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Funder: VTCT Foundation Fellowship, BACKGROUND: Auriculocondylar syndrome (ARCND) is a rare genetic disease that affects structures derived from the first and second pharyngeal arches, mainly resulting in micrognathia and auricular malformations. To date, pathogenic variants have been identified in three genes involved in the EDN1-DLX5/6 pathway (PLCB4, GNAI3 and EDN1) and some cases remain unsolved. Here we studied a large unsolved four-generation family. METHODS: We performed linkage analysis, resequencing and Capture-C to investigate the causative variant of this family. To test the pathogenicity of the CNV found, we modelled the disease in patient craniofacial progenitor cells, including induced pluripotent cell (iPSC)-derived neural crest and mesenchymal cells. RESULTS: This study highlights a fourth locus causative of ARCND, represented by a tandem duplication of 430 kb in a candidate region on chromosome 7 defined by linkage analysis. This duplication segregates with the disease in the family (LOD score=2.88) and includes HDAC9, which is located over 200 kb telomeric to the top candidate gene TWIST1. Notably, Capture-C analysis revealed multiple cis interactions between the TWIST1 promoter and possible regulatory elements within the duplicated region. Modelling of the disease revealed an increased expression of HDAC9 and its neighbouring gene, TWIST1, in neural crest cells. We also identified decreased migration of iPSC-derived neural crest cells together with dysregulation of osteogenic differentiation in iPSC-affected mesenchymal stem cells. CONCLUSION: Our findings support the hypothesis that the 430 kb duplication is causative of the ARCND phenotype in this family and that deregulation of TWIST1 expression during craniofacial development can contribute to the phenotype.

PURPOSE Li-Fraumeni syndrome (LFS) is rare in the worldwide population, but it is highly prevalent in the Brazilian population because of a founder mutation, TP53 p.R337H, accounting for 0.3% of south and southeastern population. Clinical criteria for LFS may not identify all individuals at risk of carrying the Brazilian founder mutation because of its lower penetrance and variable expressivity. This variant is rarely described in databases of somatic mutations. Somatic findings in tumor molecular profiling may give insight to identify individuals who might be carriers of LFS and allow the adoption of risk reduction strategies for cancer. MATERIALS AND METHODS We determined the frequency of the TP53 p.R337H variant in tumor genomic profiling from 755 consecutive Brazilian patients with pan-cancer. This is a retrospective cohort from January 2013 to March 2020 at a tertiary care center in Brazil. RESULTS The TP53 p.R337H variant was found in 2% (15 of 755) of the samples. The mutation allele frequency ranged from 30% to 91.7%. A total of seven patients were referred for genetic counseling and germline testing after tumor genomic profiling results were disclosed. All the patients who proceeded with germline testing (6 of 6) confirmed the diagnosis of LFS. Family history was available in 12 cases. Nine patients (9 of 12) did not meet LFS clinical criteria. CONCLUSION The identification of the TP53 p.R337H variant in tumor genomic profiling should be a predictive finding of LFS in the Brazilian population and should prompt testing for germline status confirmation.

A valuable approach to understand how individual and population genetic differences can predispose to disease is to assess the impact of genetic variants on cellular functions (e.g., gene expression) of cell and tissue types related to pathological states. To understand the genetic basis of nonsyndromic cleft lip with or without cleft palate (NSCL/P) susceptibility, a complex and highly prevalent congenital malformation, we searched for genetic variants with a regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle [OOM]), of affected individuals. From 46 OOM samples, which are frequently discarded during routine corrective surgeries on patients with orofacial clefts, we derived mesenchymal stem cells and correlated the individual genetic variants with gene expression from these cultured cells. Through this strategy, we detected significant cis-eQTLs (i.e., DNA variants affecting gene expression) and selected a few candidates to conduct an association study in a large Brazilian cohort (624 patients and 668 controls). This resulted in the discovery of a novel susceptibility locus for NSCL/P, rs1063588, the best eQTL for the MRPL53 gene, where evidence for association was mostly driven by the Native American ancestry component of our Brazilian sample. MRPL53 (2p13.1) encodes a 39S protein subunit of mitochondrial ribosomes and interacts with MYC, a transcription factor required for normal facial morphogenesis. Our study illustrates not only the importance of sampling admixed populations but also the relevance of measuring the functional effects of genetic variants over gene expression to dissect the complexity of disease phenotypes.

