Higher Cell Abundance Research Articles

Expression of lipid-metabolism genes is correlated with immune microenvironment and predicts prognosis of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors. This study was aimed to identify a lipid metabolism-related signature associated with the HCC microenvironment to improve the prognostic prediction of HCC patients. Clinical information and expression profile data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, including the GEO dataset GSE76427. The gene expression profile of lipid metabolism was downloaded from Molecular Signatures Database (MSigDB) database. The infiltrating immune cells were estimated by the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE), MCP-counter, and TIMER algorithms. Functional analysis, including Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene set enrichment analysis (GSEA) were performed to elucidate the underlying mechanisms. The prognostic risk model was performed by Least absolute shrinkage and selection operator (LASSO) algorithm and Cox regression analysis. Two distinct subgroups of survival were identified. Better prognosis was associated with high immune score, high abundance of immune infiltrating cells, and high immune status. GO and KEGG analysis showed that differentially expressed genes (DEGs) between the two subgroups were mainly enriched in immune related pathways. GSEA analysis suggested that the expression of lipid metabolism related genes (LMRGs) was related to dysregulation of immune in the high-risk group. Risk models and clinical features based on LMRGs predicted HCC prognosis. This study indicated that the lipid metabolism-related signature was important for the prognosis of HCC. The expression of LMRGs was related to the immune microenvironment of HCC patients and could be used to predict the prognosis of HCC.

Characterizing the Tumor Microenvironment and Its Prognostic Impact in Breast Cancer.

The tumor microenvironment (TME) is crucial in cancer development and therapeutic response. Immunotherapy is increasingly recognized as a critical component of cancer treatment. While immunotherapies have shown efficacy in various cancers, including breast cancer, patient responses vary widely. Some patients receive significant benefits, while others experience minimal or no improvement. This disparity underscores the complexity and diversity of the immune system. In this study, we investigated the immune landscape and cell-cell communication within the TME of breast cancer through integrated analysis of bulk and single-cell RNA sequencing data. We established profiles of tumor immune infiltration that span across a broad spectrum of adaptive and innate immune cells. Our clustering analysis of immune infiltration identified three distinct patient groups: high T cell abundance, moderate infiltration, and low infiltration. Patients with low immune infiltration exhibited the poorest survival rates, while those in the moderate infiltration group showed better outcomes than those with high T cell abundance. Moreover, the high cell abundance group was associated with a greater tumor burden and higher rates of TP53 mutations, whereas the moderate infiltration group was characterized by a lower tumor burden and elevated PIK3CA mutations. Analysis of an independent single-cell RNA-seq breast cancer dataset confirmed the presence of similar infiltration patterns. Further investigation into ligand-receptor interactions within the TME unveiled significant variations in cell-cell communication patterns among these groups. Notably, we found that the signaling pathways SPP1 and EGF were exclusively active in the low immune infiltration group, suggesting their involvement in immune suppression. This work comprehensively characterizes the composition and dynamic interplay in the breast cancer TME. Our findings reveal associations between the extent of immune infiltration and clinical outcomes, providing valuable prognostic information for patient stratification. The unique mutations and signaling pathways associated with different patient groups offer insights into the mechanisms underlying diverse tumor immune infiltration and the formation of an immunosuppressive tumor microenvironment.

Impact of Krill Meal on Enhancing Skin Mucosal Health and Reducing Sea Lice in Atlantic Salmon

The salmon industry’s challenges with skin health and sea lice emphasize the necessity for fish-sensitive measures like functional nutrition to boost skin health and fish welfare. The present study investigated the efficacy of krill meal (KM) for skin mucosal health and sea lice in Atlantic salmon (170 g). Following an 8-week feeding period, in duplicate tanks, on test diets (8% KM, 12% KM, and the control group), fish underwent a 2-week sea lice challenge, reaching 350 g. The 8% KM diet group had thicker skin epithelium (72.3 µ) compared to the 12% KM (51.3 µ) and the control groups (43.8 µ) after 8 weeks. Additionally, skin mucosal health parameters—cell size (208 µ2), cell density (25.2%), and defense activity (1.19)—were significantly enhanced with 8% KM compared to the 12% KM (cell size: 162.3 µ2, cell density: 17%, defense activity: 1.04) and the control group (cell size: 173.5 µ2, cell density: 16.4%, defense activity: 0.93). Furthermore, fish fed with 8% KM significantly showed the lowest sea lice, along with reduced cell size while maintaining a high abundance of skin mucous cells, suggesting efficient turnover of the skin mucosal layer to remove sea lice effectively. This study highlights the potential of KM as part of a functional nutrition strategy to enhance skin mucosal health and mitigate sea lice challenges.

