Gene Expression In Cancer Cells Research Articles

MiR-548 K regulatory effect on the ABCG2 gene expression in MDR breast cancer cells.

multidrug resistance (MDR) is One of the foremost challenges in overcoming breast cancer. Various molecular processes are involved in the development of MDR in breast cancer cells, including over expression of ABC transporters such as ABCG2 (BCRP), increase breast cancer stem cells drug resistance, and epithelial mesenchymal transition. In the present study, we used bioinformatics and experimental analysis to investigate the role of miR-548 K, in the modulating of ABCG2, in MDR breast cancer cells. In silico inspections introduce 14 microRNAs targeting 3'-UTR region of ABCG2 transcripts, which are probably involved in breast cancer drug resistance. An association was highlighted between miR-548 k with ABC transporter family. The expression level of ABCG2 gene in MCF7-MX cell lines was significantly more than MCF7 cell lines. On the other hand, we increased the expression of miR-548 K in MCF7-MX and MCF7 cell lines through its transfection, which dramatically coincided with decreasion in the ABCG2 transcripts level. Additional studies on patient samples revealed that the expression of ABCG2 showed an increase in ABCG2 level in neoadjuvant chemotherapy drugs resistance (NCDR) patients compared to primary pre-operative chemotherapy drugs response (PCDR) patients. Also, a reduction in the expression of miR-548 K in NCDR patients was revealed. The results of our study suggest that miR-548 K may be involved in modulating the expression of ABCG2 in MDR breast cancer cells.

SiRNA and apoptosis in breast cancer cells: A minireview

Small interfering RNA (siRNA), is a class of double-stranded RNA at first non-coding RNA molecules, operating within the RNA interference (RNAi) pathway. It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation. siRNAs have been widely used to study gene function and extensively exploited for their potential therapeutic applications. siRNAs have gained attention as a potential therapeutic reagent due to their ability to inhibit specific genes in cancer cells. Increased resistance to apoptosis is a challenging issue for treatment of many cancers, including breast cancer. It has been recently reported that siRNAs and RNAi technology can be used to increase the apoptotic susceptibility of cancer cells. It has been shown that apoptosis is induced in cancer cells by siRNA-mediated silencing of the livin/ML-IAP/KIAP gene. Association of siRNA with apoptosis via mitochondrial depolarization and caspase-3 activation has been highlighted in cancer cells. Although many aspects of siRNA actions in cancer cells have been revealed through in vivo and in vitro studies, the biological mechanisms underlying siRNA mediated knockdown of gene expression and apoptosis induction in cancer cells are not yet fully understood. The main aim of this review is to investigate the effects of siRNAs on apoptosis induction in breast cancer cells.

ADAM9 drives immunosuppressive environment for lung tumor progression

Abstract Cancer cells develop the immune suppressive tumor environment, but the underlying molecular mechanism for it is still elusive. Here, we demonstrated that ADAM9 contributed to lung tumor progression and promoted IFN-related gene expression in lung cancer cells that participated in immune regulation in the tumor environment. ADAM9 knockout (KO) lung cancer cells reduced lung cancer metastasis with a decrease in neutrophil infiltration and an increase in CD8+ T cell infiltration. By performing the genome-wide approach to explore ADAM9-regulated genes in lung cancer cells, we revealed that ADAM9 regulated cytokine production and lymphocyte activation. It enhanced the master transcription factor of IFN signaling, STAT1 activation in lung cancer cells. Moreover, ADAM9 promoted IL6/IL6 receptor-STAT3 axis signaling that lead to suppression of IL12p40 secretion and MHC class II expression in dendritic cells and macrophages. Notably, we found that type I IFN related-proteins and steroid biosynthesis-related proteins were related to ADAM9-mediated STAT signaling activation by LC-MS/MS analysis. We demonstrated that ADAM9 created an immune suppressive environment by regulating IFN signaling for tumor progression. Supported by grants from NHRI (NHRI-EX112-11219BI)

Polypropylene microplastics promote metastatic features in human breast cancer

Microplastics (MPs) are now a global issue due to increased plastic production and use. Recently, various studies have been performed in response to the human health risk assessment. However, these studies have focused on spherical MPs, which have smooth edges and a spherical shape and account for less than 1% of MPs in nature. Unfortunately, studies on fragment-type MPs are very limited and remain in the initial stages. In this study, we studied the effect that 16.4 µm fragment type polypropylene (PP) MPs, which have an irregular shape and sharp edges and form naturally in the environment, had on breast cancer. The detrimental effects of PPMPs on breast cancer metastasis were examined. Here, 1.6 mg/ml of PPMP, which does not induce cytotoxicity in MDA-MB-231, was used, and at this concentration, PPMP did not induce morphological changes or cellular migrating in the MDA-MB-231 and MCF-7 cells. However, PPMP incubation for 24 hours in the MDA-MB-231 cells significantly altered the level of cell cycle-related transcripts in an RNA-seq analysis. When confirmed by qRT-PCR, the gene expression of TMBIM6, AP2M1, and PTP4A2 was increased, while the transcript level of FTH1 was decreased. Further, secretion of the pro-inflammatory cytokine IL-6 from cancer cells was elevated with the incubation of PPMP for 12 hours. These results suggest that PPMP enhances metastasis-related gene expression and cytokines in breast cancer cells, exacerbating breast cancer metastasis.

