Treatment Efficacy Outcomes Combining Dual Checkpoint Immunotherapy with Ablative Radiation to All Sites of Oligometastatic Non-Small Cell Lung Cancer: Survival Analysis of a Phase IB trial

PURPOSE/OBJECTIVE(S)

Aggressivelocal treatment to a limited number of metastatic sites in patients with oligometastatic NSCLC increases progression free survival (PFS) and overall survival (OS). Prior studies have shown the safety of combining high dose stereotactic body radiation therapy (SBRT) with single agent anti-PD1/PD-L1 therapy. Here, we report secondary survival endpoint outcomes from a phase Ib clinical trial investigating the safety of combining ablative, high dose radiation with dual checkpoint, anti-CTLA-4 and anti-PD-L1 immunotherapy for patients with oligometastatic NSCLC.

MATERIALS/METHODS

Patients with up to 6 sites of extracranial metastatic disease were eligible for trial enrollment. All sites of disease were treated with stereotactic body radiation therapy to a dose of 30 - 50 Gy in 5 fractions. Dual checkpoint immunotherapy was started 7 days following completion of radiation utilizing anti-CTLA-4 (Tremelimumab) and anti-PD-L1 (Durvalumab) immunotherapy for a total of four cycles followed by durvalumab alone until dose limiting toxicity or progression was observed. Primary toxicity outcomes were previously reported. Progression free and overall survival was analyzed using Kaplan Meier statistical methods.

RESULTS

Fifteen patients were treated with SBRT and received at least one dose of dual agent immunotherapy per protocol. The median follow up was 43 months. The median number of extracranial metastatic sites was 2. Seven patients had 3 or more sites of extracranial disease. The most commonly treated sites were separate metastatic pulmonary lesions or osseous metastatic lesions. Median progression free survival (PFS) was 42 months and median overall survival (OS) was 48 months. Seven patients remain alive without evidence of progressive disease. Prior history of brain metastases was associated with significantly worse PFS (Median PFS 4 months vs 42 months, HR 6.1 (95% CI 1.6 - 37.0) p = 0.0248), but no difference in OS (Median OS 24 vs 42 months, HR 1.9 (95% CI 0.3 - 10.4).

CONCLUSION

Ablative SBRT radiation to up to 6 sites of disease followed by dual checkpoint immunotherapy in oligometastatic NSCLC resulted in a favorable progression free survival (42 months) and overall survival (48 months) compared to historical controls. These findings suggest potential benefit to patient outcomes compared to immunotherapy or radiation alone in this patient population and warrant further investigation.

Fragmentomic analysis of circulating tumor DNA-targeted cancer panels

BACKGROUND

The isolation of cell-free DNA (cfDNA) from the bloodstream can be used to detect and analyze somatic alterations in circulating tumor DNA (ctDNA), and multiple cfDNA-targeted sequencing panels are now commercially available for Food and Drug Administration (FDA)-approved biomarker indications to guide treatment. More recently, cfDNA fragmentation patterns have emerged as a tool to infer epigenomic and transcriptomic information. However, most of these analyses used whole-genome sequencing, which is insufficient to identify FDA-approved biomarker indications in a cost-effective manner.

PATIENTS AND METHODS

We used machine learning models of fragmentation patterns at the first coding exon in standard targeted cancer gene cfDNA sequencing panels to distinguish between cancer and non-cancer patients, as well as the specific tumor type and subtype. We assessed this approach in two independent cohorts: a published cohort from GRAIL (breast, lung, and prostate cancers, non-cancer, n = 198) and an institutional cohort from the University of Wisconsin (UW; breast, lung, prostate, bladder cancers, n = 320). Each cohort was split 70%/30% into training and validation sets.

RESULTS

In the UW cohort, training cross-validated accuracy was 82.1%, and accuracy in the independent validation cohort was 86.6% despite a median ctDNA fraction of only 0.06. In the GRAIL cohort, to assess how this approach performs in very low ctDNA fractions, training and independent validation were split based on ctDNA fraction. Training cross-validated accuracy was 80.6%, and accuracy in the independent validation cohort was 76.3%. In the validation cohort where the ctDNA fractions were all <0.05 and as low as 0.0003, the cancer versus non-cancer area under the curve was 0.99.

CONCLUSIONS

To our knowledge, this is the first study to demonstrate that sequencing from targeted cfDNA panels can be utilized to analyze fragmentation patterns to classify cancer types, dramatically expanding the potential capabilities of existing clinically used panels at minimal additional cost.

A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer

BACKGROUND

miR-346 was identified as an activator of Androgen Receptor (AR) signalling that associates with DNA damage response (DDR)-linked transcripts in prostate cancer (PC). We sought to delineate the impact of miR-346 on DNA damage, and its potential as a therapeutic agent.

METHODS

RNA-IP, RNA-seq, RNA-ISH, DNA fibre assays, in vivo xenograft studies and bioinformatics approaches were used alongside a novel method for amplification-free, single nucleotide-resolution genome-wide mapping of DNA breaks (INDUCE-seq).

