Gene Status Research Articles

Mutations and intron polymorphisms in voltage-gated sodium channel genes of different geographic populations of Culex pipiens pallens/Culex pipiens quinquefasciatus in China

BackgroundCulex pipiens pallens and Culex pipiens quinquefasciatus are the dominant species of Culex mosquitoes in China and important disease vectors. Long-term use of insecticides can cause mutations in the voltage-gated sodium channel (vgsc) gene of mosquitoes, but little is known about the current status and evolutionary origins of vgsc gene in different geographic populations. Therefore, this study aimed to determine the current status of vgsc genes in Cx. p. pallens and Cx. p. quinquefasciatus in China and to investigate the evolutionary inheritance of neighboring downstream introns of the vgsc gene to determine the impact of insecticides on long-term evolution.MethodsSampling was conducted from July to September 2021 in representative habitats of 22 provincial-level administrative divisions in China. Genomic DNA was extracted from 1308 mosquitoes, the IIS6 fragment of the vgsc gene on the nerve cell membrane was amplified using polymerase chain reaction, and the sequence was used to evaluate allele frequency and knockdown resistance (kdr) frequency. MEGA 11 was used to construct neighbor-joining (NJ) tree. PopART was used to build a TCS network.ResultsThere were 6 alleles and 6 genotypes at the L1014 locus, which included the wild-type alleles TTA/L and CTA/L and the mutant alleles TTT/F, TTC/F, TCT/S and TCA/S. The geographic populations with a kdr frequency less than 20.00% were mainly concentrated in the regions north of 38° N, and the geographic populations with a kdr frequency greater than 80.00% were concentrated in the regions south of 30° N. kdr frequency increased with decreasing latitude. And within the same latitude, the frequency of kdr in large cities is relatively high. Mutations were correlated with the number of introns. The mutant allele TCA/S has only one intron, the mutant allele TTT/F has three introns, and the wild-type allele TTA/L has 17 introns.ConclusionsCx. p. pallens and Cx. p. quinquefasciatus have developed resistance to insecticides in most regions of China. The neighboring downstream introns of the vgsc gene gradually decreased to one intron with the mutation of the vgsc gene. Mutations may originate from multiple mutation events rather than from a single origin, and populations lacking mutations may be genetically isolated.Graphical

Lethal phenotypes in Mendelian disorders

PurposeExisting resources that characterize the essentiality status of genes are based on either proliferation assessment in human cell lines, viability evaluation in mouse knockouts, or constraint metrics derived from human population sequencing studies. Several repositories document phenotypic annotations for rare disorders; however, there is a lack of comprehensive reporting on lethal phenotypes. MethodsWe queried Online Mendelian Inheritance in Man for terms related to lethality and classified all Mendelian genes according to the earliest age of death recorded for the associated disorders, from prenatal death to no reports of premature death. We characterized the genes across these lethality categories, examined the evidence on viability from mouse models and explored how this information could be used for novel gene discovery. ResultsWe developed the Lethal Phenotypes Portal to showcase this curated catalog of human essential genes. Differences in the mode of inheritance, physiological systems affected, and disease class were found for genes in different lethality categories, as well as discrepancies between the lethal phenotypes observed in mouse and human. ConclusionWe anticipate that this resource will aid clinicians in the diagnosis of early lethal conditions and assist researchers in investigating the properties that make these genes essential for human development.

Cadmium toxicity promotes hormonal imbalance and induces the expression of genes involved in systemic resistances in barley.

Cadmium (Cd) is a widely distributed pollutant that adversely affects plants' metabolism and productivity. Phytohormones play a vital role in the acclimation of plants to metal stress. On the other hand, phytohormones trigger systemic resistances, including systemic acquired resistance (SAR) and induced systemic resistance (ISR), in plants in response to biotic interactions. The present study aimed to investigate the possible induction of SAR and ISR pathways in relation to the hormonal alteration of barley seedlings in response to Cd stress. Barley seedlings were exposed to 1.5mgg-1 Cd in the soil for three days. The nutrient content, oxidative status, phytohormones profile, and expression of genes involved in SAR and ISR pathways of barley seedlings were examined. Cd accumulation resulted in a reduction in the nutrient content of barley seedlings. The specific activity of superoxide dismutase and the hydrogen peroxide content significantly increased in response to Cd toxicity. Abscisic acid, jasmonic acid, and ethylene content increased under Cd exposure. Cd treatment resulted in the upregulation of NPR1, PR3, and PR13 genes in SAR pathways. The transcripts of PAL1 and LOX2.2 genes in the ISR pathway were also significantly increased in response to Cd treatment. These findings suggest that hormonal-activated systemic resistances are involved in the response of barley to Cd stress.

