Oncogenic Phenotype Research Articles

Recurrent exon-deleting activating mutations in AHR act as drivers of urinary tract cancer

Bladder cancer has a high recurrence rate and low survival of advanced stage patients. Few genetic drivers of bladder cancer have thus far been identified. We performed in-depth structural variant analysis on whole-genome sequencing data of 206 metastasized urinary tract cancers. In ~ 10% of the patients, we identified recurrent in-frame deletions of exons 8 and 9 in the aryl hydrocarbon receptor gene (AHRΔe8-9), which codes for a ligand-activated transcription factor. Pan-cancer analyses show that AHRΔe8-9 is highly specific to urinary tract cancer and mutually exclusive with other bladder cancer drivers. The ligand-binding domain of the AHRΔe8-9 protein is disrupted and we show that this results in ligand-independent AHR-pathway activation. In bladder organoids, AHRΔe8-9 induces a transformed phenotype that is characterized by upregulation of AHR target genes, downregulation of differentiation markers and upregulation of genes associated with stemness and urothelial cancer. Furthermore, AHRΔe8-9 expression results in anchorage independent growth of bladder organoids, indicating tumorigenic potential. DNA-binding deficient AHRΔe8-9 fails to induce transformation, suggesting a role for AHR target genes in the acquisition of the oncogenic phenotype. In conclusion, we show that AHRΔe8-9 is a novel driver of urinary tract cancer and that the AHR pathway could be an interesting therapeutic target.

Abstract 324: Discovery of novel functional TROP2 antibodies for treatment of epithelial cancers

Abstract Trophoblast cell surface antigen-2 (TROP2) is a membrane-bound protein expressed during development and at lower levels in normal adult tissues. TROP2 has pleiotropic functions including formation of cell-cell junctions by mediating interactions with extracellular and intracellular proteins. In situations of TROP2 deficiency its role in normal tissues appears to be compensated by expression of EpCAM, a highly related family member. In cancer, the levels of TROP2 are increased in many epithelial tumor types. Overexpression of TROP2 confer oncogenic behavior in several in vitro and in vivo models. Both its extracellular and intracellular domains play a role in modulating interactions with ligands and/or receptors and with intracellular signaling partners to result in an oncogenic phenotype. In many solid tumors TROP2 upregulation is associated with increased tumor aggressiveness, metastasis, and decreased survival in large groups of difficult-to-treat cancers, making it an attractive target for cancer therapy. TROP2-based ADCs have been developed and one has been approved for therapeutic use in triple negative breast cancer and advanced bladder cancer. The toxicity associated with the toxin payload limits their use including in combination with chemotherapy in the earlier lines of treatment, and by the development of resistance to the payload. We isolated several anti-TROP2 heavy chain-only antibodies (HCAb) by immunization of a proprietary transgenic HCAb mouse. In this abstract, we describe the properties and activity of several of these antibodies. These antibodies are characterized by potent in vivo antitumor activity in established tumor models in NCG mice in the absence of ADCC, and by the inhibition of tumor cell viability in vitro, directly and in the absence of any effector cells. In NCG mice, which are characterized by a short antibody half-life, anti-TROP2 HCAbs displayed a T1/2 of approximately 3.5 days. These antibodies displayed very potent anti-tumor activity in established tumor xenograft models, causing tumor regression at 2 mg/kg and 80% TGI at 0.5 mg/kg in NCG mice when administered once per week. They also caused tumor regression when dosed once every three weeks in NCG mice and in tumors of very large sizes. Therefore, these antibodies directly target one or more aspects of TROP2 tumor biology that have a profound and long-lasting effect on the cancer cells. Upon glycoengineering, the afucosylated version of the antibodies displayed a strongly enhanced ADCC activity. In vitro they are characterized by different internalization rates which define several non-overlapping epitopes on TROP2. They are characterized by picomolar binding affinity to recombinant human TROP2 as determined by SPR. These antibodies bind with greater affinity to human and cyno but bind poorly to mouse, rat and rabbit. These potent naked TROP2 antibodies represent new opportunities to address TROP2 expressing cancers. Citation Format: Israel Matos, Yahya Ashraf, Hiba Zahreddine, Liying Gong, Amanda Baumholtz, Alex Zhou, Claire Bonfils, Aniel Moya-Torres, Yun Cui, Xiaowei Wang, Richard Wargachuk, Tiffany Cheng, Elijus Undzys, Shugang Yao, Jacynthe Linda Tolouse, Dominic Hou, Gordon Ngan, Luis daCruz, David Young. Discovery of novel functional TROP2 antibodies for treatment of epithelial cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 324.