RESULTS

miR-346 induces rapid and extensive DNA damage in PC cells - the first report of microRNA-induced DNA damage. Mechanistically, this is achieved through transcriptional hyperactivation, R-loop formation and replication stress, leading to checkpoint activation and cell cycle arrest. miR-346 also interacts with genome-protective lncRNA NORAD to disrupt its interaction with PUM2, leading to PUM2 stabilisation and its increased turnover of DNA damage response (DDR) transcripts. Confirming clinical relevance, NORAD expression and activity strongly correlate with poor PC clinical outcomes and increased DDR in biopsy RNA-seq studies. In contrast, miR-346 is associated with improved PC survival. INDUCE-seq reveals that miR-346-induced DSBs occur preferentially at binding sites of the most highly-transcriptionally active transcription factors in PC cells, including c-Myc, FOXA1, HOXB13, NKX3.1, and importantly, AR, resulting in target transcript downregulation. Further, RNA-seq reveals widespread miR-346 and shNORAD dysregulation of DNA damage, replication and cell cycle processes. NORAD drives target-directed miR decay (TDMD) of miR-346 as a novel genome protection mechanism: NORAD silencing increases mature miR-346 levels by several thousand-fold, and WT but not TDMD-mutant NORAD rescues miR-346-induced DNA damage. Importantly, miR-346 sensitises PC cells to DNA-damaging drugs including PARP inhibitor and chemotherapy, and induces tumour regression as a monotherapy in vivo, indicating that targeting miR-346:NORAD balance is a valid therapeutic strategy.

CONCLUSIONS

A balancing act between miR-346 and NORAD regulates DNA damage and repair in PC. miR-346 may be particularly effective as a therapeutic in the context of decreased NORAD observed in advanced PC, and in transcriptionally-hyperactive cancer cells.

Effects of different types of zinc supplement on the growth, incidence of diarrhea, immune function, and rectal microbiota of newborn dairy calves

Neonatal diarrhea in dairy calves causes huge economic and productivity losses in the dairy industry. Zinc is an effective anti-diarrheal agent, but high doses may pose a threat to the environment. Therefore, we aimed to evaluate the effects of low-dose zinc supplementation on the growth, incidence of diarrhea, immune function, and rectal microbiota of newborn Holstein dairy calves. Thirty newborn calves were allocated to either a control group (without extra zinc supplementation), or groups supplemented with either 104 mg of zinc oxide (ZnO, equivalent to 80 mg of zinc/d) or 457 mg of zinc methionine (Zn-Met, equivalent to 80 mg of zinc/d) and studied them for 14 d. The rectal contents were sampled on d 1, 3, 7, and 14, and blood samples were collected at the end of the study. Supplementation with ZnO reduced the incidence of diarrhea during the first 3 d of life, and increased serum IgG and IgM concentrations. The Zn-Met supplementation increased growth performance and reduced the incidence of diarrhea during the first 14 d after birth. The results of fecal microbiota analysis showed that Firmicutes and Proteobacteria were the predominant phyla, and Escherichia and Bacteroides were the dominant genera in the recta of the calves. As the calves grew older, rectal microbial diversity and composition significantly evolved. In addition, dietary supplementation with ZnO reduced the relative abundance of Proteobacteria in 1-d-old calves, and increased that of Bacteroidetes, Lactobacillus, and Faecalibacterium in 7-d-old calves, compared with the control group. Supplementation with Zn-Met increased the relative abundance of the phylum Actinobacteria and the genera Faecalibacterium and Collinsella on d 7, and that of the genus Ruminococcus after 2 wk, compared with the control group. Thus, the rectal microbial composition was not affected by zinc supplementation but significantly evolved during the calves' early life. Zinc supplementation reduced the incidence of diarrhea in young calves. In view of their differing effects, we recommend ZnO supplementation for dairy calves during their first 3 d of life and Zn-Met supplementation for the subsequent period. These findings suggest that zinc supplementation may be an alternative to antibacterial agents for the treatment of newborn calf diarrhea.

Short communication: Decrease of lipid profiles in cow milk by ultra-high-temperature treatment but not by pasteurization

Triglyceride (TG) and fatty acid profiles of raw (RM), pasteurized (PM, 85°C for 15 s), and indirect UHT-treated (UM, 135°C for 15 s) cow milk were investigated by a lipidomics approach. Ninety-four TG were identified and all were present at significantly lower concentrations in UM than in RM or PM, and free fatty acid contents were significantly higher in UM than in RM and PM, indicating that TG lipolysis occurred to a greater degree in UM than in RM and PM. In addition, UM contained significantly fewer unsaturated fatty acids (14 types) than those in RM and PM, including C14:1n-5, C15:1n-5, C16:1n-7, C17:1n-7, C18:1n9 cis, C18:2n-6 cis, C18:3n-3, C18:3n-6, C20:1, C20:2, C20:3n-6, C20:3n-3, C20:4n-6, and C20:5n-3. However, we detected no significant differences between RM and PM in these fatty acids. In conclusion, UHT treatment, but not pasteurization, caused loss of the nutritional quality and bioactivity of cow milk lipid profiles.

Determination of sulbactam in raw bovine milk by isotope dilution-ultra-high-performance liquid chromatography-tandem mass spectrometry

We developed a sensitive and selective isotope dilution ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the determination of sulbactam residue in raw bovine milk. Sulbactam and internal standard, sulbactam-d₅, were extracted from raw bovine milk via liquid-liquid extraction and enriched with strong anion exchange solid-phase extraction cartridges and finally analyzed by using UPLC-MS/MS with multiple reaction monitoring mode. The method was validated according to European regulations. The calibration curve showed good linearity, with a correlation coefficient of 0.9998. Decision limit and detection capability of sulbactam were determined by matrix calibration curve and were 0.0445 and 0.0517 μg/L, respectively. The recoveries of sulbactam in fortified raw bovine milk ranged from 72.1 to 91.5%, with the intra- and interday relative standard deviations ranging from 3.0 to 18.9%. Furthermore, the developed method was applied to analyzing real raw bovine milk samples collected from dairy farms in Beijing, China. Sulbactam was not determined in all samples. The proposed method could ultimately serve as a methodological foundation for the determination of sulbactam in different types of raw milk and dairy products.

