Microarray Format Research Articles

Immuno-RCA for highly sensitive detection of the antigen-antibody complex in the blood group antigen model

The problem of detecting tiny quantities of analytes by immunochemical methods has been tried for a long time. One approach is to use nucleic acid amplification methods to amplify the signal from a single antigen-antibody interaction. An amplification method suitable for microarrays is the rolling circle amplification reaction. The principle of the method is usage of a conjugate of a detecting antibody with a primer and subsequent isothermal amplification. The generation of a huge single-stranded reaction product starts after adding the necessary components for amplification reaction: circular oligonucleotides, which serves as a template for amplification and phage phi29 polymerase with the other components. This reaction product consists of a lot of repeats of a nucleotide sequence, that is complementary to the circular template. The fluorescent DNA probe can hybridize to each repeat on the product molecule, resulting in a significantly higher level of fluorescence than with fluorescently labeled antibody or streptavidin development systems. In addition, the reaction product remains immobilized on the surface, allowing usage of this approach for the detection of antigen-antibody interactions in other solid-phase analysis systems, such as microarrays. A common problem with such approaches is the nonspecific sorption of components of the immunochemical reaction or amplification reaction, leading to a high background. It is obvious that no matter how highly sensitive the analysis is in theory, a high background will reduce the entire potential of the method to nothing. Herein, we have developed a method that makes it possible to detect small amounts of antibodies to glycans in blood serum and in swabs from tumor cells in a microarray format using a model of blood group antigens. It was possible to obtain a 30 to 70-fold increase of fluorescence level from a specific interaction compared to the use of fluorescently labeled streptavidin. The method we are developing is promising, as it allows us to significantly increase the signal from the specific antigen/antibody interaction in the glycochip format, which will make it possible to detect antibodies to glycans in samples with a very low concentrations of antibodies, for example, in washes from tumor cells.

Microarray-based evaluation of selected recombinant timothy grass allergens expressed in E. Coli and N. Benthamiana

BackgroundTimothy grass (Phleum pratense) is a significant source of allergens, and recombinant allergens are increasingly used for diagnostic purposes. However, the performance of different recombinant allergen production systems in diagnostic assays needs further investigation to optimize their use in clinical settings.ObjectiveThe main objective of this study was to analyze and compare the diagnostic performance of recombinant timothy grass allergens produced in E. coli and N. benthamiana using a custom-made microarray chip.MethodsRecombinant timothy grass allergens Phl p 1, Phl p 2, Phl p 5, Phl p 6, Phl p 11, and Phl p 12 were produced in E. coli and/or N. benthamiana. A total of 113 patient serum samples were tested to evaluate the diagnostic sensitivity, specificity, inter-assay variability, and correlation of allergen-specific IgE detection compared to commercial multiplex tests (ALEX and ISAC). Additionally, the prevalence of sIgE to these allergens was assessed.ResultsPhl p 1, Phl p 2, Phl p 5, Phl p 6 and Phl p 11 showed high or very high positive correlation in immunoreactivity with other commercial multiplex tests. Notably, Phl p 11 fused with maltose-binding protein (MBP) demonstrated high diagnostic specificity and sensitivity, with a 0.3 arbitrary cut-off value. However, a high intra-assay variation was observed. The study also assessed specific IgE prevalence to timothy grass allergens within the tested patient cohort.ConclusionsRecombinant allergens from both E. coli and N. benthamiana demonstrated strong diagnostic potential on the microarray platform, with Phl p 11 (MBP-fused) showing particularly high performance. High intra-assay variation highlights the need for further optimization in allergen formulation and microarray storage conditions. These results highlight the potential of recombinant allergens for diagnostic applications, despite challenges with allergen stability in microarray formats. Specific IgE prevalence to timothy allergens revealed a sensitization profile consistent with findings from multiple studies.Graphical

Abstract A028: MTAP deficiency is frequent and mostly homogeneous in ductal adenocarcinomas of the pancreas

Abstract Complete expression loss of S-methyl-5′-thioadenosine phosphorylase (MTAP) is caused by homozygous 9p21 deletion and results in a critical vulnerability of cancer cells towards drugs targeting multiple different pathways. MTAP deficiency is common in ductal adenocarcinoma of the pancreas, but data on its intratumoral heterogeneity - a potential obstacle for targeted therapies - are lacking. To learn more on the role and potential heterogeneity of MTAP deficiency in pancreatic adenocarcinoma, 236 primary tumors were analyzed in a tissue microarray (TMA) format by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) for MTAP expression and 9p21 deletions. The cohort included 236 cancers from which 6 samples were taken from as many as possible different tumor containing primary tumor blocks and 3 samples were added from as many as possible lymph node metastases to construct a “heterogeneity TMA”. All available tumor containing blocks (average 4) from 6 selected cancers were also analyzed by IHC and FISH on whole sections. Complete absence of MTAP staining was seen in 350 (38.6%) of 907 interpretable TMA samples. 284 (98.6%) of 288 samples with a complete MTAP expression loss and FISH data had a homozygous 9p21 deletion while there were only two tumor spots with homozygous deletions within 557 samples with retained MTAP expression (99.6% concordance). On a patient level, an MTAP deficiency was found in 64 (41.0%) of 156 tumors for which at least 3 different samples were interpretable on the TMAs. 62 (96.9%) of these patients showed an MTAP loss in all interpretable samples (homogeneous MTAP deficiency). The TMA data were confirmed on whole sections in 5 of 6 patients. In the discrepant case a focal MTAP loss was identified in a tumor considered MTAP wild type based on the TMA results. It is concluded that MTAP expression loss is frequent and highly homogeneous in ductal adenocarcinomas of the pancreas. Given the high concordance rate between homozygous deletion and MTAP expression loss homozygous deletion may represent the only mechanism for MTAP deficiency in pancreatic cancer. MTAP IHC is an excellent tool for identification of MTPA deficient cases. MTAP IHC may also have considerable diagnostic value as even low-grade cancer glands can be easily identified in small biopsies from MTAP deficient cases. Considering also their aggressive clinical behavior, pancreatic adenocarcinomas may represent an ideal cancer type for studying new drugs targeting MTAP deficient cancer cells in clinical trials. Citation Format: Natalia Gorbokon, Katharina Teljuk, Frank Jacobsen, Till Krech, Till Clauditz, Stefan Steurer, Ronald Simon, Guido Sauter, Sarah Minner, Lukas Bubendorf, Thilo Hackert, Nina Schraps, Faik G Uzunoglu, Martina Kluth. MTAP deficiency is frequent and mostly homogeneous in ductal adenocarcinomas of the pancreas [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A028.

