Molecular Omics

Phosphoproteomics guides low dose drug combination of cisplatin and silmitasertib against concurrent chemoradiation resistant cervical cancer

Abstract Cisplatin-based concurrent chemoradiotherapy (CCRT) is the standard treatment for cervical patients with locally advanced disease. Despite the improved survival rates and prognosis observed in patients undergoing CCRT, over 30–40% do not achieve complete response and are at risk of locoregional recurrence. Targeting crucial molecules that confer resistance may improve the clinical outcomes of the treatment resistant patient cohort. Herein, we employed a liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based phosphoproteomic approach to identify the altered phosphophorylation events, activated kinases and dysregulated pathways involved in treatment resistance. We quantified 2531 unique phosphopeptides mapping to 1099 proteins of which 74 proteins were differentially phosphorylated between the cohorts. Pathway analysis revealed dysregulation of the DNA repair pathway and the proteins involved in DNA repair in the non-responder cohort. Additionally, we identified kinase signature associated with CCRT resistance. Kinases such as CSNK2A1, PRKDC, PLK-1, NEK2, ATM and CDK1 are predicted to be activated in non-responders. In particular, we showed that CSNK2A1 is involved in oncogenesis of cervical cancer and pharmacological inhibition led to reduced cell proliferation, migration and colony formation. Moreover, the combination of the CSNK2A1 inhibitor, silmitasertib with cisplatin demonstrated synergism (combination index < 1) and yielded a beneficial reduction in dosage. The dose reduced combination potentially reduced the proliferative, migratory and colony formation ability in vitro. Our findings highlight the potential of phosphoproteomics to identify clinically significant targets and pathways implicated in CCRT resistance. Our study also indicates that combination therapy could serve as an effective treatment strategy to improve the efficacy of patients undergoing CCRT.

A multi-omics study of the anti-cancer effect of a ferulic acid derivative FA-30

Abstract The active ingredients of Traditional Chinese Medicine are an important source of bioactive molecules and play an important role in the research and development of innovative drugs. FA-30, which is a derivative of natural product ferulic acid, inhibited cervical cancer cell proliferation and induced apoptosis as well. To understand the underlying mechanisms of FA-30, a complementary multi-omics study was conducted. Cysteine and methionine metabolism and aminoacyl-tRNA biosynthesis pathways were significantly changed both at the metabolic level and proteomic level. This may help us to get a better understanding of cervical cancer and FA-30 at the same time.

An altered proteome in ovarian cancer stem-like cells: profiling of the mDivi-1 induced proteome and its clinical significance

Abstract A three-dimensional (3D) spheroid culture mimics in vivo conditions and reproduces the tumor microenvironment, thus providing more physiological relevance to disease conditions. Mapping the proteome profile in 3D-cultured ovarian cancer (OC) spheroids helps identify novel and potential therapeutic targets in ovarian cancer stem cells. We used mass-spectrometry-based comparative proteome profiling for two-dimensional (2D)-cultured adherent and 3D-cultured OC spheroids and identified 94 upregulated and 54 downregulated proteins in 3D-cultured A2780 spheroids compared to 2D-cultured adherent A2780 cells. In SKOV-3 cells, we identified 127 upregulated proteins and 192 downregulated proteins in 3D-cultured spheroids compared to 2D-cultured adherent cells. The differentially expressed proteins were enriched in proteins regulating oxidative phosphorylation, the acetyl-CoA metabolic process, RNA polymerase core enzyme binding, and growth factor binding. In addition, we also mapped the proteome profile after the treatment with a mitochondrial fission inhibitor, mDivi-1, of 3D-cultured cells and defined the correlation between significantly upregulated and downregulated genes and their association with the progression-free survival of OC patients.

KDM4B, a potential prognostic biomarker revealed by large-scale public databases and clinical samples in uterine corpus endometrial carcinoma

