Microarray Studies Research Articles

Emerging roles of circular RNAs in osteoporosis.

Osteoporosis is one bone disease characterized with skeletal impairment, bone strength reduced and fracture risk enhanced. The regulation processes of bone metabolism are associated with several factors such as mechanical stimulation, epigenetic regulation and hormones. However, the mechanism of osteoporosis remains unsatisfactory. Increasing high‐throughput RNA sequencing and circular RNAs (circRNAs) microarray studies indicated that circRNAs are differentially expressed in osteoporosis. Growing functional studies further pinpointed specific deregulated expressed circRNAs (e.g., circ_28313, circ_0016624, circ_0006393, circ_0076906 and circ_0048211) for their functions involved in bone metabolism, including bone marrow stromal cells (BMSCs) differentiation, proliferation and apoptosis. Moreover, CircRNAs (circ_0002060, Circ_0001275 and Circ_0001445) may be acted as diagnostic biomarkers for osteoporosis. This review discussed recent progresses in the circRNAs expression profiling analyses and their potential functions in regulating BMSCs differentiation, proliferation and apoptosis.

Network-Based Integrated Analysis of Transcriptomic Studies in Dissecting Gene Signatures for LPS-Induced Acute Lung Injury.

–Acute lung injury (ALI) is a type of serious clinical syndrome leading to morbidity and mortality. However, the precise pathogenesis of ALI remains elusive. Here, we implemented an integrative meta-analysis of six GEO microarray studies with 76 samples in the ALI mouse model. A total of 958 differentially expressed genes (DEGs) were identified in LPS relative to normal samples. Then, a network-based meta-analysis was used to mine core DEGs and to unfold the interactions among these genes. We found that Ebi3 was the top upregulated genes in the LPS-induced ALI. GO, KEGG, and GSEA analyses were performed for functional annotation. qRT-PCR revealed augmented expression of six candidate genes (Stat1, Syk, Jak3, Rac2, Ripk1, and Traf6) in the established ALI mouse model with LPS exposure. Taken together, our study investigated comprehensively hub DEGs and their networks for LPS-stimulated ALI, which might afford an additional approach to determine biomarkers and therapeutic targets and explore the molecular pathophysiology toward ALI.SUPPLEMENTARY INFORMATIONThe online version contains supplementary material available at 10.1007/s10753-021-01518-8.

Evaluation of postmortem microarray data in bipolar disorder using traditional data comparison and artificial intelligence reveals novel gene targets

Large-scale microarray studies on post-mortem brain tissues have been utilized to investigate the complex molecular pathology of bipolar disorder. However, a major challenge in characterizing the dysregulation of gene expression in patients with bipolar disorder includes the lack of convergence between different studies, limiting comprehensive understanding from individual results. In this study, we aimed to identify genes that are both validated in published literature and are important classification features of unsupervised machine learning analysis of Stanley Brain Bank microarray database, followed by augmented intelligence method to identify distinct patient molecular subgroups. Through combining traditional literature approaches and machine learning, we identified TBL1XR1, SMARCA2, and CHMP5 to be replicated in 3 of the 4 studies included our analysis. The expression of these genes segregated unique subgroups of patients with bipolar disorder. Our study suggests the involvement of PPARγ pathway regulation in patients with bipolar disorder.

DNA methylation and noncoding RNA in OA: Recent findings and methodological advances

IntroductionOsteoarthritis (OA) is a chronic musculoskeletal disease characterized by progressive loss of joint function. Historically, it has been characterized as a disease caused by mechanical trauma, so-called ‘wear and tear’. Over the past two decades, it has come to be understood as a complex systemic disorder involving gene-environmental interactions. Epigenetic changes have been increasingly implicated. Recent improvements in microarray and next-generation sequencing (NGS) technologies have allowed for ever more complex evaluations of epigenetic aberrations associated with the development and progression of OA. MethodsA systematic review was conducted in the Pubmed database. We curated studies that presented the results of DNA methylation and noncoding RNA research in human OA and OA animal models since 1985. ResultsHerein, we discuss recent findings and methodological advancements in OA epigenetics, including a discussion of DNA methylation, including microarray and NGS studies, and noncoding RNAs. Beyond cartilage, we also highlight studies in subchondral bone and peripheral blood mononuclear cells, which highlight widespread and potentially clinically important alterations in epigenetic patterns seen in OA patients. Finally, we discuss epigenetic editing approaches in the context of OA. ConclusionsAlthough a substantial body of literature has already been published in OA, much is still unknown. Future OA epigenetics studies will no doubt continue to broaden our understanding of underlying pathophysiology and perhaps offer novel diagnostics and/or treatments for human OA.

