Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two microbial groups mediating nitrification, yet little is presently known about their abundances and community structures at the transcriptional level in wastewater treatment systems (WWTSs). This is a significant issue, as the numerical abundance of AOA or AOB at the gene level may not necessarily represent their functional role in ammonia oxidation. Using amoA genes as molecular markers, this study investigated the transcriptional abundance and community structure of active AOA and AOB in 14 WWTSs. Quantitative PCR results indicated that the transcriptional abundances of AOB amoA (averaged: 1.6 × 10⁸ copies g^-1 dry sludge) were higher than those of AOA (averaged: 3.4 × 10⁷ copies g^-1 dry sludge) in all WWTSs despite several higher abundances of AOA amoA at the gene level. Moreover, phylogenetic analysis demonstrated that Nitrosomonas europaea and unknown clusters accounted for 37.66% and 49.96% of the total AOB amoA transcripts, respectively, suggesting their dominant role in driving ammonia oxidation. Meanwhile, AOA amoA transcripts were only successfully retrieved from 3 samples, and the Nitrosospaera sister cluster dominated, accounting for 83.46%. Finally, the substrate utilization kinetics of different AOA and AOB species might play a fundamental role in shaping their niche differentiation, community composition, and functional activity. This study provides a basis for evaluating the relative contributions of ammonia-oxidizing microorganisms (AOMs) to nitrogen conversions in WWTSs.

A metagenomic-based method to study hospital air dust resistome

As a symbol of the defense mechanisms that bacteria have evolved over time, the genes that make bacteria resist antibiotics are overwhelmingly present in the environment. Currently, bacterial antibiotic resistance genes (ARGs) in the air are a serious concern. Previous studies have identified bacterial communities and summarized putative routes of transmissions for some dominant hospital-associated pathogens from hospital indoor samples. However, little is known about the possible indoor air ARG transportation. In this study, we mainly surveyed air-conditioner air dust samples under different airflow conditions and analyzed these samples using a metagenomic-based method. The results show air dust samples exhibited a complex resistome, and the average concentration is 0.00042 copies/16S rRNA gene, which is comparable to some other environments. The hospital air-conditioners can form resistome over time and accumulate pathogens. In addition, our results indicate that the Outpatient hall is one of the main ARG transmission sources, which can distribute ARGs to other departments (explains >80% resistome). We believe that the management should focus on ARG carrier genera such as Staphylococcus, Micrococcus, Streptococcus, and Enterococcus in this hospital and our novel evidence-based network strategy proves that plasmid-mediated ARG transfer can occur frequently. Overall, these results provide insights into the characteristics of air dust resistome and possible route for how ARGs are spread in air.

Spatiotemporal distribution, risk assessment and source appointment of metal(loid)s in water and sediments of Danjiangkou Reservoir, China

Danjiangkou Reservoir is the biggest artificial reservoir in China. But spatiotemporal distribution and risks of metal(loid)s in it were still unclear after the operation of Middle Route of South-to-North Water Diversion Project. In this study, distribution pattern of fifteen metal(loid)s in the Danjiangkou Reservoir was investigated. It was shown that metal(loid)s concentrations in the water were much lower than the drinking water quality standards in China, while Sb, Co, Cd and Cr were identified as the major pollutants in the sediments. Environment-metal(loid)s correlation analysis revealed total organic carbon, sulfate, temperature, dissolved oxygen and total phosphorus markedly controlled metal(loid)s distribution in the water, while organic carbon, total phosphorus and ammonia nitrogen shaped their distribution in the sediments. Results of risk assessment further revealed that the sediments of Danjiangkou Reservoir were minor to moderate polluted, and Sb, Cd exhibited the highest potential ecological risk. Additionally, source identification showed agricultural activities (25.3%), industrial and mining activities (17.5%) and natural processes (57.2%) were the dominant sources of metal(loid)s burden in the sediments. Overall, the results are of significance to understanding the ecological risk and pollution sources in the Danjiangkou Reservoir, which is essential for the effective management of metal(loid)s pollution.

