Cancer Molecular Subtypes Research Articles

Abstract 1064: Cancer-specific molecular subtypes of pancreatic cancer reveal clinically relevant molecular dependency

Abstract Introduction: Pancreatic cancer is lethal, showing dismal prognosis and therapeutic resistance. Previous molecular subtypes from genome or transcriptome did not show clinical relevance regarding precision strategy for optimal therapeutic options followed by precise patient classification. This study aims to uncover consensus molecular subtypes from cancer-specific multi-omics data showing clinically relevant therapeutic opportunities. Methods: We performed comprehensive analyses using the dataset from the cancer dependency map (DepMap) project, including cancer-specific molecular characterization with multi-omics data, genome-wide loss-of-function screening using the CRISPR-Cas9 system, and cancer drug sensitivity. The subtype-specific molecular signatures were validated in independent translational cohorts (TCGA-PAAD; n=150, ICGC-PACA-AU; n=461, ICGC-PACA-CA; n=317). Results: Integrative profiling of multi-omics molecular layers (Mutational signature, Copy number alteration, Transcriptome, MicroRNA, Chromatic profile, Proteome, and Metabolome) from pancreatic cancer cell lines (n=59) from the Cancer Cell Line Encyclopedia (CCLE) revealed a total of three cancer-specific molecular subtypes showing distinct tumor biology through all omics layer as well as clinical relevance with unique molecular dependency. Major molecular features of each subtype were reproducible in the validation cohorts. Subtype-specific molecular biomarkers, including mutational signatures and metabolites, were identified. Finally, the target drug with subtype-specific genetic dependency was analyzed to provide a precision strategy according to distinct subtypes’ molecular characterization. Conclusions: Integrative profiling from multi-omics molecular layers revealed precision strategies based on cancer-specific molecular subtypes of pancreatic cancer in terms of tumor classification and discriminative therapeutic opportunities. Prospective translational studies companion with clinical trials based on cancer-specific molecular subtypes is mandatory to establish the precision strategy for managing pancreatic cancer. Citation Format: Sung Hwan Lee, Jiyeon Park, Sunyoung Lee, Ju-Seog Lee. Cancer-specific molecular subtypes of pancreatic cancer reveal clinically relevant molecular dependency [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 1064.

Abstract 6535: Identification of coding and non-coding genes associated with survival outcomes in uterine cancer

Abstract Endometrial (or uterine) cancer is the most commonly diagnosed cancer in the female reproductive system and it disproportionately affects Black women, who are twice as likely to die from the disease than White women. In this study, we focused on the molecular characterization of copy-number high (CN-high) molecular subclassification of uterine cancer tumors, which includes most serous and serous-like endometroid tumors. These poorly characterized subcategories account for less than 10% of all uterine cancers but are responsible for over 80% of the mortality in uterine cancers and occur more commonly in Black women.We leveraged publicly available Pan-Cancer Atlas data to perform differential gene expression analyses between control and cancer samples in the Black and White CN-high groups with the aim of identifying relevant genes that could play a role in the aggressiveness of this cancer. We then performed survival analysis using the genes of interest using Kaplan-Meier estimators to ascertain the gene-specific survival outcomes.In the significantly upregulated subset of genes, we found that the high expression of the candidate gene was associated with higher survival in both White patients (p=0.046), and Black patients (p=0.021). Additionally, the expression levels of one of the noncoding genes were associated with differential survival between the groups, with low expression being associated with higher survival in White patients (p=0.0045), and high expression associated with higher survival in Black patients (p=0.018). This differential association of survival was also observed in one of the most downregulated genes in both groups, with low expression predicting higher survival in white patients (p=0.004), and Black patient survival is associated with high expression (p=0.0082). We also identified novel non-coding genes that predicted different survival outcomes in both groups, with high expression predicting better survival in Black patients and low expression predicting better survival in White patients (p=0.048 and p=0.039, respectively). These results showcase the identification of both coding and noncoding potential genomic targets that are associated with clinical outcomes in the aggressive CN-high molecular subtype of uterine cancer. These targets merit further characterization and experimental validation to elucidate their molecular roles in the progression of endometrial cancer. Acknowledgments S.S.G. is a CPRIT scholar in cancer research and is supported by a First-time Faculty Recruitment Award from the Cancer Prevention and Research Institute of Texas (CPRIT; RR170020). S.S.G. is also supported by a) the Lizanell and Colbert Coldwell Foundation, b) The Edward N. and Margaret G. Marsh Foundation, and c) the American Cancer Society. Citation Format: Enrique I. Ramos, Axel M. Hidalgo, Ken Y. Lin, Shrikanth S. Gadad. Identification of coding and non-coding genes associated with survival outcomes in uterine 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 6535.