A prognostic neural epigenetic signature in high-grade glioma

Neural–tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is limited. We present an epigenetically defined neural signature of glioblastoma that independently predicts patients’ survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals a high abundance of malignant stemcell-like cells in high-neural glioblastoma, primarily of the neural lineage. These cells are further classified as neural-progenitor-cell-like, astrocyte-like and oligodendrocyte-progenitor-like, alongside oligodendrocytes and excitatory neurons. In line with these findings, high-neural glioblastoma cells engender neuron-to-glioma synapse formation in vitro and in vivo and show an unfavorable survival after xenografting. In patients, a high-neural signature is associated with decreased overall and progression-free survival. High-neural tumors also exhibit increased functional connectivity in magnetencephalography and resting-state magnet resonance imaging and can be detected via DNA analytes and brain-derived neurotrophic factor in patients’ plasma. The prognostic importance of the neural signature was further validated in patients diagnosed with diffuse midline glioma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant. High-neural gliomas likely require a maximized surgical resection approach for improved outcomes.

Identifying an immunogenic cell death-related gene signature contributes to predicting prognosis, immunotherapy efficacy, and tumor microenvironment of lung adenocarcinoma.

Immunogenic cell death (ICD) is a regulated form of cell death that triggers an adaptive immune response. The objective of this study was to investigate the correlation between ICD-related genes (ICDGs) and the prognosis and the immune microenvironment of patients with lung adenocarcinoma (LUAD). ICD-associated molecular subtypes were identified through consensus clustering. Subsequently, a prognostic risk model comprising 5 ICDGs was constructed using Lasso-Cox regression in the TCGA training cohort and further tested in the GEO cohort. Enriched pathways among the subtypes were analyzed using GO, KEGG, and GSVA. Furthermore, the immune microenvironment was assessed using ESTIMATE, CIBERSORT, and ssGSEA analyses. Consensus clustering divided LUAD patients into three ICDG subtypes with significant differences in prognosis and the immune microenvironment. A prognostic risk model was constructed based on 5 ICDGs and it was used to classify the patients into two risk groups; the high-risk group had poorer prognosis and an immunosuppressive microenvironment characterized by low immune score, low immune status, high abundance of immunosuppressive cells, and high expression of tumor purity. Cox regression, ROC curve analysis, and a nomogram indicated that the risk model was an independent prognostic factor. The five hub genes were verified by TCGA database, cell sublocalization immunofluorescence analysis, IHC images and qRT-PCR, which were consistent with bioinformatics analysis. The molecular subtypes and a risk model based on ICDGs proposed in our study are both promising prognostic classifications in LUAD, which may provide novel insights for developing accurate targeted cancer therapies.

DMRTA2 supports glioma stem-cell mediated neovascularization in glioblastoma

Glioblastoma (GBM) is the most common and lethal brain tumor in adults. Due to its fast proliferation, diffusive growth and therapy resistance survival times are less than two years for patients with IDH-wildtype GBM. GBM is noted for the considerable cellular heterogeneity, high stemness indices and abundance of the glioma stem-like cells known to support tumor progression, therapeutic resistance and recurrence. Doublesex- and mab-3–related transcription factor a2 (DMRTA2) is involved in maintaining neural progenitor cells (NPC) in the cell cycle and its overexpression suppresses NPC differentiation. Despite the reports showing that primary GBM originates from transformed neural stem/progenitors cells, the role of DMRTA2 in gliomagenesis has not been elucidated so far. Here we show the upregulation of DMRTA2 expression in malignant gliomas. Immunohistochemical staining showed the protein concentrated in small cells with high proliferative potential and cells localized around blood vessels, where it colocalizes with pericyte-specific markers. Knock-down of DMRTA2 in human glioma cells impairs proliferation but not viability of the cells, and affects the formation of the tumor spheres, as evidenced by strong decrease in the number and size of spheres in in vitro cultures. Moreover, the knockdown of DMRTA2 in glioma spheres affects the stabilization of the glioma stem-like cell-dependent tube formation in an in vitro angiogenesis assay. We conclude that DMRTA2 is a new player in gliomagenesis and tumor neovascularization and due to its high expression in malignant gliomas could be a biomarker and potential target for new therapeutic strategies in glioblastoma.

