Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

BACKGROUND: Most single nucleotide variants (SNVs) occur in noncoding sequence where millions of transcription factor binding sites (TFBS) reside. Here, a comparative analysis of CRISPR-mediated homology-directed repair (HDR) versus the recently reported prime editing 2 (PE2) system was carried out in mice over a TFBS called a CArG box in the Tspan2 promoter. RESULTS: Quantitative RT-PCR showed loss of Tspan2 mRNA in aorta and bladder, but not heart or brain, of mice homozygous for an HDR-mediated three base pair substitution in the Tspan2 CArG box. Using the same protospacer, mice homozygous for a PE2-mediated single-base substitution in the Tspan2 CArG box displayed similar cell-specific loss of Tspan2 mRNA; expression of an overlapping long noncoding RNA was also nearly abolished in aorta and bladder. Immuno-RNA fluorescence in situ hybridization validated loss of Tspan2 in vascular smooth muscle cells of HDR and PE2 CArG box mutant mice. Targeted sequencing demonstrated variable frequencies of on-target editing in all PE2 and HDR founders. However, whereas no on-target indels were detected in any of the PE2 founders, all HDR founders showed varying levels of on-target indels. Off-target analysis by targeted sequencing revealed mutations in many HDR founders, but none in PE2 founders. CONCLUSIONS: PE2 directs high-fidelity editing of a single base in a TFBS leading to cell-specific loss in expression of an mRNA/long noncoding RNA gene pair. The PE2 platform expands the genome editing toolbox for modeling and correcting relevant noncoding SNVs in the mouse.

Induced pluripotent stem cells have similar immunogenic and more potent immunomodulatory properties compared with bone marrow-derived stromal cells in vitro.

AIM: To evaluate the in vitro immunogenic and immunomodulatory properties of induced pluripotent stem cells (iPSCs) compared with bone marrow-derived mesenchymal stromal cells (MSCs). MATERIALS & METHODS: Mouse embryonic fibroblasts (MEFs) were isolated from C3HeB/FeJ and C57BL/6J mice, and reprogrammed to generate iPSCs. Mixed leukocyte reactions were performed using MHC-matched and -mismatched responder leukocytes and stimulator leukocytes, iPSCs or MSCs. To assess immunogenic potential, iPSCs and MSCs were used as stimulator cells for responder leukocytes. To assess immunomodulatory properties, iPSCs and MSCs were cultured in the presence of stimulator and responder leukocytes. MEFs were used as a control. RESULTS: iPSCs had similar immunogenic properties but more potent immunomodulatory effects than MSCs. Co-culture of MHC-mismatched leukocytes with MHC-matched iPSCs resulted in significantly less responder T-cell proliferation than observed for MHC-mismatched leukocytes alone and at more responder leukocyte concentrations than with MSCs. In addition, MHC-mismatched iPSCs significantly reduced responder T-cell proliferation when co-cultured with MHC-mismatched leukocytes, while MHC-mismatched MSCs did not. CONCLUSION: These results provide important information when considering the use of iPSCs in place of MSCs in both regenerative and transplantation medicine.

Genetic background affects induced pluripotent stem cell generation.

INTRODUCTION: The influence of genetic background on the ability to generate induced pluripotent stem cells (iPSCs) has the potential to impact future applications, but has yet to be examined in detail. The purpose of this study was to determine if genetic background affects the efficiency of generating iPSCs during early reprograming as well as the pluripotent stability of the iPSCs during later stages of reprograming. METHODS: Mouse embryonic fibroblasts (MEFs) were isolated from six strains of mice (NON/LtJ; C57BL/6J; DBA/2J; BALB/cJ; 129S1/SvlmJ; CAST/EiJ) that were selected based on genetic diversity and differences in ability to produce embryonic stem cell (ESC) lines. MEFs were reprogramed via doxycycline-inducible lentiviral transduction of murine Oct4, Klf4, Sox2, and c-Myc. Differences in efficiency to generate iPSCs were assessed by comparing the total number of colonies, the percentage of colonies positive for alkaline phosphatase staining and the percentage of cells positive for SSEA1. iPSC colonies were expanded to establish doxycycline-independent cell lines whose pluripotency was then evaluated via ability to form teratomas in NOD.CB17-Prkdcscid/J mice. Proliferation of non-transduced parent MEFs from each strain was also examined over ten days under conditions that simulated reprograming. RESULTS: NON/LtJ and CAST/EiJ strains were more efficient than other strains in generating iPSCs for all parameters measured and parent MEFs from these strains were more proliferative than those from other strains. Doxycycline-independent iPSC lines were established using standard conditions for all strains except BALB/cJ, which required a higher concentration (5x) of leukemia inhibitory factor (LIF). iPSCs from all strains were capable of producing teratomas in NOD.CB17-Prkdcscid/J mice. CONCLUSIONS: The results of this study suggest that genetic background does affect iPSC generation and pluripotent stability. In addition, our results demonstrate that strain differences in efficiency to generate iPSCs during the early stages of reprograming are correlated with those observed in proliferation of parent MEFs. These findings have important implications both for future iPSC applications as well as for future investigation into determining the genes responsible for reprograming efficiency and stability.