Abstract 5673: The role of NMDA receptors subunits in the progression of inflammatory breast cancer (IBC)

Abstract Inflammatory Breast Cancer (IBC) has a 73% incidence of metastasis to the brain as compared to other cancer types like breast, lung, and bone cancer. Previous research showed that tumor cells from different breast cancer subtypes (-HR/-HER2) and (-HR/+ HER2) have a high incidence of crossing the blood-brain barrier and inducing increased expression of glutamate receptors NMDA subunits (NMDAR1 and NMDR2) in the brain. IBC is the most aggressive and rare type of breast cancer. The absence of a solid tumor is replaced by swelling, redness, and skin changes, resulting in many cases in misdiagnosis of an infection in the invasion and migration phase; this type of cancer blocks blood and lymphatic vessels in the breast's skin, causing local inflammation and rapid metastasis. However, little is known of the role that these glutamatergic receptors have in the development and/or progression of IBC. The present work provides a new understanding of the cellular and molecular effects NMDA receptors (NMDAR) have on oncogenic phenotypes in IBC. The detection and quantification of the NMDAR were evaluated by RT-qPCR, Western blot, and immunofluorescence (IF) techniques in deferments breast cancer cell lines (MCF7, MDA-MB-231) and IBC cell lines (SUM149, and SUM190). Also, NMDAR antagonists (memantine and dizocilpine "MK-801") were used in 2D and 3D cell cultures to see the pro-oncogenic effects of migration and proliferation in cell models. In addition to this, the autocrine regulation of Glutamate in IBC cell lines is verified. Results showed a significant increase in the expression of NMDARs in IBC cell lines. In the functional cell culture assays with NMDAR antagonists, a decrease in migration and proliferation in IBC cell lines was found. These findings may be related to the high aggressiveness and the high rate of metastasis by IBC within the brain. Our results have high clinical relevance since having extensive knowledge of the role of NMDARs in IBC progression could complement therapeutic approaches for patients with IBC. Citation Format: Laura L. Mendez Santacruz, Xavier S. Bittman-Soto, Keishla M. Rodriguez-Martir, Jesus M. Padilla Escalona, Esther Peterson, Carmen Maldonado-Vlaar. The role of NMDA receptors subunits in the progression of inflammatory breast cancer (IBC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5673.

Abstract 6200: MANGO: pipeline for identifying genomic translocations with key biological significance in inflammatory breast cancer

Abstract Genomic instability in cancer is essential for aberrant gene expression and translocation events that potentiate oncogenesis. Thus gene fusions, nonsense mutations and gene deregulation are key contributors to oncogenic phenotypes. Certain genomic translocations have been linked to cancer subtypes, such BCR—ABL1 for chronic myeloid leukemia (CML) serving as potential onco-biomarkers. Inflammatory breast cancer (IBC) is the rarest and most lethal subtype of breast cancer with a 5-year survival rate below 50%. Ethnic disparities for breast cancer exist; negative estrogen (ER) and progesterone (PR) hormone receptor status is more frequent in Hispanic and African American women. In addition, inflammatory breast cancer lacks defined molecular markers limiting its early onset detection which leads to poorer overall prognosis. Thus, we hypothesized that profiling IBC translocations, including its subtypes, show valuable insights to better understand this complex disease. We developed MANGO, a pipeline that leverages STAR, STAR-Fusion, FusionInspector, and Trinity to identify, visualize and assemble gene fusions from IBC sequencing data. Using the SUM149PT cell line as a model for IBC, we identified and experimentally validated a model fusion gene ZDHHC5—EPB41L5. Fusion unaware sequence assemblies cross-validated the fusion and its multiple splice sites, one of which encodes a fusion peptide. Differential gene expression between SUM149PT and SUM190PT, an IBC cell line without evidence for the identified translocation, showed loss of expression of ZDHHC5 but no change in EPB41L5, suggesting the latter retained its expression in its new genomic localization. Furthermore, in-silico functional predictions for experimental results reveals an in-frame fusion peptide with transmembrane signals in EPB41L5. Genomic translocation mapping reveals triple-negative IBC diverges from traditional breast cancer translocation patterns. In short, MANGO serves as a powerful tool to identify biologically significant translocations involved in IBC and other cancer classifications. Citation Format: Carlos S. Morales-Rivera, Emilia R. Driscoll, Esther A. Peterson-Peguero. MANGO: pipeline for identifying genomic translocations with key biological significance in inflammatory breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6200.

