Ovarian carcinosarcoma genomics and pre-clinical models highlight the N-MYC pathway as a key driver and susceptibility to EMT-targeting therapy

Ovarian carcinosarcoma (OCS) is an aggressive and rare tumour type with limited treatment options. OCS is hypothesised to develop via the combination theory from a single progenitor, resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). We show OCS from 18 women to be monoclonal through analysis of DNA variants from isolated carcinoma and sarcoma components. RNA sequencing indicated the carcinoma components were more mesenchymal when compared with pure ovarian carcinomas, supporting the conversion theory. We used pre-clinical OCS models to test the efficacy of microtubule-targeting drugs, including eribulin, which has been shown to reverse EMT characteristics. We demonstrated that microtubule inhibitors, vinorelbine and eribulin, were more effective than standard-of-care platinum-based chemotherapy. Eribulin reduced mesenchymal characteristics, N-MYC expression and cholesterol biosynthesis. Finally, eribulin induced a strong immune response, supporting immunotherapy combinations in the clinic.

[1]  E. Noguchi,et al.  Treatment Outcome of Second-Line Chemotherapy for Gynecologic Carcinosarcoma , 2020, Oncology.

[2]  T. Noda,et al.  Clinically relevant molecular subtypes and genomic alteration-independent differentiation in gynecologic carcinosarcoma , 2019, Nature Communications.

[3]  T. H. van der Kwast,et al.  An actionable sterol-regulated feedback loop modulates statin sensitivity in prostate cancer , 2019, Molecular metabolism.

[4]  D. Powell,et al.  Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list , 2019, Genome Biology.

[5]  Melissa J. Davis,et al.  Single sample scoring of molecular phenotypes , 2018, BMC Bioinformatics.

[6]  K. Hirakawa,et al.  Eribulin Promotes Antitumor Immune Responses in Patients with Locally Advanced or Metastatic Breast Cancer. , 2018, Anticancer research.

[7]  Fangfang Jiang,et al.  SREBP2 contributes to cisplatin resistance in ovarian cancer cells , 2018, Experimental biology and medicine.

[8]  R. Reynolds,et al.  Comparison of first-line chemotherapy regimens for ovarian carcinosarcoma: a single institution case series and review of the literature , 2018, BMC Cancer.

[9]  C. Frezza,et al.  Metabolic reprogramming and epithelial‐to‐mesenchymal transition in cancer , 2017, The FEBS Journal.

[10]  Sancha Martin,et al.  The Driver Mutational Landscape of Ovarian Squamous Cell Carcinomas Arising in Mature Cystic Teratoma , 2017, Clinical Cancer Research.

[11]  T. Akagi,et al.  Antitumor effects of eribulin depend on modulation of the tumor microenvironment by vascular remodeling in mouse models , 2017, Cancer science.

[12]  M. Menezes,et al.  The LIN28/let-7 Pathway in Cancer , 2017, Front. Genet..

[13]  E. Giannoni,et al.  Targeting the Metabolic Reprogramming That Controls Epithelial-to-Mesenchymal Transition in Aggressive Tumors , 2017, Front. Oncol..

[14]  Rob Patro,et al.  Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.

[15]  S. Tomita,et al.  Use of Tumor-infiltrating lymphocytes (TILs) to predict the treatment response to eribulin chemotherapy in breast cancer , 2017, PloS one.

[16]  M. Tibiletti,et al.  Two Cases of Carcinosarcomas of the Ovary Involved in Hereditary Cancer Syndromes. , 2017, International journal of gynecological pathology : official journal of the International Society of Gynecological Pathologists.

[17]  Matthew J. Wakefield,et al.  SurvivalVolume: interactive volume threshold survival graphs , 2016, J. Open Source Softw..

[18]  S. Mane,et al.  Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial–mesenchymal transition , 2016, Proceedings of the National Academy of Sciences.

[19]  Shuang Huang,et al.  Transcriptional Profiling Reveals a Common Metabolic Program in High-Risk Human Neuroblastoma and Mouse Neuroblastoma Sphere-Forming Cells. , 2016, Cell reports.

[20]  Joshua F. McMichael,et al.  DoCM: a database of curated mutations in cancer , 2016, Nature Methods.

