DRD1 suppresses cell proliferation and reduces EGFR activation and PD-L1 expression in NSCLC

Dopamine (DA) acts in various key neurological and physiological processes as both a neurotransmitter and circulating hormone. Over the past several decades, the DA signaling network has been shown to regulate the progression of several types of solid tumors, and considerable evidence has shown it is a druggable pathway in the cancer cell context. However, the specific activity and effect of these pathway components appears to be tissue-type and cell-context-dependent. In the present study, expression and methylation of dopamine receptor D1 (DRD1) were measured using RNA sequencing (RNAseq) and reverse transcription polymerase chain reaction (RT-PCR) in non-small cell lung cancer (NSCLC) samples, and validated using publicly available datasets, including The Cancer Genome Atlas (TCGA). In vitro and in vivo functional experiments were performed for cell proliferation and tumor growth, respectively. Mechanistic analyses of the transcriptome and kinome in DRD1-modulated cells informed further experiments, which characterized the effects on the epidermal growth factor receptor (EGFR) pathway and programmed cell death 1 ligand 1 (PD-L1) proteins. Through these experiments, we identified the DRD1 gene as a negative regulator of disease progression in NSCLC. We show that DRD1, as well as other DA pathway components, are expressed in normal human lung tissue, and that loss of DRD1 expression through promoter hypermethylation is a common feature in NSCLC patients and is associated with worse survival. At the cellular level, DRD1 affects proliferation by inhibiting the activation of EGFR and mitogen-activated protein kinase 1/2 (ERK1/2). Interestingly, we also found that DRD1 regulates the expression of PD-L1 in lung cancer cells. Taken together, these results suggest that DRD1 methylation may constitute a biomarker of poor prognosis in NSCLC patients while other components of this pathway could be targeted to improve response to EGFR- and PD-L1-targeted therapies.

Marine phycotoxin levels in shellfish-14 years of data gathered along the Italian coast

Along the Italian coasts, toxins of algal origin in wild and cultivated shellfish have been reported since the 1970s. In this study, we used data gathered by the Veterinary Public Health Institutes (IZS) and the Italian Environmental Health Protection Agencies (ARPA) from 2006 to 2019 to investigate toxicity events along the Italian coasts and relate them to the distribution of potentially toxic species. Among the detected toxins (OA and analogs, YTXs, PTXs, STXs, DAs, AZAs), OA and YTX were those most frequently reported. Levels exceeding regulatory limits in the case of OA (≤2,448 μg equivalent kg-1) were associated with high abundances of Dinophysis spp., and in the case of YTXs (≤22 mg equivalent kg-1) with blooms of Gonyaulax spinifera, Lingulodinium polyedra, and Protoceratium reticulatum. Seasonal blooms of Pseudo-nitzschia spp. occur all along the Italian coast, but DA has only occasionally been detected in shellfish at concentrations always below the regulatory limit (≤18 mg kg-1). Alexandrium spp. were recorded in several areas, although STXs (≤13,782 µg equivalent kg-1) rarely and only in few sites exceeded the regulatory limit in shellfish. Azadinium spp. have been sporadically recorded, and AZAs have been sometimes detected but always in low concentrations (≤7 µg equivalent kg-1). Among the emerging toxins, PLTX-like toxins (≤971 μg kg-1 OVTX-a) have often been detected mainly in wild mussels and sea urchins from rocky shores due to the presence of Ostreopsis cf. ovata. Overall, Italian coastal waters harbour a high number of potentially toxic species, with a few HAB hotspots mainly related to DSP toxins. Nevertheless, rare cases of intoxications have occurred so far, reflecting the whole Mediterranean Sea conditions.

Diverse eukaryotic phytoplankton from around the Marquesas Islands documented by combined microscopy and molecular techniques

Oceanic phytoplankton serve as a base for the food webs within the largest planetary ecosystem. Despite this, surprisingly little is known about species composition, function and ecology of phytoplankton communities, especially for vast areas of the open ocean. In this study we focus on the marine phytoplankton microflora from the vicinity of the Marquesas Islands in the Southern Pacific Ocean collected during the Tara Oceans expedition. Multiple samples from four sites and two depths were studied in detail using light microscopy, scanning electron microscopy, and automated confocal laser scanning microscopy. In total 289 taxa were identified, with Dinophyceae and Bacillariophyceae contributing 60% and 32% of taxa, respectively, to phytoplankton community composition. Notwithstanding, a large number of cells could not be assigned to any known species. Coccolithophores and other flagellates together contributed less than 8% to the species list. Observed cell densities were generally low, but at sites of high autotrophic biomass, diatoms reached the highest cell densities (1.26 × 10⁴ cells L^-1). Overall, 18S rRNA metabarcode-based community compositions matched microscopy-based estimates, particularly for the main diatom taxa, indicating consistency and complementarity between different methods, while the wide range of microscopy-based methods permitted several unknown and poorly studied taxa to be revealed and identified.

Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma

BACKGROUND

Squamous cell carcinoma (SqCC) is a subtype of non-small cell lung cancer for which patient prognosis remains poor. The extracellular matrix (ECM) is critical in regulating cell behavior; however, its importance in tumor aggressiveness remains to be comprehensively characterized.

METHODS

Multi-omics data of SqCC human tumor specimens was combined to characterize ECM features associated with initiation and recurrence. Penalized logistic regression was used to define a matrix risk signature for SqCC tumors and its performance across a panel of tumor types and in SqCC premalignant lesions was evaluated. Consensus clustering was used to define prognostic matreotypes for SqCC tumors. Matreotype-specific tumor biology was defined by integration of bulk RNAseq with scRNAseq data, cell type deconvolution, analysis of ligand-receptor interactions and enriched biological pathways, and through cross comparison of matreotype expression profiles with aging and idiopathic pulmonary fibrosis lung profiles.

RESULTS

This analysis revealed subtype-specific ECM signatures associated with tumor initiation that were predictive of premalignant progression. We identified an ECM-enriched tumor subtype associated with the poorest prognosis. In silico analysis indicates that matrix remodeling programs differentially activate intracellular signaling in tumor and stromal cells to reinforce matrix remodeling associated with resistance and progression. The matrix subtype with the poorest prognosis resembles ECM remodeling in idiopathic pulmonary fibrosis and may represent a field of cancerization associated with elevated cancer risk.

CONCLUSIONS

Collectively, this analysis defines matrix-driven features of poor prognosis to inform precision medicine prevention and treatment strategies towards improving SqCC patient outcome.

LKB1 phosphorylation and deactivation in lung cancer by NNAL, a metabolite of tobacco-specific carcinogen, in an isomer-dependent manner

LKB1 loss of function is one key oncogenic event in lung cancer. Clinical data suggest that LKB1 loss of function is associated with patients' smoking status. The responsible ingredients and molecular mechanisms in tobacco for LKB1 loss of function, however, are not defined. In this study, we reported that NNAL, a major metabolite of a tobacco-specific carcinogen NNK, induces LKB1 phosphorylation and its loss of function via the β-AR/PKA signaling pathway in an isomer-dependent manner in human lung cancer cells. NNAL exposure also resulted in enhanced lung cancer cell migration and chemoresistance in an LKB1-dependent manner. A 120-day NNAL exposure in lung cancer cells, mimicking its chronic exposure among smokers, resulted in more prominent LKB1 phosphorylation, cell migration, and chemoresistance even in the absence of NNAL, indicating the long-lasting LKB1 loss of function although such an effect eventually disappeared after NNAL was removed for two months. These observations were confirmed in a lung cancer xenograft model. More importantly, human lung cancer tissues revealed elevated LKB1 phosphorylation in comparison to the paired normal lung tissues. These results suggest that LKB1 loss of function in human lung cancer could be extended to its phosphorylation, which may be mediated by NNAL from tobacco smoke in an isomer-dependent manner via the β-AR/PKA signaling pathway.

Phenological segregation suggests speciation by time in the planktonic diatom Pseudo‐nitzschia allochrona sp. nov

The processes leading to the emergence of new species are poorly understood in marine plankton, where weak physical barriers and homogeneous environmental conditions limit spatial and ecological segregation. Here, we combine molecular and ecological information from a long‐term time series and propose Pseudo‐nitzschia allochrona, a new cryptic planktonic diatom, as a possible case of speciation by temporal segregation. The new species differs in several genetic markers (18S, 28S and ITS rDNA fragments and rbcL) from its closest relatives, which are morphologically very similar or identical, and is reproductively isolated from its sibling species P. arenysensis. Data from a long‐term plankton time series show P. allochrona invariably occurring in summer–autumn in the Gulf of Naples, where its closely related species P. arenysensis, P. delicatissima, and P. dolorosa are instead found in winter–spring. Temperature and nutrients are the main factors associated with the occurrence of P. allochrona, which could have evolved in sympatry by switching its phenology and occupying a new ecological niche. This case of possible speciation by time shows the relevance of combining ecological time series with molecular information to shed light on the eco‐evolutionary dynamics of marine microorganisms.

