Progress report for SRDCP on the Atlantic-wide study on the age and growth of shortfin mako shark

The ICCAT Shark Research and Data Collection Program (SRDCP) aims to develop and coordinate science and science-related activities needed to support provision of sound scientific advice for the conservation and management of pelagic sharks in the Atlantic. This Program was developed in 2013-2014 by the Sharks Species Group, and framed within the 2015-2020 SCRS Strategic Plan. Within this Program, a specific study on the age and growth of shortfin mako in the Atlantic was developed, with the purpose of contributing to the 2017 ICCAT SMA stock assessment. In the paper, we provide an update of the project, including preliminary growth models for the North Atlantic Ocean.Project "LL-Sharks: Mitigação das capturas de tubarões na pescaria de palangre de superfície (Ref: 31-03-05-FEP-44, funded by PROMAR)", Project "MAKO-WIDE - "A wide scale inter-hemispheric and inter-disciplinary study aiming the conservation of the shortfin mako shark in the Atlantic Ocean (Ref: FAPESP/19740/2014)", funded by FCT (Portuguese Foundation for Science and Technology) and FAPESP (São Paulo Research Foundation, Brazil), and Project SAFEWATERS SC7 (The provision of advice on the conservation of pelagic sharks associated to fishing activity under EU Sustainable Fisheries Partnership Agreements in the Atlantic Ocean) under the Framework Contract MARE/2012/21, funded by the European Commission. Additional satellite tags were acquired by NOAA in US-Uruguay and US-Portugal-Uruguay collaboration initiatives. Rui Coelho is supported by an Investigador-FCT contract from the Portuguese Foundation for Science and Technology (FCT) supported by the EU European Social Fund and the Programa Operacional Potencial Humano (Ref: IF/00253/2014). Catarina C. Santos is supported by an FCT Doctoral grant (Ref: SFRH/BD/139187/2018).info:eu-repo/semantics/draf

Age and growth of shortfin mako in the South Atlantic

The shortfin mako, Isurus oxyrinchus (Lamnidae), is regularly caught as by-catch in pelagic longline fisheries and is among the most vulnerable sharks to this fishery. The age and growth of I. oxyrinchus was studied along a wide South Atlantic region. Data from 332 specimens ranging in size from 90 to 330 cm fork length (FL) for females and 81 to 250 cm FL for males were analysed. Growth models were fitted using the von Bertalanffy growth equation re-parameterised to calculate L0, instead of t0, and a modification of this equation using the known size at birth. The von Bertalanffy growth equation with fixed L0 (size at birth = 63 cm FL) with resulting growth parameters of Linf = 218.5 cm FL, k = 0.170 year-1 for males and Linf = 263.1 cm FL, k = 0.112 year-1 for females, seemed to underestimate maximum length for this species, while overestimating k. Given the poorly estimated parameters we cannot, to this point, recommend the use of the South Atlantic growth curves.info:eu-repo/semantics/publishedVersio

Shark Research and Data Collection Program: progress on the age and growth of the shortfin mako in the Atlantic Ocean

This paper presents an update of the age and growth study within the ICCAT Shark Research and Data Collection Program (SRDCP), including the current development status and plans for the 2nd phase of the project. There are currently 469 vertebrae samples (205 females, 257 males and 7 specimens with unidentified sex) collected and processed from both the North and Southern hemispheres. The sample distribution is much more complete in the north, while in the south at this stage there are only samples from the equatorial region. The size range of the samples varies from 52 cm to 366 cm FL. The next steps of this projects is proposing a workshop on age reading and growth in order to prepare a reference set of vertebrae that can be used as a guideline for the readings of the remaining sample, and also discuss aspects of age validation and band deposition periodicity. The final results will be presented to the SCRS sharks working group in 2017, in order to contribute to the 2017 shortfin mako stock assessment.info:eu-repo/semantics/publishedVersio

