Clinical utility of expanded non-invasive prenatal screening and chromosomal microarray analysis in high-risk pregnancy

OBJECTIVE

To evaluate the utility of expanded non-invasive prenatal screening (NIPS), compared with chromosomal microarray analysis (CMA), for the detection of chromosomal abnormalities in high-risk pregnancies.

METHODS

This was a multicenter retrospective study of singleton pregnancies at high risk for chromosomal abnormality. Patients who underwent expanded NIPS and CMA sequentially during pregnancy from 2015 to 2019 were included in the analysis. Pregnancies with a positive result for sex chromosome aneuploidy were excluded as the full details could not be retrieved. The utility of expanded NIPS and CMA for detection of chromosomal abnormalities in this cohort was compared by assessing the concordance between the results.

RESULTS

Of the 774 included high-risk pregnancies, 550 (71.1%) had a positive NIPS result, while a positive CMA result was detected in 308 (39.8%) cases. The rate of full or partial concordance between NIPS and CMA was 82.2%, 59.6% and 25.0% for trisomies 21, 18 and 13, respectively. For rare aneuploidies and segmental imbalances, NIPS and CMA results were fully or partially concordant in 7.5% and 33.3% of cases, respectively. Copy-number variants < 5 Mb were detected more often by CMA, with an incidence of 7.9% (61/774) compared with 3.1% (24/774) by NIPS. A genetic aberration was detected by CMA in 1 in 17 (5.8%) high-risk pregnancies that had a negative or non-reportable NIPS result.

CONCLUSION

CMA allows for comprehensive detection of genome-wide chromosomal abnormalities in high-risk pregnancies. CMA should be offered instead of expanded NIPS for high-risk pregnancies. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.

[Use of Trichosanthis fructus and the core drug pair Trichosanthis fructus-Glycyrrhizae radix et rhizoma in traditional Chinese prescriptions: molecular mechanisms in network pharmacology and molecular docking]

OBJECTIVE

To analyze the rationale for use of Trichosanthis fructus in traditional Chinese prescriptions and explore the molecular mechanism of the core drug pair Trichosanthis fructus-Glycyrrhizae radix et rhizoma for treatment of phlegm syndrome diseases.

OBJECTIVE

We analyzed the cumulative frequency of the use of Trichosanthis fructus in traditional Chinese prescriptions and the disease spectrum treated using the prescriptions containing Trichosanthis fructus. We searched TCMSP database for the chemical components of Trichosanthis fructus and Glycyrrhizae radix et rhizoma and explored their target proteins using Swiss Target Prediction database. We also searched the CooLGeN and GeneCards databases for the potential disease target proteins using the key words "phlegm syndrome". The chemical component-target protein-signal pathway network was constructed using DAVID database to analyze the molecular mechanism of Trichosanthis fructus-Glycyrrhizae radix et rhizoma drug pair for treatment of phlegm syndrome diseases, and the result was verified by molecular docking technology.

OBJECTIVE

A total of 1700 prescriptions containing Trichosanthis fructus were retrieved, which were used for treatment of 28 diseases. Phlegm syndrome was the most frequent among the 28 diseases (14.0%). The Trichosanthis fructus-Glycyrrhizae radix et rhizoma drug pair had a cumulative frequency of 113 for use in treatment of phlegm diseases, and was the core drug pair in prescriptions containing Trichosanthis fructus. Fifty-two chemical components related to phlegm syndrome diseases were identified in the drug pair (9 in Trichosanthis fructus and 43 in Glycyrrhizae radix et rhizoma), and their therapeutic effects were mediated by a total of 41 target proteins involving the cancer pathway, NOD-like receptor signaling pathway and another 17 signal pathways. The results of molecular docking showed that 40 chemical components docking with 10 target protein molecules had total scores greater than 5.

OBJECTIVE

The different formulations of Trichosanthis fructus containing prescriptions serve different therapeutic purposes. The mechanisms of the Trichosanthis fructus-Glycyrrhizae radix et rhizoma drug pair for treatment of phlegm syndrome diseases involve multiple pathways for regulating cell proliferation, apoptosis and other biological processes.

ZNF416 is a pivotal transcriptional regulator of fibroblast mechanoactivation

Matrix stiffness is a central regulator of fibroblast function. However, the transcriptional mechanisms linking matrix stiffness to changes in fibroblast phenotype are incompletely understood. Here, we evaluated the effect of matrix stiffness on genome-wide chromatin accessibility in freshly isolated lung fibroblasts using ATAC-seq. We found higher matrix stiffness profoundly increased global chromatin accessibility relative to lower matrix stiffness, and these alterations were in close genomic proximity to known profibrotic gene programs. Motif analysis of these regulated genomic loci identified ZNF416 as a putative mediator of fibroblast stiffness responses. Genome occupancy analysis using ChIP-seq confirmed that ZNF416 occupies a broad range of genes implicated in fibroblast activation and tissue fibrosis, with relatively little overlap in genomic occupancy with other mechanoresponsive and profibrotic transcriptional regulators. Using loss- and gain-of-function studies, we demonstrated that ZNF416 plays a critical role in fibroblast proliferation, extracellular matrix synthesis, and contractile function. Together, these observations identify ZNF416 as novel mechano-activated transcriptional regulator of fibroblast biology.

Alendronate promotes the gene expression of extracellular matrix mediated by SP-1/SOX-9

BACKGROUND AND PURPOSE

Osteoarthritis (OA) is a disease with significant degenerative changes of articular cartilage, which is reported to be closely related to the integrity of chondrocytes extracellular matrix (ECM). Alendronate belongs to the family of bisphosphonates with promising cartilage repair function. In the present study, the effects of Alendronate on the gene expression of chondrocytes ECM and the potential mechanism will be investigated to explore the potential therapeutic property of Alendronate on OA.