Choline intake exceeding current dietary recommendations preserves markers of cellular methylation in a genetic subgroup of folate-compromised men.

Severe choline deficiency adversely affects cellular methylation and DNA integrity, with potentially serious implications for disease risk. As part of a 12-wk controlled choline intervention study conducted in folate-compromised Mexican-American men (n = 60; 18-55 y) differing in the methylenetetrahydrofolate reductase (MTHFR) C677T genotype (21 677CC, 29 677TT), this study evaluated the effects of varied choline intakes (300, 550, 1100, and 2200 mg/d) on the change (i.e. wk 12-0) in markers of cellular methylation and DNA integrity. Choline intake affected the change in plasma S-adenosylmethionine (P = 0.044), with decreases tending to be greater (P < or = 0.08) in the 300 and 550 mg/d groups than in the 2200 mg/d group. Choline intake also interacted with the MTHFR C677T genotype to affect the change in genomic DNA methylation and DNA damage. In men with the MTHFR 677CC genotype, choline intake affected (P = 0.007) the change in DNA methylation, with a greater decrease (P < 0.02) in the 300 mg/d group than in the 1100 and 2200 mg/d groups. In men with the MTHFR 677CC genotype, choline intake also affected (P = 0.047) the change in DNA damage, with the increase tending to be greater (P = 0.07) in the 550 mg/d group than in the 2200 mg/d group. Choline intake did not affect these variables in men with the MTHFR 677TT genotype. Overall, these data suggest that choline intake exceeding current dietary recommendations preserves markers of cellular methylation and attenuates DNA damage in a genetic subgroup of folate-compromised men.

Choline status is not a reliable indicator of moderate changes in dietary choline consumption in premenopausal women.

For the prevention of liver dysfunction in women, a choline adequate intake of 425 mg/day was established. To date, the relationship between dietary choline intake and plasma concentrations of choline moieties remains relatively unexplored. As an extension of our previous work, this 14-week controlled feeding study investigated the relationship between moderate changes in dietary choline intake and blood indicators of status. The influences of folate intake and the methylenetetrahydrofolate reductase (MTHFR) C677T genotype were also considered. Healthy premenopausal women (n=45, 18-46 years) with the MTHFR 677CC (n=28) or TT (n=17) genotype consumed a folate-restricted diet for 2 weeks followed by randomization to one of four dietary treatments (n=6-9/group) differing in total choline (344-486 mg/day), betaine (122-349 mg/day) and/or folate (400-800 microg dietary folate equivalents/day) content for 12 weeks. Responses to treatment were assessed as changes in the plasma levels of choline moieties (i.e., betaine, choline, phosphatidylcholine and sphingomyelin) and/or leukocyte global DNA methylation between pretreatment (Week 2) and posttreatment (Week 14) values. No significant changes were detected in the measured variables in response to dietary increases in choline (i.e., 41% increase) or betaine (i.e., 286% increase) intake. However, the MTHFR C677T genotype, alone or together with a diet, influenced betaine (P=.03) and phosphatidylcholine (P=.03). These data suggest that choline status is not a reliable indicator of moderate changes in dietary choline intake possibly due to the engagement of compensatory mechanisms. In addition, the MTHFR C677T genotype appears to influence the direction and use of choline moieties in this group of women.

Adequate Intake levels of choline are sufficient for preventing elevations in serum markers of liver dysfunction in Mexican American men but are not optimal for minimizing plasma total homocysteine increases after a methionine load.