Abstract 5267: Effects of polyphenon E treatment on gene expression in DU145 prostate cancer cells

Abstract One promising focus of prostate cancer (PCa) research is the chemopreventive effects of Polyphenon E (Poly E), a defined mixture of green tea polyphenols. A previous study utilizing the TRAMP model of human PCa, displayed chemopreventive activity as a result of Poly E oral administration in a dose-dependent pattern. Human clinical trials of Poly E treatment exhibited activity in PCa of those previously diagnosed with atypical small acinar proliferation or high-grade prostate intraepithelial neoplasia. The molecular mechanisms of these Poly E chemopreventive activities against PCa are not well established. Our hypothesis is that Poly E treatment influences expression of genes involved in key cellular signaling pathways. DU145 prostate cancer cells were cultured in complete growth media supplemented with varied Poly E concentrations (100, 200, 300 mg/L) for 24 hrs. RNA was isolated for comparative microarray (0 vs. 200 mg/L Poly E) and qRT-PCR analyses. Microarray data for 54,613 genes were filtered for > 2-fold expression level changes, with 5,272 increased and 6,467 genes decreased. Nine genes, (CASP8, CBLB, CCNB1, HDAC4, MXD1, RGCC, RGS4, TBC1D7, ZNF462) involved in key signaling pathways with >2-fold gene expression changes were selected for subsequent qRT-PCR analyses. Microarray probe set IDs and fold change gene expression values for these nine genes analyzed are listed (Table 1). From qRT-PCR analyses, six of these genes had significant gene expression changes between Poly E treatment levels, MXD1 (14.20-fold; p = 0.0122), RGCC (0.6748-fold; p < 0.0001), TBC1D7(0.2416-fold; p = 0.0037), ZNF462 (0.7030-fold; p = 0.0173), CASP8 (0.4856-fold; p = 0.0136), and CBLB (2.149-fold; p = 0.0036). We conclude that two thirds (6/9) of the genes selected from the microarray data for qRT-PCR analyses had significant Poly E induced gene expression changes. Future experimental directions include cell cycle profiling and annexin V apoptosis analysis, as well as inclusion of other established PCa cell lines. Microarray Data from Poly E-treated DU145 Cells Affymetrix Probe ID Gene Symbol Log2-Fold Changes 207686_s_at CASP8 1.79 213373_s_at CASP8 -1.13 1553306_at CASP8 -2.02 208348_s_at CBLB 7.79 209682_at CBLB 2.27 227900_at CBLB -1.13 228729_at CCNB1 -2.55 214710_s_at CCNB1 -2.70 1554322_a_at HDAC4 -2.06 228813_at HDAC4 -4.74 204225_at HDAC4 -5.43 206877_at MXD1 17.87 228846_at MXD1 8.04 226275_at MXD1 3.80 218723_s_at RGCC 2.54 239827_at RGCC -3.90 204339_s_at RGS4 7.74 204338_s_at RGS4 -1.33 204337_at RGS4 -1.80 1563839_at TBC1D7 47.08 223461_at TBC1D7 1.17 232393_at ZNF462 28.62 226575_at ZNF462 -1.38 244007_at ZNF462 -1.61 Citation Format: Ethan J. Vallebuona, Ashley N. Gannon, Corrine M. Costello, Ricardo Cordova, Ricardo A. Declet-Bauzo, Seung Joon Kim, Nagi Kumar, Jong Y. Park, L. Michael Carastro. Effects of polyphenon E treatment on gene expression in DU145 prostate cancer cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5267.