METHODS

Human SW1353 chondrocytes were stimulated with 1 and 2 μM Alendronate for 12 h. The gene expression of Col2α1, COL9α2, and Acan in the treated chondrocytes was determined by qRT-PCR. QRT-PCR and western blot analysis were used to evaluate the expression level of SOX-9 in the treated chondrocytes. The expression level of SP-1 was checked by qRT-PCR and immunostaining. SiRNA against SP-1 was transfected into chondrocytes to knockdown the expression of SP-1. The levels of p-ERK1/2 and total ERK1/2 were examined using western blot analysis. TNF-α was used to induce an OA-like in vitro model in the chondrocytes for therapeutic evaluations.

RESULTS

Treatment with Alendronate increased the levels of ECM related genes (Col2α1, COL9α2, and Acan) in a dose-dependent manner through increasing the expression of SOX-9, a central regulator of ECM genes. Additionally, our findings demonstrate that the effects of Alendronate in the expression of SOX-9 are mediated by SP-1 as silencing of SP-1 abolished these effects. Notably, Alendronate increased the phosphorylation of ERK1/2 and inhibition of ERK1/2 using its specific inhibitor U0126 blocked the expression of SP-1. Finally, we found that treatment with Alendronate could rescue TNF-α-induced reduction of Col2α1, COL9α2, Acan and SOX-9.

CONCLUSION

Our data indicated that Alendronate might promote the gene expression of extracellular matrix through SOX-9 mediated by the ERK1/2/SP1 signaling pathway.

[The glorious history of the treatment for ocular trauma in China in the past seven decades]

With the unremitting efforts of several generations of experts in ocular trauma, great progresses have been achieved in the field of ocular trauma in terms of the treatment, scientific research, international communication, talent team construction and cultural inheritance. The purpose of looking back on the development history of the past 70 years is to commemorate our predecessors and inspire the followers to continue to strive for the progress of this subspecialty in China. We would like to send congratulations on the 70th anniversary of Chinese Journal of Ophthalmology with this article. (Chin J Ophthalmol, 2020, 56: 801-804).

Prognostic value of age-adjusted d-dimer cutoff thresholds in patients with myocardial infarction treated by percutaneous coronary intervention

Introduction

The association between D-dimer and outcomes of patients with myocardial infarction (MI) remains controversial. Using age-adjusted D-dimer cutoff thresholds significantly improves the accuracy of diagnosis for thrombotic diseases. This study aimed to investigate the prognostic value of age-adjusted D-dimer in MI patients treated by percutaneous coronary intervention (PCI).

Methods

In this observational study, 3614 consecutive patients with MI treated by PCI were retrospectively recruited. The baseline age-adjusted D-dimer threshold was 500 ng/mL, and was calculated as age × 10 in patients older than 50 years. Cox regression was used for outcome analysis. The primary outcome was all-cause death. Discrimination and reclassification were calculated to assess the additional prognostic value of D-dimer when combined with established clinical risk factors and the Global Registry of Acute Coronary Events (GRACE) risk score.

Results

During a median follow-up of 652 days, a total of 194 deaths occurred. High D-dimer level, as defined by age-adjusted thresholds, was an independent predictor for all-cause death (hazard ratio:1.67, 95% confidence interval: 1.23–2.27, P=0.001). Addition of D-dimer level (high or low) significantly improved risk classification for death when combined with established clinical risk factors (net reclassification index [NRI]: 0.601, P&lt;0.001; integrated discrimination improvement [IDI]: 0.011, P=0.046) and GRACE score (NRI: 0.618, P&lt;0.001; IDI: 0.015, P=0.011).

Conclusions

In patients with MI treated by PCI, D-dimer elevation defined by age-adjusted thresholds was an independent predictor for adverse outcomes, and provided additional prognostic value when combined with clinical risk factors and GRACE score.

Funding Acknowledgement

Type of funding source: Public Institution(s). Main funding source(s): Chinese Academy of Medical Sciences

Association between pre-infarction angina and culprit-lesion morphology in patients with ST-segment elevation myocardial infarction: an optical coherence tomography study

Background

Previous studies reported the cardiac protection effect of pre-infarction angina (PIA) in patients with acute myocardial infarction (AMI). However, the association between PIA and culprit plaques characteristics in AMI patients through optical coherence tomography (OCT)assessment remains unclear.

Purpose

We sought to identify culprit-plaque morphology associated with PIA in patients with ST-segment elevation myocardial infarction (STEMI) using OCT.

Methods

A total of 279 STEMI patients who underwent intravascular OCT of culprit-lesion were included. Baseline clinical data and culprit-plaque characteristics were compared between the PIA group the non-PIA group.

Results

Patients with PIA represented 54.8% of the study population (153 patients). No differences were observed in clinical and angiographic data between two groups, except STEMI onset with exertion was significantly less common in PIA group (24.2% versus 40.5%, P=0.004). Patients with PIA exhibited a significantly lower incidence of plaque rupture (40.5% versus 61.9%, P&lt;0.001) and lipid-rich plaques (48.4% versus 69.0%, P=0.001). The thin-cap fibroatheroma (TCFA) prevalence was lower in PIA group, presenting a thicker fibrous cap thickness, although statistically significant differences were not observed (20.3% versus 30.2%, P=0.070; 129.1±92.0μm versus 111.4±78.1μm, P=0.088; respectively). Multivariate logistic regression analysis indicated that PIA was an independent negative predictor for plaque rupture (odds ratio: 0.44, 95% confidence interval: 0.268–0.725, P=0.001).

Conclusion

STEMI patients with PIA showed a significantly lower prevalence of plaque rupture and lipid-rich plaques in culprit-lesion than non-PIA group, implying different mechanisms of STEMI attack.