[21]  M. C. Archer,et al.  The interplay between cell signalling and the mevalonate pathway in cancer , 2016, Nature Reviews Cancer.

[22]  M. Birrer,et al.  "Carcinosarcoma of the ovary, fallopian tube, and peritoneum: Prognostic factors and treatment modalities". , 2016, Gynecologic oncology.

[23]  J. Schorge,et al.  Patterns of care, predictors and outcomes of chemotherapy for ovarian carcinosarcoma: A National Cancer Database analysis. , 2016, Gynecologic oncology.

[24]  T. Yamane,et al.  In vivo imaging of eribulin-induced reoxygenation in advanced breast cancer patients: a comparison to bevacizumab , 2016, British Journal of Cancer.

[25]  J. Blay,et al.  Eribulin versus dacarbazine in previously treated patients with advanced liposarcoma or leiomyosarcoma: a randomised, open-label, multicentre, phase 3 trial , 2016, The Lancet.

[26]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[27]  Tom Walsh,et al.  Inherited Mutations in Women With Ovarian Carcinoma. , 2016, JAMA oncology.

[28]  J. Matsui,et al.  Antimitotic and Non-mitotic Effects of Eribulin Mesilate in Soft Tissue Sarcoma. , 2016, Anticancer research.

[29]  Jaime Rodriguez-Canales,et al.  A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition , 2015, Clinical Cancer Research.

[30]  B. Chetaille,et al.  Prognostic value of HMGA2, CDK4, and JUN amplification in well-differentiated and dedifferentiated liposarcomas , 2015, Modern Pathology.

[31]  T. Herzog,et al.  2771 BRCA1 and BRCA2 mutations in 1691 epithelial ovarian tumors identify subgroups with distinct molecular characteristics , 2015 .

[32]  G. Giaever,et al.  Genome-wide RNAi analysis reveals that simultaneous inhibition of specific mevalonate pathway genes potentiates tumor cell death , 2015, Oncotarget.

[33]  Nazneen Rahman,et al.  CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting , 2015, Genome Medicine.

[34]  Ying Liang,et al.  Low-molecular-mass secretome profiling identifies HMGA2 and MIF as prognostic biomarkers for oral cavity squamous cell carcinoma , 2015, Scientific Reports.

[35]  Dong Wang,et al.  Aberrant regulation of the LIN28A/LIN28B and let-7 loop in human malignant tumors and its effects on the hallmarks of cancer , 2015, Molecular Cancer.

[36]  S. Weroha,et al.  Conventional Chemotherapy and Oncogenic Pathway Targeting in Ovarian Carcinosarcoma Using a Patient-Derived Tumorgraft , 2015, PloS one.

[37]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[38]  Ethan Cerami,et al.  Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes , 2014, Nature Communications.

[39]  Y. Oda,et al.  Eribulin mesylate reduces tumor microenvironment abnormality by vascular remodeling in preclinical human breast cancer models , 2014, Cancer science.

[40]  T. Tan,et al.  Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients , 2014, EMBO molecular medicine.

[41]  M. Ko,et al.  A genetically engineered ovarian cancer mouse model based on fallopian tube transformation mimics human high‐grade serous carcinoma development , 2014, The Journal of pathology.

[42]  S. Fox,et al.  Molecular correlates of platinum response in human high‐grade serous ovarian cancer patient‐derived xenografts , 2014, Molecular oncology.

[43]  Michael F. Lawrence,et al.  Scalable Genomics with R and Bioconductor , 2014, Statistical science : a review journal of the Institute of Mathematical Statistics.

[44]  T. Yoshida,et al.  Eribulin mesilate suppresses experimental metastasis of breast cancer cells by reversing phenotype from epithelial–mesenchymal transition (EMT) to mesenchymal–epithelial transition (MET) states , 2014, British Journal of Cancer.

[45]  Peter J. Campbell,et al.  Subclonal variant calling with multiple samples and prior knowledge , 2014, Bioinform..

[46]  Daniel R. Zerbino,et al.  Ensembl 2014 , 2013, Nucleic Acids Res..

[47]  C. Chung,et al.  RKIP and HMGA2 regulate breast tumor survival and metastasis through Lysyl Oxidase and Syndecan-2 , 2013, Oncogene.

