HEIDI: an experiment-management platform enabling high-throughput fragment and compound screening

The Swiss Light Source facilitates fragment-based drug-discovery campaigns for academic and industrial users through the Fast Fragment and Compound Screening (FFCS) software suite. This framework is further enriched by the option to utilize the Smart Digital User (SDU) software for automated data collection across the PXI, PXII and PXIII beamlines. In this work, the newly developed HEIDI webpage (https://heidi.psi.ch) is introduced: a platform crafted using state-of-the-art software architecture and web technologies for sample management of rotational data experiments. The HEIDI webpage features a data-review tab for enhanced result visualization and provides programmatic access through a representational state transfer application programming interface (REST API). The migration of the local FFCS MongoDB instance to the cloud is highlighted and detailed. This transition ensures secure, encrypted and consistently accessible data through a robust and reliable REST API tailored for the FFCS software suite. Collectively, these advancements not only significantly elevate the user experience, but also pave the way for future expansions and improvements in the capabilities of the system.

[Epidemic characteristics and trend analysis of major injuries deaths among children and adolescents in Jiangsu Province from 2012 to 2021]

Objective: To understand the situation and epidemic characteristics of injury deaths among children aged 5 to 24 years in Jiangsu Province from 2012 to 2021 and the trend of annual changes. Methods: The main injury mortality data of children and adolescents was collected, and the crude and standardized mortality rates of road traffic accidents, drowning, suicide, and accidental falls among children and adolescents over a decade and the annual average percentage of change (AAPC) were calculated. The main injury mortality characteristics and trends of children and adolescents of different age groups and genders were analyzed. Results: The total number of injury deaths among 5 to 24 adolescents in Jiangsu Province was 16 052, with a standardized mortality rate of 9.58/100 000. There was no significant trend in the overall standardized mortality rate of injuries (AAPC=-3.450%, P=0.055). The standardized mortality rate of road traffic injuries among children and adolescents showed a decreasing trend over the past decade, with statistical significance (AAPC=-9.406%, P<0.001). The standardized suicide mortality rate showed an upward trend over the past decade, with statistical significance (AAPC=9.000%, P=0.001). The overall injury mortality rate showed an upward trend with age. Suicide rates in males and females were on the rise and both have statistical significance (AAPC=9.420% and AAPC=9.607%, both P<0.05). The standardized mortality rates of female traffic accidents, drowning, and male traffic accidents showed a decreasing trend and were statistically significant (AAPC for female traffic accidents=-7.364%, AAPC for female drowning=-5.352%, and AAPC for male traffic accidents=-10.242%, all P<0.05). The standardized mortality rate of urban and rural traffic accidents showed a decreasing trend and was statistically significant(AAPC=-7.899% and AAPC=-9.421%, both P<0.001). The standardized suicide mortality rate showed an upward trend and statistical significance (AAPC=11.009% and AAPC=7.528%, both P<0.05). Conclusions: The overall injury situation of children and adolescents in Jiangsu Province improved in the past decade from 2012 to 2021, but the suicide mortality rate was on the rise. It is necessary to focus on the mental health issues of this age group and to strengthen the prevention and control of suicide among children and adolescents, in Jiangsu.

Changes in anisometropia by age in children with hyperopia, myopia, and antimetropia

Anisometropia is a unique condition of both eyes and it is associated with vision problems such as amblyopia and reduced stereoacuity. Previous studies have not reported its change pattern by age and its correlation with the refractive condition of both eyes. This study aims to compare the changes in anisometropia by age in children with hyperopia, myopia, and antimetropia. In total, 156 children were included. Children aged 3-11 years with anisometropia ≥ 1.00 D were followed up for ≥ 1 year with ≥ 2 visits at two medical centers in Taiwan. Refractive errors by cycloplegic autorefractometry, best-corrected visual acuity, eye position, and atropine use were recorded. The children were divided into hyperopic, myopic, and antimetropic groups. The results showed that anisometropia decreased in children aged < 6 years (3.34-2.96 D; P = 0.038) and increased in older children (2.16-2.55 D; P = 0.005). In children aged 3, 4, 5, and 6 years, the mean anisometropia was higher in children with myopia and antimetropia than in those with hyperopia (P = 0.005, 0.002, 0.001, and 0.011, respectively). The differences were not significant in children aged > 6 years (all P > 0.05). The factors associated with changes in anisometropia were age, refractive group, amblyopia, and strabismus. Anisometropia decreased with age in children younger than 6 years, and the changes in anisometropia was found in children with myopia and antimetropia.

[Investigation of familial tendency of endometriosis]

Objective: To investigate the familial heritability of endometriosis and to compare the clinical characteristics of patients with or without a family history of endometriosis. Methods: From January 2020 to June 2022, 850 patients with endometriosis confirmed by laparotomy or laparoscopy in Peking University Third Hospital were included in this study. Clinical data were collected, family history was followed up, and the differences of clinical indicators between patients with and without family history of endometriosis were compared. Results: A total of 850 patients were enrolled, with an average age of (33.8±7.0) years old, 315 (37.1%, 315/850) patients in stage Ⅲ and 496 (58.4%, 496/850) patients in stage Ⅳ. There were 100 patients with family history of endometriosis, accounting for 11.8% (100/850). Most of the 113 relatives involved were mothers, daughters and sisters (76.1%, 86/113), 81.5% (22/27) of the second and third degree relatives were maternal relatives. The median ages of patients with and without family history of endometriosis were 30 and 33 years old respectively at the time of diagnosis. The unmarried rate of patients with family history was higher [42.0% (42/100) vs 26.3% (197/750)]. The percentage of dysmenorrhea patients with family history was higher [89.0% (89/100) vs 55.5% (416/750)]. The medians of dysmenorrhea score in patients with and without family history were 6 and 2, and the median durations of dysmenorrhea were 10 and 1 years. There were significant differences in age, marital status, percentage of dysmenorrhea, dysmenorrhea score and duration (all P<0.001). The median levels of serum cancer antigen (CA) 125 in patients with family history and patients without family history at the time of diagnosis were 57.5 and 46.9 kU/L respectively, with a statistically significant difference (P<0.05). However, there were no significant differences between the two groups in nationality, bady mass index, menarche age, menstrual cycle, menstrual period, menstrual volume, serum CA_19-9 level, cyst location and size, stage, history of adverse pregnancy and childbirth, infertility, adenomyosis and deep infiltrating endometriosis (all P>0.05). By comparing the specific conditions of dysmenorrhea patients with and without family history of endometriosis, there were no significant differences between the two groups in terms of the age of onset of dysmenorrhea, duration of dysmenorrhea, primary and secondary dysmenorrhea, and progressive aggravation of dysmenorrhea (all P>0.05). The difference in the degree of dysmenorrhea in dysmenorrhea patients with family history of endometriosis was significant (P<0.001). Conclusions: The incidence of endometriosis has a familial tendency, and most of the involved relatives are the first degree relatives. Compared with patients without family history of endometriosis, endometriosis patients with family history are diagnosed at an earlier age, with higher percentage of dysmenorrhea, had more severe dysmenorrhea and higher serum CA₁₂₅ level.

Continuous wave dual-wavelength Nd:YVO4 laser at 1342 and 1525 nm for generating a 714-nm emission

Continuous wave dual-wavelength lasers at 1342 and 1525 nm are developed by using separate Nd:YVO₄ and YVO₄ crystals to form compactly coupled cavities for fundamental and Raman waves, respectively. The design of the coupled cavity not only reduces the thermal lensing effect in the Nd:YVO₄ crystal, but also improves the stimulated Raman scattering (SRS) efficiency in the undoped YVO₄ crystal. In addition, the Raman crystal is coated to form a highly reflective mirror to minimize cavity losses. By using a plano-concave cavity with a pump power of 40 W, the output powers of the fundamental and Raman waves are 470 mW and 310 mW, respectively. Changed to a concave cavity, the output powers of fundamental and Raman waves are 220 mW and 510 mW, respectively. Basis on the dual-wavelength operation, the maximum output power at 714 nm can reach 2.0 W via the sum frequency generation. A light source at 714 nm can be used for laser spectroscopy of atomic and ionic radium isotopes.

[Clinical application of bipolar tweezers-clamp for hepatic parenchymal transection]

Objective: To investigate the clinical value of the bipolar tweezers-clamp for the hepatic parenchymal transection in the resection of hepatocellular carcinoma. Methods: From January 2020 to January 2021,63 patients with the hepatocellular carcinoma for hepatectomy at Department of Hepatopancreatobiliary Surgery,Yuebei People's Hospital Affiliated to Shantou University Medical College were analyzed retrospectively.According to the different instruments used in the hepatic parenchymal transection,the patients were divided into bipolar tweezers-clamp group and ultrasonic scalpel group.There were 32 patients in bipolar tweezers-clamp group,with age of (55.5±10.5)years(range:37 to 78 years),including 22 males and 10 females,tumor size was (6.0±3.4)cm(range:2.4 to 13.4 cm). There were 6 patients with portal vein tumor thrombus and 5 patients with portal hypertension. There were 31 patients in ultrasonic scalpel group,with aged(57.8±10.1)years(range:37 to 79 years),including 27males and 4 females,tumor size was(7.9±5.1)cm(range: 2.4 to 21.3 cm),3 patients with portal vein tumor thrombus and 2 patients with portal hypertension. The preoperative baseline data,operation time,blood loss,postoperative liver function and the complications were compared between two groups using t test,χ² test and Fisher exact probabilityrespectively. Results: The operation was successfully completed in both groups.Compared with the ultrasonic scalpel group,the operation time was significantly shorter((219.3±76.4)minutes vs.(294.0±100.8)minutes,t=-3.322,P=0.002),the blood loss was less((250(475)ml vs. 500(1 050)ml,t=-2.307,P=0.026),the concentrate red blood cells transfusion volume was less(0.92(0.88)U vs. 2.32(4.00)U,Z=-1.987,P=0.047) in the bipolar tweezers-clamp group.The postoperative serum ALB level was higher in the bipolar tweezers-clamp group than that in the ultrasonic scalpel group((33.5±6.1)g/L vs. (29.5±4.2)g/L,t=3.226,P=0.020) on postoperative day 1;((35.7±4.5)g/L vs.(30.1±3.2)g/L,t=5.575,P<0.01) on postoperative day 3;((33.2±3.7)g/L vs. (31.0±4.4)g/L,t=3.020,P=0.004) on postoperative day 7. There was no significant difference in serum ALT,TBIL and PT level between the two groups(all P>0.05).No postoperative bile leakage occurred in both groups.The postoperative complications occurred in 8 cases(25.0%)in the bipolar tweezers-clamp group,including liver failure in one,and in 11 cases(35.5%)in the ultrasonic scalpel group,including liver failure in two(P>0.05). Conclusion: The bipolar tweezers-clamp is a safe and reliable method for the hepatic parenchymal transaction,which is quick and less bleeding during the hepatic resection.

