Reduction of chromatin assembly factor 1 p60 and C21orf2 protein, encoded on chromosome 21, in Down syndrome brain

Pathogenicity and functional analysis of CFAP410 mutations causing cone-rod dystrophy with macular staphyloma

Background

Cone-rod dystrophy (CORD) caused by pathogenic variants in CFAP410 is a very rare disease. The mechanisms by which the variants caused the disease remained largely unknown. CFAP410 pathogenic variants were identified in a cone-rod dystrophy with macular staphyloma patient. We explored the pathogenicity and performed functional analysis of two compound heterozygous mutations.

Methods

A 6-year-old boy complained decreased vision for 1 year, underwent ocular examinations together with systemic X-ray check. Blood sample was taken for targeted next generation sequencing (Tg-NGS). Pathogenicity of identified variants was determined by ACMG guideline. Mutated plasmids were constructed and transferred to HEK293T cells. Cell cycle, protein stability, and protein ubiquitination level was measured.

Results

The best-corrected visual acuity of proband was 0.20 bilaterally. Fundus showed macular staphyloma and uneven granular pigment disorder in the periphery of the retina. SS-OCT showed thinning and atrophy of the outer retina, residual ellipsoid zone (EZ) in the fovea. Scotopic and photopic ERG responses severe reduced. Two heterozygous missense pathogenic variants, c.319 T > C (p.Tyr107His) and c.347 C > T (p.Pro116Leu) in exon 4 of the CFAP410, were found and were pathogenic by the ACMG guideline. In vitro, pathogenic variants affect cell cycle. Immunofluorescence and western blotting showed that the mutant proteins decreased expression levels protein stability. Meanwhile, co-IP data suggested that ubiquitination level was altered in cells transferred with the mutated plasmids.

Conclusion

Compound heterozygous pathogenic variants c.319 T > C and c.347 C > T in CFAP410 caused CORD with macular staphyloma. The pathogenic mechanisms may be associated with alternations of protein stability and degradation through the ubiquitin-proteasome pathway.

Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1

Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly process is lacking. In this work, we report the crystal structure of human CAF-1 in the absence of histones and the cryo-electron microscopy structure of CAF-1 in complex with histones H3 and H4. One histone H3-H4 heterodimer is bound by one CAF-1 complex mainly through the p60 subunit and the acidic domain of the p150 subunit. We also observed a dimeric CAF-1-H3-H4 supercomplex in which two H3-H4 heterodimers are poised for tetramer assembly and discovered that CAF-1 facilitates right-handed DNA wrapping of H3-H4 tetramers. These findings signify the involvement of DNA in H3-H4 tetramer formation and suggest a right-handed nucleosome precursor in chromatin replication.

An Amyotrophic Lateral Sclerosis-Associated Mutant of C21ORF2 Is Stabilized by NEK1-Mediated Hyperphosphorylation and the Inability to Bind FBXO3

C21ORF2 and NEK1 have been identified as amyotrophic lateral sclerosis (ALS)-associated genes. Both genes are also mutated in certain ciliopathies, suggesting that they might contribute to the same signaling pathways. Here we show that FBXO3, the substrate receptor of an SCF ubiquitin ligase complex, binds and ubiquitylates C21ORF2, thereby targeting it for proteasomal degradation. C21ORF2 stabilizes the kinase NEK1, with the result that loss of FBXO3 stabilizes not only C21ORF2 but also NEK1. Conversely, NEK1-mediated phosphorylation stabilizes C21ORF2 by attenuating its interaction with FBXO3. We found that the ALS-associated V58L mutant of C21ORF2 is more susceptible to phosphorylation by NEK1, with the result that it is not ubiquitylated by FBXO3 and therefore accumulates together with NEK1. Expression of C21ORF2(V58L) in motor neurons induced from mouse embryonic stem cells impaired neurite outgrowth. We suggest that inhibition of NEK1 activity is a potential therapeutic approach to ALS associated with C21ORF2 mutation.

