Liquid biopsy by combining 5-hydroxymethylcytosine signatures of plasma cell-free DNA and protein biomarkers for diagnosis and prognosis of hepatocellular carcinoma

BACKGROUND

Liquid biopsy based on 5-hydroxymethylcytosine (5hmC) signatures of plasma cell-free DNA (cfDNA) originating from tumor cells provides a novel approach for early diagnosis in hepatocellular carcinoma (HCC). Here, we sought to develop a reliable model using cfDNA 5hmC signatures and protein biomarkers for diagnosis and prognosis of HCC.

PATIENTS AND METHODS

We carried out genome-wide 5hmC sequencing of cfDNA samples collected from 165 healthy volunteers, 62 liver cirrhosis (LC) patients and 135 HCC patients. A sensitive 5hmC diagnostic model was developed based on 5hmC signatures selected by sparse Partial Least Squares Discriminant Analysis and cross-validation to define the weighted diagnostic score (wd-score). Then, we combined protein biomarkers with the wd-score to build a more robust score (HCC score) by logistic regression.

RESULTS

The distribution pattern of differential 5hmC regions could clearly distinguish HCC patients, LC patients and healthy volunteers. The wd-score based on 64 5hmC signatures in cfDNA achieves 93.24% of area under the curve (AUC) to distinguish HCC patients from non-HCC patients, and the HCC score by combing protein biomarkers achieves 92.75% of AUC to distinguish HCC patients from LC patients. Meanwhile, the HCC score showed high capacity for screening high recurrence risk patients after receiving surgical resection, and appeared to be an independent indicator for both relapse-free survival (P = 0.00865) and overall survival (P = 0.000739). Furthermore, the values of the HCC score in patients' longitudinal plasma samples were positively associated with tumor burden dynamics during follow-up.

CONCLUSION

We have developed and validated a novel non-invasive liquid biopsy strategy for HCC diagnosis, prognosis and surveillance during HCC progression.

Horizontal orientation of zygomorphic flowers: significance for rain protection and pollen transfer

Floral traits are recognized to have evolved under selection for abiotic and biotic factors. Complex zygomorphic flowers usually face horizontally. It has been proved that a horizontal orientation facilitates pollinator recognition and pollination efficiency, but its significance in adaptation to abiotic factors remains unknown. The floral orientation of Abelia × grandiflora naturally varies around horizontal (with an angle of -30 to +33° between the floral main axis and the horizontal). We examined whether three different floral orientations affected flower thermal conditions, response to rain and pollination. Results showed that floral orientation had no effect on diurnal variations in flower temperature. The anthers of all three flower orientations were wetted by rainfall, but the inclined upward-facing flowers contained significantly more rainwater. The horizontal flowers received significantly higher visitation by hawkmoths and had a higher stigmatic pollen load. In contrast, the upward flower orientation reduced pollination precision, while downward-facing flowers had decreased pollinator attraction. This study indicates that horizontal flowers may have evolved as a trade-off between rain protection and pollination. Zygomorphic flowers that deviate from a horizontal orientation may have lower fitness because of flower flooding by rainwater and decreased pollen transfer.

N-Ethyl-2-Pyrrolidinone-Substituted Flavan-3-Ols with Anti-inflammatory Activity in Lipopolysaccharide-Stimulated Macrophages Are Storage-Related Marker Compounds for Green Tea

Fresh green tea (GT) is commonly considered to have better sensory flavor and higher commercial value than long-term-stored GT; however, the chemical variations during storage are unclear. In this study, the chemical profiles of stored GT were surveyed among time-series samples from 0 to 19 months using a nontargeted metabolomics method. Seven N-ethyl-2-pyrrolidinone-substituted flavan-3-ols (EPSFs) increased from 0.022 ± 0.019 to 3.212 ± 0.057 mg/g within 19 months (correlation coefficients with storage duration ranging from 0.936 to 0.965), and they were the most significantly increased compounds among the 127 identified compounds. Two representative EPSFs (R-EGCG-cThea and S-EGCG-cThea) possess potential anti-inflammatory properties by suppressing the expression, phosphorylation, and nuclear translocation of nuclear factor kappa-B (NF-κB) p65 in lipopolysaccharide-stimulated macrophages based on western blotting and immunofluorescence results. In conclusion, EPSFs were found to be marker compounds for stored GT and showed potential anti-inflammatory activity by regulating the NF-κB signaling pathway.

