Gene Expression In Tumor Tissue Research Articles

Upstream regulation of neurotransmitter signaling genes in metastatic colorectal cancer (mCRC) patients: Data from CALGB/SWOG 80405 trial (Alliance) and MONSTAR-SCREEN-2.

3523 Background: Evidence suggests neurotransmitter signaling may play a crucial role in tumorigenesis of gastrointestinal (GI) cancers, including migration, proliferation, and apoptosis, as well as angiogenesis and the microenvironment. We developed and applied a strategy to identify upstream regulators of neurotransmitters and their associations with patient outcomes. Methods: Prior literature yielded 85 neurotransmitter signaling genes mapped to RNA-seq gene expression in tumor tissue from 545 patients with mCRC enrolled in the phase III CALGB/SWOG 80405 trial. These samples were also sequenced by FoundationOne CDx for DNA damage. Using Cox proportional hazards regression, we identified a subset of CDx genes associated with overall survival (OS) or progression-free survival (PFS). We extended the Causal Inference Test (CIT) for time-to-event data and identified a subset of the 85 signaling genes consistent with mediation of DNA mutation effects on OS and PFS. Another CIT analysis identified potential upstream neurotransmitter regulators, gene expression mediators of mutation effects on the signaling genes. Top genes were then assessed in whole-transcriptome sequencing (WTS) expression data with Caris MI profile collected from 398 patients with advanced CRC enrolled in the MONSTAR-SCREEN-2 trial. Results: At the 0.05 alpha level, we identified 20 signaling genes with gene expression associated with PFS and/or OS, and 68 genes with evidence of DNA mutations associated with PFS and/or OS. False discovery rate (FDR) < 0.05 was applied to filter the 56,674 expression features on PFS and OS associations, yielding 173 unique genes as possible mediators. The CIT yielded 53 putative mediators at FDR < 0.05, suggesting upstream regulation of neurotransmitter signaling. Five genes were identified as targeting at least 8 signaling genes each, PIGU, ANO9, LY6G6D, and GPR160, and FSCN1, where the first 4 are favorable and only FSCN1 is a poorer prognostic. Following up on these 5 genes in MONSTAR-SCREEN-2 by dichotomizing at the median value of WTS expression, 3 were nominally associated with OS, PIGU ( P = 0.050; HR, 0.59; 95%CI, 0.34-1.00), ANO9( P = 0.029; HR, 0.55; 95%CI, 0.32-0.95), LY6G6D( P = 0.0024; HR, 0.44; 95%CI, 0.25-0.76), and FSCN1 was suggestive ( P = 0.079; HR, 1.62; 95%CI, 0.94-2.77), with direction of effects in agreement with 80405 results for all four. Conclusions: Our novel approach identified previously unknown upstream regulators of neurotransmitter signaling associated with treatment outcomes in mCRC. PIGU, FSCN1, and LY6G6D have been suggested in prior literature as targets for CRC and ANO9 has been suggested as a target for GI cancer. These results bolster the strategy of using mediation analysis with large-scale molecular data to identify new therapeutic targets in CRC. NCT00265850.

Abstract CT053: Exploration of potential biomarkers correlated with efficacy of ociperlimab (anti-TIGIT) plus tislelizumab (anti-PD-1) in 1L PD-L1+ non-small cell lung cancer (NSCLC)