Pre-accumulation and in-situ destruction of diclofenac by a photo-regenerable activated carbon fiber supported titanate nanotubes composite material: Intermediates, DFT calculation, and ecotoxicity

Pharmaceuticals and personal care products (PPCPs) have been widely detected in ecosystems. However, effective water purification technologies for PPCPs degradation are lacking. In this work, an active activated carbon fiber supported titanate nanotubes (TNTs@ACF) composite was synthesized via one-step hydrothermal process, which was applied for adsorption and photocatalytic degradation of PPCPs under simulated solar light. Characterizations indicated that the successful grafting of TNTs onto ACF was achieved and surface modification occurred. Diclofenac (DCF, a model PPCPs) was rapidly adsorbed onto TNTs@ACF, and subsequently photodegraded (98.8 %) under solar light within 2 h. TNTs@ACF also performed well over a wide range of pH, and was resistant to humic acid. The good adsorption and photocatalytic activity of TNTs@ACF was attributed to the well-defined hybrid structure, enabling corporative adsorption of DCF by TNTs and ACF, and extending the light absorbance to visible region. Furthermore, the description of degradation pathway and evaluation of ecotoxicity for DCF and its intermediates/byproduct were proposed based on experimental analysis, density functional theory (DFT) calculation and quantitative structure-activity relationship (QSAR) analysis, respectively, indicating the photocatalytic degradation of DCF can offer the step-by-step de-toxicity. Our study is expected to offer new strategy as "pre-accumulation and in-situ destruction" for environmental application.

Radical attack and mineralization mechanisms on electrochemical oxidation of p-substituted phenols at boron-doped diamond anodes

Degradation of phenols with different substituent groups (including -OCH₃, -CHO, -NHCOCH₃, -NO₂, and -Cl) at boron-doped diamond (BDD) anodes has been studied previously based on the removal efficiency and •OH detection. Innovatively, formations of CO₂ gas and various inorganic ions were examined to probe the mineralization process combined with quantitative structure-activity relationship (QSAR) analysis. As results, all phenols were efficiently degraded within 8 h with high COD removal efficiency. Three primary intermediates (hydroquinone, 1,4-benzoquinone and catechol) were identified during electrochemical oxidation and degradation pathway was proposed. More importantly, CO₂ transformation efficiency ranked as: no N or Cl contained phenols (p-CHO, p-OCH₃ and Ph) > N-contained phenols (p-NHCOCH₃ and p-NO₂) > Cl-contained phenols (p-Cl and o,p-Cl). Carbon mass balance study suggested formation of inorganic carbon (H₂CO₃, CO₃^2- and HCO₃^-) and CO₂ after organic carbon elimination. Inorganic nitrogen species (NH₄⁺, NO₃^- and NO₂^-) and chlorine species (Cl^-, ClO₃^- and ClO₄^-) were also formed after N- and Cl-contained phenols mineralization, while no volatile nitrogen species were detected. The phenols with electron-withdrawing substituents were easier to be oxidized than those with electron-donating substituents. QSAR analysis indicated that the reaction rate constant (k₁) for phenols degradation was highly related to Hammett constant (∑σ_o,m,p) and energy gap (E_LUMO - E_HOMO) of the compound (R² = 0.908), which were key parameters on evaluating the effect of structural moieties on electronic character and the chemical stability upon radical attack for a specific compound. This study presents clear evidence on mineralization mechanisms of phenols degradation at BDD anodes.

Effect of modified basic oxygen furnace slag on the controlled release of nitrate nitrogen and the functional microbial community in soil

The specific surface area and active adsorption sites of basic oxygen furnace (BOF) slag increase after BOF modification. The addition of modified BOF slag to the soil may enable the control of nitrate nitrogen (NO₃-N) leaching and also affect the functional microflora in the soil. In this study, soil column leaching experiments were conducted to explore the effects of adding modified slag to the soil on the controlled release of NO₃-N and the main functional microbial communities involved in nitrification and denitrification processes. The experimental design included seven column groups: a soil control group (CT); soil groups with 2.5%, 5%, and 10% raw slag (S1, S2, S3); and soil groups with 2.5%, 5%, and 10% modified slag (MS1, MS2, MS3) that were subjected to three cycles of leaching, each of which were comprised of five leaching treatments. After the three cycles of leaching, significantly less NO₃-N had leached from the modified slag group compared to the CT and the raw slag groups (P < 0.05). Although both slag treatments increased soil pH and decreased the oxidation reduction potential of the soil leaching solution, the addition of modified slag had less effect on soil pH than the addition of raw slag. During column leaching, the group with modified slag had a higher gene abundance of functional microflora compared with the group with raw slag. Similarly, the modified slag group had a higher diversity and richness of denitrifying bacteria, ammonia-oxidizing archaea, and ammonia-oxidizing bacteria than the raw slag group. In conclusion, the addition of modified slag to soil effectively decreased the NO₃-N leaching and had relatively little effect on the functional microbial community in the soil.

