Autism spectrum disorder is a mental illness with distinct genetic characteristics that persist throughout the life cycle. The condition is typified by external manifestations such as impaired social and communicative abilities, intellectual disability, and restricted interests or repetitive behaviors. Existing research indicates that the symptoms of ASD undergo age-dependent changes (Magiati et al., 2014; Lever and Geurts, 2018), yet the underlying pathogenetic mechanisms of these changes have not been uniformly elucidated.

The manifestation of ASD varies with age, and it is generally believed that cognitive ability improves with age and certain symptoms ameliorate throughout the lifespan (Happe et al., 2016). During the period of 6–12 years old, children’s social interaction behavior and understanding of social relationships are the most obvious characteristics of ASD. By the age of 12–15, the condition is relatively stable. Some patients’ symptoms have improved, but some will also have serious degeneration. The gray matter density of the cerebral cortex continues to increase at the age of 15–30, and stops at the age of 30 (Giedd et al., 1999; Sowell et al., 2003; Shaw et al., 2006). Since ASD is a typical neurological disorder of the brain, it is very important and meaningful to use magnetic resonance imaging technology to explore developmental alterations within the pathological regions of the brain. The functional connectivity between the cerebellum and default mode network (DMN) displays greater variations in children with ASD than adolescents (Haghighat et al., 2021), whereas adults with ASD have significantly lower DC in Wernicke’s area compared to children and adolescents (Lee et al., 2017). While the current research on the brain stratification development of ASD lacks unanimity, the abnormal changes of specific cerebral cortexes such as DMN in key age groups have become a consensus (Doyle-Thomas et al., 2015).

Genetic factors play a dominant role in the etiology of autism. Despite this, a limited number of articles have specifically explained changes in genetic transcription in stratified studies of ASD age (Rahbar et al., 2015; Bao et al., 2023). The neuropathological mechanism of autism is complex, involving abnormal synaptic function, abnormal neuronal activity patterns, abnormal genes, an abnormal immune system, etc. (Won et al., 2013; Zhang et al., 2015). For example, inhibitory neurotransmitters, such as gamma-aminobutyric acid (GABA) and glutamate, have been implicated as primary contributors to the onset of autism (Marotta et al., 2020). Increasing evidence has highlighted the biological basis of autism, and indicated that the disorder of excitatory and inhibitory regulation between neurons leads to an ASD signaling imbalance (Culotta and Penzes, 2020).

In this study, we aimed to identify alterations in brain function and gene transcription associated with ASD across four distinct age groups using transcriptomic-neuroimaging spatial association analysis. To achieve this, four metrics, namely, Amplitude of Low-Frequency Fluctuations (ALFF), fractional Amplitude of Low-Frequency Fluctuations (fALFF), Degree Centrality (DC), and Regional Homogeneity (ReHo) were calculated using a large resting-state fMRI dataset, and the resulting heterogeneous changes in ASD brain across four age groups were characterized by t-map, after ComBat Harmonization removal site effect. Finally, partial least squares analysis (PLS) was performed to interpret the weighted linear combination between brain functional activities and the genome, and the enriched significant correlation genes were identified.

The present study aims to investigate the critical stages in brain development that demand attention, with a specific focus on ASD. According to the typical clinical manifestations of ASD, patients are divided into four age groups in this paper. The study aims to explore the abnormal alterations in cerebral cortex function and potential gene transcription during the life cycle of ASD by analyzing functional neuroimaging data and brain gene transcription profiles. The results of this study would provide a better understanding of the underlying pathophysiological mechanisms underlying ASD, and underscore the significance of considering developmental stages when investigating brain-related disorders (Figures 2, 4).

Functional activity analysis revealed that the prefrontal lobe, temporal lobe, and cingulate cortex exhibited distinctive changes throughout the life cycle of individuals with ASD. Additionally, the associated genes were found to be enriched in transmembrane transport activity of inorganic molecules, regulation of protein transport, organophosphorus biosynthesis, and DNA metabolism. These findings may provide a novel perspective to understand the atypical course of brain function development and possible biological anomalies underlying ASD.