Abstract Background: PD-L1 expression was associated with anti-immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domains (TIGIT) + anti-PD-(L)1 treatment, in which a high PD-L1 subgroup showed improved efficacy. We investigated if anti-TIGIT mechanism of action (MOA)-related markers were associated with the efficacy of ociperlimab + tislelizumab in Cohort 3 (1L PD-L1+ NSCLC) of the phase 1/1b AdvanTIG-105 trial (NCT04047862) and evaluated a potential patient-enrichment strategy based on tumor tissue gene expression profile (GEP). Methods: Tumor tissue GEP was tested using TruSeq RNA Access technology. Ventana SP263 PD-L1 immunohistochemistry (IHC) assay was used to evaluate PD-L1 expression. Median progression-free survival (mPFS) by investigator was calculated descriptively by Kaplan-Meier methodology. 95% confidence intervals for mPFS were generated using the Brookmeyer method. The primary inferential PFS comparison used unstratified log-rank test with 2-sided descriptive P-values. Results: At data cutoff (Feb 2, 2023), 24 of 45 patients had GEP results. Anti-TIGIT MOA-related genes and signatures correlated with ociperlimab + tislelizumab treatment response. Patients with high (H) vs low (L) expression of TIGIT, CD226, CCR8, or a tumor-associated macrophage (TAM) signature had significantly longer mPFS (Table). Dual biomarkers combining both anti-PD-L1 (PD-L1 IHC) and one of the anti-TIGIT MOA-related factors (TIGIT, CCR8, TAM signature GEP) identified subgroups of PD-L1 H + TIGIT MOA-related factor H patients with improved PFS vs other subgroups (Table). A highly overlapped PD-L1 H + TIGIT H + CCR8 H + TAM signature H patient population was observed in dual biomarker analyses. Conclusions: Anti-TIGIT MOA-related genes and signatures correlated with efficacy in ociperlimab + tislelizumab-treated 1L PD-L1+ NSCLC. Combining anti-TIGIT MOA-related factors with PD-L1 expression identified a subgroup of patients with improved efficacy. TABLE 1. NAND Table. Efficacy Analyses in Patient Subgroups TIGITa CD226b CCR8b TAMb Subgroup H L H L H L H L n 8 16 12 12 12 12 12 12 mPFS, months (95% CI) NR (2.6, NR) 5.26 (2.07, 11.86) NR (4.21, NR) 4.68 (1.41, 15.05) 15.21 (2.6, NR) 4.7 (1.71, 7.16) 15.21 (4.21, NR) 4.17 (1.71, 5.45) PFS, P-value 0.0326 0.0327 0.0131 0.0153 PD-L1c + TIGITb PD-L1c + CCR8b PD-L1c + TAMb Subgroup TIGITHPD-L1H TIGITHPD-L1L TIGITLPD-L1H TIGITL PD-L1L CCR8HPD-L1H CCR8HPD-L1L CCR8LPD-L1H CCR8L PD-L1L TAMHPD-L1H TAMHPD-L1L TAMLPD-L1H TAML PD-L1L n 8 4 8 4 11 1 5 7 9 3 7 5 mPFS, months (95% CI) NR (1.41,NR) 4.76 (2.6,NR) 8.62 (2.07,NR) 2.94 (1.25,NR) NR (1.41,NR) 2.6 (NR,NR) 5.19 (2.07,NR) 4.21 (1.25,7.16) 23.89 (1.41,NR) 5.32 (4.21,NR) 5.29 (2.07,NR) 2.6 (1.25,NR) Cutoff: aTop 1/3; bMedian; cTC≥25% Citation Format: Se Hyun Kim, Jiayuan Zhang, Wei Tan, Han Yan, Tian Tian, Hao Zheng, Ziqi Zhou, Ruihua Wang, Yun Zhang, Zhirong Shen, Hye Ryun Kim, Diansheng Zhong, Shun Lu. Exploration of potential biomarkers correlated with efficacy of ociperlimab (anti-TIGIT) plus tislelizumab (anti-PD-1) in 1L PD-L1+ non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT053.

Whole-exome sequencing explored mechanism of selpercatinib resistance in RET-rearranged lung adenocarcinoma transformation into small-cell lung cancer: a case report

Small cell transformation was one mechanism by which EGFR-mutation NSCLC acquired resistance after tyrosine kinase inhibitors (TKIs) treatment. A few reports of small cell transformation occurred in other oncogene-driven lung cancers. We found the first case of transformation of a RET-rearranged lung adenocarcinoma to SCLC after selpercatinib, a novel highly selective RET TKIs. Whole-exome sequencing (WES) was used to explore alteration in gene expression in tumor tissue at initial diagnosis and after transformation into small cell carcinoma. We found that transformed into SCLC tumor tissue had inactivation of RB1 and TP53, with RET fusion was still present. In addition, the APOBEC family of cytidine deaminases appeared amplification. Although RET rearrangement still existed, using another RET TKIs was ineffective, and etoposide plus platinum might be an effective rescue treatment.

C-MYC-dependent transcriptional inhibition of autophagy is implicated in cisplatin sensitivity in HPV-positive head and neck cancer

Autophagy is important for the removal, degradation and recycling of damaged organelles, proteins, and lipids through the degradative action of lysosomes. In addition to its catabolic function, autophagy is important in cancer and viral-mediated tumorigenesis, including Human Papillomavirus (HPV) positive cancers. HPV infection is a major risk factor in a subset of head and neck cancer (HNC), for which no targeted therapies are currently available. Herein, we assessed autophagy function in HPV-positive HNC. We showed that HPV-positive HNC cells presented a transcriptional and functional impairment of the autophagic process compared to HPV-negative cells, which were reactivated by knocking down HPV E6/E7 oncoproteins, the drivers of cellular transformation. We found that the oncoprotein c-MYC was stabilized and triggered in HPV-positive cell lines. This resulted in the reduced binding of the MiT/TFE transcription factors to their autophagy targets due to c-MYC competition. Thus, the knock-down of c-MYC induced the upregulation of autophagic and lysosomal genes in HPV-positive HNC cells, as well as the increase of autophagic markers at the protein level. Moreover, HPV oncoprotein E7 upregulated the expression of the phosphatase inhibitor CIP2A, accounting for c-MYC upregulation and stability in HPV+ HNC cells. CIP2A mRNA expression negatively correlated with autophagy gene expression in tumor tissues from HNC patients, showing, for the first time, its implication in a transcriptional autophagic context. Both CIP2A and c-MYC knock-down, as well as pharmacological downregulation of c-MYC, resulted in increased resistance to cisplatin treatment. Our results not only show a novel way by which HPV oncoproteins manipulate the host machinery but also provide more insights into the role of autophagy in chemoresistance, with possible implications for targeted HPV-positive HNC therapy.