[Study of clinical characteristics in patients with gp210 antibody-positive primary biliary cholangitis]

Objective: To analyze the clinical characteristics and prognostic value of liver function in a large samples of patients with anti-glycoprotein 210 (gp210 antibody) positive primary biliary cholangitis (PBC). Methods: A retrospective study was performed on 931 PBC cases in Beijing You'an Hospital affiliated to Capital Medical University from 2010 to 2019. According to the detection of gp210 antibody, 318 cases were divided into gp210 antibody positive group (positive group) and 613 cases were divided into gp210 antibody negative group (negative group). The differences in demographic, medical history, clinical indicators, B-ultrasound and pathological indicators as well as the histopathological basis were compared between the two groups. SPSS 16.0 software was used for statistical analysis. Measurement data were analyzed by t-test or rank sum test, and enumeration data by χ² test. Multivariate analysis was used for logistic test, and and survival analysis was used for prognosis. Results: The positive and the negative groups were compared. The ratio of male to female was significantly higher in positive than negative group (1:5.35 vs. 1:9.73, P＜0.05), and the difference was statistically significant. The proportion of hormone use in history of past diagnosed and treated was higher in positive than negative group (12.9% vs. 3.47%, P＜0.05), and the difference was statistically significant. The detection of biochemical indexes such as alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), alkaline phosphatase (ALP), glutamyl transpeptidase (GGT) were higher in positive than the negative group (51.1 U/L vs. 41.1 U/L, 62.6 U/L vs. 49.6 U/L, 24.1 μmol/L vs. 17.9 μmol/L, 228.3 U/L vs. 169.6 U/L, 203.9 U/L vs. 147.6 U/L), (P＜0.05), and the differences were statistically significant. Antinuclear antibody (ANA)-positive rate, high titer ratio and immunoglobulin G (IgG) levels were higher in positive than negative group (95.2% vs. 81.6%, 69.7% vs. 48.8%, 17.2 g/L vs. 16.2 g/L), (P＜0.05), and the differences were statistically significant. The incidence of liver failure was higher in positive than negative group (P＜0.05). CK7 and inflammation score were higher in positive group than negative group in liver histopathological observations (0.83±0.53 vs. 0.28±0.47; 1.06±0.39 vs. 0.54±0.65), (P＜0.05), and the differences were statistically significant. Conclusion: The illness condition of patients with gp210 antibody positive PBC is more severe than patients with gp210 antibody negative PBC, and the incidence of liver failure is significantly increased. Cholangiocytes may be the histopathological basis of the clinical characteristics of gp210 antibody positive PBC patients.

[Characteristics of clinical and laboratory indexes in patients with liver disease with positive anti-liver cytosol antibody]

Objective: To analyze the characteristics of clinical and laboratory indexes in patients with liver disease with positive anti-liver cytosol antibody type 1 (anti-LC1), in order to provide references for clinical and differential diagnosis. Methods: The clinical data of 23 832 inpatients and outpatients with positive anti-LC1 autoantibodies detected in routine autoantibody test from January 2010 to January 2020 were retrospectively analyzed, and their clinical and laboratory indexes were compared. Western blotting was used to detect anti-LC1, anti-soluble liver antigen antibody (anti-SLA), anti-glycoprotein 210 antibodies and anti-nucleosome 100 antibodies. Indirect immunofluorescence assay was used to detect anti-nuclear antibody (ANA), anti-mitochondrial antibody, anti-Smooth muscle antibody (ASMA), anti-liver and kidney microsomal antibody (anti-LKM) and other autoantibodies. Normally distributed measurement data between the two groups were compared by independent-sample t-test, and the multiple groups comparison were compared by one-way analysis of variance. Non-normally distributed measurement data were compared by non-parametric rank sum test. Results: 38 anti-LC1 positive patients were detected in 23832 autoantibody tests. The age of initial diagnosis ranged from 11.0 to 84.0 (50.6 ± 16.0) years. There were 8 males (21.1%) and 30 females (78.9%). A total of 31 cases (81.6%) were positive for anti-LC1 and ANA, and the dominant karyotype was speckled pattern, accounting for 54.8%. Five cases (13.2%) were positive for ASMA, and no simultaneous positive with anti-LKM or anti-SLA. Among the 38 anti-LC1 positive patients, 9 were diagnosed with autoimmune hepatitis (AIH), 6 with possible AIH, 6 with primary biliary cholangitis (PBC), 8 with hepatitis B, 2 with hepatitis C, 1 with alcoholic liver disease, 2 with non-alcoholic fatty liver disease, 1 with drug-induced liver injury, 1 with hepatolenticular degeneration, and 2 with tumor. Confirmed and probable AIH cases accounted for 39.5% (15/38) of anti-LC1 positive cases. Among anti-LC1 positive patients, 47.4% (18/38) had entered the stage of liver cirrhosis. AIH group globulin level was higher than HBV group (P = 0.006) and other disease groups (P = 0.001). AIH group IgG level was higher than PBC group (P = 0.027), HBV group (P = 0.009) and other disease groups (P = 0.004). the of the PBC group IgM level was higher than AIH group (P = 0.003), HBV group (P = 0.003) and other disease groups (P = 0.006). Conclusion: Anti-LC1 is not only detected in AIH, but also observed in patients with primary biliary cholangitis, hepatitis B and C, alcoholic and non-alcoholic liver disease, drug-induced liver injury, hereditary metabolic liver disease and tumor. In addition, it is mainly female gender dominance and nearly half of ANA-positive young, middle-aged and elderly patients develop liver cirrhosis. For the diagnosis of type 2 autoimmune hepatitis, whether anti-LC1 is a specific antibody needs further research, but if AIH is highly suspected, this antibody can be used as a substitute.

Comparison of modeling accuracy between Radixact®and CyberKnife®Synchrony®respiratory tracking system

Synchrony Respiratory Tracking system adapted from CyberKnife has been introduced in Radixact to compensate the tumor motion caused by respiration. This study aims to compare the modeling accuracy of the Synchrony system between Radixact and CyberKnife. Two Synchrony plans based on fiducial phantoms were created for CyberKnife and Radixact, respectively. Different respiratory motion traces were used to drive a motion platform to move along the superoinferior and left-right direction. The cycle time and the amplitude of target/surrogate motion of one selected motion trace were scaled to investigate the dependence of modeling accuracy on the motion characteristic. The predicted target position, the correlation error, potential difference (Radixact only) and standard error (CyberKnife only) were extracted from raw data or log files of the two systems. The modeling accuracy was evaluated by calculating the root-mean-square (RMS) error between the predicted target positions and the input motion trace. A threshold T95 within which 95% of the potential difference or the standard error lay was defined and evaluated. Except for the motion trace with a small amplitude and a good (linear) correlation between target and surrogate motion, Radixact showed smaller RMS errors than CyberKnife. The RMS error of both systems increased with the motion amplitude and showed a decreasing trend with the increasing cycle time. No correlation was found between the RMS error and the amplitude of surrogate motion. T95 could be a good estimator of modeling accuracy for CyberKnife rather than Radixact. The correlation error defined in Radixact were largely affected by the number of fiducial markers and the setup error. In general, the modeling accuracy of the Radixact Synchrony system is better than that of the CyberKnife Synchrony system under unfavorable conditions.

Abstract 466: Differential expression of circRNAs allows discrimination of NSCLC from cancer-free lung specimens using the nCounter platform

Introduction: Lung cancer mortality ranks as the highest of the cancer-related deaths. Studies on tumor profiling at the genomic, transcriptomic and proteomic level has soared in the last decade improving overall survival of these patients by shaping the current targeted therapies; however, further investigation of novel biomarkers for an early diagnosis still remains imperative.circRNAs are a class of tissue-specific stable structures that control mammalian transcription. Their aberrant expression plays an important role in carcinogenesis and tumor progression which profiles them as valuable biomarkers; Conversely, its potential has not been fully explored in lung cancer due to several limitations of current circRNA quantification methods that prevent their clinical implementation.The nCounter technology allows for quantitative and qualitative assessment of up to 800 targets providing an accurate and factual perspective of expression levels. To our knowledge, thru this study we stand as the first on assessing circRNA differential expression with this platform for lung cancer detection both in FFPE specimens and cell lines providing preliminary evidence of their differential expression in lung cancer.

Methods: Cells were cultured under standard conditions until harvested. RNA was isolated by using Allprep DNA/RNA/miRNA universal kit (Qiagen). FFPE lung tissue samples (n=28; 18 NSCLC,10 non-cancer) were retrospectively collected and micro-dissected. RNA was isolated with High Pure FFPET RNA isolation kit (Roche) and quantified by Qubit (Thermo Fisher).Overnight hybridization and posterior nCounter FLEX processing were performed following NanoString protocol for nCounter Elements. Expression analysis was carried out based on a tailored panel of 85 circRNAs related to the biology of the disease.

Results: FFPE lung tissues revealed a cluster of differentially expressed circRNAs that allow distinction of lung cancer versus control. circFOXP1, circEPB41L2 and circBNC2 ranked as the most downregulated circRNAs, whereas circCHD9, circAASDH, circRUNX1 and circCHST15 led the catalog of most upregulated in cancer specimens. circRNA expression of A549, H2228, H3122, PC9, H1666, and HOP-62 cells was compared to the CCL-171 fibroblast cell line. circEPB41L2 and circFOXP1 were also confirmed distinctly downregulated in cancer cell lines.

Conclusion: This study presents for the first time the use of the differential expression of circRNAs in FFPE tissues for lung cancer discrimination using the nCounter platform. While more samples are currently being collected to increase the statistical power of the study, these results pave the way for the developing of future circRNA-based nCounter tests for lung cancer diagnosis. Further experiments using epithelial cells as control will be carried out and results will be pertinently updated at the time of the meeting.

Citation Format: Carlos Pedraz-Valdunciel, Miguel Ángel Molina-Vila, Stavros Giannoukakos, Nicolas Potie, Ruth Roman-Llado, Jill Bracht, Martyna Filipska, Masaoki Ito, Ana Gimenez-Capitán, Cristina Aguado-Esteban, Sarah Warren, Chung-Ying Huang, Trever Bivona, Rafael Rosell. Differential expression of circRNAs allows discrimination of NSCLC from cancer-free lung specimens using the nCounter platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 466.

Abstract 2606: A nCounter-Based mRNA signature in plasma associates with localized non-small cell lung cancer

Background: 80% of non-small cell lung cancer (NSCLC) cases are diagnosed at stages IIIB-IV and have a dismal prognosis with a median life expectancy that does not exceed 2 years. In contrast, patients diagnosed at early and locally advanced stages (I-IIIA) can undergo surgery and have the potential to be totally cured. Imaging technologies often detect lung nodules of unknown significance that pose a diagnostic challenge; some patients with benign nodules are submitted to unnecessary surgical interventions while others with small tumors are just kept in observation, risking a significant delay for treatment. A diagnostic test that could differentiate between benign and malignant masses would be of great help in this setting.

Methods: Circulating-free RNA (cfRNA) was isolated from the plasma of healthy individuals (N=21), early(I-II) stage (N=22) and stage IIIA (N=12) NSCLC patients, using an automatic extraction method(Qiasymphony, Qiagen). Purified cfRNA was quantified using Qubit, retrotranscribed and pre-amplified (14cycles) using the Low RNA Input Amplification kit (NanoString Technologies). Gene expression analysis was performed on the nCounter platform using the PanCancer IO360TM (NanoString Technologies), which can detect 770 transcripts related to tumor biology, micro-environment and the immune system.

Results: Gene expression analysis revealed differential patterns for some cf-mRNAs from localized stage NSCLC patients versus healthy controls. A bioinformatics recursive feature elimination algorithm selected a 16-gene mRNA signature that was able to distinguish between localized NSCLC and control samples with an area under the ROC curve of 0.91 to 0.95. Furthermore, the signature scores derived from the algorithm were significantly different between the two cohorts.

Conclusions: We have found an 16-gene signature that can differentiate between cfRNA of localized stages NSCLC patients and control individuals. Our results warrant validation studies in larger cohorts.

Citation Format: Ana Giménez Capitán, Jillian Bracht, Nicolas Potie, María González-Cao, Santiago Viteri, Alejandro Martínez-Bueno, Carlos Cabrera-Gálvez, Pablo Rubinstein, Clara Mayo-de-las-Casas, Joselyn Valarezo, Chung-Ying Huang, Carlos Pedraz, Richard Boykind, Sarah Warren, Rafael Rosell, Miguel Ángel Molina-Vilaa, Andrés Aguilar-Hernández. A nCounter-Based mRNA signature in plasma associates with localized non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2606.

