Norihiro Okada

Winner and loser effects can influence future aggressive behavior following social competition, but their neurogenomic basis remains poorly understood. Using Betta splendens , we integrated behavioral analyses, whole-brain RNA sequencing, and genomic coexpression network analyses to investigate how social experiences influence enduring behavioral and molecular states. Winners showed increased attack frequency, whereas losers prolonged aggressive latency, indicating effects on distinct behavioral aspects. Winners and losers initially shared acute responses in terms of both gene expression and network coordination but subsequently diverged through outcome-specific patterns of network reorganization, despite few persistent differentially expressed genes. This divergence was asymmetric and involved multiple components: immune-related networks showed notable contrasts, with winners displaying anticipated postconflict coordination but losers instead showing discoordination, whereas neuroendocrine and purinergic networks diverged over distinct temporal scales. These findings highlight transcriptomic network-level remodeling as a potential key feature of the winner–loser effect.

Clinically robust molecular biomarkers for depression have remained elusive, despite extensive transcriptomic research. This gap is consequential: depression is prevalent and heterogeneous, yet objective measures to quantify burden, stratify patients, and track recovery remain limited. Here, we review evidence that intron retention (IR) can serve as a homeostatic state variable—and therefore a sensitive biomarker—reporting stress adaptation and recovery at an upstream regulatory layer, often preceding or outperforming differential gene expression (DEG) readouts. Mechanistically, IR enables bidirectional fine-tuning of effective gene output: increased IR (IncIR) can throttle output under overload, whereas decreased IR (DecIR) releases this brake to restore gene output. Because these shifts are reversible and treatment-responsive, IR signatures can function not only as disease markers but also as pharmacodynamic metrics for blood-based monitoring of drug response and recovery. To evaluate the clinical utility of IR, we use depression as a proof of concept and focus on two interventions: (i) the Kampo formula hangekobokuto (HKT), which is associated with IR normalization consistent with reduced peripheral inflammatory load; and (ii) ketamine, where IR patterns measured before ketamine treatment in non-responders are linked to stronger innate-immune/antiviral activity, suggesting a higher inflammatory load that may limit treatment benefit. Finally, we discuss transdiagnostic extensions beyond depression, using early cognitive decline (mild cognitive impairment, MCI) as a stringent, biologically distal test case for blood-based IR/DI readouts and motivating independent cohort replication and longitudinal validation.

Major depressive disorder (MDD) lacks reliable laboratory tests for diagnosis and treatment monitoring, underscoring the need for robust molecular readouts in blood. Beyond symptom-based classification, MDD can also be viewed as a condition involving impaired homeostatic regulation across stress-responsive, immune, metabolic, and neural systems. Consistent with this perspective, altered intron retention (IR) patterns have been observed in peripheral blood in depression-related and treatment-response contexts, supporting the translational relevance of this RNA-processing layer to mood disorders. A key observation underpinning this review is that IR can function as a reversible, intervention-responsive readout of physiological state. In a pre-symptomatic stress-like state in klotho mutant mice (a premature-aging model), widespread IR increases revert toward a healthy pattern upon treatment, suggesting that IR is embedded in a controllable homeostatic layer. Against the backdrop of limited cross-cohort transferability of differential gene expression (DGE) signatures, we propose that IR provides a mechanistically grounded biomarker layer because it reports regulated RNA processing states rather than context-fragile abundance endpoints. We operationalize IR as a post-transcriptional “throttle” on effective gene output, with increased IR/detained intron (DI) states acting as a reversible brake and decreased IR acting as an accelerator that increases translation-competent mRNA supply. Mechanistic exemplars across immune, metabolic, and neuronal systems (e.g., IFNG, OGT, MAT2A, neuronal activity-triggered intron excision, and intron detention-mediated stemness/differentiation switching in adult neural stem cells) show that defined inputs can switch IR/DI states to tune output kinetics. Integrating these findings, we propose an “Intron Retention Homeostat” (IR-Homeostat) model in which cells sense deviations from physiological set points and implement feedback control of gene output through switchable IR/DI regulation. This framework positions IR not only as a robust state readout for stratification, treatment response prediction, and pharmacodynamic profiling, but also as a tractable entry point to identify the molecular sensors and mediators that couple homeostatic signals to RNA processing control.