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a complex disorder with a worldwide incidence estimated at 1:700. Among the putative susceptibility loci, the IRF6 gene and a region at 8q24.21 have been corroborated in different populations. To test the role of IRF6 in NSCL/P predisposition in the Brazilian population, we conducted a structured association study with the SNPs rs642961 and rs590223, respectively, located at 5′ and 3′ of the IRF6 gene and not in strong linkage disequilibrium (LD), in patients from five different Brazilian locations. We also evaluated the effect of these SNPs in IRF6 expression in mesenchymal stem cells (MSC). We observed association between rs642961 and cleft lip only (CLO) (P = 0.009; odds ratio (OR) for AA genotype = 1.83 [95% Confidence interval (CI), 0.64–5.31]; OR for AG genotype = 1.72 [95% CI, 1.03–2.84]). This association seems to be driven by the affected patients from Barbalha, a location which presents the highest heritability estimate (H2 = 0.85), and the A allele at rs642961 is acting through a dominant model. No association was detected for the SNP rs590223. We did not find any correlation between expression levels and genotypes of the two loci, and it is possible that these SNPs have a functional role in some specific period of embryogenesis. © 2012 Wiley Periodicals, Inc.

Recent reports have demonstrated that a significant proportion of human genes display allelic differential expression (ADE). ADE is associated with phenotypic variability and may contribute to complex genetic diseases. Here, we present a computational analysis of ADE using allele-specific serial analysis of gene expression (SAGE) tags representing 1295 human genes. We identified 472 genes for which unequal representation (>3-fold) of allele-specific SAGE tags was observed in at least one SAGE library, suggesting the occurrence of ADE. For 235 out of these 472 genes, the difference in the expression level between both allele-specific SAGE tags was statistically significant (p < 0.05). Eleven candidate genes were then subjected to experimental validation and ADE was confirmed for 8 out of these 11 genes. Our results suggest that at least 25% of the human genes display ADE and that allele-specific SAGE tags can be efficiently used for the identification of such genes.

Neste trabalho, estudamos duas malformações craniofaciais mendelianas, decorrentes de um distúrbio do desenvolvimento dos primeiro e segundo arcos faríngeos: a síndrome de Treacher Collins (STC) e a síndrome Aurículo-condilar (SAC). A identificação de genes e de mecanismos moleculares associados a essas condições, além de contribuir para a compreensão do desenvolvimento das estruturas derivadas desses arcos faríngeos, é fundamental para o desenvolvimento do diagnóstico molecular, uma ferramenta importante para diagnóstico diferencial e aconselhamento genético. Contribuímos para uma melhor caracterização clínica da SAC com a descrição de uma nova família com 11 afetados. Após excluirmos quatro genes/regiões candidatas para síndromes de 1º e 2º arcos faríngeos, realizamos estudos de ligação usando marcadores polimórficos ao longo do genoma. Mapeamos o primeiro lócus associado à SAC, 1p21.1-q23.3 (lod score=3.0), e nossos dados sugerem que há heterogeneidade genética para essa patologia. Com relação ao estudo da STC, realizamos uma extensa revisão da nomenclatura das mutações patogênicas descritas na literatura, além de investigar mecanismos mutacionais atípicos na STC, corroborando a hipótese de que mutações nos exons que sofrem splicing alternativo são capazes de gerar o fenótipo da síndrome. Demos continuidade à caracterização do espectro de mutações no gene TCOF1 e investigamos a correlação genótipo-fenótipo numa amostra de 58 pacientes com STC. A análise dos dados de polimorfismos da região codificadora do gene permitiu que fizéssemos inferências sobre o regime de seleção ao qual o TCOF1 está submetido, e os resultados sugeriram que o gene TCOF1 está sob seleção purificadora, que atua sobre mutações fracamente deletérias. Também inferimos a fase para um conjunto de polimorfismos da região codificadora, verificando se havia associação de algum haplótipo à gravidade do quadro clínico ou à predisposição para a doença. Dada a observação de ausência de correlação haplótipo/genótipo-fenótipo, testamos a hipótese de que variações nos níveis de expressão do alelo normal poderiam ser responsáveis pela variabilidade clínica observada nos pacientes portadores da STC. Para tanto, iniciamos o estudo funcional das regiões regulatórias do gene TCOF1 , inclusive, de regiões distantes do promotor mínimo, preditas como enhancers. Identificamos polimorfismos