Differential Expression Patterns Research Articles

Rewiring of a KNOXI regulatory network mediated by UFO underlies the compound leaf development in Medicago truncatula

Class I KNOTTED-like homeobox (KNOXI) genes are parts of the regulatory network that control the evolutionary diversification of leaf morphology. Their specific spatiotemporal expression patterns in developing leaves correlate with the degrees of leaf complexity between simple-leafed and compound-leafed species. However, KNOXI genes are not involved in compound leaf formation in several legume species. Here, we identify a pathway for dual repression of MtKNOXI function in Medicago truncatula. PINNATE-LIKE PENTAFOLIATA1 (PINNA1) represses the expression of MtKNOXI, while PINNA1 interacts with MtKNOXI and sequesters it to the cytoplasm. Further investigations reveal that UNUSUAL FLORAL ORGANS (MtUFO) is the direct target of MtKNOXI, and mediates the transition from trifoliate to pinnate-like pentafoliate leaves. These data suggest a new layer of regulation for morphological diversity in compound-leafed species, in which the conserved regulators of floral development, MtUFO, and leaf development, MtKNOXI, are involved in variation of pinnate-like compound leaves in M. truncatula.

Cell-specific Extracellular Vesicles and Their miRNA Cargo Released Into the Organ Preservation Solution During Cold Ischemia Storage as Biomarkers for Liver Transplant Outcomes.

Liver transplantation (LT) is crucial for end-stage liver disease patients, but organ shortages persist. Donation after circulatory death (DCD) aims to broaden the donor pool but presents challenges. Complications like acute rejection, hepatic artery thrombosis, and biliary issues still impact posttransplant prognosis. Biomarkers, including extracellular vesicles (EVs) and microRNAs (miRNAs), show promise in understanding and monitoring posttransplant events. This study explores the role of EVs and their miRNA cargo in LT, including their potential as diagnostic tools. EVs from intrahepatic end-ischemic organ preservation solution (eiOPS) in 79 donated livers were detected using different techniques (nanosight tracking analysis, transmission electron microscopy, and flow cytometry). EV-derived miRNAs were identified by quantitative real time-polymerase chain reaction. Bioinformatics analysis was performed using the R platform. Different-sized and origin-specific EVs were found in eiOPS, with significantly higher concentrations in DCD compared with donation after brain death organs. Additionally, several EV-associated miRNAs, including let-7d-5p, miR-28-5p, miR-200a-3p, miR-200b-3p, miR-200c-3p, and miR-429, were overexpressed in DCD-derived eiOPS. These miRNAs also exhibited differential expression patterns in liver tissue biopsies. Pathway analysis revealed enrichment in signaling pathways involved in extracellular matrix organization and various cellular processes. Moreover, specific EVs and miRNAs correlated with clinical outcomes, including survival and early allograft dysfunction. A predictive model combining biomarkers and clinical variables showed promise in acute rejection detection after LT. These findings provide new insights into the use of EVs and miRNAs as biomarkers and their possible influence on posttransplantation outcomes, potentially contributing to improved diagnostic approaches and personalized treatment strategies in LT.

Clinical features and molecular landscape of cuproptosis signature-related molecular subtype in gastric cancer.

Recent studies have highlighted the biological significance of cuproptosis in disease occurrence and development. However, it remains unclear whether cuproptosis signaling also has potential impacts on tumor initiation and prognosis of gastric cancer (GC). In this study, 16 cuproptosis-related genes (CRGs) transcriptional profiles were harnessed to perform the regularized latent variable model-based clustering in GC. A cuproptosis signature risk scoring (CSRS) scheme, based on a weighted sum of principle components of the CRGs, was used to evaluate the prognosis and risk of individual tumors of GC. Four distinct cuproptosis signature-based clusters, characterized by differential expression patterns of CRGs, were identified among 1136 GC samples across three independent databases. The four clusters were also associated with different clinical outcomes and tumor immune contexture. Based on the CSRS, GC patients can be divided into CSRS-High and CSRS-Low subtypes. We found that DBT, MTF1, and ATP7A were significantly elevated in the CSRS-High subtype, while SLC31A1, GCSH, LIAS, DLAT, FDX1, DLD, and PDHA1 were increased in the CSRS-Low subtype. Patients with CSRS-Low score were characterized by prolonged survival time. Further analysis indicated that CSRS-Low score also correlated with greater tumor mutation burden (TMB) and higher mutation rates of significantly mutated genes (SMG) in GC. In addition, the CSRS-High subtype harbored more significantly amplified focal regions related to tumorigenesis (3q27.1, 12p12.1, 11q13.3, etc.) than the CSRS-Low tumors. Drug sensitivity analyses revealed the potential compounds for the treatment of gastric cancer with CSRS-High score, which were experimentally validated using GC cells. This study highlights that cuproptosis signature-based subtyping is significantly associated with different clinical features and molecular landscape of GC. Quantitative evaluation of the CSRS of individual tumors will strengthen our understanding of the occurrence and development of cuproptosis and the treatment progress of GC.

La mutación del gen MIR867 provoca aborto de semillas y afecta el tamaño del fruto en la planta modelo Arabidopsis thaliana

MIR genes are genes that give rise to microRNAs (miRNAs), which are small RNAs that regulate key developmental processes such as flowering and embryogenesis. Little is known about its role in the formation of gametes, seeds and fruits. This work demonstrates that the activity of the promoter of the MIR867 gene has a specific expression pattern in male tissue during flower development. Using two T-DNA insertional mutants, a reduction in fruit size (siliques) in length and thickness, and semi-sterility phenotype was demonstrated. To find the cellular reason for the semi-sterility, the Alexander staining technique of pollen grains was used observing that there is defective pollen in the mutant lines. This study is the first report that relates the MIR gene with fruit formation and semi-sterility if seeds in the model plant Arabidopsis thaliana.

