Circulating tumor DNA analysis to reveal genomic profiles for epithelial ovarian cancer

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Background: Circulating tumor DNA (ctDNA) analysis in epithelial ovarian cancer (EOC) was previously reported, however with limited samples or limited genes. Here, we reported an analysis of ctDNA in EOC cohort using targeted sequencing with a 1021-gene panel. Methods: Patients with EOC were enrolled, and treatment-naïve tumor tissues and blood samples were collected. We utilized a 1021-gene NGS panel in matched tissue DNA and ctDNA to identify somatic mutations with white blood cell DNA as a germline control. Results: Mutations were identified in all of the 65 tissues and in 53 (81.5%) ctDNA. The median ctDNA mutation allelic frequency was 2.5%, ranging from 0.1% to 36.2%. A median of 66.7% (12.5%-100.0%) of tissue derived mutations were observed in ctDNA. Besides, there were 91 ctDNA private mutations, including TP53 gene mutations. The most frequently mutated genes were TP53 (55.4%), PIK3CA (13.8%) and ARID1A (12.3%) in ctDNA analysis, which were consistent with tissue analysis (60.0%, 26.2% and 20.0% of tissues with TP53, PIK3CA and ARID1A mutations, respectively). Mutations of TP53 (37/42) in high-grade serous ovarian carcinoma (HGSOC), PIK3CA (10/11) and ARID1A (8/11) in ovarian clear cell carcinoma, BRAF (4/5) in low-grade serous ovarian carcinoma and PIK3CA (3/5), ARID1A (2/5) and PTEN (2/5) in endometrioid carcinoma were observed as the most commonly genetic aberrations in ctDNA in different sub-types of EOC, which located in different signal pathways and suggested different pathogenesis. In total, 90.5% (38/42) of HGSOC were ctDNA positive, comparing with 65.2% (15/23) of other EOC subtypes (p = 0.012). In addition, 56.5% (13/23) of stage I~II EOC were ctDNA positive, comparing with 94.7% (36/38) of stage III (p = 0.002). No association between ctDNA positivity and other clinic characteristics was observed, including pathological differentiation, CA125, lesion density (solid vs. cystic-solid and cystic). Multivariable analysis suggested FIGO stage III (p = 0.008) as an independent predictor of ctDNA detection. Conclusions: In summary, genomic characterization of EOC may offer insights into tumorigenesis and identify potential therapeutic targets in this disease.

Serial ctDNA analysis as a real-time indicator of neoadjuvant chemoradiotherapy in rectal cancer

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Background: Neoadjuvant chemoradiotherapy (nCRT) is nowadays the standard of care for the locally advanced rectal cancer (LARC). However, there is no effective method to predict patients’ possible benefits from nCRT and monitor the response to it. Methods: Patients with locally advanced middle and low rectal cancer of stage cT3-4N0M0 or cTanyN+M0 were enrolled from August 2017 to July 2018. All patients received nCRT with long-term radiation plus fluorouracil based chemotherapy, followed by the radical surgery. Serial plasma samples were collected pre-nCRT, during nCRT, and preoperatively (8 weeks after the completion of nCRT). Somatic mutations were detected with next-generation sequencing using a 1021-gene panel with peripheral blood lymphocyte DNA as a germline control. Results: This prospective cohort study enrolled 61 patients with rectal cancer. The pathological complete response (pCR) rate and the downstage rate was 31% (19/61) and 80% (49/61), respectively. ctDNA was detectable in 77% (47/61), 18% (11/61) and 13% (8/61) of blood samples obtained pre-nCRT, during nCRT and preoperatively, respectively. No significant association was observed between pre-nCRT ctDNA status with any clinicopathological factors, including age, gender, differentiation or tumor circumferential extent. Among the 8 patients with detectable ctDNA preoperatively, pathological tumor regression grade (TRG) of CAP 2-3 were observed and hepatic metastasis was found in 4 patients within 2 months. For patients with undetectable pre-operative ctDNA, a higher proportion archived pathological downstaging (85% vs 50%). The correlation between preoperative ctDNA status and achievement of pathological downstage was independent of age, gender or differentiation (p = 0.02). In addition, preoperative ctDNA positivity was associated with the persistently involved lymph node (p = 0.02). However, neither pre-nCRT nor during-nCRT ctDNA status was associated with pathological downstaging or persistently lymph node involvement. Conclusions: Detectable ctDNA after the completion of nCRT is a predicator of unsatisfactory curative effect of patients with LARC, which might indicate novel treatment intensification studies. Clinical trial information: NCT03042000.

