fusion might contribute to molecular mechanisms of acquired resistance to icotinib in EGFR uncommon mutations NSCLC. Our study uncovered EGFR uncommon mutational profiles of NSCLC patients with icotinib resistance with potential therapeutic implications.

APC fusions analysis in Chinese non-small cell lung cancer (NSCLC) using comprehensive NGS panel: A multicenter study

e21086

Background: Currently, with the advances in detection techniques, such as next generation sequencing (NGS), more and more rare or atypical APC fusions had been identified. Such as APC-MCC, the importance of Wnt signaling in the pathogenesis of lung cancer and the efficacy of EGFR-TKI treatment had been demonstrated. Methods: A multicenter study in China was initiated from February 2014, and NSCLC patients have been enrolled as of December 2018. To determine the frequency of the APC fusions in NSCLC and other tumors, we analyzed data from 2743 clinical NSCLC cases, each of which had results from next-generation sequencing (NGS)-based 381 genes panel assay, analogous to the index patient. Results: Of this entire cohort, just two (0.07%) patients were identified with a APC fusion, including APC-MCC (1), APC-MRPL13 (1). The genes most frequently co-altered in patients with APC fusions were TP53 (100.00%), CCND1 (50.00%), ESR1 (50.00%), TNN (50.00%), MAP2K2 (50.00%) and POM121L12 (50.00%). Overall TMB in the APC fusions was low (median 2.16 mut/Mb). For treatments, both patients chose chemotherapy based on pemetrexed for first line, and a case example of advanced APC fusion NSCLC patients responding to anlotinib was actively being sought thru our database. Conclusions: The frequency of APC fusions in Chinese populations with NSCLC is extremely rare (0.08%). NGS can identify novel fusions and increase the list of actionable variants for patients. More patients can benefit from targeted treatment. In addition, for short-or long-term responses to TKI treatment, we can use the NGS assay to explore differential gene expression in the future.

Body condition alters glutathione and nuclear factor erythroid 2-like 2 (NFE2L2)-related antioxidant network abundance in subcutaneous adipose tissue of periparturient Holstein cows

Dairy cows with high body condition score (BCS) in late prepartum are more susceptible to oxidative stress (OS). Nuclear factor erythroid 2-like 2 (NFE2L2) is a major antioxidant transcription factor. We investigated the effect of precalving BCS on blood biomarkers associated with OS, inflammation, and liver function, along with mRNA and protein abundance of targets related to NFE2L2 and glutathione (GSH) metabolism in s.c. adipose tissue (SAT) of periparturient dairy cows. Twenty-two multiparous Holstein cows were retrospectively classified into a high BCS (HBCS; n = 11, BCS ≥3.5) or normal BCS (NBCS; n = 11, BCS ≤3.17) on d 28 before parturition. Cows were fed a corn silage- and wheat straw-based total mixed ration during late prepartum, and a corn silage- and alfalfa hay-based total mixed ration postpartum. Blood samples obtained at -10, 7, 15, and 30 d relative to parturition were used for analyses of biomarkers associated with inflammation, including albumin, ceruloplasmin, haptoglobin, and myeloperoxidase, as well as OS, including ferric reducing ability of plasma (FRAP), reactive oxygen species (ROS), and β-carotene. Adipose biopsies harvested at -15, 7, and 30 d relative to parturition were analyzed for mRNA (real-time quantitative PCR) and protein abundance (Western blotting) of targets associated with the antioxidant transcription regulator nuclear factor, NFE2L2, and GSH metabolism pathway. In addition, concentrations of GSH, ROS and malondialdehyde were measured. High BCS cows had lower prepartum dry matter intake expressed as a percentage of body weight along with greater BCS loss between -4 and 4 wk relative to parturition. Plasma concentrations of ROS and FRAP increased after parturition regardless of treatment. Compared with NBCS, HBCS cows had greater concentrations of FRAP at d 7 postpartum, which coincided with peak values in those cows. In addition, NBCS cows experienced a marked decrease in plasma ROS after d 7 postpartum, while HBCS cows maintained a constant concentration by d 30 postpartum. Overall, ROS concentrations in SAT were greater in HBCS cows. However, overall mRNA abundance of NFE2L2 was lower and cullin 3 (CUL3), a negative regulator of NFE2L2, was greater in HBCS cows. Although HBCS cows had greater overall total protein abundance of NFE2L2 in SAT, ratio of phosphorylated NFE2L2 to total NFE2L2 was lower, suggesting a decrease in the activity of this antioxidant system. Overall, mRNA abundance of the GSH metabolism-related genes glutathione reductase (GSR), glutathione peroxidase 1 (GPX1), and transaldolase 1 (TALDO1), along with protein abundance of glutathione S-transferase mu 1 (GSTM1), were greater in HBCS cows. Data suggest that HBCS cows might experience greater systemic OS after parturition, while increased abundance of mRNA and protein components of the GSH metabolism pathway in SAT might help alleviate tissue oxidant status. Data underscored the importance of antioxidant mechanisms at the tissue level. Thus, targeting these pathways in SAT during the periparturient period via nutrition might help control tissue remodeling while allowing optimal performance.

