Novel genetic characteristics in low-grade fetal adenocarcinoma of the lung

Background

Low‐grade fetal adenocarcinoma of the lung (L‐FLAC) is a rare subtype of lung adenocarcinoma with undetermined histological features and genetic abnormalities. In this study, we attempted to investigate the pathological characteristics and genomic profiles of L‐FLAC.

Methods

Among 9839 cases of primary lung adenocarcinoma resected at Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College between January 2011 and June 2016, three cases diagnosed with L‐FLAC were selected. An immunohistochemical profile and whole exome sequencing (WES) using tumor and normal tissues was conducted. The last follow‐up date of patients was January 2021.

Results

Three cases diagnosed with L‐FLAC were finally screened, suggesting a percentage of 0.03%. All three patients were male and diagnosed as stage I following radical lobectomy. The missense variant was found to be the major gene mutation type using WES. CTNNB1 and DICER1 were the two most frequent gene mutations. All cases demonstrated positive TTF‐1 expression. In addition, two patients showed positive expression of β‐catenin (nuclear/cytoplasmic expression), CgA and Sny. Negative expression of PD‐L1 in tumor cells was observed in all three cases. One case with a relatively high tumor mutation burden (TMB) (2.18 mut/Mb) had an inferior overall survival of 11.5 months. However, the other two cases with a lower TMB (0.12 and 0.74 mut/Mb) still acquired disease‐free status up to the last follow‐up date.

Conclusions

L‐FLAC has a specific molecular background which is different from lung adenocarcinoma. Furthermore, gene heterogeneity was found and might be the reason for a dramatically different prognosis in these L‐FLAC patients.

The Distinct Performances of Ultrasound, Mammograms, and MRI in Detecting Breast Cancer in Patients With Germline Pathogenic Variants in Cancer Predisposition Genes

A proportion of up to 10% of breast cancer resulted from hereditary germline pathogenic variants (GPVs) in cancer predisposition genes (CPGs), which been demonstrated distinct clinical features and imaging manifestations. However, the performance of imaging modalities for breast cancer surveillance in CPG mutation-carriers is still unclear, especially in Asian women. A population of 3002 breast cancer patients who received germline genetic testing of CPGs was enrolled from three hospitals in China. In total, 343 (11.6%) patients were found to harbor GPVs in CPGs, including 137 (4.6%) in BRCA1 and 135 (4.6%) in BRCA2. We compared the performances of ultrasound, mammograms, MRI, and the combining strategies in CPG mutation carriers and non-carriers. As a result, the ultrasound showed a higher detection rate compared with mammograms regardless of the mutation status. However, its detection rate was lower in CPG mutation carriers than in non-carriers (93.2% vs 98.0%, P=2.1×10^-4), especially in the BRCA1 mutation carriers (90.9% vs 98.0%, P=2.0×10^-4). MRI presented the highest sensitivity (98.5%) and the lowest underestimation rate (14.5%) in CPG mutation carriers among ultrasound, mammograms, and their combination. Supplemental ultrasound or mammograms would add no significant value to MRI for detecting breast cancer (P>0.05). In multivariate logistic regression analysis, the family or personal cancer history could not replace the mutation status as the impact factor for the false-negative result and underestimation. In summary, clinicians and radiologists should be aware of the atypical imaging presentation of breast cancer in patients with GPVs in CPGs.

High PD-L1 expression on immune cells, but not on tumor cells, is a favorable prognostic factor in urothelial carcinoma

Aims: To explore the prognostic value of high PD-L1 expression on tumor cells (TC) and tumor-infiltrating immune cells (TIIC) in urothelial carcinoma (UC). Patients & methods: 162 UC specimens were evaluated for PD-L1 expression on TIIC and TC with the SP263 assay. High PD-L1 expression was defined as ≥25% staining. Results: High PD-L1 expression on TC in UC patients with stage T1-4 disease was associated with poor overall survival. However, high PD-L1 expression on TIIC in UC patients with stage T1-4 disease revealed favorable disease-free and overall survival; more significant differences were observed in patients with stages T2-4. Multivariate analysis revealed that high PD-L1 expression on TIIC was an independent prognostic predictor for better disease-free and overall survival. Conclusion: High PD-L1 expression on TIIC, but not on TC, is a favorable prognostic factor in UC.

Identification of DNA methylation biomarkers for risk of liver metastasis in early-stage colorectal cancer

Background

Liver metastases can occur even in CRC patients who underwent curative surgery. While evidence suggested that adjuvant chemotherapy can help to reduce the occurrence of liver metastases for certain patients, it is not a recommended routine as the side effects outweigh the potential benefits, especially in Stage II CRC patients. This study aims to construct a model for predicting liver metastasis risk using differential methylation signals in primary CRC tumors, which can facilitate the decision for adjuvant chemotherapy.

Methods

Fifty-nine stage I/II and IV CRC patients were enrolled. Primary tumor, adjacent normal tissue, and metastatic tumor tissues were subject to targeted bisulfite sequencing for DNA methylation. The Least Absolute Shrinkage and Selection Operator (LASSO) algorithm was used to identify potential DMRs for predicting liver metastasis of CRC.

