The Diverse Role of CUB and Sushi Multiple Domains 1 (CSMD1) in Human Diseases

Constructing shared genetic architecture between bioavailable testosterone and luminal A breast cancer in female

BACKGROUND

Observational studies have showed a strong association between bioavailable testosterone (BT) and breast cancer. However, the role of genetic factors in their comorbidity remains unknown.

METHODS

Using large genome-wide association study (GWAS) data, we employed linkage disequilibrium score regression (LDSC) to identify the breast cancer subtype most genetically correlated with BT. We then constructed the shared genetic architecture between BT and this subtype by: (1) applied Heritability Estimation from Summary Statistics for local genetic correlations and stratified-LDSC for partitioned heritability; (2) performed a cross-trait GWAS meta-analysis to find novel single-nucleotide polymorphism (SNP) and validated through colocalization; (3) conducted both cross-tissue and single-tissue transcriptome-wide association studies (TWAS) and validated the candidate genes through Mendelian randomization (MR); (4) investigated SNP-heritability enrichment at the gene set, tissue, and cell levels using Multi-marker Analysis of GenoMic Annotation.

RESULTS

Luminal A breast cancer (Luminal ABC) was selected as it is a common subtype of breast cancer and demonstrates a superior genetic correlation with BT. We identified strong local correlations in 132 distinct genomic regions and confirmed shared SNPs including rs1432679 and rs7175852. TWAS highlighted two pleiotropic genes, MICALL1 and TRIOBP, with TRIOBP validated by MR. We also found six shared pathways and luminal cells in mammary gland pregnancy shared between BT and Luminal ABC. For tissue-specific enrichment, BT was mainly found in the liver and adrenal gland, whereas Luminal ABC was found in the minor salivary gland.

CONCLUSIONS

This study sheds light on the genetic architecture of BT and Luminal ABC and suggests new avenues for research and therapy.

Genomic Integration of Hepatitis B Virus Into Human Hepatocytes in Early Childhood Cirrhosis

BACKGROUND AND AIMS

Hepatitis B virus (HBV) remains a major global health problem. HBV DNA can be integrated into the human chromosomes. The integration in young cirrhotic chronic hepatitis B children has not been explored. This study aims to investigate HBV DNA integration in early childhood cirrhosis.

METHODS

Biopsy liver specimens from cirrhotic and matched non-cirrhotic chronic hepatitis B children were collected. HBV DNA integration was detected through targeted HBV DNA fragment capture sequencing.

RESULTS

Twenty cirrhotic and 20 non-cirrhotic children with chronic hepatitis B were included in the study. The cirrhotic group included 14 males and 6 females, and the non-cirrhotic group included 13 males and 7 females. Compared to non-cirrhotic children, cirrhotic children had lower serum HBsAg quantification (p = 0.001). The median number of HBV integrants in the cirrhotic group was 59 and that in the non-cirrhotic group was 98. No significant difference existed between the two groups (p = 0.529). In the multivariate linear regression analysis, serum HBV DNA level was correlated with the number of HBV integrants (p < 0.001, R2 = 0.322). Six differential intragenic high-frequency viral integration sites in cirrhotic children were revealed, all of which have protein-coding functions.

CONCLUSION

Several frequently integrated genes were observed in early childhood cirrhosis. Detailed associations between genetic alterations induced by HBV integration and early childhood cirrhosis need further exploration.

Genome-wide by trait interaction analyses with neuroticism reveal chronic pain-associated depression as a distinct genetic subtype

The frequent co-occurrence of chronic pain (CP) and depression is a well-known phenomenon, supported by both the high prevalence of major depression among CP patients and studies describing a substantial genetic correlation between the two phenotypes. Neuroticism, a trait characterised by maladaptive stress responses and a tendency to experience negative emotions, has been linked to both depression and the experience of pain. This study aimed to determine whether depression associated with CP represents a genetically distinct subtype and to explore the role of neuroticism in modulating genetic susceptibility to depression. To address these questions, we performed genome-wide association analyses for current depression utilising the UK Biobank dataset, followed by genome-wide by trait interaction analyses to assess the interaction effect of neuroticism, and polygenic risk score analyses to compare predictions. Our findings suggest that CP-related depression is a valid subtype of depression. In association with current depression, we identified a total of 49 novel genetic risk polymorphisms meeting the genome-wide significance threshold, including variants involved in synaptic plasticity and transcriptional regulation. Additionally, our results support that neuroticism has a prominent role in modulating the genetic risk of current depression independently of CP, which highlights the importance of considering personality traits and stress factors in understanding the genetic background of complex and heterogeneous phenotypes like depression.