Identification of Deleterious NOTCH Mutation as Novel Predictor to Efficacious Immunotherapy in NSCLC

PURPOSE

NOTCH signaling is associated with tumorigenesis, mutagenesis, and immune tolerance in non-small cell lung cancer (NSCLC), indicating its association with the clinical benefit of immune checkpoint inhibitors (ICI). We hypothesized that NOTCH mutation in NSCLC might be a robust predictor of immunotherapeutic efficacy.

EXPERIMENTAL DESIGN

Multiple-dimensional data including genomic, transcriptomic, and clinical data from cohorts of NSCLC internal and public cohorts involving immunotherapeutic patients were analyzed. Polymorphism Phenotyping v2 (PolyPhen-2) system was performed to determine deleterious NOTCH mutation (del-NOTCH ^mut). Further investigation on molecular mechanism was performed in The Cancer Genome Atlas (TCGA) data via CIBERSORT and gene set enrichment analysis.

RESULTS

Our 3DMed cohort (n = 58) and other four cohorts (Rizvi, POPLAR/OAK, Van Allen, and MSKCC; n = 1,499) uncovered marked correlation between NOTCH1/2/3 mutation and better ICI outcomes in EGFR/ALK ^WT population, including objective response rate (2.20-fold, P = 0.001), progression-free survival [HR, 0.61; 95% confidence interval (CI), 0.46-0.81; P = 0.001], and overall survival (HR, 0.56; 95% CI, 0.32-0.96; P = 0.035). Del-NOTCH ^mut exhibited better predictive function than non-deleterious NOTCH mutation, potentially via greater transcription of genes related to DNA damage response and immune activation. Del-NOTCH ^mut was not linked with prognosis in TCGA cohorts and chemotherapeutic response, but was independently associated with immunotherapeutic benefit, delineating the predictive, but not prognostic, utility of del-NOTCH ^mut.

CONCLUSIONS

This work distinguishes del-NOTCH ^mut as a potential predictor to favorable ICI response in NSCLC, highlighting the importance of genomic profiling in immunotherapy. More importantly, our results unravel a possibility of personalized combination immunotherapy as adding NOTCH inhibitor to ICI regimen in NSCLC, for the optimization of ICI treatment in clinical practice.

The prognostic value of the C-reactive protein to albumin ratio in cancer: An updated meta-analysis

BACKGROUND

Previous studies have demonstrated that the C-reactive protein to albumin ratio (CAR) is correlated with the clinical outcomes of solid tumors. However, the available data have not been systematically evaluated. The objective of the present meta-analysis was to explore the prognostic value of the CAR in solid tumors.

METHODS

Eligible studies were identified from the PubMed, EMBASE and Web of Science electronic databases. The clinical characteristics, disease -free survival (DFS) /progression-free survival (PFS) and overall survival (OS) were extracted from the eligible studies. The pooled hazard ratios (HRs) and 95% confidence intervals were calculated with STATA 12.0 software. We also performed subgroup, meta-regression and sensitivity analyses.

