Evaluation of mutagenic susceptibility of different stages in germ cell development of Caenorhabditis elegans using whole genome sequencing

In contrast to somatic mutations, mutations in germ cells affect every cell of any organism derived from the germ cell and therefore are related to numerous genetic diseases. However, there is no suitable assay to evaluate the mutagenic sensitivities of both male and female germ cells. The main type of Caenorhabditis elegans (C. elegans) is hermaphroditic, where spermatogenesis and oogenesis occur chronologically at specific stages, allowing induction of mutations in either sperm or eggs exclusively. In this study, we used the alkylating agent ethyl methanesulfonate and N-ethyl-N-nitrosourea to induce germline mutations in C. elegans at different developmental stages and analyzed mutation frequency and mutational spectrum from data gathered using next-generation sequencing (NGS) technology. Our results revealed low spontaneous mutation rates of C. elegans, along with distinct mutagenic effects elicited by the two mutagens. Our data show that the parental worms treated during germ cell mitosis, spermatogenesis, and oogenesis resulted in different mutation frequencies in their offspring, and female germ cells could be very susceptible to mutagen exposure during oogenesis. In summary, our study indicates that the use of C. elegans and its specific chronological hermaphroditism would be a promising way to explore the sensitivities of both male and female germ cells to mutagens.

Neuroprotective Effects of IVIG against Alzheimer' s Disease via Regulation of Antigen Processing and Presentation by MHC Class I Molecules in 3xTg-AD Mice

BACKGROUND

The results of clinical trials for Alzheimer's disease (AD) patients treated with Intravenous immunoglobulin (IVIG) revealed inconsistency in efficacy.

OBJECTIVE

To explore the neuroprotective effects and possible mechanisms of different IVIG in 3xTg-AD mice.

METHODS

3-month-old 3xTg-AD mice were administered intraperitoneally with different IVIG (A/B/C) for 3 months and then the therapeutic effects were observed and tested at 9 months of age. The bioavailability of IVIG and Aβ40/42 concentrations in parietotemporal cortex was measured by ELISA. Behavioral tests were performed to examine cognitive functions. Immunohistochemistry was utilized to examine the deposition of Aβ, the phosphorylation of tau, the levels of GFAP and Iba-1 in the hippocampus. Proteomics, Luminex assay and parallel reaction monitoring were performed to identify and verify the proteins that showed a marked change in the hippocampus.

RESULTS

IVIG-C was more effective than IVIG-A and IVIG-B in counteracting cognitive deficits, ameliorating Aβ deposits and tau phosphorylation, attenuating the activation of microglia and astrocytes in the hippocampus and inhibiting the secretion of pro-inflammatory factors. IVIG-C affected innate immunity and suppressed the activation of antigen processing and presentation by MHC class I molecule (APP-MHC-I).

CONCLUSION

The efficacy of different IVIG on AD was significantly different, and only IVIG-C has been confirmed to possess significant neuroprotective effects, which are related to the inhibition of APP-MHC-I. IVIG may be a potential therapeutic for AD but further research is needed to evaluate the functional of IVIG before clinical trials of AD treatment.

Analgesic dorsal root ganglion field stimulation blocks both afferent and efferent spontaneous activity in sensory neurons of rats with monosodium iodoacetate-induced osteoarthritis

OBJECTIVES

Chronic joint pain is common in patients with osteoarthritis (OA). Non-steroidal anti-inflammatory drugs and opioids are used to relieve OA pain, but they are often inadequately effective. Dorsal root ganglion field stimulation (GFS) is a clinically used neuromodulation approach, although it is not commonly employed for patients with OA pain. GFS showed analgesic effectiveness in our previous study using the monosodium iodoacetate (MIA) - induced OA rat pain model. This study was to evaluate the mechanism of GFS analgesia in this model.

METHODS

After osteoarthritis was induced by intra-articular injection of MIA, pain behavioral tests were performed. Effects of GFS on the spontaneous activity (SA) were tested with in vivo single-unit recordings from teased fiber saphenous nerve, sural nerve, and dorsal root.

RESULTS

Two weeks after intra-articular MIA injection, rats developed pain-like behaviors. In vivo single unit recordings from bundles teased from the saphenous nerve and third lumbar (L3) dorsal root of MIA-OA rats showed a higher incidence of SA than those from saline-injected control rats. GFS at the L3 level blocked L3 dorsal root SA. MIA-OA reduced the punctate mechanical force threshold for inducing AP firing in bundles teased from the L4 dorsal root, which reversed to normal with GFS. After MIA-OA, there was increased retrograde SA (dorsal root reflex), which can be blocked by GFS.

CONCLUSIONS

These results indicate that GFS produces analgesia in MIA-OA rats at least in part by producing blockade of afferent inputs, possibly also by blocking efferent activity from the dorsal horn.

Whole Exome Sequencing Reveals Genetic Variants in HLA Class II Genes Associated With Transplant-free Survival of Indeterminate Acute Liver Failure

INTRODUCTION

Indeterminate acute liver failure (IND-ALF) is a rare clinical syndrome with a high mortality rate. Lacking a known etiology makes rapid evaluation and treatment difficult, with liver transplantation often considered as the only therapeutic option. Our aim was to identify genetic variants from whole exome sequencing data that might be associated with IND-ALF clinical outcomes.

METHODS

Bioinformatics analysis was performed on whole exome sequencing data for 22 patients with IND-ALF. A 2-tier approach was used to identify significant single-nucleotide polymorphisms (SNPs) associated with IND-ALF clinical outcomes. Tier 1 identified the SNPs with a higher relative risk in the IND-ALF population compared with those identified in control populations. Tier 2 determined the SNPs connected to transplant-free survival and associated with model for end-stage liver disease serum sodium and Acute Liver Failure Study Group prognostic scores.

RESULTS

Thirty-one SNPs were found associated with a higher relative risk in the IND-ALF population compared with those in controls, of which 11 belong to the human leukocyte antigen (HLA) class II genes but none for the class I. Further analysis showed that 5 SNPs: rs796202376, rs139189937, and rs113473719 of HLA-DRB5; rs9272712 of HLA-DQA1; and rs747397929 of IDO1 were associated with a higher probability of IND-ALF transplant-free survival. Using 3 selected SNPs, a model for the polygenic risk score was developed to predict IND-ALF prognoses, which are comparable with those by model for end-stage liver disease serum sodium and Acute Liver Failure Study Group prognostic scores.

DISCUSSION

Certain gene variants in HLA-DRB5, HLA-DQA1, and IDO1 were found associated with IND-ALF transplant-free survival. Once validated, these identified SNPs may help elucidate the mechanism of IND-ALF and assist in its diagnosis and management.

POS1259 AXIAL SPONDYLOARTHRITIS, AGE AND MALE GENDER IMPACT COVID VACCINATION AEs MORE THAN RHEUMATOID ARTHRITIS

Background

Rheumatologists recommend vaccination in rheumatoid arthritis (RA) and axial spondyloarthritis (axSpA) patients, but there are few studies on the occurrence of adverse events (AEs), particularly worsening disease related activity and unrelated immune reactions in these groups.

Objectives

To evaluate the uptake of COVID vaccination in RA and axSpA patients, compare the frequency of AEs, and identify risk factors associated with vaccine AEs in two prospective cohorts comprised of these patients.

Methods

The IMPACT study is a monthly survey of two prospective cohorts of established RA and axSpA patients in northern Alberta, Canada from November 2020-2021 who answered at least one or more Redcap surveys through de-identified email link surveying demographics, disease characteristics, COVID symptoms, treatment of RA and axSpA, health care utilization, vaccination status, vaccine AEs and use of cannabis. Univariate analyses evaluated independent variables associated with the dependent variables of (1) any AE, (2) any severe AE, (3) any arthritis flare, and (4) any severe arthritis flare, followed by multivariate analyses of these four dependant variables using all clinically relevant variables from the univariate analysis.

Results

773/2167 patients (RA 574, axSpA 197) responded to at least one survey. 32/663 (5%) were single vaccinated, 631 (95%) double vaccinated and 230 (54%) triple vaccinated with 80% receiving Pfizer, 24% Moderna, 28% AstraZeneca and 30% “other”. 456 (69%) reported at least one AE (Figure 1) with 21 (3%) patients seeing a physician for their AE. Increased age was associated with all AEs. RA patients had lower reported AEs versus axSpA patients for all AE definitions except for severe arthritis flares. Generally, males reported worse AEs (Table 1). “Any arthritis flare” was lower in patients reporting cannabis use.

Table 1.

