iPSC-based modeling of helicase deficiency reveals impaired cell proliferation and increased apoptosis after NK cell lineage commitment

Cell proliferation is a ubiquitous process required for organismal development and homeostasis. However, individuals with partial loss-of-function variants in DNA replicative helicase components often present with immunodeficiency due to specific loss of natural killer (NK) cells. Such lineage-specific disease phenotypes raise questions on how the proliferation is regulated in cell type-specific manner. We aimed to understand NK cell-specific proliferative dynamics and vulnerability to impaired helicase function using iPSCs from individuals with NK cell deficiency (NKD) due to hereditary compound heterozygous GINS4 variants. We observed and characterized heterogeneous cell populations that arise during the iPSC differentiation along with NK cells. While overall cell proliferation decreased with differentiation, early NK cell precursors showed a short burst of cell proliferation. GINS4 deficiency induced replication stress in these early NK cell precursors, which are poised for apoptosis, and ultimately recapitulate the NKD phenotype.

β1 integrins regulate cellular behaviors and cardiomyocyte organization during ventricular wall formation

Aims

The mechanisms regulating the cellular behavior and cardiomyocyte organization during ventricular wall morphogenesis are poorly understood. Cardiomyocytes are surrounded by extracellular matrix (ECM) and interact with ECM via integrins. This study aims to determine whether and how β1 integrins regulate cardiomyocyte behavior and organization during ventricular wall morphogenesis in the mouse.

Methods and Results

We applied mRNA deep sequencing and immunostaining to determine the expression repertoires of α/β integrins and their ligands in the embryonic heart. Integrin β1 subunit (β1) and some of its ECM ligands are asymmetrically distributed and enriched in the luminal side of cardiomyocytes, while fibronectin surrounds cardiomyocytes, creating a network for them. Itgb1 , which encodes the β1 integrin subunit, was deleted via Nkx2.5 Cre/+ to generate myocardial-specific Itgb1 knockout (B1KO) mice. B1KO hearts display an absence of trabecular zone but a thicker compact zone. The abundances of hyaluronic acid and versican are not significantly different. Instead, fibronectin, a ligand of β1, was absent in B1KO. We examined cellular behaviors and organization via various tools. B1KO cardiomyocytes display a random cellular orientation and fail to undergo perpendicular cell division, be organized properly, and establish the proper tissue architecture to form trabeculae. The reduction of Notch1 activation was not the cause of the abnormal cellular organization in B1KO hearts. Mosaic clonal lineage tracing shows that Itgb1 regulates cardiomyocyte transmural migration and proliferation autonomously.

Conclusions

β1 is asymmetrically localized in the cardiomyocytes, and its ECM ligands are enriched in the luminal side of the myocardium and surrounding cardiomyocytes. β1 integrins are required for cardiomyocytes to attach to the ECM network. This engagement provides structural support for cardiomyocytes to maintain shape, undergo perpendicular division, and establish cellular organization. Deletion of Itgb1 , leading to ablation of β1 integrins, causes the dissociation of cardiomyocytes from the ECM network and failure to establish tissue architecture to form trabeculae.

Inflammation induced by tumor-associated nerves promotes resistance to anti-PD-1 therapy in cancer patients and is targetable by interleukin-6 blockade

While the nervous system has reciprocal interactions with both cancer and the immune system, little is known about the potential role of tumor associated nerves (TANs) in modulating anti-tumoral immunity. Moreover, while peri-neural invasion is a well establish poor prognostic factor across cancer types, the mechanisms driving this clinical effect remain unknown. Here, we provide clinical and mechniastic association between TANs damage and resistance to anti-PD-1 therapy. Using electron microscopy, electrical conduction studies, and tumor samples of cutaneous squamous cell carcinoma (cSCC) patients, we showed that cancer cells can destroy myelin sheath and induce TANs degeneration. Multi-omics and spatial analyses of tumor samples from cSCC patients who underwent neoadjuvant anti-PD-1 therapy demonstrated that anti-PD-1 non-responders had higher rates of peri-neural invasion, TANs damage and degeneration compared to responders, both at baseline and following neoadjuvant treatment. Tumors from non-responders were also characterized by a sustained signaling of interferon type I (IFN-I) - known to both propagate nerve degeneration and to dampen anti-tumoral immunity. Peri-neural niches of non-responders were characterized by higher immune activity compared to responders, including immune-suppressive activity of M2 macrophages, and T regulatory cells. This tumor promoting inflammation expanded to the rest of the tumor microenvironment in non-responders. Anti-PD-1 efficacy was dampened by inducing nerve damage prior to treatment administration in a murine model. In contrast, anti-PD-1 efficacy was enhanced by denervation and by interleukin-6 blockade. These findings suggested a potential novel anti-PD-1 resistance drived by TANs damage and inflammation. This resistance mechanism is targetable and may have therapeutic implications in other neurotropic cancers with poor response to anti-PD-1 therapy such as pancreatic, prostate, and breast cancers.

Abstract 6521: Subtype-specific molecular signatures of field cancerization in patients with sporadic breast cancer

Background: We have previously shown the presence of molecular field cancerization in patients with sporadic breast cancer. Given the heterogeneity of breast cancer, we hypothesized that such field cancerization is likely to be subtype-specific.

Methods: RNA exome sequencing was performed on 360 samples obtained from 75 breast cancer patients undergoing mastectomy; 25 cases were selected from each subtype: hormone receptor (HR) positive, Her2 positive, triple negative (TN) breast cancer. Four sites were sampled from each patient: primary tumor (A), adjacent normal parenchyma within 2cm of the tumor (B), 2 separate, histologically normal sites at least 2cm away from the tumor (C &D) or, if available, tissue from the unaffected contralateral breast (E). Normal breast tissue (N) from cancer-free controls was obtained from reduction mammoplasty. Tumor-associated genes (TAGs) were identified by comparison of primary tumor to tissue from cancer free controls. We estimated tumor content that was shared across samples B-E by applying deconvolutional analysis to the tumor associated genes, to calculate indices that ranged from 0, indicating normal, to 1, indicating tumor. Molecular field-associated genes and pathways were identified by Spearman’s correlation coefficient analysis between the differential genes/pathways and ISTC.

Results: Across all subtypes, the proportion of tumor content present in the histologically normal breast tissue samples (samples B, C, D, E) obtained from cancer patients ranged from 80% in tissue adjacent to the tumor to approximately 50% in tissue obtained from the contralateral breast. We found over 600 deregulated genes to constitute the molecular field across all of the 3 major subtypes tested (Her2+, HR, and TNBC), of which approximately 20% were shared in the molecular field of all 3 subtypes of breast cancer. Among the 664 genes noted to be part of the molecular field in TNBC, 23.8% were unique to this subtype. In contrast, only 13% of the genes that constituted the field cancerization in the Her2 and HR+ subtypes were subtype-specific. PIP3-AKT, TCR signaling, and DNA synthesis were among the top pathways specifically activated in the molecular field of the Her2+ subtype of breast cancer. The molecular field of HR+ breast cancer was uniquely characterized by upregulation in the mitotic cell cycle, G1- S transition, and RB pathway. The field of cancerization in the TNBC subtype showed an upregulation in MEK-MAPK, mTOR, and JNK-JUN-TAK1 pathways.

Conclusions: Our study suggests the presence of a breast cancer molecular field effect that extends beyond the adjacent normal breast tissue and includes the entire mammary gland. A substantial proportion of this field cancerization is subtype specific with uniquely deregulated pathways within each subtype. These findings provide new opportunities for developing subtype-specific chemoprevention strategies.

