Highly consistency of PIK3CA mutation spectrum between circulating tumor DNA and paired tissue in lung cancer patients.

Background: Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha ( PIK3CA) mutations are associated with drug resistance and prognosis in lung cancer; however, the consistency and clinical value of PIK3CA mutations between tissue and liquid samples are unknown. Methods: Circulating tumor DNA (ctDNA) and matched tumor tissue samples from 405 advanced lung cancer patients were collected at Jilin Cancer Hospital between 2018 and 2022, and the PIK3CA mutation status was sequenced using next-generation sequencing based on a 520 gene panel. The viability of different mutant lung cancer cells was detected using MTT assay. Results: PIK3CA mutations were detected in 46 (5.68 %) of 810 lung cancer samples, with 21 (5.19 %) of 405 plasma samples and 25 (6.17 %) of 405 matched tissues. p.Glu542Lys, p.Glu545Lys, and p.His1047Arg were the most common mutation types of PIK3CA in both the ctDNA and tissue samples. The concordance of PIK3CA mutations was 97.53 % between ctDNA and matched tissues (kappa: 0.770, P = 0.000), with sensitivity/true positive rate of 72.0 %, specificity/true negative rate of 99.2 %, and negative predictive value and positive predictive value of 0.982 and 0.857, respectively (AUC = 0.856, P = 0.000). Furthermore, the concordance of PIK3CA mutations was 98.26 % in lung adenocarcinoma and 96.43 % in lung squamous cell carcinoma. TP53 and EGFR were the most common concomitant mutations in ctDNA and tissues. Patients with PIK3CA mutations showed a high tumor mutational burden (TMB) (P < 0.001) and a significant correlation between bTMB and tTMB (r = 0.5986, P = 0.0041). For the tPIK3CAmut/ctDNA PIK3CAmut cohort, PI3K pathways alteration was associated with male sex (P = 0.022), old age (P = 0.007), and smoking (P = 0.001); tPIK3CAmut/ctDNA PIK3CAwt patients harbored clinicopathological factors of adenocarcinoma stage IV, with low PS score (≤1) and TMB. Conclusion: This study showed that ctDNA is highly concordant and sensitive for identifying PIK3CA mutations, suggesting that PIK3CA mutation detection in liquid samples may be an alternative clinical practice for tissues.

The predictive value of E2F7 in immunotherapy efficacy for lung adenocarcinoma: An observational study.

Lung adenocarcinoma (LUAD) is the most common pathological type of lung cancer. In recent years, immunotherapy has greatly changed the treatment pattern of advanced LUAD. However, only a small proportion of LUAD patients benefitted from immune checkpoint inhibitor therapy. There is an urgent need to develop a biomarker to predict immune therapy response. E2F7 has been shown to be closely related to immune cell infiltration and immune checkpoint expression in tumors. However, it is unclear whether the E2F7 expression is related to the immunotherapy efficacy in LUAD. Therefore, we conducted this study to investigate the clinical characteristics, function, and immunotherapy responsiveness of E2F7 expression, and to explore the potential of E2F7 as an immunotherapy response biomarker in LUAD. We analyzed the clinical characteristics and biological function of E2F7 expression based on data from the Cancer Genome Atlas and Gene Expression Omnibus database. In addition, we used single-cell sequencing data to analyze the immune regulatory effects of E2F7 in LUAD. Furthermore, we analyzed the immunotherapy response prediction ability of E2F7 expression based on the immunotherapy database. Compared to normal lung tissue, E2F7 was specifically overexpressed in LUAD, and its expression was associated with higher malignancy and poor efficacy. E2F7 high expression was an independent risk factor affecting the prognosis of LUAD. E2F7 was enriched in cell division and cell cycle functions. In addition, the expressions of immune checkpoints were correlated with the E2F7 expression. E2F7 was highly expressed in myeloid cells, and E2F7 highly expressed myeloid cells were associated with immune and inflammatory responses. Moreover, the expression level of E2F7 can effectively distinguish different immune therapy responses in LUAD patients. E2F7 was upregulated in LUAD, and high expression of E2F7 was associated with higher malignancy and poor efficacy. E2F7 high expression was an independent risk factor affecting the prognosis of LUAD. Moreover, E2F7 may exert its immunosuppressive effect by affecting the function of myeloid cells. These results indicated the potential role of E2F7 as a biomarker for predicting LUAD immunotherapy responses.