Results

We identified a total of 241,573 DMRs by comparing the DNA methylation profile of primary tumors of stage II patients who developed metastasis to those who were metastasis-free during the follow up period. 213 DMRs were associated with poor prognosis, among which 182 DMRS were found to be hypermethylated in the primary tumor of patients with metastases. Furthermore, by using the LASSO regression model, we identified 23 DMRs that contributed to a high probability of liver metastasis of CRC. The leave-one-out cross validation (LOOCV) was used to evaluate model predictive performance at an AUC of 0.701. In particular, 7 out of those 23 DMRs were found to be in the promoter region of genes that were previously reported prognostic biomarkers in diverse tumor types, including TNNI2, PAX8, GUF1, KLF4, EVI2B, CEP112, and long non-coding RNA AC011298. In addition, the model was also able to distinguish metastases of different sites (liver or lung) at an AUC of 0.933.

Conclusion

We have identified DNA methylation biomarkers associated with the risk of cancer liver metastasis in early-stage CRC patients. A risk prediction model based on those epigenetic markers was proposed for outcome assessment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13148-021-01108-3.

Platform study of genotyping-guided precision medicine for rare solid tumours: a study protocol for a phase II, non-randomised, 18-month, open-label, multiarm, single-centre clinical trial testing the safety and efficacy of multiple Chinese-approved targeted drugs and PD-1 inhibitors in the treatment of metastatic rare tumours

INTRODUCTION

Limited clinical studies have been conducted on rare solid tumours, and there are few guidelines on the diagnosis and treatment, including experiences with targeted therapy and immunotherapy, of rare solid tumours in China, resulting in limited treatment options and poor outcomes. This study first proposes a definition of rare tumours and is designed to test the preliminary efficacy of targeted and immunotherapy drugs for the treatment of rare tumours.

METHODS AND ANALYSIS

This is a phase II, open-label, non-randomised, multiarm, single-centre clinical trial in patients with advanced rare solid tumours who failed standard treatment; the study aims to evaluate the safety and efficacy of targeted drugs in patients with advanced rare solid tumours with corresponding actionable alterations, as well as the safety and efficacy of immune checkpoint (programmed death receptor inhibitor 1, PD-1) inhibitors in patients with advanced rare solid tumours without actionable alterations. Patients with advanced rare tumours who fail standardised treatment and carry actionable alterations (Epidermal growth factor receptor (EGFR) mutations, ALK gene fusions, ROS-1 gene fusions, C-MET gene amplifications/mutations, BRAF mutations, CDKN2A mutations, BRCA1/2 mutations, HER-2 mutations/overexpressions/amplifications or C-KIT mutations) will be enrolled in the targeted therapy arm and be given the corresponding targeted drugs. Patients without actionable alterations will be enrolled in the PD-1 inhibitor arm and be treated with sintilimab. After the patients treated with vemurafenib, niraparib and palbociclib acquire resistance, they will receive combination treatment with sintilimab or atezolizumab. With the use of Simon's two-stage Minimax design, and the sample size was estimated to be 770. The primary endpoint of this study is the objective response rate. The secondary endpoints are progression-free survival in the targeted treatment group and single-agent immunotherapy group; the duration of response in the targeted therapy and single-agent immunotherapy groups; durable clinical benefit in the single-agent immunotherapy group; and the incidence of adverse events.

ETHICS AND DISSEMINATION

Ethics approval was obtained from the Chinese Academy of Medical Sciences (ID: 20/132-2328). The results from this study will be actively disseminated through manuscript publications and conference presentations.

TRIAL REGISTRATION NUMBERS

NCT04423185; ChiCTR2000039310.

Two-year follow-up of single PD-1 blockade in neoadjuvant resectable NSCLC

8522

Background: Early stage non-small-cell lung cancer (NSCLC) could benefit from anti-programmed cell death-1 (PD-1) monotherapy; however, the survival profiles remain to be disclosed. Here, we presented the two-year follow-up outcomes from a phase 1b study of sintilimab, an anti-PD-1 inhibitor in the neoadjuvant setting of NSCLC. Methods: Treatment-naive pts with resectable NSCLC (stage IA–IIIB) received two cycles of sintilimab followed by surgical resection. Postoperative treatment of sintilimab was at the discretion of investigator. The primary endpoint was AE, and key secondary endpoints included major pathological response (MPR), disease free survival (DFS) rate of 1 year and 2 years, and overall survival (OS) rate of 2 years. Results: Among 40 enrolled pts, 36 (90%) underwent R0 resection and were included in the R0 resection population. By data cutoff (January 20, 2021), the median follow-up for DFS and OS for all the enrolled pts was 23.9 (IQR 20.5–24.4) months and 26.4 (IQR 24.2–29.0) months. A total of 12 (33.3%) pts experienced relapse, and 6 pts died. The 1-yr and 2-yr DFS rate was 91.7%/73.3%. The 2-yr OS rate for overall population and R0 population was 87.5%/91.7%, respectively. In the R0 resection population, the median DFS and OS were both not reached. Superior 2-year DFS rates were observed in pts who achieved MPR (MPR vs. Non-MPR: 86.7% vs. 63.8%). DFS of pts with non-squamous cell carcinoma tended to be shorter than that of pts with squamous cell carcinoma (HR 2.71 [95%CI 0.67–11.0], p=0.1479). Pts with tumor mutation burden (TMB) ≥10 mutations/Mb and PD-L1 tumor proportion score (TPS)≥50% tended to have a better 2-yr DFS rate compared to those with TMB<10 and TPS<50. [table] For the post-hoc event free survival (EFS) analysis, the same trend was observed with DFS among different subgroups, and patients with TMB ≥10 mutations/Mb had a significant improved EFS (HR 0.125[95% CI 0.02,1.03], P=0.0222). Conclusions: Anti-PD-1 monotherapy emerged to be a promising neoadjuvant therapeutic strategy for resectable NSCLC with improved clinical outcomes. MPR could serve as a surrogate efficacy biomarker in this setting. Clinical trial information: ChiCTR-OIC-17013726. [Table: see text]

