Clinical sequencing of the retinitis pigmentosa gene RPGR in over 1,000 cases of vision loss.

RPGR pathogenic variants are the major cause of X-linked retinitis pigmentosa. Here, we report the results from 1,033 clinical DNA tests that included sequencing of RPGR. A total of 184 RPGR variants were identified: 78 pathogenic or likely pathogenic, 14 uncertain, and 92 likely benign or benign. Among the pathogenic and likely pathogenic variants, 23 were novel, and most were frameshift or nonsense mutations (87%) and enriched (67%) in RPGR exon 15 (ORF15). Identical pathogenic variants found in different families were largely on different haplotype backgrounds, indicating relatively frequent, recurrent RPGR mutations. None of the 16 mother/affected son pairs showed de novo mutations; all 16 mothers were heterozygous for the pathogenic variant. These last two observations support the occurrence of most RPGR mutations in the male germline.

Atmospheric isoprene measurements reveal larger-than-expected Southern Ocean emissions.

Isoprene is a key trace component of the atmosphere emitted by vegetation and other organisms. It is highly reactive and can impact atmospheric composition and climate by affecting the greenhouse gases ozone and methane and secondary organic aerosol formation. Marine fluxes are poorly constrained due to the paucity of long-term measurements; this in turn limits our understanding of isoprene cycling in the ocean. Here we present the analysis of isoprene concentrations in the atmosphere measured across the Southern Ocean over 4 months in the summertime. Some of the highest concentrations ( >500 ppt) originated from the marginal ice zone in the Ross and Amundsen seas, indicating the marginal ice zone is a significant source of isoprene at high latitudes. Using the United Kingdom Earth System Model we show that current estimates of sea-to-air isoprene fluxes underestimate observed isoprene by a factor >20. A daytime source of isoprene is required to reconcile models with observations. The model presented here suggests such an increase in isoprene emissions would lead to >8% decrease in the hydroxyl radical in regions of the Southern Ocean, with implications for our understanding of atmospheric oxidation and composition in remote environments, often used as proxies for the pre-industrial atmosphere.

Enhanced weathering in the US Corn Belt delivers carbon removal with agronomic benefits.

Terrestrial enhanced weathering (EW) of silicate rocks, such as crushed basalt, on farmlands is a promising scalable atmospheric carbon dioxide removal (CDR) strategy that urgently requires performance assessment with commercial farming practices. We report findings from a large-scale replicated EW field trial across a typical maize-soybean rotation on an experimental farm in the heart of the United Sates Corn Belt over 4 y (2016 to 2020). We show an average combined loss of major cations (Ca2+ and Mg2+) from crushed basalt applied each fall over 4 y (50 t ha-1 y-1) gave a conservative time-integrated cumulative CDR potential of 10.5 ± 3.8 t CO2 ha-1. Maize and soybean yields increased significantly (P < 0.05) by 12 to 16% with EW following improved soil fertility, decreased soil acidification, and upregulation of root nutrient transport genes. Yield enhancements with EW were achieved with significantly (P < 0.05) increased key micro- and macronutrient concentrations (including potassium, magnesium, manganese, phosphorus, and zinc), thus improving or maintaining crop nutritional status. We observed no significant increase in the content of trace metals in grains of maize or soybean or soil exchangeable pools relative to controls. Our findings suggest that widespread adoption of EW across farming sectors has the potential to contribute significantly to net-zero greenhouse gas emissions goals while simultaneously improving food and soil security.

Chemistry-albedo feedbacks offset up to a third of forestation's CO2 removal benefits.

Forestation is widely proposed for carbon dioxide (CO2) removal, but its impact on climate through changes to atmospheric composition and surface albedo remains relatively unexplored. We assessed these responses using two Earth system models by comparing a scenario with extensive global forest expansion in suitable regions to other plausible futures. We found that forestation increased aerosol scattering and the greenhouse gases methane and ozone following increased biogenic organic emissions. Additionally, forestation decreased surface albedo, which yielded a positive radiative forcing (i.e., warming). This offset up to a third of the negative forcing from the additional CO2 removal under a 4°C warming scenario. However, when forestation was pursued alongside other strategies that achieve the 2°C Paris Agreement target, the offsetting positive forcing was smaller, highlighting the urgency for simultaneous emission reductions.