The Ca2+ -regulated protein kinase CIPK1 integrates plant responses to phosphate deficiency in Arabidopsis thaliana

Phosphate (Pi) deficiency severely restricts plant growth and development, as Pi is an essential macronutrient. Calcium (Ca²⁺ ) is a ubiquitous second messenger in plants; calcineurin B-like proteins (CBL) and CBL-interacting protein kinases (CIPK) are signalling pathways that act as an important Ca²⁺ signalling network which integrates plants to fine tune the response to stress; however, whether CIPK are involved in Pi deficiency stress remains largely unknown. In this study, we carried out a reverse genetic strategy to screen T-DNA insertion mutants of CIPK isoforms under Pi deficiency in Arabidopsis thaliana. Then Pi content, transcription of phosphate starvation-induced (PSI) genes, acid phosphatase activity and hydrogen peroxide were determined in the wild-type (WT) and cipk1 mutant, respectively. The phenotype of CIPK1 complementation lines was analysed. The cipk1 mutant had a more sensitive phenotype, with lower root elongation and root length, and decreased Pi content compared with the WT under Pi deficiency. Moreover, CIPK1 mutation caused phosphate starvation-induced (PSI) genes to be significantly induced under Pi deficiency. Histological staining demonstrated that the cipk1 mutant had increased acid phosphatase activity and hydrogen peroxide concentration under Pi deficiency. By using the yeast two-hybrid system, we further demonstrated the interaction between CIPK1 and the WRKY transcription factors, WRKY6 and WRKY42. Overall, we demonstrate that CIPK1 is involved in the Pi deficiency signalling pathway in A. thaliana, revealing the important role of Ca²⁺ in the Pi nutrition signalling pathway, and potentially providing a theoretical foundation for molecular breeding of crops with better Pi utilization efficiency.

A Food and Drug Administration analysis of survival outcomes comparing the Adjuvant Paclitaxel and Trastuzumab trial with an external control from historical clinical trials

BACKGROUND

Although the Adjuvant Paclitaxel and Trastuzumab (APT) trial has been adopted clinically, single-arm trials have limitations, and interest remains whether these patients with small node-negative human epidermal growth factor receptor 2 (HER2)-positive early breast cancer (EBC) would benefit from more intensive chemotherapy. This analysis explored whether external controls can contextualize single-arm studies to add to clinical decision making in the use of de-escalated therapy in patients with low-risk HER2-positive EBC.

PATIENTS AND METHODS

Patient-level data from five randomized trials supporting drug approval in adjuvant HER2-positive EBC were pooled, and patients with low-risk EBC were selected (n = 1770). Patients treated concurrently with trastuzumab and either anthracycline/cyclophosphamide/taxane/trastuzumab (ACTH) or taxane/carboplatin/trastuzumab (TCH; n = 1366) were matched (1:1) to patients treated with paclitaxel and trastuzumab (TH) in the APT trial (n = 406) using propensity scores. Patients treated with anthracycline/cyclophosphamide/taxane (ACT; n = 374) were also matched (1:1) to those treated with TH. Propensity scores were estimated using covariates of age, tumor stage, estrogen receptor status, progesterone receptor status, and histological grade.

RESULTS

After matching, the estimated probabilities of invasive disease-free survival (iDFS) at 3 and 5 years were 98.6% and 96.5% in the TH arm, and 96.6% and 92.9% in the ACTH/TCH arm, respectively. The estimated probabilities of overall survival (OS) at 3 and 5 years were 99.7% and 99.3% in the TH arm, and 99.0% and 97.4% in the ACTH/TCH arm, respectively. Comparing the TH arm with the ACT arm in the matched sample, the estimated difference in iDFS was 7.5% (TH 98.8% and ACT 91.3%) at 3 years and 12.6% (TH 96.1% and ACT 83.5%) at 5 years. The estimated difference in OS was 2.6% (TH 100% and ACT 97.4%) at 3 years, and 5.3% (TH 99.3% and ACT 94.0%) at 5 years.

CONCLUSIONS

Our analyses suggest that patients' outcomes in both arms were in general similar, thus providing additional reassurance regarding de-escalation of therapy.

Methyl Jasmonate-Induced Changes of Flavor Profiles During the Processing of Green, Oolong, and Black Tea

Tea aroma is one of the most important factors affecting the character and quality of tea. Here we describe the practical application of methyl jasmonate (MeJA) to improve the aroma quality of teas. The changes of selected metabolites during crucial tea processing steps, namely, withering, fixing and rolling, and fermentation, were analyzed. MeJA treatment of tea leaves (12, 24, 48, and 168 h) greatly promotes the aroma quality of green, oolong, and black tea products when comparing with untreated ones (0 h) and as confirmed by sensory evaluation. MeJA modulates the aroma profiles before, during, and after processing. Benzyl alcohol, benzaldehyde, 2-phenylethyl alcohol, phenylacetaldehyde, and trans-2-hexenal increased 1.07- to 3-fold in MeJA-treated fresh leaves and the first two maintained at a higher level in black tea and the last two in green tea. This correlates with a decrease in aromatic amino acids by more than twofold indicating a direct relation to tryptophan- and phenylalanine-derived volatiles. MeJA-treated oolong tea was characterized by a more pleasant aroma. Especially the terpenoids linalool and oxides, geraniol, and carvenol increased by more than twofold.