Immune-related histologic phenotype in pretreatment tumor biopsy predicts pathologic response to neoadjuvant anti-PD-1 treatment in squamous lung cancer

e20540

Background: The neoadjuvant platform affords a rich and valuable resource for understanding the responses to therapy and carrying out reverse translation, including pathologic morphology. We aimed to develop a pretreatment histologic scoring system reflecting the preexisting immune response to predict the efficacy of neoadjuvant immunotherapy based on the morphological changes we mastered in the pathologic assessment after neoadjuvant immunotherapy. Methods: Surgical specimens from the 31 squamous cell lung cancer patients recruited in a phase Ib study of neoadjuvant anti-PD-1 therapy and eligible paired pretreatment biopsies from 15 of them were included in this study. The posttreatment surgical specimens were assessed according to the immune-related pathologic response criteria. Immune-related histologic phenotype assessment criteria (irHPC) were developed based on the pathologic features identified after neoadjuvant anti-PD-1 treatment. Three pathologists trained for irHPC independently scored the HE slides of the 15 pretreatment tumor biopsies according to irHPC. Results: Whether necrosis was included in the calculation of percent of residual viable tumor (%RVT) or not had almost no effect on the consistency of pathologic assessment ( P= 0.811) and the histological response grouping. The inter-pathologist variability of assessing %RVT with immune-activated phenotype was not statistically significant ( P= 0.480). Four immune-related features of pretreatment biopsies were included for calculating the predictive score, including three positive features (tumor-infiltrating lymphocytes, tumor-infiltrating eosinophils and dense plasma cells in stroma) and one negative feature (tumor-infiltrating neutrophils) according to the developed irHPC scoring system. The trained pathologist accurately predicted 6 out of 8 patients in the cPR/MPR group and 5 out of 7 patients in the non-cPR/MPR group according to irHPC. For inter-observer reproducibility using “2 points” as the cut-off point, the overall percent agreement (OPA) was 77.8%. The reliability between pathologists for a binary tumor evaluation showed “moderate” agreement (κ = 0.54). Conclusions: The irHPC scoring system reflecting the preexisting immune response could be used to predict the pathologic response of neoadjuvant immunotherapy, but still needs the larger trails to verify.

An open-label, single-arm, multicenter, phase II study of RC48-ADC to evaluate the efficacy and safety of subjects with HER2 overexpressing locally advanced or metastatic urothelial cancer (RC48-C009)

4584

Background: There is still urgent medical needs in the patients with locally advanced or metastatic urothelial cancer (mUC) post to the failure of at least one line chemotherapy. RC48-ADC, a novel humanized anti-HER2 antibody-drug conjugate (ADC), has proved its efficacy in these patients (RC48-C005, NCT03507166), most of whom had received gemcitabine and platinum. Taking into consideration that taxane is another possible active agent for mUC, this study aims to further evaluate the efficacy of RC48-ADC in HER2 overexpressing mUC post to the failure of platinum, gemcitabine and taxane. Methods: This study was an open-label, multicenter, single-arm, non-randomized phase II study. Eligibility criteria included: histologically confirmed UC, HER2 overexpressing (IHC 2+ or 3+), ECOG PS 0-1, failed platinum, gemcitabine and taxane. The patients received RC48-ADC treatment alone (2 mg/kg IV infusion, q2w) until disease progression, unacceptable toxicity, withdrawal, death or study termination. The primary endpoint was objective response rate (ORR) assessed by blinded independent review committee (BIRC) according to RECIST v1.1. Progress-free survival (PFS), duration of response (DOR), overall survival (OS), and safety was also assessed. Results: Patient enrollment for this study started in December 2018 and completed in September 2020. A total of 64 patients were enrolled, with a median age of 62.5 years. At baseline, most patients (82.8%) had visceral metastasis. Fifty-five patients (85.9%) had received ≥ 2 lines treatment and 19 (29.7%) patients had prior immune checkpoint inhibitor (CPI) therapy. As of Nov 30, 2020, the confirmed ORR assessed by BIRC was 46.9% (95% CI: 34.3%, 59.8%) and the median DOR was 8.3 months (95% CI: 4.3, NE), the median PFS was 4.3 months (95% CI: 4.0, 6.8). The median OS was 14.8 months (95% CI: 8.7, 21.1). The ORR was 60.0% (15/25) in patients with HER2 IHC3+ or FISH test positive, 45.3% (24/53) in patients with visceral metastasis, 42.1% (8/19) in patients post to CPI therapy. The ORR was 55.6% (5/9), 50.0% (21/20) and 30.8% (4/13), in patients who had received 1 line, 2 lines and ≥ 3 lines treatment, respectively. Most commonly reported TRAEs were leukopenia (45.3%), AST increase (43.8%), neutropenia (42.2%), hypoesthesia (42.2%), ALT increase (37.5%) and fatigue (35.9%); Most commonly reported ≥ grade 3 TRAEs were neutropenia (9.4%) and hypoesthesia (6.3%) Conclusions: In patients with HER2 overexpressing (IHC 2+ or 3+) mUC who had failed platinum, gemcitabine and taxane, and the great majority of whom had received ≥2 prior lines treatment, RC48-ADC has demonstrated consistently excellent efficacy and benefit-risk profile compared with the RC48-C005 study which enrolled patients with mUC who had received ≥1 line prior chemotherapy. Clinical trial information: NCT03809013.

