Cancer Prognostic Biomarkers Research Articles

Abstract 3693: Molecular and functional characterization of circulating CK+/CD45+ cells in breast cancer

Abstract Background: Circulating tumor cells (CTCs) are considered a key element in metastatic progression and represent a validated prognostic biomarker in breast cancer (BC). CTCs in BC are normally defined as epithelial cells (positive for EPCAM or cytokeratin, CK) lacking the expression of the leukocyte marker CD45. Circulating cells expressing both EPCAM/CK and CD45 (dual positive, DPcells) have however been reported in BC but not investigated. It is believed that DPcells derive from the heterotypic cell fusion of tumor and immune cells, but this hypothesis has not been demonstrated yet. We recently reported, for the first time, the association of DPcells with worse survival in a cohort of 341 BC patients (pts) [Reduzzi et al. ASCO 2022] supporting their tumor origin. Here, we further investigated their malignancy and metastatic potential by molecular profiling and functional experiments. Methods: The study consisted of 2 components: A) Single CTCs and DPcells were enriched from the blood of BC patients with the CellSearch platform, and isolated with the DEPArray system. Single cells underwent whole genome amplification and lowpass whole genome sequencing for single cell copy number alteration (CNA) profiling; B) DPcells and CTCs were investigated in the blood of immunodeficient (NSG) and immunocompetent (FVB) mouse models using various cell lines (LM2, 4T1, MVT1). To test their metastatic potential, DPcells from the primary tumor of FVB donor mice were transplanted into recipient NSG mice, and the metastatic burden in the lungs and liver quantified, in comparison with control CD45- tumor cells. Results: We analyzed 73 DPcells and 18 CTCs collected from 16 BC pts: Aberrant genomes were observed in 28% and 93% of evaluable cells, respectively. When collected from the same pt, CTCs showed clonal CNA profiles, while DPcells were highly heterogeneous. In vivo, DPcells could only be detected in the blood of FVB mice but not in NSG mice. They were very rare, comprising of only about 3% of the total CTC count. When DPcells and control tumor cells were isolated from the primary tumor of 10 donor mice and transplanted into the tail vein of 10 recipient mice, we observed no significant differences in the metastatic colonization of the lungs and liver by the two population, indicating that DPcells do in fact possess metastatic ability, and to a similar extent as control cancer cells. Conclusions: DPcells can have an aberrant genome, supporting their malignancy. Contrary to CTCs, DPcells’ CNA profiles are not clonal and, in vivo, they can only be observed in immunocompetent models; both observations support the tumor/immune fusion hypothesis. Finally, DPcells show metastatic potential in mice, in line with the association with worse survival we previously observed in BC pts. Overall DPcells seem a new CTC subpopulation that should not be neglected anymore. More studies are needed to better understand their origin and phenotypic/molecular features. Citation Format: Carolina Reduzzi, Eleonora Nicolo, Lauren L. Ozimski, Marco Silvestri, Lorenzo Gerratana, Mara S. Serafini, Elisabetta Molteni, Nadia Bayou, Amanda K. Strickland, Huiping Liu, Vera Cappelletti, Nicola Aceto, Massimo Cristofanilli. Molecular and functional characterization of circulating CK+/CD45+ cells in breast 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 3693.

Abstract 7419: Seq2Karyotype (S2K): A method for deconvoluting heterogeneity of copy number alterations using single-sample whole-genome sequencing data