CD73 Is a Critical Immune Checkpoint in a Molecular Subtype of Pancreatic Cancer

Molecular stratification of patients with pancreatic ductal adenocarcinoma (PDAC) has the potential to guide clinical decision-making for therapeutic intervention. Investigating mechanisms by which different molecular subtypes of PDAC form and progress will improve patient responses to existing therapies and aid in identifying new, more specific therapeutic approaches. In this issue of Cancer Research, Faraoni and colleagues identified CD73/Nt5e-generated adenosine as a mechanism of immunosuppression specifically in pancreatic ductal-derived basal/squamous-type PDAC. Using genetically engineered mouse models targeting key genetic mutations to pancreatic acinar or ductal cells and an array of experimental and computational biology approaches, the authors found that adenosine signaling through receptor ADORA2B induces immunosuppression and tumor progression in ductal cell-derived tumors. These data demonstrate how molecular stratification of PDAC in combination with targeted approaches may enhance patient responses to therapy in this deadly cancer. See related article by Faraoni et al., p. 1111.

Clinicopathological Features and Survival Analysis in Molecular Subtypes of Muscle-Invasive Bladder Cancer.

Molecular subtyping of bladder cancer (BC) aims to capture the biological heterogeneity of this complex disease in order to provide better patient risk stratification. Immunohistochemical (IHC) markers are regarded as promising surrogates to classify BCs into luminal and basal subtypes in routine practice. We investigated the correlation between the molecular subclassification, assessed through IHC, and the conventional prognostic variables of a cohort of 93 muscle-invasive BCs (MIBCs), with a focus on the pattern of muscularis propria (MP) invasion, and evaluated their association with outcome. Basal, luminal, double-positive (DP), and double-negative (DN) phenotypes were identified according to the coordinate expression of 1 basal (CK5/6) and 2 luminal (CK20, GATA3) markers, and accounted for 33.3%, 32.3%, 3.2%, and 31.2% (Scheme #1) and 9.7%, 60.2%, 26.9%, and 3.2% (Scheme #2). There was a significant association between the pattern of MP invasion and the molecular subtypes according to Scheme #2, in that all 8 basal and DN cases, as well as 83% of DP cases, had a non-infiltrative invasion pattern. No consistent differences were observed in terms of OS and CSS between the molecular subtypes obtained through surrogate IHC markers. In keeping with previous studies, we report the correlation between the identification of BC subtypes and the presence of morphological prognostic factors, supporting the need for a comprehensive pathological evaluation, including clinicopathological and molecular parameters, in order to improve the diagnosis and management of MIBC.

Determination of the Cancer Genome Atlas (TCGA) Endometrial Cancer Molecular Subtypes Using the Variant Interpretation and Clinical Decision Support Software MH Guide

The Cancer Genome Atlas (TCGA) network (United States National Cancer Institute) identified four molecular endometrial cancer (EC) subtypes using an extensive multi-method approach. The aim of this study was to determine the four TCGA EC molecular subtypes using a single-method whole-exome sequencing (WES)-based approach provided by MH Guide (Molecular Health, Heidelberg, Germany). WES and clinical data of n = 232 EC patients were obtained from TCGA. The four TCGA EC molecular subtypes designated as (i) Mutated Polymerase ε (POLE), (ii) Microsatellite Instability (MSI), (iii) Copy Number (CN) low and, (iv) CN-high were determined using the MH Guide software. The prognostic value of the subtypes determined by MH Guide were compared with the TCGA classification. Analysis of WES data using the MH Guide software led to the precise identification of the four EC molecular subtypes analogous to the TCGA classification. Both approaches displayed high concordance in terms of prognostic significance. The multi-method-based TCGA EC molecular subtypes can reliably be reproduced by the single-method-based MH Guide approach. The easy-to-implement single-method MH Guide approach represents a promising diagnostic tool.