Recent studies have revealed that male patients are more susceptible to ASD than female patients, with a ratio of 4.5:1 (Loomes et al., 2017). Furthermore, the differences in brain development patterns and biological changes between male and female patients cannot be overlooked during the preprocessing stage (Joel et al., 2015; Wang et al., 2021). In order to better understand these atypical developmental trajectory changes associated with ASD, it is essential to strictly control for gender differences. Thus, we only utilized resting-state fMRI data of male ASD and TD to avoid errors resulting from gender differences.

Throughout all four ages, our results show that the developmental trajectories of the frontal-temporal-cingulate cortex circuitry differ in the ASD brain. Notably, the frontal cortex, which plays a crucial role in cognitive, emotional, and behavioral control, presents heterogeneous changes across all four age groups (Badre and Nee, 2018). Specifically, the left frontal lobe ALFF variation region gradually declines with age, while the abnormal ALFF region shifts to the insular cortex in young adults (stage 3). By adulthood (stage 4), the ALFF abnormalities in the frontal lobe are minimized. However, the right dorsolateral frontal cortex, responsible for higher cognitive functions such as spatial perception, vision, and spatial memory (Kleinhans et al., 2008), shows the greatest variation in young adults (stage 3). As such, we underscore the importance of considering these developmental changes in the brain circuitry when investigating ASD.

In DC, we observed significant phased changes in the precuneus, cingulate cortex, ventral prefrontal cortex, and dorsomedial prefrontal cortex of DMN. The global functional connections of the precuneus decreased at stage 1 and increased at stage 2. Prior studies conducted on children with ASD have shown that the precuneus exhibited decreased connectivity with the visual cortex, basal ganglia, and local posterior medial cortex (Lynch et al., 2013). Similarly, a study conducted on young adults with ASD showed that functional connectivity in the precuneus and cingulate cortex with other DMN core regions was decreased, and this reduction was negatively associated with symptom severity (Assaf et al., 2010).

Significant phased changes were observed in the local functional connectivity similarity (ReHo) of the dorsomedial prefrontal cortex, precuneus, and right temporal lobe of the ventromedial prefrontal cortex. The temporal lobe is a crucial brain region in the cerebral cortex and plays an important role in various advanced cognitive functions, including hearing, memory, language understanding, visual recognition, and emotional processing (Carter and Huettel, 2013). It has been reported that the area of abnormal activation of the superior temporal sulci (STS) is highly correlated with ASD in adolescents and its grayscale density decreases significantly (Williams et al., 2006; Zilbovicius et al., 2006). Additionally, children with ASD exhibit higher activity in bilateral temporal lobes compared to the TD group, indicating difficulties in understanding the communication intentions of others (Wang et al., 2006). These findings provide insights into the atypical development of local functional connectivity similarity in the temporal lobe of individuals with ASD.

Existing studies have shown that individuals with ASD exhibit reduced volume of frontal lobe parenchyma and decreased white matter density compared to neurotypical controls (Schmitz et al., 2007). Furthermore, mixed-age studies have found that individuals with ASD exhibit increased activation in the right frontal lobe and right upper temporal lobe compared to control groups (Kleinhans et al., 2008). Our findings are consistent with these studies but also reveal a non-linear temporal lobe functional activity pattern, characterized by increased activity in children (stage 1), decreased activity in young adults (stage 3), and increased activity in adults (stage 4). This non-linearity suggests that age-related changes in aberrant brain areas may not follow a linear progression. Notably, our study also identifies non-linear changes in ReHo and DC, which may represent a distinct developmental trajectory unique to ASD.

The expression of specific genes in the human genome is closely related to the brain. It is widely believed that many psychiatric diseases are caused by the intricate interplay of multiple genes, the proteins encoded by these genes may play important regulatory roles in various brain processes, such as neuronal development, interneuronal signal transmission, neural plasticity, etc. (Wu et al., 2015). If these genes are mutated or abnormally expressed, they may lead to neuron damage, neural pathway disorders, and eventually psychiatric diseases. Therefore, it is crucial to examine the relationship between neuroimaging and the genetic transcription in ASD to better understand the underlying mechanisms of the disorder.

The brain’s development and function are significantly affected by proteins, RNA, and other functional molecules encoded by genes. In cortical cells, the activation or inhibition of different genes produces different proteins, which may influence the shape, function, and connection of neurons, thereby modulating different aspects of cognitive, emotional, and behavioral brain functions (Auid et al., 2018).

