Editorial: New Trends in Connectomics

Translational network neuroscience: Nine roadblocks and possible solutions

Translational network neuroscience aims to integrate advanced neuroimaging and data analysis techniques into clinical practice to better understand and treat neurological disorders. Despite the promise of technologies such as functional MRI and diffusion MRI combined with network analysis tools, the field faces several challenges that hinder its swift clinical translation. We have identified nine key roadblocks that impede this process: (a) theoretical and basic science foundations; (b) network construction, data interpretation, and validation; (c) MRI access, data variability, and protocol standardization; (d) data sharing; (e) computational resources and expertise; (f) interdisciplinary collaboration; (g) industry collaboration and commercialization; (h) operational efficiency, integration, and training; and (i) ethical and legal considerations. To address these challenges, we propose several possible solution strategies. By aligning scientific goals with clinical realities and establishing a sound ethical framework, translational network neuroscience can achieve meaningful advances in personalized medicine and ultimately improve patient care. We advocate for an interdisciplinary commitment to overcoming translational hurdles in network neuroscience and integrating advanced technologies into routine clinical practice.

Stable Yet Destabilised: Towards Understanding Brain Network Dynamics in Psychogenic Disorders

Background: Psychogenic non-epileptic seizures (PNES) are seizure-like episodes that resemble behavioral aspects observed for epileptic seizures but are without the abnormal electrical activity typically seen in epilepsy. The lack of an etiologic model for PNES as well as limitations of available diagnostic methods largely hinders a clear-cut distinction from epilepsy and from a normal functioning brain. Methods: In this study, we investigate the brain dynamics of people with PNES and people with epilepsy during phases far-off seizures and seizure-like events as well as the brain dynamics of a control group. Probing for differences between these groups, we utilise the network ansatz and explore local and global characteristics of time-evolving functional brain networks. We observe subject-specific differences in local network characteristics across the groups, highlighting the physiological functioning of specific brain regions. Furthermore, we observe significant differences in global network characteristics-relating to communication, robustness, and stability aspects of the brain. Conclusions: Our findings may provide new insights into the mechanisms underlying PNES and offer a promising diagnostic approach to differentiate them from epilepsy.

Graph Theory and Modeling of Network Topology in Clinical Neurosurgery

The last several decades have seen a shift in understanding many neurological disorders as abnormalities in brain networks rather than specific brain regions. This conceptual revolution, coupled with advancements in computing capabilities and resources, has enabled a wealth of research on delineating and treating aberrant brain networks. One approach to network neuroscience, graph theory, involves modeling network topologies as mathematical graphs and computing various metrics that describe its characteristics. Using graph theory, researchers have derived new insights into the pathophysiology of many neuropsychiatric disorders and even developed treatments targeted at restoring network disturbances. In this chapter, we provide an overview of the principles of graph theory and how to implement it, specific applications of graph theory within clinical neurosurgery, and a discussion on the advantages and limitations of these approaches.

Bridging functional and anatomical neural connectivity through cluster synchronization

The dynamics of the brain results from the complex interplay of several neural populations and is affected by both the individual dynamics of these areas and their connection structure. Hence, a fundamental challenge is to derive models of the brain that reproduce both structural and functional features measured experimentally. Our work combines neuroimaging data, such as dMRI, which provides information on the structure of the anatomical connectomes, and fMRI, which detects patterns of approximate synchronous activity between brain areas. We employ cluster synchronization as a tool to integrate the imaging data of a subject into a coherent model, which reconciles structural and dynamic information. By using data-driven and model-based approaches, we refine the structural connectivity matrix in agreement with experimentally observed clusters of brain areas that display coherent activity. The proposed approach leverages the assumption of homogeneous brain areas; we show the robustness of this approach when heterogeneity between the brain areas is introduced in the form of noise, parameter mismatches, and connection delays. As a proof of concept, we apply this approach to MRI data of a healthy adult at resting state.

Simulation-based inference for efficient identification of generative models in computational connectomics

Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neuronal networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters, and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a fixed wiring rule to fit the empirical data, SBI considers many parametrizations of a rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rule parameters and relies on machine learning methods to estimate a probability distribution (the 'posterior distribution over parameters conditioned on the data') that characterizes all data-compatible parameters. We demonstrate how to apply SBI in computational connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data.