Tracking circulating cell-free tumor DNA in gastric cancer to detect early disease recurrence

e14571

Background: Identifying locoregional gastric cancer patients who are at high risk for relapse after resection could facilitate early intervention. By detecting molecular residual disease (MRD), circulating tumor DNA (ctDNA) has been shown to predict post-operative relapse in several cancers. Here, we aim to evaluate MRD detection by ctDNA and its association with clinical outcome in resected gastric cancer. Methods: This prospective cohort study enrolled 46 patients with stage I-III gastric cancer that underwent resection with curative intent. Resected tumor samples and plasma samples were obtained for targeted deep sequencing and longitudinal ctDNA profiling. Results: ctDNA was detected in 45% of treatment-naïve plasma samples. T stage was independently associated with pre-operative ctDNA positivity (p = 0.006). All patients with detectable ctDNA in the immediate post-operative period eventually experienced recurrence. ctDNA positivity at any time during longitudinal post-operative follow-up was associated with worse DFS and OS (HR = 14.78, 955 CI, 7.991-61.29, p < 0.0001 and HR = 7.664, 95% CI, 2.916-21.06, p = 0.002, respectively), and preceded radiographic recurrence by a median of 6 months. Conclusions: In locoregional gastric cancer patients treated with curative intent, these results indicate that ctDNA-detected MRD identifies patients at high risk for recurrence and can facilitate novel treatment intensification studies in the adjuvant setting to improve survival.

Identifying actionable somatic mutations in lung cancer using cell-free DNA from bronchial washing fluid

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Background: Bronchial washing is the most common technique for sampling the components of the alveolar space. Here, we evaluated the potential use of bronchial washing fluid (BWF) in liquid biopsy in lung cancer. Methods: This study enrolled 65 lung cancer patients. BWF (separated supernatant and precipitate) samples, peripheral blood lymphocytes (PBL) and formalin-fixed paraffin-embedded tissues were obtained and subjected to next-generation sequencing using a 1021-gene panel. Results: Mutations were identified in 58 (89.2%) of BWF precipitate (BWFp) samples and 64 (98.5%) of BWF supernatant (BWFs) samples, comparing with 61 (93.8%) of tumor tissues. In total, 461 somatic mutations were identified in tissues, of which 331 (71.8%) and 381 (82.6%) were detected in the matched BWFp and BWFs samples. In addition, there were 44.6% of patients carrying actionable variants identified in tissue DNA, including EGFR, ALK, ROS1, RET, etc. (Table). Similarly, there were 40.0% of BWFp samples and 44.6% of BWFs samples identified actionable variants. Moreover, tumor mutation burden (TMB) was also calculated. Nearly 9% of BWFp samples and 23% of BWFs samples were TMB-H (more than 9 mutations per megabase), comparing with 20% of tissues. Significantly, the combined results of three types of samples showed that, 49.2% of patients carrying actionable variants and 24.6% of patients with TMB-H, which suggested more patients benefit from targeted therapy or immunotherapy. Conclusions: In summary, liquid biopsy using BWF showed high potential to identify actionable mutations and to calculate TMB grade of patients with lung cancer, which might be implemented and standardized into clinical use. [Table: see text]

[Survival analysis of people living with HIV/AIDS in Sichuan province, 1991-2017]

Objective: To analyze the survival time of people living with HIV/AIDS and related influencing factors in Sichuan province during 1991-2017. Methods: A retrospective cohort study was conducted to analyze the data of 143 988 HIV/AIDS cases. The data were collected from Chinese HIV/AIDS Comprehensive Information Management System. Life table method was used to calculate the survival proportion of the cases, and Cox proportion hazard regression model was used to identify the factors related with survival time. Results: Among 143 988 HIV/AIDS cases a total of 30 420 cases died of AIDS related diseases (21.1%) and the average survival time was 11.51 years (95%CI: 11.39-11.64). Multivariate Cox regression analysis showed that the influencing factors for the survival of HIV/AIDS cases were gender (male vs. female, HR=1.35, 95%CI: 1.32-1.40), education level (primary school or below vs. junior middle school: HR=1.15, 95%CI: 1.12-1.18), ethnic group (Han vs. other ethnic groups, HR=1.46, 95%CI: 1.41-1.52), occupation (farmer vs. other occupations: HR=1.26, 95%CI: 1.22-1.29), age (≥55 years old vs. 15-24 years old: HR=3.18, 95%CI: 3.02- 3.36), disease phase (AIDS vs. HIV infection: HR=1.44, 95%CI: 1.39-1.48), antiretroviral therapy (ART) (receiving ART vs. receiving no ART: HR=0.20, 95%CI: 0.19-0.20), and CD(4)(+)T cell counts at diagnosis (>500 cells/μl vs.<200 cells/μl: HR=0.42, 95%CI: 0.40-0.45). Conclusions: The average survival time of HIV/AIDS cases was 11.51 years in Sichuan during 1991- 2017. The risk factors for the survival of the cases were male, education level of primary school or below, Han ethnic group, farmer, old age at diagnosis, disease phase, The protective factors for the survival of HIV/AIDS cases were receiving ART and higher CD(4)(+) T cell counts at diagnosis.