Abstract Broad copy number alterations (CNAs) at chromosomal band resolution have been used as cancer diagnostic and prognostic biomarkers for decades. These events have been characterized by cytogenetic imaging, an approach which is powerful for assessing heterogeneity but limited for locus fine mapping. While CNA detection by next-generation sequencing has become a standard analysis, existing methods rarely model CNA heterogeneity in bulk tumor samples and often require a paired normal sample for control. To overcome these limitations, we developed Seq2Karyotype (S2K, https://github.com/chenlab-sj/Seq2Karyotype), a new algorithm for in-silico karyotyping using single-sample whole-genome sequencing (WGS) data. S2K performs joint modeling of read-depth and allelic imbalance (AI) of high-quality heterozygous SNPs to identify reference diploid regions, followed by modeling and segmenting the deviation from the reference. Empirical coverage and AI of segmented regions are fitted to models of single and admixed CNAs to estimate clonality. The final karyotyping considers both the model fitness and minimization of evolution steps.To evaluate S2K’s performance, we analyzed two cell lines commonly used for benchmark test: COLO829 (melanoma) and HCT1395 (breast cancer); both had single-cell (sc) WGS for validation. For COLO829, S2K replicated the four populations detected by scWGS but derived a different clonality estimate. The predominant clone, defined by loss of 1p, 10p, and chr18, was estimated to have 67% cellular fraction (CF) by bulk sample analysis of S2K in contrast to the 10% CF by scWGS analysis. In HCT1395, S2K identified three new CNAs present in >50% of the cells of the matching germline sample which were subsequently validated by FISH, karyotyping and SKY mapping.To demonstrate S2K’s utility, we analyzed three diverse data sets: 17 neuroblastoma cell lines, 24 pediatric AML samples with karyotyping data, and two blood samples from children with myelodysplastic syndromes (MDS) known to harbor mosaic uniparental disomy (UPD). CNA-based intra-tumor heterogeneity was detected in 88% (15/17) of the neuroblastoma cell lines, comprised of 2-4 distinct populations with diverse ranges of CF (~10%-90%) and varying CNA patterns (e.g. admixture of tetraploid and diploid cells), which were validated by cytogenetics or scWGS. In the patient AML samples, S2K detected >95% of the previously reported cytogenetic events and 30% of additional copy-neutral loss-of-heterozygosity events. The mosaic UPD events in MDS patients were detected with projected clonality of 60% and 25%, respectively. These results not only demonstrate the accuracy of in-silico karyotyping performed by S2K but also reveal the dynamic intra-tumor heterogeneity in cancer cell lines, which may impact the design and interpretation of future experiments using these cell lines. Citation Format: Limeng Pu, Karol Szlachta, Virginia Valentine, Xiaolong Chen, Jian Wang, Dennis Kennetz, Daniel Putnam, Sivaraman Natarajan, Li Dong, Thomas Look, Marcin Wlodarski, Lu Wang, Steven Burden, John Easton, Xiang Chen, Jinghui Zhang. Seq2Karyotype (S2K): A method for deconvoluting heterogeneity of copy number alterations using single-sample whole-genome sequencing data [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 7419.

Unveiling the role of YARS1 in bladder cancer: A prognostic biomarker and therapeutic target.

YARS is responsible for catalysing the binding of tyrosine to its cognate tRNA and plays a crucial role in basic biosynthesis. However, its biological functions in bladder cancer remains to be proven. We analysed variations in YARS1 expression and survival in bladder cancer using multiple data sets, including TCGA-BLCA, GSE13507 and bladder cancer-specific tissue microarrays. Furthermore, we explored the biological functions of YARS1 using transcriptome data. Our findings revealed a noteworthy correlation between YARS1 and immune infiltration in bladder cancer, as determined using the XCELL algorithm and single-cell analysis. In addition, we employed the TIDE algorithm to evaluate the responsiveness of different cohorts to immune checkpoint therapy. We investigated the regulatory associations between YARS1 and various aspects of bladder cancer, including senescence, ferroptosis and stemness. Finally, we established a ceRNA network that is directly linked to the overall prognosis, YARS1 can serve as a prognostic biomarker for bladder cancer; its interaction with MYC has implications for bladder cancer cell senescence, ferroptosis and stemness. Moreover, the identified ceRNA network has potential as a therapeutic target in bladder cancer.

TP53 and/or BRCA1 Mutations Based on CtDNA Analysis as Prognostic Biomarkers for Primary Triple-Negative Breast Cancer.

Precise biomarkers for predicting the therapeutic efficacy of molecularly targeted drugs are limited at the protein level; thus, it has been important to broadly scrutinize individual cancer driver gene mutations for effective cancer treatments. Multiplex cancer genome profiling can comprehensively identify gene mutations that are therapeutic targets using next-generation sequencing (NGS). In addition, circulating tumor DNA (ctDNA) is a DNA fragment released into the blood by tumor cell-derived cell death or apoptosis. Liquid biopsy with ctDNA is a novel clinical test for identifying genetic mutations in an entire population noninvasively, in real-time, and heterogeneously. Although there are several reports on ctDNA, fewer have evaluated ctDNA with NGS before an initial treatment for breast cancer patients. Therefore, we examined whether analyzing tumor-associated gene mutations in primary breast cancer based on ctDNA could serve as a biomarker for prognosis and optimal treatment selection. Ninety-five primary breast cancer patients treated at our department from January 2017 to October 2020 were included. Pretreatment plasma samples were subjected to NGS analysis of ctDNA, and correlations with patients' clinicopathological characteristics were evaluated. Fifty-nine (62.1%) patients were positive for ctDNA. ctDNA tended to be positive in hormone receptor-negative, and TP53 (34%), BRCA1 (20%), and BRCA2 (17%) gene mutations were more frequent. Regarding recurrence-free survival, the prognosis was poor in the TP53 and/or BRCA1 mutation-positive groups, especially in triple-negative breast cancer (TNBC) patients. In conclusion, the results of this study indicate that ctDNA with liquid biopsy could identify the poor prognosis group before treatment among TNBC patients and for those for whom optimal treatment selection is desirable; additionally, optimal treatment could be selected according to the ctDNA analysis results.

