The 18q deletion syndrome and analysis of the critical region for orofacial cleft at 18q22.3

SALL Proteins; Common and Antagonistic Roles in Cancer

Simple Summary

Transcription factors play essential roles in regulating gene expression, impacting the cell phenotype and function, and in the response of cells to environmental conditions. Alterations in transcription factors, including gene amplification or deletion, point mutations, and expression changes, are implicated in carcinogenesis, cancer progression, metastases, and resistance to cancer treatments. Not surprisingly, transcription factor activity is altered in numerous cancers, representing a unique class of cancer drug targets. This review updates and integrates information on the SALL family of transcription factors, highlighting the synergistic and/or antagonistic functions they perform in various cancer types.

Abstract

SALL proteins are a family of four conserved C2H2 zinc finger transcription factors that play critical roles in organogenesis during embryonic development. They regulate cell proliferation, survival, migration, and stemness; consequently, they are involved in various human genetic disorders and cancer. SALL4 is a well-recognized oncogene; however, SALL1–3 play dual roles depending on the cancer context and stage of the disease. Current reviews of SALLs have focused only on SALL2 or SALL4, lacking an integrated view of the SALL family members in cancer. Here, we update the recent advances of the SALL members in tumor development, cancer progression, and therapy, highlighting the synergistic and/or antagonistic functions they perform in similar cancer contexts. We identified common regulatory mechanisms, targets, and signaling pathways in breast, brain, liver, colon, blood, and HPV-related cancers. In addition, we discuss the potential of the SALL family members as cancer biomarkers and in the cancer cells’ response to therapies. Understanding SALL proteins’ function and relationship will open new cancer biology, clinical research, and therapy perspectives.

Clinical Characteristics and Long-Term Recombinant Human Growth Hormone Treatment of 18q- Syndrome: A Case Report and Literature Review

BACKGROUND

18q- syndrome is a rare chromosomal disease caused by the deletion of the long arm of chromosome 18. Some cases with 18q- syndrome can be combined with growth hormone deficiency (GHD), but data on the efficacy of recombinant human growth hormone (rhGH) treatment in 18q- syndrome are limited.

METHODS

Here, we report one case of 18q- syndrome successfully treated with long-term rhGH supplement. Previously reported cases in the literature are also reviewed to investigate the karyotype-phenotype relationship and their therapeutic response to rhGH.

RESULTS

A 7.9-year-old girl was referred for evaluation for short stature. Physical exam revealed proportionally short stature with a height of 111.10 cm (-3.02 SD score (SDS)), low-set ears, a high-arched palate, a small jaw, webbed neck, widely spaced nipples, long and tapering fingers, and cubitus valgus. Thyroid function test indicated subclinical hypothyroidism. The peak value of growth hormone was 10.26 ng/ml in the levodopa provocation test. Insulin-like growth factor 1 (IGF-1) was 126 ng/ml (57-316 ng/ml). Other laboratory investigations, including complete blood cell count, liver and kidney function, gonadal function, serum adrenocorticotropin levels, and serum cortisol levels, were all within normal ranges. Karyotype analysis showed 46, XX, del (18) (q21). L-Thyroxine replacement and rhGH treatment were initiated and maintained in the following 7 years. At the age of 14.8, her height has reached 159.5 cm with a height SDS increase of 2.82 SDS (from -3.02 SDS to -0.20 SDS). No significant side effects were found during the treatment. The literature review indicated the average rhGH treatment duration of 16 patients was 5.9 ± 3.3 years, and the average height SDS significantly increased from -3.12 ± 0.94 SDS to -1.38 ± 1.29 SDS after the rhGH treatment (p < 0.0001).

CONCLUSION

The main clinical manifestations of 18q- syndrome include characteristic appearance, intellectual disability, and abnormal genital development. The literature review suggested a significant height benefit for short stature with 18q- syndrome from long-term rhGH treatment.

