High-risk Genes Research Articles

Allogeneic Hematopoietic Cell Transplantation in Patients with Relapsed or Refractory Acute Leukemia

Introduction: Current guidelines support allogeneic hematopoietic cell transplantation (allo-HCT) in patients with acute leukemia who achieve complete remission (CR) and are at high risk for relapse. Patients with primary refractory disease or those refractory to re-induction therapy after relapse have a poor prognosis in the absence of allo-HCT. While several studies have addressed the role of allo-HCT in those settings, the measurable benefit of allo-HCT has not been defined in such patients. Most previous studies have included patients who received myeloablative conditioning and did not address the possible impact of molecular genetic risk factors. Objective: The present study assessed outcomes of allo-HCT in patients with refractory or relapsed (R/R) acute leukemia receiving myeloablative (MAC) or reduced intensity conditioning (RIC) regimens. Our goal was to identify novel risk factors associated with improved outcomes to aid patient selection in the setting of R/R acute leukemia. Methods: Patients with R/R acute leukemia undergoing allo-HCT at Memorial Sloan Kettering Cancer Center (MSK) between 2009 and 2020 were included. Patients had a marrow blast count of 5% or more at the time of allo-HCT and were classified into one of the following categories: primary induction failure (PIF), at least 2 lines of induction therapy; not in CR (NCR), no more than one line of induction therapy; untreated relapse (UR); and refractory relapse (RR), no remission after at least one line of re-induction therapy for relapse. Results: We identified 101 patients with acute myeloid leukemia (AML; n=94), acute lymphoblastic leukemia (ALL; n=3), biphenotypic acute leukemia (n=2), and plasmacytoid dendritic cell leukemia (n=2). Table 1 depicts patient and transplant characteristics. Median blast count at the time of allo-HCT was 8% (IQR, 5%,15%). 37 patients had at least one genomic alteration, and 30 patients had circulating blasts at the time of transplant. Grafts were from HLA-identical siblings in 30 patients, from HLA-matched unrelated donors in 51 patients and from HLA-mismatched or HLA-haploidentical donors in 20 patients. 61 and 40 patients received MAC and RIC, respectively. Graft source was unmodified bone marrow (n=8), unmodified peripheral blood stem cells (PBSC; n=80), or CD34+ cellselected peripheral blood stem cells (n=7). Overall survival (OS) at 4 years was 25% (95% CI: 18%, 35%). In univariate analysis, RIC (HR 1.71, p=0.035), presence of circulating blasts (HR 2.21, p=0.002), and high pre-transplant ferritin levels (HR 1.43, p=0.049) were associated with inferior OS. In multivariate analysis, RIC was associated with reduced OS. The 4-year cumulative incidence of relapse/disease progression and non-relapse mortality (NRM) was 54% (95% CI: 43%, 63%) and 24% (CI, 16%, 33%) respectively. In univariate analysis, RIC, presence of circulating blasts, and elevated pre-transplant ferritin levels were associated with increased NRM. In multivariate analysis, RIC and elevated pre-transplant ferritin levels were associated with high NRM. The cumulative incidence of acute graft-vs-host disease (aGVHD) was 45% (95% CI: 35%, 54%) at day 100. There was no statistically significant effect of genomic and molecular parameters on NRM and OS. However, high risk molecular mutations (TP53, RUNX1, ASXL1 or FLT3-ITD) had borderline association with relapse/disease progression (HR 1.7, p=0.073). Conclusion: Allo-HCT provides durable remission in a select group of patients with relapsed or refractory acute leukemia with an OS of 25% at 4 years. The presence of circulating blasts and elevated ferritin levels at the time of allo-HCT was associated with increased NRM and inferior OS in this retrospective analysis. Known high-risk gene mutations did not affect outcomes in this population. The impact of these parameters should be evaluated in a larger cohort of patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

MECOM copy number alterations identify a new group of myeloid neoplasms with a poor prognosis

