Non-mutation Group Research Articles

Multi-factor dynamic analysis of ctDNA and CTC to aid the diagnostic prognosis of patients with metastatic breast cancer (MBC).

1038 Background: The monitoring of circulating tumor DNA (ctDNA) and circulating tumor cell (CTC) in patients with MBC predicts treatment resistance and prognosis. We previously reported that ESR1 alterations in ctDNA were associated with tumor tissue characteristics and CTCs which may predict metastasis and worse prognosis in MBC (2019 ASCO#1036, 2022 ASCO#1057). Furthermore, ctDNA can be used to evaluate tumor heterogeneity in MBC (2020 ASCO #1028). Here, we report a multi-factor analysis in ctDNA and CTC which may help to elucidate disease prognosis in MBC. Methods: This study included 391 MBC patients who received systemic treatment before 2022 under an IRB-approved clinical trial at NU Lurie Cancer Center. Whole blood samples (7.5ml/each) were collected from all patients at three time points including before treatment, three months, and six months after treatment for CTC enumeration using the CELLTRACKS system (Menarini). The corresponding ctDNA was analyzed by Guardant360 NGS evaluating 74-gene mutations. The maximum follow-up period was 380 months from first diagnosis. Causal Inference with Ensembel Learning was used for statistical analyses. Results: Of the 391 patients ctDNA analysis, TP53 mutations were found in 160 patients (TP53Mut, 40.92%), CDH1 mutations were found in 21 patients (CDH1Mut, 5.37%), Myc mutations were found in 53 patients (MycMut, 13.55%), and BRAF mutations were found in 35 patients (BRAFMut, 8.95%) inclusive of all timepoints. The corresponding ctDNA mutations were not detected in 231 patients for TP53 (TP53WT, 59.08%), in 370 patients for CDH1 (CDH1WT, 94.63%), in 338 patients for Myc (MycWT, 86.45%), or in 356 patients for BRAF (BRAFWT, 91.05%). There was shorter median overall survival (mOS) in the ctDNA mutated groups compared to the non-mutated groups: 88 months TP53Mut vs 184 months TP53WT, HR 1.91, P = 0.0002; 133 months CDH1WT vs 81 months CDH1Mut, HR 2.03, P = 0.02; 76 months Myc Mut vs 179 months MycWT , HR 3.24, P < 0.0001, and 77 months BRAFMut vs 146 months BRAFWT HR 2.45, P = 0.007. Furthermore, ≥5 CTCs were found in 32.42% patients. These patient had a shorter mOS compared to patients had no CTC detected at any time point (70.1 months vs 131 months; P < 0.001; HR 2.97). CTC-clusters were 50 times more likely to predict metastasis than single CTCs. We also found that greater than 5 CTC-clusters, clusters with 1-5, and no CTC-clusters were found in 12.55%, 11.25%, and 76.19% patients, respectively. Larger CTC-clusters had shorter mOS at 63 months, 121 months, and 163 months, respectively (P < 0.0001). Conclusions: In this study, we identified multiple liquid biopsy factors including ctDNA and CTC-clusters at various time points, and found that these are associated with prognosis. The synergy of multiple ctDNA mutations and CTC-clusters during treatment may expand the predictive role of liquid biopsy for the monitoring of disease progression in patients MBC.

Correlation of blood cell counts with mutant subtypes and impact prognosis in acute myeloid leukemia patients with FLT3 mutations

ABSTRACTObjectivesAcute myeloid leukemia (AML) often presents with abnormal blood cell counts and gene mutations at diagnosis. But, the correlation between blood cell counts and gene mutations and the clinical effects on AML is unclear.Methods279 AML patients with FMS-like tyrosine kinase 3(FLT3) mutations were selected. Patients with FLT3 mutations were counted by PCR amplification products direct sequencing and second-generation sequencing (NGS), and blood cell counts at the time of initial diagnosis. The relapse-free survival (RFS) and overall survival (OS) and the influence of the clinical characteristics of patients on the prognosis in different groups were analyzed.ResultsThe median of platelet (PLT) count was higher in the TET2 non-mutation group than mutation group and higher in the IDH1/2 mutation group than non-mutation group. The median of white blood cell (WBC) count was reduced in the poor prognosis group. The differences in levels of WBC and PLT count varied among the four groups binding sequence (JM-B), switching sequence (JM-S), zipper sequence (JM-Z), and high chain region (JM-H). The differences in PLT count varied between the insertion length ≥39 bp and <39 bp, and between ≥ 50 bp and <50 bp; The OS and RFS in 10 < WBC (×109/L) < 100 group and in the 30 ≤ PLT (×109/L)<80 group were better.ConclusionsIn AML patients with FLT3 mutations, the location of FLT3 mutations and the type of co-mutated genes may be correlated with blood cell counts, and different blood cell counts may have an impact on the prognosis.

Clinical Pathological Characteristics and Prognosis of Multigene Co-Mutations in Elderly Patients With Non-Small Cell Lung Cancer: A Retrospective Analysis.