Summary of Multivariate Level Mixed-Effect Logistic Regression Models Evaluating the IMPACT of RA and axSpA Disease Characteristics on Vaccine AEs

VariableAny Adverse EventOR (95 % CI) p valueSevere Adverse Event* OR 95 % CI) p valueAny Arthritis Flare or Joint Ache Adverse Event OR (95 % CI) p valueAny Severe Arthritis Flare or Joint Ache* OR (95 % CI) p valueGenderMale1.47 (0.89 – 2.43)p=0.132.10 (1.30-3.41)p=0.0032.05 (1.20 – 3.50) p=0.013.97 (1.84 – 8.57)p=0.0004FemaleAge1.06 (1.04 – 1.08)p<0.011.05 (1.03 – 1.06)p<0.011.03 (1.01 – 1.04)p=0.0031.03 (1.01 – 1.06)p=0.004Rheumatic Disease TypeRA0.42 (0.23 – 0.76)p=0.050.55 (0.31 – 0.98)p=0.040.52 (0.28 – 0.98)p=0.040.78 (0.34 – 1.78)p=0.55axSpASteroidsYes0.85 (0.40 – 1.83) P=0.680.66 (0.32 – 1.35) p=0.250.84 (0.36 – 1.95) p=0.690.38 (0.15 – 0.97)p=0.04NoNSAIDSYes1.11 (0.81 – 1.52) p=0.511.03 (0.75 – 1.41)p=0.861.05 (0.74 – 1.48)p=0.801.17 (0.73 – 1.89)p=0.52NoCurrent Disease Activity0.95 (0.88 – 1.03) p=0.230.90 (0.83 – 0.97)p=0.190.92 (0.85 – 1.00)p=0.060.82 (0.74 – 0.92)p=0.001HAQ1.08 (0.73 – 1.61) p=0.700.77 (0.52 – 1.14)p=0.010.74 (0.48 – 1.13)p=0.170.65 (0.38 – 1.11)p=0.12Nicotine productsYes1.33 (0.75 – 2.37) p=0.341.42 (0.80 – 2.52)p=0.241.15 (0.60 – 2.01)p=0.760.97 (0.43 – 2.17)p=0.94NoCannabis productsYes0.78 (0.49 – 1.25) p=0.300.87 (0.55 – 1.38)p=0.550.51 (0.31 – 0.83)p=0.070.66 (0.35 – 1.26)p=0.21NoDMARDsYes1.98 (1.28 – 3.06)p=0.0021.52 (1.01 – 2.28)p=0.051.43 (0.91 – 2.23) p=0.121.86 (1.03 – 3.36)p=0.04NoBiologic DMARDYes0.72 (0.42 – 1.25) p=0.240.79 (0.45 – 1.41) p=0.431.20 (0.66 – 2.18 p=0.541.39 (0.63 – 3.08)p=0.42No

*Severe = Any of the following: ranked moderate to severe and/or lasting more than 7 days and/or saw physician

Conclusion

RA and axSpA patients showed high uptake of COVID vaccination with largely minor AEs. Older age and male gender were associated with more general and arthritis specific AEs. The association of any AE and/or arthritis-specific AEs in SpA versus RA patients is a novel finding which may correlate with the male predominance of SpA. The association of cannabis with fewer arthritis AEs may reflect the nociceptive properties of cannabis.

Acknowledgements

Epidemiology Coordinating and Research (EPICORE) Centre provided support for the REDCAP survey and biostatistical analyses.

Disclosure of Interests

Stephanie Keeling Speakers bureau: Pfizer, Abbvie, GSK, UCB, Consultant of: Abbvie, GSK, UCB, AstraZeneca, Sandoz, Pfizer, Grant/research support from: Abbvie, Sandoz, Merck, UCB, Bo Pan: None declared, Edna Hutchings Shareholder of: BMS, Stephanie Wichuk: None declared, Mohammed Osman Speakers bureau: Boehringer Ingelheim, Takeda Pharmaceuticals, Grant/research support from: Boehringer Ingelheim and CSL-Behring, Ameeta Singh: None declared, Ashlesha Sonpar Speakers bureau: Novartis, Ilan Swartz: None declared, Walter P Maksymowych Speakers bureau: Abbvie, Janssen, Novartis, Pfizer, UCB, Consultant of: Abbvie, Boehringer Ingelheim, Celegene, Eli-Lilly, Galapagos, Novartis, Pfizer, UCB, Grant/research support from: Abbvie, Novartis, Pfizer, UCB

POS1258 LESS THAN EXPECTED IMPACT OF RHEUMATOID ARTHRITIS AND AXIAL SPONDYLOARTHRITIS DISEASE ON COVID SEVERITY

Background

Throughout the pandemic, there has been ongoing concern that people with autoimmune diseases such as rheumatoid arthritis (RA) and axial spondyloarthritis (axSpA) will have more severe COVID-19 disease due to immune dysfunction associated with autoimmune diseases and their treatment.

Objectives

We aimed to compare the severity of COVID-19 in patients with RA versus axSpA and characterize the predictors of COVID-19 severity during the pre-Omicron pandemic phases.

Methods

The IMPACT (IMPact of inflammatory Arthritis on COVID Outcomes STudy) study is a monthly survey of two established northern Alberta, Canada prospective cohorts of RA and axSpA patients from November 2020-2021 who answered Redcap surveys through de-identified email link surveying patient demographics, disease characteristics, COVID-19 symptoms, treatment of RA and axSpA, health care utilization, vaccination status and vaccine adverse events. Descriptive and univariate analyses (dependent variable = severe COVID-19) were performed followed by multivariate analyses of all significant and clinically relevant independent variables from the univariate analysis. Infection severity was defined as any patient with COVID-19 symptoms who visited a doctor, ER or required hospital admission.

Results

773 of 2167 (36%) patients (RA n=574, axSpA n=197) registered in both cohorts answered at least one baseline survey, 28 (4%) reporting positive COVID-19 tests (24 positive once). Of 442 reporting COVID-19 symptoms during the survey, 11 (3%) were admitted for a mean of 4 days, 2 requiring ICU or blood clot treatment and 1 requiring advanced therapy. 116 (26%) visited a physician for Covid symptoms. Univariate analysis showed that the use of steroids, NSAIDs and increased disease activity were associated with having less severe infection but these associations were not significant in the multivariate analysis (Table 1). There were no significant impacts of RA vs axSpA, age, gender, treatment, disease activity, or smoking.

Table 1.

Multivariate Level Mixed-Effect Logistic Regression Model: IMPACT of RA and axSpA Disease Characteristics on COVID Infection Severity Defined as Patients with COVID Symptoms Requiring Visit to Doctor, Emergency Room and/or Hospital Admission.

VariableCoefficient (S.E)Odds Ratio (95 % Confidence Interval)P-valueGenderMale0.17 (0.34)1.18 (0.61 – 2.31)0.6193FemaleReferenceAge-0.01 (0.01)0.99 (0.97 – 1.01)0.2543Rheumatic Disease TypeRA0.18 (0.40)1.20 (0.58 – 2.48)0.6213SpAReferenceSteroidsYes-0.40 (0.56)0.67 (0.23 – 2.01)0.4757NoReferenceNSAIDSYes-0.20 (0.26)0.82 (0.49 – 1.37)0.4508NoReferenceCurrent Disease Activity-0.04 (0.06)0.96 (0.85 – 1.09)0.5275HAQ-0.03 (0.29)0.97 (0.55 – 1.70)0.9041Nicotine productsYes-0.67 (0.37)0.51 (0.25 – 1.06)0.0714NoReferenceCannabis productsYes-0.45 (0.31)0.64 (0.35 – 1.18)0.1510NoReferenceDMARDsYes0.26 (0.30)1.30 (0.72 – 2.35)0.3860NoReferenceBiologic DMARDYes-0.46 (0.43)0.63 (0.27 – 1.46)0.2813NoReference

Conclusion

Possible disease related risk factors for increased COVID-19 severity in RA and axSpA patients preceding the onset of the Omicron variant including use of steroids or DMARDs were not associated with severe infection. These findings are consistent with other international studies whereby other non-rheumatic disease comorbidities played a greater role in infection severity.

Acknowledgements

Epidemiology Coordinating and Research (EPICORE) Centre provided support for the REDCAP survey and biostatistical anayses.

Disclosure of Interests

Stephanie Keeling Speakers bureau: Abbvie, GSK, Pfizer, UCB, Consultant of: Abbvie, GSK, Pfizer, Sandoz, UCB, Eli-Lilly, Galapagos, Novartis, Grant/research support from: Abbvie, UCB, Sandoz, Pfizer, Merck, Bo Pan: None declared, Edna Hutchings Shareholder of: BMS, Stephanie Wichuk: None declared, Mohammed Osman Speakers bureau: Boehringer Ingelheim, Takeda Pharmaceuticals, Grant/research support from: Yes, Boehringer Ingelheim and CSL-Behring, Ameeta Singh: None declared, Ashlesha Sonpar Speakers bureau: Novartis, Ilan Swartz: None declared, Walter P Maksymowych Speakers bureau: Abbvie, Janssen, Novartis, Pfizer, UCB

, Consultant of: Abbvie, Boehringer Ingelheim, Celegene, Eli-Lilly, Galapagos, Novartis, Pfizer, UCB, Grant/research support from: Abbvie, Novartis, Pfizer, UCB

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

BACKGROUND

Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS.