Effect of basic oxygen furnace slag on succession of the bacterial community and immobilization of various metal ions in acidic contaminated mine soil

As an immobilizing agent for metal ions, basic oxygen furnace slag may affect bacterial community succession, thus further promote metal ion immobilization in acidic contaminated soil. In this work, pot experiments were conducted to study the effects of adding 10 g/kg (S10) and 15 g/kg (S15) slag on soil properties, plant growth, bacterial community succession and various metal ion immobilization in acidic mine soils contaminated by Pb, Zn, Cu, Cr and Cd. The results showed that after 93 days of potting, the soil pH, electrical conductivity, total nitrogen and organic carbon content increased significantly (P < 0.05), and the dry weight of Poa pratensis L. increased significantly (P < 0.05) in S10 and S15 compared with in original soil group. With slag addition and plant growth, the diversity and richness indices of bacterial communities greatly improved, and at the genus level, the abundance of metal-tolerant bacteria and bacteria beneficial to plant growth increased, while the abundance of acidophiles decreased. After adding slag to the soil, the various metals were immobilized because slag could not only immobilize metal ions through ion exchange and coprecipitation, but also benefit plant growth and bacterial community succession which further promote the immobilization of metal ions.

RUNX1-activated upregulation of lncRNA RNCR3 promotes cell proliferation, invasion, and suppresses apoptosis in colorectal cancer via miR-1301-3p/AKT1 axis in vitro and in vivo

PURPOSE

Long non-coding RNAs (lncRNAs) have participated in progression of colorectal cancer. This study aims to study the role of RUNX1/RNCR3/miR-1301-3p/AKT1 axis in colorectal cancer.

METHODS

The cancer tissues were from patients with colorectal cancer. The qRT-PCR was used to determine expression of lncRNA RNCR3, miR-1301-3p, and AKT1. Both dual-luciferase reporter assay and ChIP assay were conducted to investigate the binding sites of RUNX1 on RNCR3 promoter. Western blot was performed to analyze expression of AKT1 protein. Both dual-luciferase reporter assay and RIP assay were performed to detect the interacting sites between RNCR3 and miR-1301-3p. The CCK-8 assay, soft agar assay, transwell assay, and annexin-V-FITC/PI staining were applied to analyze the cell growth, invasion, and apoptosis, respectively.

RESULTS

The data demonstrated that RNCR3 was elevated in colorectal cancer, and it was negatively correlated with expression of miR-1301-3p which was decreased in cancers. Then, RNCR3 could interact with and suppress miR-1301-3p expression in HCT116 and SW480. Knockdown of RNCR3 or miR-1301-3p overexpression significantly inhibited cell growth, invasion, and increased apoptosis through suppressing expression of Cyclin A1, PCNA, N-cadherin, Bcl-2, and promoting expression of E-cadherin, Bax in vitro and in vivo. RUNX1 was directly bound to RNCR3 promoter to activate RNCR3 expression. Furthermore, overexpression of RNCR3 blocked tumor inhibitory effects of miR-1301-3p on proliferation, colony formation, invasion, and apoptosis in vitro and in vivo. Additionally, RNCR3 and miR-1301-3p synergistically modulated AKT1 expression.

CONCLUSION

RUNX1-activated upregulation of RNCR3 promoted colorectal cancer progression by sponging miR-1301-3p to elevate AKT1 levels in vitro and in vivo.