Photoperiod-driven rhythms reveal multi-decadal stability of phytoplankton communities in a highly fluctuating coastal environment

Phytoplankton play a pivotal role in global biogeochemical and trophic processes and provide essential ecosystem services. However, there is still no broad consensus on how and to what extent their community composition responds to environmental variability. Here, high-frequency oceanographic and biological data collected over more than 25 years in a coastal Mediterranean site are used to shed light on the temporal patterns of phytoplankton species and assemblages in their environmental context. Because of the proximity to the coast and due to large-scale variations, environmental conditions showed variability on the short and long-term scales. Nonetheless, an impressive regularity characterised the annual occurrence of phytoplankton species and their assemblages, which translated into their remarkable stability over decades. Photoperiod was the dominant factor related to community turnover and replacement, which points at a possible endogenous regulation of biological processes associated with species-specific phenological patterns, in analogy with terrestrial plants. These results highlight the considerable stability and resistance of phytoplankton communities in response to different environmental pressures, which contrast the view of these organisms as passively undergoing changes that occur at different temporal scales in their habitat, and show how, under certain conditions, biological processes may prevail over environmental forcing.

A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.

A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients

Deciphering the post-transcriptional mechanisms (PTM) regulating gene expression is critical to understand the dynamics underlying transcriptomic regulation in cancer. Alternative polyadenylation (APA)-regulation of mRNA 3'UTR length by alternating poly(A) site usage-is a key PTM mechanism whose comprehensive analysis in cancer remains an important open challenge. Here we use a method and analysis pipeline that sequences 3'end-enriched RNA directly to overcome the saturation limitation of traditional 5'-3' based sequencing. We comprehensively map the APA landscape in lung cancer in a cohort of 98 tumor/non-involved tissues derived from European American and African American patients. We identify a global shortening of 3'UTR transcripts in lung cancer, with notable functional implications on the expression of both coding and noncoding genes. We find that APA of non-coding RNA transcripts (long non-coding RNAs and microRNAs) is a recurrent event in lung cancer and discover that the selection of alternative polyA sites is a form of non-coding RNA expression control. Our results indicate that mRNA transcripts from EAs are two times more likely than AAs to undergo APA in lung cancer. Taken together, our findings comprehensively map and identify the important functional role of alternative polyadenylation in determining transcriptomic heterogeneity in lung cancer.

Perceived global increase in algal blooms is attributable to intensified monitoring and emerging bloom impacts

Global trends in the occurrence, toxicity and risk posed by harmful algal blooms to natural systems, human health and coastal economies are poorly constrained, but are widely thought to be increasing due to climate change and nutrient pollution. Here, we conduct a statistical analysis on a global dataset extracted from the Harmful Algae Event Database and Ocean Biodiversity Information System for the period 1985-2018 to investigate temporal trends in the frequency and distribution of marine harmful algal blooms. We find no uniform global trend in the number of harmful algal events and their distribution over time, once data were adjusted for regional variations in monitoring effort. Varying and contrasting regional trends were driven by differences in bloom species, type and emergent impacts. Our findings suggest that intensified monitoring efforts associated with increased aquaculture production are responsible for the perceived increase in harmful algae events and that there is no empirical support for broad statements regarding increasing global trends. Instead, trends need to be considered regionally and at the species level.

Toxic marine microalgae and noxious blooms in the Mediterranean Sea: A contribution to the Global HAB Status Report

We review the spatial distribution of toxic marine microalgal species and the impacts of all types of harmful algal events (Harmful Algal Blooms, HABs) in the Mediterranean Sea (MS), including the Black Sea, the Sea of Marmara, coastal lagoons and transitional waters, based on two databases compiled in the Ocean Biogeographic Information System (OBIS). Eighty-four potentially toxic species have been detected in the MS (2,350 records), of which 16 described from these waters between 1860 and 2014 and a few suspected to have been introduced. More than half of these species (46) produce toxins that may affect human health, the remainders ichthyotoxic substances (29) or other types of toxins (9). Nevertheless, toxicity-related events are not frequent in the MS (308 records in 31 years), and mainly consist of impacts on aquaculture, caused by the dinoflagellates Dinophysis and Alexandrium, along with a few actual shellfish poisoning cases. Pseudo-nitzschia blooms are widespread, but domoic acid in shellfish rarely exceeds regulatory levels. Fish kills are probably less sporadic than reported, representing a problem at a few places along the southern MS coasts and in the Ebro River Delta. Since the last decade of the 20^th century, blooms of the benthic dinoflagellates Ostreopsis cf. ovata have regularly occurred all along rocky shores of the MS, at times with human health problems caused by toxic aerosol. New records of Gambierdiscus and Fukuyoa, until now reported for the westernmost and easternmost MS coasts, raise concerns about the risk of ciguatera, a syndrome so far known only for subtropical and tropical areas. Recent discoveries are the dinoflagellates Vulcanodinium rugosum, responsible for the presence of pinnatoxins in French lagoons' shellfish, and the azaspiracid-producers Azadinium spp. Mucilages and discolorations have a major impact on tourism in summer. Reports of toxic species and HABs have apparently increased in the MS over the last half century, which is likely related to the increased awareness and monitoring operations rather than to an actual increase of these phenomena. Indeed, while the case of Ostreopsis appears as a sudden upsurge rather than a trend, no actual increase of toxic or noxious events has so far emerged in intensively studied areas, such as the French and Spanish coasts or the Adriatic Sea. Moreover, some cases of decrease are reported, e.g., for Alexandrium minutum blooms disappearing from the Harbour of Alexandria. Overall, main HAB risks derive from cases of massive development of microalgal biomass and consequent impacts of reduced coastal water quality on tourism, which represents the largest part of the marine economy along the MS coasts.

Global harmful algal bloom status reporting

An extremely variegated picture of harmful algal bloom types and their socio-economic impacts at the regional and subregional scale emerges from the overviews presented in this special issue. The diversity of the HAB events parallels that of the causative species, which show different ranges and ecological characteristics, as well as highly variable responses to environmental changes. The intensity and frequency of specific blooms vary at regional and local scale, with increasing or decreasing trends and sudden occasional outbursts, but with no general uniform trend that can be discerned from that of increased observational efforts. In many cases intoxications and other adverse effects on human health are kept under control through increased monitoring activities, but impacts on human activities such as aquaculture, fishery, use of natural marine resources and tourism keep on posing economic activities at risk in many regions.

Whole-Exome Profiling of NSCLC Among African Americans

INTRODUCTION

Lung cancer incidence is higher among African Americans (AAs) compared with European Americans (EAs) in the United States, especially among men. Although significant progress has been made profiling the genomic makeup of lung cancer in EAs, AAs continue to be underrepresented. Our objective was to chart the genome-wide landscape of somatic mutations in lung cancer tumors from AAs.

METHODS

In this study, we used the whole-exome sequencing of 82 tumor and noninvolved tissue pairs from AAs. Patients were selected from an ongoing case-control study conducted by the National Cancer Institute and the University of Maryland.

RESULTS

Among all samples, we identified 178 significantly mutated genes (p < 0.05), five of which passed the threshold for false discovery rate (p < 0.1). In lung adenocarcinoma (LUAD) tumors, mutation rates in STK11 (p = 0.05) and RB1 (p = 0.008) were significantly higher in AA LUAD tumors (25% and 13%, respectively) compared with The Cancer Genome Atlas EA samples (14% and 4%, respectively). In squamous cell carcinomas, mutation rates in STK11 (p = 0.002) were significantly higher among AA (8%) than EA tumors from The Cancer Genome Atlas (1%). Integrated somatic mutation data with CIBERSORT (Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts) data analysis revealed LUAD tumors from AAs carrying STK11 mutations have decreased interferon signaling.

CONCLUSIONS

Although a considerable degree of the somatic mutation landscape is shared between EAs and AAs, discrete differences in mutation frequency in potentially important oncogenes and tumor suppressors exist. A better understanding of the molecular basis of lung cancer in AA patients and leveraging this information to guide clinical interventions may help reduce disparities.

