Efficient region-based test strategy uncovers genetic risk factors for functional outcome in bipolar disorder

Identifying novel proteins underlying bipolar disorder via integrating pQTLs of the plasma, CSF, and brain with GWAS summary data

Bipolar disorder (BD) presents a significant challenge due to its chronic and relapsing nature, with its underlying pathogenesis remaining elusive. This study employs Mendelian randomization (MR), a widely recognized genetic approach, to unveil intricate causal associations between proteins and BD, leveraging protein quantitative trait loci (pQTL) as key exposures. We integrate pQTL data from brain, cerebrospinal fluid (CSF), and plasma with genome-wide association study (GWAS) findings of BD within a comprehensive systems analysis framework. Our analyses, including two-sample MR, Steiger filtering, and Bayesian colocalization, reveal noteworthy associations. Elevated levels of AGRP, FRZB, and IL36A in CSF exhibit significant associations with increased BD_ALL risk, while heightened levels of CTSF and LRP8 in CSF, and FLRT3 in plasma, correlate with decreased BD_ALL risk. Specifically for Bipolar I disorder (BD_I), increased CSF AGRP levels are significantly linked to heightened BD_I risk, whereas elevated CSF levels of CTSF and LRP8, and plasma FLRT3, are associated with reduced BD_I risk. Notably, genes linked to BD-related proteins demonstrate substantial enrichment in functional pathways such as "antigen processing and presentation," "metabolic regulation," and "regulation of myeloid cell differentiation." In conclusion, our findings provide beneficial evidence to support the potential causal relationship between IL36A, AGRP, FRZB, LRP8 in cerebrospinal fluid, and FLRT3 in plasma, and BD and BD_I, providing insights for future mechanistic studies and therapeutic development.

The genetic association between bipolar disorder and dementia: a qualitative review

Bipolar disorder is a chronic disorder characterized by fluctuations in mood state and energy and recurrent episodes of mania/hypomania and depression. Bipolar disorder may be regarded as a neuro-progressive disorder in which repeated mood episodes may lead to cognitive decline and dementia development. In the current review, we employed genome-wide association studies to comprehensively investigate the genetic variants associated with bipolar disorder and dementia. Thirty-nine published manuscripts were identified: 20 on bipolar disorder and 19 on dementia. The results showed that the genes CACNA1C, GABBR2, SCN2A, CTSH, MSRA, and SH3PXD2A were overlapping between patients with bipolar disorder and dementia. In conclusion, the genes CACNA1C, GABBR2, SCN2A, CTSH, MSRA, and SH3PXD2A may be associated with the neuro-progression of bipolar disorder to dementia. Further genetic studies are needed to comprehensively clarify the role of genes in cognitive decline and the development of dementia in patients with bipolar disorder.

tRNA-Uridine Aminocarboxypropyltransferase DTW Domain Containing 2 Suppresses Colon Adenocarcinoma Progression

Background

DTW Domain Containing 2 (DTWD2) is a newly identified transfer RNA-uridine aminocarboxypropyltransferase. Dysregulated expression of DTWD1 has been reported in several malignancies, nevertheless, the role of DTWD2 in cancers remains completely unknown. Here, we aimed to initially investigate the expression and role of DTWD2 in colon adenocarcinoma.

Methods

We first evaluated the transcription and mRNA levels of DTWD2 using data from The Cancer Genome Atlas. Besides, we tested its mRNA and protein expression in our enrolled retrospective cohort. Univariate and multivariate analyses were conducted to assess its prognostic value. Cellular experiments and xenografts were also performed to validate the role of DTWD2 in colon cancer progression.

Results

DTWD2 was downregulated in colon adenocarcinoma and associated with poor prognosis. Lymph node metastasis, distant metastasis, and advanced tumor stage are all characterized by lower DTWD2 levels. Furthermore, Cox regression analysis demonstrated that DTWD2 is a novel independent prognostic factor for colon cancer patients. Finally, cellular and xenograft data demonstrated that silencing DTWD2 significantly enhanced colon cancer growth.

Conclusion

Low expression of DTWD2 may be a potential molecular marker for poor prognosis in colon cancer.

