Tumor Adjacent Normal Tissues Research Articles

The prognostic effect of ADH1B and ALDH2in lung adenocarcinoma.

e15167 Background: Alcohol dehydrogenase (ADH) and acetaldehyde dehydrogenase (ALDH) are major enzymes involved in the metabolism of carcinogenic acetaldehyde, converting alcohol to acetaldehyde and detoxifying acetaldehyde to harmless acetic acid, respectively. To investigate the role of ADH isoenzymes and ALDH isoenzymes in the development of lung adenocarcinoma (LUAD), we performed a retrospective analysis of gene expression. Methods: RNA sequencing data derived from 497 tumour samples and 54 adjacent normal samples were obtained from the Cancer Genome Atlas (TCGA) database. The transcript levels of ADH and ALDH family genes were compared between tumour tissue and adjacent normal tissue through a Wilcoxon test. The results were validated in transcriptomic data from 111 lung cancer patients available as part of a prior study. The diagnostic and prognostic value of ADH and ALDH family genes was further investigated by survival analysis and nomogram through the TCGA database. Insights into the mechanism of action were gained through gene set enrichment analysis (GSEA). Results: Numerous ADH and ALDH family genes showed nominally significant differential expression between tumour and adjacent normal tissues. The expression levels of ADH1B and ALDH2 showed significant and replicable depression in tumour tissue. Low expression of ADH1B and ALDH2 was associated with worse overall survival, with the combination of these genes providing greater prognostic value than the additive effects of these genes individually in the TCGA database. ADH1B and ALDH2 transcript levels were linked with the regulation of metabolism, cell cycle, DNA repair and cancer-associated pathways. A risk score model for predicting LUAD prognosis was developed and showed good performance in predicting 1, 3 and 5-year overall survival (OS). Consistent with TCGA results, our 111-patient replication dataset showed that the tumour-specific depression was most pronounced for ADH1B, and the lower expression was associated with vascular, pleural and lymphatic invasions. Moreover, smoking status and/or cumulative smoking history do not provide a direct, clinically accessible proxy for tumour ADH1B or ALDH2 expression. Conclusions: The combination of ADH1B and ALDH2 are potential prognostic markers in LUAD and may have utility as an independent clinical factor for evaluating the prognosis of LUAD.

Somatic mutations in tumor-adjacent normal breast tissue in young women with high risk family history.

576 Background: It’s incompletely understood why some women without germline breast cancer predisposing mutations develop early onset breast cancer. Breast cancer in young women is often more aggressive, with high histologic grade, worse prognosis, and higher risk of recurrence. We hypothesize that these women have somatic mutations in the normal breast tissue that contribute to breast cancer tumorigenesis. Methods: Whole exome sequencing (WES) data was analyzed from normal tissue adjacent to breast tumor and compared to matched peripheral blood (n=28). All patients were <50yo, had high risk family history as per NCCN guidelines, and had negative Ambry Genetics panel testing. FFPE sections were reviewed by two pathologists to identify normal breast tissue furthest away from tumor. WES was performed on Illumina HS4000 using 100-base pair paired-end reads. Samples were mapped to the human reference genome (vGRCh38). PCR duplicates were marked (Picard), and indel regions were adjusted (GATK). High-quality germline variants (HaplotypeCaller), somatic mutations (Mutect), and indels (IndelGenotyper) were called. Low-quality variants were filtered out. The classification and number of mutations per gene per sample were extracted and analyzed. Results: Majority of patients were white (86%), median age 45, with invasive ductal carcinoma (86%), ER+/PR+/HER2- (100%). Median somatic variants per sample were 97 (range: 45-285), all single nucleotide variants, mostly missense mutations, C>T conversions were seen in 45% of mutations. This suggests cytidine deaminase (APOBEC) involvement. All samples had alterations in at least one of the top ten affected genes which include transcription factors in zinc finger family (listed below). Zinc finger proteins play a key role in tumorigenesis, cancer progression and metastasis in a variety of cancers. Upregulation of zinc finger proteins has been associated with worse prognosis in breast cancer. Conclusions: We describe novel somatic mutations in zinc finger proteins in normal breast tissue adjacent to tumor that may contribute to early onset breast cancer in patients with high risk family history. [Table: see text]

Hypoxia disrupt tight junctions and promote metastasis of oral squamous cell carcinoma via loss of par3