Abstract PO-234: Relationship between increased concentrations of circulating chemokines and population differences in tumor biology

Genetic ancestry is a significant determinant of multiple aspects of tumor biology, immunity, and inflammatory responses. In lung cancer, in addition to increased incidence in African American (AA) men compared with other racial and ethnic groups in the US, differences in tumor biology between AAs and European Americans (EAs) have been identified. Natural selection is a strong driver of gene selection leading to population differences that can be linked to geographic and genetic ancestry. A classic example involves the Duffy antigen receptor for chemokines, also known as DARC. Individuals with African ancestry are more likely to lack DARC expression on their red blood cells (also known as Duffy null), as this confers resistance to malaria. Loss of erythrocyte expression of DARC is associated with increased circulating chemokine levels in the CXCR and CCR families as DARC serves as a dummy chemokine reservoir. Additionally, Duffy null individuals have lower circulating neutrophils, known as benign ethnic neutropenia. However, loss of DARC expression is exclusive to erythrocytes in Duffy null individuals. As venous endothelial cells and tumor cells also express DARC, we questioned whether the increased circulating bioavailability of DARC ligands in AAs led to increased DARC- dependent signaling in the tumor microenvironment (TME) of AA lung cancer patients. DARC expression on tumor cells is associated with increased aggressiveness and invasion, and endothelial cells have been shown to transcytose DARC ligands into the luminal space. As DARC ligands are associated with angiogenesis and granulocyte recruitment, we hypothesized that tumors of AAs would present with increased blood vessel invasion and granulocyte recruitment to the TME. Using the Somalogic multiplex proteomic assay, we observed significantly elevated levels of the ELR+ CXCR chemokines, with the exception of IL-8 (CXCL8), in serum samples from AA healthy control and stage 1 lung adenocarcinoma patients compared with EAs (samples from the NCI-UMD Case-Control Study), We did not find any evidence of increased angiogenesis as measured by CD31 immunohistochemical staining in AA patients (n= 39) compared with EA patients (n= 107). Immune cell composition did not differ between AAs and EAs as measured by CIBERSORT analysis in both healthy controls and patients between AAs and EAs. Therefore, while AAs have significantly higher levels of circulating DARC ligands compared with EAs, they do not appear to contribute to increased DARC-dependent signaling in normal and tumor lung tissue microenvironment in AAs.

Citation Format: Sheryse Taylor, Julian Candia, Adriana Zingone, John Tsang, Brid Ryan. Relationship between increased concentrations of circulating chemokines and population differences in tumor biology [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-234.

Do plankton reflect the environmental quality status? The case of a post-industrial Mediterranean Bay

While the effects of industrial contamination in coastal areas may persist for years in benthos communities, plankton should not show permanent impairments because of their high spatial dynamics, fast turnover times and pronounced seasonality. To test this hypothesis, in 2019 we conducted five surveys in the Bay of Pozzuoli (Gulf of Naples, Mediterranean Sea), in front of a dismissed steel factory and in the adjacent inshore coastal waters. High seasonal variability was observed for bacteria, phytoplankton and mesozooplankton, whereas plankton spatial gradients were relatively smooth during each survey. Plankton biomass and diversity did not reveal any effects of past industrial activities not even at the innermost stations of the Bay, which however showed some signals of present anthropogenic pressure. Hydrodynamic and morphological features likely play a prominent role in maintaining a relatively good status of the plankton of the Bay, which hints at the relevance of coastal circulation and meteorological dynamics to revitalize areas impacted by human activities.

Abstract 1265: The effects of ancestry and histology on the lung tumor methylome

Methylation-based biomarkers can provide molecular insight on the contribution of ancestry and histology to lung tumor biology. Loss of global methylation is a benchmark of aging and a signal of declining biological maintenance. In addition to aging, global loss of methylation occurs in response to some cancer-promoting exposures, including tobacco use. Reduced levels of global DNA methylation are associated with increased risk of several cancers, including lung. In lung tumors, global DNA hypomethylation is often associated with a more aggressive diseases and shorter survival time.

Several studies have identified population-level differences in global methylation present at birth. Additionally, gender and ancestry influence DNA methylation age (DNAm) and may predispose some individuals to accelerated aging. We hypothesized that differences in global hypomethylation and accelerated aging may contribute to differences in lung tumor biology by genetic ancestry. Therefore, we investigated methylome differences between European Americans (EA) and African Americans (AA) from the NCI-Maryland Case Control Study, which is overrepresented with AA patients (~40%) from the Baltimore area. We assessed lung tumor and paired non-involved adjacent tissue (NAT) methylation (n = 77 EA, n = 39 AA) using the Illumina EPIC methylation array. We used the Repetitive Element Methylation Prediction (REMP) package in R to identify roughly 20,000 predicted LINE-1 CpG's. We observed significantly decreased LINE-1 methylation in tumor tissue compared with NAT in both AA and EA. Additionally, among tumor samples we observed significantly decreased LINE-1 methylation in AA LUSC samples compared to EA LUSC, with only modest differences between AA LUAD and EA LUAD. In addition to decreased levels, LINE-1 methylation in AA LUSC tumors also had the greatest heterogeneity within CpG's of the same sample and between other AA LUSC samples. We observed accelerated aging (increased DNAm relative to chronological age) in 57/67 EA NAT samples and 28/38 AA NAT samples with no significant differences in age acceleration between ancestry or histology.

Our results show global hypomethylation of LINE-1 is a distinctive feature of LUSC in AA compared to EA, which is consistent with the enhanced genomic instability observed in AA LUSC relative to EA LUSC. We also observed accelerated aging in the vast majority of the NAT samples, which may implicate accelerated age with lung cancer risk. Future analysis will work towards completing a comprehensive analysis of the epigenetic landscape of lung cancer in AA and EA patients. We plan to study the relationship between global hypomethylation and genetic variants, smoking behaviors, and patient survival.

Citation Format: Emily L. Rossi, Isaac Zhao, Rony F. Arauz, Adriana Zingone, Bríd M. Ryan. The effects of ancestry and histology on the lung tumor methylome [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1265.

Global Trends in Marine Plankton Diversity across Kingdoms of Life

The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21^st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation.

Video Abstract

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Most epipelagic planktonic groups exhibit a poleward decline of diversity

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No latitudinal diversity gradient was observed below the photic zone

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Temperature emerges as the best predictor of epipelagic plankton diversity

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Global warming may increase plankton diversity, particularly at high latitudes

Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity

High-throughput sequencing (HTS) metabarcoding is commonly applied to assess phytoplankton diversity. Usually, haplotypes are grouped into operational taxonomic units (OTUs) through clustering, whereby the resulting number of OTUs depends on chosen similarity thresholds. We applied, instead, a phylogenetic approach to infer taxa among 18S rDNA V4-metabarcode haplotypes gathered from 48 time-series samples using the marine planktonic diatoms Chaetoceros and Bacteriastrum as test case. The 73 recovered taxa comprised both solitary haplotypes and polytomies, the latter composed each of a highly abundant, dominant haplotype and one to several minor, peripheral haplotypes. The solitary and dominant haplotypes usually matched reference sequences, enabling species assignation of taxa. We hypothesise that the super-abundance of reads in dominant haplotypes results from the homogenization effect of concerted evolution. Reads of populous peripheral haplotypes and dominant haplotypes show comparable distribution patterns over the sample dates, suggesting that they are part of the same population. Many taxa revealed marked seasonality, with closely related ones generally showing distinct periodicity, whereas others occur year-round. Phylogenies inferred from metabarcode haplotypes enable delineation of biologically meaningful taxa, whereas OTUs resulting from clustering algorithms often deviate markedly from such taxa.

Higher prevalence of homologous recombination deficiency in tumors from African Americans versus European Americans

To improve our understanding of longstanding disparities in incidence and mortality in lung cancer across ancestry, we performed a systematic comparative analysis of molecular features in tumors from African Americans (AAs) and European Americans (EAs). We find that lung squamous cell carcinoma tumors from AAs exhibit higher genomic instability-the proportion of non-diploid genome-aggressive molecular features such as chromothripsis and higher homologous recombination deficiency (HRD). In The Cancer Genome Atlas, we demonstrate that high genomic instability, HRD and chromothripsis among tumors from AAs is found across many cancer types. The prevalence of germline HRD (that is, the total number of pathogenic variants in homologous recombination genes) is higher in tumors from AAs, suggesting that the somatic differences observed have genetic ancestry origins. We also identify AA-specific copy-number-based arm-, focal- and gene-level recurrent features in lung cancer, including higher frequencies of PTEN deletion and KRAS amplification. These results highlight the importance of including under-represented populations in genomics research.