RESULTS

To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when > 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30×.

CONCLUSIONS

Our findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS.

Hidden biases in germline structural variant detection

BACKGROUND

Genomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging.

RESULTS

In this study, DNA from a Chinese family quartet is sequenced at three different sequencing centers in triplicate. A total of 288 derivative data sets are generated utilizing different analysis pipelines and compared to identify sources of analytical variability. Mapping methods provide the major contribution to variability, followed by sequencing centers and replicates. Interestingly, SV supported by only one center or replicate often represent true positives with 47.02% and 45.44% overlapping the long-read SV call set, respectively. This is consistent with an overall higher false negative rate for SV calling in centers and replicates compared to mappers (15.72%). Finally, we observe that the SV calling variability also persists in a genotyping approach, indicating the impact of the underlying sequencing and preparation approaches.

CONCLUSIONS

This study provides the first detailed insights into the sources of variability in SV identification from next-generation sequencing and highlights remaining challenges in SV calling for large cohorts. We further give recommendations on how to reduce SV calling variability and the choice of alignment methodology.

Mutagenicity of silver nanoparticles evaluated using whole-genome sequencing in mouse lymphoma cells

The increasing medical and food applications of silver nanoparticles (AgNPs) raise concerns about their safety, including the potential health consequences of human exposure. Previous studies found that AgNPs were negative in the Ames test due to both their microbicidal activity and the inability of nanoparticles to penetrate bacterial cell walls. Thus, the mutagenicity of AgNPs is still not completely clear, though they do induce chromosome damage, as suggested by many previous genotoxicity studies. In this study, whole-genome sequencing (WGS) was used to analyze the mutagenicity of AgNPs in mouse lymphoma cells expanded from single-cell clones. The cells were treated with AgNPs, 4-nitroquinolone-1-oxide (4-NQO) as the positive control, and vehicle controls. Both AgNPs and 4-NQO significantly increased mutation frequencies over their concurrent controls by 1.12-fold and 4.89-fold with mutation rates at 4-fold and 130-fold, respectively. AgNP-induced mutations mainly occurred at G:C sites with G:C > T:A transversions, G:C > A:T transitions, and deletions as the most commonly observed mutations. AgNPs also induced higher fold changes in tandem mutations. The results suggest that the WGS mutation assay conducted here can detect the low-level mutagenicity of AgNPs, providing substantial support for the use of the WGS method as a possible alternative assay with respect to the mutagenic assessment of nanomaterials.

Elucidating Interactions Between SARS-CoV-2 Trimeric Spike Protein and ACE2 Using Homology Modeling and Molecular Dynamics Simulations

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). As of October 21, 2020, more than 41.4 million confirmed cases and 1.1 million deaths have been reported. Thus, it is immensely important to develop drugs and vaccines to combat COVID-19. The spike protein present on the outer surface of the virion plays a major role in viral infection by binding to receptor proteins present on the outer membrane of host cells, triggering membrane fusion and internalization, which enables release of viral ssRNA into the host cell. Understanding the interactions between the SARS-CoV-2 trimeric spike protein and its host cell receptor protein, angiotensin converting enzyme 2 (ACE2), is important for developing drugs and vaccines to prevent and treat COVID-19. Several crystal structures of partial and mutant SARS-CoV-2 spike proteins have been reported; however, an atomistic structure of the wild-type SARS-CoV-2 trimeric spike protein complexed with ACE2 is not yet available. Therefore, in our study, homology modeling was used to build the trimeric form of the spike protein complexed with human ACE2, followed by all-atom molecular dynamics simulations to elucidate interactions at the interface between the spike protein and ACE2. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) and in silico alanine scanning were employed to characterize the interacting residues at the interface. Twenty interacting residues in the spike protein were identified that are likely to be responsible for tightly binding to ACE2, of which five residues (Val445, Thr478, Gly485, Phe490, and Ser494) were not reported in the crystal structure of the truncated spike protein receptor binding domain (RBD) complexed with ACE2. These data indicate that the interactions between ACE2 and the tertiary structure of the full-length spike protein trimer are different from those between ACE2 and the truncated monomer of the spike protein RBD. These findings could facilitate the development of drugs and vaccines to prevent SARS-CoV-2 infection and combat COVID-19.

VENTHEART is required for cardiomyocyte specification and function

Background

Long noncoding RNAs (lncRNAs) control early stages of cardiac differentiation, however their role in later specification and maturation is still not well explored.

Methods and results

We performed single cell RNA-seq for 2, 6 and 12 week-old hESC-CM. Weighted correlation network analysis (WGCNA) identified core genes significantly upregulated, along with a subset of lncRNAs. Importantly, these lncRNAs are highly abundant and unique to human heart. Through independent integrative analysis of genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL) data using human hearts, we also identified a long intergenic noncoding RNA (we call VENTHEART, VHRT) as co-regulated with core cardiac contractile genes, and strongly associated with heart failure. VHRT was highly expressed in MYL2+ hESC-CMs in our single cell dataset, and its locus is antisense and downstream of MYL2. VHRT knockdown (KD) in 6-weeks old hESC-CMs downregulated MYL2 and other key cardiac genes. Patch clamp recordings with VHRT KD cells showed a loss of the ventricular-like action potential. Concordantly, CRISPR-mediated excision of the VHRT locus led to impaired CM sarcomere formation, and loss of CM specification gene programs. VHRT transcript replacement in VHRT-KO cells was however insufficient to rescue the phenotype. Instead, we established by 3C assay, that the VHRT locus loops and interacts with the MYL2 promoter, bearing histone marks characteristic of a super-enhancer.

Conclusion

Thus, we conclude that both the VHRT lncRNA transcript and its genomic locus are required for proper CM specification and function, and may play a role in heart failure progression.

Funding Acknowledgement

Type of funding source: Other. Main funding source(s): EMBO, Singapore National Research Council

Development of a Nicotinic Acetylcholine Receptor nAChR α7 Binding Activity Prediction Model

Despite the well-known adverse health effects associated with tobacco use, addiction to nicotine found in tobacco products causes difficulty in quitting among users. Nicotinic acetylcholine receptors (nAChRs) are the physiological targets of nicotine and facilitate addiction to tobacco products. The nAChR-α7 subtype plays an important role in addiction; therefore, predicting the binding activity of tobacco constituents to nAChR-α7 is an important component for assessing addictive potential of tobacco constituents. We developed an α7 binding activity prediction model based on a large training data set of 843 chemicals with human α7 binding activity data extracted from PubChem and ChEMBL. The model was tested using 1215 chemicals with rat α7 binding activity data from the same databases. Based on the competitive docking results, the docking scores were partitioned to the key residues that play important roles in the receptor-ligand binding. A decision forest was used to train the human α7 binding activity prediction model based on the partition of docking scores. Five-fold cross validations were conducted to estimate the performance of the decision forest models. The developed model was used to predict the potential human α7 binding activity for 5275 tobacco constituents. The human α7 binding activity data for 84 of the 5275 tobacco constituents were experimentally measured to confirm and empirically validate the prediction results. The prediction accuracy, sensitivity, and specificity were 64.3, 40.0, and 81.6%, respectively. The developed prediction model of human α7 may be a useful tool for high-throughput screening of potential addictive tobacco constituents.

Persistent Organic Pollutants in Food: Contamination Sources, Health Effects and Detection Methods

Persistent organic pollutants (POPs) present in foods have been a major concern for food safety due to their persistence and toxic effects. To ensure food safety and protect human health from POPs, it is critical to achieve a better understanding of POP pathways into food and develop strategies to reduce human exposure. POPs could present in food in the raw stages, transferred from the environment or artificially introduced during food preparation steps. Exposure to these pollutants may cause various health problems such as endocrine disruption, cardiovascular diseases, cancers, diabetes, birth defects, and dysfunctional immune and reproductive systems. This review describes potential sources of POP food contamination, analytical approaches to measure POP levels in food and efforts to control food contamination with POPs.

Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38

After publication of this supplement article.

