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

•

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.

•

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.

Open-label, Multicenter, Phase II Study of RC48-ADC, a HER2-Targeting Antibody-Drug Conjugate, in Patients with Locally Advanced or Metastatic Urothelial Carcinoma

PURPOSE

To evaluate the efficacy and safety of RC48-ADC, a novel humanized anti-HER2 antibody conjugated with monomethyl auristatin E, in patients with HER2⁺ locally advanced or metastatic urothelial carcinoma (mUC) refractory to standard therapies.

PATIENTS AND METHODS

This was a phase II, open-label, multicenter, single-arm study of patients with HER2⁺ (IHC status 3+ or 2+) locally advanced or mUC who previously failed at least one line of systemic chemotherapy. The primary endpoint was the objective response rate (ORR) assessed by a blinded independent review committee (BIRC). The secondary endpoint included progression-free survival (PFS), disease control rate, duration of response, overall survival (OS), and safety.

RESULTS

Forty-three patients were enrolled. The median follow-up was 20.3 months. The overall confirmed ORR as assessed by the BIRC was 51.2% [95% confidence interval (CI), 35.5%-66.7%]. Similar responses were observed in prespecified subgroups, such as those with liver metastasis and those previously treated with anti-programmed cell death 1 (PD-1)/programmed death ligand 1 (PD-L1) therapies. The median PFS and OS were 6.9 months (95% CI, 5.6-8.9) and 13.9 months (95% CI, 9.1-NE), respectively. The most common treatment-related adverse events (TRAE) were hypoesthesia (60.5%), alopecia (55.8%), and leukopenia (55.8%). Twenty-five (58%) patients experienced grade 3 TRAEs, including hypoesthesia (23.3%) and neutropenia (14.0%). No grade 4 or grade 5 TRAEs occurred.

CONCLUSIONS

RC48-ADC demonstrated a promising efficacy with a manageable safety profile in patients with HER2⁺ locally advanced or mUC who had failed at least one line of systemic chemotherapy.

Safety, Antitumor Activity, and Pharmacokinetics of Toripalimab, a Programmed Cell Death 1 Inhibitor, in Patients With Advanced Non-Small Cell Lung Cancer: A Phase 1 Trial

IMPORTANCE

Programmed cell death 1 (PD-1) antibodies have shown substantial survival benefit in patients with advanced non-small cell lung cancer (NSCLC). Toripalimab is a promising and practicable PD-1 antibody; however, its performance in NSCLC has not been established.

OBJECTIVES

To assess the safety, antitumor activity, and pharmacokinetics of toripalimab in patients with advanced NSCLC and to evaluate the utility of JS311, a novel PD ligand 1 (PD-L1) immunohistochemistry (IHC) assay.

DESIGN, SETTING, AND PARTICIPANTS

This single-arm open-label phase 1 trial enrolled 41 patients with advanced NSCLC that had progressed after at least 3 lines of therapy between September 21, 2017, and June 5, 2018, with a median (interquartile range) follow-up of 14.9 (3.2-22.5) months and included a cohort study comparing JS311 with other PD-L1 IHC assays that included 280 NSCLC specimens collected from January 1, 2016, to May 21, 2018. Data collection was conducted from September 21, 2017, to September 27, 2019, and analysis was conducted from September 27, 2019, to December 30, 2019.

EXPOSURE

Enrolled patients were administered a single dose of toripalimab, under 2 manufacturing processes and scales (200 L and 500 L), for safety and pharmacokinetic analysis within 28 days, followed by subsequent multidose infusions every 2 weeks. PD-L1 expression was determined by IHC with JS311, comparing its results with results from 22C3, 28-8, and SP263 simultaneously.

MAIN OUTCOMES AND MEASURES

Progression-free survival (PFS) and overall survival (OS), estimated by Kaplan-Meier curves, and continuous variables compared by t test or Mann-Whitney test. Correlations between PD-L1 IHC antibodies were evaluated by Spearman correlation test.