FAM111B Acts as an Oncogene in Bladder Cancer.

Bladder cancer (BLCA) is a prevalent malignancy of the urinary system, associated with a high recurrence rate and poor prognosis. FAM111B, which encodes a protein containing a trypsin-like cysteine/serine peptidase domain, has been implicated in the progression of various human cancers; however, its involvement in BLCA remains unclear. In this study, we investigated the expression of FAM111B gene in tumor tissues compared to para-tumor tissues using immunohistochemistry and observed a significantly higher FAM111B gene expression in tumor tissues. Furthermore, analysis of clinical characteristics indicated that the increased FAM111B gene expression correlated with lymphatic metastasis and reduced overall survival. To investigate its functional role, we employed FAM111B-knockdown BLCA cell models and performed cell proliferation, wound-healing, transwell, and flow cytometry assays. The results showed that decreased FAM111B gene expression inhibited proliferation and migration but induced apoptosis in BLCA cells. In vivo experiments further validated that FAM111B knockdown suppressed tumor growth. Overall, our findings suggest that FAM111B acts as an oncogene in BLCA, playing a critical role in tumorigenesis, progression, and metastasis of BLCA. In conclusion, we have demonstrated a strong correlation between the expression of FAM111B gene and the development, progression, and metastasis of bladder cancer (BLCA). Thus, FAM111B is an oncogene associated with BLCA and holds promise as a molecular target for future treatment of this cancer.

Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis

Cancer treatment is still challenging because the disease is often caused by multiple mutations. Although genomic studies have identified many oncogenes and tumor suppressor genes, gene sets involved in tumorigenesis remain poorly understood. Xenopus, a genus of aquatic frogs, is a useful model to identify gene sets because it can be genetically and experimentally analyzed. Here, we analyzed gene expression in tumor tissues of three individuals in Xenopus tropicalis and identified 55 differentially expressed genes (DEGs). Gene ontology (GO) analysis showed that the upregulated genes in the tumor tissues were enriched in GO terms related to the extracellular matrix and collagen fibril organization. Hierarchical clustering showed that the gene expression patterns of tumor tissues in X. tropicalis were comparable to those of human connective, soft, and subcutaneous tissue-derived cancers. Additionally, pathway analysis revealed that these DEGs were associated with multiple pathways, including the extracellular matrix, collagen fibril organization, MET signaling, and keratan sulfate. We also found that the expression tendency of some DEGs that have not been well analyzed in the cancer field clearly determines the prognosis of human cancer patients. This study provides a remarkable reference for future experimental work on X. tropicalis to identify gene sets involved in human cancer.

Multi-omics data reveals novel impacts of human papillomavirus integration on the epigenomic and transcriptomic signatures of cervical tumorigenesis.

Integration of human papilloma virus (HPV) DNA into the human genome may progressively contribute to cervical carcinogenesis. To explore how HPV integration affects gene expression by altering DNA methylation during carcinogenesis, we analyzed a multiomics dataset for cervical cancer. We obtained multiomics data by HPV-capture sequencing, RNA sequencing, and Whole Genome Bisulfite Sequencing from 50 patients with cervical cancer. We detected 985 and 485 HPV-integration sites in matched tumor and adjacent paratumor tissues. Of these, LINC00486 (n = 19), LINC02425 (n = 11), LLPH (n = 11), PROS1 (n = 5), KLF5 (n = 4), LINC00392 (n = 3), MIR205HG (n = 3) and NRG1 (n = 3) were identified as high-frequency HPV-integrated genes, including five novel recurrent genes. Patients at clinical stage II had the highest number of HPV integrations. E6 and E7 genes of HPV16 but not HPV18 showed significantly fewer breakpoints than random distribution. HPV integrations occurring in exons were associated with altered gene expression in tumor tissues but not in paratumor tissues. A list of HPV-integrated genes regulated at transcriptomic or epigenetic level was reported. We also carefully checked the candidate genes with regulation pattern correlated in both levels. HPV fragments integrated at MIR205HG mainly came from the L1 gene of HPV16. RNA expression of PROS1 was downregulated when HPV integrated in its upstream region. RNA expression of MIR205HG was elevated when HPV integrated into its enhancer. The promoter methylation levels of PROS1 and MIR205HG were all negatively correlated with their gene expressions. Further experimental validations proved that upregulation of MIR205HG could promote the proliferative and migrative abilities of cervical cancer cells. Our data provides a new atlas for epigenetic and transcriptomic regulations regarding HPV integrations in cervical cancer genome. We demonstrate that HPV integration may affect gene expression by altering methylation levels of MIR205HG and PROS1. Our study provides novel biological and clinical insights into HPV-induced cervical cancer.