Reduced p63 expression is linked to unfavourable prognosis in muscle-invasive urothelial carcinoma of the bladder.

There is a shortage of established prognostic biomarkers in bladder cancer. One candidate is tumour protein 63 (p63), a transcription factor of the p53 gene family that is expressed in the normal urothelium. Recently proposed RNA expression-based molecular classifiers of bladder cancer identified high p63 expression as a component of a basal/squamous subtype linked to poor patient prognosis. In this study, p63 protein expression was analysed by immunohistochemistry on more than 2500 urothelial bladder carcinomas in a tissue microarray format to determine its relationship with clinicopathological parameters of disease progression and patient outcome. Nuclear p63 staining was seen in all cells of normal urothelium and at elevated levels in pTaG2 tumours. The rate of p63 positive cases and the staining intensity was lower in pTaG3 tumours (93.2%, p< 0.0001 for pTaG3 vs. pTaG2) and markedly lower in pT2-4 carcinomas (83.5%, p= 0.0120 for pT2-4 vs. pTaG3). Within 1018 pT2-4 carcinomas treated by cystectomy, low p63 expression was linked to nodal metastasis (p= 0.0028) and overall survival (p= 0.0005). The association with survival was independent of pT and pN (p= 0.0081). p63 expression was associated with GATA3 expression (p< 0.0001), a luminal cell type marker associated with favourable disease. A joint analysis of p63 and GATA3 did not suggest that GATA3 could provide additional prognostic information. The independent prognostic role of reduced p63 expression in advanced urothelial carcinomas suggests that p63 could be a useful biomarker to distinguish pT2-4 urothelial carcinomas.

17p13 (TP53) Deletions Are Associated With an Aggressive Phenotype but Unrelated to Patient Prognosis in Urothelial Bladder Carcinomas.

17p13 deletions including TP53 and other genes represent a common cause for reduced/lost p53 function in tumor cells. In this study, we analyzed the impact of 17p13 (TP53) deletions and p53 expression on tumor aggressiveness and patient prognosis in urothelial carcinoma. The 17p13 copy number status was analyzed by fluorescence in situ hybridization (FISH) on more than 2700 urothelial bladder carcinomas in a tissue microarray format. 17p13 deletion data were compared to p53 expression data measured by immunohistochemistry (IHC) in a previous study. Different types of p53 alterations were compared with tumor phenotype and clinical outcome data. Deletions of 17p13 occurred in 23% of 2185 analyzable carcinomas. The fraction of tumors with 17p13 deletions increased from pTa G2 low (9%) to pTa G3 (24%, p < 0.0001). In muscle-invasive carcinomas, 17p13 deletions were associated with advanced pT stage (p = 0.0246), but unrelated to patient prognosis (p > 0.5). 17p13 deletions were significantly related to p53 immunostaining (p = 0.0375). 17p13 deletions were most common in tumors with complete lack of p53 staining (31%), which supports the concept that many of these tumors have a complete loss of p53 function (p53 null phenotype). 17p13 deletions were also increased in tumors with high p53 staining (25%). In conclusion, 17p13 deletions were most commonly seen in p53 negative cancers, supporting their role as a cause for the p53 null phenotype in urothelial cancer. The association of 17p13 deletions with high grade and advanced pT stage may reflect increasing genomic instability going along with stage and grade progression.

Diagnostic QR Codes

This work describes the development of a revolutionary new class of universal perception-based sensor capable of diagnosing a wide range of diseases, and compatible with low-cost mass production. This sensor takes the form of an array of fluorescent, environmentally sensitive single walled carbon nanotubes (SWCNTs), resembling a conventional two dimensional QR code. Each group of pixels of the QR code is formed from carbon nanotubes with different surface functionalisation and different environmental sensitivity. Addition of an analyte such as serum causes each pixel to change its fluorescence, generating a unique spectral ‘fingerprint’ characteristic for each disease. A machine-learning approach is then trained to identify the disease based on their corresponding fingerprint.The basic principle of this technology has been previously described by the Heller Lab for the detection of ovarian cancer, but exclusively in a microplate-based format which requires extensive liquid handling. Translating this technology into a microarray format offers a number of significant advantages, including easier handling, lower production cost, less training required for operation, simpler read-out system that can be based on mobile phone devices and the ability to simultaneously screen for multiple diseases. In this way, this technology advances beyond the current state of the art of SWCNT-based sensors. In a microarray format, hundreds of nanotube assemblies can be analysed simultaneously.By creating an array of sufficient complexity, we hope to remove the need to tailor an array for a specific disease that act as a universal platform for diagnosis of a range of different diseases. This format also significantly lowers the number of necessary sample handling steps, reducing the potential for user error and the amount of training necessary to employ the sensor. Figure 1

Characterization of Receptor Binding Affinity for Vascular Endothelial Growth Factor with Interferometric Imaging Sensor.