Analysis of time-to-treatment discontinuation of targeted therapy, immunotherapy, and chemotherapy in clinical trials of patients with non-small-cell lung cancer

BACKGROUND

Pragmatic end points, such as time-to-treatment discontinuation (TTD), defined as the date of starting a medication to the date of treatment discontinuation or death has been proposed as a potential efficacy end point for real-world evidence (RWE) trials, where imaging evaluation is less structured and standardized.

PATIENTS AND METHODS

We studied 18 randomized clinical trials of patients with metastatic non-small-cell lung cancer (mNSCLC), initiated after 2007 and submitted to U.S. Food and Drug Administration. TTD was calculated as date of randomization to date of discontinuation or death and compared to progression-free survival (PFS) and overall survival (OS) across all patients, as well as in treatment-defined subgroups [EGFR mutation-positive treated with tyrosine kinase inhibitor (TKI), EGFR wild-type treated with TKI, ALK-positive treated with TKI, immune checkpoint inhibitor (ICI), chemotherapy doublet with maintenance, chemotherapy monotherapy].

RESULTS

Overall across 8947 patients, TTD was more closely associated with PFS (r = 0.87, 95% CI 0.86-0.87) than with OS (0.68, 95% CI 0.67-0.69). Early TTD (PFS-TTD ≥ 3 months) occurred in 7.7% of patients overall, and was more common with chemo monotherapy (15.0%) while late TTD (TTD-PFS ≥ 3 months) occurred in 6.0% of patients overall, and was more common in EGFR-positive and ALK-positive patients (12.4% and 22.9%). In oncogene-targeted subgroups (EGFR positive and ALK positive), median TTDs (13.4 and 14.1 months) exceeded median PFS (11.4 and 11.3 months).

CONCLUSIONS

At the patient level, TTD is associated with PFS across therapeutic classes. Median TTD exceeds median PFS for biomarker-selected patients receiving oncogene-targeted therapies. TTD should be prospectively studied further as an end point for pragmatic randomized RWE trials only for continuously administered therapies.

Genotyping of Circulating Tumor DNA Reveals the Clinically Actionable Mutation Landscape of Advanced Colorectal Cancer

Circulating tumor DNA (ctDNA) enables genomic profiling of colorectal cancer. We investigated therapeutic targets by performing ctDNA panel-captured sequencing of 152 blood samples from advanced stage patients, from which somatic mutations and potentially actionable targets were evaluated. An additional 11 matched tissue samples were retrospectively obtained to verify target validity. The mutation frequencies of 1,127 collective genetic variants identified in our study strongly correlated with those of multiple public databases (Pearson R ² = 0.92, P < 0.0001). The clonal fraction of driver genes was 90.3%, which was significantly higher than that of potential passenger genes (58.12%). Totally, 90 drug-sensitive genes from 56 patients (36.84%) were identified, including recurring targets PIK3CA, FBXW7, EGFR, BRAF, and NRAS Various resistance mechanisms of anti-EGFR antibodies were revealed via ctDNA profiling, with 29 patients individually exhibiting multiple mechanisms, suggesting considerable resistance heterogeneity in our study population. Of the matched tissue/blood pairs, 88.14% of tissue-derived mutations were detected in ctDNA, and 88.9% of actionable targets were validated. The mutational landscape of ctDNA was highly consistent with tissue databases, and ctDNA profiling showed favorable concordance with tumor tissues in our matched analysis. Thus, comprehensive ctDNA genotyping is a promising noninvasive alternative to biopsy-derived analysis for determining targeted therapy in advanced colorectal cancer.

A polymorphic MYC response element in KBTBD11 influences colorectal cancer risk, especially in interaction with an MYC-regulated SNP rs6983267

Background

MYC is a well-established cancer driver gene regulating the expression of numerous genes, indicating that polymorphisms in MYC response elements could affect tumorigenesis through altering MYC regulation. We performed integrative multistage study to evaluate the effects of variants in MYC response elements and colorectal cancer (CRC) risk.