A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression

Transcriptional profiling of pre- and post-malignant colorectal cancer (CRC) lesions enable temporal monitoring of molecular events underlying neoplastic progression. However, the most widely used transcriptomic dataset for CRC, TCGA-COAD, is devoid of adenoma samples, which increases reliance on an assortment of disparate microarray studies and hinders consensus building. To address this, we developed a microarray meta-dataset comprising 231 healthy, 132 adenoma, and 342 CRC tissue samples from twelve independent studies. Utilizing a stringent analytic framework, select datasets were downloaded from the Gene Expression Omnibus, normalized by frozen robust multiarray averaging and subsequently merged. Batch effects were then identified and removed by empirical Bayes estimation (ComBat). Finally, the meta-dataset was filtered for low variant probes, enabling downstream differential expression as well as quantitative and functional validation through cross-platform correlation and enrichment analyses, respectively. Overall, our meta-dataset provides a robust tool for investigating colorectal adenoma formation and malignant transformation at the transcriptional level with a pipeline that is modular and readily adaptable for similar analyses in other cancer types.

Bcl-2-associated transcription factor 1 Ser290 phosphorylation mediates DNA damage response and regulates radiosensitivity in gastric cancer

BackgroundDNA damage response plays critical roles in tumor pathogenesis and radiotherapy resistance. Protein phosphorylation is a critical mechanism in regulation of DNA damage response; however, the key mediators for radiosensitivity in gastric cancer still needs further exploration.MethodsA quick label-free phosphoproteomics using high-resolution mass spectrometry and an open search approach was applied to paired tumor and adjacent tissues from five patients with gastric cancer. The dysregulated phosphoproteins were identified and their associated-pathways analyzed using Gene Set Enrichment Analysis (GSEA). The mostly regulated phosphoproteins and their potential functions were validated by the specific antibodies against the phosphorylation sites. Specific protein phosphorylation was further analyzed by functional and clinical approaches.Results832 gastric cancer-associated unique phosphorylated sites were identified, among which 25 were up- and 52 down-regulated. Markedly, the dysregulated phosphoproteins were primarily enriched in DNA-damage-response-associated pathways. Particularly, the phosphorylation of Bcl-2-associated transcription factor 1 (BCLAF1) at Ser290 was significantly upregulated in tumor. The upregulation of BCLAF1 Ser290 phosphorylation (pBCLAF1 (Ser290)) in tumor was confirmed by tissue microarray studies and further indicated in association with poor prognosis of gastric cancer patients. Eliminating the phosphorylation of BCLAF1 at Ser290 suppressed gastric cancer (GC) cell proliferation. Upregulation of pBCLAF1 (Ser290) was found in association with irradiation-induced γ-H2AX expression in the nucleus, leading to an increased DNA damage repair response, and a marked inhibition of irradiation-induced cancer cell apoptosis.ConclusionsThe phosphorylation of BCLAF1 at Ser290 is involved in the regulation of DNA damage response, indicating an important target for the resistance of radiotherapy.

Pattern of placental alkaline phosphatase (PLAP) expression in human tumors: a tissue microarray study on 12,381 tumors.

Placental alkaline phosphatase (PLAP) is commonly expressed at high levels in testicular germ cell tumors. PLAP immunohistochemistry (IHC) is thus often used to confirm this diagnosis, especially in cases of putative metastasis. However, other tumors can also express PLAP. To comprehensively determine PLAP expression in normal and tumor tissue, a tissue microarray containing 16,166 samples from 131 different tumor types and subtypes as well as 608 samples from 76 different normal tissue types was analyzed by IHC. Moderate to strong PLAP positivity was found in 27 (21%) of 131 different tumor types including seminoma (96%), embryonal carcinoma (85%), and yolk sac tumors of the testis (56%); endometrioid carcinoma of the endometrium (28%) and the ovary (20%); gastric adenocarcinoma (22%); serous carcinoma (not otherwise specified) of the ovary (17%) and the uterus (11%); adenocarcinoma of the ampulla of Vater (15%); carcinosarcoma of the ovary (11%) and the uterus (8%); esophageal adenocarcinoma (10%); invasive urothelial carcinoma (4%); cholangiocarcinoma (2%); and adenocarcinoma of the lung (1%). Low‐level PLAP immunostaining, often involving only a small fraction of tumor cells, was seen in 21 additional tumor entities. The clinical significance of PLAP expression may vary between tumor types as high PLAP expression was linked to advanced pathological tumor stage (p = 0.0086), nodal metastasis (p = 0.0085), and lymphatic (p = 0.0007) and blood vessel invasion (p = 0.0222) in colorectal cancer, but to low pathological tumor stage in endometrial cancer (p = 0.0043). In conclusion, our data identify several tumor entities that can show PLAP expression at comparable levels to testicular germ cell tumors. These tumor entities need to be considered in cases of PLAP‐positive metastasis. Low‐level PLAP expression can be found in various other tumor entities and should generally not be viewed as a strong argument for germ cell neoplasia.