Molecular breast cancer subtype identification using photoacoustic spectral analysis and machine learning at the biomacromolecular level

Breast cancer threatens the health of women worldwide, and its molecular subtypes largely determine the therapy and prognosis of patients. However, an uncomplicated and accurate method to identify subtypes is currently lacking. This study utilized photoacoustic spectral analysis (PASA) based on the partial least squares discriminant algorithm (PLS-DA) to identify molecular breast cancer subtypes at the biomacromolecular level in vivo. The area of power spectrum density (APSD) was extracted to semi-quantify the biomacromolecule content. The feature wavelengths were obtained via the variable importance in projection (VIP) score and the selectivity ratio (Sratio), to identify the biomarkers. The PASA achieved an accuracy of 84%. Most of the feature wavelengths fell into the collagen-dominated absorption waveband, which was consistent with the histopathological results. This paper proposes a successful method for identifying molecular breast cancer subtypes and proves that collagen can be treated as a biomarker for molecular breast cancer subtyping.

Gelsolin: A comprehensive pan-cancer analysis of potential prognosis, diagnostic, and immune biomarkers.

Introduction: Gelsolin (GSN), a calcium-regulated actin-binding protein, is out of balance in various cancers. It can mediate cytoskeletal remodeling and regulate epithelial-mesenchymal conversion (EMT), but the studies on GSN function in pan-cancer are limited. Methods: We studied the transcription level, prognostic impact, diagnostic value, genetic, epigenetic modification, methylation level and immune significance of GSN in pan-cancer to fully comprehend the function of GSN in various malignancies based on multiple databases like The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Results: Pan-cancer research showed that GSN was downregulated in most tumors and expressed differently in immunological and molecular subtypes of many cancers. GSN had varying impacts on the prognosis of various tumor types. However, all had moderate to high diagnostic efficiency, and serum GSN had good diagnostic value in breast cancer patients (AUC = 0.947). Moreover, GSN was a distinguishing prognosis factor for some specific cancer types. The GSN protein was hypophosphorylated, and its promoter was hypermethylated in most cancers. GSN was linked to the infiltration level of several immunity cells and was essential in anti-tumor immune cell infiltration. KEGG and GSEA analyses showed that GSN was vital in the functions and proteoglycans processes in cancer, chemokine signaling pathway and other immune-related pathways, DNA methylation and cell cycle. Discussion: In conclusion, GSN possesses the ability to be a predictive, diagnostic, and immune indicator in pan-cancer.

Treatment options for molecular subtypes of endometrial cancer in 2023.

This article reviews treatment strategies in endometrial cancer by molecular subtype. The Cancer Genome Atlas (TCGA) classifies four molecular subtypes of endometrial cancer - mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H), copy number high (CNH)/p53abn, copy number low (CNL)/no specific molecular profile (NSMP), and POLEmut - which are validated and highly prognostic. Treatment consideration by subtype is now recommended. FDA-approved immune checkpoint inhibitors (ICIs) include pembrolizumab and dostarlimab for previously treated dMMR/MSI-H EC, and pembrolizumab/lenvatinib for mismatch repair-proficient/microsatellite-stable endometrial cancer, including CNH/p53abn and CNL/NSMP. ICIs are being studied as first-line therapy in advanced/recurrent endometrial cancer by MMR status, as well as in combination with other targeted agents. Trastuzumab is NCCN compendium listed for HER2-positive serous endometrial cancer, which are primarily p53-abnormal. Antibody-drug conjugates targeting low and high HER2 levels show promise in breast cancer, and are beginning to be studied in endometrial cancer. In addition to hormonal therapy, maintenance therapy with selinexor (XPO1-inhibitor) showed potential benefit in p53 -wildtype endometrial cancer and is being investigated prospectively. Multiple prospective trials are evaluating de-escalation of care for POLEmut endometrial cancer given favorable survival regardless of adjuvant therapy. Molecular subtyping has important prognostic and therapeutic implications and should be guiding patient management and clinical trial design in endometrial cancer.

Screening of Differentially Expressed Genes Based on the ACRG Molecular Subtypes of Gastric Cancer and the Significance and Mechanism of AGTR1 Gene Expression

The Asian Cancer Research Group (ACRG) classification is a molecular classification established based on the tissues of gastric cancer (GC) patients in Asia. Patients with different ACRG subtypes differ significantly with regard to treatment response and prognosis, which indicates that the ACRG molecular classification is more valuable than the traditional pathological classification. However, the specific differentially expressed genes (DEGs) and the value of the ACRG molecular subtypes of GC have not been studied in depth. Through the analysis of the GEO database, the DEGs in GC tissues of different ACRG molecular subtypes were investigated. The expression and mechanism of the screened angiotensin II receptor type 1 (AGTR1) gene were bioinformatically analyzed and experimentally verified. The role of AGTR1 in GC cells was mainly investigated using CCK-8, wound-healing, transwell invasion assays, qRT-PCR, and Western blotting. The bioinformatics results showed the presence of multiple DEGs in GC tissues with different ACRG molecular subtypes. Certain DEGs in GC tissues of different ACRG molecular subtypes have prognostic significance. AGTR1 levels in tumor tissues were significantly higher than in paired paracancerous tissues. The prognosis of GC patients with high expression of AGTR1 was poor (p < 0.05). The AGTR1 gene in GC samples was associated with the expression of immune pathways and immune checkpoint genes. After modifying AGTR1 expression in cell lines, cells' proliferation, invasion, and migration abilities and the expression of related genes changed. There were significant DEGs in GC tissues with different ACGR molecular types, among which the increased expression of AGTR1 was a molecular feature of MSS/EMT type gastric cancer. Further study found that AGTR1 was closely related to tumor immune infiltration and invasion and may be a new therapeutic target gene for gastric cancer.