[48]  Sheena M. Scroggins,et al.  Germline and Somatic Mutations in Homologous Recombination Genes Predict Platinum Response and Survival in Ovarian, Fallopian Tube, and Peritoneal Carcinomas , 2013, Clinical Cancer Research.

[49]  N. Fleshner,et al.  Cholesterol masks membrane glycosphingolipid tumor-associated antigens to reduce their immunodetection in human cancer biopsies. , 2013, Glycobiology.

[50]  Benjamin J. Raphael,et al.  Mutational landscape and significance across 12 major cancer types , 2013, Nature.

[51]  S. Gabriel,et al.  Pan-cancer patterns of somatic copy-number alteration , 2013, Nature Genetics.

[52]  David Tamborero,et al.  OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes , 2013, Bioinform..

[53]  Y. Okada,et al.  HMGA2 is a driver of tumor metastasis. , 2013, Cancer research.

[54]  German Tischler,et al.  biobambam: tools for read pair collation based algorithms on BAM files , 2013, Source Code for Biology and Medicine.

[55]  K. Kinzler,et al.  Cancer Genome Landscapes , 2013, Science.

[56]  Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[57]  Michael Peyton,et al.  An Epithelial–Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance , 2012, Clinical Cancer Research.

[58]  R. Stallings,et al.  LIN28B induces neuroblastoma and enhances MYCN levels via let-7 suppression , 2012, Nature Genetics.

[59]  Sven Rahmann,et al.  Snakemake--a scalable bioinformatics workflow engine. , 2012, Bioinformatics.

[60]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[61]  A. Iasonos,et al.  Eribulin mesylate (halichondrin B analog E7389) in platinum‐resistant and platinum‐sensitive ovarian cancer , 2012, Cancer.

[62]  M. Birrer,et al.  Carcinosarcoma of the ovary: a review of the literature. , 2012, Gynecologic oncology.

[63]  H. Saya,et al.  Expression profiles of carcinosarcoma of the uterine corpus—are these similar to carcinoma or sarcoma? , 2012, Genes, chromosomes & cancer.

[64]  A. Fusco,et al.  HMGA1 and HMGA2 protein expression correlates with advanced tumour grade and lymph node metastasis in pancreatic adenocarcinoma , 2012, Histopathology.

[65]  M. Gerstung,et al.  Reliable detection of subclonal single-nucleotide variants in tumour cell populations , 2012, Nature Communications.

[66]  J. Schorge,et al.  Carcinosarcoma of the ovary: a case-control study. , 2011, Gynecologic oncology.

[67]  Benjamin J. Raphael,et al.  Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.

[68]  H. Johnsen,et al.  Deregulation of MYCN, LIN28B and LET7 in a Molecular Subtype of Aggressive High-Grade Serous Ovarian Cancers , 2011, PloS one.

[69]  J. Peppercorn,et al.  Faculty Opinions recommendation of Eribulin monotherapy versus treatment of physician's choice in patients with metastatic breast cancer (EMBRACE): a phase 3 open-label randomised study. , 2011 .

[70]  A. Iafrate,et al.  Tissue-specific signatures of activating PIK3CA and RAS mutations in carcinosarcomas of gynecologic origin. , 2011, Gynecologic oncology.

[71]  Chris Twelves,et al.  Eribulin monotherapy versus treatment of physician's choice in patients with metastatic breast cancer (EMBRACE): a phase 3 open-label randomised study , 2011, The Lancet.

[72]  M. Nicolau,et al.  LOXL2-mediated matrix remodeling in metastasis and mammary gland involution. , 2011, Cancer research.

[73]  Lijun Xue,et al.  Overexpression of HMGA2 Promotes Metastasis and Impacts Survival of Colorectal Cancers , 2011, Clinical Cancer Research.

[74]  Ximing J. Yang,et al.  HMGA2: A biomarker significantly overexpressed in high-grade ovarian serous carcinoma , 2010, Modern Pathology.

[75]  Colleen A Crane,et al.  17beta-estradiol accelerates tumor onset and decreases survival in a transgenic mouse model of ovarian cancer. , 2010, Endocrinology.

[76]  L. Cantrell,et al.  Carcinosarcoma of the Ovary: A Review , 2009, Obstetrical & gynecological survey.

[77]  Kai Ye,et al.  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..

