No abstract

Neuroblastoma is a pediatric cancer with significant genomic and biological heterogeneity. p16 and ARF, two important tumor suppressor genes on chromosome 9p21, are inactivated commonly in most cancers but paradoxically overexpressed in neuroblastoma. Here we report that exon γ in p16 is also part of an undescribed long non-coding RNA (lncRNA) that we have termed CAI2 (CDKN2A/ARF Intron 2 lncRNA). CAI2 is a single exon gene with a poly A signal located in but independent of the p16/ARF exon 3. CAI2 is expressed at very low levels in normal tissue but is highly expressed in most tumor cell lines with an intact 9p21 locus. Concordant expression of CAI2 with p16 and ARF in normal tissue along with the ability of CAI2 to induce p16 expression suggested that CAI2 may regulate p16 and/or ARF. In neuroblastoma cells transformed by serial passage in vitro, leading to more rapid proliferation, CAI2, p16 and ARF expression all increased dramatically. A similar relationship was also observed in primary neuroblastomas where CAI2 expression was significantly higher in advanced stage neuroblastoma, independently of MYCN amplification. Consistent with its association with high risk disease, CAI2 expression was also significantly associated with poor clinical outcomes, although this effect was reduced when adjusted for MYCN amplification. Taken together, our findings suggested that CAI2 contributes to the paradoxical overexpression of p16 in neuroblastoma, where CAI2 may offer a useful biomarker of high-risk disease.

Self-transmissible and mobilizable plasmids contribute to the emergence and spread of multidrug-resistant bacteria by enabling the horizontal transfer of acquired antibiotic resistance. The objective of this study was to capture and characterize self-transmissible and mobilizable resistance plasmids from a coastal wetland impacted by urban stormwater runoff and human wastewater during the rainy season. Four plasmids were captured, two self-transmissible and two mobilizable, using both mating and enrichment approaches. Plasmid genomes, sequenced with either Illumina or PacBio platforms, revealed representatives of incompatibility groups IncP-6, IncR, IncN3, and IncF. The plasmids ranged in size from 36 to 144 kb and encoded known resistance genes for most of the major classes of antibiotics used to treat Gram-negative infections (tetracyclines, sulfonamides, β-lactams, fluoroquinolones, aminoglycosides, and amphenicols). The mobilizable IncP-6 plasmid pLNU-11 was discovered in a strain of Citrobacter freundii enriched from the wetland sediments with tetracycline and nalidixic acid, and encodes a novel AmpC-like β-lactamase (blaWDC-1), which shares less than 62% amino acid sequence identity with the PDC class of β-lactamases found in Pseudomonas aeruginosa. Although the IncR plasmid pTRE-1611 was captured by mating wetland bacteria with P. putida KT2440 as recipient, it was found to be mobilizable rather than self-transmissible. Two self-transmissible multidrug-resistance plasmids were also captured: the small (48 kb) IncN3 plasmid pTRE-131 was captured by mating wetland bacteria with Escherichia coli HY842 where it is seemed to be maintained at nearly 240 copies per cell, while the large (144 kb) IncF plasmid pTRE-2011, which was isolated from a cefotaxime-resistant environmental strain of E. coli ST744, exists at just a single copy per cell. Furthermore, pTRE-2011 bears the globally epidemic blaCTX-M-55 extended-spectrum β-lactamase downstream of ISEcp1. Our results indicate that urban coastal wetlands are reservoirs of diverse self-transmissible and mobilizable plasmids of relevance to human health.