Habitat Heterogeneity and Connectivity: Effects on the Planktonic Protist Community Structure at Two Adjacent Coastal Sites (the Lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) Revealed by Metabarcoding

The Lagoon of Venice (LoV) and the Gulf of Venice (GoV), two adjacent coastal Long Term Ecological Research (LTER) sites in the northern Adriatic Sea, represent a transitional/marine coupled ecosystem under the influence of regional and local factors. In this study, these sites were sampled on four dates from April 2016 to February 2017 for environmental DNA and relevant abiotic variables, aiming to assess the relative importance of habitat heterogeneity and connectivity in structuring the protist community. High Throughput Sequencing of V4-18S rRNA gene from 56 samples collected at seven stations produced ca 6 million reads, grouped into 7,336 Operational Taxonomic Units (OTUs) at 97% similarity, which were affiliated to protists belonging to 34 taxonomic groups. The whole community was dominated by Bacillariophyta, especially in spring-summer in the LoV, and by Dinophyta, mainly in the GoV. Ciliophora, Syndiniales, and Cryptophyceae were the next more abundant groups. The community structure varied across the seasons and was different in the two ecosystems, which shared 96% of the reads but showed a high proportion of OTUs distributed preferentially in one of the two sites (specialists) and a different partitioning of trophic categories. GoV specialists were mainly Dinophyceae (>56%), followed by Syndiniales and Bacillariophyta, while the LoV specialists were distributed among several groups, including Bacillariophyta, Syndiniales, Ciliophora, Cryptophyceae, and Trebouxiophyceae. The main abiotic drivers of the differences between protist communities were salinity and temperature, which however explained a minor part of the variance (17%), pointing at a higher relevance of biotic factors and inter-taxa relationships. This was more evident in the LoV, where the network analysis highlighted a higher number of OTUs’ connections than in the GoV. Overall, the metabarcoding approach allowed to depict the composition of the whole protist community in the lagoon and adjacent coastal waters with high resolution, revealing many taxa so far not reported in the area. In addition, despite no clear barrier to dispersal processes, differences in the relative abundance and temporal variability of local protist communities indicate that environmental heterogeneity, in these adjacent and connected ecosystems, can be strong enough to allow for ecological segregation.

Relationship between West African ancestry with lung cancer risk and survival in African Americans

PURPOSE

African Americans, especially men, have a higher incidence of lung cancer compared with all other racial and ethnic groups in the US. Self-reported race is frequently used in genomic research studies to capture an individual's race or ethnicity. However, it is clear from studies of genetic admixture that human genetic variation does not segregate into the same biologically discrete categories as socially defined categories of race. Previous studies have suggested that the degree of West African ancestry among African Americans can contribute to cancer risk in this population, though few studies have addressed this question in lung cancer.

METHODS

Using a genetic ancestry panel of 100 SNPs, we estimated West African, European, and Native American ancestry in 1,407 self-described African Americans and 2,413 European Americans.

RESULTS

We found that increasing West African ancestry was associated with increased risk of lung cancer among African American men (OR_{Q5 vs Q1} = 2.55 (1.45-4.48), p = 0.001), while no association was observed in African American women (OR_{Q5 vs Q1} = 0.90 (0.51-1.59), p = 0.56). This relationship diminished following adjustment for income and education.

CONCLUSIONS

Genetic ancestry is not a major contributor to lung cancer risk or survival disparities.

Ocurrence of Ostreopsis in two temperate coastal bays (SW iberia): Insights from the plankton

The benthic genus Ostreopsis contains toxic-bloom forming species and is an important cause of concern in warm-temperate and tropical waters. On the coast of Portugal, NE Atlantic, the occurrence of Ostreopsis cf. siamensis and Ostreopsis cf. ovata has been reported since 2008 and 2011, respectively. This work aims to understand the favorable conditions for high concentrations of Ostreopsis cells in the plankton at two sites, Lagos and Lisbon Bays, located in the South and West coast of Portugal, respectively. This study is based on weekly Ostreopsis abundance data in the plankton, from 2011 to 2017, daily satellite and in situ sea surface temperature (SST), and meteorological and sea state parameters, namely wind stress and significant wave height. The molecular identification of local Ostreopsis spp. is also presented. The maximum cell densities occur between late-summer and autumn. The distribution range of Ostreopsis cf. ovata is restricted to the South coast, while Ostreopsis cf. siamensis has a wider distribution range, being also present on the West coast. In the study period, there was only one occurrence of Ostreopsis spp., in Lagos Bay, with concentrations within the alert phase of monitoring. In Lagos Bay, high Ostreopsis spp. concentrations were related with positive SST anomalies. These high concentrations were often recorded after a period of almost 2-weeks to more than 4-weeks of low sea state (<0.6 m), followed by short time events of onshore wind and moderate waves (0.6-1 m). The former conditions are interpreted as favoring bloom development on the substrate and the latter as causing the re-suspension of Ostreopsis cells in the water column. In Lisbon Bay, O. cf. siamensis occurred in the plankton in few occasions and no clear relation could be established with the studied environmental variables. It is here hypothesized that the recent records of O. cf. siamensis in Lisbon Bay may correspond to an early colonization stage of an invasion process. Knowledge gained on Ostreopsis dynamics along the Portuguese coast can be used for both the improvement of benthic harmful algal blooms (BHABs) monitoring in the region and as a basis to design forecasting models.

Time series and beyond: multifaceted plankton research at a marine Mediterranean LTER site

Plankton are a pivotal component of the diversity and functioning of coastal marine ecosystems. A long time-series of observations is the best tool to trace their patterns and variability over multiple scales, ultimately providing a sound foundation for assessing, modelling and predicting the effects of anthropogenic and natural environmental changes on pelagic communities. At the same time, a long time-series constitutes a formidable asset for different kinds of research on specific questions that emerge from the observations, whereby the results of these complementary studies provide precious interpretative tools that augment the informative value of the data collected. In this paper, we review more than 140 studies that have been developed around a Mediterranean plankton time series gathered in the Gulf of Naples at the station LTER-MC since 1984. These studies have addressed different topics concerning marine plankton, which have included: i) seasonal patterns and trends; ii) taxonomic diversity, with a focus on key or harmful algal species and the discovery of many new taxa; iii) molecular diversity of selected species, groups of species or the whole planktonic community; iv) life cycles of several phyto- and zooplankton species; and v) interactions among species through trophic relationships, parasites and viruses. Overall, the products of this research demonstrate the great value of time series besides the record of fluctuations and trends, and highlight their primary role in the development of the scientific knowledge of plankton much beyond the local scale.

Circulating Inflammation Proteins Associated With Lung Cancer in African Americans

INTRODUCTION

Lung cancer incidence is higher among African Americans (AAs) compared with European Americans (EAs) in the United States. We and others have previously shown a relationship between immune and inflammation proteins with lung cancer in EAs. Our aim was to investigate the etiologic relationship between inflammation and lung cancer in AAs.

METHODS

We adopted a two-stage, independent study design (discovery cases, n = 316; control cases, n = 509) (validation cases, n = 399; control cases, n = 400 controls) and measured 30 inflammation proteins in blood using Meso Scale Discovery V- PLEX multiplex assays.

RESULTS

We identified and validated 10 proteins associated with lung cancer in AAS, some that were common between EAs and AAs (C-reactive proteins [OR: 2.90; 95% confidence interval (CI): 1.99-4.22], interferon γ [OR: 1.55; 95% CI: 1.10-2.19], interleukin 6 [OR: 6.28; 95% CI: 4.10-9.63], interleukin 8 [OR: 2.76; 95% CI: 1.92-3.98]) and some that are only observed among AAs (interleukin 10 [OR: 1.69; 95% CI: 1.20-2.38], interleukin 15 [OR: 2.83; 95% CI: 1.96-4.07], interferon gamma-induced protein 10 [OR: 1.54; 95% CI: 1.09-2.18], monocyte chemotactic protein-4 [OR: 0.54; 95% CI: 0.38-0.76], macrophage inflammatory protein-1 alpha [OR: 1.57; 95% CI: 1.12-2.21], and tumor necrosis factor β [OR: 0.52; 95% CI: 0.37-0.74]). We did not find evidence that either menthol cigarette smoking or global genetic ancestry drove these population differences.

CONCLUSIONS

Our results highlight a distinct inflammation profile associated with lung cancer in AAs compared with EAs. These data provide new insight into the etiology of lung cancer in AAs. Further work is needed to understand what drives this relationship with lung cancer and whether these proteins have utility in the setting of early diagnosis.

