Genome erosion and evidence for an intracellular niche - exploring the biology of mycoplasmas in Atlantic salmon

Mycoplasmas are the smallest autonomously self-replicating life form on the planet. Members of this bacterial genus are known to parasitise a wide array of metazoans including vertebrates. Whilst much research has been significant targeted at parasitic mammalian mycoplasmas, very little is known about their role in other vertebrates. In the current study, we aim to explore the biology of mycoplasmas in Atlantic Salmon, a species of major significance for aquaculture, including cellular niche, genome size structure and gene content. Using fluorescent in-situ hybridisation (FISH), mycoplasmas were targeted in epithelial tissues across the digestive tract (stomach, pyloric caecum and midgut) from different development stages (eggs, parr, subadult) of farmed Atlantic salmon (Salmo salar), and we present evidence for an intracellular niche for some of the microbes visualised. Via shotgun metagenomic sequencing, a nearly complete, albeit small, genome (~0.57 MB) as assembled from a farmed Atlantic salmon subadult. Phylogenetic analysis of the recovered genome revealed taxonomic proximity to other salmon derived mycoplasmas, as well as to the human pathogen Mycoplasma penetrans (~1.36 Mb). We annotated coding sequences and identified riboflavin pathway encoding genes and sugar transporters, the former potentially consistent with micronutrient provisioning in salmonid development. Our study provides insights into mucosal adherence, the cellular niche and gene catalog of Mycoplasma in the gut ecosystem of the Atlantic salmon, suggesting a high dependency of this minimalist bacterium on its host. Further study is required to explore and functional role of Mycoplasma in the nutrition and development of its salmonid host.

Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar

In recent years, a wealth of studies has examined the relationships between a host and its microbiome across diverse taxa. Many studies characterize the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterized using 16S rRNA gene MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across life cycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we found declining taxonomic and functional microbial community richness as fish mature through different life cycle stages. Alongside neutral community models applied to wild fish, we suggest that declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We found a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma spp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes, such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered.IMPORTANCE A growing number of studies have examined variation in the microbiome to determine the role in modulating host health, physiology, and ecology. However, the ecology of host microbial colonization is not fully understood and rarely tested. The continued increase in production of farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated the need to unravel the potential adaptive function of the microbiome and to distinguish resident from transient gut microbes. Between gut compartments in a farmed system, we found a majority of operational taxonomic units (OTUs) that fit the neutral model, with Mycoplasma species among the key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed across gut compartments. Unlike previous studies, our results make detailed comparisons between fish from wild and farmed environments, while also providing insight into the ecological processes underpinning microbial community assembly in this ecologically and economically important species.

Modulation of Rb phosphorylation and antiproliferative response to palbociclib: the preoperative-palbociclib (POP) randomized clinical trial

Background

The cyclin-dependent kinase 4 (CDK4)/6 inhibitor Palbociclib is a new standard treatment in hormone-receptor positive breast cancer patients. No predictive biomarkers have been identified and no pharmacodynamics has properly been described so far.

Patients and methods

Patients with early-breast cancer were randomized 3 : 1 to oral palbociclib 125 mg daily for 14 days until the day before the surgery versus no treatment. Primary objective was antiproliferative response defined as a natural logarithm of Ki67 expression at day 15 below 1. Secondary end points were subgroups analyses and safety. Exploratory analyses included search for predictive biomarkers. Immunostainings (Ki67, RB, pRB, p16, pAKT, pER, pCDK2, CyclinD1), FISH (CCND1) and gene expression (GE) arrays were carried out at baseline and at surgery. In addition, activating PIK3CA and AKT1 mutations were assessed at baseline.

Results

74 patients were allocated to palbociclib and 26 to control. Most patients (93%) were hormone-receptor (HR)-positive, whereas 8% were HER2-positive. Palbociclib led to significantly more antiproliferative responses when compared with control (58% versus 12%, P < 0.001), and to a significantly higher Ki67 decrease (P < 0.001). In the HR-positive/HER2-negative subgroup, this antiproliferative effect was even more marked in the palbociclib arm when compared with control (70% versus 9%, P < 0.001). Palbociclib treatment led also to a significantly higher decrease from baseline in phospho-Rb when compared with control (P < 0.001). Among treated patients, changes in Ki67 correlated with changes in phospho-Rb (Spearman rank r = 0.41, P < 0.0001). GE analyses confirmed a major effect on proliferation and cell cycle genes. Among treated patients, CCNE2 expression was significantly more decreased in antiproliferative responders versus nonresponders (P = 0.006).

Conclusion

Short-term preoperative palbociclib decreases Ki67 in early-breast cancer patients. Early decrease of Rb phosphorylation correlates with drug's effect on cell proliferation and could potentially identify patients with primary resistance.

Clinical trial registration

NCT02008734.

Abstract P5-21-11: Benefit from palbociclib and fulvestrant based on previous fulvestrant and/or everolimus treatment. Based on a cohort of over 200 patients treated in a French compassionate program

Background: CDK4/6 inhibitors have been approved in the recent years for the treatment of advanced hormone receptor-positive breast cancer. For patients with resistance to previous endocrine therapy, the approval is based on the results of the PALOMA-3 trial testing palbociclib in addition to fulvestrant observing a progression-free survival (PFS) of 9.2 months. Nevertheless, in this study no previous treatment with fulvestrant was allowed and no information had been reported of efficacy after everolimus administration.