Colony­stimulating factor CSF2 mediates the phenotypic plasticity of small­cell lung cancer by regulating the p­STAT3/MYC pathway.

Relapse and drug resistance are the main causes of mortality in patients with small­cell lung cancer (SCLC). Intratumoral heterogeneity (ITH) is a key biological mechanism that leads to relapse and drug resistance. Phenotypic plasticity is an important factor that leads to ITH in SCLC, although its mechanisms and key regulatory factors remain to be elucidated. In the present study, cell proliferation and cell switch assay were measured using trypan blue. Alamar Blue was used to test drug sensitivity. Differential genes were screened by RNA sequencing. Reverse transcription­quantitative PCR and western blotting were performed to assess the expressions of CSF2/p­STAT3/MYC pathway related molecules, neuroendocrine (NE)/non­neuroendocrine (non­NE), transcription factors and drug­related targets. The present study found that SCLC cell line NCI­H69 exhibited adherent (H69A) and suspensive (H69S) phenotypes, which could switch back and forth. The two phenotypic cells had significant differences in cellular NE and non­NE characteristics, drug sensitivity and expression of drug­related targets. RNA sequencing showed that granulocyte­macrophage colony­stimulating factor [i.e., colony­stimulating factor 2 (CSF2)] was the main differentially expressed gene between the two phenotypes and that H69A cells highly expressed CSF2. The inhibition of CSF2 promoted the transformation from H69A to H69S, increased drug sensitivity and NE marker expression and decreased the non­NE marker expression in H69A. The STRING, Pathway Commons and Reactome databases showed a potential regulatory relationship between CSF2 and phosphorylated signal transducer and activator of transcription 3 (p­STAT3)/MYC. p­STAT3 and MYC expression was higher in H69A cells than in H69S cells and CSF2 silencing inhibited their expression. Taken together, these results indicated that CSF2 may regulate the phenotypic plasticity of SCLC through the phosphorylated STAT3/MYC pathway, thereby limiting the transformation between cell clones with different phenotypes and changing the sensitivity of specific cell clones to targeted drugs. Targeting CSF2 may be a potential therapeutic strategy to overcome drug resistance in SCLC treatment by influencing ITH.

The Prevalence and Concurrent Pathogenic Mutations of KRAS G12C in Northeast Chinese Non-small-cell Lung Cancer Patients.

OBJECTIVE: KRAS mutation is one of important driver genes in non-small-cell lung cancer (NSCLC) and the patients with KRAS G12C mutations benefit from the inhibitor AMG510. However, the frequency, concurrent pathogenic mutations, and clinical characteristic of KRAS G12C is unknown in the NSCLC population of Northeast China. METHODS: The retrospective analysis was derived from 431 NSCLC patients in Jilin Cancer Hospital between January 2018 and June 2019. The mutation frequency and concurrent mutations of KRAS G12C in tumor or peripheral blood was detected by next-generation sequencing (NGS). RESULTS: The RAS mutant rate was observed in 10.7% (46/431) of this cohort. All RAS-driver cancers are caused by mutations in the KRAS isoform, while the NRAS and HRAS isoforms were not detected. Among KRAS-mutant patients, 42 (91.3%) showed exon 2 mutation in 12 codon and 13 codon. KRAS G12C showed a 4.6% (20/431) mutation rate in this cohort and the highest frequency (43.5%, 20/46) in KRAS-mutant-positive patients. There was no difference between tumor tissue and plasma in terms of either KRAS or KRAS G12C mutation. The most frequent co-occurrence mutations with KRAS G12C were TP53, followed by PTEN. Furthermore, KRAS G12C was exclusive with STK11 mutation. KRAS G12C mutation was associated with age, disease stage, and smoking status (P=0.024; P=0.02; P=0.006), smoking remained an independent factor for KRAS G12C mutation (P=0.037), and higher mutation frequency in patients older than 60, stage I-III, or smoking in NSCLC (P=0.0151, P=0.0343, P=0.0046, respectively). CONCLUSION: KRAS mutation was the only isoforms of RAS family, of these 43.5% harbored the KRAS G12C subtype in northeastern Chinese NSCLC patients. KRAS G12C is associated with age, pathological stage and smoking status, more commonly harbored TP53/PTEN mutations, and providing more genome profile for targeted therapy in local clinical practice.