Flow chart + Bar graphs of OCT findings

Funding Acknowledgement

Type of funding source: Public Institution(s). Main funding source(s): Association between pre-infarction angina and culprit-lesion morphology in patients with ST-segment elevation myocardial infarction: An optical coherence tomography study

8q24 clear cell renal cell carcinoma germline variant is associated with VHL mutation status and clinical aggressiveness

Background

The four most commonly-mutated genes in clear cell renal cell carcinoma (ccRCC) tumors are BAP1, PBRM1, SETD2 and VHL. And, there are currently 14 known RCC germline variants that have been reproducibly shown to be associated with RCC risk. However, the association of germline genetics with tumor genetics and clinical aggressiveness are unknown.

Methods

We analyzed 420 ccRCC patients from The Cancer Genome Atlas. Molecular subtype was determined based on acquired mutations in BAP1, PBRM1, SETD2 and VHL. Aggressive subtype was defined clinically using Mayo SSIGN score and molecularly using the ccA/ccB gene expression subtype. Publically-available Hi-C data were used to link germline risk variants with candidate target genes.

Results

The 8q24 variant rs35252396 was significantly associated with VHL mutation status (OR = 1.6, p = 0.0037) and SSIGN score (OR = 1.9, p = 0.00094), after adjusting for multiple comparisons. We observed that, while some germline variants have interactions with nearby genes, some variants demonstrate long-range interactions with target genes.

Conclusions

These data further demonstrate the link between rs35252396, HIF pathway and ccRCC clinical aggressiveness, providing a more comprehensive picture of how germline genetics and tumor genetics interact with respect to tumor development and progression.

[Optimization of ATG dose in haploid hematopoietic stem cell transplantation for hematologic malignancies]

Objective: To compare the clinical efficacy of different doses of rabbit antithymocyte globulin (rATG) in haplo-HSCT in the treatment of hematologic malignancies. Methods: Malignant hematological patients treated at our hospital from March 2013 to December 2018 were retrospectively analyzed. These patients were divided into three groups as per three doses of ATG (6 mg/kg, 7.5 mg/kg, and 9 mg/kg) in the conditioning regimens. The transplant outcomes were compared in terms of the occurrence of acute graft versus host disease (GVHD) , infection, and survival. Results: ①Total 288 patients were enrolled in the study, including 182 men and 106 women, with a median age of 18 (6-62) years. Total 110 patients were diagnosed with acute lymphoblastic leukemia (ALL) , 128 with acute myelogenous leukemia (AML) , 8 with chronic myeloid leukemia (CML) , 28 with myelodysplastic syndrome (MDS) , and 14 with mixed cell leukemia (MAL) . There were 159 patients in the ATG-6 group, 72 in the ATG-7.5 group, and 57 in the ATG-9 group. The median follow-up time of post transplantation was 14 (0.2-74) months. ②The incidence of neutrophil engraftment (96.9% , 97.2% , and 96.5% , respectively) and platelet engraftment (92.5% , 87.5% , and 86% , respectively) did not significantly differ among the ATG-6, ATG-7.5, and ATG-9 groups (P=0.972, P=0.276) . The incidence of grades 2-4 acute GVHD was 14.5% , 11.1% , and 8.8% in the three groups, respectively (P=0.493) , chronic GVHD incidence in the three group was 8.8% , 14.3% and 12.0% , respectively (P=0.493) . The infection rates of CMV and EBV in the ATG-9 group (77.2% and 12.5% ) were significantly higher than those in the ATG-6 (43.3% and 3.5% ) , and ATG -7.5 group (44.4% and 1.5% ) (P<0.001 and P=0.033, respectively) . ③Among the three groups, there were no significant difference in the 3-year overall survival [68.5% (95% CI 60.3% -77.9% ) , 60.1% (95% CI 48.3% -74.8% ) , 64.7% (95% CI 51.9% -80.7% ) ], cumulative incidences of relapse [34.6% (95% CI 34.3% -35.1% ) , 38.0% (95% CI 37.3% -38.7% ) , 20.6% (95% CI 20.0% -21.3% ) ], disease-free survival [53.3% (95% CI 44.9% -63.4% ) , 51.9% (95% CI 41% -65.8% ) , 63.9% (95% CI 51.9% -78.7% ) ] and non-relapse mortality [24.2% (95% CI 23.8% -24.5% ) , 26.0% (95% CI 25.4% -26.6% ) , 23.6% (95% CI 26.3% -28.2% ) ] (P=0.648, P=0.165, and P=0.486 and P=0.955) . Conclusion: Low dose (6 mg/kg) of rATG may increase the risk of grade Ⅱ-Ⅳ aGVHD, and a high dose (9 mg/kg) of ATG could significantly increase the risk of CMV and EBV infection. Median dose (7.5 mg/kg) of ATG is expected to reduce the incidence of moderate to severe aGVHD and viral infections without increasing the mortality.

[Research value of 50 MHz high-frequency ultrasound on sonography of normal facial skin in adult]

