Efficient regeneration of protoplasts from Solanum lycopersicum cultivar Micro-Tom

Protoplast regeneration has become a key platform for genetic and genome engineering. However, we lack reliable and reproducible methods for efficient protoplast regeneration for tomato (Solanum lycopersicum) cultivars. Here, we optimized cell and tissue culture methods for protoplast isolation, microcallus proliferation, shoot regeneration, and plantlet establishment of the tomato cultivar Micro-Tom. A thin layer of alginate was applied to protoplasts isolated from third to fourth true leaves and cultured at an optimal density of 1 × 105 protoplasts/ml. We determined the optimal culture media for protoplast proliferation, callus formation, de novo shoot regeneration, and root regeneration. Regenerated plantlets exhibited morphologically normal growth and sexual reproduction. The entire regeneration process, from protoplasts to flowering plants, was accomplished within 5 months. The optimized protoplast regeneration platform enables biotechnological applications, such as genome engineering, as well as basic research on plant regeneration in Solanaceae species.

An extremely energetic cosmic ray observed by a surface detector array

Cosmic rays are energetic charged particles from extraterrestrial sources, with the highest-energy events thought to come from extragalactic sources. Their arrival is infrequent, so detection requires instruments with large collecting areas. In this work, we report the detection of an extremely energetic particle recorded by the surface detector array of the Telescope Array experiment. We calculate the particle's energy as [Formula: see text] (~40 joules). Its arrival direction points back to a void in the large-scale structure of the Universe. Possible explanations include a large deflection by the foreground magnetic field, an unidentified source in the local extragalactic neighborhood, or an incomplete knowledge of particle physics.

Reappraisal of an Adequate Negative Margin Following Breast Conservation Therapy in Young Patients with Invasive Breast Cancer

PURPOSE/OBJECTIVE(S)

This study aimed to examine the relationship between resection margin (RM) width and ipsilateral breast tumor recurrence (IBTR). The current definition of an adequate negative margin was validated in young breast cancer patients (<40 years).

MATERIALS/METHODS

This study included 4,042 patients who underwent breast conservation therapy between 2006 and 2012. There were 595 women <40 years (14.7%). Re-excision to achieve a wider RM was not considered in patients with no ink on tumor. Systemic treatments were administered in 3,985 patients (98.6%). The impact of RM width on the incidence of IBTR was assessed using narrowly specified intervals (positive, >0 to <1 mm, 1 to <2 mm, 2 to <3 mm, and ≥3 mm).

RESULTS

A significant relationship was observed between RM width and incidence of IBTR. In young women, the 10-year cumulative incidence rates of IBTR were 21.6% for positive RM, 13.9% for >0 to <1 mm, 10.9% for 1 to <2 mm, 5.7% for 2 to <3 mm, and 5.8% for ≥3 mm (p <0.01). The corresponding incidence rates of IBTR in women ≥40 years were 8.6%, 8.0%, 4.4%, 2.7%, and 2.1%, respectively (p <0.01). The difference in the incidence of IBTR between each RM width interval increased over time, and the magnitude of the increment was greater in young women. RM width was the only risk factor for IBTR in young women.

CONCLUSION

The relationship between RM width and IBTR was definite in young women. Compared with women ≥40 years, young women might have long-term benefits from a wider RM than no ink on tumor.

Decadal stability in coral cover could mask hidden changes on reefs in the East Asian Seas

Coral reefs in the Central Indo-Pacific region comprise some of the most diverse and yet threatened marine habitats. While reef monitoring has grown throughout the region in recent years, studies of coral reef benthic cover remain limited in spatial and temporal scales. Here, we analysed 24,365 reef surveys performed over 37 years at 1972 sites throughout East Asia by the Global Coral Reef Monitoring Network using Bayesian approaches. Our results show that overall coral cover at surveyed reefs has not declined as suggested in previous studies and compared to reef regions like the Caribbean. Concurrently, macroalgal cover has not increased, with no indications of phase shifts from coral to macroalgal dominance on reefs. Yet, models incorporating socio-economic and environmental variables reveal negative associations of coral cover with coastal urbanisation and sea surface temperature. The diversity of reef assemblages may have mitigated cover declines thus far, but climate change could threaten reef resilience. We recommend prioritisation of regionally coordinated, locally collaborative long-term studies for better contextualisation of monitoring data and analyses, which are essential for achieving reef conservation goals.

Efficient Plant Regeneration System from Leaf Explant Cultures of Daphne genkwa via Somatic Embryogenesis

This study aimed to establish an efficient plant regeneration system from leaf-derived embryogenic structure cultures of Daphne genkwa. To induce embryogenic structures, fully expanded leaf explants of D. genkwa were cultured on Murashige and Skoog (MS) medium supplemented with 0, 0.1, 0.5, 1, 2, and 5 mg·L^-1 2,4-dichlorophenoxyacetic acid (2,4-D), respectively. After 8 weeks of incubation, the highest frequency of embryogenic structure formation reached 100% when the leaf explants were cultivated on MS medium supplemented with 0.1 to 1 mg·L^-1 2,4-D. At higher concentrations of 2,4-D (over 2 mg·L^-1 2,4-D), the frequency of embryogenic structure formation significantly declined. Similar to 2,4-D, indole butyric acid (IBA) and α-naphthaleneacetic acid (NAA) treatments were also able to form embryogenic structures. However, the frequency of embryogenic structure formation was lower than that of 2,4-D. In particular, the yellow embryonic structure (YES) and white embryonic structure (WES) were simultaneously developed from the leaf explants of D. genkwa on culture medium containing 2,4-D, IBA, and NAA, respectively. Embryogenic calluses (ECs) were formed from the YES after subsequent rounds of subculture on MS medium supplemented with 1 mg·L^-1 2,4-D. To regenerate whole plants, the embryogenic callus (EC) and the two embryogenic structures (YES and WES) were transferred onto MS medium supplemented with 0.1 mg·L^-1 6-benzyl aminopurine (BA). The YES had the highest plant regeneration potential via somatic embryo and shoot development compared to the EC and WES. To our knowledge, this is the first successful report of a plant regeneration system via the somatic embryogenesis of D. genkwa. Thus, the embryogenic structures and plant regeneration system of D. genkwa could be applied to mass proliferation and genetic modification for pharmaceutical metabolite production in D. genkwa.

Metabolic Discrimination between Adventitious Roots and Standard Medicinal Part of Atractylodes macrocephala Koidz. Using FT-IR Spectroscopy

This study aims to examine the metabolic discrimination between in vitro grown adventitious roots and the standard medicinal parts of Atractylodes macrocephala. To achieve this goal, firstly, in vitro culture conditions of adventitious roots such as indole-3-butyric acid (IBA) concentrations, types of media, inorganic salt strength of culture medium, and elicitor types and concentrations were optimized. The optimal culture conditions for proliferation of adventitious roots was found to consist of Murashige and Skoog (MS) medium containing 5 mg L^-1 IBA. Whole cell extracts from adventitious roots and the standard medicinal parts of A. macrocephala were subjected to Fourier transform infrared spectroscopy (FT-IR). Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) from FT-IR spectral data showed that adventitious roots and standard medicinal parts were clearly distinguished in the PCA and PLS-DA score plot. Furthermore, the overall metabolite pattern from adventitious roots was changed depending on the dose-dependent manner of chemicals. These results suggest that FT-IR spectroscopy can be applied as an alternative tool for the screening of higher metabolic root lines and for discriminating metabolic similarity between in vitro grown adventitious roots and the standard medicinal parts. In addition, the adventitious roots proliferation system established in this study can be directly applied as an alternative means for the commercial production of A. macrocephala.

Effects of TSA, NaB, Aza in Lactuca sativa L. protoplasts and effect of TSA in Nicotiana benthamiana protoplasts on cell division and callus formation

Whole-plant regeneration via plant tissue culture is a complex process regulated by several genetic and environmental conditions in plant cell cultures. Recently, epigenetic regulation has been reported to play an important role in plant cell differentiation and establishment of pluripotency. Herein, we tested the effects of chemicals, which interfere with epigenetic regulation, on the plant regeneration from mesophyll protoplasts of lettuce. The used chemicals were histone deacetylase inhibitors trichostatin A (TSA) and sodium butyrate (NaB), and the DNA methyltransferase inhibitor azacytidine (Aza). All three chemicals increased cell division, micro-callus formation and callus proliferation in lettuce protoplasts. Cell division increased by more than 20% with an optimal treatment of the three chemicals. In addition, substantial increase in the callus proliferation rates was observed. In addition, TSA enhances cell division and adventitious shoot formation in the protoplast culture of Nicotiana benthamiana. The regenerated tobacco plants from TSA-treated protoplasts did not show morphological changes similar to the control. TSA increased histone H3 acetylation levels and affected the expression of CDK, CYCD3-1, and WUS in tobacco protoplasts. Thus, we investigated the effect of TSA, NaB, and Aza on Lactuca sativa L. protoplasts and the effect of TSA on cell division and callus formation in Nicotiana benthamiana protoplasts, which facilitates plant regeneration from mesophyll protoplasts. Furthermore, these chemicals can be directly applied as media additives for efficient plant regeneration and crop improvement in various plant species.

Effect of an early invasive strategy based on time of symptom onset in patients with non-ST elevation myocardial infarction

Background

A limitation of the current guidelines of the timing of invasive coronary angiography (ICA) for patients with non-ST-segment elevation (NSTE) acute coronary syndrome is based on randomization time. So far, no study has reported the clinical outcomes of invasive strategy timing based on the time of symptom onset. Herein, we aimed to investigate the effect of invasive strategy timing from the time of symptom onset on the 3-year clinical outcomes of patients with NSTE myocardial infarction (MI).

