Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses

Programmable RNA-guided DNA nucleases perform numerous roles in prokaryotes, but the extent of their spread outside prokaryotes is unclear. Fanzors, the eukaryotic homolog of prokaryotic TnpB proteins, have been detected in genomes of eukaryotes and large viruses, but their activity and functions in eukaryotes remain unknown. Here, we characterize Fanzors as RNA-programmable DNA endonucleases, using biochemical and cellular evidence. We found diverse Fanzors that frequently associate with various eukaryotic transposases. Reconstruction of Fanzors evolution revealed multiple radiations of RuvC-containing TnpB homologs in eukaryotes. Fanzor genes captured introns and proteins acquired nuclear localization signals, indicating extensive, long-term adaptation to functioning in eukaryotic cells. Fanzor nucleases contain a rearranged catalytic site of the RuvC domain, similar to a distinct subset of TnpBs, and lack collateral cleavage activity. We demonstrate that Fanzors can be harnessed for genome editing in human cells, highlighting the potential of these widespread eukaryotic RNA-guided nucleases for biotechnology applications.

Multicenter Validation of a Urine CXCL10 Assay for Noninvasive Monitoring of Renal Transplants

BACKGROUND

Urine CXCL10 (C-X-C motif chemokine ligand 10, interferon gamma-induced protein 10 [IP10]) outperforms standard-of-care monitoring for detecting subclinical and early clinical T-cell-mediated rejection (TCMR) and may advance TCMR therapy development through biomarker-enriched trials. The goal was to perform an international multicenter validation of a CXCL10 bead-based immunoassay (Luminex) for transplant surveillance and compare with an electrochemiluminescence-based (Meso Scale Discovery [MSD]) assay used in transplant trials.

METHODS

Four laboratories participated in the Luminex assay development and evaluation. Urine CXCL10 was measured by Luminex and MSD in 2 independent adult kidney transplant trial cohorts (Basel and TMCT04). In an independent test and validation set, a linear mixed-effects model to predict (log 10 -transformed) MSD CXCL10 from Luminex CXCL10 was developed to determine the conversion between assays. Net reclassification was determined after mathematical conversion.

RESULTS

The Luminex assay was precise, with an intra- and interassay coefficient of variation 8.1% and 9.3%; showed modest agreement between 4 laboratories (R 0.96 to 0.99, P < 0.001); and correlated with known CXCL10 in a single- (n = 100 urines, R 0.94 to 0.98, P < 0.001) and multicenter cohort (n = 468 urines, R 0.92, P < 0.001) but the 2 assays were not equivalent by Passing-Bablok regression. Linear mixed-effects modeling demonstrated an intercept of -0.490 and coefficient of 1.028, showing Luminex CXCL10 are slightly higher than MSD CXCL10, but the agreement is close to 1.0. After conversion of the biopsy thresholds, the decision to biopsy would be changed for only 6% (5/85) patients showing acceptable reclassification.

CONCLUSIONS

These data demonstrate this urine CXCL10 Luminex immunoassay is robust, reproducible, and accurate, indicating it can be readily translated into clinical HLA laboratories for serial posttransplant surveillance.

Oral probiotic therapy improves motor function in a rodent model of sensorimotor stroke

Ischemic stroke is a debilitating neurological disease with few effective therapeutics. Previous work has shown that oral probiotic treatment prior to stroke can attenuate cerebral infarction and neuroinflammation, highlighting the gut-microbiota-brain axis as a novel therapeutic target. Whether a more clinically relevant, post-stroke, administration of probiotics can improve stroke outcomes is unknown. In this study, we examined the effect of post-stroke oral probiotic therapy on motor behavior in the pre-clinical mouse endothelin-1 (ET-1) model of sensorimotor stroke. We found that post-stroke oral probiotic therapy with Cerebiome^® (Lallemand, Montreal, Canada), containing B. longum R0175 and L. helveticus R0052, improved functional recovery and changed the composition of the post-stroke gut microbiota. Interestingly, oral Cerebiome^® administration did not result in alterations of lesion volume or the number of CD8+/Iba1+ cells in the injured tissue. Overall, these findings suggest that probiotic treatment following injury can improve sensorimotor function.

Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses

TnpB proteins are RNA-guided nucleases that are broadly associated with IS200/605 family transposons in prokaryotes. TnpB homologs, named Fanzors, have been detected in genomes of some eukaryotes and large viruses, but their activity and functions in eukaryotes remain unknown. We searched genomes of diverse eukaryotes and their viruses for TnpB homologs and identified numerous putative RNA-guided nucleases that are often associated with various transposases, suggesting they are encoded in mobile genetic elements. Reconstruction of the evolution of these nucleases, which we rename Horizontally-transferred Eukaryotic RNA-guided Mobile Element Systems (HERMES), revealed multiple acquisitions of TnpBs by eukaryotes and subsequent diversification. In their adaptation and spread in eukaryotes, HERMES proteins acquired nuclear localization signals, and genes captured introns, indicating extensive, long term adaptation to functioning in eukaryotic cells. Biochemical and cellular evidence show that HERMES employ non-coding RNAs encoded adjacent to the nuclease for RNA-guided cleavage of double-stranded DNA. HERMES nucleases contain a re-arranged catalytic site of the RuvC domain, similar to a distinct subset of TnpBs, and lack collateral cleavage activity. We demonstrate that HERMES can be harnessed for genome editing in human cells, highlighting the potential of these widespread eukaryotic RNA-guided nucleases for biotechnology applications.

Particulate mass and polycyclic aromatic hydrocarbons exposure from secondhand smoke in the back seat of a vehicle

CONTEXT

Exposure to secondhand smoke (SHS) has been reduced in the USA by banning smoking in public places. These restrictions have not had the same effect on children's exposure to SHS as adults suggesting that children are exposed to SHS in locations not covered by bans, such as private homes and cars.

OBJECTIVES

Assess exposure to SHS in the backseat of a stationary vehicle where a child would sit, quantify exposures to fine particulates (PM2.5), polycyclic aromatic hydrocarbons (PAH), carbon monoxide (CO) and nicotine. Estimate the impact on a child's mean daily exposure to PM2.5.

METHODS

SHS exposures in stationary vehicles with two different window configurations were monitored. A volunteer smoked three cigarettes in a one-hour period for twenty-two experiments. PM2.5, CO, nicotine and PAH where measured in the backseat of the vehicle. 16 PAH compounds were measured for in gas and particle phases as well as real-time particle phase concentrations.

RESULTS

The mean PAH concentration, 1325.1 ng/m(3), was larger than concentrations measured in bars and restaurants were smoking is banned in many countries. We estimate that a child spending only ten minutes in the car with a smoker at the mean PM2.5 concentration measured in the first window configuration--1697 mg/m(3)--will cause a 30% increase to the daily mean PM2.5 personal average of a child.

CONCLUSIONS

Estimates made using the measured data and previously reported PM2.5 daily mean concentrations for children in California showing that even short exposure periods are capable of creating large exposure to smoke.

Mutations induced in the HPRT gene by X-irradiation during G(1) or S: analysis of base pair alterations, small deletions, and splice errors

Reverse transcriptase PCR was performed with mRNA obtained from HPRT mutants that had base pair alterations, or small deletions or insertions <20bp. The frequencies of mutants yielding RT-PCR products (mRNA) were the same when human EJ30 cells were irradiated in G(1) or S (3-4-fold higher for 6 than 3Gy). However, the frequencies of mutants that did not yield RT-PCR products were approximately 10-fold higher in the cells irradiated in G(1) than in those irradiated in S. Sequence analysis of RT-PCR products and genomic DNA showed that 40% of the RT-PCR products had splice errors (one or more exons not spliced into mRNA), with 64% of them due to 1-17bp deletions. Also, the distributions of molecular alterations in exons, acceptor sites, and donor sites for mutants having splice errors (observed in this study and reported by others) were similar to those reported for mutants not yielding RT-PCR products (isolated from Russian cosmonauts). In addition, we have found previously that large deletions which eliminated 1-9 exons were preferentially induced in G(1). Therefore, we postulate that the preferential induction of mutants not yielding mRNA is due primarily to splice errors that result from deletions preferentially induced during G(1). These splice errors would then result either in no message or a message that is rapidly degraded.

Evidence that most radiation-induced HPRT mutants are generated directly by the initial radiation exposure

Radiation-induced HPRT mutants are generally assumed to arise directly from DNA damage that is misrepaired within a few hours after X-irradiation. However, there is the possibility that mutations result indirectly from radiation-induced genomic instability that may occur several days after the initial radiation exposure. The protocols that commonly employ a 5-7 day expression period to allow for expression of the mutant phenotype prior to replating for selection of mutants would not be able to discriminate between mutants that occurred initially and those that arose during or after the expression period. To address this question, we performed a fluctuation analysis in which synchronous or asynchronous populations of human bladder carcinoma cells were treated with single doses of X-irradiation. For comparison, radiation was delivered during the expression period, either from an initial dose of 1.0 Gy followed by two 1.0 Gy doses separated by 24 h or from disintegrations resulting from I125dU incorporated into DNA. The mutation frequency observed at the time of replating was used to calculate the average number of mutants in the initial irradiated culture by assuming that the mutants were induced directly at the time of irradiation. Then, this average number was used to calculate the fraction of the irradiated cultures that would be predicted by a Poisson distribution to have zero mutants. There was reasonably good agreement between the predicted poisson distribution and the observed distribution for the cultures that received single doses. Moreover, as expected, when cultures were irradiated during the expression period, the fraction of the cultures having zero mutants was significantly less than that predicted by a Poisson distribution. These results indicate that most radiation-induced HPRT mutations are induced directly by the initial DNA damage, and are not the result of radiation-induced instability during the 5-7 day expression period.