Citation Format: Anjana Bhardwaj, Zhenlin Ju, Constance Albarracin, Celestine Trinidad, Preethi Gunaratne, Jing Wang, Randa El-Zein, Isabelle Bedrosian. Subtype-specific molecular signatures of field cancerization in patients with sporadic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6521.

MicroRNA-mRNA networks are dysregulated in opioid use disorder postmortem brain: Further evidence for opioid-induced neurovascular alterations

INTRODUCTION

To understand mechanisms and identify potential targets for intervention in the current crisis of opioid use disorder (OUD), postmortem brains represent an under-utilized resource. To refine previously reported gene signatures of neurobiological alterations in OUD from the dorsolateral prefrontal cortex (Brodmann Area 9, BA9), we explored the role of microRNAs (miRNA) as powerful epigenetic regulators of gene function.

METHODS

Building on the growing appreciation that miRNAs can cross the blood-brain barrier, we carried out miRNA profiling in same-subject postmortem samples from BA9 and blood tissues.

RESULTS

miRNA-mRNA network analysis showed that even though miRNAs identified in BA9 and blood were fairly distinct, their target genes and corresponding enriched pathways overlapped strongly. Among the dominant enriched biological processes were tissue development and morphogenesis, and MAPK signaling pathways. These findings point to robust, redundant, and systemic opioid-induced miRNA dysregulation with a potential functional impact on transcriptomic changes. Further, using correlation network analysis, we identified cell-type specific miRNA targets, specifically in astrocytes, neurons, and endothelial cells, associated with OUD transcriptomic dysregulation. Finally, leveraging a collection of control brain transcriptomes from the Genotype-Tissue Expression (GTEx) project, we identified a correlation of OUD miRNA targets with TGF beta, hypoxia, angiogenesis, coagulation, immune system, and inflammatory pathways.

DISCUSSION

These findings support previous reports of neurovascular and immune system alterations as a consequence of opioid abuse and shed new light on miRNA network regulators of cellular response to opioid drugs.

Abstract 2997: Novel orthotopic patient-derived xenograft mouse models of hepatoblastoma that replicate tumor heterogeneity, chemoresistance, and refractory disease

Introduction: Hepatoblastoma (HB) is the most common pediatric primary liver tumor and has the fastest rising incidence of all pediatric solid tumors. Patients with high-risk, treatment refractory, or relapse disease have a survival rate of less than 50%. The development of clinically relevant models of these aggressive tumors will facilitate studies to identify drugs that target these cells.

Methods: Fresh, whole primary tumor samples were implanted into the livers of immunocompromised mice. Tumor growth was monitored with MRI and ELISA to measure serum human Alpha-fetoprotein (AFP), which is detectable in the blood of tumor-bearing animals. Tumors were validated with immunohistochemistry (IHC) for HB markers Glypican-3 (GPC3) and Beta-catenin; short tandem repeat (STR) DNA validation; next generation sequencing-based mutation profiling of 124 genes involved in pediatric solid tumors; and RNA sequencing (RNA-seq). Cells derived from tumors were grown in vitro and used for high throughput drug screening of candidate agents. Tumors were serially passaged in animals for further in vivo drug testing of novel targeted agents.

Results: Nine patient-derived xenograft (PDX) models were generated that represent low- and high-risk tumors, treatment refractory cases, and relapsed tumors. Passaging of these models showed consistent implantation rates at or above 80% with tumors detectable in 2 to 4 weeks. Eight of nine models secrete human serum AFP. All models mimic gene expression and histological patterns of their primary tumor counterparts as well as identical STR DNA profiles. The models also show gene expression consistent with an HB2/high-risk profile according to the Sumazin HB expression signature. Interestingly, two models represent unique sub-clones of a very aggressive HB relapse with different AFP secretion and transcriptomic expression. The nine models also demonstrate a range of DNA mutations with three or four mutations per tumor; all variants present in the original clinical samples were conserved in the PDX models. Drug screening of tumor cells support the efficacy of novel targeted agents and indicate that these tumors are resistant to frontline standard chemotherapy, cisplatin and doxorubicin. More extensive in vivo testing showed the efficacy of a dual MDM2/MDM4 inhibitor (ALRN-6924), a cyclin dependent kinase inhibitor (dinaciclib), and a histone deacetylase inhibitor (panobinostat), and use of an orthotopic animal model also revealed drug toxicities associated with compromised liver function.

Conclusions: These novel orthotopic PDX models of HB fully recapitulate the primary tumors and represent a platform for clinically relevant drug screening and testing. Further studies of the sub-clones of disease that grow in the animals will yield information about particularly aggressive HBs.

Citation Format: Sarah Elizabeth Woodfield, Roma H. Patel, Samuel R. Larson, Andrew Badachhape, Rohit K. Srivastava, Aayushi P. Shah, Brandon Mistretta, Barry Zorman, Kevin Fisher, Ilavarasi Gandhi, Jacquelyn Reuther, Richard S. Whitlock, Aryana M. Ibarra, Sakuni Rankothgedera, Kimberly R. Holloway, Stephen F. Sarabia, Martin Urbicain, Andras Heczey, Dolores Lopez-Terrada, Angshumoy Roy, Preethi Gunaratne, Pavel Sumazin, Sanjeev A. Vasudevan. Novel orthotopic patient-derived xenograft mouse models of hepatoblastoma that replicate tumor heterogeneity, chemoresistance, and refractory disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2997.

Functional and structural characterization of Hyp730, a highly conserved and dormancy-specific hypothetical membrane protein

Membrane proteins represent major drug targets, and the ability to determine their functions, structures, and conformational changes will significantly advance mechanistic approaches to both biotechnology and bioremediation, as well as the fight against pathogenic bacteria. A pertinent example is Mycobacterium tuberculosis (H37Rv), which contains ~4000 protein-coding genes, with almost a thousand having been categorized as 'membrane protein', and a few of which (~1%) have been functionally characterized and structurally modeled. However, the functions and structures of most membrane proteins that are sparsely, or only transiently, expressed, but essential in small phenotypic subpopulations or under stress conditions such as persistence or dormancy, remain unknown. Our deep quantitative proteomics profiles revealed that the hypothetical membrane protein 730 (Hyp730) WP_010079730 (protein ID Mlut_RS11895) from M. luteus is upregulated in dormancy despite a ~5-fold reduction in overall protein diversity. Its H37Rv paralog, Rv1234, showed a similar proteomic signature, but the function of Hyp730-like proteins has never been characterized. Here, we present an extensive proteomic and transcriptomic analysis of Hyp730 and have also characterized its in vitro recombinant expression, purification, refolding, and essentiality as well as its tertiary fold. Our biophysical studies, circular dichroism, and tryptophan fluorescence are in immediate agreement with in-depth in silico 3D-structure prediction, suggesting that Hyp730 is a double-pass membrane-spanning protein. Ablation of Hyp730-expression did not alter M. luteus growth, indicating that Hyp730 is not essential. Structural homology comparisons showed that Hyp730 is highly conserved and non-redundant in G+C rich Actinobacteria and might be involved, under stress conditions, in an energy-saving role in respiration during dormancy.

