Dissecting biological heterogeneity in major depressive disorder based on neuroimaging subtypes with multi-omics data

doi:10.21203/rs.3.rs-4852981/v1

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Dissecting biological heterogeneity in major depressive disorder based on neuroimaging subtypes with multi-omics data

https://doi.org/10.21203/rs.3.rs-4852981/v1

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Background

The heterogeneity of Major Depressive Disorder (MDD) has been increasingly recognized, challenging traditional symptom-based diagnostics and the development of mechanism-targeted therapies. This study aims to identify neuroimaging-based MDD subtypes and dissect their predominant biological characteristics using multi-omics data.

Method

A total of 807 participants were included in this study, comprising 327 individuals with MDD and 480 healthy controls (HC). The amplitude of low-frequency fluctuations (ALFF), a functional neuroimaging feature, was extracted for each participant and used to identify MDD subtypes through machine learning clustering. Multi-omics data, including profiles of genetic, epigenetics, metabolomics, and pro-inflammatory cytokines, were obtained. Comparative analyses of multi-omics data were conducted between each MDD subtype and HC to explore the molecular underpinnings involved in each subtype.

Results

We identified three neuroimaging-based MDD subtypes, each characterized by unique ALFF pattern alterations compared to HC. Multi-omics analysis showed a strong genetic predisposition for Subtype 1, primarily enriched in neuronal development and synaptic regulation pathways. This subtype also exhibited the most severe depressive symptoms and cognitive decline compared to the other subtypes. Subtype 2 is characterized by immuno-inflammation dysregulation, supported by elevated IL-1β levels, altered epigenetic inflammatory measures, and differential metabolites correlated with IL-1β levels. No significant biological markers were identified for Subtype 3.

Conclusion

Our results identify neuroimaging-based MDD subtypes and delineate the distinct biological features of each subtype. This provides a proof of concept for mechanism-targeted therapy in MDD, highlighting the importance of personalized treatment approaches based on neurobiological and molecular profiles.

Biological sciences/Neuroscience/Molecular neuroscience

Health sciences/Diseases/Psychiatric disorders/Depression

Health sciences/Pathogenesis/Clinical genetics

Biological sciences/Genetics/Clinical genetics

Over the last few decades, the recognition of Major Depressive Disorder (MDD) as a condition of inherent heterogeneity has posed significant challenges to the conventional diagnostic framework that relies on symptom clusters¹. This heterogeneity is characterized by a significant mismatch between symptom dimensions and their biological underpinnings, where identical symptoms may arise from different biological causes, and disparate symptoms may reflect similar biological changes^2,3. Such discrepancies make it necessary to develop precise diagnostic and therapeutic strategies based on the disease's underlying mechanisms. Despite extensive efforts, the identification of reliable biomarkers for MDD diagnosis remains elusive. Furthermore, the prevalent trial-and-error approach in the current diagnostic system yields disappointing outcomes, with less than one-third of MDD patients experiencing remission after initial treatments^4–6. About one-third of patients do not achieve clinical recovery even after undergoing 12-week courses of four distinct antidepressants over a year⁷. The intricate heterogeneity of MDD plays a significant role in these diagnostic and treatment dilemmas. Strategically redefining MDD into biologically homogeneous subtypes, guided by objective biomarkers, could pave the way for more accurate and effective precision diagnostics and treatments.

With the rapid advancement in biotechnologies, researches into MDD adopt multiple biological characteristics, including neuroimaging^8–10, electroencephalography (EEG)^11,12, and multi-omics molecular profiles^13–15, to delineate biological subtypes. Neuroimaging stands out as a pivotal intermediate phenotype bridging the gap between etiology and behavioral manifestations, ^16,17. Studies have employed functional, structural, and diffusion tensor imaging to categorize MDD patients into subgroups with homogenous neuroimaging patterns^18,19, providing significant insights into the categorization and therapeutic management of MDD. The Amplitude of Low-Frequency Fluctuations (ALFF) is a neuroimaging metric for measuring local spontaneous neuronal activity during rest. It has been validated for high test-retest reliability, establishing its utility as a regional functional measure to discern individual differences^20,21. In prior research, we observed alterations in the ALFF metric within specific brain areas, including the prefrontal cortex, occipital lobe, hippocampus, and amygdala of MDD patients, facilitating the delineation of subtypes in MDD^22,23.

