Aldh expressing stem cells mediate tumor initiation and metastasis in triple negative breast cancers across different ethnicities

TNBC is the only subtype of breast cancer for which there are no approved targeted therapies. In the US, its incidence is highest in women with African ancestry (AA); in western sub-Saharan Africa, single-institution studies show that TNBC constitutes 40- 80% of all breast cancers. Given the Caucasian/AA survival disparity in breast cancer, there is an urgent need to find actionable targets in TNBC of all ethnicities, but especially in TNBC in AA, which are suspected to be more aggressive. Breast cancer stem cells, the small population of cells that have been shown to mediate breast tumor initiation, metastasis, and resistance to conventional therapy have also been reported to mediate the heterogeneity of TNBC and are especially abundant in TNBC in AA women. Here, we sought to better understand the biology of TNBC by finding genes and pathways that are differentially expressed in the stem cell population of patient derived xenografts (PDX) from TNBC from Ghanaian (G), AA and Caucasian (C) women and the effect of these differentially expressed genes on the stem cell phenotype in these primary tumors. We isolated the ALDH+ and the CD44+/CD24- stem cell populations from the bulk cells from 15 PDXs using flow cytometry. We performed RNA sequencing (Illumina HiSeq platform) on the isolated populations and bulk cells (45). Comprehensive bioinformatics analyses led to the identificationof highly significantly differentially expressed genes and pathways between the cell populations. By principal component analysis, the tumors were very heterogeneous. However, the ALDH+ cells separated out from the CD44+/CD24- and the bulk cells. We identified 14 genes that were simultaneously differentially expressed between the ALDH+ vs the CD44+/CD24- as well as ALDH+ VS bulk (p-value \u3c0.001, FDR \u3c 0.05). The 3 most significant genes were MMP2 and PCDH7, both known to be involved in breast cancer metastasis and CPXM1, a carboxylase. Inhibiting MMP2 expression in the PDX cells grown in suspension resulted in significant reduction in the ALDH+ cell population. Also, the ALDH+ and not the CD44+/CD24- cells formed spheres in serum free media. The WNT, MAPK and TGF-beta pathways known to mediate metastasis were all significantly up-regulated in the ALDH+ population with down regulation of biosynthetic pathways which were upregulated in the CD44+/CD24- population. Further studies are ongoing on pathway modulation in ALDH1+ cells based on these findings. Our data demonstrate that the ALDH+ stem cell population is enriched for tumor initiating cells in aggressive TNBCs across different ethnicities. These cells may play a role in mediating the aggressive behavior of TNBC\u27s found in African women

Genomic landscapes of canine splenic angiosarcoma (hemangiosarcoma) contain extensive heterogeneity within and between patients.

Cancer genomic heterogeneity presents significant challenges for understanding oncogenic processes and for cancer's clinical management. Variation in driver mutation frequency between patients with the same tumor type as well as within an individual patients' cancer can shape the use of mutations as diagnostic, prognostic, and predictive biomarkers. We have characterized genomic heterogeneity between and within canine splenic hemangiosarcoma (HSA), a common naturally occurring cancer in pet dogs that is similar to human angiosarcoma (AS). HSA is a clinically, physiologically, and genomically complex canine cancer that may serve as a valuable model for understanding the origin and clinical impact of cancer heterogeneity. We conducted a prospective collection of 52 splenic masses from 43 dogs (27 HSA, 15 benign masses, and 1 stromal sarcoma) presenting for emergency care with hemoperitoneum secondary to a ruptured splenic mass. Multi-platform genomic analysis included matched tumor/normal targeted sequencing panel and exome sequencing. We found candidate somatic cancer driver mutations in 14/27 (52%) HSAs. Among recurrent candidate driver mutations, TP53 was most commonly mutated (30%) followed by PIK3CA (15%), AKT1 (11%), and CDKN2AIP (11%). We also identified significant intratumoral genomic heterogeneity, consistent with a branched evolution model, through multi-region exome sequencing of three distinct tumor regions from selected primary splenic tumors. These data provide new perspectives on the genomic landscape of this veterinary cancer and suggest a cross-species value for using HSA in pet dogs as a naturally occurring model of intratumoral heterogeneity

Frequency analysis of Arkansas 70 high-risk genes expression profile.

<p>Frequency analysis of Arkansas 70 high-risk genes expression profile.</p

Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases

<div><p>Multiple Myeloma (MM) is a plasma cell malignancy with significantly greater incidence and mortality rates among African Americans (AA) compared to Caucasians (CA). The overall goal of this study is to elucidate differences in molecular alterations in MM as a function of self-reported race and genetic ancestry. Our study utilized somatic whole exome, RNA-sequencing, and correlated clinical data from 718 MM patients from the Multiple Myeloma Research Foundation CoMMpass study Interim Analysis 9. Somatic mutational analyses based upon self-reported race corrected for ancestry revealed significant differences in mutation frequency between groups. Of interest, <i>BCL7A</i>, <i>BRWD3</i>, <i>and AUTS2</i> demonstrate significantly higher mutation frequencies among AA cases. These genes are all involved in translocations in B-cell malignancies. Moreover, we detected a significant difference in mutation frequency of <i>TP53</i> and <i>IRF4</i> with frequencies higher among CA cases. Our study provides rationale for interrogating diverse tumor cohorts to best understand tumor genomics across populations.</p></div

Population stratification by principal component analysis and STRUCTURE plot defining propositions of calculated genetic ancestry.

<p>(A) Principal component plot across all samples by self-reported race with Caucasian (blue dots) and African American (green dots) using AIMs derived from the whole-exome deep sequencing. The red circles indicate samples that have been removed from the analysis due to misclustering. PCA is calculated using SNP & Variation Suite v8.4.1 (Golden Helix, Inc.) PCA tool by eigenvalue (EV) implementation technique (Methadology). These samples were identified as the self-reported race. (B) STRUCTURE plot (K = 2; 50,000 Burnin period and 100,000 MCMC repeats) used to interfere genetic clusters and percent admixture: European Ancestry (red), African Ancestry (green).</p

Overall survival of patients based upon <i>TP53</i> locus alterations.

<p>(A) Kaplan-Meier analysis with long-rank test for overall survival data from CoMMpass IA9 cases stratified by mono-allelic (blue) versus bi-allelic (red) alteration as well as wildtype (black) of the TP53 locus.</p

Frequency analysis of Arkansas 70 high-risk genes expression profile.

<p>Frequency analysis of Arkansas 70 high-risk genes expression profile.</p

Overall survival of patients based upon <i>age of MM onset and race</i>.

<p>(A) Kaplan-Meier analysis with long-rank test for overall survival data from CoMMpass IA9 cases stratified by the impact of the early or late onset of MM. The data in the black box demonstrate the distribution of onset across the IA9 data set. The early (term used to label onset between 40–49 years), and late (term used to label onset between 70–79 years) that were significantly different using Fisher’s exact test between the stratified populations. Samples size also summarized in supplemental table (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007087#pgen.1007087.s008" target="_blank">S3 Table</a>) is as following: 25–39 [AA (4/127) vs CA (10/591)], 40–49 [AA (14/127) vs CA (27/591)], 50–59 [AA (27/127) vs CA (145/591)], 60–69 [AA (49/127) vs CA (224/591)], 70–79 [AA (118/127) vs CA (132/591)], 80–89 [AA (14/127) vs CA (48/591)], 90–99 [AA (1/127) vs CA (5/591)]. (B) Kaplan-Meier analysis with long-rank test for overall survival data from CoMMpass IA9 impact of incidents of MM by race-matched-ancestry.</p