Connectivity Analysis in EEG Data: A Tutorial Review of the State of the Art and Emerging Trends

Understanding how different areas of the human brain communicate with each other is a crucial issue in neuroscience. The concepts of structural, functional and effective connectivity have been widely exploited to describe the human connectome, consisting of brain networks, their structural connections and functional interactions. Despite high-spatial-resolution imaging techniques such as functional magnetic resonance imaging (fMRI) being widely used to map this complex network of multiple interactions, electroencephalographic (EEG) recordings claim high temporal resolution and are thus perfectly suitable to describe either spatially distributed and temporally dynamic patterns of neural activation and connectivity. In this work, we provide a technical account and a categorization of the most-used data-driven approaches to assess brain-functional connectivity, intended as the study of the statistical dependencies between the recorded EEG signals. Different pairwise and multivariate, as well as directed and non-directed connectivity metrics are discussed with a pros-cons approach, in the time, frequency, and information-theoretic domains. The establishment of conceptual and mathematical relationships between metrics from these three frameworks, and the discussion of novel methodological approaches, will allow the reader to go deep into the problem of inferring functional connectivity in complex networks. Furthermore, emerging trends for the description of extended forms of connectivity (e.g., high-order interactions) are also discussed, along with graph-theory tools exploring the topological properties of the network of connections provided by the proposed metrics. Applications to EEG data are reviewed. In addition, the importance of source localization, and the impacts of signal acquisition and pre-processing techniques (e.g., filtering, source localization, and artifact rejection) on the connectivity estimates are recognized and discussed. By going through this review, the reader could delve deeply into the entire process of EEG pre-processing and analysis for the study of brain functional connectivity and learning, thereby exploiting novel methodologies and approaches to the problem of inferring connectivity within complex networks.

Co-alteration Network Architecture of Major Depressive Disorder: A Multi-modal Neuroimaging Assessment of Large-scale Disease Effects

Major depressive disorder (MDD) exhibits diverse symptomology and neuroimaging studies report widespread disruption of key brain areas. Numerous theories underpinning the network degeneration hypothesis (NDH) posit that neuropsychiatric diseases selectively target brain areas via meaningful network mechanisms rather than as indistinct disease effects. The present study tests the hypothesis that MDD is a network-based disorder, both structurally and functionally. Coordinate-based meta-analysis and Activation Likelihood Estimation (CBMA-ALE) were used to assess the convergence of findings from 92 previously published studies in depression. An extension of CBMA-ALE was then used to generate a node-and-edge network model representing the co-alteration of brain areas impacted by MDD. Standardized measures of graph theoretical network architecture were assessed. Co-alteration patterns among the meta-analytic MDD nodes were then tested in independent, clinical T1-weighted structural magnetic resonance imaging (MRI) and resting-state functional (rs-fMRI) data. Differences in co-alteration profiles between MDD patients and healthy controls, as well as between controls and clinical subgroups of MDD patients, were assessed. A 65-node 144-edge co-alteration network model was derived for MDD. Testing of co-alteration profiles in replication data using the MDD nodes provided distinction between MDD and healthy controls in structural data. However, co-alteration profiles were not distinguished between patients and controls in rs-fMRI data. Improved distinction between patients and healthy controls was observed in clinically homogenous MDD subgroups in T1 data. MDD abnormalities demonstrated both structural and functional network architecture, though only structural networks exhibited between-groups differences. Our findings suggest improved utility of structural co-alteration networks for ongoing biomarker development.

Linking neuroanatomical abnormalities in autism spectrum disorder with gene expression of candidate ASD genes: A meta-analytic and network-oriented approach

BACKGROUND

Autism spectrum disorder (ASD) is a set of developmental conditions with widespread neuroanatomical abnormalities and a strong genetic basis. Although neuroimaging studies have indicated anatomical changes in grey matter (GM) morphometry, their associations with gene expression remain elusive.

METHODS

Here, we aim to understand how gene expression correlates with neuroanatomical atypicalities in ASD. To do so, we performed a coordinate-based meta-analysis to determine the common GM variation pattern in the autistic brain. From the Allen Human Brain Atlas, we selected eight genes from the SHANK, NRXN, NLGN family and MECP2, which have been implicated with ASD, particularly in regards to altered synaptic transmission and plasticity. The gene expression maps for each gene were built. We then assessed the correlation between the gene expression maps and the GM alteration maps. Lastly, we projected the obtained clusters of GM alteration-gene correlations on top of the canonical resting state networks, in order to provide a functional characterization of the structural evidence.

RESULTS

We found that gene expression of most genes correlated with GM alteration (both increase and decrease) in regions located in the default mode network. Decreased GM was also correlated with gene expression of some ASD genes in areas associated with the dorsal attention and cerebellar network. Lastly, single genes were found to be significantly correlated with increased GM in areas located in the somatomotor, limbic and ganglia/thalamus networks.

