Rapamycin-induced autophagy plays a pro-survival role by enhancing up-regulation of intracellular ferritin expression in acute lymphoblastic leukemia

Elevated mammalian target of rapamycin (mTOR) signaling has been reported to correlate with poor prognosis in acute lymphoblastic leukemia (ALL) patients. Rapamycin, an mTOR kinase inhibitor, and also a potent autophagy inducer, could not only effectively reverse glucocorticoid resistance, but also promote autophagy in the ALL cells. Autophagy has been suggested to play a paradoxical role in cancer treatment. The aim of this study was to address the role of the rapamycin-induced autophagy in the leukemia treatment.

MATERIALS AND METHODS

Cell proliferation was detected by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay in ALL cell lines of CEM-C1 and CEM-C7. Western Blot analysis was performed to test protein expressions.

RESULTS

Inhibition of mTOR by rapamycin could reverse glucocorticoid resistance in CEM-C1 cells, and also induce autophagy in these cells by up-regulation of LC3-II and Beclin-1 expressions. This autophagy played a pro-survival role since its inhibition by 6-amino-3-methylpurine or chroloquine could enhance rapamycin-induced cell death. Rapamycin increased the expression of intracellular ferritin, and this effect could be totally blocked by 6-amino-3-methylpurine and chroloquine, suggesting that the protective role of autophagy might be mediated through up-regulation of ferritin, the major iron-binding stress protein. Ciclopirox olamine, an iron chelator, could enhance rapamycin's anti-leukemia effect by down-regulation of intracellular ferritin expression.

CONCLUSIONS

All these findings would suggest that rapamycin-induced autophagy plays a pro-survival role in leukemia cells and this effect might be mediated by up-regulation of intracellular ferritin expression. We hypothesize that the combination of mTOR pathway inhibitors and autophagy inhibition is rational and would induce strong anti-leukemia effects in ALL.

Abstract ES10-2: Understanding breast cancer using a developmental perspective

Parallels among embryonic development, stem cells, and cancer have long been recognized. We identified, isolated, and characterized stem cells that first become committed to a mammary fate during embryogenesis; we refer to these cells as fetal mammary stem cells (fMaSCs). Lineage tracing, in vitro sphere formation, and in vivo transplantation studies by our group and many others all confirm that cells in the embryo are the bipotent progenitors of the mammary gland. There is debate, however, on whether such bipotent cells persist into the adult, or whether the luminal and basal lineages are maintained by unipotent progenitors. To gain insight into the relationships between fMaSCs and breast cancer, and to investigate their potential persistence in the adult, we have applied bulk and single cell RNA-sequencing (sc-RNA-seq) and single nucleus ATAC-sequencing (snATAC-seq) throughout mammary development. The results to be discussed demonstrate that fMaSC transcriptomes are heterogeneous, but all share co-expression of genes associated with luminal and basal cell fates. This fits a model in which the bipotent state is created by a balance of lineage specifiers. We also find that the fMaSC transcriptome is highly enriched in basal-like human breast cancers and identify potential embryonic pathways that correlate with poor prognosis. We used a variety of computational tools to infer the gene expression programs that ensue when fMaSCs commit to luminal and basal states. The data from scRNA-seq and snATAC-seq demonstrate that the transitions are gradual, not precipitous, and that luminal and basal cells exhibit significant transcriptomic and epigenetic heterogeneity. This challenges the notion that the mammary gland consists of discrete cell types defined by rigid transcriptomic parameters, and reveals a potential for intrinsic phenotypic plasticity of normal mammary cells. Using the combined databases, we identified Sox10 as a significantly differentially expressed cell state regulator. We show that tumors are heterogeneous with regard to Sox10 expression, and that locally invasive cells tend to express high Sox10 levels. Elevated Sox10 correlates with acquisition of a neural-crest like, EMT-related state. Implications for interception of metastasis by targeting neural crest-like cells will be discussed. Finally, we have generated a web resource that is available to the scientific community to enable the transcription and epigenetic characteristics of any gene of interest to be tracked through mammary development (https://wahl-labsalk.shinyapps.io/Mammary_snATAC/).