Abstract P5-12-01: A novel gene expression signature prognostic for both locoregional and distant failure and predictive for adjuvant radiotherapy

Background: Most patients with early stage breast cancer (BC) are treated with adjuvant radiotherapy (RT) following breast conserving surgery (BCS) to prevent locoregional recurrences (LRR). No predictive tools are currently available to select patients for RT, resulting in considerable over- and under treatment. We aimed to create and validate a gene expression-based classifier to prognosticate for LRR and to stratify patients for treatment with RT.

Patients and methods: A 27-gene expression signature was developed using three publicly available early stage BC gene expression datasets where patients were treated with RT and had detailed local recurrence information. The largest of the datasets was used to train the signature, and the other two datasets were used for signature refinement. As age was the strongest clinical factor for the endpoint in the training dataset, it was included in the model, resulting in a final clinical-genomic classifier of 27 genes and age. The classifier was locked before external validation in the SweBCG91-RT trial. This phase III clinical trial included primary tumors from 765 patients and for which gene expression data was available. The trial randomized node-negative BC patients to +/- RT following BCS, with sparse use of adjuvant systemic treatment (9%) and a median follow-up of 14.0 years for LRR in patients free from event. The classifier was validated using Cox regression with LRR as the primary endpoint, and hazard ratios (HRs) were calculated using the raw continuous classifier score (range: 0.5 to 2.5).

Results: The novel classifier was highly prognostic for LRR in SweBCG91-RT patients treated with RT (HR=7.5[3.3-16.9], p&lt;0.001), and remained prognostic in multivariate analysis (MVA) that included systemic treatment, subtype and grade (HR=7.2[3.1-16.4], p&lt;0.001). To a lesser extent, the classifier was also prognostic for LRR in patients not treated with RT (HR=1.9[1.0-3.5], p=0.03; MVA HR=1.9[1.0-3.3], p=0.05). Patients at high risk of LRR had a smaller effect of RT, and the treatment predictive potential was confirmed by testing for interaction (pinteraction=0.008). In patients treated with RT, age and the genomic component of the model were both prognostic for LRR (p&lt;0.01) as well as predictive for RT response (pinteraction&lt;0.05) and provided independent information (p&lt;0.01). The combined classifier has increased performance over its individual components (10-year AUC=0.72, 0.67, 0.65 for the classifier, age, and genomic component, respectively). While the novel signature was prognostic for metastasis (HR=4.3[2.3-7.8], p&lt;0.0001), calculated scores from previously published signatures to the metastasis endpoint, including the Oncotype-like score, were not prognostic for LRR.

Conclusions: This novel gene expression signature is highly prognostic for LRR, can identify patients at risk of LRR despite RT, and appears to be treatment predictive for adjuvant RT. Furthermore, the current signature is highly prognostic for metastasis. In contrast, calculated scores of previously published signatures modeled for the metastasis endpoint had inferior performance for LRR. These results underscore both the importance of signatures prognostic for LRR and the similarities in the biology of LRR and distant failure.

Citation Format: Sjöström M, Chang SL, Fishbane N, Davicioni E, Zhao SG, Hartman L, Holmberg E, Feng FY, Speers CW, Pierce LJ, Malmström P, Fernö M, Karlsson P. A novel gene expression signature prognostic for both locoregional and distant failure and predictive for adjuvant radiotherapy [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 P5-12-01.

The effect of energy restriction on fatty acid profiles of longissimus dorsi and tissue adipose depots in sheep

Sheep production systems in northwest China depend mostly on natural grasslands. Seasonal growth and maturity fluctuations can cause periodical restrictions in food quality and quantity. These fluctuations, in turn, result in variability in fat deposition and fatty acid profiles in different fat depots. Consequently, the study objective was to compare fat deposition, intramuscular fat (IMF) percentage and fatty acid profiles of the longissimus dorsi (LD), kidney fat (KF), tail fat (TF), and subcutaneous fat (SF) in lambs under ME restrictions similar to seasonal changes observed in the natural grasslands of northwest China. Nineteen male Dorper × Small Tailed Han lambs were assigned to 2 treatments, a control (CON) fed at 1.0 MJ / W × d and restricted (RES) by restricting ME sequentially every 30 d (0.56 MJ / W × d, 0.84 / W × d, 1.0 MJ / W × d, 0.84 MJ / W × d, 0.56 MJ / W × d, 0.28 MJ / W × d). All lambs were harvested at the end of the 180 d experimental period. Compared to CON fed lambs, restricting ME resulted in lesser IMF, fat deposition indexes ( < 0.05) except testicular and heart fat and greater ( < 0.05) SFA in LD, KF, and TF depots. The RES fed lambs had greater ( < 0.05) -3 PUFA, eicosatrienoic acid (C20:3n3), eicosapentaenoic acid (C20:5n3, EPA), and trans-linolelaidic acid (C18:2n6t) in LD muscle. The conjugated linoleic acids (CLA) content was greater in the SF depots of the CON fed lambs compared to the RES fed lambs. Fatty acid ratios (unsaturated fatty acid; USFA:SFA, MUFA:SFA, PUFA:SFA), and percentage USFA in RES fed lambs were lesser in muscle and adipose tissue compared to CON fed lambs ( < 0.05), except SF depots. In RES fed lambs, EFA were less ( < 0.05) in LD and KF depots and the ratios of functional fatty acids were lesser in LD and some adipose tissues ( < 0.05), including lesser n-6:n-3 in KF and SF ( < 0.05) depots, lesser USFA, SFA, MUFA, SFA in LD, KF, and TF ( < 0.05) depots, and lesser PUFA and SFA in LD and TF ( < 0.05) depots. Results from this research demonstrate that sequential energy restriction, as might be experience during seasonal forage quality and quantity changes in natural grasslands, result in lesser intramuscular fat with associated lesser quality, as well as, changes in fatty acid composition in different fat depots, which has implications for both meat quality and animal physiological functions.