Monocyte state 1 (MS1) cells in critically ill patients with sepsis or non-infectious conditions: association with disease course and host response

BackgroundSepsis is a life-threatening condition arising from an aberrant host response to infection. Recent single-cell RNA sequencing investigations identified an immature bone-marrow-derived CD14+ monocyte phenotype with immune suppressive properties termed “monocyte state 1” (MS1) in patients with sepsis. Our objective was to determine the association of MS1 cell profiles with disease presentation, outcomes, and host response characteristics.MethodsWe used the transcriptome deconvolution method (CIBERSORTx) to estimate the percentage of MS1 cells from blood RNA profiles of patients with sepsis admitted to the intensive care unit (ICU). We compared these profiles to ICU patients without infection and to healthy controls. Host response dysregulation was further studied by gene co-expression network and gene set enrichment analyses of blood leukocytes, and measurement of 15 plasma biomarkers indicative of pathways implicated in sepsis pathogenesis.ResultsSepsis patients (n = 332) were divided into three equally-sized groups based on their MS1 cell levels (low, intermediate, and high). MS1 groups did not differ in demographics or comorbidities. The intermediate and high MS1 groups presented with higher disease severity and more often had shock. MS1 cell abundance did not differ between survivors and non-survivors, or between patients who did or did not acquire a secondary infection. Higher MS1 cell percentages were associated with downregulation of lymphocyte-related and interferon response genes in blood leukocytes, with concurrent upregulation of inflammatory response pathways, including tumor necrosis factor signaling via nuclear factor-κB. Previously described sepsis host response transcriptomic subtypes showed different MS1 cell abundances, and MS1 cell percentages positively correlated with the “quantitative sepsis response signature” and “molecular degree of perturbation” scores. Plasma biomarker levels, indicative of inflammation, endothelial cell activation, and coagulation activation, were largely similar between MS1 groups. In ICU patients without infection (n = 215), MS1 cell percentages and their relation with disease severity, shock, and host response dysregulation were highly similar to those in sepsis patients.ConclusionsHigh MS1 cell percentages are associated with increased disease severity and shock in critically ill patients with sepsis or a non-infectious condition. High MS1 cell abundance likely indicates broad immune dysregulation, entailing not only immunosuppression but also anomalies reflecting exaggerated inflammatory responses.Graphical abstract

Population dynamics of dominant dinoflagellate species in the North Sea: in situ growth rates, photosynthetic potential, and losses due to parasitism

In the North Sea, Tripos and Dinophysis are commonly occurring mixotrophic planktonic dinoflagellate genera. In order to understand their bloom dynamics, an occurring bloom dominated by T. furca and D. norvegica was followed for several days. High cell abundances of these species were located to estimate: in situ growth rates from cell cycle analyses, depth distributions, growth rates sustained by photosynthesis, and parasite infection prevalence in all T. furca, T. fusus, D. norvegica and D. acuminata. Cell abundances were over 10000 cells L−1 for T. furca and up to 18000 cells L−1 for D. norvegica. Cells accumulated between 15-25 m depth and presented low specific in situ growth rates of 0.04-0.15 d−1 for T. furca and 0.02-0.16 d−1 for D. norvegica. Photosynthesis could sustain growth rates of 0.01-0.18 d−1 for T. furca and 0.02 to 0.14 d−1 for D. norvegica, suggesting that these species were relying mainly on photosynthesis. Parasite infections where generally low, with occasional high prevalence in D. norvegica (by Parvilucifera sp.) and T. fusus (by Amoebophrya sp.), while both parasites showed comparable prevalence in D. acuminata, which could offset in situ growth rates by parasite-induced host mortality. The restructuring effect of parasites on dinoflagellate blooms is often overlooked and this study elucidates their effect to cell abundances and their growth at the final stages of a bloom.

