Upregulation of Human Endogenous Retrovirus-K (HML-2) mRNAs in hepatoblastoma: Identification of potential new immunotherapeutic targets and biomarkers

PurposeHepatoblastoma is the most common liver malignancy in children. In order to advance therapy against hepatoblastoma, novel immunologic targets and biomarkers are needed. Our purpose in this investigation is to examine hepatoblastoma transcriptomes for the expression of a class of genomic elements known as Human Endogenous Retrovirus (HERVs). HERVs are abundant in the human genome and are biologically active elements that have been associated with multiple malignancies and proposed as immunologic targets in a subset of tumors. A sub-family of HERVs, HERV-K (HML-2), have been shown to be tightly regulated in fetal development, making investigation of these elements in pediatric tumors paramount.MethodsWe first created a HERVK-FASTA file utilizing 91 previously described HML-2 proviruses. We then concatenated the file onto the GRCh38.95 cDNA library from Ensembl. We used this computational tool to evaluate existing RNA-seq data from 10 hepatoblastoma tumors and 3 normal liver controls (GEO accession ID: GSE89775). Quantification and differential proviral expression analysis between hepatoblastoma and normal liver controls was performed using the pseudo-alignment program Salmon and DESeq2, respectively.ResultsHERV-K mRNA was expressed in hepatoblastoma from multiple proviral loci. All HERV-K proviral loci were expressed at higher levels in hepatoblastoma compared to normal liver controls. Five HERV-K proviruses (1q21.3, 3q27.2, 7q22.2, 12q24.33 and 17p13.1) were significantly differentially expressed (p-adjusted value < 0.05, |log2 fold change| > 1.5) across conditions. The provirus at 17p13.1 had an approximately 300-fold increased expression in hepatoblastoma as compared to normal liver. This was in part due to the near absence of HERV-K mRNA at the 17p13.1 locus in fully differentiated liver samples.ConclusionsOur investigation demonstrates that HERV-K is expressed from multiple loci in hepatoblastoma and that the expression is increased from several proviruses as compared to normal liver controls. Our results suggest that HERV-K mRNA expression may find use as a biomarker in hepatoblastoma, given the large differential expression profiles in hepatoblastoma, with very low mRNA levels in liver control samples.

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequence. We describe progressive extensions to Cactus that enable reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We show that Cactus is capable of scaling to hundreds of genomes and beyond by describing results from an alignment of over 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment yet created. Further, we show improvements in orthology resolution leading to downstream improvements in annotation.

The method of the examination of dangerous structures and rehabilitationof their robustness

There are a variety of methods concerning the examination of dangerous structures and rehabilitation of their robustness. One of the methods is uplifting and alignment of buildings with the use of hydraulic jack. Development of the uplift and alignment program is possible if there is a data, which is to be received both before the beginning of the uplift and during the process of recovery of spatial geometry of the building. The development of the uplift and alignment program automatically controls the speed rate of the hydraulic system. The suggested method enables an accurate control of a vertical reach and provides the minimal overload on deformable footing and structure of the building during its uplift and alignment.