Citation Format: GM Wahl, Z Ma, C Chung, C Dravis, BT Spike, RR Giraddi, O Balcioglu, C Fan, B Hagos, R Heinz, Herrera-Valdez J, X Hou, J Hwang, R Lasken, G Luna, NE Lytle, EM Mehrabad, M Novotny, CM Perou, O Poirion, S Preissl, B Ren, T Reya, CL Trejo, KT Varley. Understanding breast cancer using a developmental perspective [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr ES10-2.

Expression and distribution of HIF-1α, HIF-2α, VEGF, VEGFR-2 and HIMF in the kidneys of Tibetan sheep, plain sheep and goat

BACKGROUND

The objective of this study was to detect the expression and distribution characteristics of five proteins (the hypoxia-inducible factor 1alpha [HIF-1a], HIF-2a, vascular endothelial growth factor [VEGF], VEGF-2 receptor [VEGFR-2] and hypoxia-induced mitogenic factor [HIMF]) in kidney of Tibetan sheep, plain sheep and goat. The results will provide the basic information for the comparative study of sheep breeds living at different altitudes.

MATERIALS AND METHODS

The kidney tissues were collected from healthy adult Tibetan sheep, plain sheep and goats and made into paraffin sections. Histological characteristics were assessed by haematoxylin and eosin staining. Expressions of HIF-1a, HIF-2a, VEGF, VEGFR-2 and HIMF proteins were measured by immunohistochemical staining.

RESULTS

Immunohistochemistry results showed that the positive expression signals of HIF-1a, HIF-2a, VEGF and VEGFR-2 were detected in epithelial cells of renal tubules and collecting tubules, renal corpuscles in the kidneys of the three sheep breeds. Positive expression signals of HIMF were detected in epithelial cells of proximal tubules and distal tubules in Tibetan sheep and epithelial cells of distal tubules in goat. Immunostaining intensity of HIF-1a, HIF-2a, VEGF and VEGFR-2 proteins in Tibetan sheep was significantly higher than that in both plain sheep and goat (p < 0.05). Immunostaining intensity of HIMF in Tibetan sheep was higher than goat (p < 0.05). Positive expression signals of HIMF were not detected in plain sheep.

CONCLUSIONS

The expression and distribution characteristics of HIF-1a, HIF-2a, VEGF, VEGFR-2 and HIMF in the studied kidney tissues suggested that these proteins may be related to the physiological regulation of Tibetan sheep kidney in hypoxia environment, and therefore might be important regulating proteins for Tibetan sheep to adapt to high altitude hypoxia environment.

The role of G protein-coupled receptor-related genes in cytochrome P450-mediated resistance of the house fly, Musca domestica (Diptera: Muscidae), to imidacloprid

Ninety-four putative G protein-coupled receptors (GPCRs) were identified in the Musca domestica genome. They were annotated and compared with their homologues in Drosophila melanogaster. Phylogenetic analyses of the GPCRs from both species revealed that several family members shared a closer relationship based on the domain architecture. The expression profiles of these genes were examined by quantitative real-time PCR amongst three strains of the house fly, a near-isogenic line strain with imidacloprid resistance (N-IRS), the corresponding susceptible strain (CSS) and another strain derived from field populations with imidacloprid resistance (IRS). We found that five GPCR genes were upregulated in the N-IRS and eight GPCR genes were upregulated in the IRS strains compared to the CSS strain. The transgenic lines of D. melanogaster with the GPCR genes (LOC101899380 in the N-IRS strain and LOC101895664 in the IRS strain) exhibited significantly increased tolerance to imidacloprid, and higher expression of cytochrome P450 genes. Bioinformatic analysis of LOC101899380 was carried out based on its full-length nucleic acid sequence and putative amino acid sequence, and it was named Methuselah-like10 (Mthl10) owing to its homology with D. melanogaster Mthl10. A cell-base cell counting kit-8 toxicity assay demonstrated that the expression of the GPCR gene LOC101899380 in Spodoptera frugiperda (Sf9) cells using a baculovirus-mediated expression system can elevate the cell tolerance to imidacloprid, indirectly supporting the hypothesis that the GPCR gene LOC101899380 plays some role in imidacloprid resistance. These results should be useful for furthering understanding of the regulatory pathway by which house flies develop resistance.

