In late 2012 it was evidenced that most of the human genome is transcribed but only a small percentage of the transcripts are translated. This observation supported the importance of non-coding RNAs and it was confirmed in several organisms. The most abundant non-translated transcripts are long non-coding RNAs (lncRNAs). In contrast to protein-coding RNAs, they show a more cell-specific expression. To understand the function of lncRNAs, it is fundamental to investigate in which cells they are preferentially expressed and to detect their subcellular localization. Recent improvements of techniques that localize single RNA molecules in tissues like single-cell RNA sequencing and fluorescence amplification methods have given a considerable boost in the knowledge of the lncRNA functions. In recent years, single-cell transcription variability was associated with non-coding RNA expression, revealing this class of RNAs as important transcripts in the cell lineage specification. The purpose of this review is to collect updated information about lncRNA classification and new findings on their function derived from single-cell analysis. We also retained useful for all researchers to describe the methods available for single-cell analysis and the databases collecting single-cell and lncRNA data. Tables are included to schematize, describe, and compare exposed concepts.

Mitochondrial dysfunctions have been reported in bipolar disorder (BD), but their role in the etiopathogenesis of BD as well as their implications in modulating response to pharmacological treatments with psychotropic medications have been scarcely explored. Mitochondrial DNA copy number (mtDNA-cn) has been linked to mitochondria functioning, and, despite some degree of inconsistence, previous findings showed that BD patients present significant differences in mtDNA-cn compared to healthy controls. Here we measured mtDNA-cn in a sample of 89 patients with BD and 78 healthy controls (HC). Patients in the BD sample were treated either with lithium (n = 47) and characterized as responders (n = 22) or non-responders (n = 25), or with other mood stabilizers (n = 42). BD patients had larger mtDNA-cn compared to HC (adjusted model: F₂=9.832; p = 0.000095; contribution of diagnosis F₁= 10.798; p = 0.001). When the BD sample was stratified for treatment exposure, mtDNA-cn was lower in patients treated with lithium compared to those treated with other mood stabilizers (adjusted model: F₄=23.770, p = 7.0929E-13; contribution of treatment: F₁=54.300, p = 1.55E-10). Moreover mtDNA-cn was higher in patients treated with other mood stabilizers compared to controls and Li-treated BD patients (F₃=28.125, p = 1.36E-14; contribution of groups F₂=36.156, p = 1.25E-13). Finally, there was no difference in mtDNA-cn levels in lithium responders compared to non-responders and neither between the two diagnostic groups (BD type 1 and 2). Our findings suggest that BD may be associated with mitochondrial dysfunctions, and that exposure to lithium but not to other mood stabilizers may restore these abnormalities, though this does not appear correlated with the clinical efficacy of lithium.

Background: Major depressive disorder (MDD) exhibits significant heterogeneity in treatment responses, necessitating multiple pharmacological trials to achieve therapeutic success. Pharmacogenetic (PGx) testing has emerged as a promising tool to personalize antidepressant (AD) treatments, though its clinical utility remains controversial. Methods: This study assessed the efficacy of PGx-guided treatment in improving clinical outcomes among 287 MDD patients within the PANDORA trial, a prospective randomized, participant- and rater-blinded, controlled trial conducted in Italy. A total of 268 adults with moderate-to-severe MDD were randomized into Treated as Usual (TAU) or Treated with Genetic Test Guide (TGTG). Patients were assessed using the Hamilton Depression Rating Scale (HAM-D17), Beck Depression Inventory II (BDI-II), Beck Anxiety Inventory, MINI-ICF-APP for psychosocial functioning, and the UKU Side Effects Rating Scale, at baseline and at 4, 8, and 12 weeks. Results: Both groups demonstrated significant symptom improvement over the 12-week period. No significant differences were observed between the groups in terms of response and remission rates, measured by HAM-D17 and BDI-II, at weeks 8 and 12. Notably, in the BDI-II symptom cluster analysis, significant differences were found only in neurovegetative symptoms, with TGTG patients showing greater improvement at the 4-week and 8-week follow-up visits. Among patients with severe baseline symptoms, those in the TGTG group exhibited greater symptom reduction and higher response rates at week 8. Conclusions: These findings suggest that while PGx testing did not significantly improve overall treatment efficacy in MDD compared to TAU, it may offer benefits in managing patients with severe symptoms and specific symptom domains.

