Differential Gene Expression Patterns Research Articles

Centenarian hippocampus displays high levels of astrocytic metallothioneins.

The hippocampus is a brain area linked to cognition. The mechanisms that maintain cognitive activity in humans are poorly understood. Centenarians display extreme longevity which is generally accompanied by better quality of life, lower cognitive impairment, and reduced incidence of pathologies including neurodegenerative diseases. We performed transcriptomic studies in hippocampus samples from individuals of different ages (centenarians [≥97 years], old, and young) and identified a differential gene expression pattern in centenarians compared to the other two groups. In particular, several isoforms of metallothioneins (MTs) were highly expressed in centenarians. Moreover, we identified that MTs were mainly expressed in astrocytes. Functional studies in human primary astrocytes revealed that MT1 and MT3 are necessary for their homeostasis maintenance. Overall, these results indicate that the expression of MTs specifically in astrocytes is a mechanism for protection during aging.

Deciphering infected cell types, hub gene networks and cell-cell communication in infectious bronchitis virus via single-cell RNA sequencing.

Infectious bronchitis virus (IBV) is a coronavirus that infects chickens, which exhibits a broad tropism for epithelial cells, infecting the tracheal mucosal epithelium, intestinal mucosal epithelium, and renal tubular epithelial cells. Utilizing single-cell RNA sequencing (scRNA-seq), we systematically examined cells in renal, bursal, and tracheal tissues following IBV infection and identified tissue-specific molecular markers expressed in distinct cell types. We evaluated the expression of viral RNA in diverse cellular populations and subsequently ascertained that distal tubules and collecting ducts within the kidney, bursal mucosal epithelial cells, and follicle-associated epithelial cells exhibit susceptibility to IBV infection through immunofluorescence. Furthermore, our findings revealed an upregulation in the transcription of proinflammatory cytokines IL18 and IL1B in renal macrophages as well as increased expression of apoptosis-related gene STAT in distal tubules and collecting duct cells upon IBV infection leading to renal damage. Cell-to-cell communication unveiled potential interactions between diverse cell types, as well as upregulated signaling pathways and key sender-receiver cell populations after IBV infection. Integrating single-cell data from all tissues, we applied weighted gene co-expression network analysis (WGCNA) to identify gene modules that are specifically expressed in different cell populations. Based on the WGCNA results, we identified seven immune-related gene modules and determined the differential expression pattern of module genes, as well as the hub genes within these modules. Our comprehensive data provides valuable insights into the pathogenesis of IBV as well as avian antiviral immunology.

Abstract PO3-02-02: A prospective, international, observational, real-world evidence database, and collaborative platform for Investigator-Initiated Studies in Early-Stage Breast Cancer tested with MammaPrint and BluePrint– the FLEX Study