Indirect Impact of PD-1/PD-L1 Blockade on a Murine Model of NK Cell Exhaustion

The induction of exhaustion on effector immune cells is an important limiting factor for cancer immunotherapy efficacy as these cells undergo a hierarchical loss of proliferation and cytolytic activity due to chronic stimulation. Targeting PD-1 has shown unprecedented clinical benefits for many cancers, which have been attributed to the prevention of immune suppression and exhaustion with enhanced anti-tumor responses. In this study, we sought to evaluate the role of the PD-1/PD-L1 pathway in murine natural killer (NK) cell activation, function, and exhaustion. In an in vivo IL-2-dependent exhaustion mouse model, neutralization of the PD-1/PD-L1 pathway improved NK cell activation after chronic stimulation when compared to control-treated mice. These cells displayed higher proliferative capabilities and enhanced granzyme B production. However, the blockade of these molecules during long-term in vitro IL-2 stimulation did not alter the progression of NK cell exhaustion (NCE), suggesting an indirect involvement of PD-1/PD-L1 on NCE. Given the expansion of CD8 T cells and regulatory T cells (Tregs) observed upon acute and chronic stimulation with IL-2, either of these two populations could influence NK cell homeostasis after PD-L1/PD-1 therapy. Importantly, CD8 T cell activation and functional phenotype were indeed enhanced by PD-1/PD-L1 therapy, particularly with anti-PD-1 treatment that resulted in the highest upregulation of CD25 during chronic stimulation and granted an advantage for IL-2 over NK cells. These results indicate a competition for resources between NK and CD8 T cells that arguably delays the onset of NCE rather than improving its activation during chronic stimulation. Supporting this notion, the depletion of CD8 T cells reversed the benefits of PD-1 therapy on chronically stimulated NK cells. These data suggest a bystander effect of anti-PD1 on NK cells, resulting from the global competition that exists between NK and CD8 T cells for IL-2 as a key regulator of these cells’ activation. Thus, achieving an equilibrium between these immune cells might be important to accomplish long-term efficacy during anti-PD-1/IL-2 therapy

Progression of atypical parkinsonian syndromes: PROSPECT-M-UK study implications for clinical trials

The advent of clinical trials of disease-modifying agents for neurodegenerative disease highlights the need for evidence-based endpoint selection. Here we report the longitudinal PROSPECT-M-UK study of progressive supranuclear palsy, corticobasal syndrome, multiple system atrophy and related disorders, to compare candidate clinical trial endpoints. In this multicentre United Kingdom study, participants were assessed with serial questionnaires, motor examination, neuropsychiatric and magnetic resonance imaging assessments at baseline, six and twelve-months. Participants were classified by diagnosis at baseline and study end, into Richardson syndrome, progressive supranuclear palsy-subcortical (progressive supranuclear palsy-parkinsonism and progressive gait freezing subtypes), progressive supranuclear palsy-cortical (progressive supranuclear palsy-frontal, progressive supranuclear palsy-speech-and-language, and progressive supranuclear palsy-corticobasal syndrome subtypes), multiple system atrophy-parkinsonism, multiple system atrophy-cerebellar, corticobasal syndrome with and without evidence of Alzheimer’s disease pathology and indeterminate syndromes. We calculated annual rate of change, with linear mixed modelling, and sample sizes for clinical trials of disease modifying agents, according to group and assessment type. Two hundred forty-three people were recruited (117 progressive supranuclear palsy, 68 corticobasal syndrome, 42 multiple system atrophy and 16 indeterminate; 138 [56.8%] male; age at recruitment 68.7 ± 8.61 years). One hundred fifty-nine completed six-month assessment (82 progressive supranuclear palsy, 27 corticobasal syndrome, 40 multiple system atrophy and 10 indeterminate) and 153 completed twelve-month assessment (80 progressive supranuclear palsy, 29 corticobasal syndrome, 35 multiple system atrophy and 9 indeterminate). Questionnaire, motor examination, neuropsychiatric and neuroimaging measures declined in all groups, with differences in longitudinal change between groups. Neuroimaging metrics would enable lower sample sizes to achieve equivalent power for clinical trials than cognitive and functional measures, often achieving N < 100 required for one-year two-arm trials (with 80% power to detect 50% slowing). However, optimal outcome measures were disease specific. In conclusion, phenotypic variance within progressive supranuclear palsy, corticobasal syndrome and multiple system atrophy is a major challenge to clinical trial design. Our findings provide an evidence base for selection of clinical trial endpoints, from potential functional, cognitive, clinical or neuroimaging measures of disease progression

Diagnosis Across the Spectrum of Progressive Supranuclear Palsy and Corticobasal Syndrome

