TCGA RNA-seq Data Research Articles

Identification of Biomarkers and Molecular Pathways Implicated in Smoking and COVID-19 Associated Lung Cancer Using Bioinformatics and Machine Learning Approaches

Lung cancer (LC) is a significant global health issue, with smoking as the most common cause. Recent epidemiological studies have suggested that individuals who smoke are more susceptible to COVID-19. In this study, we aimed to investigate the influence of smoking and COVID-19 on LC using bioinformatics and machine learning approaches. We compared the differentially expressed genes (DEGs) between LC, smoking, and COVID-19 datasets and identified 26 down-regulated and 37 up-regulated genes shared between LC and smoking, and 7 down-regulated and 6 up-regulated genes shared between LC and COVID-19. Integration of these datasets resulted in the identification of ten hub genes (SLC22A18, CHAC1, ROBO4, TEK, NOTCH4, CD24, CD34, SOX2, PITX2, and GMDS) from protein-protein interaction network analysis. The WGCNA R package was used to construct correlation network analyses for these shared genes, aiming to investigate the relationships among them. Furthermore, we also examined the correlation of these genes with patient outcomes through survival curve analyses. The gene ontology and pathway analyses were performed to find out the potential therapeutic targets for LC in smoking and COVID-19 patients. Moreover, machine learning algorithms were applied to the TCGA RNAseq data of LC to assess the performance of these common genes and ten hub genes, demonstrating high performances. The identified hub genes and molecular pathways can be utilized for the development of potential therapeutic targets for smoking and COVID-19-associated LC.

DAB2IP Loss in Luminal A Breast Cancer Leads to NF-kB Associated Aggressive Oncogenic Phenotypes.

Despite proven therapy options for estrogen receptor (ER)-positive breast tumors, a substantial number of ER+ cancer patients exhibit relapse with associated metastasis. Loss of expression of RasGAPs leads to poor outcomes in several cancers, including breast cancer. Mining the TCGA breast cancer RNA-sequencing dataset revealed that low expression of the RasGAP DAB2IP was associated with a significant decrease in relapse-free survival in Luminal A breast cancer patients. Immunostaining demonstrated that DAB2IP loss occurred in grade 2 tumors and higher. Consistent with this, genes upregulated in DAB2IP-low Luminal A tumors were shared with more aggressive tumor subtypes and were associated with proliferation, metastasis, and altered ER signaling. Low DAB2IP expression in ER+ breast cancer cells was associated with increased proliferation, enhanced stemness phenotypes, and activation of IKK, the upstream regulator of the transcription factor NF-kB. Integrating cell-based ChIP-sequencing with motif analysis and TCGA RNA-seq data, we identified a set of candidate NF-kB target genes upregulated with loss of DAB2IP linked with several oncogenic phenotypes, including altered RNA processing. This study provides insight into mechanisms associated with aggressiveness and recurrence within a subset of the typically less aggressive Luminal A breast cancer intrinsic subtype.

Integration of transcriptomics, proteomics and loss-of-function screening reveals WEE1 as a target for combination with dasatinib against proneural glioblastoma

Glioblastoma is characterized by a pronounced resistance to therapy with dismal prognosis. Transcriptomics classify glioblastoma into proneural (PN), mesenchymal (MES) and classical (CL) subtypes that show differential resistance to targeted therapies. The aim of this study was to provide a viable approach for identifying combination therapies in glioblastoma subtypes. Proteomics and phosphoproteomics were performed on dasatinib inhibited glioblastoma stem cells (GSCs) and complemented by an shRNA loss-of-function screen to identify genes whose knockdown sensitizes GSCs to dasatinib. Proteomics and screen data were computationally integrated with transcriptomic data using the SamNet 2.0 algorithm for network flow learning to reveal potential combination therapies in PN GSCs. In vitro viability assays and tumor spheroid models were used to verify the synergy of identified therapy. Further in vitro and TCGA RNA-Seq data analyses were utilized to provide a mechanistic explanation of these effects. Integration of data revealed the cell cycle protein WEE1 as a potential combination therapy target for PN GSCs. Validation experiments showed a robust synergistic effect through combination of dasatinib and the WEE1 inhibitor, MK-1775, in PN GSCs. Combined inhibition using dasatinib and MK-1775 propagated DNA damage in PN GCSs, with GCSs showing a differential subtype-driven pattern of expression of cell cycle genes in TCGA RNA-Seq data. The integration of proteomics, loss-of-function screens and transcriptomics confirmed WEE1 as a target for combination with dasatinib against PN GSCs. Utilizing this integrative approach could be of interest for studying resistance mechanisms and revealing combination therapy targets in further tumor entities.

Loss-of-Imprinting of HM13 Leads to Poor Prognosis in Clear Cell Renal Cell Carcinoma.