Integration analysis of single-cell transcriptome reveals specific monocyte subsets associated with melanoma brain and leptomeningeal metastasis.

Melanoma central nervous system (CNS) metastasis remains a leading cause of patient mortality, and the underlying pathological mechanism has not been fully elucidated, leading to a lack of effective therapeutic strategies. In this study, we conducted an integrated analysis of single-cell transcriptomic data related to melanoma brain metastasis (MBM) and leptomeningeal metastasis (LMM). We focused on differences of subset composition and molecular expression of monocytes in blood, primary tumor, brain metastases, and leptomeningeal metastases. Significant differences were observed among monocytes in blood, primary tumor, and different CNS metastatic tissues, particularly in terms of subset differentiation and gene expression patterns. Subsequent analysis revealed the upregulation of cell proportions of six monocyte subsets in brain metastasis and leptomeningeal metastasis. Based on differential gene analysis, four of these subsets exhibited increased expression of factors promoting tumor migration and survival, including AREG+ monocytes (AREG, EREG, THBS1), FABP5+ monocytes (SPP1, CCL2, CTSL), and CXCL3+ monocytes (CXCL3, IL8, IL1B). The proportions of TPSB2+ monocytes (IL32, CCL5) were notably elevated in melanoma leptomeningeal metastasis tissues. Pathway analysis indicated the activation of signaling pathways such as NOD-like receptors, NFκB, and Toll-like receptors in these metastasis-related subsets. Our findings elucidate that AREG+, FABP5+ and CXCL3+ monocytes are associated with brain metastasis and TPSB2+ monocytes are associated with leptomeningeal metastasis in melanoma, which may be contribute to the development of therapeutic strategies focusing on monocytes or cytokines for melanoma CNS metastasis.

Identification of superior and rare haplotypes to optimize branch number in soybean

Key messageUsing the integrated approach in the present study, we identified eleven significant SNPs, seven stable QTLs and 20 candidate genes associated with branch number in soybean.Branch number is a key yield-related quantitative trait that directly affects the number of pods and seeds per soybean plant. In this study, an integrated approach with a genome-wide association study (GWAS) and haplotype and candidate gene analyses was used to determine the detailed genetic basis of branch number across a diverse set of soybean accessions. The GWAS revealed a total of eleven SNPs significantly associated with branch number across three environments using the five GWAS models. Based on the consistency of the SNP detection in multiple GWAS models and environments, seven genomic regions within the physical distance of ± 202.4 kb were delineated as stable QTLs. Of these QTLs, six QTLs were novel, viz., qBN7, qBN13, qBN16, qBN18, qBN19 and qBN20, whereas the remaining one, viz., qBN12, has been previously reported. Moreover, 11 haplotype blocks, viz., Hap4, Hap7, Hap12, Hap13A, Hap13B, Hap16, Hap17, Hap18, Hap19A, Hap19B and Hap20, were identified on nine different chromosomes. Haplotype allele number across the identified haplotype blocks varies from two to five, and different branch number phenotype is regulated by these alleles ranging from the lowest to highest through intermediate branching. Furthermore, 20 genes were identified underlying the genomic region of ± 202.4 kb of the identified SNPs as putative candidates; and six of them showed significant differential expression patterns among the soybean cultivars possessing contrasting branch number, which might be the potential candidates regulating branch number in soybean. The findings of this study can assist the soybean breeding programs for developing cultivars with desirable branch numbers.

FXR Agonism with Bile Acid Mimetic Reduces Pre-Clinical Triple-Negative Breast Cancer Burden.

Bariatric surgery is associated with improved outcomes for several cancers, including breast cancer (BC), although the mechanisms mediating this protection are unknown. We hypothesized that elevated bile acid pools detected after bariatric surgery may be factors that contribute to improved BC outcomes. Patients with greater expression of the bile acid receptor FXR displayed improved survival in specific aggressive BC subtypes. FXR is a nuclear hormone receptor activated by primary bile acids. Therefore, we posited that activating FXR using an established FDA-approved agonist would induce anticancer effects. Using in vivo and in vitro approaches, we determined the anti-tumor potential of bile acid receptor agonism. Indeed, FXR agonism by the bile acid mimetic known commercially as Ocaliva ("OCA"), or Obeticholic acid (INT-747), significantly reduced BC progression and overall tumor burden in a pre-clinical model. The transcriptomic analysis of tumors in mice subjected to OCA treatment revealed differential gene expression patterns compared to vehicle controls. Notably, there was a significant down-regulation of the oncogenic transcription factor MAX (MYC-associated factor X), which interacts with the oncogene MYC. Gene set enrichment analysis (GSEA) further demonstrated a statistically significant downregulation of the Hallmark MYC-related gene set (MYC Target V1) following OCA treatment. In human and murine BC analyses in vitro, agonism of FXR significantly and dose-dependently inhibited proliferation, migration, and viability. In contrast, the synthetic agonism of another common bile acid receptor, the G protein-coupled bile acid receptor TGR5 (GPBAR1) which is mainly activated by secondary bile acids, failed to significantly alter cancer cell dynamics. In conclusion, agonism of FXR by primary bile acid memetic OCA yields potent anti-tumor effects potentially through inhibition of proliferation and migration and reduced cell viability. These findings suggest that FXR is a tumor suppressor gene with a high potential for use in personalized therapeutic strategies for individuals with BC.