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Antibiotics are our primary approach to treating complex infections, yet we have a poor understanding of how these drugs affect microbial communities. To better understand antimicrobial effects on host-associated microbial communities we treated cultured sputum microbiomes from people with cystic fibrosis (pwCF, n = 24) with 11 different antibiotics, supported by theoretical and mathematical modeling-based predictions in a mucus-plugged bronchiole microcosm. Treatment outcomes we identified in vitro that were predicted in silico were: 1) community death, 2) community resistance, 3) pathogen killing, and 4) fermenter killing. However, two outcomes that were not predicted when antibiotics were applied were 5) community profile shifts with little change in total bacterial load (TBL), and 6) increases in TBL. The latter outcome was observed in 17.8% of samples with a TBL increase of greater than 20% and 6.8% of samples with an increase greater than 40%, demonstrating significant increases in community carrying capacity in the presence of an antibiotic. An iteration of the mathematical model showed that TBL increase was due to antibiotic-mediated release of pH-dependent inhibition of pathogens by anaerobe fermentation. These dynamics were verified in vitro when killing of fermenters resulted in a higher community carrying capacity compared to a no antibiotic control. Metagenomic sequencing of sputum samples during antibiotic therapy revealed similar dynamics in clinical samples. This study shows that the complex microbial ecology dictates the outcomes of antibiotic therapy against a polymicrobial infection.

Immunotherapy with ch14.18 (dinutuximab) has significantly improved the survival of high-risk neuroblastoma patients, though late relapses and allergic reaction remain concerning. N-glycolylneuraminic acid (Neu5Gc) and galactose alpha-1,3-galactose (α-gal) are glycans present in most mammals except human. Humans have circulating antibodies against these glycans due to their presence in dairy products and red meats. We investigated whether anti-glycan antibodies influence efficacy or allergic reactions associated with dinutuximab. Using ELISA, we measured anti-Neu5Gc and anti-α-gal IgG and IgE levels in plasma collected from courses 1 (days -1 & 6), 4 (days 80 & 90) & 5 (days 111 & 118) of patients on two immunotherapy trials of neuroblastoma (ANBL0032 n= 219; ANBL0931 n=100). Levels of IgG and IgE antibodies against both glycans were highest at pretreatment, decreasing significantly over the entire course of therapy as well as within each course of therapy (p<0.001, Wilcoxon signed rank). For patients on ANBL0032 immunotherapy, anti-α-gal was 924 ± 208 ng/ml (n=118) at pretreatment, decreasing to 102 ± 573 ng/ml (n=82) at day 118. Similar decreases in anti-glycan levels were also noted in patients treated with isotretinoin alone. No association between anti-glycan levels and the occurrence of anaphylaxis, urticaria or other allergic reaction during immunotherapy was observed. Patients were next dichotomized by median value into low vs. high anti-glycan subgroups and associations with EFS and OS assessed using log-rank test. While there was no correlation of anti-glycan levels at pretreatment with outcome, patients treated with immunotherapy on ANBL0032 with lower levels of anti-α-gal and anti-Neu5Gc IgG at later assessment times were significantly associated with better EFS. For example, patients with less than median levels of anti-α-gal on day 90 (n=93, p=0.05) and day 118 (n=86, p=0.05), and anti-Neu5Gc on day 90 (p=0.009) and day 118 (p=0.05), had better EFS. These results remained valid when the ANBL0032 and ANBL0931 cohorts were combined. In contrast, there was no significant correlation of anti-glycan levels and OS with immunotherapy, or EFS or OS in the non-immunotherapy cohort at any treatment timepoint. Our results suggest that lower levels of circulating antibodies against non-human glycans in neuroblastoma patients treated with dinutuximab are associated with better EFS, presumably due to less interaction of glycans on dinutuximab. Citation Format: Mitchell B. Diccianni, Jenna Mielke, Richard Williams, Karen Messer, Fevzi Ozkaynak, Andrew L. Gilman, Arlene Naranjo, Wendy London, Paul M. Sondel, Julie Park, Alice L. Yu, Childrens Oncology Group. Natural antibodies to non-human glycans Neu5Gc and alpha-gal correlate with outcome of high-risk neuroblastoma patients treated with dinutuximab on COG ANBL0032 and ANBL0931 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-300.

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<p>CAI2, p16 and ARF expression in normal tissue compared to levels in fibroblasts (Supp Figure S1); Growth comparison of low vs. high passage NMB7 cells (Supp Figure S2); Growth comparison of low vs. high passage NMB7 cells in the absence of serum or presence of RA (Supp Figure S3).</p>