DNA methylation and general psychopathology in childhood: an epigenome-wide meta-analysis from the PACE consortium

The general psychopathology factor (GPF) has been proposed as a way to capture variance shared between psychiatric symptoms. Despite a growing body of evidence showing both genetic and environmental influences on GPF, the biological mechanisms underlying these influences remain unclear. In the current study, we conducted epigenome-wide meta-analyses to identify both probe- and region-level associations of DNA methylation (DNAm) with school-age general psychopathology in six cohorts from the Pregnancy And Childhood Epigenetics (PACE) Consortium. DNAm was examined both at birth (cord blood; prospective analysis) and during school-age (peripheral whole blood; cross-sectional analysis) in total samples of N = 2178 and N = 2190, respectively. At school-age, we identified one probe (cg11945228) located in the Bromodomain-containing protein 2 gene (BRD2) that negatively associated with GPF (p = 8.58 × 10-8). We also identified a significant differentially methylated region (DMR) at school-age (p = 1.63 × 10-8), implicating the SHC Adaptor Protein 4 (SHC4) gene and the EP300-interacting inhibitor of differentiation 1 (EID1) gene that have been previously implicated in multiple types of psychiatric disorders in adulthood, including obsessive compulsive disorder, schizophrenia, and major depressive disorder. In contrast, no prospective associations were identified with DNAm at birth. Taken together, results of this study revealed some evidence of an association between DNAm at school-age and GPF. Future research with larger samples is needed to further assess DNAm variation associated with GPF.

Corticosterone-mediated regulation and functions of miR-218-5p in rat brain

Chronic stress is one of the key precipitating factors in major depressive disorder (MDD). Stress associated studies have underscored the mechanistic role of epigenetic master players like microRNAs (miRNAs) in depression pathophysiology at both preclinical and clinical levels. Previously, we had reported changes in miR-218-5p expression in response to corticosterone (CORT) induced chronic stress. MiR-218-5p was one of the most significantly induced miRNAs in the prefrontal cortex (PFC) of rats under chronic stress. In the present report, we have investigated how chronic CORT exposure mechanistically affected miR-218-5p expression in the rat brain and how miR-218 could trigger molecular changes on its downstream regulatory pathways. Elevated expression of miR-218-5p was found in the PFC of CORT-treated rats. A glucocorticoid receptor (GR) targeted Chromatin-Immunoprecipitation (ChIP) assay revealed high GR occupancy on the promoter region of Slit3 gene hosting miR-218-2 in its 3rd intron. RNA-sequencing data based on RNA Induced silencing Complex Immunoprecipitation (RISC-IP) with AGO2 in SH-SY5Y cells detected six consistent target genes of miR-218-5p (APOL4, DTWD1, BNIP1, METTL22, SNAPC1, and HDAC6). The expression of all five genes, except APOL4, was successfully validated with qPCR in CORT-treated rat PFC. Further, Hdac6-based ChIP-seq experiment helped in mapping major genomic loci enriched for intergenic regions in the PFC of CORT-treated rat. A proximity-based gene ontology (GO) analysis revealed a majority of the intergenic sites to be part of key genes implicated in central nervous system functions, notably synapse organization, neuron projection morphogenesis, and axonogenesis. Our results suggest that the upregulation of miR-218-5p in PFC of CORT-treated rats possibly resulted from GR biding in the promoter region of Slit3 gene. Interestingly, Hdac6 was one of the consistent target genes potentially found to regulate CNS related genes by chromatin modification. Collectively, these findings establish the role of miR-218-5p in chronic stress and the epigenetic function it plays to induce chromatin-based transcriptional changes of several CNS genes in triggering stress-induced disorders, including depression. This also opens up the scope to understand the role of miR-218-5p as a potential target for noncoding RNA therapeutics in clinical depression.

Rare variant association study of veteran twin whole-genomes links severe depression with a nonsynonymous change in the neuronal gene BHLHE22

OBJECTIVES

Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associations, but without known links to rare variation in the human genome. Here we aim to identify rare genetic variants associated with MDD using deep whole-genome sequencing data in an independent population.

METHODS

We report the sequencing of 1,688 whole genomes in a large sample of male-male Veteran twins. Depression status was classified based on a structured diagnostic interview according to DSM-III-R diagnostic criteria. Searching only rare variants in genomic regions from recent GWAS on MDD, we used the optimised sequence kernel association test and Fisher's Exact test to fine map loci associated with severe depression.

RESULTS

Our analysis identified one gene associated with severe depression, basic helix loop helix e22 (P_Adjusted = 0.03) via SKAT-O test between unrelated severely depressed cases compared to unrelated non-depressed controls. The same gene BHLHE22 had a non-silent variant rs13279074 (P_Adjusted = 0.032) based on a single variant Fisher's Exact test between unrelated severely depressed cases compared to unrelated non-depressed controls.