Growth performance, health status, gut microbiome, and expression of immune and growth-related genes of rainbow trout (Oncorhynchus mykiss) fed diets with pea protein replacement of fish meal

The need for fish meal constrains fish farming and significantly impacts sustainability of the aquaculture industry. Hence, it is important to investigate the use of plant-based protein sources in fish diets. The present study was conducted to determine the effects of different levels of fish meal (FM) replacement by pea protein (PP) in a 60-day feeding experiment in rainbow trout, Oncorhynchus mykiss. Effects on growth performance, body composition, hematology, serum biochemistry and immunology, and immune (TNF-α, IL1-ß and Il-8) and growth-related (GH and IGFI) gene expression were investigated. Five experimental diets (45% protein and 20% lipid) differed in replacement level of FM by PP at rates of 0% (control (PP0)), 25% (PP25), 50%(PP50), 75%(PP75) and 100%(PP100). Fish were fed with experimental diets in triplicate twice daily. The best growth performance was obtained in PP0 and PP25 groups. While fat ratios of fish fillets significantly differed (p < 0.05), there was no significant effects on protein ratios (p < 0.05). There was no significant change in the hematological values of fish, except those fed the PP100 diets, which displayed a reduction in eyrthocyte counts, hemoglobin content and hematocrit. As PP supplementation increased fish showed elevated serum glucose, total protein, cholesterol and myeloperoxidase activity and decreased glutamic pyruvic transaminase and alkaline phosphatase activity. Fish fed diets with between 25 and 75% replacement showed a decline in lactic acid bacteria in the gut. Significant increases in expression were observed in the liver of the PP25 fish relative to the 0% control for all immune and growth-related genes except for IL1-ß. These data suggest that up to 25% of FM can be replaced by PP without any adverse effects on rainbow trout.

UBA2 as a Prognostic Biomarker and Potential Therapeutic Target in Glioma.

Gliomas are characterized by aggressive behavior, leading to severe disability and high mortality. Ubiquitin-like modifier activating enzyme 2 (UBA2) is a subunit of the E1-activating enzyme involved in the SUMOylation (SUMO, small ubiquitin-related modifier) of numerous proteins. Although the abnormality of UBA2 is linked to the progression of various tumor types, the role of UBA2 in glioma is still unknown. A bioinformatic analysis using several public databases was conducted to examine the expression level, clinicopathological correlations, and prognostic significance of UBA2 in glioma. The correlation between UBA2 expression and drug sensitivity in cancers was also explored. Multiple cellular experiments were conducted to validate the role of UBA2 in glioma. Analysis of multiple databases and cellular experiments revealed that UBA2 was overexpressed in glioma tissues and cell lines, respectively. UBA2 expression in gliomas correlated with World Health Organization (WHO) grade, IDH gene status, 1p19q deletion, histological type, and immune cell infiltration in glioma. UBA2 expression in carcinomas also correlated with drug sensitivity. Kaplan-Meier analysis revealed that high expression of UBA2 predicted poorer survival in glioma patients. A nomogram model containing UBA2 expression was constructed for clinical practice. Knockdown of UBA2 was observed to suppress glioma cell progression and sensitize glioma cells to irradiation in vitro. Overall, this research showed that UBA2 might be involved not only in the development of glioma but also in the regulation of immunity, drug sensitivity, and radiosensitivity. Therefore, UBA2 may be a potential target for therapy and a candidate biomarker for glioma diagnosis and prognosis.

Epidemiological and clinicopathological features of KRAS, NRAS, BRAF mutations and MSI in Chinese patients with stage I-III colorectal cancer.

The selection of appropriate treatment modalities based on the presence or absence of mutations in KRAS, NRAS, BRAF, and the microsatellite instability (MSI) status has become a crucial consensus in colorectal cancer (CRC) therapy. However, the distribution pattern of these genetic mutations and the prevalence of MSI status in Chinese stage I-III CRCs remain unclear. We retrospectively analyzed clinicopathological features, mutations in the KRAS, NRAS, and BRAF genes, as well as MSI status of 411 patients with stage I-III CRC who underwent surgery from June 2020 to December 2022 in the First Affiliated Hospital of Nanjing Medical University. The mutation rates of KRAS, NRAS, and BRAF were 48.9%, 2.2%, and 3.2%, respectively, and the microsatellite instability-high rate was 9.5%. KRAS mutation was independently associated with mucinous adenocarcinoma. Multivariate analysis suggested that tumor location and mucinous adenocarcinoma were independently associated with BRAF mutation. Only T stage was associated with NRAS mutations in the univariate analysis. Multivariate analysis revealed that factors such as larger tumor size, tumor location, younger age, and poor differentiation were independently associated with microsatellite instability-high status. The results illustrate the mutation frequencies of KRAS, NRAS, BRAF genes and MSI status in stage I-III CRC from the eastern region of China. These findings further validate the associations between these genes status and various clinicopathological characteristics.