Despite prior studies having classified MDD into relatively homogeneous subtypes using neuroimaging features, limited researches have verified their underlying biological mechanisms at the multi-omics level. Most studies focused solely on comparing their symptomatology, or indirect verification through publicly available databases. It is noteworthy that existing etiological hypotheses, such as the monoamine hypothesis²⁴, polygenic hypothesis, immuno-inflammatory hypothesis²⁵, mitochondrial dysfunction²⁶, and metabolic dysregulation²⁷, offer diverse insights into the biological underpinnings of MDD. However, none of these hypotheses can fully explain the pathological mechanism of MDD²⁸, supporting the biological heterogeneity of MDD. Different subtypes may have stronger associations with particular etiological theories. Defining biologically homogeneous subtypes through neuroimaging characteristics and corroborating their biological relevance with omics data from the same neuroimaging cohort will help elucidate the leading etiological mechanisms of each subtype, offering vital directions for precision medicine of MDD.

This study aims to identify subtypes of MDD based on ALFF and investigate the biological underpinnings using multi-omics data. In the present study, we recruited 327 MDD patients and 480 healthy controls (HC) and clustered MDD patients into three subtypes based on ALFF patterns. Subsequently, we conducted comparative analyses across various molecular levels, including pro-inflammatory cytokine, epigenetics, metabolomics, and genetics profiles, to delineate the predominant molecular alterations of each subtype.

Participants

A total of 807 participants were included in this study, including 327 MDD patients and 480 healthy controls (HC). Patients with MDD were recruited from both inpatient and outpatient services at the Department of Psychiatry within the First Affiliated Hospital of China Medical University and Shenyang Mental Health Center. HC were recruited through local community advertisements and had no personal or family history of psychiatric disorders. All participants were independently evaluated by two trained psychiatrists. For participants aged 18 years and older, the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) Axis I Disorders was employed. Participants under 18 years old were diagnosed using the Schedule for Affective Disorders and Schizophrenia for School-Age Children-Present and Lifetime version (K-SADS-PL). Exclusion criteria for participation included: 1) general contraindications for MRI, 2) a history of substance or alcohol abuse/dependence, 3) head trauma with loss of consciousness lasting at least 5 minutes or any neurological disorder, and 4) any major concurrent medical disorder. The study was approved by the Medical Research Ethics Committee of China Medical University in accordance with the Declaration of Helsinki. Written informed consent was received from each subject or their legal guardian for young participants under 18 years old.

Clinical assessment

The Hamilton Depression Scale (HAMD) and the Hamilton Anxiety Scale (HAMA) were used to evaluate the severity of depressive and anxiety symptoms in all participants. Cognitive function was assessed by a computerized version of the Wisconsin Card Sorting Test (WCST), which provides five indices as follows: correct responses (CR), completed categories (CC), total errors (TE), perseverative errors (PE), and non-perseverative errors (NPE).

Neuroimaging data acquisition and preprocessing

MRI scans were acquired with a 3.0T GE Sigma system (Sigma EXCITE HDx, GE Healthcare, USA) with a standard 8-channel head coil at the First Affiliated Hospital of the China Medical University, Shenyang, China. A restraining foam pad was utilized to minimize head movement. Participants received explicit instructions to remain in a relaxed state, keep their eyes closed, and refrain from any movement or falling asleep throughout the scanning. The functional images were performed using a gradient echo planar imaging (EPI) sequence, which was as following parameters: repetition time = 2000 ms, echo time = 30 ms, flip angle = 90°, field of view = 240 × 240 mm2, and matrix = 64 × 64. A total of 35 slices were acquired, each with a thickness/gap of 3 mm/0 mm. The scanning session lasted for 6min and 40s. The images underwent processing and analysis employing two toolkits: Statistical Parametric Mapping 8 (SPM8, http://www.fil.ion.ucl.ac.uk/spm) and Data Processing Assistant for R-functional MRI-fMRI (DPARSF, http://www.restfmri.net/forum/DPARSF). The specific parameters and processing of MRI data (Supplementary Methods S1) were consistent with our prior publications ^29–31.

Identification of neuroimaging subtypes

For neuroimaging data, a total of 47,636 voxel-level ALFF values were extracted for each participant using the AAL90 atlas. We utilized the singular value decomposition (SVD) algorithm to handle the high-dimensional ALFF data³², resulting in 30 dimensions. Subsequently, we employed the K-means algorithm³³ to cluster MDD patients into three subtypes based on the 30-dimensional data. The stability of clustering results was evaluated using the Consensus Clustering method³⁴. These machine-learning algorithms were implemented using the scikit-learn library (version 0.22.2.post1)³⁵.