With the development and wide application of next-generation sequencing (NGS), multiple-gene mutations related to lung cancer are detected using this technology. Notably, even multigene concomitant mutations (co-mutations), which occur at a relatively low incidence, can be detected more effectively using NGS. It is well-known that the percentages of non-small cell lung cancer (NSCLC) in the elderly lung cancer population are also gradually increasing, while its prognosis is hard and the quality of long-term survival is poor. This study aimed at investigating the common clinicopathologic features of multigene co-mutations for better evaluating the prognosis of elderly NSCLC patients. A total of 464 NSCLC patients were divided into 3 groups according to the types of gene mutation, whose clinical data were retrospectively analyzed. In total, 38.36% (178/464) of NSCLC patients were in the nonmutation group, 50% in the single-gene mutation group, and 11.64% in the multigene co-mutation group. Nonmutation, single-gene mutation, and co-mutation groups were all prone to occur in male adenocarcinoma patients (P < .05). EGFR gene mutation rates were the highest in the single-gene mutation and co-mutation groups (54.31% and 24.35%). In the co-mutation group, the incidence of EGFR/PIK3CA, LK/KRAS, and EGFR/MET co-mutations was the highest (16.67%, 11.11%, and 7.41%). ALK/HER2/MET, EGFR/HER2/MET, and EGFR/HER2/MET/ROS1 multiple-gene co-mutations were, respectively, found in 1 case, and the multigene co-mutation patients commonly had a worse median progression-free survival (PFS) than that of single-gene mutation (7.13 vs 12.34 months, P = .013). With the application of NGS, the detectable rates of gene co-mutation are increasingly high in elderly patients with NSCLC, which mainly occurs in male adenocarcinoma patients commonly with poor PFS. It will be critically necessary to conduct multigene detections by NGS for directing targeted therapy of elderly NSCLC patients.

Comparison of clinical features of JAK2V617F gene mutation and non-mutation in patients with Budd-Chiari syndrome

Objective: To investigate the clinical features of JAK2V617F gene mutation and non-mutation in patients with Budd-Chiari syndrome (BCS). Methods: 17 and 127 BCS cases with JAK2V617F gene mutation (mutation group) and non-gene mutation (non-mutation group) who were continuously treated with interventional therapy between January 2016 to December 2020 in the Affiliated Hospital of Xuzhou Medical University were selected as the research object for a comparative study. The hospitalization and follow-up data of the two groups were analyzed retrospectively, and the deadline for follow-up was June 2021. Quantitative data group differences were analyzed using the independent sample t-test and Wilcoxon rank sum test. Qualitative data group differences were analyzed with χ2 test or Fisher's exact test. Mann-Whitney U test was used to analyze the differences between groups in rank data. Kaplan-Meier method was used to calculate the patient survival and recurrence rate. Results: Age [(35.41±17.10) years vs. (50.09±14.16) years, t=3.915, P<0.001], time of onset (median duration: 3 months vs. 12 months), and the cumulative survival rate (65.5% vs 95.1%; χ2=5.21, P=0.022) were lower in mutation than non-mutation group. Aaspartate aminotransferase, alanine aminotransferase, prothrombin time, Child-Pugh score, Rotterdam score, Model for End-stage Liver Disease score, hepatic vein thrombosis incidence, and the cumulative recurrence rate after intervention were higher in mutation than non-mutation group. The above all indexes had statistically significant differences (P<0.05) between the groups. Conclusion: Younger age, acute onset, severe liver injury, high incidence of hepatic vein thrombosis, and poor prognosis are the features of patients with BCS with JAK2V617F gene mutation than non-mutation.

Clinical and laboratory features of COVID-19 patients infected with SARS-CoV-2 variant B.1.1.7 versus those infected with other SARS-CoV-2 strains

Objective: To investigate the clinical symptoms of coronavirus disease 2019 (COVID-19) patients with and without B.1.1.7 mutation. Methods: This retrospective observational study included COVID-19 patients who were divided into two groups, the mutation and the non-mutation group. Demographics characteristics, clinical characteristics, laboratory parameters, and mortality rates were recorded and compared between the two groups. Results: A total of 196 patients were included in the study. The relationship between the mutant virus status and sex, age, comorbidity, survival status, and disease severity was not significant (P&gt;0.05). No significant differences were found in duration of hospitalization between the mutation and the non-mutation group (P&gt;0.05). However, there was a statistically significant difference between patients with and without mutant viruses in hemoglobin, mean platelet volume, procalcitonin, low density lipoprotein, ironbinding capacity, potassium, calcium, C-reactive protein, folate, creatine kinase myocardial band, D-dimer, and international normalized ratio (P&lt;0.05). Conclusions: No significant difference is found in mortality rate, disease severity or duration of hospitalization between the patients with and without variant B.1.1.7. Careful monitoring of COVID-19 patients is required for all variants.