Role of microRNA 690 in Mediating Angiotensin II Effects on Inflammation and Endoplasmic Reticulum Stress

Overactivation of the renin–angiotensin system (RAS) during obesity disrupts adipocyte metabolic homeostasis and induces endoplasmic reticulum (ER) stress and inflammation; however, underlying mechanisms are not well known. We propose that overexpression of angiotensinogen (Agt), the precursor protein of RAS in adipose tissue or treatment of adipocytes with Angiotensin II (Ang II), RAS bioactive hormone, alters specific microRNAs (miRNA), that target ER stress and inflammation leading to adipocyte dysfunction. Epididymal white adipose tissue (WAT) from B6 wild type (Wt) and transgenic male mice overexpressing Agt (Agt-Tg) in adipose tissue and adipocytes treated with Ang II were used. Small RNA sequencing and microarray in WAT identified differentially expressed miRNAs and genes, out of which miR-690 and mitogen-activated protein kinase kinase 3 (MAP2K3) were validated as significantly up- and down-regulated, respectively, in Agt-Tg, and in Ang II-treated adipocytes compared to respective controls. Additionally, the direct regulatory role of miR-690 on MAP2K3 was confirmed using mimic, inhibitors and dual-luciferase reporter assay. Downstream protein targets of MAP2K3 which include p38, NF-κB, IL-6 and CHOP were all reduced. These results indicate a critical post-transcriptional role for miR-690 in inflammation and ER stress. In conclusion, miR-690 plays a protective function and could be a useful target to reduce obesity.

Wnt signaling regulates neural plate patterning in distinct temporal phases with dynamic transcriptional outputs

The process that partitions the nascent vertebrate central nervous system into forebrain, midbrain, hindbrain, and spinal cord after neural induction is of fundamental interest in developmental biology, and is known to be dependent on Wnt/β-catenin signaling at multiple steps. Neural induction specifies neural ectoderm with forebrain character that is subsequently posteriorized by graded Wnt signaling: embryological and mutant analyses have shown that progressively higher levels of Wnt signaling induce progressively more posterior fates. However, the mechanistic link between Wnt signaling and the molecular subdivision of the neural ectoderm into distinct domains in the anteroposterior (AP) axis is still not clear. To better understand how Wnt mediates neural AP patterning, we performed a temporal dissection of neural patterning in response to manipulations of Wnt signaling in zebrafish. We show that Wnt-mediated neural patterning in zebrafish can be divided into three phases: (I) a primary AP patterning phase, which occurs during gastrulation, (II) a mes/r1 (mesencephalon-rhombomere 1) specification and refinement phase, which occurs immediately after gastrulation, and (III) a midbrain-hindbrain boundary (MHB) morphogenesis phase, which occurs during segmentation stages. A major outcome of these Wnt signaling phases is the specification of the major compartment divisions of the developing brain: first the MHB, then the diencephalic-mesencephalic boundary (DMB). The specification of these lineage divisions depends upon the dynamic changes of gene transcription in response to Wnt signaling, which we show primarily involves transcriptional repression or indirect activation. We show that otx2b is directly repressed by Wnt signaling during primary AP patterning, but becomes resistant to Wnt-mediated repression during late gastrulation. Also during late gastrulation, Wnt signaling becomes both necessary and sufficient for expression of wnt8b, en2a, and her5 in mes/r1. We suggest that the change in otx2b response to Wnt regulation enables a transition to the mes/r1 phase of Wnt-mediated patterning, as it ensures that Wnts expressed in the midbrain and MHB do not suppress midbrain identity, and consequently reinforce formation of the DMB. These findings integrate important temporal elements into our spatial understanding of Wnt-mediated neural patterning and may serve as an important basis for a better understanding of neural patterning defects that have implications in human health.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.

Single-Cell RNA-Sequencing Identifies Activation of TP53 and STAT1 Pathways in Human T Lymphocyte Subpopulations in Response to Ex Vivo Radiation Exposure

Detrimental health consequences from exposure to space radiation are a major concern for long-duration human exploration missions to the Moon or Mars. Cellular responses to radiation are expected to be heterogeneous for space radiation exposure, where only high-energy protons and other particles traverse a fraction of the cells. Therefore, assessing DNA damage and DNA damage response in individual cells is crucial in understanding the mechanisms by which cells respond to different particle types and energies in space. In this project, we identified a cell-specific signature for radiation response by using single-cell transcriptomics of human lymphocyte subpopulations. We investigated gene expression in individual human T lymphocytes 3 h after ex vivo exposure to 2-Gy gamma rays while using the single-cell sequencing technique (10X Genomics). In the process, RNA was isolated from ~700 irradiated and ~700 non-irradiated control cells, and then sequenced with ~50 k reads/cell. RNA in each of the cells was distinctively barcoded prior to extraction to allow for quantification for individual cells. Principal component and clustering analysis of the unique molecular identifier (UMI) counts classified the cells into three groups or sub-types, which correspond to CD4+, naïve, and CD8+/NK cells. Gene expression changes after radiation exposure were evaluated using negative binomial regression. On average, BBC3, PCNA, and other TP53 related genes that are known to respond to radiation in human T cells showed increased activation. While most of the TP53 responsive genes were upregulated in all groups of cells, the expressions of IRF1, STAT1, and BATF were only upregulated in the CD4+ and naïve groups, but were unchanged in the CD8+/NK group, which suggests that the interferon-gamma pathway does not respond to radiation in CD8+/NK cells. Thus, single-cell RNA sequencing technique was useful for simultaneously identifying the expression of a set of genes in individual cells and T lymphocyte subpopulation after gamma radiation exposure. The degree of dependence of UMI counts between pairs of upregulated genes was also evaluated to construct a similarity matrix for cluster analysis. The cluster analysis identified a group of TP53-responsive genes and a group of genes that are involved in the interferon gamma pathway, which demonstrate the potential of this method for identifying previously unknown groups of genes with similar expression patterns.

The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders

Schizophrenia and bipolar disorder are complex psychiatric diseases with risks contributed by multiple genes. Dysregulation of gene expression has been implicated in these disorders, but little is known about such dysregulation in the human brain. We analyzed three transcriptome datasets from 394 postmortem brain tissue samples from patients with schizophrenia or bipolar disorder or from healthy control individuals without a known history of psychiatric disease. We built genome-wide coexpression networks that included microRNAs (miRNAs). We identified a coexpression network module that was differentially expressed in the brain tissue from patients compared to healthy control individuals. This module contained genes that were principally involved in glial and neural cell genesis and glial cell differentiation, and included schizophrenia risk genes carrying rare variants. This module included five miRNAs and 545 mRNAs, with six transcription factors serving as hub genes in this module. We found that the most connected transcription factor gene POU3F2, also identified on a genome-wide association study for bipolar disorder, could regulate the miRNA hsa-miR-320e and other putative target mRNAs. These regulatory relationships were replicated using PsychENCODE/BrainGVEX datasets and validated by knockdown and overexpression experiments in SH-SY5Y cells and human neural progenitor cells in vitro. Thus, we identified a brain gene expression module that was enriched for rare coding variants in genes associated with schizophrenia and that contained the putative bipolar disorder risk gene POU3F2 The transcription factor POU3F2 may be a key regulator of gene expression in this disease-associated gene coexpression module.

Ronin Governs Early Heart Development by Controlling Core Gene Expression Programs

Ronin (THAP11), a DNA-binding protein that evolved from a primordial DNA transposon by molecular domestication, recognizes a hyperconserved promoter sequence to control developmentally and metabolically essential genes in pluripotent stem cells. However, it remains unclear whether Ronin or related THAP proteins perform similar functions in development. Here, we present evidence that Ronin functions within the nascent heart as it arises from the mesoderm and forms a four-chambered organ. We show that Ronin is vital for cardiogenesis during midgestation by controlling a set of critical genes. The activity of Ronin coincided with the recruitment of its cofactor, Hcf-1, and the elevation of H3K4me₃ levels at specific target genes, suggesting the involvement of an epigenetic mechanism. On the strength of these findings, we propose that Ronin activity during cardiogenesis offers a template to understand how important gene programs are sustained across different cell types within a developing organ such as the heart.

