Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing.

A modified version of the PGDx elioTM Plasma Resolve assay was validated as a laboratory-developed test (LDT) for clinical use in the Molecular Diagnostics Laboratory at Fox Chase Cancer Center. The test detects single nucleotide variants (SNVs) and small insertions and deletions (indels) in 33 target genes using fragmented genomic DNA extracted from plasma. The analytical performance of this assay was assessed with reference standard DNA and 29 samples from cancer patients and detected 66 SNVs and 23 indels. Using 50 ng of input DNA, the sensitivity was 95.5% to detect SNVs at 0.5% allele frequency, and the specificity was 92.3%. The sensitivity to detect indels at 1% allele frequency was 70.4%. A cutoff of 0.25% variant allele frequency (VAF) was set up for diagnostic reporting. An inter-laboratory study of concordance with an orthologous test resulted in a positive percent agreement (PPA) of 91.7%.

Transcriptomic changes in the prefrontal cortex of rats as a function of age and cognitive engagement.

Although changes in cognitive functions including attention are well documented in aging, the neurobiological basis for such alterations is not fully understood. Increasing evidence points towards the contribution of genetic factors in age-related cognitive decline. However, genetic studies have remained inconsistent in characterizing specific genes that could predict functional decline in aging. Here we utilized next generation RNA sequencing (RNA-seq) to identify patterns of differentially expressed genes in the prefrontal cortex (PFC), a brain region implicated in attention, of young and aged animals that were either cognitively trained or had limited cognitive engagement. Consistent with previous investigations, aging alone was associated with increased expression of genes involved in multiple facets of innate and adaptive immune responses. On the contrary, the expression of immunity-related transcripts was reduced by cognitive engagement. In addition, transcripts across a wide range of cellular processes, including those associated with neuronal remodeling and plasticity, were upregulated by this behavioral manipulation. Surprisingly, aged subjects accounted for higher mean counts of upregulated transcripts and lower mean counts for downregulated transcripts as compared to the young subjects. Because aged rats exhibited lower attentional capacities, it is plausible that transcriptional changes associated with performance in these animals were reflective of compensatory changes that occurred to cope with the declining integrity of PFC functioning. Interestingly, the effects of both aging and cognitive engagement resulted in an upregulation of transcripts linked to extracellular exosomes, suggesting such extracellular vesicles may moderate a reciprocal gene by environment interaction in order to facilitate the reorganization of PFC circuitry and maintain functionality. Taken together, these findings provide novel insights into the capacities of both cognitive engagement as well as aging to alter gene expression in the PFC, and how the effects of such dynamic factors relate to variation in age-related cognitive abilities.

IL27 Signaling Serves as an Immunologic Checkpoint for Innate Cytotoxic Cells to Promote Hepatocellular Carcinoma.

Although inflammatory mechanisms driving hepatocellular carcinoma (HCC) have been proposed, the regulators of anticancer immunity in HCC remain poorly understood. We found that IL27 receptor (IL27R) signaling promotes HCC development in vivo. High IL27EBI3 cytokine or IL27RA expression correlated with poor prognosis for patients with HCC. Loss of IL27R suppressed HCC in vivo in two different models of hepatocarcinogenesis. Mechanistically, IL27R sig-naling within the tumor microenvironment restrains the cytotoxicity of innate cytotoxic lymphocytes. IL27R ablation enhanced their accumulation and activation, whereas depletion or functional impairment of innate cytotoxic cells abrogated the effect of IL27R disruption. Pharmacologic neutralization of IL27 signaling increased infiltration of innate cytotoxic lymphocytes with upregulated cytotoxic molecules and reduced HCC development. Our data reveal an unexpected role of IL27R signaling as an immunologic checkpoint regulating innate cytotoxic lymphocytes and promoting HCC of different etiologies, thus indicating a therapeutic potential for IL27 pathway blockade in HCC. SIGNIFICANCE: HCC, the most common form of liver cancer, is characterized by a poor survival rate and limited treatment options. The discovery of a novel IL27-dependent mechanism controlling anticancer cytotoxic immune response will pave the road for new treatment options for this devastating disease. This article is highlighted in the In This Issue feature, p. 1825.

IL-27 receptor-regulated stress myelopoiesis drives abdominal aortic aneurysm development.