Proximity proteome mapping reveals PD-L1-dependent pathways disrupted by anti-PD-L1 antibody specifically in EGFR-mutant lung cancer cells

BackgroundPD-L1, a transmembrane ligand for immune checkpoint receptor PD1, has been successfully targeted to activate an anti-tumor immune response in a variety of solid tumors, including non-small cell lung cancer (NSCLC). Despite the success of targeting PD-L1, only about 20% of patients achieve a durable response. The reasons for the heterogeneity in response are not understood, although some molecular subtypes (e.g., mutant EGF receptor tumors) are generally poor responders. Although PD-L1 is best characterized as a transmembrane PD1 ligand, the emerging view is that PD-L1 has functions independent of activating PD1 signaling. It is not known whether these cell-intrinsic functions of PD-L1 are shared among non-transformed and transformed cells, if they vary among cancer molecular subtypes, or if they are impacted by anti-PD-L1 therapy.MethodsHere we use quantitative microscopy techniques and APEX2 proximity mapping to describe the behavior of PD-L1 and to identify PD-L1's proximal proteome in human lung epithelial cells.ResultsOur data reveal growth factor control of PD-L1 recycling as a mechanism for acute and reversible regulation of PD-L1 density on the plasma membrane. In addition, we describe novel PD-L1 biology restricted to mutant EGFR cells. Anti-PD-L1 antibody treatment of mutant EGFR cells perturbs cell intrinsic PD-L1 functions, leading to reduced cell migration, increased half-life of EGFR and increased extracellular vesicle biogenesis, whereas anti-PD-L1 antibody does not induce these changes in wild type EGFR cells.ConclusionsGrowth factor acute regulation of PD-L1 trafficking, by contributing to the control of plasma membrane density, might contribute to the regulation of PD-L1's immune checkpoint activity, whereas the specific effects of anti-PD-L1 on mutant EGFR cells might contribute to the poor anti-PD-L1 response of mutant EGFR tumors.5zzQ_mo5e1oawe5DznU6q-Video

Pan-cancer analysis highlights the role of PSENEN in the prognosis and immunology of cancer

BackgroundPresenilin enhancer-2 (PSENEN, PEN-2), one of the four components of the γ-secretase complex, has been increasingly revealed to be significant in cancer types such as pancreatic cancer, gastric cancer, and breast cancer. However, the pan-cancer clinical relevance of PSENEN remains unclear. MethodsRaw data on PSENEN expression in normal and cancer tissues were obtained from The Cancer Genome Atlas (TGCA) database and Genotype-Tissue Expression Project (GTEx). The difference of PSENEN expression was analyzed using data from the TCGA repository and TIMER2 database. Meanwhile, Cox regression analysis and KM plotter were used to analyze the pan-cancer prognostic significance of PSENEN. We also analyzed the correlation between PSENEN expression and tumor immune infiltration using the TIMER and XCELL algorithms. Moreover, we used the TISIDB database to determine PSENEN expression in different immune and molecular subtypes of human cancers. Pan-cancer analysis of genetic alteration of PSENEN was performed using online tools such as cBioPortal and UALCAN. Finally, six Gene Expression Omnibus datasets from the Gene Expression Profiling Interactive Analysis database were used to validate the expression level of PSENEN in lung adenocarcinoma (LUAD). ResultsContrary to nonmalignant tissues, the expression level of PSENEN was significantly upregulated in the cancerous tissues in 22 cancer types. Elevated PSENEN expression was correlated with worse overall survival in 7 cancer types and with worse disease-specific survival in 8 of them. By using xCell algorithm, TIMER algorithm, and Spearman's correlation analysis, we found that PSENEN expression was closely correlated with the infiltration of immune cells across all cancer types. Moreover, aberrant PSENEN expression was associated with 60 immune checkpoint pathway-related genes, microsatellite instability, and tumor mutation burden in various cancer types. Besides, PSENEN expression was significantly associated with different immune subtypes and molecular subtypes of various human cancers. Notably, ovarian epithelial tumor samples demonstrated the highest frequency of PSENEN mutation among all cancer types. ConclusionsOur pan-cancer analysis demonstrated that PSENEN might serve as a prognostic biomarker and revealed the importance of an in-depth understanding of the oncogenic role of PSENEN in various malignancies.