Overexpression of chromatin assembly factor-1/p60 predicts biological behaviour of laryngeal carcinomas

This study analysed the immunohistochemical expression of the CAF-1/p60 protein in laryngeal cancers. CAF-1/p60 assumes an independent discriminative and prognostic value in laryngeal neoplasms; the presence of this protein in carcinoma in situ compared with laryngeal precancerous and larynx infiltrating tumours. We assessed the immunohistochemical expression of CAF-1/p60 in 30 cases of moderate and/or severe dysplasia, 30 cases of carcinoma in situ and 30 cases of laryngeal squamous cell carcinoma (LSCCs). CAF-1/p60 expression increased significantly according to the high index of neoplastic cellular replication; therefore, CAF-1/p60 was overexpressed in neoplastic cells and its moderate-severe expression is correlated with poorer prognosis compared to less expression. In conclusion, overexpression of the CAF-1/p60 protein is related to a risk of higher morbidity and mortality and is a reliable independent prognostic index of laryngeal carcinoma. CAF1-p60 protein overexpression can be used in cancer management as an indicator of malignant evolution, especially in carcinoma in situ.

Genotype/phenotype correlation in a female patient with 21q22.3 and 12p13.33 duplications

Many chromosomal rearrangements that lead to copy-number gains or losses have been shown to cause distinctive and recognizable clinical phenotypes. Conventional cytogenetic analysis can detect many, but not all, rearrangements depending on its power of resolution. The wide use of whole-genome array-based comparative genomic hybridization (array-CGH) techniques has allowed the detection of novel syndromes and to establish genotype-phenotype correlations by delineating at high resolution the regions involved in specific chromosomal aberrations. We report on a two and half-year-old female patient with intellectual disability and distinctive phenotypic features resulting from a de novo duplication of about 0.3 Mb in 21q22.3 associated with duplication of about 0.3 Mb in 12p13.33. The patient's chromosomal abnormalities were identified at the cytogenetic molecular level, using SNP array analysis, while GTG banding technique revealed a normal karyotype. Clinical findings of the patient were compared with Down syndrome and 12p duplication syndrome. This study suggests that an area of contiguous genes on the distal part of chromosome 21 (21q22.3) contribute to the Down syndrome phenotype and indicates that genes in the distal region of 12p (12p13.33) account for many facial characteristics and hypotonia of trisomy 12p syndrome.

Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation

Background

The endogenous ability to dedifferentiate, re-pattern, and re-differentiate adult cells to repair or replace damaged or missing structures is exclusive to only a few tetrapod species. The Mexican axolotl is one example of these species, having the capacity to regenerate multiple adult structures including their limbs by generating a group of progenitor cells, known as the blastema, which acquire pattern and differentiate into the missing tissues. The formation of a limb regenerate is dependent on cells in the connective tissues that retain memory of their original position in the limb, and use this information to generate the pattern of the missing structure. Observations from recent and historic studies suggest that blastema cells vary in their potential to pattern distal structures during the regeneration process; some cells are plastic and can be reprogrammed to obtain new positional information while others are stable. Our previous studies showed that positional information has temporal and spatial components of variation; early bud (EB) and apical late bud (LB) blastema cells are plastic while basal-LB cells are stable. To identify the potential cellular and molecular basis of this variation, we compared these three cell populations using histological and transcriptional approaches.

Results

Histologically, the basal-LB sample showed greater tissue organization than the EB and apical-LB samples. We also observed that cell proliferation was more abundant in EB and apical-LB tissue when compared to basal-LB and mature stump tissue. Lastly, we found that genes associated with cellular differentiation were expressed more highly in the basal-LB samples.

Conclusions

Our results characterize histological and transcriptional differences between EB and apical-LB tissue compared to basal-LB tissue. Combined with our results from a previous study, we hypothesize that the stability of positional information is associated with tissue organization, cell proliferation, and pathways of cellular differentiation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12861-015-0095-4) contains supplementary material, which is available to authorized users.

The NEK1 interactor, C21ORF2, is required for efficient DNA damage repair

Defective DNA damage response is a threat to genome stability and a proven cause of tumorigenesis. C21ORF2 (chromosome 21 open reading frame 2) is a novel gene on chromosome 21, and the C21ORF2 protein is found to interact with NEK1. Earlier studies showed that C21ORF2 might be associated with some human genetic diseases including Down syndrome. However, the cellular functions of C21ORF2 remain unknown. In the present study, we reported that C21ORF2 affected cell proliferation after DNA damage induced by ionizing radiation, and DNA repair was less efficient in C21ORF2-depleted cells compared with control cells. However, C21ORF2-knockdown cells did not show defects in the activation of the G2-phase DNA damage checkpoint. Furthermore, homologous recombination, but not non-homologous end joining repair, was found to be impaired after C21ORF2 attenuation, which could be rescued by the overexpression of NEK1, indicating that C21ORF2 functions in the same pathway as NEK1 in DNA damage repair.