Identification of ALYREF in pan cancer as a novel cancer prognostic biomarker and potential regulatory mechanism in gastric cancer

ALYREF is considered as a specific mRNA m5C-binding protein which recognizes m5C sites in RNA and facilitates the export of RNA from the nucleus to the cytoplasm. Expressed in various tissues and highly involved in the transcriptional regulation, ALYREF has the potential to become a novel diagnostic marker and therapeutic target for cancer patients. However, few studies focused on its function during carcinogenesis and progress. In order to explore the role of ALYREF on tumorigenesis, TCGA and GTEx databases were used to investigate the relationship of ALYREF to pan-cancer. We found that ALYREF was highly expressed in majority of cancer types and that elevated expression level was positively associated with poor prognosis in many cancers. GO and KEGG analysis showed that ALYREF to be essential in regulating the cell cycle and gene mismatch repair in tumor progression. The correlation analysis of tumor heterogeneity indicated that ALYREF could be specially correlated to the tumor stemness in stomach adenocarcinoma (STAD). Furthermore, we investigate the potential function of ALYREF on gastric carcinogenesis. Prognostic analysis of different molecular subtypes of gastric cancer (GC) unfolded that high ALYREF expression leads to poor prognosis in certain subtypes of GC. Finally, enrichment analysis revealed that ALYREF-related genes possess the function of regulating cell cycle and apoptosis that cause further influences in GC tumor progression. For further verification, we knocked down the expression of ALYREF by siRNA in GC cell line AGS. Knockdown of ALYREF distinctly contributed to inhibition of GC cell proliferation. Moreover, it is observed that knocked-down of ALYREF induced AGS cells arrested in G1 phase and increased cell apoptosis. Our findings highlighted the essential function of ALYREF in tumorigenesis and revealed the specific contribution of ALYREF to gastric carcinogenesis through pan-cancer analysis and biological experiments.

Multi-omics analysis of TLCD1 as a promising biomarker in pan-cancer.

Background: The TLC Domain Containing 1 (TLCD1) protein, a key regulator of phosphatidylethanolamine (PE) composition, is distributed across several cellular membranes, including mitochondrial plasma membranes. Existing research has revealed the impact of TLCD1 on the development of non-alcoholic fatty liver disease. However, there remains a gap in comprehensive pan-cancer analyses of TLCD1, and the precise role of TLCD1 in cancer patient prognosis and immunological responses remains elusive. This study aims to provide a comprehensive visualization of the prognostic landscape associated with TLCD1 across a spectrum of cancers, while shedding light on the potential links between TLCD1 expression within the tumor microenvironment and immune infiltration characteristics. Methods: TLCD1 expression data were obtained from GTEx, TCGA, and HPA data repositories. Multiple databases including TIMER, HPA, TISIDB, cBioPortal, GEPIA2, STRING, KEGG, GO, and CancerSEA were used to investigate the expression pattern, diagnostic and prognostic significance, mutation status, functional analysis, and functional status of TLCD1. In addition, we evaluated the relationship between TLCD1 expression and immune infiltration, tumor mutational burden (TMB), microsatellite instability (MSI), and immune-related genes in pan-cancer. Furthermore, the association of TLCD1 with drug sensitivity was analyzed using the CellMiner database. Results: We found that TLCD1 is generally highly expressed in pan-cancers and is significantly associated with the staging and prognosis of various cancers. Furthermore, our results also showed that TLCD1 was significantly associated with immune cell infiltration and immune regulatory factor expression. Using CellMiner database analysis, we then found a strong correlation between TLCD1 expression and sensitivity to anticancer drugs, indicating its potential as a therapeutic target. The most exciting finding is that high TLCD1 expression is associated with worse survival and prognosis in GBM and SKCM patients receiving anti-PD1 therapy. These findings highlight the potential of TLCD1 as a predictive biomarker for response to immunotherapy. Conclusion: TLCD1 plays a role in the regulation of immune infiltration and affects the prognosis of patients with various cancers. It serves as both a prognostic and immunologic biomarker in human cancer.

Comprehensive Analysis Reveals Deoxyribonuclease 1 as a Potential Prognostic and Diagnostic Biomarker in Human Cancers.

