CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes.

CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

Distinct hypertrophic cardiomyopathy genotypes result in convergent sarcomeric proteoform profiles revealed by top-down proteomics.

Hypertrophic cardiomyopathy (HCM) is the most common heritable heart disease. Although the genetic cause of HCM has been linked to mutations in genes encoding sarcomeric proteins, the ability to predict clinical outcomes based on specific mutations in HCM patients is limited. Moreover, how mutations in different sarcomeric proteins can result in highly similar clinical phenotypes remains unknown. Posttranslational modifications (PTMs) and alternative splicing regulate the function of sarcomeric proteins; hence, it is critical to study HCM at the level of proteoforms to gain insights into the mechanisms underlying HCM. Herein, we employed high-resolution mass spectrometry-based top-down proteomics to comprehensively characterize sarcomeric proteoforms in septal myectomy tissues from HCM patients exhibiting severe outflow track obstruction (n = 16) compared to nonfailing donor hearts (n = 16). We observed a complex landscape of sarcomeric proteoforms arising from combinatorial PTMs, alternative splicing, and genetic variation in HCM. A coordinated decrease of phosphorylation in important myofilament and Z-disk proteins with a linear correlation suggests PTM cross-talk in the sarcomere and dysregulation of protein kinase A pathways in HCM. Strikingly, we discovered that the sarcomeric proteoform alterations in the myocardium of HCM patients undergoing septal myectomy were remarkably consistent, regardless of the underlying HCM-causing mutations. This study suggests that the manifestation of severe HCM coalesces at the proteoform level despite distinct genotype, which underscores the importance of molecular characterization of HCM phenotype and presents an opportunity to identify broad-spectrum treatments to mitigate the most severe manifestations of this genetically heterogenous disease.

An Unbiased Proteomics Method to Assess the Maturation of Human Pluripotent Stem Cell-Derived Cardiomyocytes.

RATIONALE: Human pluripotent stem cell (hPSC)-derived cardiomyocytes exhibit the properties of fetal cardiomyocytes, which limits their applications. Various methods have been used to promote maturation of hPSC-cardiomyocytes; however, there is a lack of an unbiased and comprehensive method for accurate assessment of the maturity of hPSC-cardiomyocytes. OBJECTIVE: We aim to develop an unbiased proteomics strategy integrating high-throughput top-down targeted proteomics and bottom-up global proteomics for the accurate and comprehensive assessment of hPSC-cardiomyocyte maturation. METHODS AND RESULTS: Utilizing hPSC-cardiomyocytes from early- and late-stage 2-dimensional monolayer culture and 3-dimensional engineered cardiac tissue, we demonstrated the high reproducibility and reliability of a top-down proteomics method, which enabled simultaneous quantification of contractile protein isoform expression and associated post-translational modifications. This method allowed for the detection of known maturation-associated contractile protein alterations and, for the first time, identified contractile protein post-translational modifications as promising new markers of hPSC-cardiomyocytes maturation. Most notably, decreased phosphorylation of α-tropomyosin was found to be associated with hPSC-cardiomyocyte maturation. By employing a bottom-up global proteomics strategy, we identified candidate maturation-associated markers important for sarcomere organization, cardiac excitability, and Ca2+ homeostasis. In particular, upregulation of myomesin 1 and transmembrane 65 was associated with hPSC-cardiomyocyte maturation and validated in cardiac development, making these promising markers for assessing maturity of hPSC-cardiomyocytes. We have further validated α-actinin isoforms, phospholamban, dystrophin, αB-crystallin, and calsequestrin 2 as novel maturation-associated markers, in the developing mouse cardiac ventricles. CONCLUSIONS: We established an unbiased proteomics method that can provide accurate and specific assessment of the maturity of hPSC-cardiomyocytes and identified new markers of maturation. Furthermore, this integrated proteomics strategy laid a strong foundation for uncovering the molecular pathways involved in cardiac development and disease using hPSC-cardiomyocytes.

BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes.

Polycomb repressive epigenetic complexes are recurrently dysregulated in cancer. Unlike polycomb repressive complex 2 (PRC2), the role of PRC1 in oncogenesis and therapy resistance is not well-defined. Here, we demonstrate that highly recurrent mutations of the PRC1 subunits BCOR and BCORL1 in leukemia disrupt assembly of a noncanonical PRC1.1 complex, thereby selectively unlinking the RING-PCGF enzymatic core from the chromatin-targeting auxiliary subcomplex. As a result, BCOR-mutated PRC1.1 is localized to chromatin but lacks repressive activity, leading to epigenetic reprogramming and transcriptional activation at target loci. We define a set of functional targets that drive aberrant oncogenic signaling programs in PRC1.1-mutated cells and primary patient samples. Activation of these PRC1.1 targets in BCOR-mutated cells confers acquired resistance to treatment while sensitizing to targeted kinase inhibition. Our study thus reveals a novel epigenetic mechanism that explains PRC1.1 tumor-suppressive activity and identifies a therapeutic strategy in PRC1.1-mutated cancer. SIGNIFICANCE: We demonstrate that BCOR and BCORL1 mutations in leukemia unlink PRC1.1 repressive function from target genes, resulting in epigenetic reprogramming and activation of aberrant cell signaling programs that mediate treatment resistance. Our study provides mechanistic insights into the pathogenesis of PRC1.1-mutated leukemia that inform novel therapeutic approaches. This article is highlighted in the In This Issue feature, p. 85.