Wet Age-related macular degeneration (AMD) is the leading cause of vision loss in industrialized nations, often resulting in blindness. Biologics, therapeutic agents derived from biological sources, have been effective in AMD, albeit at a high cost. Due to the high cost of AMD treatment, it is critical to determine the binding affinity of biologics to ensure their efficacy and make quantitative comparisons between different drugs. This study evaluates the in vitro VEGF binding affinity of two drugs used for treating wet AMD, monoclonal antibody-based bevacizumab and fusion protein-based aflibercept, performing quantitative binding measurements on an Interferometric Reflectance Imaging Sensor (IRIS) system. Both biologics can inhibit Vascular Endothelial Growth Factor (VEGF). For comparison, the therapeutic molecules were immobilized on to the same support in a microarray format, and their real-time binding interactions with recombinant human VEGF (rhVEGF) were measured using an IRIS. The results indicated that aflibercept exhibited a higher binding affinity to VEGF than bevacizumab, consistent with previous studies using ELISA and SPR. The IRIS system's innovative and cost-effective features, such as silicon-based semiconductor chips for enhanced signal detection and multiplexed analysis capability, offer new prospects in sensor technologies. These attributes make IRISs a promising tool for future applications in the development of therapeutic agents, specifically biologics.

High-throughput transcriptome profiling indicates ribosomal RNAs to be associated with resistance to immunotherapy in non-small cell lung cancer (NSCLC)

BackgroundDespite the impressive outcomes with immune checkpoint inhibitor (ICI) in non-small cell lung cancer (NSCLC), only a minority of the patients show long-term benefits from ICI. In this study, we...

Multiplex gradient immunochip for detection of post-vaccinal antibodies in poultry.

Multiplex analysis as an immunochip-in-a well format for simultaneous detection of post-vaccinal antibodies to three poultry infections (Newcastle disease, infectious bronchitis and bursal disease) in one chicken sera was developed. The immunochip had a microarray format printed on the bottom of a standard microtiter plate well and consisted of 36 microspots (d = 400μm each) with three lines of viral antigens absorbed in a gradient of five decreasing concentrations. Optimization of assay conditions revealed the necessity of careful choice of the reaction buffer due to the high tendency of chicken IgY to exhibit unspecific binding. The best results were obtained for PBS buffer (pH 6.0) supplied with 0.1% Tween 20. Assay results were visualized by a number of coloured microspots that were correlated with the specific antibody titre in the analysed serum. High (> 8000), medium (3000-8000) or low (1000-3000) antibody titre level for each of three infections could be quickly assessed in one probe visually or with the help of smartphone. ELISA results (antibody titres) and visual gradient immunochip results interpretation (high, medium, low antibody level/titre) for 63 chicken sera with multiple levels of post-vaccinal antibodies against Newcastle disease, infectious bronchitis and bursal disease were in good correlation.

Abstract B018: KDM6A and MTAP expression loss enable identification of a large fraction of low grade non-invasive urothelial neoplasia of the urinary bladder

Abstract The identification of low-grade urothelial neoplasia in cytologic samples or in biopsies with dysplastic lesions poses a particular problem for pathologists in routine diagnostics. Improved diagnosis of low-grade urothelial neoplasia could help to reduce the number of cystoscopic follow-up examinations. KDM6A, also known as UTX (ubiquitously transcribed X chromosome tetratricopeptide repeat protein) is an epigenetic regulator which is frequently mutated in urothelial carcinoma. Because KDM6A is localized on chromosome Xp11.3, and because of the male predominance in bladder cancer, many KDM6A mutations should result in a complete loss of KDM6A protein expression and become detectable by immunohistochemistry (IHC). Similarly, S-methyl-5′-thioadenosine phosphorylase (MTAP), a critical enzyme for DNA and RNA synthesis, is co-deleted with the CDKN2A tumor suppressor located on chromosome 9p21 in about 25% of bladder cancers, resulting in reduced or lost protein expression. To study the prevalence and diagnostic potential of immunohistochemical loss of KDM6A and MTAP expression, 928 tumors were analyzed by IHC in a tissue microarray format. The cohort included 628 non-invasive papillary tumors (pTa) and 300 tumors from patients who underwent radical cystectomy for muscle-invasive disease (pT2-4). A complete KDM6A expression loss occurred in 35% of 342 pTa G2 low-grade, 23% of 150 pTa G2 high-grade, 17.8% of 90 pTa G3 tumors, and 20.1% of 243 interpretable muscle invasive (pT2-4) cancers (p&amp;lt;0.0001). Within pTa tumors, there was a strong correlation between KDM6A loss and low tumor grade (p=0.0003), whereas no significant difference was found between pT3 G3 and muscle invasive cancers (p=0.8828). Complete absence of MTAP expression occurred in 11% of 297 pTa G2 low-grade, 29.6% of 125 pTa G2 high-grade, 18.4% of 76 pTa G3 tumors, and 26.3% of 217 muscle invasive (pT2-4) cancers (p&amp;lt;0.0001). A combined analysis of 702 cancers with interpretable data for KDM6A and MTAP showed that 6.6% of tumors had expression loss of both KDM6A and MTAP, 20% had KDM6A loss only, and 13% had MTAP loss only. The rate of expression loss of KDM6A and/or MTAP was markedly higher in pTa G2 low (41.2%) and in pTa G2 high (40.3%) than in pTa G3 tumors (29%). In summary, our data demonstrate that about 40% of low-grade non-invasive urothelial neoplasias – which are usually not detected by urine cytology – had a completed expression loss of either KDM6A or MTAP. In patients with these alterations, follow-up could be potentially facilitated by immunohistochemistry. Citation Format: Florian Viehweger, Neele Heckmann, Natalia Gorbokon, Henning Plage, Sebastian Hofbauer, Sarah Weinberger, Florian Roßner, Simon Schallenberg, Sefer Elezkurtaj, Maximilian Lennartz, Tim Mandelkow, Elena Bady, Margit Fisch, Thorsten Ecke, Stefan Koch, Nico Adamini, Ronald Simon, Guido Sauter, Tobias Klatte, Thorsten Schlomm, David Horst, Henrik Zecha, Martina Kluth, Sarah Minner. KDM6A and MTAP expression loss enable identification of a large fraction of low grade non-invasive urothelial neoplasia of the urinary bladder [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr B018.