Clinically robust molecular biomarkers for depression have remained elusive, despite extensive transcriptomic research. This gap is consequential: depression is prevalent and heterogeneous, yet objective measures to quantify burden, stratify patients, and track recovery remain limited. Here we review evidence that intron retention (IR) can serve as a homeostatic state variable—and therefore a sensitive biomarker—reporting stress adaptation and recovery at an upstream regulatory layer, often preceding or outperforming differential gene expression (DEG) readouts. Mechanistically, IR enables bidirectional fine-tuning of effective gene output: increased IR (IncIR) can throttle output under overload, whereas decreased IR (DecIR) releases this brake to restore gene output. Because these shifts are reversible and treatment-responsive, IR signatures can function not only as disease markers but also as pharmacodynamic metrics for blood-based monitoring of drug response and recovery. To evaluate the clinical utility of IR, we use depression as a proof-of-concept and focus on two interventions: (i) the Kampo formula hangekobokuto (HKT), which is associated with IR normalization consistent with reduced peripheral inflammatory load. and (ii) ketamine, where IR patterns measured before ketamine treatment in non-responders are linked to stronger innate-immune/antiviral activity, suggesting a higher inflammatory load that may limit treatment benefit. Finally, we discuss transdiagnostic extensions using early cognitive decline as a concrete example. Although peripheral blood may only indirectly reflect the primary drivers of MCI-stage dementia risk—potentially yielding smaller IR/DI effect sizes than in depression—consistent group-level shifts can still emerge in adequately powered cohorts, supporting IR as a practical blood-based readout even when causal pathology lies outside the blood.

Major depressive disorder (MDD) lacks reliable laboratory tests for diagnosis and treatment monitoring, motivating continued efforts to identify robust molecular readouts in blood. A key observation underpinning this review is that intron retention (IR) can behave as a reversible, intervention-responsive readout of physiological state: in a pre-symptomatic stress-like state in klotho mice, widespread IR increases revert toward a healthy pattern upon treatment with the traditional multi-herbal medicine juzentaihoto, suggesting that IR is embedded in a controllable homeostatic layer. Against the backdrop of limited cross-cohort transferability of differential gene expression (DEG) signatures, we propose that IR provides a mechanistically grounded biomarker layer because it reports regulated RNA-processing states rather than context-fragile abundance endpoints. We operationalize IR as a post-transcriptional “throttle” on effective gene output, with increased IR/detained intron (DI) states acting as a reversible brake and decreased IR acting as an accelerator that increases translation-competent mRNA supply. Mechanistic exemplars across immune, metabolic, and neuronal systems (e.g., IFNG, OGT, MAT2A, neuronal activity–triggered intron excision, and intron detention–mediated stemness/differentiation switching in adult neural stem cells) show that defined inputs can switch IR/DI states to tune output kinetics. Integrating these findings, we propose an “Intron Retention Homeostat” (IR-Homeostat) model in which cells sense deviations from physiological set points and implement feedback control of gene output via switchable IR/DI regulation. This framework positions IR not only as a robust state readout for stratification, treatment-response prediction, and pharmacodynamic profiling, but also as a tractable entry point to identify the molecular sensors and mediators that couple homeostatic signals to RNA-processing control.

Intron retention (IR) provides an early regulatory readout of stress, often preceding steady-state changes in mRNA expression. Here, we asked whether IR can resolve complex spaceflight stress into separable mechanistic components and map how stress information propagates across tissues. We integrated high-confidence IR profiles from mouse spaceflight experiments with datasets representing mechanical unloading (microgravity) and non-mechanical, non-gravitational (NG; radiation–oxidative) stress. IR-based analysis disentangled these stress axes and uncovered a conserved five-layer regulatory architecture—mechanical input, signaling-gate, nuclear/genome-integrity, RNA/splicing–proteostasis/trafficking, and immune–metabolic adaptive output layers—through which immune organs interpret spaceflight stress. Microgravity and NG stress entered this hierarchy through distinct routes yet converged at IR as a common mode of upstream control, preceding most downstream transcriptional changes. This IR-centered framework provides a general strategy for decomposing complex, multi-factorial stress into interpretable modules. Leveraging this resolution, we identified a subset of IRGs whose normalization tracked the recovery of interacting structural partners, revealing a network-coupled “drag” phenomenon detectable when stress programmes are partitioned at the IR level. Together, our results establish IR as a unifying regulatory code—a command tier—that organizes stress-response hierarchies and exposes emergent network behaviors across mechanical, radiative, and immune perturbations.

