Noninvasive fetal genotyping in pregnancies at risk for PKU using a comprehensive quantitative cSMART assay for PAH gene mutations: a clinical feasibility study

OBJECTIVE

To assess the diagnostic performance of a novel circulating single molecule amplification and re-sequencing technology (cSMART) method for noninvasive prenatal testing (NIPT) of Phenylketonuria (PKU).

DESIGN

Blinded NIPT analysis of pregnancies at high risk for PKU.

SETTING

Shanghai Xinhua Hospital and Hunan Jiahui Genetics Hospital, China.

POPULATION

Couples (n = 33) with a child diagnosed with PKU.

METHODS

Trio testing for pathogenic PAH mutations was performed by Sanger sequencing. In second pregnancies, invasive prenatal diagnosis (IPD) was used to determine fetal genotypes. NIPT was performed using a PAH gene-specific cSMART assay. Based on the plasma DNA mutation ratio relative to the fetal DNA fraction, fetal genotypes were assigned using a maximum-likelihood algorithm.

MAIN OUTCOME MEASURES

Concordance of fetal genotyping results between IPD and NIPT, and the sensitivity and specificity of the NIPT assay.

RESULTS

Compared with gold standard IPD results, 32 of 33 fetuses (96.97%) were accurately genotyped by NIPT. The sensitivity and specificity of the NIPT assay was 100.00% (95% CI 59.04-100.00%) and 96.15% (95% CI 80.36-99.90%), respectively.

CONCLUSIONS

The novel cSMART assay demonstrated high accuracy for correctly calling fetal genotypes. We propose that this test has useful clinical utility for the rapid screening of high-risk and low-risk pregnancies with a known history of PKU on one or both sides of the family.

TWEETABLE ABSTRACT

NIPT of couples at high risk for PKU using a full-coverage cSMART PAH gene test.

Enzyme-Responsive Mesoporous Ruthenium for Combined Chemo-Photothermal Therapy of Drug-Resistant Bacteria

The rapid mutation of drug-resistant bacteria and the serious lag of development of new antibiotics necessitate research on novel antibacterial agents. Nanomaterials with unique size effect and antibacterial mechanism could serve as an alternative for antibiotics, since they showed low possibility to develop drug-resistant bacteria. Here, an enzyme-responsive nanosystem, AA@Ru@HA-MoS₂, with a synergistic chemo-photothermal therapy function is proposed to treat bacterial infections. Mesoporous ruthenium nanoparticles (Ru NPs) were used as nanocarriers, loading prodrug ascorbic acid (AA) and encapsulated by hyaluronic acid (HA). Then, molybdenum disulfide (MoS₂) precoated with ciprofloxacin was used as a catalyst with targeting effect binding to the outer surface. When the nanosystem gathered at the infection site, Hyal secreted by bacteria could degrade the HA capping and trigger the release of AA and then generated hydroxyl radicals (^•OH) in situ by the catalysis of MoS₂. In addition, taking advantage of the good photothermal property of Ru NPs, combined chemo-photothermal antibacterial therapy could be achieved. The nanosystem exhibited potent bactericidal activity against drug-resistant Gram-positive and Gram-negative bacteria. Furthermore, it could break down the biofilm, inhibit the contained bacteria, and prevent the formation of a new biofilm. The in vivo bacterium-infected model also proved accelerated wound healing. The study showed a high potential of AA@Ru@HA-MoS₂ as a novel enzyme-responsive nanosystem for combating drug-resistant bacterial infection.

[Transmastoidslotted labyrinthotomy approach cochlear implantation with customized electrode for patients with common cavity deformity]

Objective: To discuss the benefit of using transmastoid slotted labyrinthotomy approach (TSLA) and customized electrode for common cavity deformity (CCD) patients, and to evaluate the audiological outcomes. Methods: A retrospective analysis of the intraoperative monitoring data and postoperative auditory outcomes of 10 CCD cases who received cochlear implantation in Beijing Tongren Hospital,Capital Medical University from April 2016 to December 2017, was conducted using TSLA and customized electrod as a test group.At the same time, 10 cases of age and gender matched children with severe or severe sensorineural hearing loss and normal inner ear structures were recorded as a control group. Four questionnaires were collected from the two groupspre-operative, 6 months and 1 year after start-up. The Wilcoxon signed rank sum test was used to compare the scores of different time points. Rank sum test of two independent samples was used to compare the scores between different groups. Results: None of the patients exhibited CSF leakage or facial paralysis after operation. The average impedance of 8 CCD children in the experimental group was below 5 kΩ. The total extraction rate of auditory neural response telemetry (ART) of all stimulating electrodes was 55% (33/60), and the amplitude of the electricity induced complex action potential (ECAP) of electrodes at different positions ranged from 50.69 to 170.3 μV.The average surgical time of the TSLA group was 46.4 min, shorter than the traditional approach.There was significant difference between the scores of pre-operative, 6 months and 1 year after start-up for the TSLA group(categories of auditory performance,CAP: 2.0 (2.0,3.0) vs. 4.0 (3.8,4.0) , Z=-3.109, P=0.002; speech intelligibility rating,SIR: 2.0 (2.0,2.3) vs. 3.0 (2.8,4.0) , Z=-2.952, P=0.003; meaningful use of speech scale,MUSS: 4.0 (3.3,6.0) vs. 9.0 (6.0,11.8) , Z=-3.421, P=0.001; meaningful auditory integration scale, MAIS or infant-toddler and meaningful auditory integration scale, IT-MAIS: 5.5 (3.8,9.0) vs. 15.5 (10.8,18.5) , Z=-3.522, P=0.000 for the latter two).In addition, The scores of the TSLA group were significantly worse than the control group at 6 months and 1 year after start-up.The high-resolution CT scan showed good adhesion of the electrodes without displacementone week and one year after surgery. Conclusions: For CCD patients, TSLA and customized electrode is recommended due to lower surgical difficulty and post-operative risk, shortened surgical time; Intraoperative ART monitoring can be used to determine the integrity of the auditory pathway. Children with common cavity deformity have a longer period of auditory rehabilitation, and the individual differences in speech rehabilitation are significantly different, which is significantly worse than those with normal structure.