Abstract TIPS SABCS 2023 A prospective, international, observational, real-world evidence database, and collaborative platform for Investigator-Initiated Studies in Early-Stage Breast Cancer tested with MammaPrint and BluePrint– the FLEX Study Background: Clinical trials have been an invaluable tool in providing improvements in the discovery, treatment, and quality of life for various diseases and disorders including breast cancer, which impacts millions of people each year. The MammaPrint 70-gene assay along with BluePrint 80-gene subtype analysis are tools to provide such improvements in treatment planning. Historically, patient trial populations have not been racially diverse. Current efforts are focused on improving diversity and inclusion to promote efficacy and health equity across all races/ethnicities. Given recent publications supporting the ability of MammaPrint and BluePrint to identify genomic differences in outcomes of black women with breast cancer, the ongoing multi-center FLEX trial (NCT03053193) has proven to be an unparalleled source for improvement in breast cancer care. With a target of 30,000 enrolled patients, the collaborative research network within FLEX will use MammaPrint, BluePrint, full transcriptome, and clinical data to explore clinical and genomic differences in (sub)populations of interest to promote and advance precision medicine for patients with early-stage breast cancer. Methods: FLEX is the first of its kind to link clinical data with full transcriptome data. It is a prospective, observational trial that enrolls patients who are ≥ 18 years old with histologically proven stage I-III breast cancer with up to 3 positive lymph nodes. Patient eligibility for study enrollment include standard of care MammaPrint testing with or without BluePrint and consent to clinically annotated full transcriptome data collection. The study’s infrastructure facilitates the generation of hypotheses for targeted sub-studies that are important for breast cancer management. The FLEX network fosters collaboration with 99 active sites, including Canada, Greece, and Israel. All proposed substudies are vetted and approved by both internal and external research and scientific review committees. Since launching in April 2017, 13,547 patients have been enrolled including those who have been historically underrepresented in trials (Black n =1032; Latin n= 373; AAPI n =276), 43 investigator initiated sub-studies have been approved and are in progress on a varied number of approaches like MammaPrint/Blueprint clinical utilities, racial disparities, neoadjuvant treatment planning in ER+, and or HER2+ breast cancer with 31 abstracts accepted in national and international congresses. Five ongoing sub-studies within FLEX address differences in underlying biology and treatment response/management among Black, Latina, and Asian American patients with early-stage breast cancer. These studies provide a broader understanding of how differential gene expression patterns, identified with MammaPrint and BluePrint, are unique to racial/ethnic groups and can impact treatment outcomes. Overall, the FLEX study strives to use MammaPrint, BluePrint, and newly developed immune signature, ImPrint, along with full transcriptome data to improve precision medicine in early-stage breast cancer. Citation Format: JJ Alberty-Oller, Lee Riley, Laila Samiian, Sarah Thayer, Olexiy Aseyev, Karen Tedesco, Victoria Poillucci, William Audeh, Danijela Jelovac, Joyce O'Shaughnessy. A prospective, international, observational, real-world evidence database, and collaborative platform for Investigator-Initiated Studies in Early-Stage Breast Cancer tested with MammaPrint and BluePrint– the FLEX Study [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-02-02.

Transcriptional signatures of fentanyl use in the mouse ventral tegmental area.

Synthetic opioids such as fentanyl contribute to the vast majority of opioid-related overdose deaths, but fentanyl use remains broadly understudied. Like other substances with misuse potential, opioids cause lasting molecular adaptations to brain reward circuits, including neurons in the ventral tegmental area (VTA). The VTA contains numerous cell types that play diverse roles in opioid use and relapse; however, it is unknown how fentanyl experience alters the transcriptional landscape in specific subtypes. Here, we performed single nuclei RNA sequencing to study transcriptional programs in fentanyl-experienced mice. Male and female C57/BL6 mice self-administered intravenous fentanyl (1.5μg/kg/infusion) or saline for 10days. After 24 h abstinence, VTA nuclei were isolated and prepared for sequencing on the 10× platform. We identified different patterns of gene expression across cell types. In dopamine neurons, we found enrichment of genes involved in growth hormone signalling. In dopamine-glutamate-GABA combinatorial neurons, and some GABA neurons, we found enrichment of genes involved in Pi3k-Akt signalling. In glutamate neurons, we found enrichment of genes involved in cholinergic signalling. We identified transcriptional regulators for the differentially expressed genes in each neuron cluster, including downregulated transcriptional repressor Bcl6, and upregulated transcription factor Tcf4. We also compared the fentanyl-induced gene expression changes identified in mouse VTA with a published rat dataset in bulk VTA, and found overlap in genes related to GABAergic signalling and extracellular matrix interaction. Together, we provide a comprehensive picture of how fentanyl self-administration alters the transcriptional landscape of the mouse VTA that serves as the foundation for future mechanistic studies.

Transcriptomics and starch biosynthesis analysis in leaves and developing seeds of mung bean provide a basis for genetic engineering of starch composition and seed quality.