[78]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[79]  Oliver Greiner,et al.  An efficient and versatile system for acute and chronic modulation of renal tubular function in transgenic mice , 2008, Nature Medicine.

[80]  R. Tothill,et al.  Novel Molecular Subtypes of Serous and Endometrioid Ovarian Cancer Linked to Clinical Outcome , 2008, Clinical Cancer Research.

[81]  M. Jordan,et al.  Inhibition of centromere dynamics by eribulin (E7389) during mitotic metaphase , 2008, Molecular Cancer Therapeutics.

[82]  Sun-Mi Park,et al.  Let-7 Prevents Early Cancer Progression by Suppressing Expression of the Embryonic Gene HMGA2 , 2007, Cell cycle.

[83]  E. Kistner,et al.  Let-7 expression defines two differentiation stages of cancer , 2007, Proceedings of the National Academy of Sciences.

[84]  Anindya Dutta,et al.  The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. , 2007, Genes & development.

[85]  David P. Bartel,et al.  Supporting Online Material Materials and Methods Fig. S1 Tables S1 and S2 References Database S1 Disrupting the Pairing between Let-7 and Hmga2 Enhances Oncogenic Transformation , 2022 .

[86]  M. Piccart,et al.  Current management of ovarian carcinosarcoma , 2006, International Journal of Gynecologic Cancer.

[87]  M. Jordan,et al.  The primary antimitotic mechanism of action of the synthetic halichondrin E7389 is suppression of microtubule growth , 2005, Molecular Cancer Therapeutics.

[88]  M. Burns,et al.  Case-Control Study , 2020, Definitions.

[89]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[90]  T. Motoyama,et al.  Carcinosarcomas (Malignant Mullerian Mixed Tumors) of the Uterus and Ovary: A Genetic Study With Special Reference to Histogenesis , 2003, International journal of gynecological pathology : official journal of the International Society of Gynecological Pathologists.

[91]  K. Rajewsky,et al.  Stringent doxycycline dependent control of CRE recombinase in vivo. , 2002, Nucleic acids research.

[92]  J. Boyd,et al.  Carcinosarcoma of the ovary in a patient with a germline BRCA2 mutation: evidence for monoclonal origin. , 2000, Gynecologic oncology.

[93]  R. Hruban,et al.  Frequent genetic heterogeneity in the clonal evolution of gynecological carcinosarcoma and its influence on phenotypic diversity. , 2000, Cancer research.

[94]  C. Morton,et al.  HMGIC expression in human adult and fetal tissues and in uterine leiomyomata , 1999, Genes, chromosomes & cancer.

[95]  S. Finkelstein,et al.  Carcinosarcomas (malignant mixed mullerian tumors) of the female genital tract: comparative molecular analysis of epithelial and mesenchymal components. , 1998, Human pathology.

[96]  G. Fleuren,et al.  Molecular genetic evidence for the conversion hypothesis of the origin of malignant mixed Müllerian tumours , 1997, Journal of Pathology.

[97]  P. Rogalla,et al.  HMGI-C expression patterns in human tissues. Implications for the genesis of frequent mesenchymal tumors. , 1996, The American journal of pathology.

[98]  M. Costa,et al.  p53 gene mutation in female genital tract carcinosarcomas (malignant mixed müllerian tumors): a clinicopathologic study of 74 cases. , 1994, Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc.

[99]  J. Boyd,et al.  Mutation and over‐expression of the P53 tumor suppressor gene frequently occurs in uterine and ovarian sarcomas , 1994, Obstetrics and gynecology.

[100]  M. Nissen,et al.  The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. , 1990, The Journal of biological chemistry.

[101]  Y. Yip,et al.  Toxicity of enzymically-oxidized low-density lipoprotein. , 1987, Biochemical and biophysical research communications.

[102]  M. Nissen,et al.  Specific A . T DNA sequence binding of RP-HPLC purified HMG-I. , 1987, Biochemical and biophysical research communications.

[103]  M. Solomon,et al.  A mammalian high mobility group protein recognizes any stretch of six A.T base pairs in duplex DNA. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[104]  A. Varshavsky,et al.  A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome , 1984, Cell.

[105]  John Aitchison,et al.  The Statistical Analysis of Compositional Data , 1986 .