Efficient adsorption of europium (III) and uranium (VI) by titanate nanorings: Insights into radioactive metal species

Radioactive wastewater containing high concentration of radionuclides poses severe threats to ecosystem and human health, so efficient removal of these toxic heavy metals is urgently needed. Titanate nanomaterials have been demonstrated good adsorbents for heavy metals due to ion exchange property. In this study, titanate nanorings (TNRs) were synthesized using the facile hydrothermal-cooling method. The TNRs were composed of sodium trititanate, with a chemical formula of Na_0.66H_1.34Ti₃O₇•0.27H₂O and a Na content of 2.38 mmol/g. The TNRs demonstrated sufficient adsorption performance to radionuclides europium (Eu) and uranium (U) ions. Specifically, even at a high initial concentration of 50 mg/L, 86.5% and 92.6% of the two metal ions can be rapidly adsorbed by the TNRs within 5 min, and equilibrium was reached within 60 min at pH 5. The maximum adsorption capacity (Q _max) obtained by the Langmuir isotherm model was 115.3 mg/g for Eu(III) and 282.5 mg/g for uranium U(VI) at pH 5, respectively. The adsorption capacities of the two metals under various water chemical conditions were highly related to their species. Ion exchange between metal cations and Na⁺ in the TNR interlayers was the dominant adsorption mechanism, and adsorption of U(VI) was more complicated because of the co-existence of various uranyl (UO₂ ²⁺) and uranyl-hydroxyl species. The spent TNRs were effectively regenerated through an acid-base or ethylenediamine tetraacetic acid (EDTA) treatment and reused. Considering the large adsorption capacity and quick kinetic, TNRs are promising materials to remove radionuclides in environmental purification applications, especially emergent treatment of leaked radionuclides.

Metagenomic insights into the profile of antibiotic resistomes in a large drinking water reservoir

Reservoirs play a vital role in the control and management of surface water resources. However, the long water residence time in the reservoir potentially increases the storage and accumulation of antibiotic resistant genes (ARGs). The full profiles and potential health risks of antibiotic resistomes in reservoirs are largely unknown. In this study, we investigated the antibiotic resistomes of water and sediment during different seasons in the Danjiangkou Reservoir, which is one of the largest reservoirs in China, using a metagenomic sequencing approach. A total of 436 ARG subtypes belonging to 20 ARG types were detected from 24 water and 18 sediment samples, with an average abundance of 0.138 copies/cell. The overall ARG abundance in the sediment was higher than that in the water, and bacitracin and vancomycin resistance genes were the predominant ARG types in the water and sediment, respectively. The overall ARG abundance in the dry season was higher than that in the wet season, and a significant difference in ARG subtype compositions was observed in water, but not in the sediment, between the different seasons. The potential horizontal gene transfer frequency in the water was higher than that in the sediment, and the ARGs in water mainly came from the sediment upstream of the reservoir. The metagenomic assembly identified 14 contigs as ARG-carrying pathogens including Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa, and 3 of 14 carried virulence factors. Overall, the potential public health risks posed by resistomes in the water of the Danjiangkou Reservoir were higher in the dry season than in the wet season. Based on these results, strategies including sediment control and pathogen monitoring are suggested for water safety management in drinking water reservoirs.

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Complete ammonia oxidizing bacteria (CAOB) have been recognized as a new member of ammonia-oxidizing microorganisms (AOMs) due to its single-step nitrification capability. However, the abundance and diversity of CAOB in environmental ecosystems were still far from known owing to the lack of specific molecular marker. Herein, a universal primer set specifically targeting both clades of CAOB amoA gene with high specificity and coverage was successfully designed. Intriguingly, real-time quantitative PCR tests revealed that CAOB were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that clade A existed in all the five types of ecosystems, while clade B were only detected in soil and sediment samples. Four sub-clusters were further classified within clade A, in which N. nitrosa cluster dominated CAOB amoA in activated sludge samples while the new recognized soil cluster was the primary constitute in soils. Moreover, the niche specialization between different CAOB species and the environmental conditions were supposed to be the primary driven force to shape the diversity and community of CAOB. This study provided a strong evidence in support of the ubiquities and high abundances of CAOB in various environmental ecosystems and highlighted the significance of including CAOB as the new member of AOMs to re-evaluate the biogeochemical nitrogen cycle.