Patients and methods

We systematically integrated ChIP-Seq, DNase-Seq and transcription factor motif data to screen variants with potential ability to affect the MYC binding affinity. Then, we conducted a two-stage case-control study, totally consisting of 4830 CRC cases and 4759 controls in Chinese population to identify risk polymorphisms and interactions. The effects of risk variants were confirmed by functional assays in CRC LoVo, SW480 and HCT15 cells.

Results

We identified a novel polymorphism rs11777210 in KBTBD11 significantly associated with CRC susceptibility (P = 2.43 × 10-12). Notably, we observed a significant interaction between rs11777210 and MYC nearby rs6983267 (P-multi = 0.003, P-add = 0.005), subjects carrying rs6983267 GG and rs11777210 CC genotypes showing higher susceptibility to CRC (2.83-fold) than those carrying rs6983267 TT and rs11777210 TT genotypes. We further demonstrated that rs6983267 T > G increased MYC expression, and MYC bound to and negatively regulated KBTBD11 expression when the rs11777210 C risk allele was present. KBTBD11 was downregulated in tumor tissues, and KBTBD11 knockdown promoted cell proliferation and inhibited cell apoptosis.

Conclusion

The rs11777210 is a potential predictive biomarker of CRC susceptibility, and KBTBD11 functions as a putative tumor suppressor in tumorigenesis. Our study highlighted the high CRC risk of people carrying rs6983267 G and rs11777210 C alleles, and provided possible biological mechanism of the interaction.

Curcumin attenuates palmitic acid-induced cell apoptosis by inhibiting endoplasmic reticulum stress in H9C2 cardiomyocytes

Diabetic cardiomyopathy is mediated by multiple molecular mechanisms including endoplasmic reticulum (ER) stress. Curcumin, a phenolic compound, has cytoprotective properties, but its potential protective action against diabetic cardiomyopathy and the related molecular mechanisms are not fully elucidated. In this study, we evaluated the effects of curcumin on cell viability and apoptosis in palmitic acid (PA)-treated H9C2 cardiomyocytes and investigated the signaling pathways involved. Treatment with PA reduced cell viability, induced apoptosis, enhanced apoptosis-related protein expression (Caspase 3 and BCL-2 associated X protein (BAX)), and activated ER stress marker protein expression (glucose-regulated protein 78 (GRP78) and CCAAT/enhancer binding protein homologous protein (CHOP)). Curcumin attenuated PA-induced reduction in cell viability and activation of apoptosis, Caspase 3 activity, BAX, CHOP, and GRP78 expression. 4-Phenylbutyric acid (4-PBA) attenuated the PA-induced effects on cell viability and apoptosis, similar to curcumin. Both curcumin and 4-PBA also attenuated PA-induced increase in ER stress protein (CHOP and GRP78) expression. Curcumin also protected against cytotoxicity, apoptosis, and ER stress induced by thapsigargin. These findings indicate that PA triggers apoptosis in H9C2 cells via ER stress pathways and curcumin protects against this phenomenon.

Abstract P1-08-25: Withdrawn

This abstract was withdrawn by the authors.

Citation Format: Zhao H, Gong Y, Ye F, Ling H, Hu X. Withdrawn [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-08-25.

Abstract P2-01-13: The splicing factor PHD finger protein 5A inhibits apoptosis to promote breast cancer progression

Background: All the widely accepted hallmarks of cancer are known to be affected by aberrant splicing (AS), and splicing dysregulation itself is considered a valuable therapeutic target. Understanding the AS that promote cancer progression is crucial for the development of effective strategies for treating breast cancer.

Methods: An in vivo CRISPR screen targeting RNA-binding proteins (RBPs) was performed to reveal the key splicing modulator (PHD finger protein 5A, PHF5A) of breast tumor progression. Immunohistochemistry method and survival analysis were performed using a tissue microarray (TMA) containing 450 breast carcinoma. Proliferation, transwell migration and in vivo tumor formation assays were utilized to assess the biological role of PHF5A. RNA sequencing and RT-PCR assay were used to identify PHF5A-regulated AS events in breast cancer cells. Biological functions and molecular pathways of the affected genes were investigated through a gene ontology (GO) analysis. Flow cytometry and Western blot analysis were used for apoptotic assessments. The correlation between PHF5A expression and AS events was further analysed using mRNA-Seq data of 40 paired breast cancer and adjacent normal breast tissues. And the correlation between the levels of PHF5A and cleaved caspase-3 were evaluated in the TMA.