Elevated aspartate aminotransferase and monocyte counts predict unfavorable prognosis in patients with malignant pleural mesothelioma

Limited biomarkers predicting prognosis of malignant pleural mesothelioma (MPM) have been identified. The present study aims to assess potential laboratory prognostic factors of MPM. We retrospectively reviewed the clinical data of 105 patients with MPM. The overall survival and prognostic factors were assessed by Kaplan-Meier curves and Cox regression analysis. A receiver operating characteristic (ROC) curve analysis was performed to determine the optimal cut-off values. The mean age of the 105 patients (62 men, 43 women) was 56.0 years. The major clinical presentations were dyspnea, cough and chest pain. The most common laboratory abnormalities were thrombocytosis and elevated monocyte count. Significant prognostic factors on univariate analysis were performance status (PS), serum albumin, aspartate aminotransferase (AST), lactate dehydrogenase (LDH), alkaline phosphatase (ALP), monocyte, platelet to lymphocyte ratio (PLR), lymphocyte to monocyte ratio (LMR) and treatment strategy. Multivariate analysis showed PS, AST, monocyte, and treatment strategy were statistically significant (p<0.05). Higher AST level and monocyte count were both related to the presence of anemia (p=0.001 and 0.010, respectively) and higher ALP level (p=0.049 and 0.001, respectively). A higher AST level was also associated with higher alanine aminotransferase (ALT) and LDH level (p<0.05). A higher monocyte count was also correlated with male patients, higher white blood cell (WBC), platelet, neutrophil counts, lower red blood cell (RBC) and LMR counts (p<0.05). In conclusion, our data show that PS<2, normal AST level, lower monocyte count, and multimodality treatment are independent positive prognostic factors of MPM. The elevated AST and monocyte levels represent unfavorable prognostic biomarkers of MPM.

Similarities and differences between variants called with human reference genome HG19 or HG38

Background

Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: HG19 or HG38. To date, the impact of genome version on SNV identification has not been rigorously assessed.

Methods

We conducted analysis comparing the SNVs identified based on HG19 vs HG38, leveraging whole genome sequencing (WGS) data from the genome-in-a-bottle (GIAB) project. First, SNVs were called using 26 different bioinformatics pipelines with either HG19 or HG38. Next, two tools were used to convert the called SNVs between HG19 and HG38. Lastly we calculated conversion rates, analyzed discordant rates between SNVs called with HG19 or HG38, and characterized the discordant SNVs.

Results

The conversion rates from HG38 to HG19 (average 95%) were lower than the conversion rates from HG19 to HG38 (average 99%). The conversion rates varied slightly among the various calling pipelines. Around 1.5% SNVs were discordantly converted between HG19 or HG38. The conversions from HG38 to HG19 had more SNVs which failed conversion and more discordant SNVs than the opposite conversion (HG19 to HG38). Most of the discordant SNVs had low read depth, were low confidence SNVs as defined by GIAB, and/or were predominated by G/C alleles (52% observed versus 42% expected).

Conclusion

A significant number of SNVs could not be converted between HG19 and HG38. Based on careful review of our comparisons, we recommend HG38 (the newer version) for NGS SNV analysis. To summarize, our findings suggest caution when translating identified SNVs between different versions of the human reference genome.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2620-0) contains supplementary material, which is available to authorized users.

Abstract P1-03-05: Long term survival and tumor biology of screen-detected small non-palpable breast cancer in Chinese women: The smaller, the better?

Background: Tumor biology would reflect the prognosis and potentially the lead time and over-diagnosis rate of screen-detected small breast cancer [PMID: 28591529, 21452022 and 24888816]. Chinese women had earlier peak age of breast cancer incidence and used ultrasound as the primary screening imaging test on a hospital-basis [2016 SABCS P5-02-05, PMID: 27689334]. In our previous work, we showed that US detected non-palpable breast cancer (NPBC) had higher percentage of invasive and lymph node positive cancer, yet still could be regarded as low-risk cancer [PMID:27689334, 28412736]. This study was performed to investigate the prognostic impact of immunohistochemical subtypes and tumor size: the smaller the NPBC, the better the tumor biology and prognosis?

Methods: From January 2001 to December 2017, 6,423 consecutive asymptomatic women underwent mammography (MG) or ultrasound (US) guided biopsy in Peking Union Medical College Hospital. Among them, 159 T1a, 239 T1b, 377 T1c and 72 T2 NPBC were diagnosed and treated. The clinicopathological features, treatment choice, 10-year disease-free survival (DFS) and overall survival (OS) of the small NPBC (defined as≤1.0cm, T1a+b) were reviewed and compared with T1c and T2 NPBC. Prognostic factors of these subgroups of invasive NPBC were identified.

Results: Compared to big NPBC, the T1a+b small NPBC showed more lymph node negative (p&lt;0.001) and low Ki67 (&lt;14%, p&lt;0.001) cancers with earlier TNM stage (p&lt;0.001), more luminal A subtype (p=0.003) and significantly improved 10-year DFS and OS (p=0.004). T1c+T2 NPBC had more triple-negative subtype and received more chemotherapy (p&lt;0.001) and targeted therapy (p=0.008). Breast conserving rate and the use of radiation and endocrine therapy showed no significant difference.

Table 1.Comparison of clinicopathological factors and long term survival of small vs big screen-detected NPBCScreen-detected NPBC(2001-2017    Clinical&prognostic factors T1a+T1b(n=398)T1c+T2(n=449)P valueScreening methodUS-NPBC(n,%)336(84.4)406(90.4)0.008 MG-NPBC(n,%)62(15.6)43(9.6) Lymph node statusNegative(n,%)343(86.2)315(70.2)&lt;0.001 Positive(n,%)55(13.8)134(29.8) TNM stageI(n,%)344(86.4)277(61.7)&lt;0.001 II(n,%)37(9.3)134(29.8)  III(n,%)17(4.3)38(8.5) Ki67&lt;14%(n,%)208(52.2)168(37.4)&lt;0.001 ≥14%(n,%)183(46.0)274(61.0) SubtypeLuminal A(n,%)164(41.3)135(30.1)0.003 Luminal B(n,%)155(38.9)218(48.6)  Her2(n,%)28(7.0)27(6.0)  TNBC(n,%)31(7.8)52(11.6)  Unknown(n,%)20(5.0)17(3.7) 10-year survivalDFS(%)94.688.80.004 OS(%)100.096.4 

Conclusion: Small asymptomatic NPBCs were detected when small because they were good in terms of low Ki67 index, favorable subtype, tumor biology and long term prognosis. On the contrary, T1c and T2 NPBCs were screened when already big or even with positive nodes without clinical symptoms indicating that they might have larger chance of becoming interval cancers.

Citation Format: Xu Y, Pan B, Yao R, Zhou Y-D, Mao F, Zhu Q-L, Wu H-W, Lin Y, Shen S-j, Sun Q. Long term survival and tumor biology of screen-detected small non-palpable breast cancer in Chinese women: The smaller, the better? [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 P1-03-05.

Abstract P2-14-30: Survival outcomes of breast conserving surgery versus mastectomy for ultrasound detected non-palpable breast cancer in hospital-based screening among Chinese women

Background: Some population-base studies have reported similar or improved survival for breast-conserving surgery (BCS) plus radiotherapy compared with mastectomy (Mx) in early breast cancer [PMID: 22373563, 27344114]. Among the screening detected early breast cancer, ultrasound (US) could detect more invasive non-palpable breast cancer (NPBC) with positive lymph nodes in hospital-based asymptomatic Chinese women, who could achieve comparable 10-year DFS and OS as mammography (MG)-detected NPBC [2016 SABCS P5-02-05, PMID: 27689334]. However, there is little data about the surgical outcomes of BCS verse Mx in the low-risk screening detected NPBC with US as the initial imaging test.

Methods: From 2001 to 2017, 6,423 consecutive asymptomatic women underwent mammography or ultrasound guided biopsy in Peking Union Medical College Hospital. Among them, 1130 NPBC including 914 US-detected and 216 MG-detected NPBC were diagnosed and treated. There were 349 (30.9%) patients underwent BCS including 286 (25.3%) patients received radiation therapy and 63 (5.6%) elderly patients (&gt;70 years) who did not. The clinicopathological features, treatment choice, 10-year disease-free survival (DFS) and overall survival (OS) were compared between breast conservingsurgery (BCS) versus mastectomy(Mx) in all NPBC and between the US-detected and MG-detected NPBC.

Result: Compared to those who received BCS, the 781 (69.1%) patients who underwent Mx had more cancers with relatively higher histologic grade (p=0.003), positive lymph node (18.8% vs 12.0%, p=0.005), ER-negative (22.5% vs 11.5%, p&lt;0.001), PR-negative (29.6% vs 16.3, p&lt;0.001), Her2-positive (16.3% vs 8.9%, p=0.001), and received chemotherapy (37.6% vs 28.7%, p=0.003). The breast conserving rates of US-NPBCwere higher than that of MG-NPBC (32.6% vs 23.6%, p=0.010), but the breast conserving rates were similar between ductal carcinoma in situ (DCIS) and invasive cancers. The 10-year DFS and OS were similar among BCS with radiation therapy, BCS without radiation therapy and Mx as well as among US-NPBC with BCS, US-NPBC with Mx, MG-NPBC with BCS and MG-NPBC with Mx. However, MG-NPBC with Mx had favorable 10-year DFS than that of MG-NPBC with BCS (p=0.041).