Outcome of postmastectomy radiotherapy after primary systemic treatment in patients with clinical T1-2N1 breast cancer

PURPOSE

The role of postmastectomy radiotherapy following primary systemic treatment in patients with clinical T1-2N1 breast cancer remains a controversial issue. The purpose of this study was to evaluate the benefit of postmastectomy radiotherapy following primary systemic treatment.

PATIENTS AND METHODS

Between 2005 and 2012, in two independent institutions, female patients with T1-2N1 breast cancer receiving primary systemic treatment followed by mastectomy and lymph node dissection because bad response, then treated with or without chest wall and regional lymph node irradiation have been studied retrospectively. The patients received normofractionated radiotherapy using 3D conformal photons or electron techniques. Locoregional recurrence-free survival, distant metastasis-free survival and disease-free survival were calculated using Kaplan-Meier method. Univariate analysis of potential prognostic factors was performed using log-rank test.

RESULTS

Eighty-eight patients have been studied. Of them, 75 patients received postmastectomy radiotherapy. At surgery, 53 patients achieved ypN0. Median follow-up was 67 months. Postmastectomy radiotherapy significantly improved locoregional recurrence-free survival, with a 5-year rate of 96.9% versus 78.6% in the group that did not have postmastectomy radiotherapy. In the subgroup of 53 patients achieving ypN0, postmastectomy radiotherapy improved locoregional recurrence-free survival (a 5-year rate of 94.7% vs. 72.9%), distant metastasis-free survival (a 5-year rate of 92.8% vs. 75%) and disease-free survival (a 5-year rate of 92.9% vs. 62.5%). By univariate analysis, postmastectomy radiotherapy was the only significant prognostic factor affecting locoregional recurrence-free survival.

CONCLUSIONS

For patients with clinical T1-2N1 disease, postmastectomy radiotherapy could significantly improve locoregional recurrence-free survival after primary systemic treatment and be even more therapeutic in the subgroup of patients with good response for primary systemic treatment by improving locoregional recurrence-free, distant metastasis-free and disease-free survival. Larger prospective studies are needed to confirm our findings.

d-Glucose and amino acid deficiency inhibits casein synthesis through JAK2/STAT5 and AMPK/mTOR signaling pathways in mammary epithelial cells of dairy cows

Amino acids and energy deficiency lead to lower milk protein content in dairy cows. However, the known mechanisms involved in this process do not adequately explain the variability of milk protein concentration in the mammary gland. We hypothesized that a deficiency in d-glucose (d-Glc) or AA would inhibit casein synthesis by regulating signaling pathways in mammary epithelial cells. Cow mammary epithelial cells (CMEC) were subjected to combinations of 1 of 3 concentrations of d-Glc (0, 2.50, or 17.5 mM) and 1 of 3 concentrations of AA (0, 1.03, or 7.20 mM). The effect of each mixture on cell cycle stage was assessed by flow cytometry. The expression levels of β-casein and κ-casein (encoded by CSN2 and CSN3) were measured by quantitative real-time PCR and Western blotting. Phosphorylation of Janus kinase 2 (Jak2), signal transducer and activator of transcription 5a (Stat5a), AMP-activated protein kinase (AMPK), mammalian target of rapamycin (mTOR), ribosomal protein S6 kinase 1 (S6K1), and eukaryotic factor 4E-binding protein 1 (4EBP1) were analyzed by Western blotting. The percentages of cells in the DNA postsynthetic (G2) and DNA synthesis (S) phases would decrease, with the level of d-Glc or AA declining individually, but no interaction was observed between the d-Glc and AA effects. The CSN2 and CSN3 mRNA and protein were downregulated when d-Glc or AA decreased individually from 17.5 to 2.50 mM or from 7.20 to 1.03 mM, but d-Glc deficiency had a greater effect according to the regression analysis. The phosphorylation ratio of Jak2 (Tyr^1007/1008), Stat5a (Tyr⁶⁹⁴), mTOR (Ser²⁴⁴⁸), S6K1 (Thr³⁸⁹), and 4EBP1 (Thr³⁷) was downregulated with the level of d-Glc or AA decline, whereas the phosphorylation ratio of AMPK (Thr^183/172) was upregulated. And the change of d-Glc level had a more marked effect than AA in regulating the activity of these signaling protein above according to the regression analysis. Thus, d-Glc or AA deficiency likely reduced casein transcription via inhibition of the Jak2/Stat5 pathway, and reduced translation via suppression of the mTOR pathway by activation of AMPK, but d-Glc deficiency had a more marked effect. These indicated that deficiency of AA, and especially Glc, suppressed proliferation of CMEC and casein gene and protein expression, associated with inhibition of JAK2/STAT5 and AMPK/mTOR signaling pathways.