Results: According to RNA sequencing analysis of MCF10 cell series (MCF10A, MCF10AT, MCF10DCIS and MCF10CA1a), 159 RBPs were found to be up-regulated in cancer cells compared with non-cancer cells. And the CRISPR screen targeting these 159 RBPs systematically identified highest-ranking genes including PHF5A. In TMA cohort, high PHF5A expression was correlated with poor disease-free survival. PHF5A is frequently up-regulated in breast cancer and is essential for cancer cell proliferation, migration and tumor formation. Knockdown of PHF5A induces genome-wide AS events. The RT-PCR assay of MCF10CA1a cells showed that splicing changes of nine arbitrarily selected target genes were all modulated by PHF5A. GO analysis showed that PHF5A-regulated AS events were involved in apoptotic and anti-apoptotic pathways, among which FAS-activated serine/threonine kinase (FASTK) AS showed significant PSI (percent spliced in) difference. PHF5A knockdown appeared to switch full-length FASTK (FASTK-L) to an intron 5-retained variant (herein termed FASTK short, FASTK-S) in MCF10CA1a cells. The knockdown of PHF5A resulted in cleavage of caspase-3 and poly-ADP-ribose polymerase and conversion of the FASTK-L (61 kDa) and FASTK-S (42 kDa) proteins. Intriguingly, cells transduced with exogenous FASTK-S showed the most significant apoptotic effect, whereas the FASTK-L group presented a decreased apoptotic effect. The PHF5A ratios of paired non-tumor to tumor tissue were negatively correlated with the FASTK PSI differences between non-tumor and tumor tissues. A strong negative correlation was found between the PHF5A and cleaved caspase-3 levels in TMA.

Conclusions: PHF5A depletion sensitizes cancer cells to apoptotic signaling partially through AS-mediated FASTK isoform conversion. This apoptotic suppressor plays a key role in breast cancer progression and acts as a prognostic indicator, and should be critically considered for optimization of the current therapeutic strategy.

Citation Format: Zheng Y-Z, Xue M-Z, Shen H-J, Li X-G, Ma D, Gong Y, Hu X, Shao Z-M. The splicing factor PHD finger protein 5A inhibits apoptosis to promote breast cancer progression [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-01-13.

Abstract P4-09-09: Association between socioeconomic factors at diagnosis and survival in non-metastatic breast cancer: A population-based study

Background: Breast cancer is a severe public health problem for women worldwide. Race disparities and regional disparities are documented regarding incidence, mortality, and survival of breast cancer patients. However, the associations between socioeconomic status and survival outcomes of breast cancer remain unclear and require a comprehensive large-scale investigation of specific socioeconomic factors. Furthermore, no model has included both histological and socioeconomic factors together to predict survival of breast cancer. In this study, we sought to develop nomograms to predict overall survival (OS) and breast cancer-specific survival (BCSS) with consideration of socioeconomic factors for non-metastasis breast cancer.

Methods: We included a total of 274,108 female patients, diagnosed with malignant breast cancer between 2007 and 2014from the Surveillance, Epidemiology, and End Results (SEER) database. Socioeconomic factors involving marital status, insurance status, residence, median household income, poverty rate, unemployment rate and education level were included in the analysis. OS and BCSS were evaluated with log-rank tests and Kaplan-Meier estimates. We identified and integrated significant prognostic factors for OS and BCSS using univariate and multivariate Cox regression analysis to construct nomograms. Calibration plots and concordance indexes were used to evaluate the accuracy and discrimination of the models.

Results: Among different age subgroups, insured patients were more likely to have better survival than uninsured patients or patients with Medicaid (P&lt;0.001), and especially for patients who were aged 18 to 35 years old at diagnosis, uninsured patients associated with poor BCSS than Medicaid patients (P&lt;0.05). Through multivariate analysis, we found non-Hispanic black patients experienced worst survival compared with the White and other races (P&lt;0.001). Interestingly, married (vs. single vs. separated/divorced/widowed; P&lt;0.001) and insured (vs. Medicaid vs. uninsured; P&lt;0.001) patients had a better prognosis. Living in the non-metro area increased the risk of death (hazard ratio [HR], 1.084, P&lt;0.05). Furthermore, living in counties with higher median household income (&gt;US $72,800) had favorable impacts on OS (HR 0.843, P&lt;0.001). Four and five socioeconomic factors were involved in constructing the nomograms for 3 years-, 5 years- and 7 years- OS and BCSS, respectively. The C-indexes of the final nomograms were higher than those of the TNM staging system for predicting OS (0.776 vs 0.678; P &lt; 0.001) and BCSS (0.842 vs 0.776; P &lt; 0.001), respectively. The performance of the nomograms for predicting OS was significantly lower when excluding the socioeconomic factors (P &lt; 0.001).