A single-cell transcriptome atlas of Lueyang black-bone chicken skin

As the largest organ of the body, the skin participates in various physiological activities, such as barrier function, sensory function, and temperature regulation, thereby maintaining the balance between the body and the natural environment. To date, compositional and transcriptional profiles in chicken skin cells have not been reported. Here, we report detailed transcriptome analyses of cell populations present in the skin of a black-feather chicken and a white-feather chicken using single-cell RNA sequencing (scRNA-seq). By analyzing cluster-specific gene expression profiles, we identified 12 cell clusters, and their corresponding cell types were also characterized. Subsequently, we characterized the subpopulations of keratinocytes, myocytes, mesenchymal cells, fibroblasts, and melanocytes. It is worth noting that we have identified a subpopulation of keratinocytes involved in pigment granule capture and a subpopulation of melanocytes involved in pigment granule deposition, both of which have a higher cell abundance in black-feather chicken compared to white-feather chicken. Meanwhile, we also compared the cellular heterogeneity features of Lueyang black-bone chicken skin with different feather colors. In addition, we also screened out 12 genes those could be potential markers of melanocytes. Finally, we validated the specific expression of SGK1, WNT5A, CTSC, TYR, and LAPTM5 in black-feather chicken, which may be the key candidate genes determining the feather color differentiation of Lueyang black-bone chicken. In summary, this study first revealed the transcriptome characteristics of chicken skin cells via scRNA-seq technology. These datasets provide valuable information for the study of avian skin characteristics and have important implications for future poultry breeding.

Evaluation of immune microenvironment in IgG4-related sialadenitis.

IgG4-related sialadenitis is a systemic autoimmune disease that can lead to fibro-inflammatory conditions. This study aims to investigate the immune microenvironment and potential signaling pathways associated with IgG4-related sialadenitis. Datasets related to IgG4-related sialadenitis were retrieved from the GEO database. Immune cell infiltration analysis was conducted using the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) method. Differentially immune-related expressed genes (DIEG) and immune-related functional enrichment were identified. Moreover, potential treatment targets for IgG4-related sialadenitis were predicted using The Connectivity Map. Only two datasets from GEO were included for further analysis. The CIBERSORT results indicated dominant immune cell populations in IgG4-related sialadenitis, including CD8+ T cells, resting NK cells, monocytes, and naïve B cells in peripheral blood mononuclear cells. Additionally, high abundance of plasma cells was observed in labial salivary gland tissues. Furthermore, a total of 42 DIEGs were identified, with tumor necrosis factor (TNF) signaling via the NF-Kappa B signaling pathway and the p53 signaling pathway being highly enriched. Autophagy inhibitors and DNA topoisomerase inhibitors were strongly associated with potential targets for the treatment of IgG4-related sialadenitis (P<0.05). This study reveals altered immune microenvironment in peripheral blood mononuclear cells and labial salivary gland tissues in IgG4-related sialadenitis. Autophagy inhibitors and DNA topoisomerase inhibitors show promise as potential targets for treating IgG4-related sialadenitis, providing a novel therapeutic strategy for this disease.