CEA (CEACAM5) expression is common in muscle-invasive urothelial carcinoma of the bladder but unrelated to the disease course.

Carcinoembryonic antigen (CEA) is a cell surface glycoprotein that represents a promising therapeutic target. Serum measurement of shedded CEA can be utilized for monitoring of cancer patients. To evaluate the potential clinical significance of CEA expression in urothelial bladder neoplasms, CEA was analysed by immunohistochemistry in more than 2500 urothelial bladder carcinomas in a tissue microarray format. CEA staining was largely absent in normal urothelial cells but was observed in 30.4% of urothelial bladder carcinomas including 406 (16.7%) with weak, 140 (5.8%) with moderate, and 192 (7.9%) with strong staining. CEA positivity occurred in 10.9% of 411 pTaG2 low-grade, 32.0% of 178 pTaG2 high-grade, and 43.0% of 93 pTaG3 tumours (p < 0.0001). In 1335 pT2-4 carcinomas, CEA positivity (34.1%) was lower than in pTaG3 tumours. Within pT2-4 carcinomas, CEA staining was unrelated to pT, pN, grade, L-status, V-status, overall survival, recurrence free survival, and cancer specific survival (p > 0.25). CEA increases markedly with grade progression in pTa tumours, and expression occurs in a significant fraction of pT2-4 urothelial bladder carcinomas. The high rate of CEA positivity in pT2-4 carcinomas offers the opportunity of using CEA serum measurement for monitoring the clinical course of these cancers. Moreover, CEA positive urothelial carcinomas are candidates for a treatment by targeted anti-CEA drugs.

Gold-nanoparticle-embedded membrane (GEM) for highly sensitive multiplexed sandwich immunoassays

For early disease diagnostics, highly sensitive biosensing methods are required to detect disease-related biomolecules in biofluids at low concentrations. Further, for complex diseases such as cancer, multiplexed detection is required to simultaneously measure multiple analytes in a single assay. Current technologies either lack sensitivity, multiplexing capabilities, or require complicated micro/nano-fabrication processes and specialized instrumentation, limiting their broader use in the biomedical research community as well as in clinical diagnostic applications. In this work, we have developed a gold-nanoparticle-embedded membrane (GEM) platform that consists of 3D nitrocellulose membranes preloaded with gold nanoparticles in microliter compartments for highly sensitive, multiplexed metal enhanced fluorescence (MEF)-based detection. After the development of the compartmentalized GEM and the optimization of size, shape, and concentration of the gold nanoparticles to achieve optimal MEF, we demonstrated its application for scalable multiplexed sandwich immunoassays in a microarray format for the quantification of three cancer-related proteins in blood plasma. In PBS buffer solution, the limit of detection for GM-CSF, TNF-α, and EGFR were improved by 287-folds, 949-folds, and 9.8-folds, respectively, when using the GEM compared to conventional ELISA. When spiked in pooled human plasma, low pg/mL sensitivity was also achieved for each protein, demonstrating its application for complex samples. Long-term storage was demonstrated for potential distribution of the GEM for wide availability among the biomedical and clinical community, facilitating technology dissemination. This technology offers simple, highly sensitive, and multiplexed detection capabilities with low reagent and sample consumption, suitable for accurate and early disease diagnostics.

Abstract 3804: Multiparameter cell-cycle measurement enables a better assessment of cancer aggressiveness than Ki67 LI alone

Abstract Background: Ki67 is expressed in the G1, S, G2 and M phase of the cell cycle. Immunohistochemical determination of the Ki67 labeling index (LI) is a clinically well-established tool for assessing the proliferative activity of tumors and critical clinical decisions are based on this parameter. Other cell cycle associated proteins have been evaluated for clinical utility much less intensively. This for example includes minichromosome maintenance-3 (MCM3) which is expressed earlier in the cell cycle than Ki67. Design: To evaluate the difference and potential synergy between of Ki67 and MCM3 based proliferation indices, both proteins were analyzed by multiplex fluorescent immunohistochemistry in more than 1,580 colorectal carcinomas that were available in a tissue microarray format and results were compared with clinico-pathological parameters (pT, pN, grade, MSI, p53 status). A deep learning-based framework comprising a deep-learning based algorithm for automated cell and marker detection was used for image analysis. Results: In our 1,583 evaluable colorectal cancers, the average Ki67 LI was 69% and the average MCM3-LI was 67%. There was a significant overlap between Ki67 and MCM3 staining: Of all panCK positive tumor cells, 56% were positive for both Ki67 and MCM3, 11% were only positive for Ki67, 8% showed positivity only for MCM3, and 25% were negative for both markers. According to the expression of Ki67 and MCM3, the following compartments of proliferating cells were defined: early (MCM3+/Ki67−), intermediate (MCM3+/Ki67+), and late phase of the cell cycle (MCM3−/Ki67+) as well as full proliferation (MCM3+ or Ki67+). Comparison with clinico-pathological parameters revealed the best p-values for the MCM3 LI in the comparison with pT (p=2.7e−8), nodal metastasis (p=0.0002), and p53 alterations (p=6e−11) while the “full proliferation” LI was most tightly linked to microsatellite instability (p=1e−10). The Ki67 LI was best correlated to the grade (p=0.01). Conclusion: The combined analysis of MCM3 and Ki67 enables the distinction of cells in early, intermediate, and late phase of the cell cycle. At least in colorectal cancer - a highly proliferative neoplasm - MCM3 quantification alone or in combination with Ki67 often resulted in stronger relationships with clinicopathological parameters than the Ki67 LI alone. These results suggest that a more subtle analysis of cell cycle proteins might enable a better evaluation of cancer aggressiveness than Ki67 measurement alone. Citation Format: Jan H. Mueller, Julia Ebner, Zhihao Huang, Maximilian Lennartz, Claudia Hube-Magg, Frank Jacobsen, Stefan Steurer, Christian Bernreuther, Till S. Clauditz, Andreas H. Marx, Till Krech, Eike Burandt, Guido Sauter, Ronald Simon, Sarah Minner, Elena Bady. Multiparameter cell-cycle measurement enables a better assessment of cancer aggressiveness than Ki67 LI alone [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 3804.