Abstract P5-07-08: Evaluating the risk of cardiotoxicity associated with concurrent trastuzumab emtansine (TDM1) and radiation therapy in patients with early-stage HER2 positive breast cancer

Abstract BACKGROUND: HER2-positive breast cancers, which accounts for 20% of breast cancers, is associated with aggressive clinical behavior and inferior survival. The approval of HER2 targeted therapy has changed the landscape of this disease and has reduced disease recurrence by 50% and has improved survival by 33%. (1) However, cardiotoxicity is a well-recognized adverse event associated with HER2-targeted therapies. Adjuvant trastuzumab emtansine (TDM1) is the current standard of care for patients with residual breast cancer after neoadjuvant HER2-targeted therapy. TDM1 is associated with a risk of cardiotoxicity defined as a decline in left ventricular ejection fraction (LVEF). In a pooled analysis of data from seven metastatic breast cancer trials with TDM1, the incidence of cardiac events such as congestive heart failure (CHF), cardiac ischemia, cardiac arrhythmia or grade 1/2 LVEF drop was 3.37%. Adjuvant breast radiation (RT) is routinely offered for patients at high risk for recurrence. Breast RT is also associated with long-term increased risk of cardiac disease more than 10 years after RT. The HERA trial which studied use of adjuvant trastuzumab showed that rates of cardiotoxicity were higher in patients receiving concurrent RT with trastuzumab (left sided &amp;gt; right sided breast cancer) compared to those who did not receive adjuvant RT, although not statistically significant. In the multivariate analysis, no treatment or baseline cardiovascular risk factors were strongly correlated with LVEF, but radiation therapy showed a borderline correlation (adjusted HR, 1.258; 95% CI, 1.00-1.58; P = .049). The risk of cardiotoxicity with concurrent TDM1 and RT has not been well studied. With increasing use of TDM1 in the adjuvant setting, it is important to understand the cardiotoxic effects of combination therapy in early-stage breast cancer. METHODS: We undertook a review of our clinical database to identify patients who received adjuvant TDM1 with concurrent RT for Stage I-III breast cancer from 1/2020 to 01/2022. Clinical parameters including age, date of diagnosis, history of cardiac disorders, echocardiogram findings, radiation dose, final pathologic stage and molecular subtypes of cancer were extracted. All patients had ejection fraction to monitor cardiac fraction. Global longitudinal strain (GLS), which is a more sensitive and reproducible indicator of cardiac dysfunction than LVEF, was also collected, if available. RESULTS: Of 32 patients identified in our retrospective analysis, two patients (6%) developed a drop in ejection fraction post radiation. Median age of patients was 57y. Majority of the patients were Caucasian (44%) followed by Hispanic (28%). 19 (60%) patients had right sided breast cancers and 13(40%) patients had left sided cancers. The mean pre-radiation ejection fraction was 60% and post radiation was 61%. Using paired t-testing, there was no statically significant difference in ejection fraction after radiation (p=0.343). Comparative GLS measurements were available for 16 patients and there was no statical difference with concurrent radiation (p=0.18). All patients tolerated radiation with mostly grade 2 skin dermatitis except four patients who had grade 3 skin dermatitis. One patient had to discontinue radiation early given grade 3 skin dermatitis. CONCLUSION: This institutional review of 32 patients suggests that adjuvant TDM1 with concurrent RT did not result in a significant change in ejection fraction or GLS. Most patients tolerated radiation without significant skin toxicities. One of the limitations of the study is the small sample size. A larger study should look at more broader conclusions; however this data has strong clinical implications. Cardiac Parameters pre and post RT Citation Format: Faheem Farooq, Dillon Cason, Nisha Ohri, Shicha Kumar, Allison Grann, Anna Litvak, Shridar Ganesan, Bruce G. Haffty, Deborah Toppmeyer, Coral Omene, Mridula A. George. Evaluating the risk of cardiotoxicity associated with concurrent trastuzumab emtansine (TDM1) and radiation therapy in patients with early-stage HER2 positive breast cancer [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 P5-07-08.