Elevated Serum Megakaryocyte Potentiating Factor as a Predictor of Poor Survival in Patients with Mesothelioma and Primary Lung Cancer

Background

There is an urgent need for a companion assay to work with mesothelin-targeted therapeutic agents and for noninvasive and accurate prognostication of malignant mesothelioma (MM) patients. We report the development and validation of a blood-based assay for megakaryocyte potentiating factor (MPF) and the evaluation of its effectiveness for prognosis in MM and lung cancer patients.

Methods

Using electrochemiluminescence technology, we developed a sensitive MPF assay and performed both analytical and clinical validations. Further, the effectiveness of the MPF assay in predicting prognosis was evaluated for 95 MM and 272 lung cancer patients.

Results

We performed comprehensive analytical and clinical validation, including precision and accuracy, interference, preanalytical variables, sensitivity, and specificity for mesothelioma. In MM patients, increased serum MPF is a predictor of poor survival with a hazard ratio (HR) = 2.46 (log-rank P = 0.003; n = 95). In refractory MM patients, increased MPF is a strong predictor of poor outcome with an HR = 6.12 (log-rank P = 0.0007; n = 57). In a lung cancer patient cohort, increased MPF is a predictor of poor survival, with an HR = 1.57 (log-rank P = 0.003; n = 272).

Conclusions

The MPF assay has robust technical characteristics, with strong analytic and clinical validation. Clinical studies indicate that increased serum MPF is a predictor of poor survival for MM patients, throughout the course of the disease. Increased MPF is also associated with poor overall survival for patients with newly diagnosed lung cancer.

Relationship between Circulating Inflammation Proteins and Lung Cancer Diagnosis in the National Lung Screening Trial

BACKGROUND

Previously, we observed a strong relationship between circulating serum inflammation proteins in relation to lung cancer diagnosis and risk, both in case-control and prospective cohorts. Low-dose computed tomography (LDCT) screening has a high prevalence of false-positive nodules, thus companion noninvasive biomarkers that can distinguish between benign and malignant nodules could have clinical utility and positive impact on patient outcomes.

METHODS

We conducted a nested case-control study within the National Lung Screening Trial. Concentrations of 30 inflammation proteins were measured on plasma samples of 262 cases and 528 controls using a highly sensitive and analytically validated electrochemiluminescence V-PLEX immunoassay.

RESULTS

Comparing the fourth quartile with the first quartile, we found increased IFNγ and IL12/IL23p40 associated with increased odds of a lung cancer diagnosis [OR 1.89, 95% confidence intervals (CI), 1.16-3.09; OR 2.49, 95% CI, 1.46-4.23, respectively]. Confirming our previous observations, we also detected a relationship between increased IL6, IL8, and C-reactive protein (CRP) with lung cancer diagnosis. These relationships were significant after adjustment for age, gender, race, smoking, body mass index (BMI), family history of lung cancer, and previous diagnoses of inflammatory conditions. However, none of these proteins could distinguish between a benign and malignant lung nodule (IL6: OR 1.25, 95% CI, 0.59-2.64; IL8: OR 1.40, 95% CI, 0.70-2.81; CRP: OR 0.98, 95% CI, 0.45-2.12).

CONCLUSIONS

We have discovered new associations for IFNγ and IL12/IL23p40 with lung cancer but have no evidence that these proteins can distinguish between benign and malignant lung nodules.

IMPACT

Circulating inflammation proteins are unlikely to have utility as companion LDCT biomarkers.

Comparative Transcriptome Profiling Reveals Coding and Noncoding RNA Differences in NSCLC from African Americans and European Americans

Purpose: To determine whether racial differences in gene and miRNA expression translates to differences in lung tumor biology with clinical relevance in African Americans (AAs) and European Americans (EAs).Experimental Design: The NCI-Maryland Case Control Study includes seven Baltimore City hospitals and is overrepresented with AA patients (∼40%). Patients that underwent curative NSCLC surgery between 1998 and 2014 were enrolled. Comparative molecular profiling used mRNA (n = 22 AAs and 19 EAs) and miRNA (n = 42 AAs and 55 EAs) expression arrays to track differences in paired fresh frozen normal tissues and lung tumor specimens from AAs and EAs. Pathway enrichment, predicted drug response, tumor microenvironment infiltration, cancer immunotherapy antigen profiling, and miRNA target enrichment were assessed.Results: AA-enriched differential gene expression was characterized by stem cell and invasion pathways. Differential gene expression in lung tumors from EAs was primarily characterized by cell proliferation pathways. Population-specific gene expression was partly driven by population-specific miRNA expression profiles. Drug susceptibility predictions revealed a strong inverse correlation between AA resistance and EA sensitivity to the same panel of drugs. Statistically significant differences in M1 and M2 macrophage infiltration were observed in AAs (P < 0.05); however, PD-L1, PD-L2 expression was similar between both.Conclusions: Comparative transcriptomic profiling revealed clear differences in lung tumor biology between AAs and EAs. Increased participation by AAs in lung cancer clinical trials are needed to integrate, and leverage, transcriptomic differences with other clinical information to maximize therapeutic benefit in both AAs and EAs. Clin Cancer Res; 23(23); 7412-25. ©2017 AACR.

Abstract 5850: Nrf2-mediated oxidative stress response is altered during acquired resistance to the proteasome inhibitor, oprozomib, in multiple myeloma

Multiple myeloma (MM) is a hematologic neoplasm characterized by malignant proliferation of plasma cells in the bone marrow. Proteasome inhibitors are widely used in treatment regimens for MM. Although initial responses to PI (e.g., bortezomib, carfilzomib) treatments have been promising, patients often develop resistance and become refractory to disease. Understanding molecular alterations in signaling cascades influenced by proteasome inhibitors and mechanisms underlying acquired resistance is needed. In this study, we have established a clinically relevant oproxomib-resistant subline (KMS28BMONYX) of the MM cell line KMS28BM. The KMS28BMONYX cell line is pan-resistant to PIs with a 10-fold increase in IC50 for oprozomib as compared to the parental line. To identify genes involved in modulating drug resistance, we analyzed gene expression profiles of both parental and resistant cell lines using the Affymetrix GeneChip Human Genome U133 Plus 2.0 array. Ingenuity Pathway Analysis of microarray data comparing the parental and resistant cells revealed an acute dependence on stress response proteins to maintain PI-resistance. Activation of nuclear factor-erythroid 2 (NF-E2)-related factor 2 (Nrf2; gene symbol NFE2L2) coupled with elevated levels of sequestosome 1/p62 (SQSTM1/p62) were prominent features of the KMS28BMONYX cell line. Altered levels of SQSTM1 correlated with resistance to oprozomib in several MM cell lines. Simultaneously, the KMS28BMONYX cell line showed increased expression of MYC and MCL1. Oprozomib treatment stabilized c-Myc expression in the KMS28BMONYX line. The Champion ChiP Transcription Factor Search Portal database DECODE predicted two c-Myc transcription factor binding sites in the SQSTM1 promoter. CHIP-seq data for MYC in MM1s cells also indicates strong binding in the promoter region of SQSTM1. Our data suggest that therapies targeting the SQSTM1/p62-Nrf2 pathway may help overcome proteasome inhibitor resistance in refractory MM patients.

Citation Format: Snehal M. Gaikwad, Adriana Zingone, Aleksandra Michalowski, Susana Najera, Anaisa Quintanilla-Artega, Sayeh Gorjifard, John Simmons, Nick Watson, Ola Landgren, Jing Huang, Beverly Mock. Nrf2-mediated oxidative stress response is altered during acquired resistance to the proteasome inhibitor, oprozomib, in multiple myeloma [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 5850.

Plankton dynamics across the freshwater, transitional and marine research sites of the LTER-Italy Network. Patterns, fluctuations, drivers

A first synoptic and trans-domain overview of plankton dynamics was conducted across the aquatic sites belonging to the Italian Long-Term Ecological Research Network (LTER-Italy). Based on published studies, checked and complemented with unpublished information, we investigated phytoplankton and zooplankton annual dynamics and long-term changes across domains: from the large subalpine lakes to mountain lakes and artificial lakes, from lagoons to marine coastal ecosystems. This study permitted identifying common and unique environmental drivers and ecological functional processes controlling seasonal and long-term temporal course. The most relevant patterns of plankton seasonal succession were revealed, showing that the driving factors were nutrient availability, stratification regime, and freshwater inflow. Phytoplankton and mesozooplankton displayed a wide interannual variability at most sites. Unidirectional or linear long-term trends were rarely detected but all sites were impacted across the years by at least one, but in many case several major stressor(s): nutrient inputs, meteo-climatic variability at the local and regional scale, and direct human activities at specific sites. Different climatic and anthropic forcings frequently co-occurred, whereby the responses of plankton communities were the result of this environmental complexity. Overall, the LTER investigations are providing an unparalleled framework of knowledge to evaluate changes in the aquatic pelagic systems and management options.