Methods and results

Among 13,104 patients from the Korea Acute Myocardial Infarction Registry-National Institutes of Health, we evaluated 5,856 patients with NSTEMI. The patients were categorized according to symptom-to-catheter (StC) time (&lt;48 h and ≥48 h). The primary outcome was 3-year all-cause mortality, and the secondary outcome was a 3-year composite of all-cause mortality, recurrent MI, and hospitalization for heart failure. Overall, 3,919 (66.9%) patients were classified into the StC time &lt;48 h group. This group had lower all-cause mortality than the StC time ≥48 h group (7.3% vs. 13.4%, p&lt;0.001). The continuous association of StC time and risk of primary and secondary endpoints showed shorter StC time (reference: 48 h), and lower adjusted hazard ratio reduction was observed. In multivariable analysis, independent predictors of delayed ICA were older age, non-specific symptoms, no use of emergency medical services, no ST-segment deviation, chronic kidney disease, and Global Registry of Acute Coronary Events score &gt;140.

Conclusion

Early invasive strategy based on the StC time improves all-cause mortality in patients with NSTEMI.

Funding Acknowledgement

Type of funding sources: None.

Analysis of predisposing factors in unilateral maxillary sinus fungal ball: the predictive role of odontogenic and anatomical factors

BACKGROUND

The pathogenesis of maxillary sinus fungal ball (MSFB) is explained by aerogenic and odontogenic factors. We evaluated the predisposing factors, including intranasal anatomical and dental factors for increased diagnostic accuracy.

METHODOLOGY

In this study, 117 patients who underwent endoscopic sinus surgery for unilateral MSFB were included. Preoperative computed tomography (CT) scans were used to analyze the presence of anatomical variations (anterior and posterior nasal septal deviation (NSD), concha bullosa (CB), infraorbital cell (haller cell), paradoxical middle turbinate, everted uncinate process and MS size). Dental factors including history of dental procedures and findings on CT scans were reviewed.

RESULTS

Anterior and posterior NSD toward non-affected side were significantly associated with the presence of FB. The presence of CB and infraorbital cell was higher in the non-affected side rather than in the lesion side. Compared to non-affected MS, FB-presence MS was shallower and had a larger height to depth ratio. The presence of dental history was significantly higher on FB-presence MS than non-affected MS. In multivariable analysis, posterior NSD toward non-affected side, dental history increased the aOR of MSFB, while the presence of CB and infraorbital cell decreased the aOR of MSFB.

CONCLUSIONS

The occurrence of MSFB seems to be associated with ipsilateral odontogenic factors, followed by anatomic variations including posterior NSD toward non-affected side and absence of CB and infraorbital cell.

Development of late-bolting plants by CRISPR/Cas9-mediated genome editing from mesophyll protoplasts of lettuce

KEY MESSAGE

CRISPR/Cas9-mediated introduction of a single base mutation in SOC1, a transcription factor that regulates flowering time, results in late-bolting phenotypes in lettuce. Lettuce is a widely consumed leafy vegetable crop. One of the molecular approaches that can increase leaf yield of lettuce is to delay the onset of flowering. Flowering time or time-to-bolting is not only a valuable trait for lettuce, but also a sought-after phenotype for other leafy vegetable crops. This is because delayed flowering enables more extensive vegetative growth, which leads to higher leaf numbers, and possibly larger leaves. Here, we deployed the most recent gene-editing technique to reduce the expression of SOC1, which is a gene that encodes one of several transcription factors that regulate the onset of flowering in plants. By inducing a single base mutation in SOC1 through Cas9 protein-gRNA ribonucleoproteins (RNPs) system, we showed that the time to first flower bud formation in lettuce is longer than that of wild type. In addition, expression of the floral regulatory genes including LsLFY, LsFUL, LsAPL1, and LsAPL2, was lower in the SOC1 gene edited plants than that of the wild type. The gene-editing technique established in this study could be directly applied for diverse quality improvement of lettuce by direct RNP transfer from protoplasts. Furthermore, it is expected that direct RNP transfer from protoplasts can be used as a useful mean for developing various gene edited crops.

First Report of Pseudomonas cichorii Causing Bacterial vein necrosis on Perilla plants [Perilla frutescens (L.) Britton.] in South Korea

Perilla (Perilla frutescens L.) is the second most important upland crop and the third largest edible oil crop in Korea (Shin and Kim 1994). During a disease survey in Busan, Korea in September 2021, symptoms of vein necrosis were observed in perilla plants, with incidences of approximately 30% and 50% in two fields. Symptoms of spots on the perilla appeared as leaf dryness and spots with water-soaked blotches largely concentrated on the mid-veins of leaves. The lesions were initiated with water-soaked spots on the leaf or stem and gradually turned black or brown. Necrosis was also observed in the stems. A bacterium was isolated on Luria-Bertani (LB) agar from diseased leaf tissues that were surface-disinfected with 70% ethyl alcohol for 3-5 min and then washed with sterile water three times. Three pieces of sterilized leaf tissue (size: 0.5 × 0.5 cm) were mixed with 500 µL sterile water for 30 min, and then the suspension was serially diluted and spread on LB agar. Subsequently, isolates were cultivated on LB agar and King's Medium B agar (KMB) (Schaad et al. 2001), and they were predominantly cream-colored and circular bacterial colonies with undulated margins. The bacterial colonies on KMB displayed fluorescence under 365 nm UV light. The isolates were analyzed with the GEN III MicroPlate (Biolog, Hayward, CA, USA), and all isolates were identified as Pseudomonas cichorii, a devastating plant bacterium that damages a wide range of host plants worldwide, including in South Korea (Hikichi et al. 2013; Ramkumar et al. 2015). To identify the species of the bacterial pathogen, genomic DNA of four isolates (BS4922, BS4167, BS4345, and BS4560) was extracted, and the 16S rRNA gene and hrcRST gene were amplified with universal primers, 27F/1492R and Hcr1/Hcr2, and sequencing was then done (Patel et al. 2019). In the BLAST analysis, the 16S rRNA sequences (GenBank OM060656, OM275434, OM275435, OM275436) showed a 100% and 99% similarity to P. cichorii strains MAFF 302698 (AB724286) and P. cichorii strain Pc-Gd-4 (KU923373), respectively. Further, hrcRST gene sequences (GenBank OM143596, OM268864, OM268865, and OM268866) showed high similarity (>99%) with P. cichorii strain P16-51 (MG518230). A pathogenicity test of the four isolates was performed on 3 - 4 weeks old perilla plants by creating wounds with a needle on the lower leaves and stems, and then the plants were inoculated by spraying inoculum (108 CFU/ml). The plants that served as the negative control were wounded and sprayed with unsterilized water. The inoculated perilla plants were placed in a greenhouse at 28 ± 2oC , 80-85% relative humidity, and a natural photoperiod. The inoculation site began to show symptoms of water-soaked brown lesions. Disease symptoms such as leaf dryness, water-soaked blotches on the mid-vein of leaves, and necrosis on plant stems were observed in the inoculated plants 7-10 days after inoculation, whereas the plants of the negative control group did not show any symptoms. The bacteria were re-isolated from the diseased tissues of the plants, and DNA sequence analysis identified them as P. cichorii. Additionally, all isolates induced hypersensitivity reactions in tobacco and tomato leaves within 24 h after inoculation. To our knowledge, this is the first report of P. cichorii infecting perilla in South Korea. The findings in this study will provide the basic information for the development of diagnostic tools and management measures against P. cichorii in perilla.

Impacts of weaning weights and mycotoxin challenges on jejunal mucosa-associated microbiota, intestinal and systemic health, and growth performance of nursery pigs

Background

This study aimed at investigating the effects of mycotoxin challenge on the growth and physiology of nursery pigs with different weaning weights.

Results

At weaning, 10 pigs were euthanized to collect jejunal mucosa and 90 pigs were assigned following a randomized complete block design in a 2 × 2 factorial arrangement of treatments with 3 pigs per pen. Factors were: weaning weight (light: body weight, BW < 7.5 kg or heavy: BW > 9.0 kg); and dietary mycotoxins (supplementation of 0.2 mg/kg aflatoxins, 2.0 mg/kg deoxynivalenol). All diets had titanium dioxide as an external marker at 0.5%. Growth performance and fecal score were recorded until pigs achieved 20 kg BW (light pigs average BW = 21.1 kg and heavy pigs average BW = 20.5 kg). Pigs were sampled for blood, ileal digesta, jejunal tissue and mucosa at 20 kg BW. Data were analyzed using the mixed procedure of SAS. At weaning, light pigs had decreased (P < 0.05) jejunal interleukin-8, increased (P < 0.05) tumor necrosis factor-α, and increased (P < 0.05) α-diversity indexes of jejunal mucosa-associated microbiota. At 20 kg of BW, light pigs had decreased (P < 0.05) average daily gain (ADG), average daily feed intake (ADFI), and gain to feed ratio (G/F). Mycotoxins decreased (P < 0.05) BW, ADG, ADFI, and G/F. Light pigs tended to have increased fecal score on d 0 (P = 0.080), d 10 (P = 0.069), and increased (P < 0.05) fecal score at 20 kg. Mycotoxins decreased the apparent ileal digestibility of nitrogen (P < 0.05). Light pigs had increased (P < 0.05) intestinal malondialdehydes and interleukin 8. Mycotoxins tended to increase (P = 0.060) intestinal tumor necrosis factor-α.

Conclusions

Nursery pigs with light weaning weight were more susceptible to jejunal inflammation and had impaired intestinal health due to weaning stress, whereas mycotoxins diminished the health and growth of nursery pigs regardless of weaning weight.

Increased risk of cardiovascular diseases in patients with chronic rhinosinusitis: a longitudinal follow-up study using a national health screening cohort

BACKGROUND

Chronic rhinosinusitis (CRS) is one of the most common chronic inflammatory diseases and is characterized by sinonasal inflammation that lasts longer than 12 weeks. Whether the effect of chronic inflammation caused by CRS on cardiovascular diseases (CVDs) is similar to its effect on other inflammatory disorders has not been thoroughly evaluated. We aimed to demonstrate whether CRS patients have a higher prevalence of CVDs, including stroke and ischemic heart disease (IHD).

METHODOLOGY

We compared the prevalence of various comorbidities between CRS and control participants through a case-control cohort study from 2002 to 2015 that included 514,866 participants. CRS (n=6,552) and control (n=26,208) participants who were over 40 years old were selected by matching age, sex, income, and area of residence at a 1:4 ratio.