Genomic imprinting refers to the epigenetic silencing of one of both alleles in a parent-of-origin-specific manner, particularly in genes regulating growth and development. Impaired genomic imprinting leading to the activation of the silenced allele, also called canonical loss-of-imprinting (LOI), is considered an early factor in oncogenesis. As LOI studies in clear cell renal cell carcinoma (ccRCC) are limited to IGF2, we performed a genome-wide analysis in 128 kidney normal solid tissue and 240 stage 1 ccRCC samples (TCGA RNA-seq data) to screen for canonical LOI in early oncogenesis. In ccRCC, we observed LOI (adj. p = 2.74 × 10-3) of HM13 (Histocompatibility Minor 13), a signal peptide peptidase involved in epitope generation. HM13 LOI samples featured HM13 overexpression, both compared to normal solid tissues (p = 3.00 × 10-7) and non-LOI (p = 1.27 × 10-2) samples. Upon adjustment for age and sex, HM13 expression was significantly associated with poor survival (p = 7.10 × 10-5). Moreover, HM13 overexpression consistently exacerbated with increasing tumor stage (p = 2.90 × 10-8). For IGF2, LOI was observed in normal solid tissues, but the prevalence did not increase in cancer. In conclusion, HM13 LOI is an early event in ccRCC, causing overexpression leading to poor prognosis.

Abstract 6727: QL335, a novel T cell engager with enhanced safety profile targeting MSS colorectal cancer

Abstract Colorectal cancer (CRC) is the fourth leading cause of death in the world with a global mortality rate of over 700,000 annually. While recent advancement in diagnosis and prevention has reduced the overall number of deaths, the lack of effective and durable treatment has not significantly improved survival rate. Emerging modalities in immunotherapy such as T cell engagers have paved new ways for disease management. However, a common challenge to advancing T cell engagers in the clinic is poor target specificity and high toxicity associated with non-specific T cell activation and cytokine release. To overcome these shortcomings, we have developed QL335, a bispecific antibody bridging LY6G6D antigen on tumor cells and CD3 on T cells. LY6G6D or Lymphocyte Antigen 6 Family Member G6D, is a GPI-anchored membrane protein that, according to TCGA RNAseq data, is highly expressed in microsatellite stable (MSS) colorectal cancer but not in normal tissues. We analyzed LY6G6D expression by IHC in over 200 CRC patient tumors and 40+ normal tissue samples from different organs, confirming its highly restricted CRC expression pattern. We constructed our bispecific antibody in a 2+1 format, comprising two high affinity LY6G6D binding domains and one reduced affinity CD3 binding domain. Such format allows for higher tumor accumulation while mitigating non-specific T cell activation in the periphery. In vitro evaluation showed that QL335 induced potent yet highly specific T cell activation and killing of only target cells expressing LY6G6D. QL335 demonstrated robust anti-tumor efficacy in vivo against human colon cancer xenograft models with human PBMC reconstitution. Importantly, QL335 was well tolerated in cynomolgus monkeys dosed up to 50 mg/kg, supporting the enhanced safety profile by design of this therapeutic candidate. QL335 is currently being evaluated in a phase 1 clinical trial. Citation Format: Shenda Gu, Guangjie Guo, Helena Yee, Hieu V. Tran, Shihao Chen, Chuanzeng Cao, Ke Liu, Chunyan Jin, Weihua Lun, Ruixue Ma, Lele Ren. QL335, a novel T cell engager with enhanced safety profile targeting MSS colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6727.

Abstract 5847: Characterizing mechanisms of BRAF/MEK inhibitor resistance in BRAF V600 mutant colorectal cancer vs. melanoma