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Ronin displays complex expression patterns during embryogenesis

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Ronin is critical for heart growth

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Ronin regulates genetic growth programs

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Ronin binding influences H3K4me₃ levels at target genes

Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes

TP63 is required to maintain stem cell pluripotency and suppresses the metastatic potential of cancer cells through multiple mechanisms. These functions are differentially regulated by individual isoforms, necessitating a deeper understanding of how the distinct transcriptional programs controlled by these isoforms affect cancer progression and outcomes. In this study, we conducted a pan-cancer analysis of The Cancer Genome Atlas to identify transcriptional networks regulated by TAp63 and ΔNp63 using transcriptomes derived from epidermal cells of TAp63^-/- and ΔNp63^-/- mice. Analysis of 17 cancer developmental and 27 cancer progression signatures revealed a consistent tumor suppressive pattern for TAp63. In contrast, we identified pleiotropic roles for ΔNp63 in tumor development and found that its regulation of Lef1 was crucial for its oncogenic role. ΔNp63 performed a distinctive role as suppressor of tumor progression by cooperating with TAp63 to modulate key biological pathways, principally cell-cycle regulation, extracellular matrix remodeling, epithelial-to-mesenchymal transition, and the enrichment of pluripotent stem cells. Importantly, these TAp63 and ΔNp63 signatures prognosticated progression and survival, even within specific stages, in bladder and renal carcinomas as well as low-grade gliomas. These data describe a novel approach for understanding transcriptional activities of TP63 isoforms across a large number of cancer types, potentially enabling identification of patient subsets most likely to benefit from therapies predicated on manipulating specific TP63 isoforms.Significance: Transcriptomic analyses of patient samples and murine knockout models highlight the prognostic role of several critical mechanisms of tumor suppression that are regulated by TP63. Cancer Res; 78(2); 451-62. ©2017 AACR.

Protective properties of n-3 fatty acids and implications in obesity-associated breast cancer

Obesity is well documented as a risk factor for developing breast cancer, especially in postmenopausal women. Adipose tissue in the breast under obese conditions induces inflammation by increasing macrophage infiltration and pro-inflammatory cytokines that in turn up-regulates genes and signaling pathways, resulting in increased inflammation, cell proliferation and tumor growth in the breast. Due to their potent anti-inflammatory effects, n-3 polyunsaturated fatty acids (n-3 PUFA) are a promising and safe dietary intervention in reducing breast cancer risk. Here, we briefly review current status of breast cancer and its relationship with obesity. We then review in depth, current research and knowledge on the role of n-3 PUFA in reducing/preventing breast cancer cell growth in vitro, in vivo and in human studies, and how n-3 PUFA may modulate signaling pathways mitigating their effects on breast cancer development.

Abstract P4-15-03: Regulation of miRNA-29c and its gene targets in preneoplastic progression of triple negative breast cancer

Introduction: Little is understood about the early molecular drivers of the triple negative breast cancer making identification of women at risk and development of targeted therapy for prevention a significant challenge. Methods: Here, by deep sequencing of TNBC- cell line based breast cancer progression system we have identified miRNA-29c and its functional gene targets to be potentially involved in the normal to preneoplastic transition during TNBC progression. We have used cell line based functional assays that are relevant in early tumorigenesis such cell proliferation (ki67), and colony formation assay to study the growth inhibitory potential of these miRNA and their gene targets. To identify direct gene targets of miRNA-29c, we cloned the 3'untranslated region containing miRNA-29c binding sites from predicted gene targets in a luciferase reporter vector, pmiRGLO and studied the potential of miRNA-29c overexpression on the repression of luciferase reporter activity indicating their direct gene regulation. Results: Our deep sequencing results and their further validation by QPCR revealed miRNA-29c to be lost during the TNBC progression, and its forced expression to inhibit cell proliferation and colony formation of preneoplastic (MCF10AT1) and ductal carcinoma in situ (MCF10DCIS) cells. We found miRNA-29c to directly bind in 3'UTR of TGIF2, CREB5, AKT3 and CDK6 and regulate their expression as shown by our luciferase assays. We also found miRNA-29c binding to 3'UTR of these gene targets to be functionally relevant as TGIF2, CREB5 and AKT3 were able to rescue the inhibition in cell proliferation and colony formation assay caused by loss of miRNA-29c in preneoplastic cells. Further confirming the relevance of these miRNA-29c gene targets and pathways in TNBC tumorigenesis, inhibition of PI3K, which is upstream of AKT3, inhibits cell proliferation in MCF10AT1 and DCIS cells. We also examined the regulation of tumor suppressor miRNA-29c to study the mechanisms responsible for its loss during breast cancer development. We found c-myc and EZH2 driven epigenetic mechanism as well as DNA methylation in part to cause the loss of miRNA-29c during TNBC progression. Consistently, we found a pan HDAC inhibitor and a DNA methylation inhibitor to relieve the suppression of miRNA-29c. Conclusions: Together, these results indicate that loss of miRNA-29c plays a central role in preneoplastic development of breast cancer and efforts directed at inhibition of its target pathways or rescue of miRNA-29c itself may provide novel opportunities for prevention of TNBC.Introduction: Little is understood about the early molecular drivers of the triple negative breast cancer making identification of women at risk and development of targeted therapy for prevention a significant challenge. Methods: Here, by deep sequencing of TNBC- cell line based breast cancer progression system we have identified miRNA-29c and its functional gene targets to be potentially involved in the normal to preneoplastic transition during TNBC progression. We have used cell line based functional assays that are relevant in early tumorigenesis such cell proliferation (ki67), and colony formation assay to study the growth inhibitory potential of these miRNA and their gene targets. To identify direct gene targets of miRNA-29c, we cloned the 3'untranslated region containing miRNA-29c binding sites from predicted gene targets in a luciferase reporter vector, pmiRGLO and studied the potential of miRNA-29c overexpression on the repression of luciferase reporter activity indicating their direct gene regulation. Results: Our deep sequencing results and their further validation by QPCR revealed miRNA-29c to be lost during the TNBC progression, and its forced expression to inhibit cell proliferation and colony formation of preneoplastic (MCF10AT1) and ductal carcinoma in situ (MCF10DCIS) cells. We found miRNA-29c to directly bind in 3'UTR of TGIF2, CREB5, AKT3 and CDK6 and regulate their expression as shown by our luciferase assays. We also found miRNA-29c binding to 3'UTR of these gene targets to be functionally relevant as TGIF2, CREB5 and AKT3 were able to rescue the inhibition in cell proliferation and colony formation assay caused by loss of miRNA-29c in preneoplastic cells. Further confirming the relevance of these miRNA-29c gene targets and pathways in TNBC tumorigenesis, inhibition of PI3K, which is upstream of AKT3, inhibits cell proliferation in MCF10AT1 and DCIS cells. We also examined the regulation of tumor suppressor miRNA-29c to study the mechanisms responsible for its loss during breast cancer development. We found c-myc and EZH2 driven epigenetic mechanism as well as DNA methylation in part to cause the loss of miRNA-29c during TNBC progression. Consistently, we found a pan HDAC inhibitor and a DNA methylation inhibitor to relieve the suppression of miRNA-29c. Conclusions: Together, these results indicate that loss of miRNA-29c plays a central role in preneoplastic development of breast cancer and efforts directed at inhibition of its target pathways or rescue of miRNA-29c itself may provide novel opportunities for prevention of TNBC.

Citation Format: Bhardwaj A, Tachibana K, Ganesan N, Rajapakshe K, Singh H, Gunaratne P, Coarfa C, Bedrosian I. Regulation of miRNA-29c and its gene targets in preneoplastic progression of triple negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-15-03.

Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates

Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over 700,000 cases in USA annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). To identify potential targets for molecularly targeted chemoprevention, here we perform integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar ultraviolet radiation-driven Hairless mouse model. We identify the major transcriptional drivers of this progression sequence, showing that the key genomic changes in cuSCC development occur in the normal skin to AK transition. Our data validate the use of this ultraviolet radiation-driven mouse cuSCC model for cross-species analysis and demonstrate that cuSCC bears deep molecular similarities to multiple carcinogen-driven SCCs from diverse sites, suggesting that cuSCC may serve as an effective, accessible model for multiple SCC types and that common treatment and prevention strategies may be feasible.

Mesp1 Marked Cardiac Progenitor Cells Repair Infarcted Mouse Hearts

Mesp1 directs multipotential cardiovascular cell fates, even though it's transiently induced prior to the appearance of the cardiac progenitor program. Tracing Mesp1-expressing cells and their progeny allows isolation and characterization of the earliest cardiovascular progenitor cells. Studying the biology of Mesp1-CPCs in cell culture and ischemic disease models is an important initial step toward using them for heart disease treatment. Because of Mesp1's transitory nature, Mesp1-CPC lineages were traced by following EYFP expression in murine Mesp1(Cre/+); Rosa26(EYFP/+) ES cells. We captured EYFP+ cells that strongly expressed cardiac mesoderm markers and cardiac transcription factors, but not pluripotent or nascent mesoderm markers. BMP2/4 treatment led to the expansion of EYFP+ cells, while Wnt3a and Activin were marginally effective. BMP2/4 exposure readily led EYFP+ cells to endothelial and smooth muscle cells, but inhibition of the canonical Wnt signaling was required to enter the cardiomyocyte fate. Injected mouse pre-contractile Mesp1-EYFP+ CPCs improved the survivability of injured mice and restored the functional performance of infarcted hearts for at least 3 months. Mesp1-EYFP+ cells are bona fide CPCs and they integrated well in infarcted hearts and emerged de novo into terminally differentiated cardiac myocytes, smooth muscle and vascular endothelial cells.

Abstract LB-321: TP63 isoforms regulate distinct and cooperative transcriptional signatures that drive cancer progression and predict clinical outcomes

TP63 is required to maintain stem cell pluripotency and suppresses the metastatic potential of cancer cells through multiple mechanisms. Even though roles for Tp63 in cancer have been described, the transcriptional roles of TP63 isoforms, namely TAp63 and ΔNp63, in tumor development and progression have been perplexing due to their variable expression in tissues, their complex interaction with each other and with TP53, and the lack of adequate antibodies to distinguish between their isoforms. Of concern is the use of total p63 as a diagnostic marker for many epithelial cancers in the clinic with disregard of the existence and functions of the various isoforms, which may lead to improper diagnosis. These notions necessitate a deeper understanding of how the distinct transcriptional programs controlled by TP63 isoforms affect cancer progression and patient outcomes. To shed light on the activities of the TP63 isoforms in cancer development and progression, we conducted a pan-cancer analysis of The Cancer Genome Atlas (TCGA) to identify the transcriptional networks regulated by TAp63 and ΔNp63 using transcriptomes derived from epidermal cells of TAp63-/- and ΔNp63-/- mice. We then derived 17 cancer developmental (tumor versus corresponding normal) and 27 cancer progression (high stage versus low stage) signatures. Our analysis revealed a consistent tumor suppressive pattern for TAp63. In contrast, we identified pleiotropic roles for ΔNp63 in tumor development and progression. Our findings revealed a cooperative role between TAp63 and ΔNp63 via their gene signatures that predict survival and correlates with progression of cancer patients in bladder cancer (BLCA), clear cell renal cell carcinoma (KIRC), papillary renal cell carcinoma (KIRP) and low grade glioma. Importantly, we found that ΔNp63 transcriptional activity integrates the remodeling of extracellular matrix remodeling to provide an ideal environment in these cancers to undergo epithelial to mesenchymal transition and gain pluripotent stem cell characteristics, thus supporting tumor progression, while TAp63 activity acts to regulate the cell cycle required in stem cell maintenance which may further allow tumors to progress. These signatures are not only predictive of survival across stages, but can even stratify patients within the same stage into different survival groups in the genitourinary tumors as well as in low grade gliomas. We then validated our findings in independent cohorts. Our data describe a global approach for understanding transcriptional activities of TP63 isoforms across a large number of cancer types, potentially enabling the identification of patient subsets most likely to benefit from therapies predicated on manipulating specific TP63 isoforms in order to inhibit the acquisition of pluripotency potential.

Citation Format: Hussein Abbas, Kimal Rajapakshe, Justin Wong, Ngoc Hoang Bao Bui, Preethi Gunaratne, Kenneth Tsai, Cristian Coarfa, Elsa Flores. TP63 isoforms regulate distinct and cooperative transcriptional signatures that drive cancer progression and predict clinical outcomes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-321.

Abstract 1920: Novel molecular targets for chemoprevention of squamous cell carcinoma

INTRODUCTION: It is estimated that cancer prevention efforts can reduce cancer incidence by over 50%. Unlike for advanced disease, effective molecularly-driven interventions and risk assessment are not available for clinically normal tissues that may be have been exposed to carcinogens or for precancerous lesions. Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers and has the most accessible and clinically well-characterized progression sequence of any human cancer, from a distinct precancerous lesion, the actinic keratosis (AK), to invasive carcinoma. Thus, it is an ideal model for establishing a paradigm of molecularly targeted cancer chemoprevention.

METHODS: Here, we performed next-generation sequencing of total RNA and miRNA (Illumina HiSeq) on matched isogenic samples of human cuSCC, surrounding normal (chronically irradiated) skin (NS), and AK. In parallel, we profiled matched samples from a UV-driven Hairless mouse model of cuSCC for cross-species analysis, to identify the most important drivers of progression from NS to AK to cuSCC.

RESULTS: Unsupervised clustering of both mRNA and miRNA expression changes showed that preneoplastic AKs span a continuum indistinguishable from cuSCC or surrounding NS, whereas cuSCC and NS were easily distinguished. Through cross-species computational analysis of mRNA-miRNA functional pairs, we identified miR-21, miR-205, miR-31, let-7B, and miR-497 and their mRNA targets as core drivers of cuSCC development through the AK intermediate. We show that several of these miRNAs are modulated by UV exposure, regulate susceptibility to apoptosis, and regulate cell motility. Several miRNAs are being inhibited in our mouse model to validate them as chemoprevention targets. TRANSFAC analysis identified E2F, SP1, AP1, and TCF3 as key transcriptional regulators of SCC development. We tested the global mRNA and miRNA expression similarities to other tumor types profiled by the NIH TCGA effort, showing that cuSCC is most closely related to head & neck SCC, lung SCC, and basal subtype of breast cancer. Exome analysis confirmed a high frequency of TP53, NOTCH1/2, and CDKN2A mutations in cuSCC, with mutational loads of >30/Mb that are strongly dominated by UVB signature lesions. Surprisingly, NS contains evidence of numerous mutations reflecting UV-induced somatic mosaicism.

CONCLUSIONS: We report the first integrated transcriptomic characterization of the development of cuSCC through the preneoplastic AK. AKs are indistinguishable from cuSCC, suggesting that chemoprevention efforts should be directed at UV-exposed skin prior to the emergence of lesions. Key transcriptional responses in miRNAs and transcription factor networks were identified in our cross-species analysis, which have been functionally validated. Finally, SCCs of diverse anatomic sites share deep genomic commonalities suggesting that there may be common chemoprevention strategies applicable to multiple SCC types.