Table 1.Kaplan-Meier estimated 10-year DFS and OS of all NPBC§Patients (No.)NPBC GroupNumber (%)10-year DFS (%)P value10-year OSP valueAll NPBC (1130)BCS without Radiotherapy63 (5.6)85.00.10592.30.722 BCS with Radiotherapy286 (25.3)92.7 99.5  Mastectomy781 (69.1)93.2 98.7        All NPBC (1130)US+BCS298 (26.4)90.40.24896.30.542 US+Mx616 (64.5)92.4 98.4  MG+BCS51 (4.5)90.3 100.0  MG+Mx165 (14.6)96.1 100.0 § Kaplan-Meier survival curves would be displayed in the poster.

Conclusion: The 10-year DFS and OS of breast conserving surgery versus mastectomy were similar among all NPBC patients. As the current initial imaging test, US-detected NPBC patients would receive significantly more BCS compared to MG. There was no significant difference in surgical outcomes among BCS and Mx in US-detected NPBC. However, among MG-detected NPBC, patients with Mx reached a better DFS but a similar OS than those with BCS. The radiation therapy could be safely omitted in the elderly patients (&gt;70 years) with NPBC.

Citation Format: Yao R, Pan B, Xu Y, Zhou Y, Zhu Q, Zhang J, Wu H, Mao F, Lin Y, Shen S, Sun Q. Survival outcomes of breast conserving surgery versus mastectomy for ultrasound detected non-palpable breast cancer in hospital-based screening among Chinese women [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 P2-14-30.

Abstract P1-03-06: Risk stratification by ultrasound for screen-detected non-palpable breast cancer in Chinese women: Regular low risk versus ultra-low risk?

Background: Mammography (MG) screen-detected breast cancer has been established as low-risk in the western world. However, ultrasound (US) is currently the 'real-world' initial imaging test for breast cancer in China. In our previous work, we firstly showed with a multi-center randomized controlled trial that US could detect breast cancer with improved sensitivity and accuracy in high risk Chinese women [PMID: 25668012]. Then we demonstrated on a hospital-screening basis that US and MG detected non-palpable breast cancer (NPBC) had similar survival [2016 SABCS P5-02-05, PMID: 27689334]. This study was performed to test the hypothesis [Hypothesis would be published in the journal of Medical Hypothesis, 118 (2018):9-12] whether MG+/US- NPBC could be taken as ultra-low risk cancer which had more favorable clinical characteristics and survival than the regular low-risk NPBC.

Methods: From 2015-2017, 1,478 consecutive patients received biopsy with initial positive screening US (BI-RADS 4 and 5) at Peking Union Medical College Hospital. Among them, 206 US+/MG- and 135 US+/MG+ NPBC were diagnosed. Meanwhile, 371 patients who had negative initial screening US (BI-RADS 1, 2 and 3) and positive additional MG (BI-RADS 4 and 5) underwent MG-guided biopsies, and 88 MG+/US- NPBC were diagnosed. Clinical characteristics, treatment and 3-year disease free survival (DFS) and overall survival (OS) were analyzed and compared. Prognostic factors were identified.

Results: There was no significant difference in age, lymph node status, hormone receptor status, endocrine therapy, chemotherapy, targeted-therapy among the three subgroups of NPBC. MG detected significantly more ductal carcinoma in situ (DCIS, 59.1% vs 22.8% and 28.1%, p&lt;0.001) whereas ultrasound diagnosed more invasive cancers (77.2% and 71.9% vs 40.9%, p&lt;0.001), multifocal cancer (p=0.020) and patients who received breast-conserving surgery (p&lt;0.001) and needed radiotherapy (P=0.001). No significant difference was found for 3-year DFS and 3-year OS were all 100%, although MG+/US- NPBC showed a trend of better DFS.

Table 1.Comparison of positive predictive value (PPV), pathology and prognosis of US+/MG-, US+/MG+ and MG+/US- NPBCPathologyRadiology (2015-2017)US-detected NPBL (N=1,478)US-detected NPBL(N=1,478)MG-detected NPBL (N=371)MG & US positivityUS+/MG- (N=1,108)US+/MG+ (N=370)MG+/US- (N=371)Imaging presentationNoduleNodule + micro-calcificationsMicro-calcificationsBreast cancer (PPV %)206 (18.6%)135 (36.5%)88 (23.7%)Pathology (p&lt;0.001)   DCIS (%)47 (22.8)38 (28.1)52 (59.1)Invasive (%)159 (77.2)97 (71.9)36 (40.9)3-Year survival   DFS (%)92.391.196.5OS (%)100.0100.0100.0

Conclusion: MG+/US- NPBC had satisfactory prognosis, higher percentage of DCIS and might be taken as 'ultra-low risk' cancer. Hence US had the potential of stratifying the screen-detected NPBC into regular low risk (US+/MG+ and US+/MG-) and ultra-low risk (MG+/US-).

Citation Format: Xu Y, Pan B, Yao R, Zhou Y-d, Mao F, Zhu Q-L, Zhang J, Lin Y, Shen S-j, Sun Q. Risk stratification by ultrasound for screen-detected non-palpable breast cancer in Chinese women: Regular low risk versus ultra-low risk? [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 P1-03-06.

Abstract P1-02-02: Is ultrasound screening justified for non-palpable breast cancer in asymptomatic Chinese women: A real-world study based on long-term survival of consecutive cohort (2001-2017)

Background: Ultrasound (US) is an effective initial screening test for breast cancer both in Caucasian and Chinese women [PMID: 26712110, 26715161, and 25668012]. The real-world modality of breast cancer screening in the China is hospital-based screening among asymptomatic self-referred women. In our previous study, we showed that US and mammography (MG) detected non-palpable breast cancer (NPBC) had similar long-term survival and that US detected more invasive NPBC with positive lymph node [2016 SABCS P5-02-05, PMID: 27689334]. This study was to investigate whether these findings would be still true with more NPBC cases included and longer follow-up in the consecutive hospital cohort.

Methods: From 2001 to 2017, 5,264 asymptomatic women with positive (BI-RADS 4 and 5) initial screening US underwent biopsies in PUMC Hospital, and 914 US-NPBC in 883 women were diagnosed. Meanwhile, women without dense breasts (defined as BI-RADS category C and D) also received screening MG after physical examination and US. There were 1,159 patients with positive (BI-RADS 4 and 5) MG and normal US (BI-RADS 1, 2 and 3) underwent MG-guided biopsies and 216 MG-NPBC were diagnosed in 214 women. The clinicopathological characteristics and 10-year disease-free survival (DFS) and overall survival (OS) were reviewed and compared between the US-NPBC and MG-NPBC. Prognostic factors of NPBC were identified by univariate and multivariate Cox analysis.

Result: Compared to MG, US could detect more invasive (81.2% vs 48.6%, p&lt;0.001), lymph node positive (18.3% vs 10.2%, p&lt;0.001), stage II+III (21.7% vs 12.5%, p&lt;0.001) and low grade cancer (p=0.001).Between invasive US-NPBC and MG-NPBC, no significant difference was identified for lymph node status, TNM stage or subtype.US-NPBC received more breast conserving surgery (32.6% vs 24.1%, p&lt;0.001) and chemotherapy (37.5% vs 23.6%, p&lt;0.001). There was no significant difference in DFS or OS between US- vs MG-NPBC among ductal carcinoma in situ (DCIS), invasive and all NPBC. For the US-NPBC, the DFS factors included TNM stage and Hormone receptor status whereas OS-predictors were pN and subtype.

Table 1.Kaplan-Meier estimates of DFS and OS between US-NPBC and MG-NPBC§Patients (No.) 10-year DFS (%)P value10-year OS (%)P valueAllUS-NPBC (914)92.40.57098.20.143 MG-NPBC (216)94.7 100.0 DCISUS-NPBC (172)97.70.170100.0- MG-NBPC (111)95.3 100.0 InvasiveUS-NPBC (742)91.20.45897.90.251 MG-NPBC (105)94.4 100.0 § Kaplan-Meier survival curves between each two subgroups would be displayed in the poster.

Conclusion: Overall, US could detect more invasive NPBC patients with positive lymph node and advanced stage compared to MG, and screen invasive NPBC at similar TNM stage and subtype distribution as MG. US-NPBC patients received more breast conserving surgery and chemotherapy, and could achieve comparable 10-year DFS and OS as MG-detected NPBC. Hence US is justified in the real-world as the initial imaging modality in hospital-based screening Chinese women.

Citation Format: Yao R, Pan B, Xu Y, Zhou Y, Zhu Q, Zhang J, Wu H, Mao F, Lin Y, Shen S, Sun Q. Is ultrasound screening justified for non-palpable breast cancer in asymptomatic Chinese women: A real-world study based on long-term survival of consecutive cohort (2001-2017) [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 P1-02-02.