Abstract 329: Understanding the role of GPR30 in the estrogen non-genomic signaling in inflammatory breast cancer

Abstract Inflammatory Breast Cancer (IBC) is rare and the most aggressive subtype of all breast cancers, reporting rapid progression, poor prognosis, and a unique clinical diagnosis (blockage of lymph vessels by tumor emboli). Approximately, 40% of IBC cases are classified as triple-negative breast cancer (TNBC), meaning they test negative for hormone receptors (estrogen and progesterone) and the amplification of the epidermal growth factor receptor 2 (HER2), which leads to no effective targeted therapies availability. However, 17β-estrogen (E2) has been found to enhance the migration and invasion phenotypes of TN-IBC cells and it has been associated with the presence of a membrane G-protein coupled estrogen receptor (GPR30) and a novel cytoplasmic estrogen receptor (ERα36 isoform) that can undergo an estrogen non-genomic (rapid) cell’s response. Recent studies have also reported a crosstalk between these estrogen non-genomic receptors and the epidermal growth factor receptor (EGFR) signaling pathway in the presence of E2, inducing phosphorylation of the extracellular signal-regulated kinase (ERK1/2) and promoting oncogenic phenotypes (migration & invasion) in TN-IBC cells. However, the exact role of GPR30 and ERα36 in the non-genomic signaling pathway remains elusive in TN-IBC. We hypothesis that GPR30 and ERα36 are necessary to undergo de estrogen non-genomic signaling and promote oncogenic phenotypes in TN-IBC SUM149 cells after E2 treatment. Methods: We have measured migratory activity and tumor emboli formation of SUM149 cells (by wound-healing and 3D-cell proliferation assay), and phosphorylation levels of ERK1/2 and AKT kinases (by western-blot) after treatments in time-points with E2 alone and in combination with G15 (GPR30 antagonist drug). We are also working to identify protein partners of GPR30 (by Ip and Mass-spec) after E2 treatment, including physical interaction with ERα36, in TN-IBC and other types of breast cancers. Results: G15 treatment in Sum149 cells significantly reduced E2-induced ERK1/2 phosphorylation, indicating that GPR30 is necessary for the estrogen non-genomic signaling pathway and has direct involvement with the EGFR signaling cascade. Data acquired from these experiments will contribute to a better understanding of TN-IBC’s molecular structure and create new opportunities to develop novel targeted therapies. Citation Format: Xavier S. Bittman Soto, Adrian J. Rivera Lopez, Esther A. Peterson. Understanding the role of GPR30 in the estrogen non-genomic signaling in inflammatory breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 329.

Abstract 5717: Novel evidence for FTO as an oncogenic player and mediator of chemoresistance in colorectal cancer

Abstract Background: Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide. Although, 5-flurouracil (5FU) based chemotherapy and surgical resection are considered most effective treatments for CRC patients, the 5-year survival rates remain poor primarily due to distant metastasis, local recurrence and acquired drug resistance. Fat mass and obesity-associated protein (FTO), an RNA N6-methyladenosine demethylase, has recently been reported to be upregulated in various cancers, including CRC. However, thus far, the molecular mechanism underlying the role of FTO in CRC and/or acquisition of 5FU resistance remains unclear. Methods: To study the relevance of FTO overexpression in CRC, we adopted various approaches: a) lentiviral-mediated stable depletion of FTO or (b) CS1-mediated pharmacological inhibition in CRC cells, c) lentiviral-mediated FTO overexpression in normal colonic epithelial cells (NCM460), and thereafter analyzed the effect on cell viability, cell cycle, wound healing, invasion, epithelial-mesenchymal transition (EMT), cancer stemness, 5FU drug response and tumor forming capability in nude mice. Expression of markers of cell proliferation and apoptosis in the tumor extracts were analyzed by western blotting. To augment the clinical relevance, we evaluated the effect of CS1 on the growth and response to 5FU in patient-derived organoids (PDOs). Kaplan Meier analysis was performed to correlate the significance of FTO overexpression with survival in CRC patient cohorts. Results: A significant upregulation of both mRNA and protein expression of FTO was found in various CRC cells compared to NCM460 cells. Notably, FTO inhibition hampered the proliferative, migratory and invasive capabilities of CRC cells whilst, ectopic overexpression of FTO in the NCM460 cells promoted oncogenic phenotype. Furthermore, FTO depletion in CRC cells led to EMT reversal, impaired tumor-sphere formation and stemness traits, which in turn was reflected in the sensitization towards 5FU in otherwise resistant cells. Moreover, xenograft tumor forming capabilities of CRC cells was severely hindered in FTO depleted cells. Besides, FTO-depleted xenografts displayed a significant decrease in the expression of markers of cell survival and proliferation (p-AKT and PCNA), while there was an increment in the apoptotic marker, Caspase 9. The relevance of our in vitro and in vivo findings was further strengthened as CS1-mediated inhibition not only decrease the number and size of PDO, but also sensitized them towards 5FU. In addition, we unambiguously demonstrate a significant correlation between FTO upregulation and poor overall and recurrence-free-survival of CRC patients. Conclusions: Our study establishes the functional importance of FTO in CRC and provides novel evidence for the potential use of FTO inhibitor as an adjunctive treatment to 5FU based chemotherapy for CRC patients. Citation Format: Rachana Garg, Laleh Melstorm, Jianjun Chen, Chuan He, Ajay Goel. Novel evidence for FTO as an oncogenic player and mediator of chemoresistance in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5717.