Role of sludge retention time in mitigation of nitrous oxide emission from a pilot-scale oxidation ditch

Nitrous oxide (N₂O) emission from wastewater treatment plants (WWTPs) has become a focus of attention due to its significant greenhouse effect. In this study, the role of sludge retention time (SRT) in mitigation of N₂O emission from a pilot-scale oxidation ditch was systematically investigated. The activated sludge system that operated at SRT of 25 days demonstrated significantly lower N₂O emission factor, higher resistance to ammonia overload and aeration failure shock than those obtained at SRT of 15 days no matter which hydraulic retention time (HRT) was adopted. Batch experiments revealed that nitrifier denitrification (ND) was the primary mechanism of N₂O generation. However, more microbes affiliated with Nitrospira genera were harbored in the system at SRT 25 d, which could effectively avoid nitrite accumulation, a key factor promoting N₂O generation by ND. PICRUSt results further suggested the system at SRT 25 d possessed higher genetic potential for N₂O reduction reflected by the more abundant nitrous-oxide reductase.

The immune profile of small HER2-positive breast cancers: a secondary analysis from the APT trial

BACKGROUND

Previous data suggest that the immune microenvironment plays a critical role in human epidermal growth factor receptor 2 (HER2) -positive breast cancer; however, there is little known about the immune profiles of small HER2-positive tumors. In this study, we aimed to characterize the immune microenvironment of small HER2-positive breast cancers included in the Adjuvant paclitaxel and trastuzumab for node-negative, HER2-positive breast cancer (APT) trial and to correlate the immune markers with pathological and molecular tumor characteristics.

PATIENTS AND METHODS

The APT trial was a multicenter, single-arm, phase II study of paclitaxel and trastuzumab in patients with node-negative HER2-positive breast cancer. The study included 406 patients with HER2-positive, node-negative breast cancer, measuring up to 3 cm. Exploratory analysis of tumor infiltrating lymphocytes (TIL), programmed death-ligand 1 (PD-L1) expression (by immunohistochemistry), and immune gene signatures using data generated by nCounter PanCancer Pathways Panel (NanoString Technologies, Seattle, WA), and their association with pathological and molecular characteristics was carried out.

RESULTS

Of the 406 patients, 328 (81%) had at least one immune assay carried out: 284 cases were evaluated for TIL, 266 for PD-L1, and 213 for immune gene signatures. High TIL (≥60%) were seen with greater frequency in hormone-receptor (HR) negative, histological grades 2 and 3, as well in HER2-enriched and basal-like tumors. Lower stromal PD-L1 (≤1%) expression was seen with greater frequency in HR-positive, histological grade 1, and in luminal tumors. Both TIL and stromal PD-L1 were positively correlated with 10 immune cell signatures, including Th1 and B cell signatures. Luminal B tumors were negatively correlated with those signatures. Significant correlation was seen among these immune markers; however, the magnitude of correlation did not indicate a monotonic relationship between them.

CONCLUSION

Immune profiles of small HER2-positive breast cancers differ according to HR status, histological grade, and molecular subtype. Further work is needed to explore the implication of these findings on disease outcome.

CLINICAL TRIAL REGISTRATION

clinicaltrials.gov identifier: NCT00542451.

Prospective evaluation of the cardiac safety of HER2-targeted therapies in patients with HER2-positive breast cancer and compromised heart function: the SAFE-HEaRt study

Purpose

HER2-targeted therapies have substantially improved the outcome of patients with breast cancer, however, they can be associated with cardiac toxicity. Guidelines recommend holding HER2-targeted therapies until resolution of cardiac dysfunction. SAFE-HEaRt is the first trial that prospectively tests whether these therapies can be safely administered without interruptions in patients with cardiac dysfunction.

Methods

Patients with stage I–IV HER2-positive breast cancer candidates for trastuzumab, pertuzumab or ado-trastuzumab emtansine (TDM-1), with left ventricular ejection fraction (LVEF) 40–49% and no symptoms of heart failure (HF) were enrolled. All patients underwent cardiology visits, serial echocardiograms and received beta blockers and ACE inhibitors unless contraindicated. The primary endpoint was completion of the planned HER2-targeted therapies without developing either a cardiac event (CE) defined as HF, myocardial infarction, arrhythmia or cardiac death or significant asymptomatic worsening of LVEF. The study was considered successful if planned oncology therapy completion rate was at least 30%.