Adding venetoclax to fludarabine/busulfan RIC transplant for high-risk MDS and AML is feasible, safe, and active.

Adding the selective BCL-2 inhibitor venetoclax to reduced-intensity conditioning chemotherapy (fludarabine and busulfan [FluBu2]) may enhance antileukemic cytotoxicity and thereby reduce the risk of posttransplant relapse. This phase 1 study investigated the recommended phase 2 dose (RP2D) of venetoclax, a BCL-2 selective inhibitor, when added to FluBu2 in adult patients with high-risk acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and MDS/myeloproliferative neoplasms (MPN) undergoing transplant. Patients received dose-escalated venetoclax (200-400 mg daily starting day -8 for 6-7 doses) in combination with fludarabine 30 mg/m2 per day for 4 doses and busulfan 0.8 mg/kg twice daily for 8 doses on day -5 to day -2 (FluBu2). Transplant related-toxicity was evaluated from the first venetoclax dose on day -8 to day 28. Twenty-two patients were treated. At study entry, 5 patients with MDS and MDS/MPN had 5% to 10% marrow blasts, and 18 (82%) of 22 had a persistent detectable mutation. Grade 3 adverse events included mucositis, diarrhea, and liver transaminitis (n = 3 each). Neutrophil/platelet recovery and acute/chronic graft-versus-host-disease rates were similar to those of standard FluBu2. No dose-limiting toxicities were observed. The RP2D of venetoclax was 400 mg daily for 7 doses. With a median follow-up of 14.7 months (range, 8.6-24.8 months), median overall survival was not reached, and progression-free survival was 12.2 months (95% confidence interval, 6.0-not estimable). In patients with high-risk AML, MDS, and MDS/MPN, adding venetoclax to FluBu2 was feasible and safe. To further address relapse risk, assessment of maintenance therapy after venetoclax plus FluBu2 transplant is ongoing. This study was registered at clinicaltrials.gov as #NCT03613532.

Pistachio nuts reduce triglycerides and body weight by comparison to refined carbohydrate snack in obese subjects on a 12-week weight loss program.

OBJECTIVE: There is a widely held view that, due to high fat content, snacking on nuts will lead to weight gain, ultimately causing unhealthy changes in lipid profiles. This study is designed to study the effects of pistachio snack consumption on body weight and lipid levels in obese participants under real-world conditions. METHODS: Participants were randomly assigned to consume 1 of 2 isocaloric weight reduction diets for 12 weeks, with each providing 500 cal per day less than resting metabolic rate. Each diet included an afternoon snack of either 53 g (240 cal) of salted pistachios (n  =  31) or 56 g of salted pretzels (220 cal; n  =  28). RESULTS: Both groups lost weight during the 12-week study (time trend, p < 0.001), but there were significant differences in the changes in body mass index between the pretzel and pistachio groups (pistachio, 30.1 ± 0.4 to 28.8 ± 0.4 vs. pretzel, 30.9 ± 0.4 to 30.3 ± 0.5). At 6 and 12 weeks, triglycerides were significantly lower in the pistachio group compared with the pretzel group (88.04 ± 9.80 mg/dL vs. 144.56 ± 18.86 mg/dL, p  =  0.01 at 6 weeks and 88.10 ± 6.78 mg/dL vs. 132.15 ± 16.76 mg/dL, p  =  0.02 at 12 weeks), and there was a time trend difference between the 2 groups over the 12 weeks (p < 0.01). There were no significant differences in total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, insulin, or glucose between the 2 groups. CONCLUSION: Pistachios can be consumed as a portion-controlled snack for individuals restricting calories to lose weight without concern that pistachios will cause weight gain. By comparison to refined carbohydrate snacks such as pretzels, pistachios may have beneficial effects on triglycerides as well.

Absorption of silicon from artesian aquifer water and its impact on bone health in postmenopausal women: a 12 week pilot study.