RESULTS

A stratified Cox proportional hazards model was utilized to assess the hazard ratio (HR) of CRS for stroke and IHD. The HRs for stroke and IHD were significantly increased in CRS patients compared to controls after adjusting for obesity, alcohol consumption, smoking, systolic and diastolic blood pressure, fasting blood glucose, total cholesterol, hemoglobin, and Charlson Comorbidity Index (CCI) scores. The HR of stroke was significantly higher in the absence of nasal polyps than in the presence of nasal polyps. The HR of IHD was significantly increased in the CRS group regardless of the presence of nasal polyps.

CONCLUSIONS

This study showed that CRS participants had a significantly higher prevalence of stroke and IHD.

Plant Growth Promotion by Two Volatile Organic Compounds Emitted From the Fungus Cladosporium halotolerans NGPF1

Microbial volatiles have beneficial roles in the agricultural ecological system, enhancing plant growth and inducing systemic resistance against plant pathogens without being hazardous to the environment. The interactions of plant and fungal volatiles have been extensively studied, but there is limited research specifically elucidating the effects of distinct volatile organic compounds (VOCs) on plant growth promotion. The current study was conducted to investigate the impact of VOCs from Cladosporium halotolerans NGPF1 on plant growth, and to elucidate the mechanisms for the plant growth-promoting (PGP) activity of these VOCs. The VOCs from C. halotolerans NGPF1 significantly promoted plant growth compared with the control, and this PGP activity of the VOCs was culture medium-dependent. Headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) identified two VOC structures with profiles that differed depending on the culture medium. The two compounds that were only produced in potato dextrose (PD) medium were identified as 2-methyl-butanal and 3-methyl-butanal, and both modulated plant growth promotion and root system development. The PGP effects of the identified synthetic compounds were analyzed individually and in blends using N. benthamiana plants. A blend of the two VOCs enhanced growth promotion and root system development compared with the individual compounds. Furthermore, real-time PCR revealed markedly increased expression of genes involved in auxin, expansin, and gibberellin biosynthesis and metabolism in plant leaves exposed to the two volatile blends, while cytokinin and ethylene expression levels were decreased or similar in comparison with the control. These findings demonstrate that naturally occurring fungal VOCs can induce plant growth promotion and provide new insights into the mechanism of PGP activity. The application of stimulatory volatiles for growth enhancement could be used in the agricultural industry to increase crop yield.

Anti-Inflammatory Effects of Weigela subsessilis Callus Extract via Suppression of MAPK and NF-κB Signaling

Weigela subsessilis is used in folk medicine to treat pain and allergic syndromes in Korea. However, the antibacterial and anti-inflammatory activities of W. subsessilis callus extract remain unexplored. In this study, we aimed to evaluate the W. subsessilis callus of pharmacological activity. Therefore, we first established in vitro calluses of W.subsessilis via plant tissue culture methods. We then evaluated the antioxidant and anti-inflammatory effects of W. subsessilis callus extract in lipopolysaccharide (LPS)-treated RAW264.7 macrophage cells. The W. subsessilis callus extract showed antioxidant and anti-inflammatory effects. These effects were regulated via suppression of mitogen-activated protein kinase signaling through LPS-induced translocation of nuclear factor kappa B (NF-κB) p65 from the cytoplasm to the nucleus. W. subsessilis callus extract also showed antibacterial and anti-inflammatory activities in Propionibacterium acnes-treated HaCaT keratinocyte cells. These results indicate that W. subsessilis callus extract has antioxidant, antibacterial and anti-inflammatory activities, suggesting its possible application in the treatment of inflammatory disorders.

Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila

An aerobic, Gram-stain-negative, weak-motile, short-rod-shaped bacterial strain, designated JBR3-12^T, was isolated from halophyte Carex pumila plants, and its taxonomic position was investigated by using a polyphasic taxonomic approach. The strain produced a pink pigment on tryptic soy agar and grew optimally at 25 °C, pH 8 and in the presence of 3 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain JBR3-12^T formed a lineage within the genus Pedobacter and was most closely related to Pedobacter sandarakinus DS-27^T (98.0 %) and Pedobacter agri PB92^T (97.6 %). The DNA G+C content of the genome was 41.3 mol%; the whole genome length was 5 426 070 bp. The major fatty acids of JBR3-12^T were iso-C_15 : 0, summed feature 3 (comprising C_16 : 1  ω6c and/or C_16 : 1  ω7c) and iso-C_17 : 0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant quinone was menaquinone-7. Based on its phenotypic, phylogenetic and genotypic features, strain JBR3-12^T is proposed to represent a novel species of the genus Pedobacter, for which the name is Pedobacter endophyticus sp. nov. The type strain is JBR3-12^T (=KCTC 82363^T=NBRC 114901^T).

TSA Promotes CRISPR/Cas9 Editing Efficiency and Expression of Cell Division-Related Genes from Plant Protoplasts

Trichostatin A (TSA) is a representative histone deacetylase (HDAC) inhibitor that modulates epigenetic gene expression by regulation of chromatin remodeling in cells. To investigate whether the regulation of chromatin de-condensation by TSA can affect the increase in the efficiency of Cas9 protein-gRNA ribonucleoprotein (RNP) indel formation from plant cells, genome editing efficiency using lettuce and tobacco protoplasts was examined after several concentrations of TSA treatments (0, 0.1, 1 and 10 μM). RNP delivery from protoplasts was conducted by conventional polyethylene glycol (PEG) transfection protocols. Interestingly, the indel frequency of the SOC1 gene from TSA treatments was about 3.3 to 3.8 times higher than DMSO treatment in lettuce protoplasts. The TSA-mediated increase of indel frequency of the SOC1 gene in lettuce protoplasts occurred in a concentration-dependent manner, although there was not much difference. Similar to lettuce, TSA also increased the indel frequency by 1.5 to 1.8 times in a concentration-dependent manner during PDS genome editing using tobacco protoplasts. The MNase test clearly showed that chromatin accessibility with TSA treatments was higher than that of DMSO treatment. Additionally, TSA treatment significantly increased the level of histone H3 and H4 acetylation from lettuce protoplasts. The qRT-PCR analysis showed that expression of cell division-related genes (LsCYCD1-1, LsCYCD3-2, LsCYCD6-1, and LsCYCU4-1) was increased by TSA treatment. These findings could contribute to increasing the efficiency of CRISPR/Cas9-mediated genome editing. Furthermore, this could be applied for the development of useful genome-edited crops using the CRISPR/Cas9 system with plant protoplasts.

Optimization of protoplast regeneration in the model plant Arabidopsis thaliana

BACKGROUND

Plants have a remarkable reprogramming potential, which facilitates plant regeneration, especially from a single cell. Protoplasts have the ability to form a cell wall and undergo cell division, allowing whole plant regeneration. With the growing need for protoplast regeneration in genetic engineering and genome editing, fundamental studies that enhance our understanding of cell cycle re-entry, pluripotency acquisition, and de novo tissue regeneration are essential. To conduct these studies, a reproducible and efficient protoplast regeneration method using model plants is necessary.

RESULTS

Here, we optimized cell and tissue culture methods for improving protoplast regeneration efficiency in Arabidopsis thaliana. Protoplasts were isolated from whole seedlings of four different Arabidopsis ecotypes including Columbia (Col-0), Wassilewskija (Ws-2), Nossen (No-0), and HR (HR-10). Among these ecotypes, Ws-2 showed the highest potential for protoplast regeneration. A modified thin alginate layer was applied to the protoplast culture at an optimal density of 1 × 106 protoplasts/mL. Following callus formation and de novo shoot regeneration, the regenerated inflorescence stems were used for de novo root organogenesis. The entire protoplast regeneration process was completed within 15 weeks. The in vitro regenerated plants were fertile and produced morphologically normal progenies.

CONCLUSION

The cell and tissue culture system optimized in this study for protoplast regeneration is efficient and reproducible. This method of Arabidopsis protoplast regeneration can be used for fundamental studies on pluripotency establishment and de novo tissue regeneration.

Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots

A Gram-stain-positive, facultatively anaerobic, rod-shaped, endospore-forming, oxidase-positive, and catalase-negative strain designated as BRMEA1^T was isolated from the surface-sterilized Selaginella involvens roots. Growth of strain BRMEA1^T was found to occur at pH 6.0-8.0 (optimum, pH 7.0), 15-50 °C (optimum, 25-30 °C) and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BRMEA1^T formed a lineage within the genus Neobacillus (family Bacillaceae) and showed the highest sequence similarity to Neobacillus drentensis DSM 15600^T (98.3 %) and Neobacillus fumarioli KCTC 13885^T (98.2 %), and less than 98.2 % 16S rRNA gene sequence similarity to the other members of the genus Neobacillus. Whole-genome analysis of strain BRMEA1^T comprised a circular chromosome (5 632 809 bp in size) with 38.5 mol% G+C content. Digital DNA-DNA hybridization analyses revealed that strain BRMEA1^T showed 20.5 and 22.0% genomic DNA relatedness with the closest species, N. drentensis DSM 15600^T and N. fumarioli KCTC 13885^T, respectively. The whole-genome sequence of strain BRMEA1^T showed the presence of 11 specific conserved signature indels for the genus Neobacillus. The major cellular fatty acids (>10 %) of strain BRMEA1^T were found to be iso-C_15 : 0 and anteiso-C_15 : 0, while the major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Polyphasic analysis results revealed that BRMEA1^T represents a novel species of the genus Neobacillus, with the proposed name Neobacillus endophyticus sp. nov. The type strain is BRMEA1^T (=KCTC 43208^T=CCTCC AB 2020071^T).