Results

Of 31 enrolled patients, 30 were evaluable. Fifteen patients were treated with trastuzumab, 14 with trastuzumab and pertuzumab, and 2 with TDM-1. Mean LVEF was 45% at baseline and 46% at the end of treatment. Twenty-seven patients (90%) completed the planned HER2-targeted therapies. Two patients experienced a CE and 1 had an asymptomatic worsening of LVEF to ≤ 35%.

Conclusion

This study provides safety data of HER2-targeted therapies in patients with breast cancer and reduced LVEF while receiving cardioprotective medications and close cardiac monitoring. Our results demonstrate the importance of collaboration between cardiology and oncology providers to allow for delivery of optimal oncologic care to this unique population.

Electronic supplementary material

The online version of this article (10.1007/s10549-019-05191-2) contains supplementary material, which is available to authorized users.

Antibiotics in water and sediments of Danjiangkou Reservoir, China: Spatiotemporal distribution and indicator screening

Danjiangkou Reservoir is the largest artificial freshwater lake in China. The occurrence and spatiotemporal distribution of 77 antibiotics in water and sediment samples from Danjiangkou Reservoir were investigated. Approximately 90% of the detectable concentrations of the 61 and 54 antibiotics found in water and sediment samples were lower than 5.0 ng/L and 1.0 ng/g, respectively. Sulfamethoxazole was the most abundant antibiotic found in water (1.65-149 ng/L, median 6.25 ng/L). In sediment samples, macrolides were frequently detected (42.7-54.5%) at concentrations of ND-4.34 ng/g. Greater diversity and higher levels of antibiotics were generally found in both water and sediment samples in spring than in the other seasons. Composition profiles of antibiotics differed between the two tributary river basins of Danjiangkou Reservoir, indicating different sources of contamination and the influence of water and sediment properties. Four criteria, namely widespread occurrence, correlation with the total antibiotic concentration, and risk to aquatic organisms or to human health, were suggested to select specific indicators for monitoring and pollution control of antibiotics. Five antibiotics were selected as appropriate indicators for Danjiangkou Reservoir, namely sulfamethoxazole, trimethoprim, clarithromycin, roxithromycin, and anhydrochlortetracycline. This study adds to the understanding of the occurrence of antibiotics in water reservoirs and can assist authorities in regulating antibiotic contamination and designing effective strategies for risk minimization.

Abstract P2-09-07: Preoperative pembrolizumab (Pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC)

Background: Radiation therapy (RT) induces immune-mediated cell death and could generate a rich supply of tumor antigens if administered in the pre-operative, curative-intent setting. The addition of PD-1 mediated checkpoint blockade to pre-operative RT could thus, generate robust anti-tumor immune responses, induce long-term tumor-specific memory, and ultimately, improve cure rates. This study aims to establish the safety of pre-operative pembrolizumab (pembro)-mediated immune modulation with a RT “boost” equivalent in patients with operable triple negative breast cancer (TNBC) for whom lumpectomy and adjuvant RT are planned (NCT03366844). Serial research biopsies permit interrogation of conventional biomarkers including tumor infiltrating lymphocytes (TILs) and novel immune correlates as potential predictors of response to pembro alone versus pembro with RT.

Methods: Ten women with operable, primary TNBC &gt;2cm for whom breast-conserving therapy is planned are being enrolled in this single-institution pilot study. Study treatment consists of 1 cycle of pre-operative pembro (200 mg IV) alone, followed 3 weeks later by a RT boost (24 Gy/3 fractions) to the primary breast tumor concurrently with pembro (+/- 5 days). Curative-intent, standard-of-care, neoadjuvant chemotherapy (NAC) or breast-conserving surgery is then undertaken within 8 weeks of study enrollment (i.e. within 5 weeks of pembro #2). Adjuvant RT is administered per standard-of-care after surgery, but without a boost dose. Research blood and fresh tumor biopsies are obtained at baseline and after cycles 1 and 2 of pembro. Co-primary endpoints are: 1) safety/tolerability, as defined by the number of patients who do not necessitate a delay in standard-of-care chemotherapy or surgery and 2) change in TIL score. Secondary endpoints include safety/toxicity up to 19 weeks after study enrollment, pCR rates and disease-free survival. Correlative analysis will include single-cell RNA sequencing of the tumor immune infiltrate and multispectral immunohistochemistry