An integrative analysis of enhancer of yellow 2 homolog (ENY2) as a molecular biomarker in pan-cancer.

ENY2 (Enhancer of yellow 2 transcription factor) is a transcription nuclear protein and primarily participates in the course of mRNA export and histone deubiquitination to influence gene expression. Current studies have shown that the expression of ENY2 is significantly upregulated in multiple cancers. However, the exact association between ENY2 and pan-cancers has not been fully established. Here, we comprehensively analyzed ENY2 from the online public database and The Cancer Genome Atlas (TCGA) database, including gene expression level in pan-cancer, comparison of ENY2 expression in different molecular and immune subtypes of pan-cancer, targeted protein, biological functions, molecular signatures, diagnostic and prognostic value in pan-cancer. Moreover, we focused on head and neck squamous cell carcinoma (HNSC) and explored ENY2 from the perspective of the correlations with clinical characteristics, prognosis, co-expression genes, differentially expressed genes (DEGs) and immune Infiltration. Our findings showed that the expression of ENY2 differed enormously not only in most cancer types but also in different molecular and immune subtypes of cancers. High accuracy in predicting cancers and notable correlations with prognosis of certain cancers suggested that ENY2 might be a potential diagnostic and prognostic biomarker of cancers. In addition, ENY2 was identified to be significantly correlated with clinical stage, gender, histologic grade and lymphovascular invasion in HNSC. Overexpression of ENY2 could lead to a worse overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in HNSC, especially in different clinical subgroups of HNSC. Taken together, ENY2 showed strong correlation with the diagnosis and prognosis of pan-cancer, and was an independent prognostic risk factor of HNSC, which may serve as a potential target for cancer management.

A Database of Lung Cancer-Related Genes for the Identification of Subtype-Specific Prognostic Biomarkers

The molecular subtype is critical for accurate treatment and follow-up in patients with lung cancer; however, information regarding subtype-associated genes is dispersed among thousands of published studies. Systematic curation and cross-validation of the scientific literature would provide a solid foundation for comparative genetic studies of the major molecular subtypes of lung cancer. Here, we constructed a literature-based lung cancer gene database (LCGene). In the current release, we collected and curated 2507 unique human genes, including 2267 protein-coding and 240 non-coding genes from comprehensive manual examination of 10,960 PubMed article abstracts. Extensive annotations were added to aid identification of differentially expressed genes, potential gene editing sites, and non-coding gene regulation. For instance, we prepared 607 curated genes with CRISPR knockout information in 43 lung cancer cell lines. Further comparison of these implicated genes among different subtypes identified several subtype-specific genes with high mutational frequencies. Common tumor suppressors and oncogenes shared by lung adenocarcinoma and lung squamous cell carcinoma, for example, exhibited different mutational frequencies and prognostic features, suggesting the presence of subtype-specific biomarkers. Our retrospective analysis revealed 43 small cell lung cancer-specific genes. Moreover, 52 tumor suppressors and oncogenes shared by lung adenocarcinoma and squamous cell carcinoma confirmed the different molecular mechanisms of these two cancer subtypes. The subtype-based genetic differences, when combined, may provide insight into subtype-specific biomarkers for genetic testing.

Rare molecular subtypes of lung cancer.

Oncogenes that occur in ≤5% of non-small-cell lung cancers have been defined as 'rare'; nonetheless, this frequency can correspond to a substantial number of patients diagnosed annually. Within rare oncogenes, less commonly identified alterations (such as HRAS, NRAS, RIT1, ARAF, RAF1 and MAP2K1 mutations, or ERBB family, LTK and RASGRF1 fusions) can share certain structural or oncogenic features with more commonly recognized alterations (such as KRAS, BRAF, MET and ERBB family mutations, or ALK, RET and ROS1 fusions). Over the past 5 years, a surge in the identification of rare-oncogene-driven lung cancers has challenged the boundaries of traditional clinical grade diagnostic assays and profiling algorithms. In tandem, the number of approved targeted therapies for patients with rare molecular subtypes of lung cancer has risen dramatically. Rational drug design has iteratively improved the quality of small-molecule therapeuticagents and introduced a wave of antibody-based therapeutics, expanding the list of actionable de novo and resistance alterations in lung cancer. Getting additional molecularly tailored therapeutics approved for rare-oncogene-driven lung cancers in a larger range of countries will require ongoing stakeholder cooperation. Patient advocates, health-care agencies, investigators and companies with an interest in diagnostics, therapeutics and real-world evidence have already taken steps to surmount the challenges associated with research into low-frequency drivers.