Surgical resection of primary tumor is associated with prolonged survival in low-grade pancreatic neuroendocrine tumors.

INTRODUCTION: The incidence of pancreatic neuroendocrine tumors (PNETs) is increasing over the past few decades. Surgery for low-grade and small PNETs of less than 2cm and N0M0 is still debated. The purpose of this study is to examine the association between surgical resection and survival in patients with low-grade nonfunctioning PNETs. MATERIALS AND METHODS: Patients diagnosed with PNETs between 2004 and 2015 were extracted from SEER. Kaplan-Meier methods and Cox proportional hazard models were used to estimate independent predictors in PNETs patients. RESULTS: A total of 2637 patients (2147 underwent surgical resection and 490 did not undergo surgery) with histologically confirmed low-grade PNETs in this cohort study. Overall survival (OS) and cancer-specific survival (CSS) of patients with surgery was better than those without surgery (log rank test POS<0.001, PCSS<0.001). Multivariate Cox regression analysis showed that surgical status was an independent prognostic factor associated with OS (HR 3.257, 95%CI: 2.635, 4.026) and CSS (HR 3.546, 95%CI: 2.798, 4.493). Subgroup analysis suggested the patients receiving surgery apparently had better OS and CSS regardless of tumor size (all log rank test POS<0.001, all log rank test PCSS<0.001) and SEER stage (all log rank test POS<0.001, all log rank test PCSS<0.001), compared to patients without removal of the primary tumor. CONCLUSIONS: Surgical resection of primary tumor may have a significant benefit on survival for patients with low-grade nonfunctioning PNETs. To determine the optimal management, grade, stage and tumor size should be considered comprehensively.

Elevated serum lipid level can serve as early signal for metastasis for Non-Small Cell Lung Cancer patients: A retrospective nested case-control study.

Objective: To investigate the association between serum lipid levels in patients with primary non-small cell lung cancer and the risk of developing metastases, a retrospective cohort-based nested case-control study was conducted. Material and method: Patients with primary non-small cell lung cancer admitted to the First and the Third Hospitals of Jilin University from January 2008 through December 2015 were recruited retrospectively based on their electronic medical records. A total of 524 patients were initially considered, consisting of 138 in the case group and 386 as control. Out of these, 110 were finally included in the case group and 110 as control based on additional selection criteria. The following information is collected from all the patients, total cholesterol (TC), low-density lipoprotein (LDL-C), high density lipoprotein (HDL-C) and triglyceride (TG). Logistic regressions were conducted to estimate the odds ratios (ORs) and 95% confidence intervals (95% CI) for non-small cell lung cancer (NSCLC) patients to have metastasis risk when having elevated serum lipid levels. Restricted cubic spline (RCS) curves were used to demonstrate the association between serum lipid levels and the risk of metastasis. Results: Patients with high TC level (P = 0.025, 0R = 1.35, 95% CI: 1.03-1.74) and patients with high LDL-C level (Q4: > 3.47 vs Q1: ≤2.54, P = 0.002, OR = 3.92, 95% CI: 1.31-11.77) are found to have an increased metastasis risk; and their dose-response relationship was validated by our restricted cubic spline analysis (TC: P overall association=0.02, P non-linear association = 0.73; LDL-C: P overall association=0.02, P non-linear association = 0.10). These associations were statistically significant, particularly in men who smoked, never drank, and were 65 years of age or younger. In addition, patients with simultaneously high levels of TC and LDL-C have a 60% increased risk of metastasis compared with patients with high levels of TC and normal LDL-C. Conclusion: Dyslipidemia may be a risk factor for metastasis among NSCLC patients. Examination of serum lipid level on a regular basis can provide early signal of metastasis for NSCLC patients.