Features in genomics and tumor immune microenvironment in NSCLC treated with neoadjuvant PD-1 blockade

9063

Background: Results from several clinical trials have preliminarily demonstrated the safety and effectiveness of single PD-1 inhibitors in neoadjuvant setting for resectable non-small cell lung cancer (NSCLC). However, only around 40% patients could achieve Major Pathological Response. How to select patients who could benefit from single PD-1 blockade remains elusive. Methods: In this study, we aimed to assess the association of PD-L1 expression, tumor mutation burden (TMB), copy number alteration (CNA, including copy number gain and loss) burden with the pathological response to neoadjuvant PD-1 blockade. We also evaluated the dynamic changes of tumor immune microenvironment (TIME) by analyzing pre-immunotherapy treatment tumor biopsy samples from twenty-nine NSCLC patients as well as the matched post-surgery samples after neoadjuvant sintilimab treatment and resection. Targeted DNA sequencing (543 genes), PD-L1 immunochemistry staining (22C3) and multiplex immunofluorescence (CD4, CD8, CD9) were applied. Results: The degree of pathological regression and major pathological response (MPR), were positively correlated with tumor proportion score (TPS) of PD-L1 (R = 0.40, p = 0.04) and negatively correlated with copy number gain (CNgain) burden (R = -0.44, p = 0.04). Of note, the combination of CNgain burden and TPS can better stratify MPR patients compared to CNgain or TPS alone. Whereas, TMB only had a marginal association with pathological response (R = 0.32, p = 0.15). Additionally, PD-1 blockade led to an increase in CD8+PD-1-T cells in the tumor region (p = 0.04, Mann-Whitney U test for paired samples) and a reduction in Tregs and M2 macrophages in the stromal region (p < 0.05, Mann-Whitney U test for paired samples). Further investigation showed that the degree of CD8+PD-1-T cell increase was significantly associated with MPR (p < 0.05, Mann-Whitney U test). Intriguingly, we also observed a substantial reduction in CD19+ cells in the non-MPR group but not in the MPR group, indicating the involvement of B cells in improving neoadjuvant immunotherapy response in NSCLC patients. Conclusions: TPS and CNgain burden were correlated with pathological response to neoadjuvant immunotherapy in NSCLC patients. This may provide potential selective indicators for future clinical trials of neoadjuvant immunotherapy. The dynamic changes of components in the tumor immune microenvironment may provide novel insight into the immune responses induced by neoadjuvant PD-1 blockade therapy.

Cytoplasmic MSH2 Related to Genomic Deletions in the MSH2/EPCAM Genes in Colorectal Cancer Patients With Suspected Lynch Syndrome

Background

A large proportion of patients with Lynch syndrome (LS) have MSH2 abnormalities, but genotype-phenotype studies of MSH2 mutations in LS are still lacking. The aim of this study was to comprehensively analyze the clinicopathological characteristics and molecular basis of colorectal cancer (CRC) in patients with uncommon MSH2 cytoplasmic expression.

Methods

We retrospectively reviewed 4195 consecutive cases of CRC patients diagnosed between January 2015 and December 2017 at the Cancer Hospital Chinese Academy of Medical Sciences. Of the 4195 patients with CRC, 69 were indicated to have abnormal MSH2 expression through tumor immunohistochemical staining. Genetic tests, such as next-generation sequencing, large genomic rearrangement (LGR) analysis, microsatellite instability status analysis and genomic breakpoint analysis, were performed. Clinicopathological and molecular characteristics and clinical immunotherapy response were analyzed.

