<p>Chromothripsis and corresponding cancer gene amplifications and losses. <b>A,</b> Representative Circos plots of SVs and CNAs across the genome by WGS. Outer band shows an ideogram of chromosome positions and cytogenetic bands. Second band depicts total CN, and third band shows minor allele CN. The inner circle depicts SVs as arcs connecting the two relevant genomic points as identified by three algorithms (see “Methods”). CNAs in key cancer genes in the regions of chromothripsis (red, amplifications; blue, deletions) are displayed. Circos plots for all cases are shown in Supplementary Fig. S6. <b>B,</b> CN log ratio plots from the FACETS algorithm displaying the distinctive oscillating CN states on chromosomes with chromothripsis. CN segments are shown in red. Focal segments (<2 MB in size) are shown as enlarged points for visual purposes. Selected amplifications are indicated (yellow). <b>C,</b> Summary of chromosomal location of chromothriptic events in cases analyzed by WGS and tNGS. Also shown are selected amplifications and losses in oncogenes and tumor suppressors, respectively, localized to the chromothriptic chromosomes. Full list is provided in Supplementary Table S7. <b>D,</b> Schematic summary for the rate of major genomic mechanisms detected in the set analyzed by WGS (<i>n</i> = 11) and in the full cohort (<i>n</i> = 20). In the lower diagram, major chromosomes involved by chromothripsis are indicated in the inner doughnut, and corresponding recurrent gene amplifications are indicated in the outer doughnut. <b>E,</b> Total number of SVs identified in samples analyzed by WGS. Variants are color-coded by type. <b>F,</b> Number of fusions predicted in samples with available RNA-seq. <b>G,</b> Diagram illustrating putative enhancer hijacking in case A17 with chromothripsis on chromosome 2 resulting in translocation between <i>SH3RF3</i> on chromosome 2 and upstream regulatory region of <i>CCND1</i> on chromosome 11. Epigenetic landscape surrounding the breakpoint was extrapolated from data from multiple tissue types (Epilogos search tool). ChrT, chromothripsis.</p>
Abstract Primary open-angle glaucoma (POAG), the leading cause of irreversible blindness worldwide, disproportionately affects African Americans. Large-scale POAG genetic studies have focused on individuals of European and Asian ancestry, limiting our understanding of disease biology. Here we report genetic analysis of the largest-ever deeply phenotyped African American population (n=5950), identifying a novel POAG-associated SNP on chromosome 11 near the TRIM66 gene (rs112369934). POAG trait association also implicated SNPs in genes involved in trabecular meshwork homeostasis and retinal ganglion cell maintenance. These new loci deepen our understanding of the pathophysiology of POAG in African Americans.
Age-related macular degeneration (AMD) predominantly affects the retina and retinal pigment epithelium in the posterior eye. While there are numerous studies investigating the non-coding transcriptome of retina and RPE, few significant differences between AMD and normal tissues have been reported. Strand specific RNA sequencing of both peripheral retina (PR) and RPE-Choroid-Sclera (PRCS), in both AMD and matched normal controls were generated. The transcriptome analysis reveals a highly significant and consistent impact on anti-sense transcription as well as moderate changes in the regulation of non-coding (sense) RNA. Hundreds of genes that do not express anti-sense transcripts in normal PR and PRCS demonstrate significant anti-sense expression in AMD in all patient samples. Several pathways are highly enriched in the upregulated anti-sense transcripts-in particular the EIF2 signaling pathway. These results call for a deeper exploration into anti-sense and noncoding RNA regulation in AMD and their potential as therapeutic targets.
PURPOSE Ewing sarcoma (ES) is a primitive sarcoma defined by EWSR1-ETS fusions as the primary driver alteration. To better define the landscape of cooperating secondary genetic alterations in ES, we analyzed clinical genomic profiling data of 113 patients with ES, a cohort including more adult patients (> 18 years) and more patients with advanced stage at presentation than previous genomic cohorts. METHODS The data set consisted of patients with ES prospectively tested with the US Food and Drug Administration–cleared Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets large panel, hybrid capture-based next-generation sequencing assay. To assess the functional significance of ERF loss, we generated ES cell lines with increased expression of ERF and lines with knockdown of ERF. We assessed cell viability, clonogenic growth, and motility in these ES lines and performed transcriptomic and epigenetic analyses. Finally, we validated our findings in vivo using cell line xenografts. RESULTS Novel subsets were defined by recurrent secondary alterations in ERF, which encodes an ETS domain transcriptional repressor, in 7% of patients (five truncating mutations, one deep deletion, and two missense mutations) and in FGFR1 in another 2.7% (one amplification and two known activating mutations). ERF alterations were nonoverlapping with STAG2 alterations. In vitro, increased expression of ERF decreased tumor cell growth, colony formation, and motility in two ES cell lines, whereas ERF loss induced cellular proliferation and clonogenic growth. Transcriptomic analysis of cell lines with ERF loss revealed an increased expression of genes and pathways associated with aggressive tumor biology, and epigenetic, chromatin-based studies revealed that ERF competes with EWSR1-FLI1 at ETS-binding sites. CONCLUSION Our findings open avenues to new insights into ES pathobiology and to novel therapeutic approaches in a subset of patients with ES.
