Genetic mosaicism at the insulin locus in liver associated with childhood hepatoblastoma

A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers

Mounting evidence supports the idea that transcriptional patterns serve as more specific identifiers of active enhancers than histone marks; however, the optimal strategy to identify active enhancers both experimentally and computationally has not been determined. Here, we compared 13 genome-wide RNA sequencing assays in K562 cells and showed that the nuclear run-on followed by cap-selection assay (GRO/PRO-cap) has advantages in eRNA detection and active enhancer identification. We also introduced a tool, Peak Identifier for Nascent Transcript Starts (PINTS), to identify active promoters and enhancers genome-wide and pinpoint the precise location of the 5′ transcription start sites. Finally, we compiled a comprehensive enhancer candidate compendium based on the detected eRNA TSSs available in 120 cell and tissue types that can be accessed at https://pints.yulab.org. With the knowledge of the best available assays and pipelines, this large-scale annotation of candidate enhancers will pave the way for selection and characterization of their functions in a time- and labor-efficient manner in the future.

An 8-cM interstitial deletion on 4q21-q22 in DNA from an infant with hepatoblastoma overlaps with a commonly deleted region in adult liver cancers

We performed molecular analysis of a germline interstitial deletion of chromosome 4 [del(4)(q21.22q23)], which had been observed in a male infant manifesting early-onset hepatoblastoma (HBL). The chromosomal anomaly in this child was associated with a unique congenital syndrome including HBL, atrial septal defect, ventricular septal defect, patent ductus arteriosus, mental retardation, and seizures. However, the patient did not exhibit a megalencephaly typical of 4q21-22 deletions. His HBL was associated with an increasing serum alpha-fetoprotein level and rapid growth. To define the chromosomal deletion at the molecular level in this child, we analyzed his lymphoblasts with fluorescence in situ hybridization, using as probes a panel of BAC/PAC genomic clones containing STS markers covering the 4q12-27 region. The analysis revealed that the affected chromosome had an 8-cM deletion within 4q21-q22, flanked by markers D4S2964 and D4S2966. This microdeletion overlaps with the commonly deleted region at 4q21-q22 that was recently defined in adult hepatocellular carcinomas.

Analysis of CDKN2A, CDKN2B, CDKN2C, and cyclin Ds gene status in hepatoblastoma

The status and the expression of cyclin-dependent kinase inhibitor A (CDKN2A) family genes, named CDKN2A, CDKN2B, and CDKN2C and of cyclin Ds (D1, D2, and D3) genes were investigated in 14 cases of human hepatoblastomas. These genes were selected because: 1) CDKN2A and CDKN2B are very frequently inactivated in human cancers; 2) cyclin Ds are overexpressed in several tumors and 3) CDKN2A is posttranscriptionally silenced in hepatocellular carcinomas. Structural analysis of the CDKN2A, CDKN2B, and CDKN2C genes in hepatoblastoma cases showed the absence of deletions and/or point mutations. Moreover, a detailed investigation of loss of heterozygosity at 9p21 and 1p32 (the chromosomal regions where CDKN2A genes are located) rules out the possible loss of one allele. Messenger RNA (mRNA) analysis showed that CDKN2C is expressed in all hepatoblastoma samples studied, while both CDKN2A and CDKN2B genes are not transcribed in the cancer specimens as well as in the matched normal liver tissues. Interestingly, an alternative mRNA expressed by the CDKN2A gene (beta-transcript) is detectable in 100% of the samples investigated. The analysis of cyclin D genes expression revealed that cyclin D1 is highly transcribed in normal hepatic tissue while cyclin D2 or D3 genes were extensively expressed in the matched transformed samples. Investigation at protein level confirmed the data obtained on RNA analysis. Indeed, p16INK4A and p15INK4B (products of expression of CDKN2A and CDKN2B respectively) were not observable while pl8INK4C (which is codified by CDKN2C) was clearly detectable in the samples analyzed. Moreover, a noticeable decrease of cyclin D1 content and increase of cyclin D3 level were observable in tumor tissues versus normal counterparts. Our findings demonstrated the following: 1) CDKN2A, CDKN2B, and CDKN2C genes are structurally unmodified in human hepatoblastoma, and 2) CDKN2A (alpha-transcript) and CDKN2B are transcriptionally silenced in normal liver whereas CDKN2A (beta-transcript) and CDKN2C were clearly expressed. Finally, a clear shift in cyclin D type expression was observable during malignant transformation. These results show that CDKN2A gene family alterations are not involved in hepatoblastoma development, whereas changes in cyclin D types might play a role in this type of tumor. Furthermore, a highly regulated expression of CDKN2A seems to occur in normal hepatic tissue.

Hepatic malignancies in childhood and adolescence (hepatoblastoma, hepatocellular carcinoma, and embryonal sarcoma)

Hepatoblastoma is the most common malignant liver tumor of childhood. Clinical trials have demonstrated its responsiveness to chemotherapy, especially with platinum-based chemotherapeutic agents. In patients with completely resected tumors, recurrent disease is effectively controlled by adjuvant chemotherapy. In patients with initially unresectable tumors, chemotherapy can induce tumor shrinkage sufficient to allow complete extirpation of tumor and also to prevent recurrent disease. The child with tumor resistant to primary therapy or with recurrent disease presents a special problem requiring individualized and innovative therapies, including consideration of orthotopic liver transplant. Hepatocellular carcinoma in children and adolescents carries a much poorer prognosis compared to hepatoblastoma. Complete resection of tumor offers the only hope of cure, but these tumors are unfortunately resistant or partially resistant to conventional doses of chemotherapy. A number of innovative treatment strategies have been employed, but optimal treatment remains elusive. Transplant for tumor localized to the liver may offer the only hope of cure. Embryonal (undifferentiated) sarcoma of the liver is a rare tumor that has not been studied prospectively in any clinical trial. Small published series indicate that it can be responsive to chemotherapy, and cure may be possible.

Hepatoblastoma in children: a review

The past 25 years have seen a dramatic improvement in results of treatment of children with HBL; formerly, < 25% were cured, and today, 65 to 75% may be cured. New, active agents are still needed, and the late effects of therapy, especially on the heart and kidneys, remain a concern. Nevertheless, it is clear that treatment of HBL is indeed "a bit of a success story" (42).