Abstract 2201: Effect of opioid and cannabinoid receptors gene expression on survival of patients with colorectal cancer

Abstract Introduction: Colorectal cancer (CRC) is one of the leading causes of cancer death in the world. CRC patients are often treated with opioid (e.g., morphine, or synthetic opioid piritramide) analgesia for pain, nausea, and side effects of chemotherapy. These analgesics act through opioid and cannabinoid receptors, which pathways are involved in tumor progression and metastases and thus can negatively affect the survival of patients. In our previous studies, we analyzed the presence of circulating tumor cells (CTCs) in two groups of CRC patients. One group received morphine analgesia (MA) and second piritramide analgesia (PA). We found that MA associated with increased CTCs levels and significantly shorter cancer-specific survival (CSS). These findings lead to further analysis of the opioid and cannabinoid receptors tumor gene expressions. We expected that the different expression of specific receptors in tumor tissue makes a difference between the effects of MA and PA on patients´ survival. Methods: Gene expression of opioid receptors µ (OPRM), κ (OPRK), δ (OPRD), nociceptin (OPRL) and cannabinoid receptors 1 and 2 (CB1, CB2) was analyzed in RNA purified from tumor tissues in 131 patients with CRC. Expression of markers was detected using real-time RT-PCR on LightCycler 1536 from Roche. Β-actin gene expression was used for gene expression normalization. Specific cut-off values were calculated for each marker using maxstat R software, ver. 3.3.1. Relationship between expression of receptors in tumor tissue and patients’ survival was analyzed using COX regression, Kruskal-Wallis/ANOVA test, and Kaplan-Meier method. Results: In total, 118 patients (45 females and 73 males, average age 68 years), of clinical stage-III were analyzed. It was found that MA in CRC patients was associated with significantly shorter cancer-specific survival (CSS; p=0,027). The univariate survival analysis revealed that CRC patients with high OPRM tumor tissue gene expression had significantly longer overall survival (OS; p=0.017) and patients with CB2 gene expression had significantly longer disease-free survival (DFS; p=0,029). All other tested opioid receptors expressions had no statistically significant effect on patients’ survival. Conclusion: The diverse opioid receptors’ expressions on tumor and immune cells can affect the survival of cancer patients treated with opioid analgesia. Morphine perioperative analgesia seems to shorten the CCS in CRC patients in our study. However, further research is required to elucidate the effect of opioids on different cell populations. Acknowledgement: This study was supported by Ministry of Health of the Czech Republic [NV18-03-00470]; Palacky University Olomouc [LF 2022_012]; European Regional Development Fund [ENOCHCZ.02.1.01/0.0/0.0/16_019/0000868) and European Union - Next Generation EU (EXCELES LX22NPO5102). Citation Format: Monika Vidlarova, Josef Srovnal, Emil Berta, Sona Gurska, Alona Rehulkova, Pavla Kourilova, Marian Hajduch. Effect of opioid and cannabinoid receptors gene expression on survival of patients with colorectal 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 2201.

Biological Effects of Low Dose Radiation (LDR) on Peri-Tumoral and Tumoral Areas with Squamous Cell Skin Cancer

<h3>Purpose/Objective(s)</h3> Low dose radiation (LDR) may have paradoxically beneficial effects via an adaptive response. We aimed to assess the adaptive response of healthy and malignant skin tissue to low doses of radiation and explore the molecular details behind the induced adaptive response. <h3>Materials/Methods</h3> We conducted a prospective, randomized pilot study (N=8) to ascertain the biological effects of integrating 0.1 Gy of LDR into standard radiotherapy sessions (2.0 Gy fractions) over the first two weeks of radiotherapy for patients 18-80 years of age (both sexes) diagnosed with squamous cell carcinoma of skin (lesions of 1 – 10 cm). Radiation treatment was done with a linear accelerator. The patients received definitive radiation for the tumor as determined by the treating physician using 2.0 Gy fractions. In addition, 0.1 Gy of LDR was integrated into the standard radiotherapy course on day 0 and day 6 over the first two weeks of treatment. Radiation delivery to healthy tissue was with a 1.5 cm margin around the tumor using a mask over the tumor. We obtained partial thickness skin biopsy samples of the tumor and peri-tumoral normal tissue before treatment from four patients (for control). An additional four patients (actively treated) were biopsied before and 24 hours after 0.1 Gy of LDR (day 0, 1 and day 6, 7). RNA was obtained from skin biopsies and processed for genetic expression (138K genes). <h3>Results</h3> The change in gene expression in healthy peri-tumoral tissues due to LDR exposure was relatively low (only 325 genes: 170 upregulated, 155 downregulated). The <i>senescence and autophagy in cancer</i> and <i>genotoxicity pathway</i> genes showed the most significant downregulation in peritumoral healthy tissue comparing days 0 and 1. The biological pathways in peritumoral healthy tissue comparing days 6 and 7 showed predominantly downregulation of genes with most pronounced downregulation seen in <i>electron transport chain in mitochondria</i> and genes involved in <i>non-alcoholic fatty liver disease</i>. In contrast to normal peritumoral tissue, the difference in gene expression in tumor tissue due to LDR exposure was significantly more pronounced (5,651 genes: 2,896 upregulated, 2,755 downregulated) The <i>allograft rejection</i> genes and <i>nuclear receptor meta-pathway</i> were the most upregulated in the tumoral tissues comparing days 0 and 1. The nuclear receptor meta-pathway were the most upregulated in the tumoral tissues on days 6 and 7. The <i>Allograft rejection pathway in skin cancer</i> was among those upregulated. <h3>Conclusion</h3> LDR had a modest effect on miRNA expression when applied to healthy peritumoral skin. Downregulated pathways predominate, and DNA repair mechanisms are stimulated by the first dose in healthy tissue. In contrast, a more pronounced effect on gene expression (as measured by miRNA profiles), including upregulation of several key relevant pathways, was induced by LDR to malignant tissue.