RESULTS

A total of 41 patients (29 [70.7%] men) with a median (interquartile range) age of 59 (53 to 63) years who experienced disease progression following chemotherapy were included. The most common treatment-related adverse events were rash (6 [14.6%]), increased amylase level (5 [12.2%]), and increased aspartate aminotransferase level (5 [12.2%]). In 35 patients included in the pharmacokinetic analysis, drug exposure and area under curve after 1 dose was similar under both manufacturing processes and scales (mean [SD] for 200-L group: 12 465.28 [4128.17] hour × μg/mL; for 500-L group: 12 331.42 [2472.58] hour × μg/ml). In 28 patients included in the response and survival analysis, the median PFS and OS were 2.8 (95% CI, 2.7 to 4.6) months and 13.8 months (95% CI, 10.0 months to not reached), respectively. Stratified by PD-L1 tumor proportion score of at least 50%, 1% to 49%, and less 1%, median PFS rates were 11.2 months (95% CI, 2.3 months to not evaluable), 2.3 (95% CI, 1.7 to 2.7) months, and 2.8 (95% CI, 2.7 to 4.6) months, respectively. A total of 4 anti-PD-L1 IHC antibodies were compared during PD-L1 staining, using 280 NSCLC specimens. The consistency rates between the 4 antibodies were 80.8% to 89.5% (ρ, 0.619 to 0.790) and 93.3% to 95.5% (ρ, 0.691 to 0.773), with PD-L1 tumor proportion scores of 1% and 50% as cut points, respectively.

CONCLUSIONS AND RELEVANCE

In this study, toripalimab exhibited encouraging antitumor activity and manageable safety profiles among patients with heavily treated NSCLC. The novel PD-L1 IHC antibody JS311 was highly consistent with previously verified PD-L1 IHC assays.

Integrated molecular characterization reveals potential therapeutic strategies for pulmonary sarcomatoid carcinoma

Pulmonary sarcomatoid carcinoma (PSC) is a rare subtype of lung cancer with poor prognosis. Here, we perform multi-omics analysis of 56 PSC samples, 14 of which are microdissected to analyze intratumoral heterogeneity. We report the mutational landscape of PSC. The epithelial and sarcomatoid components share numerous genomic alterations, indicating a common progenitor. We find that epithelial-mesenchymal transition (EMT) plays important roles in the carcinogenesis of PSC. The pan-cancer analysis reveals high tumor mutation burden and leukocyte fraction of PSC. Integrated molecular classification shows three subgroups with distinct biology, prognosis and potential therapeutic strategies. Actionable mutations are enriched in C1 and C2, patients in C3 have a significantly longer overall survival, and C1 and C2 exhibit T-cell inflamed microenvironments. The three subgroups show molecular similarities to specific subtypes of conventional lung cancer. In conclusion, our study reveals the molecular characteristics and provides entry points for the treatment of PSC.

Pulmonary sarcomatoid carcinoma (PSC) is a rare subtype of lung cancer with poor prognosis. Here the authors performed multi-omics analysis of human samples to investigate the mutational landscape of PSC and show three subgroups of PSC with distinct biology, prognosis and potential therapeutic strategies.

DLBCL with amplification of JAK2/PD-L2 exhibits PMBCL-like CNA pattern and worse clinical outcome resembling those with MYD88 L265P mutation

Background

Recently, copy number alteration (CNA) of 9p24.1 were demonstrated in 10% of diffuse large b-cell lymphoma (DLBCL), with gene expression and mutation profiles that were similar to those of primary mediastinal large B-cell lymphoma (PMBCL). However, their CNA-based profile and clinical impact still remain unclear.

Methods

Multiplex ligation-dependent probe amplification were employed to investigate the prevalence of JAK2/PD-L2 amplification in DLBCL and their CNA-based pattern of driver genes. The clinical outcome and characteristics were also analyzed.