Mung bean starch is distinguished by its exceptional high amylose content and regulation of starch biosynthesis in leaves and storage tissues, such as seeds, share considerable similarities. Genetic engineering of starch composition and content, requires detailed knowledge of starch biosynthetic gene expression and enzymatic regulation. In this study we applied detailed transcriptomic analyses to unravel the global differential gene expression patterns in mung bean leaves and in seeds during various stages of development. The objective was to identify candidate genes and regulatory mechanisms that may enable generation of desirable seed qualities through the use of genetic engineering. Notable differences in gene expression, in particular low expression of the Protein Targeting to Starch (PTST), starch synthase (SS) 3, and starch branching enzyme1 (SBE1) encoding genes in developing seeds as compared to leaves were evident. These differences were related to starch molecular structures and granule morphologies. Specifically, the starch molecular size distribution at different stages of seed development correlated with the starch biosynthesis gene expression of the SBE1, SS1, granule-bound starch synthases (GBSS) and isoamylase 1 (ISA1) encoding genes. Furthermore, putative hormonal and redox controlled regulation were observed, which may be explained by abscisic acid (ABA) and indole-3-acetic acid (IAA) induced signal transduction, and redox regulation of ferredoxins and thioredoxins, respectively. The morphology of starch granules in leaves and developing seeds were clearly distinguishable and could be correlated to differential expression of SS1. Here, we present a first comprehensive transcriptomic dataset of developing mung bean seeds, and combined these findings may enable generation of genetic engineering strategies of for example starch biosynthetic genes for increasing starch levels in seeds and constitute a valuable toolkit for improving mung bean seed quality.

Long Non-Coding RNAs as Determinants of Thyroid Cancer Phenotypes: Investigating Differential Gene Expression Patterns and Novel Biomarker Discovery.

Thyroid Cancer (TC) is the most common endocrine malignancy, with increasing incidence globally. Papillary thyroid cancer (PTC), a differentiated form of TC, accounts for approximately 90% of TC and occurs predominantly in women of childbearing age. Although responsive to current treatments, recurrence of PTC by middle age is common and is much more refractive to treatment. Undifferentiated TC, particularly anaplastic thyroid cancer (ATC), is the most aggressive TC subtype, characterized by it being resistant and unresponsive to all therapeutic and surgical interventions. Further, ATC is one of the most aggressive and lethal malignancies across all cancer types. Despite the differences in therapeutic needs in differentiated vs. undifferentiated TC subtypes, there is a critical unmet need for the identification of molecular biomarkers that can aid in early diagnosis, prognosis, and actionable therapeutic targets for intervention. Advances in the field of cancer genomics have enabled for the elucidation of differential gene expression patterns between tumors and healthy tissue. A novel category of molecules, known as non-coding RNAs, can themselves be differentially expressed, and extensively contribute to the up- and downregulation of protein coding genes, serving as master orchestrators of regulated and dysregulated gene expression patterns. These non-coding RNAs have been identified for their roles in driving carcinogenic patterns at various stages of tumor development and have become attractive targets for study. The identification of specific genes that are differentially expressed can give insight into mechanisms that drive carcinogenic patterns, filling the gaps of deciphering molecular and cellular processes that modulate TC subtypes, outside of well-known driver mutations.

The genome regulatory landscape of Atlantic salmon liver through smoltification.

The anadromous Atlantic salmon undergo a preparatory physiological transformation before seawater entry, referred to as smoltification. Key molecular developmental processes involved in this life stage transition, such as remodeling of gill functions, are known to be synchronized and modulated by environmental cues like photoperiod. However, little is known about the photoperiod influence and genome regulatory processes driving other canonical aspects of smoltification such as the large-scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. Here we generate transcriptome, DNA methylation, and chromatin accessibility data from salmon livers across smoltification under different photoperiod regimes. We find a systematic reduction of expression levels of genes with a metabolic function, such as lipid metabolism, and increased expression of energy related genes such as oxidative phosphorylation, during smolt development in freshwater. However, in contrast to similar studies of the gill, smolt liver gene expression prior to seawater transfer was not impacted by photoperiodic history. Integrated analyses of gene expression, chromatin accessibility, and transcription factor (TF) binding signatures highlight chromatin remodeling and TF dynamics underlying smolt gene regulatory changes. Differential peak accessibility patterns largely matched differential gene expression patterns during smoltification and we infer that ZNF682, KLFs, and NFY TFs are important in driving a liver metabolic shift from synthesis to break down of organic compounds in freshwater. Overall, chromatin accessibility and TFBS occupancy were highly correlated to changes in gene expression. On the other hand, we identified numerous differential methylation patterns across the genome, but associated genes were not functionally enriched or correlated to observed gene expression changes across smolt development. Taken together, this work highlights the relative importance of chromatin remodeling during smoltification and demonstrates that metabolic remodeling occurs as a preadaptation to life at sea that is not to a large extent driven by photoperiod history.