Lentinan enhances the antitumor effects of Delta-like 1 via neutrophils

BackgroundSelective activation of Delta-like 1 (DLL1)-Notch signaling is a new approach to activate CD8+ T cell and suppress tumor growth, while the efficacy remains modest. Lentinan (LNT) is a clinically used immunomodulation agent. Thus, we hypothesized that LNT could improve the efficacy of DLL1.MethodsThe effects of LNT combined with DLL1 on tumor growth were evaluated by growth curve and tumor weight in EO771 breast and LAP0297 lung tumor models. The impacts on immune cells and gene expression in tumor tissues were determined by flow cytometry, qPCR. Neutrophil depletion was used to investigate the mechanism of the combination therapy on tumor growth. The data sets were compared using unpaired student’s t-test or ordinary one-way ANOVA.Results LNT treatments additively improved the antitumor effects of DLL1 in EO771 breast tumor growth. Remarkably, LNT treatments synergistically enhanced the suppression of DLL1 on LAP0297 lung tumor growth, resulting in tumor regression. Mechanically, the combination of LNT and DLL1 interventions not only promoted the accumulation and activation of CD8+ T cells, but also increased intratumoral CD45+CD11b+Ly6G+ neutrophils. Reduced neutrophils by anti-Gr1 antibody administrations reversed the improved antitumor effects by LNT treatments in LAP0297 lung tumor. These results suggest that LNT treatments improve the inhibition of DLL1 on tumor growth via neutrophils.ConclusionsOur findings indicates that LNT and DLL1 may induce synergistical antitumor immunity via simultaneous modulating lymphoid and myeloid cell populations regardless of the type of tumor, providing a potential new strategy to potentiate cancer immunotherapy.

Inhibitory effects and gene expression analysis of chemotherapeutic photodynamic therapy by using a liposomally formulated indocyanine green derivative

BackgroundPhotodynamic therapy (PDT) utilizes the enhanced permeability retention effect of photosensitizers and is less invasive and more selective than traditional chemotherapy. We constructed a chemotherapeutic PDT (chemo-PDT) nanoscale drug delivery system using a liposomally formulated indocyanine green derivative (ICG-Lipo) that encapsulated carboplatin and docetaxel (ICG-Lipo-C&D). MethodsThe antitumor effect of chemo-PDT mediated by ICG-Lipo-C&D was evaluated in a murine colon 26 CDF1 mouse model. Gene expression in tumor tissues was analyzed by RNA sequencing. ResultsChemo-PDT using ICG-Lipo-C&D demonstrated an even stronger PDT-enhancing effect than did ICG-Lipo due to the synergistic effect of carboplatin and docetaxel. In addition, gene expression analysis showed that PDT with ICG-Lipo-C&D increased the expression of immune-related genes and decreased the expression of cytoskeleton-related genes. ConclusionsChemo-PDT using ICG-Lipo as a photosensitizer as well as a drug delivery system with an enhanced permeability retention effect may be a promising cancer therapy.

Analysis of CFTR gene expression as an immunological and prognostic biomarker in pan-cancers

Cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-activated chloride channel that regulates fluid homeostasis via ATP binding and uses energy to transport relevant substrates across cytomembranes. It has been reported that CFTR plays a crucial role in the incidence and development of various types of cancers by regulating proliferation, metastasis, invasion and apoptosis. However, aberrant CFTR gene expression across different cancers makes it difficult to propose CFTR as a possible pan-cancer biomarker. Here, multiple databases (ONCOMINE, PrognoScan, Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA)), were accessed to investigate the relationship between CFTR gene expression with the immunological and prognostic roles in pan-cancers. The results showed higher CFTR gene expression in tumor tissues compared to normal tissues for most cancers except for CHOL, ESCA, KICH, LAML, SKCM and STAD. Higher expression of the CFTR gene directly correlated with better prognosis for BRCA, GBM, COAD, KIRP, LAML, LUAD, PRAD, SARC and STAD, and CFTR gene expression was higher in stage Ⅰ_Ⅱ compared to stage Ⅲ_ Ⅳ. Furthermore, CFTR gene expression levels were significantly associated with immune infiltrates and immunocytes, in particular, immune checkpoints, in COAD, LIHC, LUAD and LUSC. In conclusion, CFTR can be used as a prognostic marker for nine types of cancers examined in this study where CFTR expression levels play a vital role in forecasting the clinical efficacy of immune checkpoint suppression therapy.