Conclusion: Some certain socioeconomic factors (i.e., marital status, insurance status, median household income, and residence) play essential roles in predicting survival of non-metastasis breast cancer. We constructed and validated nomograms including socioeconomic factors to provide more comprehensive and realistic survival estimation. Besides, these findings may highlight the importance of developing health-related policies and the necessity of targeted social support-based interventions for those high-risk patients.

Citation Format: Ji P, Gong Y, Hu X, Hong D, Shao Z-M. Association between socioeconomic factors at diagnosis and survival in non-metastatic breast cancer: A population-based study [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-09-09.

Abstract P2-08-36: Comparing prognostic performance of different lymph node staging systems among patients with breast cancer

Background: Metastatic regional lymph nodes (LN) is a strong predictor of worse long-term outcome after resection of breast cancer. This study aimed to compare the prognostic performance of American Joint Committee on Cancer (AJCC) N stage relative to lymph node ratio (LNR), log odds of metastatic lymph nodes (LODDS), number of removed lymph nodes (NRLNs), and number of negative lymph nodes (NNLNs) in breast cancer patients.

Methods: All of the breast cancer patients who underwent surgery between 2004 and 2012 were identified from the Surveillance, Epidemiology, and End Results database. Restricted cubic spline functions were used to characterize the association between continuous variables and the risk of death and determine the optimal cut-off points. The Cox proportional hazards models were constructed, and the relative discriminative abilities of the different LN staging systems were assessed using the Akaike's Information Criterion (AIC) and the Harrell's concordance index (C-index).

Results: A total of 264,096 breast cancer patients were enrolled, and 177,598 (67.2%) had no lymph node metastasis, whereas 86,498 (32.8%) had lymph node metastasis. 187,785 (71.1%) patients had a limited number of LNs harvested (NRLN &lt;10). The median follow-up time was 73 months, and the 8-year overall survival (OS) and breast cancer-specific survival (BCSS) were 82.6% and 90.4%, respectively. LNR, LODDS, NRLNs, and NNLNs were all nonlinearly associated with OS and BCSS. Patients with metastatic LN had an increased risk of OS (hazards ratio: 2.32, 95% confidence interval: 2.27–2.37; P &lt; 0.001) and BCSS (hazards ratio: 4.53, 95% confidence interval: 4.40–4.66; P &lt; 0.001). When LNR was equal to 0 or 1, there was a heterogeneity of outcomes, and LODDS still yielded informative values compared to LNR. Among the entire cohort, LNR modeled as a continuous variable had a somewhat better prognostic performance (AIC: 923231.4 and C-index: 0.722 for OS; AIC: 482962.3 and C-index: 0.817 for BCSS) than any of other LN staging systems. However, a model with AJCC N stage showed the best fit in patients with a limited number of LNs harvested (AIC: 501321.8 and C-index: 0.699 for OS; AIC: 212605.6 and C-index: 0.809 for BCSS). When assessed among patients with metastatic LN, LODDS outperformed other staging systems including AJCC N stage, LNR, NRLNs and NNLNs, whenever assessed using continuous (AIC: 428626.2 and C index: 0.728 for OS; AIC: 296886.8 and C index: 0.770 for BCSS) or categorical (AIC: 429527.5 and C index: 0.722 for OS; AIC: 297796.6 and C index: 0.762 for BCSS) cutoff values.

Conclusions: Although LNR assessed as a continuous variable was the most potent method to stratify patients regardless of LN status, the prognostic superiority of LNR is confounded by a limited LN harvest. LODDS was a better and more powerful predictor of survival when patients were LN positive, especially among those patients with either very low or high LNR.

Citation Format: Gong Y, Ji P, Jiang Y-Z, Hu X, Shao Z-M. Comparing prognostic performance of different lymph node staging systems among patients with breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-08-36.

Abstract OT3-05-04: Phase II study of atezolizumab, cobimetinib, and eribulin in patients with recurrent or metastatic inflammatory breast cancer (IBC)

Background: IBCs that do not completely respond to chemotherapy often have dysregulated immune pathways, and novel therapies are needed to improve outcomes in recurrent/metastatic disease. One-third of IBCs express the atezolizumab target PD-L1, and cobimetinib increases PD-L1 expression; thus, we hypothesize that atezolizumab and cobimetinib may act synergistically in IBC. The FDA-approved agent eribulin is active in IBC and has anti-stem cell activity and can reverse the IBC phenotype of epithelial-to-mesenchymal transition. Hence the use of eribulin as a chemotherapy backbone in combination with other novel agents is well justified.