Association of MAD1L1 polymorphism (rs871925) with prenatal famine exposure and schizophrenia in a Chinese population: A case-control study.

Schizophrenia (SCZ) is a complex, frequently disabling psychiatric disorder. Prenatal exposure to famine, an environmental factor, plays a significant role in the cause of SCZ. We used DNA methylation related sites to analyze their association with prenatal famine exposure and SCZ risk in a Northeast Han Chinese population. A total of 967 subjects (446 patients with SCZ/521 health controls) were recruited. Five single-nucleotide polymorphisms (rs2300149 in ITIH1, rs2675956 in NGEF, rs3758543 in NT5C2, rs7003288 in NA, and rs871925 in MAD1L1) were selected and genotyped. Genotype distribution and allele frequency analysis indicated that rs871925 was significantly associated with SCZ. We also found a significant association between prenatal exposure to famine and rs871925 in the recessive model in the health control group. The generalized multifactor dimensionality reduction analysis suggested a five-locus interaction model association with the risk of developing SCZ. Our data suggested that MAD1L1 rs871925 was associated with prenatal famine exposure and SCZ susceptibility in a Northeast Han Chinese population.

Fibrinogen and Kininogen are Potential Serum Protein Biomarkers for Depressive Disorder.

BACKGROUND: Depressive disorder is a debilitating psychiatric mental disease. However, no biological methods are used for the diagnosis of this disorder. Proteomic approaches for biomarker discovery may provide an important objective tool for diagnostics of depression. This study aimed to identify serum protein biomarkers for diagnosis of depressive disorder. METHODS: We screened for potential depression biomarkers in 175 serum samples from 86 patients and 89 healthy controls. Serum protein spectrums were detected by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). Differentially expressed peptides among the two groups were analyzed and followed by sequence analysis to identify these peptides. RESULTS: Five peaks were found to have a significant different between the depression and healthy control groups. Among them, up-regulated m/z 1,466.21 and down-regulated m/z 1,944.99 are identified as the fractions of fibrinogen alpha chain and kininogen 1, respectively. CONCLUSIONS: Fibrinogen and kininogen may be potential serum protein biomarkers in the diagnosis and prognosis of depressive disorders.

Kininogen-1 as a protein biomarker for schizophrenia through mass spectrometry and genetic association analyses.

BACKGROUND: Schizophrenia (SCZ) is a complex and severe mental illness. There is a lack of effective biomarkers for SCZ diagnosis. The aim of this study was to explore the possibility of using serum peptides for the diagnosis of SCZ as well as analyze the association of variants in genes coding for these peptides and SCZ. METHODS: After bead-based fractionation, the matrix-assisted laser desorption ionization/time-of-flight mass spectrometry technique was used to identify peptides that showed different expressions between 166 SCZ patients and 201 healthy controls. Differentially expressed peptides were verified in a second set of samples (81 SCZ patients and 103 healthy controls). The association of SCZ and three tagSNPs selected in genes coding for differentially expressed peptides was performed in 1,126 SCZ patients and 1,168 controls. RESULTS: The expression level of peptides with m/z 1,945.07 was significant lower in SCZ patients than in healthy controls (P < 0.000001). The peptide with m/z 1,945.07 was confirmed to be a fragment of Kininogen-1. In the verification tests, Kininogen-1 had a sensitivity of 95.1% and a specificity of 97.1% in SCZ prediction. Among the three tagSNPs (rs13037490, rs2983639, rs2983640) selected in the Cystatin 9 gene (CST9) which encodes peptides including Kininogen-1, tagSNP rs2983640 had its genotype distributions significantly different between SCZ patients and controls under different genetic models (P < 0.05). Haplotypes CG (rs2983639-rs2983640) and TCG (rs13037490-rs2983639-rs2983640) were significantly associated with SCZ (CG: OR = 1.21, 95% CI [1.02-1.44], P = 0.032; TCG: OR = 24.85, 95% CI [5.98-103.17], P < 0.0001). CONCLUSIONS: The present study demonstrated that SCZ patients had decreased expression of Kininogen-1 and genetic variants in Kininogen-1 coding gene CST9 were significantly associated with SCZ. The findings from both protein and genetic association studies suggest that Kininogen-1 could be a biomarker of SCZ.