Deoxyribonuclease 1 (DNASE1) is an important gene associated with several cancers, including liver, bladder, and gastric cancer. It has been linked to autoimmune illnesses, including systemic lupus erythematosus, which may lead to cancer formation. However, the role of DNASE1 in cancer has not beenstudied. We performed a pan-cancer analysis using bioinformatics tools, including Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), and University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN) databases, Kaplan-Meier plotter, and cBioPortal, to investigate the expression of DNASE1 across various cancers as well as its association with immune infiltration and genetic alterations. Public datasets were used to validate DNASE1 expression in kidney renal clear cell carcinoma (KIRC) and kidney papillary renal cell carcinoma (KIRP) samples. DNASE1 was found to be highly expressed in many cancers, such as bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), and was lowly expressed in other cancers, including KIRC, KIRP, and thyroid carcinoma (THCA). Additionally, TIMER results showed an association of DNASE1 with immune cell infiltration in KIRC and KIRP. Survival analysis indicated that high DNASE1 expression was associated with poor prognosis in KIRC. We also discovered that altered DNASE1 expression was related to poor prognosis in The Cancer Genome Atlas (TCGA) tumors. DNASE1 could potentially be used as a prognostic and diagnostic biomarker for KIRC and as a diagnostic biomarker for KIRP.

Loss of AR-regulated AFF3 contributes to prostate cancer progression and reduces ferroptosis sensitivity by downregulating ACSL4 based on single-cell sequencing analysis.

Prostate cancer (PCa) is one of the most common cancers affecting the health of men worldwide. Castration-resistant prostate cancer (CRPC), the advanced and refractory phase of prostate cancer, has multiple mechanisms of resistance to androgen deprivation therapy (ADT) such as AR mutations, aberrant androgen synthase, and abnormal expression of AR-related genes. Based on the research of the AR pathway, new drugs for the treatment of CRPC have been developed in clinical practice, such as Abiraterone and enzalutamide. However, many areas in this pathway are still worth exploring. In this study, single-cell sequencing analysis was utilized to scrutinize significant genes in the androgen receptor (AR) pathway related to CRPC. Our analysis of single-cell sequencing combined with bulk-cell sequencing revealed a substantial downregulation of AR-regulated AFF3 in CRPC. Overexpression of AFF3 restricted the proliferation and migration of prostate cancer cells whilst also increasing their sensitivity towards enzalutamide, while knockdown of AFF3 had the opposite effect. To elucidate the mechanism of tumor inhibition by AFF3, we applied GSVA and GSEA to investigate the metabolic pathways related to AFF3 and revealed that AFF3 had an impact on fatty acids metabolism and ferroptosis through the regulation of ACSL4 protein expression. Based on correlation analysis and flow cytometry, we can speculate that AFF3 can impact the sensitivity of the CRPC cell lines to the ferroptosis inducer (RSL3) by regulating ACSL4. Therefore, our findings may provide new insights into the mechanisms of drug resistance in CRPC, and AFF3 may serve as a novel prognostic biomarker in prostate cancer.

Survival and clinicopathological significance of B7-H3 in bladder cancer: a systematic review and meta-analysis

BackgroundB7-H3 has been implicated in clinical pathological features and prognosis across various cancer types, suggesting its potential as a cancer biomarker. Nevertheless, consensus remains elusive regarding its clinical-pathological and prognostic significance in bladder cancer. To address this gap, we conducted a systematic review and meta-analysis.MethodsWe systematically searched PubMed, Embase, Web of Science, Cochrane, and CNKI databases from their inception up to October 6, 2022. We evaluated the literature’s quality using the Newcastle-Ottawa Scale. We performed meta-analysis using Review Manager 5.3 and STATA 12.0, synthesizing data and calculating odds ratios (ORs) or hazard ratios (HRs) with corresponding 95% confidence intervals (CIs).ResultsAfter applying eligibility criteria and conducting assessments, we included data from 8 studies, encompassing 1622 bladder cancer patients. Bladder tumor tissues exhibited significantly elevated B7-H3 protein expression compared to normal bladder tissues. Elevated B7-H3 expression was notably associated with patient age, tumor infiltration, and recurrence in bladder cancer. However, no significant correlations were observed with other clinical characteristics. Our pooled HR analysis indicated no significant association between B7-H3 expression and overall survival in bladder cancer patients.ConclusionOur meta-analysis unveils the complex role of B7-H3 in bladder cancer progression. It appears to be directly involved in tumor infiltration and recurrence but cannot definitively serve as a prognostic biomarker for bladder cancer. To validate these findings, further well-designed studies, encompassing larger sample sizes and diverse racial backgrounds, are warranted.PROSPERO registrationNo. CRD42022364688.