Abstract 3077: Leveraging a 3D organoid library to identify novel therapeutic targets during ESCC initiation and progression

Abstract Esophageal squamous cell carcinoma (ESCC) is a devastating and common disease worldwide. Despite recent advances annotating the genetic and epigenetic changes underlying the initiation and development of ESCC and its precursor lesion, esophageal squamous dysplasia, more work is needed to translate these findings into novel therapeutic strategies. This gap is due in part to the lack of tractable models of ESCC initiation and development that can then be manipulated ex vivo for preclinical testing. Currently, the large-scale studies characterizing the aforementioned molecular changes have used primary tissue for their analyses and have subsequently been unable to test the specific hypotheses that arise from their data using the original tissue that they profiled. To address this gap, we have generated a large (n = 54) three-dimensional organoid library from the esophagi of mice treated with the carcinogen 4-Nitroquinoline N-oxide (4-NQO) representing each stage of esophageal squamous cell initiation and progression from early intraepithelial dysplasia through lung metastasis. We have determined that these organoids faithfully recapitulate the molecular biology, histology, and oncogenic phenotype of their tissue of origin. Through integrative analysis of both RNA sequencing and whole exome sequencing data, we have identified several novel therapeutic targets that contribute to ESCC initiation and development including the DNA damage response and NOTCH1 signaling. Together, our work capitalizes on the intersection of large-scale multiomics and sophisticated 3D organoid models to identify novel therapeutic targets for the treatment of a devastating disease. Citation Format: Samuel Flashner, Masataka Shimonosono, Satoshi Takada, Norihiro Matsuura, Yasuto Tomita, Xiao Chen, Alison Taylor, Andres Klein-Szanto, Fatameh Momen-Heravi, J. Alan Diehl, Chao Lu, Hiroshi Nakagawa. Leveraging a 3D organoid library to identify novel therapeutic targets during ESCC initiation and progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3077.

Ecdysoneless Overexpression Drives Mammary Tumorigenesis through Upregulation of C-MYC and Glucose Metabolism.

We demonstrate ECD overexpression in the mammary gland of mice led to the development of a tumor progression model through upregulation of c-MYC signaling and glucose metabolism.

Leveraging Bulk and Single-Cell RNA Sequencing Data of NSCLC Tumor Microenvironment and Therapeutic Potential of NLOC-15A, A Novel Multi-Target Small Molecule.

Lung cancer poses a serious threat to human health and has recently been tagged the most common malignant disease with the highest incidence and mortality rate. Although epidermal growth factor (EGFR)-tyrosine kinase inhibitors (TKIs) have significantly improved the prognosis of advanced non-small cell lung cancer (NSCLC) patients with EGFR mutations, patients often develop resistance to these drugs. There is therefore a need to identify new drug candidates with multitarget potential for treating NSCLC. We hereby provide preclinical evidence of the therapeutic efficacy of NLOC-015A a multitarget small-molecule inhibitor of EGFR/mitogen-activated protein (MAP) kinase kinase 1 (MAP2K1)/mammalian target of rapamycin (mTOR)/yes-associated protein 1 (YAP1) for the treatment NSCLC. Our multi-omics analysis of clinical data from cohorts of NSCLC revealed that dysregulation of EGFR/MAP2K1/mTOR/YAP1 signaling pathways was associated with the progression, therapeutic resistance, immune-invasive phenotypes, and worse prognoses of NSCLC patients. Analysis of single-cell RNA sequencing datasets revealed that MAP2K1, mTOR, YAP1 and EGFR were predominantly located on monocytes/macrophages, Treg and exhaustive CD8 T cell, and are involved in M2 polarization within the TME of patients with primary and metastatic NSCLC which further implied gene’s role in remodeling the tumor immune microenvironment. A molecular-docking analysis revealed that NLOC-015A bound to YAP1, EGFR, MAP kinase/extracellular signal-related kinase kinase 1 (MEK1), and mTOR with strong binding efficacies ranging –8.4 to –9.50 kcal/mol. Interestingly, compared to osimertinib, NLOC-015 bound with higher efficacy to the tyrosine kinase (TK) domains of both T790M and T790M/C797S mutant-bearing EGFR. Our in vitro studies and sequencing analysis revealed that NLOC-015A inhibited the proliferation and oncogenic phenotypes of NSCLC cell lines with concomitant downregulation of expression levels of mTOR, EGFR, YAP1, and MEK1 signaling network. We, therefore, suggest that NLOC-015A might represent a new candidate for treating NSCLC via acting as a multitarget inhibitor of EGFR, mTOR/NF-κB, YAP1, MEK1 in NSCLC.

TET1 Isoforms Have Distinct Expression Pattern, Localization and Regulation in Breast Cancer.