Anti-Inflammatory Activities of an Extract of In Vitro Grown Adventitious Shoots of Toona sinensis in LPS-Treated RAW264.7 and Propionibacterium acnes-Treated HaCaT Cells

Toona sinensis has been traditionally used to treat dysentery, enteritis, flatulence, and itchiness. However, the existence of anti-inflammatory effects of T. sinensis on Propionibacterium acnes-induced skin disease is unknown. In vitro cultures of plant cells and tissues produced under controlled conditions offer a continuous production platform for plant natural products including pigments and anti-inflammatory agents. In this study, we determine the anti-inflammatory activities of an extract of in vitro grown adventitious shoots of T. sinensis on P. acnes, the etiologic agent of skin inflammation. The extract of T. sinensis showed antioxidant and anti-inflammatory activity in LPS-treated RAW264.7 cells. It also had antibacterial activity and anti-inflammatory effects on P. acnes-treated HaCaT cells. In addition, these effects were regulated by suppression of the mitogen-activated protein kinase (MAPK) pathways. These results suggesting the potential application of adventitious shoots of T. sinensis grown with an in vitro proliferation system as a medicine for treating P. acnes-induced inflammatory skin disease.

The Effect of Sodium Butyrate on Adventitious Shoot Formation Varies among the Plant Species and the Explant Types

Histone acetylation plays an important role in plant growth and development. Here, we investigated the effect of sodium butyrate (NaB), a histone deacetylase inhibitor, on adventitious shoot formation from protoplast-derived calli and cotyledon explants of tobacco (Nicotiana benthamiana) and tomato (Solanum lycopersicum). The frequency of adventitious shoot formation from protoplast-derived calli was higher in shoot induction medium (SIM) containing NaB than in the control. However, the frequency of adventitious shoot formation from cotyledon explants of tobacco under the 0.1 mM NaB treatment was similar to that in the control, but it decreased with increasing NaB concentration. Unlike in tobacco, NaB decreased adventitious shoot formation in tomato explants in a concentration-dependent manner, but it did not have any effect on adventitious shoot formation in calli. NaB inhibited or delayed the expression of D-type cyclin (CYCD3-1) and shoot-regeneration regulatory gene WUSCHEL (WUS) in cotyledon explants of tobacco and tomato. However, compared to that in control SIM, the expression of WUS was promoted more rapidly in tobacco calli cultured in NaB-containing SIM, but the expression of CYCD3-1 was inhibited. In conclusion, the effect of NaB on adventitious shoot formation and expression of CYCD3-1 and WUS genes depended on the plant species and whether the effects were tested on explants or protoplast-derived calli.

Temporal and Spatial Expression Analysis of Shoot-Regeneration Regulatory Genes during the Adventitious Shoot Formation in Hypocotyl and Cotyledon Explants of Tomato (CV. Micro-Tom)

Enhancing the competence for plant regeneration in tissue culture studies is an important issue not only for efficient genetic transformation of commercial crops but also for the reproducibility of scientific reports. In this study, we investigated optimization of several tissue culture conditions including plant growth regulators, types and ages of explants, culture densities, and plant position in order to improve the competence of adventitious shoot formation of the tomato (Solanum lycopersicum cv. Micro-Tom). In addition, we examined the differential expression of D-type cyclin (CYCD3-1) and several shoot regeneration regulatory genes from hypocotyl and cotyledon explants of tomato during shoot organogenesis. A treatment of 1 mg L-1 Zeatin and 0.1 mg L-1 Indole-3-acetic acid (IAA) in Murashige and Skoog (MS) medium containing 3% sucrose was optimal for adventitious shoot formation from hypocotyl and cotyledon explants. The younger explants exhibited more shoot formation regardless of explant types. Additionally, those closest to the shoot apical meristem produced more shoots compared to the other regions in the hypocotyl and the cotyledon explants. Gene expression of CYCD3-1, SHOOT MERISTEMLESS (STM), and cytokinin dependent WUSCHEL (WUS) was significantly higher in younger explants than in older ones. Furthermore, an increase in CYCD3-1, STM, and WUS expression was evident at the distal part of hypocotyls and the proximal part of cotyledons compared to other regions. These differential gene expression profiles exhibited good agreement with the results of shoot formation obtained from diverse explants of tomato. These results suggest that temporal and spatial gene expression of shoot regeneration regulatory genes plays an important role in enhancing the competence and the reproducibility of adventitious shoot formation from tomato explants.

Induced extracellular production of stilbenes in grapevine cell culture medium by elicitation with methyl jasmonate and stevioside

We report the high production of stilbenes, including resveratrol and viniferin, in grapevine (Vitis labruscana L.) cell cultures through elicitation with methyl jasmonate (MeJA) and stevioside (STE). Methyl-β-cyclodextrin (MeβCD) is widely used as a solubilizer for resveratrol production. For the first time, we used STE as a solubilizer for stilbene production in plant cell cultures. MeJA was most effective elicitor in activating VvSTS expression and stimulating stilbene biosynthesis in grapevine cell cultures. The maximum concentration of δ-viniferin (892.2 mg/L) production with a small amount of trans-resveratrol (12.2 mg/L) was observed in the culture medium by co-treatment of cells with MeJA and STE, whereas the highest level of trans-resveratrol (371.9 mg/L) with a slight amount of δ-viniferin (11.5 mg/L) was accumulated in the culture medium of cells treated with MeJA and MeβCD. However, neither trans-resveratrol nor δ-viniferin were significantly elevated within the cells by the applications. Notably, predominant production of δ-viniferin and trans-resveratrol was observed in shake and static flask culture medium, respectively, by co-treatment of MeJA and STE. Furthermore, stilbene compounds of resveratrol, ε-viniferin, and δ-viniferin were mainly produced in a 3-L bioreactor culture following elicitation of cells with MeJA and STE. These results provide new strategies for conditional, high-level production of resveratrol and viniferin in cell cultures by utilizing the solubilizing properties of STE or MeβCD.

The Synergistic Effect of Co-Treatment of Methyl Jasmonate and Cyclodextrins on Pterocarpan Production in Sophora flavescens Cell Cultures

Pterocarpans are derivatives of isoflavonoids, found in many species of the family Fabaceae. Sophora flavescens Aiton is a promising traditional Asian medicinal plant. Plant cell suspension cultures represent an excellent source for the production of valuable secondary metabolites. Herein, we found that methyl jasmonate (MJ) elicited the activation of pterocarpan biosynthetic genes in cell suspension cultures of S. flavescens and enhanced the accumulation of pterocarpans, producing mainly trifolirhizin, trifolirhizin malonate, and maackiain. MJ application stimulated the expression of structural genes (PAL, C4H, 4CL, CHS, CHR, CHI, IFS, I3’H, and IFR) of the pterocarpan biosynthetic pathway. In addition, the co-treatment of MJ and methyl-β-cyclodextrin (MeβCD) as a solubilizer exhibited a synergistic effect on the activation of the pterocarpan biosynthetic genes. The maximum level of total pterocarpan production (37.2 mg/g dry weight (DW)) was obtained on day 17 after the application of 50 μM MJ on cells. We also found that the combined treatment of cells for seven days with MJ and MeβCD synergistically induced the pterocarpan production (trifolirhizin, trifolirhizin malonate, and maackiain) in the cells (58 mg/g DW) and culture medium (222.7 mg/L). Noteworthy, the co-treatment only stimulated the elevated extracellular production of maackiain in the culture medium, indicating its extracellular secretion; however, its glycosides (trifolirhizin and trifolirhizin malonate) were not detected in any significant amounts in the culture medium. This work provides new strategies for the pterocarpan production in plant cell suspension cultures, and shows MeβCD to be an effective solubilizer for the extracellular production of maackiain in the cell cultures of S. flavescens.

Clinical Characteristics of Developmentally Delayed Children based on Interdisciplinary Evaluation

The aim of this study is to examine the clinical characteristics of children suspected to have neurodevelopmental disorders and to present features that could be helpful diagnostic clues at the clinical assessment stage. All children who visited the interdisciplinary clinic for developmental problems from May 2001 to December 2014 were eligible for this study. Medical records of the children were reviewed. A total of 1,877 children were enrolled in this study. Most children were classified into four major diagnostic groups: global developmental delay (GDD), autism spectrum disorder (ASD), developmental language disorder (DLD) and motor delay (MD). GDD was the most common (43.9%), and boys were significantly more predominant than girls in all groups. When evaluating the predictive power of numerous risk factors, the probability of GDD was lower than the probability of ASD among boys, while the probability of GDD increased as independent walking age increased. Compared with GDD and DLD, the probability of GDD was increased when there was neonatal history or when the independent walking age was late. Comparison of ASD and DLD showed that the probability of ASD decreased when a maternal history was present, whereas the probability of ASD increased with male gender. To conclude, the present study revealed the clinical features of children with various neurodevelopmental disorders. These results are expected to be helpful for more effectively flagging children with potential neurodevelopmental disorders in the clinical setting.

Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses

The genus Izhakiella was established and designated as a member of the family Enterobacteriaceae in 2016. Although the taxonomical classification of most members in this family has been relatively resolved after two reclassifications in 2016 and 2017, the classification of the genus Izhakiella remains ambiguous. In this study, a polyphasic approach was used to provide evidence supporting the fact that the genus Izhakiella should no longer be considered a member of Enterobacteriaceae and proposes its reclassification into the family Erwiniaceae. The phylogenetic tree of type species in the families Enterobacteriaceae and Erwiniaceae based on the sequences of the 16S rRNA gene, rpoB housekeeping gene, and the whole-genome comprising the 92 core genes revealed that the genus Izhakiella forms a phylogenetic lineage within the family Erwiniaceae. The average nucleotide identity (ANI) value of the type species with genus Izhakiella was found to be higher for the family Erwiniaceae than that for the family Enterobacteriaceae. Notably, 12 conserved signature indels (CSIs) that are exclusively shared among the Erwiniaceae clade members were found in the type strains of the genus Izhakiella. Based on these analyses, this study suggests the reclassification of I. capsodis and I. australiensis into the family Erwiniaceae.

Humeral shaft fracture and radial nerve palsy in Korean soldiers: focus on arm wrestling related injury

INTRODUCTION

Humeral shaft fractures can lead to radial nerve injury and may require surgery and rehabilitation. We determined the causative events of humeral fracture, including arm wrestling, in young Korean soldiers and examined whether humeral fracture is related to demographic characteristics and the presence of radial nerve palsy.