Results

Using unsupervised hierarchical clustering, a small group of DLBCL (10.5%, 8/76) was clustered together with PMBCL as Cluster_2, demonstrating amplification of JAK2 (100%,8/8) and PD-L2 (75.0%,6/8). This subgroups of DLBCL demonstrated significant higher expression of PD-L1 than those with MYD88 L265P mutation(p = 0.024). And they exhibited dismal OS and PFS as compared with DLBCL_others(p = 0.003 and 0.001, respectively), which is similar to DLBCL with MYD88 L265P mutation.

Conclusions

DLBCL with amplification of JAK2/PD-L2 exhibits CNA pattern that is similar to PMBCL, and demonstrates unfavorable clinical outcome that resembles those with MYD88 L265P mutation. It is essential to identify this subgroup of DLBCL who may acquire more benefits from the JAK2 and PD-L1 signaling inhibition.

Development and external validation of a nomogram to predict four or more positive nodes in breast cancer patients with one to three positive sentinel lymph nodes

Objective

To develop a nomogram for predicting the possibility of four or more positive nodes in breast cancer patients with 1–3 positive sentinel lymph nodes (SLN).

Materials and methods

Retrospective analysis of data of patients from two institutions was conducted. The inclusion criteria were: invasive breast cancer; clinically node negative; received lumpectomy or mastectomy plus SLN biopsy followed by axillary lymph node dissection (ALND); and pathologically confirmed T1-2 tumor, with 1–3 positive SLNs. Patients from one institution formed the training group and patients from the other the validation group. Univariate and multivariate analyses were performed to identify the predictors of four or more positive nodes. These predictors were used to build the nomogram. The area under the receiver operating characteristic curve (AUC) was calculated to assess the accuracy of the model.

Results

Of the 1480 patients (966 patients in the training group, 514 in the validation group), 306 (20.7%) had four or more positive nodes. Multivariate stepwise logistic regression showed number of positive (p < .001) and negative SLN (p < .001), extracapsular extension (p < .001), pT stage (p = .016), and tumor location in outer upper quadrant (p = .031) to be independent predictors of four or more positive nodes. The nomogram was built using these five factors. The AUC was 0.845 in the training group and 0.804 in the validation group.

Conclusion

The proposed nomogram appears to accurately estimate the likelihood of four or more positive nodes and could help radiation oncologists to decide on use of regional nodal irradiation (RNI) for breast cancer patients with 1–3 positive nodes but no ALND.

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Five predictors of four or more positive nodes in breast cancer patients were identified.

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A nomogram was built using these five factors.

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The nomogram was validated on an external cohort.

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The proposed nomogram predicts four or more positive nodes with high accuracy.

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The nomogram can help in decision making on use of regional nodal irradiation.

PDCD6 cooperates with C-Raf to facilitate colorectal cancer progression via Raf/MEK/ERK activation

Background

Colorectal cancer (CRC) is one of the most common malignancies, and it’s expected that the CRC burden will substantially increase in the next two decades. New biomarkers for targeted treatment and associated molecular mechanism of tumorigenesis remain to be explored. In this study, we investigated whether PDCD6 plays an oncogenic role in colorectal cancer and its underlying mechanism.

Methods

Programmed cell death protein 6 (PDCD6) expression in CRC samples were analyzed by immunohistochemistry and immunofluorescence. The prognosis between PDCD6 and clinical features were analyzed. The roles of PDCD6 in cellular proliferation and tumor growth were measured by using CCK8, colony formation, and tumor xenograft in nude mice. RNA-sequence (RNA-seq), Mass Spectrum (MS), Co-Immunoprecipitation (Co-IP) and Western blot were utilized to investigate the mechanism of tumor progression. Immunohistochemistry (IHC) and quantitative real-time PCR (qRT-PCR) were performed to determine the correlation of PDCD6 and MAPK pathway.