Abstract 1048: Loss of MTAP expression is strongly linked to homozygous 9p21 deletion, unfavorable tumor phenotype and non-inflamed microenvironment in urothelial bladder cancer

Abstract 9p21 deletions are common in urothelial carcinoma and mostly include S-methyl-5′-thioadenosine phosphorylase (MTAP) a critical enzyme for DNA and RNA synthesis. Homozygous MTAP deletions result in a complete loss of expression which can be visualized by immunohistochemistry (IHC). Evidence is emerging that MTAP deficiency results in a critical vulnerability of cancer cells towards drugs targeting multiple different pathways that depend on a functional MTAP gene and causes resistance to immune checkpoint inhibitors. To determine the prevalence and clinical significance of MTAP deficiency and its relationship with the tumor microenvironment in urothelial bladder carcinomas, more than 2,500 tumors were analyzed by fluorescence in-situ hybridization (FISH) and IHC in a tissue microarray format, and the data were compared with existing data on intratumoral lymphocyte subsets and PD-L1 expression. The cohort included 1,826 patients that underwent radical cystectomy for muscle-invasive disease (pT2-4). 9p21 deletion was homozygous in 364 (21.3%) and heterozygous in 334 (19.5%) of 1,711 analyzable tumors. The rate of 9p21 deleted tumors increased from pTa G2 low (9.2% homozygous, 25.8% heterozygous) to pTa G2 high (32.6%, 20.9%; p&amp;lt;0.0001) but was slightly lower in pTa G3 (16.7% each). In pT2-pT4 carcinomas, 9p21 deletions were homozygous in 23.3% and heterozygous in 17.9%. Within muscle-invasive cancers, 9p21 deletions were tied to high pT (p=0.0014) and poor overall survival (p=0.0461). MTAP expression loss was strongly linked to homozygous 9p21 deletions. Complete absence of MTAP staining was seen in 96.1% of homozygous deleted cancers while only 4 of 249 MTAP negative cancers had retained at least one 9p21 copy (p&amp;lt;0.0001). Accordingly, absence of MTAP staining was also linked to advanced pT status and poor overall survival (p&amp;lt;0.05 each). Tumors with heterozygous 9p21 deletion did often show preserved but low-level expression of MTAP. 9p21 deletions were associated with low numbers of PD-L1 positive tumor cells (p&amp;lt;0.0001), CD8 (p=0.01) and CD4 positive lymphocytes (p=0.009), M2-macrophages (p&amp;lt;0.0001), and dendritic cells (p=0.0007). A similar tendency was observed for MTAP expression loss, but the level of significance was only reached for PD-L1 positive tumor cells (p&amp;lt;0.0001), M2 macrophages (p=0.001) and dendritic cells (p=0.012). Complete MTAP expression loss is common in urinary bladder cancer and strongly tied to homozygous 9p21 loss, aggressive disease, and non-inflamed microenvironment. Drugs targeting MTAP-deficiency may be highly useful in bladder cancer. MTAP IHC is an excellent surrogate for the detection of MTAP deficiency in this tumor entity. Citation Format: Natalia Gorbokon, Niklas Wößner, Viktoria Ahlburg, Simon Schallenberg, Henning Plage, Sebastian Hofbauer, Kira Furlano, Sarah Weinberger, Paul G. Bruch, Florian Roßner, Sefer Elezkurtaj, Maximilian Lennartz, Niclas C. Blessin, Andreas H. Marx, Henrik Samtleben, Margit Fisch, Michael Rink, Marcin Slojewski, Krystian Kaczmarek, Thorsten Ecke, Steffen Hallmann, Stefan Koch, Nico Adamini, Sarah Minner, Ronald Simon, Guido Sauter, Henrik Zecha, David Horst, Tobias Klatte, Thorsten Schlomm, Martina Kluth. Loss of MTAP expression is strongly linked to homozygous 9p21 deletion, unfavorable tumor phenotype and non-inflamed microenvironment in urothelial bladder 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 1048.

Abstract 6449: KDM6A expression loss is a common feature in low grade non-invasive urothelial carcinomas of the urinary bladder

Abstract KDM6A, also known as UTX (ubiquitously transcribed X chromosome tetratricopeptide repeat protein) is an epigenetic regulator which is frequently mutated in urothelial carcinoma. Because KDM6A loss causes a dependency on EZH2, a potential therapeutic target, KDM6A analysis may have therapeutic importance. Most data on KDM6A mutations are derived from next generation sequencing (NGS). However, because of the combination of a high rate of truncating KDM6A mutations, the localization of KDM6A on chromosome Xp11.3, and the male predominance in bladder cancer, many KDM6A mutations should result in a complete loss of KDM6A protein expression and become detectable by immunohistochemistry (IHC). To study the prevalence and the potential diagnostic and clinical role of KDM6A expression loss, more than 2,100 tumors were analyzed by IHC in a tissue microarray format. The cohort included 1,128 patients who underwent radical cystectomy for muscle-invasive disease (pT2-4). A complete KDM6A expression loss occurred in 36% of 350 pTa G2 low-grade, 23% of 152 pTa G2 high-grade, and 18.5% of 92 pTa G3 tumors (p=0.0002). As compared to pTa G3 tumors, the frequency of KDM6A expression loss did not differ significantly in pT2 (17.2%), pT3 (21.9%), and pT4 (18.2%) cancers. Within pT2-4 carcinomas, KDM6A staining was unrelated to pT, pN, grade, L-status, V-status, overall survival, recurrence-free survival, and cancer-specific survival (p≥0.18 each). A KDM6A loss was more common in male (22.2%) than in female patients (15.4%; p&amp;lt;0,0001), and within male patients, a KDM6A loss was more frequent in tumors with Y-chromosome loss (36.1%) than in cancers without a Y-chromosome loss (16.3%; p&amp;lt;0.0001). KDM6A expression loss was significantly associated with increased p63 expression (p&amp;lt;0.0001) and high uroplakin 1b staining (p=0.0013) but unrelated to CK20, GATA3, UpK1b, and p53 staining. In summary, our data demonstrate that truncating KDM6A mutations occur in a significant subset of urothelial carcinomas which is linked to low-grade non-invasive cancer, male gender and loss of the Y chromosome. The predominance of KDM6A loss in low grade tumors makes KDM6A IHC a promising new tool for identification of low grade dysplasia in biopsies and early bladder cancer detection in cytology. Citation Format: Florian Viehweger, Natalia Gorbokon, Henning Plage, Sebastian Hofbauer, Kira Furlano, Sarah Weinberger, Bernhard Ralla, Antonia Franz, Annika Fendler, Michela de Martino, Florian Roßner, Simon Schallenberg, Sefer Elezkurtaj, Maximilian Lennartz, Tim Mandelkow, Elena Bady, Andreas H. Marx, Henrik Samtleben, Margit Fisch, Michael Rink, Marcin Slojewski, Krystian Kaczmarek, Thorsten Ecke, Stefan Koch, Nico Adamini, Ronald Simon, Guido Sauter, Joachim Weischenfeldt, Tobias Klatte, Thorsten Schlomm, David Horst, Henrik Zecha, Martina Kluth, Sarah Minner. KDM6A expression loss is a common feature in low grade non-invasive urothelial carcinomas of the urinary bladder [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 6449.