BackgroundOral squamous cell carcinoma (OSCC) is a highly malignant tumor that is frequently associated with lymph node metastasis, resulting in poor prognosis and survival in patients. In the tumor microenvironment, hypoxia plays an important role in regulating cellular responses such as progressive and rapid growth and metastasis. In these processes, tumor cells autonomously undergo diverse transitions and acquire functions. However, hypoxia-induced transition of OSCC and the involvement of hypoxia in OSCC metastasis remain unclear. Therefore, in this study, we aimed to elucidate the mechanism of hypoxia-induced OSCC metastasis and particularly, its impact on tight junctions (TJs).MethodsThe expression of hypoxia-inducible factor 1-alpha (HIF-1α) was detected in tumor tissues and adjacent normal tissues from 29 patients with OSCC using reverse transcription quantitative real-time polymerase chain reaction (qRT-PCR), western blotting, and immunohistochemistry (IHC). The migration and invasion abilities of OSCC cell lines treated with small interfering (si)RNA targeting HIF-1α or cultured in hypoxic conditions were analyzed using Transwell assays. The effect of HIF-1α expression on in vivo tumor metastasis of OSCC cells was evaluated using lung metastasis model.ResultsHIF-1α was overexpressed in patients with OSCC. OSCC metastasis was correlated with HIF-1α expression in OSCC tissues. Hypoxia increased the migration and invasion abilities of OSCC cell lines by regulating the expression and localization of partitioning-defective protein 3 (Par3) and TJs. Furthermore, HIF-1α silencing effectively decreased the invasion and migration abilities of OSCC cell lines and restored TJ expression and localization via Par3. The expression of HIF-1α was positively regulated the OSCC metastasis in vivo.ConclusionsHypoxia promotes OSCC metastasis by regulating the expression and localization of Par3 and TJ proteins. HIF-1α positively correlates to OSCC metastasis. Lastly, HIF-1α expression could regulate the expression of Par3 and TJs in OSCC. This finding may aid in elucidating the molecular mechanisms of OSCC metastasis and progression and developing new diagnostic and therapeutic approaches for OSCC metastasis.

Genomic–transcriptomic evolution in lung cancer and metastasis

Intratumour heterogeneity (ITH) fuels lung cancer evolution, which leads to immune evasion and resistance to therapy1. Here, using paired whole-exome and RNA sequencing data, we investigate intratumour transcriptomic diversity in 354 non-small cell lung cancer tumours from 347 out of the first 421 patients prospectively recruited into the TRACERx study2,3. Analyses of 947 tumour regions, representing both primary and metastatic disease, alongside 96 tumour-adjacent normal tissue samples implicate the transcriptome as a major source of phenotypic variation. Gene expression levels and ITH relate to patterns of positive and negative selection during tumour evolution. We observe frequent copy number-independent allele-specific expression that is linked to epigenomic dysfunction. Allele-specific expression can also result in genomic–transcriptomic parallel evolution, which converges on cancer gene disruption. We extract signatures of RNA single-base substitutions and link their aetiology to the activity of the RNA-editing enzymes ADAR and APOBEC3A, thereby revealing otherwise undetected ongoing APOBEC activity in tumours. Characterizing the transcriptomes of primary–metastatic tumour pairs, we combine multiple machine-learning approaches that leverage genomic and transcriptomic variables to link metastasis-seeding potential to the evolutionary context of mutations and increased proliferation within primary tumour regions. These results highlight the interplay between the genome and transcriptome in influencing ITH, lung cancer evolution and metastasis.

Aberrant methylation in neurofunctional gene serves as a hallmark of tumorigenesis and progression in colorectal cancer

BackgroundDNA methylation is one of the most promising biomarkers in predicting the prognosis of colorectal cancer (CRC). We aimed to develop a DNA methylation biomarker that could evaluate the prognosis of CRC.MethodsA promising DNA methylation biomarker was developed by hypermethylated genes in cancer tissue that were identified from Illumina EPIC methylation arrays. A cohort comprising 30 pairs of snap-frozen tumor tissue and adjacent normal tissue was used for correlation analysis between the methylation and expression status of the marker. The other cohort comprising 254 formalin-fixed paraffin-embedded (FFPE) tumor tissue from 254 CRC patients was used for prognosis analysis.ResultsRegulating synaptic membrane exocytosis 2 (RIMS2) was hypermethylated and lowly expressed in CRC comparing to adjacent normal tissue. Hypermethylation of RIMS2 in CRC was correlated with less frequent KRAS mutant and high differentiation. RIMS2 promoter methylation showed independent predictive value for survival outcome (P = 0.015, HR 1.992, 95% CI [(1.140–3.48)]), and a combination of RIMS2 methylation with KRAS status could predict prognosis better.ConclusionsRIMS2 is frequently hypermethylated in CRC, which can silence the expression of RIMS2. RIMS2 methylation is a novel biomarker for predicting the prognosis of CRC.