IMPORTANCE: Patients with atypical parkinsonian syndromes (APS), including progressive supranuclear palsy (PSP), corticobasal syndrome (CBS) and multiple system atrophy (MSA), may be difficult to distinguish in early stages and are often misdiagnosed as Parkinson’s disease (PD). The diagnostic criteria for PSP have been updated to encompass a range of clinical subtypes, but have not been prospectively studied. OBJECTIVE: To define the distinguishing features of PSP and CBS, and to assess their usefulness in facilitating early diagnosis and separation from PD. DESIGN, SETTING, PARTICIPANTS: Cohort study which recruited APS and PD patients from movement disorder clinics across the UK from September 2015 to December 2018, and will follow up patients over 5 years. APS patients were stratified into PSP-Richardson syndrome, PSP-subcortical (including PSP-parkinsonism and PSP-progressive gait freezing cases), PSP-cortical (including PSP-frontal and PSP/CBS overlap cases), MSA-parkinsonism, MSA-cerebellar, CBS-Alzheimer’s and CBS-non-Alzheimer’s groups. MAIN OUTCOME MEASURES: Baseline group comparisons were conducted using: 1) Clinical trajectory; 2) Cognitive screening scales; 3) Serum neurofilament light chain (NF-L); 4) TRIM11, ApoE and MAPT genotypes; 5) Volumetric MRI. RESULTS: 222 APS cases (101 PSP, 55 MSA, 40 CBS and 26 indeterminate) were recruited (58% male; mean age at recruitment, 68.3 years). Age-matched controls (n=76) and PD cases (n=1967) were also included. Concordance between the ante-mortem clinical diagnosis and pathological diagnosis was achieved in 12/13 (92%) of PSP and CBS cases coming to post-mortem. Applying the MDS PSP diagnostic criteria almost doubled the number of patients diagnosed with PSP. 49/101 (49%) of reclassified PSP patients did not have classical PSP-Richardson syndrome. PSP-subcortical patients had a longer diagnostic latency and a more benign clinical trajectory than PSP-Richardson syndrome and PSP-cortical (p<0.05). PSP-subcortical was distinguished from PSP-cortical and PSP-Richardson syndrome by cortical volumetric MRI measures (AUC 0.84-0.89), cognitive profile (AUC 0.80-0.83), serum NF-L (AUC 0.75-0.83) and TRIM11 rs564309 genotype. Midbrain atrophy was a common feature of all PSP subtypes. 8/17 (47%) of CBS patients with CSF analysis were identified as having CBS-Alzheimer’s. CBS-Alzheimer’s patients had a longer diagnostic latency, relatively benign clinical trajectory, greater cognitive impairment and higher APOE-ε4 allele frequency than CBS-non-Alzheimer’s (p<0.05, AUC 0.80-0.87). Serum NF-L levels distinguished PD from PSP and CBS (p<0.05, AUC 0.80). CONCLUSIONS AND RELEVANCE: Clinical, therapeutic and epidemiological studies focusing on PSP-Richardson syndrome are likely to miss a large number of patients with underlying PSP-tau pathology. CSF analysis defines a distinct CBS-Alzheimer’s subgroup. PSP and CBS subtypes have distinct characteristics that may enhance their early diagnosis

Polymorphisms within autophagy-related genes as susceptibility biomarkers for multiple myeloma: a meta-analysis of three large cohorts and functional characterization

Functional data used in this project have been meticulously catalogued and archived in the BBMRI-NL data infrastructure (https://hfgp.bbmri.nl/, accessed on 12 February 2020) using the MOLGENIS open-source platform for scientific data.Multiple myeloma (MM) arises following malignant proliferation of plasma cells in the bone marrow, that secrete high amounts of specific monoclonal immunoglobulins or light chains, resulting in the massive production of unfolded or misfolded proteins. Autophagy can have a dual role in tumorigenesis, by eliminating these abnormal proteins to avoid cancer development, but also ensuring MM cell survival and promoting resistance to treatments. To date no studies have determined the impact of genetic variation in autophagy-related genes on MM risk. We performed meta-analysis of germline genetic data on 234 autophagy-related genes from three independent study populations including 13,387 subjects of European ancestry (6863 MM patients and 6524 controls) and examined correlations of statistically significant single nucleotide polymorphisms (SNPs; p < 1 × 10−9) with immune responses in whole blood, peripheral blood mononuclear cells (PBMCs), and monocyte-derived macrophages (MDM) from a large population of healthy donors from the Human Functional Genomic Project (HFGP). We identified SNPs in six loci, CD46, IKBKE, PARK2, ULK4, ATG5, and CDKN2A associated with MM risk (p = 4.47 × 10−4−5.79 × 10−14). Mechanistically, we found that the ULK4rs6599175 SNP correlated with circulating concentrations of vitamin D3 (p = 4.0 × 10−4), whereas the IKBKErs17433804 SNP correlated with the number of transitional CD24+CD38+ B cells (p = 4.8 × 10−4) and circulating serum concentrations of Monocyte hemoattractant Protein (MCP)-2 (p = 3.6 × 10−4). We also found that the CD46rs1142469 SNP corre lated with numbers of CD19+ B cells, CD19+CD3− B cells, CD5+ IgD− cells, IgM− cells, IgD−IgM− cells, and CD4−CD8− PBMCs (p = 4.9 × 10−4−8.6 × 10−4 ) and circulating concentrations of interleukin (IL)-20 (p = 0.00082). Finally, we observed that the CDKN2Ars2811710 SNP correlated with levels of CD4+EMCD45RO+CD27− cells (p = 9.3 × 10−4 ). These results suggest that genetic variants within these six loci influence MM risk through the modulation of specific subsets of immune cells, as well as vitamin D3−, MCP-2−, and IL20-dependent pathways.This work was supported by the European Union’s Horizon 2020 research and innovation program, N° 856620 and by grants from the Instituto de Salud Carlos III and FEDER (Madrid, Spain; PI17/02256 and PI20/01845), Consejería de Transformación Económica, Industria, Conocimiento y Universidades and FEDER (PY20/01282), from the CRIS foundation against cancer, from the Cancer Network of Excellence (RD12/10 Red de Cáncer), from the Dietmar Hopp Foundation and the German Ministry of Education and Science (BMBF: CLIOMMICS [01ZX1309]), and from National Cancer Institute of the National Institutes of Health under award numbers: R01CA186646, U01CA249955 (EEB).This work was also funded d by Portuguese National funds, through the Foundation for Science and Technology (FCT)—project UIDB/50026/2020 and UIDP/50026/2020 and by the project NORTE-01-0145-FEDER-000055, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)