Abstract P4-04-11: A small amount of primary breast cancer shows high tumor mutation burden that may benefit from immune checkpoint inhibitor therapy

Background: Targeted therapy using immune checkpoint inhibitors (ICIs) is a major breakthrough in cancer treatment in the last decade. ICIs like PD1 or PD-L1 antibodies have been shown to be quite effective in cancer like melanoma. However, in most other tumor types including breast cancer, the situation is not as optimistic. Only a small percentage of those patients respond to ICIs therapy. This highlights the importance of identifying biomarkers to predict which patients may benefit from such treatment. Tumor Mutation Burden (TMB) has been shown to be a sensitive marker for ICI treatment. This study is to investigate whether TBM could be used as a biomarker for breast cancer treatment.

Methods: We reviewed next generation sequencing studies of breast cancer. Two such studies with raw data provided were included in our analysis. One study entitled METABRIC performed targeted sequencing of 173 cancer-related genes in around 2500 primary breast cancer tissues. The other study was from TCGA breast cancer project, which performed Whole Exome Sequencing (WES) of around 1000 primary breast cancer samples. Mutation data were downloaded from public data deposit. The number of mutations per sample was calculated. TBM was calculated by divide the coverage in million base pair from that of the total mutation counts.

Results: In METABRIC study, 17272 mutations were identified in 2369 samples, with a median of 7 mutations per sample (95% CI: 6 ˜ 7). The median TMB of METABRIC dataset was 5.8 SNVs/Mb (95% CI: 5 ˜ 5.8). Totally 30 out 2369 (1.3%) samples had a TMB equal or large than 20 SNVs/Mb. In another cohort from TCGA breast cancer study using WES technology, 90172 mutations were identified in 977 samples, with a median of 44 mutations per sample (95% CI: 39 ˜ 50). The median TMB was 1 SNVs/Mb (95% CI: 0.9 ˜ 1.1). Totally 13 out 977 (1.3%) samples had a TMB equal or large than 20 SNVs/Mb.

Conclusions: Breast cancer shows middle to low mutation burden compared to other cancer types. Around 1.3% of breast cancer has quite high TMB of at least 20 SNVs/Mb, which may be qualified for immune checkpoint inhibitors therapy. Our study indicates that TMB may be incorporated as a standard test for late stage breast cancer patients in the clinical practice.

Keywords: Breast cancer, Tumor Mutation Burden, Whole exome sequencing, Targeted sequencing, Immune checkpoint

Citation Format: Wang J, Chen W, Jiang Z, Lin X, Qin T, Yang X, Liu T, Hu H, Li Z, Xie D, Yao H, Song E. A small amount of primary breast cancer shows high tumor mutation burden that may benefit from immune checkpoint inhibitor therapy [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 P4-04-11.

[A meta-analysis of the effect of occupational exposure to 1-bromopropane on workers' nerve conduction velocity]

Objective: To analysis the occupational exposure to 1-bromopropane on the worker's nerve conduc-tion velocity. Methods: To PubMed, Wanfang, VIP, Chinese Journal Full-text Database (CNKI) and other databases as a data source, searched and screened database to October 2017 on occupational exposure to 1-bromopropane workers on the role of nerve conduction in the paper. According to inclusion and exclusion criteria, we screened literatures, extracted data and evaluated the quality of the included studies, using RevMan5.3 software to test the heterogeneity of the results and us-ing the corresponding mathematical model for data combination analysis. Results: A total of 5 articles were included in the literature. The results showed that the tibial nerve MCV of workers in the 1-bromopropane exposure group was slower than that in the control group (SMD=-0.47,95%CI=-0.70~-0.24) , the difference was statistically significant (Z=4.06, P<0.01). The tibial nerve DL of the exposure group was more prolonged than that of the control group (SMD=0.35,95%CI=0.00~0.69) , with a statistically significant difference (Z=1.99, P=0.05). The sural nerve SCV of the exposure group was slower than that of the control group (SMD=-0.47, 95%CI=-0.78~-0.15), with a statistically significant difference (Z=2.88,P<0.01). Conclusion: Occupational exposure to 1-bromopropane may have an effect on the worker's nerve conduction ve-locity.It's necessary to do broader and deeper neurotoxicity studies about 1-bromopropane.