Abstract 777: Super-resolution imaging of heterochromatin structure detects early events in lung cancer

Abstract Early detection of lung cancer is essential to reduce lung cancer-related morbidity and mortality. Despite significant efforts, current approaches suffer from high false-positive rates or limited sensitivity. There is a critical need for non-invasive, cost-effective technologies that detect the early changes in lung carcinogenesis with high sensitivity and specificity. Abnormal chromatin structure is one of the hallmarks of cancer cells and is independent of molecular pathways making it an attractive target for early cancer detection. In this study, we assessed the use of super-resolution stochastic optical reconstruction microscopy (STORM) to detect abnormal heterochromatin disruption in lung carcinogenesis. First, utilizing a mouse model of tobacco carcinogen (NNK)-induced lung adenocarcinoma, we analyzed heterochromatin structure in the lungs of NNK-treated mice at 8, 15 and 20 weeks post-NNK exposure together with non-treated control mice at the same time points. Super-resolution images of NNK-induced lung lesions at all time points showed significant disruption of condensed heterochromatin nanodomains compared to normal alveolar epithelial cells from the control mice, consistent with our data from other tumor types. Importantly, the normal-appearing bronchial epithelial cell nuclei from NNK-treated mice also showed significant heterochromatin disruption in NNK-treated mice at 15 and 20 weeks (P< 0.0001), demonstrating that this method can detect early changes. Next, we sought to confirm this in humans. Super-resolution imaging showed that, compared to normal alveolar and bronchial epithelial cells from control subjects without cancer, the heterochromatin structure was more disrupted in tumor cells from patients with lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). We also observed significant disrupted heterochromatin structure in tumor-adjacent normal tissue at the tumor margin. Lastly, we performed a pilot study on bronchial epithelial cells isolated from sputum samples from 11 cigarette smokers with or without lung cancer. The heterochromatin structure in the bronchial epithelial cells collected from lung cancer patients at the time of diagnosis was significantly more disrupted than those from smokers without lung cancer (P= 0.004). Our results support disrupted heterochromatin structure as an early event in lung carcinogenesis and demonstrate the feasibility of utilizing super-resolution imaging of heterochromatin structure for early detection of lung cancer using sputum samples. Citation Format: Laura P. Stabile, Xuejiao Sun, Jianquan Xu, Beatriz Kanterewicz, David O. Wilson, Sanja Dacic, Lora H. Rigatti, Brenda Diergaarde, Yang Liu. Super-resolution imaging of heterochromatin structure detects early events in lung 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 777.

Abstract NG06: Investigating biological mediators of social and environmental risk factors on cancer health disparities

Abstract NG06: Investigating biological mediators of social and environmental risk factors on cancer health disparities

MPP7 is a potential prognostic marker and is associated with cancer metabolism and immune infiltration in clear cell renal cell carcinoma: a bioinformatics analysis based on the TCGA database.

Metastasis is a major negative prognostic marker in clear cell renal cell carcinoma (ccRCC). Membrane palmitoylated proteins (MPPs) are a class of cell polarity-associated proteins that function in both cell-cell junction and adhesion. However, the relationship between MPP7 and the prognosis of ccRCC remains elusive. In this study, we aimed to investigate the associations between MPP7 expression with clinical prognosis of ccRCC using bioinformatics analyses. The messenger RNA (mRNA) and protein expression patterns of MPP7 in different cancer types were examined using The Cancer Genome Atlas (TCGA) and Human Protein Atlas (HPA) databases, with key clinical characteristics (TNM and pathological stages, pathological grade, survival status) included. A nomogram model using MPP7 expressions and other clinical factors was built to predict the survival probability. The Kaplan-Meier plotter and Cox regression were employed to investigate the clinical significance and prognostic value of MPP7 in ccRCC. MPP7 expression-associated signaling pathways with were analyzed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) tools. The Tumor Immune Estimation Resource (TIMER) database was used to investigate the correlation between MPP7 and the infiltration patterns of immune cells. By analyzing TCGA-kidney renal clear cell carcinoma (TCGA-KIRC) and HPA databases, we found that MPP7 was differentially expressed in tumor tissues and adjacent normal tissues (P<0.001). The MPP7 expression patterns were associated with pathological stage (P<0.001), histological grade (P<0.01), and survival status (P<0.001). Using nomogram model, Cox regression and survival analysis, it showed that MPP7 expressions combined with key clinical factors could accurately predict the clinical prognosis. The promoter methylation patterns of MPP7 were correlated with the clinical factors of ccRCC patients. Furthermore, the KEGG and GO analyses demonstrated that MPP7 is associated with mitochondrial oxidative metabolism. MPP7 expression was associated with multiple types of immune cells and correlated with the enrichment of these cells. MPP7 is a critical gene links with ccRCC prognosis and is associated with tumor immune status and metabolism. MPP7 could become a potential biomarker and important therapeutic target for ccRCC patients.

Transcriptomic data in tumor-adjacent normal tissues harbor prognostic information on multiple cancer types.