Abdominal aortic aneurysm (AAA) is a prevalent life-threatening disease, where aortic wall degradation is mediated by accumulated immune cells. Although cytokines regulate inflammation within the aorta, their contribution to AAA via distant alterations, particularly in the control of hematopoietic stem cell (HSC) differentiation, remains poorly defined. Here we report a pathogenic role for the interleukin-27 receptor (IL-27R) in AAA, as genetic ablation of IL-27R protects mice from the disease development. Mitigation of AAA is associated with a blunted accumulation of myeloid cells in the aorta due to the attenuation of Angiotensin II (Ang II)-induced HSC expansion. IL-27R signaling is required to induce transcriptional programming to overcome HSC quiescence and increase differentiation and output of mature myeloid cells in response to stress stimuli to promote their accumulation in the diseased aorta. Overall, our studies illuminate how a prominent vascular disease can be distantly driven by a cytokine-dependent regulation of bone marrow precursors.

BRCA1 intronic Alu elements drive gene rearrangements and PARP inhibitor resistance.

BRCA1 mutant carcinomas are sensitive to PARP inhibitor (PARPi) therapy; however, resistance arises. BRCA1 BRCT domain mutant proteins do not fold correctly and are subject to proteasomal degradation, resulting in PARPi sensitivity. In this study, we show that cell lines and patient-derived tumors, with highly disruptive BRCT domain mutations, have readily detectable BRCA1 protein expression, and are able to proliferate in the presence of PARPi. Peptide analyses reveal that chemo-resistant cancers contain residues encoded by BRCA1 intron 15. Mechanistically, cancers with BRCT domain mutations harbor BRCA1 gene breakpoints within or adjacent to Alu elements in intron 15; producing partial gene duplications, inversions and translocations, and terminating transcription prior to the mutation-containing BRCT domain. BRCA1 BRCT domain-deficient protein isoforms avoid mutation-induced proteasomal degradation, support homology-dependent DNA repair, and promote PARPi resistance. Taken together, Alu-mediated BRCA1 gene rearrangements are responsible for generating hypomorphic proteins, and may represent a biomarker of PARPi resistance.

Gene expression pattern and hormonal regulation of small proline-rich protein 2 family members in the female mouse reproductive system during the estrous cycle and pregnancy.

Small proline-rich proteins (SPRR) are known to construct the cornified cell envelope (CE) in the stratified squamous epithelial cell. Their functions in the simple epithelium such as the uterine epithelium are not clear hitherto. In the present study, the mRNA expression patterns of sprr2 family members in the mouse uterus and vagina during the estrous cycle and pregnancy as well as their regulation by steroids were investigated. Using semi-quantitative RT-PCR, it was revealed that the transcripts of sprr2b, 2e and 2g genes were up-regulated in the proestrous and estrous uteri, and sprr2d was up-regulated only in the estrous uterus. In the vagina, transcription of sprr2a, 2b, 2d, 2e and 2k genes were up-regulated at the metestrous stage. Northern blot analysis demonstrated that the overall expression of sprr2 was highly up-regulated in the estrous uterus and the metestrous vagina. During pregnancy, the sprr2 mRNA in the uterus was sharply repressed from day 3 postcoitus on, and began to be induced around labor time. In situ hybridization showed that the sprr2 transcripts were localized in uterine luminal and glandular epithelial cells as well as vaginal stratified epithelial cells. In ovariectomized mice, the expression of sprr2a, 2d, 2e and 2f genes in the uterus were induced by estrogen, and the effect of estrogen on sprr2d and 2e expression could be partly abolished by progesterone. The data indicate that the sprr2 genes have unique regulation patterns in different reproductive tissues under different physiological conditions, and the encoded proteins might play diverse functions in the female reproductive system.

Determination of genes involved in the early process of embryonic implantation in rhesus monkey (Macaca mulatta) by suppression subtractive hybridization.

Embryonic implantation is a temporally and spatially restricted process that involves a precise cross talk between the embryo and the receptive maternal endometrium. Underlying the complex changes in the uterus during implantation is the alteration in gene expression pattern, which is not fully understood for the primates. In the present study, suppression subtractive hybridization (SSH) was performed to screen genes that were differentially expressed in the implantation site of the pregnant rhesus monkey, and a subtractive cDNA library was constructed. Furthermore, with dot blot analysis, reverse Northern blot analysis, and semiquantitative reverse transcription-polymerase chain reaction, 76 of 376 clones randomly selected from the library were proven to be differentially expressed in the implantation site. With DNA sequencing and BLAST analysis against the GenBank/EMBL database, it was demonstrated that the cDNA fragments carried by 73 clones shared high homology with 31 human genes. Among them, 15 positive clones represented the S100A10 gene and 10 positive ones corresponded with the secreted frizzled-related protein 4 gene. The other two clones shared homology with one human EST. There was one clone homologous to a human DNA sequence, which indicated that it might be a novel gene. To our knowledge, this is the first report to determine genes involved in the early implantation stage in the rhesus monkey with high throughput technology.