APPLYING NEXT-GENERATION CANCER GENOME SEQUENCING APPROACHES TO OVARIAN CANCER

Ovarian cancer is the leading cause of death from gynecologic cancers. The ten year survival is less than 30% and has not improved significantly over the last 30 years. We employed next generation sequencing to address three common areas where previous studies have been lacking and insight into disease etiology would help improve survival and treatment of patients with ovarian cancer. Firstly, one of the challenges to improved diagnostic and therapeutic intervention in ovarian cancer has been a limited understanding of the natural history of the disease. It has been proposed that fallopian tube cancers may be precursors of high-grade serous ovarian carcinoma (HGSOC) but evolutionary evidence for this hypothesis has been limited. We performed 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. Secondly, to improve our understanding of ovarian cancer, we performed genome-wide analyses of 45 commonly used ovarian cancer cell lines. Lastly, endometrioid and mucinous ovarian cancers represent nearly a quarter of ovarian cancers and their molecular characteristics and pathologic origins are poorly understood. Whole exome sequencing analyses of HGSOC samples demonstrated that p53 signatures and STICs are precursors of ovarian carcinoma and identified a window of seven years between development of a STIC and initiation of ovarian carcinoma, with metastases following rapidly thereafter. Whole genome sequencing analyses of 45 ovarian cancer cell lines showed dose-response analyses to targeted therapies revealed unique molecular dependencies, including increased sensitivity of tumors with PIK3CA and PPP2R1A alterations to PI3K inhibitor GNE-493, MYC amplifications to PARP inhibitor BMN673, and SMAD3/4 alterations to MEK inhibitor MEK162. Finally, whole exome and genome sequencing analyses on less common ovarian cancer subtypes revealed ovarian and GI mucinous tumors were epigenetically distinct. In contrast, the number of alterations and affected genes in ovarian and uterine endometrioid cancers were not distinguishable, suggesting that these tumors may have a similar tissue of origin. Together these analyses provide insights into the etiology of ovarian cancer, have implications for prevention, early detection and therapeutic intervention of this disease

Goblet cell differentiation in colorectal cancer

Colorectal stem cells give rise to three cell types in the colorectal crypt: enterocytes, enteroendocrince cells and goblet cells. In colorectal cancer this stem cell differentiation is dysregulated and absence of differentiation usually confers a worse prognosis for the patient. In order to understand goblet cell differentiation in colorectal cancer we first investigated novel goblet cell markers. REG4 was found as a marker through examination of our microarray data on 96 colorectal cell lines and confirmed through flow cytometry and immunohistochemistry. Dll4 was also examined as a potential goblet cell marker but instead stained a separate population of cells that may prove to either influence goblet cell differentiation or be goblet cell progenitors. We then examined the roles of goblet cell differentiation regulators such as Notch and the homeobox genes CDX1 and CDX2 in colorectal cell lines. Treatment of colorectal cell lines with inhibitors of the Notch pathway, including the γ-secretase inhibitor DBZ and anti-Dll4, increased the number of goblet cells. Knockdown of CDX1 and CDX2 decreased the number of goblet cells in goblet cell producing cell lines. Further research will elucidate the mechanisms by which these regulators influence differentiation, which could yield a treatment for colorectal cancer; inducing goblet cell differentiation and abating further tumor growth.</p

Goblet cell differentiation in colorectal cancer

Colorectal stem cells give rise to three cell types in the colorectal crypt: enterocytes, enteroendocrince cells and goblet cells. In colorectal cancer this stem cell differentiation is dysregulated and absence of differentiation usually confers a worse prognosis for the patient. In order to understand goblet cell differentiation in colorectal cancer we first investigated novel goblet cell markers. REG4 was found as a marker through examination of our microarray data on 96 colorectal cell lines and confirmed through flow cytometry and immunohistochemistry. Dll4 was also examined as a potential goblet cell marker but instead stained a separate population of cells that may prove to either influence goblet cell differentiation or be goblet cell progenitors. We then examined the roles of goblet cell differentiation regulators such as Notch and the homeobox genes CDX1 and CDX2 in colorectal cell lines. Treatment of colorectal cell lines with inhibitors of the Notch pathway, including the γ-secretase inhibitor DBZ and anti-Dll4, increased the number of goblet cells. Knockdown of CDX1 and CDX2 decreased the number of goblet cells in goblet cell producing cell lines. Further research will elucidate the mechanisms by which these regulators influence differentiation, which could yield a treatment for colorectal cancer; inducing goblet cell differentiation and abating further tumor growth

Combining PARP with ATR inhibition overcomes PARP inhibitor and platinum resistance in ovarian cancer models

Patients with ovarium cancer frequently develop resistance to platinum chemotherapy and PARP inhibitors (PARPi). Here, the authors show that the combination of PARP and ATR inhibitors increases the therapeutic response in PARPi and platinum resistant ovarium cancer PDX models

High grade serous ovarian carcinomas originate in the fallopian tube

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