Metabolomics Investigation Reveals That 8-C N-Ethyl-2-pyrrolidinone-Substituted Flavan-3-ols Are Potential Marker Compounds of Stored White Teas

White teas of different stored ages have varied flavor, bioactivity, and commercial value. In this study, a liquid chromatography-mass spectrometry-based metabolomics investigation revealed that there are distinct differences among the compound patterns of Baihaoyinzhen (BHYZ) and Baimudan (BMD) white teas with various storage durations. The levels of flavan-3-ols, procyanidins, theasinensins, theaflavins, flavonol- O-glycosides, flavone- C-glycosides, and most of the amino acids were reduced after long-term (>4 years) storage. More importantly, 8-C N-ethyl-2-pyrrolidinone-substituted flavan-3-ols (EPSFs), including seven novel compounds discovered in white teas for the first time, were formed from theanine and flavan-3-ols during storage, and their contents were positively correlated with the storage duration. These findings were further confirmed by the linearly increasing formation of EPSFs in reaction solution and BMD white teas stored in an environment-controlled cabinet. In conclusion, EPSFs were detected in white teas for the first time and were discovered as marker compounds and potential indicators for long-term storage of white tea.

Detection of carcinoembryonic antigen in peritoneal fluid of patients undergoing laparoscopic distal gastrectomy with complete mesogastric excision

Background

Surgery for gastric cancer may result in free intraperitoneal cancer cells. This study aimed to determine whether laparoscopic gastrectomy with complete mesogastric excision (D2 + CME) reduces the number of free intraperitoneal cancer cells.

Methods

Patients with gastric cancer who had a conventional D2 or D2 + CME laparoscopic distal gastrectomy between April 2015 and February 2017 were included in the study. Intraoperative peritoneal washings were collected before and after tumour resection. Reverse transcriptase–quantitative real-time PCR for carcinoembryonic antigen (CEA) was used to assess the presence of gastric cancer cells.

Results

Eighty-five patients underwent conventional D2 lymphadenectomy and 76 had the D2 + CME procedure. Of 161 peritoneal fluid samples obtained before gastrectomy, 137 (D2, 72; D2 + CME, 65) had low CEA expression indicative of no cancer cells. After gastrectomy, high CEA expression was detected in 23 of the 72 samples (32 per cent) from patients in the D2 group, and in ten of the 65 samples (15 per cent) from the D2 + CME group. In the overall cohort, mean CEA expression level after gastrectomy was lower in the D2 + CME group than in the D2 group (P = 0·0038). In patients with low CEA expression before gastrectomy, disease-free survival in the D2 + CME group was better than that in the D2 group (P = 0·033).

Conclusion

Laparoscopic distal gastrectomy with complete mesogastric excision reduces the number of free intraperitoneal cancer cells and is associated with a better disease-free survival than conventional D2 gastrectomy.

Abstract 4479: Protein arginine methyltransferase PRMT6 regulates cancer stemness through CRAF methylation in hepatocellular carcinoma

Arginine methylation is a post-translational modification that plays pivotal roles in signal transduction and gene transcription during cell fate determination. We found protein methyltransferase 6 (PRMT6) to be frequently down-regulated in hepatocellular carcinoma (HCC) cells and its expression to negatively correlate with aggressive cancer features in HCC patients. Silencing of PRMT6 promoted the tumor-initiating, metastasis and therapy resistance potential of HCC cells. Consistently, loss of PRMT6 expression aggravated liver tumorigenesis in a DEN+CCL4 HCC induced PRMT6-/- mouse model. Integrated transcriptome and protein-protein interaction studies revealed an enrichment of genes implicated in RAS signaling and that PRMT6 interacted with CRAF, and likely other RAF family members, and their methylation at conserved arginine 100, negatively regulating its activity, and as a consequence resulting in enhanced MEK/ERK signaling. Our work uncovered a critical repressive function for PRMT6 in maintenance of HCC cells by regulating the MEK/ERK pathway via arginine methylation of RAF, providing a new avenue of molecular mechanism by which ERK mediated stemness in HCC cells are developed.

Citation Format: LH Chan, L Zhou, Kai Yu Ng, TL Wong, TK Lee, YP Ching, YF Yuan, D Xie, S Richard, MS Huen, XY Guan, S Ma. Protein arginine methyltransferase PRMT6 regulates cancer stemness through CRAF methylation in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4479.