Background and Objectives: Treatment-resistant depression (TRD) is a major clinical challenge in the management of major depressive disorder (MDD). While pharmacogenetics has been suggested to be clinically useful in guiding antidepressant treatment, few studies have explored if and how pharmacogenes can be involved in TRD pathophysiology and its clinical outcomes. Material amd Methods: We explored the role of differences in metabolizer phenotypes, gene expression levels, and microRNAs of three key pharmacogenes (CYP2D6, CYP2C19, CYP2B6) in TRD pathophysiology and antidepressant response in a cohort of 300 patients with MDD from the PROMPT consortium. Results: CYP2D6 phenotype distribution did not differ significantly between TRD and non-TRD groups, but mRNA expression was significantly upregulated in TRD. Hsa-miR-26b-5p, a microRNA predicted to regulate CYP2D6, was significantly downregulated in TRD. For CYP2C19, intermediate metabolizers (IMs) were underrepresented in TRD versus non-TRD (IMs vs. normal metabolizers (NMs): χ² = 6.07, p = 0.019). microRNA hsa-let-7d-5p and hsa-miR-27a-3p, predicted to regulate CYP2C19, were significantly downregulated in TRD. No significant differences were found for CYP2B6. Conclusions: This study contributes valuable insights to the PROMPT project on how pharmacokinetic gene variants and their expression and regulatory mechanisms may influence antidepressant response and resistance in MDD.

Early life stress (ELS) increases vulnerability to major depressive disorder (MDD) and treatment-resistant depression (TRD) through lasting neurobiological and epigenetic alterations. MicroRNAs (miRNAs), key post-transcriptional regulators of gene expression, are emerging as potential biomarkers linking environmental stressors and depression pathophysiology. This study employed a miRNomic approach to investigate plasma miRNA changes associated with trauma-focused psychotherapy in TRD patients with a history of ELS. Twenty-four patients received either trauma-focused cognitive behavioural therapy (TF-CBT) or eye movement desensitization and reprocessing (EMDR) over eight weeks, with depressive symptoms assessed by the Montgomery-Åsberg Depression Rating Scale (MADRS) at baseline (T0) and post-treatment (T8). Plasma levels of 188 miRNAs were quantified using qRT-PCR. Of these, 148 passed quality control and were included in the analysis. Twenty-two miRNAs were nominally significantly downregulated after psychotherapy, with miR-132-3p remaining significant after correction for multiple testing, and four (let-7f-5p, miR-195-5p, miR-29c-3p, miR-32-5p) showing trends toward significance. Pathway enrichment analyses identified 120 pathways involved in inflammation, neuroplasticity, and stress response, including Hippo, TGF-β, TNF, Wnt, PI3K-Akt, Neurotrophin, glutamatergic synapse, and dopaminergic signaling. Subgroup analyses identified nominal downregulation of miRNAs following EMDR (miR-132-3p and let-7f-5p) and TF-CBT (miR-32-5p and let-7f-5p), with none remaining significant after correction. Correlational analyses between miRNAs changes and treatment outcomes showed, in the whole sample, that miR-139-5p downregulation was nominally associated with greater improvements in overall depressive symptoms, as well as cognitive and neurovegetative symptom domains. Subgroup correlational analyses identified significant nominal associations between miR-125b-5p downregulation and improvements in overall depressive symptoms, mood, and neurovegetative domains following TF-CBT, and between miR-139-5p downregulation and overall depressive symptoms (trend significant) and neurovegetative symptom improvement following EMDR; however, none of these associations survived multiple-testing correction. These findings suggest that trauma-focused psychotherapies may induce peripheral miRNA modulation linked to clinical response, with miR-132-3p, miR-125b-5p, and miR-139-5p emerging as potential biomarkers of treatment response. The results support a role for miRNA-mediated neuroplastic and inflammatory mechanisms in the molecular underpinnings of psychotherapy efficacy in TRD patients exposed to ELS.