DNA methylation regulates the secondary metabolism of saponins to improve the adaptability of Eleutherococcus senticosus during drought stress

Plant growth and development can be significantly impacted by drought stress. Plants will adjust the synthesis and accumulation of secondary metabolites to improve survival in times of water constraint. Simultaneously, drought stress can lead to modifications in the DNA methylation status of plants, and these modifications can directly impact gene expression and product synthesis by changing the DNA methylation status of functional genes involved in secondary metabolite synthesis. However, further research is needed to fully understand the extent to which DNA methylation modifies the content of secondary metabolites to mediate plants’ responses to drought stress, as well as the underlying mechanisms involved. Our study found that in Eleutherococcus senticosus (E. senticosus), moderate water deprivation significantly decreased DNA methylation levels throughout the genome and at the promoters of EsFPS, EsSS, and EsSE. Transcription factors like EsMYB-r1, previously inhibited by DNA methylation, can re-bind to the EsFPS promotor region following DNA demethylation. This process promotes gene expression and, ultimately, saponin synthesis and accumulation. The increased saponin levels in E. senticosus acted as antioxidants, enhancing the plant’s adaptability to drought stress.

LXRα Promotes Abdominal Aortic Aneurysm Formation Through UHRF1 Epigenetic Modification of miR-26b-3p.

Abdominal aortic aneurysm (AAA) is a severe aortic disease without effective pharmacological approaches. The nuclear hormone receptor LXRα (liver X receptor α), encoded by the NR1H3 gene, serves as a critical transcriptional mediator linked to several vascular pathologies, but its role in AAA remains elusive. Through integrated analyses of human and murine AAA gene expression microarray data sets, we identified NR1H3 as a candidate gene regulating AAA formation. To investigate the role of LXRα in AAA formation, we used global Nr1h3-knockout and vascular smooth muscle cell-specific Nr1h3-knockout mice in 2 AAA mouse models induced with angiotensin II (1000 ng·kg·min; 28 days) or calcium chloride (CaCl2; 0.5 mol/L; 42 days). Upregulated LXRα was observed in the aortas of patients with AAA and in angiotensin II- or CaCl2-treated mice. Global or vascular smooth muscle cell-specific Nr1h3 knockout inhibited AAA formation in 2 mouse models. Loss of LXRα function prevented extracellular matrix degeneration, inflammation, and vascular smooth muscle cell phenotypic switching. Uhrf1, an epigenetic master regulator, was identified as a direct target gene of LXRα by integrated analysis of transcriptome sequencing and chromatin immunoprecipitation sequencing. Susceptibility to AAA development was consistently enhanced by UHRF1 (ubiquitin-like containing PHD and RING finger domains 1) in both angiotensin II- and CaCl2-induced mouse models. We then determined the CpG methylation status and promoter accessibility of UHRF1-mediated genes using CUT&Tag (cleavage under targets and tagmentation), RRBS (reduced representation bisulfite sequencing), and ATAC-seq (assay for transposase-accessible chromatin with sequencing) in vascular smooth muscle cells, which revealed that the recruitment of UHRF1 to the promoter of miR-26b led to DNA hypermethylation accompanied by relatively closed chromatin states, and caused downregulation of miR-26b expression in AAA. Regarding clinical significance, we found that underexpression of miR-26b-3p correlated with high risk in patients with AAA. Maintaining miR-26b-3p expression prevented AAA progression and alleviated the overall pathological process. Our study reveals a pivotal role of the LXRα/UHRF1/miR-26b-3p axis in AAA and provides potential biomarkers and therapeutic targets for AAA.

Postpartum Breast Cancer and Survival in Women With Germline BRCA Pathogenic Variants