Epigenetic silencing of SALL3 is an independent predictor of poor survival in head and neck cancer

Background

This study examined Sal-like protein (SALL)3 methylation profiles of head and neck cancer (HNSCC) patients at diagnosis and follow-up and evaluated their prognostic significance and value as a biomarker. SALL3 expression was examined in a panel of cell lines by quantitative reverse transcription polymerase chain reaction (RT-PCR). The methylation status of the SALL3 promoter was examined by quantitative methylation-specific PCR.

Results

SALL3 promoter methylation was associated with transcriptional inhibition and was correlated with disease recurrence in 64.8% of cases, with an odds ratio of 1.914 (95% confidence interval: 1.157–3.164; P = 0.011) by multivariate Cox proportional hazard regression analysis. SALL3 promoter hypermethylation showed highly discriminatory receiver operator characteristic curve profiles that clearly distinguished HNSCC from adjacent normal mucosal tissue, and was correlated with reduced disease-free survival (DFS) (log-rank test, P = 0.01). Hypermethylation of tumor-related genes was higher among patients with SALL3 methylation than among those without methylation (P < 0.001). Furthermore, SALL3 hypermethylation was associated with expression of TET1, TET2, and DNMT3A genes.

Conclusions

This study suggests that CpG hypermethylation is a likely mechanism of SALL3 gene inactivation, supporting the hypothesis that the SALL3 gene may play a role in the tumorigenesis of HNSCC and may serve as an important biomarker.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-017-0363-1) contains supplementary material, which is available to authorized users.

Systematic analysis of copy number variants of a large cohort of orofacial cleft patients identifies candidate genes for orofacial clefts

Orofacial clefts (OFCs) represent a large fraction of human birth defects and are one of the most common phenotypes affected by large copy number variants (CNVs). Due to the limited number of CNV patients in individual centers, CNV analyses of a large number of OFC patients are challenging. The present study analyzed 249 genomic deletions and 226 duplications from a cohort of 312 OFC patients reported in two publicly accessible databases of chromosome imbalance and phenotype in humans, DECIPHER and ECARUCA. Genomic regions deleted or duplicated in multiple patients were identified, and genes in these overlapping CNVs were prioritized based on the number of genes encompassed by the region and gene expression in embryonic mouse palate. Our analyses of these overlapping CNVs identified two genes known to be causative for human OFCs, SATB2 and MEIS2, and 12 genes (DGCR6, FGF2, FRZB, LETM1, MAPK3, SPRY1, THBS1, TSHZ1, TTC28, TULP4, WHSC1, WHSC2) that are associated with OFC or orofacial development. Additionally, we report 34 deleted and 24 duplicated genes that have not previously been associated with OFCs but are associated with the BMP, MAPK and RAC1 pathways. Statistical analyses show that the high number of overlapping CNVs is not due to random occurrence. The identified genes are not located in highly variable genomic regions in healthy populations and are significantly enriched for genes that are involved in orofacial development. In summary, we report a CNV analysis pipeline of a large cohort of OFC patients and identify novel candidate OFC genes.

Central hypogonadotropic hypogonadism: genetic complexity of a complex disease

Central hypogonadotropic hypogonadism (CHH) is an emerging pathological condition frequently associated with overweight, metabolic syndrome, diabetes, and midline defects. The genetic mechanisms involve mutations in at least twenty-four genes regulating GnRH neuronal migration, secretion, and activity. So far, the mechanisms underlying CHH, both in prepubertal and in adulthood onset forms, remain unknown in most of the cases. Indeed, all detected gene variants may explain a small proportion of the affected patients (43%), indicating that other genes or epigenetic mechanisms are involved in the onset of CHH. The aim of this review is to summarize the current knowledge on genetic background of CHH, organizing the large amount of data present in the literature in a clear and concise manner, to produce a useful guide available for researchers and clinicians.