Objective: To observe the differences in normal facial skin thickness and echo density by different ages and sites of healthy adults of the same sex using 50 MHz high-frequency ultrasound. Methods: From January to June 2019, 200 healthy adult volunteers with normal facial skin who were from Sichuan, Yunnan, Guizhou, and Chongqing and met the inclusion criteria were recruited by the Affiliated Hospital of Southwest Medical University with simple random sampling method, and then were included in this cross-sectional investigation study. Then 50 MHz high-frequency ultrasound was used to obtain skin ultrasonogram of volunteers' forehead, canthus, eyelid, and cheek. According to the ages, 100 female volunteers were divided into 20-29 years old (30 females), 30-39 years old (25 females), 40-49 years old (20 females), and 50-70 years old (25 females) groups; 100 male volunteers were divided into 20-29 years old (30 males), 30-39 years old (25 males), 40-49 years old (20 males), and 50-70 years old (25 males) groups. The thickness of full-skin, the upper dermal echo density, and the lower dermal echo density of the female and male volunteers'forehead, canthus, eyelid, and cheek were recorded respectively. Data were statistically analyzed with one-way analysis of variance, analysis of variance for repeated measurement, least significant difference test, and Bonferroni correction. Results: (1) The thickness of full-thickness skin in forehead, canthus, eyelid, and cheek of female and male volunteers in 20-29 years old group were (1.86±0.26), (1.36±0.11), (1.24±0.25), and (1.90±0.21) mm, (2.45±0.37), (1.64±0.19), (1.44±0.16), and (2.53±0.26) mm, respectively, in 30-39 years old group were (1.98±0.24), (1.43±0.13), (1.15±0.15), and (2.12±0.13) mm, (2.34±0.27), (1.63±0.27), (1.50±0.38), and (2.43±0.40) mm, respectively, in 40-49 years old group were (1.90±0.21), (1.43±0.18), (1.24±0.27), and (1.98±0.12) mm, (2.14±0.24), (1.54±0.25), (1.28±0.14), and (2.39±0.36) mm, respectively, in 50-70 years old group were (1.64±0.25), (1.36±0.19), (1.16±0.12), and (1.89±0.29) mm, (2.28±0.27), (1.73±0.25), (1.58±0.18), and (2.38±0.32) mm, respectively. There were no statistically significant differences between female volunteers in the 4 groups and male volunteers in the 4 groups in thickness of full-thickness skin in canthus, eyelid, and cheek (F=0.677, 0.666, 0.136, 0.697, 0.294, 0.888, P>0.05). The thickness of full-thickness skin in forehead and cheek of the female volunteers in the 4 groups and male volunteers in the 4 groups was similar (P>0.05), and was significantly higher than that of canthus and eyelid (P<0.05). The thickness of full-thickness skin in canthus and eyelid of female volunteers in 20-29 years old, 40-49 years old, and 50-70 years old group was similar (P>0.05), while thickness of full-thickness skin in canthus and eyelid of male volunteers in the 4 groups was similar (P>0.05). (2) The upper dermal echo density of forehead, canthus, eyelid, and cheek of female volunteers in 50-70 years old group was significantly lower than that in 20-29 years old and 30-39 years old groups (P<0.05). The upper dermal echo density of forehead, canthus, eyelid, and cheek of male volunteers in 50-70 years old group was significantly lower than that in 20-29 years old group (P<0.05). The upper dermal echo density of forehead, canthus, eyelid, and cheek of female and male volunteers in 20-29 years old and 30-39 years old groups was similar (P>0.05). The upper dermal echo density of forehead and cheek of female volunteers in 20-29 years old, 40-49 years old, and 50-70 years old groups was significantly lower than that of canthus and eyelid (P<0.05). The echo density of upper dermis of cheek of male volunteers in the 4 groups was significantly lower than that of canthus and eyelid (P<0.05). The upper dermal echo density of canthus and eyelid of female volunteers in the 4 groups and male volunteers in the 4 groups was similar (P>0.05), the upper dermal echo density of forehead and cheek was similar (P>0.05). (3) The lower dermal echo density of forehead, canthus, eyelid, and cheek of female volunteers in 50-70 years old group was significantly higher than that in 20-29 years old and 30-39 years old groups (P<0.05). The lower dermal echo density of forehead, canthus, eyelid, and cheek of male volunteers in 50-70 years old group was significantly higher than that in 20-29 years old group (P<0.05). The echo density of the lower dermis of forehead, eyelid, and cheek of female and male volunteers in 20-29 years old, 30-39 years old, and 40-49 years old groups was similar (P>0.05). The lower dermal echo density of forehead and cheek of female volunteers in the 4 groups was significantly lower than that of canthus and eyelid (P<0.05). The lower dermal echo density of forehead and cheek of male volunteers in 30-39 years old, 40-49 years old, and 50-70 years old groups was significantly lower than that of canthus and eyelid (P<0.05). The lower dermal echo density between canthus and eyelid and between forehead and check of female volunteers in the 4 groups and male volunteers in the 4 groups was similar (P>0.05). Conclusions: The 50 MHz high-frequency ultrasonography shows that the thickness of full-thickness skin of canthus, eyelid, and cheek is similar in all age groups of female and male adult volunteers with normal facial skin. In the same age group, the thickness of full-thickness skin of forehead and cheek of male and female volunteers is significantly higher than that of canthus and eyelid. The upper dermal echo density of forehead, canthus, eyelid, and cheek of female and male volunteers shows a decreasing trend with age, while the lower dermal echo density shows an increasing trend with age. In addition, the echo density of upper and lower dermis of canthus and eyelid was significantly higher than that of cheek in all the four age groups.

miR-21 regulates the proliferation and apoptosis of ovarian cancer cells through PTEN/PI3K/AKT

OBJECTIVE

Phosphatase and tensin homologue deleted on chromosome ten (PTEN) regulates cell proliferation and apoptosis by inhibiting phosphatidylinositol-3 kinase (PI3K) and protein kinase (AKT) signaling. High expression of miR-21 was associated with ovarian cancer. This study aims to investigate whether miR-21 regulates PTEN/PI3K/AKT signaling as well as its role in the proliferation and apoptosis of ovarian cancer cells.

MATERIALS AND METHODS

Bioinformatics analysis was used to identify the binding site between miR-21 and the 3'-UTR of PTEN mRNA. A dual-luciferase reporter gene assay was performed to confirm the relationship between miR-21 and PTEN. The expression of miR-21, PTEN, and p-AKT was measured in normal ovarian cell IOSE80, ovarian cancer cell lines A2780, and SKOV3. miR-NC or miR-21 inhibitor was transfected into A2780 or SKOV3 cells followed by the analysis of the expression of miR-21, PTEN, p-AKT, cell apoptosis by flow cytometry, and proliferation by EdU assay.