em sua região promotora, sendo um deles capaz de diminuir os níveis de transcrição e de afetar a ligação do fator de transcrição YY1 ao promotor do TCOF1 . Caracterizamos a ação de YY1 como repressora in vitro. Testamos também a hipótese de haploinsuficiência como mecanismo associado à STC. Quantificamos os níveis de transcritos do TCOF1 em indivíduos afetados e normais e observamos uma diferença significativa. Nosso trabalho corrobora a hipótese de haploinsuficiência e mostra pela primeira vez que pacientes têm degradação de transcritos. Também investigamos a possibilidade de os níveis de transcritos estarem correlacionados à variabilidade fenotípica. Comparamos os dados de expressão de cada paciente à freqüência de nove sinais clínicos principais da STC, mas nenhuma correlação foi observada. Investigamos o padrão de metilação da ilha CpG do gene TCOF1 em pacientes e em controles, com o intuito de verificar se diferentes níveis de metilação inter-individual estariam associados à grande variação na expressão gênica. Demonstramos que a metilação da ilha CpG não é o mecanismo regulatório por trás dessa ampla variação de expressão do TCOF1 In the present study, we investigate two craniofacial mendelian disorders, resulting from abnormalities in the development of the first and second pharyngeal arches: the Treacher Collins Syndrome (TCS ) and the auriculo condylar syndrome (ACS). The identification of genes and molecular mechanisms associated to these conditions, in addition to contributing to the understanding of the development of structures derived from these pharyngeal arches, is fundamental for the development of molecular diagnostics, an important tool for differential diagnosis and genetic counseling. We contributed to a better clinical characterization of ACS with a description of a new family with 11 affected individuals. After excluding four candidate genes/regions for syndromes of the 1st and 2nd pharyngeal arches, we carried out linkage studies using polymorphic markers throughout the genome. We mapped the first locus associated to ACS, 1p21.1-q23.3 (lod score=3.0), and our data suggest genetic heterogeneity exists for this pathology. With respect to the study of TCS , we carried out an extensive review of the nomenclature for the pathogenic mutations described in the literature, in addition to investigating atypical mutation mechanisms in TCS , corroborating the hypothesis that mutations in the exons that undergo alternative splicing can result in the TCS phenotype. We continued the characterization of the mutation spectrum for TCOF1 and we investigated the genotype-phenotype correlation in a sample of 58 patients with TCS . The analysis of polymorphisms in the coding region allowed us to make inferences about the selective regime experienced by TCOF1 , and our results suggested that TCOF1 is under purifying selection, which acts upon weakly deleterious mutations. We also inferred the phase for a set of polymorphisms in the coding region, testing whether there was association between any haplotype and the severity of the phenotype or the susceptibility to the disease. Given the observation of no correlation between haplotype/genotype and phenotype, we tested the hypothesis that variation in the levels of expression of the normal allele could be responsible for the clinical variability observed in TCS patients. To do this, we started a functional study of the TCOF1 regulatory regions, including regions distant from the minimal promoter, predicted to be enhancers. We identified polymorphisms in the promoter region, one of which reduced the levels of transcription and affected the binding of the YY1 transcription factor to the TCOF1 promoter. Using an in vitro assay we characterized YY1 as a repressor. We also tested the hypothesis of haploinsufficiency as a mechanism associated to TCS . We quantified the levels of TCOF1 transcripts in normal and affected individuals and found a significant difference. Our study corroborates the haploinsufficiency hypothesis and for the first time shows that patients have transcript degradation. We also investigated the possibility that transcripts levels are correlated to phenotypic variability. We compared the expression data for each patient with the frequency of nine clinical signs of TCS , but no correlation was found. We investigated the pattern of methylation on the CpG island of TCOF1 in patients and controls, in order to test whether different levels of methylation among individuals were associated to the great variation in gene expression. We demonstrated that methylation of the CpG island is not the regulatory mechanisms underlying the broad variation in TCOF1 expression.