In identifying prognostic markers in cancer, the roles of tumor-adjacent normal tissues are often confined to drawing expression differences between tumor and normal tissues rather than being treated as the main targets of investigations. Thus, differential expression analysis between tumors and adjacent normal tissues is performed prior to prognostic analysis in previous studies. However, recent studies have suggested that the prognostic relevance of differentially expressed genes (DEGs) is insignificant for some cancers, contradicting conventional approaches METHODS: This study investigated the prognostic efficacy of transcriptomic data from tumors and adjacent normal tissues using The Cancer Genome Atlas dataset. Prognostic analysis using Cox regression models and survival prediction using machine-learning models and feature selection methods were employed. The results revealed that for kidney, liver, and head and neck cancer, adjacent normal tissues harbored higher proportions of prognostic genes and exhibited better survival prediction performance than tumor tissues and DEGs in machine-learning models. Furthermore, the application of a distance correlation-based feature selection method to kidney and liver cancer using external datasets revealed that the selected genes for adjacent normal tissues exhibited higher prediction performance than those for tumor tissues. The study results suggest that the expression levels of genes in adjacent normal tissues are potential prognostic markers. The source code of this study is available at https://github.com/DMCB-GIST/Survival_Normal.

Characterization and Clinical Relevance of Endometrial CAFs: Correlation between Post-Surgery Event and Resistance to Drugs.

Cancer-associated fibroblasts (CAFs) within a solid tumor can support the progression of cancer. We studied the identification and characterization of patient-derived endometrial CAFs in the context of their clinical relevance in endometrial cancers. We established patient-derived primary cultures of CAFs from surgically resected tumors (TCAF) and tumor-adjacent normal (NCAF) tissues in 53 consented patients with success rates of 97.7% and 75%, respectively. A passage of CAF was qualified by the (1) absence of CK 8,18,19, EpCAM, CD45, and CD31, and (2) presence of SMAalpha, S100A4, CD90, FAP, TE-7, CD155, PD-L1, TGFB, PDGFRA (qRT-PCR, flow cytometry, Western blot, ICC). Out of the 44 established CAFs, 31 were aggressive (having an early, i.e., 4-7 week, establishment time and/or >3 passages) compared to 13 which were non-aggressive. A post-surgery-event (PSE) was observed in 7 out of 31 patients bearing aggressive CAFs, 2 of whom were also positive for CTCs, while none of the 13 patients bearing non-aggressive CAFs had events. A positive correlation was found between patients with grade 3 (p = 0.025) as well as stage 3/4 diseases (p = 0.0106) bearing aggressive CAFs and the PSE. Finally, aggressive TCAFs from patients with PSE resisted the effects of paclitaxel and lenvatinib on the growth of HUVEC and endometrial tumor cells. Our study is the first to report a correlation between the PSE and the aggressive nature of CAFs in endometrial cancers and provides an undeniable reason to study the in-depth mechanism of CAF function towards the development of treatment resistance in endometrial cancers.

Transcriptome sequencing identifies prognostic genes involved in gastric adenocarcinoma.

Gastric adenocarcinoma (GAC) is one of the world's most lethal malignant tumors. It has been established that the occurrence and progression of GAC are linked to molecular changes. However, the pathogenesis mechanism of GAC remains unclear. In this study, we sequenced 6 pairs of GAC tumor tissues and adjacent normal tissues and collected GAC gene expression profile data from the TCGA database. Analysis of this data revealed 465 differentially expressed genes (DEGs), of which 246 were upregulated and 219 were downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that DEGs were observably enriched in ECM-receptor interaction, protein digestion and absorption, and gastric acid secretion pathways. Six key genes (MATN3, COL1A1, COL5A2, P4HA3, SERPINE1 and VCAN) associated with poor GAC prognosis were screened from the protein‒protein interaction (PPI) network by survival analysis, and P4HA3 and MATN3 have rarely been reported to be associated with GAC. We further analyzed the function of P4HA3 in the GAC cell line SGC-7901 by RT‒qPCR, MTT, flow cytometry, colony formation, wound healing, Transwell and western blot assays. We found that P4HA3 was upregulated in the SGC-7901 cell line versus normal control cells. The outcomes of the loss-of-function assay illustrated that P4HA3 significantly enhanced the ability of GAC cells to proliferate and migrate. This study provides a new basis for the selection of prognostic markers and therapeutic targets for GAC.

Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients

BackgroundPrevious investigations of transcriptomic signatures of cancer patient survival and post-therapy relapse have focused on tumor tissue. In contrast, here we show that in colorectal cancer (CRC) transcriptomes derived from normal tissues adjacent to tumors (NATs) are better predictors of relapse.ResultsUsing the transcriptomes of paired tumor and NAT specimens from 80 Korean CRC patients retrospectively determined to be in recurrence or nonrecurrence states, we found that, when comparing recurrent with nonrecurrent samples, NATs exhibit a greater number of differentially expressed genes (DEGs) than tumors. Training two prognostic elastic net-based machine learning models—NAT-based and tumor-based in our Samsung Medical Center (SMC) cohort, we found that NAT-based model performed better in predicting the survival when the model was applied to the tumor-derived transcriptomes of an independent cohort of 450 COAD patients in TCGA. Furthermore, compositions of tumor-infiltrating immune cells in NATs were found to have better prognostic capability than in tumors. We also confirmed through Cox regression analysis that in both SMC-CRC as well as in TCGA-COAD cohorts, a greater proportion of genes exhibited significant hazard ratio when NAT-derived transcriptome was used compared to when tumor-derived transcriptome was used.ConclusionsTaken together, our results strongly suggest that NAT-derived transcriptomes and immune cell composition of CRC are better predictors of patient survival and tumor recurrence than the primary tumor.