TET1 regulates gene expression by demethylating their regulatory sequences through the conversion of 5-methylcytosine to 5-hyroxymethylcytosine. TET1 plays important roles in tissue homeostasis. In breast cancer, TET1 was shown to play controversial roles. Moreover, TET1 has at least two isoforms (long and short) that have distinct expression pattern and apparently different functions in tissue development and disease including breast cancer. We hypothesized that TET1 isoforms have different expression patterns, localization and regulation in different types of breast cancer. To prove our hypothesis, we studied the expression of TET1 isoforms in basal and luminal breast cancer cell lines, as well as in basal and luminal breast cancer animal models. We also studied the effect of different hormones on the expression of the two isoforms. Moreover, we assessed the distribution of the isoforms between the cytoplasm and nucleus. Finally, we overexpressed the full length in a breast cancer cell line and tested its effect on cancer cell behavior. In this study, we demonstrate that while Estrogen and GnRH downregulate the expression of long TET1, they lead to upregulation of short TET1 expression. In addition, we uncovered that luminal cells show higher expression level of the long isoform. We also show that while all TET1 isoforms are almost depleted in a basal breast cancer animal model, the expression of the short isoform is induced in luminal breast cancer model. The short form is expressed mainly in the cytoplasm while the long isoform is expressed mainly in the nucleus. Finally, we show that long TET1 overexpression suppresses cell oncogenic phenotypes. In conclusion, our data suggest that TET1 isoforms have distinct expression pattern, localization and regulation in breast cancer and that long TET1 suppresses oncogenic phenotypes, and that further studies are necessary to elucidate the functional roles of different TET1 isoforms in breast cancer.

Comprehensive analysis of microRNAs and their target genes in oral submucous fibrosis.

The objective of the study is to understand the role of experimentally validated microRNAs (miRNAs) contributing to the acquisition of oncogenic phenotype in oral submucous fibrosis (OSF) by computational analysis. A comprehensive review was carried out to corroborate and summarize altered miRNA expression in OSF by retrieving relevant publications querying MEDLINE, Web of Science, Embase, and Scopus. The association between the miRNA-mRNA was performed using miRTarBase 8.0. The visualization of the miRNA-mRNA interaction was plotted using Cytoscape. MIENTURNET was used for the pathway analysis. Enrichment analysis was carried out for elucidating the hierarchical functions of miRNAs related to the acquisition of biological processes involved in the development of cancer. Thirteen miRNAs (hsa-miR-499a, hsa-miR-200b, hsa-miR-200c, hsa-miR-1246, hsa-miR-31, hsa-miR-10b, hsa-miR-21, hsa-miR-203, hsa-miR-455, hsa-miR-760, hsa-miR-623, hsa-miR-610, and hsa-miR-509-3-5p) were found to be deregulated in OSF. A total of 371 experimentally validated genes were shown to be interacting with the OSF-associated miRNAs. The targets of antifibrotic and profibrotic miRNAs were enriched in the cancer-related pathways. Dysregulated miRNAand its target genes illustrate the physiological role of miRNAs in fibrosis. Understanding the miRNA-mediated fibrotic signaling and targetting the specific miRNA-target gene interaction might provide relevant cues to ameliorate the fibrotic disease.

Circ_0092012 knockdown restrains non-small cell lung cancer progression by inhibiting cell malignant phenotype and immune escape through microRNA-635/programmed death ligand 1 axis

ABSTRACT Circular RNAs have been reported to play roles in non-small cell lung cancer (NSCLC) progression. Herein, this work aimed to investigate the potential value of circ_0092012 in NSCLC progression. Levels of genes and proteins were detected using quantitative reverse transcription-polymerase chain reaction and Western blot, respectively. The growth, malignant phenotypes and immune escape in NSCLC were investigated. The binding between microRNA (miR)-635 and circ_0092012 or programmed death ligand 1 (PDL1) was verified. Circ_0092012 was highly expressed in NSCLC. Circ_0092012 deficiency suppressed NSCLC cell proliferation, invasion and migration, moreover, as well as was able to inhibit the apoptosis of CD8 + T cells and induce higher interferon-γ and tumor necrosis factor-α levels when co-cultured with peripheral blood mononuclear cells. Mechanistically, circ_0092012 sponged miR-635, which targeted PDL1. Further rescue experiments suggested that the anticancer effects of circ_0092012 knockdown were reversed by miR-635 inhibition. Additionally, miR-635 re-expression suppressed NSCLC cell malignant phenotypes mentioned above and immune escape, which were attenuated by PDL1 overexpression. Moreover, circ_0092012 deletion retarded NSCLC growth in vivo. In all, circ_0092012 knockdown suppressed NSCLC cell oncogenic phenotypes and immune escape by miR-635/PDL1 axis.