Genome-wide Association Study on Platinum-induced Hepatotoxicity in Non-Small Cell Lung Cancer Patients

Platinum-based chemotherapy has been shown to improve the survival of advanced non-small cell lung cancer (NSCLC) patients; the platinum-induced toxicity severely impedes the success of chemotherapy. Genetic variations, such as single nucleotide polymorphisms (SNPs), may contribute to patients’ responses to the platinum-based chemotherapy. To identify SNPs that modify the risk of hepatotoxicity in NSCLC patients receiving platinum-based chemotherapy, we performed a genome-wide association scan in 334 subjects followed by a replication study among 375 subjects. Consistent associations with platinum-induced hepatotoxicity risk was identified for SNP rs2838566 located at 21q22.3, as the minor A allele could significantly increase the risk of liver injury (OR = 3.78, 95%CI = 1.99–7.19, P = 4.90 × 10⁻⁵ for GWAS scan, OR = 1.89, 95%CI = 1.03–3.46, P = 0.039 for replication, and OR = 2.56, 95%CI = 1.65–3.95, P = 2.55 × 10⁻⁵ for pooled population). These results suggested that genetic variants at 21q22.3 may contribute to the susceptibility of platinum-induced hepatotoxicity in NSCLC patients.

Overexpression of chromatin assembly factor-1 p60, poly(ADP-ribose) polymerase 1 and nestin predicts metastasizing behaviour of oral cancer

Aims

The natural history of oral squamous cell carcinomas (OSCCs) is variable and difficult to predict. This study aimed to assess the value of the expression of poly(ADP-ribose) polymerase 1 (PARP-1), chromatin assembly factor-1 (CAF-1)/p60 and the stem cell markers CD133, CD166, CD44, CD44v6 and nestin as markers of outcome and progression-free survival in OSCC patients.

Methods

Clinical data were collected from 66 patients (41 male and 25 female, aged 29–92 years) who underwent surgery for OSCC of the tongue, floor, lips, and palate. During follow-up (range: 12–131 months), 14 patients experienced relapse/metastasis and/or death. The study was performed by immunohistochemistry on paraffin-embedded tumour tissues, western blot analysis of tumour protein lysates and human cell lines, and RNA silencing assays. In addition, the human papillomavirus (HPV) status of primary tumours was evaluated by immunohistochemistry and viral subtyping. Univariate and multivariate analyses were performed to determine the correlation between these parameters and the clinical and pathological variables of the study population.

Results and conclusions

We found that a PARP-1^high/CAF-1 p60^high/nestin^high phenotype characterized the OSCCs with the worst prognosis (all HPV-negative). This may be of benefit in clinical management, since radio-enhancing anti-PARP-1 and/or anti-CAF-1/p60 agents may allow radioresistance to be bypassed in the nestin-overexpressing, metastasizing OSCC cells.

New cerebellar phenotypes in YAC transgenic mouse in vivo library of human Down syndrome critical region-1

Down syndrome (DS) is the most frequent genetic cause of mental retardation (MR) associated with neurological alterations. To allow a genetic dissection of DS phenotype, we studied eight transgenic mouse lines carrying YACs containing human DNA fragments covering DS critical region (DCR-1), as an in vivo library. Herein, we found an increased brain size in the 152F7-mice containing DYRK1A gene. We also identified a new cerebellar alteration in two independent lines carrying 230E8-YAC. These mice showed significant elongation of the cerebellar antero-posterior axis (p<0.001), determined by increased length of rostral folia of the vermis (lobule II-V, p<0.0001; lobule VI, p<0.001). In addition, we identified a major neurological defect in culmen and declivus lobules in the 230E8-mice. We analyzed P30, P12, and P9 stages and detected high significant increased lengths of anterior lobules (II-VI) of 230E8-mice at P30 and P12 (lobule II-V, p<0.0001; lobule VI, p<0.05), but not at P9, indicating that this new phenotype appears between P9 and P12. Interestingly, 230E8-mice also present increased cortical cell density and mild learning defects. 230E8-YAC contains seven genes, some of which could be potentially responsible for this phenotype. Between them, we proposed DOPEY2 as potential candidate gene for these cerebellar alterations considering its high expression in the brain and that its homologous genes in yeast, Caenorhabditis elegans and Drosophila are involved in morphogenesis, suggesting a conserved role of DOPEY2 as a patterning gene.