Abstract 409: A pre-treatment plasma extracellular vesicle-mRNA signature associates with checkpoint inhibitor pneumonitis in lung cancer patients

Introduction: Immune checkpoint inhibitors (ICIs) have demonstrated clinical efficacy in non-small cell lung cancer (NSCLC) patients (p). However, ICIs can also trigger a self-reactive response in the adjacent healthy lung tissue that can eventually lead to life-threatening immune-related adverse events (irAEs), like checkpoint inhibitor pneumonitis (CIP). We hypothesized that a pre-treatment state of chronic inflammation or immune system imbalance could predict which p are at higher risk of developing CIP.

Methodology: We retrospectively collected pre-ICI-treatment FFPE tumor tissue and matching plasma samples from 17 CIP- and 24 non-CIP lung cancer p. An additional 40 plasma samples, including 3 CIP and 37 non-CIP p were used as a validation cohort. The miRCURY exosome isolation kit (Qiagen) was used for extracellular vesicle (EV) enrichment from 500 μL of plasma and RNA was extracted using TRI-reagent. EV-mRNA was then pre-amplified (10 cycles) using the Low RNA Input Amplification kit (NanoString Technologies). FFPE mRNA was extracted using the High Pure FFPET RNA Isolation Kit (Roche). Gene expression analysis was performed on tissue and EV-derived mRNA using the NanoString nCounter platform with the Human PanCancer IO360 panel, which targets 770 genes related to tumor biology, immune response and microenvironment. Differential expression (DE) analysis was carried out based on the development of CIP. Finally, a classifier was created using a bioinformatic recursive feature elimination and a leave-one-out cross validation algorithm to predict which combination of genes is most effective to predict CIP development.

Results: DE analysis revealed 54 differentially expressed genes (DEGs) in pre-treatment tissue of CIP vs. non-CIP p. An 8-gene CIP mRNA signature was able to distinguish between the two cohorts with areas under the ROC curve (AUC) of 0.81-0.95. When analyzing plasma EV samples, we found 57 DEGs. The tissue CIP signature was not translatable to EVs, yielding AUCs of only 0.53-0.54. Therefore, we developed a new 4-gene EV-based mRNA signature that could differentiate CIP vs. non-CIP developing p with AUCs of 0.82-0.90 and an overall accuracy of 89.9%. The negative- and positive predictive values (NPV and PPV) were 92.7% and 78.6%, respectively with a Youden´s index of 0.67. The 4 genes included in the EV signature were upregulated in CIP p and were found to be involved in T-cell activation and immune cell localization to the tumor.

Conclusions: We have created a 4-gene EV-mRNA signature that associates with CIP development upon ICI treatment. Our results also indicate that plasma EV-mRNA was non-inferior to invasive tissue biopsy analysis in predicting CIP development. Validation studies in larger patient cohorts are ongoing.

Citation Format: Jillian Wilhelmina Bracht, Santiago Viteri-Ramirez, Andrés Aguilar, Silvia Calabuig-Fariñas, Juan José García-Mosquera, Chung-Ying Huang, Elena Duréndez-Sáez, Nicolas Potie, Erika Aldeguer, Ana Gimenez-Capitán, Sonia Rodriguez, Ruth Roman, Cristina Aguado, Sarah Warren, Carlos Camps, Rafael Rosell, Eloisa Jantus-Lewintre, Miguel-Angel Molina-Vila, Maria González-Cao. A pre-treatment plasma extracellular vesicle-mRNA signature associates with checkpoint inhibitor pneumonitis in lung cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 409.

Probiotic Escherichia coli Nissle inhibits IL-6 and MAPK-mediated cardiac hypertrophy during STZ-induced diabetes in rats

Escherichia coli Nissle (EcN), a probiotic bacterium protects against several disorders. Multiple reports have studied the pathways involved in cardiac hypertrophy. However, the effects of probiotic EcN against diabetes-induced cardiac hypertrophy remain to be understood. We administered five weeks old Wistar male (271±19.4 g body weight) streptozotocin-induced diabetic rats with 10⁹ cfu of EcN via oral gavage every day for 24 days followed by subjecting the rats to echocardiography to analyse the cardiac parameters. Overexpressed interleukin (IL)-6 induced the MEK5/ERK5, JAK2/STAT3, and MAPK signalling cascades in streptozotocin-induced diabetic rats. Further, the upregulation of calcineurin, NFATc3, and p-GATA4 led to the elevation of hypertrophy markers, such as atrial and B-type natriuretic peptides. In contrast, diabetic rats supplemented with probiotic EcN exhibited significant downregulated IL-6. Moreover, the MEK5/ERK5 and JAK2/STAT3 cascades involved during eccentric hypertrophy and MAPK signalling, including phosphorylated MEK, ERK, JNK, and p-38, were significantly attenuated in diabetic rats after supplementation of EcN. Western blotting and immunofluorescence revealed the significant downregulation of NFATc3 and downstream mediators, thereby resulting in the impairment of cardiac hypertrophy. Taken together, the findings demonstrate that supplementing probiotic EcN has the potential to show cardioprotective effects by inhibiting diabetes-induced cardiomyopathies.

Initial clinical experience of patient-specific QA of treatment delivery in online adaptive radiotherapy using a 1.5 T MR-Linac

Purpose. This study aims to evaluate the performance of a commercial 1.5 T MR-Linac by analyzing its patient-specific quality assurance (QA) data collected during one full year of clinical operation.Methods and Materials. The patient-specific QA system consisted of offline delivery QA (DQA) and online calculation-based QA. Offline DQA was based on ArcCHECK-MR combined with an ionization chamber. Online QA was performed using RadCalc that calculated and compared the point dose calculation with the treatment planning system (TPS). A total of 24 patients with 189 treatment fractions were enrolled in this study. Gamma analysis was performed and the threshold that encompassed 95% of QA results (T95) was reported. The plan complexity metric was calculated for each plan and compared with the dose measurements to determine whether any correlation existed.Results. All point dose measurements were within 5% deviation. The mean gamma passing rates of the group data were found to be 96.8 ± 4.0% and 99.6 ± 0.7% with criteria of 2%/2mm and 3%/3mm, respectively. T95 of 87.4% and 98.2% was reported for the overall group with the two passing criteria, respectively. No statistically significant difference was found between adaptive treatments with adapt-to-position (ATP) and adapt-to-shape (ATS), whilst the category of pelvis data showed a better passing rate than other sites. Online QA gave a mean deviation of 0.2 ± 2.2%. The plan complexity metric was positively correlated with the mean dose difference whilst the complexity of the ATS cohort had larger variations than the ATP cohort.Conclusions. A patient-specific QA system based on ArcCHECK-MR, solid phantom and ionization chamber has been well established and implemented for validation of treatment delivery of a 1.5 T MR-Linac. Our QA data obtained over one year confirms that good agreement between TPS calculation and treatment delivery was achieved.

MicroRNA-126 inhibits pathological retinal neovascularization via suppressing vascular endothelial growth factor expression in a rat model of retinopathy of prematurity

Vascular endothelial growth factor (VEGF) is the principal growth factor responsible for the retinal neovascularization in the pathogenesis of retinopathy of prematurity (ROP). Current therapies for ROP include laser ablation and intravitreal anti-VEGF injection. However, these treatments either destroy the peripheral retina or associate with problems of persistent peripheral avascular retina or later recurrence of ROP. In the present study we investigated a new therapeutic approach by exploring the potential role of a specific microRNA, miR-126, in regulating VEGFA expression and retinal neovascularization in a rat oxygen-induced retinopathy (OIR) model. We demonstrated that miR-126 mimic and plasmid effectively suppresses VEGFA mRNA expression in both human and rat retinal pigment epithelium cell lines, quantified with qRT-PCR. Animal experiments on rat OIR model revealed that intravitreal injection of miR-126 plasmid efficiently downregulated VEGFA expression in the intraocular fluid and retinal tissues measured by ELISA, and significantly suppressed retinal neovascularization, which was confirmed by calculating sizes of neovascularization areas on fluorescence microscopic images of flat mounted retina stained with Alexa Fluor 594-conjugated isolectin B4 to visualize blood vessels. Together, these results showed that intravitreal injection of miR-126 plasmid could inhibit retinal neovascularization by down-regulating VEGFA expression, suggesting a potential therapeutic effect for ROP.

Multiplex Detection of Clinically Relevant Mutations in Liquid Biopsies of Cancer Patients Using a Hybridization-Based Platform

BACKGROUND

With the advent of precision oncology, liquid biopsies are quickly gaining acceptance in the clinical setting. However, in some cases, the amount of DNA isolated is insufficient for Next-Generation Sequencing (NGS) analysis. The nCounter platform could be an alternative, but it has never been explored for detection of clinically relevant alterations in fluids.

METHODS

Circulating-free DNA (cfDNA) was purified from blood, cerebrospinal fluid, and ascites of patients with cancer and analyzed with the nCounter 3 D Single Nucleotide Variant (SNV) Solid Tumor Panel, which allows for detection of 97 driver mutations in 24 genes.

RESULTS

Validation experiments revealed that the nCounter SNV panel could detect mutations at allelic fractions of 0.02-2% in samples with ≥5 pg mutant DNA/µL. In a retrospective analysis of 70 cfDNAs from patients with cancer, the panel successfully detected EGFR, KRAS, BRAF, PIK3CA, and NRAS mutations when compared with previous genotyping in the same liquid biopsies and paired tumor tissues [Cohen kappa of 0.96 (CI = 0.92-1.00) and 0.90 (CI = 0.74-1.00), respectively]. In a prospective study including 91 liquid biopsies from patients with different malignancies, 90 yielded valid results with the SNV panel and mutations in EGFR, KRAS, BRAF, PIK3CA, TP53, NFE2L2, CTNNB1, ALK, FBXW7, and PTEN were found. Finally, serial liquid biopsies from a patient with NSCLC revealed that the semiquantitative results of the mutation analysis by the SNV panel correlated with the evolution of the disease.

CONCLUSIONS

The nCounter platform requires less DNA than NGS and can be employed for routine mutation testing in liquid biopsies of patients with cancer.

High-Throughput Simultaneous mRNA Profiling Using nCounter Technology Demonstrates That Extracellular Vesicles Contain Different mRNA Transcripts Than Their Parental Prostate Cancer Cells

Extracellular vesicles (EVs) are nano-sized lipid bilayer encapsulated particles with a molecular cargo that appears to play important roles within the human body, such as in cell-to-cell communication. Unraveling the composition of EV cargos remains one of the most fundamental steps toward understanding the role of EVs in intercellular communication and the discovery of new biomarkers. One of the unmet needs in this field is the lack of a robust, sensitive, and multiplexed method for EV mRNA profiling. We established a new protocol using the NanoString low RNA input nCounter assay by which the targeted mRNA transcripts in EVs can be efficiently and specifically amplified and then assayed for 770 mRNAs in one reaction. Prostate cancer cells with epithelial (PC3-Epi) or mesenchymal (PC3-EMT) phenotypes and their progeny EVs were analyzed by the same panel. Among these mRNAs, 157 were detected in PC3-Epi EVs and 564 were detected in PC3-EMT EVs. NOTCH1 was the most significantly abundant mRNA transcripts in PC3-EMT EVs compared to PC3-Epi EVs. Our results demonstrated that when cells undergo epithelial-to-mesenchymal transition (EMT), a more active loading of cancer progression-related mRNA transcripts may occur. The mRNA cargos of EVs derived from mesenchymal prostate cancer cells may contribute to the pro-EMT function. We found that mRNA transcripts are different in progeny EVs compared to parental cells. EV cargos are not completely reflective of their cell origin, and the underlying mechanism of cargo sorting is complicated and needs to be further elucidated.