Short communication: Microbiological quality of raw cow milk and its association with herd management practices in Northern China

Contamination of raw milk with bacterial pathogens is potentially hazardous to human health. The aim of this study was to evaluate the total bacteria count (TBC) and presence of pathogens in raw milk in Northern China along with the associated herd management practices. A total of 160 raw milk samples were collected from 80 dairy herds in Northern China. All raw milk samples were analyzed for TBC and pathogens by culturing. The results showed that the number of raw milk samples with TBC <2 × 10⁶ cfu/mL and <1 × 10⁵ cfu/mL was 146 (91.25%) and 70 (43.75%), respectively. A total of 84 (52.50%) raw milk samples were Staphylococcus aureus positive, 72 (45.00%) were Escherichia coli positive, 2 (1.25%) were Salmonella positive, 2 (1.25%) were Listeria monocytogenes positive, and 3 (1.88%) were Campylobacter positive. The prevalence of S. aureus was influenced by season, herd size, milking frequency, disinfection frequency, and use of a Dairy Herd Improvement program. The TBC was influenced by season and milk frequency. The correlation between TBC and prevalence of S. aureus or E. coli is significant. The effect size statistical analysis showed that season and herd (but not Dairy Herd Improvement, herd size, milking frequency, disinfection frequency, and area) were the most important factors affecting TBC in raw milk. In conclusion, the presence of bacteria in raw milk was associated with season and herd management practices, and further comprehensive study will be powerful for effectively characterizing various factors affecting milk microbial quality in bulk tanks in China.

Cell cycle-coupled expansion of AR activity promotes cancer progression

The androgen receptor (AR) is required for prostate cancer (PCa) survival and progression, and ablation of AR activity is the first line of therapeutic intervention for disseminated disease. While initially effective, recurrent tumors ultimately arise for which there is no durable cure. Despite the dependence of PCa on AR activity throughout the course of disease, delineation of the AR-dependent transcriptional network that governs disease progression remains elusive, and the function of AR in mitotically active cells is not well understood. Analyzing AR activity as a function of cell cycle revealed an unexpected and highly expanded repertoire of AR-regulated gene networks in actively cycling cells. New AR functions segregated into two major clusters: those that are specific to cycling cells and retained throughout the mitotic cell cycle ('Cell Cycle Common'), versus those that were specifically enriched in a subset of cell cycle phases ('Phase Restricted'). Further analyses identified previously unrecognized AR functions in major pathways associated with clinical PCa progression. Illustrating the impact of these unmasked AR-driven pathways, dihydroceramide desaturase 1 was identified as an AR-regulated gene in mitotically active cells that promoted pro-metastatic phenotypes, and in advanced PCa proved to be highly associated with development of metastases, recurrence after therapeutic intervention and reduced overall survival. Taken together, these findings delineate AR function in mitotically active tumor cells, thus providing critical insight into the molecular basis by which AR promotes development of lethal PCa and nominate new avenues for therapeutic intervention.

Abstract P1-10-02: A signature predictive of early vs. late recurrence after radiation treatment (RT) for breast cancer that may inform the biology of early, aggressive recurrences

Purpose: Unmet clinical needs in breast cancer (BC) management include the identification of patients (pts) at high risk to fail locally despite standard local therapy including RT and understanding the biology of these recurrences. We previously reported1 a RT response signature and here extend those studies to identify a signature predictive of timing of recurrence after completion of RT (before or after 3 years).

Methods: Two independent patient cohorts (treated with BCS) from non-randomized clinical trials were used for training and validation. The training cohort included 119 pts with in-breast tumor recurrence and the validation cohort had 25 pts with recurrences. Initial feature selection used Spearman's rank correlation correlating gene expression (14,806 genes) to recurrence time. Genes with sig. correlation (FDR &lt;0.1) and large expression range (fold change &gt;2) were used to train an elastic net penalized Poisson regression model. This model was locked and then applied to the validation dataset. Cox regression was used for both univariate and multivariable analyses (UVA and MVA). To identify biological-related concepts, Spearman's corr. coefficients of recurrence time to gene expression within the training cohort were used to generate a pre-ranked list upon which GSEA pathway analysis was performed.

Results: Spearman's correlation identified 485 genes whose expression was significantly associated with recurrence time (early vs. late). Feature reduction further refined the gene list to 41 genes, which were retained within the signature and locked for further validation. In the training dataset the Spearman's correlation of the continuous score to recurrence time was 0.852 with a P-value of 1.3x10-34 and an AUC of 0.92. Application of this early vs late signature to an independent BC validation set accurately identifies pts with early vs. late recurrences (Spearman's corr.=0.537, p-value&lt;0.007, AUC=0.74, sensitivity=0.71, specificity=0.73, PPV=0.77, NPV=0.67). In UVA and MVA the early vs. late recurrence signature remained the most significant factor associated with recurrence time. Although independent of intrinsic subtype, GSEA analysis of the 41 genes retained within the signature identifies proliferation and EGFR concepts associated with early recurrences and luminal and ER-signaling pathways associated with late recurrences. Knockdown of genes associated with the early and late recurrences is currently underway to assess phenotypic changes (proliferation and clonogenic survival as a measure of early and durable RT response) associated with the early and late recurrence-associated genes.

Conclusion: In this study we derive a BC-specific RT signature predictive of early vs. late recurrence with biologic relevance and validate this signature for prediction of timing of recurrence in an independent clinical dataset. By identifying pts with tumors likely to recur sooner vs. later this signature has the potential to allow for a furthered understanding of the biology underlying early and late recurrences and has a potential to personalize RT, particularly in patients for whom treatment intensification is needed.

1. Clin Cancer Res. 2015 Aug 15;21(16):3667-77.

Citation Format: Speers C, Chang L, Santola A, Liu M, Zhao SG, Chandler B, Olsen E, Bartelink H, Feng FY, Pierce LJ. A signature predictive of early vs. late recurrence after radiation treatment (RT) for breast cancer that may inform the biology of early, aggressive recurrences [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-10-02.