Abstract Background: BRAF V600 mutations comprise ~80% of all oncogenic BRAF mutations in metastatic colorectal cancer (mCRC). While most cancers with BRAF V600 mutations can be effectively treated with combined BRAF and MEK inhibition, BRAF V600 mutant mCRC acquire resistance through EGFR-mediated signaling. The profound difference in response rates to BRAF/MEK inhibitors in BRAF V600 mutant mCRC (12%) vs. melanoma (63-68%) is not sufficiently explained by increased EGFR signaling in CRC. Therefore, we sought to characterize the differences that exist between BRAF V600 mutant CRC and melanomas that could explain the differential sensitivity to BRAF/MEK inhibition and identify more effective treatments for BRAF V600 mutant CRC. Methods: We assessed cell survival by clonogenic assay in the presence of small molecule inhibitors. In parallel, we mined TCGA RNAseq data to calculate the MAPK Pathway Activity Score (MPAS). RTK expression was assessed in TCGA data from patients with BRAF V600 mutant CRC vs. melanoma. We developed cells with acquired resistance to BRAF+MEK inhibitors (Encorafenib+Binimetinib; E+B) by culturing cells in increasing concentrations of drug over several months. RNA-sequencing and analysis was performed on parental and resistant cells treated with vehicle control or BRAF+MEK inhibitors. Results: When comparing the efficacy of BRAF+MEK inhibitors across BRAF V600 mutant cells, we found that BRAF V600 mutant CRC cell lines (n=2) were less sensitive than melanoma cell lines (n=2). MPAS scores were significantly lower in BRAF V600 mutant CRC (n=46) vs. melanoma (n=188) tumors. We interrogated protein array data from the DepMap and identified increased activation of several RTKs (EGFR, HER2, HER3) in BRAF V600 CRC (n=8) vs. melanoma (n=39) cell lines. Similarly, we established resistant HT29 (BRAF V600 CRC) cells and observed sustained MAPK pathway activity despite a lack of difference in EGFR activity in the presence of BRAF+MEK inhibitor treatment. Both HT29 parental and resistant cells showed re-establishment of MAPK signaling after 72 hours. Resistant SkMel28 (BRAF V600 melanoma) cells showed increased pERK levels compared to resistant HT29 cells. RNAseq revealed increased expression of multiple RTKs (PDGFRB, ERBB2, ERBB3) and ligands/growth factors for multiple RTKs (FGF3, PDGFA, HB-EGF) in resistant HT29 cells. Shp2 is a protein tyrosine phosphatase that regulates signaling of multiple RTKs to activate the MAPK pathway. Accordingly, we assessed the efficacy of an inhibitor of Shp2 (TNO155) overcoming MAPKi resistance in BRAF V600 CRC cells. We confirmed that E+B+TNO155 more effectively inhibited cell growth and MAPK pathway activity in BRAF V600 CRC cell lines (n=2) in vitro. Conclusion: Together, these data identify key, actionable drivers of MAPK inhibitor resistance in CRC and highlight Shp2 as a potential therapeutic target for BRAF V600 CRC. Citation Format: Jennifer Maxwell, Emmanuelle Rousselle, Lucy An, April Rose. Characterizing mechanisms of BRAF/MEK inhibitor resistance in BRAF V600 mutant colorectal cancer vs. melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5847.

IGSF8 is a potential target for the treatment of gliomas

BackgroundImmunoglobulin superfamily member 8, or IGSF8, is a member of the recently identified immunoglobulin family of proteins. It is mostly produced on cell membranes and has a unique transmembrane structure. It has recently been demonstrated that there is a strong correlation between the expression variation of IGSF8 and the growth of gliomas. Therefore, we used data from the TCGA and CGGA databases to evaluate the function of IGSF8. MethodsThe TCGA and GTEx data sets' RNA-seq data were utilized to examine IGSF8 expression. The Gene Cards database was utilized to get IGSF8 protein data. The Cluster Profiler data package was used to carry out the IGSF8 enrichment study. The GO and KEGG databases were used to examine the relationship between IGSF8 and cellular physiological and biochemical processes. The TCGA immune cell infiltration scores were obtained from online databases and published studies. Clinical survival data from TCGA and CGGA were used to investigate the predictive significance of IGSF8. ResultsTGGA revealed that the majority of cancers had differential expression of IGSF8. IGSF8 was discovered to be enriched in numerous significant pathways in tumor cells by GO and KEGG. Moreover, a strong correlation was seen between the expression of IGSF8 and the immunomodulatory interactions that occur between non-lymphocytes and lymphocytes. T-cell infiltration, immunological checkpoints, immune-activating and immune-suppressive genes, chemokines, and chemokine receptors were all strongly correlated with IGSF8 expression. Lastly, the TCGA and CGGA databases showed a strong correlation between IGSF8 and the grade and prognosis of gliomas. ConclusionAccording to our findings, IGSF8 may be a glioma marker. In order to control the immunological microenvironment, IGSF8 may cooperate with a number of immune checkpoints. This information may be utilized to create novel targeted immunotherapy medications.

Metabolic subtypes and immune landscapes in esophageal squamous cell carcinoma: prognostic implications and potential for personalized therapies

BackgroundThis study aimed to identify metabolic subtypes in ESCA, explore their relationship with immune landscapes, and establish a metabolic index for accurate prognosis assessment.MethodsClinical, SNP, and RNA-seq data were collected from 80 ESCA patients from the TCGA database and RNA-seq data from the GSE19417 dataset. Metabolic genes associated with overall survival (OS) and progression-free survival (PFS) were selected, and k-means clustering was performed. Immune-related pathways, immune infiltration, and response to immunotherapy were predicted using bioinformatic algorithms. Weighted gene co-expression network analysis (WGCNA) was conducted to identify metabolic genes associated with co-expression modules. Lastly, cell culture and functional analysis were performed using patient tissue samples and ESCA cell lines to verify the identified genes and their roles.ResultsMolecular subtypes were identified based on the expression profiles of metabolic genes, and univariate survival analysis revealed 163 metabolic genes associated with ESCA prognosis. Consensus clustering analysis classified ESCA samples into three distinct subtypes, with MC1 showing the poorest prognosis and MC3 having the best prognosis. The subtypes also exhibited significant differences in immune cell infiltration, with MC3 showing the highest scores. Additionally, the MC3 subtype demonstrated the poorest response to immunotherapy, while the MC1 subtype was the most sensitive. WGCNA analysis identified gene modules associated with the metabolic index, with SLC5A1, NT5DC4, and MTHFD2 emerging as prognostic markers. Gene and protein expression analysis validated the upregulation of MTHFD2 in ESCA. MTHFD2 promotes the progression of ESCA and may be a potential therapeutic target for ESCA.ConclusionThe established metabolic index and identified metabolic genes offer potential for prognostic assessment and personalized therapeutic interventions for ESCA, underscoring the importance of targeting metabolism-immune interactions in ESCA. MTHFD2 promotes the progression of ESCA and may be a potential therapeutic target for ESCA.