Correlation between Mycoplasma pneumoniae drug resistance and clinical characteristics in bronchoalveolar lavage fluid of children with refractory Mycoplasma pneumoniae pneumonia

BackgroundTo investigate the resistance-gene mutation of Mycoplasma pneumoniae (MP) in the bronchoalveolar lavage fluid of children with Mycoplasma pneumoniae pneumonia (MPP) and the clinical characteristics of refractory Mycoplasma pneumoniae pneumonia (RMPP) correlation.MethodsForty-eight children with MPP were selected and placed in RMPP and non-RMPP groups based on their clinical status – whether they had worsening clinical symptoms, persistent fever and a worsening lung image. They were also separated into drug-resistance gene mutation and non-mutated groups using nucleic acid detection. The participants’ data were collected on high-sensitivity C-reactive protein and MP-DNA loads, fever time, hospitalisation time, macrolide antibiotic application time and fever regression time after application. The differences in imaging manifestations were determined by using multivariate logistic regression to analyse the clinical characteristics of RMPP. Additionally, the correlation between drug-resistance gene mutations and the clinical characteristics of RMPP was summarised.ResultsAmong the 48 MPP children, 31 (64.6%) had A2063G and/or A2064G gene mutation, 31 (64.6%) had RMPP and 23 (74.2%) had drug-resistance gene mutation. The children in the drug-resistance gene mutation group had higher high-sensitivity C-reactive protein and MP-DNA loads, longer fever time, hospitalisation time, macrolide antibiotic application time, fever regression time after application and extrapulmonary complications. There were more symptoms and more severe changes under bronchoscopy. The difference was statistically significant (P < 0.05). Logistic multivariate regression analysis showed that the mutation of drug-resistance genes had no significant correlation with RMPP.ConclusionThe mutation rate of drug-resistance genes in children with MPP is high, the inflammatory index and MP-DNA load are high, the course of the disease is long, and the changes under bronchoscopy are severe. The occurrence of RMPP is not only determined by drug-resistance genes but may also be the result of a combination of factors.

Identification and in silico analysis of noval alteration Arg420Gly in KIT proto oncogene among acute myeloid leukemia patients

A number of studies have reported frequent incidence of c-kit gene mutations in association with core binding factor acute myeloid leukemia (CBF-AML). These genetic changes have become important prognostic predictors in patients with abnormal karyotype. Aim of this study was the detection of nucleotide alterations in newly diagnosed acute myeloid leukemia patients for three exons of c-kit gene, including cytogenetically normal patients. Thirty-one de novo AML patients were screened for any possible variations in exon 8, 11 and 17 sequences of c-kit proto-oncogene leading to amino acid substitutions or frame shift. Sanger sequencing method was employed followed by sequence analysis. Mutation data was then correlated with clinical and hematological parameters of patients and prognostic significance of genetic changes was assessed as well. The computational tools were then used to further understand the extent of damage caused by these mutations to c-kit protein. Fifteen (48.4%) mutant patients were observed with single, double or multiple mutations in one, two or all three exons studied. The analysis revealed eight new alterations which were not reported previously. Significant variation among mutant and non-mutant group of patients was observed with respect to FAB subtypes (x2 = 12.524, p = 0.029), Spleen size (x2 = 4.288, p = 0.038) and Red blood cell count (x2 = 8.447, p = 0.007). The survival analysis indicates poor overall and event free survival outcomes in mutant individuals. Furthermore, the in silico analysis suggests that changes in nucleotide sequences can possibly damage the protein structure and effect it’s function. This study emphasizes the need to consider screening of c-kit gene alterations not only in CBF-AML but in cytogenetically normal AML patients as well. In current investigation the effect of mutation Arg420Gly on structure and function of c-kit protein was investigated, as this was the most observed substitution in present cohort. Various bioinformatics tools and techniques were employed, which determined that Arg420Gly is possibly non-pathogenic mutation.

FAT2 mutation is associated with better prognosis and responsiveness to immunotherapy in uterine corpus endometrial carcinoma.

Uterine corpus endometrial carcinoma (UCEC) ranks sixth among malignant tumors in women and the mortality is still rising. FAT2 gene has been considered to be related to the survival and prognosis of some certain diseases in previous studies, but the FAT2 mutation status in UCEC and its prognostic value has been rarely studied. Hence, the purpose of our study was to explore the role of FAT2 mutations for predicting prognosis and responsiveness to immunotherapy in patients with UCEC. UCEC samples from the Cancer Genome Atlas database were analyzed. We evaluated the impact of FAT2 gene mutation status and clinicopathological characteristics on the prognosis of UCEC patients and used univariate and multivariate Cox analysis risk scores to independently predict patient overall survival (OS). Tumor mutation burden (TMB) values of the FAT2 mutant and non-mutant groups were computed by Wilcoxon rank sum test. The correlation of FAT2 mutation and half maximal inhibitory concentration (IC50) values of various anticancer drugs was analyzed. Gene Ontology data and Gene Set Enrichment Analysis (GSEA) were employed to examine the differential expression of genes between the two groups. Finally, a single-sample GSEA arithmetic was utilized to measure the abundance of tumor-infiltrating immune cells in UCEC patients. FAT2 mutations suggested better OS (p < 0.001) and disease-free survival (DFS) (p=0.007) in UCEC. The IC50 values of 18 anticancer drugs were upregulated in FAT2 mutation patients (p < 0.05). The TMB and microsatellite instability values of patients with FAT2 mutations were significantly higher (p < 0.001). Next, the Kyoto Encyclopedia of Genes and Genomes functional analysis and GSEA revealed the potential mechanism of FAT2 mutation on the tumorigenesis and progression of UCEC. In addition, in reference to the UCEC microenvironment, the infiltration levels of activated CD4/CD8 T cells (p < 0.001/p=0.001) and plasmacytoid dendritic cells (p=0.006) were upregulated in the non-FAT2 mutation group, and Type 2 T helper cells (p=0.001) were downregulated in the FAT2 mutation group. UCEC patients with FAT2 mutations have better prognosis and are more likely to respond to immunotherapy. FAT2 mutation may be a valuable predictor for prognosis and responsiveness to immunotherapy in UCEC patients.