RESULTS

In total, twenty-seven eligible studies including 10556 patients were enrolled in the present meta-analysis. The pooled HRs with 95% confidence intervals showed that the CAR was significantly associated with poor OS (HR = 1.95, 95% CI: 1.71-2.22) and DFS/PFS (HR = 1.82, 95% CI: 1.61-2.07) in patients with solid tumors. Although publication bias was found in the studies with regard to OS, a further trim and fill analysis revealed that the adjusted HR was 1.82 (95% CI: 1.69-1.96), which was close to the original HR. Subgroup analysis confirmed the CAR as a strong prognostic marker in patients with solid tumors, regardless of the tumor type, detection time, cut-off value, sample size and area.

CONCLUSION

Our meta-analysis indicated that a high CAR might be an unfavorable prognostic marker for OS and DFS/PFS in patients with solid tumors.

The Rise of China as an Economic Power

In the twenty years since the Cultural Revolution, China has maintained fast real growth. This occurred despite China having similar problems to other transitional economies, e.g. loss-making State Owned Enterprises (SOEs), eroding fiscal revenues and inflation, (Section 3).

Although China initially adopted the Soviet central planning model, after the 1950s break Chinese planning changed towards a regionally-based system with local planning (Section 2). In contrast to the centrally-based, functionally-specialised (U-form or unitary structure) Soviet model, the Chinese economy is organised on a multi-layer-multi-regional (M-form) basis. This encour aged development of small size township and village enterprises (TVEs), the main engine of Chinese growth.

Power and control remained with the Party and the State, but was diffused much more widely, regionally and locally. This allowed initiatives at lower (political) levels to establish institutions, both in agriculture (the ‘household responsibility system’) and industry (TVEs), without state protection. Even among regionally controlled SOEs, ‘tournament rivalry’ between regions, etc., and between SOEs and TVEs provided competition.

Controlled Release of Oxycodone as an Opioid Titration for Cancer Pain Relief: A Retrospective Study

BACKGROUND In 2014, a Chinese expert consensus was proposed regarding a titration protocol with controlled-release (CR) oxycodone as a background dose for relieving the moderate to severe cancer pain. This work aimed to summarize its efficacy and safety in our hospital. MATERIAL AND METHODS The Good Pain Management (GPM) protocol comprises a CR morphine or oxycodone given every 12-hours as a background dose and an immediate-release (IR) opioid as a rescue dose. Cancer patients with moderate to severe cancer pain were treated with this protocol, and the successful titration (numerical rating scale [NRS] ≤3 within 3 days) rate was analyzed. SPSS was used for statistical analysis. Differences of variables between opioid intolerant patients and opioid tolerant patients were analyzed using the Mann-Whitney U test. The chi square test was used for comparison of frequencies in different groups. A P-value.

[Clinicopathological features of dedifferentiated liposarcomas with meningothelial-like whorls: report of six cases]

Objective: To investigate the histopathologic, immunohistochemical, molecular genetic characteristics of dedifferentiated liposarcomas with meningothelial-like whorls(DDLMW). Methods: Six cases of DDLMW diagnosed at Jiangsu Province Hospital(the First Affiliated Hospital of Nanjing Medical University) from March 2012 to August 2018 were enrolled. The cases were analyzed by routine HE staining, immunohistochemistry(MDM2, CDK4 and p16) and fluorescent in-situ hybridization(FISH) on MDM2 gene. Related literatures were also reviewed. Results: Three of the 6 patients were male.The patient ages ranged from 40 to 77 years (mean, 58 years). Four tumors occurred in the retroperitoneum and two in the mediastinum. Histologically, the tumors showed, in addition to foci of well-differentied liposarcoma, characteristic, scattered meningothelial-like concentrical whorls. The whorls were composed of tightly, concentrically arranged, spindle to ovoid cells with mild to mederate cytological atypia. Metaplastic bone was present within or in their immediate vicinity in four case. The tumors cell also showed strong and diffuse immunoreactivity to MDM2, CDK4 and p16, but no immunoreactivity to S-100 protein, SMA, SOX10, EMA, CD21, CD23 or CD35. The Ki-67 labeling indexes were low, while FISH showed high levels of MDM2 amplification in all cases. Conclusions: DDLMW is a rare morphologic variant of dedifferentiated liposarcoma. The whorls in DDLMW do not represent perineurial or follicular dendritic differentiation. Recognition and familiarity with its existence, as well as combined application of immunohistochemical staining and MDM FISH, are important to avoid confusion with other lesions.