Results: Seven patients enrolled between 12/19/17 and 7/1/18. As of 7/1/18, 5 patients have completed the experimental pembro/RT phase of the trial and are currently completing standard-of-care NAC; 1 patient is currently being treated in the experimental pembro/RT phase; and 1 patient with a cT2N0 tumor at baseline achieved a pathologic complete response (pCR, ypT0/Tis ypN0) after completing the experimental pembro/RT phase followed by anthracycline- and taxane-based NAC. No grade 3 or 4 toxicities have been observed during pembro/RT in the 6 patients completing the experimental phase to date. Three additional patients will be enrolled

Conclusions: This is the first trial of curative-intent, pre-operative checkpoint blockade with RT in breast cancer and the strategy appears to be well tolerated to date. At the time of presentation, safety, change in TIL score, and pCR rates for all patients completing the experimental and NAC phases of the study will be reported.

Citation Format: McArthur HL, Basho R, Shiao SL, Park D, Mita M, Chung A, Arnold B, Martin C, Dang C, Karlan S, Knott S, Giuliano A, Ho A. Preoperative pembrolizumab (Pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC) [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 P2-09-07.

Abstract P3-08-04: Transient state change, but not permanent subtype change, after HER2-targeted therapy for HER2-positive breast cancer

Background: In CALGB 40601 (Alliance, NCT00770809), a neoadjuvant phase III trial of paclitaxel and trastuzumab with or without lapatinib for 12 weeks for patients with HER2-positive breast cancer, 33% of pretreatment tumors were Luminal A subtype, however, 69% of post-treatment samples with residual disease were Luminal A subtype. In addition, 71% of Luminal B (12/17) and 67% of HER2-Enriched (6/9) tumors changed into Luminal A, while 80% of Luminal A (20/24) remained Luminal A (Carey et al. J Clin Oncol. 2016). It is not known whether this shift to Luminal A was transient or permanent.

Methods: We selected matched pairs of pre- and post-treatment 40601 samples with tumor purity &gt;10% based upon DNA analyses to ensure all samples contained tumor. PAM50 intrinsic subtyping was applied to the 40601 samples gene expression data using a two-step normalization process based on The Genome Cancer Atlas, and PAM50 training set. In addition, a HER2-enriched expression subtype patient-derived xenograft (PDX) tumor called WHIM35, was studied and was either untreated (n=10), or treated with lapatinib at 220 mg/kg for 1 week (wk) (n=5), for 2 wks (n=8), or for 3 wks (n=4). We also treated WHIM35 tumors with lapatinib for 2 wks (on) and then removed laptinib for 1 wk (off) (n=6), or for 2 wks on and 2-4 wk off (n=6), and finally for 3 wks on, and 1 wk off (n=3). PAM50 intrinsic subtyping was applied to the PDX gene expression data and subtype assessed as well as a genomic-based proliferation score. ANOVA p-values were calculated by comparing median values across all gene signature or correlation scores.

Results: We found 10 pairs of 40601 samples that kept their tumor purity values, however, their subtype changed to Luminal A after treatment (i.e., in the residual disease), and in these cases no minor tumor subclone became a dominant clone in the post treatment sample. Pretreatment subtypes were 6 Luminal B, 3 Luminal A, and 1 HER2-enriched. The tumor purity values did not change after the treatments, but correlation to Luminal A was significantly higher (p=0.01), while correlation to HER2-enriched (p=0.004) and proliferation signature scores (p=0.003) were significantly lower in the post-treatment samples. Among the WHIM35 PDX tumors, one sample changed its subtype from HER2-enriched to Luminal A after the lapatinib treatment and the rest remained HER2-enriched, suggesting environmental differences between patient samples and the PDX model. However, correlation to Luminal A was significantly higher in all lapatinib treated WHIM35 samples (p=8.3e-12), and notably went back to the initial low levels just one week after removing lapatinib. Likewise, correlation to HER2-enriched (p=1.2e-10) and proliferation signature scores (p=6.2e-12) also got lower while treated with lapatinib, but went back to the initial levels after cessation of treatment.

