A cup half full: the first assessment on the distribution, ecology and need for conservation of the threatened Neptune's cup sponge, Cliona patera, in the Gulf of Thailand.

The Neptune's cup sponge is an iconic species found in marine soft sediment habitats in the Indo-West Pacific, with a history of overharvesting and extreme population declines. Access to SCUBA diving surveys has allowed for its rediscovery at Singapore, its type locality; however, with fewer than ten living individuals documented in the twenty-first century, the species is believed to be in need of conservation. Here, we share the results from surveys across the Gulf of Thailand, allowing for a documentation of 29 additional individuals, with information on their ecology and distribution. Of the 29 individuals, extensive damage or mortality caused by marine debris is recorded for six individuals, and one further individual is believed to be lost due to an unknown cause. Documented threats from the Gulf of Thailand differ from those in Singapore; however, low population sizes and poor connectivity remain a significant concern for the survival of the species.

The association of low birthweight and prematurity on outcomes in children and adults with nephrotic syndrome-a NEPTUNE cohort study.

BACKGROUND: In single-center studies, both preterm birth and low birth weight (LBW) are associated with worse outcomes in childhood nephrotic syndrome. Using the Nephrotic Syndrome Study Network (NEPTUNE) observational cohort, we tested the hypothesis that in patients with nephrotic syndrome, hypertension, proteinuria status, and disease progression would be more prevalent and more severe in subjects with LBW and prematurity singly or in combination (LBW/prematurity). METHODS: Three hundred fifty-nine adults and children with focal segmental glomerulosclerosis (FSGS) or minimal change disease (MCD) and available birth history were included. Estimated glomerular filtration rate (eGFR) decline and remission status were primary outcomes, and secondary outcomes were kidney histopathology, kidney gene expression, and urinary biomarkers. Logistic regression was used to identify associations with LBW/prematurity and these outcomes. RESULTS: We did not find an association between LBW/prematurity and remission of proteinuria. However, LBW/prematurity was associated with greater decline in eGFR. This decline in eGFR was partially explained by the association of LBW/prematurity with APOL1 high-risk alleles, but the association remained after adjustment. There were no differences in kidney histopathology or gene expression in the LBW/prematurity group compared to normal birth weight/term birth. CONCLUSION: LBW and premature babies who develop nephrotic syndrome have a more rapid decline in kidney function. We did not identify clinical or laboratory features that distinguished the groups. Additional studies in larger groups are needed to fully ascertain the effects of (LBW) and prematurity alone or in combination on kidney function in the setting of nephrotic syndrome.

NEPTUNE China cohort: First-line durvalumab plus tremelimumab in Chinese patients with metastatic non-small-cell lung cancer.

OBJECTIVES: The phase 3 NEPTUNE study (NCT02542293) evaluated first-line durvalumab plus tremelimumab (DT) versus chemotherapy for metastatic NSCLC. Prespecified exploratory analyses were conducted in an extended cohort enrolled in China. MATERIALS AND METHODS: Patients were randomized (1:1) to DT or standard chemotherapy, stratified by PD-L1 tumor cell (TC) expression (≥25 % vs < 25 %), histology, and smoking history. The primary analysis for this cohort was overall survival (OS) in patients with PD-L1 TC < 1 %. Secondary analyses included OS and progression-free survival (PFS) in the ITT population and PD-L1 subgroups, and safety. No alpha was allocated to these cohort analyses (data cut-off, 21-September-2020). RESULTS: 78 and 82 patients were randomized to DT and chemotherapy, respectively; 26 and 29 had PD-L1 TC < 1 % (median follow-up, 31.2 and 29.7 months [censored patients]). Among patients with PD-L1 TC < 1 %, OS favored DT versus chemotherapy (HR 0.60; 95 % CI, 0.32-1.11), with medians of 15.0 months (95 % CI, 10.5-27.4) and 11.7 months (95 % CI, 8.6-20.5), respectively; 24-month rates were 36.0 % (95 % CI, 18.2-54.2) and 17.9 % (95 % CI, 6.5-33.7). In the ITT population, OS was prolonged with DT versus chemotherapy (HR 0.70; 95 % CI, 0.48-1.02); medians were 20.0 and 14.1 months and 24-month rates were 44.2 % and 30.4 %. PFS was similar in the PD-L1 TC < 1 % (HR 1.13; 95 % CI, 0.59-2.14) and ITT (HR 0.95; 95 % CI, 0.66-1.36) populations; 12-month rates were 15.6 % versus 11.3 % and 23.9 % versus 16.6 %. Grade 3/4 treatment-related adverse events (TRAEs) occurred in 31.2 % with DT and 52.6 % with chemotherapy; 3.9 % versus 10.3 % discontinued due to TRAEs. CONCLUSIONS: In exploratory analyses, first-line DT showed a trend towards improved OS versus chemotherapy among Chinese patients in the PD-L1 TC < 1 % population and ITT population, with 24-month OS and 12-month PFS rates indicating benefit in survival curve tails. DT was well tolerated with no new safety signals.