<div>AbstractPurpose:<p>Desmoplastic small round cell tumor (DSRCT) is a highly lethal intra-abdominal sarcoma of adolescents and young adults. DSRCT harbors a t(11;22)(p13:q12) that generates the EWSR1-WT1 chimeric transcription factor, the key oncogenic driver of DSRCT. EWSR1-WT1 rewires global gene expression networks and activates aberrant expression of targets that together mediate oncogenesis. EWSR1-WT1 also activates a neural gene expression program.</p>Experimental Design:<p>Among these neural markers, we found prominent expression of neurotrophic tyrosine kinase receptor 3 (NTRK3), a druggable receptor tyrosine kinase. We investigated the regulation of NTRK3 by EWSR1-WT1 and its potential as a therapeutic target <i>in vitro</i> and <i>in vivo</i>, the latter using novel patient-derived models of DSRCT.</p>Results:<p>We found that EWSR1-WT1 binds upstream of <i>NTRK3</i> and activates its transcription. NTRK3 mRNA is highly expressed in DSRCT compared with other major chimeric transcription factor–driven sarcomas and most DSRCTs are strongly immunoreactive for NTRK3 protein. Remarkably, expression of <i>NTRK3</i> kinase domain mRNA in DSRCT is also higher than in cancers with <i>NTRK3</i> fusions. Abrogation of NTRK3 expression by RNAi silencing reduces growth of DSRCT cells and pharmacologic targeting of NTRK3 with entrectinib is effective in both <i>in vitro</i> and <i>in vivo</i> models of DSRCT.</p>Conclusions:<p>Our results indicate that EWSR1-WT1 directly activates NTRK3 expression in DSRCT cells, which are dependent on its expression and activity for growth. Pharmacologic inhibition of NTRK3 by entrectinib significantly reduces growth of DSRCT cells both <i>in vitro</i> and <i>in vivo</i>, providing a rationale for clinical evaluation of NTRK3 as a therapeutic target in DSRCT.</p></div>
e16070 Background: Intestinal dysbiosis has been hypothesized as a possible etiology of the increasing incidence of early-onset colon cancer (EO-CC). Here, we compare the microbiome signature in nonmetastatic, microsatellite stable (MSS) EO-CC to average-onset colon cancer (AO-CC). Methods: Specimens from patients with resected stage I-III MSS colon cancer from 2014-2019 were sequenced by MSK-IMPACT, a large panel next generation sequencing (NGS) assay. A validated technique using non-human read sequences from NGS analysis was used to identify the microbial species in tumor tissue. The tumor microbial alpha diversity and differentially abundant microbiome were compared between patients younger than 40 years (EO-CC) with those older than 60 years (AO-CC). Results: Of 275 patients with MSS, 24 (mean 33.6, range 24-39) and 114 patients (mean 70, range 61-90) had EO-CC and AO-CC, respectively. There was no significant difference in clinicopathological features including gender, tumor stage and neoadjuvant treatment between the two groups. EO-CC was more likely to present with left sided disease compared to AO-CC (81% vs. 45%, p = 0.001). There was no significant difference in the tumor microbial diversity (alpha diversity) between the EO-CC and AO-CC (p Shannon = 0.95). Although there was a relative abundance of microbial species from bacterial phylum such as Actinobacteria, Deinococcus-Thermus, α-proteobacteria, γ-proteobacteria and δ-proteobacteria in EO-CC compared to AO-CC, this difference was not significant after controlling for multiple comparisons (Table). Conclusions: Our analysis did not reveal a significant difference between EO-CC and AO-CC in both the abundance and diversity of tumor microbial species, suggesting intestinal dysbiosis may not be a major driver in early onset colorectal cancer pathogenesis. However, additional studies with a larger sample size are warranted for further analysis and subgroup comparison. [Table: see text]
Abstract Circulating cell-free DNA (cfDNA) from blood plasma of cancer patients can be used to interrogate somatic tumor alterations non-invasively or when adequate tissue is unavailable. We have developed and clinically implemented MSK-ACCESS (Analysis of Circulating cfDNA to Evaluate Somatic Status), an NGS assay for detection of very low frequency somatic alterations in select exons and introns of 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 98% for a priori mutation profiling. To evaluate the performance and utility of MSK-ACCESS, we report results from the first 681 prospective blood samples (617 patients) that underwent clinical analysis to guide patient management. Somatic mutations, copy number, and/or structural variants were detected in 73% of the samples, and 56% of these circulating-tumor DNA (ctDNA) positive samples had clinically actionable alterations. The utilization of matched white blood cell sequencing allowed retention of somatic alterations while filtering out over 10,000 germline and clonal hematopoiesis variants, thereby greatly enhancing the specificity of the assay. Taken together, our experience illustrates the importance of analyzing a matched normal sample when interpreting cfDNA results and highlights the potential of cfDNA profiling to guide treatment selection, monitor treatment response, and identify mechanisms of treatment resistance.