Measure of pro-inflammatory cytokines

Levels of three common pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β) were measured using the Human Premixed Multi-Analyte Kit (R&D Systems, Inc., Minneapolis, MN, United States) with the Human Magnetic Luminex Assay (Leptin [BR51]). Samples were magnetically labeled using a human, magnetic, premixed, microparticle cocktail of antibodies (Kit Lot Number L120614).

Multi-omics data acquisition

Peripheral blood samples were collected from participants for multi-omics profiling. Genomic, epigenomic, and metabolomic profiles were measured in this study. To obtain genomic data, we genotyped DNA samples following standard procedures, employing the Illumina Global Screening Chip-24 v1.0 BeadChip for Han Chinese populations. This BeadChip comprises 642,824 predetermined genetic variants and 53,411 custom-designed mutation sites. Epigenomic profiles were derived using the Illumina Infinium Methylation EPIC BeadChip³⁶, facilitating the quantitative analysis of over 850,000 methylation sites across the genome with single-nucleotide precision. For the metabolomic profile, untargeted metabolomics and lipid-omics analyses were conducted on the Ultimate 3000 Ultra Performance Liquid Chromatography coupled with the Q Interactive Quadrupole-Orbitrap High Resolution Mass Spectrometer (UPLC-HRMS)³⁷. Detailed information could be check in our prior publications^29,38.

Calculation of epigenetic inflammation score (EIS)

We utilized the ChAMP R package³⁹ to load the raw DNA methylation data, and filter probes and samples by default parameters (Supplementary Methods S2). Then the probes were normalized and corrected for technical batch effects and cell heterogeneity. All DNA methylation levels were expressed as β values, ranging from 0 to 1, calculated as M/(M + U), where M is the signal from methylated beads, and U is the signal from unmethylated beads at the targeted CpG site.

The calculation of epigenetic inflammation scores (EIS) is informed by methodologies established in prior research⁴⁰. Specifically, we utilized findings from both the discovery and validation phases of a large-scale meta-analysis, involving 9 cohorts (n = 8,863) and 4 cohorts (n = 4,111) respectively, to select seven methylation sites significantly associated with plasma C-reactive protein (CRP) levels⁴⁰. Due to the exclusion of one CpG site (cg06126421) from our dataset during quality control, our analysis proceeded with the six remaining CpG sites. The calculation involved multiplying the beta values of the six CpG sites by their respective regression weights and summing them to generate a composite score for each participant⁴¹. Given that all regression weights from the EWAS were negative, a lower EIS score is indicative of a higher state of inflammation, thus establishing a direct correlation between epigenetic markers and inflammation levels.

Estimation of epigenetic immune cell proportions

We utilized the reference-based GLINT method to assess the proportions of various immune cell types within each sample, relying on their methylation profiles⁴². This method estimates the proportion of monocytes, CD8 + cells, CD4 + cells, NK cells, B cells, neutrophils, and eosinophils according to the Houseman model, using a panel of 300 highly informative methylation sites in blood⁴³ and reference data collected from sorted blood cells⁴⁴. It provides relative data of cell counts rather than absolute counts.

Identification of differential metabolites (DMs)

Following standard quality control procedures, a total of 669 metabolites were quantified. We applied linear regression modeling to identify the differential metabolites (DMs) associated with each subtype, incorporating 'group' as the independent variable and the relative abundance of each metabolite as the dependent variable, while adjusting for age, gender, BMI, and medication status as covariates. To account for multiple testing, we applied the Benjamini-Hochberg False Discovery Rate (FDR) correction, considering adjusted p-values values below 0.05 as statistically significant⁴⁵.

Calculation of polygenic risk scores (PRS)

Quality control of genomic data and imputation were performed before the calculation of polygenic risk scores (PRS). The process included the exclusion of single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) below 1%, a call rate less than 95%, or deviation from Hardy-Weinberg equilibrium (P-value < 10^− 5), and the exclusion of participants with more than 5% missing data, gender mismatches, or an identity-by-descent (IBD) score greater than 0.9. The refined genotype data were imputed using the GenoImpute engine⁴⁶. The international MDD GWAS results published by the Psychiatric Genomics Consortium were used as discovery samples (https://pgc.unc.edu/), and our imputed genotyping data were used as a target sample. In the paper by the Major depressive disorder Working Group of the Psychiatric Genomics Consortium, the specific genetic factors contributing to MDD were analysed in 135,458 people with MDD and 344,901 controls⁴⁷. PRSs were generated using PRSice software (www.PRSice.info). P-value-informed clumping was performed with a cut-off of r 2 = 0.1 in a 250 kb window. Seven PRSs at different P-value thresholds (10^− 8, 10^− 7, 10^− 6, 10^− 5, 10^− 4, 0.001, 0.01) were derived for each study participant.