Persistent decrease in viability as a function of X irradiation of human bladder carcinoma cells in G1 or S phase

A persistent decrease in viability after treatment with a variety of mutagenic agents has been observed previously, but the dependence of the decrease on the phase of the cell cycle in which the cells are treated has not been fully explored. Synchronous human bladder carcinoma cells (EJ30-15) were obtained by mitotic selection (88-96% in or near mitosis). As monitored by microscopy and pulse labeling with [3H]dThd, approximately 98% of the cells were in G1 phase when they were irradiated after 3 h of incubation, and approximately 80% were in S phase when they were irradiated after 14 h of incubation. The initial plating efficiencies demonstrated no difference in cell survival when cells were irradiated in G1 or S phase, with normalized clonogenic survival and standard error of 60+/-6% for 3 Gy and 13+/-2% for 6 Gy. However, when the cell populations were allowed to incubate and were replated 5 to 33 days later (5.5 to 36 doublings), a difference between the populations irradiated in G1 and S phase became clear. Cells that were irradiated with 6 Gy regained and maintained the high plating efficiencies (67.9+/-3.6%) of the unirradiated populations much sooner when they were irradiated in S phase compared with irradiation in G1 phase, i.e. 11 days (12 cell doublings) for S phase compared to approximately 20 days (22 cell doublings) for G1 phase. During these periods when the plating efficiencies were increasing, the populations irradiated in G1 phase were multiplying at rates lower than those for the populations irradiated in S phase. Furthermore, after 6 Gy, more giant cells and multinucleated cells were seen in the populations irradiated in G1 phase than in the populations irradiated in S phase. These results indicate that, although the clonogenic survival was the same for cells irradiated in G1 or S phase, the residual damage in progeny of the irradiated cells persisted longer (approximately 20 days compared to 11 days) when cells were irradiated in G1 phase than when they were irradiated in S phase.

Comparisons of the frequencies and molecular spectra of HPRT mutants when human cancer cells were X-irradiated during G1 or S phase

In an attempt to elucidate mechanisms underlying the variation in radiosensitivity during the cell cycle, mutations in the HPRT gene were selected with 6-thioguanine, quantified and characterized in synchronous human bladder carcinoma cells (EJ30-15) that were irradiated in G1 or S phase with 3 or 6 Gy. Synchronous cells were obtained by mitotic selection, with approximately 98% of the cells in G1 phase when they were irradiated after 3 h of incubation, and 75% in S phase when they were irradiated after 14 h of incubation. The mutant frequencies were approximately 4-fold higher (P < 0.01) when cells were irradiated in G1 phase compared with S phase, and the lowest frequency (1.5 x 10(-5) for 3 Gy during S phase) was approximately 10-fold higher than the spontaneous frequency. Exon analysis by multiplex polymerase chain reaction was performed on DNA isolated from each independent mutant. The different types of mutants were categorized as class 1, which consisted of base-pair changes or small deletions less than 20 bp; class 2, which consisted of deletions greater than 20 bp but with one or more HPRT exons present; and class 3, which consisted of deletions encompassing the entire HPRT gene and usually genomic markers located 350-750 kbp from the 5' end of the gene and/or 300-1400 kbp from the 3' end. A "hotspot" for class 2 deletions was observed between exons 6 and 9 (P < 0.01). For cells irradiated during G1 phase, the percentages for the different classes (total of 78 mutants) were similar for 3 and 6 Gy, with a selective induction of class 3 mutants (34-38%) compared with spontaneous mutants (3%, total 20). When S-phase cells were irradiated with 3 Gy, there were fewer class 1 mutants (21%, total 37) than when cells were irradiated in G1 phase with 3 Gy (45%, total 42) (P < 0.01). The greatest change was observed when the dose was increased in S phase from 3 Gy to 6 Gy (total of 43 mutants), with the frequency of class 2 mutants decreasing dramatically from 30% to 1% (P < 0.005). A similar decrease in class 2 mutants with an increase in dose has been observed by others in asynchronous cultures of normal human fibroblasts. We hypothesize that these differences occur because: (a) there is more error-free repair of double-strand breaks (DSBs) during S than G1 phase; (b) a single DSB within the HPRT gene causes a class 2 mutation or a certain percentage of class 1 mutations, while two DSBs, with one in each approximately 1-Mbp region 5' and 3' of the gene, cause a class 3 mutation; and (c) a repair process that is induced when the dose during S phase is increased from 3 to 6 Gy results in a preferential decrease in class 2 mutations.