Genome-Wide Identification and Expression Analysis of Fifteen Gene Families Involved in Anthocyanin Synthesis in Pear

Anthocyanins play a crucial role in imparting red coloration to pear fruits. However, the specific number and expression patterns of each member within the anthocyanin biosynthesis-related gene families in pears require systematic exploration. In this study, based on the pear genome we identified 15 gene families involved in the anthocyanin biosynthesis pathway using the BLASTP and Hidden Markov Model search methods, comprising a total of 94 enzyme genes. Through phylogenetic analysis, conserved domains, motif, and gene structure analysis, these gene families were further categorized into eight distinct lineages. Subsequent collinearity analysis revealed that the expansion of anthocyanin synthesis-related gene families primarily originated from segmental duplications. Analysis of cis-element in the promoter regions of genes related to anthocyanin synthesis unveiled the presence of light-responsive elements and various hormone-responsive elements. This suggests that changes in light stimulation and hormone levels may influence anthocyanin synthesis. RNA-Seq and qRT-PCR analyses indicated differential expression of anthocyanin biosynthesis-related genes between the peel and flesh tissues. During the accumulation of anthocyanins in red-fleshed pears, upstream genes in the anthocyanin biosynthesis pathway such as PbrPAL2, PbrC4H2, PbrC4H3, Pbr4CL2, Pbr4CL17, PbrF3H5, and PbrF3H6 exhibited high expression levels, likely contributing significantly to the red coloration of pear flesh. In summary, we have identified the number of gene family members involved in pear anthocyanin biosynthesis and analyzed the expression patterns of the genes related to pear anthocyanin biosynthesis. These findings provide a solid foundation for further research on the regulatory mechanisms underlying pear anthocyanin biosynthesis and the breeding of red pear varieties.

Kidney toxicity and transcriptome analyses of male ICR mice acutely exposed to the mushroom toxin α-amanitin

Amatoxins are responsible for most fatal mushroom poisoning cases, as it causes both hepatotoxicity and nephrotoxicity. However, studies on amatoxin nephrotoxicity are limited. Here, we investigated nephrotoxicity over 4 days and nephrotoxicity/hepatotoxicity over 14 days in mice. The organ weight ratio, serological indices, and tissue histology results indicated that a nephrotoxicity mouse model was established with two stages: (1) no apparent effects within 24 h; and (2) the appearance of adverse effects, with gradual worsening within 2–14 days. For each stage, the kidney transcriptome revealed patterns of differential mRNA expression and significant pathway changes, and Western blot analysis verified the expression of key proteins. Amanitin-induced nephrotoxicity was directly related to RNA polymerase II because mRNA levels decreased, RNA polymerase II-related pathways were significantly enriched at the transcription level, and RNA polymerase II protein was degraded in the early poisoning stage. In the late stage, nephrotoxicity was more severe than hepatotoxicity. This is likely associated with inflammation because inflammation-related pathways were significantly enriched and NF-κB activation was increased in the kidney.

Abstract 2536: Multimodal stratification of predictive biomarkers in head and neck cancers: A focus on cytokine-based immunotherapy

Abstract Background Immunotherapy, particularly cytokine-based therapy, has been gaining traction in the treatment of head and neck cancers. Cytokines are small proteins that play a crucial role in the immune response to cancer. However, not all patients respond to cytokine-based immunotherapies, and some may experience severe side effects. The ability to predict which patients are most likely to benefit from these therapies could greatly improve the efficacy and tolerability of treatment. In this context, the study of predictive biomarkers, such as the expression of immune checkpoint molecules like PD-L1 and TIGIT, and the profiling of cytokines within the tumor microenvironment, has become crucial. These biomarkers could provide valuable information about the patient's immune response to the tumor and their likelihood of responding to cytokine-based immunotherapies. Method A multimodal approach to stratify predictive biomarkers in head and neck cancers was used. The methodology was founded on combining metabolic, transcriptomic, and proteomic data to offer a comprehensive understanding of potential biomarkers. The data from different modalities were integrated using bioinformatics and machine learning algorithms. This comprehensive dataset was analyzed to identify multimodal biomarker signatures that could predict patient responses to cytokine-based therapies. Result Preliminary finding showed significant heterogeneity in the expression of PD-L1, TIGIT, and various cytokines across the tumor microenvironment. This underscored the complexity of head and neck cancers. Certain multimodal biomarker signatures, which included specific patterns of immune checkpoint molecule expression, cytokine profiles, and immune cell infiltration, correlated robustly with patient responses to cytokine-based therapies. Conclusion Our study demonstrates the considerable potential of a multimodal stratification approach in deciphering the complexity of head and neck cancers and predicting responses to cytokine-based immunotherapies. By integrating metabolomic, transcriptomic, and proteomic data, we identified unique biomarker signatures that strongly correlated with therapy responses. This work underscores the invaluable role of integrated predictive biomarker profiles in enhancing the precision of immunotherapy. Citation Format: Corinne Ramos, Richard Ruez, Sandra Delebecq, Victor Senechal. Multimodal stratification of predictive biomarkers in head and neck cancers: A focus on cytokine-based immunotherapy [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 2536.