RIG-I Promotes Tumorigenesis and Confers Radioresistance of Esophageal Squamous Cell Carcinoma by Regulating DUSP6.

We investigated the expression and biological function of retinoic acid inducible gene I (RIG-I) in esophageal squamous cell carcinoma (ESCC). Materials and methods: An immunohistochemical analysis was performed on 86 pairs of tumor tissue and adjacent normal tissue samples of patients with ESCC. We generated RIG-I-overexpressing ESCC cell lines KYSE70 and KYSE450, and RIG-I- knockdown cell lines KYSE150 and KYSE510. Cell viability, migration and invasion, radioresistance, DNA damage, and cell cycle were evaluated using CCK-8, wound-healing and transwell assay, colony formation, immunofluorescence, and flow cytometry and Western blotting, respectively. RNA sequencing was performed to determine the differential gene expression between controls and RIG-I knockdown. Tumor growth and radioresistance were assessed in nude mice using xenograft models. RIG-I expression was higher in ESCC tissues compared with that in matched non-tumor tissues. RIG-I overexpressing cells had a higher proliferation rate than RIG-I knockdown cells. Moreover, the knockdown of RIG-I slowed migration and invasion rates, whereas the overexpression of RIG-I accelerated migration and invasion rates. RIG-I overexpression induced radioresistance and G2/M phase arrest and reduced DNA damage after exposure to ionizing radiations compared with controls; however, it silenced the RIG-I enhanced radiosensitivity and DNA damage, and reduced the G2/M phase arrest. RNA sequencing revealed that the downstream genes DUSP6 and RIG-I had the same biological function; silencing DUSP6 can reduce the radioresistance caused by the overexpression of RIG-I. RIG-I knockdown depleted tumor growth in vivo, and radiation exposure effectively delayed the growth of xenograft tumors compared with the control group. RIG-I enhances the progression and radioresistance of ESCC; therefore, it may be a new potential target for ESCC-targeted therapy.

Abstract P1-05-18: Orphan non-coding RNAs for early detection of breast cancer with liquid biopsy

Abstract Background: Early detection of breast cancer is crucial for optimal patient outcomes but cannot always be accomplished based on symptoms or screening mammography. Biomarker-based screening could aid early detection of breast cancer by improving sensitivity and specificity. Exai Bio has developed a novel liquid biopsy technology that detects and analyzes small non-coding RNAs that are cancer specific, termed orphan non-coding RNAs (oncRNAs). Previous work in patients with diagnosed breast cancer demonstrated that changes in oncRNAs in serum reflected treatment response and event-free survival. In this study, we developed an assay that measures oncRNAs in serum to detect breast cancer across the range of tumor stages and sizes. Methods: Previously, a library of ~260,000 oncRNAs from 32 different cancers was compiled based on smRNA sequences found in tumor tissues and largely absent in tumor-adjacent normal tissues from The Cancer Genome Atlas (TCGA). To refine this library for applications in serum, we sequenced smRNA in 31 control serum samples. These smRNA sequences were filtered from the larger library, reducing its size to 250,332 oncRNAs. The diagnostic performance of these oncRNAs was then assessed in an independent cohort of archived serum samples from 96 female patients with clinically diagnosed, untreated breast cancer and 95 age- and sex-matched individuals with no known history of cancer. We sequenced smRNAs at an average depth of 17.7 million 50-bp single-end reads per sample. Of the 250,332 oncRNAs in our library, 171,981 (68.7%) were detected in our independent study cohort. An ensemble of logistic regression models was trained with 5-fold cross-validation, using only those oncRNAs yielding an odds ratio &amp;gt;1 and observed in &amp;gt;6% of samples within each training set. Results: The cohort of 96 breast cancer patients and 95 matched controls had mean ages of 59.4 and 56.3 years, respectively. Area under the receiver operating characteristic curve (AUC) for detecting breast cancer was 0.94 (95% CI, 0.85–0.96). Sensitivities for detecting breast cancer at 95% specificity ranged from 0.75 to 0.87 among the four breast cancer stages, including a sensitivity of 0.81 for tumor stage I (Table 1); and from 0.67 to 0.87 among the four main TNM T categories (Table 2). Sensitivities at 95% specificity were relatively high for small tumors, at 0.75 (95% CI, 0.40–0.97) for T1b (&amp;gt;5mm to ≤10mm; n = 9) and 0.80 (0.68–0.94) for T1c (&amp;gt;10mm to ≤20mm; n = 37). Conclusions We have demonstrated the potential value of an oncRNA-based liquid biopsy assay by showing that oncRNAs can be used to detect breast cancer in serum samples with high sensitivity, and that detection requires fewer reads than are needed with other platforms. Moreover, we found that this oncRNA-based assay performed well in detecting early-stage breast cancer and small tumors. This suggests that an oncRNA-based liquid biopsy assay may be beneficial for early detection of breast cancer. Table 1. Model sensitivity by tumor stage. For the indicated numbers of cases (N), sensitivity and Pearson-Clopper 95% confidence intervals are reported for tumor detection by the oncRNA-based model at 95% specificity by tumor stage, as defined by the AJCC 7th Edition breast cancer staging system. Table 2. Model sensitivity by tumor size. For the indicated numbers of cases (N), sensitivity and Pearson-Clopper 95% confidence intervals are reported for tumor detection by the oncRNA-based model at 95% specificity by TNM T category, as defined by the AJCC 7th Edition breast cancer staging system. Citation Format: Taylor B. Cavazos, Jeffrey Wang, Oluwadamilare I. Afolabi, Alice Huang, Dung Ngoc Lam, Seda Kilinc, Jieyang Wang, Lisa Fish, Xuan Zhao, Andy Pohl, Helen Li, Kimberly H. Chau, Patrick A. Arensdorf, Fereydoun Hormozdiari, Hani Goodarzi, Babak Alipanahi. Orphan non-coding RNAs for early detection of breast cancer with liquid biopsy [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-05-18.