Optical and polarization properties of nonpolar InGaN-based light-emitting diodes grown on micro-rod templates

We have demonstrated non-polar a-plane InGaN multiple-quantum-well (MQW) light-emitting diodes (LEDs) on sapphire, achieved by overgrowing on a micro-rod template with substantially improved crystal quality. Photoluminescence measurements show one main emission peak at 418 nm along with another weak peak at 448 nm. Wavelength mapping measurements carried out by using a high spatial-resolution confocal PL system indicate that the two emissions origin from different areas associated with the underlying micro-rod patterns. Electroluminescence measurements exhibit a negligible blue-shift of 1.6 nm in the peak wavelength of the main emission when the driving current increases from 10 to 100 mA, indicating that the quantum confined Stark effect is effectively suppressed in in the nonpolar LED. A polarization ratio of 0.49 is obtained for the low-energy emission (~448 nm), while the main emission (~418 nm) shows a polarization ratio of 0.34. Furthermore, the polarization ratios are independent of injection current, while the energy separation between m-polarized and c-polarized lights increases with the injection current for both emissions.

[Role of PD-1/PD-L1 in microenvironment of breast cancer]

Programmed cell death protein 1 (PD-1), as a checkpoint of the immune signaling pathway, is a hotspot in the field of immuno-oncology. Its binding with ligand (PD-L1) is an important negative regulatory mechanism. Application of PD-1/PD-L1 inhibitors in treatments of breast cancer is still being explored at present. Fully understanding the mechanism of PD-1/PD-L1 in the microenvironment of breast cancer will help their inhibitors play a full role. This review will start with the discovery of PD-1 and PD-L1, describe their main signaling pathways, introduce the common types and applications of PD-1/PD-L1 inhibitors, especially in breast cancer, summarize the basic research of PD-1 and PD-L1 in breast cancer microenvironment in recent years, and seek new strategies of PD-1/PD-L1 inhibitors in breast cancer treatment.

[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.

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.

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.

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 recessive C locus in the MITF gene plays a key regulatory role in the plumage colour pattern of duck (Anas platyrhynchos)

1. The c/c alleles are responsible for the white plumage colour of ducks; however, the gene corresponding to this locus is still unclear. In order to identify the locus-related candidate gene associated with duck's plumage colour pattern, it was necessary to analyse the whole genome resequencing data. 2. A total of 929,465 SNPs in chromosome 13 and 1,688 SNPs in the region of the Microphthalmia-Associated Transcription Factor (MITF) gene were identified from whole genome resequencing data analysis. After construction of an F_ST plot from chromosome 13, MITF was highlighted as a candidate gene, possessing the highest F_ST value (0.811) on chromosome 13. 3. Six novel SNPs were discovered, located in the intronic region of the MITF gene. F2 progeny of Kaiya × Liancheng ducks (N = 1,061) were selected for genotyping by the Restriction Fragment Length Polymorphism (RFLP) technique. Association analysis using Haploview software was used for validation of the results. 4. Association results between SNPs and phenotypes showed significant association with corresponding phenotypes. All the significantly associated SNPs were located in the identified candidate gene. 5. The identified candidate gene provided novel information which is important in marker-assisted selection and breeding of duck and for the investigation of the C locus recessive white genetic mechanisms underlying plumage colour pattern.

Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce

BACKGROUND

The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition.

RESULTS

Following a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with auxiliary activities from carbohydrate-active enzyme (CAZy) families AA3 and AA5. In addition, a lytic polysaccharide monooxygenase from family AA9 was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi.

CONCLUSIONS

The inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of specific sequences within large glycoside hydrolase families (e.g., GH5 and GH16), and permitted co-expression analyses that identified new targets for study, including non-catalytic proteins and proteins with unknown function.