Abstract 5477: An investigation to study differential gene expression of lung cancer cells, tumor associated macrophages, and bone marrow derived mesenchymal stems cells in the tumor microenvironment

Abstract Cancer is a public health crisis affecting approximately 19.3 million globally, annually. Lung cancer has the highest percentage of incidence and is responsible for 27% of cancer-related deaths. The prevalence of lung cancer worldwide led us to investigate differential gene expression in lung adenocarcinoma and small cell lung cancer cell lines in comparison to a healthy lung cell line. We also investigated the effect of lung tumor microenvironment to bone marrow derived pluripotent mesenchymal stem cells (PMSC) and tumor associated macrophages. This research involved cancer and healthy cell line culture with appropriate medium. Whole transcriptomic and small non-coding RNA sequencing and analysis by Ingenuity Pathway Analysis (Qiagen, USA), Quantitative RT-PCR and ELISA assays. We further studied morphological changes and differential gene expression in extracellular vesicles(exosomes) isolated from the TAM and TME exposed PMCs by atomic force microscopy and RNA sequencing techniques. The results of our investigation showed differential gene expression and novel core canonical pathways in the lung cancer cells, TME exposed TAM, and PMSC. We also observed morphological changes in TME derived exosomes from TAM and PMSC. RNA sequencing results showed differential gene expression of both coding and non-coding RNAs including tRNA fragments. Thus, our findings of this investigation led to identification of multiple cancer related genes and small non-coding microRNA, long non-coding RNA, and tRNA fragments which will have potential diagnostic and therapeutic target value that demands further future research. Acknowledgement: This research is supported by a grant from US NIH-NIGMS- 5T34GM100831-08 and US-NIH Grant# U 54 MD007597-31-5959. Citation Format: Hirendra N. Banerjee, Joseph Hedley, Cheslsey Aurelus, Narendra Banerjee, Kuldeep Rawat, Quentin Reaves, Shennel Brown, Darla Gilmartin, Makieyah Liverman, Jazmine Cuffee, Elizabeth Cagle, Erik Armstrong, Brent Lake, Santosh Mandal, Somiranjan Ghosh, Stephen Beebe, Kamal Asadipour, Christopher Krauss, Santanu Bhattacharya, Tanmay Kulkarni, Zahidur Abedin. An investigation to study differential gene expression of lung cancer cells, tumor associated macrophages, and bone marrow derived mesenchymal stems cells in the tumor microenvironment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5477.

Abstract 5754: Determining the regulatory logic of breast cancer cells using single-cell multi-omics

Abstract Cancer cells rewire regulatory elements scattered throughout the genome (such as enhancers) to drive aberrant gene expression. Thus, deconvoluting the regulatory mechanisms that contribute to oncogenic gene expression in cancer cells is key to understanding tumor biology. To this end, we have charted the transcriptional and epigenetic landscape of breast cancer at single-cell resolution to quantitatively link variation in chromatin accessibility to gene expression across malignant and non-malignant cell types. Our comprehensive dataset profiles the chromatin landscape (scATAC-seq) in concert with the transcriptional profiles (scRNA-seq) of 4 breast cancer cell lines, 12 primary breast tumors, and 4 normal mammary reduction tissue specimens collected and processed immediately after surgical resection. This dataset, encompassing over 250,000 individual cells, allowed us to define the regulatory logic of cancer cells by 1) revealing how the epigenome underlies cellular heterogeneity of these tumors in comparison to normal mammary tissue, 2) defining how malignant cells hijack enhancer elements to drive key transcriptional programs in a subtype-specific manner, and 3) annotating which cancer-specific enhancer-to-gene connections portend a worse outcome in patients. Notably, we discovered that cancer cells acquire de novo non-coding enhancer elements to modulate hallmark cancer pathways that were previously hidden using bulk genomics approaches. This highlights the potential for cancer-specific enhancers to serve as markers with diagnostic and prognostic potential, or even serve as tractable targets for therapeutic intervention. Together these data enable the annotation of the cellular composition, transcriptional, and epigenetic landscape of breast tumors to help pinpoint clinically relevant mechanisms of tumorigenesis. Citation Format: Matthew J. Regner, Aatish Thennavan, Susana Garcia-Recio, Kamila Wisniewska, Philip M. Spanheimer, Joel S. Parker, Charles M. Perou, Hector L. Franco. Determining the regulatory logic of breast cancer cells using single-cell multi-omics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5754.

Abstract 2235: A treatment for glioblastoma with a novel epigenetic inhibitor and identification of its target