Draft genome of the cotton aphid Aphis gossypii

The cotton aphid Aphis gossypii Glover is a worldwide agricultural pest that feeds on cotton, melon, and other landscape plants, causing a high level of economic loss. In addition to the common characteristics shared with other aphids, Ap. gossypii has evolved multiple biotypes that present substantial differences in host adaption. These intriguing biological features are of interest from both a fundamental and applied perspective. However, the molecular studies of Ap. gossypii have been restrained by the lack of a reference genome. Furthermore, in order to establish a platform for the development of novel and sustainable control methods, it is necessary to generate genomic resources for Ap. gossypii. Here, we present a 294 Mb draft genome sequence of Ap. gossypii, which consists of 4,724 scaffolds with an N50 size of 438 kb. Compared to other aphid species with published genomes, Ap. gossypii presents the most compact genome size. A total of 14,694 protein-coding genes were predicted and annotated in the consensus gene set, 98.03% of CEGMA genes and 93.5% of BUSCO genes were captured respectively. Genome-wide selection analyses revealed that significantly evolving pathways in the genus Aphis are related to biological processes of detoxification, steroid biosynthesis, and ethylbenzene degradation. The acquisition of the genome of Ap. gossypii makes it possible to understand the molecular mechanism of intricate biological traits of this species, and will further facilitate the study of aphid evolution.

Computational prediction models for assessing endocrine disrupting potential of chemicals

Endocrine disrupting chemicals (EDCs) mimic natural hormones and disrupt endocrine function. Humans and wildlife are exposed to EDCs might alter endocrine functions through various mechanisms and lead to an adverse effects. Hence, EDCs identification is important to protect the ecosystem and to promote the public health. Leveraging in-vitro and in-vivo experiments to identify potential EDCs is time consuming and expensive. Hence, quantitative structure-activity relationship is applied to screen the potential EDCs. Here, we summarize the predictive models developed using various algorithms to forecast the binding activity of chemicals to the estrogen and androgen receptors, alpha-fetoprotein, and sex hormone binding globulin.

[The role of IL-22 in T cell reconstitution after thymus damage induced by ionizing radiation]

Objective: To explore the levels of IL-22 in thymus damaged by γ-ray total body irradiation (TBI), and to study the role of IL-22 in T cell reconstitution after thymic injury induced by TBI. Methods: To induce thymic injury, mice were treated by sub-lethal TBI. Levels of intra-thymic and circulatory IL-22 were detected by using ELISA assay. Untreated mice were used as control. After receiving sub-lethal TBI, mice were intraperitoneally injected with PBS or recombinant mouse IL-22, which were marked as TBI+PBS or TBI+IL-22, respectively. Mice were monitored for counts of total thymic cells and circulatory white blood cells. Flow cytometry was applied to analyze percentages of thymic epithelial cells (TEC), thymocyte subsets and circulatory T cells. Real-time PCR assay was applied to analyze the mRNA expression levels of Foxn1, Ccl25, Aire and Dll4 in thymus. Results: ①Sub-lethal TBI treated mice expressed higher levels of intra-thymic and circulatory IL-22, compared with untreated ones (all P<0.05). ②After injection of recombinant IL-22, TBI+IL-22 mice had higher levels of intra-thymic IL-22 than TBI+PBS mice (all P<0.05). ③On day 14 after irradiation, real-time PCR assay showed that TBI+IL-22 mice had higher mRNA levels of Foxn1, Ccl25, Aire and Dll4 in thymus compared with TBI+PBS ones. Meanwhile, the TBI+IL-22 mice had higher counts of total thymic cells[(5.93±3.19)×10(6)/ml vs (1.42±0.46)×10(6)/ml, t=3.128, P=0.033] and circulatory white blood cells[(3.08±0.94)×10(6)/ml vs (1.43±0.30)×10(6)/ml, t=3.730, P=0.015] than those of TBI+PBS mice. Flow cytometry analysis indicated that TBI+IL-22 mice had higher counts of TEC and thymocytes than TBI+PBS mice on day 14 after irradiation (all P<0.05). On days 7 and 14 after irradiation, TBI+IL-22 mice had higher counts of circulatory white blood cells and T cells than TBI+PBS mice (all P<0.05). Conclusion: Sub-lethal TBI induces upregulation of intra-thymic IL-22, and injecting of recombinant IL-22 increases level of IL-22 in thymus. Injecting of recombinant IL-22 improves recovery of TEC and increases numbers of thymocyte subsets and circulatory T cell after thymic injury.

Structural Changes Due to Antagonist Binding in Ligand Binding Pocket of Androgen Receptor Elucidated Through Molecular Dynamics Simulations

When a small molecule binds to the androgen receptor (AR), a conformational change can occur which impacts subsequent binding of co-regulator proteins and DNA. In order to accurately study this mechanism, the scientific community needs a crystal structure of the Wild type AR (WT-AR) ligand binding domain, bound with antagonist. To address this open need, we leveraged molecular docking and molecular dynamics (MD) simulations to construct a structure of the WT-AR ligand binding domain bound with antagonist bicalutamide. The structure of mutant AR (Mut-AR) bound with this same antagonist informed this study. After molecular docking analysis pinpointed the suitable binding orientation of a ligand in AR, the model was further optimized through 1 μs of MD simulations. Using this approach, three molecular systems were studied: (1) WT-AR bound with agonist R1881, (2) WT-AR bound with antagonist bicalutamide, and (3) Mut-AR bound with bicalutamide. Our structures were very similar to the experimentally determined structures of both WT-AR with R1881 and Mut-AR with bicalutamide, demonstrating the trustworthiness of this approach. In our model, when WT-AR is bound with bicalutamide, Val716/Lys720/Gln733, or Met734/Gln738/Glu897 move and thus disturb the positive and negative charge clumps of the AF2 site. This disruption of the AF2 site is key for understanding the impact of antagonist binding on subsequent co-regulator binding. In conclusion, the antagonist induced structural changes in WT-AR detailed in this study will enable further AR research and will facilitate AR targeting drug discovery.

[Application of vascular replacement technique with allogenic blood vessel in radical resection for pancreatic carcinoma: a report of 33 cases]

Objective: To analyze the application of vascular replacement technique with allogenic blood vessel in radical resection for pancreatic carcinoma. Methods: The clinical data of 33 patients with vascular invasion of pancreatic carcinoma who underwent radical resection from April 2013 to April 2017 in Department of Hepatobiliary Surgery, Beijing Chaoyang Hospital were retrospectively analyzed. There were 14 males and 19 females with age of (62.5±10.6)years(ranging from 35 to 78 years). Vascular replacement technique with allogenic blood vessel was used on all patients who underwent radical resection for pancreatic carcinoma. The operation procedure was made according to the specific location of the carcinoma, and the allogenic blood vessel was selected according to the type of vascular invasion. The matching vessel was selected for replacement to the patient who was invaded only one vessel. And the "Y" type of iliac vein was selected for replacement to the patient who was invaded the confluence of portal vein, splenic vein and superior mesenteric vein. After the operation, the patients were followed up by telephone and outpatient review. Results: All of 33 patients were successfully completed the operations. There were 28 patients underwent pancreaticoduodenectomy with vascular replacement, and 5 patients underwent total pancreatectomy with vascular replacement. All the patients were confirmed pancreatic carcinoma and R0 resection according to the postoperative pathology. There were 16 patients with the carcinoma invasion the confluence of portal vein, splenic vein and superior mesenteric vein, 12 patients with the carcinoma invasion the superior mesenteric vein, and 5 patients with the carcinoma invasion the portal vein. There was no perioperative death in this group and no complications related to allogenic blood vessel. The incidence of postoperative complications was 18.2% (6/33), and the incidence of pancreatic fistula was 6.1% (2/33), all of which were biochemical fistula. There were 32 patients were followed up, and the follow-up rate was 96.9%. The median survival time was 14.6 months. The half-year, 1-year and 2-year survival rates were 75.6%, 37.6% and 27.4%. Conclusion: The application of vascular replacement technique with allogenic blood vessel for pancreatic carcinoma has a great significance for improving the R0 resection rate and the prognosis of patients.

Endocrine Disrupting Chemicals Mediated through Binding Androgen Receptor Are Associated with Diabetes Mellitus

Endocrine disrupting chemicals (EDCs) can mimic natural hormone to interact with receptors in the endocrine system and thus disrupt the functions of the endocrine system, raising concerns on the public health. In addition to disruption of the endocrine system, some EDCs have been found associated with many diseases such as breast cancer, prostate cancer, infertility, asthma, stroke, Alzheimer’s disease, obesity, and diabetes mellitus. EDCs that binding androgen receptor have been reported associated with diabetes mellitus in in vitro, animal, and clinical studies. In this review, we summarize the structural basis and interactions between androgen receptor and EDCs as well as the associations of various types of diabetes mellitus with the EDCs mediated through androgen receptor binding. We also discuss the perspective research for further understanding the impact and mechanisms of EDCs on the risk of diabetes mellitus.