IMMU-11. NLRP3+ TUMOR-ASSOCIATED MYELOID CELLS ARE ENRICHED IN ASTROCYTIC GLIOMAS AND REPRESENT A THERAPEUTIC VULNERABILITY

Abstract BACKGROUND Tumor-associated myeloid cells (TAMs) are known drivers of immunosuppression and glioma progression. Hence novel approaches for repolarizing TAMs from a protumorigenic to an antitumorigenic phenotype is an active area of investigation. While single-cell RNA sequencing (scRNA-seq) studies have characterized glioma TAMs in great detail, their uniqueness or similarity to TAMs in other tumors remains unknown. Cross-comparison of glioma TAMs with TAM subsets from other tumor types will aid in identifying novel TAM-targeted immunotherapies. METHODS We performed scRNA-seq of ~26K myeloid cells from nine patients with high-grade astrocytoma (n=3) and oligodendroglioma (n=6). The scRNA-seq findings were validated using TCGA RNA-seq data, public scRNA-Seq data, and immunohistochemistry (IHC) analysis. RESULTS The TAM clusters in gliomas predominantly exhibited a microglia-specific gene signature, while macrophage and monocyte clusters were also identified. Utilizing canonical TAM markers, we identified three major TAM subtypes, SPP1+ regulatory, FOLR2+ tissue-resident, and NLRP3+ inflammatory, enriched in astrocytomas. A gene set enrichment analysis of the three TAM subtype genes confirmed their enrichment in astrocytomas (IDHMut-non-codel) (P=0.0005; normalized enrichment score [NES]=1.79) in the TCGA bulk RNAseq data from IDH1-mutant LGGs. Investigation of the three TAM subtype markers in public scRNA-seq data confirmed their enrichment in immune/myeloid clusters across multiple glioma types (gangliogliomas, pilocytic astrocytomas, astrocytomas, diffuse midline gliomas, and glioblastomas). Finally, IHC analysis of 14 astrocytomas demonstrated regional variation in NLRP3 and FOLR2 expression in all cases, with a trend toward an inverse association between NLRP3 and FOLR2 expression. CONCLUSIONS 1) Astrocytomas (IDHMut-non-codel) comprise TAM subsets common across multiple tumor types. 2) The FOLR2+ TAMs predict favorable outcomes, while the NLRP3+ TAMs are immunosuppressive and predict adverse outcomes in breast cancer. Given the inverse expression of NLRP3 and FOLR2 in astrocytomas, we hypothesize that NLRP3 TAMs+ are immunosuppressive and a potential immunotherapeutic target in astrocytomas.

EPCO-31. THE PROGNOSTIC IMPLICATIONS OF THE RELATIVE ABUNDANCE OF DECONVOLVED TUMOR AND NON-TUMORAL SUBPOPULATIONS IN MULTI-REGIONAL BIOPSIES OF HIGH GRADE GLIOMA WITH BULK RNA-SEQ

Abstract High-grade glioma continues to have dismal survival owing in part to its intra- and inter-patient heterogeneity. Standard clinical protocol collects tumor samples with the aim of providing or confirming a diagnosis and determining the status of a few key genes (e.g. IDH1, MGMT). However, this protocol is unable to capture the diversity within tumor regions, immune expression or normal cell abundances that play key roles in the development of the disease. To overcome this, during surgery we collect image-localized multi-regional biopsies to characterize this disease heterogeneity. Data collection is ongoing, and we currently have 202 samples from 58 patients with available bulk RNA-Seq. With a single-cell reference dataset from Columbia University, we used CIBERSORTx, a deconvolution method, to predict relative abundances of 7 normal, 6 glioma, and 5 immune cell subpopulations for each sample. We used Cox proportional hazard models with first-order statistics (mean, minimum, maximum) of abundances within patients to determine whether these are prognostic, then used TCGA RNA-Seq data to validate these findings. We found that one glioma proneural subtype was significantly beneficial for patient survival relative to other glioma subtypes across all statistics (and showed significance in TCGA). Proliferative and mesenchymal glioma subtypes also showed significance for one or two of the calculated statistics. Oligodendrocyte progenitor cell abundances were consistently significantly beneficial for patient survival in our cohort, while an increased abundance of abnormal (reactive) astrocytes is associated with poor prognosis. We also ran these analyses within invasive margin and core tumor regions to determine location-specific population abundances associated with patient survival. In conclusion, understanding the in vivo diversity of cellular subpopulations within high grade glioma is important for treatment stratification and patient benefit.