Chemistry-driven changes strongly influence climate forcing from vegetation emissions.

Biogenic volatile organic compounds (BVOCs) affect climate via changes to aerosols, aerosol-cloud interactions (ACI), ozone and methane. BVOCs exhibit dependence on climate (causing a feedback) and land use but there remains uncertainty in their net climatic impact. One factor is the description of BVOC chemistry. Here, using the earth-system model UKESM1, we quantify chemistry's influence by comparing the response to doubling BVOC emissions in the pre-industrial with standard and state-of-science chemistry. The net forcing (feedback) is positive: ozone and methane increases and ACI changes outweigh enhanced aerosol scattering. Contrary to prior studies, the ACI response is driven by cloud droplet number concentration (CDNC) reductions from suppression of gas-phase SO2 oxidation. With state-of-science chemistry the feedback is 43% smaller as lower oxidant depletion yields smaller methane increases and CDNC decreases. This illustrates chemistry's significant influence on BVOC's climatic impact and the more complex pathways by which BVOCs influence climate than currently recognised.

Updated variant curation expert panel criteria and pathogenicity classifications for 251 variants for RYR1-related malignant hyperthermia susceptibility.

The ClinGen malignant hyperthermia susceptibility (MHS) variant curation expert panel specified the American College of Medical Genetics and Genomics/Association of Molecular Pathologists (ACMG/AMP) criteria for RYR1-related MHS and a pilot analysis of 84 variants was published. We have now classified an additional 251 variants for RYR1-related MHS according to current ClinGen standards and updated the criteria where necessary. Criterion PS4 was modified such that individuals with multiple RYR1 variants classified as pathogenic (P), likely pathogenic (LP), or variant of uncertain significance (VUS) were not considered as providing evidence for pathogenicity. Criteria PS1 and PM5 were revised to consider LP variants at the same amino-acid residue as providing evidence for pathogenicity at reduced strength. Finally, PM1 was revised such that if PS1 or PM5 are used PM1, if applicable, should be downgraded to supporting. Of the 251 RYR1 variants, 42 were classified as P/LP, 16 as B/LB, and 193 as VUS. The primary driver of 175 VUS classifications was insufficient evidence supporting pathogenicity, rather than evidence against pathogenicity. Functional data supporting PS3/BS3 was identified for only 13 variants. Based on the posterior probabilities of pathogenicity and variant frequencies in gnomAD, we estimated the prevalence of individuals with RYR1-related MHS pathogenic variants to be between 1/300 and 1/1075, considerably higher than current estimates. We have updated ACMG/AMP criteria for RYR1-related MHS and classified 251 variants. We suggest that prioritization of functional studies is needed to resolve the large number of VUS classifications and allow for appropriate risk assessment. RYR1-related MHS pathogenic variants are likely to be more common than currently appreciated.

Variant curation expert panel recommendations for RYR1 pathogenicity classifications in malignant hyperthermia susceptibility.

PURPOSE: As a ClinGen Expert Panel (EP) we set out to adapt the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) pathogenicity criteria for classification of RYR1 variants as related to autosomal dominantly inherited malignant hyperthermia (MH). METHODS: We specified ACMG/AMP criteria for variant classification for RYR1 and MH. Proposed rules were piloted on 84 variants. We applied quantitative evidence calibration for several criteria using likelihood ratios based on the Bayesian framework. RESULTS: Seven ACMG/AMP criteria were adopted without changes, nine were adopted with RYR1-specific modifications, and ten were dropped. The in silico (PP3 and BP4) and hotspot criteria (PM1) were evaluated quantitatively. REVEL gave an odds ratio (OR) of 23:1 for PP3 and 14:1 for BP4 using trichotomized cutoffs of ≥0.85 (pathogenic) and ≤0.5 (benign). The PM1 hotspot criterion had an OR of 24:1. PP3 and PM1 were implemented at moderate strength. Applying the revised ACMG/AMP criteria to 44 recognized MH variants, 29 were classified as pathogenic, 13 as likely pathogenic, and 2 as variants of uncertain significance. CONCLUSION: Curation of these variants will facilitate classification of RYR1/MH genomic testing results, which is especially important for secondary findings analyses. Our approach to quantitatively calibrating criteria is generalizable to other variant curation expert panels.