[Characteristic analysis of organic fluorosis caused by appliying of touch screen anti-fingerprint nanocoating material]

Objective: To analysis pathogenic conditions and pathogenic characteristics of organic fluorosis caused by applying of anti-fingerprint coating material on touch screen glass of the mobile phone. Methods: To collect clinical data and analyze the causes and pathogenic characteristics of poisoning through surveying occupational health, detecting occupational hazards in the workplace, collecting clinical data and diagnosing of occupational diseases. 6 employees in workshop 1 of packaging were as the organic fluorine exdposed group, and 16 employees in other workshops were as the non-exposed group. Results: Organic fluorine chemicals (perfluoro-1, 3-dimethylcyclohexane, hexadecafluoroheptane, perfluoro-hexane, perfluoromethy lopentane, perfluoro-2-methyl-2-pentene, etc.) can be volatilized by spraying and baking of anti-fingerprint nano-coating material on touch screen. The relative percentage of volatile components in air is 85.65%. Four cases of acute poisoning were caused by organic fluorosis deposited in a dustless air conditioning workshop with poor ventilation.The clinical manifestations of the patients were acute bronchitis, pulmonary edema and/or myocarditis. The average concentration of urine fluorine in the organic fluorine exposed group was 13.7± 4.4 mmol/mol creatinine, which was 4-5 times higher than that of other non-organic fluorine exposed groups. The difference of urine fluorine level between the organic fluorine exposed group and non exposed group was statistically significant (P<0.01) . The main indicators were abnormal for the blood oxygen saturation of finger pulse under suction air, leukocytes, neutrophils, monocytes, hypersensitivec-reactive protein, procalcitonin, l-lactate dehydrogenase, forebrain diuretic natriuretic peptide, hypersensitive troponin T in the four cases. One case was myocardial ischemia, four cases had bilateral lung symmetrically exudative lesions, one case was accompanied by a small amount of pleural pericardial effusion. Conclusion: Acute organofluorine poisoning can caused by the applying of the fingerprint nano-coating material on touch screen of the mobile phone. Attention should be paid to occupational poisoning caused by the applying of the small molecular perfluoroalkanes (olefins) in new industries, new processes and new materials.

Genome-wide association study for growth and fatness traits in Chinese Sujiang pigs

Growth and fatness traits are complex and economically important traits in the pig industry. The molecular basis underlying porcine growth and fatness traits remains largely unknown. To uncover genetic loci and candidate genes for these traits, we explored the GeneSeek GGP Porcine 80K SNP chip to perform a GWAS for seven growth and fatness traits in 365 individuals from the Sujiang pig, a recently developed breed in China. We identified two, 17, one and 11 SNPs surpassing the suggestively significant threshold (P < 1.86 × 10^-5 ) for body weight, chest circumference, chest width and backfat thickness respectively. Of these SNPs, 20 represent novel genetic loci, and five and four SNPs were respectively associated with chest circumference and backfat thickness at a genome-wide significant threshold (P < 9.31 × 10^-7 ). Eight SNPs had a pleiotropic effect on both chest circumference and backfat thickness. The most remarkable locus resided in a region between 72.95 and 76.27 Mb on pig chromosome 4, harboring a number of previously reported quantitative trait loci related to backfat deposition. In addition to two reported genes (PLAG1 and TAS2R38), we identified four genes including GABRB3, ZNF106, XKR4 and MGAM as novel candidates for body weight and backfat thickness at the mapped loci. Our findings provide insights into the genetic architecture of porcine growth and fatness traits and potential markers for selective breeding of Chinese Sujiang pigs.

Detection of hepatitis E virus genotypes 3 and 4 in donkeys in northern China

BACKGROUND

Hepatitis E virus (HEV) is the causative agent of acute self-limiting hepatitis in humans in developing countries. Hepatitis E virus RNA was first detected in donkeys in Spain, but little is known about the possible presence of HEV in donkeys in China.

OBJECTIVES

To investigate the prevalence of HEV in donkeys in northern China.

STUDY DESIGN

Investigation of the prevalence of HEV in donkeys using serological, molecular and phylogenetic approaches.

METHODS

A total of 401 donkey serum specimens were tested for serological and molecular detection of HEV via enzyme-linked immunosorbent assay and quantitative reverse transcription polymerase chain reaction. The amplified products were cloned in pMD18-T vector and sequenced. The alignment and phylogenetic analysis of partial HEV ORF2 genes were compared with the corresponding sequences of the obtained HEV representative strains.