METHODS

We reviewed 7.5 years (July 2012 to June 2019) of medical records covering patients who had experienced a humeral shaft fracture after entering military service and had received surgery for open reduction and internal fixation. Data were obtained on basic demographics, initial event provoking the fracture, presence of radial nerve palsy, initial and follow-up severity of the weakness, and any discharge from military service because of prolonged radial nerve palsy.

RESULTS

Of 123 cases, arm wrestling was the leading cause (52.8%). A high energy injury, such as falling from a height (11.4%), and sports related slips (10.6%) were other causes. All humeral shaft fractures caused by forceful contraction were spiral, while 40% of the fractures caused by external force related events were of a transverse type. The percentage of left-sided fractures was significantly higher for fractures arising from an external force than in those caused by forceful contraction related events. Radial nerve palsy was found in 34 patients (27.6%), and 16 were discharged from the military because of prolonged radial nerve palsy 6 months after the fracture. The causative events and other factors did not affect the presence of radial nerve palsy.

CONCLUSION

Arm wrestling was the leading cause of humeral fracture in young Korean soldiers but the chance of developing comorbid radial nerve palsy did not differ from that of other causes. These epidemiologic findings in this young active group may help in understanding the causes of humeral shaft fracture in soldiers and in the wider young population.

Elective neck dissection versus observation for early-stage oral squamous cell carcinoma: Systematic review and meta-analysis

INTRODUCTION

Oral squamous cell carcinoma (OSCC) is the seventh most common cancer globally, and has been identified as a growing health concern. This study aims to evaluate the current literature comparing elective neck dissection to observation in the treatment of early-stage tongue SCC, focusing on nodal recurrence, overall survival, disease specific survival statistics from randomised controlled trials comparing the two interventions.

METHODS

Systematic review and meta-analysis was conducted according to PRISMA guidelines. The odds ratio (OR) was used as a summary statistic.

RESULTS

From 8 studies, there was a total of 372 cases of recurrence, 98 (15.1%) in END group and 274 (41.5%) in the Observation group. There was a significantly lower rate of recurrence in the END group compared to observation (OR 0.25, 95% CI 0.16-0.39, I² = 54%, P < 0.00001). END was associated with higher overall survival rates when compared with observation (OR 1.95, 95% CI 1.40-2.73, I² = 14%, P < 0.0001). END was also associated with higher disease-specific survival compared with observation (OR 1.88, 95% CI 1.21-2.93), I² = 47%, P = 0.005), with no significant heterogeneity noted.

CONCLUSIONS

END was associated with significantly lower recurrence rates and higher overall and disease-specific survival compared to a conservative observation approach in early-stage oral SCC with clinically N0 neck.

European Position Paper on Rhinosinusitis and Nasal Polyps 2020

The European Position Paper on Rhinosinusitis and Nasal Polyps 2020 is the update of similar evidence based position papers published in 2005 and 2007 and 2012. The core objective of the EPOS2020 guideline is to provide revised, up-to-date and clear evidence-based recommendations and integrated care pathways in ARS and CRS. EPOS2020 provides an update on the literature published and studies undertaken in the eight years since the EPOS2012 position paper was published and addresses areas not extensively covered in EPOS2012 such as paediatric CRS and sinus surgery. EPOS2020 also involves new stakeholders, including pharmacists and patients, and addresses new target users who have become more involved in the management and treatment of rhinosinusitis since the publication of the last EPOS document, including pharmacists, nurses, specialised care givers and indeed patients themselves, who employ increasing self-management of their condition using over the counter treatments. The document provides suggestions for future research in this area and offers updated guidance for definitions and outcome measurements in research in different settings. EPOS2020 contains chapters on definitions and classification where we have defined a large number of terms and indicated preferred terms. A new classification of CRS into primary and secondary CRS and further division into localized and diffuse disease, based on anatomic distribution is proposed. There are extensive chapters on epidemiology and predisposing factors, inflammatory mechanisms, (differential) diagnosis of facial pain, allergic rhinitis, genetics, cystic fibrosis, aspirin exacerbated respiratory disease, immunodeficiencies, allergic fungal rhinosinusitis and the relationship between upper and lower airways. The chapters on paediatric acute and chronic rhinosinusitis are totally rewritten. All available evidence for the management of acute rhinosinusitis and chronic rhinosinusitis with or without nasal polyps in adults and children is systematically reviewed and integrated care pathways based on the evidence are proposed. Despite considerable increases in the amount of quality publications in recent years, a large number of practical clinical questions remain. It was agreed that the best way to address these was to conduct a Delphi exercise . The results have been integrated into the respective sections. Last but not least, advice for patients and pharmacists and a new list of research needs are included. The full document can be downloaded for free on the website of this journal: http://www.rhinologyjournal.com.

367 Combinational use of sodium butyrate and phytogenics on intestinal health of nursery pigs

The effects of encapsulated sodium butyrate (SB), phytogenics (PH), or a combination were studied on intestinal health of nursery pigs. Phytogenics were blends of dry herbs and essential oil components. Forty-eight weaned pigs (21-d-old; 6.9 ± 0.6 kg BW) were individually housed, blocked by initial BW and sex, allotted to 4 dietary treatments (n = 12) in a RCBD, and fed for 33-d (P1: 0–7; P2: 7–19; and P3: 19–33). Treatments were arranged by 2 factors: SB (P1: 0.2% and P2: 0.1%) and PH (P3: 0.033%). Diets were formulated to meet or exceed NRC (2012) nutrient requirements and pigs were fed ad libitum. For each phase, ADG, ADFI, and G:F were measured. Fecal scores were assessed during d 3–19 and d 26–33. Blood samples were drawn in P2 and P3 to measure tumor necrosis factor alpha (TNF-α), IL-6, and immunoglobulin G (IgG). Four pigs at P2 and 8 pigs in P3 from each treatment were euthanized to collect jejunal tissue, jejunal mucosa, and ileal digesta to measure gut histology, TNF-α, IL-6, myeloperoxidase (MPO), malondialdehyde (MDA), and protein carbonyl. Data were analyzed using PROC MIXED of SAS. Fixed effects were treatments and random effects were blocks. In P2 and P1-2, SB decreased (P &lt; 0.05) ADFI whereas no effect on ADG and G:F. In P2, SB tended to decrease (P = 0.063) villus height to crypt depth ratio (VH:CD) whereas increased (P &lt; 0.05) enterocyte proliferation in P3. In P3 and overall, PH increased (P &lt; 0.05) G:F. No changes were found in TNF-α, IL-6, MPO, MDA, IgG, and protein carbonyl. Conclusively, SB and a combinational use of SB and PH showed minimal effects on growth performance and gut health when added to the diets of nursery pigs. However, PH supplementation increased feed efficiency of nursery pigs during 19–33 d post-weaning.

137 Effects of dietary supplementation with xylanase and probiotics on growth performance and gut health of newly weaned pigs

This study was to evaluate the supplemental effects of xylanase and probiotics on growth performance and gut health of newly weaned pigs. One hundred and forty-four pigs at 3 weeks of age with an initial body weight (BW) at 6.47 ± 0.03 kg were allotted (4 pigs per pen) to 3 dietary treatments based on a randomized complete block design with sex (gilts and barrow) and initial BW as blocks. The treatments were CON (no supplement), XYL (xylanase at 10,000 XU/kg, Xylamax, BRI, Durham, NC), and PRO (Bacillus spp. 6 x 109 CFU/kg plus xylanase 10,000 XU/kg, EnzaPro, BRI). All diets met the NRC (2012) requirements in 3 phases (P1 for 7 d, P2 for 14 d, and P3 for 14 d). The ADG, ADFI, and G/F were measured weekly. On d 21, 1 pig representing a median BW of each pen was euthanized to collect jejunal samples to measure the immune and oxidative stress status, microbiome, and histology. Data were analyzed using the MIXED procedure of SAS. Treatment was a fixed effect and blocks were random effects. There were no fixed effects among treatments on growth performance, immune and oxidative stress status, and histology. Use of xylanase increased (P &lt; 0.05) the Chao1 index in jejunal mucosa of pigs (24.6 to 29.5). Relative abundance of the Enterobacteriaceae in jejunal mucosa tended to decrease (P = 0.083) with the use of xylanase (16.2 to 1.6%). The PRO increased (P &lt; 0.05) the relative abundance of Mitsuokella compared with others treatments (0.9 vs. 4.8%). In conclusion, supplementation of xylanase or Mitsuokella can enhance the microbiome in jejunal mucosa by increasing the diversity and beneficial bacterial abundance, whereas by reducing pathogenic bacterial abundance without affecting the growth performance, histology, immune, and oxidative stress status.

365 Effects of weaning ages on growth performance of nursery pigs fed diets with increasing lactose levels during at 7 to 11 kg body weight

Lactose is an effective carbohydrate source for nursery pigs. Weaning age could influence needs for lactose. Weaning ages can vary among producers depending on preferred management programs. This study aimed to evaluate optimum levels of lactose for pigs at 7 kg BW weaned at different ages. A total of 1,632 pigs were weaned at d21 (d 21.2 ± 1.3) or d25 (d 24.6 ± 1.1). Pigs had a common diet until they reach 7 kg BW. Within a same weaning age group, when pigs reached 7 kg body weight, they were allotted to 4 dietary treatments with 6, 9, 12, and 15% lactose. Feed intake and BW were measured after 10d feeding when pigs reached 11 kg BW. Data were analyzed using the MIXED procedure of SAS for a slope ratio analysis to test effects of lactose levels on growth performance of pigs influenced by their weaning ages. Pigs weaned at d21 had Phase 1 for 11 days whereas pigs weaned at d 25 had Phase 1 for 2 days to reach 7 kg BW. According to the slope ratio analysis, as increasing lactose intake, ADG of pigs weaned at d21 responded greater (P &lt; 0.05, 68.5%) than growth of pigs weaned at d25. There was no change of slope in feed intake of pigs weaned at d 25 by increasing lactose intake. However, G:F of pigs weaned at d 25 responded greater (P &lt; 0.05, 250%) than G:F of pigs weaned at d21. In conclusion, pigs weaned at d21 grew faster from 7 to 11 kg BW as lactose intake increased compared with pigs weaned at d25 potentially because pigs weaned at d21 had an extended time for adaptation and recovery from weaning stress until they reached 7 kg BW.