Abstract P2-20-06: Anti-B7-H3 Antibody (T-1A5) Blocks Immunomodulatory Function of B7-H3 and Enhances NK and T Cell–Mediated Cytotoxicity against Breast Cancer Cells

Abstract One of the main factors contributing to breast cancer (BC) initiation and metastasis is immune suppression by tumor cells. Immune checkpoint blockade has recently been shown to overcome tumor-induced immune suppression, but a significant proportion of patients do not respond, implying that more effective cancer immunotherapies are required. B7-H3 belongs to B7 family of immune checkpoint proteins that is overexpressed in various human malignancies. Here, we hypothesize that blocking B7-H3 using monoclonal antibodies (mAbs) enhances immune cell proliferation and function. To test our hypothesis, B7-H3 expression was determined using RNA-seq data from primary and metastatic breast tumors, and adjacent normal tissues, from the TCGA and METABRIC databases. To assess B7-H3 protein expression in BC, we performed immunohistochemistry (IHC) on frozen primary tumor tissues (n=50) and adjacent normal tissues (n=23) from TNBC patients. In addition, to investigate the immunomodulatory effect of B7-H3 in BC, we performed IHC for T-cell markers in subsets of patient tissues with high and low levels of B7-H3 expression. Next, we assessed B7-H3 expression in over 13 BC cell lines, including TNBC and ER+, PR+, and HER2+ cell lines, as well as TNBC PDX-derived cells. Moreover, to determine the effect of B7-H3 knockdown on NK- and T-cell activity, we co-cultured control and B7H3–KD BC cells in the presence and absence of NK and T cells and measured the induction of apoptosis in BC cells through IncuCyte live-cell imaging system. The effect of a novel B7H3-blocking mAb (clone T-1A5, isotype IgG1) on NK-cell and T-cell-mediated cytotoxicity in BC cell lines was examined using live-cell imaging. In the TCGA and METABRIC databases, B7-H3 was found to be significantly overexpressed (P&amp;lt; 0.0001) in tumor tissues than in adjacent normal tissues of BC patients. A survival analysis by the log-rank test indicated that patients with B7-H3high tumors had significantly lower progression-free (P=0.01) and relapse-free (P=0.0026) survival than patients with B7-H3low tumors. Moreover, B7-H3 is significantly upregulated in all the BC subtypes including basal, luminal A, luminal B and Her2-enriched with highest expression in basal type BC. Relative mRNA quantification and flow cytometry analysis demonstrated strong B7-H3 expression in most of the BC cell lines including TNBC and ER+, PR+, and HER2+ cell lines, as well as TNBC PDX-derived cells. Furthermore, IHC analysis revealed that compared to the matched normal tissue, B7-H3 expression was substantially higher in tumor tissue (N=16, P&amp;lt; 0.001). Also, patients with high B7-H3 expression had significantly lower numbers of CD3+, CD4+, and CD8+ T-cell, compared to patients with low B7-H3 expression (P&amp;lt; 0.001), indicating immunosuppressive role of B7-H3. Furthermore, NK cell and T cell mediated killing was significantly higher in B7H3-KD BC cell lines compared to control cells. We observed a significant increase in the killing of BC cells by NK cells and T cells in the presence of anti-B7H3 mAb T-1A5 in a concentration dependent manner (P &amp;lt; 0.001), suggesting that anti-B7H3 antibodies suppress the immunomodulatory function of B7-H3 and enhance NK and T cell–mediated ADCC in BC. To determine the antibody-dependent cell-mediated cytotoxicity, we developed a human-mouse chimera of T-1A5 (chT-1A5) and tested in combination with NK cells. Interestingly, we found a concentration and time dependent increase in ADCC in BC cells in the presence of chT-1A5 antibody. Our data suggests that B7-H3 is overexpressed in primary BC and inhibits immune-cell infiltration. Moreover, blocking the immunomodulatory functions of B7-H3 using anti-B7H3 antibody T-1A5 enhances NK and T cell–mediated killing of BC cells. Citation Format: Vivek Anand, Anudishi Tyagi, Venkata Lokesh Battula. Anti-B7-H3 Antibody (T-1A5) Blocks Immunomodulatory Function of B7-H3 and Enhances NK and T Cell–Mediated Cytotoxicity against Breast Cancer Cells [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-20-06.