CONCLUSION

The gene BHLHE22 shows compelling genetic evidence of directly impacting the severe depression phenotype. Together these results advance understanding of the genetic contribution to major depressive disorder in a new cohort and link a rare variant to severe forms of the disorder.

The Sins of Our Forefathers: Paternal Impacts on De Novo Mutation Rate and Development

Spermatogonial stem cells (SSCs) are generally characterized by excellent DNA surveillance and repair, resulting in one of the lowest spontaneous mutation rates in the body. However, the barriers to mutagenesis can be overwhelmed under two sets of circumstances. First, replication errors may generate age-dependent mutations that provide the mutant cells with a selective advantage, leading to the clonal expansions responsible for dominant genetic diseases such as Apert syndrome and achondroplasia. The second mechanism centers on the vulnerability of the male germline to oxidative stress and the induction of oxidative DNA damage in spermatozoa. Defective repair of such oxidative damage in the fertilized oocyte results in the creation of mutations in the zygote that can influence the health and well-being of the offspring. A particular hot spot for such oxidative attack on chromosome 15 has been found to align with several mutations responsible for paternally mediated disease, including cancer, psychiatric disorders, and infertility.

Predictors of Functional Outcome in Patients With Bipolar Disorder: Effects of Cognitive Psychoeducational Group Therapy After 12 Months

Background: Cognitive deficits are known as a core feature in bipolar disorder. Persisting neurocognitive impairment is associated with low psychosocial functioning. The aim of this study was to identify potential cognitive, clinical and treatment-dependent predictors for functional impairment, symptom severity and early recurrence in bipolar patients, as well as to analyze neurocognitive performance compared to healthy controls. Methods: Forty three remitted bipolar patients and 40 healthy controls were assessed with a neurocognitive battery testing specifically attention, memory, verbal fluency and executive functions. In a randomized controlled trial, remitted patients were assigned to two treatment conditions as add-on to state-of-the-art pharmacotherapy: cognitive psychoeducational group therapy over 14 weeks or treatment-as-usual. At 12 months after therapy, functional impairment and severity of symptoms were assessed. Results: Compared to healthy controls, bipolar patients showed lower performance in executive function (perseverative errors p < 0.01, categories correct p < 0.001), sustained attention (total hits p < 0.001), verbal learning (delayed recall p < 0.001) and verbal fluency (p-words p < 0.002). Cognitive psychoeducational group therapy and attention predicted occupational functioning with a hit ratio of 87.5%. Verbal memory recall was found to be a predictor for symptom severity (hit ratio 86.8%). Recurrence in the follow-up period was predicted by premorbid IQ and by years of education (hit ratio 77.8%). Limitations: Limitations of the present study result mainly from a small sample size. The extent of cognitive impairment appears to impact occupational disability, clinical outcome as well as recurrence rate. This result must be interpreted with caution because statistical analysis failed to show higher significance. Conclusions: Bipolar patients benefit from cognitive psychoeducational group therapy in the domain of occupational life. Deficits in sustained attention have an impact on occupational impairment. Implications for treatment strategies are discussed. Further evaluation in larger studies is needed.

Biogenesis and functions of aminocarboxypropyluridine in tRNA

Transfer (t)RNAs contain a wide variety of post-transcriptional modifications, which play critical roles in tRNA stability and functions. 3-(3-amino-3-carboxypropyl)uridine (acp3U) is a highly conserved modification found in variable- and D-loops of tRNAs. Biogenesis and functions of acp3U have not been extensively investigated. Using a reverse-genetic approach supported by comparative genomics, we find here that the Escherichia coli yfiP gene, which we rename tapT (tRNA aminocarboxypropyltransferase), is responsible for acp3U formation in tRNA. Recombinant TapT synthesizes acp3U at position 47 of tRNAs in the presence of S-adenosylmethionine. Biochemical experiments reveal that acp3U47 confers thermal stability on tRNA. Curiously, the ΔtapT strain exhibits genome instability under continuous heat stress. We also find that the human homologs of tapT, DTWD1 and DTWD2, are responsible for acp3U formation at positions 20 and 20a of tRNAs, respectively. Double knockout cells of DTWD1 and DTWD2 exhibit growth retardation, indicating that acp3U is physiologically important in mammals.