366 Efficacy of mycotoxin deactivators on health and growth of newly weaned pigs under chronic dietary challenges of deoxynivalenol

The efficacy of mycotoxin deactivators on health and growth performance of newly weaned pigs (27 d-old) fed diets naturally contaminated with deoxynivalenol was investigated. Sixty pigs were housed individually and assigned to 5 treatments for 34 d subdivided into 3 phases: NC (no added deoxynivalenol); PC (deoxynivalenol at 2 mg/kg); CYC (PC + clay/yeast culture based product, 0.2%); CYE (PC + clay/yeast cell wall/plant extracts/antioxidants based product, 0.2%); and CYB (PC + clay/inactivated yeast/botanicals/antioxidants based product, 0.2%). Blood was taken at d 14 and 34. Intestinal mucosa was taken at d 34. Data were analyzed using Proc Mixed of SAS with pre-planned contrasts. Deoxynivalenol reduced (P &lt; 0.05) ADG in P3. Pigs fed CYC had greater (P &lt; 0.05) ADG during overall period, ADFI during P3, and gain/feed during P2 than PC. At d 14, deoxynivalenol reduced (P &lt; 0.05) BUN/creatinine and tended to reduce (P = 0.088) BUN. Pigs fed CYB tended to have greater (P = 0.059) AST than PC. At d 34, pigs fed CYC (P = 0.083) and CYB (P = 0.068) tended to have lower serum CPK than PC. Pigs fed CYE had lower (P &lt; 0.05) BUN/creatinine than PC. Deoxynivalenol tended to increase (P = 0.068) malondialdehydes and decrease (P = 0.072) glutathione in jejunal mucosa. Pigs fed CYE and CYB had lower (P &lt; 0.05) malondialdehydes, whereas pigs fed CYB had greater (P &lt; 0.05) glutathione and tended to have lower (P = 0.079) jejunal IgA than PC. Pigs fed CYC (P = 0.066) and CYE (P = 0.099) tended to have lower jejunal IL8 than PC. In conclusion, deoxynivalenol compromised growth performance and intestinal health. The mycotoxin deactivators could enhance intestinal health of pigs fed diets with deoxynivalenol without affecting liver function.

126 Evaluation of true ileal amino acid digestibility of fermented soybean meal fed to nursery pigs

Fermented soybean meal (FSBM) has smaller peptides and reduced anti-nutritional factors compared with those in conventional SBM. Apparent and true ileal digestibilities (AID and TID) of AA in FSBM were measured using both a direct method and a substitution method. Forty eight (24 barrows and 24 gilts) pigs at 7 kg BW were allotted to 4 dietary treatments (n = 12) based on a randomized complete block design with sex and initial body weight as blocks. Treatments includes NFD (semi-purified N free diet to measure endogenous AA loss), NFSB (NFD with 20% FSBM; Genebiotech Co., Ltd. and Nutraferma, Inc), CBD (corn basal diet), and CBSB (CBD at 80% and FSBM at 20%). NFD and NFSB were used to directly measure AID and TID AA of FSBM, whereas NFD, CBD, and CBSB were used to indirectly calculate AID and TID AA of FSBM using a substitution method. Experimental diets included TiO2 (0.4%). Pigs were fed experimental diets for 10 days. Feed allowance was based on 0.09 x BW0.75 kg per day. All pigs were euthanized at the end of the experiments to collect ileal digesta. Diets and ileal digesta were used to quantify TiO2 and AA. Data were analyzed using Mixed Procedure of SAS 9.4. Dietary treatment was the main effect and blocks were random effects. Endogenous AA loss was 2.48 g. When measured by a direct method, AID and TID of Lys, Met, Thr, and Trp were 72.1 and 89.8%, 74.9 and 92.1%, 61.0 and 88.5%, and 72.2 and 92.2%, respectively. When measured by a substitution method, AID and TID of Lys, Met, Thr, and Trp were 64.7 and 84.4%, 60.5 and 77.9%, 36.2 and 57.0%, and 58.2 and 81.0%, respectively. Overall, a direct method showed higher AID and TID AA in FSBM than those measured by a substitution method.

Production of Handmade Open Pulled Straw (OPS) Using Digital Heating Gun for the Vitrification Process

BACKGROUND

Vitrification is the most popular technique for the cryopreservation of oocytes and embryos, replacing slow freezing methods.

MATERIALS AND METHODS

This study evaluated the efficient manufacturing methods of handmade open pulled straw (OPS) with a digital heating gun that could be proposed for vitrification.

RESULTS

Production efficiency of OPS using 0.5 mL straw was detected at 0, 66.1, 90.5 and 85.7% for 1~2 s and 9.5, 33.3, 47.6 and 23.8% for 2~3 s of heating time at 250, 350, 400 and 450°C respectively. The production rate of OPS using 0.25 mL straw was perceived at 33.3, 76.2, 83.3, 95.2 and 57.6 % for 1.5~2.5 s time with the optimized heat setting at 330, 340, 350, 360 and 370°C respectively. The desired inner diameter (200~300 μm) of OPS could be varied according to the gamete size, embryo developmental stages or cell lines of different species. Based on our data, the production efficiency of OPS using 0.25-mL straw were increased beyond using a 0.5-mL straw.

CONCLUSION

Handmade OPSs could be efficiently produced with a digital heating gun to generate a vitrification device for freezing gametes, embryos and cell lines.

P997Improving left atrial appendage occluder size determination by using 3-dimensional printing model of the left atrial appendage

Introduction

Given the complexity of left atrial appendage (LAA) structure, current 2D based LAA occluder (LAAO) size prediction system using transesophageal echocardiography (TEE) has limitations.

Objective

To assess the accuracy of LAAO size determination method by implantation simulation using a 3D printed model compared with a conventional method based on TEE.

Methods

We retrospectively reviewed 57 cases with percutaneous LAAO using Amplatzer Cardiac Plug and Amulet from 2014 to 2018. We excluded cases without cardiac CT (21 cases) or with peri-device leakage or inappropriate position of the device on six months follow up TEE (6 cases), or with paroxysmal atrial fibrillation (2 cases). We finally included 28 cases with anatomically and physiologically properly implanted LAAO, using the final size of the implanted devices as a standard for the size prediction accuracy. We generated 3D printing model from cardiac CT images. LAAO size was determined with device implantation simulation using 3D printing model and occluder devices (Figure C), and conventional 2D TEE measurements by two experienced cardiologists who were blinded to the size of the finally implanted device.

Results

The accuracy in size of 3D printed left atrium (LA) models, compared with CT image sources, were validated by measuring the distance between artifacts which were intentionally implanted to LA model during image processing. There was minimal bias (−0.11 mm) between 3D images and printed LA models (Figure A). As plotted in Figure B, LAAO sizing by implantation simulation with 3D printing model showed excellent agreement with actually implanted LAAO size (r=0.927; bias=0.7±2.5), while LAAO sizing by 2D TEE measurements remained poor (r=0.544; bias 2.3±6.7).

Conclusions

LAAO size determination by using 3D printing model of LAA showed excellent accuracy. A prospective study to evaluate the clinical utility of this method should be done in future.

P4776Age-dependent anti-thrombotic therapy for atrial fibrillation patients with intermediate risk (CHA2DS2-VASc Score of 1 or 2) of ischemic stroke

Background

Although older age is one of the most important risk factor for stroke in atrial fibrillation (AF), it is unclear whether oral anticoagulants are beneficial for AF patients with intermediate CHA2DS2-VASc score (1 for male or 2 for female) according to age threshold. We sought to investigate the effect of age-dependent antithrombotic therapy for ischemic stroke in Korean intermediate risk AF patients.

Methods

We enrolled 29,592 patients (males with CHA2DS2-VASc score of 1 and females with CHA2DS2-VASc score of 2) using the Korean National Health Insurance Service database. The clinical endpoint was the occurrence of ischemic stroke. The propensity score matching method was used to balance covariates across treated and untreated patients.

Results

Treated male AF patients were 6,570 (67.1%) with age <55 years, 7,115 (70.9%) with 55–64 years and 6,470 (68.3%) with 65–74 years in each age risk criterion. Also, treated female AF patients were 3,156 (71.3%) with age <55 years, 2,838 (71.0%) with 55–64 years and 3,440 (72.6%) with 65–74 years in each age risk criterion. Among male and female patients (age <55 years and 55–64 years) with 1 risk factor, an annual ischemic stroke rate was not significantly different between treated and untreated patients at full follow-up. However, treated AF patients who are in age 65–74 year without other risk factor had a much lower annual risk of ischemic stroke [(1.05%/year (male) and 1.04%/year (female)] compared with untreated patients [(1.77%/year (male) (p<0.026) and 1.86%/year (female) (p<0.041).

Conclusions

Age is an important predictor in determining the risk of ischemic stroke in AF patients with intermediate CHA2DS2-VASc scores (1 for male or 2 for female). We suggest that the benefit of anti-thrombotic therapy for intermediate risk AF patients depends on age threshold.

Whole-genome sequence data and analysis of Saccharibacillus sp. ATSA2 isolated from Kimchi cabbage seeds

Saccharibacillus sp. ATSA2 was isolated from Kimchi cabbage seeds grown in Gyeongbuk province in the Republic of Korea. Whole-genome sequencing of Saccharibacillus sp. ATSA2 was performed using the PacBio RSII and Illumina HiSeq platforms, and it features a 5,619,468 bp circular chromosome with 58.4% G + C content. The genome includes 4543 protein-coding genes, 104 RNA genes (70 transfer RNA genes, 30 ribosomal RNA genes, and 4 non-coding RNA), and 73 pseudogenes. Multiple gene clusters associated with stress responses, nitrogen and phosphorus metabolism, and plant hormone biosynthesis were annotated in the genome. The genome information will provide fundamental knowledge of this organism as well as insight for understanding microbial activity in the agricultural application. The whole-genome sequence of Saccharibacillus sp. ATSA2 is available at GenBank/EMBL/DDBJ under accession number CP041217.