Analysis of extracellular vesicle mRNA derived from plasma using the nCounter platform

Extracellular vesicles (EVs) are double-layered phospholipid membrane vesicles that are released by most cells and can mediate intercellular communication through their RNA cargo. In this study, we tested if the NanoString nCounter platform can be used for the analysis of EV-mRNA. We developed and optimized a methodology for EV enrichment, EV-RNA extraction and nCounter analysis. Then, we demonstrated the validity of our workflow by analyzing EV-RNA profiles from the plasma of 19 cancer patients and 10 controls and developing a gene signature to differentiate cancer versus control samples. TRI reagent outperformed automated RNA extraction and, although lower plasma input is feasible, 500 μL provided highest total counts and number of transcripts detected. A 10-cycle pre-amplification followed by DNase treatment yielded reproducible mRNA target detection. However, appropriate probe design to prevent genomic DNA binding is preferred. A gene signature, created using a bioinformatic algorithm, was able to distinguish between control and cancer EV-mRNA profiles with an area under the ROC curve of 0.99. Hence, the nCounter platform can be used to detect mRNA targets and develop gene signatures from plasma-derived EVs.

Assessment of the Feasibility and Safety of Durvalumab for Treatment of Solid Tumors in Patients With HIV-1 Infection: The Phase 2 DURVAST Study

Importance

Therapies targeting the programmed cell death 1 (PD-1) receptor or its ligand (PD-L1), such as the humanized monoclonal antibody durvalumab, have shown durable clinical responses in several tumor types. However, concerns about the safety and feasibility of PD-1/PD-L1 blockade in HIV-1-infected individuals have led to the exclusion of these patients from clinical trials on cancer immunotherapies.

Objective

To evaluate the feasibility and safety of durvalumab treatment in patients with advanced cancer and virologically controlled HIV-1 infection.

Design, Setting, and Participants

The DURVAST study was a nonrandomized, open-label, phase 2 clinical trial in patients with any solid tumor type in which anti-PD-1 or anti-PD-L1 antibodies have approved indications or for which there are data of antitumoral activity with no other available curative therapy. All patients had basal undetectable plasma viremia while undergoing combination antiretroviral therapy.

Interventions

Treatment consisted of intravenous infusion of durvalumab (1500 mg every 4 weeks) until disease progression or unacceptable toxic effects.

Main Outcomes and Measures

Adverse events were graded with the use of the National Cancer Institute Common Terminology Criteria for Adverse Events, version 4.03. Tumor response was evaluated using the Response Evaluation Criteria in Solid Tumors version 1.1.

Results

A total of 20 HIV-1-infected patients with advanced cancer were enrolled; 16 (80%) were male, the median (range) age was 54 (30-73) years, and 12 (60%) had progressed with previous cancer treatment lines. A median (range) of 4 (1-16) cycles of durvalumab were administered. Drug-related adverse events were observed in 50% of patients, and all were grade 1 and 2 (mainly diarrhea, asthenia, and arthromyalgia). Four of 16 response-evaluable patients (25%) had a partial response. Five patients (31%) had stable disease, including 4 with durable stable disease (disease control rate of 50%). CD4+ and CD8+ T-cell counts and plasma HIV-1 viremia remained stable throughout the study.

Conclusions and Relevance

Durvalumab treatment was feasible and safe in HIV-1-infected patients with cancer receiving combination antiretroviral therapy. HIV-1-infected patients on suppressive antiretroviral therapy with advanced cancer should have access to cancer immunotherapy treatments.

Trial Registration

ClinicalTrials.gov Identifier: NCT03094286.

Yuan-Hu Zhi Tong Prescription Mitigates Tau Pathology and Alleviates Memory Deficiency in the Preclinical Models of Alzheimer's Disease

Alzheimer's disease (AD) is characterized by memory dysfunction, Aβ plaques together with phosphorylated tau-associated neurofibrillary tangles. Unfortunately, the present existing drugs for AD only offer mild symptomatic cure and have more side effects. As such, developments of effective, nontoxic drugs are immediately required for AD therapy. Present study demonstrates a novel role of Chinese medicine prescription Yuan-Hu Zhi Tong (YZT) in treating AD, and it has substantiated the in vivo effectiveness of YZT in two different transgenic mice models of AD, namely P301S tau and 3XTg-AD mice. Oral treatment of YZT significantly ameliorates motor dysfunction as well as promotes the clearance of aggregated tau in P301S tau mice. YZT improves the cognitive function and reduces the insoluble tau aggregates in 3XTg-AD mice model. Furthermore, YZT decreases the insoluble AT8 positive neuron load in both P301S tau and 3XTg-AD mice. Using microarray and the "Connectivity Map" analysis, we determined the YZT-induced changes in expression of signaling molecules and revealed the potential mechanism of action of YZT. YZT might regulate ubiquitin proteasomal system for the degradation of tau aggregates. The research results show that YZT is a potential drug candidate for the therapy of tau pathogenesis and memory decline in AD.

Abstract 342: Profiling mRNAs of parental prostate cancer cells with different phenotypes and their daughter extracellular vesicles using the NanoString low RNA input nCounter assay

Introduction and objective: Cell plasticity regulated by the balance between the epithelial-to-mesenchymal transition (EMT) and MET is critical in the metastatic cascade. Extracellular vesicles (EVs) may play an important role in this balance by shuttling molecular cargos into recipient cells. This study aims to evaluate the feasibility of profiling mRNAs of parental prostate cancer (PCa) cells with different phenotypes and their daughter EVs using the NanoString low RNA input nCounter assay.

Methods: PC3-Epi and PC3-EMT cell lines representing epithelial and mesenchymal phenotype, respectively, were generated from original PC3 cell line. The cell culture supernatant was collected after 48 h of serum starvation of cells and processed by differential ultracentrifugation. The supernatant was first pre-cleared for any dead cells and debris by centrifugation at 2000×g for 20 min. Without disturbing the pellet, the supernatant was then transferred to a fresh ultracentrifuge tube and centrifuged at 10,000×g for 20 min at 4 °C. The remaining SN was then centrifuged to isolate the EVs at 100,000×g for 120 min at 4 °C. The EVs pellet was further washed in 1× PBS followed by a second centrifugation at 100,000×g for 120 min at 4 °C. The final EVs pellet was resuspended in 1×PBS for subsequent characterization (transmission electron microscopy, nanoparticle tracking analysis and Western blot) and nCounter assays. The total RNA of cells and their daughter EVs were assayed by the nCounter PanCancer Progression Panel to determine expression of 770 selected mRNAs. The NanoString nCounter Low RNA Input Kit with the multiplex 770-gene primer pool was used for the pre-amplification of mRNA and overnight hybridization with the PanCancer Progression panel. Each sample type was submitted to the assay in biological triplicate.

Results: When comparing all 12 samples, Eisen Cluster analysis separated all the cells and all EVs into two groups, regardless of their phenotypes. In subgroup analysis, the expression patterns between PC3-Epi and PC3-EMT cells were significantly different. CLEC2B, KDR, CRIP2, IL13RA2, CC2D1B were significantly upregulated in PC3-EMT cells, while CXCL8, EPCAM, LAD1, SERPINH1, ESRP1, CLDN7, CLDN1, TACSTD2, TGFB2, TMEM30B, CDH1, S100A14, ST14, NOX5, OVOL2 were significantly downregulated in PC3-EMT cells. The expression patterns between PC3-Epi and PC3-EMT cells were also significantly different. TBX1, CAV1, COL4A1, SLC35A3, MYC, ITGB2, TIMP4, CAMK2B, PTGDS, P3H2, PECAM1, CXCL13, CNN1, TFPI2, MTDH, STAB2, ITGB6, VIM, GTF2I, ZNF143, STAT3 were all significantly downregulated in PC3-EMT cell derived EVs.

Conclusions: The NanoString low RNA input nCounter assay can provide reliable mRNA expression profiling of EVs. The mRNA expression patterns are very different between cells and their daughter EVs. Both cells and EVs with different phenotypes have different gene expressions.

Citation Format: Liang Dong, Chung-Ying Huang, Richard Zieren, Kengo Horie, Sarah R. Amend, Kenneth J. Pienta. Profiling mRNAs of parental prostate cancer cells with different phenotypes and their daughter extracellular vesicles using the NanoString low RNA input nCounter assay [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 342.

Abstract 809: nCounter for detection of clinically relevant alterations in exosomes of non-small cell lung cancer cells and patients

Background: ALK, ROS1 and RET fusions and MET exon 14 skipping variant (METex14) are present in 10-15% of advanced non-small-cell lung cancer (NSCLC) patients and their accurate identification is critical to guide targeted therapies. In a significant number of cancer patients, the tumor tissue available is insufficient for genetic analysis and repeated tissue biopsies for monitoring the course of the disease and the emergence of resistance are not feasible. Liquid biopsies constitute the only alternative available in these cases, but NGS techniques have shown insufficient sensitivity for fusion detection in blood samples. The nCounter technology has been adapted to detect fusions and skipping variants in FFPE tumor biopsies and we aimed to validate it for exosomes.

Methods: Exosomes were purified using a miRCURY kit (Qiagen) and RNA was extracted using the TRI reagent (MRC Inc). A customized nCounter panel (Nanostring) for detection ALK, ROS1 and RET fusion transcripts and MET ex14 mRNA was used with a 10-cycles preamp step. First, proof-of-concept experiments were run by testing exosomes isolated from the culture medium of cell lines. Next, we tested exosomes isolated from the blood of NSCLC patients with know genotypes.

Results: nCounter fusion probes successfully detected ALK, RET and ROS1 fusion transcripts in exosomes isolated from the culture medium of the cell lines H3122 (EML4-ALKv1), H2228 (EML4-ALKv3), HCC78 (SLC34A2-ROS1) and LC/2-Ad (CCDC6-RET). Exosomes from a cell line established from a patient progressing to alectinib were also positive for EML4-ALKv1and showed high MET expression levels, while exosomes from the fusion-negative cell lines A549 and H23 tested negative. Finally, fusion transcripts were detected in exosomes purified from the blood of fusion positive NSCLC patients but not in fusion negative cases.

Conclusions: nCounter can detect ALK, RET and ROS1 fusion transcripts in exosomes purified from the blood of advanced NSCLC patients

Citation Format: Ana Giménez Capitán, Jill Bracht, Chung-Ying Huang, Cristina Teixidó, Noemí Reguart, Rich Boykin, Sarah Warren, Joseph M Beechem, Santiago Viteri Ramirez, Juan José García, Andrés Aguilar, Rafael Rosell Costa, Jay Gerlach, Miguel Angel Molina-Vila. nCounter for detection of clinically relevant alterations in exosomes of non-small cell lung cancer cells and patients [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 809.

Abstract 929: Transcriptomic analysis of pre-treatment tissue samples to predict clinical benefit to durvalumab in HIV-infected cancer patients

Introduction: Treatment with anti PD-1/PD-L1 antibodies has demonstrated clinical activity in different types of solid tumors, but only 20 to 30% of patients (pts) respond to these immune checkpoint inhibitors (ICIs). Therefore, predictive biomarkers of response that can assist in pt selection are urgently needed. Single biomarker expression, like PD-L1, may not provide enough information about cancer cells and the tumor microenviroment. Novel technologies, analyzing hundreds of genes at the same time, are needed to yield better predictive gene signatures of ICI response. The DURVAST trial analyzed the feasibility of durvalumab treatment in HIV-infected cancer pts, which are usually excluded from ICI clinical trials. The trial included 20 patients with different tumor types and yielded a disease control rate of 56%.

