Baylor Scott and White Research Institute

Choquet, K., D. Forget, E. Meloche, M. J. Dicaire, G. Bernard, A. Vanderver, R. Schiffmann, M. R. Fabian, M. Teichmann, B. Coulombe, B. Brais and C. L. Kleinman (2019). “Leukodystrophy-associated POLR3A mutations down-regulate the RNA polymerase III transcript and important regulatory RNA BC200.” J Biol Chem Mar 21. [Epub ahead of print].

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RNA polymerase III (Pol III) is an essential enzyme responsible for the synthesis of several small non-coding RNAs, a number of which are involved in mRNA translation. Recessive mutations in POLR3A, encoding the largest subunit of Pol III, cause POLR3-related hypomyelinating leukodystrophy (POLR3-HLD), characterized by deficient central nervous system myelination. Identification of the downstream effectors of pathogenic POLR3A mutations has been so far elusive. Here, we used CRISPR-Cas9 to introduce the POLR3A mutation c.2554A>G (p.M852V) into human cell lines and assessed its impact on Pol III biogenesis, nuclear import, DNA occupancy, transcription, and protein levels. Transcriptomic profiling uncovered a subset of transcripts vulnerable to Pol III hypofunction, including a global reduction in tRNA levels. The brain cytoplasmic BC200 RNA (BCYRN1), involved in translation regulation, was consistently affected in all our cellular models, including patient-derived fibroblasts. Genomic BC200 deletion in an oligodendroglial cell line led to major transcriptomic and proteomic changes, having a larger impact than those of POLR3A mutations. Upon differentiation, mRNA levels of the MBP gene, encoding myelin basic protein, were significantly decreased in POLR3A-mutant cells. Our findings provide the first evidence for impaired Pol III transcription in cellular models of POLR3-HLD and identify several candidate effectors, including BC200 RNA, having a potential role in oligodendrocyte biology and involvement in the disease.

Rhodes, C. J., K. Batai, M. Bleda, M. Haimel, L. Southgate, M. Germain, M. W. Pauciulo, C. Hadinnapola, J. Aman, B. Girerd, A. Arora, J. Knight, K. B. Hanscombe, J. H. Karnes, M. Kaakinen, H. Gall, A. Ulrich, L. Harbaum, I. Cebola, J. Ferrer, K. Lutz, E. M. Swietlik, F. Ahmad, P. Amouyel, S. L. Archer, R. Argula, E. D. Austin, D. Badesch, S. Bakshi . . . and M. R. Wilkins (2019). “Genetic determinants of risk in pulmonary arterial hypertension: international genome-wide association studies and meta-analysis.” Lancet Respir Med 7(3): 227-238.

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BACKGROUND: Rare genetic variants cause pulmonary arterial hypertension, but the contribution of common genetic variation to disease risk and natural history is poorly characterised. We tested for genome-wide association for pulmonary arterial hypertension in large international cohorts and assessed the contribution of associated regions to outcomes. METHODS: We did two separate genome-wide association studies (GWAS) and a meta-analysis of pulmonary arterial hypertension. These GWAS used data from four international case-control studies across 11 744 individuals with European ancestry (including 2085 patients). One GWAS used genotypes from 5895 whole-genome sequences and the other GWAS used genotyping array data from an additional 5849 individuals. Cross-validation of loci reaching genome-wide significance was sought by meta-analysis. Conditional analysis corrected for the most significant variants at each locus was used to resolve signals for multiple associations. We functionally annotated associated variants and tested associations with duration of survival. All-cause mortality was the primary endpoint in survival analyses. FINDINGS: A locus near SOX17 (rs10103692, odds ratio 1.80 [95% CI 1.55-2.08], p=5.13 x 10(-15)) and a second locus in HLA-DPA1 and HLA-DPB1 (collectively referred to as HLA-DPA1/DPB1 here; rs2856830, 1.56 [1.42-1.71], p=7.65 x 10(-20)) within the class II MHC region were associated with pulmonary arterial hypertension. The SOX17 locus had two independent signals associated with pulmonary arterial hypertension (rs13266183, 1.36 [1.25-1.48], p=1.69 x 10(-12); and rs10103692). Functional and epigenomic data indicate that the risk variants near SOX17 alter gene regulation via an enhancer active in endothelial cells. Pulmonary arterial hypertension risk variants determined haplotype-specific enhancer activity, and CRISPR-mediated inhibition of the enhancer reduced SOX17 expression. The HLA-DPA1/DPB1 rs2856830 genotype was strongly associated with survival. Median survival from diagnosis in patients with pulmonary arterial hypertension with the C/C homozygous genotype was double (13.50 years [95% CI 12.07 to >13.50]) that of those with the T/T genotype (6.97 years [6.02-8.05]), despite similar baseline disease severity. INTERPRETATION: This is the first study to report that common genetic variation at loci in an enhancer near SOX17 and in HLA-DPA1/DPB1 is associated with pulmonary arterial hypertension. Impairment of SOX17 function might be more common in pulmonary arterial hypertension than suggested by rare mutations in SOX17. Further studies are needed to confirm the association between HLA typing or rs2856830 genotyping and survival, and to determine whether HLA typing or rs2856830 genotyping improves risk stratification in clinical practice or trials. FUNDING: UK NIHR, BHF, UK MRC, Dinosaur Trust, NIH/NHLBI, ERS, EMBO, Wellcome Trust, EU, AHA, ACClinPharm, Netherlands CVRI, Dutch Heart Foundation, Dutch Federation of UMC, Netherlands OHRD and RNAS, German DFG, German BMBF, APH Paris, INSERM, Universite Paris-Sud, and French ANR.