Glioblastoma That Does Not Improve with Standard Treatment: Poor Prognostic Factors and Future Perspectives

The 5-year survival of glioblastoma (GBM) is at approximately 15%, and prognostic factors of GBM are age, Karnofsky performance status (KPS), extent of resection, and MGMT promoter methylation status. The reasons for the poor prognosis of GBM are as follows: 1)median age of onset of GBM is 68 years; 2)half of the patients have KPS≤70; 3)rapid growth of the tumor; 4)half of the patients undergo total resection; and 5)available drugs are only temozolomide and bevacizumab. The comprehensive genome profiling test is performed to analyze exome gene mutations, amplifications, deletions, and fusion gene expression in tumor tissues with a next-generation sequencer to identify tumor-specific driver genes. This test has been covered by public medical insurance for patients with cancer, including malignant brain tumors, in Japan since 2019. It detects the driver genes of GBM, such as BRAF and FGFR gene mutations, leading to clinical application by those inhibitors.

LncRNA NCK1-AS1 Aggravates Hepatocellular Carcinoma by the miR-22-3p/YARS Axis to Activate PI3K/AKT Signaling.

Hepatocellular carcinoma (HCC) is frequently diagnosed at late stages when curative treatments are no more appliable. Many studies have proved the active role of long non-coding RNAs (lncRNAs) in cancers' biology; here, the functional role of lncRNA NCK1-AS1 in HCC was identified. Gene expression in tumor tissues of HCC was evaluated by examining online databases and 88 collected HCC samples from our hospital. The interactions of miR-22-3p with NCK1-AS1 and tyrosyl-tRNA synthetase (YARS) were tested by conducting bioinformatics analysis, luciferase report, and RNA pulldown experiments. CCK-8, colony formation, flow cytometry, wound healing, transwell experiments were used to dissect the role of the NCK1-AS1/miR-22-3p/YARS axis in HCC. NCK1-AS1 was overexpressed in HCC cells and tissues. Functional assays depicted that depletion of NCK1-AS1 hampered malignant character of HCC cells. NCK1-AS1 controlled the availability of miR-22-3p, resulting in YARS upregulation. YARS was found to have a clinical value for HCC diagnosis. Moreover, rescue experiments revealed that miR-22-3p inhibition or YARS overexpression partially blocked the function of NCK1-AS1 deficiency in HCC cells. As for the downstream signaling pathway, we discovered that NCK1-AS1 activated PI3K/AKT signaling by the miR-22-3p/YARS axis. The present study verified that NCK1-AS1 could promote HCC progression via the miR-22-3p/YARS axis to activate PI3K/AKT signaling.

RNA m6A demethylase FTO-mediated epigenetic up-regulation of LINC00022 promotes tumorigenesis in esophageal squamous cell carcinoma

BackgroundLong non-coding RNA (LncRNA) controls cell proliferation and plays a significant role in the initiation and progression of esophageal squamous cell carcinoma (ESCC). N6-methyladenosine (m6A) modification now is recognized as a master driver of RNA function to maintain homeostasis in cancer cells. However, how m6A regulates LncRNA function and its role in tumorigenesis of ESCC remain unclear.MethodsMultiple ESCC datasets were used to analyze gene expression in tumor tissues and normal tissues. Kaplan-Meier method and the ROC curve were conducted to evaluate the prognostic value and diagnostic value of LINC00022 in ESCC, respectively. Both gain-of-function and loss-of-function experiments were employed to investigate the effects of LINC00022 on ESCC growth in vitro and in vivo. Bioinformatics analysis, colorimetric m6A assay, RIP, MeRIP and co-IP was performed to explore the epigenetic mechanism of LINC00022 up-regulation in ESCC.ResultsHere we report that m6A demethylation of LncRNA LINC00022 by fat mass and obesity-associated protein (FTO) promotes tumor growth of ESCC in vivo. Clinically, we revealed that LINC00022 was up-regulated in primary ESCC samples and was predictive of poor clinical outcome for ESCC patients. Mechanistically, LINC00022 directly binds to p21 protein and promotes its ubiquitination-mediated degradation, thereby facilitating cell-cycle progression and proliferation. Further, the elevated FTO in ESCC decreased m6A methylation of LINC00022 transcript, leading to the inhibition of LINC00022 decay via the m6A reader YTHDF2. Over-expression of FTO was shown to drive LINC00022-dependent cell proliferation and tumor growth of ESCC.ConclusionsThus, this study demonstrated m6A-mediated epigenetic modification of LncRNA contributes to the tumorigenesis in ESCC and LINC00022, specific target of m6A, serves as a potential biomarker for this malignancy.

Elevated Flt3L Predicts Long-Term Survival in Patients with High-Grade Gastroenteropancreatic Neuroendocrine Neoplasms.