Gene expression profiles of white bass (Morone chrysops) and hybrid striped bass (M. chrysops x M. saxatilis) gill tissue following Flavobacterium covae infection

Columnaris disease is a prevalent disease in freshwater environments caused by the ubiquitous aquatic pathogen Flavobacterium species. Adhesion to the external mucosal surfaces of fishes is the initial stage of infection, and the gills specifically have been identified as both a primary target and release site for this pathogen. Demonstrated here and in previous research, the hybrid striped bass (Morone chrysops x M. saxatilis), a prominent United States aquaculture product, is more susceptible to infection with F. covae than the maternal white bass (M. chrysops) parental species. To further elucidate the mechanisms underlying differences in resistance between these fish we examined gill gene expression profiles using RNA sequencing at different timepoints after F. covae infection. Patterns of differential gene expression and association with key enrichment terms indicate the effective immune response observed in white bass includes the up-regulation of multiple cytokines (IL-1β, IL-17C, TNF-α, G-CSF, IL-8, CCL16, CXCL9), hepcidins (HAMP and HAMP2), ribosomal subunit components (e.g., RPL13), and, interestingly, the down-regulation of leptin (LEPA) during initial (1 – 4 h) stages of infection. Conversely, up-regulation of the same genes was not detected in hybrid striped bass until 24 h after infection, indicating a delay in immune response mechanisms that is ultimately ineffective in protecting the host, as this was concurrent with the onset of mortality in these fish. Collectively, the presented results include several putative pathways and candidate genes for further investigation toward characterizing immune defense mechanisms underlying the resistance (white bass) and susceptibility (hybrid striped bass) for selective breeding efforts and/or biotechnological intervention.

Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana (Scleropages formosus).

Asia arowana (Scleropages formosus) is an ornamental fish with high economic value, while its sex determination mechanism is still poorly understood. By far, no morphological evidence or molecular marker has been developed for effective distinguishment of genders, which poses a critical challenge to our captive breeding efforts. In this study, we sequenced gonadal transcriptomes of adult Asian arowanas and revealed differential expression profiling of sex-related genes. Based on the comparative transcriptomics analysis of testes (n = 3) and ovaries (n = 3), we identified a total of 8,872 differentially expressed genes (DEGs) and 18,490 differentially expressed transposable elements (TEs) between male and female individuals. Interestingly, the expression of TEs usually has been more significantly testis-biased than related coding genes. As expected, several genes related to females (such as foxl2 and cyp19a1a) are significantly transcribed in the ovary, and some genes related to male gonad development (such as dmrt1, gsdf and amh) are highly expressed in the testis. This sexual dimorphism is valuable for ascertaining the differential expression patterns of sex-related genes and enriching the genetic resources of this economically important species. These valuable genetic materials thereby provide instructive references for gender identification and one-to-one breeding practices so as to expand fish numbers for a rapid elevation of economic value.

Gene expression variation in geographically diverse populations of two North American songbird species

The range distributions of many bird species cover extensive geographic distances, exposing each local population to unique ecological challenges. Understanding the molecular basis of how species adapt to diverse habitats across their geographic range is crucial for identifying populations at risk and implementing effective conservation strategies. In this study, we employed two passerine species, the black-capped chickadee (Poecile atricapillus) and the American goldfinch (Spinus tristis), which are widely distributed across North America. This study focused on examining changes in gene expression within their distinct populations inhabiting diverse habitats across various geographical locations. A comparative transcriptomic study was conducted on wild-caught birds from two geographically separate locations, Boston, Massachusetts, and Kent, Ohio, characterized by considerable annual variability in winter severity. We tested the hypothesis that populations of both species in Kent and Boston would show differential gene expression patterns in their brains in response to unique local environmental conditions. Analyzing the differentially expressed genes (DEGs) in black-capped chickadees revealed associations with neural processes such as the generation and maintenance of neurons, activity-dependent plasticity, and cognitive ability. Many of these genes were linked to brain variation in chickadee populations related to spatial cognition associated with food caching. We also compared changes in gene expression levels with coding sequence variability to explore the underlying basis of differential gene expression patterns. We tested the hypothesis that expression differences are driven by underlying genetic variation. A population genetic analysis on transcriptome data from both species revealed no highly divergent genetic variants (single nucleotide polymorphisms or SNPs) in the coding regions of genes identified as differentially expressed. However, some of the DEGs themselves were transcription factors or regulatory molecules, as were some of the genes with highly divergent SNPs. These findings suggest that the genetic architecture underlying the differential gene expression patterns is mostly regulatory rather than protein-coding changes.