BACKGROUND: An adequate intake of 550 mg choline/d was established for the prevention of liver dysfunction in men, as assessed by measuring serum alanine aminotransferase concentrations. OBJECTIVE: This controlled feeding study investigated the influence of choline intakes ranging from 300 to 2200 mg/d on biomarkers of choline status. The effect of the methylenetetrahydrofolate reductase (MTHFR) C677T genotype on choline status was also examined. DESIGN: Mexican American men (n = 60) with different MTHFR C677T genotypes (29 677TT, 31 677CC) consumed a diet providing 300 mg choline/d plus supplemental choline intakes of 0, 250, 800, or 1900 mg/d for total choline intakes of 300, 550, 1100, or 2200 mg/d, respectively, for 12 wk; 400 mug/d as dietary folate equivalents and 173 mg betaine/d were consumed throughout the study. RESULTS: Choline intake affected the response of plasma free choline and betaine (time x choline, P < 0.001); the highest concentrations were observed in the 2200 mg/d group. Phosphatidylcholine (P = 0.026) and total cholesterol (P = 0.002) were also influenced by choline intake; diminished concentrations were observed in the 300 mg/d group. Phosphatidylcholine was modified by MTHFR genotype (P = 0.035; 677TT < 677CC). After a methionine load (100 mg/kg body wt), choline intakes of 1100 and 2200 mg/d attenuated (P = 0.016) the rise in plasma homocysteine, as did the MTHFR 677TT genotype (P < 0.001). Serum alanine aminotransferase was not influenced by the choline intakes administered in this study. CONCLUSIONS: These data suggest that 550 mg choline/d is sufficient for preventing elevations in serum markers of liver dysfunction in this population under the conditions of this study; higher intakes may be needed to optimize other endpoints.

Ethnicity and folate influence choline status in young women consuming controlled nutrient intakes.

OBJECTIVE: We previously demonstrated that choline and folate are interrelated and that African American women have lower folate nutriture than Caucasian and Mexican American women under conditions of controlled folate intake. The present study sought to examine the influences of ethnicity and controlled folate intake on choline status. METHODS: Forty-two women of Mexican American (n = 14), African American (n = 14), and Caucasian American (n = 14) descent consumed a folate restricted diet (135 microg DFE/d) for 7 weeks, followed by 7 weeks of folate treatment with either 400 or 800 microg DFE/d. Total choline intake remained unchanged throughout the study at approximately 350 mg/d. Plasma choline and its derivatives were measured by LC-MS/MS at weeks 0, 7, and 14. RESULTS: Plasma phosphatidylcholine declined during folate restriction (P < 0.001) and tended to increase in response to 800 microg DFE/d (week x folate, P = 0.099) in Mexican American and Caucasian women. For African American women, however, phosphatidylcholine continued to decline (week x race, P = 0.056). Plasma betaine was modified by ethnicity and level of folate intake (week x race x folate, P = 0.039) however no clear patterns emerged. CONCLUSIONS: The phosphatidylcholine data suggest that the lower folate status observed in African American women may also be associated with lower choline status. In turn, diseases linked to folate may also be linked to choline.

Folate intake and the MTHFR C677T genotype influence choline status in young Mexican American women.

Numerous studies have reported a relationship between folate status, the methylenetetrahydrofolate reductase (MTHFR) 677C-->T variant and disease risk. Although folate and choline metabolism are inter-related, only limited data are available on the relationship between choline and folate status in humans. This study sought to examine the influences of folate intake and the MTHFR 677C-->T variant on choline status. Mexican-American women (n=43; 14 CC, 12 CT and 17 TT) consumed 135 microg/day as dietary folate equivalents (DFE) for 7 weeks followed by randomization to 400 or 800 microg DFE/day for 7 weeks. Throughout the study, total choline intake remained unchanged at approximately 350 mg/day. Plasma concentrations of betaine, choline, glycerophosphocholine, phosphatidylcholine and sphingomyelin were measured via LC-MS/MS for Weeks 0, 7 and 14. Phosphatidylcholine and sphingomyelin declined (P=.001, P=.009, respectively) in response to folate restriction and increased (P=.08, P=.029, respectively) in response to folate treatment. The increase in phosphatidylcholine occurred in response to 800 (P=.03) not 400 (P=.85) microg DFE/day (week x folate interaction, P=.017). The response of phosphatidylcholine to folate intake appeared to be influenced by MTHFR C677T genotype. The decline in phosphatidylcholine during folate restriction occurred primarily in women with the CC or CT genotype and not in the TT genotype (week x genotype interaction, P=.089). Moreover, when examined independent of folate status, phosphatidylcholine was higher (P<.05) in the TT genotype relative to the CT genotype. These data suggest that folate intake and the MTHFR C677T genotype influence choline status in humans.