Narrowing the critical region for congenital vertical talus in patients with interstitial 18q deletions

Interstitial deletions of 18q lead to a number of phenotypic features, including multiple types of foot deformities. Many of these associated phenotypes have had their critical regions narrowly defined. Here we report on three patients with small overlapping deletions of chromosome 18q determined by microarray analysis (chr18:72493281-73512553 hg19 coordinates). All of the patients have congenital vertical talus (CVT). Based on these findings and previous reports in the literature and databases, we narrow the critical region for CVT to a minimum of five genes (ZNF407, ZADH2, TSHZ1, C18orf62, and ZNF516), and propose that TSHZ1 is the likely causative gene for CVT in 18q deletion syndrome.

Chromosome 18q-syndrome and 1p terminal duplication in a patient with bilateral vesico-ureteral reflux: case report and literature revision

Background

Vesico-ureteral reflux (VUR) is a dynamic event in which a retrograde flow of urine is present into the upper tracts. VUR may occur isolated or in association with other congenital abnormalities or as part of syndromic entities. We present a patient with a bilateral primary VUR, syndromic disease caused by a large deletion of 18q (18q21.3-qter) and terminal duplication of 1p (1p36.32-p36.33).

Case report

The patient was 8 years old female with a disease including moderate growth retardation, psychomotor retardation, facial dysmorphism, single umbilical artery, umbilical hernia, urachal remnant, bilateral congenital clubfeet and renal-urinary disease. Chromosomal analysis and Array-CGH revealed two heterozygous chromosomal rearrangements: 1p terminal duplication and de novo 18q terminal deletion. She referred to our clinic to evaluation of bilateral hydronephrosis and right renal cortex thinning. Voiding cystourethrography demonstrated bilateral grade IV VUR and dimercaptosuccinic acid renal scintigraphy confirmed right renal cortex thinning and showed a cortical uptake of 75% of the left kidney and 25% of the right kidney. The patient underwent ureterovesical reimplantation after failure of 3 endoscopic submeatal Deflux injections with VUR resolution.

Conclusions

This is the first report involving a patient with 18q-syndrome and contemporary presence of 1p chromosomal terminal duplication. The coexistence of two chromosomal rearrangements complicates the clinical picture and creates a chimeric disorder (marked by characteristics of both chromosomal anomalies). Kidney problems, primarily VUR is reported in 15% of patients affected by 18-q syndrome and no cases is reported in the literature regarding a correlation between VUR and 1p36 chromosomal duplication.

Aberrant methylation and downregulation of sall3 in human hepatocellular carcinoma

AIM: To investigated whether sall3 transcription was regulated by promoter CpG island hypermethylation in hepatocellular carcinoma (HCC).

METHODS: The cell lines Huh7, HepG2, SK-HEP1, SMMC7721, Bel7402, QGY7703 and a cohort of 38 HCC tissue specimens and corresponding nontumorous tissues were subjected to analysis for sall3 promoter CpG island methylation and mRNA transcription. sall3 promoter CpG island methylation levels were determined using the MassARRAY platform and mRNA transcription levels of the gene were detected by quantitative real-time polymerase chain reaction.

RESULTS: The levels of sall3 mRNA were decreased by more than twofold in 33 of 38 tumor tissues compared to adjacent noncancerous tissues. Among these 33 tumor tissues with lower levels of sall3 mRNA, 24 showed higher levels of methylation. Based on these results, we hypothesized that the decrease in sall3 mRNA transcription level was likely due to promoter CpG island hypermethylation. Changes in sall3 mRNA transcription and promoter CpG island methylation were determined in the above six cell lines after treatment with 0, 0.1, 0.5 and 2.5 μmol 5-aza-2-deoxycytidine, a demethylating agent. Promoter CpG island methylation levels decreased in a dose-dependent manner in all six cell lines, while the mRNA transcription level increased dose-dependently in Huh7, HepG2, SK-HEP1 and SMMC7721 cells and irregularly in Bel7402 and QGY7703 cells.

CONCLUSION: These results indicated that promoter CpG island hypermethylation contributes to the downregulation of sall3 mRNA transcription in HCC.