Abstract LB017: Potential role of kinesin family member C1 (KIFC1) in melanoma

Abstract According to the Surveillance, Epidemiology, and End Results (SEER) analyses, based on 2017-2019 data, approximately ~2.1 percent of men and women will be diagnosed with melanoma at some point during their lifetime. Melanoma can be fatal if not surgically removed at an early stage, with the 5-year survival being a dismal 29.8% for a stage IV melanoma. Melanoma mortality is primarily due to the distant organ metastases and its resistance to treatment, even with newly developed immunotherapy and/or targeted therapies (BRAF and MEK inhibitors). Thus, the discovery of novel melanoma targets is crucial as they may be able to provide alternative treatment options or be used alone or in combination with current therapies. KIFC1 (kinesin family member C1; also known as HSET, an ortholog in Drosophila melanogaster), a nonessential kinesin motor protein, has an established role in centrosome clustering which is utilized by cancer cells to evade apoptosis and mitotic arrest. This occurs when replicating cells harbor additional centrosomes, a hallmark of cancer. The requirement of KIFC1 in mitosis of cancer cells harboring abnormal centrosomes, but not that of normal cells, makes it a potential drug target for cancer management. The goal of this study was to determine the role and significance of KIFC1 in melanoma. Differential expression analysis of GTEX and TCGA RNA-seq data identified significantly higher levels of KIFC1 in both primary and metastatic melanoma as compared to normal skin. In addition, higher expression of KIFC1 was found to be associated with poorer overall survival of melanoma patients. Furthermore, a quantitative protein estimation with the automated ProteinSimple Jess capillary western blotting system demonstrated higher KIFC1 expression in several melanoma cell lines when compared to normal melanocytes. In addition, we also found significantly increased expression of KIFC1 mRNA in mouse melanoma tumors obtained from the genetically engineered BrafV600E/PtenNULL mice, as compared to the normal skin. Next, we determined the effect of a small molecule KIFC1 inhibitor, AZ82 on A375, G361 and Hs294T melanoma cells. AZ82 is an ATP-competitive inhibitor that binds the KIFC1-microtubule complex, blocking the release of ADP and negating its role as a motor protein. Employing RealTime-Glo MT cell viability assay as well as the endpoint XTT growth assay, we found that AZ82 treatment resulted in a significant growth inhibition of human melanoma cells at 2-3.5 µM concentrations. Additionally, AZ82 treatments resulted in a significant decrease in clonogenic survival in all three human melanoma cell lines. Collectively, our data suggests a potential role of KIFC1 in melanoma progression, and merits further investigation to determine the roles and functional and therapeutic significance of KIFC1 in melanoma. Citation Format: Davis S. Mau, Mary A. Ndiaye, Gabriella R. Zaemisch, Chandra K. Singh, Jess Vera, Sean R. McIlwain, Nihal Ahmad. Potential role of kinesin family member C1 (KIFC1) in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB017.

Abstract 2534: Targeting defective necroptosis in colorectal cancer to overcome therapeutic resistance

Abstract Colorectal cancer (CRC) is a leading cause of cancer related deaths in the United States. CRC patients are often treated with the chemotherapeutic drug 5-fluorouracil (5-FU), but resistance often occurs. It is well-established that 5-FU induces apoptosis in cancer cells, but apoptosis inhibition does not block the anticancer effect of 5-FU, suggesting a role of non-apoptotic cell death. Necroptosis is a regulated form of necrosis controlled by Receptor-Interacting Protein kinase 1 (RIP1), RIP3, and Mixed Lineage Kinase domain-Like (MLKL), and its role in anticancer therapy remains unclear. TCGA RNAseq data show that RIP3 is significantly downregulated in primary CRC tumors, which is correlated with worse outcomes. RIP3 downregulation also occurs in established CRC cell lines and is associated with decreased 5-FU sensitivity. Therefore, we hypothesize that necroptosis may play a critical role in anticancer therapy and that restoring defective necroptosis may enhance therapeutic sensitivity. Our studies show that RIP3-expressing (RIP3+) CRC cells undergo both apoptosis and necroptosis in response to 5-FU. As expected, knock-out of RIP3 in RIP3+ CRC cells resulted in decreased 5-FU sensitivity, as well as abrogated necroptosis induction. Additionally, stable restoration of RIP3 in RIP3-silenced (RIP3-) CRC cells appeared to enhance 5-FU response, under conditions where apoptosis was inhibited. Furthermore, we explored alternative ways to induce necroptosis in RIP3-silenced cells. Together, our results suggest that necroptosis plays an important role in 5-FU-induced cell death in CRC. These results provide novel insights into the role of necroptosis in anticancer therapy in CRC, which could be used for development of improved therapies and personalized medicine based on RIP3 status. Citation Format: Kaylee Ermine, Dongshi Chen, Xinyan Lu, Jian Yu, Lin Zhang. Targeting defective necroptosis in colorectal cancer to overcome therapeutic resistance [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 2534.

