Molecular cytogenetic characterisation of a novel de novo ring chromosome 6 involving a terminal 6p deletion and terminal 6q duplication in the different arms of the same chromosome

Identification of cell specific biomarkers for intellectual disability via single cell RNA sequencing and transcriptomic bioinformatics approaches

Limitations in cognitive functioning and adaptive behavior are hallmarks of Intellectual Disability (ID), a neurodevelopmental disease. Specific genetic disorders that result in ID can also have immune system anomalies, such as changes in T (CD4+ and CD8+) cell activity. This work aimed to compare single-cell RNA-sequencing (scRNA-seq) and transcriptome data to find biomarkers linked to T cells that could potentially be utilized for the diagnosis and assessment of ID. After integrating genes and performing a comparative analysis 196 genes were identified as differentially expressed genes (DEGs). Furthermore, the DAVID online platform and FunRich software were utilized to detect signal transduction and translation, immune response, MHC (Major Histocompatibility Complex) class II, antigen processing and presentation, allograft rejection and important pathways of type I diabetes mellitus. In this investigation, six ribosomal proteins (RPS27A, RPS21, RPS18, RPS7, RPS5, and RPL9) have been identified as the hub genes of ID from PPI. Additionally, eleven topological algorithms discovered only one hub protein, namely RPS27A from the protein-protein interaction (PPI) network. Through the analysis of the regulatory network, we have identified several crucial transcriptional factors (TFs) including FOXC1, FOXL1, and GATA2; microRNAs such as mir-92a-3p, and mir-16-5p were investigated by procedural data analysis. This study used scRNA-seq and transcriptomics data analysis to define unique biomarkers associated with T cell types throughout the progression of ID. Ongoing research on the activity of ID genes is contributing to a greater understanding of the pathophysiology of ID and will become more scientific and research-based in future.

Genetic diversity, demographic history, and selective signatures of Silkie chicken

BACKGROUND

Silkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl.

RESULTS

In total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie.

CONCLUSIONS

Our study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts.

Axenfeld-Rieger syndrome: A systematic review examining genetic, neurological, and neurovascular associations to inform screening

Axenfeld-Rieger Syndrome (ARS) is comprised of a group of autosomal dominant disorders that are each characterized by anterior segment abnormalities of the eye. Mutations in the transcription factors FOXC1 or PITX2 are the most well-studied genetic manifestations of this syndrome. Due to the rarity this syndrome, ARS-associated neurological manifestations have not been well characterized. The purpose of this systematic review is to characterize and describe ARS neurologic manifestations that affect the cerebral vasculature and their early and late sequelae. PRISMA guidelines were followed; studies meeting inclusion criteria were analyzed for study design, evidence level, number of patients, patient age, whether the patients were related, genotype, ocular findings, and nervous system findings, specifically neurostructural and neurovascular manifestations. 63 studies met inclusion criteria, 60 (95%) were case studies or case series. The FOXC1 gene was most commonly found, followed by COL4A1, then PITX2. The most commonly described structural neurological findings were white matter abnormalities in 26 (41.3%) of studies, followed by Dandy-Walker Complex 12 (19%), and agenesis of the corpus callosum 11 (17%). Neurovascular findings were examined in 6 (9%) of studies, identifying stroke, cerebral small vessel disease (CSVD), tortuosity/dolichoectasia of arteries, among others, with no mention of moyamoya. This is the first systematic review investigating the genetic, neurological, and neurovascular associations with ARS. Structural neurological manifestations were common, yet often benign, perhaps limiting the utility of MRI screening. Neurovascular abnormalities, specifically stroke and CSVD, were identified in this population. Stroke risk was present in the presence and absence of cardiac comorbidities. These findings suggest a relationship between ARS and neurovascular findings; however, larger scale studies are necessary inform therapeutic decisions.

Novel maternal duplication of 6p22.3-p25.3 with subtelomeric 6p25.3 deletion: new clinical findings and genotype-phenotype correlations

BACKGROUND

Copy-number variants (CNVs) drive many neurodevelopmental-related disorders. Although many neurodevelopmental-related CNVs can give rise to widespread phenotypes, it is necessary to identify the major genes contributing to phenotypic presentation. Copy-number variations in chromosome 6, such as independent 6p deletion and 6p duplication, have been reported in several live-born infants and present widespread abnormalities such as intellectual disability, growth deficiency, developmental delay, and multiple dysmorphic facial features. However, a contiguous deletion and duplication in chromosome 6p regions have been reported in only a few cases.