RESULTS

There was a targeted relationship between miR-21 and PTEN. Compared with IOSE80 cell, levels of miR-21 and p-AKT were significantly elevated in A2780 and SKOV3 cells, with the statistical reduction of PTEN expression (p<0.05). The inhibition of miR-21 significantly reduced the expressions of miR-21 and p-AKT and induced PTEN level in A2780 and SKOV3 cells, which also restricted cell proliferation and promoted cell apoptosis.

CONCLUSIONS

The miR-21 expression is found elevated in ovarian cancer cells. The suppression of miR-21 increases PTEN expression, inhibits PI3K/AKT activity, promotes cell apoptosis, and reduces cell proliferation. This finding provides new leads to the future treatment of ovarian cancer.

Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas

Adenosquamous cancer of the pancreas (ASCP) is a subtype of pancreatic cancer that has a worse prognosis and greater metastatic potential than the more common pancreatic ductal adenocarcinoma (PDAC) subtype. To distinguish the genomic landscape of ASCP and identify actionable targets for this lethal cancer, we applied DNA content flow cytometry to a series of 15 tumor samples including five patient-derived xenografts (PDX). We interrogated purified sorted tumor fractions from these samples with whole-genome copy-number variant (CNV), whole-exome sequencing, and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analyses. These identified a variety of somatic genomic lesions targeting chromatin regulators in ASCP genomes that were superimposed on well-characterized genomic lesions including mutations in TP53 (87%) and KRAS (73%), amplification of MYC (47%), and homozygous deletion of CDKN2A (40%) that are common in PDACs. Furthermore, a comparison of ATAC-seq profiles of three ASCP and three PDAC genomes using flow-sorted PDX models identified genes with accessible chromatin unique to the ASCP genomes, including the lysine methyltransferase SMYD2 and the pancreatic cancer stem cell regulator RORC in all three ASCPs, and a FGFR1-ERLIN2 fusion associated with focal CNVs in both genes in a single ASCP. Finally, we demonstrate significant activity of a pan FGFR inhibitor against organoids derived from the FGFR1-ERLIN2 fusion-positive ASCP PDX model. Our results suggest that the genomic and epigenomic landscape of ASCP provide new strategies for targeting this aggressive subtype of pancreatic cancer. SIGNIFICANCE: These data provide a unique description of the ASCP genomic and epigenomic landscape and identify candidate therapeutic targets for this dismal cancer.

[Epidemiological characteristics of serum vitamin B(12) and folate levels in women awaiting delivery]

Objectives: To analyze the epidemiological characteristics and levels of vitamin B(12) and folate as well as their relationship in women awaiting delivery, in Shaanxi province. Methods: Data were collected from healthy pregnant women who gave birth at six top hospitals in Shaanxi, from January 2014 to December 2016. Blood samples were taken prenatally to determine the levels of vitamin B(12) and folate. Quantile regression model was used to analyze the relationship between the levels of vitamin B(12) and folates in women awaiting delivery. Results: A total of 1 277 women awaiting delivery were included in this study. Among them, the median level of serum vitamin B(12) was 164.7 pg/ml, in women at late pregnancy, with the deficiency rate as 69.6%, while the median level of serum folate was 7.6 ng/ml, with the deficiency rate as 12.1%. 58.4% of these women presented simple vitamin B(12) deficiency and 0.9% with simple folate deficiency. Women living in rural areas showed lower levels of both vitamin B(12) and folate than the women from the urban areas. Both the levels of vitamin B(12) and folate increased with age but were significantly lower in women under the age of 25. Among those with or without folate deficiency, the average difference in the levels of vitamin B(12) was 37.62 pg/ml. Quantile regression models showed that the vitamin B(12) levels in women with folate deficiency were significantly lower than those without, despite the different levels of vitamin B(12). This difference appeared increasing along with the increase of the vitamin B(12) levels. Conclusions: Our data showed that both vitamin B(12) and folate were deficient in women awaiting delivery, in Shaanxi. We suggest that vitamin B(12) should also be added into the folic acid supplementation program, together with the reinforcement on health education program to improve the awareness of nutrient supplementation in rural and young women. Hopefully, these strategies could increase the levels of both vitamin B(12) and folate, in the province.

High-sensitivity nanoscale chemical imaging with hard x-ray nano-XANES

Resolving chemical species at the nanoscale is of paramount importance to many scientific and technological developments across a broad spectrum of disciplines. Hard x-rays with excellent penetration power and high chemical sensitivity are suitable for speciation of heterogeneous (thick) materials. Here, we report nanoscale chemical speciation by combining scanning nanoprobe and fluorescence-yield x-ray absorption near-edge structure (nano-XANES). First, the resolving power of nano-XANES was demonstrated by mapping Fe(0) and Fe(III) states of a reference sample composed of stainless steel and hematite nanoparticles with 50-nm scanning steps. Nano-XANES was then used to study the trace secondary phases in lithium iron phosphate (LFP) particles. We observed individual Fe-phosphide nanoparticles in pristine LFP, whereas partially (de)lithiated particles showed Fe-phosphide nanonetworks. These findings shed light on the contradictory reports on Fe-phosphide morphology in the literature. Nano-XANES bridges the capability gap of spectromicroscopy methods and provides exciting research opportunities across multiple disciplines.

A novel bacteriocin BM1029: physicochemical characterization, antibacterial modes and application

AIM

Bacteriocins with antimicrobial activity are considered as potential natural bio-preservatives to control the growth of food spoilage bacteria. The aim of this work was to characterize a novel bacteriocin BM1029 discovered from Lactobacillus crustorum MN047 and evaluate its antibacterial mechanism.

METHODS AND RESULTS

Bacteriocin BM1029 was purified by cation-exchange chromatography and reversed-phase chromatography. Antibacterial activity assay showed that BM1029 is antagonistic against both Gram-positive and Gram-negative bacteria. Furthermore, it was found that BM1029 showed low haemolysis with high stability to the pretreatment with different temperatures, pH and surfactants. Moreover electron microscopy and flow cytometry suggested that BM1029 inhibit indicator strains by damaging the cell envelope integrity. Cell cycle assay suggested that BM1029 arrested cell cycle in R-phase.