White blood cell counts by automated and manual methods with backlighting

White blood cell (WBC) counts were compared in the presence of "backlighting" using the Coulter S-Plus Jr and a manual system. Platelet aggregates and large platelets in specimens anticoagulated with ethylenediamine tetraacetic acid (EDTA) cause interference and prompt the WBC count on the Coulter S-Plus Jr to backlight. This means that the background behind the count on the data terminal display lights up, alerting the operator to a questionable result. A total of 29 automated backlighted WBC counts of blood samples collected in sodium and potassium salts of EDTA tubes were compared with the results by hemocytometer method. Values for WBC count by both methods showed good agreement. Smear examination detected platelet clumps and large platelets in 66% of the Na 2EDTA tubes. Only low WBC counts prompted backlighting in K 3EDTA. tubes. Liquid K 3EDTA is a preferred anticoagulant for whole blood analysis because of its rapid solubility, eliminating clumping of platelets and thus backlighting.

Early effect of myo-inositol deficiency on phosphatidylinositol metabolism in rat liver

Young rats (100 g) were fed either a myo-inositol-deficient or supplemented (control) diet for up to 14 days following a 12 h fast. At various times during this period animals were killed, livers were removed, and a microsomal fraction was prepared and assayed for CDPdiacylglycerol inositol transferase activity and for phosphatidylinositol-inositol exchange activity. Within 2 days after beginning the regimen, rats consuming the deficient diet had a 40% lower activity of the transferase than rats consuming the control diet. This difference was maintained throughout the feeding period and developed simultaneously with the accumulation of triacylglycerol in the deficient livers. In contrast, the specific activity of the exchange enzyme was unchanged by feeding the deficient diet.

Densitometry and microchromatography compared for determination of the hemoglobin C and A2 proportions in hemoglobin C and hemoglobin SC disease and in hemoglobin C trait

Using both densitometry and anion-exchange microchromatography, we measured hemoglobin C (Hb C) and Hb A2 proportions in 11 patients, eight of whom had Hb AC, two Hb SC, and one Hb CC. For one patient with Hb SC, we made the determinations before and after a transfusion. The mean (and SD) for the sum of Hb C + Hb A2 by densitometry and anion-exchange microchromatography for the nine patients with Hb AC and Hb CC were 45 (18) and 40 (18)%, respectively (p greater than 0.1, r = 0.98); for the three determinations involving the two Hb SC patients, the respective proportions were 40 (9.9) and 38 (6.6)% (r = 0.88). Electrophoretic analysis of microchromatographic eluates from the Hb AC and Hb CC patients showed that 6% of the absorbance of the late high-ionic-strength eluate was due to Hb C, which was responsible for the statistically insignificant difference between densitometric and chromatographic values for Hb C + A2 values. Electrophoresis on cellulose acetate of concentrated eluates of the Hb C + A2 fraction from the two Hb SC patients revealed no contamination by Hb S. Evidently, microchromatography can be used to determine Hb C + A2 in patients with Hb C or Hb SC disease or Hb C trait.

Densitometry and microchromatography compared for determination of the hemoglobin C and A2 proportions in hemoglobin C and hemoglobin SC disease and in hemoglobin C trait

Using both densitometry and anion-exchange microchromatography, we measured hemoglobin C (Hb C) and Hb A2 proportions in 11 patients, eight of whom had Hb AC, two Hb SC, and one Hb CC. For one patient with Hb SC, we made the determinations before and after a transfusion. The mean (and SD) for the sum of Hb C + Hb A2 by densitometry and anion-exchange microchromatography for the nine patients with Hb AC and Hb CC were 45 (18) and 40 (18)%, respectively (p greater than 0.1, r = 0.98); for the three determinations involving the two Hb SC patients, the respective proportions were 40 (9.9) and 38 (6.6)% (r = 0.88). Electrophoretic analysis of microchromatographic eluates from the Hb AC and Hb CC patients showed that 6% of the absorbance of the late high-ionic-strength eluate was due to Hb C, which was responsible for the statistically insignificant difference between densitometric and chromatographic values for Hb C + A2 values. Electrophoresis on cellulose acetate of concentrated eluates of the Hb C + A2 fraction from the two Hb SC patients revealed no contamination by Hb S. Evidently, microchromatography can be used to determine Hb C + A2 in patients with Hb C or Hb SC disease or Hb C trait.