Angiogenesis is Differentially Modulated by Anthocyanin and Phenolic Acid Extracts from Wild Blueberry (V. angustifolium) Through PI3K Pathway.

Wild blueberries rank very high in anthocyanins (ACNs) and phenolic acids (PA) among other berries. Previous work from our group has documented their beneficial effects. In this study, human umbilical vein endothelial cells were used, and ACNs, PAs, and their combination (ACNs:PAs) at concentrations of 0.002, 8, 15, 60, and 120 µg/mL were tested for endothelial tube formation. Treatment with ACNs decreased, while treatment with PAs and ACNs:PAs increased overall endothelial cell tube formation compared to control. Endothelial cells exposed to ACNs downregulated gene expression of AKT1 and endothelial nitric oxide synthase (eNOS), while PAs upregulated AKT1 and vascular endothelial growth factor (VEGF) gene expression. Combination of ACNs:PAs decreased gene expression of AKT1 and eNOS, while protein levels of AKT1 increased. In summary, based on the type of wild blueberry extract, angiogenesis is differentially modulated and is concentration dependent. Further experiments will delineate the mechanism(s) of the differential action of the aforementioned extracts on angiogenesis.

Minimal Climate Impacts From Short-Lived Climate Forcers Following Emission Reductions Related to the COVID-19 Pandemic.

We present an assessment of the impacts on atmospheric composition and radiative forcing of short-lived pollutants following a worldwide decrease in anthropogenic activity and emissions comparable to what has occurred in response to the COVID-19 pandemic, using the global composition-climate model United Kingdom Chemistry and Aerosols Model (UKCA). Emission changes reduce tropospheric hydroxyl radical and ozone burdens, increasing methane lifetime. Reduced SO2 emissions and oxidizing capacity lead to a decrease in sulfate aerosol and increase in aerosol size, with accompanying reductions to cloud droplet concentration. However, large reductions in black carbon emissions increase aerosol albedo. Overall, the changes in ozone and aerosol direct effects (neglecting aerosol-cloud interactions which were statistically insignificant but whose response warrants future investigation) yield a radiative forcing of -33 to -78 mWm-2. Upon cessation of emission reductions, the short-lived climate forcers rapidly return to pre-COVID levels; meaning, these changes are unlikely to have lasting impacts on climate assuming emissions return to pre-intervention levels.

Genomic Screening for Malignant Hyperthermia Susceptibility.

It is timely to consider the utility and practicability of screening for malignant hyperthermia susceptibility using genomic testing. Here the authors pose a simple, but bold question: what would it take to end deaths from malignant hyperthermia? The authors review recent advances and propose a scientific and clinical pathway toward this audacious goal to provoke discussion in the field.

Phenolic and anthocyanin fractions from wild blueberries (V. angustifolium) differentially modulate endothelial cell migration partially through RHOA and RAC1.

The present study investigates the effect of anthocyanin (ACN), phenolic acid (PA) fractions, and their combination (ACNs:PAs) from wild blueberry powder (Vaccinum angustifolium) on the speed of endothelial cell migration, gene expression, and protein levels of RAC1 and RHOA associated with acute exposure to different concentrations of ACNs and PAs. Time-lapse videos were analyzed and endothelial cell speed was calculated. Treatment with ACNs at 60 µg/mL inhibited endothelial cell migration rate ( P ≤ 0.05) while treatment with PAs at 0.002 µg/mL ( P ≤ 0.0001), 60 µg/mL ( P ≤ 0.0001), and 120 µg/mL ( P ≤ 0.01) significantly increased endothelial cell migration rate compared with control. Moreover, exposure of HUVECs to ACNs:PAs at 8:8 µg/mL ( P ≤ 0.05) and 60:60 µg/mL increased ( P ≤ 0.001) endothelial cell migration. Gene expression of RAC1 and RHOA significantly increased 2 hours after exposure with all treatments. No effect of the above fractions was observed on the protein levels of RAC1 and RHOA. Findings suggest that endothelial cell migration is differentially modulated based on the type of blueberry extract (ACN or PA fraction) and is concentration-dependent. Future studies should determine the mechanism of the differential action of the above fractions on endothelial cell migration.

T Cells Deficient in Diacylglycerol Kinase ζ Are Resistant to PD-1 Inhibition and Help Create Persistent Host Immunity to Leukemia.