Methods: Pre-ICI-treatment FFPE tumor tissue samples from 14 HIV-infected cancer pts (including 11 lung, 1 melanoma, 1 anal and 1 bladder cancer) were analyzed using the nCounter NanoString platform with the IO360 panel, including 770 genes involved in tumor biology, microenvironment and immune response. Gene expression results were correlated with clinical benefit (CB) (objective response and stable disease of more than 24 weeks by RECIST1.1 criteria), and compared to other predictive markers.

Results: Exploratory analysis of pre-treatment gene expression profiles (GEPs) revealed differentially expressed genes (DEGs) between the pts with- and without CB. Panel-incorporated biological signatures related to tumor and immune activities were evaluated and some of the most DEGs (based on higher log2FC values and nominal p-values ≤0.05) were shown to be involved in cytokine and chemokine signaling. Although not significant, pts without CB tend to have lower expression of genes involved in cytokine and chemokine signaling (p = 0.097). In contrast, pts without CB tended to have a higher TGF beta signature scores (p = 0.318). When combining both signatures, we obtained an aggregated signature score that was significantly different between pts with- and without CB (p = 0.017). While the positive predictive values were the same for all tests, our signature score outperformed PD-L1 expression positivity by immunohistochemistry and PD-L1 RNA expression as predictors for clinical benefit with a two-fold higher sensitivity and negative predictive value.

Conclusion: Gene expression analysis of pre-treatment tumor samples revealed distinct GEPs between HIV-infected cancer pts with- and without CB, where combined high baseline recruitment and activation of immune cells by cytokine and chemokine signaling pathways and low immunosuppressive TGF beta signaling pathways predict CB from durvalumab treatment. This predictive score outperformed other predictive markers of CB. These findings need further validation in an external and non-HIV infected pt cohort, in addition to a pt cohort treated with other ICIs.

Citation Format: Jillian Wilhelmina Bracht, Maria Gonzalez-Cao, Teresa Moran, Judith Dalmau, Javier Garcia-Corbacho, Reyes Bernabe, Oscar Juan, Javier de Castro, Ana Gimenez-Capitan, Remedios Blanco, Erika Aldeguer, Sonia Rodriguez, Ana Drozdowskyj, Jordi Argilaguet, Julian Blanco, Julia Prado, Christian Brander, Jorge Carrillo, Bonaventura Clotet, Bartomeu Massuti, Mariano Provencio, Chung-Ying Huang, Clara Mayo de las Casas, Monica Garzon, Andres Felipe Cardona, Oscar Arrieta, Andreas Meyerhans, Miguel Angel Molina-Vila, Javier Martinez-Picado, Rafael Rosell. Transcriptomic analysis of pre-treatment tissue samples to predict clinical benefit to durvalumab in HIV-infected cancer patients [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 929.

Abstract 5365: Profiling circulating tumor cell RNA from a large blood screening volume: A pilot study using diagnostic leukapheresis followed by the NanoString low RNA input nCounter assay

Introduction and objective: The presence of circulating tumor cells (CTC) is associated with poor prognosis in metastatic prostate cancer (mPCa) patients. The aim of this study is to evaluate the feasibility of using diagnostic leukapheresis (LP) followed by gene profiling using the NanoString low RNA input nCounter assay to achieve reliable CTC gene profiling.

Methods: Blood samples were collected from 4 mPCa patients and 3 healthy donors. In the LP procedure, different blood elements were separated based on density. The mononuclear cell layer (presumed to contain any CTCs) was collected. The Alere™ CTC AdnaTest (AdnaGen, Langenhagen, Germany), an EpCAM positive selection method for isolation of EpCAM+ CTCs, followed by RT-qPCR for PSA, PSMA, and HOXB13 was used to detect CTCs from LP. The Ct value thresholds for positive CTC signal by RT-qPCR were set based on healthy donor LP subjected to AdnaTest as a negative control (PSA 36.3, PSMA 36.82, HOXB13 40). The cDNA of cells captured by EpCAM+ selection (including putative CTCs) and of the EpCAM+ depleted white blood cells (WBC) were assayed by the nCounter PanCancer Progression Panel to determine expression of 770 selected mRNAs. The NanoString nCounter Low RNA Input Kit with the multiplex 770-gene primer pool was used for the pre-amplification of cDNA and overnight hybridization with the PanCancer Progression panel. To validate the assay, healthy donor LPs were spiked with known numbers of PCa cell line LN95 cells.

Results: For mPCa patients, the LP procedure took 136.2±10.6 min, with a screening volume of 10L of peripheral blood. The mean volume of mPCa LP product was 123.64±12.23 ml. The WBC concentration was 69.75±28.2×109/L. All samples were subjected to AdnaTest in triplicate and CTCs were identified in 3 out of 4 patients. The positive Ct values of PSA were 33.86±0.81, 32.14±0.31 and 33.09±0.34; PSMA were 35.55±1.02, 33.55±0.83 and 35.30±0.65; HOXB13 were 36.25±0.34, 37.15±0.22 and 37.09±0.33. To assess profiling of CTCs isolated from LP using the nCounter platform, 100, 500, and 1000 LN95 cells were spiked in healthy LPs and were analyzed with the AdnaTest. Within each spiking group, pre-spiking WBC, captured CTC, post-capture WBC, and LN95 cells in PBS alone were subjected to the Nanostring assay. Eisen Cluster analysis separated pre- and post- WBCs, captured CTCs, LN95 cells into three groups. The gene expression of captured CTCs correlated with those of LN95 cells, and the correlation increased with the spiking cancer cell number (R2=0.45, 0.57, and 0.70, respectively). The gene expression of pre-spiked WBCs were highly correlated with those of post-capture WBCs regardless of spiking cancer cell number (R2=0.83, 0.84 and 0.85).

Conclusions: Analyzing CTCs in LP samples by AdnaTest is feasible and offers a promising method for liquid biopsy of mPCa patients. The NanoString low RNA input nCounter assay can provide reliable gene expression profiling of CTC.

Citation Format: Liang Dong, Chung-Ying Huang, Changxue Lu, Diane Reyes, Sarah R. Amend, Jun Luo, Kenneth Pienta. Profiling circulating tumor cell RNA from a large blood screening volume: A pilot study using diagnostic leukapheresis followed by the NanoString low RNA input nCounter assay [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 5365.

Abstract 760: miRNA and mRNA detection in plasma-derived extracellular vesicles (EVs) using the nCounter NanoString platform

Introduction: Although genetic and transcriptomic analysis of tumor tissue can provide useful information for prognosis and treatment decision making, 5-20% of advanced-stage lung cancer patients cannot be biopsied, or the amount of tumor tissue is insufficient for successful analysis. In addition, repeated sampling is often not possible. Liquid biopsies have shown potential to be used as minimally invasive, safe and sensitive alternative for tissue biopsies, but lack of standardized protocols is hampering implementation in the clinic. The nCounter platform could provide the solution for this problem, with an easy-to-use technical workflow and straightforward data analysis. Extracellular vesicles (EVs) are mediators of intercellular communication and may play a role in early cancer development. Therefore, RNA found within EVs can be used as a biomarker for cancer development and progression. In addition, the lipid bilayer of EVs makes their cargo particularly stable and allows the use of biobank stored samples.

Methods: EVs were isolated from 600 μL plasma of 19 cancer patients and 10 healthy donors, using the miRCURY® Exosome Serum/Plasma Kit (Qiagen), and total RNA was extracted using TRI Reagent® (MRC Inc) or the automated QIAsymphony® System (Qiagen) with the DSP Virus/Pathogen Kit, after RNAse A (Sigma-Aldrich) treatment to remove plasma cell-free RNA. The Human Immune V2 panel (NanoString Technologies), including 600 mRNA targets, was used to analyze EV-derived mRNA after a pre-amplification (pre-amp) step with the Low RNA Input Amplification Kit. In addition, the Human V3 miRNA panel (NanoString Technologies), including 800 miRNA targets, was used to analyze the same EV samples without pre-amp.

Results: Total amount of RNA isolated from EVs was found to be significantly higher using TRI Reagent®, versus automated RNA isolation. In addition, the conditions for the pre-amp step were tested and optimized. A pre-amp of 10 cycles for the mRNA panel was shown to be sufficient to detect mRNA targets in EVs without saturation, and the NanoString retrotranscription (RT) enzyme outperformed the other RT enzyme tested. In addition, supernatant collected during EV isolation was also analyzed, and results showed that the RNA targets were derived from within the EVs. On average, 337 mRNA targets were detected within the EVs, while 157 miRNA targets were detected in the same samples without pre-amp, with no significant differences between cancer patients and healthy donors. Interestingly, most differentially expressed (DE) mRNAs were shown to be lower expressed in cancer patients, while most DE miRNAs were found to be higher expressed in cancer patients.

Conclusion: Our results demonstrate that the nCounter NanoString platform can be used for miRNA and mRNA detection in plasma-derived EVs from cancer patients and healthy donors. Further studies will focus on specific mRNA and miRNA expression differences between these two cohorts.

Citation Format: Jillian Wilhelmina Bracht, Ana Gimenez-Capitan, Chung-Ying Huang, Carlos Pedraz-Valdunciel, Joselyn Valarezo, Sarah Warren, Rafael Rosell, Miguel Angel Molina-Vila. miRNA and mRNA detection in plasma-derived extracellular vesicles (EVs) using the nCounter NanoString platform [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 760.

Myopia in school-aged children with preterm birth: the roles of time spent outdoors and serum vitamin D

AIMS

To analyse the factors associated with myopia in school-aged children with preterm birth and with or without retinopathy of prematurity (ROP).

METHODS

Children born prematurely between January 2010 and December 2011 were enrolled in this cross-sectional study when they reached school age between April 2017 and June 2018 in a referral centre. The main parameters were cycloplegic refraction, time spent outdoors and serum 25-hydroxyvitamin D (25(OH)D) concentration.

RESULTS

A total of 99 eyes from 99 children with a mean age of 6.8 years underwent analysis. The average time spent outdoors was significantly higher in the non-myopic group (0.9 ± 0.5 hours/day) than in the myopic group (0.7 ± 0.3 hours/day) (p = 0.032). After adjustment for age, sex, number of myopic parents, ROP severity, near-work time and serum 25(OH)D concentration, more time spent outdoors was correlated with a lower odds of myopia (OR, 0.13 per additional hour per day; 95% CI, 0.02-0.98; p = 0.048). Mean serum 25(OH)D concentrations were similar between the myopic and non-myopic groups (49.7 ± 13.6 and 48.8 ± 14.0 nmol/mL; p = 0.806) and were not correlated with spherical equivalence power (r = -0.09; p = 0.418). Vitamin D insufficiency was present in 57% of the participants.

CONCLUSIONS

Among preterm children with or without ROP, more time spent outdoors was associated with lower odds of myopia. The serum 25(OH)D concentration was not associated with myopia, but a high proportion of the participants had insufficient levels.

Correlation between higher-order aberrations and visual acuity recovery (CoHORT) after spectacles treatment for pediatric refractive amblyopia: A pilot study using iDesign measurement

Purpose

To determine the correlation between higher-order aberrations (HOAs) and best-corrected visual acuity (BCVA) recovery speed after spectacles treatment using iDesign measurements in refractive amblyopic children.

Methods

This is a prospective case series. Children aged from 3 to 7 years with refractive amblyopia (Landolt C equivalent < 0.8) were recruited. All participants were followed for at least 6 months after full correction of the refraction error by spectacles. The HOAs were measured using iDesign before and after cycloplegia at first visit and at 3-month intervals. Then correlation between BCVA recovery after treatment for 6 months and HOAs was determined.