Prognosis of surgical hernia repair in cirrhotic patients with refractory ascites

BACKGROUND

Abdominal wall hernias are common in patients with ascites. Elective surgical repair is recommended for the treatment of abdominal wall hernias. However, surgical hernia repair in cirrhotic patients with refractory ascites is controversial. In this study, we aimed to evaluate the outcomes of elective surgical hernia repair in patients with liver cirrhosis with and without refractory ascites.

METHOD

From January 2005 to June 2018, we retrospectively reviewed the records of consecutive patients with liver cirrhosis who underwent a surgical hernia repair.

RESULTS

This study included 107 patients; 31 patients (29.0%) had refractory ascites. Preoperatively, cirrhotic patients with refractory ascites had a higher median model for end-stage liver disease (MELD) score (13.0 vs 11.0, P = 0.001) than those without refractory ascites. The 30-day mortality rate (3.2% vs 0%, P = 0.64) and the risk of recurrence (hazard ratio 0.410; 95% CI 0.050-3.220; P = 0.39) did not differ significantly between cirrhotic patients with refractory ascites and cirrhotic patients without refractory ascites. Among cirrhotic patients with refractory ascites, albumin (P = 0.23), bilirubin (P = 0.37), creatinine (P = 0.97), and sodium levels (P = 0.35) did not change significantly after surgery.

CONCLUSION

In advanced liver cirrhosis patients with refractory ascites, hernias can be safely treated with elective surgical repair. Mortality rate within 30 days did not differ by the presence or absence of refractory ascites. Elective hernia repair might be beneficial for treatment of abdominal wall hernia in cirrhotic patients with refractory ascites.

Recent advances in the development of gene delivery systems

Background

Gene delivery systems are essentially necessary for the gene therapy of human genetic diseases. Gene therapy is the unique way that is able to use the adjustable gene to cure any disease. The gene therapy is one of promising therapies for a number of diseases such as inherited disorders, viral infection and cancers. The useful results of gene delivery systems depend open the adjustable targeting gene delivery systems. Some of successful gene delivery systems have recently reported for the practical application of gene therapy.

Main body

The recent developments of viral gene delivery systems and non-viral gene delivery systems for gene therapy have briefly reviewed. The viral gene delivery systems have discussed for the viral vectors based on DNA, RNA and oncolytic viral vectors. The non-viral gene delivery systems have also treated for the physicochemical approaches such as physical methods and chemical methods. Several kinds of successful gene delivery systems have briefly discussed on the bases of the gene delivery systems such as cationic polymers, poly(L-lysine), polysaccharides, and poly(ethylenimine)s.

Conclusion

The goal of the research for gene delivery system is to develop the clinically relevant vectors such as viral and non-viral vectors that use to combat elusive diseases such as AIDS, cancer, Alzheimer, etc. Next step research will focus on advancing DNA and RNA molecular technologies to become the standard treatment options in the clinical area of biomedical application.

Abstract P3-08-12: PIK3CA mutations in breast cancer: Mutational landscape and clinical implications in ER+/HER2- subtype

Introduction: PIK3CA mutation is one of the most frequent genomic alterations in breast cancer. We evaluated PIK3CA mutational status including spatial and temporal heterogeneity, clinical characteristics and prognostic impact focused on ER+/HER2- subtype.

Methods: We performed targeted ultra-deep sequencing (CancerSCAN™) of breast cancer tissue in a prospective cohort. Burden of disease was assessed by metabolic tumor volume(MTV) in 18F-FDG-PET scan. Association with clinical characteristics or survival were tested in ER+/HER2- subtype, using Chi square test or Kaplan-Meier method.

Results: PIK3CA analyses were performed in 1274 breast cancer specimens from 1091 patients. 957 patients had early breast cancer. PIK3CA alterations were found in 397 patients(36.3%), and frequency of PIK3CA mutation was significantly lower in triple negative breast cancer(19.0%), compared with 40.4% in ER+/HER2-, 40.9% in ER+/HER2+, and 45.2% in ER-/HER2+ subtype(p&lt;0.0001). 158 patients had more than two biopsies. Among 92 patients with second biopsy within one month, 11%(10/92) had spatial heterogeneity of PIK3CA mutation. After neoadjuvant chemotherapy, 10%(3/30) of patients had change of PIK3CA mutational status. Serial biopsy at time of recurrence revealed loss or gain of PIK3CA mutation in 10 out of 59 patients (17%). In ER+/HER2- subtype, PIK3CA had a trend toward longer distant disease free survival without statistical significance. In patients with stage IV ER+/HER2- disease, PIK3CA hotspot mutations were associated with significant longer overall survival(OS) (71.0 vs. 37.8 months, p=0.048) and better progression free survival(PFS) at 1st line palliative treatment (37.7 vs. 9.4 months, p = 0.0004). Frequency of symptomatic recurrence, recurrence as oligometastases, and specific metastatic sites were not associated with PIK3CA mutational status, except that bone metastases at first distant metastases was less prevalent in patients with PIK3CA hotspot mutations(35.6% vs. 53.8% in PIK3CA wt, p=0.048). Metabolic tumor volume(MTV) at time of first distant metastases was not associated with presence of PIK3CA mutation.

Conclusion: We observed variations in PIK3CA mutational status in more than 10% of patients with &gt;1 repeated biopsy. In stage IV ER+/HER2- disease, PIK3CA hotspot mutation seemed to be associated with longer PFS and OS, however metabolic tumor burden was not associated with PIK3CA alterations.

Citation Format: Ahn HK, Park S, Hyun SH, Park K, Lee E, Kim J-Y, Nam SJ, Kim SW, Lee JE, Lee SK, Yu JH, Ahn JS, Im Y-H, Park YH. PIK3CA mutations in breast cancer: Mutational landscape and clinical implications in ER+/HER2- subtype [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-08-12.

Abstract P1-09-11: Prognostication of genetic alterations of ESR 1 in estrogen receptor positive metastatic breast cancers using targeted ultra-deep sequencing data analysis

Introduction: Genetic alteration of Estrogen Receptor 1(ESR1) gene have been associated with acquired endocrine resistance and occurred in about 20% of endocrine resistant estrogen receptor(ER)-positive metastatic breast cancer(MBC). Mutations in ligand binding domain of ESR1 lead to constitutive activity of the ER without ligand estrogen and stimulated down stream cell growth signal. Therefore, ESR1 ligand binding domain alteration is known resistant mechanism of aromatase inhibitor. Among these ESR1 mutations, Y537S, one of the ligand binding domain mutations, caused ER antagonist, fulvestrant resistance. Therefore, assessment of ESR1 mutation in ER-positive MBC had significant benefit to further precision medicine for MBCs. In this study, we explored to identify the frequency and type of ESR1 genetic alterations of ER-positive MBC.

Methods: We performed targeted ultra-deep sequencing (CancerSCAN™) using BC tissue specimens. This sequencing was covered entire coding area of ESR1 gene and also detected copy number alteration and translocation of ESR1.

Results: Targeted ultra-deep sequencing of ESR1 was performed using 990 BC tissues. Of 990 tissue samples, 341(34.5%) were MBCs. Of MBCs, 112(11.3%) were ER-positive and human epidermal growth factor receptor 2(HER2)-negative BCs. In ER-positive HER2-negative MBCs (N=112), 21 ESR1 genetic alterations were identified in 19 BCs (17.0%). Nineteen were single nucleotide variats (SNVs) and three were copy number (CN) amplification. Most commonly detected single nucleotide variant (SNV) was D538G (6 of 19, 31.6%) followed by Y537N, Y537S, V382I (4, 2 and 2 cases, respectively). Three mutations occurred in non-ligand binding domain (G415V, V392I and P79A). Two BC samples harbored two ESR1 mutations, respectively (Y537S and D538G, L536P and Y537N). In terms of treatment, 11 of 12 patients with ER-positive MBC harboring ESR1 mutation received palliative endocrine therapies. Eight patients received aromatase inhibitor and two patients received tamoxifen. One patient received letrozole plus palbociclib. In 2 MBCs with Y537S mutation, progression free survival (PFS) of endocrine therapy was 1.4 and 5.3 months. MBCs with D538G had 12.3months of PFS (range, 5.3-23.7(months)) and BCs harboring another ligand binding domain mutations (Y537N, L536H and L536P) had 15.7months of PFS of endocrine therapy (range, 8.4-17.3(months)). BC with mutation observed in non-lignand binding domain had short PFS (1.8 (V392I) and 2.7 (P79A) months, respectively). In terms of ESR1 CN amplification, patients could not receive endocrine therapy because their BCs rapidly progressed and extensive distant metastases were occurred within 3 months after curative surgery.

Conclusion: In this exploratory study, ESR1 genetic alterations were detected in about 20% of ER-positive MBC. The type of genetic alterations varied including SNVs, CNAs. Each locus of ESR1 mutation predicted endocrine resistance. In addition, we might suggest that ESR1 CN amplification is prognostic marker of ER-positive BCs.

Citation Format: Kim J-Y, Park KH, Park W-Y, Nam SJ, Kim SW, Lee JE, Lee SK, Yu JH, Ahn JS, Im Y-H, Park YH. Prognostication of genetic alterations of ESR 1 in estrogen receptor positive metastatic breast cancers using targeted ultra-deep sequencing data analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-09-11.

Abstract P4-08-30: Prognostication of immune related gene expression in patients with triple negative breast cancer

Introduction: To date, the role of immunotherapy with check point inhibitors and/or vaccines in the treatment of breast cancer (BC) is still debating, and the main focus of immunotherapy in BC is on triple negative subtype as a target population in many ongoing clinical trials. Translational research into identifying predictive and prognostic immune biomarkers is of particular clinical relevance, but, there are currently no definite prognostic and predictive immune biomarkers in BC, especially in triple negative breast cancer(TNBC). We investigated the expression profiles of immune genes in patients with TNBC to identify the prognostic value of immune genes in search of clinical implications.