In young-onset breast cancer (YOBC), a diagnosis within 5 to 10 years of childbirth is associated with increased mortality. Women with germline BRCA1/2 pathogenic variants (PVs) are more likely to be diagnosed with BC at younger ages, but the impact of childbirth on mortality is unknown. To determine whether time between most recent childbirth and BC diagnosis is associated with mortality among patients with YOBC and germline BRCA1/2 PVs. This prospective cohort study included women with germline BRCA1/2 PVs diagnosed with stage I to III BC at age 45 years or younger between 1950 and 2021 in the United Kingdom, who were followed up until November 2021. Data were analyzed from December 3, 2021, to November 29, 2023. Time between most recent childbirth and subsequent BC diagnosis, with recent childbirth defined as 0 to less than 10 years, further delineated to 0 to less than 5 years and 5 to less than 10 years. The primary outcome was all-cause mortality, censored at 20 years after YOBC diagnosis. Mortality of nulliparous women was compared with the recent post partum groups and the 10 or more years post partum group. Cox proportional hazards regression analyses were adjusted for age, tumor stage, and further stratified by tumor estrogen receptor (ER) and BRCA gene status. Among 903 women with BRCA PVs (mean [SD] age at diagnosis, 34.7 [6.1] years; mean [SD] follow-up, 10.8 [9.8] years), 419 received a BC diagnosis 0 to less than 10 years after childbirth, including 228 women diagnosed less than 5 years after childbirth and 191 women diagnosed 5 to less than 10 years after childbirth. Increased all-cause mortality was observed in women diagnosed within 5 to less than 10 years post partum (hazard ratio [HR], 1.56 [95% CI, 1.05-2.30]) compared with nulliparous women and women diagnosed 10 or more years after childbirth, suggesting a transient duration of postpartum risk. Risk of mortality was greater for women with ER-positive BC in the less than 5 years post partum group (HR, 2.35 [95% CI, 1.02-5.42]) and ER-negative BC in the 5 to less than 10 years post partum group (HR, 3.12 [95% CI, 1.22-7.97]) compared with the nulliparous group. Delineated by BRCA1 or BRCA2, mortality in the 5 to less than 10 years post partum group was significantly increased, but only for BRCA1 carriers (HR, 2.03 [95% CI, 1.15-3.58]). These findings suggest that YOBC with germline BRCA PVs was associated with increased risk for all-cause mortality if diagnosed within 10 years after last childbirth, with risk highest for ER-positive BC diagnosed less than 5 years post partum, and for ER-negative BC diagnosed 5 to less than 10 years post partum. BRCA1 carriers were at highest risk for poor prognosis when diagnosed at 5 to less than 10 years post partum. No such associations were observed for BRCA2 carriers. These results should inform genetic counseling, prevention, and treatment strategies for BRCA PV carriers.

THE EFFECT OF PRIMARY LOCALIZATION OF COLORECTAL CANCER&#x0D; ON KRAS STATUS AND ITS PROGNOSTIC VALUE

Relevance: Colorectal cancer (CRC), arising from the right-sided or left-sided colon, is a separate clinical and pathological unit. The status&#x0D; of KRAS and its predictive value in CRC remain controversial.&#x0D; The study aimed to explore the effect of primary tumor localization on KRAS gene status in CRC.&#x0D; Methods: The study included 60 patients with colon and rectal cancer. The KRAS mutation test was performed on paraffin-coated tumor samples&#x0D; using PCR methods. Colon cancer was divided into right-sided colon cancer (RSCC) and left-sided colon cancer (LSCC).&#x0D; Results: KRAS mutation was found much more often in rectal cancer (RC) and sigmoid colon (SC) (p=0.413) than in tumors in other parts&#x0D; of the colon. A combined analysis of our data and previously published data showed that KRAS mutation was more common in PSTC, especially&#x0D; in the area of the hepatic bend of the colon than in LSTC (p=0.120). The association of the KRAS mutation with the patient’s age (p&lt;0.012) and&#x0D; the duration of hospitalization (p&lt;0.001) was established.&#x0D; Conclusion: Our study revealed no significant difference in the KRAS status between colon cancer and rectal cancer. However, KRAS&#x0D; mutation was much more common in RSCC compared to LSCC. Patients with RSCC with mutated KRAS also had a worse prognosis and&#x0D; required longer hospitalization compared to wild-type KRAS. However, patients with LSCC did not demonstrate a similar effect.

Exploring Epigenetic and Genetic Modulation in Animal Responses to Thermal Stress.

There is increasing evidence indicating that global temperatures are rising significantly, a phenomenon commonly referred to as 'global warming', which in turn is believed to be causing drastic changes to the global climate. Global warming (GW) directly impacts animal health, reproduction, production, and welfare, presenting several challenges to livestock enterprises. Thermal stress (TS) is one of the key consequences of GW, and all animal species, including livestock, have diverse physiological, epigenetic and genetic mechanisms to respond to TS. As a result, TS can significantly affect an animals' health, immune responsiveness, metabolic pathways etc. which can also influence the productivity, performance, and welfare of animals. Moreover, prolonged exposure to TS can lead to transgenerational and intergenerational changes that are mediated by epigenetic changes. For example, in several animal species, the effects of TS are encoded epigenetically during the animals' growth or productive stage, and these epigenetic changes can be transmitted intergenerationally. Such epigenetic changes can affect animal productivity by changing the phenotype so that it aligns with its ancestors' environment, irrespective of its immediate environment. Furthermore, epigenetic and genetic changes can also help protect cells from the adverse effects of TS by modulating the transcriptional status of heat-responsive genes in animals. This review focuses on the genetic and epigenetic modulation and regulation that occurs in TS conditions via HSPs, histone alterations and DNA methylation.