RESULTS

Serological results showed that 49 donkeys (12.22%, 95% CI: 9.18-15.83%) were positive for anti-HEV-specific antibodies, and 17 donkeys (4.24%, 95% CI: 2.49-6.70%) were positive for HEV viral RNA. On the basis of sequence alignment and phylogenetic analysis, all isolated HEV strains belonged to genotype 3 (HEV-3) or HEV-4, sharing more than 76.2-96.3% identities with 67 other HEV representative strains of HEV-1 to HEV-8.

MAIN LIMITATIONS

Further studies about the prevalence of HEV in organs or faecal samples from donkeys are needed to evaluate the possible role of HEV reservoir and to determine the risk factors associated with the transmission of this zoonotic virus in donkeys in China.

CONCLUSIONS

This is the first report documenting the molecular analysis of donkey HEV strains worldwide and the serological evidence of HEV infection in donkeys in northern China. The results suggest that young donkeys are more susceptible to HEV infection compared with older donkeys. Further investigation is required to determine whether donkeys should be considered reservoirs for zoonotic HEV. The Summary is available in Chinese - see Supporting information.

High temperature strain sensing with alumina ceramic derived fiber based Fabry-Perot interferometer

A Fabry-Perot interferometer (FPI) based on an alumina ceramic derived fiber (CDF) is proposed and demonstrated for high temperature strain sensing. The strain sensor is constructed by splicing a piece of CDF between two standard single-mode fibers (SMFs). The strain properties of the sensor are investigated from room temperature to 1200 °C. Experimental results show that the wavelength shift of the CDF-FPI presents a linear relationship with the tensile strain at both room temperature and high temperature with up to 1000 °C. The strain sensitivity is calculated to be 1.5 pm/µɛ at 900 °C, and the linear response is repeatable within 0-3000 µɛ. Moreover, for each applied force at 1000 °C, the wavelength shift versus time shows the stability of the developed CDF-FPI sensor within 0-2000 µɛ. The obtained results show that such a CDF-FPI has potential application in various engineering areas, such as aeronautics, metallurgy, and gas boiler.

Effects of bisphenol A exposure on DNA integrity and protamination of mouse spermatozoa

BACKGROUND

Bisphenol A is widely used in the manufacture of polycarbonate plastics and has caused increasing concern over its potential adverse impacts on spermatogenesis. However, the effect of bisphenol A on spermiogenesis is yet to be explored.

OBJECTIVES

To evaluate whether bisphenol A has adverse effects on DNA integrity and protamination of spermatogenic cell.

MATERIALS AND METHODS

Newborn male mice were subcutaneously injected with bisphenol A (0.1, 5 mg/kg body weight, n = 15) or coin oil (control group, n = 20) daily from post-natal day 1 until 35. At post-natal day 70, epididymis caudal spermatozoa and testes were collected. Sperm count, sperm motility, and sperm morphology were analyzed. The sperm chromatin structure assay was performed to examine the sperm DNA fragmentation. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) method was used to assess apoptosis of spermatogenic cells. The ultrastructural features of testicular sections were examined under a transmission electron microscope. Western blot and RT-PCR were used to detect the expression levels of transition protein (Tnp) 1 and Tnp2, protamine (Prm) 1 and Prm2 protein, and mRNA in mice testes.

RESULTS

Bisphenol A significantly reduced sperm counts, impaired sperm motility, and increased the percentage of malformed spermatozoa. Poor sperm chromatin integrity and increased TUNEL-positive spermatogenic cells were also observed in mice exposed to bisphenol A. Ultrastructural analysis of testes showed that bisphenol A exposure caused incomplete chromatin condensation, retention of residual cytoplasm, and abnormal acrosome formation. In addition, the relative expression levels of Tnp2 and Prm2 in mice testes decreased significantly in bisphenol A groups.

DISCUSSION AND CONCLUSION

Our findings identified that neonatal bisphenol A exposure may negatively contribute to the sperm quality in adult mice. Mechanistically, we showed that bisphenol A reduced sperm chromatin integrity along with increased DNA damage, which may be due to poor protamination of spermatozoa.