We wish to draw the attention of cancer geneticists to a particular genetic variant of the Prolactin-Induced Protein (PIP) gene that may be an important predisposing factor to cancer because of its high frequency and significant association with cancer, as determined in this study. In an initial copy number variation (CNV) screen for germ-line deletions in 123 Brazilian cancer patients selected as high risk either because of early age of onset (pediatric cancer) or a positive family history (TP53-negative Li–Fraumeni and APC/MUTYH-negative Familial Adenomatous Polyposis patients), a previously undescribed microdeletion was discovered in four patients. The deletion carried in these patients was apparently identical (Figure 1), with a size of 69 kb and similar base-pair position in chromosome region 7q34. All four deletions were validated by qPCR and found to harbor only the PIP and TAS2R39 (taste receptor type 2 member 39) genes. TAS2R39 is a member of ∼30 TAS2R bitter taste receptors,1 several of which are known to exhibit variation in copy number. It is unlikely that TAS2R39 has a role in tumorigenesis, and will not be considered further in this submission. We here refer to the deletion encompassing the PIP gene as PIP-Sao Paulo, following the convention of adding the place of discovery to the gene name. This deletion was not detected in a control group of 260 non-related individuals from the Sao Paulo urban area that had attended our genetic service for reasons other than cancer (normal relatives of patients with intellectual disabilities). The difference in deletion frequency between patients and controls was significant at the 0.01 level (Fisher's exact test). Another example of the PIP-Sao Paulo deletion was serendipitously detected in a TP53-mutated patient who was not part of these cohorts, but had been investigated by aCGH for presenting with an atypically severe course of cancer that commenced at 4 years of age with the diagnosis of a rhabdomyosarcoma, followed by choroid plexus tumor (7 years of age), liposarcoma and osteochondroma (10 years of age), and finally passed away at 11 years. This patient was not included in the statistics of the patient–control comparison; however, a possible interaction between the TP53 mutation and PIP-Sao Paulo deletion may have contributed to the severity of the cancer progression. Figure 1 PIP-Sao Paulo microdeletion at 7q34, detected by array-CGH in cancer patients. Array-CGH profile of a chromosome region at 7q34 (microarray platform Agilent 180K—Agilent Technologies, Santa Clara, CA, USA), showing heterozygous losses ... Following our initial observations, we interrogated the 1000 Genomes Project database and found a comparable deletion to be present in 13 out of 1097 individuals: 9 of European and 4 of Latin-American origin (see Supplementary Table 1). Manual review of the sequence data in this region indicated that 7 out of the 13 individuals had sufficient sequence depth to determine that they shared identical breakpoints. From this information, we designed PCR primers and were able to amplify across the breakpoints in all the five Brazilian deletion cases. Subsequent sequencing of the PCR fragments (see Supplementary Figure 1) demonstrated that all identified PIP-Sao Paulo deletions were identical to the deletions present in the 1000 Genomes Project data set. In a replicate study, we determined by breakpoint PCR the frequency of PIP deletions in an independent Brazilian cancer group (219 individuals) that had either presented with more than one primary cancer prior to 60 years of age (166 individuals) or were probands of hereditary melanoma families (53 individuals with no CDKN2A or CDK4 mutations). This identified a further 6 individuals, who had had cancer and carried the PIP deletion (2.6%), as opposed to 10 out of 847 individuals (1.2%) from a second control group. As in the initial study, the deletion frequency in the replicate study in cancer patients was higher than that in controls, although this was not significant at the 5% level (P=0.11). However, when cancer and control samples from both studies were pooled, statistical significance was attained (P=0.04, Fisher's exact test). Importantly, heterogeneity tests demonstrated that no significant differences existed at the 0.05 level between the two control and two patient samples, respectively. We conclude that the relatively frequent germ-line deletion of the PIP gene has more than a two-fold increase in frequency in the Brazilian cancer patients compared with the Brazilian controls. The clinical phenotype, mutation status, type of tumor and age of diagnosis of all patients carrying the PIP-Sao Paulo deletion are summarized in