Abstract Glioblastoma multiforme (GBM) is one of the deadliest human cancers. Despite extensive efforts to develop a new treatment, the prognoses of patients have not changed dramatically over the past several decades. LSD1 plays an essential role in the epigenetic regulation of gene expression in many cancer cells, including GBM, as it removes methyl groups from histone H3 lysine (K) 4me1/2 and H3K9me1/2. Since it was reported that suppression of LSD1 induced apoptosis of glioblastoma stem cells (GSCs), LSD1 has been expected as an effective therapeutic target for GBMs, particularly enriched with GSCs. We newly discovered an LSD inhibitor (S2172) that suppressed the LSD1 enzymatic activity effectively and sufficiently penetrated into brain. We found that S2172 showed a strong inhibitory effect on cell growth not only in GCS cells but also in differentiated GBM cells in vitro. In GBM cell line U251, IC50 of S2172 was lower than that of other LSD1 inhibitors (IC50 10.5 μM, 29.5 μM, 11.0 μM treated with S2172, Ory-1001, and CC-90011, respectively). We also found a robust suppression of transcription of oncogene Myc in differentiated GBM cells after S2172 treatment, which is highly expressed in most GBM cells and considered as a key element to maintain its stemness and proliferation. Consistent with the expression analysis, chromatin immunoprecipitation-sequencing (ChIP-seq) revealed that enrichment of H3K4m2 and H3K4m3 was efficiently altered by S2172 treatment along with the change of Myc expression. Finally, we treated U251 brain tumor mouse model with S2172. While S2172 had a strong effect in vitro, S2172 seemed unsuccessful in killing differentiated GBM cells in vivo. These data suggests that treatment of S2172 is less effective to differentiated GBM cells and this is consistent with previous report that LSD1 as a candidate therapeutic target in stem-like tumor propagating cells in GBM. Citation Format: Tokunaga Kota. A treatment for glioblastoma with a novel epigenetic inhibitor and identification of its target [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2235.

Abstract 5249: Polyphenon E effects MXD1 and RGS4 gene expression in PC-3 prostate cancer cells

Abstract Polyphenon E (Poly E) is a standardized, caffeine-free green tea extract with defined polyphenol content. Oral Poly E administration confers chemoprotective activity against prostate cancer (PCa) progression in the TRAMP model of human PCa. Poly E has limited activity against human PCa, but only in those previously diagnosed with atypical small acinar proliferation or high-grade prostate intraepithelial neoplasia. The molecular mechanisms underpinning Poly E chemopreventive activities against PCa are not fully understood. We hypothesized Poly E treatment of PCa cells induces gene expression changes, which could involve molecular mechanisms underpinning the limited Poly E chemoprevention activity against PCa. PC-3 cells were cultured in complete growth media supplemented with varied Poly E concentrations (0, 100, 200, or 300 mg/L) for 24 hr. RNA was isolated for comparative DNA microarray (0 vs. 200 mg/L Poly E) and subsequent qRT-PCR analyses for validation. Microarray data for 54,613 genes were filtered for > 2-fold expression level changes, with 8,319 increased and 6,176 genes decreased. Seven genes (CASP8, CBLB, CCNB1, HDAC4, MXD1, RGCC, RGS4) involved in key cellular signaling pathways and with > 2-fold expression level changes, as well as a control gene (RB1), were selected for qRT-PCR analyses. These eight genes are listed with corresponding fold-change gene expression values for each microarray probe set (Table 1). The qRT-PCR analyses identified two genes with significantly increased expression, MXD1 (13.98-fold; p=0.0003) and RGS4 (21.98-fold; p=0.0011), between poly E treatment levels. The significantly increased MXD1 and RGS4 gene expression in Poly E-treated PC-3 cells, and the Poly E-dose dependence of MXD1 gene expression increases, could implicate MXD1 and RGS4 in the PCa chemopreventive activity of Poly E. Future experimental directions include cell cycle profile and Annexin V analyses, immunoblotting analyses, and including other established PCa cell lines in these studies. Microarray Data from Poly E-treated PC-3 Cells Affymetrix Probe ID Gene symbol Log2-Fold Change 213373_s_at CASP8 -2.23 1553306_at CASP8 -3.20 208348_s_at CBLB 19.01 209682_at CBLB 3.83 214710_s_at CCNB1 -2.77 228729_at CCNB1 -3.47 1554322_a_at HDAC4 -2.47 204225_at HDAC4 -3.23 228813_at HDAC4 -4.45 206877_at MXD1 13.56 228846_at MXD1 7.35 226275_at MXD1 1.91 211540_s_at RB1 1.85 203132_at RB1 -1.43 218723_s_at RGCC 23.12 239827_at RGCC 1.22 204338_s_at RGS4 20.54 204337_at RGS4 6.12 204339_s_at RGS4 3.69 Citation Format: L. Michael Carastro, Ethan J. Vallebuona, Ricardo Cordova, Ashley N. Gannon, Corrine M. Costello, Ricardo A. Declet-Bauzo, Seung Joon Kim, Nagi Kumar, Jong Y. Park. Polyphenon E effects MXD1 and RGS4 gene expression in PC-3 prostate cancer cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5249.