DNA methylation markers for risk of metastasis in a cohort of men with localized prostate cancer

ABSTRACT Accurately identifying life-threatening prostate cancer (PCa) at time of diagnosis remains an unsolved problem. We evaluated whether DNA methylation status of selected candidate genes can predict the risk of metastasis beyond clinical risk factors in men with untreated PCa. A nested case-control study was conducted among men diagnosed with localized PCa at Kaiser Permanente California between 01/01/1997–12/31/2006 who did not receive curative treatments. Cases were those who developed metastasis within 10 years from diagnosis. Controls were selected using density sampling. Ninety-eight candidate genes were selected from functional categories of cell cycle control, metastasis/tumour suppressors, cell signalling, cell adhesion/motility/invasion, angiogenesis, and immune function, and 41 from pluripotency genes. Cancer DNA from diagnostic biopsy blocks were extracted and analysed. Associations of methylation status were assessed using CpG site level and principal components-based analysis in conditional logistic regressions. In 215 cases and 404 controls, 27 candidate genes were found to be statistically significant in at least one of the two analytical approaches. The agreement between the methods was 25.9% (7 candidate genes, including 2 pluripotency markers). The DNA methylation status of several candidate genes was significantly associated with risk of metastasis in untreated localized PCa patients. These findings may inform future risk prediction models for PCa metastasis beyond clinical characteristics.

Abstract 5170: Novel dSTRIDE-HR assays can accurately assess DNA repair defects in human cancers and distinguish HR status of tumors

Abstract Accurate patient stratification is crucial for the successful application of targeted anti-cancer therapeutic approaches. It has been shown that PARP inhibitors are synthetic lethal with defective homologous recombination (HR) repair, with genes such as BRCA1 and BRCA2 identified as conferring therapy resistance or sensitivity, depending on their mutational status. Moreover, there is evidence of patient benefit of carboplatin-based therapy in HR deficient (HRD) tumors. With a growing emphasis on HRD in cancer treatment, efforts have been made to define the HRD phenotype. Nonetheless, the current approaches employed in the clinic, such as Next Generation Sequencing (NGS), HRD score or RAD51 assays have significant limitations and their interpretation can be unclear. To answer the need for a functional HR-specific biomarker, we have recently developed and introduced two new assays, called collectively dSTRIDE-HR. The assays are based on the STRIDE platform technology that enables direct and sensitive detection of single- or double-strand DNA breaks in situ in fixed cells. Novel dSTRIDE-HR explicitly detect double-strand DNA breaks localized in close proximity to RPA (dSTRIDE-RPA) or RAD51 (dSTRIDE-RAD51) proteins. The assays have been shown to be reliable reporters of HR activation in cellular models after exogenous DNA damage induction, yet their potential to predict HR status in an in vivo setting has not been tested so far. To assess the suitability of the dSTRIDE-HR assays for determining the HR status of patients’ tumor cells, we applied these assays in FFPE sections from biopsies derived from breast cancer patients with a different mutational status of BRCA1 and BRCA2 genes. The assays showed low dSTRIDE-RPA and dSTRIDE-RAD51 readouts in BRCA1/2 mutated tumors in comparison to wild type tumors, as well as a great concordance of readouts within a given genetic background. Additionally, the cell cycle analysis proved nearly twofold increase in foci numbers of dSTRIDE-RPA and dSTRIDE-RAD51 in G2/S phase. Our study unveils a potential of dSTRIDE-HR assays to become predictive biomarkers reporting on the status of HR repair in breast tumors, although more patient samples need to be tested to confirm initial findings. Citation Format: Monika Jarosz, Zsombor Prucsi, Franek Sierpowski, Karolina Stepien, Sophie Ostrowska-Paton, Szymon Koman, Nadeem Riaz, Simon Powell, Fresia Pareja, Edaise da Silva, Magdalena Kordon-Kiszala, Kamil Solarczyk. Novel dSTRIDE-HR assays can accurately assess DNA repair defects in human cancers and distinguish HR status of 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 5170.