Prediction of response to neoadjuvant chemotherapy of patients with muscle invasive bladder cancer by molecular subtyping and radioligand target quantitation: Preview of the Bladder BRIDGister.

543 Background: Patients with muscle invasive urothelial carcinoma achieving pathological complete response (pCR) upon neoadjuvant chemotherapy (NACT) have improved prognosis. Molecular subtypes of bladder cancer differ markedly with regard to sensitivity to cisplatinum based chemotherapy and harbour FGFR treatment targets to various content. Previously we did show that lumina tumors respond better to NACT, while FGFR1 expression is associated with chemo resistance (Ecke et al. 2022). The objective of this study was to determine wether radioligand therapy may be an appropriate option in chemoresistent tumors to justify subsequent prospective validation within the "Bladder BRIDGister". Methods: Formalin fixed paraffin embedded (FFPE) tissues from transurethral resections (TUR) before chemotherapy and cystectomy samples after NACT of 36 patients were retrospectively collected. RNA from FFPE tissues were extracted by commercial kits, relative gene expression of subtyping markers (KRT5, KRT20, FGFR1) and radioligand target genes (CXCR4, FAP) were analyzed by standardized RT-qPCR systems (STRATIFYER Molecular Pathology GmbH, Cologne). Spearman correlation, hierarchical clustering, Kruskal-Wallis, chi square and contingency tests were done by JMP 9.0.0 (SAS software). Results: The neoadjuvant cohort consisted of 36 patients (median age: 69, male 83% vs. female 17%) with 92% of patients being histopathologically node negative. When comparing pretreatment with post treatment samples the median expression of KRT20 dropped 128fold, while FGFR1, CXCR4 and FAP mRNA expression increased 6,8fold, 1,9 fold and 2,9 fold, respectively. FAP was positively associated with KRT5, FGFR1 and CXCR4 in treatment naïve TUR biopsies (r=0.4051 p=0.0141, r=0.6458 p&lt;0.0001 and r=0.7586 p&lt;0.0001, respectively), but negatively associated with KRT20 (r=-0.3879 p=0.0194). As previously described, FGFR1 was negatively associated with pCR (r=-0.6418 p&lt;0.0001). Similarly, CXCR4 and FAP trended to be negatively associated with pCR (r=-0.3181 p=0.0586; r=-0.3072 p=0.0684). Hierarchical clustering revealed that CXCR4 and FAP are elevated in stromal rich, KRT5 &amp; KRT20 negative tumors not responding to NACT. Elevated FAP above median mRNA expression was significantly associated with resistance to NACT (chi2 4.314 p=0,0378). Combining elevated FAP and CXCR4 mRNA expression did identify 28% of the patients to be at high risk of NACT resistance (90%). Conclusions: Expression of the radioligand targets CXCR4 and FAP are associated with basal/stromal enriched tumors and resistance to NACT. Theranostic targeting of CXCR4 and FAP before NACT might increase response towards NACT in this poor prognosis group.

Prediction of response to neoadjuvant chemotherapy of patients with muscle invasive bladder cancer by molecular subtyping and antibody drug conjugate target gene quantitation: Preview of Bladder BRIDGister.