Abstract 1761: Dual inhibition of HSP27 and FAO as a novel therapeutic strategy for cisplatin-resistant ovarian cancer

Abstract Cisplatin is the most commonly employed chemotherapeutic drug for ovarian cancer treatment. However, most ovarian cancer patients experience recurrent cisplatin-resistant cancer, for which treatment options are limited. We have previously shown that inhibition of heat shock protein 27 (HSP27) or fatty acid oxidation (FAO) sensitizes cisplatin-resistant ovarian cancer cells to cisplatin. However, it is unknown if HSP27 and FAO pathways interact to promote cisplatin resistance in ovarian cancer cells. Therefore, we tested whether cisplatin-resistant ovarian cancer cells are sensitive to concurrent HSP27 and FAO inhibition. Strikingly, dual inhibition of HSP27 and FAO, with the clinically employed drugs ivermectin and perhexiline respectively, dramatically decreased the viability of A2780CIS, a cisplatin-resistant ovarian cancer cell line. We also found that HSP27 knockdown cancer cells are more sensitive to cisplatin and perhexiline dual treatment. Thus, we sought to test the hypothesis that cisplatin-resistant ovarian cancer cells rely on FAO upon HSP27 inhibition to maintain cisplatin resistance. To test if FAO is affected by HSP27 inhibition, we measured AMPK activity and CPT1A expression, an inducer of FAO and the rate limiting enzyme of FAO respectively. We found that AMPK is activated and CPT1A is upregulated in HSP27 knockdown cancer cells. It has been shown that cisplatin induces reactive oxygen species (ROS) and that HSP27 is a negative regulator of ROS. Thus, we treated HSP27 knockdown cancer cells with cisplatin and measured the levels of mitochondrial and cellular ROS, oxidized/reduced lipids, and reduced thiols using MitoSOX, CellROX, Image -iT Lipid Peroxidation, and ThiolTracker fluorescent dyes, respectively. Our data demonstrates that HSP27 inhibition increases mitochondrial ROS, cellular ROS, and the ratio of oxidized to reduced lipids in cisplatin-treated cells. Additionally, HSP27 inhibition decreases levels of reduced thiols in this context. Our preliminary data also suggests that cisplatin-treated HSP27 knockdown cells have decreased expression of glucose-6-phosphate dehydrogenase (G6PD) and glutathione reductase (GSR), key enzymes that facilitate the reduction of glutathione into its reduced form (GSH). Additionally, we demonstrate that attenuation of cisplatin-induced ROS with N-Acetyl cysteine (NAC) prevented cisplatin-induced apoptosis and ferroptosis. NAC also attenuated cisplatin-mediated induction of HSP27 and FAO gene expression in cisplatin-resistant ovarian cancer cells. Collectively, our results demonstrate that HSP27 and FAO are two parallel pathways that promote cisplatin resistance in ovarian cancer cells by attenuating cisplatin-induced ROS. Future studies will determine the in vivo efficacy of this combination therapy and if dual inhibition leads to synergistic cell death through a ROS based mechanism. Citation Format: James P. Heiserman, Zenab Minhas, Dong-Joo Cheon. Dual inhibition of HSP27 and FAO as a novel therapeutic strategy for cisplatin-resistant ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1761.

Abstract 5401: Computational cancer cell gene expression deconvolution from tumor bulk RNA-seq via the machine learning algorithm Helenus

Abstract Background: Biomarker gene expression is becoming more commonly utilized for clinical decision-making in oncology clinical practice. However, complex tumor tissue comprises a population of cancer cells (CC) and the tumor microenvironment (TME), causing expression signals belonging to the CC and TME calculated from bulk RNA-seq of the tumor tissue to be indistinguishable. To circumvent this, Helenus, a gene expression deconvolution tool, was developed to estimate TME-specific gene expression, consequently, providing precise CC-specific gene expression. Methods: Helenus performs the “subtraction” of TME gene expression from the total expression calculated from bulk RNA-seq of the tumor tissue. To accurately reconstruct the CC expression profile, LightGBM gene models were trained on artificial transcriptomes created from > 1,000 different solid tumor cancer cell lines and > 3,000 samples of various TME cellular proportions. The LighGBM gene models included genes expressed predominantly in the TME (e.g., CD3E), both the TME and the CC (e.g., BCL6), or in the CC (e.g., HER2). The input features included: 1) RNA percentages of TME cell types predicted by the cell deconvolution tool Kassandra (Zaitsev et al., 2022); 2) evaluation of TME target gene expression via the estimation of its weighted average expression profile in TME cell populations; and 3) a set of TME- and CC-specific genes. The resulting predictions were adjusted based on the CC cell fraction. To evaluate Helenus’ performance, CC and TME RNA were mixed at different ratios using various cancer cell lines and peripheral blood-derived TME cell populations and suspensions of tumor cells prepared from cancer tissue across multiple tumor purity dilutions. Results: Helenus deconvolution resulted in an increased concordance correlation value from 0.73 to 0.98 between the real gene expression profile of pure CC and the reconstructed CC expression from bulk RNA-seq. Helenus showed high concordance between the gene expression profile of sorted cancer cell lines and the deconvolved gene expression across a wide range of CC RNA concentrations (20-90%) mixed with imitated TME RNA at varying concentrations. Helenus demonstrated high performance calculating gene expression of multiple clinically relevant biomarkers in the TME:cancer cell line mixes: CD274 (PD-L1) (mean absolute error [MAE] ~3.5-fold reduction); HLA-A (~2.8-fold MAE reduction); MKI67 (Ki-67, ~2.2-fold MAE reduction), ERBB2 (HER2, ~1.7-fold MAE reduction). Helenus deconvolved CC expression and found significant correlations with CC gene amplifications and deletions (e.g., BCL-2, VNN3) independent of tumor purity (p < 0.003). Conclusion: Helenus, the CC gene expression deconvolution tool, was developed with high accuracy to contribute to tumor diagnosis, disease monitoring, treatment decisions, and clinically relevant biomarker identification. Citation Format: Valentina Beliaeva, Ekaterina Ivleva, Boris Shpak, Daniil Litvinov, Anastasia Zotova, Krystle Nomie, Daniiar Dyikanov, Alexander Kuznetsov, Maria Savchenko, Aleksandr Zaitsev, Nathan Fowler, Alexander Bagaev. Computational cancer cell gene expression deconvolution from tumor bulk RNA-seq via the machine learning algorithm Helenus. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5401.