Abstract A015: Targeting necroptosis and RIP3 in colorectal cancer to overcome chemotherapeutic resistance

Abstract Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States. When metastatic, chemotherapeutic drug 5-fluorouracil (5-FU) is typically used for treatment, but resistance often occurs. Many studies have shown that 5-FU induces apoptosis in cancer cells, but when apoptosis is inhibited, cell death can still occur, suggesting that other forms of cell death are occurring. Necroptosis, or regulated necrosis, is an alternative form of cell death, controlled by RIP1, RIP3, and MLKL, and its role in anticancer therapy remains unclear. TCGA RNAseq data show that RIP3 is significantly downregulated in primary CRC tumors, with RIP3 downregulation correlating with worse clinical outcomes. Analysis of numerous established CRC cell lines revealed that RIP3 expression was downregulated in ~50% of the cell lines, with low RIP3 expression being associated with decreased 5-FU sensitivity. These data led us to hypothesize that RIP3 expression and necroptosis may play a critical role in response to anticancer therapies, such as 5-FU, and that restoring defective necroptosis may enhance therapeutic sensitivity. Our preliminary studies have shown that RIP3-expressing (RIP3+) CRC cell lines are able to undergo both apoptosis and necroptosis in response to 5-FU, which could explain the enhanced sensitivity. As expected, knock-out of RIP3 in RIP3+ cells resulted in decreased 5-FU sensitivity, as well as abrogated necroptosis induction. Additionally, transient restoration of RIP3 in RIP3-silenced (RIP3-) CRC cells appeared to enhance 5-FU sensitivity, and so, we generated a stable RIP3-expressing cell line through retroviral infection. Although the stable RIP3-expressing cell line did not appear to be more sensitive to 5-FU alone, it did show enhanced sensitivity under conditions where apoptosis is inhibited. Together, our results suggest that RIP3 plays an important role in 5-FU-induced cell death in CRC, and that restoring RIP3 when the apoptosis pathway is implicated could provide a way to enhance 5-FU sensitivity and overcome resistance. The results from this project provide novel insight into the role of RIP3 in mediating response to anticancer therapy in CRC, which could be used for development of improved therapies and personalized medicine based on RIP3 status in the clinic. Citation Format: Kaylee A. Ermine, Dongshi Chen, Peng Wang, Jian Yu, Lin Zhang. Targeting necroptosis and RIP3 in colorectal cancer to overcome chemotherapeutic resistance [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr A015.

BIOM-48. HOXD12 IS AN INDEPENDENTLY PROGNOSTIC AGE-ASSOCIATED INDICATOR FOR POOR SURVIVAL IN OLIGODENDROGLIOMA

Abstract BACKGROUND Oligodendroglioma, IDH-mutant and 1p/19q-codeleted has variable outcomes that are strongly influenced by patient age. This study aimed to discover novel molecular biomarkers that may characterize an aggressive subgroup of oligodendroglioma that is associated with, but independently prognostic of patient age. METHODS Differential gene expression analysis, gene ontology analysis, and gene set enrichment analysis were conducted on TCGA RNA-seq data (N=169) to identify genes and pathways that differ significantly between older and younger patients. Genes whose expression was associated with age and survival in multivariate analyses were further studied using DNA methylation (N=171). The prognostic value of their expression and methylation profiles was then compared to known genomic biomarkers, radiographic features, and histopathologic features. RNA-seq and DNA methylation validation data were obtained from the CGGA (N=44) and a cohort published by Capper et al. (N=144), respectively. RESULTS Highly activated pathways in older oligodendrogliomas were linked to developmental transcription factors. Overexpression of HOXD12 was associated with patient age and survival in the TCGA (FDR< 0.01, FDR=1e-5) and the CGGA (p=0.03, p< 1e-3). Hypermethylation of HOXD12 was associated with age, tumor grade, and survival in the TCGA (p< 1e-5, p< 0.001, p< 1e-3) and with age and tumor grade in Capper et al. (p< 0.02, p=0.001). In the TCGA, HOXD12 hypermethylation and overexpression were independently prognostic of NOTCH1 and PIK3CA mutations, loss of 15q, and MYC activation as well as mitotic figures, Ki-67 index, microvascular proliferation, and necrosis. HOXD12 overexpression was also independently prognostic of T1-post contrast enhancement, whole tumor volume, and peritumoral edema volume. We developed a risk-stratification nomogram predicting 5- and 10-year overall survival using patient age, HOXD12 methylation, and WHO grade. CONCLUSIONS HOXD12 overexpression and hypermethylation are associated with an aggressive subtype of oligodendroglioma and may serve as superior prognostic biomarkers than previously reported genomic, radiographic, and histopathologic features.