Abstract 169: Prevalence, immune checkpoint expression and spatial interplay of intraepithelial lymphocytes, macrophages, and dendritic cells in 4740 human carcinomas

Abstract Background: Although there is raising evidence that the density and the level of immune checkpoint expression of immune cell subpopulations that are in direct contact to the tumor cells (intraepithelial) can predict response to immune checkpoint therapy and patient’s outcome, a comprehensive assessment of intraepithelial immune cell subpopulations and their spatial interplay is lacking. Material and methods: To comprehensively assess the density, level of immune checkpoint expression, and spatial interplay of 48 immune checkpoint expressing intraepithelial leukocyte subpopulations in 46 carcinoma entities, 4740 tumor samples in a tissue microarray format were stained with 21 antibodies using our BLEACH&amp;STAIN mfIHC approach. A deep learning-based framework comprising 18 different convolutional neuronal networks (U-Net and DeepLabv3+) were used for image analysis. Results: The mean intraepithelial immune cell density of CD8+ cytotoxic T-cells, CD4+ T-helper cells, FOXP3+ Tregs, CD20+ B-cells, M1/M2 macrophages and CD11c+ dendritic cells varied markedly between tumor entities and individual tumors. For example, 88 (±90) cells/mm2 were found in tubular breast cancer, 661 (±729) cells/mm2 in colorectal cancer, and 1280 (±1334) to 2325 (±2131) cells/mm2 in squamous cell cancers from various origins. The abundance of T-cell subpopulations, M2 macrophages, and dendritic cells was highly concordant (range r=0.49 to 0.92) across all tumor entities, while the density of M1 macrophages was unrelated (r=0.1, p&amp;lt;0.001). Unsupervised hierarchical clustering across all tumor entities revealed a cluster A of 634 patients from almost all different tumor entities with an exceptionally high density of intraepithelial immune cells, thus a highly inflamed tumor microenvironment that was characterized by the strongest interaction between intraepithelial CD8+ T-cell and CD4+ T-helper cells, M2 macrophages, as well as dendritic cells (DC, p&amp;lt;0.002 each) along with the highest expression level of TIM3, PD-1, CLTA-4 and PD-L1. In contrast, a cluster C of 2245 patients with the lowest intraepithelial immune cell infiltration was characterized by a significantly increased M1 proportion (p&amp;lt;0.001) and an enriched proportion of regulatory T-cells (p&amp;lt;0.001). Across all analyzed tumor entities, the intraepithelial highly inflamed cluster A was significantly linked to low pT (p&amp;lt;0.001). Conclusion: The data from this study provide a comprehensive characterization of intraepithelial immune cells across 46 different human carcinomas and identify an inflamed phenotype defined by strong interactions of intraepithelial CD8+ cytotoxic T-cells, CD4+ T-cells, dendritic cells, and M2 macrophages along with highest levels of TIM3, PD-1, PD-L1, and CTLA-4 expression that is linked to a favorable tumor phenotype. Citation Format: Zhihao Huang, Tim Mandelkow, Jan H. Müller, Andreas H. Marx, Till Krech, Guido Sauter, Julia Ebner, Maximilian Lennartz, Ronald Simon, Martina Kluth, Claudia Hube-Magg, Sarah Minner, Elena Bady, Niclas C. Blessin. Prevalence, immune checkpoint expression and spatial interplay of intraepithelial lymphocytes, macrophages, and dendritic cells in 4740 human carcinomas [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 169.

Abstract 4893: Role of MGMT expression in the genomic landscape and immunogenicity in human colorectal carcinomas