Identification of serum inflammatory markers as classifiers of lung cancer mortality for stage I adenocarcinoma

BACKGROUND

Lung cancer is the leading cause of cancer-related mortality worldwide. Low-dose CT (LDCT) imaging is now recommended to screen high-risk lung cancer individuals in the USA. LDCT has resulted in increased detection of stage I lung cancer for which the current standard of care is surgery alone. However, approximately 30% of these patients develop recurrence and therefore are in need of further treatment upon diagnosis. This study aims to explore blood-based inflammatory biomarkers to identify patients at high-risk of mortality for which additional treatment modalities can be offered at time of diagnosis.

PATIENTS AND METHODS

Recent work on a small panel of circulating cytokines identified elevated levels of IL-6, a pro-inflammatory cytokine, as an indicator of poor survival for lung cancer patients. To reflect the broader role of inflammation in lung cancer, we examined a large panel of 33 inflammatory proteins in the sera of 129 lung cancer patients selected from the National Cancer Institute-Maryland case-control study. To reduce heterogeneity, we specifically focused our study on stage I lung adenocarcinoma patients.

RESULTS

We replicated the previous observations that IL-6 is associated with prognosis of lung cancer and extended its utility to prognosis in this highly-selected population of stage I lung adenocarcinoma patients. In addition, we developed a multi-marker, combined prognostic classifier that includes the pro-inflammatory Th-17 cell effector cytokine, IL-17. Patients with high levels of IL-6 and IL-17A had a significantly adverse survival compared with patients with low levels (P for trend <0.0001). Patients in the high risk group, with high levels of both proteins had a 5-year survival rate of 46% in comparison to 93% for those with low levels of both markers. Furthermore, we validated the same trends for the IL-6 and IL-17A prognostic signature in an independent data set.

CONCLUSIONS

The results identified here justify further investigation of this novel, combined cytokine prognostic classifier for the identification of high-risk stage I lung adenocarcinoma patients. This classifier has the much-needed potential to identify patients at high risk of recurrence and thus prospectively identify the subset of patients requiring more aggressive treatment regimens at the time of diagnosis.

The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean

Diatoms are a diverse and ecologically important group of phytoplankton. Although most species are considered free living, several are known to interact with other organisms within the plankton. Detailed imaging and molecular characterization of any such partnership is, however, limited, and an appraisal of the large-scale distribution and ecology of such consortia was never attempted. Here, observation of Tara Oceans samples from the Benguela Current led to the detection of an epibiotic association between a pennate diatom and a tintinnid ciliate. We identified the diatom as Fragilariopsis doliolus that possesses a unique feature to form barrel-shaped chains, associated with seven different genera of tintinnids including five previously undescribed associations. The organisms were commonly found together in the Atlantic and Pacific Ocean basins, and live observations of the interaction have been recorded for the first time. By combining confocal and scanning electron microscopy of individual consortia with the sequencing of high-resolution molecular markers, we analyzed their distribution in the global ocean, revealing morpho-genetically distinct tintinnid haplotypes and biogeographically structured diatom haplotypes. The diatom was among the most abundant in the global ocean. We show that the consortia were particularly prevalent in nutrient-replete conditions, rich in potential predators. These observations support the hypothesis of a mutualistic symbiosis, wherein diatoms acquire increased motility and tintinnids benefit from silicification through increased protection, and highlight that such associations may be more prevalent than currently appreciated.

Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus

Background

Flagella have been lost in the vegetative phase of the diatom life cycle, but they are still present in male gametes of centric species, thereby representing a hallmark of sexual reproduction. This process, besides maintaining and creating new genetic diversity, in diatoms is also fundamental to restore the maximum cell size following its reduction during vegetative division. Nevertheless, sexual reproduction has been demonstrated in a limited number of diatom species, while our understanding of its different phases and of their genetic control is scarce.

Results

In the transcriptome of Leptocylindrus danicus, a centric diatom widespread in the world’s seas, we identified 22 transcripts related to the flagella development and confirmed synchronous overexpression of 6 flagellum-related genes during the male gamete formation process. These transcripts were mostly absent in the closely related species L. aporus, which does not have sexual reproduction. Among the 22 transcripts, L. danicus showed proteins that belong to the Intra Flagellar Transport (IFT) subcomplex B as well as IFT-A proteins, the latter previously thought to be absent in diatoms. The presence of flagellum-related proteins was also traced in the transcriptomes of several other centric species. Finally, phylogenetic reconstruction of the IFT172 and IFT88 proteins showed that their sequences are conserved across protist species and have evolved similarly to other phylogenetic marker genes.

Conclusion

Our analysis describes for the first time the diatom flagellar gene set, which appears to be more complete and functional than previously reported based on the genome sequence of the model centric diatom, Thalassiosira pseudonana. This first recognition of the whole set of diatom flagellar genes and of their activation pattern paves the way to a wider recognition of the relevance of sexual reproduction in individual species and in the natural environment.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4210-8) contains supplementary material, which is available to authorized users.

Baseline mutational patterns and sustained MRD negativity in patients with high-risk smoldering myeloma

Early results of a prospective phase 2 clinical trial of carfilzomib, lenalidomide, and dexamethasone followed by lenalidomide maintenance in high-risk smoldering myeloma showed promising results that were previously published. Here, we provide novel insights into the genetic landscape of high-risk smoldering myeloma and information on sustained minimal residual disease (MRD) negativity with an expanded cohort of patients. Eighteen patients with high-risk smoldering myeloma were enrolled between 29 May 2012, and 14 January 2014. We included patients with newly diagnosed multiple myeloma enrolled in a parallel trial who received the same therapy (reference group). The overall response rate was 100%. With median potential follow-up of 43.3 months, 10 (63%) remain in MRD negativity, and the estimated 4-year progression-free and overall survival rates are 71% and 100%, respectively. Importantly, we report differences in mutational patterns in patients with high-risk smoldering myeloma and newly diagnosed multiple myeloma, reflected in a lower frequency of mutations in significant myeloma genes (6.6% vs 45%) and NFKB pathway genes (6.6% vs 25%). Treatment with carfilzomib, lenalidomide, and dexamethasone followed by lenalidomide maintenance was associated with a 100% response rate and 63% MRD negativity with a safety profile consistent with previous reports for this regimen. This study had a small numbers of participants, but there seemed to be important differences in the genetic landscape of patients with high-risk smoldering myeloma and those with newly diagnosed multiple myeloma, suggestive of a more treatment-responsive biology in early disease.

Circulating Adiponectin Levels Differ Between Patients with Multiple Myeloma and its Precursor Disease

OBJECTIVE

An increased risk of multiple myeloma (MM) has been observed among individuals with low prediagnostic circulating levels of adiponectin, a metabolic hormone that is typically underexpressed among those with overweight or obesity. To assess whether adiponectin may influence myeloma development or progression to frank MM, circulating adiponectin levels were compared across patients with different stages of MM and its precursor, monoclonal gammopathy of undetermined significance (MGUS).

METHODS

Adiponectin was measured in 213 patients with MGUS, smoldering MM, or fully developed MM. Differences in adiponectin levels across patient groups were assessed using multivariate linear regression.

RESULTS

Relative to MGUS patients, adiponectin levels were statistically significantly lower among those with smoldering and fully developed MM, both overall (16%-20% decrease; P = 0.048) and among those with IgG/IgA isotypes (26%-28% decrease; P = 0.004). Among MGUS patients, adiponectin levels were significantly lower for those with the higher-risk IgM isotype compared with those who had IgG/IgA isotypes (42% decrease; P = 0.036).

CONCLUSIONS

The findings of this study, the largest to investigate adiponectin levels in patients with different stages of MM and the first to evaluate associations with clinical characteristics, suggest that reduced expression of adiponectin may be associated with progression from MGUS to MM.

Abstract 4658: Inflammatory based diagnostic markers of lung cancer in African Americans

African Americans have a higher risk of developing lung cancer compared with all other ethnic groups in the USA. Previous studies based on a small panel of markers suggested that certain circulating cytokines were associated with lung cancer. Given the complexity of the immune response in lung cancer and the multitude of cell types involved, we reasoned that examining a broad panel of inflammatory markers—including cytokines, chemokines, angiogenic and other pro-inflammatory factors—might identify a diagnostic signature of lung cancer for African American patients.