In this study, we employed PLS to detect genes linked with regions exhibiting atypical brain function in ASD and subsequently conducted a functional enrichment analysis of these genes. In general, these genes are mainly related to synaptic organization, protein transport regulation, neuronal projection development, and DNA metabolism. ASD is a typical neurodevelopmental disorder characterized by complex and heterogeneous etiology and pathogenesis. Notwithstanding the uncertainty in the field, existing literature suggests that abnormal brain neuron function could play a pivotal role in the onset of ASD (Bernier et al., 2014).

Our analysis revealed that genes associated with resting-state functional connectivity metrics, such as ReHo and DC, were significantly enriched in terms related to mRNA processing during stage 1 and stage 4 of brain development. Interestingly, several studies have demonstrated that mutations in specific genes or abnormal expression of mRNA can impair the function, development, and signal transduction of neurons, which has been implicated in ASD pathology (Bagni and Zukin, 2019). Studies have also shown that it is related to cognition. Furthermore, the concentration of the emotion-associated dopamine receptor D4 (DRD4-mRNA) was significantly reduced in children and adolescents with ASD (Taurines et al., 2011). It is worth mentioning that the synaptic structure of neuron cells was found to be significantly enriched with genes associated with global functional connectivity (DC) during stages 1, 3, and 4. The release of neurotransmitters to alter the potential of receiving neurons or trigger physiological responses is the primary purpose of synapses. The NRXN, NLGN, and SHANK genes are mutated most frequently at synapses, according to several studies. Thus, it is possible that synaptic disruption plays a key role in the etiology of ASD (Gai et al., 2012; Guang et al., 2018). These findings demonstrate that genes associated with abnormal brain regions are involved in and influence neuronal dysfunction across the lifespan of ASD, which could ultimately lead to abnormal neural function in ASD individuals. In addition, we found that genes associated with different resting-state functional connectivity metrics were enriched in distinct biological processes during different stages of brain development. Specifically, the associated genes identified in stage 2 using the four calculation methods of ALFF, hair ALFF, DC, and ReHo were mainly enriched in terms such as molecular metabolism, regulation, and differentiation of cells. The genes associated with ALFF, fALFF, and ReHo in stage 4 are all involved in the transmembrane transport of ions between cells. Although the results in DC do not involve this process, the activity of gated channels is regulated by the transmembrane transport of ions (Randak and Welsh, 2003; Hwang and Kirk, 2013). Voltage-controlled calcium channels, which are regulated by the transmembrane transport of ions, play a crucial role in dendritic growth and arborization of neuronal cells (Krey et al., 2013). However, knocking out genes encoding voltage-gated channels in mice did not lead to neurological symptoms (Pinggera and Striessnig, 2016). Collectively, our findings suggest that genes associated with different resting-state functional connectivity metrics could contribute to distinct biological processes, which could potentially be targeted for the development of novel ASD therapeutics.

The present study has several limitations that should be taken into consideration. Firstly, the age divisions utilized in our analysis were limited and may not fully capture the intricacies of the developmental trajectory of ASD. To gain a more nuanced understanding of the progression of autism, future research could benefit from utilizing more refined age categories or collecting longitudinal data.

The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.

The data used in this study is obtained from the open-source dataset from ABIDE. The ethical considerations pertaining to human participants in this study were meticulously examined and approved by the Institutional Review Board. Written informed consent was obtained from all patients/participants prior to their involvement in the study. For instance, The studies involving human participants were reviewed and approved by Ethical approval was obtained from the St. James’s Hospital/AMNCH (ref: 2010/09/07) and the Linn Dara CAMHS Ethics Committees (ref: 2010/12/07). Written informed consent to participate in this study was provided by the participants’ legal guardian/next of kin.

To ensure the experiments’ progress and caliber, YL created the research plan, planned the experimental procedure, and was in charge of the majority of the experiments. FZ oversaw the data gathering, experimental collation, in-depth analysis of the findings, and creation of the manuscript. RL oversaw organizing the background information and the border of connected technical domains in the manuscript and presents some fresh theoretical stances and concepts. JG and JH assisted in the revision of the work and edited the expression and structure to make it more quality and readable. All authors contributed to the article and approved the submitted version.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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