Abstract Micro-environmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the development of prevention strategies and the safe testing of treatment de-escalation. We addressed methodological barriers and characterized the mutational, transcriptional, histological and microenvironmental landscape across 85 multiple micro-dissected regions from 39 cases. Most somatic alterations, including whole genome duplications, were clonal, but genetic divergence increased with physical distance. Phenotypic and subtype heterogeneity frequently associated with underlying genetic heterogeneity and regions with low-risk features preceded those with high-risk features according to the inferred phylogeny. B- and T-lymphocytes spatial analysis identified 3 immune states, including an epithelial excluded state located preferentially at DCIS regions, and characterized by histological and molecular features of immune escape, independently from molecular subtypes. Such breast pre-cancer atlas with uniquely integrated observations will help scope future expansion studies and build finer models of outcomes and progression risk.
Abstract Breast cancer cells bearing similarities to normal mammary stem cells play a key role in tumor progression. Here, we characterize a unique stem-like tumor cell population that expresses the integrin αvβ3 and is associated with aggressive patient disease. We now show that αvβ3+ cells that also express EpCAMLow represent a functionally and transcriptomically distinct breast cancer cell type. Rare αvβ3+ cells enrich for stemness properties such as anchorage-independent colony formation, self-renewal, differentiation and tumor initiation at limiting dilution. Unbiased whole transcriptome analysis by RNA-Seq identified several genes specifically upregulated in αvβ3+ cells that are also enriched in normal adult mammary stem cells. Phospho-array profiling of major signaling pathways revealed increased activation of the proto-oncogene c-Jun in αvβ3+ stem-like cells. Inhibition of JNK/c-Jun signaling further identified the receptor tyrosine kinase AXL as a critical downstream target gene necessary for tumorsphere formation. Our findings reveal a c-Jun/AXL signaling pathway required for stemness properties in αvβ3+ tumor cells important for breast cancer progression. Citation Format: Qi Sun, Yufen Wang, Adam Officer, Olivier Harismendy, Jay S. Desgrosellier. An integrin αvβ3+ stem-like tumor cell subset promotes breast cancer progression via c-Jun/AXL signaling [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6024.
<p>Inferred evolutionary trajectory derived from CNAs. Cases showing linear (<b>A</b>) and branched (<b>B</b>) evolution are depicted. For each case, evolutionary tree and segmentation plots are shown with HapLOHseq calls represented in lavender background. Branches are drawn to scale based on the number of CNA events. Chromosomal aberrations associated to the branch with the largest HG clone are shown. Red indicates gains and blue losses. Patient IDs highlighted in red indicate cases with coexisting PDAC. SNVs associated with each branch are labeled. Red arrow labels the branch with larger HG clone.</p>
<p>Genomic landscapes of IPMN lesions. <b>A,</b> SNVs identified in <i>KRAS</i> and <i>GNAS</i> in LG and HG IPMNs. Dark purple: somatic mutations detected for <i>KRAS</i> and <i>GNAS</i>. Light purple: mutations detected by retesting. <b>B,</b> SNVs and CNAs identified in ND, LG, HG, and PDAC regions and classified by relevant PDAC-related pathways. For A and B, samples were arranged by histological type and labeled at the top of each heat map.</p>
<div>Abstract<p>Intraductal papillary mucinous neoplasms (IPMN) are cystic precursor lesions to pancreatic ductal adenocarcinoma (PDAC). IPMNs undergo multistep progression from low-grade (LG) to high-grade (HG) dysplasia, culminating in invasive neoplasia. While patterns of IPMN progression have been analyzed using multiregion sequencing for somatic mutations, there is no integrated assessment of molecular events, including copy-number alterations (CNA) and transcriptional changes that accompany IPMN progression. We performed laser capture microdissection on surgically resected IPMNs of varying grades of histologic dysplasia obtained from 23 patients, followed by whole-exome and whole-transcriptome sequencing. Overall, HG IPMNs displayed a significantly greater aneuploidy score than LG lesions, with chromosome 1q amplification being associated with HG progression and with cases that harbored co-occurring PDAC. Furthermore, the combined assessment of single-nucleotide variants (SNV) and CNAs identified both linear and branched evolutionary trajectories, underscoring the heterogeneity in the progression of LG lesions to HG and PDAC. At the transcriptome level, upregulation of MYC-regulated targets and downregulation of transcripts associated with the MHC class I antigen presentation machinery as well as pathways related to glycosylation were a common feature of progression to HG. In addition, the established PDAC transcriptional subtypes (basal-like and classical) were readily apparent within IPMNs. Taken together, this work emphasizes the role of 1q copy-number amplification as a putative biomarker of high-risk IPMNs, underscores the importance of immune evasion even in noninvasive precursor lesions, and reinforces that evolutionary pathways in IPMNs are heterogenous, comprised of both SNV and CNA-driven events.</p>Significance:<p>Integrated molecular analysis of genomic and transcriptomic alterations in the multistep progression of IPMNs, which are bona fide precursors of pancreatic cancer, identifies features associated with progression of low-risk lesions to high-risk lesions and cancer, which might enable patient stratification and cancer interception strategies.</p></div>
Abstract Tumor initiation represents the first step in tumorigenesis during which normal progenitor cells undergo cell fate transition to cancer. Capturing this process as it occurs in vivo, however, remains elusive. Here we employ spatiotemporally controlled oncogene activation and tumor suppressor inhibition together with multiomics to unveil the processes underlying oral epithelial progenitor cell reprogramming into tumor initiating cells at single cell resolution. Tumor initiating cells displayed a distinct stem-like state, defined by aberrant proliferative, hypoxic, squamous differentiation, and partial epithelial to mesenchymal invasive gene programs. YAP-mediated tumor initiating cell programs included activation of oncogenic transcriptional networks and mTOR signaling, and recruitment of myeloid cells to the invasive front contributing to tumor infiltration. Tumor initiating cell transcriptional programs are conserved in human head and neck cancer and associated with poor patient survival. These findings illuminate processes underlying cancer initiation at single cell resolution, and identify candidate targets for early cancer detection and prevention.