Results

Forty-five of 69 patients were identified to have LS with pathogenic germline mutations in MSH2 and/or EPCAM. Of these LS patients, 26.7% were confirmed to harbor large genomic rearrangements (LGRs). Of note, three tumors from two unrelated family pedigrees exhibited a rare cytoplasmic MSH2 staining pattern that was found in LS patients with EPCAM/MSH2 deletions. RNA analysis showed that two novel mRNA fusions of EPCAM and MSH2 resulted in the predicted protein fusion with MSH2 cytoplasmic localization. Analyses of genomic breakpoints indicated that two novel deletions of EPCAM and MSH2 originated from Alu repeat-mediated recombination events. Our study also provides clinical evidence for the beneficial effect of the PD-1 inhibitor pembrolizumab for CRC patients that exhibit cytoplasmic MSH2 staining.

Conclusion

Our study demonstrates that the rare cytoplasmic MSH2 staining pattern should be fully recognized by pathologists and geneticists. Given the specific genotype-phenotype correlation in LS screening, we advocate that all CRC patients with cytoplasmic MSH2 staining in histology should be screened for LGRs of EPCAM and MSH2.

Tumor-Associated Stromal Cellular Density as a Predictor of Recurrence and Mortality in Breast Cancer: Results from Ethnically Diverse Study Populations

PURPOSE

Tumor-associated stroma is comprised of fibroblasts, tumor-infiltrating lymphocytes (TIL), macrophages, endothelial cells, and other cells that interactively influence tumor progression through inflammation and wound repair. Although gene-expression signatures reflecting wound repair predict breast cancer survival, it is unclear whether combined density of tumor-associated stromal cells, a morphologic proxy for inflammation and wound repair signatures on routine hematoxylin and eosin (H&E)-stained sections, is of prognostic relevance.

METHODS

By applying machine learning to digitized H&E-stained sections for 2,084 breast cancer patients from China (n = 596; 24-55 years), Poland (n = 810; 31-75 years), and the United States (n = 678; 55-78 years), we characterized tumor-associated stromal cellular density (SCD) as the percentage of tumor-stroma that is occupied by nucleated cells. Hazard ratios (HR) and 95% confidence intervals (CI) for associations between SCD and clinical outcomes [recurrence (China) and mortality (Poland and the United States)] were estimated using Cox proportional hazard regression, adjusted for clinical variables.

RESULTS

SCD was independently predictive of poor clinical outcomes in hormone receptor-positive (luminal) tumors from China [multivariable HR (95% CI)_{fourth(Q4) vs. first(Q1) quartile} = 1.86 (1.06-3.26); P _trend = 0.03], Poland [HR (95% CI)_{Q4 vs. Q1} = 1.80 (1.12-2.89); P _trend = 0.01], and the United States [HR (95% CI)_{Q4 vs. Q1} = 2.42 (1.33-4.42); P _trend = 0.002]. In general, SCD provided more prognostic information than most classic clinicopathologic factors, including grade, size, PR, HER2, IHC4, and TILs, predicting clinical outcomes irrespective of menopausal or lymph nodal status. SCD was not predictive of outcomes in hormone receptor-negative tumors.

CONCLUSIONS

Our findings support the independent prognostic value of tumor-associated SCD among ethnically diverse luminal breast cancer patients.

IMPACT

Assessment of tumor-associated SCD on standard H&E could help refine prognostic assessment and therapeutic decision making in luminal breast cancer.

A modified screening strategy for Lynch syndrome among MLH1-deficient CRCs: Analysis from consecutive Chinese patients in a single center

BACKGROUND

The low prevalence of the BRAF V600E mutation in colorectal cancers (CRCs) in Chinese populations has stimulated concern about the efficacy of BRAF mutation analysis for Lynch syndrome (LS) screening.

METHODS

In total, 169 of 4104 consecutive CRC patients with absent MLH1 staining were analyzed to compare the utility of the BRAF V600E mutation testing with MLH1 promoter methylation analysis in the Chinese population. Germline genetic testing was performed in patients with wild-type BRAF/methylated MLH1.

RESULTS

Compared with BRAF genotyping, the use of MLH1 methylation testing alone to evaluate patients with MLH1 deficiency reduced referral rates for germline testing by 1.8-fold (82.8% vs. 47.1%). However, 6 patients harboring MLH1 promoter methylation were verified to have LS through germline genetic testing. It is notable that all 6 patients had a family history of CRC in at least 1 first-degree relative (FDR) or second-degree relative (SDR). The combination of MLH1 promoter methylation analysis and a family history of CRC could preclude significantly more patients from germline genetic testing than from BRAF mutation testing alone (45.5% vs. 17.2%, p<0.001) and decrease the number of misdiagnosed LS patients with MLH1 promoter methylation.

CONCLUSION

The combination of a family history of CRC with MLH1 promoter methylation analysis showed better performance than BRAF mutation testing in the selection of patients in the Chinese population for germline genetic testing.

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

BACKGROUND

Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.

RESULTS

All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.

CONCLUSION

This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.

Heterogeneous Response to First-Generation Tyrosine Kinase Inhibitors in Non-Small-Cell Lung Cancers with Different EGFR Exon 19 Mutations

BACKGROUND

Epidermal growth factor receptor (EGFR) exon 19 deletions (19dels) appear in a large number of variants, which has not been distinguished in previously published trials despite differences in deletion and insertion locations.