Abstract 358: Restoring necroptosis in colorectal cancer cells to overcome chemotherapeutic resistance

Abstract Colorectal cancer (CRC) is a leading cause of cancer related deaths in the United States. CRC patients are often treated with chemotherapeutic drugs, such as 5-fluorouracil (5-FU), and resistance to chemotherapy is a major clinical problem. It is well-established that 5-FU induces apoptosis in cancer cells, but apoptosis inhibition does not block the anticancer effect of 5-FU, suggesting a role of non-apoptotic cell death. Necroptosis is a regulated form of necrosis controlled by Receptor-Interacting Protein kinase 1 (RIP1), RIP3, and Mixed Lineage Kinase domain-Like (MLKL). TCGA RNA-Seq data reveal that RIP1 and RIP3 are frequently downregulated in CRC, with RIP3 downregulation correlating with worse clinical outcomes. We found that loss of RIP3 expression in CRC cells is associated with decreased 5-FU sensitivity. RIP3 silencing in CRC was shown to be caused by promoter hypermethylation. However, the exact functional role of RIP3 in response to anticancer therapies remains unclear. Our studies reveal that RIP3-expressing CRC cells were able to undergo both apoptosis and necroptosis in response to 5-FU treatment, which was abrogated upon knock-out or inhibition of RIP3. Restoration of RIP3 in RIP3-silenced CRC cells by transfection enhanced 5-FU sensitivity, along with restored necroptosis and enhanced apoptosis. Furthermore, we have shown that RIP3 expression can be restored in RIP3-silenced CRC cells by the DNA methyltransferase 1 inhibitor 5-aza-2’-deoxycytidine (5-aza-dC), which also enhances 5-FU sensitivity. This effect of 5-aza-dC is partially dependent on RIP3 and suppressed by a RIP3 inhibitor. Together, our results suggest RIP3 plays a critical role in response to 5-FU and other chemotherapeutic agents, and that restoring RIP3 expression can be used to potentiate chemotherapy. These results provide novel insight into the functional role of RIP3 in CRC chemotherapy, which could be explored for developing improved and personalized CRC treatments based on RIP3 status. Citation Format: Kaylee Ermine, Dongshi Chen, Peng Wang, Jian Yu, Lin Zhang. Restoring necroptosis in colorectal cancer cells to overcome chemotherapeutic resistance [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 358.

Abstract 5843: Truncated APC & AXIN2 expression contribute to maintaining β-catenin/WNT signaling at the “Just Right” level for CRC cell proliferation

Abstract Adenomatous polyposis coli (APC) mutation leads to increased WNT signaling and stem cell overpopulation, which drives development of colorectal cancer (CRC). APC mutations often encode a truncated protein that has loss of APC’s domains that mediate APC interaction with AXIN2. A substantial body of scientific evidence indicates that truncated APC is essential for CRC cell proliferation by maintaining beta-catenin levels and WNT signaling at the “just right” level (known as the “Just Right” Hypothesis). Thus, AXIN2 is of particular interest because both wild-type APC and AXIN2 are part of the beta-catenin destruction complex, which is essential for tumor-suppressing ability. Hypothesis: the degree of AXIN2 expression, in the context of truncated APC, is critical to maintain WNT-signaling activity at the “just right” level which is optimal for CRC cell proliferation. Accordingly, we evaluated the effect of AXIN2 levels in CRC cells that contain APC protein-truncating mutations on WNT signaling (Top Flash assay), expression of WNT-targeted genes, and CRC cell proliferation and differentiation. We found that modulating AXIN2 expression altered WNT signaling, expression of WNT-targeted genes, and CRC cell proliferation in CRC cell lines with different APC-truncation causing mutations. Indeed, western blot results showed that knock down of AXIN2 gene expression increased truncated-APC and AXIN1 protein expression, and decreased expression of several WNT-target genes (e.g. LGR5, CD44, c-Jun, c-Myc, Cyclin D1), particularly genes that have reported roles in cell cycle regulation. These findings were consistent with our independent bioinformatics analyses of NCI TCGA RNA-seq data on CRC patients. Overall, our study suggests that i) The beta-catenin destruction complex is still functional at a certain level despite APC-truncating mutations; ii) Perturbing AXIN2 expression leads to changes in WNT-signaling activity that deviate from a level that is “just right” for malignant cell proliferation, likely by affecting the function of the destruction complex; iii) Deviation from “just right” WNT signaling levels alters WNT-target gene expression and diminishes the ability of APC-mutant CRC cells to maintain uncontrolled proliferation. Citation Format: Chi Zhang, Caroline O. Facey, Katherine Funk, Lynn M. Opdenaker, Bruce M. Boman. Truncated APC & AXIN2 expression contribute to maintaining β-catenin/WNT signaling at the “Just Right” level for CRC cell proliferation [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 5843.

Inconsistency in the expression pattern of a five-lncRNA signature as a potential diagnostic biomarker for gastric cancer patients in bioinformatics and in vitro.