Efforts to improve the efficacy of adoptive T-cell therapies and immune checkpoint therapies in myelogenous leukemia are desired. In this study, we evaluated the antileukemia activity of adoptively transferred polyclonal cancer antigen-reactive T cells deficient in the regulator diacylglycerol kinase zeta (DGKζ) with or without PD-1/PD-L1 blockade. In the C1498 mouse model of myeloid leukemia, we showed that leukemia was eradicated more effectively in DGKζ-deficient (DGKζ-/-) mice than wild-type mice. T cells transferred from DGKζ-deficient mice to wild-type tumor-bearing recipients conferred this benefit. Leukemia clearance was similar to mice treated with anti-PD-L1. Strikingly, we found that the activity of adoptively transferred DGKζ-/- T cells relied partly on induction of sustainable host T-cell immunity. Transferring DGKζ-deficient T cells increased the levels of IFNγ and other cytokines in recipient mice, especially with coadministration of anti-PD-L1. Overall, our results offered evidence that targeting DGKζ may leverage the efficacy of adoptive T-cell and immune checkpoint therapies in leukemia treatment. Furthermore, they suggest that DGKζ targeting might decrease risks of antigen escape or resistance to immune checkpoint blockade. Cancer Res; 77(20); 5676-86. ©2017 AACR.

Adoptive cell therapy using PD-1+ myeloma-reactive T cells eliminates established myeloma in mice.

BACKGROUND: Adoptive cellular therapy (ACT) with cancer antigen-reactive T cells following lymphodepletive pre-conditioning has emerged as a potentially curative therapy for patients with advanced cancers. However, identification and enrichment of appropriate T cell subsets for cancer eradication remains a major challenge for hematologic cancers. METHODS: PD-1+ and PD-1- T cell subsets from myeloma-bearing mice were sorted and analyzed for myeloma reactivity in vitro. In addition, the T cells were activated and expanded in culture and given to syngeneic myeloma-bearing mice as ACT. RESULTS: Myeloma-reactive T cells were enriched in the PD-1+ cell subset. Similar results were also observed in a mouse AML model. PD-1+ T cells from myeloma-bearing mice were found to be functional, they could be activated and expanded ex vivo, and they maintained their anti-myeloma reactivity after expansion. Adoptive transfer of ex vivo-expanded PD-1+ T cells together with a PD-L1 blocking antibody eliminated established myeloma in Rag-deficient mice. Both CD8 and CD4 T cell subsets were important for eradicating myeloma. Adoptively transferred PD-1+ T cells persisted in recipient mice and were able to mount an adaptive memory immune response. CONCLUSIONS: These results demonstrate that PD-1 is a biomarker for functional myeloma-specific T cells, and that activated and expanded PD-1+ T cells can be effective as ACT for myeloma. Furthermore, this strategy could be useful for treating other hematologic cancers.

E-cadherin re-expression shows in vivo evidence for mesenchymal to epithelial transition in clonal metastatic breast tumor cells.

Substantial experimental evidence has shown that dedifferentiation from an epithelial state to a mesenchymal-like state (EMT) drives tumor cell metastasis. This transition facilitates tumor cells to acquire motility and invasive features. Intriguingly, tumor cells at the metastatic site are primarily epithelial, and it is believed that they differentiate back to an epithelial state by a process called mesenchymal to epithelial transition (MET). However, there is little in vivo evidence to support the MET process. To investigate EMT and MET in vivo, we generated two epithelial (E) and two mesenchymal (M) primary clonal cell lines from a spontaneous mouse mammary tumor (Tg MMTV/neu). These cells were labeled with reporters (GFP and luciferase), and tracked in vivo during primary tumor growth and subsequent secondary metastasis. Once E cells were implanted into the mammary fat pad, E-cadherin expression progressively decreased and continued to decrease as the primary tumor enlarged over time. A greater percentage of E tumor cells expressed E-cadherin at the secondary metastatic site as compared to the corresponding primary tumor site. Collectively, these data provide direct in vivo evidence that epithelial tumor cells have metastatic potential, undergo EMT at the primary tumor site, and MET at the metastatic site.

Mitochondria-Targeted Analogues of Metformin Exhibit Enhanced Antiproliferative and Radiosensitizing Effects in Pancreatic Cancer Cells.