OBJECTIVE

The aim of this study was to investigate the therapeutic response of patients with different EGFR exon 19dels to first-generation tyrosine kinase inhibitors (TKIs) and the mechanisms by which their tumors acquire resistance to these TKIs.

PATIENTS AND METHODS

The clinical outcomes of 195 patients harboring EGFR exon 19dels and receiving first-generation EGFR TKIs between July 2011 and June 2019 were retrospectively analyzed.

RESULTS

A total of twenty EGFR exon 19dels variants were identified. The patients were divided into three groups according to the first residue of the deletion, including E746, L747, and other residues (T751 or S752). The median progression-free survival (PFS) of patients treated with EGFR TKIs was significantly different between groups (p < 0.001). Patients harboring EGFR exon 19dels starting at T751 or S752 had the shortest median PFS (2.9 months), followed by those with E746 (11.4 months) and those with L747 (17.2 months). Analyzing 140 patients who had progressed on therapy, EGFR exon 19dels beginning at T751 or S752 were associated with a low incidence of the T790M mutation (16.7%).

CONCLUSIONS

Deletion location and type variants (with or without an insertion and/or a substitution) might affect first-generation TKI efficacy, and different EGFR exon 19dels should be considered when making decisions on which EGFR TKI should be used.

Whole exome sequencing (WES) analysis of transformed small cell lung cancer (SCLC) from lung adenocarcinoma (LUAD)

Background

Histologic transformation of non-small cell lung cancer (NSCLC) to small cell lung cancer (SCLC) is a rare mechanism of acquired resistance to epidermal growth factor receptor (EGFR)-targeted tyrosine kinase inhibitors. However, the SCLC transformation has also been observed in non-

EGFR

mutant NSCLC. In these cases, whether SCLC initially co-exists with NSCLC or originates from initial NSCLC remains to be determined.

Methods

Whole exome sequencing was performed on 10 samples from 5 patients with SCLC transformation from lung adenocarcinoma (LUAD), a main subtype of NSCLC. Somatic mutations and copy number variations (CNVs) were analyzed to explore the differences between initial LUAD and transformed SCLC, as well as the origin of transformed SCLC.

Results

After SCLC transformation, the mutation spectrum changed, with decreased C>T and increased C>A. Compared with initial LUAD, the CNV burden of transformed SCLC was greatly increased (39.0 vs. 61.1, Wilcoxon P=0.4). The higher the CNV burden of LUAD, the shorter the time to SCLC transformation was observed to be; and the higher the CNV burden of transformed SCLC, the shorter the overall survival (OS) after transformation. Clonal evolution analysis showed different clonal components between initial LUAD and transformed SCLC.

Conclusions

The transformation of LUAD into SCLC may be promoted by CNV events rather than mutational events. CNV burden was associated with the time to SCLC transformation and with the OS of patients following SCLC transformation. Transformed SCLC did not evolve directly from the initial LUAD but branched off from LUAD before the time of initial diagnosis.

Serum alpha-fetoprotein as a predictive biomarker for tissue alpha-fetoprotein status and prognosis in patients with hepatocellular carcinoma

Background

Alpha-fetoprotein (AFP) expression is closely related to hepatocarcinogenesis, and it is an important prognostic factor for hepatocellular carcinoma (HCC). We aimed to investigate the relationship between serum AFP concentration and tissue AFP status and identify the prognostic value of serum and tissue AFP for HCC.

Methods

This is a retrospective review of 248 patients with HCC from January 2012 to December 2018. Receiver operating characteristic (ROC) curves were plotted to investigate the predictive value of serum AFP for tissue AFP status. Overall survival (OS) was analyzed using the Kaplan-Meier method and log-rank tests were used for comparison between two groups. Multivariate Cox proportional hazards regression analysis was performed for various risk factors.

Results

The serum AFP level in patients with tissue AFP-positive HCC was higher than those with tissue AFP-negative HCC (506.7 vs. 7.7 ng/mL, P<0.0001). Youden’s index yielded an optimal cut-off value of serum AFP for tissue AFP status of 92.33 ng/mL with a sensitivity and specificity of 0.84 (95% CI: 0.74–0.90) and 0.88 (95% CI: 0.82–0.92), respectively. Moreover, high serum AFP concentrations (≥92.33 ng/mL) were significantly correlated with positive hepatitis B virus (HBV, P=0.012), tumor size (P=0.025) and histological grade (P=0.001); tissue AFP-positive status was associated with positive HBV (P=0.006), tumor number (P=0.033) and histological grade (P<0.001). Further, serum AFP level ≥92.33 ng/mL and tissue AFP-positive status were associated with poorer OS, and positive HBV (Positive: HR 3.496; 95% CI: 1.349–9.064; P=0.010) and larger tumor size (≥5; HR 2.617; 95% CI: 1.372–4.992; P=0.003) were independent factors of OS.

Conclusions

This study showed that serum AFP level could be a highly predictive biomarker for tissue AFP status in patients with HCC. Furthermore, serum AFP levels ≥92.33 ng/mL and tissue AFP-positive status were associated with poorer OS but were not independent factors of OS.