In situ phytoplankton photosynthetic characteristics and their controlling factors in the eastern Indian Ocean

Photosynthesis is the most important bioenergy conversion process on Earth. Capturing instantaneous changes in in situ photosynthesis in open ocean ecosystems remains a major challenge. In this study, fast repetition rate fluorometry (FRRF), which can obtain nondestructive, real-time and in situ estimates of photosynthetic parameters, was used for the first time to continuously observe the spatial variation in in situ photosynthetic parameters in the eastern Indian Ocean (EIO). We further formulated new insights regarding abiotic and biotic factors of potential importance in determining photosynthetic performance. First, we found that the distributions of micro/nano- and picophytoplankton were opposite under the control of nutrient concentrations. Micro/nanophytoplankton had higher cell abundances in the nearshore and upwelling regions, while picophytoplankton had higher abundances in the open ocean, and Prochlorococcus was the dominant group. Second, based on the FRRF technology, we obtained the high-precision and high-density vertical profile map of photosynthetic parameters in the euphotic layer. It was observed that values of the maximum photochemical efficiency (Fv/Fm; 0.14–0.55, unitless) and the functional absorption cross-section of PSII (σPSII; 1.71–4.90 nm2 RCII−1) increased with increasing depth, while high values of the photosynthetic electron transfer rates (ETRRCII; 0.0019–17.0292 mol e− mol RCII−1 s−1) and the nonphotochemical quenching (NPQNSV; 0.35–7.26, unitless) occurred in the shallow 50 m layer, and the values decreased as the depth increased. Finally, we discussed limiting factors that regulated the distribution of photosynthetic parameters and concluded that optical properties varied significantly with changes in the ocean physico-chemical parameters and taxonomic composition of phytoplankton assemblages in the EIO. Picophytoplankton (especially cyanobacteria), rather than the micro/nanophytoplankton community, was the dominant factor influencing photosynthesis. Among abiotic factors, photosynthetically active radiation (PAR) was the proximal limiting factor affecting photosynthetic efficiency, followed by temperature and dissolved inorganic nitrogen (DIN). Consequently, phytoplankton photosynthetic parameters exhibited great variability, allowing rapid responses to environmental condition changes. In this study, we established the basis for detecting future changes in primary production in this oligotrophic area.

Identify and validate circadian regulators as potential prognostic markers and immune infiltrates in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneity pathological malignant cancer with leading causes of morbidity and mortality. EGFR inhibitors, immune checkpoint inhibitors have become novel treatments. However, the mechanism still remained uncertain. Several studies have confirmed that the circadian rhythms induce multiple malignancies developing. We utilized multi-omics analysis to demonstrate the crosstalk between circadian clock genes and tumor microenvironment in HNSCC. Firstly, we performed the LASSO Cox regression analysis based on the 16 important clock genes. A 7-gene risk model was successfully established in TCGA and validated in GEO datasets. Next, CIBERSORT and ESTIMATE methods were performed to display the immune landscape of high risk and low risk groups, and the results showed that high abundance of mast cells activated, dendritic cells activated and neutrophils were positively correlated with poor OS. To further identify hub genes, Kaplan Meier plot was applied in all TCGA and GEO datasets and two hub genes (PER2, and PER3) were identified, especially PER3, which was found strongly associated with immune score, PDCD1, CD4 + and CD8 + T cells in HNSCCC. Moreover, to explore the innate mechanism of circadian-induced pathway, we constructed a circadian-related ceRNA regulatory network containing 34 lncRNAs, 3 miRNAs and 4 core circadian genes. In-vitro experiments also verified that Per2 or Per3 could suppressed the proliferation, migration and invasion of HNSC. This study unraveled the association between PER3 and prognosis in patients with HNSC and the innate mechanism remains to be elucidated.

Characterisation of macrophage infiltration and polarisation based on integrated transcriptomic and histological analyses in Primary Sjögren's syndrome.