CONCLUSION

The novel bacteriocin BM1029 showed high bactericidal activity against Escherichia coli and Staphylococcus aureus through a cell envelope-associated mechanism.

SIGNIFICANCE AND IMPACT OF THE STUDY

Application of BM1029 inhibited the growth of indicator strains on beef meat storage at 4°C suggesting that this bacteriocin is promising to be used as a novel preservative in food processing and preservation.

Abstract 6466: Serum immunoglobulins are an independent prognostic marker of time to first therapy in newly diagnosed chronic lymphocytic leukemia (CLL) and monoclonal B-cell lymphocytosis (MBL)

Immune dysfunction is a hallmark of CLL/MBL; ~25% individuals with newly diagnosed CLL have hypogammaglobulinemia at diagnosis. In this study of newly diagnosed CLL/MBL, we sought to a) investigate the association between serum immunoglobulins and specific mutations identified by next generation sequencing, and b) determine if serum immunoglobulin levels predict TFT, independent of the CLL-International Prognostic Index (CLL-IPI) and tumor mutational load (TML).

We used the Mayo Clinic CLL Resource to identify newly diagnosed CLL/MBL individuals consented within 2 years of diagnosis. Baseline clinical characteristics and the CLL-IPI score was ascertained on all individuals. DNA was extracted from peripheral blood CD5+/CD19+ clonal B-cells; and the entire coding regions of 60 somatically recurring mutated CLL driver genes were enriched using a customized Agilent SureSelect gene panel and sequenced in Illumina Hiseq4000. Serum immunoglobulins were quantitated by radial immunodiffusion using Immunoplates. The relationship between serum immunoglobulins was assessed: a) with individual gene mutations (mutated vs. not); and b) using the TML score (using a value of 0, 1, and 2 or greater [2+] mutated genes). The impact of serum immunoglobulin levels on TFT was analyzed for all individuals.

Of 356 individuals identified, 80 (22%) had MBL, median age was 63 years (28-87), 261 (73%) were male, and the CLL-IPI distribution was: low risk (n=149, 42%), intermediate risk (n=112, 32%), and high/very high risk (n=94, 26%). We observed 43%, 39%, and 18% individuals with 0, 1, or 2+ mutated genes, respectively. The most commonly mutated genes were NOTCH1 (13%), SF3B1 (13%), TP53 (8%), ATM (8%), BIRC3 (7%), and NFKBIE (7%). Using standard cutoffs, 135 (38%) individuals had low serum IgG, 73 (21%) had low serum IgA, and 154 (44%) had low serum IgM at diagnosis.

There were no differences in individual gene mutation frequencies between individuals with low and normal serum IgG. In contrast, individuals with low serum IgA were more likely to have mutations in NOTCH1 (25% vs 10%) and ATM (14% vs 7%) compared to those with normal IgA, and individuals with low serum IgM were more likely to have mutations in NOTCH1 (19% vs 9%) and BIRC3 (11% vs 4%) compared to those with normal IgM (all p-values &lt;0.05). There were no significant differences in individuals with low serum IgG based on TML scores of 0, 1, and 2+ (31%, 35%, 40%, respectively, p=0.28). However, individuals with low serum IgA and low serum IgM were more likely to have a higher TML (8%, 20%, 36% for IgA, p&lt;0.0001; and 35%, 45%, 54% for IgM, p&lt;0.0001, for TML scores of 0, 1, and 2+, respectively).

After a median follow-up of 6.9 years, 157 individuals required CLL therapy. After adjusting for CLL-IPI and TML, low serum IgG, low serum IgA, and low serum IgM (hazard ratio [HR]: 1.8, 2.3, and 2.4, respectively, all p-values &lt;0.05) were independently associated with a shorter TFT.

Our study shows that individuals with CLL/MBL who harbor mutations in NOTCH1, ATM and BIRC3 are more likely to have low serum IgA and IgM at diagnosis. Serum IgA and IgM (but not serum IgG) levels decrease with an increase in the TML score. Finally, low serum immunoglobulins can predict TFT, independent of the CLL-IPI and TML, which has important implications for risk stratification in newly diagnosed CLL/MBL.

Citation Format: Sameer A. Parikh, Cristine Allmer, Geffen Kleinstern, Nicholas J. Boddicker, Shulan Tian, Cecilia B. De Campos, Laura A. Bruins, Daniel R. o"brien, Brian F. Kabat, Kari G. Rabe, Aaron D. Norman, Huihuang Yan, Xing Li, Timothy G. Call, Wei Ding, Jose F. Leis, Saad J. Kenderian, Celine M. Vachon, James R. Cerhan, Neil E. Kay, Susan L. Slager, Esteban Braggio. Serum immunoglobulins are an independent prognostic marker of time to first therapy in newly diagnosed chronic lymphocytic leukemia (CLL) and monoclonal B-cell lymphocytosis (MBL) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6466.