Identification of genetic associations of ECHS1 gene with milk fatty acid traits in dairy cattle

Our previous genome-wide association study identified 83 genome-wide significant SNPs and 20 novel promising candidate genes for milk fatty acids in Chinese Holstein. Among them, the enoyl-CoA hydratase, short chain 1 (ECHS1) and enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH) genes were located near two SNPs and one SNP respectively, and they play important roles in fatty acid metabolism pathways. We herein validated whether the two genes have genetic effects on milk fatty acid traits in dairy cattle. By re-sequencing the full-length coding region, partially adjacent introns and 3000 bp up/downstream flanking sequences, we identified 12 SNPs in ECHS1: two in exons, four in the 3' flanking region and six in introns. The g.25858322C>T SNP results in an amino acid replacement from leucine to phenylalanine and changes the secondary structure of the ECHS1 protein, and single-locus association analysis showed that it was significantly associated with three milk fatty acids (P = 0.0002-0.0013). The remaining 11 SNPs were found to be significantly associated with at least one milk fatty acid (P = <0.0001-0.0040). Also, we found that two haplotype blocks, consisting of nine and two SNPs respectively, were significantly associated with eight milk fatty acids (P = <0.0001-0.0125). However, none of polymorphisms was observed in the EHHADH gene. In conclusion, our findings are the first to indicate that the ECHS1 gene has a significant genetic impact on long-chain unsaturated and medium-chain saturated fatty acid traits in dairy cattle, although the biological mechanism is still undetermined and requires further in-depth validation.

[Analysis on the standardized management of hospitalized asthmatic patients: a single center 10-years experience]

Objective: To analyze the outcome of standardized management on the hospitalized asthmatic patients in the past 10 years in a single center. Methods: Clinical data of 2 207 asthmatic patients, who were hospitalized in the Center of Respiratory Medicine and Allergic Diseases, the General Hospital of Northern Military District from January 1, 2008 to December 31, 2017, was retrospectively collected and analyzed. Results: Asthmatic in-patients accounted for 11.5% of total hospitalized patients(2 207/19 134) over the 10-year study period. The highest percentage of asthmatic patients over the total hospitalized patients (16.9%, 207/1 223) was in the year 2008, and it was gradually reduced from 2009 through 2017: a median of 13.2% (221/1 674) from 2009 to 2013 with 3.7% decrease, and a median of 9.4% (224/2 385) from 2014 to 2017 with 7.5% decrease. There was a significant difference in the percentages between the year of 2008 (16.9%) and the years from 2009 through 2017 (P<0.05). Over the 10-year study period, 69.1% (1 526/2 207) of the asthmatic in-patients were hospitalized only once, 13.3% (294/2 207) were twice, and 3.8% (85/2 207) were hospitalized more than twice. Totally 1,553 patients were hospitalized with acute asthmatic attack, which accounted for 8.1% (1 553/19 134) of the total in-patient number over the 10 years, and 14.2% (174/1 223) of which was in the year 2008, while 9.7% (163/1 674) was in the years from 2009 through 2013 with a decrease of 4.5% from 2008, and 5.9% (141/2 385) was in 2014 through 2017 with a decrease of 8.3% from 2008. The differences between the 2008 incidence and that of 2009-2013 or 2014-2017 were statistically significant (P<0.05). However, the incidence of acute exacerbation of comorbid conditions was lowest in 2008 (15.9%, 33/207), while it was 25.8% (58/221) from 2009 to 2013 with an increase of 9.9% from 2008, and 37.0% (83/224) from 2013 to 2017 with an increase of 21.1% compared to 2008. Asthmatic hospitalization peaked in March (9.2%, 150/1 628) and August (9.7%, 157/1 612), respectively, while it was lowest in February (7.1%,101/1 423). The difference between the peak months (March and August) and February was statistically significant (P<0.05), while there was no significant difference between February and the rest of months (P>0.05). When the risk factors for acute asthmatic attack was analyzed by grouping single-time attack (n=1 074) versus multiple-time attack (hospitalized ≥ 2 times, n=479), we found the following risk factors were significant: airway infection (OR=2.006), male (OR=1.355), age ≥ 65 years old (OR=1.364), wet rales on physical examination (OR=1.762), hospitalization ≥ 14 days (OR=1.892), and invasive mechanical ventilation (OR=1.798). In addition, there were significant differences in per capital cost comparison between the following pairs (P<0.05): multiple-time (16 219±16 628, n=681) vs single-time asthmatic hospitalization (13 752±20 692, n=1 526), multiple-time (13 933±13 036, n=479) vs single-time hospitalization with acute asthmatic attack (11 208±13 853, n=1 074), multi-time asthmatic hospitalization (n=681) vs multi-time hospitalization with acute asthmatic attack (n=479), and single-time asthmatic hospitalization (n=1 526) vs single-time hospitalization with acute asthmatic attack (n=1 074). Conclusions: Standardized management of asthma could significantly reduce the risk of hospitalization as well as acute asthmatic attack. Findings of the current study suggested that risk factors for acute and recurrent asthmatic attack should be assessed and managed efficiently in order to reduce incidence of multiple hospitalization for asthma.