Differential Expression of Nuclear Body Component, Zc3h8, Disrupts DNA Double Strand Break Repair

The processes of DNA damage recognition and repair are paramount to maintaining genome integrity in the cell. Failure to do so results in genetic instability and the accumulation of mutations. Double strand breaks have the greatest potential to introduce mutations because rearrangements, non‐homologous end joining, deletions, or insertions may result. Unrepaired or incorrectly repaired DNA double strand breaks can lead to cell death, apoptosis, or disease such as cancer. We previously demonstrated that the C3H1 zinc finger‐containing protein Zc3h8 (also called Fliz1) promotes oncogenic phenotypes when overexpressed in cells, while oncogenic phenotypes are suppressed when expression is reduced. In mice, Zc3h8 expression affected tumorigenesis and tumor size in vivo. Higher expression of Zc3h8 led to more frequent tumors and larger tumors in mice. In humans Zc3h8 is overexpressed in 2‐6% of cancers and is a statistically significant prognostic indicator for poor rates of survival. The Zc3h8 protein has been localized to nuclear bodies including promyelocytic leukemia (PML) and Cajal Bodies where key cellular processes including transcription, translation, post‐translational modifications, and RNA processing are regulated. PML Bodies, in particular, have a role in DNA damage response and repair since P53 is located in PML Bodies along with DAXX, ATRX, and CK2. Since Zc3h8 co‐localized with DNA damage response and repair proteins in PML bodies and promotes oncogenic properties in cells, we investigated if Zc3h8 expression alters how cells respond to DNA damage such as double strand breaks and how this damage is mitigated in cells. Differential expression of Zc3h8 affected mouse mammary tumor cell’s ability to repair double strand breaks caused by the topoisomerase II inhibitor etoposide as indicated by the presence of γH2AX, a marker for unrepaired double strand breaks. Using a Comet assay, we found extensive DNA fragmentation in cells with elevated Zc3h8 expression despite high rates of proliferation and migration. Furthermore, Zc3h8 increases cellular tolerance for DNA damage and alters apoptosis. These phenotypes promote further mutation and may indicate a molecular cause for highly aggressive and progressive cancers with elevated Zc3h8 expression. These conclusions suggest a DNA damage repair and response pathway that is altered by Zc3h8 expression levels can affect multiple aspects of cellular behavior and promote oncogenic phenotypes.

The role of NMDA receptors subunits in the progression of inflammatory breast cancer (IBC)

Inflammatory Breast Cancer (IBC) has a 73% incidence of metastasis to the brain as compared to other cancer types like breast, lung, and bone cancer. Previous research showed that tumor cells from different breast cancer subtypes (‐HR / ‐HER2) and (‐HR / + HER2) have a high incidence of crossing the blood‐brain barrier and inducing increased expression of glutamate receptors NMDA subunits (NMDAR1 and NMDR2) in the brain. IBC is the most aggressive and rare type of breast cancer. The absence of a solid tumor is replaced by swelling, redness, and skin changes, resulting in many cases in misdiagnosis of an infection in the invasion and migration phase; this type of cancer blocks blood and lymphatic vessels in the breast's skin, causing local inflammation and rapid metastasis. However, little is known of the role that these glutamatergic receptors have in the development and/or progression of IBC. The present work provides a new understanding of the cellular and molecular effects NMDA receptors (NMDAR) have on oncogenic phenotypes in IBC. The detection and quantification of the NMDAR were evaluated by RT‐qPCR, Western blot, and immunofluorescence (IF) techniques in deferments breast cancer cell lines (MCF7, MDA‐MB‐231) and IBC cell lines (SUM149, and SUM190). Also, NMDAR antagonists (memantine and dizocilpine “MK‐801”) were used in 2D and 3D cell cultures to see the pro‐oncogenic effects of migration and proliferation in cell models. In addition to this, the autocrine regulation of Glutamate in IBC cell lines is verified. Results showed a significant increase in the expression of NMDARs in IBC cell lines. In the functional cell culture assays with NMDAR antagonists, a decrease in migration and proliferation in IBC cell lines was found. These findings may be related to the high aggressiveness and the high rate of metastasis by IBC within the brain. Our results have high clinical relevance since having extensive knowledge of the role of NMDARs in IBC progression could complement therapeutic approaches for patients with IBC.

GPR30: A potential therapeutic target in Triple‐negative Inflammatory Breast Cancer