Primary Sjögren's syndrome (pSS) is a progressive inflammatory autoimmune disease. Immune cell infiltration into glandular lobules and ducts and glandular destruction are the pathophysiological hallmarks of pSS. Macrophages are one of the most important cells involved in the induction and regulation of an inflammatory microenvironment. Although studies have reported that an abnormal tissue microenvironment alters the metabolic reprogramming and polarisation status of macrophages, the mechanisms driving macrophage infiltration and polarisation in pSS remain unclear. Immune cell subsets were characterised using the single-cell RNA sequencing (scRNA-seq) data of peripheral blood mononuclear cells (PBMCs) from patients with pSS (n = 5) and healthy individuals (n = 5) in a public dataset. To evaluate macrophage infiltration and polarisation in target tissues, labial salivary gland biopsy tissues were subjected to histological staining and bulk RNA-seq (pSS samples, n = 24; non-pSS samples, n = 12). RNA-seq data were analysed for the construction of macrophage co-expression modules, enrichment of biological processes and deconvolution-based screening of immune cell types. Detailed mapping of PBMCs using scRNA-seq revealed five major immune cell subsets in pSS, namely, T cells, B cells, natural killer (NK) cells, dendritic cells (DCs) and monocyte-macrophages. The monocyte-macrophage subset was large and had strong inflammatory gene signatures. This subset was found to play an important role in the generation of reactive oxygen species and communicate with other innate and adaptive immune cells. Histological staining revealed that the number of tissue-resident macrophages was high in damaged glandular tissues, with the cells persistently surrounding the tissues. Analysis of RNA-seq data using multiple algorithms demonstrated that the high abundance of pro-inflammatory M1 macrophages was accompanied by the high abundance of other infiltrating immune cells, senescence-associated secretory phenotype and evident metabolic reprogramming. Macrophages are among the most abundant innate immune cells in PBMCs and glandular tissues in patients with pSS. A bidirectional relationship exists between macrophage polarisation and the inflammatory microenvironment, which may serve as a therapeutic target for pSS.

Single-cell morphological and topological atlas reveals the ecosystem diversity of human breast cancer

Digital pathology allows computerized analysis of tumor ecosystem using whole slide images (WSIs). Here, we present single-cell morphological and topological profiling (sc-MTOP) to characterize tumor ecosystem by extracting the features of nuclear morphology and intercellular spatial relationship for individual cells. We construct a single-cell atlas comprising 410 million cells from 637 breast cancer WSIs and dissect the phenotypic diversity within tumor, inflammatory and stroma cells respectively. Spatially-resolved analysis identifies recurrent micro-ecological modules representing locoregional multicellular structures and reveals four breast cancer ecotypes correlating with distinct molecular features and patient prognosis. Further analysis with multiomics data uncovers clinically relevant ecosystem features. High abundance of locally-aggregated inflammatory cells indicates immune-activated tumor microenvironment and favorable immunotherapy response in triple-negative breast cancers. Morphological intratumor heterogeneity of tumor nuclei correlates with cell cycle pathway activation and CDK inhibitors responsiveness in hormone receptor-positive cases. sc-MTOP enables using WSIs to characterize tumor ecosystems at the single-cell level.

Warburg effect-related risk scoring model to assess clinical significance and immunity characteristics of glioblastoma.

Glioblastoma (GBM), the most common primary malignant brain tumor, has a poor prognosis, with a median survival of only 14.6 months. The Warburg effect is an abnormal energy metabolism, which is the main cause of the acidic tumor microenvironment. This study explored the role of the Warburg effect in the prognosis and immune microenvironment of GBM. A prognostic risk score model of Warburg effect-related genes (Warburg effect signature) was constructed using GBM cohort data from The Cancer Genome Atlas. Cox analysis was performed to identify independent prognostic factors. Next, the nomogram was built to predict the prognosis for GBM patients. Finally, the drug sensitivity analysis was utilized to find the drugs that specifically target Warburg effect-related genes. Age, radiotherapy, chemotherapy, and WRGs score were confirmed as independent prognostic factors for GBM by Cox analyses. The C-index (0.633 for the training set and 0.696 for the validation set) and area under curve (>0.7) indicated that the nomogram exhibited excellent performance. The calibration curve also indicates excellent consistency of the nomogram between predictions and actual observations. In addition, immune microenvironment analysis revealed that patients with high WRGs scores had high immunosuppressive scores, a high abundance of immunosuppressive cells, and a low response to immunotherapy. The Cell Counting Kit-8 assays showed that the drugs targeting Warburg effect-related genes could inhibit the GBM cells growth invitro. Our research showed that the Warburg effect is connected with the prognosis and immune microenvironment of GBM. Therefore, targeting Warburg effect-related genes may provide novel therapeutic options.