Increased uptake of oxLDL does not exert lipotoxic effects in insulin-secreting cells

Modified lipoproteins can negatively affect beta cell function and survival. However, the mechanisms behind interactions of modified lipoproteins with beta cells - and in particular, relationships to increased uptake - are only partly clarified. By over-expressing the scavenger receptor CD36 (Tet-on), we increased the uptake of fluorescent low-density modified lipoprotein (oxLDL) into insulin-secreting INS-1 cells. The magnitude of uptake followed the degree of CD36 over-expression. CD36 over-expression increased concomitant efflux of 3H-cholesterol in proportion to the cellular contents of 3H-cholesterol. Exposure to concentrations of oxLDL from 20 to 100 µg/mL dose-dependently increased toxicity (evaluated by MTT) as well as apoptosis. However, the increased uptake of oxLDL due to CD36 over-expression did not exert additive effects on oxLDL toxicity - neither on viability, nor on glucose-induced insulin release and cellular content. Reciprocally, blocking CD36 receptors by Sulfo-N-Succinimidyl Oleate decreased the uptake of oxLDL but did not diminish the toxicity. Pancreatic islets of CD36-/- mice displayed reduced uptake of 3H-cholesterol-labeled oxLDL vs wild type but similar toxicity to oxLDL. OxLDL was found to increase the expression of CD36 in islets and INS-1 cells. In summary, given the experimental conditions, our results indicate that (1) increased uptake of oxLDL is not responsible for toxicity of oxLDL, (2) increased efflux of the cholesterol moiety of oxLDL counterbalances, at least in part, increased uptake and (3) oxLDL participates in the regulation of CD36 in pancreatic islets and in INS-1 cells.

Crystallization-induced refractive index modulation on sapphire-derived fiber for ultrahigh temperature sensing

We have demonstrated crystallization-induced refractive index (RI) modulation on sapphire-derived fiber (SDF) showing superheat resistance and developed the SDF based Fabry-Perot interferometers (FPIs) for ultrahigh temperature sensing. The SDF is a special fiber with high concentration of alumina to silica in the fiber core region. Reheating and cooling the SDF by arc discharge generates mullite particles in the core region, which achieves RI modulation up to ~0.015. Such crystallized region in the SDF is explored as mirrors for FPI, showing a good linear response to temperature with sensitivity of ~13.2 pm/°C. Benefiting from superheat resistance of the crystallized SDF being mirrors, the developed SDF-FPI sensor is capable to withstand high temperature up to 1600°C, which is the highest working temperature for amorphous fiber. Moreover, the SDF-FPI sensor exhibits 6-hour stability at 1200°C. The crystallized SDF-FPIs with compactness, wide temperature working range, high sensitivity, and robustness show great potential application in harsh environment such as turbine engines, power plants, petrochemical, gas industry, etc.

Genetic association of DDIT3, RPL23A, SESN2 and NR4A1 genes with milk yield and composition in dairy cattle