Patients and methods: We collected information from patients treated with palbociclib + fulvestrant in the context of a French compassionate access. We aimed at determining the benefit of this treatment in a real population to provide information about PFS in non-selected patients as well as efficacy of palbociclib and fulvestrant in patients previously treated with fulvestrant and/or everolimus. Median PFS were assessed by Kaplan-Meier survival analysis and compared with log-rank test.

Results: 206 patients were identified from 5 institutions. Mean age at treatment was 61 years (range 28 – 85). 55% presented with visceral disease. Lines at where palbociclib + fulvestrant treatment was administered were as follows: 1% 1st line, 8.3% 2nd line, 19.4% 3rd line, 13.6% 4th line, 10.2% 5th lignes and the remaining 47.6% had received ≥6 lines (median: 5 lines, range 1 to 15).

A total of 48% patients had previously been treated with fulvestrant. In a subsample of patient where the information was available (n=146), 67.8% patients had received everolimus in combination with endocrine therapy before palbociclib administration.

A total of 77 patients were still on treatment. Median PFS on fulvestrant-palbociclib treatment at the date of data cut-off was of 5.46 months (95% CI; 4.6 to 6.6 months). In a univariate analysis, there were no significant differences in median PFS for patients treated or not with previous fulvestrant, suggesting a potential effect of palbociclib to recover sensitivity to fulvestrant (4.7 months for previous fulvestrant treatment [95% CI 4.07 - 6.3 months] vs 6.1 months for no previous fulvestrant [95% CI; 6.3 - 8.02 months], p=0.3559).

Similarly, in the subsample of n=146 patients where information about previous everolimus treatment was available at data cut-off, benefit from palbociclib-fulvestrant was not affected by previous everolimus treatment (median PFS 4.8 months for previously treated [95% CI; 4.01 -7.8 months] vs 5.4 months for the untreated everolimus group [95% CI; 4.07 - 9.59 months], p=0.374).

Conclusions: Fulvestrant-palbociclib in the real life is associated with a median PFS of 5.5 months, which is below the results provided in the PALOMA-3 trial, reflecting a much more advanced population. Importantly, neither previous everolimus treatment nor fulvestrant therapy affected benefit from fulvestrant-palbociclib in this population in univariate analyses suggesting a potential recovery of fulvestrant sensitivity with CDK4/6 inhibition. Results from multivariate analyses and more detailed information about patients' characteristics and benefit from previous therapies will be provided.

Citation Format: Arnedos M, Rusquec P, Morelle M, Lebreton C, Jacquet E, Emile G, Aires J, Debled M, Frenel J-S, Augereau P, Cheaib B, Levy C, Bachelot T. Benefit from palbociclib and fulvestrant based on previous fulvestrant and/or everolimus treatment. Based on a cohort of over 200 patients treated in a French compassionate program [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-21-11.

Neoadjuvant chemotherapy (NACT) increases immune infiltration and programmed death-ligand 1 (PD-L1) expression in epithelial ovarian cancer (EOC)

Background

Lymphocytic infiltration at diagnosis is prognostic in EOC, however, the impact of NACT on tumour infiltrating lymphocytes (TILs) or PD-L1 expression remains poorly described.

Patients and methods

Patients with EOC and sequential samples (pre-NACT, post-NACT or relapse) were retrospectively identified. TILs were evaluated on whole sections; stromal TILs (sTILs) scored as percentage of stromal area with high sTILs defined as ≥50%; intra-epithelial TILs (ieTILs) scored semi-quantitatively (0-3) with high ieTILs ≥2. A smaller number were available for PD-L1 evaluation, cut-off for positivity was ≥5% staining.

Results

sTILs were detected in all tumours at diagnosis (range 2-90%, median 20%), with 22% (25/113) showing high sTILs. Among evaluable paired pre/post-NACT samples (N = 83), an overall increase in median sTILs from 20% to 30% was seen following NACT (P = 0.0005); individually the impact of NACT varied with sTILs increasing in 51% (42/83), decreasing in 25%, and stable in 24%. Post-NACT sTILs were predictive of platinum-free interval (PFI), patients with PFI ≥6 months had significantly higher post-NACT sTILs (sTILs 28% versus 18% for PFI <6 months, P = 0.026); pre-NACT sTILS were not predictive. At diagnosis, 23% showed high ieTILs, and following NACT 33% showed increasing ieTILs. Proportion of tumours with PD-L1-positive immune cells was 30% (15/50) pre-NACT and 53% (27/51) post-NACT (P = 0.026). Among paired tumours, 63% of PD-L1-negative tumours became positive after NACT, furthermore cisplatin induced PD-L1 expression in PD-L1-negative EOC cell lines. On multivariate analysis, high sTILs both pre- and post-NACT were independent prognostic factors for progression-free survival (PFS) (HR 0.49, P = 0.02 and HR 0.60, P = 0.05, respectively). No prognostic impact of ieTILs or PD-L1 expression was detected.

Conclusions

In EOC, sTILs levels are prognostic at diagnosis and remain prognostic after NACT. TILs and PD-L1 expression increase following NACT. Evaluation of immune parameters in the post-NACT tumour may help select patients for immunotherapy trials.