Evaluation of chemical mutagenicity using next generation sequencing: A review

Mutations are heritable changes in the nucleotide sequence of DNA that can lead to many adverse effects. Genotoxicity assays have been used to identify chemical mutagenicity. Recently, next generation sequencing (NGS) has been used for this purpose. In this review, we present the progress in NGS application for assessing mutagenicity of chemicals, including the methods used for detecting the induced mutations, bioinformatics tools for analyzing the sequencing data, and chemicals whose mutagenicity has been evaluated using NGS. Available information suggests that NGS technology has unparalleled advantages for evaluating mutagenicity of chemicals can be applied for the next generation of mutagenicity tests.

FOXC1 overexpression is a marker of poor response to anthracycline-based adjuvant chemotherapy in sporadic triple-negative breast cancer

Purpose

Because of its aggressive characteristics and poor prognosis, triple-negative breast cancer (TNBC) has become a hot topic in cancer research. Chemotherapy is currently the only treatment for patients with TNBC. The transcription factor FOXC1 has been associated with TNBC prognosis, but little is known about its effect on chemosensitivity. The aim of this study was to investigate the effects of FOXC1 on chemosensitivity.

Methods

A case–control study was performed on 25 TNBC patients who experienced relapse and/or metastasis. Another 25 patients without relapse or metastasis were randomly selected as controls. Medical records were reviewed for relevant information, and immunohistochemistry was performed to measure FOXC1 levels. The Kaplan–Meier method and Cox analysis were used to analyze differences in disease-free survival (DFS) and overall survival (OS). The correlation of FOXC1 expression with chemosensitivity was analyzed. Data were analyzed using SPSS 21.0 software, and a P value <0.05 was considered to be statistically significant.

Results

In 15 of 22 case patients, FOXC1 was overexpressed, whereas only 8 control patients exhibited FOXC1 overexpression (P < 0.05). FOXC1 expression had no correlation with pathological indicators. An anthracycline-based regimen was administered to 21 study patients and 23 control patients. FOXC1 expression was significantly associated with a worse DFS (HR 2.62, 95% CI 1.05–6.50, P = 0.038) but presented no correlation with OS (HR 2.53, 95% CI 0.76–8.40, P = 0.131) among these 44 patients.

Conclusions

This study shows that FOXC1 is correlated with chemosensitivity to anthracycline and could be used as an indicator of chemosensitivity in sporadic TNBC.

Electronic supplementary material

The online version of this article (doi:10.1007/s00280-017-3319-4) contains supplementary material, which is available to authorized users.

S phase arrest in lymphocytes induced by urinary 1-hydroxypyrene and alcohol drinking in coke oven workers

Arrest of the cell cycle after DNA damage is believed to promote DNA repair. We aim to investigate the main factors affecting cell cycle arrest of lymphocytes in coke oven workers. A total of 600 workers were included in this study, and their urinary levels of four polycyclic aromatic hydrocarbons (PAH) metabolites, 8-hydroxydeoxyguanosine (8-OHdG), and cell cycle distribution were determined. Urinary PAH metabolites were significantly increased in coke oven workers ( p < 0.01). It was found that only urinary 2-hydroxynaphthalene and 1-hydroxypyrene showed significant positive linear dose–response effects on 8-OHdG in this study population ( ptrend = 0.025 and 0.017, respectively). The dose–response effect was also observed for smoking and drinking on 8-OHdG ( ptrend < 0.001 and 0.034, respectively). Multivariate logistic regression analysis revealed that high levels of urinary 1-hydroxypyrene were associated with a significantly increased risk of S phase arrest (odds ratio (OR) = 1.32, p = 0.03), so as heavy alcohol drinking (OR = 1.31, p = 0.02). Drinking can significantly modify the effects of urinary 1-hydroxypyrene on S phase arrest, during co-exposure to both heavy drinking and median or high 1-hydroxypyrene levels (OR = 3.31, 95% confidence interval (CI) = 1.21–7.63 and OR = 2.56, 95% CI = 1.08–6.06, respectively). Our findings demonstrate that coke oven workers with heavy drinking will cause S phase arrest so as to repair more serious DNA damage.

Abstract P5-02-05: Biology and long-term prognosis of screening detected non-palpable breast cancer by ultrasound in hospital-based Chinese population (2001-2014)

Background: Milestone studies showed that ultrasound (US) was an effective primary screening test for breast cancer both in the western world and in China [PMID: 26712110, 26715161, and 25668012]. Ultrasound has been officially designated to be the initial imaging test for breast cancer screening in Beijing and several other cities in China, due to its improved sensitivity in Chinese women who usually have denser breasts and develop breast cancer earlier than Caucasian counterparts. Study showed that it would take 40 years to screen each woman in the target age group once [PMID: 26808342].The mainstay modality of breast cancer screening in China is the hospital-based opportunistic screening among asymptomatic self-referred women. However, there is little data about the tumor biology and long-term survival of the US-detected non-palpable breast cancer (NPBC) in hospital-based Chinese population.

Methods: From January 2001 to December 2014, 3,786 asymptomatic women with positive (BI-RADS 4 and 5) initial screening US underwent biopsies in Peking Union Medical College Hospital, and 572 NPBC in 556 women were diagnosed. Women without dense breasts (defined as BI-RADS category C and D) also received screening mammography (MG) after physical examination and ultrasound. 788 patients with positive (BI-RADS 4 and 5) mammogram (MG) and normal US (BI-RADS 1, 2 and 3) underwent MG-guided biopsies and another 127 NPBC were diagnosed in 126 women. The clinicopathological features, treatment choice, 10-year disease-free survival (DFS) and overall survival (OS) were reviewed and compared between the US-detected and MG-detected NPBC. Prognostic factors of NPBC were identified.

Results: Overall, US could detect more invasive NPBC (83.4% vs 54.3%, p&lt;0.001), lymph node positive cancer (19.1% vs 10.2%, p&lt;0.001)and multifocal cancer (19.2% vs 6.3%, p&lt;0.001). In invasive NPBC, US detected more low grade cancer (21.4% vs 10.2%, p=0.001), multifocal cancer (20.7% vs 2.9%, p&lt;0.001), Her2 negative cancer (77.6% vs 62.3%, p=0.001) and larger tumor (pT1c+pT2, 53.3% vs 37.6%, p&lt;0.001). There was no significant difference in immunophenotype/subtype, treatment methods, DFS or OS between US- and MG-NPBC among ductal carcinoma in situ (DCIS), invasive and all NPBC. For all NPBC and the US-NPBC, the common DFS-factors included pT, pN and p53 whereas OS-predictors were pN and immunophenotype/subtype.

Table 1. Kaplan-Meier estimates of DFS and OS between US-NPBC and MG-NPBC§.Patients (No.)10-year DFS (%)P value10-year OS (%)P valueAllUS-NPBC (572)90.60.73896.10.142 MG-NPBC (127)92.7 100.0 DCISUS-NPBC (94)100.00.060100.0- MG-NPBC (58)93.8 100.0 InvasiveUS-NPBC (478)88.60.68095.20.239 MG-NPBC (69)92.0 100.0 § Kaplan-Meier survival curves between each two subgroups would be displayed in the poster.

Conclusion: Compared to MG, US detected more invasive NPBC with positive lymph node in hospital-based asymptomatic self-referred Chinese women, who could achieve comparable 10-year DFS and OS as MG-detected NPBC. US could serve as the feasible initial imaging modality in hospital-based opportunistic screening Chinese women.

Citation Format: Yao R, Pan B, Zhu Q, Xu Q, Zhou Y, Zhang J, Mao F, You S, Lin Y, Shi J, Guan J, Wang X, Zhang Y, Zhang X, Shen S, Zhong Y, Xu Y, Liang Z, Jiang Y, Sun Q. Biology and long-term prognosis of screening detected non-palpable breast cancer by ultrasound in hospital-based Chinese population (2001-2014) [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 P5-02-05.

Malignant pericardial mesothelioma : A systematic review of current practice

BACKGROUND

Malignant mesothelioma is a rare but aggressive tumor, with a high misdiagnosis rate and overall bleak prognosis. In 0.7% of all cases, the origin is the pericardium.

METHODS

The present study is a review of the literature published in recent decades focusing on the advances in clinical manifestations, radiological findings, diagnosis, differential diagnosis, and treatment of malignant pericardial mesothelioma (MPM).