Familial 4.8 MB deletion on 18q23 associated with growth hormone insufficiency and phenotypic variability

The deletion of the long arm of chromosome 18 causes a contiguous gene deletion syndrome with a highly variable phenotype, usually related to the extent of the deleted region. The most commonly reported clinical features include: decreased growth, microcephaly, facial abnormalities, hypotonia, developmental delay, intellectual disability, congenital aural atresia with hearing impairment and limb anomalies. Here we report on a familial terminal deletion of 18q23 region transmitted from a mother to two daughters, resulting in a remarkable phenotypic variability. The deletion was first detected by conventional cytogenetic analysis in one daughter and subsequently characterized using fluorescence in situ hybridization (FISH) and array-CGH. FISH analysis using subtelomeric 18p and 18q probes confirmed the 18qter deletion in the three patients, and FISH with a whole chromosome painting probe specific for chromosome 18 excluded rearrangements with other chromosomes. Array-CGH analysis allowed us to precisely define the extent of the deletion, which spans 4.8 Mb from 71,236,891 to 76,093,303 genomic positions and includes GALR1 and MBP genes, among others. High-resolution analysis of the deletion, besides a detailed clinical assessment, has provided important data for phenotype-genotype correlation and genetic counseling in this family. Furthermore, this study adds valuable information for phenotype-genotype correlation in 18q- syndrome and might facilitate future search for candidate genes involved in each phenotypic trait.

Oculoauriculovertebral spectrum with a full range of severe clinical manifestations--case report

Oculoauriculovertebral spectrum (OAVS) is a rare congenital malformation consisting of epibulbar dermoids, lid colobomas, auricular deformities, hypoplasia of the soft and bony tissues of the face, associated oral deformities and vertebral anomalies. This report presents a child with a choroid of the right eye, coloboma of the upper eyelid, epibulbar dermoid of the left eye, mandibular hypoplasia, facial asymmetry, bilateral complete cleft lip and palate, hypoplasia of the left alar cartilage, appendage of the left nose, butterfly vertebral defects of Th-1, Th-2 and abnormality of rib XI. Widened sulci of frontal and parietal lobes, bilateral white matter density decrease and calcifications of falx cerebelli were noted. Axial hypotony and delayed psycho-motor development were apparent. This rare case presents a range of severe clinical manifestations of oculoauriculovertebral spectrum. Despite a normal cervical vertebral column, tracheostenosis was present. It caused difficulties in tracheal intubation, creating the need for a tracheostomy, and death after a failed attempt at decannulation. This case indicates that in patients with clinical manifestations including cerebral anomalies, a risk of respiratory insufficiency should be always taken under consideration, when planning surgery.

Rare and frequent promoter methylation, respectively, of TSHZ2 and 3 genes that are both downregulated in expression in breast and prostate cancers

Background

Neoplastic cells harbor both hypomethylated and hypermethylated regions of DNA. Whereas hypomethylation is found mainly in repeat sequences, regional hypermethylation has been linked to the transcriptional silencing of certain tumor suppressor genes. We attempted to search for candidate genes involved in breast/prostate carcinogenesis, using the criteria that they should be expressed in primary cultures of normal breast/prostate epithelial cells but are frequently downregulated in breast/prostate cancer cell lines and that their promoters are hypermethylated.

Methodology/Principal Findings

We identified several dozens of candidates among 194 homeobox and related genes using Systematic Multiplex RT-PCR and among 23,000 known genes and 23,000 other expressed sequences in the human genome by DNA microarray hybridization. An additional examination, by real-time qRT-PCR of clinical specimens of breast cancer, further narrowed the list of the candidates. Among them, the most frequently downregulated genes in tumors were NP_775756 and ZNF537, from the homeobox gene search and the genome-wide search, respectively. To our surprise, we later discovered that these genes belong to the same gene family, the 3-member Teashirt family, bearing the new names of TSHZ2 and TSHZ3. We subsequently determined the methylation status of their gene promoters. The TSHZ3 gene promoter was found to be methylated in all the breast/prostate cancer cell lines and some of the breast cancer clinical specimens analyzed. The TSHZ2 gene promoter, on the other hand, was unmethylated except for the MDA-MB-231 breast cancer cell line. The TSHZ1 gene was always expressed, and its promoter was unmethylated in all cases.