Abstract 7047: Comparative analysis of transcriptomic and immunological profiles in treatment-naïve black and non-Hispanic White women with high-grade serous ovarian cancer

Abstract Background: Ovarian cancer is a highly lethal gynecological malignancy and high-grade serous histology (HGSOC) accounts for the majority of cases. Platinum-based chemotherapy is the primary treatment. Notably, Black women face the highest mortality-to-incidence ratio across all ethnic groups. This study investigated transcriptomic and immunological differences in tumors from Black compared to NHW women that might explain the poor clinical outcomes observed within this patient cohort. Methods: We collected primary tumor specimens from 36 Black and 31 treatment-naïve NHW patients. After RNA isolation, RNA sequencing (RNA-seq) identified differentially expressed transcripts and Enrichr performed pathway enrichment studies. To confirm the observed gene expression differences, we employed quantitative reverse transcription PCR (qRT-PCR), western blotting, and multiplex immunohistochemistry (mIHC). Additionally, we conducted cell proliferation, colony formation, and cell viability assays to functionally validate potential target genes of interest. Results: Our findings revealed 277 genes with significant differential expression between Black and NHW patients (FDR-adjusted p-value < 0.05). Among these, 103 coding genes were up-regulated, while 81 coding genes were down-regulated in tumors from Black compared to NHW patients. Gene Ontology analyses of these significantly differentially expressed genes highlighted enriched pathways related to DNA damage response, including the insulin receptor (INSR) gene, p53/apoptosis signaling components such as Forkhead box proteins A1 (FOXA1) and FOXB1, as well as genes involved in the cholesterol/lipid modulation pathway, including Low-density lipoprotein (LDL) receptor and Stearoyl-CoA Desaturase (SCD). Notably, silencing INSR and FOXA1 enhanced sensitivity to platinum-based drugs and inhibited cell growth and colony formation. Furthermore, we identified differences in the proportions of key immune cell types between the two patient groups, with tumors from Black patients exhibiting a significantly lower proportion of CD4+ Naïve T-cells and CD4+ regulatory T-cells (Tregs). Conclusions: Overall, our study reveals significant differential gene expression patterns between HGSOC tumors from Black and NHW patients, as well as differences in the proportions of immune cell types. These discoveries provide valuable insights into the biological mechanisms underlying the disparities in outcomes observed between black and NHW patients afflicted with HGSOC. It is critical to further investigate how these biological differences affect clinical outcomes and treatment response in Black women. Citation Format: Hao Huang, Russel Keathley, Ujin Kim Kim, Horacio Cardenas, Ping Xie, Jianjun Wei, Guangyuan Zhao, Emma L. Barber, Ernst Lengyel, Kenneth P. Nephew, Victoria Bae-Jump, Bin Zhang, Daniela Matei. Comparative analysis of transcriptomic and immunological profiles in treatment-naïve black and non-Hispanic White women with high-grade serous ovarian 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 7047.

Abstract 4354: Long noncoding RNA DUXAP10 serves as a putative driver of carcinogenic transformation in anaplastic thyroid cancer

Abstract Anaplastic Thyroid Cancer (ATC) is the most aggressive thyroid cancer subset, with a <4% five-year survival rate. ATC is completely refractory to traditional therapy and newer immunotherapeutic options. Unlike other lethal cancers, ATC has a low mutational burden, warranting the need for a comprehensive study of differential gene expression patterns. Transcriptomic regulators known as long non-coding RNAs (lncRNA) have been described as pivotal orchestrators of gene expression and drivers of carcinogenic patterns. Thus, we present the role of novel lncRNAs in shaping the ATC genotype and phenotype. ​​Publicly available ATC vs. normal thyroid tissue transcriptomic datasets (Gene Expression Omnibus; GSE33630, GSE85457) were investigated to identify genomic transcripts that are differentially expressed in ATC samples using GEO2R. Bioinformatic analysis identified Double Homeobox A Pseudogene 10 (DUXAP10), as a highly upregulated lncRNA in ATC patient tissue samples in both databases (40-fold and 20-fold). Gene Expression Profiling Interactive Analysis statistically correlated high DUXAP10 expression with decreased survival in thyroid cancer patients. DUXAP10 expression was similarly upregulated in ATC cell line, T238, compared to immortalized “normal” thyroid epithelial cell line, Nthy-ori-3-1. Our T238-CRISPRi knockdown model of DUXAP10 was evaluated in vitro to assess consequences of overexpression. CRISPRi knockdown of DUXAP10 in T238 significantly reduced its migratory capabilities by 50%, invasion index by 30%, clonogenicity by 70%, cell viability by 67%, 60%, and 50% at 24, 48, and 72 hours, respectively, proliferation by 28%, 45%, and 36% at 24, 48, and 72 hours, respectively, and global transcription rate by 65%. Further, our DUXAP10-CRISPRi knockdown exhibited a downregulation of N-Cadherin and mediators of beta-catenin signaling- confirming a role in regulatory cross-talk of central carcinogenic pathways. We are currently evaluating proteins and miRNAs bound to and “sponged” by DUXAP10 in vitro utilizing RNA-centric methodology. These data reveal the novelty of DUXAP10, and that its over-expression may increase the negative consequences of ATC metastasis. Thus, we have identified DUXAP10 as a putative determinant for ATC diagnosis, prognosis, and therapeutic targeting. Citation Format: Nicole R. DeSouza, Michelle Carnazza, Danielle Quaranto, Tara Jarboe, Kaci Kopec, Robert Suriano, Kate Nielsen, Augustine Moscatello, Humayun Islam, Jan Geliebter, Raj K. Tiwari. Long noncoding RNA DUXAP10 serves as a putative driver of carcinogenic transformation in anaplastic thyroid 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 4354.