VHL and DNA damage repair pathway alterations as potential clinical biomarkers for first-line TKIs in metastatic clear cell renal cell carcinomas

PurposeVascular endothelial growth factor receptor tyrosine kinase inhibitors (VEGFR-TKIs) are being used for the first-line treatment of metastatic clear cell renal cell carcinoma (mccRCC). Here, we set out to explore associations between genomic statuses, gene expression clusters and clinical outcomes of mccRCCs upon the application of VEGFR-TKIs.MethodsA retrospective study of 56 patients with mccRCC who received first-line VEGFR-TKIs and who underwent genomic profiling and whole transcriptome sequencing was conducted. Survival analysis was carried out using log-rank tests and Cox regression analyses, and Kaplan–Meier curves were plotted. Clustering was performed using the K-means method.ResultsAmong the 56 patients tested, 17 harbored DNA Damage and Repair (DDR) pathway alterations and 35 VHL mutations. The median progression-free survival (PFS) rates for the DDR and VHL alteration groups were 18 and 18 months, respectively, compared with 14 and 10 months for the nonmutant groups. DDR mutations, VHL mutations and co-mutations were identified as prognostic biomarkers of a longer PFS (p = 0.017, 0.04, 0.014). K-means clustering of expressed transcripts revealed three clusters of 40 patients: C_1, C_2 and C_3. The C_1 cluster exhibited the best PFS and objective response rate (ORR) to TKI therapy, with the highest proportion of DDR and VHL mutations. Further analysis of the tumor immune environment revealed that the C_1 cluster was enriched in activated CD8 T cells and effector CD4 T cells, whereas the C_2 cluster was enriched in eosinophils, mast cells and DC cells and, thus, in immunosuppressive cells.ConclusionsWe found that patients with mccRCC harboring DDR and VHL alterations were more likely to benefit from first-line VEGF-TKI systemic therapy than patients with wild-type disease. In addition, we found that a three-cluster prognostic model based on gene expression can predict PFS and ORR, which was well-matched with activated TIL infiltration.

SCG2: A Prognostic Marker That Pinpoints Chemotherapy and Immunotherapy in Colorectal Cancer.

BackgroundFluorouracil (FU)-based chemotherapy regimens are indispensable in the comprehensive treatment of colorectal cancer (CRC). However, the heterogeneity of treated individuals and the severe adverse effects of chemotherapy results in limited overall benefit.MethodsFirstly, Weighted gene co-expression network analysis (WGCNA) identified modules tightly associated with chemotherapy response. Then, the in-house cohort and prognostic cohorts from TCGA and GEO were subjected to Cox proportional hazards model and survival analysis to ascertain the predictable function of SCG2 on the prognosis of CRC patients. Finally, we performed In vitro experiments, functional analysis, somatic mutation, and copy number variation research to explore the biological characteristics of SCG2.ResultsWe identified red and green as the modules most associated with chemotherapy response, in which SCG2 was considered a risky factor with higher expression predicting poorer prognosis. SCG2 expression in the APC non-mutation group was remarkably higher than in the mutation group. The mutation frequencies of amplified genes differed significantly between different SCG2 expression subgroups. Besides, CRC cell lines with SCG2 knockdown have reduced invasive, proliferative, and proliferative capacity. We discovered that the SCG2 high expression subgroup was the immune hot type and considered more suitable for immunotherapy.ConclusionThis study demonstrates the clinical significance and biological characteristics of SCG2, which could serve as a promising biomarker to identify patients who may benefit from chemotherapy and immunotherapy.