EGFR mutation is positively correlated with C-Met protein expression: a study of 446 resected lung adenocarcinoma

BACKGROUND

Epidermal growth factor receptor (EGFR) mutation and mesenchymal-epithelial transition factor (C-Met) amplification are known factors for primary resistance to EGFR tyrosine kinase inhibitors (EGFR-TKIs) in advanced primary lung adenocarcinoma. However, little is known about the relationship between high expression of C-Met protein and primary EGFR mutation. This research aims to investigate the correlation between EGFR mutation and C-Met protein expression in resected primary lung adenocarcinoma.

METHODS

Four hundred and forty-six surgically resected lung adenocarcinoma between 2013-2015 were collected for EGFR mutation analysis by real-time PCR (RT-PCR) and C-Met protein expression by immunohistochemistry (IHC). The relationship between the two biomarkers and clinicopathological features were analyzed.

RESULTS

The positive rate of EGFR mutation and C-Met protein expression were 66.4% (296/446) and 96.4% (430/446). EGFR mutation was significantly higher in female, mild to moderate differentiation, lepidic, acinar and papillary histological subtypes (P<0.05). C-Met expression was more prominent in female than male (201 vs. 123, 45.07% vs. 27.57%). EGFR mutation was found positively correlated with C-Met protein expression (P<0.05).

CONCLUSIONS

EGFR mutation and C-Met protein expression are prone to have a female predominance, and are positively correlated with each other in surgically resected lung adenocarcinoma specimens. This finding may be beneficial in explaining some of the resistance mechanisms of EGFR-mutated cases, which is worth further study.

Different pathologic responses to neoadjuvant anti-PD-1 in primary squamous lung cancer and regional lymph nodes

Neoadjuvant immunotherapy provides a unique opportunity for understanding therapeutic responses. We analyzed pathologic responses in surgical specimens obtained from 31 squamous non-small cell lung cancer (NSCLC) patients receiving neoadjuvant anti-PD-1 treatment. Fifteen (48.4%) patients achieved pathologic complete response (pCR) or major pathologic response (MPR). Among them, seven (46.7%) were assessed as radiological partial response and eight (53.3%) as stable disease. Among 20 patients with pathologically identified tumor beds in lymph nodes (LNs), 10 and six patients achieved pCR/MPR in primary tumors and paired LNs, respectively. pCR was achieved in 6/19 N1 nodes and 1/7 N2 nodes. Residual viable tumor (RVT) cells in 8/9 MPR specimens had 100% immune-activated phenotype, while a median of 80% of RVT cells in pathologic nonresponse specimens presented immune-excluded/desert phenotype. These findings demonstrated that assessment of pathologic responses in both primary tumor and LNs may be important as a surrogate for assessing neoadjuvant immunotherapeutic efficacy.

Potential Unreliability of Uncommon ALK, ROS1, and RET Genomic Breakpoints in Predicting the Efficacy of Targeted Therapy in NSCLC

INTRODUCTION

Variable genomic breakpoints have been identified through the application of target-capture DNA next-generation sequencing (NGS) for ALK, ROS1, and RET fusion detection in NSCLC. We investigated whether ALK, ROS1, and RET genomic breakpoint location can predict matched targeted therapy efficacy.

METHODS

NSCLCs were analyzed by DNA NGS, target-specific RNA NGS, whole-transcriptome sequencing, and immunohistochemistry.

RESULTS

In total, 3787 NSCLC samples were analyzed. DNA NGS detected ALK, ROS1, and RET fusions in 241, 59, and 76 cases, respectively. These fusions were divided into canonical (single EML4-ALK, CD74/EZR/TPM3/SDC4-ROS1, and KIF5B/CCDC6-RET fusions), noncanonical (single non-EML4-ALK, non-CD74/EZR/TPM3/SDC4-ROS1, and non-KIF5B/CCDC6-RET fusions), and primary/reciprocal (both primary and reciprocal rearrangements were detected) subtypes on the basis of genomic breakpoint position, and noncanonical and primary/reciprocal subtypes were defined as uncommon fusions. Further RNA sequencing and immunohistochemistry revealed that six of 47 (12.8%) uncommon fusions were actually nonproductive rearrangements that generated no aberrant transcripts or proteins. Moreover, genomic breakpoints of canonical ALK and RET, but not ROS1, fusions always predicted breakpoints at the transcript level, whereas 85.4% (35 of 41) of uncommon fusions actually produced canonical fusion transcripts. Patients with uncommon ALK fusion (n = 31) who received first-line crizotinib exhibited shorter median progression-free survival than those with canonical ALK fusion (n = 53, 8.4 mo versus 12.0 mo, p = 0.004). However, no difference in progression-free survival was observed when only ALK RNA or protein-positive cases were analyzed (p = 0.185).

CONCLUSIONS

Uncommon ALK, ROS1, and RET genomic breakpoint is an unreliable predictor of matched targeted therapy efficacy. Functional validation by RNA or protein assay may add value for the accurate detection and interpretation of rare fusions.