Copresence of High-Risk Human Papillomaviruses and Epstein-Barr Virus in Colorectal Cancer: A Tissue Microarray and Molecular Study from Lebanon.

Colorectal cancer (CRC) is the third most common cause of cancer-related deaths worldwide. Human papillomaviruses (HPVs) and Epstein–Barr virus (EBV) have been reported to be present in different types of human cancers, including CRCs, where they can play a key role in the onset and/or progression of these cancers. Thus, we herein explored the prevalence of high-risk HPVs and EBV in a cohort of 94 CRC tissue samples and 13 colorectal normal tissues from the Lebanese population using polymerase chain reaction, immunohistochemistry, and tissue microarray methodologies. We found that high-risk HPVs are present in 64%, while EBV is present in 29% of our CRC samples. Additionally, our data showed that high-risk HPV types (16, 18, 35, 58, 51, 45, 52, 31, and 33) are the most frequent in CRC in the Lebanese cohort, respectively. Our data point out that HPVs and EBV are copresent in 28% of the samples. Thus, this study clearly suggests that high-risk HPVs and EBV are present/copresent in CRCs, where they could play an important role in colorectal carcinogenesis. Nevertheless, further investigations using a larger cohort are needed to elucidate the possible cooperation between these oncoviruses in the development of CRC.

Anti-inflammatory and Pro-apoptotic Effects of 18beta-Glycyrrhetinic Acid In Vitro and In Vivo Models of Rheumatoid Arthritis.

18β-Glycyrrhetinic acid (18β-GA), an active component from Glycyrrhiza glabra L. root (licorice), has been demonstrated to be able to protect against inflammatory response and reduce methotrexate (MTX)-derived toxicity. This study was therefore designed to test the therapeutic possibility of 18β-GA on rheumatoid arthritis (RA) and to explore the underlying mechanism. LPS or TNF-α-induced inflammatory cell models and collagen-induced arthritis (CIA) animal models were applied in this study. Real-time quantitative PCR (RT-qPCR) was used to measure the mRNA levels of various cytokines and FOXO family members. The protein levels of molecules in the MAPK/NF-κB signaling pathway were analyzed using western blot. The cell proliferation assay and colony-forming assay were used to test the influence of 18β-GA on cell viability. The cell apoptosis assay and cell cycle assay were performed to detect the effect of 18β-GA on cell proliferative capacity by using flow cytometry. Hematoxylin and eosin (H&E) staining was performed to evaluate pathological changes after drug administration. The enzyme-linked immunosorbent assay (ELISA) was carried out for the detection of cytokines in serum. In vitro, we found that 18β-GA decreased the mRNA levels of IL-1β, IL-6, and COX-2 by inhibiting the MAPK/NF-κB signaling pathway in MH7A and RAW264.7 cell lines. Moreover, 18β-GA was able to suppress cell viability, trigger cell apoptosis, and G1 phase cell cycle arrest in our in vitro studies. 18β-GA dramatically enhanced the mRNA level of FOXO3 in both TNF-α- and LPS-induced inflammation models in vitro. Interestingly, after analyzing GEO datasets, we found that the FOXO3 gene was significantly decreased in the RA synovial tissue as compared to healthy donors in multiple microarray studies. In vivo, 18β-GA exhibited a promising therapeutic effect in a collagen-induced arthritis mouse model by alleviating joint pathological changes and declining serum levels of TNF-α, IL-1β, and IL-6. Finally, we observed that 18β-GA administration could mitigate liver damage caused by collagen or MTX. Collectively, the current study demonstrates for the first time that 18β-GA can inhibit inflammation and proliferation of synovial cells, and the underlying mechanism may be associated with its inhibition of MAPK/NF-κB signaling and promotion of FOXO3 signaling. Therefore, 18β-GA is expected to be a new drug candidate for RA therapy.