PTCH1 and AXIN2 modulation of AR copy number effects on AR gene overexpression in metastatic castration resistant prostate cancer (mCRPC).

e17026 Background: Androgen receptor (AR) signaling is a critical pathway in prostate cancer progression. Reactivation of the AR pathway is a key driver in mCRPC. Patients with mCRPC often develop resistance to novel AR signaling inhibitors (ARSIs) such as enzalutamide. AR inhibitor resistance leads to shorter overall and progression-free survival and can be attributed to AR gene amplification with subsequent AR overexpression and androgen-sensitization in prostate tumors. Identifying novel modulators of AR amplification in patients progressing on ARSIs may lead towards potential targets in drug discovery. Methods: In this cross-sectional study, an in silico patient model was developed on prescribed drug therapies and failed therapies patient information, PSA measures, ̃100 mutation variables including somatic, germline, and gain/loss mutations, and ̃1K gene expressions data from 275 mCRPC patients obtained from the Tempus database using GNS Healthcare’s Causal artificial intelligence technology, REFS. A causal network model was reconstructed based on patient data with inferred effect estimates. The network model was topologically surveyed for biological interactions. Results: Causal analysis of this model uncovered two germline mutations, located in PTCH1 and AXIN2, which modify the effect of AR copy number gain ( ARgain+ : copy number 6, ARgain- : copy number &lt; 6) on AR gene expression. For PTCH1-mutant group, there was a 2-fold increase in AR gene expression in ARgain+ patients compared to ARgain- patients (p = 2.1e-12), while only 1.4 fold increase in AR gene expression from the PTCH1 non-mutant group (p = 6.3e-08). Similarly, there was a 2-fold increase in AR gene expression in ARgain+ patients compared to ARgain- patients (p = 7.2e-16) for the AXIN2-mutant group, while only one-fold increase in AR gene expression with the AXIN2 non-mutant group (p = 0.001). The C to T missense mutation in codon 3746 in PTCH1 and codon 148 in AXIN2 have higher prevalences, 55% and 72%, respectively in this mCRPC cohort compared to their population allele frequencies, 38% and 47%, respectively. Conclusions: PTCH1 and AXIN2 mutations from our analyses is consistent with a literature reported role for Hedgehog signaling and Wnt/-catenin signaling pathways, respectively, influencing the disease progression in castration-resistant prostate cancer. Our findings suggest that the missense germline mutations in PTCH1 and AXIN2 predicts response to enzalutamide and other ARSIs in CRPC setting, and propose potential targets for combination therapy to overcome ARSI drug resistance in hormone-refractory prostate cancer. [Table: see text]

Analysis of clinical characteristics and related genetic variation of juvenile myasthenia gravis

Objective: To analyze the clinical characteristics and related genetic variation of juvenile myasthenia gravis (MG) patients. Methods: We collected the clinical data of adolescent MG patients who were treated in the Department of Neurology of the First Affiliated Hospital of Sun Yat-sen University from June 2019 to May 2020. After obtaining the patient's informed consent, the blood samples were collected. The Whole Exome Sequencing (WES) was performed on peripheral blood samples. And use biological information software and SPSS 22.0 for data processing and result analysis. Results: According to the inclusion and exclusion criteria, 54 patients with juvenile MG were included, 28 males and 26 females. And the average age of onset was (3.79±0.89) years. Among the enrolled patients, there were 52 (96.3%) patients with ocular MG, the MG-ADL scores of 54 patients were (3.44±0.44) points, and the titer of AChR antibody was (5.88±2.45) nmol/L. Two patients had thymic hyperplasia, and 5 patients had a family history of MG.A total of 169 variant genes were found in 54 patients, of which TTN gene variants had the largest number, with a total of 17 variants (31.5%). In the TTN gene variant group, 7(41.2%) patients had eye fixation symptoms, and 4 (10.8%) patients in the non-mutation group had eye fixation symptoms. And The difference between the two groups was statistically significant (P=0.016). In addition, the synaptic nucleus envelope protein-1 (SYNE1) and the ryanodine receptor-1 (RYR1) gene variations were also found in 7 cases (13.2%), and no clear relationship between these gene variations and clinical manifestations of MG was found. Conclusions: The incidence of juvenile MG was preschoolers with no gender difference, and ocular MG was more common. The proportion of TTN gene variation in adolescent MG was higher, suggesting that this gene may be a potential therapeutic target for juvenile MG patients.

Ovarian Reserve and ART Outcomes in Blepharophimosis-Ptosis-Epicanthus Inversus Syndrome Patients With FOXL2 Mutations.

ObjectiveTo characterize the status of ovarian reserve and ART outcomes in BPES women and provide informative reference for clinical diagnosis and treatment.MethodsTwenty-one women with BPES were screened for mutations in the FOXL2 gene and underwent assisted reproductive technology (ART) treatment. Indicators for ovarian reserve and ART outcomes were compared between patients with and without FOXL2 mutations. Additionally, ART outcomes were compared among patients with different subtypes of FOXL2 mutations.ResultsA total of 13 distinct heterozygous variants in the FOXL2 gene were identified in 80.95% of BPES women, including 4 novel mutations with plausible pathogenicity (c.173_175dup, c.481C>T, c.576del and c.675_714del). Compared to non-mutation group, patients with FOXL2 mutations had elevated levels of FSH (P=0.007), decreased AMH levels (P=0.012) and less AFC (P=0.015). They also had worse ART outcomes with large amount of Gn dosage (P=0.008), fewer oocytes (P=0.001), Day3 good quality embryos (P=0.001) and good quality blastocysts (P=0.037), and a higher cancellation rate (P=0.272). High heterogeneity of ART outcomes existed in BPES patients with different FOXL2 mutation types.ConclusionsBPES patients with FOXL2 mutations had diminished ovarian reserve and adverse ART outcomes. The genotype-reproductive phenotype correlations were highly heterogeneous and cannot be generalized. Genetic counseling for fertility planning and preimplantation or prenatal genetic diagnosis to reduce offspring inheritance are recommended.