Abstract 1256: Widespread alterations of chromatin accessibility in chronic lymphocytic leukemia (CLL)

Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in western countries that has a strong genetic basis. Using data from both chromatin immunoprecipitation and sequencing (ChIP-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq), recent studies have uncovered alterations of chromatin landscape in CLL. However, the spectrum of epigenetic changes and the mechanisms of casualtyare only partially understood. In this study, we used ATAC-seq to profile chromatin accessibility across the two major CLL subtypes, IGHV-mutated (n=19) and IGHV-unmutated (n=22). DNA library of accessible chromatin regions was generated from purified CD5+/CD19+ leukemiacells. All libraries were assessed to have high data quality based on the ENCODE quality metrics. Additionally, publicly available ATAC-seq data (GSE118189 and GSE111015) from total (n=5), memory (n=6) and naïve B cells (n=6) were analyzed in parallel and used as normal reference. ATAC-seq peaks from CLL and normal B cells were merged to generate a consensus list of 107,928 high-confidence peaks that did not overlap ENCODE blacklisted regions, were present in at least two CLL or two normal B-cell samples, and had ≥1 counts-per-million in at least 10% of the samples. Raw read counts were Trimmed Mean of M-values normalized and log2 transformed. K-means clustering of differential peaks revealed an extensive reprogramming of chromatin accessibility landscape in CLL, with over 11,000 lost and nearly 9,000 gained open chromatin regions relative to normal B-cells. In particular, we identified two clusters comprising 1,401 regions that were largely open either in IGHV-mutated(571 peaks) or in IGHV-unmutated CLL (830 peaks). Open chromatin regions gained in IGHV-mutatedwere preferentially linked to genes in the B cell receptor signaling pathway and those in IGHV-mutatedto genes enriched in the interferon type I signaling pathway. These discriminatory regions are highly enriched with DNA binding motifs for transcription factors (TFs) with key roles in B cell development, such as PU.1, AP-1, c-Jun, BATF, and TCF family. In addition, 94% of the 1,401 peaks were located in distal regulatory regions, being ≥2.5 kb away from transcription start sites of genes; two-third of these distal regulatory regions overlapped H3K27ac peaks from CLL patients or immune cell types in the Roadmap reference epigenomes,indicating that enhancers are the prime sites of epigenetic differentiation between the two subtypes. Together, our analyses provide new insights into the global alterations of regulatory regions in CLL. Given the noticeable heterogeneity of chromatin landscape, further integration with histone modifications, TF binding, chromatin interaction, gene expression and genetic variation data are needed to understand the roles of epigenetic dysregulation and its interaction with genetic lesions in CLL pathogenesis.

Citation Format: Huihuang Yan, Zhiquan Wang, Shulan Tian, Geffen Kleinstern, Nicholas Boddicker, Xing Li, Susan Slager, Esteban Braggio. Widespread alterations of chromatin accessibility in chronic lymphocytic leukemia (CLL) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1256.

Wnt-induced, TRP53-mediated Cell Cycle Arrest of Precursors Underlies Interstitial Cell of Cajal Depletion During Aging

BACKGROUND & AIMS

Gastric dysfunction in the elderly may cause reduced food intake, frailty, and increased mortality. The pacemaker and neuromodulator cells interstitial cells of Cajal (ICC) decline with age in humans, and their loss contributes to gastric dysfunction in progeric klotho mice hypomorphic for the anti-aging Klotho protein. The mechanisms of ICC depletion remain unclear. Klotho attenuates Wnt (wingless-type MMTV integration site) signaling. Here, we examined whether unopposed Wnt signaling could underlie aging-associated ICC loss by up-regulating transformation related protein TRP53 in ICC stem cells (ICC-SC).

METHODS

Mice aged 1-107 weeks, klotho mice, APC^Δ468 mice with overactive Wnt signaling, mouse ICC-SC, and human gastric smooth muscles were studied by RNA sequencing, reverse transcription-polymerase chain reaction, immunoblots, immunofluorescence, histochemistry, flow cytometry, and methyltetrazolium, ethynyl/bromodeoxyuridine incorporation, and ex-vivo gastric compliance assays. Cells were manipulated pharmacologically and by gene overexpression and RNA interference.

RESULTS

The klotho and aged mice showed similar ICC loss and impaired gastric compliance. ICC-SC decline preceded ICC depletion. Canonical Wnt signaling and TRP53 increased in gastric muscles of klotho and aged mice and middle-aged humans. Overstimulated canonical Wnt signaling increased DNA damage response and TRP53 and reduced ICC-SC self-renewal and gastric ICC. TRP53 induction persistently inhibited G₁/S and G₂/M cell cycle phase transitions without activating apoptosis, autophagy, cellular quiescence, or canonical markers/mediators of senescence. G₁/S block reflected increased cyclin-dependent kinase inhibitor 1B and reduced cyclin D1 from reduced extracellular signal-regulated kinase activity.

CONCLUSIONS

Increased Wnt signaling causes age-related ICC loss by up-regulating TRP53, which induces persistent ICC-SC cell cycle arrest without up-regulating canonical senescence markers.

Genome-wide Analyses Identify a Novel Risk Locus for Nonsyndromic Cleft Palate

The 3 major subphenotypes observed in patients with nonsyndromic orofacial clefts (NSOFCs) are nonsyndromic cleft lip only (NSCLO), nonsyndromic cleft lip with palate (NSCLP), and nonsyndromic cleft palate only (NSCPO). However, the genetic architecture underlying NSCPO is largely unknown. Here we performed a 2-stage genome-wide association study (GWAS) on NSCPO and replication analyses of selected variants in other NSOFCs from the Chinese Han population. We identified a novel locus (15q24.3) and a known locus (1q32.2) where variants in or near the gene reached genome-wide significance (2.80 × 10^-13 < P < 1.72 × 10^-08) in a test for association with NSCPO in a case-control design. Although a variant from 15q24.3 was found to be significantly associated with both NSCPO and NSCLP, the direction of estimated effects on risk were opposite. Our functional annotation of the risk alleles within 15q24.3 coupled with previously established roles of the candidate genes within identified risk loci in periderm development, embryonic patterning, and/or regulation of cellular processes supports their involvement in palate development and the pathogenesis of cleft palate. Our study advances the understanding of the genetic basis of NSOFCs and provides novel insights into the pathogenesis of NSCPO.

Contribution of single-gene defects to congenital cardiac left-sided lesions in the prenatal setting

OBJECTIVES

To explore the contribution of single-gene defects to the genetic cause of cardiac left-sided lesions (LSLs), and to evaluate the incremental diagnostic yield of whole-exome sequencing (WES) for single-gene defects in fetuses with LSLs without aneuploidy or a pathogenic copy-number variant (pCNV).