Results

Higher expression levels of PDCD6 in tumor tissues were associated with a poorer prognosis in patients with CRC. Furthermore, PDCD6 increased cell proliferation in vitro and tumor growth in vivo. Mechanistically, RNA-seq showed that PDCD6 could affect the activation of the MAPK signaling pathway. PDCD6 interacted with c-Raf, resulting in the activation of downstream c-Raf/MEK/ERK pathway and the upregulation of core cell proliferation genes such as MYC and JUN.

Conclusions

These findings reveal the oncogenic effect of PDCD6 in CRC by activating c-Raf/MEK/ERK pathway and indicate that PDCD6 might be a potential prognostic indicator and therapeutic target for patients with colorectal cancer.

Erratum: Evolution of π^{0} Suppression in Au+Au Collisions from sqrt[s_{NN}]=39 to 200 GeV [Phys. Rev. Lett. 109, 152301 (2012)]

This corrects the article DOI: 10.1103/PhysRevLett.109.152301.

Transdifferentiation of tumor infiltrating innate lymphoid cells during progression of colorectal cancer

Innate lymphoid cells (ILCs) reside in mucosal surfaces to potentiate immune responses, sustain mucosal integrity and maintain tissue homeostasis. However, how tumor infiltrating ILCs modulate tumor development and progression is unclear. Here we profiled tumor infiltrating ILCs during colorectal cancer (CRC) progression by single-cell RNA sequencing. We identified six clusters of tumor infiltrating ILCs with unique features. ILC1s expressed inhibitory receptors and underwent inhibitory functional conversion at the late stage of CRC. ILC2s were classified into three subsets (called ILC2-A, -B, -C), of which ILC2-C subset could facilitate tumor progression. HS3ST1 and PD1 were highly expressed in ILC2s of late stage CRC tumors and deficiency of HS3ST1 or PD1 in ILC2s suppressed tumor growth. Moreover, ILC3s transdifferentiated into ILCregs during CRC progression and ILCregs promoted tumor growth. Of note, TGF-β signaling initiated the conversion of ILC3s to ILCregs and blockade of TGF-β signaling could disrupt the ILCreg transdifferentiation and inhibited tumor growth. Thus, intervention of ILC conversions might be a potential strategy for CRC immunotherapy.

The prognostic value of a Methylome-based Malignancy Density Scoring System to predict recurrence risk in early-stage Lung Adenocarcinoma

Current NCCN guidelines do not recommend the use of adjuvant chemotherapy for stage IA lung adenocarcinoma patients with R0 surgery. However, 25% to 40% of patients with stage IA disease experience recurrence. Stratifying patients according to the recurrence risk may tailor adjuvant therapy and surveillance imaging for those with a higher risk. However, prognostic markers are often identified by comparing high-risk and low-risk cases which might introduce bias due to the widespread interpatient heterogeneity. Here, we developed a scoring system quantifying the degree of field cancerization in adjacent normal tissues and revealed its association with disease-free survival (DFS).

Methods: We recruited a cohort of 44 patients with resected stage IA lung adenocarcinoma who did not receive adjuvant therapy. Both tumor and adjacent normal tissues were obtained from each patient and subjected to capture-based targeted genomic and epigenomic profiling. A novel methylome-based scoring system namely malignancy density ratio (MD ratio) was developed based on 39 patients by comparing tumor and corresponding adjacent normal tissues of each patient. A MD score was then obtained by Wald statistics. The correlations of MD ratio, MD score, and genomic features with clinical outcome were investigated.

Results: Patients with a high-risk MD ratio showed a significantly shorter postsurgical DFS compared with those with a low-risk MD ratio (HR=4.47, P=0.01). The MD ratio was not associated with T stage (P=1), tumor cell fraction (P=0.748) nor inflammatory status (p=0.548). Patients with a high-risk MD score also demonstrated an inferior DFS (HR=4.69, P=0.039). In addition, multivariate analysis revealed EGFR 19 del (HR=5.39, P=0.012) and MD score (HR= 7.90, P=0.01) were independent prognostic markers.