A Unified Computational Framework to Compare Direct and Sequential False Discovery Rate Algorithms for Exploratory DNA Microarray Studies

The problem of detecting differential gene expression with mi croarray data has led to further innovative approaches to controlling false positives in multiple testing. False discovery rate (FDR) has been widely used as a measure of error in this multiple testing context. Direct estima tion of FDR was recently proposed by Storey (2002, Journal of the Royal Statistical Society, Series B 64, 479-498) as a substantially more powerful al ternative to the traditional sequential FDR controlling procedure, pioneered by Benjamini and Hochberg (1995, Journal of the Royal Statistical Society, Series B 57, 289-300). Direct estimation to FDR requires fixing a rejection region of interest and then conservatively estimating the associated FDR. On the other hand, sequential FDR procedure requires fixing a FDR control level and then estimating the rejection region. Thus, sequential and direct approaches to FDR control appear very different. In this paper, we intro duce a unified computational framework for sequential FDR methods and propose a class of more powerful sequential FDR algorithms, that link the direct and sequential approaches. Under the proposed unified compuational framework, both approaches simply approximate the least conservative (op timal) sequential FDR procedure. We illustrate the FDR algorithms and concepts with some numerical studies (simulations) and with two real ex ploratory DNA microarray studies, one on the detection of molecular signa tures in BRCA-mutation breast cancer patients and another on the detection of genetic signatures during colon cancer initiation and progression in the rat.

Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Ulcerative Colitis

Background: Ulcerative colitis (UC) is a chronic, complicated, inflammatory disease with an increasing incidence and prevalence worldwide. However, the intrinsic molecular mechanisms underlying the pathogenesis of UC have not yet been fully elucidated.Methods: All UC datasets published in the GEO database were analyzed and summarized. Subsequently, the robust rank aggregation (RRA) method was used to identify differentially expressed genes (DEGs) between UC patients and controls. Gene functional annotation and PPI network analysis were performed to illustrate the potential functions of the DEGs. Some important functional modules from the protein-protein interaction (PPI) network were identified by molecular complex detection (MCODE), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG), and analyses were performed. The results of CytoHubba, a plug for integrated algorithm for biomolecular interaction networks combined with RRA analysis, were used to identify the hub genes. Finally, a mouse model of UC was established by dextran sulfate sodium salt (DSS) solution to verify the expression of hub genes.Results: A total of 6 datasets met the inclusion criteria (GSE38713, GSE59071, GSE73661, GSE75214, GSE87466, GSE92415). The RRA integrated analysis revealed 208 significant DEGs (132 upregulated genes and 76 downregulated genes). After constructing the PPI network by MCODE plug, modules with the top three scores were listed. The CytoHubba app and RRA identified six hub genes: LCN2, CXCL1, MMP3, IDO1, MMP1, and S100A8. We found through enrichment analysis that these functional modules and hub genes were mainly related to cytokine secretion, immune response, and cancer progression. With the mouse model, we found that the expression of all six hub genes in the UC group was higher than that in the control group (P < 0.05).Conclusion: The hub genes analyzed by the RRA method are highly reliable. These findings improve the understanding of the molecular mechanisms in UC pathogenesis.

Immunoexpression of SDHB, FH, and CK20 among eosinophilic renal tumors: A tissue microarray study

BackgroundDifferential diagnosis can be a challenge for eosinophilic subtypes of renal cell tumors due to their overlapping histomorphological and immunohistochemical features. We aimed to investigate the frequency of rare variants of renal cell carcinomas (RCCs) such as succinate dehydrogenase-deficient RCC (SDDRCC), hereditary leiomyomatosis and RCC (HLRCC)-associated RCC, and eosinophilic, solid, and cystic RCC (ESCRCC) in our population. Materials and methodsRenal tumors which could be considered in the eosinophilic tumor category were included: 91 conventional clear cell RCCs with eosinophilic cytoplasm, 72 papillary RCCs, 74 chromophobe RCCs, 88 oncocytomas, and 37 other rare subtypes. Using the tissue microarray method, succinate dehydrogenase B (SDHB), fumarate hydratase (FH), and cytokeratin 20 (CK20) antibodies were performed by immunohistochemistry. Immunohistochemistry was repeated on whole block sections for selected cases. The utility of these antibodies in the differential diagnosis was also investigated. ResultsLoss of SDHB expression was detected in three tumors, two of which showed typical morphology for SDDRCC. In additional two tumors, SDHB showed weak cytoplasmic expression without a mitochondrial pattern (possible-SDHB deficient). None of the tumors showed loss of FH expression. Heterogeneous reactions were observed with SDHB and FH antibodies. Only one ESCRCC was detected with diffuse CK20 positivity. ConclusionSDDRCCs, HLRCC-associated RCCs, and ESCRCCs are very rare tumors depending on the population. Possible weak staining and focal loss of SDHB and FH expression should be kept in mind and genetic testing must be included for equivocal results.