Simple SummaryNeuroendocrine tumors of the gastrointestinal tract (GEP-NEN) are a rare type of tumor with considerable variability in the course of disease, which makes clinical management particularly challenging. Biomarkers that are able to guide personalized treatment decisions would be of importance, but are not yet available. In this study, we demonstrate that tissue expression, as well as circulating levels of the cytokine Flt3L in advanced and aggressive tumors, predict survival and time to progression. Increased tumoral Flt3L was also associated with upregulation of genes related to immune activation, suggesting Flt3L as a surrogate marker of host anti-tumor immunity. Therefore, Flt3L measurements in serum may hold promise as a biomarker of disease outcome that could support personalized treatment decisions in GEP-NEN patients, potentially guiding researchers towards viable immunotherapies.Background: The clinical management of high-grade gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN) is challenging due to disease heterogeneity, illustrating the need for reliable biomarkers facilitating patient stratification and guiding treatment decisions. FMS-like tyrosine kinase 3 ligand (Flt3L) is emerging as a prognostic or predictive surrogate marker of host tumoral immune response and might enable the stratification of patients with otherwise comparable tumor features. Methods: We evaluated Flt3L gene expression in tumor tissue as well as circulating Flt3L levels as potential biomarkers in a cohort of 54 patients with GEP-NEN. Results: We detected a prominent induction of Flt3L gene expression in individual G2 and G3 NEN, but not in G1 neuroendocrine tumors (NET). Flt3L mRNA expression levels in tumor tissue predicted the disease-related survival of patients with highly proliferative G2 and G3 NEN more accurately than the conventional criteria of grading or NEC/NET differentiation. High level Flt3L mRNA expression was associated with the increased expression of genes related to immunogenic cell death, lymphocyte effector function and dendritic cell maturation, suggesting a less tolerogenic (more proinflammatory) phenotype of tumors with Flt3L induction. Importantly, circulating levels of Flt3L were also elevated in high grade NEN and correlated with patients’ progression-free and disease-related survival, thereby reflecting the results observed in tumor tissue. Conclusions: We propose Flt3L as a prognostic biomarker for high grade GEP-NEN, harnessing its potential as a marker of an inflammatory tumor microenvironment. Flt3L measurements in serum, which can be easily be incorporated into clinical routine, should be further evaluated to guide patient stratification and treatment decisions.

Abstract 665: Cannabinoid receptor 2 tumor tissue gene expression positively affects lung cancer survival following radical surgery

Abstract Background: Non-small cell lung cancer (NSCLC) is a leading cause of cancer-related death with a 5-year survival rate of 21%. New treatment options are thus required, and the endogenous cannabinoid system is a potential new therapeutic target. We therefore analysed the expression of cannabinoid 1 and 2 receptor (CB1 and CB2) genes in NSCLC tissue and its influence on survival following radical surgery. Method: CB1 and CB2 gene expression in tumor tissue samples collected from 100 NSCLC patients was analysed using the quantitative real-time polymerase chain reaction. Since gene expression may not correlate with protein production, the presence of the CB2 protein was validated by immunohistochemistry. CB2 gene expression was correlated with disease stage, the presence of lymph node and distant metastases, tumor size, tumor grade, and survival. Result: Patients with tumors expressing CB2 gene had significantly longer overall survival (OS) (p&amp;lt;0.001), cancer-specific survival (CSS) (p=0.002), and disease-free survival (DFS) (p&amp;lt;0.001). They also had less advanced disease stage (p=0.047) and fewer lymph node metastases (p=0.011) at the time of surgery. A multivariate analysis showed that CB2 tumor tissue gene expression was a positive prognostic factor for OS (Hazard ratio (HR) = 0.402, p=0.013), CSS (HR=0.344, p=0.025), and DFS (HR=0.274, p=0.003). CB1 gene expression had no effect on survival. CB1 and CB2 gene expression was detected in 50% and 79.6% of the tumor tissue samples, respectively, and immunohistochemistry confirmed a correlation between CB2 gene expression and the presence of the CB2 protein in tumor tissues. Conclusion: In NSCLC patients undergoing radical surgery, CB2 gene expression in tumor tissue is associated with less advanced disease stage, fewer lymph node metastases, and longer survival (OS, CSS, DFS). Acknowledgement: This study was supported by Ministry of Health of the Czech Republic (NV18-03-00470), Ministry of Education, Youth and Sport of the Czech Republic (LM2018132), Palacky University Olomouc (LF 2020_007), Technological Agency of the Czech Republic (TN01000013), European Regional Development Fund (ENOCH CZ.02.1.01/0.0/0.0/16_019/0000868) and Cancer Research Czech Republic. Citation Format: Josef Srovnal, Monika Vidlarova, Emil Berta, Petr Prasil, Pavla Kourilova, Josef Chudacek, Marian Hajduch. Cannabinoid receptor 2 tumor tissue gene expression positively affects lung cancer survival following radical surgery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 665.