Trial Design: This single-arm, open-label trial is enrolling patients with recurrent IBC or de novo metastatic IBC that has progressed on at least 1 line of standard chemotherapy. During a 4-week pharmacodynamic window, patients have an upfront biopsy, receive atezolizumab and cobimetinib treatment for 4 weeks, and have a second biopsy. Triple-combination treatment then commences, with standard eribulin dosing. After 4 cycles of eribulin, patients receive maintenance targeted therapy until disease progression or intolerable toxicity.

Eligibility Criteria: Patients with metastatic IBC of any molecular subtype must have measurable disease (per RECIST 1.1) amenable to biopsy. Patients with HER2+ disease must have received both pertuzumab and T-DM1. Patients with treated stable brain metastases are allowed. Patients must have recovered from the acute effects of any prior therapies and have adequate hematologic, organ, and cardiac function. Patients with autoimmune diseases or a history of pneumonitis are ineligible.

Specific Aims: The primary objective is to determine the overall response rate (ORR) of the combination therapy. Secondary objectives include determining the safety and tolerability, clinical benefit rate, response duration, progression-free survival, 2-year overall survival rate and predictive biomarker analyses.

Statistical Methods: The trial will enroll up to 9 patients in its phase I/safety lead-in portion and up to 33 patients total. A Bayesian optimal interval design is used to efficiently determine the maximum tolerated cobimetinib dose in phase I. Patients start cobimetinib at the FDA-approved dose of 60 mg/day with a target toxicity rate is 0.3. Phase II will enroll 24 patients to determine the efficacy of the triple-combination therapy. The historical ORR in metastatic IBC is 10%; our sample size provides 80% power to detect an ORR improvement to 25%.

Accrual: The trial has enrolled 7 patients since its start in August 2017.

Citation Format: Alexander A, Marx AN, Reddy SM, Reuben JM, Le-Petross HC, Lane D, Huang ML, Krishnamurthy S, Gong Y, Gombos DS, Patel N, Tung CI, Allen RC, Kandl TJ, Wu J, Liu S, Patel AB, Futreal A, Wistuba I, Layman RM, Valero V, Tripathy D, Ueno NT, Lim B. Phase II study of atezolizumab, cobimetinib, and eribulin in patients with recurrent or metastatic inflammatory breast cancer (IBC) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT3-05-04.

Clinical factors associated with circulating tumor DNA (ctDNA) in primary breast cancer

Noninvasive circulating tumor DNA (ctDNA) can be used to predict breast cancer recurrence and prognosis. In this study, we detected 226 and 114 somatic variants in tumor DNA from 70 primary breast cancer (PBC) patients (98.59%) and ctDNA from 48 patients (67.61%), respectively. Gene frequencies of tumor DNA and ctDNA significantly correlated (R²  = 0.9532, P < 0.0001), and tumor-derived variants were detectable in the blood of 43 patients. ctDNA was more often detected in locally advanced/metastatic and nonluminal patients. Multivariate analysis revealed that individual N stage (P < 0.001) and hormone receptor (HR) status (P = 0.001) could independently predict the detectability of tumor-derived mutations in blood. The maximal variant allele frequency of ctDNA was significantly higher in patients with stage IV/M1 (P = 0.0136) and stage T3/T4 (P = 0.0085) cancers. Finally, clonal variants in tumor DNA were more easily traced in ctDNA than subclonal variants (84.62% vs 48.75%). In conclusion, ctDNA fragments concordant with tumor DNA can be consistently detected in the majority of tested PBC patients, which may enable noninvasive genomic profiling of PBC, particularly for patients with advanced-stage tumors and positive HR status.

Monolithic multiple colour emission from InGaN grown on patterned non-polar GaN

A novel overgrowth approach has been developed in order to create a multiple-facet structure consisting of only non-polar and semi-polar GaN facets without involving any c-plane facets, allowing the major drawbacks of utilising c-plane GaN for the growth of III-nitride optoelectronics to be eliminated. Such a multiple-facet structure can be achieved by means of overgrowth on non-polar GaN micro-rod arrays on r-plane sapphire. InGaN multiple quantum wells (MQWs) are then grown on the multiple-facet templates. Due to the different efficiencies of indium incorporation on non-polar and semi-polar GaN facets, multiple-colour InGaN/GaN MQWs have been obtained. Photoluminescence (PL) measurements have demonstrated that the multiple-colour emissions with a tunable intensity ratio of different wavelength emissions can be achieved simply through controlling the overgrowth conditions. Detailed cathodoluminescence measurements and excitation-power dependent PL measurements have been performed, further validating the approach of employing the multiple facet templates for the growth of multiple colour InGaN/GaN MQWs. It is worth highlighting that the approach potentially paves the way for the growth of monolithic phosphor-free white emitters in the future.