Introduction: In contemporary aging societies, preventing and ameliorating mental and physical frailty is essential. Kampo formulas, including ninjinyoeito (NYT) and juzentaihoto (JTT), have been used traditionally to treat frailty in the elderly. NYT has been reported to alleviate psychological frailty such as depression and anxiety. This study aimed to clarify the mechanisms underlying the effects of these two Kampo formulas in the early stages of neurodegeneration associated with psychiatric disorders. Methods: Genes affected by Kampo formulas were comprehensively investigated by administering JTT or NYT to senescence accelerated mouse prone 8 (SAMP8) mice, from 7 weeks, and by RNA sequencing of the hippocampus at 19 weeks when depression and anxiety behaviors typically emerge. Additionally, we examined the impact of these Kampo formulas on neuroinflammation induced by lipopolysaccharide (LPS). Results: The two Kampo formulas alleviated the depressive-like behavior of SAMP8 mice, as demonstrated by the restoration of microglial cell activation, DNA repair, stress-responsive transcription factor expression, and nervous system development-related gene expression. However, the NYT-administrated group presented a greater number of recovered genes than did the JTT-administrated group, and NYT additionally suggests that the potential inhibition of age-related mitochondrial dysfunction and increased oxidative stress. The administration of LPS resulted in elevated expression levels of immune and inflammation-related genes and increased astrocyte activity in SAMP8 mice. JTT mitigated these effects by suppressing the expression of the LPS receptor TLR4 and its downstream target NF-κB. In contrast to JTT, NYT maintained and increased the expression of genes associated with neuroprotective functions in microglia. Discussion: The two Kampo formulas exerted neuroprotective effects by enhancing neural and glial stress responses in the early stages of neurodegeneration. Under condition of acute inflammation, JTT and NYT alleviated neuronal damage via the suppression of microglial activity and the enhancement of microglial neuroprotection, respectively. These findings provide novel insights into the mechanism of action of NYT, which has been reported to ameliorate psychological frailty associated with aging, and further suggest that JTT may exert effects against inflammatory neurodegeneration.

In response to stress, the body attempts to maintain protein homeostasis through intron retention (IR). By identifying the genes that undergo IR in response to stress, possibly we can identify what type of stress the body is experiencing. Using this principle, we reanalyzed RNA sequencing data of patients with treatment-resistant depression and examined IR genes to investigate their characteristics to ketamine. The ketamine nonresponders were characterized by a state of elevated viral infection. Several IR genes related to viral infection were restored to a healthy state by ketamine, regardless of whether the individual was a nonresponder or a responder. Accordingly, it was more reasonable to describe nonresponders not as individuals for whom ketamine is ineffective but rather as individuals for whom ketamine is insufficient to overcome the extremely elevated inflammatory state of these individuals. This study is pioneering in its exploration of the molecular underpinnings that differentiate between nonresponders and responders.

Background: Peripheral inflammation is often associated with depressive disorders, and immunological biomarkers of depression remain a focus of investigation.Methods: We performed RNA-seq analysis of RNA transcripts of human peripheral blood mononuclear cells from a case-control study including subjects with self-reported depression in the pre-symptomatic state of major depressive disorder and analyzed differentially expressed genes (DEGs) and the frequency of intron retention (IR) using rMATS.Results: Among the statistically significant DEGs identified, the 651 upregulated DEGs were particularly enriched in the term “bacterial infection and phagocytosis”, whereas the 820 downregulated DEGs were enriched in the terms “antigen presentation” and “T-cell proliferation and maturation”. We also analyzed 158 genes for which the IR was increased (IncIR) and 211 genes for which the IR was decreased (DecIR) in the depressed subjects. Although the Gene Ontology terms associated with IncIR and DecIR were very similar to those of the up- and downregulated genes, respectively, IR genes appeared to be particularly enriched in genes with sensor functions, with a preponderance of the term “ciliary assembly and function”. The observation that IR genes specifically interact with innate immunity genes suggests that immune-related genes, as well as cilia-related genes, may be excellent markers of depression. Re-analysis of previously published RNA-seq data from patients with MDD showed that common IR genes, particularly our predicted immune- and cilia-related genes, are commonly detected in populations with different levels of depression, providing validity for using IR to detect depression.Conclusion: Depression was found to be associated with activation of the innate immune response and relative inactivation of T-cell signaling. The DEGs we identified reflect physiological demands that are controlled at the transcriptional level, whereas the IR results reflect a more direct mechanism for monitoring protein homeostasis. Accordingly, an alteration in IR, namely IncIR or DecIR, is a stress response, and intron-retained transcripts are sensors of the physiological state of the cytoplasm. The results demonstrate the potential of relative IR as a biomarker for the immunological stratification of depressed patients and the utility of IR for the discovery of novel pathways involved in recovery from depression.