Metformin (Met) is an approved antidiabetic drug currently being explored for repurposing in cancer treatment based on recent evidence of its apparent chemopreventive properties. Met is weakly cationic and targets the mitochondria to induce cytotoxic effects in tumor cells, albeit not very effectively. We hypothesized that increasing its mitochondria-targeting potential by attaching a positively charged lipophilic substituent would enhance the antitumor activity of Met. In pursuit of this question, we synthesized a set of mitochondria-targeted Met analogues (Mito-Mets) with varying alkyl chain lengths containing a triphenylphosphonium cation (TPP(+)). In particular, the analogue Mito-Met10, synthesized by attaching TPP(+) to Met via a 10-carbon aliphatic side chain, was nearly 1,000 times more efficacious than Met at inhibiting cell proliferation in pancreatic ductal adenocarcinoma (PDAC). Notably, in PDAC cells, Mito-Met10 potently inhibited mitochondrial complex I, stimulating superoxide and AMPK activation, but had no effect in nontransformed control cells. Moreover, Mito-Met10 potently triggered G1 cell-cycle phase arrest in PDAC cells, enhanced their radiosensitivity, and more potently abrogated PDAC growth in preclinical mouse models, compared with Met. Collectively, our findings show how improving the mitochondrial targeting of Met enhances its anticancer activities, including aggressive cancers like PDAC in great need of more effective therapeutic options. Cancer Res; 76(13); 3904-15. ©2016 AACR.

The Effects of Local Warming on Surgical Site Infection.

BACKGROUND: Surgical site infections (SSI) account for a major proportion of hospital-acquired infections. They are associated with longer hospital stay, readmissions, increased costs, mortality, and morbidity. Reducing SSI is a goal of the Surgical Care Improvement Project and identifying interventions that reduce SSI effectively is of interest. In a single-blinded randomized controlled trial (RCT) we evaluated the effect of localized warming applied to surgical incisions on SSI development and selected cellular (immune, endothelial) and tissue responses (oxygenation, collagen). METHODS: After Institutional Review Board approval and consent, patients having open bariatric, colon, or gynecologic-oncologic related operations were enrolled and randomly assigned to local incision warming (6 post-operative treatments) or non-warming. A prototype surgical bandage was used for all patients. The study protocol included intra-operative warming to maintain core temperature ≥36°C and administration of 0.80 FIO2. Patients were followed for 6 wks for the primary outcome of SSI determined by U.S. Centers for Disease Control (CDC) criteria and ASEPSIS scores (additional treatment; presence of serous discharge, erythema, purulent exudate, and separation of the deep tissues; isolation of bacteria; and duration of inpatient stay). Tissue oxygen (PscO2) and samples for cellular analyses were obtained using subcutaneous polytetrafluoroethylene (ePTFE) tubes and oxygen micro-electrodes implanted adjacent to the incision. Cellular and tissue ePTFE samples were evaluated using flow cytometry, immunohistochemistry, and Sircol™ collagen assay (Biocolor Ltd., Carrickfergus, United Kingdom). RESULTS: One hundred forty-six patients participated (n=73 per group). Study groups were similar on demographic parameters and for intra-operative management factors. The CDC defined rate of SSI was 18%; occurrence of SSI between groups did not differ (p=0.27). At 2 wks, warmed patients had better ASEPSIS scores (p=0.04) but this difference was not observed at 6 wks. There were no significant differences in immune, endothelial cell, or collagen responses between groups. On post-operative days one to two, warmed patients had greater PscO2 change scores with an average PscO2 increase of 9-10 mm Hg above baseline (p<0.04). CONCLUSIONS: Post-operative local warming compared with non-warming followed in this study, which included intra-operative warming to maintain normothermia and FIO2 level of 0.80, did not reduce SSI and had no effect on immune, endothelial cell presence, or collagen synthesis. PscO2 increased significantly with warming, however, the increase was modest and less than expected or what has been observed in studies testing other interventions.

Immune modulating effects of cyclophosphamide and treatment with tumor lysate/CpG synergize to eliminate murine neuroblastoma.