Objective(s):Due to diagnosis of gastric cancer in advanced stages as well as its poor prognosis, finding biomarkers is essential. In this study, using the TCGA RNAseq data of gastric cancer patients, we evaluated the diagnostic value of lncRNAs that had differential expression.Materials and Methods:We evaluated P-value, FDR, and log fold change for whole transcripts. Next, by comparison of the RNAseq gene names with the total known lncRNA names, we identified differential expressed lncRNAs. Following this, specificity and sensitivity for lncRNAs coming from the previous step were calculated. For more confirmation, we predicted target genes and performed GO and KEGG signaling pathway analysis. In the end, we examined reliability and consistency of expression of this signature in three gastric cancer cell lines and one of them in twenty tumors and tumor-adjacent normal tissue samples using qRT-PCR.Results:Five lncRNAs had proper sensitivity and specificity and had target genes involved in cancer-related signaling pathways; however, they showed different expression patterns in TCGA data and in vitro.Conclusion:The results of our study demonstrated that the five-lncRNAs PART1, UCA1, DIRC3, HOTAIR, and HOXA11AS require more investigation to be confirmed as diagnostic biomarkers in gastric cancer.

Long noncoding RNA TLNC1 promotes the growth and metastasis of liver cancer via inhibition of p53 signaling

BackgroundLong non-coding RNAs (lncRNAs) have been demonstrated to play vital roles in cancer development and progression. However, their biological roles and function mechanisms in liver cancer remain largely unknown.MethodsRNA-seq was performed with clinical hepatoma tissues and paired adjacent normal liver tissues to identify differentially expressed lncRNAs. qPCR was utilized to examine the expression levels of lncRNAs. We studied the function of TLNC1 in cell growth and metastasis of hepatoma with both cell and mouse models. RNA-seq, RNA pull-down coupled with mass spectrometry, RNA immunoprecipitation, dual luciferase reporter assay, and surface plasmon resonance analysis were used to analyze the functional mechanism of TLNC1.ResultsBased on the intersection of our own RNA-seq, TCGA RNA-seq, and TCGA survival analysis data, TLNC1 was identified as a potential tumorigenic lncRNA of liver cancer. TLNC1 significantly enhanced the growth and metastasis of hepatoma cells both in vitro and in vivo. TLNC1 exerted its tumorigenic function through interaction with TPR and inducing the TPR-mediated transportation of p53 from nucleus to cytoplasm, thus repressing the transcription of p53 target genes and finally contributing to the progression of liver cancer.ConclusionsTLNC1 is a promising prognostic factor of liver cancer, and the TLNC1-TPR-p53 axis can serve as a potential therapeutic target for hepatoma treatment.

Identification of Prognosis Biomarkers for High-Grade Serous Ovarian Cancer Based on Stemness

In this paper, high-grade serous ovarian cancer (HGSOC) is studied, which is the most common histological subtype of ovarian cancer. We use a new analytical procedure to combine the bulk RNA-Seq sample for ovarian cancer, mRNA expression-based stemness index (mRNAsi), and single-cell data for ovarian cancer. Through integrating bulk RNA-Seq sample of cancer samples from TCGA, UCSC Xena and single-cell RNA-Seq (scRNA-Seq) data of HGSOC from GEO, and performing a series of computational analyses on them, we identify stemness markers and survival-related markers, explore stem cell populations in ovarian cancer, and provide potential treatment recommendation. As a result, 171 key genes for capturing stem cell characteristics are screened and one vital cancer stem cell subpopulation is identified. Through further analysis of these key genes and cancer stem cell subpopulation, more critical genes can be obtained as LCP2, FCGR3A, COL1A1, COL1A2, MT-CYB, CCT5, and PAPPA, are closely associated with ovarian cancer. So these genes have the potential to be used as prognostic biomarkers for ovarian cancer.

Immuno-genomic characterisation of high-grade serous ovarian cancer reveals immune evasion mechanisms and identifies an immunological subtype with a favourable prognosis and improved therapeutic efficacy.

Immunotherapy has revolutionised the field of cancer therapy and immunology, but has demonstrated limited therapeutic efficacy in high-grade serous ovarian cancer (HGSOC). Multi-omics data of 495 TCGA HGSOC tumours and RNA-seq data of 1708 HGSOC tumours were analyzed. Multivariate Cox regression analysis and meta-analyses were used to identify prognostic genes. The immune microenvironment was characterised using the ssGSEA methods for 28 immune cell types. Immunohistochemistry staining of tumour tissues of 14 patients was used to validate the key findings further. A total of 1142 genes were identified as favourable prognostic genes, which are prevailing in immune-related pathways and the infiltration of most immune subpopulations was observed to be associated with a favourable prognosis suggesting that tumour immunogenicity was the most prominent factor associated with improved clinical outcomes and response to chemotherapy of HGSOC. We identified multiple genomic and transcriptomic determinants of immunogenicity, including the copy loss of chromosome 4q and deficiencies of the homologous recombination pathway. Finally, an immunological subtype characterised by increased infiltration of activated CD8 T cells and decreased Tregs was associated with favourable prognosis and improved therapeutic efficacy. Our study characterised the immunogenomic landscape and refined the immunological classifications of HGSOC. This may improve the selection of patients with HGSOC who are suitable candidates for immunotherapy.