Showing papers by "Ie Ming Shih published in 2017"
TL;DR: Genetic aberrances in fallopian tube lesions, ovarian cancers, and metastases from HGSOC patients are analyzed and evolutionary analyses reveal that p53 signatures and STICs are precursors of ovarian carcinoma and identify a window of 7 years between development of a STIC and initiation of ovarian cancer, with metastases following rapidly thereafter.
Abstract: High-grade serous ovarian carcinoma (HGSOC) is the most frequent type of ovarian cancer and has a poor outcome. It has been proposed that fallopian tube cancers may be precursors of HGSOC but evolutionary evidence for this hypothesis has been limited. Here, we perform whole-exome sequence and copy number analyses of laser capture microdissected fallopian tube lesions (p53 signatures, serous tubal intraepithelial carcinomas (STICs), and fallopian tube carcinomas), ovarian cancers, and metastases from nine patients. The majority of tumor-specific alterations in ovarian cancers were present in STICs, including those affecting TP53, BRCA1, BRCA2 or PTEN. Evolutionary analyses reveal that p53 signatures and STICs are precursors of ovarian carcinoma and identify a window of 7 years between development of a STIC and initiation of ovarian carcinoma, with metastases following rapidly thereafter. Our results provide insights into the etiology of ovarian cancer and have implications for prevention, early detection and therapeutic intervention of this disease.
467 citations
TL;DR: It is found that lesions in deep infiltrating endometriosis, which are associated with virtually no risk of malignant transformation, harbor somatic cancer driver mutations.
Abstract: BackgroundEndometriosis, defined as the presence of ectopic endometrial stroma and epithelium, affects approximately 10% of reproductive-age women and can cause pelvic pain and infertility. Endometriotic lesions are considered to be benign inflammatory lesions but have cancerlike features such as local invasion and resistance to apoptosis. MethodsWe analyzed deeply infiltrating endometriotic lesions from 27 patients by means of exomewide sequencing (24 patients) or cancer-driver targeted sequencing (3 patients). Mutations were validated with the use of digital genomic methods in microdissected epithelium and stroma. Epithelial and stromal components of lesions from an additional 12 patients were analyzed by means of a droplet digital polymerase-chain-reaction (PCR) assay for recurrent activating KRAS mutations. ResultsExome sequencing revealed somatic mutations in 19 of 24 patients (79%). Five patients harbored known cancer driver mutations in ARID1A, PIK3CA, KRAS, or PPP2R1A, which were validated by Safe...
403 citations
TL;DR: It is shown that epigenetic therapy in a mouse model of ovarian cancer increases the numbers of activated immune cells, and that this is dependent on the interferon antiviral response, which indicates that the type I IFN response is required for effective in vivo antitumorigenic actions of the DNMTi 5-azacytidine (AZA).
Abstract: Ovarian cancer is the most lethal of all gynecological cancers, and there is an urgent unmet need to develop new therapies. Epithelial ovarian cancer (EOC) is characterized by an immune suppressive microenvironment, and response of ovarian cancers to immune therapies has thus far been disappointing. We now find, in a mouse model of EOC, that clinically relevant doses of DNA methyltransferase and histone deacetylase inhibitors (DNMTi and HDACi, respectively) reduce the immune suppressive microenvironment through type I IFN signaling and improve response to immune checkpoint therapy. These data indicate that the type I IFN response is required for effective in vivo antitumorigenic actions of the DNMTi 5-azacytidine (AZA). Through type I IFN signaling, AZA increases the numbers of CD45+ immune cells and the percentage of active CD8+ T and natural killer (NK) cells in the tumor microenvironment, while reducing tumor burden and extending survival. AZA also increases viral defense gene expression in both tumor and immune cells, and reduces the percentage of macrophages and myeloid-derived suppressor cells in the tumor microenvironment. The addition of an HDACi to AZA enhances the modulation of the immune microenvironment, specifically increasing T and NK cell activation and reducing macrophages over AZA treatment alone, while further increasing the survival of the mice. Finally, a triple combination of DNMTi/HDACi plus the immune checkpoint inhibitor α-PD-1 provides the best antitumor effect and longest overall survival, and may be an attractive candidate for future clinical trials in ovarian cancer.