TPM2 attenuates progression of prostate cancer by blocking PDLIM7-mediated nuclear translocation of YAP1

BackgroundProstate cancer (PCa) is a common malignant tumor of the genitourinary system. Clinical intervention in advanced PCa remains challenging. Tropomyosins 2 (TPM2) are actin-binding proteins and have been found as a biomarker candidate for certain cancers. However, no studies have explored the role of TPM2 in PCa and its regulatory mechanism.MethodsTPM2 expression was assessed in Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) PCa patient dataset. The effect of TPM2 on PCa progression was assessed in vitro and in vivo by quantifying proliferation, migration, invasion and tumor growth assays, and the mechanism of TPM2 in PCa progression was gradually revealed by Western blotting, immunoprecipitation, and immunofluorescence staining arrays.ResultsTPM2 was found to be severely downregulated in tumor tissues of PCa patients compared with tumor-adjacent normal tissues. In vitro experiments revealed that TPM2 overexpression inhibited PCa cell proliferation, invasion and androgen-independent proliferation. Moreover, TPM2 overexpression inhibited the growth of subcutaneous xenograft tumors in vivo. Mechanistically, this effect was noted to be dependent on PDZ-binding motif of TPM2. TPM2 competed with YAP1 for binding to PDLIM7 through the PDZ-binding motif. The binding of TPM2 to PDLIM7 subsequently inhibited the nuclear transport function of PDLIM7 for YAP1. YAP1 sequestered in the cytoplasm phosphorylated at S127, resulting in its inactivation or degradation which in turn inhibited the expression of YAP1 downstream target genes.ConclusionsThis study investigated the role of TPM2, PDLIM7, and YAP1 in PCa progression and castration resistance. TPM2 attenuates progression of PCa by blocking PDLIM7-mediated nuclear translocation of YAP1. Accordingly, targeting the expression or functional modulation of TPM2, PDLIM7, or YAP1 has the potential to be an effective therapeutic approach to reduce PCa proliferation and prevent the progression of castration-resistant prostate cancer (CRPC).

HNRNPA2B1 as a potential therapeutic target for thymic epithelial tumor recurrence: An integrative network analysis

Thymic epithelial tumors (TETs) are rare malignant tumors, and the molecular mechanisms of both primary and recurrent TETs are poorly understood. Here we established comprehensive proteomic signatures of 15 tumors (5 recurrent and 10 non-recurrent) and 15 pair wised tumor adjacent normal tissues. We then proposed an integrative network approach for studying the proteomics data by constructing protein-protein interaction networks based on differentially expressed proteins and a machine learning-based score, followed by network modular analysis, functional enrichment annotation and shortest path inference analysis. Network modular analysis revealed that primary and recurrent TETs shared certain common molecular mechanisms, including a spliceosome module consisting of RNA splicing and RNA processing, but the recurrent TET was specifically related to the ribosome pathway. Applying the shortest path inference to the collected seed gene module identified that the ribonucleoprotein hnRNPA2B1 probably serves as a potential target for recurrent TET therapy. The drug repositioning combined molecular dynamics simulations suggested that the compound ergotamine could potentially act as a repurposing drug to treat recurrent TETs by targeting hnRNPA2B1. Our study demonstrates the value of integrative network analysis to understand proteotype robustness and its relationships with genotype, and provides hits for further research on cancer therapeutics.

