Any-way and Sparse Analyses for Multimodal Fusion and Imaging Genomics

This dissertation aims to develop new algorithms that leverage sparsity and mutual information across data modalities built upon the independent component analysis (ICA) framework to improve the performance of current ICA-based multimodal fusion approaches. These algorithms are further applied to both simulated data and real neuroimaging and genomic data to examine their performance. The identified neuroimaging and genomic patterns can help better delineate the pathology of mental disorders or brain development. To alleviate the signal-background separation difficulties in infomax-decomposed sources for genomic data, we propose a sparse infomax by enhancing a robust sparsity measure, the Hoyer index. Hoyer index is scale-invariant and well suited for ICA frameworks since the scale of decomposed sources is arbitrary. Simulation results demonstrate that sparse infomax increases the component detection accuracy for situations where the source signal-to-background (SBR) ratio is low, particularly for single nucleotide polymorphism (SNP) data. The proposed sparse infomax is further extended into two data modalities as a sparse parallel ICA for applications to imaging genomics in order to investigate the associations between brain imaging and genomics. Simulation results show that sparse parallel ICA outperforms parallel ICA with improved accuracy for structural magnetic resonance imaging (sMRI)-SNP association detection and component spatial map recovery, as well as with enhanced sparsity for sMRI and SNP components under noisy cases. Applying the proposed sparse parallel ICA to fuse the whole-brain sMRI and whole-genome SNP data of 24985 participants in the UK biobank, we identify three stable and replicable sMRI-SNP pairs. The identified sMRI components highlight frontal, parietal, and temporal regions and associate with multiple cognitive measures (with different association strengths in different age groups for the temporal component). Top SNPs in the identified SNP factor are enriched in inflammatory disease and inflammatory response pathways, which also regulate gene expression, isoform percentage, transcription expression, or methylation level in the frontal region, and the regulation effects are significantly enriched. Applying the proposed sparse parallel ICA to imaging genomics in attention-deficit/hyperactivity disorder (ADHD), we identify and replicate one SNP component related to gray matter volume (GMV) alterations in superior and middle frontal gyri underlying working memory deficit in adults and adolescents with ADHD. The association is more significant in ADHD families than controls and stronger in adults and older adolescents than younger ones. The identified SNP component highlights SNPs in long non-coding RNAs (lncRNAs) in chromosome 5 and in several protein-coding genes that are involved in ADHD, such as MEF2C, CADM2, and CADPS2. Top SNPs are enriched in human brain neuron cells and regulate gene expression, isoform percentage, transcription expression, or methylation level in the frontal region. Moreover, to increase the flexibility and robustness in mining multimodal data, we propose aNy-way ICA, which optimizes the entire correlation structure of linked components across any number of modalities via the Gaussian independent vector analysis and simultaneously optimizes independence via separate (parallel) ICAs. Simulation results demonstrate that aNy-way ICA recover sources and loadings, as well as the true covariance patterns with improved accuracy compared to existing multimodal fusion approaches, especially under noisy conditions. Applying the proposed aNy-way ICA to integrate structural MRI, fractal n-back, and emotion identification task functional MRIs collected in the Philadelphia Neurodevelopmental Cohort (PNC), we identify and replicate one linked GMV-threat-2-back component, and the threat and 2-back components are related to intelligence quotient (IQ) score in both discovery and replication samples. Lastly, we extend the proposed aNy-way ICA with a reference constraint to enable prior-guided multimodal fusion. Simulation results show that aNy-way ICA with reference recovers the designed linkages between reference and modalities, cross-modality correlations, as well as loading and component matrices with improved accuracy compared to multi-site canonical correlation analysis with reference (MCCAR)+joint ICA under noisy conditions. Applying aNy-way ICA with reference to supervise structural MRI, fractal n-back, and emotion identification task functional MRIs fusion in PNC with IQ as the reference, we identify and replicate one IQ-related GMV-threat-2-back component, and this component is significantly correlated across modalities in both discovery and replication samples.Ph.D

Structural brain alterations and their association with cognitive function and symptoms in Attention-deficit/Hyperactivity Disorder families

Gray matter disruptions have been found consistently in Attention-deficit/Hyperactivity Disorder (ADHD). The organization of these alterations into brain structural networks remains largely unexplored. We investigated 508 participants (281 males) with ADHD (N = 210), their unaffected siblings (N = 108), individuals with subthreshold ADHD (N = 49), and unrelated healthy controls (N = 141) with an age range from 7 to 18 years old from 336 families in the Dutch NeuroIMAGE project. Source based morphometry was used to examine structural brain network alterations and their association with symptoms and cognitive performance. Two networks showed significant reductions in individuals with ADHD compared to unrelated healthy controls after False Discovery Rate correction. Component A, mainly located in bilateral Crus I, showed a ADHD/typically developing difference with subthreshold cases being intermediate between ADHD and typically developing controls. The unaffected siblings were similar to controls. After correcting for IQ and medication status, component A showed a negative correlation with inattention symptoms across the entire sample. Component B included a maximum cluster in the bilateral insula, where unaffected siblings, similar to individuals with ADHD, showed significantly reduced loadings compared to controls; but no relationship with individual symptoms or cognitive measures was found for component B. This multivariate approach suggests that areas reflecting genetic liability within ADHD are partly separate from those areas modulating symptom severity

Discrepancies of polygenic effects on symptom dimensions between adolescents and adults with ADHD