Author Correction: Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer

The original version of this Article contained an error in Fig. 2, in which the left y-axis labels 'tDNA' and 'ctDNA' were inadvertently inverted. This has been corrected in the PDF and HTML versions of the Article.

Clinical factors associated with circulating tumor DNA (ctDNA) in primary breast cancer

Noninvasive circulating tumor DNA (ctDNA) can be used to predict breast cancer recurrence and prognosis. In this study, we detected 226 and 114 somatic variants in tumor DNA from 70 primary breast cancer (PBC) patients (98.59%) and ctDNA from 48 patients (67.61%), respectively. Gene frequencies of tumor DNA and ctDNA significantly correlated (R²  = 0.9532, P < 0.0001), and tumor-derived variants were detectable in the blood of 43 patients. ctDNA was more often detected in locally advanced/metastatic and nonluminal patients. Multivariate analysis revealed that individual N stage (P < 0.001) and hormone receptor (HR) status (P = 0.001) could independently predict the detectability of tumor-derived mutations in blood. The maximal variant allele frequency of ctDNA was significantly higher in patients with stage IV/M1 (P = 0.0136) and stage T3/T4 (P = 0.0085) cancers. Finally, clonal variants in tumor DNA were more easily traced in ctDNA than subclonal variants (84.62% vs 48.75%). In conclusion, ctDNA fragments concordant with tumor DNA can be consistently detected in the majority of tested PBC patients, which may enable noninvasive genomic profiling of PBC, particularly for patients with advanced-stage tumors and positive HR status.

Indoleamine 2,3-Dioxygenase (IDO) Regulates Th17/Treg Immunity in Experimental IgA Nephropathy

IgA nephropathy (IgAN) is the most common glomerulonephritis worldwide. Current studies have shown that the Th17/Treg immune balance may be involved in the occurrence of IgAN, but the exact mechanism is still unclear. Indoleamine 2,3-dioxygenase (IDO) is an enzyme that catalyses degradation of tryptophan (Trp) through the kynurenine (Kyn) pathway; it can control inflammation and immune response by inducing Trp starvation. IDO may be a key molecule in regulating the Th17/Treg immune balance. However, it is not clear whether IDO is involved in the IgAN disease occurrence by regulating the Th17/Treg immune balance. In this study, an IgAN mouse model was established. The mice were intraperitoneally inoculated with IDO inhibitor 1-MT or agonist ISS-ODN to observe whether the IDO signalling pathway participates in the occurrence and development of IgAN by regulating the Th17/Treg immune balance. The results showed that IDO inhibitor 1-MT significantly increased renal injury and glomerular IgA accumulation and up-regulated Th17/Treg and Th17-related cytokine expression in IgAN mice, while ISS-ODN significantly decreased renal injury and glomerular IgA accumulation, down-regulated Th17/Treg expression and inhibited Th17-related cytokine expression in IgAN mice. In conclusion, IDO was involved in the occurrence and progress of IgAN by regulating the Th17/ Treg balance.

The DnaJ Gene Family in Shiitake Culinary-Medicinal Mushroom, Lentinus edodes (Agaricomycetes): Comprehensive Identification, Characterization, and Expression Profiles under Different Conditions

The DnaJ proteins, also called heat-shock protein 40 based on their molecular weight, play significant roles in organism growth and development and resistance to abiotic and biotic stresses. However, studies on the DnaJ gene family in Lentinus edodes (= Lentinula edodes) are less well known. In this study, 29 putative L. edode DnaJ genes (LeDnaJ01 to LeDnaJ29) were identified using bioinformatics analysis and were classified into four groups according to the presence of the J protein and zinc finger as well as C-terminal domain. Multiple cis elements related to the phytohormone and stresses were found in the promotor region of the LeDnaJ genes. In addition, qRT-PCR analysis revealed that 79.31% of LeDnaJ genes were induced by cadmium, 55.17% were induced by Trichoderma atroviride, and 37.93% were induced by heat stress, indicating that the LeDnaJ proteins might participate in the response of L. edodes to the multiple stresses. Meanwhile, qRT-PCR analysis also revealed that all LeDnaJs are expressed in at least one development stage, indicating that they could be involved in the process of L. edodes growth and development and the response to the abiotic and biotic stresses. Taken together, these results advance the functional analysis of DnaJ genes in Basidiomycetes.