EVA1A, a novel and promising prognostic biomarker in colorectal cancer.

The purpose of this study was to investigate the potential of EVA1A as a prognostic biomarker for Colorectal cancer (CRC). The study utilized public databases to analyze the difference in Evala mRNA expression between CRC tumor tissues and adjacent normal tissues. Additionallymunohistochemical staining was performed on 90 paired tissue samples to detect EVA1A expression. The relationship between EVA1A and clinicopathological features was examined, and a Kaplan-Meier survival analysis was conducted. Univariate and multivariate Cox analyses were employed to identify prognostic factors affecting the overall survival (OS) of CRC patients. The analysis revealed a significant increase in Evala mRNA expression in CRC tumor cells compared to normal controls from public databases (P< 0.05). Immunohistochemical staining further confirmed a significant upregulation of EVA1A expression in CRC tissues (P< 0.05). High EVA1A expression was associated with age, pathological M stage, total tumor stage, and Carbohydrate antigen CA19-9 (CA19-9). Kaplan-Meier analysis demonstrated a significant association between high EVA1A expression and poor OS. Univariate and multivariate analysis identified EVA1A as an independent risk factor for CRC prognosis. The study suggests that EVA1A is increased in CRC tumor tissues and may serve as a potential biomarker for poor prognosis in CRC.

Exosome circATP8A1 induces macrophage M2 polarization by regulating the miR-1-3p/STAT6 axis to promote gastric cancer progression

Circular RNAs (circRNAs) play important roles in gastric cancer progression but the regulatory role of circRNAs in controlling macrophage function remains elusive. Exosomes serve as cargo for circRNAs and play a crucial role as mediators in facilitating communication between cancer cells and the tumor microenvironment. In this study, we found that circATP8A1, a previously unreported circular RNA, is highly expressed in both gastric cancer tissues and exosomes derived from plasma. Increased circATP8A1 was associated with advanced TNM stage and worse prognosis in patients with gastric cancer. We showed that the circATP8A1 knockdown significantly inhibited gastric cancer proliferation and invasion in vitro and in vivo. Functionally, exosome circATP8A1 induced the M2 polarization of macrophages through the STAT6 pathway instead of the STAT3 pathway. Mechanistically, circATP8A1 was shown to activate the STAT6 pathway through competitive binding to miR-1-3p, as confirmed by Fluorescence In Situ Hybridization (FISH), RNA immunoprecipitation, RNA pulldown, and Luciferase reporter assays. The reversal of circATP8A1-induced STAT6 pathway activation and macrophage polarization was observed upon blocking miR-1-3p. Macrophages treated with exosomes from gastric cancer cells overexpressing circATP8A1 were able to promote gastric cancer migration, while knockdown of circATP8A1 reversed these effects in vivo. In summary, exosome-derived circATP8A1 from gastric cancer cells induce macrophages M2 polarization via the circATP8A1/miR-1-3p/STAT6 axis, and tumor progression. Our results highlight circATP8A1 as a potential prognostic biomarker and therapeutic target in gastric cancer.

Impact of NDUFAF6 on breast cancer prognosis: linking mitochondrial regulation to immune response and PD-L1 expression

BackgroundBreast cancer is a major global health concern, and there is a continuous search for novel biomarkers to predict its prognosis. The mitochondrial protein NDUFAF6, previously studied in liver cancer, is now being investigated for its role in breast cancer. This study aims to explore the expression and functional significance of NDUFAF6 in breast cancer using various databases and experimental models.MethodsWe analyzed breast cancer samples from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Human Protein Atlas (HPA) databases, supplemented with immunohistochemistry (IHC) staining to assess NDUFAF6 expression. A breast cancer cell xenograft mouse model was used to evaluate tumor growth, apoptosis, and NDUFAF6 expression. Survival probabilities were estimated through Kaplan–Meier plots and Cox regression analysis. A Protein–Protein Interaction (PPI) network was constructed, and differentially expressed genes related to NDUFAF6 were analyzed using GO, KEGG, and GSEA. The relationship between NDUFAF6 expression, immune checkpoints, and immune infiltration was also evaluated.ResultsNDUFAF6 was found to be overexpressed in breast cancer patients and in the xenograft mouse model. Its expression correlated with worse clinical features and prognosis. NDUFAF6 expression was an independent predictor of breast cancer outcomes in both univariate and multivariate analyses. Functionally, NDUFAF6 is implicated in several immune-related pathways. Crucially, NDUFAF6 expression correlated with various immune infiltrating cells and checkpoints, particularly promoting PD-L1 expression by inhibiting the NRF2 signaling pathway.ConclusionThe study establishes NDUFAF6 as a potential prognostic biomarker in breast cancer. Its mechanism of action, involving the inhibition of NRF2 to upregulate PD-L1, highlights its significance in the disease's progression and potential as a target for immunotherapy.