Abstract Background: Uterine corpus endometrial carcinoma (UCEC) is the fourth most common cancer among women worldwide. The 5 year survival rate for patients with advanced UCEC is only 17%. Lysine-specific demethylase 4B (KDM4B), a histone demethylase, is overexpressed or dysregulated in various cancers and is associated with tumor progression and poor prognosis. We performed bioinformatics analysis and in vitro assays to assess the role of KDM4B in UCEC. Additionally, the role of KDM4B in the tumor immune microenvironment was explored. Methods: The mRNA and protein levels of KDM4B in UCEC were evaluated using The Cancer Genome Atlas (TCGA), The Human Protein Atlas (HPA), and Gene Expression Omnibus (GEO) databases. Immunohistochemistry and western blotting were performed to verify the protein expression level of KDM4B in two batches of clinical samples. Kaplan–Meier survival, univariate, and multivariate analyses were performed to assess the correlation between KDM4B expression and the prognosis of patients with UCEC. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to predict the function and mechanism of KDM4B, and four immune-related databases (TIMER, CIBERSORT, TISIDB, and EPIC) were used to explore their relevance in a tumor immune microenvironment. Results: First, KDM4B was significantly overexpressed in UCEC tissues at the mRNA and protein levels. Immunohistochemistry and western blotting confirmed the abnormal overexpression of KDM4B. Additionally, upregulation of KDM4B was associated with different clinicopathological prognostic factors. Second, the overexpression of KDM4B was also associated with shorter overall survival (OS) and progression-free survival (PFS). Univariate and multivariate analyses confirmed that KDM4B was an independent prognostic factor for poor survival. Then, GO and KEGG analysis revealed that KDM4B is enriched in biological processes and cellular signaling pathways closely related to the immune response. Finally, KDM4B expression was closely associated with immune cell infiltration and expression of immune checkpoint molecules, indicating that it may be a new immune-related potential oncogene in UCEC. Conclusions: KDM4B may be a new potential oncogene that is clinically significant in patients with UCEC. KDM4B may not only be used to assess the clinical prognosis of patients with UCEC but may also be a target for immunotherapy or targeted gene therapy.

Models for measuring metabolic chemical changes in the metastasis of high grade serous ovarian cancer: fallopian tube, ovary, and omentum

Abstract Ovarian cancer (OC) is the most lethal gynecologic malignancy and high grade serous ovarian cancer (HGSOC) is the most common and deadly subtype, accounting for 70–80% of OC deaths. HGSOC has a distinct pattern of metastasis as many believe it originates in the fallopian tube and then it metastasizes first to the ovary, and later to the adipose-rich omentum. Metabolomics has been heavily utilized to investigate metabolite changes in HGSOC tumors and metastasis. Generally, metabolomics studies have traditionally been applied to biospecimens from patients or animal models; a number of recent studies have combined metabolomics with innovative cell-culture techniques to model the HGSOC metastatic microenvironment for the investigation of cell-to-cell communication. The purpose of this review is to serve as a tool for researchers aiming to model the metastasis of HGSOC for metabolomics analyses. It will provide a comprehensive overview of current knowledge on the origin and pattern of metastasis of HGSOC and discuss the advantages and limitations of different model systems to help investigators choose the best model for their research goals, with a special emphasis on compatibility with different metabolomics modalities. It will also examine what is presently known about the role of small molecules in the origin and metastasis of HGSOC.

Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer

Abstract Women coinfected with human immunodeficiency virus type 1 (HIV-1) and human papillomavirus (HPV) are six times as likely to develop invasive cervical carcinoma compared to those without HIV. Unlike other HIV-associated cancers, the risk of cervical cancer development does not change when HPV/HIV coinfected women begin antiretroviral therapy, suggesting HIV-associated immune suppression is not a key driver of cervical cancer development in coinfected women. Here, we investigated whether the persistent secretion of inflammatory factors in HIV-positive patients on antiretroviral therapy could enhance cancer signaling in HPV-infected cervical cells via endocrine mechanisms. We integrated previously reported HIV-induced secreted inflammatory factors (Hi-SIFs), HIV and HPV virus–human protein interactions, and cervical cancer patient genomic data using network propagation to understand the pathways underlying disease development in HPV/HIV coinfection. Our results pinpointed the PI3K-AKT signaling pathway to be enriched at the interface between Hi-SIFs and HPV–host molecular networks, in alignment with PI3K pathway mutations being prominent drivers of HPV-associated, but HIV independent, cervical cancer development. Furthermore, we experimentally stimulated cervical cells with 14 Hi-SIFs to assess their ability to activate PI3K-AKT signaling. Strikingly, we found 8 factors (CD14, CXCL11, CXCL9, CXCL13, CXCL17, AHSG, CCL18, and MMP-1) to significantly upregulate AKT phosphorylation (pAKT-S473) relative to a phosphate buffered saline control. Our findings suggest that Hi-SIFs cooperate with HPV infection in cervical cells to over-activate PI3K-AKT signaling, effectively phenocopying PI3K-AKT pathway mutations, resulting in enhanced cervical cancer development in coinfected women. Our insights could support the design of therapeutic interventions targeting the PI3K-AKT pathway or neutralizing Hi-SIFs in HPV/HIV coinfected cervical cancer patients.