The Relationship between Gene Polymorphism of miRNAs Regulating FGA and Schizophrenia.

AIM: To investigate the relationship between the polymorphism of related gene loci of miRNAs regulated fibrinopeptide A and schizophrenia. Lay the foundation for the aetiology of schizophrenia. METHODS: Adapt to the phase match of sex and age case-control study, a total of 513 Chinese Han patients with schizophrenia were selected as the case group, 513 normal healthy persons as a control group. Obtaining SNPs information of the FGA gene by querying the dbSNP database, and reference HapMap database included SNPs site frequency information for screening. The frequency distributions of SNPs were genotyped by iMLDR® SNP detection technology. Two SNPs (pre-hsa-miR-605rs2043556 T>C, pre-hsa-miR-499a/pre-hsa-miR-499brs4909237 T < C) were analyzed to demonstrate their association with susceptibility to schizophrenia. RESULTS: There were no significant differences between patients and controls in genotype and allele distribution of SNPs rs2043556 and rs4909237 in the precursor region of hsa-miR-605 and pre-hsa-miR-499a/pre-hsa-miR-499b. Their gene-gene interaction, which suggests that the polymorphisms of miRNA genes might not contribute to schizophrenia susceptibility in the Han Chinese population. CONCLUSION: No significant difference existed between schizophrenic patients and controls in SNP (rs2043556 and rs4909237) in the precursor region of hsa-miR-605 and pre-hsa-miR-499a/pre-hsa-miR-499b. There may not regulate FGA gene expression. Thus, hsa-miR-605 and pre-hsa-miR-499a/pre-hsa-miR-499b may not influence the risks of schizophrenia.

CACNA1C Polymorphism (rs2283291) Is Associated with Schizophrenia in Chinese Males: A Case-Control Study.

Recent research has shown that prenatal famine exposure may be one of the risk factors for schizophrenia and that people born in famine years may be at an increased risk of schizophrenia due to alteration of the DNA methylation of genes. In this study, the association of rs2283291/rs4648635 and the incidence of schizophrenia and prenatal famine exposure at the genetic level were investigated to provide clues to the pathogenesis of schizophrenia. A total of 960 participants were recruited, comprising 473 prenatal famine-exposed individuals (225 patients and 248 controls) and 487 prenatal non-famine-exposed individuals (220 patients and 267 controls). The association of prenatal famine, schizophrenia, and their interaction with DNA methylation levels was analyzed using SPSS and GMDR software. Gender stratification analysis revealed a significant association between the rs2283291 genotype and schizophrenia in male patients (P = 0.017), and difference still existed after correction by the Bonferroni method. It was also found that an increasing risk of schizophrenia was associated with rs2283291 in males (OR: 1.62, 95% CI: 1.13-2.33, P = 0.0086, AIC = 669.7) in an overdominant model. The results of gene-environment interaction and gene-gene interaction revealed no association with the risk of schizophrenia. This study reported for the first time that rs2283291 was associated with schizophrenia in Chinese males.

Relationship of Gallbladder Diseases with Sociodemographic Characteristics, Lifestyle, and Chronic Diseases in Northeastern China.