Statistical Analysis

We performed a descriptive analysis to evaluate the demographic and clinical characteristics of the participants. The normality of continuous variables was determined using the Shapiro-Wilk test. These variables are presented as means ± standard deviations (SD), while categorical data are expressed as frequencies and percentages. To investigate differences among subtypes, ANOVA analyses were conducted for continuous variables, and chi-square tests were utilized for categorical variables. In the evaluation of clinical measures, encompassing both clinical symptoms and cognitive performance, we employed ANOVA to assess statistical differences among the identified subtypes and HC. This was followed by post-hoc comparisons using Tukey's Honestly Significant Difference test to discern specific pairwise differences between the groups. A threshold of p < 0.05 was set to determine statistical significance.

To delineate the neuroimaging distinctions between subtypes and HC, we conducted a voxel-based two-sample t-test using the DPABI tool. Age and sex were included as covariates to mitigate potential biases, with statistical significance thresholds set at voxel P-value of < 0.001 and cluster P-value of < 0.05, corrected using the Gaussian random field (GRF) method.

Differences in pro-inflammatory cytokines, EIS, and proportions of seven immune cell types among the subtypes and HC were evaluated using ANOVA analysis respectively. To identify specific pairwise group differences, a post-hoc analysis was performed using Tukey's Honestly Significant Difference test. A p-value of less than 0.05 was considered to denote a statistically significant difference.

Pearson correlation analysis was used to investigate associations between DMs and pro-inflammatory cytokines.

The association of PRS-MDD with each subtype was investigated using logistic regression embedded in the software PRSice, adjusted for the first 20 principal components, age, and gender. Nagelkerke’s pseudo-R2 was calculated to measure the proportion of variance explained. To explore the biological pathways associated with these genetic variants, we conducted gene ontology (GO) enrichment analysis on the genes mapped to the significant PRS. This analysis, performed using the "clusterProfiler" package in R⁴⁸, covered three categories: cellular components (CC), molecular functions (MF), and biological processes (BP). To account for multiple testing, we applied the Benjamini-Hochberg FDR correction, considering p-adjusted values below 0.05 as statistically significant⁴⁵. We visually presented the top 10 significant pathways within each category to clearly represent the results.

Characteristics of participants

Demographic and clinical characteristics of 327 MDD patients and 480 HC are presented in Table 1. There were significant differences between MDD patients and HC in age, gender, BMI, and education level. In clinical assessment, WCST scores (CC, CR, TE, PE, NPE), HAMD-17, and HAMA scores were significantly higher in MDD patients than in HC.