Seasonal dynamics and ecology of the Pseudo-nitzschia delicatissima group in the Black Sea

Seasonal dynamics, including the Pseudo-nitzschia delicatissima (PDG) group's vertical and spatial distribution, were analysed based on field data collected in the Black Sea from 1948 to 2020. The main annual bloom occurred in February-March when the abundance in the upper mixed layer could reach 5 × 106 cells m−3. Bloom was most intense in the centre of the sea and on the outer shelf waters. In April, the bloom subsided, and in summer, only small peaks could be found in the deep-sea waters. On the contrary, high cell abundance was observed in the shelf areas in summer and autumn. Three periods with different levels of biomass were distinguished in the centre of the deep-water basin: highest (February-March), moderate (April-June), and lowest (July-December). Nutrient levels varied during these three periods, contributing to different growth-promoting phases. Six experiments with natural phytoplankton conducted in April-June showed that dissolved nitrate (N) and phosphate (P) were growth-limiting factors for PDG. Very low dissolved silicate (DSi) in October likely limited growth, as evidenced by the algae's lack of response to N and P additions. In February-March, dissolved inorganic nutrient concentrations were highest, with dissolved inorganic nitrogen (DIN), P, and DSi above 2.0 µM, 0.2 µM, and 2.5 µM, respectively. During the moderate growth period, DIN (˂ 1.2 µM) and P (˂ 0.15 µM) were expected to significantly limit the growth of PDG, while DSi was too high (> 3.5 µM) to have such an effect. In the second half of the year, DSi fell below 2.0 µM, which could severely inhibit cell growth in addition to DIN and P. Thus, after June, low DIN, P, and DSi combined resulted in the lowest PDG biomass.

Studies on the complex Warnowiaceae (Dinophyceae) I. Lohmann’s Pouchetia parva refound and renamed Nematodinium parvum comb. nov. (= Warnowia parva)

ABSTRACT The dinoflagellate family Warnowiaceae has often been considered to include some of the most complex cells among the protists. The number of described species is around 40, but both the species and generic concepts are in need of revision. Warnowiaceans are often fragile and readily change morphology under the light microscope, and they are usually regarded to be rare. They are particularly famous for the eye-like structures, termed ocelloids. Studies on warnowiaceans are hampered by lack of cultures, and our studies are therefore based on cells obtained directly from field samples. We provide a description of Nematodinium parvum comb. nov. (syn. Pouchetia parva, Warnowia parva), based on light, scanning and transmission electron microscopy, combined with phylogenetic analyses of ribosomal genes. It was described in 1908 by Lohmann from Kieler Bay, but is often common in Danish waters, allowing observations on distribution and behaviour. Crucial conditions for finding high cell abundances were periods of warm temperatures and a calm sea. Cells were yellowish, photosynthetic, and contained a net-like chloroplast, in addition to an ocelloid, trichocysts and harpoon-like nematocysts. They divided asexually but planozygotes were also seen. Following the demonstration of nematocysts, the species, which has been known as Warnowia parva since 1928, is transferred to Nematodinium. The finding of a peduncle indicates mixotrophy but all feeding experiments failed to identify a suitable prey. The phylogenetic analyses based on single-cell PCR and sequence determinations of small and large subunit rDNA confirmed that the systematics of Nematodinium and Warnowia is in a state of flux.

Assessing the bioavailability of black carbon-derived dissolved organic matter for marine heterotrophic prokaryotes