Tobacco exposure in adults and children with proteinuric glomerulopathies: a NEPTUNE cohort study.

BACKGROUND: Tobacco exposure has been recognized as a risk factor for cardiovascular disease (CVD) and progression of kidney disease. Patients with proteinuric glomerulopathies are at increased risk for cardiovascular morbidity and mortality. Multiple studies have linked tobacco exposure to CVD and chronic kidney disease, but the relationships between smoking and proteinuric glomerulopathies in adults and children have not been previously explored. METHODS: Data from the Nephrotic Syndrome Study Network (NEPTUNE), a multi-center prospective observational study of participants with proteinuric glomerulopathies, was analyzed. 371 adults and 192 children enrolled in NEPTUNE were included in the analysis. Self-reported tobacco exposure was classified as non-smoker, active smoker, former smoker, or exclusive passive smoker. Baseline serum cotinine levels were measured in a sub-cohort of 178 participants. RESULTS: The prevalence of active smokers, former smokers and exclusive passive smoking among adults at baseline was 14.6%, 29.1% and 4.9%, respectively. Passive smoke exposure was 16.7% among children. Active smoking (reference non-smoking) was significantly associated with greater total cholesterol among adults (ß 17.91 95% CI 0.06, 35.76, p = 0.049) while passive smoking (reference non-smoking) was significantly associated with greater proteinuria over time among children (ß 1.23 95% CI 0.13, 2.33, p = 0.03). Higher cotinine levels were associated with higher baseline eGFR (r = 0.17, p = 0.03). CONCLUSION: Tobacco exposure is associated with greater risk for CVD and worse kidney disease outcomes in adults and children with proteinuric glomerulopathies. Preventive strategies to reduce tobacco exposure may help protect against future cardiovascular and kidney morbidity and mortality in patients with proteinuric glomerulopathies.

NEPTUNE: Phase 3 Study of First-Line Durvalumab Plus Tremelimumab in Patients With Metastatic NSCLC.

INTRODUCTION: NEPTUNE, a phase 3, open-label study, evaluated first-line durvalumab plus tremelimumab versus chemotherapy in metastatic NSCLC (mNSCLC). METHODS: Eligible patients with EGFR and ALK wild-type mNSCLC were randomized (1:1) to first-line durvalumab (20 mg/kg every 4 weeks until progression) plus tremelimumab (1 mg/kg every 4 weeks for up to four doses) or standard chemotherapy. Randomization was stratified by tumor programmed death-ligand 1 expression (≥25% versus <25%), tumor histologic type, and smoking history. The amended primary end point was overall survival (OS) in patients with blood tumor mutational burden (bTMB) greater than or equal to 20 mutations per megabase (mut/Mb). Secondary end points included progression-free survival (PFS) in patients with bTMB greater than or equal to 20 mut/Mb and safety and tolerability in all treated patients. RESULTS: As of June 24, 2019, 823 patients were randomized (intention-to-treat [ITT]); 512 (62%) were bTMB-evaluable, with 129 of 512 (25%) having bTMB greater than or equal to 20 mut/Mb (durvalumab plus tremelimumab [n = 69]; chemotherapy [n = 60]). Baseline characteristics were balanced in the intention-to-treat. Among patients with bTMB greater than or equal to 20 mut/Mb, OS improvement with durvalumab plus tremelimumab versus chemotherapy did not reach statistical significance (hazard ratio 0.71 [95% confidence interval: 0.49-1.05; p = 0.081]; median OS, 11.7 versus 9.1 months); the hazard ratio for PFS was 0.77 (95% confidence interval, 0.51-1.15; median PFS, 4.2 versus 5.1 months). In the overall safety population, incidence of grade 3 or 4 treatment-related adverse events was 20.7% (durvalumab plus tremelimumab) and 33.6% (chemotherapy). CONCLUSIONS: NEPTUNE did not meet its primary end point of improved OS with durvalumab plus tremelimumab versus chemotherapy in patients with mNSCLC and bTMB greater than or equal to 20 mut/Mb. Despite the amended study design, with a resultant small primary analysis population, therapeutic activity was aligned with expectations based on mechanistic biology and previous studies.