196 citations
TL;DR: The data suggest that the molecular features of HGSCs with and without associated STIC lesions are mostly shared, indicating a common biologic origin, likely to be the distal fallopian tube among all cases.
Abstract: Many high-grade serous carcinomas (HGSCs) of the pelvis are thought to originate in the distal portion of the fallopian tube. Serous tubal intra-epithelial carcinoma (STIC) lesions are the putative precursor to HGSC and identifiable in ~ 50% of advanced stage cases. To better understand the molecular etiology of HGSCs, we report a multi-center integrated genomic analysis of advanced stage tumors with and without STIC lesions and normal tissues. The most significant focal DNA SCNAs were shared between cases with and without STIC lesions. The RNA sequence and the miRNA data did not identify any clear separation between cases with and without STIC lesions. HGSCs had molecular profiles more similar to normal fallopian tube epithelium than ovarian surface epithelium or peritoneum. The data suggest that the molecular features of HGSCs with and without associated STIC lesions are mostly shared, indicating a common biologic origin, likely to be the distal fallopian tube among all cases. High-grade serous carcinomas (HGSCs) are associated with precursor lesions (STICs) in the fallopian epithelium in only half of the cases. Here the authors report the molecular analysis of HGSCs with and without associated STICs and show similar profiles supporting a common origin for all HGSCs.
151 citations
TL;DR: A strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq), and the development of a machine-learning–based computational pipeline, TIPseqHunter, to identify insertion sites with high precision and reliability.
Abstract: Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These mobile DNAs are self-propagating, and their continued transposition is a source of both heritable structural variation as well as somatic mutation in human genomes. Tailored approaches to map these sequences are useful to identify insertion alleles. Here, we describe in detail a strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq). We also report the development of a machine-learning-based computational pipeline, TIPseqHunter, to identify insertion sites with high precision and reliability. We demonstrate the utility of this approach to detect somatic retrotransposition events in high-grade ovarian serous carcinoma.
81 citations
TL;DR: The data regarding the association between endometriosis and ovarian cancer and the potential correlation of endometRIosis with other cancers are critically appraised.
Abstract: Endometriosis is defined as the presence of viable endometrial glands and stroma outside of the uterus. It is a common disease, occurring in 5 to 15% of all women. Endometriosis is associated with chronic pelvic pain and infertility and often requires surgical intervention for definitive treatment. Although it is a benign gynecologic condition, endometriosis shares pathophysiologic features with cancer. In recent years, both histologic and epidemiologic evidence has accumulated, suggesting that ovarian endometriosis may give rise to malignant ovarian tumors, primarily those that are epithelial in origin, known as endometriosis-associated ovarian carcinoma (EAOC) including ovarian clear cell carcinoma, endometrioid carcinoma, and the least common, seromucinous tumors. Women with endometriosis have a two- to threefold increase in absolute risk of developing epithelial ovarian cancer, especially clear cell and endometrioid subtypes. Somatic mutations, such as ARID1A, PIK3CA, and PTEN, may promote the progression of benign endometriosis to carcinoma. Endometriosis has been implicated in the development of other malignancies, including endometrial and breast cancer. In this review, we critically appraise the data regarding the association between endometriosis and ovarian cancer and the potential correlation of endometriosis with other cancers.
64 citations
TL;DR: It is suggested that gene copy-number gain and upregulation of CCNE1 occur in ovarian clear cell carcinoma and are associated with a worse clinical outcome, dictating the survival of early-stage patients, and that these molecular alterations are unique to clear cell cancer among different types of endometriosis-related ovarian neoplasms.
49 citations
TL;DR: The tumor microenvironment (TME) of primary and recurrent EOC was evaluated for CD8+ T cells, FOXP3+ regulatory T cells (Tregs), CD68+ tumor-associated macrophages, programmed cell death protein 1 (PD-1) and programmed cellDeath ligand 1 ( PD-L1).
34 citations
TL;DR: Critical data imply that ZIP4 is a new and important cancer stem cell regulator in ovarian cancer, and provide an innovative interpretation for the apparent disconnection between low levels of zinc and up-regulation of ZIP4 in Ovarian cancer tissues.