Abstract 3034: Krüppel-like factors in regulation of gastric cancer progression

Abstract Introduction: Gastric cancer (GC) is the third leading cause of cancer-associated mortality and the fifth most frequently diagnosed cancer worldwide. The development and progression of GC is a complicated multistage process subjected to dynamic changes in gene regulation. Investigating the effects of these changes is therefore critical for improving our knowledge about GC initiation and progression. Krüppel-like factors (KLFs) are evolutionarily conserved zinc finger-containing transcription factors with altered expressions and diverse regulatory functions in GC. We previously reported that there is loss of KLF4 in GC. Here we report that KLF4 is a crucial regulator of KLF5 expression and vice versa and together they regulate GC cell behavior. Methods: The Cancer Genome Atlas (TCGA) and pan cancer data of differential expressions of KLFs in GC was analyzed. TCGA RNAseq and clinical data for the differential expression status of KLF genes in normal and cancerous tissues and the clinicopathological association was accessed from the UALCAN web portal. The expressions of KLF4 and KLF5 in human normal stomach and GC and orthotopic xenografts were detected by immunohistochemistry (IHC). KLF4, KLF5 cross regulation was evaluated by gene manipulation of each gene individually and checking the expression of the other factor in GC cells. The effect of KLFs on GC cell proliferation, migration, and invasion was determined by Ki67 staining of tissues, PrestoBlue cell viability assay, scratch wound and transwell cell invasion assays. Results and Conclusion: Our results indicated that not only KLF4 and KLF5 have contrasting expressions and effects in GC but also these two factors cross regulate each other. While lower expressions of KLF4 was found in human GC and orthotopic xenografts, increased expression of KLF5 was found in both human GC tissue and orthotopic xenografts. KLF4 silencing and CRISPR/Cas9 knockdown in human GC cells resulted in increased expression of KLF5 which was associated with increased GC cell proliferation and invasiveness. Interestingly, KLF5 knockdown by CRISPR/Cas9 in human GC cells on the other hand resulted in increased expression of KLF4, which was associated with decreased GC cell growth. Our data therefore suggests that the differential expressions of KLF4 and KLF5 might serve as valuable prognostic markers in GC. Citation Format: Sooraj Kakkat, Prabhat Suman, Sandeep Goswami, Sujit Basu, Martin J. Heslin, Elba A. Turbat-Herrera, Veronica Ramirez Alcantara, Chandrani Sarkar, Debanjan Chakroborty. Krüppel-like factors in regulation of gastric cancer progression [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 3034.

Abstract 7001: Profiling the CpG methylation patterns of Epstein-Barr virus DNA in lymphoma patients from Ethiopia

Abstract Introduction: Epstein-Barr virus (EBV) is a tumor virus associated with various malignancies, driven by genetic mutations and epigenetic alterations, including DNA methylation. Abnormal CpG methylation holds promise as a diagnostic and therapeutic biomarker for EBV-associated tumors. However, the understanding of EBV's epigenetic mechanisms remain limited. Determining the methylation profile of EBV is crucial for gaining insights into the pathogenesis of EBV-associated tumors, developing diagnostic biomarkers, and exploring potential therapeutic strategies. Therefore, our study aimed to assess the CpG methylation profile of EBV DNA in lymphoma patients from Ethiopia. Methods: This study enrolled 115 lymphoma patients from Tikur Anbessa Specialized Hospital in Addis Ababa, Ethiopia. Plasma and formalin-fixed paraffin-embedded blocks were collected from the participants, and isolation of DNA was performed from these samples. The methylation analysis was performed using the methylation-iPLEX assay. iPLEX capture and extension primers were designed to amplify and target EBV CpGs from bisulfite-converted DNA sequences. Ethical approval was also obtained from respected institutions. Results: Among the 115 participants, 65.2% (n = 75) were male patients. The largest proportion (n = 35, 30.4%) fell within the 41-60 age group. Non-Hodgkin lymphoma (NHL) was diagnosed in 96 patients, while 19 had Hodgkin lymphoma (HL). In the NHL group, the majority (n = 27, 28.1%) were classified as diffuse large cell lymphoma, followed by follicular lymphoma (n = 24, 25%). Out of the different EBV genome methylation sites, we have identified 24 EBV genes to assess the methylation status of the EBV genome. Average methylation levels of these genes were ranged from 45% to 50%. Notably, the HL group exhibited significant heterogeneity in methylation levels, while the CpG methylation status of EBV genes in NHL subtypes demonstrated a consistent pattern. A significant proportion of our samples exhibited methylation loss in the lytic gene BZLF1 and at the origin of replication associated with lytic replication. Conclusions: This study presents the first data from East Africa, shedding light on the EBV DNA methylation status in a diverse group of lymphoma patients. Further investigations in different locations are necessary to elucidate the impact of EBV DNA methylation on tumor progression. Citation Format: Seifegebriel T. Feleke, Kidist Z. Shita, Abdulaziz A. Sherif, Fisihatsion T. Woldegebriel, Christoph Weigel, Elshafa H. Ahmed, Tamrat A. Zeleke, Robert A. Baiocchi. Profiling the CpG methylation patterns of Epstein-Barr virus DNA in lymphoma patients from Ethiopia [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 7001.