Abstract 7089: Proteomic evaluation of combination data in acute myeloid leukemia to inform mechanism of action and new targets

Abstract Background: Acute myeloid leukemia (AML) is a prevalent adult leukemia. In the US, around 20,380 individuals were diagnosed with AML in 2023. Despite standard therapies, relapse and resistance persist. Cyclin-dependent kinase 9 (CDK9) has been recognized an actionable therapeutic target in AML. The potent inhibitor, AZD4573, induces durable apoptosis and suppresses tumor growth. Our study reveals that combining AZD4573 with standard-of-care (SoC) treatments deepens cell death responses in multiple AML cell models. We also used proteomics tools to understand the mechanisms underlying the vulnerability and resistance in SoC and CDK9 combinations. Methods: In the drug combination study, three SoC agents (cytarabine, decitabine, and venetoclax) were evaluated in combination using a 6 × 6 dose-response matrix in four AML cell models (MOLM13, MOLM16, MV411, and OCI-AML2). The HSA synergy score and Emax drug activity were used to assess the benefits of the drug combinations. In the proteomics evaluation study, MOLM13 cells treated for 7 days under different conditions - (1) vehicle control; (2) cytarabine alone; (3) decitabine alone; (4) venetoclax alone; (5) AZD4573 alone; (6) AZD4573+cytarabine; (7) AZD4573+decitabine; (8) AZD4573+venetoclax - were collected for proteomics analysis using LC-MS/MS. Differential expression and missing pattern analyses were used to identify dysregulated proteins. Functional enrichment analysis was employed to identify dysregulated biological processes and pathways in response to different treatments. Results: Our drug combination screens demonstrated the efficacy of AZD4573 in combination with cytarabine, decitabine, and venetoclax in 3 of 4 AML cell models. In our proteomic analysis, we took two approaches. First, we compared the proteomes of AML cells treated with SoC agents, identifying shared downregulated pathways such as serine biosynthesis, notably pointing to the rate-limiting enzyme PHGDH as a potential therapeutic target in AML. Cytarabine and decitabine induced an inflammatory response, while venetoclax increased the expression of cell division regulators like Aurora kinase B (AURKB). Interestingly, targeting AURKB with AZD2811 has been shown to overcome venetoclax resistance in AML. Second, we compared proteome changes induced by various AZD4573 combinations. We identified IRF2BP2 as a shared vulnerable protein across the three AZD4573 combinations. POUF2F2 expression was significantly induced by cytarabine but suppressed when combined with AZD4573. Given that POUF2F2 activates the PDK1-Akt pathway, our findings suggest that AZD4573-induced POUF2F2 downregulation suppresses the PDK1-AKT pathway, inhibiting tumor progression. Conclusions: Our proteomics analysis identifies vulnerable and resistant pathways and proteins, shedding light on the mechanism of action and revealing potential new targets for AML. Citation Format: Lori Chan, Zuleyha Ozen, Anthony Iannetta, Eric Miele, Funda Kar, Andrew Jarnuczak, Geoff Nelson, Aleksandra Markovets, Justine Roderick-Richardson, Jelena Urosevic, Lisa Drew, Jerome Mettetal. Proteomic evaluation of combination data in acute myeloid leukemia to inform mechanism of action and new targets [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 7089.

Abstract 6622: Identification of early oncogenic lesions following concomitant Vhl and Pbrm1 loss in the murine kidney

Abstract Characterizing the early events preceding tumorigenesis is a major challenge in understanding cancer. To address this, we are investigating the paradigm of clear cell renal cell carcinoma (ccRCC) that is driven by the biallelic loss of the von Hippel Lindau (VHL) tumor suppressor gene. Though VHL loss is required, additional mutations have been found in the evolution of the cancer, most commonly in Polybromo-1 (PBRM1), a subunit of the PBAF SWI/SNF chromatin remodeling complex. Concomitant Vhl and Pbrm1 deletion, but not Vhl deletion alone, in the renal tubular epithelium (RTE) has been reported to be sufficient to drive the formation of renal tumors in mice. However, the early in vivo consequences of Vhl loss, and the exact requirement for Pbrm1 loss to tumorigenesis remain poorly studied. We have previously reported the development of a novel lineage-tracing model of Vhl deletion that directly couples loss of a conditional Vhl allele to the expression of a tdTomato reporter and allows accurate identification and retrieval of marked Vhl-null cells. In the work reported here, we have combined this system with conditional Pbrm1 deletion using an RTE-restricted Pax8-CreERT2 to precisely identify and assay Vhl/Pbrm1-null cells. We describe the histological abnormalities specifically comprising Vhl/Pbrm1-null cells observed at early (1-3 weeks), intermediate (10 months), and late (17 months) intervals post recombination. We found that Vhl/Pbrm1-null cells formed extensive ‘tumorlets’, disorganized, multilayered tubules, and cystic dilated tubules specifically in the renal cortex at 17 months post recombination. Immunohistochemistry confirmed that all epithelial cells in the lesions were Vhl/Pbrm1 null and expressed HIF1 and HIF2. These lesions contained cycling cells as identified by dual tdTomato/Ki67 staining, foci of immune cells and were strikingly surrounded by cells expressing high levels of p-ERK. We then traced these lesions to earlier timepoints, and observed Vhl/Pbrm1-null lesions resembling ‘tumorlet’ precursors and disorganized tubules at 10 months post recombination specifically in the renal cortex. Interestingly, these precursors were encompassed by macrophages and could be discerned in situ by a ring of p-ERK-expressing cells surrounding these lesions. No similar lesions were detected at 3 weeks after recombination. Interestingly, the presence of cortical lesions was associated with a region-specific expansion of the total Vhl/Pbrm1-null population over time. Our data suggest that morphological abnormalities arise after a general proliferation of Vhl/Pbrm1-null cells in the renal cortex and from a subset of cells expressing specific markers. We are now comparing the differential gene expression patterns of Vhl-null cells and Vhl/Pbrm1-null normal and transformed cells at single cell resolution to expand on these observations. Citation Format: Joanna Lima, Samvid Kurlekar, Norma Masson, Ayslan B. Barros, Maria Fernanda Soares, Christopher W. Pugh, Julie Adam, Peter J. Ratcliffe. Identification of early oncogenic lesions following concomitant Vhl and Pbrm1 loss in the murine kidney [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 6622.