Effect of swine leukocyte antigen-DQA gene variation on diarrhea in Large White, Landrace, and Duroc piglets

Piglet diarrhea is one of the most common factors that affects the benefits of the swine industry. Although recent studies have shown that exon 2 of SLA-DQA is associated with piglet resistance to diarrhea, contributions of genetic variation in the additional exon coding regions of this gene remain unclear. Here, we investigated variation in exons 1, 3 and 4 of the SLA-DQA gene and evaluated their effects on diarrheal infection in 425 suckling piglets. No variation was identified in exon 1. In exon 3, there were eight alleles detected, generated by 14 single nucleotide polymorphisms (SNPs) and three nucleotide deletions, eight SNPs being newly identified. Four allele sequences and three SNPs were identified in exon 4, only one SNP being newly identified. Statistical analysis showed that the genotypes of exon 3 are significantly associated with piglet diarrhea; indeed, genotypes DQA*wb01/wb02 and wb04/wb05 are clearly associated with resistance to piglet diarrhea, as they have the lowest probabilities of infection (P < 0.05). However, no significant association was found between the genotypes of exon 4 and diarrhea (P > 0.05). These results provide important new information concerning the level of genetic diversity at the SLA-DQA locus and suggest that further genetic association studies of piglet diarrhea resistance should include analyses of both exons 2 and 3 of this locus.

Genetic association of sequence variation in exon 3 of the swine leukocyte antigen-DQA gene with piglet diarrhea in Large White, Landrace, and Duroc piglets

Piglet diarrhea is one of the primary factors that affects the benefits of the swine industry. Recent studies have shown that exon 2 of the swine leukocyte antigen-DQA gene is associated with piglet resistance to diarrhea; however, the contributions of additional exon coding regions of this gene remain unclear. Here, we detected and sequenced variants in the exon 3 region and examined their associations with diarrhea infection in 425 suckling piglets using the polymerase chain reaction-single-strand conformational polymorphism and sequencing analysis. The results revealed that exon 3 of the swine leukocyte antigen-DQA gene is highly polymorphic and pivotal to both diarrhea susceptibility and resistance in piglets. We identified 14 genotypes (AA, AB, BB, BC, CC, EE, EF, BE, BF, CF, DD, DH, GG, and GF) and eight alleles (A-H) that were generated by 14 nucleotide variants, eight of which were novel, and three nucleotide deletions. Statistical analyses revealed that the genotypes AB and EF were associated with resistance to diarrheal disease (P < 0.05), and the genotype DD may contribute to diarrhea susceptibility but was unique to Large White pigs (P > 0.05). These results elucidate the genetic and immunological background to piglet diarrhea, and provide useful information for resistance breeding programs.

Effects of tail docking on the expression of genes related to lipid metabolism in Lanzhou fat-tailed sheep

To evaluate stearoyl-CoA desaturase (SCD), hormone-sensitive lipase (HSL), lipoprotein lipase (LPL), and peroxisome proliferator-activated receptor (PPARγ) expression in Lanzhou fat-tailed sheep (with and without docked tails), 18 rams were randomly divided into two equal groups (docked group, LT; control group, LC). These data were also used to increase the understanding of sheep fat deposition and metabolism. All animals were harvested at the age of 18 months, and expression was determined for 10 tissues. The results indicated that the fat weight of each tissue in LT was higher than in LC (P < 0.05). SCD expression in semitendinosus, omentum majus fat (OF), subcutaneous fat, kidney fat (KF), and subcutaneous rump fat was higher in LT than in LC rams (P < 0.05). Trends (P < 0.10) associated with higher HSL expression of LC in comparison to that of LT rams in intestinal fat, OF, and KF tissues were detected. Numerically, LPL expression was the highest in KF, OF, and kidney tissues, but there were few differences (P > 0.10). PPARγexpression was greater in LT than in LC rams in liver tissues (P < 0.05), but there were few differences in other tissues. No significant differences were found with regard to the regression analysis of expression and adipose tissue weights, but the two indices exhibited the same trend. The results indicated that changes in fatty deposits may be due to the common control of docking management and the minor effects associated with the regulation of SCD, HSL, LPL, and PPARγexpression.

Association between polymorphisms of the swine MHC-DQA gene and diarrhoea in three Chinese native piglets

Swine leucocyte antigen (SLA) is a highly polymorphic multigene family that plays a crucial role in swine immune response and disease resistance. Here, we identified polymorphisms and gene variations of SLA-DQA exon 2 using polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and DNA sequencing analysis, and further investigated the correlation between the polymorphisms and piglet diarrhoea in three Chinese native pig breeds (Bamei, Juema and Gansu Black pigs). Consequently, 12 genotypes and 8 alleles including two novel alleles were detected. Nucleotide polymorphism was compared with the actual functional polymorphism in the peptide-binding region (PBR), binding pockets P1, P6 and P9, and the antigen-binding groove, variations in the antigen-binding groove of alleles DQA*01xa01, DQA*01xa03, DQA*01xb01, DQA*We02, DQA*03xb03 and DQA*wy06 were higher than alleles DQA*03xa01 and DQA*03xa03, while amino acid variations in peptide-binding pockets of allele DQA*03xa03 were most abundant among all alleles. The results of association analysis showed the diarrhoea score of Gansu Black pigs (-0.08 ± 0.78) was significantly higher than Bamei and Juema pigs (P < 0.01), and genotype DQA*03xa0103xa01 (0.39 ± 0.54) was significantly higher relative to other genotypes (P < 0.01), while that of genotype DQA*03xa0303xa03 (-1.31 ± 0.88) was markedly lower than scores obtained with genotypes DQA*03xa0103xa01 and DQA*03xa0101xa01 (P < 0.01), as well as DQA*01xa0101xa01 (P < 0.05), indicating that amino acid variations in the peptide-binding pockets play a more important role than the antigen-binding groove in piglet diarrhoea resistance. Further studies on other SLA molecules of native pigs are required to validate the link between this gene complex and diarrhoea.