Citation Format: Vida Chitsazzadeh, Cristian Coarfa, Tri H. Nguyen, Aaron K. Joseph, Preethi Gunaratne, Li Shen, Hui Yao, Weimin Xiao, Xiaoping Su, Jennifer Drummond, David Wheeler, Elsa R. Flores, Kenneth Y. Tsai. Novel molecular targets for chemoprevention of squamous cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1920. doi:10.1158/1538-7445.AM2015-1920

Large conserved domains of low DNA methylation maintained by Dnmt3a

Gains and losses in DNA methylation are prominent features of mammalian cell types. To gain insight into the mechanisms that promote shifts in DNA methylation and contribute to changes in cell fate, including malignant transformation, we performed genome-wide mapping of 5-methylcytosine and 5-hydroxymethylcytosine in purified mouse hematopoietic stem cells. We discovered extended regions of low methylation (canyons) that span conserved domains frequently containing transcription factors and are distinct from CpG islands and shores. About half of the genes in these methylation canyons are coated with repressive histone marks, whereas the remainder are covered by activating histone marks and are highly expressed in hematopoietic stem cells (HSCs). Canyon borders are demarked by 5-hydroxymethylcytosine and become eroded in the absence of DNA methyltransferase 3a (Dnmt3a). Genes dysregulated in human leukemias are enriched for canyon-associated genes. The new epigenetic landscape we describe may provide a mechanism for the regulation of hematopoiesis and may contribute to leukemia development.

G-CSF receptor positive neuroblastoma subpopulations are enriched in chemotherapy-resistant or relapsed tumors and are highly tumorigenic

Neuroblastoma is a neural crest-derived embryonal malignancy, which accounts for 13% of all pediatric cancer mortality, primarily due to tumor recurrence. Therapy-resistant cancer stem cells are implicated in tumor relapse, but definitive phenotypic evidence of the existence of these cells has been lacking. In this study, we define a highly tumorigenic subpopulation in neuroblastoma with stem cell characteristics, based on the expression of CSF3R, which encodes the receptor for granulocyte colony-stimulating factor (G-CSF). G-CSF receptor positive (aka G-CSFr(+) or CD114(+)) cells isolated from a primary tumor and the NGP cell line by flow cytometry were highly tumorigenic and capable of both self-renewal and differentiation to progeny cells. CD114(+) cells closely resembled embryonic and induced pluripotent stem cells with respect to their profiles of cell cycle, miRNA, and gene expression. In addition, they reflect a primitive undifferentiated neuroectodermal/neural crest phenotype revealing a developmental hierarchy within neuroblastoma tumors. We detected this dedifferentiated neural crest subpopulation in all established neuroblastoma cell lines, xenograft tumors, and primary tumor specimens analyzed. Ligand activation of CD114 by the addition of exogenous G-CSF to CD114(+) cells confirmed intact STAT3 upregulation, characteristic of G-CSF receptor signaling. Together, our data describe a novel distinct subpopulation within neuroblastoma with enhanced tumorigenicity and a stem cell-like phenotype, further elucidating the complex heterogeneity of solid tumors such as neuroblastoma. We propose that this subpopulation may represent an additional target for novel therapeutic approaches to this aggressive pediatric malignancy.

Abstract B14: Synergy of small-molecule inhibitors in cutaneous T-cell lymphoma cells: A discovery tool to define new therapeutic targets

Cutaneous T-Cell Lymphomas (CTCL) represent a heterogeneous group of hematopoietic malignancies that account for 5-10% of Non-Hodgkin Lymphomas. The initial disease presentation is characterized by the infiltration of the skin by malignant clonal CD4+ lymphocytes that possess a mature memory helper T-cell phenotype. CTCL patients present in a spectrum of defined disease phenotypes, Mycosis Fungoides (MF) and Sézary Syndrome (SS) being the most common. Thus, it is not surprising that no underlying molecular basis for disease has been identified. Standard treatment protocols are designed to provide palliation, as no chemotherapeutic compound(s) has demonstrated increased long-term or disease-free survival. Currently, no curative therapy for CTCL exists. Our long-term goal is to gain a better understanding of the pathways governing CTCL cell survival and proliferation while identifying druggable targets for the development of new and more effective therapeutics. The principles of chemical biology, to discover and elucidate molecular pathways fundamental in cellular, developmental, and disease biology through synthetic organic chemistry, are readily applied to the field drug discovery. Using these methods, we have previously observed that inhibition of protein kinase C (PKC) β with the small molecule Enzastaurin (Enz), combined with inhibition of glycogen synthase kinase 3 (GSK3) with AR-A014418 (ARA), causes synergistic apoptosis in CTCL cell lines (Hut78 and H9). Critically, this cell death is dependent on the increase in active β-catenin protein expression. Treatment of cells with ICAT, a protein that prevents the interaction of β-catenin and TCF, demonstrated that β-catenin-mediated transcriptional activity participates in the combined compound—induced cell death. In order to assess potential targets of Enz and ARA treatment, we recently screened downstream β-catenin-mediated targets with a commercially available signaling pathway PCR array and validated them with qRT-PCR. Several targets of β-catenin were differentially regulated by the combined small-molecule treatment. We decreased cellular β-catenin by either siRNA knockdown or shRNA in stable cell lines and determined that β-catenin is required for compound-induced cytotoxicity of CTCL cell lines. In contrast, overexpression of β-catenin in CTCL cell lines demonstrated β-catenin alone is not sufficient to induce apoptosis. Thus, while we have identified β-catenin as a key regulator of CTCL viability, there are likely additional undescribed mechanisms of cell death stimulated by the combined inhibition of PKC and GSK3. From these data, we conclude that the combined inhibition of PKC and GSK signaling in CTCL causes cell death by impacting β-catenin specific targets as well as by stimulating cell death independent of β-catenin. To further elucidate these mechanisms we are assaying drug-treatment induced changes in global gene expression through a microarray approach. We are identifying transcripts that are significantly regulated after combined inhibition of PKC and GSK3 with Enz and ARA respectively. These data will provide the basis for downstream target identification for further drug development.

Citation Format: Meghan Bliss-Moreau, Weimin Xiao, Preethi Gunaratne, Nancy L. Krett, Steven T. Rosen. Synergy of small-molecule inhibitors in cutaneous T-cell lymphoma cells: A discovery tool to define new therapeutic targets. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B14.

Abstract 2331: Deletion of ΔNp63 and ΔNp73 in p53 deficient mice results in TAp63 and TAp73 compensation of p53 tumor suppression in vivo

p53 tumor suppressor undergoes mutational loss in majority of cancers contributing to tumor formation. Therapeutic strategies are aimed towards p53 overexpression in tumors or to identify targets that compensate for p53-functional loss. p63 & p73, share structural similarities to p53, making them excellent candidates for therapeutic compensation of p53. Unlike p53, p63 and p73 do not undergo mutational loss and their role in tumorigenesis is being delineated. p63 and p73 have two major isoforms, the transactivation (TA), with activities similar to p53 and the delta (Δ)N- isoform with oncogenic functions. Inhibition of TAp63 and TAp73 is observed in cancers as a consequence of overexpression of ΔN isoforms of p63 and p73. In disparity, recent studies report, tumor suppressive properties of ΔNp63 and ΔNp73 in activating genes involved in DNA repair and apoptosis.