NOR Expression increases in interphase lymphocytes of Down syndrome babies/children as AgNORs surface, according to the mitogen concentration in the culture medium

The extra chromosome 21 of Down syndrome (DS) or trisomy 21 patients contains an average of 40 extra copies of rRNA genes and the in vivo/in vitro regulation of the activity of these genes is not fully understood. The objective of this work was to compare the NORs expression pattern in interphase lymphocytes of DS patients with regular trisomy 21 and control individuals according to phytohemagglutinin (PHA) concentration (0.37, 0.75, 1.48 and 2.21 ml) per 100 ml of medium. Because the AgNOR staining is an indicator of the active rRNA genes, comparison of the image analysis values of the AgNOR area in 72 h cultivated lymphocytes for each concentration of PHA between DS patients (N=30) and controls (N=24) provided a plausible conclusion on the regulation of the extra rRNA genes in DS lymphocytes. The nucleolus organizer regions area/total nuclear area (NORa/TNa) was calculated using an in-house computer program. Fifty consecutive interphases per PHA concentration were analysed for each individual, for determination of the NORa/TNa. In contrast to healthy controls, NORa/TNa of lymphocytes from DS patient babies/children (0-8 years old) increased gradually in parallel with the PHA concentration in the culture medium: 10.44+/-1.72% for 0.37 ml of PHA, 11.74+/-1.93% for 0.75 ml of PHA, 13.25+/-2.03% for 1.48 ml of PHA and 13.43+/-2.08% for 2.21 ml of PHA per 100 ml of medium. Contrary to control cells (in which the NORa/TNa ratio according to PHA concentration in the culture medium remains constant), DS interphase lymphocytes in culture do not down-regulate their NOR expression. These results obtained from interphase NORs are consistent with the previous results obtained by evaluating the mean of AgNOR+ chromosome number in metaphase cells, also in relation to the mitogen concentration in the culture medium.

Age-dependent decreases in mitogen-stimulation level and RNA content in peripheral blood mononuclear cells of down syndrome patients

OBJECTIVE

The aim of the present study was to determine whether or not the phytohemagglutinin (PHA)-activated proliferation and average RNA content in peripheral blood mononuclear cells (PBMC) of Down syndrome (DS) patients change with age.

METHOD

Stimulated portion of PBMC and total RNA levels in these cells after 72 h of PHA stimulation from 38 DS patients were compared with 28 age-matched healthy controls using flow cytometric measurement.

RESULTS

Decreased ratio of PBMC from DS patients undergoes mitogenic stimulation with age (r = -0.84, P = 0.000). This decrease is not observed in the cells of control individuals (r = 0.03, P = 0.869). Stimulated PBMC in infants with DS have higher level of RNA contents compared to controls (Z = 2.227, P = 0.026). While RNA content in mitogen-stimulated PBMC of DS decreased progressively and significantly with age (r = -0.70, P = 0.000), no significant age-related change in RNA content was found among the cells of healthy individuals in the range of 0-27 year old (r = 0.275, P = 0.157, P > 0.05).

CONCLUSION

Age-dependent decreases in mitogen-activated proliferation ratio and average RNA content of PBMC from DS patients appear as regular events. These results may contribute to the explanation of the immune deficiency seen in DS patients since the PHA-stimulated cells are principally T-lymphocytes. This is the first report on the decrease in PHA-stimulated proliferation ratio (stimulability) and RNA level in PBMC of DS patients in relation to age.