CASE PRESENTATION

In this study, we reported the first duplication of chromosome band 6p25.3-p22.3 with deletion of 6p25.3 in a pedigree. This is the first case reported involving CNVs in these chromosomal regions. In this pedigree, we reported a 1-year-old boy with maternal 6p25-pter duplication characterized by chromosome karyotype. Further analysis using CNV-seq revealed a 20.88-Mb duplication at 6p25.3-p22.3 associated with a contiguous 0.66-Mb 6p25.3 deletion. Whole exome sequencing confirmed the deletion/duplication and identified no pathogenic or likely pathogenic variants related with the patient´s phenotype. The proband presented abnormal growth, developmental delay, skeletal dysplasia, hearing loss, and dysmorphic facial features. Additionally, he presented recurrent infection after birth. CNV-seq using the proband´s parental samples showed that the deletion/duplication was inherited from the proband´s mother, who exhibited a similar phenotype to the proband. When compared with other cases, this proband and his mother presented a new clinical finding: forearm bone dysplasia. The major candidate genes contributing to recurrent infection, eye development, hearing loss features, neurodevelopmental development, and congenital bone dysplasia were further discussed.

CONCLUSIONS

Our results showed a new clinical finding of a contiguous deletion and duplication in chromosome 6p regions and suggested candidate genes associated with phenotypic features, such as FOXC1, SERPINB6, NRN1, TUBB2A, IRF4, and RIPK1.

Mechanisms of structural chromosomal rearrangement formation

Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead to genetic instability. Most of these rearrangements arise from recombination, repair, or replication mechanisms that occur after a double-strand break or the stalling/breakage of a replication fork. Here, we review the mechanisms of formation of structural rearrangements, highlighting their main features and differences. The most important mechanisms of constitutional chromosomal alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling and Template Switching (FoSTeS), and Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis and in the formation of complex chromosomal rearrangements, inverted duplications associated with terminal deletions, and ring chromosomes is also outlined. We reinforce the importance of high-resolution analysis to determine the DNA sequence at, and near, their breakpoints in order to infer the mechanisms of formation of structural rearrangements and to reveal how cells respond to DNA damage and repair broken ends.

Intellectual disability associated with craniofacial dysmorphism due to POLR3B mutation and defect in spliceosomal machinery

Background

Intellectual disability (ID) is a clinically important disease and a most prevalent neurodevelopmental disorder. The etiology and pathogenesis of ID are poorly recognized. Exome sequencing revealed a homozygous missense mutation in the POLR3B gene in a consanguineous family with three Intellectual disability with craniofacial anomalies patients. POLR3B gene encoding the second largest subunit of RNA polymerase III.

Methods

We performed RNA sequencing on blood samples to obtain insights into the biological pathways influenced by POLR3B mutation. We applied the results of our RNA-Seq analysis to several gene ontology programs such as ToppGene, Enrichr, KEGG.

Results

A significant decrease in expression of several spliceosomal RNAs, ribosomal proteins, and transcription factors was detected in the affected, compared to unaffected, family members.

Conclusions

We hypothesize that POLR3B mutation dysregulates the expression of some important transcription factors, ribosomal and spliceosomal genes, and impairments in protein synthesis and splicing mediated in part by transcription factors such as FOXC2 and GATA1 contribute to impaired neuronal function and concurrence of intellectual disability and craniofacial anomalies in our patients. Our study highlights the emerging role of the spliceosome and ribosomal proteins in intellectual disability.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01237-5.

De Novo Subtelomeric 6p25.3 Deletion with Duplication of 6q23.3-q27: Genotype-Phenotype Correlation

Duplications of 6q and deletions of 6p have been reported in more than 30 cases of live born infants and given rise to widespread abnormalities recognizable as a specific clinical syndrome. Different phenotypes have been described with variable clinical signs. Most cases involve the coexistence of unbalanced translocations affecting one or the other of the chromosomes. However, duplication of both chromosome 6q and deletion of 6p regions have been reported in only a few cases. Here, we report the first duplication of chromosome band 6q23.3-q27 with deletion of 6p25.3. This is the first case in the literature involving changes to these specific chromosomal regions; a medium size duplication of the distal long arm and smaller deletion of the terminal short arm of chromosome 6. In the literature, there are no other cases where these two specific chromosomal aberrations are observed together. Conventional chromosome analysis was performed to investigate the patient. Chromosome structure was identified using fluorescence in situ hybridization for subtelomeric regions of chromosome 6 and array comparative genomic hybridization analysis (array-CGH).