Association Between RET Fusions and Efficacy of Pemetrexed-based Chemotherapy for Patients With Advanced NSCLC in China: A Multicenter Retrospective Study

BACKGROUND

Rearranged during transfection (RET) proto-oncogene gene fusions are rare in non-small-cell lung cancer (NSCLC). We compared the efficacy of pemetrexed-based chemotherapy with other chemotherapy regimens in patients with NSCLC with different RET fusion subtypes.

PATIENTS AND METHODS

A retrospective, multicenter study of patients with pathologically confirmed stage IIIB/IV lung adenocarcinomas was conducted. RET rearrangements were detected using next generation sequencing. We analyzed the clinical characteristics of patients with RET-rearranged NSCLC and the efficacy of chemotherapy regimens. We also evaluated the efficacy between groups of patients with and without KIF5B-RET-rearranged lung cancer.

RESULTS

We evaluated 62 patients with NSCLC and RET rearrangements, including 41 with KIF5B-RET, 15 with CCDC6-RET, and 6 with other rare fusion subtypes. Of these 62 patients, 50 had stage IIIB/IV. We also evaluated 40 patients with first-line chemotherapy information available. The median progression-free survival was significantly different between those receiving pemetrexed-based chemotherapy and those receiving other chemotherapy regimens (9.2 vs. 5.2 months; P = .007). The median progression-free survival for patients with KIF5B-RET fusion and non-KIF5B-RET fusion was not significantly different statistically (7.8 vs. 11.2 months; P = .847). For second-line chemotherapy, a statistically significant difference was found between the chemotherapy regimens (4.9 vs. 2.8 months; P = .049). Survival follow-up data were available for 38 patients with advanced NSCLC. The median overall survival was 26.4 months. The overall survival of the patients with RET-rearranged NSCLC who had received pemetrexed-based chemotherapy versus no pemetrexed-based chemotherapy was 35.2 versus 22.6 months (P = .052). No difference in survival was observed between the patients with KIF5B-RET and non-KIF5B-RET rearrangements.

CONCLUSIONS

Pemetrexed-based treatment should be considered first when selecting the chemotherapy regimen for patients with NSCLC and RET rearrangements.

Mixed Germ Cell Tumor of the Endometrium: A Case Report and Literature Review

Germ cell tumors (GCTs) localized extragonadally are rare, with only 14 reported cases of a yolk sac tumor in the endometrium. Here we report a case of mixed endometrium GCTs in a 65-year-old postmenopausal woman with abnormal vaginal bleeding. An ultrasound examination showed an oval-shaped mass in the patient’s uterine cavity. Biochemical examination revealed elevated serum α-fetoprotein (AFP) at 359 ng/mL, whereas the tumor markers CA-125, CA-199, and CEA were all within normal range. Total hysterectomy and bilateral salpingo-oophorectomy were performed;. a histological examination revealed that the malignant components contained a yolk sac tumor, embryonal carcinoma, and focal immature teratoma. Immunohistochemical staining showed that AFPs were diffusively distributed in both the yolk sac tumor and embryonal carcinoma. The stem cell marker OCT3/4 was positive in the embryonal carcinoma component and that the pan-cytokeratin AE1/AE3 staining was positive in glandular areas. GFAPs (Glial Fibrillary Acidic Proteins) were positive in neuroectodermal tubules; the Ki-67 protein was positive in 90% of the tumor cells, whereas CD117 and placental alkaline phosphatase (PLAP) were negative. The cumulative evidence indicated mixed GCTs of endometrium as the final histopathological diagnosis. The patient received three courses of adjunct chemotherapy that provided good therapeutic efficacy as evidenced by the decreased serum AFP level. Our report on this rare case of mixed GCTs of the endometrium, supported by associated histological patterns and immunophenotypes and successful adjunct chemotherapy after surgery, could provide insight on future treatment of this rare but lethal disease.