Inflammatory Breast Cancer (IBC) is rare and the most aggressive subtype of all breast cancers, with reported rapid progression, poor prognosis, and a unique clinical diagnosis (blockage of lymph vessels by tumor emboli). Approximately, 40% of IBC cases are classified as triple‐negative breast cancer (TNBC), meaning they test negative for hormone receptors (estrogen and progesterone) and the amplification of the epidermal growth factor receptor 2 (HER2), which result in no effective targeted therapies to date. However, 17β‐estrogen (E2) has been found to induce a non‐genomic cellular response to enhance oncogenic phenotypes in TN‐IBC and this has been associated with the presence of alternative estrogen receptors, including a novel G‐protein coupled estrogen receptor (GPR30). Recent studies have also reported a crosstalk between GPR30 and the epidermal growth factor receptor (EGFR) signaling pathway in the presence of E2, which enhances the phosphorylation of the extracellular signal‐regulated kinase (ERK1/2) and protein kinase B (AKT), and promotes migration and invasion phenotypes in TN‐BC cells. However, the exact role of GPR30 in the non‐genomic signaling pathway in TN‐IBC remains elusive. We hypothesize that GPR30 is necessary to undergo the estrogen non‐genomic signaling pathway to induce ERK1/2 and AKT phosphorilation levels and enhance migration and proliferation activities in TN‐IBC cells after treatment with E2.MethodsWe measured phosphorylation levels of ERK1/2 and AKT kinases (by western‐blot), migratory activity (by wound‐healing assay), and tumor emboli formation (by 3D‐cell proliferation assay) after treatments in time‐points with E2 alone and in combination with G15, GPR30 antagonist drug, in TN‐IBC cells SUM149PT.ResultsThe combined G15 + E2 treatment significantly reduced E2‐induced ERK1/2 and AKT phosphorylation levels, as well as decreased migratory activity in SUM149PT cells, suggesting that GPR30 is necessary to undergo the estrogen non‐genomic signaling pathway and can regulate the ERK1/2 and AKT signaling cascade in TN‐IBC. Data acquired from these experiments will contribute to a better understanding of TN‐IBC’s molecular structure and create new opportunities to develop novel targeted therapies.

MANGO: pipeline for identifying genomic translocations with key biological significance in inflammatory breast cancer

Genomic instability in cancer is essential for aberrant gene expression and translocation events that potentiate oncogenesis. Thus gene fusions, nonsense mutations and gene deregulation are key contributors to oncogenic phenotypes. Certain genomic translocations have been linked to cancer subtypes, such BCR—ABL1 for chronic myeloid leukemia (CML) serving as potential onco‐biomarkers. Inflammatory breast cancer (IBC) is the rarest and most lethal subtype of breast cancer with a 5‐year survival rate below 50%. Ethnic disparities for breast cancer exist; negative estrogen (ER) and progesterone (PR) hormone receptor status is more frequent in Hispanic and African American women. In addition, inflammatory breast cancer lacks defined molecular markers limiting its early onset detection which leads to poorer overall prognosis. Thus, we hypothesized that profiling IBC translocations, including its subtypes, show valuable insights to better understand this complex disease. We developed MANGO, a pipeline that leverages STAR, STAR‐Fusion, FusionInspector, and Trinity to identify, visualize and assemble gene fusions from IBC sequencing data. Using the SUM149PT cell line as a model for IBC, we identified and experimentally validated a model fusion gene ZDHHC5—EPB41L5. Fusion unaware sequence assemblies cross‐validated the fusion and its multiple splice sites, one of which encodes a fusion peptide. Differential gene expression between SUM149PT and SUM190PT, an IBC cell line without evidence for the identified translocation, showed loss of expression of ZDHHC5 but no change in EPB41L5, suggesting the latter retained its expression in its new genomic localization. Furthermore, in‐silico functional predictions for experimental results reveals an in‐frame fusion peptide with transmembrane signals in EPB41L5. Genomic translocation mapping reveals triple‐negative IBC diverges from traditional breast cancer translocation patterns. In short, MANGO serves as a powerful tool to identify biologically significant translocations involved in IBC and other cancer classifications.

Targeting Estrogen Non‐Genomic Signaling in a Three‐Dimensional (3D) in VitroModel of Inflammatory Breast Cancer

Inflammatory Breast Cancer (IBC) is the most aggressive form of breast cancer with a low overall 5‐year survival rate of ~30‐60%. To this date the molecular signature associated with IBC has not been fully characterized, which lead to a lack of effective targeted therapeutics, especially for those patients that account for the 20‐40% of triple‐negative (TNBC) IBC cases. Several studies established that molecular signature of IBC shows important differences from the other breast cancer subtypes, such as overexpression of ErbB receptors, RhoC GTPase and Cox‐2, E‐cadherin aberrant expression, and loss of WISP3, among others. However, these molecular alterations do not explain completely the aggressive and rapid IBC progression. Recently, several studies have shown that estrogen can exert non‐genomic effect in triple‐negative IBC and other TNBCs, mediated by the expression of alternate estrogen receptors, including ERα36 and GPR30. Estrogen non‐genomic signaling refers to the rapid action of these alternate estrogen receptors that upon estrogen binding activates protein‐kinase cascades in the cytoplasm. We hypothesize that estrogen can elicit a specific non‐genomic signaling cascade that promotes the acquisition of aggressive oncogenic phenotypes in IBC and that targeting this pathway can be an effective anticancer therapy for IBC. To test this hypothesis, we used pharmacological inhibitors of the Epidermal Growth Factor Receptor (EGFR) alone and GPR30 alone or in combination. The first approach was to determine if inhibiting estrogen non‐genomic signaling by targeting one of the alternate receptors, GPR30, affects cell proliferation in a 3D colony formation assay using Matrigel. Preliminary observations showed that after G15 treatment (GPR30 inhibitor), there was a slight reduction in cell proliferation compared to E2, but when combined with IRESSA (EGFR inhibitor) there was a further decreased on proliferation when compared to IRESSA alone. Ongoing experiments include the effects of Icaritin (modulator of ERα36) and knockdown of ERα36 using siRNA experiments to test the effects in cell proliferation, migration and invasion. Also, we are in the process of determining the half‐maximal inhibitory concentration (IC50) of G15, IRESSA and IRESSA + G15 by performing a dose response curve (Alamar Blue cell viability assay) of SUM149 cell line, to observe if there is an additive effect when combined the pharmacological inhibitors of EGFR and GPR30. This study will provide the foundation for further characterization of the role estrogen non‐genomic signaling in the progression of IBC and to test its potential as a therapeutic target.