Association between Genetic Polymorphism in the Swine Leukocyte Antigen-DRA Gene and Piglet Diarrhea in Three Chinese Pig Breeds

The swine leukocyte antigen (SLA)-DRA locus is noteworthy among other SLA class II loci for its limited variation and has not been investigated in depth. This study was investigated to detect polymorphisms of four exons of SLA-DRA gene and its association with piglet diarrhea in Landrace, Large White and Duroc pigs. No polymorphisms were detected in exon 3, while 2 SNPs (c.178G>A and c.211T>C), 2 SNPs (c.3093A>C and c.3104C>T) and 5 SNPs (c.4167A>G, c.4184A>G, c.4194A>G, c.4246A>G and c.4293G>A) were detected in exon 1, exon 2 and exon 4 respectively, and 1 SNP (c.4081T>C) in intron 3. Statistical results showed that genotype had significant effect on piglet diarrhea, individuals with genotype BC had a higher diarrhea score when compared with the genotypes AA, AB, AC and CC. Futhermore, genotype AC had a higher diarrhea score than the genotype CC in exon 1 (p<0.05); diarrhea scores of genotype AA and BB were higher than those of genotypes AC and CC in exon 2 (p<0.05); individuals with genotype AA had a higher diarrhea score than individuals with genotype AB and BB in exon 4 (p<0.05). Fourteen common haplotypes were founded by haplotype constructing of all SNPs in the three exons, its association with piglet diarrhea appeared that Hap2, 5, 8, 10, and 14 may be the susceptible haplotypes and Hap9 may be the resistant haplotype to piglet diarrhea. The genetic variations identified of the SLA-DRA gene may potentially be functional mutations related to piglet diarrhea.

Swine Leukocyte Antigen-DQA Gene Variation and Its Association with Piglet Diarrhea in Large White, Landrace and Duroc

The swine leukocyte antigen class II molecules are possibly associated with the induction of protective immunity. The study described here was to investigate the relationship between polymorphisms in exon 2 of the swine DQA gene and piglet diarrhea. This study was carried out on 425 suckling piglets from three purebred pig strains (Large White, Landrace and Duroc). The genetic diversity of exon 2 in swine DQA was detected by PCR-SSCP and sequencing analysis, eight unique SSCP patterns (AB, BB, BC, CC, CD, BD, BE and DD) representing five specific allele (A to E) sequences were detected. Sequence analysis revealed 21 nucleotide variable sites and resulting in 12 amino acid substitutions in the populations. A moderate level polymorphism and significant deviations from Hardy-Weinberg equilibrium of the genotypes distribution were observed in the populations (p<0.01). The association analysis indicated that there was a statistically significant difference in the score of piglet diarrhea between different genotypes, individuals with genotype CC showed a lower diarrhea score than genotypes AB (0.98±0.09), BB (0.85±0.77) and BC (1.25±0.23) (p<0.05), and significantly low than genotype BE (1.19±0.19) (p<0.01), CC genotype may be a most resistance genotype for piglet diarrhea.

Efficacy of intratumoral chemotherapy using arsenic trioxide (As2O3) sustained release tablets for the treatment of neurogliocytoma in nude mice

OBJECTIVE

This study aimed to investigate the inhibiting effect of arsenic trioxide (As2O3) on neurogliocytoma in nude mice and the mechanism responsible for this effect.

MATERIALS AND METHODS

Neurogliocytoma implantation models were constructed in nude mice, which were assigned to three groups: the control group, the sustained release tablet-polylactic acid-glycolic acid polymer (50:50) group (PLGA group) and the As2O3-polylactic acid-glycolic acid polymer (50:50) (As2O3-PLGA group). One tablet of As2O3-PLGA was implanted in the tumor of the As2O3-PLGA group. Intratumoral implantation was also performed in the other groups using a different type of tablet. The sustained releasing As2O3 had an inhibiting effect on the tumors. The TUNEL assay was used to determine the apoptosis rates in the implanted tumors. Immunohistochemical staining and Western blotting was carried out to determine the expression levels of caspase-3 and Bcl-2.

RESULTS

No inhibitory effect was observed on the tumor in the PLGA group, and there was no significant difference between this group and the control group. Subcutaneous tumor growth in nude mice was significantly inhibited in the As2O3-PLGA group relative to that in the control group, and the difference was statistically significant (p < 0.01). The tumor inhibition rate was 60.8%. The percentage of apoptotic tumor cells in the As2O3-PLGA group was 30.8%, which was significantly higher than that in the control group (3.92%) and that in the PLGA group (4.08%). The expression of Bcl-2 in the implanted tumor tissue was significantly reduced, but the expression of caspase-3 increased significantly.

CONCLUSIONS

As2O3 has a potent inhibiting effect on the growth of neurogliocytoma in vivo and can induce the apoptosis of tumor cells. The molecular mechanism of this effect may be related to the downregulation of Bcl-2 expression and the upregulation of caspase-3 expression.