Abstract 2601: Using chaperonin containing TCP1 as a marker to track clinically relevant circulating tumor cells

Abstract Current methods for assessing circulating tumor cells (CTC) in blood focus on capture and enumeration with epithelial markers that provide little information about the aggressive and invasive potential of CTC. As a result, valuable knowledge that improves monitoring of cancer recurrence and metastasis is lacking. To provide actionable information on CTC, we developed a CTC identification method based on detection of the second subunit of Chaperonin Containing TCP1 (CCT2). CCT is a macromolecular protein folding complex composed of eight subunits (CCT1-8) that drives expression of many tumorigenic factors. Bioinformatic analysis in multiple cancers, such as breast cancer, revealed increased gene expression in tumor tissue compared to normal tissue for CCT1-8 (p&amp;lt; 0.0001), with the largest differences observed in CCT2 and CCT3. Genomic alteration of CCT2 inversely correlated with cancer patient survival, and depletion of CCT2 prevented growth of murine breast tumors. In a correlative study of blood and tumor tissues from metastatic breast cancer patients, high CTC counts positively correlated with detectable CCT2 in tumor tissues. These results support CCT2 as a possible marker for CTC. To determine this, antibodies to CCT2 were validated for use in the CellSearch System (CSS), currently the only FDA approved CTC enrichment platform, and tested with breast cancer cells spiked into healthy human blood. Recovery using CCT2 for identification, led to increased collection up to 6% of spiked breast cancer cells that would have been lost by standard CTC classification using cytokeratin (CK). With prognostic thresholds around 3-5 CTC/tube of blood, increased detection of even 1-2 more CTC can be significant for assessing patients' risks. Analysis in an open software program called ACCEPT (Automated CTC Classification, Enumeration and PhenoTyping) confirmed that the majority of recovered spiked cancer cells expressed CCT2. Flow cytometry analysis of spiked cancer cells confirmed that CCT2+ enriched cells expressed cancer markers CD44 or estrogen receptor (ER). These results show that the addition of CCT2 staining to a CTC detection protocol has positive implications for enumeration of CTC from blood, such as increased detection of CTC with low expression of epithelial markers. This experiment was repeated using small cell lung cancer cell lines with similar results. The combined bioinformatics, histologic and experimental results indicate that identification of CCT2-expressing CTC can be incorporated into CTC detection platforms to monitor those patients with a heightened risk for cancer recurrence or metastasis. Citation Format: Amanda Cox, Ana Martini, Eunkyung Lee, Rebecca Moroose, Amr Khaled, Annette R. Khaled. Using chaperonin containing TCP1 as a marker to track clinically relevant circulating tumor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2601.

Serum levels of cytoskeleton remodeling proteins and their mRNA expression in tumor tissue of metastatic laryngeal and hypopharyngeal cancers

Actin-binding proteins (ABPs) and various signaling systems are involved in the process of squamous cell carcinoma of the larynx and hypopharynx (SCCLH) metastasis. The clinical significance of these proteins has not yet been determined. We analyzed the relationship between the mRNA levels of cofilin 1 (CFL1), profilin 1 (PFN1), adenylyl cyclase-associated protein 1 (CAP1), SNAI1 and RND3 and SCCLH metastasis. The serum levels of the above ABPs were estimated and the relationship between them and their mRNA expressions was analyzed. The expression levels of ABP mRNAs were measured by real-time RT-PCR in paired tissue samples taken from 54 patients with SCCLH (T1-4N0-1M0). Expression analysis was performed using the 2-ΔΔCT method. The levels of ABPs in the blood serum were measured by ELISA. Statistical analysis was carried out using the SPSS Statistica 20.0 software package. No significant difference in the mRNA gene expression in tumor tissue of patients with T1-3N0M0 SCCLH and patients with T2-4N1-2M0 SCCLH was found. High expression of RND3 mRNA was accompanied by an increase in mRNA expression of all studied ABPs. In the blood serum of T2-4N1-2M0 patients, the level of PFN1 was lower by 21% and the level of CAP1 was higher by 75% than those observed in T1-4N0M0 patients. The data obtained showed that RND3 is involved in the regulation of molecular cascades of SCCLH metastasis. PFN1 and CAP1 serum levels can be good classifiers of metastases in patients with SCCLH.

Identification of molecular heterogeneity of hepatocellular carcinoma based on immune gene expression signatures.

Although various molecular subtypes of hepatocellular carcinoma (HCC) have been investigated, most of these studies identify HCC subtype based on genomic profiling. Few studies have investigated the classification based on immune signatures, and none have classified HCC based on Immune activation and immunosuppressive. We performed immune gene expression of tumor tissue in 374 HCC patients from The Cancer Genome Atlas (TCGA) database and used unsupervised consensus clustering to stratify tumors. We then used HCC patients from the International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) as replication datasets. Based on the expression of 782 immune-related genes, HCC was stratified into four distinct immune subtypes. Tumors in one cluster (high immune activation; high-IA) indicate a higher level of Immune activation, which was characterized by higher anti-tumor immunity, higher pro-tumor immune-suppressive cell types, higher fractions of CD8+ T cells and M0 Macrophages compared with other subtypes. The high-IA also presents higher cancer-related hallmark signatures, such as epithelial-mesenchymal transition (EMT), angiogenesis, and apoptosis. We also found subpopulations of regulatory and exhaustion T lymphocyte were characterized by an opposite trend in high-IA, though samples in high-IA response to immunotherapy with better survival. The comparison of the immune profile in tumor and normal tissue indicates the activation of immune responses which only occurred in high-IA patients, while we conducted comparison of cirrhosis and non-cirrhosis tumor immune signatures, immune response activation was almost occurred in high-IA, but some of immune responses occurred in low-IA (low immune activation).