To define the functional roles of ΔNp63 and ΔNp73 in cancer, mouse models targeting the ΔN isoforms were generated. We observed that, ΔNp63+/- and ΔNp73−/− mice on a p53−/− background had lower thymic lymphoma incidence compared to the p53−/− mice. I found TAp63 and TAp73 up regulated in the double mutant mice that correspond with an increase in p53-downstream apoptotic (PUMA, Noxa, BAX) and cell cycle targets (p21, p16, PML). This suggests that ablation of ΔN isoforms mediate TAp63 and TAp73 up regulation inducing apoptosis or cell cycle arrest by activation of p53-downstream targets. To further demonstrate this, I ablated ΔNp63 and ΔNp73 in vivo in p53−/- mice thymic lymphoma by administering adenoviral-CRE specifically to the thymus. The CRE-treated mice had a significant thymic lymphoma regression within 3 weeks as imaged by MRI in comparison to the mock-treated mouse cohorts. Additionally, RNA-Seq analysis from CRE-treated versus untreated mice, has identified novel metabolic genes with apoptotic or cell-cycle functions. We further report, ΔNp63 and ΔNp73 to bind to promoter site of TAp63 and TAp73 by chromatin immunoprecipitation (ChIP). This supports the notion that ablation of ΔN isoforms of p63 and p73 restores the function of TAp63 and TAp73 thus compensating for p53-tumor suppressive function in vivo. To test, if ablation of ΔN isoforms reduces tumorigenesis in human cancers, ΔNp63 and ΔNp73 were knocked down in human cancer cell lines were p53 expression was ablated or mutated. TAp63 and TAp73 were upregulated in ΔNp63/ΔNp73 knock down human cancer cell lines. However, induction of apoptosis or cell-cycle arrest was observed in p53-deleted cancer cell lines in comparison to the p53-mutated cell lines. This highlights the co-repressive effect of mutant p53, preventing activation of TAp63/TAp73 downstream targets. Current work is aimed towards overcoming mutant p53 effect in these cancer cell lines. Thus, targeting the ΔNp63/ΔNp73 compensates for p53-functional loss mediating tumor suppression.

Citation Format: Avinashnarayan Venkatanarayan, Deepavali Chakravarti, Xiaohua Su, Santosh Sandur, Lingzhi Liu, Eliot Fletcher Sananikone, Payal Raulji, Cristian Coarfa, William Norton, Preethi Gunaratne, Elsa Renee Flores. Deletion of ΔNp63 and ΔNp73 in p53 deficient mice results in TAp63 and TAp73 compensation of p53 tumor suppression in vivo. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2331. doi:10.1158/1538-7445.AM2013-2331

Molecular and functional characteristics of ovarian surface epithelial cells transformed by KrasG12D and loss of Pten in a mouse model in vivo

Ovarian cancer is a complex and deadly disease that remains difficult to detect at an early curable stage. Furthermore, although some oncogenic (Kras, Pten/PI3K and Trp53) pathways that are frequently mutated, deleted or amplified in ovarian cancer are known, how these pathways initiate and drive specific morphological phenotypes and tumor outcomes remain unclear. We recently generated Pten(fl/fl); Kras(G12D); Amhr2-Cre mice to disrupt the Pten gene and express a stable mutant form of Kras(G12D) in ovarian surface epithelial (OSE) cells. On the basis of histopathologic criteria, the mutant mice developed low-grade ovarian serous papillary adenocarcinomas at an early age and with 100% penetrance. This highly reproducible phenotype provides the first mouse model in which to study this ovarian cancer subtype. OSE cells isolated from ovaries of mutant mice at 5 and 10 weeks of age exhibit temporal changes in the expression of specific Mullerian epithelial marker genes, grow in soft agar and develop ectopic invasive tumors in recipient mice, indicating that the cells are transformed. Gene profiling identified specific mRNAs and microRNAs differentially expressed in purified OSE cells derived from tumors of the mutant mice compared with wild-type OSE cells. Mapping of transcripts or genes between the mouse OSE mutant data sets, the Kras signature from human cancer cell lines and the human ovarian tumor array data sets, documented significant overlap, indicating that KRAS is a key driver of OSE transformation in this context. Two key hallmarks of the mutant OSE cells in these mice are the elevated expression of the tumor-suppressor Trp53 (p53) and its microRNA target, miR-34a-c. We propose that elevated TRP53 and miR-34a-c may exert negatively regulatory effects that reduce the proliferative potential of OSE cells leading to the low-grade serous adenocarcinoma phenotype.

Abstract 2029: Identification of novel tumor suppressor microRNAs implicated in epithelial ovarian cancer from the 19q13.41 non-coding RNA cluster

Background: Epithelial ovarian cancer is the 5th leading cause of cancer death in women. Our objective was to identify key genetic events important for the pathogenesis of this lethal disease. Methods: Levels of microRNA (miRNA) expression were examined in specimens of primary papillary serous carcinomas, normal ovary and distal fallopian tube using Next Generation Sequencing and a custom expression array. Chromosomal gains and losses were also examined by CGH. SYBR Green reagents were used to measure relative expression of target gene expression by quantitative real-time PCR. Functional impact of altered miRNA expression was tested using standard MTT and Caspase 3/7 assays to measure proliferation and apoptosis (Promega). Key outcome demographics were coded and correlated with miRNA and gene expression by Kaplan-Meier analysis. Results: A total of 140 miRNAs were differentially expressed when papillary serous ovarian cancers were compared to either fimbrae of normal fallopian or normal ovary. Of these, 36 miRNAs were found to correlate with either overall survival, disease free interval (DFI) or platinum sensitivity. Nineteen (19) of these clinically significant miRNAs mapped to single primate-specific genomic locus located at 19q13.41. This locus spanned 125 Kb of non-coding DNA and encoded a total of 44 miRNAs, most all of which showed significant copy number variation in papillary serous ovarian cancers (n = 178) and showed copy losses in the majority of tumors. Using established algorithms for target prediction, we found that this miRNA cluster collectively targeted more than 2800 distinct genes. Key loci included gene products implicated in the epithelial-to-mesenchymal transition (Snail, Slug) as well as both the G1-S and G2-M cell cycle checkpoints (MYCN and Wee1). Transfection of established ovarian cancer cell lines with individual 19q13.41 miRNAs significantly reduced expression of Snail, Slug, Wee1, resulting in altered proliferation and apoptosis. Conclusions: Altered expression of 19q13.41 cluster miRNAs correlate with significant clinical outcomes for women with papillary serous ovarian cancers. These miRNAs appear to play a key role in regulating the expression of gene products critical for the ongoing proliferation and metastasis of ovarian cancer. Future work will focus on dissecting the role of individual 19q13.41 miRNAs in ovarian and other cancers as well as validating the novel nanoparticle-based strategies we have developed for therapeutic miRNA delivery. Supported by NIH TCGA and the Ovarian Cancer Research Foundation (OCRF)

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2029.

The genome of a songbird

The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.

A genome-wide screen for copy number alterations in Aicardi syndrome

Aicardi syndrome is a severe neurodevelopmental disorder that affects females or rarely males with a 47,XXY karyotype. Therefore, it is thought to be caused by heterozygous defects in an essential X-linked gene or by defects in an autosomal gene with sex-limited expression. Because all reported cases are sporadic with one exception, traditional linkage analysis to identify the mutant gene is not possible, and the de novo mutation rate must be high. As an alternative approach to localize the mutant gene, we screened the DNA of 38 girls with Aicardi syndrome by high-resolution, genome-wide array comparative genomic hybridization for copy number gains and losses. We found 110 copy number variants (CNVs), 97 of which are known, presumably polymorphic, CNVs; 8 have been seen before in unrelated studies in unaffected individuals. Four previously unseen CNVs on autosomes were each inherited from a healthy parent. One subject with Aicardi syndrome had a de novo loss of X-linked copy number in a region without known genes. Detailed analysis of this and flanking regions did not reveal CNVs or mutations in annotated genes in other affected subjects. We conclude that, in this study population of 38 subjects, Aicardi syndrome is not caused by CNVs detectable with the high-resolution array platform that was used.