545 Background: Patients with muscle invasive urothelial carcinoma achieving pathological complete response (pCR) upon neoadjuvant chemotherapy (NACT) have improved prognosis. Molecular subtypes of bladder cancer differ markedly with regard to sensitivity to cisplatinum based chemotherapy. Previously we did show that luminal tumors respond better to NACT, while FGFR1 expression is associated with chemo resistance (Ecke et al. 2022). The objective of this study was to determine which patients may benefit from Antibody Drug Conjugate (ADC) treatment in addition to NACT to justify subsequent prospective analysis within the "Bladder BRIDGister". Methods: Formalin fixed paraffin embedded (FFPE) tissues from transurethral resections (TUR) before chemotherapy and cystectomy samples after NACT of 36 patients were retrospectively collected. RNA from FFPE tissues were extracted by commercial kits, relative gene expression of subtyping markers (KRT5, KRT20, FGFR1) and radioligand target genes (NECTIN4, TROP2) were analyzed by standardized RT-qPCR systems (STRATIFYER Molecular Pathology GmbH, Cologne). Spearman correlation, hierarchical clustering, Kruskal-Wallis, chi square and contingency tests were done by JMP 9.0.0 (SAS software). Results: The neoadjuvant cohort consisted of 36 patients (median age: 69, male 83% vs. female 17%) with 92% of patients being pathohistologically node negative. When comparing pretreatment with post treatment samples the median expression of KRT20 dropped 128fold, while FGFR1 expression increased 6.8 fold. Interestingly, TROP2 and NECTIN4 mRNA expression also dropped significantly upon NACT by 5.7 fold and 7.1 fold, respectively. TROP2 and NECTIN4 were positively associated with the response marker KRT20 in therapy naïve TUR biopsies (r=0.5562 p=0.0004; r=0.5833 p=0.0002), but negatively associated with the resistance marker FGFR1 (r=-0.2903 p=0,0858; r=-0.3396 p=0,0427). However, TROP2 and NECTIN4 were not associated with pCR in spearman analysis with minor trend for TROP2 (r=0,2139 p=0,2103). Cluster analysis revealed a subgroup of KRT20 positive and FGFR1 negative tumors expression TROP2 and NECTIN4, which achieved 80% pCR. In addition elevated TROP2 and NECTIN4 expression was found in KRT20 positive tumors coexpressing FGFR1 and being resistant to NACT. Conclusions: Expression of the ADC targets TROP2 and NECTIN4 is associated with KRT20 positive, luminal tumors being highly sensitive to neoadjuvant chemotherapy alone. KRT5 positive, basal tumors do exhibit only very low expression of TROP2 and NECTIN4 mRNA. In view of toxicities the addition of TROP2 and NECTIN4 treatment to NACT might be considered only in luminal tumors exhibiting elevated FGFR1 expression as resistance mechanism and therefore do not respond to NACT.

Assessing Epstein–Barr virus in gastric cancer: clinicopathological features and prognostic implications

BackgroundEpstein–Barr virus (EBV)-associated gastric cancer (EBVaGC) was a unique molecular subtype of gastric cancer (GC). However, the clinicopathological characteristics and prognostic role of EBV infection remains unclear. We aimed to evaluate the clinicopathological features of EBVaGC and its role on prognosis.MethodsEBV-encoded RNA (EBER) in situ hybridization method was used to evaluate the EBV status in GC. The serum tumor markers AFP, CEA, CA19-9 and CA125 of patients were detected before treatment. HER2 expression and microsatellite instability (MSI) status was evaluated according to established criteria. The relationship between EBV infection and clinicopathological factors as well as its role on prognosis were investigated.Results420 patients were enrolled in the study and of 53 patients (12.62%) were identified as EBVaGC. EBVaGC was more common in males (p = 0.001) and related to early T stage (p = 0.045), early TNM stage (p = 0.001) and lower level of serum CEA (p = 0.039). No association could be found between EBV infection and HER2 expression, MSI status and other factors (p all > 0.05). Kaplan–Meier analysis revealed that both the overall survival and disease-free survival of EBVaGC patients were similar to that of EBV-negative GC (EBVnGC) patients (p = 0.309 and p = 0.264, respectively).ConclusionEBVaGC was more common in males and in patients with the early T stage and TNM stage as well as patients with lower serum CEA level. Difference in overall survival and disease-free survival between EBVaGC and EBVnGC patients cannot be detected.

Identification and Validation of Molecular Subtype and Prognostic Signature for Bladder Cancer Based on Neutrophil Extracellular Traps

Neutrophil extracellular traps (NETs) could promote tumor growth and distant metastases. Molecular subtypes of bladder cancer were identified with consensus cluster analysis. A NETs-related prognostic signature was constructed with LASSO cox regression analysis. As a result, we identified three subtypes of bladder cancer, which had a distinct difference in prognosis, immune microenvironment, TIDE score, mRNAsi score and IC50 score. We also developed a prognostic signature based on 5 NETs-related genes, which had a good performance in clinical outcome prediction of bladder cancer. These results may provide more data about the vital role of NETs in bladder cancer.

The past, present, and future of immunotherapy for colorectal cancer

Colorectal cancer is prevalent worldwide, with various factors influencing the survival rate of late-stage metastatic cases. Current standard treatments include surgical removal, adjuvant chemotherapy, and neoadjuvant chemotherapy. Novel immunotherapy research shows promising results for various cancer types, including colorectal cancer. Current immunotherapy options are limited to specific molecular subtypes of colorectal cancer, while the remaining are limited to standard protocol. This review article summarizes approved, developing, and potential sources for novel colorectal cancer immunotherapy treatment through active-specific, checkpoint inhibitor, cytokine, cytotoxic, and adoptive T-cell immunotherapy. Such a study would be beneficial to patients with colorectal cancer.