Walters, D. C., E. Arning, T. Bottiglieri, E. E. W. Jansen, G. S. Salomons, M. N. Brown, M. A. Schmidt, G. R. Ainslie, J. B. Roullet and K. M. Gibson (2019). “Metabolomic analyses of vigabatrin (VGB)-Treated mice: GABA-transaminase inhibition significantly alters amino acid profiles in murine neural and non-neural tissues.” Neurochem Int.

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The anticonvulsant vigabatrin (VGB; Sabril(R)) irreversibly inhibits GABA transaminase to increase neural GABA, yet its mechanism of retinal toxicity remains unclear. VGB is suggested to alter several amino acids, including homocarnosine, beta-alanine, ornithine, glycine, taurine, and 2-aminoadipic acid (AADA), the latter a homologue of glutamic acid. Here, we evaluate the effect of VGB on amino acid concentrations in mice, employing a continuous VGB infusion (subcutaneously implanted osmotic minipumps), dose-escalation paradigm (35-140mg/kg/d, 12 days), and amino acid quantitation in eye, visual and prefrontal cortex, total brain, liver and plasma. We hypothesized that continuous VGB dosing would reveal numerous hitherto undescribed amino acid disturbances. Consistent amino acid elevations across tissues included GABA, beta-alanine, carnosine, ornithine and AADA, as well as neuroactive aspartic and glutamic acids, serine and glycine. Maximal increase of AADA in eye occurred at 35mg/kg/d (41+/-2nmol/g (n=21, vehicle) to 60+/-8.5 (n=8)), and at 70mg/kd/d for brain (97+/-6 (n=21) to 145+/-6 (n=6)), visual cortex (128+/-6 to 215+/-19) and prefrontal cortex (124+/-11 to 200+/-13; mean+/-SEM; p<0.05), the first demonstration of tissue AADA accumulation with VGB in mammal. VGB effects on basic amino acids, including guanidino-species, suggested the capacity of VGB to alter urea cycle function and nitrogen disposal. The known toxicity of AADA in retinal glial cells highlights new avenues for assessing VGB retinal toxicity and other off-target effects.

Tecson, K. M., K. Bass, J. Felius, S. A. Hall, A. K. Jamil and S. A. Carey (2019). “Patient “Activation” of Patients Referred for Advanced Heart Failure Therapy.” Am J Cardiol 123(4): 627-631.

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Advanced heart failure (HF) is a devastating chronic illness requiring complex treatment regimens and patient engagement. Having the information, motivation, and skills to live with a medical condition are conceptualized by the term, “activation.” Patients referred for advanced HF therapy and their unpaid family caregiver were invited to participate in this study by completing the 10-item patient activation measure (PAM) questionnaire. Anxiety and depression were assessed via the hospital anxiety and depression scale. We compared activation, anxiety, and depression between those selected versus not selected for advanced HF therapy (left ventricular assist device or heart transplantation). We analyzed those who subsequently underwent advanced HF therapy in regards to activation and 1-year survival. There were 133 (68%) patients selected for therapy. Neither depression nor anxiety differed by selection status, but PAM levels did (p=0.02). Those not selected for therapy were approximately 4 times more likely to have lower activation than those who were selected (8% vs 2%). Of the 133 selected patients, 110 (84%) subsequently underwent advanced HF therapy and 15 (14%) of those died within 1 year. Survival was independent of baseline anxiety (p=0.92) and depression (p=0.70), as well as patient and caregiver PAM (p=0.50 and 0.77, respectively). In conclusion, patients with higher activation were more likely to be selected for advanced HF therapy.

Carl, E., S. M. Witcraft, B. Y. Kauffman, E. M. Gillespie, E. S. Becker, P. Cuijpers, M. Van Ameringen, J. A. J. Smits and M. B. Powers (2019). “Psychological and pharmacological treatments for generalized anxiety disorder (GAD): a meta-analysis of randomized controlled trials.” Cogn Behav Ther Feb 14: p. 1-21. [Epub ahead of print].

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The purpose of this meta-analysis was to provide updated pooled effect sizes of evidence-based psychotherapies and medications for generalized anxiety disorder (GAD) and to investigate potential moderators of outcomes. Seventy-nine randomized controlled trials (RCT) including 11,002 participants with a diagnosis of GAD were included in a meta-analysis that tested the efficacy of psychotherapies or medications for GAD. Psychotherapy showed a medium to large effect size (g = 0.76) and medication showed a small effect size (g = 0.38) on GAD outcomes. Psychotherapy also showed a medium effect on depression outcomes (g = 0.64) as did medications (g = 0.59). Younger age was associated with a larger effect size for psychotherapy (p < 0.05). There was evidence of publication bias in psychotherapy studies. This analysis found a medium to large effect for empirically supported psychotherapy interventions on GAD outcomes and a small effect for medications on GAD outcomes. Both groups showed a medium effect on depression outcomes. Because medication studies had more placebo control conditions than inactive conditions compared to psychotherapy studies, effect sizes between the domains should not be compared directly. Patient age should be further investigated as a potential moderator in psychotherapy outcomes in GAD.