Lung RNA profiling suggests an essential role for micro RNAs in regulating allergic lung disease (91.9)

MicroRNAs (miRNAs) are small non-coding RNAs, which negatively regulate gene expression by translational inhibition of target mRNAs. In vertebrates, miRNAs are produced in most organs, including lungs. In the current study, we hypothesized that the expression of miRNAs would correlate inversely with expression of critically important target genes involved in the pathogenesis of allergic lung disease. After intranasal challenge of mice with a potent allergen derived from Aspergillus oryzae on alternating days for 2 weeks, lungs were isolated, high quality RNA was extracted and subjected to microarray analysis in comparison to naïve lungs obtained in parallel. In allergic lungs, ~ 30 known miRNAs were suppressed and ~100 were induced, including many new miRNA candidates uncovered through genome-wide predictions. Bioinformatics analysis revealed that miRNA 199a*, which was suppressed, and miR-144 which was induced in allergic lungs, are candidate regulators of STAT-6, GATA-3 and costimulatory factors, all of which are critical mediators of allergic lung disease. These studies suggest the existence of many new miRNAs and pivotal role for miRNA 199a* in controlling the expression of allergic lung disease.

The DNA sequence, annotation and analysis of human chromosome 3

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

The finished DNA sequence of human chromosome 12

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

Identification of prognosis markers in pediatric high-risk acute lymphoblastic leukemia

Gene expression profiling may improve the understanding of the biology behind relapse in pediatric acute lymphoblastic leukemia. Using suppression subtractive hybridization (SSH), cDNA concatenated sequencing (CCS), and reverse transcriptase real-time quantitative polymerase chain reaction (RT-RQ-PCR) on high-risk patient samples with nondeterminant chromosomal translocation, the authors identified 3 genes that were significantly overexpressed in the nonrelapsed patients: the calcium/calmodulin-dependent serine protein kinase (CASK), subunit 2 of the cofactor required for SP1 transcriptional activation (CRSP2), and granzyme K (GZMK). The level of expression of these biomarkers may help identify patients with potentially good prognosis within a group otherwise at high risk of relapse.

The DNA sequence of the human X chromosome

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

Novel potential ALL low-risk markers revealed by gene expression profiling with new high-throughput SSH-CCS-PCR

The current systems of risk grouping in pediatric acute lymphoblastic leukemia (ALL) fail to predict therapeutic success in 10-35% of patients. To identify better predictive markers of clinical behavior in ALL, we have developed an integrated approach for gene expression profiling that couples suppression subtractive hybridization, concatenated cDNA sequencing, and reverse transcriptase real-time quantitative PCR. Using this approach, a total of 600 differentially expressed genes were identified between t(4;11) ALL and pre-B ALL with no determinant chromosomal translocation. The expression of 67 genes was analyzed in different cytogenetic ALL subgroups and B lymphocytes isolated from healthy donors. Three genes, BACH1, TP53BPL, and H2B/S, were consistently expressed as a significant cluster associated with the low-risk ALL subgroups. A total of 42 genes were differentially expressed in ALL vs normal B lymphocytes, with no specific association with any particular ALL subgroups. The remaining 22 genes were part of a specific expression profile associated with the hyperdiploid, t(12;21), or t(4;11) subgroups. Using an unsupervised hierarchical cluster analysis, the discriminating power of these specific expression profiles allowed the clustering of patients according to their subgroups. These genes could help to understand the difference in treatment response and become therapeutical targets to improve ALL clinical outcomes.

Transcriptional regulation of the murine erythroid-specific 5-aminolevulinate synthase gene

5-Aminolevulinate synthase (ALAS) catalyzes the first step of the heme biosynthetic pathway in mammalian cells. Separate genes encode the two isoforms: ubiquitously expressed ALAS (ALAS1) and erythroid-specific ALAS (ALAS2). Transcription of the ALAS2 gene is only activated during erythroid cell differentiation. This stimulation allows for the formation of hemoglobin-specific heme. The 5'-flanking region of the mouse ALAS2 gene was studied in order to define its erythroid-specific function in transcriptional activation. Putative binding sites for the erythroid-specific nuclear factors GATA-1, NF-E2, and EKLF were identified within the first 300bp region of the mouse ALAS2 5'-flanking region. However, this 300bp region alone did not efficiently activate transient expression in erythroid MEL and K562 cell lines. Additional DNA regulatory sequences found within 300-718bp upstream of the transcription start site were required for maximal transcriptional activation, even though these regions stimulated similar expression in the non-erythroid HeLa and NIH/3T3 cells. This suggests that cis-acting elements present in the 5'-flanking region are not responsible for maintenance of transcriptional silencing in non-erythroid cell lines and that tissue-specific regulation of ALAS2 depends on other regions of the gene or on chromatin remodeling. A putative hypoxia inducible factor 1 (HIF-1) response element was identified within the 300-718bp upstream region. Significantly, two proximal GATA-1-binding sites (-118/-113 and -98/-93) and a region located within -518 to -315bp of the mouse ALAS2 promoter were essential for transcriptional activation during chemically induced differentiation of MEL cells, implying their importance in conferring erythroid specificity to the ALAS2 transcriptional activation. This is the first study to delimit the cis-acting region responsible for activation of the ALAS2 promoter upon dimethyl-sulfoxide induction in MEL cells.

Duplication of the PMP22 gene in 17p partial trisomy patients with Charcot-Marie-Tooth type-1 neuropathy

Autosomal dominant Charcot-Marie-Tooth type-1A neuropathy (CMT1A) is a demyelinating peripheral nerve disorder that is commonly associated with a submicroscopic tandem DNA duplication of a 1.5-Mb region of 17p11.2p12 that contains the peripheral myelin gene PMP22. Clinical features of CMT1A include progressive distal muscle atrophy and weakness, foot and hand deformities, gait abnormalities, absent reflexes, and the completely penetrant electrophysiologic phenotype of symmetric reductions in motor nerve conduction velocities (NCVs). Molecular and fluorescense in situ hybridization (FISH) analyses were performed to determine the duplication status of the PMP22 gene in four patients with rare cytogenetic duplications of 17p. Neuropathologic features of CMT1A were seen in two of these four patients, in addition to the complex phenotype asociated with 17p partial trisomy. Our findings show that the CMT1A phenotype of reduced NCV is specifically associated with PMP22 gene duplications, thus providing further support for the PMP22 gene dosage mechanism for CMT1A.

Protein tyrosyl phosphatase-1B is expressed by normal human epidermis, keratinocytes, and A-431 cells and dephosphorylates substrates of the epidermal growth factor receptor

In the epidermis tyrosine kinases such as those found in the epidermal growth factor receptor (EGF-R) phosphorylate regulatory molecules on tyrosine and play an important role in controlling epidermal growth. Phosphotyrosyl phosphatases (PTPase) that dephosphorylate EGF-R and other proteins phosphorylated on tyrosine must also play an important role in controlling epidermal growth. The presence and metabolism of one such PTPase, PTP-1B, was detected and studied in human skin using biochemical, immunochemical, and molecular biologic methods. The message for PTP-1B was expressed in human epidermis, in keratinocytes cultured from human epidermis, and in human keratinocyte cell lines. The 49-kDa but not the 37-kDa form of PTP-1B was identified in membranes prepared from these cells and tissues by immunodetection on Western blots. Nearly all of the labeled proteins identified by gel electrophoresis of an A-431 particulate fraction phosphorylated with [gamma-32P] ATP in the presence of epidermal growth factor are substrates for PTP-1B because their labeling decreased after incubation with a catalytically active and purified PTP-1B fusion protein. Immunohistochemical methods were used to show that PTP-1B was primarily localized to the basal cell layers in normal thick epidermis. The presence of PTP-1B in intact human epidermis suggests that this molecule is not an artifact limited to cultured cells but is an important molecule in the in vivo regulation of epidermal functions.