SG-Transunet: A segmentation-guided Transformer U-Net model for KRAS gene mutation status identification in colorectal cancer

Accurately identifying the Kirsten rat sarcoma virus (KRAS) gene mutation status in colorectal cancer (CRC) patients can assist doctors in deciding whether to use specific targeted drugs for treatment. Although deep learning methods are popular, they are often affected by redundant features from non-lesion areas. Moreover, existing methods commonly extract spatial features from imaging data, which neglect important frequency domain features and may degrade the performance of KRAS gene mutation status identification. To address this deficiency, we propose a segmentation-guided Transformer U-Net (SG-Transunet) model for KRAS gene mutation status identification in CRC. Integrating the strength of convolutional neural networks (CNNs) and Transformers, SG-Transunet offers a unique approach for both lesion segmentation and KRAS mutation status identification. Specifically, for precise lesion localization, we employ an encoder–decoder to obtain segmentation results and guide the KRAS gene mutation status identification task. Subsequently, a frequency domain supplement block is designed to capture frequency domain features, integrating it with high-level spatial features extracted in the encoding path to derive advanced spatial-frequency domain features. Furthermore, we introduce a pre-trained Xception block to mitigate the risk of overfitting associated with small-scale datasets. Following this, an aggregate attention module is devised to consolidate spatial-frequency domain features with global information extracted by the Transformer at shallow and deep levels, thereby enhancing feature discriminability. Finally, we propose a mutual-constrained loss function that simultaneously constrains the segmentation mask acquisition and gene status identification process. Experimental results demonstrate the superior performance of SG-Transunet over state-of-the-art methods in discriminating KRAS gene mutation status.

Transcriptomic Analysis of Alzheimer's Disease Pathways in a Pakistani Population.

Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder that is most prevalent in elderly individuals, especially in developed countries, and its prevalence is now increasing in developing countries like Pakistan. Our goal was to characterize key genes and their levels of expression and related molecular transcriptome networks associated with AD pathogenesis in a pilot case-control study in a Pakistani population. To obtain the spectrum of molecular networks associated with pathogenesis in AD patients in Pakistan (comparing cases and controls), we used high-throughput qRT-PCR (TaqMan Low-Density Array; n = 33 subjects) coupled with Affymetrix Arrays (n = 8) and Ingenuity Pathway Analysis (IPA) to identify signature genes associated with Amyloid processing and disease pathways. We confirmed 16 differentially expressed AD-related genes, including maximum fold changes observed in CAPNS2 and CAPN1. The global gene expression study observed that 61% and 39% of genes were significantly (p-value 0.05) up- and downregulated, respectively, in AD patients compared to healthy controls. The key pathways include, e.g., Amyloid Processing, Neuroinflammation Signaling, and ErbB4 Signaling. The top-scoring networks in Diseases and Disorders Development were Neurological Disease, Organismal Injury and Abnormalities, and Psychological Disorders. Our pilot study offers a non-invasive and efficient way of investigating gene expression patterns by combining TLDA and global gene expression method in AD patients by utilizing whole blood. This provides valuable insights into the expression status of genes related to Amyloid Processing, which could play potential role in future studies to identify sensitive, early biomarkers of AD in general.

Effect of rifampicin on TLR4-signaling pathways in the nucleus accumbens of the rat brain during abstinence of long-term alcohol treatment.

The treatment with the antibiotic rifampicin (Rif) led to a decrease in the frequency of neurodegenerative pathologies. There are suggestions that the mechanism of action of Rif may be mediated by its effect on toll-like receptor (TLR)4-dependent pathways. We evaluated the expression status of TLR4-dependent genes during abstinence from long-term alcohol treatments in the nucleus accumbens (NAc) of the rat brain, and also studied the effects of Rif to correct these changes. The long-term alcohol treatment was performed by intragastric delivery of ethanol solution. At the end of alcohol treatment intraperitoneal injections of Rif (100mg/kg) or saline were made. Extraction of the brain structures was performed on the 10th day of abstinence from alcohol. We used the SYBR Green qPCR method to quantitatively analyze the relative expression levels of the studied genes. The long-term alcohol treatment promotes an increase in the level of TLR4 mRNA and mRNA of its endogenous ligand high-mobility group protein B1 during abstinence drop alcohol in NAc of rats. The use of Rif in our study led to a decrease in the increased expression of high-mobility group protein B1, Tlr4, and proinflammatory cytokine genes (Il1β, Il6) in the NAc of the rat brain during abstinence of long-term alcohol treatment. In addition, Rif administration increased the decreased mRNA levels of anti-inflammatory cytokines (Il10, Il11). The data obtained indicate the ability of Rif to correct the mechanisms of the TLR4 system genes in the NAc of the rat brain during alcohol abstinence.