CONCLUSIONS

This approach allowed us to combine the well beaten path of genetic and brain imaging in a novel way, to specifically investigate the relation between gene expression and brain with structural damage, and individuate genes of potential interest for further investigation in the functional domain.

Clinical applications of magnetic resonance imaging based functional and structural connectivity

Advances in computational neuroimaging techniques have expanded the armamentarium of imaging tools available for clinical applications in clinical neuroscience. Non-invasive, in vivo brain MRI structural and functional network mapping has been used to identify therapeutic targets, define eloquent brain regions to preserve, and gain insight into pathological processes and treatments as well as prognostic biomarkers. These tools have the real potential to inform patient-specific treatment strategies. Nevertheless, a realistic appraisal of clinical utility is needed that balances the growing excitement and interest in the field with important limitations associated with these techniques. Quality of the raw data, minutiae of the processing methodology, and the statistical models applied can all impact on the results and their interpretation. A lack of standardization in data acquisition and processing has also resulted in issues with reproducibility. This limitation has had a direct impact on the reliability of these tools and ultimately, confidence in their clinical use. Advances in MRI technology and computational power as well as automation and standardization of processing methods, including machine learning approaches, may help address some of these issues and make these tools more reliable in clinical use. In this review, we will highlight the current clinical uses of MRI connectomics in the diagnosis and treatment of neurological disorders; balancing emerging applications and technologies with limitations of connectivity analytic approaches to present an encompassing and appropriate perspective.

Navigable maps of structural brain networks across species

Connectomes are spatially embedded networks whose architecture has been shaped by physical constraints and communication needs throughout evolution. Using a decentralized navigation protocol, we investigate the relationship between the structure of the connectomes of different species and their spatial layout. As a navigation strategy, we use greedy routing where nearest neighbors, in terms of geometric distance, are visited. We measure the fraction of successful greedy paths and their length as compared to shortest paths in the topology of connectomes. In Euclidean space, we find a striking difference between the navigability properties of mammalian and non-mammalian species, which implies the inability of Euclidean distances to fully explain the structural organization of their connectomes. In contrast, we find that hyperbolic space, the effective geometry of complex networks, provides almost perfectly navigable maps of connectomes for all species, meaning that hyperbolic distances are exceptionally congruent with the structure of connectomes. Hyperbolic maps therefore offer a quantitative meaningful representation of connectomes that suggests a new cartography of the brain based on the combination of its connectivity with its effective geometry rather than on its anatomy only. Hyperbolic maps also provide a universal framework to study decentralized communication processes in connectomes of different species and at different scales on an equal footing.

Reduced Salience and Enhanced Central Executive Connectivity Following PTSD Treatment

Background

In soldiers with posttraumatic stress disorder, symptom provocation was found to induce increased connectivity within the salience network, as measured by functional magnetic resonance imaging and global brain connectivity with global signal regression (GBCr). However, it is unknown whether these GBCr disturbances would normalize following effective posttraumatic stress disorder treatment.

Methods

Sixty-nine US Army soldiers with (n = 42) and without posttraumatic stress disorder (n = 27) completed functional magnetic resonance imaging at rest and during symptom provocation using subject-specific script imagery. Then, participants with posttraumatic stress disorder received six weeks (12 sessions) of group cognitive processing therapy or present-centered therapy. At week 8, all participants repeated the functional magnetic resonance imaging scans. The primary analysis used a region-of-interest approach to determine the effect of treatment on salience GBCr. A secondary analysis was conducted to explore the pattern of GBCr alterations posttreatment in posttraumatic stress disorder participants compared to controls.

Results

Over the treatment period, present-centered therapy significantly reduced salience GBCr (p = .02). Compared to controls, salience GBCr was high pretreatment (present-centered therapy, p = .01; cognitive processing therapy, p = .03) and normalized post-present-centered therapy (p = .53) but not postcognitive processing therapy (p = .006). Whole-brain secondary analysis found high GBCr within the central executive network in posttraumatic stress disorder participants compared to controls. Post hoc exploratory analyses showed significant increases in executive GBCr following cognitive processing therapy treatment (p = .01).

Conclusion

The results support previous models relating cognitive processing therapy to central executive network and enhanced cognitive control while unraveling a previously unknown neurobiological mechanism of present-centered therapy treatment, demonstrating treatment-specific reduction in salience connectivity during trauma recollection.