Deconstructing neutrophil to lymphocyte ratio (NLR) in early breast cancer: lack of prognostic utility and biological correlates across tumor subtypes

PurposeThe prognostic utility and biological correlates of neutrophil to lymphocyte ratio (NLR), a potential biomarker of the balance between immune response and the inflammatory status, are still uncertain in breast cancer (BC).MethodsWe analysed a cohort of 959 women with early breast cancer, mostly treated with neoadjuvant or adjuvant chemotherapy. Clinical and pathological data, survival, NLR (continuous and categorical) and stromal tumor infiltrating lymphocytes (sTIL) were evaluated.ResultsNLR was only weakly associated with Ki67, while no association was found for grade, histology, immunohistochemical subtype or stage. Lymphocyte infiltration of the tumor did not correlate with NLR (Rho: 0.05, p = 0.30). These results were similar in the whole group and across the different BC subtypes, with no differences in triple negative BC. Relapse free interval (RFI), breast cancer specific survival (BCSS) and overall survival (OS) changed according to pre-treatment NLR neither in the univariate nor in the multivariate Cox models (RFI: HR 0.948, p = 0.61; BCSS: HR 0.920, p = 0.57; OS: HR 0.96, p = 0.59).ConclusionThese results question the utility of NLR as a prognostic biomarker in early breast cancer and suggest the lack of correlation of NLR with tumor microenvironment immune response.

SPARC is a Novel Prognostic Biomarker for Ovarian Cancer and Associated with Immune Signatures and Drug Response

SPARC is a Novel Prognostic Biomarker for Ovarian Cancer and Associated with Immune Signatures and Drug Response

Pan-cancer integrated analysis of ANKRD1 expression, prognostic value, and potential implications in cancer

There is substantial evidence demonstrating the crucial role of inflammation in oncogenesis. ANKRD1 has been identified as an anti-inflammatory factor and is related to tumor drug resistance. However, there have been no studies investigating the prognostic value and molecular function of ANKRD1 in pan-cancer. In this study, we utilized the TCGA, GTEx, GSCALite, ENCORI, CTRP, DAVID, AmiGO 2, and KEGG databases as well as R language, to explore and visualize the role of ANKRD1 in tumors. We employed the ROC curve to explore its diagnostic significance, while the Kaplan–Meier survival curve and Cox regression analysis were used to investigate its prognostic value. Additionally, we performed Pearson correlation analysis to evaluate the association between ANKRD1 expression and DNA methylation, immune cell infiltration, immune checkpoints, TMB, MSI, MMR, and GSVA. Our findings indicate that ANKRD1 expression is dysregulated in pan-cancer. The ROC curve revealed that ANKRD1 expression is highly sensitive and specific in diagnosing CHOL, LUAD, LUSC, PAAD, SKCM, and UCS (AUC > 85.0%, P < 0.001). Higher ANKRD1 expression was related to higher overall survival (OS) in LGG, but with lower OS in COAD and STAD (P < 0.001). Moreover, Cox regression and nomogram analyzes suggested that ANKRD1 is an independent factor for COAD, GBM, HNSC, and LUSC. Dysregulation of ANKRD1 expression in pan-cancer involves DNA methylation and microRNA regulation. Using the CTRP database, we discovered that ANKRD1 may influence the half-maximal inhibitory concentration (IC50) of several anti-tumor drugs. ANKRD1 expression showed significant correlations with immune cell infiltration (including cancer-associated fibroblast and M2 macrophages), immune checkpoints, TMB, MSI, and MMR. Furthermore, ANKRD1 is involved in various inflammatory and immune pathways in COAD, GBM, and LUSC, as well as cardiac functions in HNSC. In vitro experiments demonstrated that ANKRD1 promotes migration, and invasion activity, while inhibiting apoptosis in colorectal cancer cell lines (Caco2, SW480). In summary, ANKRD1 represents a potential prognostic biomarker and therapeutic target in human cancers, particularly in COAD.