Estimation of highly increased concentrations of fetal hemoglobin in Fanconi's anemia

We report a case of Fanconi's anemia with an extremely high proportion of fetal hemoglobin (Hb F). A three-year-old girl with multiple birth defects, mental retardation, and aplastic anemia consistent with Fanconi's anemia showed Hb AF by electrophoresis; the Kleihauer smear showed Hb F in 70% of her erythrocytes. Total Hb concentration was 34 g/L, mean corpuscular volume 119 fL. The proportion of Hb F was 45% by densitometry, 36% by radial immunodiffusion, and 30% by cation-exchange microchromatography. The Hb A2 was 0.5%; glycated Hb was 7.8% by affinity chromatography. Sample volume was insufficient for alkali denaturation. As exemplified with this patient, we recommend microchromatographic cation-exchange assay when Hb F exceeds 30% by densitometry. Here the effect of contamination by Hb A1 was lessened by the high proportion of Hb F. Cation-exchange microchromatography provides clinically relevant Hb F values more quickly than radial immunodiffusion and more conveniently than alkali denaturation.

Estimation of highly increased concentrations of fetal hemoglobin in Fanconi's anemia

We report a case of Fanconi's anemia with an extremely high proportion of fetal hemoglobin (Hb F). A three-year-old girl with multiple birth defects, mental retardation, and aplastic anemia consistent with Fanconi's anemia showed Hb AF by electrophoresis; the Kleihauer smear showed Hb F in 70% of her erythrocytes. Total Hb concentration was 34 g/L, mean corpuscular volume 119 fL. The proportion of Hb F was 45% by densitometry, 36% by radial immunodiffusion, and 30% by cation-exchange microchromatography. The Hb A2 was 0.5%; glycated Hb was 7.8% by affinity chromatography. Sample volume was insufficient for alkali denaturation. As exemplified with this patient, we recommend microchromatographic cation-exchange assay when Hb F exceeds 30% by densitometry. Here the effect of contamination by Hb A1 was lessened by the high proportion of Hb F. Cation-exchange microchromatography provides clinically relevant Hb F values more quickly than radial immunodiffusion and more conveniently than alkali denaturation.

Proportion of glycosylated hemoglobin in erythrocytes of a person with hemoglobins A, S, and G Philadelphia

The apparent proportion of column-chromatographically measured glycosylated hemoglobin in erythrocytes from an individual with hemoglobins A, S, and G was only 2.3% because the slow glycosylated variant hemoglobins were retarded in the column. In contrast, the value for glycosylated hemoglobin was 7.8% by a new cellulose acetate electrophoretic method that includes use of dextran sulfate buffer. The erythrocyte metalloprotein, carbonic anhydrase B, was shown to co-migrate with glycosylated hemoglobin by this technique, however. Thus carbonic anhydrase B, HbF, and HbA all have weak attraction for negative charges at acid pH. We believe that carbonic anhydrase B should contribute significantly (at least 10-20% absorbance) to the HbA1 by this electrophoretic method. We conclude that microcolumn chromatography should remain the method of choice for HbA1 determination, that subject-based reference intervals should be used for HbS or HbC heterozygotes, and that electrophoretic HbA1 methods should be reserved for use with both HbS and HbC homozygotes and HbSC disease.

Proportion of glycosylated hemoglobin in erythrocytes of a person with hemoglobins A, S, and G Philadelphia

The apparent proportion of column-chromatographically measured glycosylated hemoglobin in erythrocytes from an individual with hemoglobins A, S, and G was only 2.3% because the slow glycosylated variant hemoglobins were retarded in the column. In contrast, the value for glycosylated hemoglobin was 7.8% by a new cellulose acetate electrophoretic method that includes use of dextran sulfate buffer. The erythrocyte metalloprotein, carbonic anhydrase B, was shown to co-migrate with glycosylated hemoglobin by this technique, however. Thus carbonic anhydrase B, HbF, and HbA all have weak attraction for negative charges at acid pH. We believe that carbonic anhydrase B should contribute significantly (at least 10-20% absorbance) to the HbA1 by this electrophoretic method. We conclude that microcolumn chromatography should remain the method of choice for HbA1 determination, that subject-based reference intervals should be used for HbS or HbC heterozygotes, and that electrophoretic HbA1 methods should be reserved for use with both HbS and HbC homozygotes and HbSC disease.