Table 1, demonstrating that several types of cancer are involved in this study and that no single type or group of cancers predominates. Presence of the PIP-Sao Paulo deletion was investigated in paraffin blocks from several different primary tumors taken from four of the deleted patients. In all samples, except for one from patient 7, the PIP-Sao Paulo deletion was detected (Supplementary Figure 1); additionally, at least one exon of the PIP gene was amplified from each of the tested samples, indicating that one allele was retained, similar to blood. Unfortunately, DNA quality did not allow sequence screening for point mutations or other deletions that may have occurred in the remaining allele. We conclude that if the PIP-Sao Paulo deletion is directly responsible for tumor induction, this has not occurred by induction of homozygosity of the deletion itself in the cases studied. Table 1 Characteristics of the PIP-Sao Paulo deletion patients: mutation status, clinical phenotype, type of tumor and age at diagnosis To date, several publications have reported association between PIP expression and tumor progression, particularly for prostate and breast cancers.2, 3 The gene has been implicated in multiple functions, including apoptosis, cell proliferation and migration,4 but mutations have only been studied in tumor cell lines and never investigated as germ-line mutations. According to the TCGA database (http://cancergenome.nih.gov/), PIP gains in tumors are more frequent than deletions; however, data in different type of tumors are very heterogeneous and difficult to interpret. We have no specific insights into the mechanisms through which the PIP-Sao Paulo deletion could be oncogenic. It is evident from the foregoing that the PIP-Sao Paulo deletion is not specific to Brazil. Inspection of the HapMap3 database shows that the haplotype adjacent to the deletion (Table 2) is either absent or extremely rare in African populations. Interestingly, although about ∼25% of the 1094 individuals sequenced in data set 1 of the 1000 Genome Project were of African origin, none of the 13 individuals carrying the deletion were African and, except for one Colombian and two Mexican individuals from Los Angeles, CA, USA, all others were of European origin. Ethnic certainty of Brazilian cancer patients and controls is obscured by miscegenation and ethnic diversity; however, they are most likely to be mainly Caucasians, given the relatively high Caucasian composition of Sao Paulo, and through hospital attendance preferences and other socioeconomic differences. It is probable that PIP-Sao Paulo arose in an European population as a founder mutation that was subsequently exported to the New World. Table 2 SNPs, genomic positions (Hg19) and the common haplotype deduced from the proximal region of the patients with 7q34 deletion The crucial question of whether the PIP-Sao Paulo deletion constitutes a widespread cancer risk can only be answered by similar investigations in other countries, which we hope will be stimulated by this report. However, maintenance of a deletion variant associated with cancer at such high frequency is surprising and probably implies that, if the cancer association is confirmed by independent studies, PIP-Sao Paulo appears to have a relatively low cancer penetrance rate so that many carriers either do not manifest cancer or do so at later age, following transmission of the deletion to their offspring, similar to the well-documented Brazilian TP53 variant R337H4. Whereas R337H has an estimated population frequency of ∼0.3% in Southern Brazil and exhibits an ∼8% penetrance rate in families with adrenocortical cancer,5 PIP-Sao Paulo is practically an order of magnitude more frequent (estimated at ∼2% in European populations from the 1000 Genome Project data set) and appears as a very frequent factor associated with increased cancer risk. Further, if the PIP-Sao Paulo deletion frequency is at least two-fold higher in European cancer patients than in controls, as in the Sao Paulo study, then even allowing for a low penetrance rate, there would be an increased cancer risk for Europeans. In the case of PIP-Sao Paulo, it is the high frequency and not the penetrance that constitutes the main risk parameter. This completely unanticipated aspect deserves a rapid, coordinated response to confirm whether indeed such an increased risk exists, and if so, to establish its magnitude and specificity. Rapid and cost-effective detection of the deletion can be performed using either PCR across the breakpoints, or copy number estimates by RT-PCR, MLPA and so on. The exact genome location of PIP-Sao Paulo is chr7: 142824847-142893913 (Genome build GRCh37/hg19).