Conclusions: Our findings suggest that the apparent subtype change during HER2-targeting therapy is not permanent, but is more likely a transient state change from a HER2-enriched subtype into a more Luminal A-like state. When we plan additional treatment strategies using residual disease phenotypes, it may not be clear what is the true subtype of the sample due to this inherent plasticity.

Citation Format: Tanioka M, Parker JS, Henry LN, Tolaney S, Dang C, Krop IE, Harris L, Polley M, Berry DA, Winer EP, Carey LA, Perou CM. Transient state change, but not permanent subtype change, after HER2-targeted therapy for HER2-positive 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 P3-08-04.

Abstract P6-18-30: Phase Ib/II study of capecitabine 7/7 schedule with neratinib in patients with HER2-positive metastatic breast cancer (MBC)

Background: Neratinib (N) is a potent irreversible inhibitor of HER1, HER2, and HER4 and has been shown to have antitumor activity in patients (pts) with human epidermal growth factor receptor 2 (HER2) - positive breast cancer. A previous study of combination of neratinib with capecitabine (X) was associated with &gt; G 3 diarrhea in &gt; 20% of patients. Currently, the NALA study is evaluating this combination of N with X at standard schedule against control. X at 7 day on and 7 day off schedule (7/7) has been shown to be well-tolerated with less ≥G3 toxicities. We are conducting a phase Ib/II study of N with X (7/7) in pts with pretreated HER2+ MBC (NCT03377387). Methods: Eligible pts had HER2+ MBC, normal left ventricular ejection fraction (LVEF ≥ 50%); pts can have any and up to 4 prior chemotherapy-based treatments in phase Ib and II portions, respectively. Primary endpoints are to define maximum tolerated dose and efficacy in phase I and phase II portions, respectively. Secondary endpoints include safety and tolerability; exploratory endpoint is to quantify cell-free DNA to correlate with response for phase II portion. There were 4 cohorts for phase Ib with dose level 1 with starting dose of X at 1500 mg BID at 7/7 schedule with N at 240 mg daily. Results: As of July 1, 2018 8 pts have been enrolled in 2 cohorts. The median age is 63y (range: 57-79), and median ECOG is 0 (range: 0-1). 4 patients were treated at dose level 1 and 2 of 4 patients experienced dose-limiting toxicity with G3 diarrhea during cycle 1. Other significant toxicities included G3 hand foot syndrome (n=1), G3 fatigue (n=1) and G3 nausea (n=1). Three pts have now been treated at dose level -1 (X at 1000 mg twice daily 7/7 and N at 240 mg daily) and no ≥ G3 toxicities has been noted. Once MTD is reached, the phase II portion will occur to assess the efficacy and to further establish the safety and tolerability of capecitabine and neratinib at the MTD. Conclusions: The phase Ib/II study combining neratinib and capecitabine 7/7 is ongoing and updated result will be presented.

Citation Format: Wang R, Singh J, Sterlin V, Goldstein M, Lake D, Wong S, Baselga J, Norton L, Dang C. Phase Ib/II study of capecitabine 7/7 schedule with neratinib in patients with HER2-positive metastatic breast cancer (MBC) [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 P6-18-30.

Newly designed primer pair revealed dominant and diverse comammox amoA gene in full-scale wastewater treatment plants

The discovery of complete ammonia oxidizing bacteria (CAOB) capable of performing the two-step nitrification process on their own has fundamentally upended our traditional perception. However, their environmental distribution and ecological significance in driving ammonia oxidation are still urgently awaited to be assessed. In this study, the diversity and abundance of CAOB amoA gene in wastewater treatment plants (WWTPs) were presented taking advantage of a newly designed primer pair specifically targeting CAOB amoA gene. Phylogenetic results demonstrated the novel amoA gene formed a clearly distinct cluster from the canonical amoA and pmoA genes. Among the five well-supported sub-clusters, Nitrospira nitrosa cluster accounted for 94.34% of all the currently retrieved sequences from WWTPs. More importantly, qPCR results demonstrated a remarkably high abundance of CAOB amoA gene, which were up to 182.7-fold more abundant than AOB amoA gene. This study provided new dimension and fundamental basis for future researches towards biogeochemical nitrogen cycle.