Abstract: // Qipeng Fan 1 , Qingchun Cai 1 , Pengfei Li 1, 2 , Wenyan Wang 1, 3 , Jing Wang 1, 4 , Emily Gerry 5 , Tian-Li Wang 5 , Ie-Ming Shih 5 , Kenneth P Nephew 6 and Yan Xu 1 1 Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202, USA 2 Pharmaceutical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, PR China 3 Department of Obstetrics and Gynecology, The Second Hospital of Anhui Medical University, Hefei City, 230601, PR China 4 MASDINO (Beijing) Medical Research Co Ltd, Beijing, 100123, PR China 5 Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA 6 Medical Sciences, Indiana University School of Medicine, Jordan Hall 302, Bloomington, IN 47405, USA Correspondence to: Yan Xu, email: xu2@iupuiedu Keywords: ZIP4, LPA, ovarian cancer, cancer stem cells (CSC) Received: June 07, 2017 Accepted: August 26, 2017 Published: September 30, 2017 ABSTRACT Our RNAseq analyses revealed that ZIP4 is a top gene up-regulated in more aggressive ovarian cancer cells ZIP4’s role in cancer stem cells has not been reported in any type of cancer In addition, the role and regulation of ZIP4, a zinc transporter, have been studied in the context of extracellular zinc transporting Factors other than zinc with ZIP4 regulatory effects are essentially unknown ZIP4 expression and its regulation in epithelial ovarian cancer cells was assessed by immunoblotting, quantitative PCR, or immunohistochemistry staining in human ovarian tissues Cancer stem cell-related activities were examined to evaluate the role of ZIP4 in human high-grade serous ovarian cancer cells in vitro and in vivo RNAi and CRISPR techniques were used to knockdown or knockout ZIP4 and related genes Ovarian cancer tissues overexpressed ZIP4 when compared with normal and benign tissues ZIP4 knockout significantly reduced several cancer stem cell-related activities in EOC cells, including proliferation, anoikis-resistance, colony-formation, spheroid-formation, drug-resistance, and side-population in vitro ZIP4-expressing side-population highly expressed known CSC markers ALDH1 and OCT4 ZIP4 knockout dramatically reduced tumorigenesis and ZIP4 overexpression increased tumorigenesis in vivo In addition, the ZIP4-expressing side-population had the tumor initiating activity Moreover, the oncolipid lysophosphatic acid effectively up-regulated ZIP4 expression via the nuclear receptor peroxisome proliferator-activated receptor gamma and lysophosphatic acid ’s promoting effects in cancer stem cell-related activities in HGSOC cells was at least partially mediated by ZIP4 in an extracellular zinc-independent manner Our critical data imply that ZIP4 is a new and important cancer stem cell regulator in ovarian cancer Our data also provide an innovative interpretation for the apparent disconnection between low levels of zinc and up-regulation of ZIP4 in ovarian cancer tissues
26 citations
TL;DR: Results indicate that, although recurrent NRAS mutations are present, their low prevalence indicates that NRAS plays a limited role in the development of LGSC, and further studies to identify other oncogenic events that drive LGSC progression are warranted.
21 citations
30 Sep 2017
TL;DR: Xu et al. as mentioned in this paper showed that the role and regulation of ZIP4, a zinc transporter, have been studied in the context of extracellular zinc transporting, which implies that ZIP4 is a new important cancer stem cell regulator in ovarian cancer.