Childhood glaucoma genes and phenotypes: Focus on FOXC1 mutations causing anterior segment dysgenesis and hearing loss

Childhood glaucoma is an important cause of blindness world-wide. Eleven genes are currently known to cause inherited forms of glaucoma with onset before age 20. While all the early-onset glaucoma genes cause severe disease, considerable phenotypic variability is observed among mutations carriers. In particular, FOXC1 genetic variants are associated with a broad range of phenotypes including multiple forms of glaucoma and also systemic abnormalities, especially hearing loss. FOXC1 is a member of the forkhead family of transcription factors and is involved in neural crest development necessary for formation of anterior eye structures and also pharyngeal arches that form the middle ear bones. In this study we review the clinical phenotypes reported for known FOXC1 mutations and show that mutations in patients with reported ocular anterior segment abnormalities and hearing loss primarily disrupt the critically important forkhead domain. These results suggest that optimal care for patients affected with anterior segment dysgenesis should include screening for FOXC1 mutations and also testing for hearing loss.

Ring chromosome 6 in a child with anterior segment dysgenesis and review of its overlap with other FOXC1 deletion phenotypes

Here, we report a patient with ring chromosome 6 [r(6)], associated with anterior segment dysgenesis (ASD) and other anomalies. The phenotype was due to a 1880 kb microdeletion at 6p25.3 identified by whole-genome array analysis, and was mainly attributable to a FOXC1 haploinsufficiency. Currently 37 patients with r(6) have been reported. We found that facial dysmorphism, ASD, heart anomalies, brain anomalies, and hearing loss are constant features only in severe cases of r(6), mainly related to hemizygosity of FOXC1. Thus, overlaps with other FOXC1 related phenotypes, such as the 6p25 deletion syndrome, Axenfeld-Rieger syndrome type 3, and ASD type 3. Contrarily, those patients whose r(6) does not disrupt FOXC1, have mild or moderate phenotypes and do not exhibit ASD.

A child with intellectual disability and dysmorphism due to complex ring chromosome 6: identification of molecular mechanism with review of literature

Background

Ring chromosome 6 (r(6)) is a rare disorder that mainly occurs as a ‘de novo’ event. Nonetheless, a wide phenotypic spectrum has been reported in r(6) cases, depending on breakpoints, size of involved region, copy number alterations and mosaicism of cells with r(6) and/or monosomy 6 due to loss of r(6).

Case presentation

An 11-year-old male was referred with developmental delay, intellectual disability and microcephaly. Physical examination revealed additionally short stature and multiple facial dysmorphisms. Banding cytogenetic studies revealed a karyotype of mos 46,XY,r(6)(p25.3q27)[54]/45,XY,-6[13]/46,XY,r(6)(::p25.3→q27::p25.3→q27::)[13]/46,XY[6]/47,XY,r(6)(p25.3q27)×2[2]dn. Additionally, molecular karyotyping and molecular cytogenetics confirmed the breakpoints and characterized a 1.3 Mb contiguous duplication at 6p25.3.

Conclusion

The present study has accurately identified copy number alterations caused by ring chromosome formation. A review of the literature suggests that hemizygous expression of TBP gene in 6q27~qter, is likely to be the underlying cause of the phenotype. The phenotypic correlation and clinical severity in r(6) cases continue to remain widely diverse in spite of numerous reports of genomic variations.

[Clinical and genetic features of ring chromosome 13 syndrome: an analysis of one case]

A girl aged 5 months was admitted due to developmental delay. Physical examination showed delayed physical development, unusual facies (microcephalus, hypertelorism, low-set ears, wide nasal bridge, and short philtrum), and an absence of the labium minus at one side. The peripheral blood karyotype was 46,XX,r(13)(p11q33)[82]/45,XX,-13[10]/46,XX,r(13;13)(p11q33;p11q33)[8], and array-based comparative genomic hybridization showed an 87.5 Mb duplication in 13q11q33.2 region and an 8.2 Mb deletion in 13q33.2q34 region. Fluorescence in situ hybridization showed terminal depletion of the long arm of the ring chromosome 13. The girl was diagnosed with ring 13 syndrome. This syndrome has various clinical phenotypes and is closely associated with the amount and site of the loss of genetic material in chromosomal band and different rates of chimerism.