Factors affecting outcome in resected EGFR-mutated lung cancer

Introduction Long-term data on disease trajectory of EGFR-mutated early-stage non-small cell lung cancer (NSCLC) is still limited. This is relevant in the context of the recently approved introduction of adjuvant EGFR-targeting therapy, specifically osimertinib in resected stage II–III EGFR-mutated NSCLC. Methods Long-term data on patients with resected adenocarcinoma of the lung and known EGFR-status were analysed with focus on site of relapse and detailed cause of death. Patients resected in the period 2006 to 2018 were included. Results Of 503 patients (286 (57%) females, median age 67.3 years), 62 (12%) harboured an EGFR-mutation, 286 (57%) were in stage I. After a median follow-up of 8.0 years, 241 (48%) patients relapsed. Recurrence occurred in 30% and 53% of EGFR-positive stage IA and IB patients, respectively. Median overall survival was longer in EGFR-mutated versus non-mutated patients (128 versus 88 months). The recurrence rate, time to recurrence and rate of brain metastases was not different between EGFR-mutated and non-mutated groups. Median time from recurrence to death was longer in EGFR-mutated patients (31 months) compared with non-mutated patients (15 months). More patients without EGFR-mutation succumbed to non-cancer related death (18%) compared to patients with EGFR-mutations (8%). Conclusions The recurrence pattern in EGFR-mutated and non-mutated NSCLC-patients is similar and the rate is high in early stages. Time from recurrence to death and overall survival is longer in the EGFR-mutated group, due to lower risk of non-lung cancer deaths, and efficient treatment upon relapse.

Single-Cell Sequencing Identifies the Heterogeneity of CD8+ T Cells and Novel Biomarker Genes in Hepatocellular Carcinoma.

CD8+ T cells are required for the establishment of antitumor immunity, and their substantial infiltration is associated with a good prognosis. However, CD8+ T cell subsets in the tumor microenvironment may play distinct roles in tumor progression, prognosis, and immunotherapy. In this study, we used the scRNA-seq data of hepatocellular carcinoma (HCC) to reveal the heterogeneity of different CD8+ T cell subsets. The scRNA-seq data set GSE149614 was obtained from the GEO database, and the transcriptome and sample phenotypic data of TCGA-LIHC were obtained from the TCGA database. CD8+ T cell subtypes and metabolic gene sets were obtained from published reports. The data processing and analysis of CD8+ T cell groups was performed by R language. The PPI network was constructed to obtain the hub genes, and the KM survival curve of the hub genes was further plotted to determine the hub genes with differences in survival. CD8+ T cells in HCC were divided into 7 subsets, and the cytotoxic CD8 T cells 4 subset showed considerable differences between the TP53-mutant and nonmutant groups, as well as between different degrees of cirrhosis, HCC grades, stages, ages, and body weights. Cytotoxic CD8 T cells 4 differential genes were analyzed by TCGA-LIHC data and single-cell sequencing data set. 10 hub genes were found: FGA, ApoA1, ApoH, AHSG, FGB, HP, TTR, TF, HPX, and APOC3. Different subsets of CD8+ T cells were found to contribute to heterogeneous prognosis and pathway activity in HCC. Alterations in the cytotoxic and immune checkpoint gene expression during CD8+ T cell differentiation were also identified. We found that cytotoxic CD8 T cells 4 is closely associated with survival and prognosis of HCC and identified four differential genes that can be used as biological markers for survival, prognosis, and clinically relevant characteristics of HCC. Results of this study could help finding targets for immunotherapy of HCC and aid in the accelerated development of immunotherapy for HCC.