Abstract: // Qipeng Fan 1 , Qingchun Cai 1 , Pengfei Li 1, 2 , Wenyan Wang 1, 3 , Jing Wang 1, 4 , Emily Gerry 5 , Tian-Li Wang 5 , Ie-Ming Shih 5 , Kenneth P. Nephew 6 and Yan Xu 1 1 Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202, USA 2 Pharmaceutical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, P.R. China 3 Department of Obstetrics and Gynecology, The Second Hospital of Anhui Medical University, Hefei City, 230601, P.R. China 4 MASDINO (Beijing) Medical Research Co. Ltd., Beijing, 100123, P.R. China 5 Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA 6 Medical Sciences, Indiana University School of Medicine, Jordan Hall 302, Bloomington, IN 47405, USA Correspondence to: Yan Xu, email: xu2@iupui.edu Keywords: ZIP4, LPA, ovarian cancer, cancer stem cells (CSC) Received: June 07, 2017 Accepted: August 26, 2017 Published: September 30, 2017 ABSTRACT Our RNAseq analyses revealed that ZIP4 is a top gene up-regulated in more aggressive ovarian cancer cells. ZIP4’s role in cancer stem cells has not been reported in any type of cancer. In addition, the role and regulation of ZIP4, a zinc transporter, have been studied in the context of extracellular zinc transporting. Factors other than zinc with ZIP4 regulatory effects are essentially unknown. ZIP4 expression and its regulation in epithelial ovarian cancer cells was assessed by immunoblotting, quantitative PCR, or immunohistochemistry staining in human ovarian tissues. Cancer stem cell-related activities were examined to evaluate the role of ZIP4 in human high-grade serous ovarian cancer cells in vitro and in vivo . RNAi and CRISPR techniques were used to knockdown or knockout ZIP4 and related genes. Ovarian cancer tissues overexpressed ZIP4 when compared with normal and benign tissues. ZIP4 knockout significantly reduced several cancer stem cell-related activities in EOC cells, including proliferation, anoikis-resistance, colony-formation, spheroid-formation, drug-resistance, and side-population in vitro . ZIP4-expressing side-population highly expressed known CSC markers ALDH1 and OCT4. ZIP4 knockout dramatically reduced tumorigenesis and ZIP4 overexpression increased tumorigenesis in vivo . In addition, the ZIP4-expressing side-population had the tumor initiating activity. Moreover, the oncolipid lysophosphatic acid effectively up-regulated ZIP4 expression via the nuclear receptor peroxisome proliferator-activated receptor gamma and lysophosphatic acid ’s promoting effects in cancer stem cell-related activities in HGSOC cells was at least partially mediated by ZIP4 in an extracellular zinc-independent manner. Our critical data imply that ZIP4 is a new and important cancer stem cell regulator in ovarian cancer. Our data also provide an innovative interpretation for the apparent disconnection between low levels of zinc and up-regulation of ZIP4 in ovarian cancer tissues.
TL;DR: It is demonstrated that ferryl haemoglobin in peritoneal fluid could prevent cell death from DNA‐damaged fimbrial epithelial cells, facilitating ovulation‐induced carcinogenesis of tubal epithelium, providing new insight into the tumour initiation event in HGSC.
Abstract: Ovarian high-grade serous carcinoma (HGSC) is the most malignant neoplasm of the gynaecological tract. While the origins of many human malignant neoplasms are clear, the origin of HGSC remains poorly understood. This lack of knowledge limits our understanding of its pathogenesis and compromises efforts devoted to developing better early detection tools and effective preventative interventions. The paradigm of the tubal origin of HGSC has been advanced since the initial report of dysplastic lesions (now known as serous tubal intraepithelial carcinomas or STICs) that morphologically resemble HGSC in the Fallopian tube. These were observed in a group of patients with a genetic predisposition to ovarian cancer who were undergoing risk-reducing salpingo-oophorectomy. Since then, a series of clinico-pathological and molecular studies have characterized STICs and their concurrent HGSCs, and the results support the new paradigm of a tubal origin of many 'ovarian' HGSCs. Reactive oxygen species-containing ovulatory follicular fluid has been thought to be the major culprit behind DNA damage in tubal epithelial cells, leading to either cell death or, if the cells survive, mutagenesis. A recent report from this journal demonstrates that ferryl haemoglobin (Hb) in peritoneal fluid could prevent cell death from DNA-damaged fimbrial epithelial cells, facilitating ovulation-induced carcinogenesis of tubal epithelium. This timely study provides new insight into the tumour initiation event in HGSC. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
TL;DR: The CINdex Bioconductor package calculates the chromosome instability (CIN) index, a novel measurement that quantitatively characterizes genome-wide copy number alterations (CNAs) as a measure of CIN, which enables in-depth systems biology–based network analysis and assessment of the impact of CNA on various biological processes or clinical outcomes.
Abstract: The CINdex Bioconductor package addresses an important area of high-throughput genomic analysis. It calculates the chromosome instability (CIN) index, a novel measurement that quantitatively characterizes genome-wide copy number alterations (CNAs) as a measure of CIN. The advantage of this package is an ability to compare CIN index values between several groups for patients (case and control groups), which is a typical use case in translational research. The differentially changed cytobands or chromosomes can then be linked to genes located in the affected genomic regions, as well as pathways. This enables in-depth systems biology-based network analysis and assessment of the impact of CNA on various biological processes or clinical outcomes. This package was successfully applied to analysis of DNA copy number data in colorectal cancer as a part of multi-omics integrative study as well as for analysis of several other cancer types. The source code, along with an end-to-end tutorial, and example data are freely available in Bioconductor at http://bioconductor.org/packages/CINdex/.