T-cell receptor diversity in minimal change disease in the NEPTUNE study.

BACKGROUND: Minimal change disease (MCD) is the major cause of childhood idiopathic nephrotic syndrome, which is characterized by massive proteinuria and debilitating edema. Proteinuria in MCD is typically rapidly reversible with corticosteroid therapy, but relapses are common, and children often have many adverse events from the repeated courses of immunosuppressive therapy. The pathobiology of MCD remains poorly understood. Prior clinical observations suggest that abnormal T-cell function may play a central role in MCD pathogenesis. Based on these observations, we hypothesized that T-cell responses to specific exposures or antigens lead to a clonal expansion of T-cell subsets, a restriction in the T-cell repertoire, and an elaboration of specific circulating factors that trigger disease onset and relapses. METHODS: To test these hypotheses, we sequenced T-cell receptors in fourteen MCD, four focal segmental glomerulosclerosis (FSGS), and four membranous nephropathy (MN) patients with clinical data and blood samples drawn during active disease and during remission collected by the Nephrotic Syndrome Study Network (NEPTUNE). We calculated several T-cell receptor diversity metrics to assess possible differences between active disease and remission states in paired samples. RESULTS: Median productive clonality did not differ between MCD active disease (0.0083; range: 0.0042, 0.0397) and remission (0.0088; range: 0.0038, 0.0369). We did not identify dominant clonotypes in MCD active disease, and few clonotypes were shared with FSGS and MN patients. CONCLUSIONS: While these data do not support an obvious role of the adaptive immune system T-cells in MCD pathogenesis, further study is warranted given the limited sample size. A higher resolution version of the Graphical abstract is available as Supplementary information.

Reactive oxygen species, the trident of Neptune in the hands of hecate; role in different diseases, signaling pathways, and detection methods.

Free radicals are highly reactive molecules with short lifetime which are now well accepted to act as regulators for different signaling pathways and hence can affect various cellular processes. Furthermore, they play pivotal role in different physiological/pathophysiological processes including homeostasis, metabolism, immunity, proliferation, differentiation, and cancer. Meanwhile, free radicals play a positive role in pathogen resistance that any imbalances in their productions/regulation could be harmful to cell macromolecules such as proteins, lipids, and nucleic acids and finally cells' fate, which may be results in different diseases. Some modalities, especially in cancer therapy, are based on ROS elevation/decreasing. Based on the inevitable importance of ROS various detection methods have been developed. These methods should have fundamental criteria including cell-permeability and physiological pH compatibility. In this review first we will bring up about different free radicals, their role in diseases, and underlying signaling pathways; after that various detection methods with their pros and cons will be discussed.

Construction and characterization of microsatellite markers for the Neptune whelk, Neptunea cumingii.

BACKGROUND: The Neptune whelk, Neptunea cumingii, is an economic gastropod endemic to the East Asia Warm Temperate Biotic Subregion. The study of the development in microsatellite markers maybe beneficial for assessing the genetic diversity and conservation of resources on this dwindling species. METHODS AND RESULTS: The microsatellite markers were constructed and characterized through Illumina high-throughput sequencing and capillary electrophoresis techniques. Eleven polymorphic microsatellite loci were screened and validated. The observed heterozygosity and expected heterozygosity of each locus showed a range from 0.0600 to 0.6508 and from 0.7380 to 0.9375, respectively. The average Shannon's information index and polymorphism information content were 2.0828 and 0.8325, respectively. Deviation from all loci was generated from Hardy-Weinberg equilibrium. CONCLUSIONS: The 11 microsatellite markers developed in this study show polymorphic status. These markers are expected to be highly informative for further analysis of genetic diversity in N. cumingii.

NEPTUNE: A novel computational approach for accurate and large-scale identification of tumor homing peptides.