Anti-Cancer Effect of Dorema Ammoniacum Gum by Targeting Metabolic Reprogramming by Regulating APC, P53, KRAS Gene Expression in HT-29 Human Colon Cancer Cells.

Colorectal cancer is a heterogeneous disease that leads to metabolic disorders due to multiple upstream genetic and molecular changes and interactions. The development of new therapies, especially herbal medicines, has received much global attention. Dorema ammoniacum is a medicinal plant. Its gum is used in healing known ailments. Studying metabolome profiles based on nuclear magnetic resonance 1HNMR as a non-invasive and reproducible tool can identify metabolic changes as a reflection of intracellular fluxes, especially in drug responses. This study aimed to investigate the anti-cancer effects of different gum extracts on metabolic changes and their impact on gene expression in HT-29 cell. Extraction of Dorema ammoniacum gum with hexane, chloroform, and dichloromethane organic solvents was performed. Cell inhibition growth percentage and IC50 were assessed. Following treating the cells with dichloromethane extract, p53, APC, and KRAS gene expression were determined. 1HNMR spectroscopy was conducted. Eventually, systems biology software tools interpreted combined metabolites and genes simultaneously. The lowest determined IC50 concentration was related to dichloromethane solvent, and the highest was hexane and chloroform. The expression of the KRAS oncogene gene decreased significantly after treatment with dichloromethane extract compared to the control group, and the expression of tumor suppressor gene p53 and APC increased significantly. Most gene-altered convergent metabolic phenotypes. This study's results indicate that the dichloromethane solvent of Dorema ammoniacum gum exhibits its antitumor properties by altering the expression of genes involved in HT-29 cells and the consequent change in downstream metabolic reprogramming.

Collagen cross‐linking in oral cancer

AbstractCarcinogenesis is widely recognized to be caused by qualitative and quantitative genetic changes. These changes include abnormalities in gene structure itself and/or in transcriptional mechanisms involved in gene expression in cancer cells and cancer‐associated cells. Emerging evidence has also revealed that the nature of the extracellular matrix (ECM) in the tumor microenvironment actively regulates cancer cell growth, migration, and metastasis. The most abundant protein in the ECM surrounding cancer cells is fibrillar type I collagen that accumulates and stiffens through formation of specific types of covalent intermolecular cross‐links. Alterations in the physicochemical nature of ECM proteins like fibrillar type I collagen can affect cancer cell behavior. This review provides an overview of collagen cross‐linking and its roles in oral cancer as well as possible clinical applications.

Epigenetic modification of gene expression in cancer cells by terahertz demethylation

Terahertz (THz) radiation can affect the degree of DNA methylation, the spectral characteristics of which exist in the terahertz region. DNA methylation is an epigenetic modification in which a methyl (CH3) group is attached to cytosine, a nucleobase in human DNA. Appropriately controlled DNA methylation leads to proper regulation of gene expression. However, abnormal gene expression that departs from controlled genetic transcription through aberrant DNA methylation may occur in cancer or other diseases. In this study, we demonstrate the modification of gene expression in cells by THz demethylation using resonant THz radiation. Using an enzyme-linked immunosorbent assay, we observed changes in the degree of global DNA methylation in the SK-MEL-3 melanoma cell line under irradiation with 1.6-THz radiation with limited spectral bandwidth. Resonant THz radiation demethylated living melanoma cells by 19%, with no significant occurrence of apurinic/apyrimidinic sites, and the demethylation ratio was linearly proportional to the power of THz radiation. THz demethylation downregulates FOS, JUN, and CXCL8 genes, which are involved in cancer and apoptosis pathways. Our results show that THz demethylation has the potential to be a gene expression modifier with promising applications in cancer treatment.