Table 1

Demographic and clinical differences between MDD subtypes and HC.
	MDD patients (N = 327)	Health controls (N = 480)	P value^# M-W U test	Subtype 1 (N = 93)	Subtype 2 (N = 93)	Subtype 3 (N = 141)	P value^## ANCOVA/χ2	F/χ2	Post hoc Turkey test
Demographics
Gender, female (%)	67.9	59.8	0.02	73.1	55.9	72.3	< 0.001	4.5	Subtype 3 > HC
Age, mean (S.D.), years	27.6 (10.6)	30.9 (11.8)	< 0.001	30.4 (10.6)	24.3 (9.7)	27.9 (10.6)	0.004	10.6	Subtype 2 < Subtype 1,HC; Subtype 3 < HC
Education, mean (S.D.), years	12.3 (3.3)	14.1 (3.7)	< 0.001	12.4 (3.2)	12.2 (2.9)	12.4 (3.6)	< 0.001	15.5	Subtype 1, Subtype 2, Subtype 3 < HC
BMI, mean (S.D.)	21.9 (3.8)	22.6 (3.9)	0.02	21.7 (3.6)	22.9 (4.1)	21.5 (3.6)	0.009	3.9	Subtype 3 < Subtype 2, HC
Clinical characteristics
Age of onset, mean (S.D.), years	24.9 (10.1)	—		27.9 (10.4)	22.7 (9.7)	24.9 (10.2)	0.009	4.7	Subtype 1 > Subtype 2
Duration, mean (S.D.), months	21.9 (41.8)	—		20.3 (31.4)	24.4 (36.1)	22.6 (51.1)	0.838	0.2
Anti-depressants use
Any (%)	23.5	0		47.3	63.4	61.0	0.050	3.0
SSRI (%)	13.3	0		30.1	35.5	32.6	0.543	0.6
TCA (%)	0	0		0	0	0	—	—
MAO (%)	0	0		0	0	0	—	—
Others (%)	17.6	0		36.6	44.1	47.5	0.484	0.7
Clinical symptoms
HAMD total score, mean (S.D.)	18.5 (9.9)	1.3 (2.3)	< 0.001	21.1 (10.1)	18.1 (10.0)	17.4 (9.6)	< 0.001	443.7	Subtype 1 > HC, Subtype 2, Subtype 3; Subtype 2, Subtype 3 > HC
HAMA total score, mean (S.D.)	16.3 (10.4)	1.2 (2.5)	< 0.001	17.4 (10.3)	17.8 (10.2)	16.0 (11.1)	< 0.001	293.5	Subtype 1, Subtype 2, Subtype 3 > HC
Cognition performance (WCST)	N = 253	N = 383		N = 62	N = 76	N = 115
CR score of WCST, mean (S.D.)	28.5 (10.9)	30.2 (12.3)	0.008	24.9 (10.8)	30.0 (10.1)	29.4 (11.2)	0.013	3.6	Subtype 1 < Subtype 2
CC score of WCST, mean (S.D.)	3.6 (1.9)	3.9 (2.3)	0.052	3.2 (1.9)	3.9 (1.9)	3.7 (2.0)	0.099	2.1
TE score of WCST, mean (S.D.)	19.5 (10.8)	17.8 (12.4)	0.01	23.1 (10.8)	17.9 (10.1)	18.6 (10.8)	0.012	3.7	Subtype 1 > Subtype 2
PE score of WCST, mean (S.D.)	7.1 (6.8)	6.4 (7.0)	0.014	9.4 (8.2)	6.5 (6.7)	6.3 (5.9)	0.013	3.6	Subtype 1 > Subtype 3
NPE score of WCST, mean (S.D.)	12.3 (6.7)	11.4 (7.2)	0.027	13.7 (6.3)	11.4 (5.9)	12.2 (7.2)	0.109	2.0
Data are presented as either number (%) or means (standard deviations). SZ, schizophrenia; BD, bipolar disorder; MDD, major depressive disorder; HC, healthy control; HAMD, Hamilton Depression Scale; HAMA, Hamilton Anxiety Scale; WCST, Wisconsin Card Sorting Test. FD, framewise-displacement. N/A, not available/not applicable.
# The examination between the MDD patients and HC groups.
## The examination among the subtypes and HC groups.

Identification of neuroimaging-based subtypes and their ALFF patterns

327 MDD patients were clustered into three subtypes based on ALFF data using the K-means algorithm: Subtype 1 (44%), Subtype 2 (28%), and Subtype 3 (28%). Each subtype exhibited unique functional imbalance patterns in ALFF. In Subtype 1, ALFF was significantly elevated in limbic areas including the hippocampus, cingulate, amygdala, and thalamus, but notably decreased in the primary cortices such as the occipital and postcentral cortex, in comparison to HC as depicted in Fig. 1. Subtype 2 showed a marked increase in ALFF within the frontal cortex and a decrease in the primary sensory cortex relative to HC. Conversely, Subtype 3 demonstrated a significant reduction in ALFF in the frontal cortex and an increase in the primary sensory cortex compared to HC. Detailed information about these region-specific alterations, aligned with the Automated Anatomical Labeling (AAL) atlas, is available in the Supplementary Results S1.

Demographic and clinical characteristics of the subtypes

In the comparison of demographic characteristics across the three identified subtypes and HC, significant differences were observed in gender, age, education and BMI level among the four groups (Table 1). The results of subsequent post-hoc analyses are presented in Table 1. Regarding clinical symptoms, Post-hoc comparisons revealed that Subtype 1 had significantly higher HAMD-17 scores than both Subtype 2 and Subtype 3. Subtype 1 also demonstrated more pronounced cognitive impairments in WCST than both Subtype 2 and Subtype 3. Specifically, Subtype 1 exhibited significantly lower CR scores and higher TE scores compared to Subtype 2. Subtype 1 had higher PE scores than Subtype 3. Detailed demographic and clinical statistical results are presented in Table 1.