Abstract 2560: Plasticity-related signaling pathways in the medial prefrontal cortex and hippocampus as potential targets of the antidepressant vortioxetine in reversing cognitive impairments after androgen deprivation therapy for prostate cancer

Abstract Androgen deprivation therapy (ADT) is a frontline treatment for prostate cancer but induces profound cognitive impairment in more than half of patients. This significantly reduces quality of life for cancer survivors and their families. Deficits occur in cognitive domains associated with function of the hippocampus (Hipp) and medial prefrontal cortex (mPFC) and increase in severity with duration of treatment. Therefore, it may be possible to slow or reverse the impairment. In preclinical studies, we reported that vortioxetine, a novel multi-modal antidepressant that has been shown to improve cognitive impairment in depressed patients, may reverse the ADT-induced impairment. Our lab established a rodent model of ADT in which surgically castrated rats display deficits in cognitive flexibility and visuospatial recognition, measures of prefrontal executive function and hippocampal spatial learning, respectively. We also found that castration reduces response of the mPFC to activation of the afferent pathway from the vHipp in anesthetized animals. Chronic dietary vortioxetine (28mg/kg/day) normalized response in this pathway and reversed the cognitive impairments associated with both the mPFC and Hipp. In a microarray study (Agilent Technologies, Inc.) of tissue collected from the mPFC, dorsal-, and ventral-Hipp, we found that castration altered over 1,000 genes in each of these regions (adjusted p &amp;lt;0.05). Vortioxetine did not have a significant main effect on individual genes, but pathway analysis revealed significant changes in processes involved in synaptic plasticity, such as synapse formation, axonogenesis, and MAPK signaling. In the present study, qPCR and western blot analyses were used to investigate potential ADT- and vortioxetine-induced changes in candidate factors. Factors were identified in the top-hit pathways from the vortioxetine x castration microarray analysis and confirmed by qPCR. These included plasticity-related proteins such as Arc, Akt, CREB, mGlur1, and PSD95, among others. Changes in expression and phosphorylation were further determined using western blots. Early results indicate that vortioxetine selectively reversed the reduced expression induced by castration for some, but not all, of these proteins, including CREB and mGlur1 (p&amp;lt;0.05). Experiments are underway to identify potential alterations in protein phosphorylation, as changes in activation rather than expression may also be important to the beneficial effects of vortioxetine. These results suggest that vortioxetine may reverse deficits in executive function and visuospatial recognition after ADT by modulating structural and functional plasticity in mPFC and Hipp. Citation Format: Alexandra M. Vaiana, Roman Fernandez, Jonathan Gelfond, Teresa L. Johnson-Pais, Robin Leach, Chethan Ramamurthy, Ian Thompson, David A. Morilak. Plasticity-related signaling pathways in the medial prefrontal cortex and hippocampus as potential targets of the antidepressant vortioxetine in reversing cognitive impairments after androgen deprivation therapy for prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2560.

Abstract 2891: Protein phosphatase 5 regulation of cell motility

Abstract Metastasis has been considered as one of the cancer hallmarks. Approximately 90% of cancer-related death is due to cancer metastasis. Tumor cell migration is a prerequisite for cancer metastasis. Protein phosphatase 5 (PP5) is a serine/threonine protein phosphatase that belongs to the phosphoprotein phosphatase (PPP) family including PP1 and PP2A. It is well known that PP5 regulates apoptosis, proliferation, and stress response. However, the role of PP5 in the regulation of cell motility is only beginning to be recognized, and the mechanism of PP5 regulation of cell motility is largely unknown. In this study, our tissue microarray (TMA) studies showed the expression of PP5 increased with the stages of prostate cancer, which is consistent with the previous findings that there is a positive correlation between PP5 overexpression and breast cancer metastases. Furthermore, by the single-cell motility assay, we found that overexpression of PP5 increased the motility of various tumor cells, whereas knockdown of PP5 decreased the cell motility, suggesting that PP5 positively regulates cell motility. As focal adhesion kinase (FAK) is a key regulator of cell motility, and a report has shown that PP5 forms a complex with ASK1, FAK, CXCR4 in wounded alveolar epithelial cancer cells, we examined whether PP5 activates FAK. The Western blotting results showed that overexpression of PP5 did not obviously affect the phosphorylation of FAK. The results suggest that PP5 regulates cell motility through a new mechanism. Further research is on the way to identify how PP5 positively regulates cell motility. (Supported by the Feist-Weiller Cancer Center, LSU Health Sciences Center, Shreveport, LA, USA.) Citation Format: n Li, Shile Huang. Protein phosphatase 5 regulation of cell motility [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2891.