Design and optimization various formulations of PEGylated niosomal nanoparticles loaded with phytochemical agents: potential anti-cancer effects against human lung cancer cells.

Phytochemicals and their derivatives are good options to improve treatment efficiency in cancer patients. Artemisinin (ART) and metformin (MET) are widely used phytochemicals to treat various types of cancers. However, their application because of their dose-dependent side effects, and poor bioavailability brings several challenges. Niosome is a novel nanocarrier that is the best choice to encapsulate both lipophilic and hydrophilic drugs. In this study, we synthesized and characterized various formulations of PEGylated (polyethylene glycol) niosomal nanoparticles co-loaded with ART-MET and evaluated their anticancer effect on A549 lung cancer cells. Various formulations of PEGylated noisome were prepared by the thin-film hydration method and characterized in size, morphology, release pattern, and physicochemical structure. The cytotoxic effect of the free ART-MET and optimized PEGylated niosomal nanoparticles loaded with ART-MET on A549 cells were evaluated by MTT assay. Furthermore, the Real-time PCR (RT-PCR) technique used to evaluate apoptotic and anti-apoptotic gene expression. The size, encapsulation efficiency (EE), and polydispersity index (PDI) of the optimized nanoparticles are 256nm, 95%, and 0.202, respectively. Additionally, due to the PEGylation hydrophilic character, there is a major consideration of the high impact of PEGylation on reducing niosome size. According to the results of the MTT assay, free ART-MET and ART-MET-loaded niosomal nanoparticles showed dose-dependent toxicity and inhibits the growth of A549 lung cancer cells. Furthermore, the RT-PCR results indicated that ART-MET-loaded niosomal nanoparticles have a higher anti-proliferative effect by inhibiting anti-apoptotic and inducing apoptotic gene expression in A549 lung cancer cells. Our study revealed that the simultaneous use of ART and MET in the optimized PEGylated niosomal nanoparticles delivery system could be an appropriate approach to improve the effectiveness of lung cancer treatment.

Comprehensive analysis of the correlation of the pan-cancer gene HAUS5 with prognosis and immune infiltration in liver cancer

Liver hepatocellular carcinoma (LIHC) is one of the most common malignancies and places a heavy burden on patients worldwide. HAUS augmin-like complex subunit 5 (HAUS5) is involved in the occurrence and development of various cancers. However, the functional role and significance of HAUS5 in LIHC remain unclear. The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE) and Gene Expression Omnibus (GEO) databases were used to analyze the mRNA expression of HAUS5. The value of HAUS5 in predicting LIHC prognosis and the relationship between HAUS5 and clinicopathological features were assessed by the Kaplan–Meier plotter and UALCAN databases. Functional enrichment analyses and nomogram prediction model construction were performed with the R packages. The LinkedOmics database was searched to reveal co-expressed genes associated with HAUS5. The relationship between HAUS5 expression and immune infiltration was explored by searching the TISIDB database and single-sample gene set enrichment analysis (ssGSEA). The Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Human Protein Atlas (HPA) databases were used to evaluate HAUS5 protein expression. Finally, the effect of HAUS5 on the proliferation of hepatoma cells was verified by CCK-8, colony formation and EdU assays. HAUS5 is aberrantly expressed and associated with a poor prognosis in most tumors, including LIHC. The expression of HAUS5 is significantly correlated with clinicopathological indicators in patients with LIHC. Functional enrichment analysis showed that HAUS5 was closely related to DNA replication, cell cycle and p53 signaling pathway. HAUS5 may serve as an independent risk factor for LIHC prognosis. The nomogram based on HAUS5 had area under the curve (AUC) values of 0.74 and 0.77 for predicting the 3-year and 5-year overall survival (OS) of LIHC patients. Immune correlation analysis showed that HAUS5 was significantly associated with immune infiltration. Finally, the results of in vitro experiments showed that when HAUS5 was knocked down, the proliferation of hepatoma cells was significantly decreased. The pan-oncogene HAUS5 is a positive regulator of LIHC progression and is closely associated with a poor prognosis in LIHC. Moreover, HAUS5 is involved in immune infiltration in LIHC. HAUS5 may be a new prognostic marker and therapeutic target for LIHC patients.

Transcription of Autophagy Associated Gene Expression as Possible Predictors of a Colorectal Cancer Prognosis.