Differences of Subtypes in molecular levels

Significant alteration of pro-inflammatory cytokine in Subtype 2

We compared the differences in pro-inflammatory cytokines among three subtypes and HC using ANCOVA and post-hoc analysis. We found that IL-1β in Subtype 2 was more significantly elevated than HC (Fig. 2). TNF-alpha and IL-6 presented a trend of increased levels in Subtype 2, but did not reach statistical significance. This result indicated that Subtype 2 was in a higher inflammatory state than Subtype 1 and Subtype 2. Next, we further illuminate the inflammatory characteristics of Subtype 2 with multiple omics data.

Significant changes of inflammation indicators in methylation level underlying Subtype 2

Epigenetic Inflammation Scores (EIS) are refined indicators of chronic low-grade inflammation⁴⁹. Distinct from traditional markers like plasma CRP levels, which are prone to significant variations in response to acute inflammatory stimuli, EIS provides a steadier reflection of chronic inflammation^50,51. The EIS, in particular, showcases enhanced test-retest reliability when compared to serum CRP levels, underscoring its value in offering a more reliable measure of inflammation's temporal stability⁴¹. Subtype 2 exhibited a significantly lower EIS compared to HC, indicating a higher state of inflammation (Fig. 3A). Subtype 1 and Subtype 3 did not show significant differences in EIS, as illustrated in Fig. 3A.

In the analysis of proportions of seven immune cell types derived from methylation data, Subtype 2 demonstrated a significantly higher proportion of neutrophils relative to HC, while the other six immune cell types showed no statistical significance (Fig. 3B-3H). Subtype 1 and Subtype 3 did not show significant differences in the proportions of the seven immune cell types. Neutrophils are responsible for the first line of the host immune response against invading pathogens. They employ various mechanisms, including chemotaxis, phagocytosis, the release of reactive oxygen species (ROS) and granular proteins, and the production and release of cytokines, all of which contribute to inflammation. These findings suggest that Subtype 2 is primarily associated with increased inflammation.

Significant metabolomic alterations and the correlation with IL-1β level underlying Subtype 2

In the analysis of DMs, we observed significant metabolic disturbances in Subtype 2. Compared to HC, Subtype 2 exhibited 36 DMs, while Subtype 1 and Subtype 3 did not show any DMs (Fig. 4A- 4C). In 36 DMs, 9 fatty acids, 8 triglycerides, 1 peptide, and 1 microbiome metabolite showed higher abundance, while 7 organic acids, 6 amino acids, 1 carbohydrate, and 3 unclassified metabolites showed decreased abundance in Subtype 2 compared to HC (Fig. 4D, 4E).

Pearson correlation analysis was used to further test the associations of DMs with IL-1β level, which was significantly higher in Subtype 2. 44% (16/36) of DMs significantly correlated with IL-1β levels in Subtype 2. Specifically, five of six amino acids - N-Acetylleucine, Acetyl-N-formyl-5-methoxykynurenamine, N-Acetylisoleucine, N-Lactoylvaline, and Methylglutaconic acid - were negatively correlated with plasma IL-1β. Similarly, six of the seven organic acids, including Fumaric acid, Isobutyric acid, Glutaric acid, Succinic acid semialdehyde, Dihydroxybutanoic acid, and Furoic acid, demonstrated significant negative associations with IL-1β (Fig. 4F).

Significant genetic predispositions underlying Subtype 1

PRS analysis revealed variation in genetic predispositions across the three MDD subtypes (Fig. 5). Only Subtype 1 demonstrated significant genetic predisposition associated with MDD at PTs of 0.01 and 0.001 after adjusting for multiple comparisons. Subtype 2 and Subtype 3 did not exhibit a genetic liability related to MDDs. Specifically, PRS-MDD at PT of 0.001 (P = 0.011, NSNPs = 1325) and 0.01 (P = 0.002, NSNPs = 4769) accounted for 5.9% and 8.1% of the phenotypic variance in Subtype 1, respectively. 4769 SNPs of PRS-MDD at the most significance threshold of PT = 0.01 were mapped to 2169 genes and found to be significantly enriched in pathways related to neuronal development and synaptic regulation. The top ten Gene Ontology (GO) terms within each category were presented in Fig. 5, mainly involved in 'synapse organization', 'regulation of neuron projection development', 'axonogenesis', 'postsynaptic membrane', 'neuron to neuron synapse', and 'monoatomic ion gated channel activity'.