Abstract 2775: PD-L1 expression in human tumors: a tissue microarray study on 5,561 tissue samples and 87 tumor types

Abstract The programmed death protein 1 (PD-1) and his ligand PD-L1 are frequently expressed in human cancers and immune checkpoint inhibitor therapies targeting the PD1/PD-L1 pathway are increasingly employed in a growing number of tumor types. However, a unanimous picture on PD-L1 expression in cancer cells and immune cells in various cancer types are so far lacking. In this study we analyzed PD-L1 expression in 5,561 tumor samples by immunohistochemistry in a highly standardized way to define the relative importance of PD-L1 expression and its relationship with tumor infiltrating CD8 positive lymphocytes across 87 human tumor types and subtypes. At a cut-off level of 10% positive tumor cells, PD-L1 positivity was seen in 62 of 87 (71%) tumor types. More than 50% PD-L1 positive cases were found in 7 (8%) tumor types, including thymoma (100%), Hodgkin lymphoma (93%), anaplastic thyroid carcinoma (67%), as well as squamous cell carcinomas of the penis (67%), cervix (65%), oral cavity (61%), and pharynx (50%). PD-L1 immunostaining in tumor cells was absent in 25 (29%) tumor types, including non-Hodgkin lymphomas, seminoma, endometrial malignant mixed Müllerian tumors, and mucinous carcinoma of the ovary. In immune cells, PD-L1 positivity was detectable in 79 (91%) tumor types, with the highest positivity rates in tumors of haemotopoetic and lymphoid tissues (75% to 100%), seminoma (85%), Warthin tumors of the parotid glands (83%), and Merkel cell carcinoma (82%). Immune cell PD-L1 positivity was absent in only 8 (9%) tumor types (e.g. chondosarcoma, pleomorphic adenoma of the salivary gland, and chromophobe renal cell carcinoma). PD-L1 positivity in tumor cells was significantly correlated with the number of intratumoral CD8 positive lymphocytes across all tumor types as well as in the separate analyses of several individual tumor types, such as basal cell carcinoma (p&amp;lt;0.0001), chondrosarcoma (p=0.0013), gastrointestinal stromal tumors (p=0.0028), and adrenal cortical carcinoma (p=0.0001). In summary, these data provide a ranking list of tumors according to their PD-L1 positivity rate. The strong association with the frequency of CD8 positive lymphocytes supports the concept, that PD-L1 expression in tumor cells represent a mechanism of highly immunogenic tumors to enable immune evasion. Citation Format: Katharina Möller, Ronald Simon, Martina Kluth, Guido Sauter, Claudia Hube-Magg, Christoph Fraune, Niclas Blessin, Maximilian Lennartz, Doris Höflmayer, Sarah Minner, Eike Burandt, Sören Weidemann, Andreas Luebke. PD-L1 expression in human tumors: a tissue microarray study on 5,561 tissue samples and 87 tumor types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2775.

Abstract 2833: Mesothelin expression in human tumor types: a tissue microarray study on more than 13,000 tumor samples