Abstract B019: Assessing Circulating TumOur DNA as a prognostic biomarker in endometrial cancer (The CODEC Study)

Abstract Introduction/Background: Endometrial cancer (EC) is the most common gynecological cancer in the developing world. While significant progress has been made through molecular sub-classification, the treatment of EC for many women remains contentious and better biomarkers are required to guide therapy selection. Circulating tumor DNA (ctDNA) a ‘liquid biopsy’, involves collection of tumor specific DNA via a blood test and can quantify cancer burden and detect tumor specific genomic information. The CODEC study is a prospective pilot study to assess the utility of ctDNA as a prognostic biomarker in EC with the hope that it may help predict relapse and guide selection of adjuvant therapy. Methodology: Women with Type 2 EC planned for surgery and consenting to the collection of biospecimens were enrolled prior to surgery and followed prospectively. Blood was collected perioperatively and then every three months for up to two years and at relapse. Broad sequencing of participants’ tumors was performed, the results of which guided the design of personalized droplet digital PCR (ddPCR) assays for ctDNA analysis. ctDNA was extracted from 5ml of plasma and tested in quadruplicate. PET defined metabolic tumor volume was compared to ctDNA and analysis of ctDNA and relapse free survival (RFS) performed using a Cox proportional hazards regression model. Results: Somatic mutations to guide ddPCR analysis were detected in 45 enrolled women stages 1- 4 including pathogenic variants in POLE. ctDNA results are currently available for 30 participants (remaining results awaited). 12/30 participants had detectable ctDNA preoperatively and 5/25 at Time Point 3 (2-6 weeks post-surgery). ctDNA levels varied significantly across the cohort but results to date indicate that perioperative ctDNA positivity is associated with relapse. Interestingly in those that had detectable ctDNA preoperatively, the majority had a rise in ctDNA intraoperatively. Conclusion: This proof-of-concept analysis showed that ctDNA can successfully be detected in the perioperative setting and is the first study in EC to compare ctDNA with PET findings. Although testing is still underway, the early results indicate that ctDNA maybe a useful biomarker to predict relapse and guide the selection of adjuvant therapy. Citation Format: Rachel Delahunty, Rainier Arnolda, Thuan Tzen Koh, Michael Hofman, Hayley Johnston, Patricia Wojtowicz, Caitlyn Nguyen, Nicole Brooks, Kym Reid, Julie Lamont, Thomas Jobling, Deborah Neesham, Vanessa Obers, Clair Shadbolt, Brooke Sawyer, Paul Smith, Jennifer Ellis, Geradline Goss, Mila Volcheck, Madawa Jayawardana, Sandun Silva, Chelsee Hewitt, Kate Jones, Andrew Fellowes, Orla McNally, Stephen Wong, Elizabeth Christie, Costas Yannakou. Assessing Circulating TumOur DNA as a prognostic biomarker in endometrial cancer (The CODEC Study) [abstract]. In: Proceedings of the AACR Special Conference on Endometrial Cancer: Transforming Care through Science; 2023 Nov 16-18; Boston, Massachusetts. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(5_Suppl):Abstract nr B019.

COL10A1 as a Prognostic Biomarker in Association with Immune Infiltration in Prostate Cancer.

The collagen type X alpha 1 (COL10A1) has recently been found to play an important role in the development and progression of cancer. However, the link between COL10A1 and the tumor immune microenvironment remains understood scantily. In the current study, the pan-cancer data of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were used to investigate the expression mode, the clinical prognostic and diagnostic value of COL10A1 in different tumors. We used TCGA data to assess the correlations between COL10A1 and clinical symptoms of prostate cancer. The R packages "edgR" and "clusterProfiler" were used for differential expression gene and enrichment analysis of COL10A1. Immunohistochemistry was further employed to corroborate the expression of COL10A1 gene in prostate cancer. After that, we used TIMER to evaluate the pertinence of COL10A1 expression to immune infiltration level in prostate cancer. On the whole, COL10A1 was expressed at significantly higher levels in a variety of tumor tissues than in the corresponding normal tissues. Besides, significant correlations with tumor prognosis and relative exactitude in predicting tumors show that COL10A1 may be a probable prognostic and diagnostic biomarker of prostate cancer. In addition, the evidence indicates a significant correlation between COL10A1 and clinical symptoms of prostate cancer. Furthermore, the main molecular functions of COL10A1 included humoral immune response, complement activation, immunoglobulin, regulation of complement activation, and regulation of humoral immune response. Finally, we found that COL10A1 expression is positively correlated with enhanced macrophage and M2 macrophage infiltration in prostate cancer. The study indicates that COL10A1 might participate in M2 macrophage polarization in prostate cancer. COL10A1 might be an innovative biomarker to evaluate tumor microenvironment immune cell infiltration and prognosis in prostate cancer.