Results

We analyzed 24 eyes of 12 children (mean age, 4.5 years). Baseline mean BCVA was logarithm of minimal angle of resolution (logMAR) 0.335 (Landolt C equivalent 0.46), which improved to logMAR 0.193 (Landolt C equivalent 0.64) after treatment with full-correction spectacles for 6 months. The amblyopic eye BCVA recovery was negatively correlated with tetrafoil with/without cycloplegia (P = 0.006 and 0.022, respectively) and trefoil with cycloplegia (P = 0.049).

Conclusions

trefoil and tetrafoil measured with iDesign negatively correlates with the BCVA recovery speed of refractive amblyopic eyes after spectacles treatment in this pilot study. The current study results may aid in further investigation for diagnosis and treatment of refractory refractive and idiopathic amblyopia.

[Years of potential life lost due to premature death of cardiovascular diseases among residents in Suzhou from 1987 to 2017]

From 1987 to 2017, cardiovascular disease (CVD) had been ranking the first cause of death in Suzhou, and the mortality rate showed an upward trend annual percentage changes (APC=0.62%, P=0.001), while the standardized mortality rate showed a downward trend (APC=-2.65%, P<0.001). The probability of premature death of CVD declined consistently from 7.06% in 1987 to 2.00% in 2017 (APC=-4.45%, P<0.001). When the life expectancy was set at 70, the potential years of life lost rate (PYLLR) decreased from 6.35‰ in 1987 to 3.30‰ in 2017, and the standardized PYLLR decreased from 7.30‰ to 2.68‰. When the life expectancy was set at 75, the PYLLR decreased from 10.12‰ to 5.19‰, and the standardized PYLLR decreased from 11.44‰ to 3.88‰. With the increase of years, all PYLLR and standardized PYLLR showed a significantly downward trend (APC=-2.51%--3.89%, P<0.001).

P2602Inhaled iloprost improves echocardiographic myocardial performance during exercise in heart failure with preserved ejection fraction

Introduction

The pathophysiology of HFpEF is complicated and treatments that improve outcomes in HFrEF have no substantial benefits in HFpEF. Impairments in LV global longitudinal strain (GLS) and LV diastolic function parameters have been regarded as novel echocardiographic markers to predict cardiovascular events in HFpEF. Preliminary trials indicate that iloprost, an inhaled prostacyclin analougue, improves exercise hemodynamics in both patients with pulmonary artery hypertension and pulmonary hypertension associated with HFpEF.

Purpose

We aim to investigate the impact of inhaled iloprost on LV global longitudinal strain, LV diastolic function and RV function during exercise in HFpEF population.

Methods

34 patients diagnosed with HFpEF were included with exclusion of severe pulmonary, coronary artery, valvular heart and pericardial diseases. Subjects were randomized 1:1 to inhalation of iloprost or placebo. Transthoracic echocardiography was performed at rest and after 6-minute supine bicycle exercise at 20-Watt workload. We utilized tissue speckle tracking by QLAB software to derive LV GLS and global strain rate during LV isovolumetric relaxation period (SRIVR). E/e', E/SRIVR, tricuspid regurgitation pressure gradient (TRPG), tissue Doppler imaging of RV lateral tricuspid annulus and tricuspid annular plane systolic excursion (TAPSE) were measured to evaluate changes of myocardial performance.

Results

LV GLS during exercise significantly enhanced after iloprost use. E/SRIVR, a novel predictor of LV filling pressure, was significantly decreased. E/e' was also lower in iloprost group by trend. Improvements in RV function and degree of pulmonary hypertension during exercise with iloprost were observed in this study.

Echocardiographic myocardial function endpoints during 20-Watt excercise between iloprost and placebo groups Iloprost (N=17) Placebo (N=17) P value LV global longitudinal strain, % −4.96±1.20 −0.75±3.00 <0.001 E/SRIVR, cm 206.41±113.55 454.13±262.98 0.005 E/e' mean 10.77±2.39 14.41±12.14 0.235 TAPSE, cm 2.62±0.62 2.37±0.56 0.221 TRPG, mmHg 28.37±12.47 44.25±9.29 <0.001 TDI lateral tricuspid annulus, cm/s 16.41±4.61 14.77±2.92 0.222

Effects of iloprost at rest and exercise

Conclusions

Our study is the first to demonstrate that, in patients with HFpEF, inhaled iloprost favorably enhances LV GLS reserves, decreases LV diastolic filling load, reduces pulmonary hypertension and thereby improves RV function during exercise.

Acknowledgement/Funding

This work was supported in part by the National Science Council of the Republic of China, Taiwan (NSC107-2314-B-002-265-MY3)

Abstract 1384: nCounter for detection of clinically relevant alterations in liquid biopsies of solid tumor patients

Background: With the advent of precision medicine, screening for clinically relevant mutations and gene fusions is mandatory in many tumor types. However, in a significant number of cancer patients, the tumor tissue available is insufficient for genetic analysis. In addition, repeated tissue biopsies for monitoring the course of the disease and the emergence of mechanisms of resistance to targeted therapies are not feasible. Liquid biopsies constitute the only alternative available in these cases. The nCounter technology has been adapted to detect mutations and gene fusions in FFPE biopsies from cancer patients with a minimum requirement of tumor material and sample handling, a short turnaround time and a straightforward data analysis. However, nCounter has not been tested in liquid biopsy samples.

Methods: For mutation analysis, the SNV Solid Tumor Panel was used, which allows for detection of 97 driver mutations in 24 genes. For fusions, a customized panel for ALK, ROS1, RET, and NTRK1 fusion transcripts was used with a 14-cycles preamp step. First, proof-of-concept experiments were run by spiking plasma samples with a mixture of genomic DNAs or RNAs from positive cell lines. Next, 65 circulating-free DNA (cfDNA) samples from advanced cancer patients, previously genotyped by other techniques, were analyzed using the SNV panel. Of those, 60 had been purified from plasma, 4 from ascites and 1 from the pleural effusion. Nineteen were positive for EGFR mutations, 20 for KRAS, 13 for BRAF, 5 for PIK3CA, 2 for NRAS, and 6 were pan-negative. Finally, 8 circulating cell-free RNA samples isolated from plasma were tested with the nCounter Low RNA Input Kit and the lung fusion panel. Of those, 6 corresponded to lung cancer patients harboring ALK or ROS1 rearrangements in tumor tissue, but previous RT-PCR only detected fusions transcripts in 2.

Results: Spiking experiments revealed that the nCounter SNV Panel was able to detect mutations at allelic fractions as low as 0.2% for most of the drivers. When testing liquid biopsies, 63/65 cfDNA samples from cancer patients were evaluable, despite having DNA concentrations lower than 1 ng/µL. The SNV Panel successfully detected EGFR, KRAS, BRAF, PIK3CA and NRAS mutations with a concordance rate of 97.5% with previous genotyping by NGS, Therascreen® or Taqman® with PNA, corresponding to a Cohen’s kappa of 0,913. In the case of the lung fusion panel, ALK, ROS1 and RET fusion transcripts were detected in all spiked plasma cfRNA. Two samples from lung cancer patients with positive RT-PCR results were also detected by the nCounter low-input lung fusion panel. Research is ongoing to further improve the performance of the nCounter low-input fusion panel in liquid biopsy samples.

Conclusions: Our results demonstrate the feasibility of mutation analysis in the cfDNA of advanced cancer patients using nCounter. The nCounter technology also shows promise for the detection of gene fusions in cfRNA

Citation Format: Ana A. Giménez-Capitán, Chung-Ying Huang, Jill Bracht, Rich Boykin, Clara Mayo-de-las-Casas, Joseph M. Beechem, Cristina Teixidó, Ariadna Balada-Bel, Beatriz Garcia-, Sergio Villatoro, Monica Garzón, Nuria Jordana-Ariza, Cristina Aguado, Santiago Viteri, Juan José García, Rafael Rosell, Jay Gerlach, Noemi Reguart, Miguel Angel Molina-Vila. nCounter for detection of clinically relevant alterations in liquid biopsies of solid tumor patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1384.

[Sero-prevalence of Babesia infection among voluntary blood donors in Jiangsu Province]

OBJECTIVE

To evaluate the sero-positivity of Babesia infection in voluntary blood donors in Jiangsu region, so as to provide the evidence for transfusion safety.

METHODS

A total of 950 blood samples were collected from voluntary blood donors in Jiangsu Provincial Blood Center from February to May, 2017, and detected by double antigen sandwich ELISA targeting peptides derived from B. microti-secreted antigen 1 (BmSA1). The positive samples were confirmed by microscopy and nested-PCR to determine parasitemia. The prevalence of anti-BmSA1 was analyzed between/among different genders, ages and occupations of the blood donors.

RESULTS

Of the 950 blood screened samples, 5 were positive for anti-BmSA1, and the sero-prevalence of Babesia infection was 0.53%. The 5 samples were all negative by microscopy and nested-PCR. There were no gender- (χ² = 0.01, P =0.92) or age-specific differences (χ² = 0.11, P = 0.95) in the sero-prevalence of Babesia infection; however, there was an occupation-specific difference detected in the sero-prevalence of Babesia infection (χ² = 11.93, P < 0.05).

CONCLUSIONS

Babesia infection is detected in voluntary blood donors in Jiangsu region, which should be paid much attention.

[The new classifications of biliary tract diseases based on actual anatomy]

In order to facilitate the treatment strategies for biliary tract injury, hilar cholangiocarcinoma, bile duct tumor thrombus, cholangiocellular carcinoma and bile duct cystic dilatation, many classifications have been made, even more than 10 types for one disease. Each type is represented by numbers or English alphabet, which are not only confusing but also difficult to remember. The Academician Mengchao Wu divided the liver into five sections and four segments base on its anatomy, this classification is very direct and visual, thus had been using till now. In order to overcome those complicated problems, it is considered to develop a new classification based on actual anatomic location similar to that for liver cancer, which is easy to remember and to directly determine the treatment strategy. All kinds of classifications have their own characteristics and advantages and disadvantages. This practical classifications avoid the complexity and may be useful for clinicians.

Application of wavelet analysis on transient reflectivity in ultra-thin films

Applications of wavelet analysis in ultra-thin film transient reflectivity (TR) measurements have been investigated. Advantages of utilizing different localized wavelet bases, in position and time, have been addressed on the residual TR signals. Morse wavelets have been used to obtain information from the abrupt oscillatory modes in the signal, which are not distinguishable with conventional methods such as Fourier transforms. These abrupt oscillatory modes are caused by the surface, interface, or any short-lived oscillatory modes which are suppressed in the TR signal in ultra-thin films. It is demonstrated that by choosing different Morse wavelets, information regarding different oscillatory modes in the TR signal of a heterostructure thin film is achievable. Moreover, by performing wavelet analysis on multiferroic heterostructures, oscillatory modes with very close energy ranges are easily distinguishable. For illustration, residuals of the TR signals have been obtained by a pump-probe setup in reflectivity mode on La_0.7Sr_0.3MnO₃/SrTiO₃ and BaTiO₃/La_0.7Sr_0.3MnO₃/SrTiO₃ samples, where sufficient signal to noise ratios have been achieved by taking multiple scans. The residual signals have been analyzed with Morse wavelets, and multiple oscillatory modes with close energy ranges have been observed and distinguished. This approach can isolate the location of various oscillatory modes at the surface, interface and in the bulk of the heterostructure sample.

Neurodevelopmental Outcomes after Intravitreal Bevacizumab Therapy for Retinopathy of Prematurity: A Prospective Case-Control Study

PURPOSE

To evaluate the neurodevelopmental and ocular developmental outcomes in premature children who have undergone intravitreal bevacizumab injection (IVB) for treatment of type 1 retinopathy of prematurity (ROP).