Conclusion: The novel methylome-based scoring system, developed by comparing the signatures between tumor and corresponding adjacent normal tissues of individual patients, largely minimizes the bias of interpatient heterogeneity and reveals a robust prognostic value in patients with resected lung adenocarcinoma.

Evaluation of the fully automated Idylla EGFR Mutation Assay in Chinese patients with lung adenocarcinoma

e21716

Background: Epidermal growth factor receptor ( EGFR) mutation testing is nowadays an essential part of lung adenocarcinoma diagnosis. Its rapid detection is of utmost significance in order to ensure that patients receive timely and appropriate treatment. However, the current techniques for EGFR examination in China, ARMS-PCR and NGS, often take 3~7 days to deliver the final results. In contrast, the fully automated Idylla EGFR assay could detect 51 EGFR mutations directly from formalin-fixed, paraffin-embedded (FFPE) samples within 2.5 hours with < 2 minutes of hands-on time. The test has proven both accurate and robust among Caucasian lung adenocarcinoma patients but has never been clinically validated in Chinese patients. Methods: FFPE samples were retrospectively collected from 94 lung adenocarcinoma patients followed by EGFR testing using the Idylla system. Seventy-eight samples were also previously assessed with ARMS-PCR, 9 with NGS and 7 with both. In case of discordance, repeat testing was performed on the same tissue block with a third method. The sensitivity and specificity of the Idylla EGFR assay were evaluated against ARMS-PCR or NGS. Mutations beyond the scope of detection by the Idylla EGFR assay were not included in the analyses. Results: Of the 94 tumors enrolled, 77 were stage I-II. The Idylla system was consistent with ARMS-PCR or NGS for the EGFR mutational profiles of 92 tumors: 80 positive and 12 negative. Among the 2 cases of discrepancy, one was wild-type using Idylla but were found to harbor G719X/S768I using ARMS-PCR (and confirmed by NGS), while the other one carried L858R according to Idylla, as confirmed by ARMS-PCR, but was discovered to have an additional mutation L861Q using NGS. The Idylla EGFR test had a sensitivity of 97.6%, a specificity of 100% and an overall concordance of 97.9%. Conclusions: The Idylla system provides a rapid, accurate and user-friendly solution to EGFR characterization, especially in time-sensitive scenarios where special expertise and staff training could be a challenge.

DNA methylation signatures predicting liver metastasis of colorectal cancer: A proof-of-concept pilot study

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Background: Liver metastasis (LIM) is the leading cause of death in colorectal cancer (CRC) patients. Early detection of LIM may improve outcome in CRC patients. The aim of this study was to evaluate the feasibility of predicting LIM of CRC using methylation profiles. Methods: We performed Roche targeted (~5.5 million methylation sites) bisulfite sequencing of matched primary, metastatic and their adjacent normal tissue samples from 5 CRC patients with LIM, 5 patients with lung metastasis (LUM) and 8 patients without metastasis in the training cohort (n = 48 samples). Differential methylation regions (DMR) of LUM were identified and a predictive model was developed. The model was further validated in primary tumor sample from nine patients (6 with LIM). Results: By comparing primary tumor vs adjacent normal tissues and metastatic tumor vs adjacent normal tissues in CRC patients with LIM, we identified 28954 common DMRs which indicating the methylation characteristic of CRC with LIM. Similarly, 16187 DMRs were identified in patients with LUM. 9179 DMRs are shared in both LIM and LUM comparisons which should be the common characteristic of CRC tumor tissue regardless of the location of metastasis. 7008 DMRs are LUM specific and 19775 DMRs are LIM specific. In order to predict LIM in primary, early changes in LIM specific DMRs should be identified. Hence, we further selected 4134 DMRs by chossing significantly differentically methylated regions between LIM primary tissues and LUM primary tissues. To increase the ability of distinguishing LIM from other normal tissues and non-matastasis CRC tumors, 1215 DMRs were finally selected which also showed increasing or decreasing trend of methylation level through the progression of CRC. The final 1215 biomarkers were used to construct a random forest model using methlylation profile of 5 CRC patients with LIM as positive training data and 5 CRC patients with LUM as well as 8 patients without metastasis as negative training data. Through the feature recursive elimination method, one methylation site (chr8.72468901-72469000) was identified with ROC of 0.9 in the training dataset. The predictive model was validated in an independent dataset which is composed of 6 patients with LIM and 3 patients without metastasis, and achieved an AUC of 0.87. Conclusions: Our findings demonstrate the utility of methylation biomarkers for the molecular characterization of metastatic precursors, with implications for prediction and early detection of liver metastasis in CRC.