A Novel Nucleic Acid Sensing-related Genes Signature for Predicting Immunotherapy Efficacy and Prognosis of Lung Adenocarcinoma.

As a novel pillar for lung adenocarcinoma (LUAD) treatment, immunotherapy has limited efficiency in LUAD patients. The nucleic acid sensing (NAS) pathways are critical in the anti-tumor immune response, but their role in LUAD remains controversial. The study aims to develop a classification system to identify immune subtypes of LUAD based on nucleic acid sensing-related genes so that it can help screen patients who may respond to immunotherapy. We performed a comprehensive bioinformatics analysis of the NAS molecule expression profiles across multiple public datasets. Using qRT-PCR to verify the NAS genes in multiple lung cancer cell lines. Molecular docking was performed to screen drug candidates. The NAS-activated subgroup and NAS-suppressed subgroup were validated based on the different patterns of gene expression and pathways enrichment. The NAS-activated subgroup displayed a stronger immune infiltration and better prognosis of patients. Moreover, we constructed a seven nucleic acid sensing-related risk score (NASRS) model for the convenience of clinical application. The predictive values of NASRS in prognosis and immunotherapy were subsequently fully validated in the lung adenocarcinoma dataset and the uroepithelial carcinoma dataset. Additionally, five potential drugs binding to the core target of the NAS signature were predicted through molecular docking. We found a significant correlation between nucleic acid sensing function and the immune treatment efficiency in LUAD. The NASRS can be used as a robust biomarker for the predicting of prognosis and immunotherapy efficiency and may help in clinical decisions for LUAD patients.

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.

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 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.

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 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 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.

Modulation of neural gene networks by estradiol in old rhesus macaque females.

The postmenopausal decrease in circulating estradiol (E2) levels has been shown to contribute to several adverse physiological and psychiatric effects. To elucidate the molecular effects of E2 on the brain, we examined differential gene expression and DNA methylation (DNAm) patterns in the nonhuman primate brain following ovariectomy (Ov) and subsequent subcutaneous bioidentical E2 chronic treatment. We identified several dysregulated molecular networks, including MAPK signaling and dopaminergic synapse response, that are associated with ovariectomy and shared across two different brain areas, the occipital cortex (OC) and prefrontal cortex (PFC). The finding that hypomethylation (p = 1.6 × 10-51) and upregulation (p = 3.8 × 10-3) of UBE2M across both brain regions provide strong evidence for molecular differences in the brain induced by E2 depletion. Additionally, differential expression (p = 1.9 × 10-4; interaction p = 3.5 × 10-2) of LTBR in the PFC provides further support for the role E2 plays in the brain, by demonstrating that the regulation of some genes that are altered by ovariectomy may also be modulated by Ov followed by hormone replacement therapy (HRT). These results present real opportunities to understand the specific biological mechanisms that are altered with depleted E2. Given E2's potential role in cognitive decline and neuroinflammation, our findings could lead to the discovery of novel therapeutics to slow cognitive decline. Together, this work represents a major step toward understanding molecular changes in the brain that are caused by ovariectomy and how E2 treatment may revert or protect against the negative neuro-related consequences caused by a depletion in estrogen as women approach menopause.

Retracted: Discovering Common Pathophysiological Processes between COVID-19 and Cystic Fibrosis by Differential Gene Expression Pattern Analysis.

[This retracts the article DOI: 10.1155/2022/8078259.].