DESIGN

Prospective case-control study.

PARTICIPANTS

We enrolled 3 groups of premature patients: premature children who had no history of ROP (group 0), premature children with history of ROP without treatment (group 1), and premature children with ROP who had received a single IVB (0.625 mg; group 2).

METHODS

Ocular developmental assessment, including cycloplegic refractometry, axial length, Cardiff acuity, and neurodevelopmental assessment via the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley III), were performed at 1 to 3 years of age and were compared between groups.

MAIN OUTCOME MEASURES

Ocular developmental outcomes and Bayley III scores.

RESULTS

A total of 148 patients (85 boys and 63 girls) were included. The mean age at assessment was 1.49±0.59 years. Group 0 patients demonstrated significantly higher gestational age (GA), birth weight, and Apgar scores compared with group 1 and 2 patients. There were no significant differences between groups 1 and 2 in demographics or systemic risk factors except for lower GA in group 2. The cylindrical power was significantly larger in groups 1 and 2 compared with group 0. The spherical equivalent was significantly more myopic and the Cardiff acuity was significantly poorer in group 2 than in group 0. There were no significant differences between groups 1 and 2 in refractive status, axial length, or Cardiff acuity. Neurodevelopmental assessment using Bayley III showed no significant difference among the 3 groups in any aspect after adjusting for GA and other systemic risk factors. The risks for poor neurodevelopmental outcomes also were not significantly different.

CONCLUSIONS

At the mean age of 1.5 years, children with prior history of IVB (group 2) showed similar refractive and visual outcomes and similar neurodevelopmental outcomes compared with premature patients with ROP without requirement of treatment (group 1), although there is a possibility that a small but clinically significant difference may not have been detected in the current study.

Medicolegal Identification of Medical Malpractices in Orthopaedic Surgery

OBJECTIVES

To analyze the characteristics of medical malpractices in orthopaedic surgeries, to explore principles and methods in medical legal identification, and to provide basic data for uniform medicolegal standard for the future medical identification.

METHODS

A retrospective analysis was conducted on 100 cases of medical malpractices in orthopaedic surgery, among the 364 cases archived in Medicolegal Expertise Center of Xi'an Jiaotong University during 2002-2015.

RESULTS

In the 100 cases of orthopedic medical malpractices, with 104 hospitals involved in, 95 cases were judged with medical errors and the other 9 cases with no error. The top 3 reasons for errors were （1） inadequate observation or estimation of diseases （27.9%）, （2） intraoperative improper operation （17.3%）, and （3） delayed or missed diagnosis and treatment （12.5%）. The consequences of medical malpractices were mostly disability （61%）, followed by prolonged diseases （31%） and death （8%）. With regard to the causal relationship between medical errors and consequences, 95 cases （91.4%） were with causality and the other 9 cases （8.6%） with no causality. Specifically, 56 cases （53.9%） were with medical errors as the secondary causes accounting for 25% causative potency, and 20 cases （19.2%） were with medical errors as the major causes accounting for 75% causative potency.

CONCLUSIONS

It is pivotally important for determining the causative potency of medical errors to analyse the causes of damages in orthopaedic surgery and to distinguish subjective factors from objective ones of medical errors.

[Research on risk factors of short-term outcome in AIDS patients with pneumocystis pneumonia]

Objective: To investigate the prognostic risk factors of acquired immunodeficiency syndrome (AIDS) patients with pneumocystis pneumonia (PCP), and to establish risk models for predicting early outcome. Methods: The clinical data of 418 AIDS patients with PCP admitted to Department of Infectious Diseases, Beijing You'an Hospital, Capital Medical University from January 2008 to May 2016 were retrospectively analyzed.The patients were divided into death group and survival group according to clinical outcome during hospitalization.Data of the two groups were collected including general information and laboratory test results.Multivariate Logistic regression was used to analyze risk factors affecting prognosis of patients, establish prognostic models and evaluate predictive value of the model. Results: Of the 418 AIDS patients with PCP, 388 cases were male and 30 cases were female, aged from 5 to 82 years, mean age was (40±12) years.There were 82 patients in the death group and 336 patients in the survival group.Disease course, bacterial infection and alveolar-arterial oxygen pressure difference(P(A-a)O(2)), serum lactate dehydrogenase(LDH), white blood cell (WBC), neutrophil (N), alanine aminotransferase (AST), urea nitrogen (BUN) and serum potassium (K) were significantly higher in the death group than those in the survival group (all P<0.05), and arterial oxygen pressure (PaO(2)), blood oxygen saturation (SpO(2)), CD4(+) T lymphocyte count, lymphocyte (L) , hemoglobin (Hb), platelet (PLT), albumin (ALB), prealbumin (PALB), cholinesterase (CHE), cholesterol (CHO), serum chlorine (Cl) and serum sodium (Na) were significantly lower in the death group than those in the survival group (all P<0.05). Multivariate Logistic regression analysis showed that P(A-a)O(2, )ALB, LDH, N and CD4(+) T lymphocyte count were prognostic factors of AIDS complicated with PCP.Prognostic index=9.736+ 0.112×P(A-a)O(2)-0.719×ALB+ 0.006×LDH+ 0.355×N-0.021×CD4.ROC curve of the short-term prognostic model was 0.985 (95%CI 0.977-0.994), with P value 0.000, cut-off value 0.907, sensitivity 92.0% and specificity 98.8%.The mortality rate increased with the increase of equation value. Conclusions: P(A-a)O(2, )ALB, LDH, N and CD4(+) T lymphocyte count are independent risk factors to predict short-term prognosis in these patients.The short-term prognostic model based on independent risk factors is useful in guiding clinical treatment.

A systematic review of the safety and efficacy of aerobic exercise during cytotoxic chemotherapy treatment

PURPOSE

Aerobic exercise improves prognosis and quality of life (QoL) following completion of chemotherapy. However, the safety and efficacy of aerobic exercise during chemotherapy is less certain. A systematic review was performed of randomised trials of adult patients undergoing chemotherapy, comparing an exercise intervention with standard care.

METHOD

From 253 abstracts screened, 33 unique trials were appraised in accordance with PRISMA guidance, including 3257 patients. Interventions included walking, jogging or cycling, and 23 were of moderate intensity (50-80% maximum heart rate).

RESULTS

Aerobic exercise improved, or at least maintained fitness during chemotherapy. Moderately intense exercise, up to 70-80% of maximum heart rate, was safe. Any reported adverse effects of exercise were mild and self-limiting, but reporting was inconsistent. Adherence was good (median 72%). Exercise improved QoL and physical functioning, with earlier return to work. Two out of four studies reported improved chemotherapy completion rates. Four out of six studies reported reduced chemotherapy toxicity. There was no evidence that exercise reduced myelosuppression or improved response rate or survival.

CONCLUSIONS

Exercise during chemotherapy is safe and should be encouraged because of beneficial effects on QoL and physical functioning. More research is required to determine the impact on chemotherapy completion rates and prognosis.

[Characteristics of IgH-CDR3 repertoire of peripheral B cells in a patient with primary biliary cholangitis: a preliminary study using high-throughput sequencing]

Objective: To analyze the characteristics of immunoglobulin heavy chain complementarity-determining region (IgH-CDR3) repertoire of peripheral B cells in a patient with primary biliary cholangitis (PBC) and to investigate the diversity of the immune system. Methods: Arm-PCR was used to amplify the IgH-CDR3 region of circulating B cells isolated from a PBC patient, and high-throughput sequencing was used to analyze the amplified product. The characteristics of immune repertoire were analyzed by bioinformatics. Results: In total, 329219 sequence reads were generated from the sample, with 325540 total CDR3 sequences and 72774 distinct CDR3 sequences, and the D50 of IGH-CDR3 was 7.7. The dominant CDR3 length of the sample was 45 nt (9.6%); the N addition with the highest frequency ranged from 13 to 14 nt (5.25%); the J trimming with the highest frequency was 0 nt (12.7%); the three most frequent V alleles were V4-59 (9.5%), V3-23 (8.1%), and V1-69 (6.4%). Conclusion: The diversity of IgH-CDR3 repertoire is relatively low in this patient with PBC, with several B-cell clonal expansions. The specificity needs to be further verified after increasing the sample size.

[Clinical value of anti-liver/kidney microsomal-1 antibody in patients with liver disease]

Objective: To investigate the clinical and laboratory features of patients with liver disease and positive anti-liver/kidney microsomal-1 (anti-LKM-1) antibody, and to provide a reference for clinical diagnosis and differential diagnosis. Methods: The clinical data of patients with positive anti-LKM-1 antibody who were treated in our hospital from 2006 to 2016 were collected, and clinical and laboratory features were analyzed and compared. An analysis was also performed for special cases. Results: The measurement of related autoantibodies was performed for about 100 thousand case-times, and 15 patients were found to have positive anti-LKM-1 antibody. Among the 15 patients, 7 were diagnosed with type 2 autoimmune hepatitis (AIH) with an age of 11.0 ± 9.0 years and were all adolescents with acute onset; 8 were diagnosed with hepatitis C with an age of 51.5 ± 9.0 years, among whom 7 were middle-aged patients and 1 was a child aged 12 years, and all of them had an insidious onset. Compared with the patients with hepatitis C, the AIH patients had significantly higher levels of alanine aminotransferase (1 003.9 ± 904.3 U/L vs 57.0 ± 84.1 U/L, P < 0.05), aspartate aminotransferase (410.7 ± 660.3 U/L vs 34.9 ± 42.9 U/L, P < 0.05), and total bilirubin (98.0 ± 191.0 μmol/L vs 15.4 ± 6.0 μmol/L, P < 0.05). There was a reduction in immunoglobulin G after the treatment with immunosuppressant, compared with the baseline. Of all 8 patients with hepatitis C, 6 received antiviral therapy with interferon and ribavirin, and 5 out of them achieved complete response, among whom 4 had a reduction in the level of anti-LKM-1 antibody after treatment; however, a 12-year-old child developed liver failure after interferon treatment and died eventually. Conclusion: Positive anti-LKM-1 antibody is commonly seen in patients with type 2 AIH or hepatitis C, but there are differences between these two groups of patients in terms of age, disease onset, liver function, and the level of anti-LKM-1 antibody. The hepatitis C patients with a confirmed diagnosis and exclusion of autoimmune hepatitis can achieve good response to interferon under close monitoring, even if anti-LKM-1 antibody is positive. As for adolescent patients with hepatitis C and positive anti-LKM-1 antibody, the possibility of AIH should be excluded.

[Terminal branches portal vein embolization for planed hepatectomy]

OBJECTIVE

To explore the application of the technique of terminal branches portal vein embolization(TBPVE)for planed hepatectomy.

METHODS

From February 2016 to June 2016, 4 patients with hepatocellular carcinoma underwent TBPVE and liver resection in Yuebei People's Hospital (n=3) and Jiangxi Ji'an Central People's Hospital (n=1). All of them were male and were 50, 64, 39 and 47 years old respectively. All the tumors located in the right lobe. All patients had the liver function of Child-Pugh A classification and liver cirrhosis level of G2S4. The standard liver volume (SLV) were 1 291, 1 109, 1 177 and 1 242 ml and estimated future liver remnant(FLR) were 315, 347, 306 and 323 ml respectively. The puncture site of TBPVE was determined by the three-dimensional reconstruction of portal vein. Three patients were punctured in the segment Ⅵ and the other one punctured in the segment Ⅲ. CT scan was repeated 2 weeks after TBPVE and FLR and FLR/SLV were calculated. All patients underwent right hepatectomy 2 weeks after TBPVE.