(1) Background: Autophagy plays a dual role in oncogenesis-it contributes to the growth of the tumor and can inhibit its development. The aim of this study was to assess changes in the transcriptional activity of LAMP-2, BECN1, PINK1, and FOXO1 genes involved in the autophagy process in histopathologically confirmed adenocarcinoma sections of colorectal cancer: (2) Methods: A gene expression profile analysis was performed using HG-U133A and the RT-qPCR reaction. The transcriptional activity of genes was compared in sections of colorectal cancer in the four clinical stages (CSI-CSIV) concerning the control group; (3) Results: In CSI, the transcriptional activity of the PINK1 gene is highest; in CS II, the LAMP-2 gene is highest, while FOXO1 increases gradually from CSI reaching a maximum in CSIII. There is no BECN1 gene expression in colorectal cancer cells; (4) Conclusions: The observed differences in the mRNA concentration profile of autophagy-related genes in colon cancer specimens may indicate the role of autophagy in the pathogenesis of this cancer. Genes involved in autophagy may be diagnostic tools for colorectal cancer screening and personalized therapy in the future.

Shear loaded osteocyte-like-cells affect epithelial and mesenchymal gene expression in DU145 prostate cancer cells, while decreasing their invasion in vitro

Once prostate cancer (PC) metastasizes towards bone the 5-year survival rates drop with 70%, but it is largely unknown why. Bone is continuously mechanically loaded, which likely modulates the paracrine signaling from osteocytes towards PC cells to affect tumor behavior. We hypothesize that shear loaded osteocytes affect PC cell proliferation, invasion and epithelial and mesenchymal-related gene and protein expression. We cultured human DU145 cells, a commonly used cell line for prostate cancer metastases, in the conditioned medium (CM) from shear loaded or unloaded human osteocyte-like-cells (OCYLCs) for 1 and 3 days and assessed their number by staining nuclei with DAPI, their invasion by performing an invasion assay, and epithelial-to-mesenchymal (EMT)-related gene and protein expression by qPCR and immunocytochemistry. CM of shear loaded OCYLCs did not affect DU145 cell number compared to CM of static cultured OCYLCs, but decreased their invasion 1.34-fold. CM of shear loaded OCYLCs enhanced expression of epithelial genes: SYND1 and CDH1 after day 1, while it also enhanced CDH1 after day 3. CM of shear loaded osteocytes enhanced mesenchymal genes: VMN, Snail and MIP2 after day 1, while it decreased expression of mesenchymal CYR61 after day 3. We conclude that CM of shear loaded OCYLCs does not affect DU145 cell proliferation, but decreases their invasion, and differentially affects their EMT-related gene expression. Identifying paracrine signals from shear loaded osteocytes that decrease PC cell invasion may provide novel leads in developing treatments for bone metastases from PC.

The Effect of Different Anesthetic Techniques on Proliferation, Apoptosis, and Gene Expression in Colon Cancer Cells: A Pilot In Vitro Study.

Colorectal cancer is highly common and causes high mortality rates. Treatment for colorectal cancer is multidisciplinary, but in most cases the main option remains surgery. Intriguingly, in recent years, a number of studies have shown that a patient's postoperative outcome may be influenced by certain anesthetic drugs. Our main objective was to compare the effect of propofol-total intravenous anesthesia (TIVA) with sevoflurane anesthesia and to investigate the potential role of intravenous lidocaine on colon cancer cell functions. We tested the effects of serum from colorectal cancer patients undergoing TIVA vs. sevoflurane anesthesia with or without lidocaine on HCT 116 cell lines; on proliferation, apoptosis, migration, and cell cycles; and on cancer-related gene expressions. 60 patients who were scheduled for colorectal cancer surgery were randomized into four different groups (two groups with TIVA and two groups with sevoflurane anesthesia with or without intravenous lidocaine). Blood samples were collected at the start and at the end of surgery. HCT 116 cells were exposed to the patients' serum. 15 patients were included in each of the study groups. We did not find any significant difference on cell viability or apoptosis between the study groups. However, there was an increased apoptosis in propofol groups, but this result was not statistically significant. A significant increase in the expression profile of the TP53 gene in the propofol group was registered (p = 0.029), while in the other study groups, no significant differences were reported. BCL2 and CASP3 expressions increased in the sevoflurane-lidocaine group without statistical significance. In our study, serum from patients receiving different anesthetic techniques did not significantly influence the apoptosis, migration, and cell cycle of HCT-116 colorectal carcinoma cells. Viability was also not significantly influenced by the anesthetic technique, except the sevoflurane-lidocaine group where it was increased. The gene expression of TP53 was significantly increased in the propofol group, which is consistent with the results of similar in vitro studies and may be one of the mechanisms by which anesthetic agents may influence the biology of cancer cells. Further studies that investigate the effects of propofol and lidocaine in different plasma concentrations on different colon cancer cell lines and assess the impacts of these findings on the clinical outcome are much needed.

Retracted: Differential Control of Growth, Apoptotic Activity, and Gene Expression in Human Breast Cancer Cells by Extracts Derived from Medicinal Herbs Zingiber officinale.

[This retracts the article DOI: 10.1155/2012/614356.].