The schizophrenia-associated gene CSMD1 encodes a complement classical pathway inhibitor predominantly expressed by astrocytes and at synapses in mice and humans

CUB and sushi multiple domains 1 (CSMD1) is predominantly expressed in brain and robustly associated with schizophrenia risk; however, understanding of which cells express CSMD1 in brain and how it impacts risk is lacking. CSMD1 encodes a large transmembrane protein including fifteen tandem short consensus repeats (SCRs), resembling complement C3 convertase regulators. CSMD1 complement regulatory activity has been reported and mapped to SCR17-21. We expressed two SCR domains of CSMD1, SCR17-21 and SCR23-26, and characterised their complement regulatory activity using a panel of functional assays testing convertase and terminal pathway inhibition. Both domains inhibited the classical pathway C3 convertase by acting as factor I cofactors; neither domain caused any inhibition in alternative or terminal pathway assays. Novel anti-CSMD1 monoclonal antibodies cross-reactive with human and mouse CSMD1 were generated that detected endogenous CSMD1 in human and rodent brain; immunostaining showed predominantly astrocyte and synaptic localisation of CSMD1, the latter confirmed using isolated synapses. Using iPSC-derived cells, astrocyte expression was confirmed and expression on cortical neurons demonstrated. We show that CSMD1 is a classical pathway-specific complement regulator expressed predominantly on astrocytes, neurons, and synapses in human and mouse brain. These findings will help reveal the mechanism by which CSMD1 impacts schizophrenia risk.

Regulatory Plasticity of the Human Genome

Evolutionary turnover in noncoding regions has driven phenotypic divergence during past speciation events and continues to facilitate environmental adaptation through variants. We used a deep learning model to identify the substrates of regulatory turnover using genome-wide mutations mimicking three evolutionary pathways: recent history (human-chimp substitutions), modern population (human population variation), and mutational susceptibility (random mutations). We observed enhancer turnover in approximately 6% of the whole genome, with more than 80% of the novel activity arising from repurposing of enhancers between cell types. Frequency of turnover in a cell type is remarkably similar across the three pathways, despite only ∼19% overlap in the source regions. The majority of turnover loci were found to be localized within 100 kb of a gene, with the highest turnover occurring near neurodevelopmental genes including CNTNAP2, NPAS3, and AUTS2. Flanking enhancers of these genes undergo high turnover irrespective of the mutational model pathway, suggesting a high plasticity in neurocognitive evolution. Based on susceptibility to random mutations, these enhancers were identified as vulnerable by nature and feature a higher abundance of cell type-specific transcription factor binding sites. Our findings suggest that enhancer repurposing within vulnerable loci drives regulatory innovation while keeping the core regulatory networks intact.

Identification of genetic fingerprint of type I interferon therapy in visceral metastases of melanoma

Malignant melanoma is a difficult-to-treat skin cancer with increasing incidence worldwide. Although type-I interferon (IFN) is no longer part of guidelines, several melanoma patients are treated with type-I interferon (IFN) at some point of the disease, potentially affecting its genetic progression. We run genome-wide copy number variation (CNV) analysis on previously type-I IFN-treated (n = 17) and control (n = 11) visceral metastases of melanoma patients. Results were completed with data from the TCGA and MM500 databases. We identified metastasis- and brain metastasis-specific gene signatures mostly affected by CN gains. Some cases were genetically resistant to IFN showing characteristic gene alterations (e.g. ABCA4 or ZEB2 gain and alterations of DNA repair genes). Analysis of a previously identified type-I IFN resistance gene set indicates that only a proportion of these genes was exclusive for the IFN-treated metastases reflecting a possible selective genomic pressure of endogenous IFNs during progression. Our data suggest that previous type-I IFN treatment and/or endogenous IFN production by immune response affect genomic progression of melanoma which may have clinical relevance, potentially influence immune checkpoint regulation in the tumor microenvironment.

AXL expression reflects tumor-immune cell dynamics impacting outcome in non-small cell lung cancer patients treated with immune checkpoint inhibitor monotherapy

Introduction

AXL receptor expression is proposed to confer immune-checkpoint inhibitor (ICI)-resistance in non-small cell lung cancer (NSCLC) patients. We sought to interrogate AXL expression in conjunction with mutational and tumor-microenvironmental features to uncover predictive mechanisms of resistance in ICI-treated NSCLC patients.