METHODS

Between 10 April 2015 and 30 October 2018, we recruited 80 pregnant women diagnosed with a LSL who had termination of pregnancy and genetic testing. Eligible LSLs were aortic valve atresia or stenosis, coarctation of the aorta, mitral atresia or stenosis and hypoplastic left heart syndrome (HLHS). CNV sequencing (CNV-seq) and WES were performed sequentially on specimens from these fetuses and their parents. CNV-seq was used to identify aneuploidies and pCNVs, while WES was used to identify diagnostic genetic variants in cases without aneuploidy or pCNV.

RESULTS

Of 80 pregnancies included in the study, 27 (33.8%) had a genetic diagnosis. CNV-seq analysis identified six (7.5%) fetuses with aneuploidy and eight (10.0%) with pCNVs. WES analysis of the remaining 66 cases revealed diagnostic genetic variants in 13 (19.7%) cases, indicating that the diagnostic yield of WES for the entire cohort was 16.3% (13/80). KMT2D was the most frequently mutated gene (7/66 (10.6%)) in fetuses with LSL without aneuploidy or pCNVs, followed by NOTCH1 (4/66 (6.1%)). HLHS was the most prevalent cardiac phenotype (4/7) in cases with a KMT2D mutation in this cohort. An additional six (9.1%) cases were found to have potentially deleterious variants in candidate genes.

CONCLUSIONS

Single-gene defects contribute substantially to the genetic etiology of fetal LSLs. KMT2D mutations accounted for approximately 10% of LSLs in our fetal cohort. WES has the potential to provide genetic diagnoses in fetuses with LSLs without aneuploidy or pCNVs. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Tumor mutational load predicts time to first treatment in chronic lymphocytic leukemia (CLL) and monoclonal B-cell lymphocytosis beyond the CLL international prognostic index

Next-generation sequencing identified about 60 genes recurrently mutated in chronic lymphocytic leukemia (CLL). We examined the additive prognostic value of the total number of recurrently mutated CLL genes (i.e., tumor mutational load [TML]) or the individually mutated genes beyond the CLL international prognostic index (CLL-IPI) in newly diagnosed CLL and high-count monoclonal B-cell lymphocytosis (HC MBL). We sequenced 59 genes among 557 individuals (112 HC MBL/445 CLL) in a multi-stage design, to estimate hazard ratios (HR) and 95% confidence intervals (CI) for time-to-first treatment (TTT), adjusted for CLL-IPI and sex. TML was associated with shorter TTT in the discovery and validation cohorts, with a combined estimate of continuous HR = 1.27 (CI:1.17-1.39, P = 2.6 × 10^-8 ; c-statistic = 0.76). When stratified by CLL-IPI, the association of TML with TTT was stronger and validated within low/intermediate risk (combined HR = 1.54, CI:1.37-1.72, P = 7.0 × 10^-14 ). Overall, 80% of low/intermediate CLL-IPI cases with two or more mutated genes progressed to require therapy within 5 years, compared to 24% among those without mutations. TML was also associated with shorter TTT in the HC MBL cohort (HR = 1.53, CI:1.12-2.07, P = .007; c-statistic = 0.71). TML is a strong prognostic factor for TTT independent of CLL-IPI, especially among low/intermediate CLL-IPI risk, and a better predictor than any single gene. Mutational screening at early stages may improve risk stratification and better predict TTT.

[Analysis of chloroquine-resistant gene polymorphisms in Plasmodium falciparum imported into China in 2012 and 2018]

OBJECTIVE

To detect the chloroquine-resistant molecular marker polymorphisms in Plasmodium falciparum imported into China, investigate the mutation types of P. falciparum chloroquine resistant transporter (Pfcrt) gene at positions 72 to 76, and analyze the specificity of the P. falciparum specimens with different origins.

METHODS

A total of 674 filter paper blood samples were collected from the National Malaria Diagnosis Reference Laboratory of China in 2012 and 2018. The amino acid po- sitions 72 to 76 of the Pfcrt gene on chromosome 7 were amplified using nested PCR assay and sequenced, and the sequencing results of the target gene fragment and the geographical region-specific prevalence of the mutations in the Pfcrt gene were analyzed.

RESULTS

Among the 674 imported P. falciparum malaria cases in China in 2012 and 2018, 99.5% (644/674) were from Africa, which were predominantly from western and central Africa (80.4%, 518/644), and 4.5% (30/674) from Southeast Asia and Oceania (Papua New Guinea). A total of 4 site mutations (C72S, M74I, N75E and K76T) and 5 haplotypes (CVMNK, CVIET and SVMNT and two mixed types) were identified, with haplotypes CVMNK and CVIET present in parasites of both African and Southeast Asian origins, SVMNT detected in Southeast Asia (Myanmar) and Papua New Guinea isolates, the mixed type of haplo- types CVMNK/CVIET detected in P. falciparum of African and Southeast Asian origins, and the mixed type of haplotypes CVMNK/SVMNT detected only in the Myanmar isolate. Most P. falciparum parasites of the African origin carried the wild-type Pfcrt allele (77.7%, 478/615), and 68.0% (17/25) of the P. falciparum parasites of the Southeast Asian and Papua New Guinea or- igins harbored chloroquine resistant molecular markers (χ² = 28.5, P < 0.05). The constituent ratio of the wild- and mutant-type Pfcrt allele varied in different geographical regions of Africa (P < 0.01), and the lowest prevalence of the wild-type Pfcrt allele was seen in western Africa.

CONCLUSIONS

Among the 674 imported malaria cases in China in 2012 and 2018, the P. falciparum imported from Sotheast Asia habors a higher proportion of resistance to chloroquine and a higher molecular polymophism at ami- no acid positions 72 to 76 of the Pfcrt gene than the parasite of the African origin.