Methods : We investigated expression profiles of 770 pan-cancer immune related genes using the nCounter mRNA expression assay (NanoString®) from paraffin-embedded tumor tissues in 200 patients diagnosed as TNBC who received curative surgery at Samsung Medical Center from 2000 to 2004. We analyzed the relationship between stage adjusted level of gene expressions and patients' survival outcomes using Cox regression model.

Results: Of 770 genes, 186 genes were selected from univariate analysis with clinical stage adjustment. In multivariate analysis using Cox regression, expressions of CD1B, CD45, CD53, CT45A1, GTF3C1, IL11RA, IL1RN, LRRN3, MAPK1, NEFL, PRKCE, SPACA3 and RANKL were associated with distant recurrence free survival (p&lt;0.05, respectively). Among these 13 genes, expression of MAPK1, NEFL, CD45, SPACA3 and RANKL were correlated with favorable outcome in terms of distant recurrence free survival (p&lt;0.05, respectively). In terms of overall survival, C3, IL1RL1, IL1RN, IL7 and PRKCE were associated with poor prognosis (p&lt;0.05, respectively) and expression of SAA1 CXCL9 and RANKL resulted in favorable outcome (p&lt;0.05, respectively).

Table 1ParameterParameter EstimateStandard Errorp-valueHazard Ratio95% Confidence Interval(a) distant recurrence free survival     Stage2.487350.680570.000312.0293.169, 45.661CD1B1.141910.2753&lt;.00013.1331.826, 5.374CD531.531650.34851&lt;.00014.6262.336, 9.159CT45A10.426110.134210.00151.5311.177, 1.992GTF3C11.193110.579720.03963.2971.059, 10.271IL11RA1.671120.461750.00035.3182.151, 13.146IL1RN0.980280.24657&lt;.00012.6651.644, 4.321LRRN31.424170.28742&lt;.00014.1542.365, 7.297MAPK1-0.542740.258240.03560.5810.35, 0.964NEFL-1.12170.335610.00080.3260.169, 0.629PRKCE2.378340.49659&lt;.000110.7874.076, 28.549CD45-2.736780.43154&lt;.00010.0650.028, 0.151SPACA3-0.745930.272270.00610.4740.278, 0.809RANKL-1.288920.2976&lt;.00010.2760.154, 0.494(b) overall survival     Stage1.359280.497810.00633.8931.468, 10.329C30.329830.150350.02831.3911.036, 1.867CXCL9-0.379190.100680.00020.6840.562, 0.834IL1RL10.679360.262940.00981.9731.178, 3.303IL1RN0.437130.172370.01121.5481.104, 2.171IL70.507280.206250.01391.6611.109, 2.488PRKCE0.835340.272910.00222.3061.35, 3.936SAA1-0.564250.13449&lt;.00010.5690.437, 0.74RANKL-0.604990.234510.00990.5460.345, 0.865

Conclusion: High expression of IL1RN, PRKCE were associated with short distant recurrence free survival and overall survival in patients with TNBCs who received curative surgery. In contrast, RANKL expression resulted in prolonged distant recurrence free survival and overall survival.

Citation Format: Kim J-Y, Jung HH, Lim JE, Cho EY, Lee SK, Yu JH, Lee JE, Kim SW, Nam SJ, Park YH, Ahn JS, Im Y-H. Prognostication of immune related gene expression in patients with triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-30.

Abstract P2-08-52: A predictive model for distant metastasis in breast cancer patients using machine learning

Introduction

Tumor metastasis is a major clinical challenge accounting for the vast majority of cancer related deaths.In previous studies, prediction of distant metastasis was based on subtypes,clinical status and sometimes gene expression were used however clinical application was difficult.

In this study, we develop the easy to use prediction tool for distant metastasis using clinical characteristics and gene profiles which came from CancerSCANTM, Next Generation Sequencing based targeted-sequencing platform designed at Samsung Medical Center(SMC).

Methods

We performed a retrospective chart review of 326 breast cancer patients who underwent surgery and CancerSCAN TM between Jan 2001 and Dec 2014 at SMC. Median follow up period was 83 months (Range 1˜190). Cancer scanTM cover 381 genes but 27 genes and 34 occasions (loss of function, mutation or copy number variation) were selected for analysis through gradient boosting and Wilcoxon Signed rank test. Azure Machine Learning is a cloud service that enables the execution of machine learning processes.This was accomplished using the steps of (1) edit the data, (2) split the data, (3) train the model, (4) score the model, and (5) evaluate the model. We split the modeling data into training and testing sets using a randomized 50–50 split. Two-class Decision Forest method was used. After deploying the Azure ML predictive model as a web service, we used a Representational State Transfer application programming interface to send data and obtained predictions in real-time.

Results

No distant metastasis group and distant metastasis group consisted of 267 and 59 patients, respectively. HR-/HER2+ and 50 years old and over patients were higher in metastasis group (p-value = 0.003 and p-value = 0.000). Nuclear grade 3 and N2,3 were higher in metastasis group (p-value = 0.010 and p-value = 0.000, p-value = 0.001 respectively). Stage III was also higher in metastasis group (p-value = 0.000). Among 59 patients with distantmetastasis, multiple sites metastasis was 21 cases (35.6%) and then lung metastasis was 19 cases (32.2%). In the 21 cases of multiple sites metastasis, triple sites was 6 cases (28.6%) and double sites was 15 cases (71.4%). PIK3CA mutation was the most frequent gene variation in all patients (34.5% of no metastasis group and 27.1% of metastasis group) but there was no difference between two groups(p-value = 0.278). BRCA 1 loss of function and BRCA2 loss of function were more frequent in metastasis group than no metastasis group(p-value = 0.033 and p-value = 0.024, respectively) but total counts was too small. We assessed the area under the curve (AUC) of the receiver operating characteristic (ROC) curve for predictive value. The AUC of ROC curve was 1.000 and also accuracy, precision, recall were 1.000. In addition, we conducted internal validation using 83 patients during 2015. When we applied a 0.5 threshold value with our predictive model, true negative was 81 and true positive was 2 among 83 patients. Finally, the accuracy of validation was 1.000.

Conclusion

Our predicted model could represent a useful and easy-to-access tool for the selection of patients with distant metastasis. After additional evaluation with large data and external validation, worldwide use of our model could be expected.

Citation Format: Kim I, Choi HJ, Ryu JM, Lee SK, Yu JH, Kim SW, Nam SJ, Seo SW, Lee JE. A predictive model for distant metastasis in breast cancer patients using machine learning [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-08-52.

Abstract PD5-08: Neoadjuvant chemotherapy alters the genomic landscape and immune microenvironment of breast cancers

Understanding how standard-of-care drug treatments affect tumor intrinsic biology and microenvironment is critical for elucidating drug resistance mechanisms and developing better combination therapies as well as new therapies. To characterize the effects of neoadjuvant chemotherapy (NAC) on the genome, transcriptome and tumor infiltrating leukocytes (TILs), we have conducted whole exome and whole transcriptome sequencing of a large longitudinal breast cancer cohort consisting of 146 cases and 281 paired tumor samples. In total, 52 (38%) patients achieved pathologic complete response (pCR) while 85 patients (62%) had residual disease with standard chemotherapy regimen. Tumor biopsies were collected for each patient at three time points – pre-treatment, three weeks after the first cycle of anthracycline and cyclophosphamide (AC) and at the time of surgery after 3 more cycles of AC followed by 4 cycles of taxane or taxane plus Herceptin in case of HER2+ subtype. We detected 5,955 protein-altering somatic mutations affecting 4,414 genes in pretreatment samples and 502 acquired mutations in surgery samples affecting 477 genes including 19recurrently mutated genes such as TP53 and NOTCH1. Across all subtypes, 4,346 genes were differentially expressed (DE) following NAC treatment and significantly enriched in pathways such as cell cycle, ER signaling, PI3K/mTOR, immune and metabolism. Expression-based virtual microdissection analysis indicated that NAC treatment induced an increase in the fractions of stromal and adjacent normal tissue compartment, consistent with observed reduction in tumor cellularity. To assess the NAC induced changes in the molecular landscape of these tumors, we compared molecular features including gene expression signatures, mutation prevalence and copy number alteration between three time points while adjusting for confounding effects of molecular subtype and tumor cellularity. We found that NAC induced dynamic changes in gene expression signatures associated with proliferation and immunomodulatory treatment response. We further validated the observed pattern of change in TILs through histopathology and digital imaging analyses. In pretreatment tumors, 116 genes were DE between patients with pCR vs. those with residual disease with significant enrichment in immune/inflammatory pathways. Further, pre-treatment TIL levels were found to be significantly associated with pCR, echoing previous reports in breast cancers that implicated anti-tumor immunity in mediating the efficacy of chemotherapies. Our analyses also revealed associations between NAC response and baseline genomic attributes such as genomic alterations that affect DNA damage repair pathways. Taken together, these results suggest that NAC induced a multitude of changes on the genomic landscape and immune microenvironment of breast cancers, some of which point to combination strategies with immunomodulatory therapies and therapies that target DNA damage repair.

Citation Format: Kan Z, Lal S, Ding Y, Lee JE, Lee S-H, Lee SK, Yu JH, Choi Y-l, Kim SW, Nam SJ, Kim J-Y, Ram S, Powell E, Ching K, Cho SY, Bonato V, Deng S, Park W-Y, Rejto P, Bienkowska J, Park Y-H. Neoadjuvant chemotherapy alters the genomic landscape and immune microenvironment of breast cancers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD5-08.

Abstract P1-15-18: Not presented

This abstract was not presented at the conference.

Citation Format: Choi HJ, Kim SW, Ryu JM, Kim I, Nam SJ, Yu J, Lee SK, Lee JE. Not presented [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-15-18.