In this research, the utilization of machine learning clustering techniques on functional neuroimaging features (ALFF) in MDD patients identified three distinct subtypes—Subtype 1, Subtype 2, and Subtype 3. Each subtype was characterized by unique ALFF patterns. These distinctions were further substantiated through comprehensive multi-omics biological profiling, enriching our understanding of the specific etiological factors underlying each subtype. Subtype 1 features an imbalance of brain activity between the limbic system and primary cortices, with increased ALFF in the hippocampus, cingulate, and amygdala, and decreased ALFF in the primary visual, sensory, and motor cortices. This subtype indicates a strong genetic predisposition toward MDD, primarily enriched in neuronal development and synaptic regulation pathways, accompanied by severe depressive symptoms and cognitive decline. Subtype 2 reveals a different pattern of ALFF imbalance, with increased activity in the higher-order cortices, notably the prefrontal cortex, and decreased activity in the primary cortices. Immune-inflammation dysregulation existed in Subtype 2, supported by multidimensional molecular evidence, including elevated IL-1β level, altered epigenetic inflammatory measures, and differential metabolites correlated with IL-1β level. Contrary to Subtype 2 in the ALFF pattern, Subtype 3 presents decreased activity in the prefrontal cortex and increased activity in primary cortices. There were no significant biological markers identified in Subtype 3. Our study showed that three subtypes may exhibit unique etiological mechanisms, with Subtype 1 predominantly influenced by genetic factors involved in neuronal development and synaptic regulation and Subtype 2 linked to immune-inflammatory processes. The variability of multidimensional features of subtypes reveals the complexity of MDD and highlights the potential of using neuroimaging-based subtypes to forge a path towards precision therapy in MDD.

Interestingly, all three subtypes demonstrate alterations in the primary sensory cortices, emphasizing their significance in MDD. Traditionally, the higher-order cortices and limbic system, known for their roles in cognitive and emotional regulation, have been the focus of the studies of neural mechanisms of MDD^52,53. The primary sensory cortices, tasked mainly with sensory input processing, have received less attention in MDD research. However, recent findings highlight the involvement of primary sensory cortices in higher-order functions, especially the visual cortex, suggesting its potential as a neuroregulatory target for alleviating depressive symptoms and improving cognitive function⁵⁴. Our initial results from the MAM animal model, which revealed an imbalanced functional neuroimaging pattern between higher-order and primary cortices, showed that abnormal activity in the primary cortex has begun in adolescence, preceding abnormalities in the higher-order cortices that have appeared in early adulthood⁵⁵. Studies by Jiang et al. on schizophrenia (SZ) patients examined the evolution of functional imaging features throughout the disease progression, revealing a gradual shift from the primary to higher-order cortices and subcortical areas as the disease advances⁵⁶. These consistent observations indicate that changes in the primary cortex may be early indicators of psychiatric conditions like MDD and SZ, potentially making it a viable target for early intervention. Moreover, our prior animal study provided further support for these observations by demonstrating that targeted high-frequency repetitive Transcranial Magnetic Stimulation (rTMS) of the visual cortex during adolescence can reverse the abnormal functional connectivity in the higher-order cortex observed in early adulthood in a rat model of depression⁵⁷. This outcome is further bolstered by human studies, where interventions targeting the visual cortex have proved effective for reversing abnormal neuroimaging and alleviating clinical symptoms⁵⁸ in mood disorders patients. Furthermore, one of our clinical trials showed that visual cortex stimulation significantly improved cognitive function in bipolar disorder (BD) patients⁵⁹. These findings collectively suggest that primary cortices-targeted interventions may hold promising clinical utility.

The multi-omics evidence consistently indicates that immune-inflammatory dysregulation primarily drives the pathogenesis of Subtype 2. We observed a significant elevation of the pro-inflammatory cytokine IL-1β and pronounced metabolic dysregulation in Subtype 2 compared to HC. Notably, the disturbances in fatty acid, triglyceride, and amino acid metabolism were significantly correlated with IL-1β level. The association between immune-inflammatory damage and MDD has been robustly supported by human and animal research^60,61. Studies have identified increased levels of pro-inflammatory cytokines and acute response proteins in the plasma⁶², central nervous system⁶³, and cerebrospinal fluid⁶⁴ of MDD patients, along with a rise in immune cells like neutrophils and monocytes^65,66. Clinical observations have shown that cytokine therapy, such as using IFN-α for chronic hepatitis, can lead to depressive-like behaviors, including anhedonia, anorexia, and reduced libido^67,68. Animal studies corroborate these findings, showing that inflammatory inducers like lipopolysaccharide (LPS) triggered depressive-like behaviors, such as decreased activity, appetite loss, and lowered sexual drive⁶⁹. These findings suggest that at least a subset of MDD patients have immune-inflammatory damage.