Seeking for associations of I/D polymorphism of ACE gene with self-reported work performance, memory, and cardiovascular health in a professional leadership community

Introduction. Maintaining labor efficiency, working under conditions of stress and uncertainty, high level of requirements to the functional state of workers in various professions actualize the occupational health study of work performance. Methodological applications of predictive medicine and psychogenetics make it possible to identify specific hereditary (biological) predispositions of individuals, to carry out professional orientation of a person, to provide humanistic recommendations on occupation of a certain type of professional activity.&#x0D; The study aims to identify a correlation between ACE genotypes and work performance capability in individuals from a professional leadership community.&#x0D; Materials and methods. Individuals from a professional leadership community, after dividing into two cohorts consisting of entrepreneurs and non-entrepreneurs, were interviewed and genotyped for evidence of genotype-by-insertion/deletion (I/D) polymorphism associations of the angiotensin I converting enzyme (ACE) gene and health status. Answers to 4 questions characterized the state of work performance and memory, and another 4 questions characterized the cardiovascular system. The mean age was 37±1.7 years for entrepreneurs and 34.23±0.66 years for non-entrepreneurs. There were 44 females and 129 males among them.&#x0D; Results. Analysis of genotyping of 173 people (25 entrepreneurs and 148 non-entrepreneurs) revealed a significant deviation of actual frequencies of I and D alleles from theoretically expected values in the whole group of managers and between non-entrepreneurs (p=0.95, χ2&gt;3.8). In all groups, there was a marked increase in the frequency of the I/I genotype at the expense of a decrease in the frequency of the D/D genotype compared to the literature data. A significant difference between D/D and I/D genotypes in work performance was found in entrepreneurs (p=0.9817), which coincides with a significant difference between their representatives by age (p&gt;0.99). Contrary to expectations, representatives of the D/D genotype, at least entrepreneurs, demonstrated the most optimal level of functioning of the autonomic nervous system. No associations were found between the genotype for the ACE gene (rs4646994) and work performance and memory.&#x0D; Conclusion. In the total sample of leaders and among the subgroup of non-entrepreneurs, a strong and reliable change in the frequencies of alleles I and D was found compared to the theoretically expected (frequencies). There was a significant increase in the frequency of I/I genotype in all groups. The significant difference in the rates between the D/D and I/D groups coincides with a significant difference between their representatives in terms of age. According to the results of test answers, representatives of entrepreneurs of D/D genotype had the most optimal level of vegetative nervous system functioning.

The value of minimal residual disease and IKZF1 deletion for predicting prognosis in adult patients with B-cell acute lymphoblastic leukemia

Objective: To reassess the prognostic value of minimal residual disease (MRD) and IKZF1 gene deletions in adults with B-cell acute lymphoblastic leukemia (B-ALL) who received pediatric-specific chemotherapy regimens during the Nanfang Hospital PDT-ALL-2016 trial. Methods: We retrospectively analyzed the prognosis of 149 adult patients with B-ALL who were admitted to Nanfang Hospital from January 2016 to September 2020. Prognostic factors were identified using Cox regression models. Results: The complete remission rate was 93.2% in 149 patients, with a 5-year overall survival (OS) rate of (54.3±5.0) % and a cumulative incidence of relapse (CIR) of (47.5±5.2) %. The Cox regression analysis revealed that MRD positivity at day 45 (MRD(3)) after induction therapy was independently associated with relapse risk (HR=2.535, 95%CI 1.122-5.728, P=0.025). Deletion of IKZF1 gene was independently associated with mortality risk (HR=1.869, 95%CI 1.034-3.379, P=0.039). Based on MRD(3) and IKZF1 gene status, we categorized adult patients with B-ALL into the low-risk (MRD(3)-negative and IKZF1 gene deletion-negative) and high-risk (MRD(3)-positive and/or IKZF1 gene wild type) groups. The 5-year OS and CIR rates were (45.5±6.0) % vs (69.4±8.6) % (P<0.001) and (61.6±8.3) % vs (25.5±6.5) % (P<0.001), respectively, in the high-risk and low-risk groups, respectively. The multivariate analysis showed that the high-risk group was an independent risk factor for OS (HR=3.937, 95%CI 1.975-7.850, P<0.001) and CIR (HR=4.037, 95%CI 2.095-7.778, P<0.001) . Conclusion: The combined use of MRD and IKZF1 gene in prognostic stratification can improve clinical outcome prediction in adult patients with B-ALL, helping to guide their treatment.