FGFR2-BICC1: A Subtype Of FGFR2 Oncogenic Fusion Variant In Cholangiocarcinoma And The Response To Sorafenib

Fibroblast growth factor receptor (FGFR) family includes four highly conserved receptor tyrosine kinases. Particularly, FGFR2 has been identified as a potential target for tyrosine kinase inhibitor (TKI) treatment. Except for immunohistochemistry and fluorescence in situ hybridization, next-generation sequencing (NGS) technology represents a novel tool for FGFR2 detection that covers a wide range of fusion genes. In the present work, we present a case of cholangiocarcinoma who had FGFR2-BICC1 rearrangement detected by NGS. A 76-year-old female diagnosed with cholangiocarcinoma underwent four cycles of chemotherapy. The NGS assay showed that the tumor had a FGFR2-BICC1 rearrangement. The patient had a favorable tumor response to sorafenib. Herein, we report the first case with cholangiocarcinoma harboring FGFR2-BICC1 who is sensitive to sorafenib therapy.

Unique Access to u-Channel Physics: Exclusive Backward-Angle Omega Meson Electroproduction

Backward-angle meson electroproduction above the resonance region, which was previously ignored, is anticipated to offer unique access to the three quark plus sea component of the nucleon wave function. In this Letter, we present the first complete separation of the four electromagnetic structure functions above the resonance region in exclusive ω electroproduction off the proton, ep→e^{'}pω, at central Q^{2} values of 1.60, 2.45  GeV^{2}, at W=2.21  GeV. The results of our pioneering -u≈-u_{min} study demonstrate the existence of a unanticipated backward-angle cross section peak and the feasibility of full L/T/LT/TT separations in this never explored kinematic territory. At Q^{2}=2.45  GeV^{2}, the observed dominance of σ_{T} over σ_{L}, is qualitatively consistent with the collinear QCD description in the near-backward regime, in which the scattering amplitude factorizes into a hard subprocess amplitude and baryon to meson transition distribution amplitudes: universal nonperturbative objects only accessible through backward-angle kinematics.

MiRNA-337 leads to podocyte injury in mice with diabetic nephropathy

OBJECTIVE

To elucidate the function of miRNA-337 in the pathogenesis of diabetic nephropathy (DN) and its underlying mechanism.

MATERIALS AND METHODS

Type 2 diabetes db/db mice were assigned into db/db group, vehicle group, and si-miR group, and age-matched db/m mice were in the db/m group. Differences in mouse serum glucose, body weight, serum creatinine, and albumin/creatinine ratio (ACR) among the four groups were compared at 6 weeks, 10 weeks, 14 weeks, 18 weeks, and 22 weeks of age. The expression level of miRNA-337 in mouse kidney tissues was determined by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). Correlation between miRNA-337 expression with ACR was analyzed. Through Western blot analysis, protein levels of interleukin 6 (IL-6), IL-18, podocin, nephrin, and desmin in mouse kidney tissues were detected.

RESULTS

With the increasing age, serum glucose, body weight, serum creatinine, and ACR in db/db mice gradually increased, which were remarkably higher than age-matched db/m mice. After treatment with miRNA-337 inhibitor in db/db mice, no remarkable changes in serum glucose and body weight were found, while serum creatinine and ACR decreased. Compared with db/m mice, miRNA-337 expression in kidney tissues of db/db mice upregulated, which was positively correlated with ACR. Expression levels of IL-6 and IL-18 in kidney tissues of db/db mice increased relative to db/m mice, but they were downregulated by miRNA-337 inhibitor treatment. Moreover, podocin and nephrin downregulated, while desmin upregulated in kidney tissues of db/db mice than db/m mice. By miRNA-337 inhibitor treatment in db/db mice, levels of podocin and nephrin increased, whereas desmin level decreased. We obtained similar results at their cellular level.

CONCLUSIONS

We showed that miRNA-337 expression increases in db/db mice with diabetic nephropathy, which leads to podocyte injury by upregulating levels of IL-6 and IL-18.