Here we investigated the bioavailability of black carbon (BC)-derived dissolved organic matter (DOM) for a natural mixed community of marine heterotrophic prokaryotes. We ran an in vitro biodegradation experiment that took place over 3 months and exposed a community of organisms collected in the northwestern Mediterranean Sea (Bay of Marseille, France) to three different soluble fractions of BC prepared in the laboratory from various fossil fuel combustion particulates: standard diesel (DREF), oxidized diesel (DREF-OX), and natural samples of ship soot (DSHIP). Over the course of the three months, we observed significant decreases in the concentrations of dissolved organic carbon (DOC; from 9 to 21 %), dissolved BC (DBC; from 22 to 38 %) and dissolved polycyclic aromatic hydrocarbons (d-PAH; from 24 to 64 %) along with variability in the growth dynamics and activity of the heterotrophic prokaryotic community. The heterotrophic prokaryotic community exposed to DREF-OX treatment showed the highest values of respiration and production and the highest cell abundance, associated with the highest decrease in DOC (21 %) and d-PAH (64 %) concentrations. In the DREF and DSHIP treatments, prokaryotic activity was oriented towards anabolism. DREF treatment led to the highest decrease in DBC concentration (38 %). DSHIP treatment, which presented a substantially different d-PAH and dissolved metals content to the other two treatments, showed the lowest decreases in DOC, DBC and d-PAH concentrations, as well as the lowest prokaryotic activity and biomasses. Our results indicate that BC-derived DOM, including the most condensed fraction of this material, is partly bioavailable and therefore likely to be assimilated by marine prokaryotes. The origin of BC/soot deposited at the ocean surface turns out to be a key parameter that dictates the efficiency of biodegradation of its dissolved fraction by heterotrophic prokaryotes.

Application of a Quantitative PCR to Investigate the Distribution and Dynamics of Two Morphologically Similar Species, Karenia mikimotoi and K. papilionacea (Dinophyceae) in Korean Coastal Waters.

Species of the marine dinoflagellate genus Karenia are known to produce various potent biotoxins and can form noxious blooms that cause mass mortalities of fish and shellfish. To date, harmful blooms of the species K. mikimotoi have been reported in Korea, but K. papilionacea was recently recorded off the southern coast of Korea. Here, we developed a quantitative real-time PCR (qRT-PCR) assay with specific primer pairs for the accurate detection and quantification of these two similar-looking unarmored species, K. mikimotoi and K. papilionacea, and investigated their distribution and dynamics in Korean coastal waters. Overall, K. papilionacea had not only a wider distribution, but also higher cell abundances (15-2553 cells L-1) than K. mikimotoi (3-122 cells L-1) in surface waters. Of 18 sampling sites, the two Karenia species were found to coexist at two sites. During monitoring at a fixed station (S5), K. papilionacea was generally predominant over K. mikimotoi; however, the two species exhibited similar dynamics and occasionally co-occurred. Both Karenia species showed similar physiological responses to temperature and salinity, requiring similar conditions for optimum growth. These results suggest that blooms of the two species may co-occur and induce a synergistic adverse effect on marine environments.

Retrospective study of transcriptomic profiling identifies Thai triple-negative breast cancer patients who may benefit from immune checkpoint and PARP inhibitors.

Triple-negative breast cancer (TNBC) is a rare and aggressive breast cancer subtype. Unlike the estrogen receptor-positive subtype, whose recurrence risk can be predicted by gene expression-based signature, TNBC is more heterogeneous, with diverse drug sensitivity levels to standard regimens. This study explored the benefit of gene expression-based profiling for classifying the molecular subtypes of Thai TNBC patients. The nCounter-based Breast 360 gene expression was used to classify Thai TNBC retrospective cohort subgroups. Their expression profiles were then compared against the previously established TNBC classification system. The differential characteristics of the tumor microenvironment and DNA damage repair signatures across subgroups were also explored. Thai TNBC cohort could be classified into four main subgroups, corresponding to the LAR, BL-2, and M subtypes based on Lehmann's TNBC classification. The PAM50 gene set classified most samples as basal-like subtypes except for Group 1. Group 1 exhibited similar enrichment of the metabolic and hormone response pathways to the LAR subtype. Group 2 shared pathway activation with the BL-2 subtype. Group 3 showed an increase in the EMT pathway, similar to the M subtype. Group 4 showed no correlation with Lehmann's TNBC. The tumor microenvironment (TME) analysis showed high TME cell abundance with increased expression of immune blockade genes in Group 2. Group 4 exhibited low TME cell abundance and reduced immune blockade gene expressions. We also observed distinct signatures of the DNA double-strand break repair genes in Group 1. Our study reported unique characteristics between the four TNBC subgroups and showed the potential use of immune checkpoint and PARP inhibitors in subsets of Thai TNBC patients. Our findings warrant further clinical investigation to validate TNBC's sensitivity to these regimens.