Clinical trials have demonstrated promising evidence that anti-inflammatory treatments, both standalone and adjunct, can ameliorate depressive symptoms⁷⁰. Targeted anti-inflammatory therapy, considering the biological heterogeneity of MDD, is especially crucial for patients with immune-inflammatory profiles. The challenge lies in accurately identifying this subgroup. Recent research has extended the use of molecular markers from cardiovascular to psychiatric domains, primarily utilizing molecular markers in peripheral blood for clinical stratification, such as CRP > 3 as an indicator of chronic inflammation⁶. These approaches offer valuable insights, yet the variability and potential somatic condition confounders of traditional peripheral inflammation markers hinder their clinical applicability. Neuroimaging features, serving as a conduit between peripheral inflammation and the central nervous system^71,72, emerge as promising markers for identifying inflammatory subtypes in psychiatric disorders. In our study, distinct subtypes of MDD were identified based on ALFF, of which Subtype 2 was characterized by immune-inflammatory dysregulation and anti-inflammatory therapies would offer a promising adjunctive treatment modality for this subgroup.

Compared to Subtypes 1 and 2, our multi-omics analysis did not definitively reveal the pathogenic mechanisms of Subtype 3, which shows neither significant genetic risk factors nor notable changes in inflammatory markers. We speculate that the etiology and pathological mechanisms of Subtype 3 are more complex and heterogeneous.

Limitation

Several limitations should be considered with regard to interpreting the current findings. Firstly, our whole-genome genetics and epigenetics data are limited in sample size, thus lacking the statistical power to identify specific genes or pathways associated with each subtype. This limitation prompted us to complement our analysis with large-sample-based validated results and summarized measures from whole-genome data, such as PRS and EIS, given the well-established understanding of MDD as a polygenic disorder. Secondly, not all MDD patients are medication-free, although there is no significant variation in medication use status among the three subtypes. Notably, medication does not influence the genetic profile. To address potential confounding effects, we included medication status as a covariate in our analysis of epigenetics and metabolomics data. Lastly, our study is cross-sectional, precluding the determination of direct causal effects of molecular alterations on each subtype. Future longitudinal studies are essential to explore the presence of causal relationships.

This study leveraged functional imaging to decipher the biological heterogeneity of MDD and employed multi-omics data to identify the primary biological mechanisms underlying the homogenous imaging subtypes: Subtype 1 is driven by genetic anomalies; Subtype 2 by immune-inflammatory dysregulation; and Subtype 3 by a complex mix. Our results offer a proof of concept for mechanism-targeted therapy in MDD.

Acknowledgements:

Funding

This work was supported by grants from NSFC-Guangdong Joint Fund [U20A6005 to Fei Wang], Jiangsu Provincial Key Research and Development Program [BE2021617 to Fei Wang], Strategic Topics Grant of University Grants Committee [STG1/M-501/23-N to FeiWang], Jiangsu Provincial Medical Innovation Team, Key Project supported by Medical Science and Technology Development Foundation, Jiangsu Commission of Health [ZD2021026 to Rongxin Zhu], Jiangsu Provincial Key Research and Development Program [BE2022160 to Rongxin Zhu], Natural Science Foundation of Jiangsu Province [BK20231126 to Rongxin Zhu], China Postdoctoral Science Foundation [2022M721681 to Junjie Zheng]. We would like to thank all participants who took part in this study.

Declaration of interest：

None

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Dissecting biological heterogeneity in major depressive disorder based on neuroimaging subtypes with multi-omics data

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Version 1

Abstract

Background

Method

Results

Conclusion

Figures

Introduction

Materials and methods

Participants

Clinical assessment

Neuroimaging data acquisition and preprocessing

Identification of neuroimaging subtypes

Measure of pro-inflammatory cytokines

Multi-omics data acquisition

Calculation of epigenetic inflammation score (EIS)

Estimation of epigenetic immune cell proportions

Identification of differential metabolites (DMs)

Calculation of polygenic risk scores (PRS)

Statistical Analysis

Results

Characteristics of participants

Identification of neuroimaging-based subtypes and their ALFF patterns

Demographic and clinical characteristics of the subtypes

Differences of Subtypes in molecular levels

Significant alteration of pro-inflammatory cytokine in Subtype 2

Significant changes of inflammation indicators in methylation level underlying Subtype 2

Significant metabolomic alterations and the correlation with IL-1β level underlying Subtype 2

Significant genetic predispositions underlying Subtype 1

Discussion

Limitation

Conclusion

Declarations

References

Additional Declarations

Supplementary Files

Status:

Version 1