BACKGROUND: Neuroblastoma is a pediatric cancer of neural crest origin. Despite aggressive treatment, mortality remains at 40 % for patients with high-risk disseminated disease, underscoring the need to test new combinations of therapies. In murine tumor models, our laboratory previously showed that T cell-mediated anti-tumor immune responses improve in the context of lymphopenia. The goal of this study was to incorporate lymphodepletion into an effective immune therapy that can be easily translated into neuroblastoma standard of care. Based on the lymphodepleting effects of cyclophosphamide, we hypothesized that cyclophosphamide would synergize with the TLR9 agonist, CpG oligodeoxynucleotide (ODN), to produce a T cell-mediated anti-neuroblastoma effect. METHODS: To test this hypothesis, we used the AgN2a aggressive murine model of neuroblastoma. Mice bearing subcutaneous tumors were treated with cyclophosphamide followed by treatment with tumor cell lysate mixed with CpG ODN injected at the tumor site. RESULTS: Subcutaneous neuroblastoma regressed only in mice that were treated with 100 mg/kg cyclophosphamide prior to receiving treatments of tumor lysate mixed with CpG ODN. The anti-neuroblastoma response was T cell-mediated. Synergy between cyclophosphamide and the tumor lysate/CpG ODN treatment influenced the production of anti-tumor CD8 T cell effectors, and dendritic cell homeostasis. For clinical consideration, an allogeneic tumor lysate was used effectively with this protocol to eliminate AgN2a tumor in vivo. CONCLUSION: Synergistic immune modulating effects of cyclophosphamide and a treatment containing tumor cell lysate and CpG ODN provide T cell-mediated anti-tumor activity against murine neuroblastoma.

Combined immune checkpoint protein blockade and low dose whole body irradiation as immunotherapy for myeloma.

BACKGROUND: Multiple myeloma is characterized by the presence of transformed neoplastic plasma cells in the bone marrow and is generally considered to be an incurable disease. Successful treatments will likely require multi-faceted approaches incorporating conventional drug therapies, immunotherapy and other novel treatments. Our lab previously showed that a combination of transient lymphodepletion (sublethal whole body irradiation) and PD-1/PD-L1 blockade generated anti-myeloma T cell reactivity capable of eliminating established disease. We hypothesized that blocking a combination of checkpoint receptors in the context of low-dose, lymphodepleting whole body radiation would boost anti-tumor immunity. METHODS: To test our central hypothesis, we utilized a 5T33 murine multiple myeloma model. Myeloma-bearing mice were treated with a low dose of whole body irradiation and combinations of blocking antibodies to PD-L1, LAG-3, TIM-3, CD48 (the ligand for 2B4) and CTLA4. RESULTS: Temporal phenotypic analysis of bone marrow from myeloma-bearing mice demonstrated that elevated percentages of PD-1, 2B4, LAG-3 and TIM-3 proteins were expressed on T cells. When PD-L1 blockade was combined with blocking antibodies to LAG-3, TIM-3 or CTLA4, synergistic or additive increases in survival were observed (survival rates improved from ~30% to >80%). The increased survival rates correlated with increased frequencies of tumor-reactive CD8 and CD4 T cells. When stimulated in vitro with myeloma cells, CD8 T cells from treated mice produced elevated levels proinflammatory cytokines. Cytokines were spontaneously released from CD4 T cells isolated from mice treated with PD-L1 plus CTLA4 blocking antibodies. CONCLUSIONS: These data indicate that blocking PD-1/PD-L1 interactions in conjunction with other immune checkpoint proteins provides synergistic anti-tumor efficacy following lymphodepletive doses of whole body irradiation. This strategy is a promising combination strategy for myeloma and other hematologic malignancies.

Ferrocene-Boronic Acid-Fructose Binding Based on Dual-Plate Generator-Collector Voltammetry and Square-Wave Voltammetry.

The interaction of ferrocene-boronic acid with fructose is investigated in aqueous 0.1 m phosphate buffer at pH 7, 8 and 9. Two voltammetric methods, based on 1) a dual-plate generator-collector micro-trench electrode (steady state) and 2) a square-wave voltammetry (transient) method, are applied and compared in terms of mechanistic resolution. A combination of experimental data is employed to obtain new insights into the binding rates and the cumulative binding constants for both the reduced ferrocene-boronic acid (pH dependent and weakly binding) and for the oxidised ferrocene-boronic acid (pH independent and strongly binding).