RESULTS

On the 14(th) day after TBPVE, the FLR of 4 patients were 529, 462, 469 and 498 ml which increased 67.9%, 33.1%, 53.3% and 54.2% compared with that before TBPVE, and FLR/SLV were 41.0%, 41.7%, 39.8% and 40.1% respectively. No severe complication occurred. Right hepatectomy were performed 2 weeks after TBPVE. No inflow blood control applied during the liver resection. The mean blood loss was 950 ml and the mean operating time was 3.3 hours (ranging from 3 to 4 hours). One patient had respiratory infection and two had slight jaundice and ascites for a short period. No other complication occurred.

CONCLUSION

The TBPVE could induce a rapid and large FLR volume that give chances to patients with small FLR to have liver resection for hepatocellular carcinoma.

Abstract 2441: NanoString 3D Biology™ technology: simultaneous digital counting of DNA, RNA and protein

Introduction: Development of improved cancer diagnostics and therapeutics requires detailed understanding of the genomic, transcriptomic, and proteomic profiles in the tumor microenvironment. Current technologies can excel at measuring a single analyte, but it remains challenging to simultaneously collect high-throughput DNA, RNA, and protein data from small samples. We have developed an approach that uses optical barcodes to simultaneously profile DNA, RNA, and protein from as little as 5ng DNA, 25ng RNA, and 250ng protein or just 2 5µm FFPE slides, and simplifies data analysis by generating digital counts for each analyte.

Methods: The approach uses paired capture and reporter oligonucleotide probes and optical barcodes to enumerate up to 800 targets. The platform was initially developed to measure RNA, and we have adapted it to measure DNA single nucleotide variants (SNVs), proteins, and phospho-proteins. SNVs are detected by direct hybridization of sequence discriminating probes to the wild-type and mutant sequence of interest. Proteins are detected via binding of oligonucleotide-conjugated antibodies.

Results: Combinations of DNA, RNA, and protein in biological and experimental contexts. SNV probes are able to detect variant alleles down to 5% abundance within a wild type population and can discriminate variants within mutation hotspots. It was &gt;96% accurate at identifying variants from samples displaying a range of allele frequencies and DNA integrity when benchmarked against next-generation sequencing. Protein detection has been developed for cell surface, cytosolic, and nuclear proteins, as well as phospho-proteins. It was validated against flow cytometry, western blot, and mass spectrometry using cell lines with ectopic target expression and primary cells. To demonstrate concurrent measurement of DNA, RNA, and protein from a single system, BRAFWT or BRAFV600E cell lines were treated with the BRAFV600E inhibitor vemurafenib and the MEK inhibitor trametinib. We measured the allele usage at the BRAFV600 locus, as well as BRAFV600E dependent changes in mRNA expression, protein expression and protein phosphorylation in a single experiment.

Conclusions: 3D Biology has several advantages over other analytical approaches. Direct, single-molecule digital counting allows detection over a broad dynamic range with high reproducibility, often over 98% concordance between technical replicates. The simultaneous interrogation of DNA, RNA, and protein maximizes the amount of data obtained from precious samples and minimizes instrumentation demands by leveraging a single detection platform. The 3D Biology approach allows holistic, digital analysis of biological samples with high specificity and precision. This technology is currently available for research use, but may also have clinical application in the future.

Citation Format: Chris Lausted, Yong Zhou, Jinho Lee, Christopher Vellano, Karina A. Eterovic, Ping Song, Lin-ya Tang, Gloria Fawcett, Tae-Beom Kim, Ken Chen, Gary Geiss, Gavin Meredith, Qian Mei, Gokhan Demirkan, Dwayne Dunaway, Dae Kim, P. Martin Ross, Elizabeth Manrao, Nathan Elliott, Sarah Warren, Christina Bailey, Chung-Ying Huang, Joseph Beechem, Gordon Mills, Leroy Hood. NanoString 3D Biology™ technology: simultaneous digital counting of DNA, RNA and protein [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2441. doi:10.1158/1538-7445.AM2017-2441

[Effect of Krüppel like zinc finger transcription factor 2 on γ-glutamylcysteine synthetase in bronchial epithelial cells of chronic obstructive pulmonary disease]

Objective: To research the regulation effects of Krüppel like zinc finger transcription factor 2 (KLF2) on γ-glutamylcysteine synthetase (γ-GCS) in airway epithelial cells of chronic obstructive pulmonary disease (COPD). Methods: (1) Human specimen experiment: lung tissue of pulmonary lobectomy patients with lung cancer with or without COPD was collected from Department of Thoracic Surgery of Hunan Cancer Hospital from December 2008 to December 2009. The patients were divided into COPD group and control group without COPD. The levels of KLF2, γ-GCS mRNA and protein expression in lung tissues were measured by immunohistochemistry and in situ hybridization (ISH). Then, the correlation between KLF2 and γ-GCS mRNA and protein expression levels were analyzed, as well as the correlation between KLF2 or γ-GCS protein and smoking index, percentage of forced expiratory volume in one second to predicted value (FEV1%), percentage of forced expiratory volume in one second to forced vital capacity (FVC/FEV1). (2) Animal experiment: the primary bronchial epithelial cells of rats were extracted by enzyme digestion. After 6 hours of incubation with 10% tobacco smoke extract (TSE), cellular glutathione (GSH) was measured by enzyme linked immunosorbent assay (ELISA) method. The cells were transfected by specific inhibitor of KLF2 through the liposom, which inhibited the protein expression of KLF2. Then, the cells were divided into KB group (blank control group without any treatment), KB+ TSE group (treated with TSE), NC group (control group transfected with miRNA), NC+ TSE group (treated with miRNA and TSE), 92a group (transfected with KLF2 inhibitor), 92a+ TSE group (treated with KLF2 inhibitor transfection and TSE) based in the treatment. After that, the changes of KLF2 and γ-GCS mRNA and protein expression in the cells of each group were measured by reverse transcriptase-polymerase chain reaction (RT-PCR) and Western blot method. Results: (1) Human specimen experiment: The expressions of KLF2 mRNA, protein and γ-GCS mRNA, protein in the lung tissue of COPD patients were strong positive and higher than those in control group (0.32±0.04 vs 0.19±0.03, 0.35±0.05 vs 0.22±0.03; 0.28±0.03 vs 0.16±0.03, 0.31±0.05 vs 0.21±0.03; all P<0.01). Linear correlation analysis showed that KLF2 mRNA and protein were positively correlated with γ-GCS mRNA and protein (r=0.705, 0.722; both P<0.01). The KLF2 and γ-GCS protein were positively correlated with smoking index, FEV1% and FEV1/FVC (r=0.552, 0.728, 0.670, and r=0.631, 0.727, 0.657; all P<0.01). (2) Animal experiment: The level of GSH in KB+ TSE group was significantly higher than that in KB group[(28.05±2.04) vs (7.27±0.33) nmol/mg, P<0.01]. The KLF2 mRNA, protein and γ-GCS mRNA, protein in KB+ TSE group (1.715±0.026, 1.842±0.028 and 2.117±0.067, 1.879±0.065) were higher than those in KB group (1.130±0.017, 1.177±0.033 and 1.378±0.053, 1.177±0.042; all P<0.05), and those in 92a group (0.472±0.028, 0.634±0.025 and 0.582±0.025, 0.554±0.021) were significantly lower than those in KB group, NC group (1.047±0.056, 1.092±0.045 and 1.303±0.037, 1.252±0.037), and those in TSE+ 92a group (0.262±0.017, 0.288±0.017 and 0.337±0.022, 0.321±0.022) were significantly lower than those in KB+ TSE group, 92a group and NC+ TSE group (1.576±0.036, 1.646±0.066 and 1.948±0.093, 1.843±0.078) (all P<0.05). Conclusion: KLF2 exerts antioxidative effect by regulating the expression of γ-GCS in the bronchial epithelial cells of chronic obstructive pulmonary disease.

Relationship of lifestyle and body stature growth with the development of myopia and axial length elongation in Taiwanese elementary school children

Context:

The development of myopia and growth of the eye, occur at a time when body stature is increasing.

Aims:

To investigate the relationship of lifestyle and body growth with axial elongation and myopia development among schoolchildren aged 7 to 9 years.

Settings and Design:

Prospective study.

Materials and Methods:

Children in elementary schools without serious eye disorders were invited to participate. We measured cycloplegic refraction, corneal curvature, intraocular pressure, axial length, body height, and weight. Questionnaires about the children's daily lifestyles, family members’ myopia and parents’ socio-demographic status were completed. The children were followed up every 6 months in a 3-year period.

Statistical Analysis Used:

Bivariate correlations, simple and multiple regression.

Results:

Eighty-eight children participated in this study. Forty-eight were myopic at the beginning of the study, and their myopia correlated with longer axial length and parental myopia (P = 0.015, 0.012). Sixty-five children (74%) completed the study, and the rates of change per year were -0.43 ± 0.58 (mean + standard deviation) diopters in spherical equivalence, 0.32 ± 0.25 mm in axial length (AL), 5.73 ± 2.71 cm in body height, and 3.84 ± 2.23 kg in weight. The axial length change was positively correlated with the height change (P < 0.001). The myopia shift was correlated to axial length change (P = 0.000) but not correlated to height change. Using multiple regression test, near work was the only significant risk factor for myopia progression (P = 0.022).

Conclusions:

Our study showed that body height increment was correlated to axial length elongation but not to myopia shift in children aged 7-9 years. Genetic factors such as parental myopia and body height had a possible influence on myopia development, and the environment factor as near work intensity was related to myopia progression.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell type would be transformative for understanding systems-level properties as well as specific pathways in physiology and disease. Here, we describe the generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins by the widely accessible, sensitive, and robust targeted mass spectrometric method selected reaction monitoring, SRM. This human SRMAtlas provides definitive coordinates that conclusively identify the respective peptide in biological samples. We report data on 166,174 proteotypic peptides providing multiple, independent assays to quantify any human protein and numerous spliced variants, non-synonymous mutations, and post-translational modifications. The data are freely accessible as a resource at http://www.srmatlas.org/, and we demonstrate its utility by examining the network response to inhibition of cholesterol synthesis in liver cells and to docetaxel in prostate cancer lines.

No increased risk of coronary heart disease for patients receiving androgen deprivation therapy for prostate cancer in Chinese/Taiwanese men

The relationship between androgen deprivation therapy (ADT) and coronary heart disease (CHD) remains controversial. Furthermore, the majority of such studies focused on Caucasian populations, and there is still a paucity of studies among Asian populations. This population-based study aimed to investigate the relationship between ADT and CHD in an ethnic Chinese (i.e., Taiwanese) population. We used data sourced from the Taiwan 'Longitudinal Health Insurance Database'. This study included 1278 patients with prostate cancer in the study group and 1278 subjects without prostate cancer in the comparison group. Each patient was individually tracked for a 3-year period to identify those who had subsequently received a diagnosis of CHD. The results showed that the incidence rate of CHD during the 3-year follow-up period was 4.69 (95% CI: 2.99-5.48) per 100 person-years and 2.67 (95% CI: 2.15-3.27) per 100 person-years for the study and comparison cohort, respectively. The Cox proportional hazard regression showed that the hazard ratio for CHD during the 3-year follow-up period for prostate cancer patients was 1.65 (95% confidence interval (CI) = 1.25-2.16) compared with comparison subjects after adjusting for patients' geographic location, monthly income, urbanization level, hypertension, diabetes, hyperlipidemia, and stroke. However, we failed to find a significant difference in the adjusted hazard of CHD during the 3-year follow-up period between prostate cancer patients who did and those who did not receive ADT (hazard ratio = 1.12, 95% CI = 0.79-1.59). We concluded that prostate cancer but not ADT was significantly associated with CHD. In addition, a common cause of prostate cancer and coronary heart disease could exist.