Differences in 30 inflammatory marker serum levels were measured in 316 African-American cases and 508 African American controls from the National Cancer Institute-Maryland (NCI-MD) case-control study using a Mesoscale (MSD) multiplex platform. The panel of 30 serum inflammatory markers included chemokines, cytokines and other inflammatory related proteins. Logistic regression analyses were conducted to investigate the association between levels of inflammatory marker expression and lung cancer risk. Expression levels above the median threshold defined within the control samples were considered high. Statistical models were also adjusted for potential confounding factors such as age, gender, pack-years and smoking status.

Nineteen inflammatory markers (CRP, IFN-ϒ, IL-10, IL-15, IL-17A, IL-1α, IL-1β, IL-4, IL-5, IL-6, IL-7, IL-8, IP-10, MCP-4, MIP-1α, TARC, TNF-α, TNF-β and VEGF) were significantly different among African American cases compared with African American controls (P&lt;0.05). In agreement with our previous observations, levels of IL-10, IL-1β, IL-6, IL-8, and TNF-α were associated with lung cancer risk. In addition, we found that CRP, IFN-ϒ, IL-15, IL-7, IP-10, MCP-4, MIP-1 α, TARC, TNF-β and VEGF were associated with lung cancer in African Americans. The associations between CRP, IFN-ϒ, IL-10, IL-15, IL-1β, IL-5, IL-6, IL-7, IL-8, IP-10, MCP-4, MDC, MIP-1α, TNF-α and TNF-β levels and lung cancer among African Americans was significant after adjustment for additional potential confounding factors.

Serum cytokine levels vary by race and might contribute to lung cancer differently in African Americans and European Americans. The findings presented here build upon recent work that identified associations between elevated levels of IL-10, IL-1β, IL-6, IL-8, TNF-α and lung cancer specifically among African Americans. By analyzing a broader spectrum of inflammatory measures, we have identified additional markers of lung cancer for African American patients. Further to this, we have integrated GWAS and MSD data for 137 cases and 203 controls that allows us to examine the genetic basis to the relationship between risk of lung cancer and modulated inflammatory marker expression. Markers identified here as significant for lung cancer risk will be further analyzed using case-control samples from an independent African American validation cohort.

Citation Format: Claire L. Meaney, Khadijah A. Mitchell, Adriana Zingone, Derek Brown, Wei Tang, Yunkai Yu, Liang Cao, Angela S. Wenzlaff, Ann G. Schwartz, Brid M. Ryan. Inflammatory based diagnostic markers of lung cancer in African Americans [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4658. doi:10.1158/1538-7445.AM2017-4658

Abstract 4423: Deep sequencing of lung cancer samples using different library preparation methods produces discordant short non-coding RNA profiles

Background: RNA-seq is the new standard for profiling coding and non-coding RNAs in a cell. This study compared two methods for miRNA library preparation from NEB and Qiagen. Our goal was to evaluate overall performance in terms of coverage, known miRNA detection, novel miRNA detection, isomiR detection, and tRNA fragment (tRF) detection.

Methods: We performed short RNA-seq on 4 lung cancer tumor-normal pairs. We used two library preparation kits: NEB Next Small RNA kit and Qiagen Qiaseq. All 16 preparations were sequenced on an Illumina NextSeq 550 using NextSeq High V2 chemistry and 75 bp single-end reads were obtained. After adapter removal and quality trimming reads were mapped to the hg19 human genome assembly using the Bowtie2 and SHRiMP packages.

Results: On average read yield was 46 million reads. A significantly higher portion of the sequenced reads survived adapter removal and quality trimming in the NEB preparations (96.5%) compared to the Qiagen (72.9%). The portion that could be uniquely mapped to hg19 was lower for the NEB kit (41.1%) than for the Qiagen (50.8%).NEB performed better (39.6%) compared with Qiagen (36.9%). Qiagen preparations had lengths between 20 and 25 bp whereas more than half of the mapped reads in the NEB preparation were 26 bp or longer.

At the miRNA arm level the Qiagen kit detected significantly more known miRNAs (792) with 10 or more reads, compared with NEB (576). The same 530 miRNA arms were identified by both kits. There was no discernible pattern in the ID’s or the sequence composition of the miRNAs that were identified by each kit. The detection of novel miRNAs was also higher with Qiagen (102), compared with NEB (82). The same 79 novel miRNAs were identified by both.

The Qiagen kit detected nearly twice as many isomiRs (5,316) with 10 or more reads compared to NEB (2,958). The same 2,631 isomiRs were identified by both kits. However, isomiR detection across samples was more consistent with the NEB kit.

When we computed pairwise Pearson correlations of normal samples, using the most highly expressed miRNAs in each sample, the NEB kit exhibited higher consistency (0.98) compared with the Qiagen kit (0.95). Pearson correlations of tumor samples showed even higher consistency for NEB (0.96) than Qiagen (0.89). Unsurprisingly, Pearson correlations of like samples across the NEB and Qiagen kits was very low: 0.42 for normal and 0.56 for tumor samples. RIN value did not seem to affect the overall performance of either kit.

Lastly, we compared tRFs. Here, the differences were very pronounced. For multiple choices of the support threshold the NEB and Qiagen profiles agreed on approximately 33% of the reported tRFs.

Conclusions: Library preparation kits give rise to both consistent and divergent results. End users interested in the detection of miRNAs, isomiRs or tRFs may derive greater utility by selecting one kit over another.

Citation Format: Brid M. Ryan, Phillipe Loher, Khadijah Mitchell, Adriana Zingone, Yongmei Zhao, Jyoti Shetty, Bao Tran, Isidore Rigoutsos. Deep sequencing of lung cancer samples using different library preparation methods produces discordant short non-coding RNA profiles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4423. doi:10.1158/1538-7445.AM2017-4423

Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation

Cancer treatments often require combinations of molecularly targeted agents to be effective. mTORi (rapamycin) and HDACi (MS-275/entinostat) inhibitors have been shown to be effective in limiting tumor growth, and here we define part of the cooperative action of this drug combination. More than 60 human cancer cell lines responded synergistically (CI<1) when treated with this drug combination compared with single agents. In addition, a breast cancer patient-derived xenograft, and a BCL-XL plasmacytoma mouse model both showed enhanced responses to the combination compared with single agents. Mice bearing plasma cell tumors lived an average of 70 days longer on combination treatment compared with single agents. A set of 37 genes cooperatively affected (34 downregulated; 3 upregulated) by the combination responded pharmacodynamically in human myeloma cell lines, xenografts, and a P493 model, and were both enriched in tumors, and correlated with prognostic markers in myeloma patient datasets. Genes downregulated by the combination were overexpressed in several untreated cancers (breast, lung, colon, sarcoma, head and neck, myeloma) compared with normal tissues. The MYC/E2F axis, identified by upstream regulator analyses and validated by immunoblots, was significantly inhibited by the drug combination in several myeloma cell lines. Furthermore, 88% of the 34 genes downregulated have MYC-binding sites in their promoters, and the drug combination cooperatively reduced MYC half-life by 55% and increased degradation. Cells with MYC mutations were refractory to the combination. Thus, integrative approaches to understand drug synergy identified a clinically actionable strategy to inhibit MYC/E2F activity and tumor cell growth in vivoMol Cancer Ther; 16(9); 2008-21. ©2017 AACR.

Relationship between anti-depressant use and lung cancer survival

OBJECTIVES

In recent years, the anti-cancer properties of several commonly used drugs have been explored, with drugs such as aspirin and beta-blockers associated with improved cancer outcomes. Previous preclinical work demonstrated that tricyclic anti-depressants have antitumor efficacy in lung cancer. Our goal was to examine the association between anti-depressant use and survival in lung cancer.

MATERIALS AND METHODS

We examined the association between use of common anti-depressants and survival in 1,097 lung cancer patients from the NCI-Maryland lung cancer study. The types of anti-depressants included in the study were norepinephrine and dopamine reuptake inhibitors, serotonin reuptake inhibitors, selective serotonin reuptake inhibitors, non-selective serotonin reuptake inhibitors, and tricyclic anti-depressants. Anti-depressant use was extracted from the medical history section of a detailed interviewer-administered questionnaire. Specific use in the three months before a lung cancer diagnosis was determined. Cox portioned hazards modeling was used to estimate the association between anti-depressant use with lung cancer-specific death with adjustment for potential confounding co-factors.