A significant proportion of individuals with attention-deficit/hyperactivity disorder (ADHD) show persistence into adulthood. The genetic and neural correlates of ADHD in adolescents versus adults remain poorly characterized. We investigated ADHD polygenic risk score (PRS) in relation to previously identified gray matter (GM) patterns, neurocognitive, and symptom findings in the same ADHD sample (462 adolescents & 422 adults from the NeuroIMAGE and IMpACT cohorts). Significant effects of ADHD PRS were found on hyperactivity and impulsivity symptoms in adolescents, hyperactivity symptom in adults, but not GM volume components. A distinct PRS effect between adolescents and adults on individual ADHD symptoms is suggested

Gray matter networks associated with attention and working memory deficit in ADHD across adolescence and adulthood

Contains fulltext : 231759.pdf (publisher's version ) (Open Access)Attention-deficit/hyperactivity disorder (ADHD) is a childhood-onset neuropsychiatric disorder and may persist into adulthood. Working memory and attention deficits have been reported to persist from childhood to adulthood. How neuronal underpinnings of deficits differ across adolescence and adulthood is not clear. In this study, we investigated gray matter of two cohorts, 486 adults and 508 adolescents, each including participants from ADHD and healthy controls families. Two cohorts both presented significant attention and working memory deficits in individuals with ADHD. Independent component analysis was applied to the gray matter of each cohort, separately, to extract cohort-inherent networks. Then, we identified gray matter networks associated with inattention or working memory in each cohort, and projected them onto the other cohort for comparison. Two components in the inferior, middle/superior frontal regions identified in adults and one component in the insula and inferior frontal region identified in adolescents were significantly associated with working memory in both cohorts. One component in bilateral cerebellar tonsil and culmen identified in adults and one component in left cerebellar region identified in adolescents were significantly associated with inattention in both cohorts. All these components presented a significant or nominal level of gray matter reduction for ADHD participants in adolescents, but only one showed nominal reduction in adults. Our findings suggest although the gray matter reduction of these regions may not be indicative of persistency of ADHD, their persistent associations with inattention or working memory indicate an important role of these regions in the mechanism of persistence or remission of the disorder

Network modules linking expression and methylation in prefrontal cortex of schizophrenia

Tremendous work has demonstrated the critical roles of genetics, epigenetics as well as their interplay in brain transcriptional regulations in the pathology of schizophrenia (SZ). There is great success currently in the dissection of the genetic components underlying risk-conferring transcriptomic networks. However, the study of regulating effect of epigenetics in the etiopathogenesis of SZ still faces many challenges. In this work, we investigated DNA methylation and gene expression from the dorsolateral prefrontal cortex (DLPFC) region of schizophrenia patients and healthy controls using weighted correlation network approach. We identified and replicated two expression and two methylation modules significantly associated with SZ. Among them, one pair of expression and methylation modules were significantly overlapped in the module genes which were significantly enriched in astrocyte-associated functional pathways, and specifically expressed in astrocytes. Another two linked expression-methylation module pairs were involved ageing process with module genes mostly related to oligodendrocyte development and myelination, and specifically expressed in oligodendrocytes. Further examination of underlying quantitative trait loci (QTLs) showed significant enrichment in genetic risk of most psychiatric disorders for expression QTLs but not for methylation QTLs. These results support the coherence between methylation and gene expression at the network level, and suggest a combinatorial effect of genetics and epigenetics in regulating gene expression networks specific to glia cells in relation to SZ and ageing process

A deep generative multimodal imaging genomics framework for Alzheimer's disease prediction

Alzheimer's disease (AD) is a neurodegenerative process characterized by the accumulation of amyloid-beta plaques and neurofibrillary tangles and is the most common cause of dementia. Studies have been striving to analyze the disease using available physiological and behavioral data. Functional/structural neuroimaging and genomics are complementary modalities for exploring the mechanisms subserving the development of AD. In this paper, we present a deep multimodal generative data fusion framework for integrating these sources in a classification task involving AD patients and healthy controls from the ADNI database. Biological data fusion has the potential to improve the fmal prediction, but at the same time, it is particularly challenging due to the unavailability of all sources of input for the entire cohort of subjects. Our proposed model allows us to perform prediction even if individuals are missing certain modalities. Our method addresses the missing modalities problem via knowledge transfer from two generative adversarial networks. The model exhibits superior performance for predicting AD versus healthy control, even with missing modalities. This could have an important impact from the patient point of view since certain clinical tests may not be necessary or available to a given individual

Neural correlates of cognitive function and symptoms in attention-deficit/hyperactivity disorder in adults

Contains fulltext : 195462.pdf (publisher's version ) (Open Access

Structural brain alterations and their association with cognitive function and symptoms in Attention-deficit/Hyperactivity Disorder families

Gray matter disruptions have been found consistently in Attention-deficit/Hyperactivity Disorder (ADHD). The organization of these alterations into brain structural networks remains largely unexplored. We investigated 508 participants (281 males) with ADHD (N = 210), their unaffected siblings (N = 108), individuals with subthreshold ADHD (N = 49), and unrelated healthy controls (N = 141) with an age range from 7 to 18 years old from 336 families in the Dutch NeuroIMAGE project. Source based morphometry was used to examine structural brain network alterations and their association with symptoms and cognitive performance. Two networks showed significant reductions in individuals with ADHD compared to unrelated healthy controls after False Discovery Rate correction. Component A, mainly located in bilateral Crus I, showed a ADHD/typically developing difference with subthreshold cases being intermediate between ADHD and typically developing controls. The unaffected siblings were similar to controls. After correcting for IQ and medication status, component A showed a negative correlation with inattention symptoms across the entire sample. Component B included a maximum cluster in the bilateral insula, where unaffected siblings, similar to individuals with ADHD, showed significantly reduced loadings compared to controls; but no relationship with individual symptoms or cognitive measures was found for component B. This multivariate approach suggests that areas reflecting genetic liability within ADHD are partly separate from those areas modulating symptom severity