The MST1R/RON Tyrosine Kinase in Cancer: Oncogenic Functions and Therapeutic Strategies.

Simple SummaryMST1R/RON receptor tyrosine kinase is a highly conserved transmembrane protein present on epithelial cells, macrophages, and recently identified in a T-cell subset. RON activation attenuates inflammation in healthy tissue. Interestingly, it is overexpressed in several epithelial neoplasms with increasing levels of expression associated with worse outcomes. Though the mechanisms involved are still under investigation, RON is involved in carcinogenesis via immune modulation of the immune tumor microenvironment, activation of numerous oncogenic pathways, and is protective under cellular stress. Alternatively, inhibition of RON abrogates tumor progression in both animal and human tissue models. Given this, RON is a targetable protein of great interest for cancer treatment. Here, we review RON’s function in tissue inflammation and cancer progression, and review cancer clinical trials to date that have used agents targeting RON signaling.The MST1R/RON receptor tyrosine kinase is a homologue of the more well-known MET receptor. Like MET, RON orchestrates cell signaling pathways that promote oncogenesis and enable cancer cell survival; however, it has a more unique role in the regulation of inflammation. RON was originally described as a transmembrane receptor expressed on tissue resident macrophages and various epithelial cells. RON is overexpressed in a variety of cancers and its activation modifies multiple signaling pathways with resultant changes in epithelial and immune cells which together modulate oncogenic phenotypes. While several RON isoforms have been identified with differences in structure, activation, and pathway regulation, increased RON expression and/or activation is consistently associated with worse outcomes. Tyrosine kinase inhibitors targeting RON have been developed, making RON an actionable therapeutic target.

High-throughput RNA sequencing transcriptome analysis of ABC-DLBCL reveals several tumor evasion strategies

Activated B-cell (ABC) lymphoma, a distinct molecular entity within diffuse large B-cell lymphoma (DLBCL), remains highly incurable, showing a worse response to standard immunochemotherapy. The discouraging results obtained in several clinical trials using proteasome inhibitors, tyrosine kinase inhibitors, or immunomodulators, lead to an intense search for new, potentially druggable biomarkers in DLBCL. In this study, we designed an experimental strategy for DLBCL to discover high- and low-abundance RNA-seq-derived transcripts involved in the oncogenic phenotype in patients diagnosed with ABC-DLBCL. Based on the results of a comparative analysis, 79 DE genes and two enriched gene sets related to metabolism and immunity were selected. Genes related to drug resistance, anti-inflammatory response, and tumor-cell dissemination were found to be up-regulated, while tumor suppressor genes were down-regulated. Then, we searched for the perturbagens most suitable for gene expression profiling (GEP) by iLINCS-CMap. Herein, we present a novel experimental approach that connects the omics signature of DLBCL with potential drugs for more accurate treatments.

Analysis of Yes-Associated Protein-1 (YAP1) Target Gene Signature to Predict Progressive Breast Cancer.

Breast cancers are treated according to the ER/PR or HER2 expression and show better survival outcomes with targeted therapy. Triple-negative breast cancers (TNBCs) with a lack of expression of ER/PR and HER2 are treated with systemic therapy with unpredictable responses and outcomes. It is essential to investigate novel markers to identify targeted therapies for TNBC. One such marker is YAP1, a transcription co-activator protein that shows association with poor prognosis of breast cancer. YAP1 transcriptionally regulates the expression of genes that drive the oncogenic phenotypes. Here, we assess a potential YAP target gene signature to predict a progressive subset of breast tumors from METABRIC and TCGA datasets. YAP1 target genes were shortlisted based on expression correlation and concordance with YAP1 expression and significant association with survival outcomes of patients. Hierarchical clustering was performed for the shortlisted genes. The utility of the clustered genes was assessed by survival analysis to identify a recurring subset. Expression of the shortlisted target genes showed significant association with survival outcomes of HER2-positive and TNBC subset in both datasets. The shortlisted genes were verified using an independent dataset. Further validation using IHC can prove the utility of this potential prognostic signature to identify a recurrent subset of HER2-positive and TNBC subtypes.