RESULTS

Anti-depressant use was associated with extended lung cancer-specific survival. In an analysis of specific classes of anti-depressant use, NDRIs and TCAs were associated with improved survival. Importantly, the extended survival associated with anti-depressants was maintained after adjustment for the clinical indications for these drugs, suggestive of a direct effect on lung cancer biology.

CONCLUSIONS

Considering the manageable and largely tolerable side effects of anti-depressants, and the low cost of these drugs, these results indicate that evaluation of anti-depressants as adjunct therapeutics with chemotherapy may have a translational effect for lung cancer patients.

Mediterranean Azadinium dexteroporum (Dinophyceae) produces six novel azaspiracids and azaspiracid-35: a structural study by a multi-platform mass spectrometry approach

Azadinium dexteroporum is the first species of the genus described from the Mediterranean Sea and it produces different azaspiracids (AZA). The aims of this work were to characterize the toxin profile of the species and gain structural information on azaspiracids produced by the A. dexteroporum strain SZN-B848 isolated from the Gulf of Naples. Liquid chromatography-mass spectrometry (LC-MS) analyses were carried out on three MS systems having different ion source geometries (ESI, TurboIonSpray®, ESI ION MAX) and different MS analyzers operating either at unit resolution or at high resolution, namely a hybrid triple quadrupole-linear ion trap (Q-Trap MS), a time of flight (TOF MS), and a hybrid linear ion trap Orbitrap XL Fourier transform mass spectrometer (LTQ Orbitrap XL FTMS). As a combined result of these different analyses, A. dexteroporum showed to produce AZA-35, previously reported from Azadinium spinosum, and six compounds that represent new additions to the AZA-group of toxins, including AZA-54 to AZA-58 and 3-epiAZA-7, a stereoisomer of the shellfish metabolite AZA-7. Based on the interpretation of fragmentation patterns, we propose that all these molecules, except AZA-55, have the same A to I ring system as AZA-1, with structural modifications all located in the carboxylic side chain. Considering that none of the azaspiracids produced by the Mediterranean strain of A. dexteroporum is currently regulated by European food safety authorities, monitoring programs of marine biotoxins in the Mediterranean area should take into account the occurrence of the new analogues to avoid an underestimation of the AZA-related risk for seafood consumers. Graphical Abstract A multi-platform MS approach reveals known and new azaspiracids in a Mediterranean strain of Azadinium dexteroporum.

Enzymatic activities of circulating plasma proteasomes in newly diagnosed multiple myeloma patients treated with carfilzomib, lenalidomide and dexamethasone

The proteasome inhibitor carfilzomib is highly effective in the treatment of multiple myeloma. It irreversibly binds the chymotrypsin-like active site in the β5 subunit of the 20S proteasome. Despite impressive response rates when carfilzomib is used in combination with immunomodulatory agents in newly diagnosed multiple myeloma patients; no biomarker exists to accurately predict response and clinical outcomes. We prospectively assessed the activity in peripheral blood of the chymotrypsin-like (CHYM), caspase-like (CASP) and trypsin-like (TRYP) proteolytic sites in 45 newly diagnosed multiple myeloma patients treated with eight cycles of carfilzomib, lenalidomide and dexamethasone (CRd) (NCT01402284). Samples were collected per protocol and proteasome activity measured through a fluorogenic assay. Median CHYM levels after one dose of carfilzomib decreased by >70%. CHYM and CASP activity decreased throughout treatment reaching a minimum after eight cycles of treatment. Higher levels of proteasome activity associated with higher disease burden (r > 0.30; p < 0.05) and higher disease stage (0.10 < p <0.20). No association was found with the probability of achieving a complete response, minimal residual disease negativity or time to best response. Further studies evaluating proteasome activity in malignant plasma cells may help elucidate how proteasome activity can be used as a biomarker in multiple myeloma.

Abstract 3406: The identification of serum cytokine inflammatory markers as classifiers of lung cancer mortality for stage I lung adenocarcinoma: a retrospective cohort study

Lung cancer is the leading cause of cancer-related mortality worldwide. Low-dose CT (LDCT) imaging is now recommended to screen high-risk lung cancer individuals in the USA. The sensitivity of LDCT has resulted in increased detection of stage I lung cancer and a 20% reduction in lung cancer mortality. The current standard of care for stage 1 lung cancer patients is surgery alone. However, between 20% and 30% of these patients will develop recurrence and therefore are in need of further treatment upon diagnosis.

This study aims to explore and validate biomarkers to identify patients at high-risk of mortality so that additional treatment modalities can be offered at time of diagnosis. Our recent work on a small panel of circulating cytokines identified elevated levels of IL-6, a pro-inflammatory cytokine, as an indicator of poor survival. To further examine the potential of inflammatory biomarkers as prognostic indicators, 125 stage I lung adenocarcinoma cases were selected from the National Cancer Institute-Maryland lung cancer case-control study. This is an on-going prospective study of non-small cell lung cancer based in the greater Baltimore region of the USA.

A panel of 33 inflammatory markers was measured for each case using the Mesoscale V-Plex assay. The magnitude of association between serum inflammatory marker expression levels and lung cancer-specific survival was tested using multivariable Cox proportional hazards regression modeling (Stata 12.0 statistical software). All calculations were adjusted for age, gender, stage and smoking status. Maximum follow up time was 15 years.

Five analytes were significantly associated with shorter survival. In concordance with the previous study, IL-6 was again associated with shorter survival (HR, 2.63; 95% CI, 1.25-5.56). Other cytokines associated with shorter survival included CRP (HR, 2.25; 95% CI, 1.09-4.65), Eotaxin-3 (HR, 2.20; 95% CI, 0.97-4.86), IL-12p40 (HR 1.98; 95% C.I. 1.00 - 3.91), and IL-17 (HR, 2.22; 95% CI, 1.08-4.58). Although IL6 and CRP were positively correlated (Rho = 0.451, P&lt;0.0001), the association between IL-6 and survival was independent of CRP (HR, 2.46; 95% CI, 1.19-5.09).

These results support the potential of cytokine markers as a prognostic tool to further classify stage I lung cancer and thus identify patients in need of additional treatment. The associations identified here justify further investigation of a novel, combined cytokine prognostic classifier to serve as a robust predictor of stage I lung adenocarcinoma survival.

Citation Format: Claire L. Meaney, Adriana Zingone, Derek Brown, Yunkai Yu, Liang Cao, Brid M. Ryan. The identification of serum cytokine inflammatory markers as classifiers of lung cancer mortality for stage I lung adenocarcinoma: a retrospective cohort study. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3406.

Benthic protists: the under-charted majority

Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.

Monoclonal gammopathy-associated pure red cell aplasia

Pure red cell aplasia (PRCA) is a rare disorder characterized by inhibition of erythroid precursors in the bone marrow and normochromic, normocytic anaemia with reticulocytopenia. Among 51 PRCA patients, we identified 12 (24%) patients having monoclonal gammopathy, monoclonal gammopathy of undetermined significance or smouldering multiple myeloma, with presence of monoclonal protein or abnormal serum free light chains and atypical bone marrow features of clonal plasmacytosis, hypercellularity and fibrosis. Thus far, three patients treated with anti-myeloma based therapeutics have responded with reticulocyte recovery and clinical transfusion independence, suggesting plasma cells play a key role in the pathogenesis of this specific monoclonal gammopathy-associated PRCA.

Subtle reproductive impairment through nitric oxide-mediated mechanisms in sea urchins from an area affected by harmful algal blooms

The health of the sea urchin Paracentrotus lividus, a key species in the Mediterranean Sea, is menaced by several pressures in coastal environments. Here, we aimed at assessing the reproductive ability of apparently healthy P. lividus population in a marine protected area affected by toxic blooms of Ostreospsis cf. ovata. Wide-ranging analyses were performed in animals collected prior to and during the bloom, as well as at several times thereafter, during the reproductive season. Adults showed a low fertilization rate, along with high nitric oxide (NO) levels in the gonads and the nitration of the major yolk protein toposome, which is an important player in sea urchin development. Serious developmental anomalies were observed in the progeny, which persist several months after the bloom. NO levels were high in the different developmental stages, which also showed variations in the transcription of several genes that were found to be directly or indirectly modulated by NO. These results highlight subtle but important reproductive flaws transmitted from the female gonads to the offspring with the NO involvement. Despite a recovery along time after the bloom, insidious damages can be envisaged in the local sea urchin population, with possible reverberation on the whole benthic system.