BACKGROUND: Nonsyndromic cleft lip with or without cleft palate is a relatively common craniofacial defect with multifactorial inheritance. The association of the rs987525 single nucleotide variant, located in a gene desert at 8q24.21 region, has been consistently replicated in European populations. We performed a structured association approach combined with transcriptional analysis of the MYC gene to dissect the role of rs987525 in oral clefting susceptibility in the ethnically admixed Brazilian population. METHODS: We performed the association study conditioned on the individual ancestry proportions in a sample of 563 patients and 336 controls, and in an independent sample of 221 patients and 261 controls. The correlation between rs987525 genotypes and MYC transcriptional levels in orbicularis oris muscle mesenchymal stem cells was also investigated in 42 patients and 4 controls. RESULTS: We found a significant association in the larger sample (p 5 0.0016; OR 5 1.80 [95% confidence interval {CI}, 1.21–2.69], for heterozygous genotype, and 2.71 [95% CI, 1.47–4.96] for homozygous genotype). We did not find a significant correlation between rs987525 genotypes and MYC transcriptional levels (p 5 0.14; r 52 0.22, Spearman Correlation). CONCLUSIONS: We present a positive association of rs987525 in the Brazilian population for the first time, and it is likely that the European contribution to our population is driving this association. We also cannot discard a role of rs987515 in MYC regulation, because this locus behaves as an expression quantitative locus of MYC in another tissue. Birth Defects Research (Part A) 94:464–468, 2012. 2012 Wiley Periodicals, Inc.

Nonsyndromic cleft lip and palate (NSCL/P) is a complex disease resulting from failure of fusion of facial primordia, a complex developmental process that includes the epithelial-mesenchymal transition (EMT). Detection of differential gene transcription between NSCL/P patients and control individuals offers an interesting alternative for investigating pathways involved in disease manifestation. Here we compared the transcriptome of 6 dental pulp stem cell (DPSC) cultures from NSCL/P patients and 6 controls. Eighty-seven differentially expressed genes (DEGs) were identified. The most significant putative gene network comprised 13 out of 87 DEGs of which 8 encode extracellular proteins: ACAN, COL4A1, COL4A2, GDF15, IGF2, MMP1, MMP3 and PDGFa. Through clustering analyses we also observed that MMP3, ACAN, COL4A1 and COL4A2 exhibit co-regulated expression. Interestingly, it is known that MMP3 cleavages a wide range of extracellular proteins, including the collagens IV, V, IX, X, proteoglycans, fibronectin and laminin. It is also capable of activating other MMPs. Moreover, MMP3 had previously been associated with NSCL/P. The same general pattern was observed in a further sample, confirming involvement of synchronized gene expression patterns which differed between NSCL/P patients and controls. These results show the robustness of our methodology for the detection of differentially expressed genes using the RankProd method. In conclusion, DPSCs from NSCL/P patients exhibit gene expression signatures involving genes associated with mechanisms of extracellular matrix modeling and palate EMT processes which differ from those observed in controls. This comparative approach should lead to a more rapid identification of gene networks predisposing to this complex malformation syndrome than conventional gene mapping technologies. Electronic supplementary material The online version of this article (doi:10.1007/s12015-010-9197-3) contains supplementary material, which is available to authorized users.

Treacher Collins syndrome (TCS) is an autosomal dominant craniofacial malformation caused by null mutations in the TCOF1 gene. High inter and intra familial clinical variability, ranging from mild malar hypoplasia to perinatal death due to airway collapse is observed, but, to date, no genotype-phenotype correlation has been reported. Considering haploinsufficiency as the molecular mechanism underlying the disease, we have hypothesized that mutations in the promoter region of the gene, which has never been previously characterized, in trans with a pathogenic mutation, could modulate the phenotype. Therefore, the aims of the present study were to determine the TCOF1 gene's core promoter and to identify mutations in this region that could contribute to the phenotypic variation observed in this syndrome. We have delimitated the minimal promoter to a region of less than 150 bp, with 63% of identity among 5 different species. We screened 1.2 kbp of the TCOF1 5' flanking sequence in the DNA obtained from 21 patients and 51 controls and identified four new single nucleotide polymorphisms (SNPs), one of which (-346C>T), was proved to be functional, as it decreased the promoter activity by 38%. Electrophoretic mobility shift assay (EMSA) analysis demonstrated that the -346T allele impairs DNA-binding to the YY1 transcription factor. This promoter variant represents a candidate allele to explain the clinical variability in patients bearing TCS.