Abstract Mesothelin is a glycoprotein which is normally expressed in only few non-vital tissues. Due to its membranous location and expression in various cancer types, it represents an attractive molecule for target-specific cancer therapies. To examine, what tumor types might benefit most from anti-mesothelin therapies, a set of tissue microarrays containing samples from 13,298 tumors from 122 different tumor types and 608 samples from 76 different normal tissue categories were analyzed for mesothelin expression by immunohistochemistry. Sixty-six (54%) of these 122 tumor types and subtypes showed at least occasional weak staining, including 49 tumor types with at least one strongly positive sample. Tumor types with highest prevalence of mesothelin positivity included ovarian cancers (serous 97%, clear cell 83%, endometroid 77%, mucinous 71%, Müllerian mixed tumors 65%), pancreatic adenocarcinoma (81%), endometrial cancers (clear cell 71%, serous 57%, Müllerian mixed tumors 50%, endometroid 45%), malignant mesothelioma (71%), and lung adenocarcinoma (55%). Mesothelin positivity was particularly rare or absent in urothelial carcinoma (10% positive out of 925), breast cancer (6% of 1,285), renal cell cancer (7% of 1,049), adenocarcinoma of the prostate (0 of 498), thyroid carcinomas (0 of 238), and soft tissue tumors (0 of 920). Significant associations with patient outcome or parameters of malignancy were not observed in 1,072 breast cancers of no special type, 925 urinary bladder cancers, 386 serous ovarian cancers, 266 lung cancers or 373 stomach cancers. Taken together, our systematic and highly standardized analysis identified numerous clinically important cancer types with frequent and high level mesothelin expression. These tumor types might benefit most from future anti-mesothelin therapies. The prognostic relevance of mesothelin appears to be low in the analyzed tumor types. Citation Format: Sören Weidemann, Natalia Gorbokon, Doris Höflmayer, Katharina Möller, David Dum, Andreas Luebke, Martina Kluth, Claudia Hube-Magg, Niclas Blessin, Guido Sauter, Jakob Izbicki, Ronald Simon, Stefan Steurer, Andreas Marx, Till Krech, Kristina Jansen, Maximilian Lennartz. Mesothelin expression in human tumor types: a tissue microarray study on more than 13,000 tumor samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2833.

Lack of GD3 synthase (St8sia1) attenuates malignant properties of gliomas in genetically engineered mouse model.

High expression of gangliosides GD3 and GD2 is observed in human gliomas. The functions of GD3 and GD2 in malignant properties have been reported in glioma cells in vitro, but those functions have not yet been investigated in vivo. In this study, we showed that deficiency of GD3 synthase (GD3S, St8sia1) attenuated glioma progression and clinical and pathological features in a platelet‐derived growth factor B‐driven murine glioma model. Lack of GD3S resulted in the prolonged lifespan of glioma‐bearing mice and low‐grade pathology in generated gliomas. Correspondingly, they showed reduced phosphorylation levels of Akt, Erks, and Src family kinases in glioma tissues. A DNA microarray study revealed marked alteration in the expression of various genes, particularly in MMP family genes, in GD3S‐deficient gliomas. Re‐expression of GD3S restored expression of MMP9 in primary‐cultured glioma cells. We also identified a transcription factor, Ap2α, expressed in parallel with GD3S expression, and showed that Ap2α was critical for the induction of MMP9 by transfection of its cDNA and luciferase reporter genes, and a ChIP assay. These findings suggest that GD3S enhances the progression of gliomas by enhancement of the Ap2α‐MMP9 axis. This is the first report to describe the tumor‐enhancing functions of GD3S in vivo.

A reversible microarray immobilization strategy based on thiol-quinone reaction

Microarray technology has been widely applied in biomedical research. The key to microarray study is to develop efficient immobilization method. In this study, we designed a new reversible microarray immobilization method based on thiol-quinone reaction. A quinone-functionalized slide was fabricated through H2O2 treatment of dopamine-coated slides. Various thiol-containing molecules can be anchored onto the quinone-functionalized slides via thioether linker, which could be cleaved under H2O2 treatment to regenerate quinone groups on the surface. The highly versatile approach can be widely used for immobilization of various thiol-containing molecules.

Comprehensive transcriptome analysis of erythroid differentiation potential of olive leaf in haematopoietic stem cells.

Anaemia is one of the leading causes of disability in young adults and is associated with increased morbidity and mortality in elderly. With a global target to reduce the disease burden of anaemia, recent researches focus on novel compounds with the ability to induce erythropoiesis and regulate iron homeostasis. We aimed to explore the biological events and potential polypharmacological effects of water‐extracted olive leaf (WOL) on human bone marrow–derived haematopoietic stem cells (hHSCs) using a comprehensive gene expression analysis. HPLC analysis identifies six bioactive polyphenols in the WOL. Treatment with WOL for 12 days regulated gene expressions related to erythroid differentiation, oxygen homeostasis, iron homeostasis, haem metabolism and Hb biosynthesis in hHSCs. Functional clustering analysis reveals several major functions of WOL such as ribosomal biogenesis and mitochondrial translation machinery, glycolytic process, ATP biosynthesis and immune response. Additionally, the colonies of both primitive and mature erythroid progenitors, CFU‐E and BFU‐E, were significantly increased in WOL‐treated hHSCs. The expressions of erythroid markers, CD47, glycophorin A (GYPA), and transferrin receptor (TFRC) and adult Hb subunits‐HBA and HBB were also confirmed in immunofluorescent staining and flow cytometer analysis in WOL‐treated hHSCs. It is well known that induction of lineage‐specific differentiation, as well as the maturation of early haematopoietic precursors into fully mature erythrocytes, involves multiple simultaneous biological events and complex signalling networks. In this regard, our genome‐wide transcriptome profiling with microarray study on WOL‐treated hHSCs provides general insights into the multitarget prophylactic and/or therapeutic potential of WOL in anaemia and other haematological disorders.