Analysis of Coexisting Gene with NRAS in Acute Myeloid Leukemia

To investigate the coexisting mutations and clinical significance of Homo sapiens neuroblastoma RAS viral oncogene homolog (NRAS) gene in acute myeloid leukemia (AML) patients. High-throughput DNA sequencing and Sanger sequencing were used to detect 51 gene mutations. The occurrence, clinical characteristics and treatment efficacy of coexisting genes with NRAS were investigated. A total of 57 NRAS mutations (17.5%) were detected in 326 patients with AML. Compared with the patients in NRAS non-mutation group, patients in the mutant group were younger (P=0.018) and showed lower platelet count (P=0.033), but there was no significant difference in peripheral leukocyte count, hemoglobin, and sex. For FAB classification, NRAS mutation and M2 subtype showed mutually exclusive (P=0.038). Among 57 patients carried with NRAS mutation, 51 (89.5%) patients carried with other gene mutations, 25 (43.9%) carried with double gene mutations, 10 (17.5%) carried with 3 gene mutations, and 16 (28.1%) corried with ≥ 4 gene mutations. The most common coexisting gene mutation was KRAS (24.6%, 14/57), followed by FLT3-ITD (14.0%, 8/57), RUNX1 (12.3%, 7/57), NPM1 (10.5%, 6/57), PTPN11 (10.5%, 6/57), DNMT3A (10.5%, 6/57) and so on. The age (P=0.013, P=0.005) and peripheral platelet count (P=0.007, P=0.021) of patients with NPM1 or DNMT3A mutations were higher than those of the patients with wild type, but there was no significant difference in peripheral leukocyte count and hemoglobin. Also, there was no significant difference in age, peripheral leukocyte count, hemoglobin, and peripheral platelet count between the patients in KRAS, FLT3-ITD, RUNX1 or PTPN11 mutant group and the wild group. Patients with FLT3-ITD mutations showed a lower complete remission (CR) rate (P=0.044). However, there was no significant difference in CR rate between the patients with KRAS, NPM1, RUNX1, PTPN11 or DNMT3A mutations and the wild group. The CR rate of the patents with single gene mutation, double gene mutations, 3 gene mutations, and≥ 4 gene mutations were decreased gradually, and there was no significant difference in CR rate between pairwise comparisons. The mutation rate of NRAS mutation is 17.5%, 89.5% of AML patients with NRAS mutation coexist with additional gene mutations. The type of coexisting mutations has a certain impact on clinical characteristics and CR rate of patients with AML.

Immunohistochemical Evaluation of BAP1 Expression in Breast Cancer with Known BRCA1 and BRCA2 Mutations and Comparison with Histopathological Features.

Introduction. BRCA-mutated breast cancers have specific pathological characteristics. BAP1 is a tumor suppressor gene that is important in many cancers with different pathways. The relationship between BRCA1 mutation and BAP1 immunohistochemical staining is still unclear. Our aim is to determine whether BAP1 immunohistochemical expression indicates BRCA mutation status in breast carcinomas with specific pathological characteristics. In addition, we aim to determine the histopathological characteristics of tumors according to BRCA mutations. Methods. Histomorphology, molecular subtypes and BAP1 immunohistochemical expression patterns of the BRCA1/BRCA2 mutated and non-mutated tumors were evaluated. The BAP1 immunohistochemical stain was applied to nine tumor tissues with the BRCA1 mutation, six tumor tissues with the BRCA2 mutation, and 16 tumor tissues without any BRCA mutation. Pearson's chi square test and the Fisher Freeman Halton test were used to analyze the associations between the datas. The statistical significance was considered as P value of <.05. Results. Immunohistochemical BAP1 loss was not detected in any mutated or non-mutated tumor group. BRCA1 mutated tumors had the statistically highest histopathological grade (P = .04) and BRCA1/2 mutated tumors had significant immunohistochemical triple negative expression pattern (P = .01). Conclusions. Intrinsic and histopathological characteristics may vary between BRCA1 mutated and non-BRCA1 mutated tumors. Also, BAP1 loss was not detected in BRCA mutated breast tumors because of several effects of BAP1 that are non-related with BRCA in the cell cycle.

Mutational spectrum and its prognostic significance in childhood acute lymphoblastic leukemia based on next-generation sequencing technology

目的分析儿童急性淋巴细胞白血病（ALL）的基因突变谱及其预后意义。方法回顾性分析2016年11月至2019年12月福建医科大学附属协和医院采用二代测序技术（NGS）行基因突变检测的141例初治ALL患儿的临床资料，分析基因突变谱及其对ALL患儿预后的影响。结果141例患儿中，83例（58.9％）检出体细胞突变，包括37个Ⅰ类及123个Ⅱ类突变位点。单核苷酸变异（SNV）为最常见的突变类型。KRAS（20/160，12.5％）为最常见的突变基因，其次为NOTCH1（11.9％）及NRAS（10.6％）。RAS通路（KRAS、FLT3、PTPN11）、PAX5及TP53突变仅在B-ALL患儿中检出，而FBXW7、PTEN突变仅在T-ALL患儿中检出；NRAS突变主要在B-ALL中检出，而NOTCH1突变主要在T-ALL中检出。每例T-ALL患儿检出的平均基因突变个数显著高于B-ALL患儿（4.16±1.33对2.04±0.92，P＝0.004）。按照有无遗传变异将患儿分为突变组和无突变组，两组的性别、年龄、初诊白细胞计数、微小残留病监测结果、预计3年无事件生存（EFS）率及总生存（OS）率差异均无统计学意义（P值均>0.05）；但突变组T-ALL以及融合基因阴性患儿的比例显著高于无突变组（P值分别为0.021和<0.001）。进一步亚组分析，在融合基因阴性的患儿中，有Ⅰ类突变的患儿预计3年EFS率显著低于无Ⅰ类突变的患儿（85.5％对100.0％，P＝0.039）；在B-ALL患儿中，伴TP53突变的患儿预计3年EFS率显著低于不伴有TP53突变的患儿（37.5％对91.2％，P<0.001）。结论体细胞突变在儿童ALL中较为常见，与临床表型及预后具有一定的相关性，NGS可作为传统MICM分型检查的重要补充。

Low-level gastrokine 2 promoted progress of NSCLC and as a potential biomarker.