RESULTS

No clear relationship has been established between the etiologies and the development of MPM. Clinical symptoms and signs are nonspecific when present. The main presentations are chest pain and dyspnea. Imaging plays an important role in the detection, characterization, staging, and posttreatment follow-up. The definitive diagnosis is made on the basis of pathological findings. Chest radiography and echocardiography are common techniques used initially, but their roles are limited. Computed tomography and magnetic resonance imaging have an advantage in depicting the thickened pericardium, mediastinal lymph node, tumor, and the extension of adjacent structures. Surgery is the most important treatment modality and remains palliative in most cases, while the roles of chemo- and radiotherapy are unsatisfactory.

CONCLUSION

Clinical trials of malignant pleural and peritoneal mesothelioma remain important for MPM management. Multimodality treatment of surgery, chemotherapy, radiotherapy, and immunotherapy is expected to have a role in the treatment of MPM.

Diastolic dysfunction and cardiac troponin I decrease in aging hearts

Cardiac tropnoin I (cTnI) plays a critical role in the regulation of diastolic function, and its low expression may result in cardiac diastolic dysfunction, which is the most common form of cardiovascular disorders in older adults. In this study, cTnI expression levels were determined in mice at various ages and cardiac function was measured and compared between young adult mice (3 and 10 months) and older mice (18 months). The data indicated that the cTnI levels reached a peak high in young adult hearts (3 months), but decreased in older hearts (18 months). Furthermore, the older hearts showed a significant diastolic dysfunction observed by P-V loop and echocardiography measurements. To further define the mechanism underlying the cTnI decrease in aging hearts, we tested DNA methylation and histone acetylation modifications of cTnI gene. We found that acetylation of histone near the promoter region of cTnI gene played an important role in regulation of cTnI expression in the heart at different ages. Our study indicates that epigenetic modification caused cTnI expression decrease is one of the possible causes that result in a reduced cTnI level and diastolic dysfunction in the older hearts.

Abstract P6-08-03: Functional detection and inhibition of the targetable oncogenic kinome of chemotherapy-treated triple-negative breast cancer cells

Background: Triple-negative breast cancer (TNBC) accounts for 10-15% of all breast cancer cases. A major area of innovation in TNBC is identifying potential treatment targets, especially in TNBC cells which survive chemotherapy. Our previous study showed that TNBC cells displayed deregulated kinase-dependent signaling cascades, and uniquely divergent phospho-circuits could be distinguished between TNBC vs non-TNBC cell lines [2014 SABCS abstract 1672, poster P2-05-09]. We further hypothesized that specific dysfunctional phospho-signaling network played a key role in the early adaptive changes in DNA damage response of TNBC cells exposed to DNA damaging chemotherapeutic agents.

Methods: TNBC cell lines MDA-MB-231 and MDA-MB-436 were treated with 5-fluorouracil (5-Fu), carboplatin and doxorubicin at their respective half maximal inhibitory concentrations (ic50s). MiSeq gene sequencing of the untreated vs treated TNBC cells was performed to investigate whether exposure to chemotherapy agents for 3-day's duration would induce additional adaptive genetic mutation. Apoptosis and cell-cycle distribution of the untreated and treated TNBC cells were analyzed with flow cytometry. The functional phospho-signature of each TNBC cell sample was analyzed using a high throughput experimental platform that monitors the level of activity of myriad kinases at once. This technique used over 450 phospho-sensing probes, including over 150 controls in an aqueous-based assay to simultaneously and directly measure the phospho-catalytic activity of phosphorylating enzymes in cell lysates. The kinome activities of the untreated vs treated TNBC cell lines were compared respectively, and the most significantly deranged and functionally altered phospho-signaling cascades and their related kinases were identified as the early adaptive changes of the survived TNBC cells after the 3-day exposure to DNA damage chemotherapies.

Results: Using the two TNBC cell lines treated with the three chemotherapies, we made 8 cell line samples, including 6 treated and 2 untreated as the control. MiSeq gene sequencing showed no significant additional adaptive genetic mutations in the treated TNBC cells after the 3-day short-term exposure to 5-Fu, carboplatin and doxorubicin. 36 phospho-signatures were generated and validated for repeatability and robustness. The kinase activity signature of each TNBC sample was analyzed and compared to each other using unsupervised hierarchical clustering. The phospho-sensing assay revealed that phospho-signaling cascades related to CHK1/2 and IKK kinases were differentially altered in the untreated vs treated TNBC cell lines, which, when respectively inhibited by AZD7762 and IKK16, successfully increased growth inhibition and cell death of TNBCs.

Conclusions: We identified specific phospho-fingerprints of the early adaption of TNBC cell lines and combinatorial targeted therapies that improve treatment outcome. Our next goal is to identify specific phosphorylation cascades in a broader range of cell lines and tumor tissues, to explore the actionable, kinase-dependent mechanisms critical to the DNA damage-induced adaptive reprogramming of TNBCs and early changes driving drug-resistance.

Citation Format: Pan B, Olow A, Sun Q, Mori M, Lee PRE, Hartog M, Wang C, Wolf D, Yau C, van 't Veer L, Coppé J-P. Functional detection and inhibition of the targetable oncogenic kinome of chemotherapy-treated triple-negative breast cancer cells. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-08-03.

Abstract P6-05-12: Prognosis of subtypes of the mucinous breast carcinoma in Chinese women: A population-based study of 32-year experience (1983-2014)

Background: The heterogeneous nature of the mucinous breast cancer (MBC), with its subtypes of pure (PMBC) and mixed carcinoma (MMBC), calls for more precise individualized prognosis assessment. PMBC showed favorable prognosis in both Chinese and Caucasian women, with nodal status and TNM stage as the prognostic predictors [PMID: 18026874, 22451233]. However, few studies had investigated tumor biology and prognosis of MMBC in Chinese population, especially with respect to the different co-existing cancer components.

Methods: From January 1983 to December 2014, 197 consecutive MBC patients, including 117 PMBC and 80 MMBC, received breast cancer surgery in Peking Union Medical College Hospital. The clinicopathological characteristics, treatment choice, disease-free survival (DFS) and overall survival (OS) were compared both between PMBC vs MMBC, and among subgroups of MMBC according to the mixed entities, including 24 women with ductal caricinoma in situ (DCIS) and 45 with IDC. Univariate and Cox multivariate analyses were performed to identify the prognostic factors.

Results: The 197 MBC comprised 1.9% of contemporary 10,192 breast cancer (BC). Compared to PMBC, MMBC had significantly more lymph node metastasis (p=0.038), Her2 positivity (p=0.036), high Ki-67 index (defined as &gt;20%, p=0.026) and anti-Her2 targeted therapy (p=0.006). All these differences remained significant when the comparison were performed among PMBC, MBC+DCIS and MBC+IDC, and additional significant difference were identified in tumor size (p=0.036), pTNM stage (p=0.003) and chemotherapy (p=0.003). However, no significant difference was found in DFS or OS between any two subtypes/subgroups of MBC, including PMBC, MMBC, MBC+DCIS and MBC+IDC.

Table 1. Comparison of survival outcomes among PMBC, MBC+DCIS and MBC+IDC§SurvivalPMBC (N=117, Median, range, and Mean±SD)MBC+DCIS (N=24, Median, range, and Mean±SD)MBC+IDC (N=45, Median, range, and Mean±SD)P-ValueDFS (months)43 (1-233), 52.7±45.227 (1-84), 34.3±25.326 (1-113), 33.1±26.60.187OS (months)46 (1-312), 56.9±51.827 (1-84), 34.4±25.326 (1-113), 34.8±28.70.628§ Kaplan-Meier survival curves would be displayed in the poster

High Ki-67 index (p=0.046) appeared to be the significant DFS related prognostic factor for PMBC, whereas estrogen receptor (ER) status (univariate p=0.000, multivariate p=0.062) and immunophenotype (luminal, her2, or triple-negative, univariate p=0.000, multivariate p=0.079) might be the potential DFS predictors for MMBC. None of the above-mentioned clinicopathological factors could serve as OS predictors for MBC.

Conclusion: This population-based study showed that there were significant difference in nodal status, Ki-67, Her2 positivity and targeted therapy between PMBC and MMBC, and furthermore in tumor size, stage and chemotherapy among PMBC and subgroups of MMBC such as MBC+DCIS and MBC+IDC. However, survival outcomes were similar between these clinical entities and subgroups, suggesting the intra-tumoral heterogeneity might not interfere with survival outcomes of MBC in Chinese woman. High Ki-67 index was identified as the significant DFS related prognostic factor for PMBC, whereas ER status and immunophenotype as the potential DFS predictors for MMBC.

Citation Format: Yao R, Pan B, Sun Q, Zhou Y, Mao F, Lin Y, Guan J, Wang X, Zhang Y, Zhang X, Shen S, Zhong Y, Xu Y, Shi J, Zhu Q, Cai F, Liang Z. Prognosis of subtypes of the mucinous breast carcinoma in Chinese women: A population-based study of 32-year experience (1983-2014). [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-05-12.