Tumor homing peptides (THPs) play a crucial role in recognizing and specifically binding to cancer cells. Although experimental approaches can facilitate the precise identification of THPs, they are usually time-consuming, labor-intensive, and not cost-effective. However, computational approaches can identify THPs by utilizing sequence information alone, thus highlighting their great potential for large-scale identification of THPs. Herein, we propose NEPTUNE, a novel computational approach for the accurate and large-scale identification of THPs from sequence information. Specifically, we constructed variant baseline models from multiple feature encoding schemes coupled with six popular machine learning algorithms. Subsequently, we comprehensively assessed and investigated the effects of these baseline models on THP prediction. Finally, the probabilistic information generated by the optimal baseline models is fed into a support vector machine-based classifier to construct the final meta-predictor (NEPTUNE). Cross-validation and independent tests demonstrated that NEPTUNE achieved superior performance for THP prediction compared with its constituent baseline models and the existing methods. Moreover, we employed the powerful SHapley additive exPlanations method to improve the interpretation of NEPTUNE and elucidate the most important features for identifying THPs. Finally, we implemented an online web server using NEPTUNE, which is available at http://pmlabstack.pythonanywhere.com/NEPTUNE. NEPTUNE could be beneficial for the large-scale identification of unknown THP candidates for follow-up experimental validation.

Preparation of Nereid oligopeptide and investigation of the mechanism underlying the induction of apoptosis in human lung cancer H1299 cells.

In the present study, oligopeptides from Nereid (Perinereis aibuhitensis) were prepared via enzymatic hydrolysis, and the mechanism underlying the induction of apoptosis in H1299 cells was investigated. According to the analysis of the inhibition rate on proliferation, alkaline protease demonstrated the best enzymatic efficiency. The optimal conditions for hydrolysis were as follows: 50˚C and pH 10 for 6 h; a material­to­liquid ratio of 1:1 (g/ml); and addition of 400 U/g enzyme. The hydrolysates were purified using ultrafiltration, anion chromatography, gel filtration chromatography, and high­performance liquid chromatography. The Nereid oligopeptide (NOP), with a molecular weight of 841 kDa and an amino acid sequence of glutamine­isoleucine­asparagine­glutamine­histidine­leucine, was obtained. NOP inhibited the proliferation of H1299 cells in a time­ and dose­dependent manner. Morphological changes and apoptosis were also induced by NOP in H1299 cells. The western blot analysis revealed that the B­cell lymphoma 2/Bcl­2 associated X (Bcl­2/Bax) ratio was reduced by 24.7% in the NOP treatment group compared with the control group. The relative expression levels of cleaved caspase­9 (cleaved­CASP9) and cleaved caspase­3 (cleaved­CASP3) in the NOP treatment group were 2.55­ and 1.71­fold higher than those measured in the control group, respectively. These results suggested that NOP exerts antitumor effects by influencing the proliferation and apoptosis of H1299 cells.

Murine Neural Plate Targeting by In Utero Nano-Injection (NEPTUNE) at Embryonic Day 7.5.

Manipulating gene expression in the developing mouse brain in utero holds great potential for functional genetics studies. However, it has previously largely been restricted to the manipulation of embryonic stages post-neurulation. A protocol was developed to inject the amniotic cavity at embryonic day (E)7.5 and deliver lentivirus, encoding cDNA or shRNA, targeting >95% of the neural plate and neural crest cells, contributing to the future brain, spinal cord, and peripheral nervous system. This protocol describes the steps necessary to achieve successful transduction, including grinding of the glass capillary needles, pregnancy verification, developmental staging using ultrasound imaging, and optimal injection volumes matched to embryonic stages. Following this protocol, it is possible to achieve transduction of >95% of the developing brain with high-titer lentivirus and thus perform whole-brain genetic manipulation. In contrast, it is possible to achieve mosaic transduction using lower viral titers, allowing for genetic screening or lineage tracing. Injection at E7.5 also targets ectoderm and neural crest contributing to distinct compartments of the eye, tongue, and peripheral nervous system. This technique thus offers the possibility to manipulate gene expression in mouse neural-plate- and ectoderm-derived tissues from preneurulation stages, with the benefit of reducing the number of mice used in experiments.

The conserved core of the nereid brain: Circular CNS, apical nervous system and lhx6-arx-dlx neurons.

When bilaterian animals first emerged, an enhanced perception of the Precambrian environment was key to their stunning success. This occurred through the acquisition of an anterior brain, as found in most extant bilaterians. What were the core circuits of the first brain, and how do they relate to today's diversity? With two landmark resources - the full connectome and a multimodal cellular atlas combining gene expression and ultrastructure - the young worm of the marine annelid Platynereis dumerilii takes center stage in comparative bilaterian neuroanatomy. The new data suggest a composite structure of the ancestral bilaterian brain, with the anterior end of a circular CNS fused to a sensory-neurosecretory apical system, and with lhx6-arx-dlx chemosensory circuits giving rise to associative centers in the descending bilaterian lineages.