Methods

Tumor samples from 111 NSCLC patients treated with ICI-monotherapy were analyzed by immunohistochemistry for tumor- and immune-AXL expression. Subsets of patients were analyzed by whole-exome sequencing (n = 44) and imaging mass cytometry (n = 14). Results were related to ICI-outcome measurements.

Results

Tumor-cell AXL expression correlated with aggressive phenotypic features including reduced OS in patients treated with ICIs (P = 0.04) after chemotherapy progression, but conversely associated with improved disease control (P = 0.045) in ICI-treated, PD-L1 high first-line patients. AXL+ immune-cell infiltration correlated with total immune-cell infiltration and improved overall outcomes (PFS: P = 0.044, OS: P = 0.054). Tumor-cell AXL-upregulation showed enrichment in mutations associated with PD-L1-upregulation and ICI-response such as MUC4 and ZNF469, as well as adverse mutations including CSMD1 and LRP1B which associated with an immune-suppressed tumor phenotype and poor ICI prognosis particularly within chemotherapy-treated patients. Tumor mutational burden had no effect on ICI-outcomes and was associated with a lack of tumor-infiltrating immune cells. Spatial-immunophenotyping provided evidence that tumor-cell AXL-upregulation and adverse mutations modulate the tumor microenvironment in favor of infiltrating, activated neutrophils over anti-tumor immune-subsets including CD4 and CD8 T-cells.

Conclusion

Tumor-cell AXL-upregulation correlated with distinct oncotypes and microenvironmental immune-profiles that define chemotherapy-induced mechanisms of ICI-resistance, which suggests the combination of AXL inhibitors with current chemoimmunotherapy regimens can benefit NSCLC patients.

Genome-Wide Association Study for Weight Loss at the End of Dry-Curing of Hams Produced from Purebred Heavy Pigs

Dissecting the genetics of production traits in livestock is of outmost importance, both to understand biological mechanisms underlying those traits and to facilitate the design of selection programs incorporating that information. For the pig industry, traits related to curing are key for protected designation of origin productions. In particular, appropriate ham weight loss after dry-curing ensures high quality of the final product and avoids economic losses. In this study, we analyzed data (N = 410) of ham weight loss after approximately 20 months of dry-curing. The animals used for ham production were purebred pigs belonging to a commercial line. A genome-wide association study (GWAS) of 29,844 SNP markers revealed the polygenic nature of the trait: 221 loci explaining a small percentage of the variance (0.3-1.65%) were identified on almost all Sus scrofa chromosomes. Post-GWAS analyses revealed 32 windows located within regulatory regions and 94 windows located in intronic regions of specific genes. In total, 30 candidate genes encoding receptors and enzymes associated with ham weight loss (MTHFD1L, DUSP8), proteolysis (SPARCL1, MYH8), drip loss (TNNI2), growth (CDCA3, LSP1, CSMD1, AP2A2, TSPAN4), and fat metabolism (AGPAT4, IGF2R, PTDSS2, HRAS, TALDO1, BRSK2, TNNI2, SYT8, GTF2I, GTF2IRD1, LPCAT3, ATN1, GNB3, CMIP, SORCS2, CCSER1, SPP1) were detected.

Tumor suppressor role of the complement inhibitor CSMD1 and its role in TNF-induced neuroinflammation in gliomas

BACKGROUND

The complement inhibitor CSMD1 acts as a tumor suppressor in various types of solid cancers. Despite its high level of expression in the brain, its function in gliomas, malignant brain tumors originating from glial cells, has not been investigated.

METHODS

Three cohorts of glioma patients comprising 1500 patients were analyzed in our study along with their clinical data. H4, U-118 and U-87 cell lines were used to investigate the tumor suppressor function of CSMD1 in gliomas. PDGFB-induced brain tumor model was utilized for the validation of in vitro data.

RESULTS

The downregulation of CSMD1 expression correlated with reduced overall and disease-free survival, elevated tumor grade, wild-type IDH genotype, and intact 1p/19q status. Moreover, enhanced activity was noted in the neuroinflammation pathway. Importantly, ectopic expression of CSMD1 in glioma cell lines led to decreased aggressiveness in vitro. Mechanically, CSMD1 obstructed the TNF-induced NF-kB and STAT3 signaling pathways, effectively suppressing the secretion of IL-6 and IL-8. There was also reduced survival in PDGFB-induced brain tumors in mice when Csmd1 was downregulated.