Clinicopathological features and prognostic analysis of 247 small cell lung cancer with limited-stage after surgery

The objective of this study was to analyze the clinical and pathological characteristics of patients with small cell lung cancer (SCLC) after curative surgery and to explore prognostic factors for disease-free survival (DFS) and overall survival (OS). Clinical data of 247 patients were collected, and clinicopathological features were retrieved, including gender, age, smoking history, tumor location, and distant metastasis. Histopathological features were also reviewed by three pathologists, including primary tumor (T), lymph node metastasis (N), pleural invasion, bronchial invasion, nerve invasion, spread through air spaces (STAS), tumor thrombosis, major cell shape (round Vs. spindle), tumor necrosis, stromal fibrosis, and tumor-infiltrating lymphocytes (TILs). Immunohistochemical staining of neuroendocrine markers (CD56, synapsin, chromogranin A) was also reviewed. All patients were followed up for recurrence, distant metastasis, and survival. Kaplan-Meier curves and log-rank tests were applied for survival analysis. The median DFS was 98 months, and the 1-year, 3-year, and 5-year DFS rates were 70.9%, 54.4%, and 52.2%, respectively. The median OS was not reached, and the 1-year, 3-year, and 5-year survival rates were 94.2%, 72.3%, and 65.4%, respectively. Univariate analysis revealed clinicopathological features with DFS (gender, smoking history, primary tumor, regional lymph node metastasis, major cell shape, and TILs) and OS (age, primary tumor, regional lymph node metastasis, distant metastasis, nerve invasion, major cell shape, and TILs). Multivariate analysis revealed DFS-related factors (smoking history, regional lymph node metastasis and major cell shape) and OS-related factors (age, primary tumor, distant metastasis in the brain, liver, bone, nerve invasion, and TILs). Age more than 65 years, smoking, advanced stage (T and N), distant metastasis, nerve invasion, major cell shape as spindle and TILs >30% were negatively correlated with survival. Neuroendocrine immunostaining markers showed no correlation with survival. Of interest, spindle cell type and TILs >30% are revealed as independent negative prognostic factors, and further molecular mechanisms need to be explored.

Genomic profile and immune microenvironment in patients with relapsed stage IA lung adenocarcinoma

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This finding may provide a novelty insight to help elucidate the mechanisms of the relapses.

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Relapsed tumours from stage IA LUAD patients exhibited a weakened immune phenotype.

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A targeted 395-gene expression NGS assay helps assess tumour immunity.

Patients with early-stage non-small cell lung cancer (NSCLC), even stage IA, are at substantial risk of relapse and death. We explored the distinct features of molecular alterations and immune-related gene expression in Formalin-fixed paraffin-embedded (FFPE) samples from 25 relapsed patients compared with 25 non-relapsed patients through using whole-exome sequencing and an immune oncology panel RNA sequencing platform. Results showed that the chemokine, cytolytic activity and tumour-associated antigen gene signatures exhibited significantly higher expression in non-relapsed tumours from stage IA lung adenocarcinoma (LUAD) than that in relapsed tumours. Besides, Kaplan–Meier survival analysis revealed that the gene signatures of chemokines and tumour-associated antigens were significantly associated with the patients’ disease-free survival (DFS), indicating their prognostic value in early-stage LUAD. Cytolytic activity displayed a similar trend but failed to reach statistical significance. These findings revealed a weakened immune phenotype in relapsed tumours and provide valuable information for improving the treatment management of these high-risk patients. Due to the overall small patient number in this study, these differences should be further validated in a larger cohort.

Clinicopathological features and prognostic implications of ASCL1 expression in surgically resected small cell lung cancer

Background

Small cell lung cancer (SCLC) is one of the most aggressive lung cancers. Treatment of SCLC has remained unchanged during the past decades. Preclinical studies have revealed ASCL1 as a transcription regulator in the neuroendocrine (NE) differentiation and carcinogenesis of SCLC. However, there are few studies on correlation of ASCL1 expression and clinicopathological factors in resected SCLCs. Here, we aimed to analyze the ASCL1 expression of SCLC and investigate its associations with clinicopathological factors and survival.

Methods

A total of 247 surgically resected pure SCLC specimens were included in this retrospective study, all of which were processed using tissue microarrays for immunohistochemistry analysis of ASCL1. A total of 48 of 247 cases were tested by NanoString for mRNA expression analysis on 50 SCLC related genes. Statistical analysis was performed using R studio and SPSS software.

Results

NE scores of 48 pure SCLC specimens were calculated by analyzing 50 preselected genes. A significant correlation between NE score with both ASCL1 mRNA expression and ASCL1 protein expression were observed. For the entire cohort of 247 patients, ASCL1 was highly expressed in 42.5% of pure SCLC patients according to IHC results. Significant differences were observed between ASCL1 high and low expression groups in variables including staging, lymph node metastasis, nerve invasion and overall survival.

Conclusions

In limited staged pure SCLC, ASCL1 expression was positively correlated with NE signature, pTNM stage, nerve invasion and OS. ASCL1 may therefore serve as a potential biomarker to predict prognosis as well as in the selection of patients for therapies targeting ASCL1‐regulated downstream molecules.