BackgroundGastrokine 2 (GKN2) is significantly downregulated in non‐small cell lung cancer (NSCLC) tissues than in normal tissues (NT), as assessed by mRNA microassay; however, the mechanism and clinical value of GKN2 is unknown in NSCLC.MethodsA total of 60 NSCLC samples and corresponding NT samples were prospectively collected GKN2 expression in NSCLC tissues was estimated. Also, the expression level of GKN2 promoter methylation and correlation with clinical data in NSCLC patients from public databases were analyzed. Cytology experiments were also carried out.ResultsThe GKN2 mRNA and protein expression level in NSCLC was significantly lower than that in the NT, and the GKN2 expression level in large tumors NSCLC was significantly lower than that in the small tumor group. Public data showed that expression of GKN2 in LUAD with P53 mutation group was lower than that of the P53 non‐mutation group, and GKN2 promoter methylation level of LUAD was significantly higher than its NT and close to age and clinical stage. Cell migration, invasion, and proliferation ability of GKN2 overexpressed were lower in A549 and PC9 groups than those in GKN2 overexpressed A549 and PC9 negative control groups, while the percentage of apoptotic cells increased in the GKN2 overexpressed A549 and PC9 groups. The DNMT3B mRNA expression levels were higher in PC9 and A549 cells than BEAS‐2B cells.ConclusionThe overexpression of GKN2 significantly inhibited cell proliferation, migration, and invasion and promoted apoptosis. Low‐level GKN2 promoted the progression of NSCLC via DNMT3B and is expected to be a biomarker for NSCLC.

JAK2 mutation may predict response and guide first line treatment in rheumatoid arthritis

BackgroundJAK (Janus kinase) inhibitors work by inhibiting the activity of one or more of the enzyme Janus kinase with a therapeutic application for treatment of cancer and inflammatory disorders such as rheumatoid arthritis (RA). We aimed to study impact of JAK2 mutation in serum of rheumatoid arthritis patients on response to first line with conventional synthetic disease-modifying anti-rheumatic drug (csDMARDS) at 3rd month by evaluating DAS28 and ACR response criteria. The study included 85 newly diagnosed rheumatoid arthritis patients and 50 matched controls. Basal JAK2 mutation assessed by PCR in blood samples, TNF-α and IL 6 were measured by ELISA in serum of patient and control groups. All patients started therapy with csDMARDs. Response assessment at 3rd month was evaluated by DAS28 and ACR response criteria. JAK2 mutation was correlated with different clinical and laboratory parameters of patients.ResultsSeventeen females (83.5%) and 14 males (16.5%) with age mean ± SD (years); (48.7 ± 7.2). Pretreatment JAK2 mutation, TNF-α and IL 6 were significantly high in patients. JAK2 mutation was detected in 45 (52.9%) patients while 40 (47.1%) patients were JAK2 non-mutant. Mutant JAK2 was significantly linked to severity of disease evaluated by DAS28; 14 (70%) of patients with DAS28 (≤ 2.6) were non-mutant JAK2 vs sex (30%) patients mutant JAK2 while 19 (73.1%) of patients with DAS28 (> 5.1) were mutant JAK2 vs 7 (26.9%) patients non-mutant JAK2 (P 0.02). JAK2 mutation found to be significantly correlated with ACR 20, 50, and 70 response criteria; 68.2% of patients with non-mutant JAK2 showed ACR 70 vs 31.8% in mutant group, 52% of patients with non-mutant JAK2 showed ACR 50 vs 48% in mutant group while 31.6% of patients with non-mutant JAK2 showed ACR 20 vs 68.4% in mutant group (P 0.02). JAK2 mutation were more presented in young age patients (mean ± SD; 47.1 ± 7.2 vs 50.4 ± 6.9 in mutant vs non-mutant JAK2 patients, respectively with P 0.03). JAK2 mutation was associated with high pretreatment TNFα and IL6 level in serum. Mean ± SD of TNFα; 49.4 ± 41.9 in mutant vs 26 ± 24.4 pg/ml in non-mutant group, with P (0.003) while mean ± SD of IL6; 83.5 ± 56.8 in mutant vs 47 ± 46.9 pg/ml in non-mutant group, with P (0.002).ConclusionsAdult RA with pretreatment JAK2 mutation significantly showed high disease activity and high pretreatment TNFα and IL6 levels. Patients with JAK2 mutation found to be linked to poor response to 1st line csDMARDs including MTX so they could get more benefit with early introduction of JAK inhibitors as first line monotherapy or when combined with csDMARDS especially those with moderate to severe active RA.Trial registrationInstitutional Research Board (IRB)-Faculty of Medicine: IRB Proposal Code: R.20.11.1075-2020/11/16. Clinicaltrials.gov registration date: 8/12/2020, code: NCT04667988.