Genome-wide transcriptional reorganization associated with senescence-to-immortality switch during human hepatocellular carcinogenesis.

Senescence is a permanent proliferation arrest in response to cell stress such as DNA damage. It contributes strongly to tissue aging and serves as a major barrier against tumor development. Most tumor cells are believed to bypass the senescence barrier (become "immortal") by inactivating growth control genes such as TP53 and CDKN2A. They also reactivate telomerase reverse transcriptase. Senescence-to-immortality transition is accompanied by major phenotypic and biochemical changes mediated by genome-wide transcriptional modifications. This appears to happen during hepatocellular carcinoma (HCC) development in patients with liver cirrhosis, however, the accompanying transcriptional changes are virtually unknown. We investigated genome-wide transcriptional changes related to the senescence-to-immortality switch during hepatocellular carcinogenesis. Initially, we performed transcriptome analysis of senescent and immortal clones of Huh7 HCC cell line, and identified genes with significant differential expression to establish a senescence-related gene list. Through the analysis of senescence-related gene expression in different liver tissues we showed that cirrhosis and HCC display expression patterns compatible with senescent and immortal phenotypes, respectively; dysplasia being a transitional state. Gene set enrichment analysis revealed that cirrhosis/senescence-associated genes were preferentially expressed in non-tumor tissues, less malignant tumors, and differentiated or senescent cells. In contrast, HCC/immortality genes were up-regulated in tumor tissues, or more malignant tumors and progenitor cells. In HCC tumors and immortal cells genes involved in DNA repair, cell cycle, telomere extension and branched chain amino acid metabolism were up-regulated, whereas genes involved in cell signaling, as well as in drug, lipid, retinoid and glycolytic metabolism were down-regulated. Based on these distinctive gene expression features we developed a 15-gene hepatocellular immortality signature test that discriminated HCC from cirrhosis with high accuracy. Our findings demonstrate that senescence bypass plays a central role in hepatocellular carcinogenesis engendering systematic changes in the transcription of genes regulating DNA repair, proliferation, differentiation and metabolism.

A novel approach for small sample size family-based association studies: sequential tests.

In this paper, we propose a sequential probability ratio test (SPRT) to overcome the problem of limited samples in studies related to complex genetic diseases. The results of this novel approach are compared with the ones obtained from the traditional transmission disequilibrium test (TDT) on simulated data. Although TDT classifies single-nucleotide polymorphisms (SNPs) to only two groups (SNPs associated with the disease and the others), SPRT has the flexibility of assigning SNPs to a third group, that is, those for which we do not have enough evidence and should keep sampling. It is shown that SPRT results in smaller ratios of false positives and negatives, as well as better accuracy and sensitivity values for classifying SNPs when compared with TDT. By using SPRT, data with small sample size become usable for an accurate association analysis.

Effects of tonsillectomy on speech spectrum.

Changes in the speech spectrum of vowels and consonants before and after tonsillectomy were investigated to find out the impact of the operation on speech quality. Speech recordings obtained from patients were analyzed using the Kay Elemetrics, Multi-Dimensional Voice Processing (MDVP Advanced) software. Examination of the time-course changes after the operation revealed that certain speech parameters changed. These changes were mainly F3 (formant center frequency) and B3 (formant bandwidth) for the vowel /o/ and a slight decrease in B1 and B2 for the vowel /a/. The noise-to-harmonic ratio (NHR) also decreased slightly, suggesting less nasalized vowels. It was also observed that the fricative, glottal consonant /h/ has been affected. The larger the tonsil had been, the more changes were seen in the speech spectrum. The changes in the speech characteristics (except F3 and B3 for the vowel /o/) tended to recover, suggesting an involvement of auditory feedback and/or replacement of a new soft tissue with the tonsils. Although the changes were minimal and, therefore, have little effect on the extracted acoustic parameters, they cannot be disregarded for those relying on their voice for professional reasons, that is, singers, professional speakers, and so forth.