Genomic and epigenomic profiles to distinguish pulmonary enteric adenocarcinoma from lung metastatic colorectal cancer

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Background: As an extremely rare variant of lung adenocarcinoma, the diagnosis of pulmonary enteric adenocarcinoma (PEAC) remains challenging in the clinic due to shared morphological and immunohistochemical features with lung metastatic colorectal cancer (mCRC). Current differentiation of PEAC and mCRC mainly relies on clinical history and pathological examination while which still remain risks of misdiagnosis. Due to their distinct treatment regimens, effective molecular markers are essential for accurate diagnosis. However, comprehensive molecular features of PEAC is still poorly understood. Methods: We performed whole-exome sequencing and targeted bisulfite sequencing of 23 PEAC and 20 mCRC and matched normal tissue to improve molecular characterization. For DNA methylation profiling, differentially methylated regions (DMR) were analyzed by comparing PEAC with normal lung tissue and with mCRC. We also trained machine learning methods to distinguish PEAC from mCRC and validated the classifier in an independent cohort with 10 PEAC and 10 mCRC. Results: Mutations of KRAS, APC, and EGFR, alterations of chromosome arms 13q, 14q and 18p were found to be the major differential genetic alterations between PEAC and mCRC (P < 0.05), yet not enough to aid clinical diagnosis. For epigenomic profile, we identified 524 DMRs (false discovery rate ≤0.05) which were further reduced to 30 DMRs according to importance rank by the random forest algorithm. Based on these DMR features, we developed a diagnostic classifier that correctly classified 95.1% of patients in this discovery cohort. We further validated this predictive model in the validation cohort, with a prediction accuracy of 90.0%. We demonstrated its clinical application in two cases with difficulties to diagnosis by traditional methods. Conclusions: We have illustrated the unique genetic and methylation profiles of PEAC and mCRC. Our approach for disease classification may have a substantial impact on diagnostic precision and therapeutic decision for PEAC.

Conjoint Analysis of DNA Methylation for Tumor Differentiation Using Cationic Conjugated Polymers

Molecular biomarkers, especially DNA methylation, are crucial discoveries for early detection of cancer. Compared with a single biomarker detection mode, using the conjoint detection mode can allow researchers to easily assess the association of the biomarkers with specific cancer. In this paper, we calculated the methylation status of RASSF1A, APC, CDKN2A/p16, and TMEFF2 genes using cationic conjugated polymers (CCPs)-based fluorescence resonance energy transfer (FRET) technique and then explored the connection between the overall DNA methylation status of the four genes and the clinical parameters of lung cancer patients. After analysis, no association was found between the methylation status of any single gene and the grade of tumor differentiation among 159 lung cancer samples analyzed. However, for conjoint analysis using the four genes, a statistically significant difference was reached between methylation status and the grade of tumor differentiation. The methylation levels in a panel of the four genes were correlated with sex, age, smoking pack-years, and lymphatic metastasis. Therefore, the conjoint analysis of DNA methylation in specific cancer-related genes could be a useful diagnostic tool for clinical implementation.