Impact of MTHFR polymorphisms on methylation of MGMT in glioma patients from Northeast China with different folate levels

Hypomethylation of the O6-methylguanine-DNA-methyltransferase (MGMT) promoter in glioma cells has been associated with temozolomide resistance. S-adenosylmethionine (SAM), which is produced during folate metabolism, is the main source of methyl groups during DNA methylation. As a key enzyme during folate metabolism, polymorphisms of 5,10-methylenetetrahydrofolate reductase (MTHFR) may regulate folate end-products. We investigated the effect of typical polymorphisms of MTHFR (C677T and A1298C) on MGMT methylation based on different serum folate levels in patients with glioma from Northeast China. A total of 275 patients with glioma and 329 without malignant tumors were tested. Serum folate concentration was assayed by using the electrochemiluminescence immunoassay. MTHFR polymorphisms were detected by Taqman-Fluorescence quantitative polymerase chain reaction (PCR). Methylation-specific PCR was used to assess MGMT methylation. The constituent ratio of glioma patients below the serum folate biological reference value was significantly higher than that of the control population (P < 0.001). In patients with oligodendroglioma and glioblastoma, heterozygotes for the A1298C mutation were found in higher frequency than homozygotes or wild types (oligodendroglioma, P < 0.001; glioblastoma, P < 0.01). When grouped by the median or biological reference value of serum folate, only homozygotes for C677T with low levels of folate were significantly associated with decreased methylation of MGMT (median, P < 0.001; biological reference value, P = 0.036). These data suggest that, in combination with a negative folate balance in glioma patients, T/T genotypes in MTHFR C677T may be associated with MGMT demethylation.

Cloning and bioinformatic analysis of an acidophilic beta-mannanase gene, Anman5A, from Aspergillus niger LW-1

Using 3' and 5' rapid amplification of cDNA ends (RACE) techniques, the full-length cDNA sequence of the AnmanSA, a gene that encodes an acidophilic beta-mannanase of Aspergillus niger LW-1 (abbreviated to AnMan5A), was identified from the total RNA. The cDNA sequence was 1417 bp in length, harboring 5'- and 3'-untranslated regions, as well as an open reading frame (ORF) which encodes a 21-aa signal peptide, a 17-aa propeptide and a 345-aa mature peptide. Based on the topology of the phylogenetic tree of beta3-mannanases from glycoside hydrolase (GH) family 5, the AnMan5A belongs to the subfamily 7 of the GH family 5. Its 3D structure was modeled by the bitemplate-based method using both MODELLER 9.9 and SALIGN programs, based on the known beta-mannanase crystal structures of Trichoderma reesei (1QNO) and Lycopersicon esculentum (1RH9) from the GH family 5. In addition, the complete DNA sequence of the Anman5A was amplified from the genomic DNA using the pUCm-T vector-mediated PCR and conventional PCR methods. The DNA sequence was 1825 bp in length, containing a 5'-flanking regulatory region, 2 introns and 3 exons when compared with the full-length cDNA.

Silencing of ferrochelatase enhances 5-aminolevulinic acid-based fluorescence and photodynamic therapy efficacy

Background:

Recurrence of glioma frequently occurs within the marginal area of the surgical cavity due to invading residual cells. 5-Aminolevulinic acid (5-ALA) fluorescence-guided resection has been used as effective therapeutic modalities to improve discrimination of brain tumour margins and patient prognosis. However, the marginal areas of glioma usually show vague fluorescence, which makes tumour identification difficult, and the applicability of 5-ALA-based photodynamic therapy (PDT) is hampered by insufficient therapeutic efficacy in glioma tissues.

Methods:

To overcome these issues, we assessed the expression of ferrochelatase (FECH) gene, which encodes a key enzyme that catalyses the conversion of protoporphyrin IX (PpIX) to heme, in glioma surgical specimens and manipulated FECH in human glioma cell lines.

Results:

Prominent downregulation of FECH mRNA expression was found in glioblastoma tissues compared with normal brain tissues, suggesting that FECH is responsible for PpIX accumulation in glioblastoma cells. Depletion of FECH by small interference RNA enhanced PpIX fluorescence after exposure to 5-ALA concomitant with increased intracellular PpIX accumulation in glioma cells. Silencing of FECH caused marked growth inhibition and apoptosis induction by PDT in glioma cells.

Conclusion:

These results suggest that knockdown of FECH is a potential approach to enhance PpIX fluorescent quality for optimising the subjective discrimination of vague fluorescence and improving the effect of 5-ALA-PDT.

Tetraethylammonium inhibits glioma cells via increasing production of intracellular reactive oxygen species

BACKGROUND

Potassium channel blockers have been shown to possess antitumor properties, but the role of apoptosis remains to be clarified. In this study, we investigated the antiproliferative effect of tetraethylammonium (TEA), a nonspecific potassium channel blocker, in rat C6 and 9L glioma cells.

METHODS

Cytotoxicity was evaluated by MTT assay. Apoptosis was detected by TUNEL and annexin V-FITC/propidium iodide assays. Protein levels were determined by Western blot analysis. Intracellular reactive oxygen species (ROS) levels were assessed flow cytometrically.

RESULTS

TEA (2-60 mM) significantly inhibited the proliferation of C6 and 9L glioma cells. In addition, increased cell apoptosis was confirmed after treatment with 40 mM TEA. Apoptosis was associated with a dramatic increase in ROS levels and altered Bcl-2/Bax protein balance.

CONCLUSION

TEA can inhibit proliferation and induce apoptosis in both cell lines; therefore, it might be associated with the increase in intracellular ROS production.

Diagnosing anorexia based on partial least squares, back propagation neural network, and support vector machines

Support vector machine (SVM), as a novel type of learning machine, for the first time, was used to develop a predictive model for early diagnosis of anorexia. It was based on the concentration of six elements (Zn, Fe, Mg, Cu, Ca, and Mn) and the age extracted from 90 cases. Compared with the results obtained from two other classifiers, partial least squares (PLS) and back-propagation neural network (BPNN), the SVM method exhibited the best whole performance. The accuracies for the test set by PLS, BPNN, and SVM methods were 52%, 65%, and 87%, respectively. Moreover, the models we proposed could also provide some insight into what factors were related to anorexia.