Highly efficient manipulation of nervous system gene expression with NEPTUNE.

Genetic loss and gain of function in mice have typically been studied by using knockout or knockin mice that take months to years to generate. To address this problem for the nervous system, we developed NEPTUNE (NEural Plate Targeting by in Utero NanoinjEction) to rapidly and flexibly transduce the neural plate with virus prior to neurulation, and thus manipulate the future nervous system. Stable integration in >95% of cells in the brain enabled long-term overexpression, and conditional expression was achieved by using cell-type-specific MiniPromoters. Knockdown of Olig2 by using NEPTUNE recapitulated the phenotype of Olig2 -/- embryos. We used NEPTUNE to investigate Sptbn2, mutations in which cause spinocerebellar ataxia type 5. Sptbn2 knockdown induced dose-dependent defects in the neural tube, embryonic turning, and abdominal wall closure, previously unreported functions for Sptbn2. NEPTUNE thus offers a rapid and cost-effective technique to test gene function in the nervous system and can reveal phenotypes incompatible with life.

Neptune: an environment for the delivery of genomic medicine.

PURPOSE: Genomic medicine holds great promise for improving health care, but integrating searchable and actionable genetic data into electronic health records (EHRs) remains a challenge. Here we describe Neptune, a system for managing the interaction between a clinical laboratory and an EHR system during the clinical reporting process. METHODS: We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. RESULTS: Neptune has been applied for the generation and delivery of over 15,000 clinical genomic reports. This work spans two clinical tests based on targeted gene panels that contain 68 and 153 genes respectively. These projects demanded customizable clinical reports that contained a variety of genetic data types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow. CONCLUSION: Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open source and available at https://gitlab.com/bcm-hgsc/neptune .

Human leukocyte antigen selected allogeneic mesenchymal stromal cell therapy in renal transplantation: The Neptune study, a phase I single-center study.

Mesenchymal stromal cells (MSC) hold promise as a novel immune-modulatory therapy in organ transplantation. First clinical studies have used autologous MSCs; however, the use of allogeneic "off-the-shelf" MSCs is more sustainable for broad clinical implementation, although with the risk of causing sensitization. We investigated safety and feasibility of allogeneic MSCs in renal transplantation, using a matching strategy that prevented repeated mismatches. Ten patients received two doses of 1.5 × 106 /kg allogeneic MSCs 6 months after transplantation in a single-center nonrandomized phase Ib trial, followed by lowering of tacrolimus (trough level 3 ng/mL) in combination with everolimus and prednisone. Primary end point was safety, measured by biopsy proven acute rejection (BPAR) and graft loss 12 months after transplantation. Immune monitoring was performed before and after infusion. No BPAR or graft loss occurred and renal function remained stable. One patient retrospectively had DSAs against MSCs, formed before infusion. No major alterations in T and B cell populations or plasma cytokines were observed upon MSC infusion. Administration of HLA selected allogeneic MSCs combined with low-dose tacrolimus 6 months after transplantation is safe at least in the first year after renal transplantation. This sets the stage to further explore the efficacy of third-party MSCs in renal transplantation.

Enhancing Fluorogold-based neural tract tracing.

BACKGROUND: Fluorogold (FG) is used by many groups to retrogradely trace nervous system pathways. Fluorogold, while a robust tracer, also is neurotoxic and causes tissue damage at the injection site and leads to motor deficits. NEW METHOD: In the current study, we describe a method for enhancing FG-uptake using Triton™ and an overall procedure for reducing FG-related tissue damage while still allowing effective quantification. RESULTS: Triton™ decreases the amount of FG, as well as the time required for long-distance transport from the thoracic spinal cord to the motor cortex by >4 fold when this distance is >10in. Although small FG concentrations and injection volumes are ideal for minimizing associated tissue damage and motor deficits, they result in difficult-to-detect fluorescence. This can be solved using FG antiserum paired with an ABC chromogen reaction. This ABC chromogen reaction product can remain stable for at least 9 years. COMPARISON WITH EXISTING METHOD(S): This study is the first to collectively address FG-induced tissue damage and describe methods for minimizing this damage. CONCLUSIONS: Triton™ enhances the uptake of FG in the nervous system, reduces the FG required, and allows for a substantial decrease in tracing time that limits FG-induced motor deficits. Small FG concentration and volume decreases tissue damage but also decreases FG fluorescent detection. Detection challenges are resolved using FG anti-serum and chromogen reactions.