BACKGROUND: Gallbladder diseases are common in Jilin, China. However, there have been few previous studies on this disease. Our study used the chronic disease database in Jilin Province to study the factors correlated with gallbladder diseases. METHODS: A total of 21,435 people were selected from the Jilin Province adult chronic disease survey conducted in 2012. Multistage stratified random cluster sampling was used in this cross-sectional study. Multiple logistic regression analysis was used to explore the independent associations of different factors with gallbladder diseases. RESULTS: There were 1876 people with gallbladder diseases, and the prevalence of the diseases was 8.8% (males 4.4%, females 12.8%). Multivariate logistic regression analysis showed that female (prevalence odds ratio (POR) = 3.13, 95% confidence intervals (CIs): 2.76⁻3.55), older people (30⁻45 years (POR = 2.79, 95% CIs: 2.06⁻3.77), 45⁻60 years (POR = 4.26, 95% CIs: 3.17⁻5.73), 60⁻79 years (POR = 4.72, 95% CIs: 3.48⁻6.41)), people living in rural areas (POR = 1.65, 95% CIs: 1.49⁻1.82), smoking (current smoker (POR = 1.15, 95% CIs: 1.01⁻1.31), former smoker (POR = 1.37, 95% CIs: 1.13⁻1.66)), high frequency of eating seafood (POR = 0.77, 95% CIs: 0.63⁻0.93), and high frequency of eating soy products (POR = 0.50, 95% CIs: 0.44⁻0.58) were associated with gallbladder diseases. CONCLUSIONS: We found that there were some factors associated with gallbladder disease, and there needs to be further studies to confirm these associations.

Association Between Polymorphisms of the Complement 3 Gene and Schizophrenia in a Han Chinese Population.

BACKGROUND/AIMS: Schizophrenia is a severe psychiatric disorder, and complement 3 (C3) is closely related to schizophrenia. We investigated the association between C3 polymorphisms and schizophrenia in a Northeast Han Chinese population. METHODS: A total of 2240 Chinese people, consisting of 1086 patients with schizophrenia and 1154 healthy controls, were recruited for this study. Ten single nucleotide polymorphisms (SNPs; rs11569562, rs344555, rs2241393, rs2241392, rs11569514, rs445750, rs451760, rs11672613, rs2230205, and rs2250656) in C3 were selected and genotyped. RESULTS: Genotype distribution analysis indicated that rs11569514 was significantly associated with schizophrenia. In the dominant model (AA vs. GG+GA genotypes), we found a significant protective effect for rs344555 against schizophrenia (odds ratio [OR]: 0.72, 95% confidence interval [CI]: 0.53-0.99, P = 0.04). In the codominant model (TT vs. AA), we found a significant risk effect for rs11569514 on schizophrenia (OR: 4.39, 95% CI: 2.06-9.37, P < 0.001). Haplotypes, including TG (rs11569562 and rs344555), TGG (rs11569562-rs344555-rs2241393), AG (rs344555-rs2241393), CGGGT (rs11569562-rs344555-rs2241393-rs2241392-rs11569514), and ACGTG (rs11569514-rs445750-rs451760-rs11672613-rs2230205), showed either a risk or protective role for schizophrenia. CONCLUSIONS: SNP rs11569514 in C3 and haplotypes of C3 variants were associated with schizophrenia in a Han Chinese population.

Kinases, homology models, and high throughput docking.

With the many protein sequences coming from the genome sequencing projects, it is unlikely that we will ever have an atomic resolution structure of every relevant protein. With high throughput crystallography, however, we will soon have representative structures for the vast majority of protein families. Thus the drug discovery and design process will rely heavily on protein modeling to address issues such as designing combinatorial libraries for an entire class of targets and engineering genome-wide selectivity over a target class. In this study we assess the value of high throughput docking into homology models. To do this we dock a database of random compounds seeded with known inhibitors into homology models of six different kinases. In five of the six cases the known inhibitors were found to be enriched by factors of 4-5 in the top 5% of the overall scored and ranked compounds. Furthermore, in the same five cases the known inhibitors were found to be enriched by factors of 2-3 in the top 5% of the scored and ranked known kinase inhibitors, thus showing that the homology models can pick up some of the crucial selectivity information.