Abstract Introduction: Colorectal cancer (CRC) is second most common cause of cancer-related mortality in the USA and most patients with advanced tumors lack effective therapeutic options. Epigenetic silencing resulting in reduced expression of O6-methylguanine-DNA methyltransferase (MGMT) has been described in diverse tumor types including CRC and it is linked with reduced DNA repair capability and increased sensitivity to alkylating agents such as temozolomide. However, the potential role and clinical significance of MGMT overexpression in cancer cells has not been studied. Methods: We used spatially resolved multiplex quantitative immunofluorescence (mQIF) analysis to concurrently measure the levels of MGMT protein, γH2AX and CD8+ tumor infiltrating lymphocytes (TILs) in a cohort of 111 CRCs and paired non-tumor colorectal mucosa from the same patient represented in tissue microarray format. To assess the genomic and immunologic context of MGMT expression, we studied the methylome, mutation profiling and mRNA expression of 526 CRCs from TCGA. The immunologic landscape of tumors was studied using GSEA and multiple transcriptomic-based tumor immune infiltration scores such as TIMER, CIBERSORT, etc. Finally, the genomic alterations and immunogenicity of SW620 human CRC cells (with baseline MGMT hypermethylation) with or without MGMT transfection were studied using in vitro co-culture preparations coupled to ultra-deep DNAseq and flow cytometry analysis. Results: On mQIF analysis, cancer-cell MGMT protein upregulation was identified in 73.9% of CRCs and was associated with reduced levels of γH2Ax in malignant cells and lower CD8+ TILs. 26.1% of cases showed MGMT protein downregulation. The genomic analysis of the TCGA cohort revealed that the mean nonsynonymous mutational load was significantly lower in MGMT-high than low tumors with marked differences in the type of variants and frequency of oncogenic mutations. The transcriptomic analysis revealed that MGMT overexpressing tumors showed lower immune infiltration than the MGMT-low group and reduced representation of immune associated signatures including interferon gamma response and TNF-alpha signaling. In contrast, DNA repair, TP53 pathways, were enriched. The exogenous expression of MGMT in SW620 cells reduced the number of nonsynonymous mutations by 15.6% (141 vs 119 mean mutations) and was also associated with low T-cell activation (CD69+/CD8+ T-cells) and cancer-cell elimination on allogenic co-cultures with human PBMCs. Conclusion: MGMT protein upregulation is common in human CRCs and is associated with reduced DNA damage response, distinct genomic features, and adaptive immune evasion. To our knowledge, this study is the first to report the biological and clinical characteristics of CRCs with MGMT overexpression that could support diagnostic and therapeutic developments. Citation Format: Barani Kumar Rajendran, Janie Zhang, Shruti Desai, Joanna Gibson, Jassim DiPalermo, Patricia LoRusso, Yong Kong, Hongyu Zhao, Michael Cecchini, Kurt Alex Schalper. Role of MGMT expression in the genomic landscape and immunogenicity in human colorectal carcinomas [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 4893.

Abstract 5220: Reduced expression of Glutathione peroxidase 2 (GPX2) is an independent predictor of poor prognosis in muscle-invasive urothelial carcinoma of the bladder

Abstract Background: The Glutathione peroxidase 2 (GPX2) is a selenium-dependent glutathione peroxidase with a pivotal role in removing potentially harming reactive oxygen species (ROS) from cells by catalyzing the reduction process of hydrogen peroxide to water. GPX2 is strongly expressed in normal urothelium but can be reduced in urothelial cancer. The aim of the study was to evaluate the potential clinical significance of GPX2 expression in urothelial bladder cancer. Design: GPX2 was analyzed by immunohistochemistry (IHC) in more than 2,500 urothelial bladder carcinomas in a tissue microarray format. Follow-up data were available for more than 600 patients with muscle-invasive disease. Results: GPX2 staining occurred in 67.5% of urothelial carcinomas including 11.4% with weak, 11.9% with moderate, and 44.2% with strong staining. While GPX2 staining was always strong in normal urothelium, it decreased markedly during grade and stage progression. Within pTa tumors, GPX2 positivity continuously decreased from pTaG2 low grade (99.4% positive) to pTa G2 high grade (97.2% positive) and to pTa G3 (90.5%; p=0.0013) while there was a marked further drop of GPX2 positivity from pTaG3 to muscle-invasive cancers (56.6%; p&amp;lt;0.0001 for pT2-4 vs. pTa G3). Within pT2-4 carcinomas, low or absent GPX2 staining was significantly linked to poor overall survival (p=0.0140), V1 (p&amp;lt;0.0001), L1 (p=0.0014), and high grade (p=0.0091), but statistically unrelated to pT and pN. In a multivariate analysis, the prognostic impact of reduced GPX2 expression (p=0.0081) was independent of pT (p&amp;lt;0.0001) and pN (p&amp;lt;0.0001) in pT2-4 tumors. GPX2 expression loss was inversely related to the expression of the luminal subtype markers GATA3 (p&amp;lt;0.0001), uroplakin 1b (p&amp;lt;0.0001) and cytokeratin 20 (p&amp;lt;0.0001) in pT2-4 carcinomas. Conclusion: GPX2 expression loss is a common event during bladder cancer progression which is strongly associated with poor prognosis in patients with pT2-4 urothelial carcinomas. GPX2 expression measurement - optimally together with other markers - could be useful for clinical risk assessment of bladder cancer patients. Citation Format: Henning Plage, Sebastian Hofbauer, Kira Furlano, Sarah Weinberger, Antonia Franz, Annika Fendler, Joachim Weischenfeldt, Florian Roßner, Simon Schallenberg, Sefer Elezkurtaj, Martina Kluth, Andreas H. Marx, Henrik Samtleben, Margit Fisch, Marcin Slojewski, Krystian Kaczmarek, Thorsten Ecke, Stefan Koch, Nico Adamini, Ronald Simon, Guido Sauter, Henrik Zecha, Tobias Klatte, Sarah Minner, David Horst, Thorsten Schlomm, Michael Rink, Maximilian Lennartz. Reduced expression of Glutathione peroxidase 2 (GPX2) is an independent predictor of poor prognosis in muscle-invasive urothelial carcinoma of the bladder [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 5220.