21 Nov 2017
TL;DR: Next-generation sequencing of tumor samples from a woman with well-differentiated endometrioid SEO tumors and a clinical “recurrent” poorly differentiated peritoneal tumor that was diagnosed 8 years after the complete resection of the SEO tumors predicted that the so-called recurrent peritoneAL tumor was derived from the same endometrial ancestor clone as the SEO tumor.
Abstract: Synchronous endometrial and ovarian (SEO) carcinomas involve endometrioid neoplasms in both the ovary and uterus at the time of diagnosis. Patients were traditionally classified as having independent primary SEO lesions or as having metastatic endometrioid carcinoma. Recent studies have supported that SEO tumors result from the dissemination of cells from one organ site to another. However, whether this can be considered a "metastasis" or "dissemination" remains unclear. In this report, we performed whole-exome sequencing of tumor samples from a woman with well-differentiated endometrioid SEO tumors and a clinical "recurrent" poorly differentiated peritoneal tumor that was diagnosed 8 years after the complete resection of the SEO tumors. Somatic mutation analysis identified 132, 171, and 1214 nonsynonymous mutations in the endometrial, ovarian, and peritoneal carcinomas, respectively. A unique mutation signature associated with mismatch repair deficiency was observed in all three tumors. The SEO carcinomas shared 57 nonsynonymous mutations, whereas the clinically suspected recurrent carcinoma shared only eight nonsynonymous mutations with the SEO tumors. One of the eight shared somatic mutations involved PTEN; these shared mutations represent the earliest genetic alteration in the ancestor cell clone. Based on analysis of the phylogenetic tree, we predicted that the so-called recurrent peritoneal tumor was derived from the same endometrial ancestor clone as the SEO tumors, and that this clone migrated and established benign peritoneal endometriosis where the peritoneal tumor later arose. This case highlights the usefulness of next-generation sequencing in defining the etiology and clonal relationships of synchronous and metachronous tumors from patients, thus providing valuable insight to aid in the clinical management of rare or ambiguous tumors.
TL;DR: This study proves the safety and establishes the dose of E39 for a larger prospective, randomized, controlled trial in HLA-A2+ EC and OC patients to prevent recurrence, and reveals that E39+GM-CSF is well-tolerated and elicits a strong, dose-dependent in vivo immune response.
01 Jan 2017
TL;DR: The clinicopathological features of representative type I tumors are described and the most recent advances in elucidating their molecular pathogenesis are summarized to discuss the ongoing and newly proposed therapeutic intervention to treat these rare types of ovarian cancer.
Abstract: Ovarian epithelial cancer is a heterogeneous group of neoplastic diseases that can be broadly classified as type I and type II tumors. While type II ovarian cancer is composed of mostly high-grade serous carcinoma (HGSC), the most common type of ovarian cancer, type I ovarian cancers, includes several histologic subtypes and each of them only constitutes a small percentage of ovarian cancer. These rare ovarian cancers are divided into three groups: (1) endometriosis-related tumors which include endometrioid, clear cell, and seromucinous carcinomas, (2) low-grade serous carcinomas, and (3) mucinous carcinomas and malignant Brenner tumors. They usually present at early stages which are amenable for curable surgical resection. They grow slowly and are always associated with precursor lesions. Molecularly, the rare (type I) tumors are characterized by frequent somatic mutations involving PTEN , CTNNB1 , ARID1A , KRAS , BRAF , ERBB2 , PIK3CA , and mismatch repair genes, which are uncommon in the conventional ovarian cancer (i.e., HGSC). The presence of mutations provides an opportunity for targeted therapy using inhibitors that inactivate individual molecular pathways. In this chapter, we will briefly describe the clinicopathological features of representative type I tumors and summarize the most recent advances in elucidating their molecular pathogenesis. Lastly, we will discuss the ongoing and newly proposed therapeutic intervention to treat these rare types of ovarian cancer.