Abstract 7046: Proteogenomic and immunologic profiles of head and neck cancer patients of African ancestry

Abstract Blacks/African Americans (BAAs) with head and neck squamous cell carcinoma (HNSCC) have worse survival than Whites. However, the complex molecular biomarkers and signatures of HNSCC among BAAs and molecular distinction associated with HNSCC disparities are largely unknown. Here we show the results of a multi-omics analysis of 500 patients (48 BAAs and 452 Whites). Comparative analyses between the racial groups were performed at the level of genomics, pathways, molecular subtype, tumor immune infiltration, protein alterations and prognosis. We found that overall survival in BAAs with HPV-unrelated HNSCC is significantly shorter than in White patients. Ancestry-related differential mutation spectrum, DNA methylation, gene and protein expression pattern and immune infiltration landscape were identified. Particularly, FAT1 mutation is significantly associated with its gene expression in BAA HNSCC and poor overall survival in this group. In BAA HNSCC, SALL3 gene expression is positively associated with its gene CNVs, while RTP4 gene expression is inversely correlated with its methylation. High EGFR_pY1068 and RAD50 levels correlate with poor prognosis in BAAs with HNSCC. The immune infiltration enrichment scores of Th17 cells, activated dendritic cells, monocytes and neutrophils in BAA HNSCC were significantly lower than those in White HNSCC. By combining multi-omics analysis and data validation using in-house-made tumor tissue arrays, this study comprehensively elucidates the genetic landscape, immune response, and tumor biology in BAA and White HNSCC patients, providing a molecular basis for future research in identifying appropriate screening modalities and therapeutic interventions leading to improved outcomes in BAAs with HNSCC. Citation Format: Fan Yang, Fanghui Chen, Chloe Shay, Nabil F. Saba, Yong Teng. Proteogenomic and immunologic profiles of head and neck cancer patients of African ancestry [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 7046.

Abstract 1103: Molecular signature for treatment-responsive and recurrent Wilms tumors

Abstract Wilms tumor is the most common solid renal malignancy in children. To better understand the biology of Wilms tumors and develop drugs especially against tumors that relapse, we sought to identify mutations in the exome, differential gene expression patterns, and tumor suppressor expression status of Wilms tumors in Kentucky. The Kentucky Cancer Registry (KCR) Virtual Tissue Repository identified 29 cases of Wilms tumor diagnosed between 2015 and 2021 at hospitals across the Commonwealth of Kentucky. The Markey Cancer Center Biospecimen Procurement and Translational Pathology Facility prepared tumor microarrays (TMAs) using Wilms tumor and matching normal tissue cores for immunohistochemistry (IHC) analysis. RNA-Seq analysis performed at the Markey Cancer Center Oncogenomics Facility identified a gene signature that was further validated by IHC and reverse-transcription quantitative-PCR (RT-qPCR). Outcome data provided by KCR indicated that increased expression of an anti-apoptotic protein in the tumor counter-intuitively provided better prognosis and outcome to treatment, indicating that the treatments either directly or indirectly targeted this protein. Loss of function of the tumor suppressor proteins in Par-4/PAWR, WT1 and p53 did not explain the higher expression of the cell survival protein. Our multidisciplinary team approach involves basic science/translational researchers, population scientists, biomedical informaticists, and clinicians and has resulted in well-characterized, Wilms tumor tissue microarrays. The next phase of the study is generating patient derived xenografts (PDXs) for a better understanding of Wilms tumor biology in children. Citation Format: Jieyun Jiang, Derek B. Allison, Ravshan Burikhanov, Saptadwipa Ganguly, Ryan A. Goettl, Jinpeng Liu, Chi Wang, Amanda F. Saltzman, Thomas Tucker, Peter H. Spielmann, Eric B. Durbin, John A. D’Orazio, Vivek M. Rangnekar. Molecular signature for treatment-responsive and recurrent Wilms tumors [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 1103.