Conclusions/Significance

TSHZ2 and TSHZ3 genes turned out to be the most interesting candidates for novel tumor suppressor genes. Expression of both genes is downregulated. However, differential promoter methylation suggests the existence of distinctive mechanisms of transcriptional inactivation for these genes.

Mosaic ring chromosome 18, ring chromosome 18 duplication/deletion and disomy 18: perinatal findings and molecular cytogenetic characterization by fluorescence in situ hybridization and array comparative genomic hybridization

OBJECTIVE

To present the perinatal findings and molecular cytogenetic analysis of a rare chromosomal abnormality involving structural and numerical abnormalities of chromosome 18.

MATERIALS, METHODS AND RESULTS

A 36-year-old woman, gravida 5, para 3, underwent amniocentesis because of her advanced maternal age. Amniocentesis revealed a karyotype of 46,XY,r(18) [27]/45,XY,-18[5]/46,XY[5]. The parents decided to continue the pregnancy. Level II ultrasound revealed ventriculomegaly. At 38 weeks of gestation, a 3,725 g male fetus was delivered. The fetus had microcephaly, hypertelorism, epicanthal folds, cleft palate, a broad flat nose, simian creases, broad hands, tapered fingers, clubfeet, micropenis, a sacral dimple, hypotonia, ventriculomegaly, and a ventricular septal defect. The peripheral blood lymphocytes revealed a karyotype of 46,XY,r(18)[81]/45,XY,-18[3]/46,XY,idic r(18)[3]/46,XY[13]. Fluorescence in situ hybridization using chromosome 18 centromeric probe (cep18) and subtelomeric (18pter, 18qter) identified four types of cells, r(18), idic r(18), monosomy 18, and disomy 18. Array comparative genomic hybridization analysis of the blood demonstrated a 14.9-Mb deletion at chromosome 18p [arr cgh 18p11.32p11.21 (0-14,941,330)× 1] and a 29.6-Mb deletion at chromosome 18q [arr cgh 18q21.2q23 (46,533,430-76,117,153) × 1]. The proband's karyotype was 46,XY,r(18)(p11.21q21.2)[81]/45,XY,-18[3]/46,XY,idic r(18)(p11.21q21.2;p11.21q21.2)[3]/46,XY[13].

CONCLUSION

Array comparative genomic hybridization is useful to determine the breakpoints of a ring chromosome, particularly in cases where the ring chromosome comprises the majority of the mosaicism.

A classification and construction of congenital lateral facial clefts

BACKGROUND

The repair of the lateral or transverse facial cleft is a surgical challenge on the account of the abnormal positioning and appearance of the cleft.

MATERIALS AND METHODS

Over a twenty-seven year period, 22 lateral facial cleft cases were evaluated at a cleft lip (CL) and palate clinic and seven children underwent reconstruction of the lateral CL.

RESULTS

Twenty-two of 3187 (0.69%) cases presented with a lateral CL. Five of these 22 cases (23%) had a bilateral, eight (36%) had a right-sided and nine (41%) had a left-sided cleft. The evaluation of these cases resulted in a new classification (namely an extension of the Tessier 7 cleft) classification for the cutaneous and muscle involvement: a superior (T7.1), middle (T7.2), inferior (T7.3) and agenetic (T7.4) lateral CL. The altered surgical construction: an internal mucosal straight-line closure, a curved cutaneous-mucosal red-lip/vermilion-lined flap for the lip commissure, muscle reconstruction at the modiolus and a positional cutaneous z-plasty for the rare lateral cutaneous cleft.

CONCLUSION

The paper introduced a new classification for the lateral CL, as well as an altered surgical reconstructive technique for the most natural functioning of the lateral part of the face.