Higher NORs-expression in lymphocyte of trisomy 21 babies/children: In vivo evaluation

Extra chromosome 21 of Down syndrome (DS) or trisomy 21 patients contains an average of 40 extra copies of rRNA genes and the in vivo regulation of these genes is not known. The objective of this work is to compare the NORs expression in interphase nuclei in non-stimulated lymphocytes of DS patients and healthy controls. Because the AgNOR staining is the indicator of the active rRNA genes, comparison of the image analysis values of AgNORs area between DS's and healthy controls' interphase lymphocytes is considered to be sufficient to evaluate the level of rDNA activities in the two groups. The Nucleolus Organizer Regions area/Total Nuclear area (NORa/TNa) was calculated using a computer program designed by us. 100 consecutive NORa/TNa per individual were evaluated. We report that 24 DS children's peripheral lymphocytes show significantly higher NORa/TNa mean value (6.32 +/- 1.77%) than that of the 20 healthy controls' cells (5.31 +/- 1.34%) (2-tailed Mann-Whitney U test, z = 19.4, P = 0.000). The same is true for the nucleolus (AgNOR spot) number per nucleus. The mean value of nucleoli number per nucleus in DS lymphocytes was significantly higher than that of the controls: z = 14.6, P = 0.000. In conclusion, extra rRNA genes on the chromosome 21 are not down-regulated in DS patients' lymphocytes. Rather, extra NORs expressions in 'in vivo' condition contribute to the increase of AgNORs area and AgNOR spots number per nucleus. This is the first work on the comparison of NORs activities in resting (non-stimulated) interphase lymphocytes between DS and healthy controls.

NOR expression increases on metaphase chromosomes of down syndrome lymphocytes in concordance with mitogen concentration in culture medium

BACKGROUND

Regulation of nucleolus organizer region (NOR) expression in trisomy 21 (Down syndrome [DS]) cells is not fully explained. This work compared NOR expression on metaphase chromosomes in gradiently stimulated lymphocytes from DS patients with those from healthy controls.

METHOD

Conventional peripheral blood culture (72 h) and chromosomal preparation procedures were used except that blood samples from each individual were cultivated in the same but gradiently increasing concentrations (0.37, 0.75, 1.48, and 2.21 ml) of phytohemagglutinin (PHA) per 100 ml of medium. One hundred consecutive metaphases per concentration were analyzed for scoring the means of the active NORs bearing chromosomes (AgNOR+ chromosome) per individual and per concentration.

RESULTS

In contrast to healthy controls (n=24), AgNOR+ chromosomal number in lymphocytes from 30 DS patients increased in concordance to the gradient of PHA concentration in the culture medium.

CONCLUSION

DS lymphocytes do not downregulate their NOR expression in the limit of control cells. This in vitro result may serve as a clue for the explanation of the DS phenotype due to the wasted energy in producing unnecessary rRNA transcripts and AgNOR proteins in utero during organogenesis. These results also indicate that precautions must be used in routine work of NOR evaluation/interpretation in DS lymphocytes.

Flow cytometric comparison of RNA content in peripheral blood mononuclear cells of down syndrome patients and control individuals

OBJECTIVE

Trisomy 21 or Down syndrome (DS) is the most common genetic cause of mental retardation associated with the immunologic and other known defects. Extra chromosome 21 of DS patients contains an average of 40 extra copies of rRNA genes and the in vivo regulation of these genes' activity is not known. Because over 80% of total cellular RNA is rRNA, the measurement of total cellular RNA provides information on rRNA content. The aim of this work was to determine whether or not the additional chromosome 21 causes any increase in total cellular RNA content in mononuclear cells from peripheral blood (PBMNCs) of these patients and whether or not this content is modified with age.

METHOD

PBMNCs of 48 patients with DS and 48 healthy controls were studied. RNA content of isolated PBMNCs was evaluated by flow cytometric measurements.

RESULTS

Average RNA content of younger DS patients' cells was significantly higher than that of healthy controls (P=0.003). Furthermore, the RNA content decreased significantly with increasing age of DS patients (r=-0.377, P=0.008) in the range of 0-26 year old, whereas no significant relationship was found between age and PBMNCs' RNA content of healthy controls in the same range of ages.

CONCLUSION

RNA content of PBMNCs from DS patients decreases rapidly with age. This is the first work on the age-dependent decrease of the RNA content in PBMNCs of DS patients.