Comprehensive multi-omics analysis and experimental verification reveal PFDN5 is a novel prognostic and therapeutic biomarker for gastric cancer

Prefoldin Subunit 5 (PFDN5) plays a critical role as a member of the prefoldins (PFDNs) in maintaining a finely tuned equilibrium between protein production and degradation. However, there has been no comprehensive analysis specifically focused on PFDN5 thus far. Here, a comprehensive multi-omics (transcriptomics, genomics, and proteomics) analysis, systematic molecular biology experiments (in vitro and in vivo), transcriptome sequencing and PCR Array were performed for identifying the value of PFDN5 in pan-cancer, especially in Gastric Cancer (GC). We found PFDN5 had the potential to serve as a prognostic and therapeutic biomarker in GC. And PFDN5 could promote the proliferation of GC cells, primarily by affecting the cell cycle, cell death and immune process etc. These findings provide novel insights into the molecular mechanisms and precise treatments of in GC.

Biological Clock Genes are Crucial and Promising Biomarkers for the Therapeutic Targets and Prognostic Assessment in Gastric Cancer.

Gastric cancer is one of the major public health problems worldwide. Circadian rhythm disturbances driven by circadian clock genes play a role in the development of cancer. However, whether circadian clock genes can serve as potential therapeutic targets and prognostic biomarkers for gastric cancer remains elusive. In this study, we comprehensively analyzed the potential relationship between circadian clock genes and gastric cancer using online bioinformatics databases such as GEPIA, cBioPortal, STRING, GeneMANIA, Metascape, TIMER, TRRUST, and GEDS. Biological clock genes are expressed differently in human tumors. Compared with normal tissues, only PER1, CLOCK, and TIMELESS expression differences were statistically significant in gastric cancer (p < 0.05). PER1 (p = 0.0169) and CLOCK (p = 0.0414) were associated with gastric cancer pathological stage (p < 0.05). Gastric cancer patients with high expression of PER1 (p = 0.0028) and NR1D1 (p = 0.016) had longer overall survival, while those with high expression of PER1 (p = 0.042) and NR1D1 (p = 0.016) had longer disease-free survival. The main function of the biological clock gene is related to the circadian rhythms and melatonin metabolism and effects. CLOCK, NPAS2, and KAT2B were key transcription factors for circadian clock genes. In addition, we also found important correlations between circadian clock genes and various immune cells in the gastric cancer microenvironment. This study may establish a new gastric cancer prognostic indicator based on the biological clock gene and develop new drugs for the treatment of gastric cancer using biological clock gene targets.

Peritoneal Tumor DNA as a Prognostic Biomarker in Gastric Cancer: A Systematic Review and Meta-Analysis.

Gastric cancers commonly spread to the peritoneum. Its presence significantly alters patient prognosis and treatment-intent; however, current methods of peritoneal staging are inaccurate. Peritoneal tumor DNA (ptDNA) is tumor-derived DNA detectable in peritoneal lavage fluid. ptDNA positivity may indicate peritoneal micrometastasis and may be more sensitive than cytology in staging the peritoneum. In this meta-analysis, we evaluated the prognostic potential of ptDNA in gastric cancer. PubMed, Embase, Scopus, and Web of Science databases were searched using PRISMA guidelines. Studies published between January 1, 1990, and April 30, 2023, containing quantitative data relating to ptDNA in gastric cancer were meta-analyzed. Six studies were analyzed. Of the total 757 patients with gastric adenocarcinoma, 318 (42.0%) were stage I, 311 (41.0%) were stage II/III, 116 (15.3%) were stage IV, and 22 (2.9%) were undetermined. Overall, ptDNA detected cytology-positive cases with a sensitivity and specificity of 85.2% (95% CI, 66.5 to 100.0) and 91.5% (95% CI, 86.5 to 96.6), respectively. Additionally, ptDNA was detected in 54 (8.5%) of 634 cytology-negative patients. The presence of ptDNA negatively correlated with pathological stage I (relative risk [RR], 0.29 [95% CI, 0.13 to 0.66]) and positively correlated with pathological stage IV (RR, 8.61 [95% CI, 1.86 to 39.89]) disease. Importantly, ptDNA positivity predicted an increased risk of peritoneal-specific metastasis (RR, 13.81 [95% CI, 8.11 to 23.53]) and reduced 3-year progression-free (RR, 5.37 [95% CI, 1.39 to 20.74]) and overall (hazard ratio, 4.13 [95% CI, 1.51 to 11.32]) survival. ptDNA carries valuable prognostic information and can detect peritoneal micrometastases in patients with gastric cancer. Its clinical utility in peritoneal staging for gastric cancer deserves further investigation.