BACKGROUND: Decreased bone mineral density and osteoporosis in postmenopausal women represents a growing source of physical limitations and financial concerns in our aging population. While appropriate medical treatments such as bisphosphonate drugs and hormone replacement therapy exist, they are associated with serious side effects such as osteonecrosis of the jaw or increased cardiovascular risk. In addition to calcium and vitamin D supplementation, previous studies have demonstrated a beneficial effect of dietary silicon on bone health. This study evaluated the absorption of silicon from bottled artesian aquifer water and its effect on markers of bone metabolism. METHODS: Seventeen postmenopausal women with low bone mass, but without osteopenia or osteoporosis as determined by dual x-ray absorptiometry (DEXA) were randomized to drink one liter daily of either purified water of low-silicon content (PW) or silicon-rich artesian aquifer water (SW) (86 mg/L silica) for 12 weeks. Urinary silicon and serum markers of bone metabolism were measured at baseline and after 12 weeks and analyzed with two-sided t-tests with p < 0.05 defined as significant. RESULTS: The urinary silicon level increased significantly from 0.016 ± 0.010 mg/mg creatinine at baseline to 0.037 ± 0.014 mg/mg creatinine at week 12 in the SW group (p = 0.003), but there was no change for the PW group (0.010 ± 0.004 mg/mg creatinine at baseline vs. 0.009 ± 0.006 mg/mg creatinine at week 12, p = 0.679). The urinary silicon for the SW group was significantly higher in the silicon-rich water group compared to the purified water group (p < 0.01). NTx, a urinary marker of bone resorption did not change during the study and was not affected by the silicon water supplementation. No significant change was observed in the serum markers of bone formation compared to baseline measurements for either group. CONCLUSIONS: These findings indicate that bottled water from artesian aquifers is a safe and effective way of providing easily absorbed dietary silicon to the body. Although the silicon did not affect bone turnover markers in the short-term, the mineral's potential as an alternative prevention or treatment to drug therapy for osteoporosis warrants further longer-term investigation in the future. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01067508.

Antioxidant-rich spice added to hamburger meat during cooking results in reduced meat, plasma, and urine malondialdehyde concentrations.

BACKGROUND: Emerging science has shown the effect of oxidation products and inflammation on atherogenesis and carcinogenesis. Cooking hamburger meat can promote the formation of malondialdehyde that can be absorbed after ingestion. OBJECTIVE: We studied the effect of an antioxidant spice mixture on malondialdehyde formation while cooking hamburger meat and its effects on plasma and urinary malondialdehyde concentrations. DESIGN: Eleven healthy volunteers consumed 2 kinds of burgers in a randomized order: one burger was seasoned with a spice blend, and one burger was not seasoned with the spice blend. The production of malondialdehyde in burgers and malondialdehyde concentrations in plasma and urine after ingestion were measured by HPLC. RESULTS: Rosmarinic acid from oregano was monitored to assess the effect of cooking on spice antioxidant content. Forty percent (19 mg) of the added rosmarinic acid remained in the spiced burger (SB) after cooking. There was a 71% reduction in the malondialdehyde concentration (mean +/- SD: 0.52 +/- 0.02 micromol/250 g) in the meat of the SBs compared with the malondialdehyde concentration (1.79 +/- 0.17 micromol/250 g) in the meat of the control burgers (CBs). The plasma malondialdehyde concentration increased significantly in the CB group as a change from baseline (P = 0.026). There was a significant time-trend difference (P = 0.013) between the 2 groups. Urinary malondialdehyde concentrations (micromol/g creatinine) decreased by 49% (P = 0.021) in subjects consuming the SBs compared with subjects consuming the CBs. CONCLUSIONS: The overall effect of adding the spice mixture to hamburger meat before cooking was a reduction in malondialdehyde concentrations in the meat, plasma, and urine after ingestion. Therefore, cooking hamburgers with a polyphenol-rich spice mixture can significantly decrease the concentration of malondialdehyde, which suggests potential health benefits for atherogenesis and carcinogenesis. This trial was registered at clinical trials.gov as NCT01027052.

Strawberry consumption is associated with increased antioxidant capacity in serum.

Strawberries are known to contain antioxidants, but the significance of ingesting antioxidant-rich fruits remains to be established. In order to determine whether the consumption of strawberries impacted measures of in vivo antioxidant capacity, frozen strawberries (250 g) were administered daily for 3 weeks to 21 healthy female volunteers. Compliance was confirmed by quantitating pelargonidin-glucuronide, urolithin A-glucuronide, and 2,5-dimethyl-4-hydroxy-3-[(2)H]furanone-glucuronide in plasma and urine by liquid chromatography-mass spectrometry and antioxidant capacity in serum measured by the increase in lag phase of low-density lipoprotein after copper sulfate exposure, DNA strand breaks in lymphocytes, and activity of phase II enzymes. Among these measures lipid peroxidation lag time increased by 20% (P < .01), whereas other measures did not change significantly. The potent antioxidant defenses in humans make determination of changes due to dietary ingestion in healthy individuals difficult. In summary, daily consumption of strawberries resulted in a modest but significant increase in antioxidant capacity in a healthy population.