Abstract 2763: A specific ribomethylome pattern in lung cancer is associated with increased risk of metastasis

Abstract Non-coding RNAs drive cancer phenotypes and are associated with patients’ outcome. SnoRNAs are required for the 2’-O-methylation (2’-O-Me) and pseudouridylation of ribosomal RNA (rRNA) thus being essential for ribosomal biogenesis and function. So far, the role of rRNA methylation (ribomethylation) for non-small cell lung cancer (NSCLC) pathogenesis is unknown. To investigate the role of ribomethylation we included samples from 92 patients with lung adenocarcinoma (pathological stage IA to IIB) for comprehensive multi-omics profiling. Amongst transcriptomics, small RNA sequencing, proteomics, and whole exome sequencing, ribomethylation as epitranscriptomic dimension was analyzed using RiboMethSeq. We focused the analysis on complete tumor resection samples. Here 47 out of 106 2’-O-Me sites were fully methylated in all tumor samples suggesting a crucial role for methylation at this position. Surprisingly, 59 sites had a dynamic methylation pattern. By combining ribomethylation sequencing data of dynamic sites with whole-exome-sequencing as well as transcriptome and proteome analyses using a multi-omics factor analysis (MOFA), we discovered a 2’-O-Me signature in a subset of NSCLC patients with a high risk of metastasis and poor prognosis. We termed the patient subset, with underlying ribomethylation signature, epitranscriptomic pro-metastatic phenotype (EPROMET). This phenotype was not associated with genetic mutations as analyzed by exome sequencing. Analysis of gene sets in both transcriptomics and proteomics showed an upregulation of secreted and extracellular matrix proteins in EPROMET patients. Alongside, the ribomethylation site with major contribution to the EPROMET signature; 18S-Um799, mediated through SNORD105/105B, was found to be the most dynamic within the dataset. It also showed the largest difference between EPROMET and non-EPROMET patients. For functional validation, lung cancer cell lines with knockout of snoRNAs contributing to EPROMET signature were generated using CRISPR/Cas9. Lung cancer cells lacking the corresponding rRNA modifications migrated slower in vitro, failed to grow at a distant site in vivo and were impaired in metastasis. Functionally, it was shown that the modulated ribomethylation signature effected translation of secreted proteins by altered mRNA binding to ribosomes. This study indicates the presence of a ribomethylome-associated phenotype of NSCLC related to metastasis and poor prognosis. Altered ribomethylation affects the ribosome function towards differential expression patterns of secreted proteins. Taken together, an epitranscriptomic pattern of 2’-O-Me is associated with invasion/migration properties of NSCLC cells and with development of metastasis. The ribomethylome may present a suitable biomarker and a potential therapeutic target. Citation Format: Cornelius Pauli, Daniel Heid, Christian Rohde, Nadja Krall, Sylvain Delaunay, Michael Kienhoefer, Christian Tischer, Michael Allgäuer, Maximilian Felix Blank, Fengbiao Zhou, Michael Kardorff, Michael Thomas, Hauke Winter, Sarah Sandmann, Marc Kriegsmann, Marc Schneider, Thomas Muley, Alexander Brobeil, Nicole Bäumer, Sebastian Bäumer, Simon Raffel, Albrecht Stenzinger, Peter Schirmacher, Junyan Lu, Judith Zaugg, Michaela Frye, Carsten Müller-Tidow. A specific ribomethylome pattern in lung cancer is associated with increased risk of metastasis [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 2763.

Abstract 5668: Long non-coding RNA LINC01614 knockdown decreases carcinogenic behavior of papillary thyroid cancer in vitro

Abstract Papillary thyroid cancer (PTC) accounts for the vast majority of thyroid cancer cases with increasing incidence over the past few decades. PTC has a significantly higher prevalence in females in their childbearing years. Despite high survival rates, disease recurrence and metastasis remain prominent issues, thus highlighting the critical need for molecular biomarker detection. A newer class of molecular regulators, known as long non-coding RNAs (lncRNAs), have demonstrated differential expression patterns in a multitude of cancers. The largest subclass of these RNA molecules in the human genome consists of long intergenic non-coding RNAs (lincRNAs) with many of their functions yet to be identified. Known functional roles of lncRNAs center on their ability to modulate gene expression and drive carcinogenic behavior, deeming them attractive biomarkers and/or therapeutic targets for study. Bioinformatic analysis of RNA sequencing data from our patient sample biobank identified LINC01614 as being significantly upregulated (~12 fold increase) in PTC, when compared to normal, matched thyroid tissue. Further, it was also upregulated ~30-fold in male PTC compared to ~5.5 fold increase in female PTC, highlighting a potential sex correlation for study. Thus, we are studying LINC01614 as a potential PTC biomarker. Gene expression analysis of LINC01614 in vitro was found to be upregulated in various thyroid cancer cell lines, specifically two PTC cell lines: TPC1 (~5 fold; RET/PTC rearrangement; female) and K1 (~2 fold; BRAFV600E; male) when compared to the immortalized “normal” thyroid cell line (Nthy-ori-3-1). For phenotypic evaluation, we utilized the CRISPRi technique to employ transcriptional repression of LINC01614 in both TPC1 and K1. LINC01614 knockdown in TPC1 and K1 resulted in decreased healing capacity (~20%), clonogenicity (~50% and ~34%, respectively), and proliferation (~55% and ~45%, respectively). Studies are currently underway to further assess invasion, morphology, and RNA localization within the cell in vitro, as well as the identification of potential protein interactions and mechanisms of action of LINC01614 in PTC. Studying lncRNAs and their regulatory roles in cancer cell function is critical in the identification of various diagnostic and prognostic biomarkers for therapeutic intervention. Our data support the potential biological role of LINC01614 in driving PTC growth and metastatic potential. Further elucidation of how LINC01614 impacts PTC development and progression is a promising avenue of exploration. Citation Format: Danielle Quaranto, Michelle Carnazza, Nicole R. DeSouza, Sina Dadafarin, Augustine Moscatello, Humayun K. Islam, Raj K. Tiwari, Jan Geliebter. Long non-coding RNA LINC01614 knockdown decreases carcinogenic behavior of papillary thyroid cancer in vitro [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 5668.