Tumor necrosis factor-α-inducible protein 8-like protein 3 (TIPE3): a novel prognostic factor in colorectal cancer

BackgroundTo explore the correlation of tumor necrosis factor-α-induced protein 8-like protein 3 (TIPE3) expressions in colorectal cancer (CRC) with tumor-immune infiltration and patient prognosis.MethodsFormalin-fixed paraffin-embedded tumor samples from CRC patients (n = 110) were used in this study. Immunohistochemistry staining of TIPE3 and three prognostic immune biomarkers (CD8, CD20, and CD66b) was conducted in the tumor tissues and adjacent normal tissues. A Cox regression analysis of univariate and multivariate variables was performed to assess the correlation between TIPE3 and patient prognosis.ResultWe found that TIPE3 was mainly expressed in the cytoplasm, with a small amount in the nucleus. The expression of TIPE3 in tumor tissues is significantly higher than in adjacent normal tissues, and it is significantly correlated with the survival rate of patients in tumor tissues (p = 0.0038) and adjacent normal tissues (p<0.0001). Patients with a high TIPE3 expression had a lower survival rate, while patients with a low TIPE3 expression had a higher survival rate. Univariate regression analysis showed that the TIPE3 expression in tumor tissues (p = 0.007), the TIPE3 expression in adjacent normal tissues (p<0.001), the number of CD8+ T cells in tumor tissues (p = 0.020), the number of CD20+ B cells in tumor tissues (p = 0.023), the number of CD20+ B cells in adjacent normal tissues (p = 0.023), the number of CD66b+ neutrophils in tumor tissues (p = 0.005), the number of CD66b+ neutrophils in adjacent normal tissues (p<0.001), lymphatic metastasis (p = 0.010), TNM stage (p = 0.013), and tumor grade (p = 0.027) were significantly correlated with overall survival (OS). These prognostic factors were then subjected to multivariate regression analysis, and the results showed that the expression of TIPE3, the number of CD8+ T cells, and the number of CD66b+ neutrophils were prognostic factors affecting the OS rate of CRC patients.ConclusionWe found that the TIPE3 protein is upregulated in CRC cancer tissues and is correlated with survival rate.

Vascular endothelial growth factor A is a potential prognostic biomarker and correlates with immune cell infiltration in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related deaths among cancer patients. Vascular endothelial growth factor A (VEGFA) is involved in regulating biological processes, such as angiogenesis and vascular permeability, and is very closely related to the pathogenesis of various tumours, especially vascular-rich, solid tumours. Clinical data of patients with HCC and other tumours were analysed through public databases, such as the TCGA database, Gene Expression Omnibus database, Human Protein Atlas database, STRING, Tumour Immune Estimation Resource and Kaplan-Meier Plotter. The tumour tissues and adjacent normal tissues of patients with HCC from Hunan Provincial People's Hospital were collected to verify the expression of VEGFA by immunohistochemistry, immunofluorescence, Western blotting and qPCR. VEGFA expression is elevated in multiple tumour types and correlates with the prognosis of tumour patients. VEGFA is involved in regulating the tumour microenvironment and immune cell function in tumour development. Inhibition of VEGFA reduces proliferation, invasion, and migration and promotes apoptosis in HCC cells. VEGFA is a potential predictive biomarker for the diagnosis and prognosis of HCC.

Prognostic and predictive value of a lncRNA signature in patients with stage II colon cancer

The current staging method is inadequate to identify high-risk recurrence patients with stage II colon cancer (CC). Using a systematic and comprehensive-biomarker discovery and validation method, we aimed to construct a lncRNA-based signature to improve the prognostic prediction of stage II CC. We identified 1,377 differently expressed lncRNAs by analyzing 16 paired stage II CC tumor tissue and adjacent normal mucosal tissue from the TCGA dataset. Subsequently, using a univariable and step multivariable Cox regression model, we trained an 11-lncRNA signature in the training cohort (n = 141), which could divide patients into high-risk and low-risk groups (AUC at 3 years = 0.801, 95% CI: 0.724–0.877; AUC at 5 years = 0.801, 95% CI: 0.718–0.885). Significantly, patients in the high-risk group had poorer recurrence-free survival (RFS) compared with the low-risk group (log-rank test, P < 0.001 in the training cohort). This lncRNA-based signature was further confirmed in the validation cohort (P < 0.001). Multivariate Cox regression and stratified survival analyses showed that the prognostic value of this signature was independent of other clinicopathological risk factors (CEA, T stage, and chemotherapy). Time-dependent receiver operating characteristic (ROC) analysis demonstrated that this signature had better prognostic ability than any other clinical risk factors or single lncRNAs (all P < 0.05). A nomogram was constructed for clinical use, which integrated both the lncRNA-based signature and clinical risk factors (CEA and T stage) and performed well in the calibration plots. Altogether, our lncRNA-based signature was an independent prognostic factor and possessed a stronger predictive power compared with the currently used clinicopathological risk factors when predicting the recurrence of patients with stage II CC. Collectively, this lncRNA-based signature might facilitate individualized treatment decisions and postoperative counseling, ultimately contributing to improved survival.