Abstract 6732: Immunomodulatory and anti-tumor effect of a CCR2-targeted STING agonist iADC in human lung cancer

Abstract Introduction: Antibody drug conjugates (ADCs) targeting cancer-cell antigens can improve therapeutic index and show prominent clinical impact. Limited studies have used ADCs to target antigens present in non-malignant cells in the tumor microenvironment or to deliver immunomodulatory agents. We developed an immune-cell directed antibody drug conjugate (iADC) TAK-500 that selectively activates STING in C-C chemokine receptor type 2 (CCR2) expressing cells to achieve enhanced efficacy over non-targeted STING agonists. Here, we spatially mapped CCR2 protein in human NSCLC and studied the immunomodulatory role and anti-tumor effect of the novel iADC TAK-500 on human lung cancer tumor explants ex vivo. Methods: Using multiplexed quantitative immunofluorescence (mQIF) panels we measured the levels of CCR2 protein, myeloid cell populations and tumor infiltrating lymphocyte (TIL) subsets in 411 primary NSCLC carcinomas from treatment-naïve patients in 2 independent cohorts and determined their clinical significance. In addition, we longitudinally studied CCR2 levels, myeloid cells (DAPI/CCR2/CD68/CD11b), TILs (DAPI/CK/CD4/CD8/CD20), T-cell functional markers (DAPI/CK/CD3/Ki-67/GZMB [Granzyme B]) and cancer-cell death/proliferation markers (DAPI/CK/TFR1/Ki-67/CC3 [Cleaved Caspase 3]) in 314 primary cultured tissue fragments from paired tumor and non-tumor specimens resected from 11 lung cancer patients at Yale New Haven Hospital between 2021-2023 (8 adenocarcinomas, 2 small cell carcinomas, and 1 squamous cell carcinoma). Each biopsy was divided into 4-mm2 fragments, cultured in extracellular matrix for 5 days with or without TAK-500 treatment. Samples were processed into FFPE tissue and stained with mQIF panels using a tissue microarray format. Results: CCR2 protein was detected in 386 of 411 (94%) NSCLCs from 2 independent cohorts predominantly localized in CD11b+ intratumor myeloid cells and CD68+ tumor-associated macrophages (TAMs). Elevated CCR2 was associated with adenocarcinoma histology, increased PD-L1, activating KRAS mutations and longer survival. Treatment with TAK-500 for 5 days reduced CCR2 levels in myeloid cells and CD68+ TAMs, without significant changes in TIL or T-cell GZMB/Ki-67 levels. TAK-500 also significantly reduced tumor proliferation (Ki-67 expression) and increased tumor cell apoptosis (CC3 levels) after 5 days of treatment. Notably, these TAK-500-induced changes were observed only in tumor specimens with high baseline CCR2 levels above the median in retrospective NSCLC cohorts. No significant effect was observed in the paired non-tumor fragments. Conclusion: Our results reveal prominent myeloid CCR2 expression in a subset of human NSCLCs with distinct clinicopathologic/molecular characteristics. Using a novel lung cancer explant ex vivo system, we demonstrate a CCR2-dependent immunomodulatory and anti-tumor effect of TAK-500 iADC. Citation Format: Angelo Porciuncula, Vicky A. Appleman, Alex Parent, Jeff Raizer, Richard C. Gregory, Neil Lineberry, Adnan O. Abu-Yousif, Kurt A. Schalper. Immunomodulatory and anti-tumor effect of a CCR2-targeted STING agonist iADC in human lung 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 6732.

Abstract 5206: High level STING expression in tumor and inflammatory cells is linked to microsatellite instability and favorable tumor parameters in a cohort of 1,900 colorectal cancer patients

Abstract Background: The stimulator of interferon genes (STING) is a transmembrane protein expressed on a variety of cell types including epithelial, inflammatory (lymphocytes and macrophages), and endothelial cells. STING expression has been described at variable levels in various tumor types where it might enhance anti-tumoral effects of the immune system and impact tumor angiogenesis. STING activating targeted therapies are currently evaluated in preclinical studies. However, the clinical significance of STING expression in tumor cells as compared to tumor-associated inflammatory cells is not fully resolved. Methods: To evaluate the potential clinical significance of STING expression in different cell types of colorectal cancer (CRC) tissue (tumor cells, lymphocytes, macrophages and endothelial cells), more than 1,900 patients were analyzed by multiplex fluorescence immunohistochemistry (CKpan, STING, CD45, CD68 and CD31) in a tissue microarray format (TMA) in combination with a deep-learning based algorithm for automated cell detection. Results: STING expression on colorectal cancer cells varied markedly. Of 1,905 evaluable cancers, 601 (31.5%) showed a strong expression in virtually all tumor cells and 428 (22.5%) lacked STING staining while 478 (25.1%) showed a weak, and 398 (20.9%) a moderate staining. High STING expression on tumor cells was associated with microsatellite instability (MSI, p&amp;lt;0.0001), low tumor stage (p=0.0013), absence of nodal metastasis (pN0, p=0.0003) and tumor localization in the right colon (p&amp;lt;0.0001). A multivariate analysis revealed that these associations were solely driven by the tight relationship between STING expression in tumor cells and MSI. Accordingly, subgroups of tumors with and without MSI lacked significant associations between STING expression on tumor cells and pT or pN categories. While the total number of lymphocytes and macrophages were related to MSI, low pT, and pN0, there were significant associations between a high percentage of STING positive macrophages and lymphocytes to low pT stage (p&amp;lt;0.0001 each) and absence of nodal metastases for high percentage of STING positive macrophages (p=0.0033). STING was regularly expressed on endothelial cells of small vessels. Although the intensity appeared to be variable, there was no link to tumor phenotype. Conclusion: In summary, the significant link between high STING expression on tumor cells, lymphocytes and macrophages with a favorable tumor phenotype supports the concept of STING representing an enhancer of anti-tumoral effects of the immune system. Citation Format: Elena Bady, Zhihao Huang, Maximilian Lennartz, Claudia Hube-Magg, Julia Ebner, Frank Jacobsen, Stefan Steurer, Christian Bernreuther, Till S. Cauditz, Andreas H. Marx, Till Krech, Eike Burandt, Guido Sauter, Ronald Simon, Sarah Minner, Jan Hendrik Mueller. High level STING expression in tumor and inflammatory cells is linked to microsatellite instability and favorable tumor parameters in a cohort of 1,900 colorectal cancer patients [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 5206.