Transcriptome Analysis of the Lymph Node Microenvironment in Chronic Lymphocytic Leukemia

Gene expression profiling with microarrays and in vivo deuterated water labeling in patients with chronic lymphocytic leukemia (CLL) have shown that tumor activation and proliferation predominantly occur in the lymph node (LN). It is thought that CLL cells actively shape the surrounding microenvironment to support tumor survival and growth.To further dissect the biology of CLL and its interactions with the tumor microenvironment, we performed total RNA sequencing of purified tumor cells from paired peripheral blood (PB) and LN in 29 patients. Samples separated by anatomic compartment in principal component analysis. A total of 883 protein-coding genes were differentially expressed (DE) between PB and LN (fold-change >2, Q <0.1). Among these DE genes, 82% were upregulated and 18% were downregulated in LN compared to PB. Gene Set Enrichment Analysis using experimentally-derived lymphoid gene signatures (https://lymphochip.nih.gov/signaturedb) revealed activation of B-cell receptor (BCR), NF-κB, JAK-STAT, cytokine and NOTCH signaling as well as increased proliferation and metabolism in LN (normalized enrichment score >1.6, Q <0.05). In contrast, PB tumor cells were characterized by a quiescent transcriptional program.Long non-coding RNAs (lncRNAs) are a novel class of transcripts with emerging significance in cancer. We detected 134 DE lncRNAs between PB and LN. To gain insight into the function of lncRNAs, DE lncRNAs and protein-coding genes were subjected to weighted gene co-expression network analysis grouping highly co-expressed transcripts into modules. One of 5 identified modules contained protein-coding genes representing BCR activation and cell proliferation. Among 36 lncRNAs in this module, CCAT1 was overexpressed in LN-resident CLL cells. Overexpression of CCAT1 has also been reported in acute myeloid leukemia and some solid tumors, in which CCAT1 regulates MYC transcription. While the function of most lncRNAs remains unknown, our data suggest a network of lncRNAs may regulate survival pathways and proliferation of CLL cells in the microenvironment.Next, we profiled the transcriptome of bulk LN samples from 33 patients with CLL and 4 normal donors to characterize the cellular composition of CLL-LNs. We applied CIBERSORT (Newman, Nat Methods 2015) to infer the relative proportion of leukocyte subsets. First, B cells were more abundant in CLL than normal LNs (median 66% versus 34% of cellular elements, Q < 0.0001). Among non-B cells, CLL-LNs had more γδ-T cells (median 12% versus 1%, Q = 0.04), but fewer CD4+ T cells (median 34% versus 57%, Q = 0.008), NK cells (median 0% versus 4%, Q = 0.008), and mast cells (median 0% versus 1%, Q = 0.01) than normal LNs. No difference was observed in the frequency of CD8+ T-cells or monocyte-macrophage lineage cells between CLL and normal LNs. Because M2-polarized tumor-associated macrophages have been implicated in tumor development, we also assessed the ratio of M1 to M2 macrophages. However, macrophages from CLL-LNs did not exhibit increased M2 polarization as compared to normal LNs.In summary, we confirmed BCR and NF-κB activation reported in prior microarray studies and additionally identified the upregulation of JAK-STAT and NOTCH signaling in LN-resident tumor cells. In addition, network analysis suggested a possible role for lncRNAs in the response of CLL cells to microenvironmental stimuli. Significant alterations in the cellular composition of CLL-LNs included the relative expansion of B cells and γδ-T cells. Our data highlight the complexity of tumor-microenvironment interactions in CLL and reveal novel aspects that merit further investigation.This research was supported by the Intramural Research Program of the NHLBI. DisclosuresWiestner:Acerta Pharma: Research Funding; Pharmacyclics: Research Funding.