Abstract 7381: Mathematical modeling and validation of mechanistic target of rapamycin and N-myristoyltransferase signaling pathways in breast cancer

Abstract Hormone receptor-positive (HR+) breast cancer (BC) makes up approximately 65% of all breast cancers diagnosed. The prognosis for early-stage disease is excellent with mainstay endocrine therapy (ET). Despite the effectiveness of standard ET, as many as 41% of HR+ early-stage BC diagnosed women will experience distant recurrence. The resistance to endocrine therapy and recurrence is partly attributed to the activation of the insulin pathway and the independence of HR+ BC cells on the ER pathway for their growth. Earlier, we demonstrated the crosstalk between insulin/mTOR and ER pathways. N-myristoyltransferase (NMT) exists in humans in two paralogues (NMT1 and NMT2) that catalyze myristoylation reaction. Recent studies from our laboratory demonstrated that NMTs are downstream targets of insulin and ER pathways. In this study, we have designed mathematical models using differential equations to study the activation of the insulin pathway and its effect on NMT. The mathematical modeling incorporated the partition of cellular organelles and the sequential flow of information with cascades of equations representing signaling reactions. The activated mathematical model was designed by activating the insulin receptor (IR) or insulin-like growth factor receptor (IGF1R) and compared with the control model. The mathematical models were validated by wet lab experiments. The HR+ BC cells (MCF7) were treated with insulin or IGF1 for short term and long term. The expression patterns of NMT1, NMT2, and mTOR were determined by cell fractionation and western blot analysis. The results revealed the correlation between the differential expression patterns of NMTs and the proliferation of MCF7 cells when the insulin pathway was activated by insulin or IGF. The mathematical modeling was validated by simulations and data fittings. The results demonstrated that differential equation-based mathematical modeling could predict the NMT-related oncogenic changes in HR+ BC cells. Citation Format: Abinash Meher, Shailly Varma Shrivastav, Anouska Agarwal, Sheen Dube, Stephanie Portet, Anuraag Shrivastav. Mathematical modeling and validation of mechanistic target of rapamycin and N-myristoyltransferase signaling pathways in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7381.

Abstract 1024: Differential gene expression of colorectal cancer biomarkers in Hispanic individuals

Abstract Colorectal cancer (CRC) is a leading cause of cancer death among men and women in Puerto Rico and the United States. About 60-70% of CRC cases are found at advanced stages (III/IV), suggesting limited adherence to available screening methods. Several molecular biomarkers have been identified as discriminatory for CRC (e.g., KRAS, NRAS, MSI), improving CRC management and patient outcomes. This study evaluates the differential expression patterns of DKK3, PKM2, IGFBP2, and SEPT9 genes between matched CRC tumors and adjacent mucosa samples. The secondary outcome was to examine the association between the presence of the selected biomarkers in tissue compared to blood samples. Using a retrospective study design, we examined 112 tissue samples of Hispanic individuals with a pathology-confirmed CRC diagnosis recruited throughout the Puerto Rico Familial Colorectal Cancer Registry (PURIFICAR). We quantified expression levels of target genes by RT-qPCR normalized with endogenous control GAPDH, using TaqMan Gene Expression Assay in the QuantStudio 3 (Applied Biosystems). Wilcoxon signed-rank test was used to calculate differences between gene expression from tumor and adjacent mucosal tissue samples. Additionally, 39 paired blood and tissue samples were analyzed to explore the association between biomarkers in these two types of samples. Protein biomarkers were measured using a commercially available ELISA kit according to manufacturer protocols (Thermo Scientific Federick, MD and Biosource San Diego, CA). mSEPT9 was measured using the Epi proColon® 2.0 CE test. The association between biomarker presence in tissue and blood samples was assessed using the Chi-square test of independence, with biomarker concentrations dichotomized at the median value. Statistical analyses were performed using Stata 17 and R version 4.3.1. DKK3 and IGFBP2 expression levels were higher among CRC tumor samples. However, expression levels of PKM2 and SEPT9 genes were slightly lower. DKK3 was the only target gene significantly different (p<0.05) when comparing overall gene expression between the matched samples. Upon comparison between early and advanced CRC stages, DKK3 expression levels were higher in advanced-stage tumor samples when compared to adjacent mucosal tissue samples (p<0.05). Moreover, a significant association between IGFBG2 presence in tissue compared to blood was detected at a 90% confidence level (p-value<0.10). This association was evident in early-stage CRC cases; there is a relationship between IGFBG2 biomarker presence in tissue and IGFBG2 biomarker presence in blood (p<0.05). Our findings indicate DKK3 and IGFBP2 as potential biomarkers for CRC progression and early detection. The study’s insights into the differential expression patterns of these biomarkers can inform targeted screening strategies. Further research is needed to assess their potential to enhance early tumor detection in Hispanics. Citation Format: Elba V. Caraballo-Rivera, Hilmaris Centeno-Girona, Gabriel De Jesus-Astacio, Camille Zenon-Melendez, Brenda Torres-Velasquez, Madeline Martir-Ocasio, Marcia R. Cruz-Correa. Differential gene expression of colorectal cancer biomarkers in Hispanic individuals [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 1024.