Polymorphisms within Autophagy-Related Genes as Susceptibility Biomarkers for Multiple Myeloma: A Meta-Analysis of Three Large Cohorts and Functional Characterization

Multiple myeloma (MM) arises following malignant proliferation of plasma cells in the bone marrow, that secrete high amounts of specific monoclonal immunoglobulins or light chains, resulting in the massive production of unfolded or misfolded proteins. Autophagy can have a dual role in tumorigenesis, by eliminating these abnormal proteins to avoid cancer development, but also ensuring MM cell survival and promoting resistance to treatments. To date no studies have determined the impact of genetic variation in autophagy-related genes on MM risk. We performed meta-analysis of germline genetic data on 234 autophagy-related genes from three independent study populations including 13,387 subjects of European ancestry (6863 MM patients and 6524 controls) and examined correlations of statistically significant single nucleotide polymorphisms (SNPs; p \u3c 1 × 10−9) with immune responses in whole blood, peripheral blood mononuclear cells (PBMCs), and monocyte-derived macrophages (MDM) from a large population of healthy donors from the Human Functional Genomic Project (HFGP). We identified SNPs in six loci, CD46, IKBKE, PARK2, ULK4, ATG5, and CDKN2A associated with MM risk (p = 4.47 × 10−4−5.79 × 10−14). Mechanistically, we found that the ULK4rs6599175 SNP correlated with circulating concentrations of vitamin D3 (p = 4.0 × 10−4), whereas the IKBKErs17433804 SNP correlated with the number of transitional CD24+CD38+ B cells (p = 4.8 × 10−4) and circulating serum concentrations of Monocyte Chemoattractant Protein (MCP)-2 (p = 3.6 × 10−4). We also found that the CD46rs1142469 SNP correlated with numbers of CD19+ B cells, CD19+CD3− B cells, CD5+IgD− cells, IgM− cells, IgD−IgM− cells, and CD4−CD8− PBMCs (p = 4.9 × 10−4−8.6 × 10−4) and circulating concentrations of interleukin (IL)-20 (p = 0.00082). Finally, we observed that the CDKN2Ars2811710 SNP correlated with levels of CD4+EMCD45RO+CD27− cells (p = 9.3 × 10−4). These results suggest that genetic variants within these six loci influence MM risk through the modulation of specific subsets of immune cells, as well as vitamin D3−, MCP-2−, and IL20-dependent pathways

AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders.

AMPA receptors (AMPARs) are tetrameric ligand-gated channels made up of combinations of GluA1-4 subunits encoded by GRIA1-4 genes. GluA2 has an especially important role because, following post-transcriptional editing at the Q607 site, it renders heteromultimeric AMPARs Ca2+-impermeable, with a linear relationship between current and trans-membrane voltage. Here, we report heterozygous de novo GRIA2 mutations in 28 unrelated patients with intellectual disability (ID) and neurodevelopmental abnormalities including autism spectrum disorder (ASD), Rett syndrome-like features, and seizures or developmental epileptic encephalopathy (DEE). In functional expression studies, mutations lead to a decrease in agonist-evoked current mediated by mutant subunits compared to wild-type channels. When GluA2 subunits are co-expressed with GluA1, most GRIA2 mutations cause a decreased current amplitude and some also affect voltage rectification. Our results show that de-novo variants in GRIA2 can cause neurodevelopmental disorders, complementing evidence that other genetic causes of ID, ASD and DEE also disrupt glutamatergic synaptic transmission