CONCLUSIONS

Our study has identified CSMD1 as a tumor suppressor in gliomas and elucidated its role in TNF-induced neuroinflammation, contributing to a deeper understanding of glioma pathogenesis.

Evidence for a Pathogenic Role of CSMD1 in Childhood Apraxia of Speech

Childhood apraxia of speech (CAS) is a pediatric motor speech disorder. The genetic etiology of this complex neurological condition is not yet well understood, although some genes have been linked to it. We describe the case of a boy with a severe and persistent motor speech disorder, consistent with CAS, and a coexisting language impairment.Whole exome sequencing in our case revealed a de novo and splicing mutation in the CSMD1 gene.

Whole Genome Sequencing Revealed Inherited Rare Oligogenic Variants Contributing to Schizophrenia and Major Depressive Disorder in Two Families

Schizophrenia and affective disorder are two major complex mental disorders with high heritability. Evidence shows that rare variants with significant clinical impacts contribute to the genetic liability of these two disorders. Also, rare variants associated with schizophrenia and affective disorders are highly personalized; each patient may carry different variants. We used whole genome sequencing analysis to study the genetic basis of two families with schizophrenia and major depressive disorder. We did not detect de novo, autosomal dominant, or recessive pathogenic or likely pathogenic variants associated with psychiatric disorders in these two families. Nevertheless, we identified multiple rare inherited variants with unknown significance in the probands. In family 1, with singleton schizophrenia, we detected four rare variants in genes implicated in schizophrenia, including p.Arg1627Trp of LAMA2, p.Pro1338Ser of CSMD1, p.Arg691Gly of TLR4, and Arg182X of AGTR2. The p.Arg691Gly of TLR4 was inherited from the father, while the other three were inherited from the mother. In family 2, with two affected sisters diagnosed with major depressive disorder, we detected three rare variants shared by the two sisters in three genes implicated in affective disorders, including p.Ala4551Gly of FAT1, p.Val231Leu of HOMER3, and p.Ile185Met of GPM6B. These three rare variants were assumed to be inherited from their parents. Prompted by these findings, we suggest that these rare inherited variants may interact with each other and lead to psychiatric conditions in these two families. Our observations support the conclusion that inherited rare variants may contribute to the heritability of psychiatric disorders.

Complement C4-deficient mice have a high mortality rate during PTZ-induced epileptic seizures, which correlates with cognitive problems and the deficiency in the expression of Egr1 and other immediate early genes

Complement system plays an important role in the immune defense against pathogens; however, recent studies demonstrated an important role of complement subunits C1q, C4, and C3 in normal functions of the central nervous system (CNS) such as non-functional synapse elimination (synapse pruning), and during various neurologic pathologies. Humans have two forms of C4 protein encoded by C4A and C4B genes that share 99.5% homology, while mice have only one C4B gene that is functionally active in the complement cascade. Overexpression of the human C4A gene was shown to contribute to the development of schizophrenia by mediating extensive synapse pruning through the activation C1q-C4-C3 pathway, while C4B deficiency or low levels of C4B expression were shown to relate to the development of schizophrenia and autism spectrum disorders possibly via other mechanisms not related to synapse elimination. To investigate the potential role of C4B in neuronal functions not related to synapse pruning, we compared wildtype (WT) mice with C3- and C4B- deficient animals for their susceptibility to pentylenetetrazole (PTZ)- induced epileptic seizures. We found that C4B (but not C3)-deficient mice were highly susceptible to convulsant and subconvulsant doses of PTZ when compared to WT controls. Further gene expression analysis revealed that in contrast to WT or C3-deficient animals, C4B-deficient mice failed to upregulate expressions of multiple immediate early genes (IEGs) Egrs1-4, c-Fos, c-Jus, FosB, Npas4, and Nur77 during epileptic seizures. Moreover, C4B-deficient mice had low levels of baseline expression of Egr1 on mRNA and protein levels, which was correlated with the cognitive problems of these animals. C4-deficient animals also failed to upregulate several genes downstream of IEGs such as BDNF and pro-inflammatory cytokines IL-1β, IL-6, and TNF. Taken together, our study demonstrates a new role of C4B in the regulation of expression of IEGs and their downstream targets during CNS insults such as epileptic seizures.