Recently, a novel exon was described in TCOF1 that, although alternatively spliced, is included in the major protein isoform. In addition, most published mutations in this gene do not conform to current mutation nomenclature guidelines. Given these observations, we developed an online database of TCOF1 mutations in which all the reported mutations are renamed according to standard recommendations and in reference to the genomic and novel cDNA reference sequences (www.genoma.ib.usp.br/TCOF1_database). We also report in this work: 1) results of the first screening for large deletions in TCOF1 by Southern blot in patients without mutation detected by direct sequencing; 2) the identification of the first pathogenic mutation in the newly described exon 6A; and 3) statistical analysis of pathogenic mutations and polymorphism distribution throughout the gene.

The MAGE-C1/CT7 encodes a cancer/testis antigen (CTA), is located on the chromosomal region Xq26–27 and is highly polymorphic in humans. MAGE-C1/CT7 is frequently expressed in multiple myeloma (MM) that may be a potential target for immunotherapy in this still incurable disease. MAGEC1/CT7 expression is restricted to malignant plasma cells and it has been suggested that MAGE-C1/CT7 might play a pathogenic role in MM; however, the exact function this protein in the pathophysiology of MM is not yet understood. Our objectives were (1) to clarify the role of MAGE-C1/CT7 in the control of cellular proliferation and cell cycle in myeloma and (2) to evaluate the impact of silencing MAGE-C1/CT7 on myeloma cells treated with bortezomib. Myeloma cell line SKO-007 was transduced for stable expression of shRNA-MAGE-C1/CT7. Downregulation of MAGE-C1/CT7 was confirmed by real time quantitative PCR and western blot. Functional assays included cell proliferation, cell invasion, cell cycle analysis and apoptosis. Western blot showed a 70–80% decrease in MAGE-C1/CT7 protein expression in inhibited cells (shRNA-MAGE-C1/CT7) when compared with controls. Functional assays did not indicate a difference in cell proliferation and DNA synthesis when inhibited cells were compared with controls. However, we found a decreased percentage of cells in the G2/M phase of the cell cycle among inhibited cells, but not in the controls (p

Background Treacher Collins syndrome (TCS) is an autosomal dominant craniofacial disorder caused by frameshift deletions or duplications in the TCOF1 gene. These mutations cause premature termination codons, which are predicted to lead to mRNA degradation by nonsense mediated mRNA decay (NMD). Haploinsufficiency of the gene product (treacle) during embryonic development is the proposed molecular mechanism underlying TCS. However, it is still unknown if TCOF1 expression levels are decreased in post-embryonic human cells. Methods We have estimated TCOF1 transcript levels through real time PCR in mRNA obtained from leucocytes and mesenchymal cells of TCS patients (n = 23) and controls (n = 18). Mutational screening and analysis of NMD were performed by direct sequencing of gDNA and cDNA, respectively. Results All the 23 patients had typical clinical features of the syndrome and pathogenic mutations were detected in 19 of them. We demonstrated that the expression level of TCOF1 is 18-31% lower in patients than in controls (p < 0.05), even if we exclude the patients in whom we did not detect the pathogenic mutation. We also observed that the mutant allele is usually less abundant than the wild type one in mesenchymal cells. Conclusions This is the first study to report decreased expression levels of TCOF1 in TCS adult human cells, but it is still unknown if this finding is associated to any phenotype in adulthood. In addition, as we demonstrated that alleles harboring the pathogenic mutations have lower expression, we herein corroborate the current hypothesis of NMD of the mutant transcript as the explanation for diminished levels of TCOF1 expression. Further, considering that TCOF1 deficiency in adult cells could be associated to pathologic clinical findings, it will be important to verify if TCS patients have an impairment in adult stem cell properties, as this can reduce the efficiency of plastic surgery results during rehabilitation of these patients.