Previously, we identified by RNA sequencing that DDIT3, RPL23A, SESN2 and NR4A1 genes were significantly differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentages; thus, these four genes are considered as promising candidates potentially affecting milk yield and composition traits in dairy cattle. In the present study, we further verified whether these genes have genetic effects on milk traits in a Chinese Holstein population. By re-sequencing part of the non-coding and the entire coding regions of the DDIT3, RPL23A, SESN2 and NR4A1 genes, a total of 35 SNPs and three insertions/deletions were identified, of which three were found in DDIT3, 12 in RPL23A, 16 in SESN2 and seven in NR4A1. Moreover, two of the insertions/deletions-g.125714860_125714872del and g.125714806delinsCCCC in SESN2-were novel and have not been reported previously. Subsequent single SNP analyses revealed multiple significant association with all 35 SNPs and three indels regressed against the dairy production traits (P-value = <0.0001-0.0493). In addition, with a linkage disequilibrium analysis, we found one, one, three, and one haplotype blocks in the DDIT3, RPL23A, SESN2 and NR4A1 genes respectively. Haplotype-based association analyses revealed that some haplotypes were also significantly associated with milk production traits (P-value = <0.0001-0.0461). We also found that 12 SNPs and two indels (two in DDIT3, two in RPL23A, nine in SESN2 and one in NR4A1) altered the specific transcription factor binding sites in the promoter, thereby regulating promoter activity, suggesting that they might be promising potential functional variants for milk traits. In summary, our findings first determined the genetic associations of DDIT3, RPL23A, SESN2 and NR4A1 with milk yield and composition traits in dairy cattle and also suggested potentially causal variants, which require in-depth validation.

Abstract P3-06-01: Clonal evolution and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy

Background: Understanding to what extent a breast tumor's genetic composition may change over the course of a few months of neoadjuvant therapy has implications for optimal therapeutic approach. However, genomic changes observed across treatment may result from either treatment-induced clonal evolution or geographically disparate sampling of a heterogeneous tumor. We sought to characterize the geographic heterogeneity in primary breast tumors, and to incorporate this information into analysis of clonal evolution with neoadjuvant therapy.

Methods: We assembled the largest cohort to date of multi-region (n=2-3) whole-exome sequenced (WES) or whole-genome sequenced untreated primary breast tumors with matched normal and adequate tumor purity for analysis: four tumors with data generated for this study and five tumors compiled from three previous studies. We also generated the first cohort of multi-region (n=2-6) WES breast tumors post-neoadjuvant HER2-targeted therapy and chemotherapy, sequencing one region from a pre-treatment diagnostic specimen, multiple regions from the post-treatment surgical specimen, and matched normal for five HER2+ breast tumors that did not achieve a pathologic complete response. We used an agent-based model of spatial tumor growth to investigate whether the mutational patterns we observed with treatment were consistent with pre-existing heterogeneity or treatment-induced selection.

Results: In untreated primary breast tumors, on average 30% (range 1-70%) of apparently clonal mutations from a single region were absent or rare in a second, spatially disparate region (high-frequency regional, or HFR). Intra-tumor heterogeneity was similar post-treatment (HFR 28%, range 10-54%), and was higher in breast tumors than in previously analyzed colon, brain, lung, and esophageal tumors. Simulation studies confirmed that with high heterogeneity as observed in breast tumors, analysis of one pre-treatment and one post-treatment region could not distinguish treatment-induced clonal evolution from pre-existing heterogeneity; however, obtaining at least two post-treatment regions allowed for detection of clonal shifts with treatment. Analysis of multi-region data revealed that clonal replacement occurred with neoadjuvant therapy in two of the five tumors. Candidate causes of therapeutic resistance included amplifications in CCND1, ERBB4, and MYC in one subclone, and functional protein-altering mutations in ERCC2, SMO, and WT1 in another. Mathematical modeling suggested that these putative resistant subclones comprised 0.02-12.5% of the overall pre-treatment cell population, substantially larger than previous estimates of resistant tumor clone size.

Conclusions: WES data from multiple regions of untreated and treated primary breast tumors revealed considerable heterogeneity that remained present throughout treatment with chemotherapy and HER2-targeted therapy, even while major clonal sweeps took place in a minority of tumors. Obtaining at least two samples for analysis from breast tumors post-neoadjuvant therapy may reveal the tumor's evolutionary path and, especially as increasing numbers of molecular and immune therapeutic targets are identified, inform new clinical strategies.

Citation Format: Caswell-Jin JL, McNamara K, Reiter JG, Sun R, Hu Z, Ma Z, Suarez CJ, Tilk S, Raghavendra A, Forte V, Chin S-F, Bardwell H, Provenzano E, Caldas C, Lang J, West R, Tripathy D, Press MF, Curtis C. Clonal evolution and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-01.