Abstract Objective Myeloid neoplasms (MNs) harboring inv(3)(q21q26)/t(3;3)(q21;q26) or MECOM gene rearrangements as identified by fluorescence in situ hybridization (FISH) are known to carry a poor prognosis. The objective of this study is to assess prognostic impact of MNs with copy number alterations (CNA) in MECOM as compared to MNs with inv(3)/t(3;3) or MECOM rearrangements. We present those initial comparative results and secondarily assess whether genetic mutations that confer a worse clinical outcome are also associated with MNs with MECOM CNA. Methods A retrospective review of electronic pathology records was performed at Beth Israel Deaconess Medical Center. All MNs from 2016 – current with MECOM FISH (Abbott Molecular, Abbott Park, IL) confirmed analyses were extracted. Other additional items extracted included karyotype and next-generation sequencing (NGS) results of a 65 gene myeloid panel (SmartGenomics Myeloid Profile, PathGroup, Nashville, TN). Kaplan-Meier and ANOVA were performed using GraphPad Prism (San Diego, CA). Results A total of 307 cases were identified in which MECOM FISH was performed. Exclusion of cases lacking inv(3)/t(3;3), MECOM rearrangement, or MECOM CNA provided an initial study cohort of 20 cases. 5 cases had MECOM rearrangement with inv(3)/t(3;3), 7 had MECOM rearrangement without inv(3)/t(3;3), and 8 had MECOM CNA. 13 of 20 cases had a complex karyotype, 13 of 20 cases had a monosomal karyotype, 10 of 20 cases had both a complex and monosomal karyotype. Of the 20 cases in which MECOM FISH demonstrated inv(3)/t(3;3), MECOM rearrangement, or CNA, NGS was performed on 16 cases. Genes known to be associated with a significant negative overall survival (OS) include ASXL1, EZH2, IDH2, KRAS, NRAS, RAD21, RUNX1, SRSF2, STAG2, TP53 with single and multiple mutations found in 9 of 20 cases. Kaplan-Meier analysis revealed no significant difference in OS among the three MECOM aberration groupings (Log-rank test; p=0.77). Single factor ANOVA analysis revealed enrichment for high risk gene mutations in MECOM CNA (p=0.04) and TP53 mutations (p=0.04) when compared to MNs with MECOM rearrangements. Summary Our analysis of MNs with MECOM aberrations by FISH reveal that MECOM with CNA display similarly poor overall survival as MNs with inv(3)/t(3;3) and MECOM rearrangements. Additionally, the MECOM CNA group was enriched for high risk gene mutations and TP53 as compared to inv(3)/t(3;3) and MECOM rearrangement groups. Overall, the initial results of this study reveal a new group of MNs harboring MECOM CNA that confer a poor prognosis and high risk mutational profile.

High-risk HPV infection-associated hypermethylated genes in oropharyngeal squamous cell carcinomas

BackgroundHPV-positive oropharyngeal squamous cell carcinomas (OPSCCs) are sensitive to chemo-radiation therapy and have favorable survival outcomes compared with HPV-negative cancers. These tumors are usually not related to tobacco and alcohol exposure. Therefore, diagnosing HPV-positive OPSCCs for the appropriate disease management is crucial, and no suitable markers are available for detecting early malignancies in HPV-infected tissues. In this study, we attempt to find HPV-specific epigenetic biomarkers for OPSCCs.MethodsA total of 127 surgical samples were analyzed for HPV positivity and promoter methylation of a panel of genes. HPV detection was performed by PCR detection of HPV E6 and E7 viral oncoproteins. In addition, promoter methylation of a total of 8 genes (DAPK, FHIT, RASSF1A, TIMP3, AGTR1, CSGALNACT2, GULP1 and VGF) was analyzed by quantitative-methylation specific PCR (QMSP), and their associations with HPV positivity or RB/p16 expressions were evaluated.ResultsAGTR1 and FHIT were frequently methylated in HPV-positive OPSCC samples with a good area under the curve (AUC over 0.70). In addition, these genes' promoter methylation was significantly associated with p16 positive and RB negative cases, which were the characteristics of OPSCC cases with favorable survival outcomes. Either AGTR1 or FHIT methylated cases were significantly associated with HPV-positive cancers with 92.0% sensitivity (P < 0.001). Also, they had significantly better overall survival (P = 0.047) than both unmethylated cases.ConclusionsA combination of AGTR1 and FHIT methylation demonstrated a suitable detection marker of OPSCCs derived from the HPV-infected field, familiar with p16-positive and RB-negative phenotypes.

THBS1, a fatty acid-related metabolic gene, can promote the development of laryngeal cancer

Laryngeal cancer is the second most prevalent head and neck tumor and it is one of the most common malignancies of the upper respiratory tract. Fatty acid metabolism affects cancer cell biology in several ways, and alterations in fatty acid metabolism are characteristic of both tumorigenesis and metastasis. Despite advances in laryngeal cancer diagnosis and treatment over the years, there has been no significant improvement in survival or mortality. Studying the role of fatty acid metabolism-related genes in laryngeal cancer will facilitate our search for valuable biomarkers to guide prognostic management and treatment selection. We constructed a prognostic risk score model for fatty acid metabolism-related genes by downloading and analyzing laryngeal cancers from the TCGA and GEO databases. We predicted survival outcomes of laryngeal cancer patients using a prognostic risk score model of fatty acid metabolism-related genes and analyzed the resistance of laryngeal cancer in different individuals to multiple drugs. In addition, the relationship between the prognostic risk score model and cellular infiltration characteristics of the tumor microenvironment were investigated. Through the prognostic risk scoring model, the genes with risk-prompting effect and related to prognosis were screened out for further research. Through the study of gene expression levels in the TCGA database, we screened out 120 differentially expressed fatty acid metabolism genes. LASSO-Cox and Cox regression analyses identified nine genes associated with prognosis to construct a prognostic risk score model for genes related to fatty acid metabolism. Both TCGA and GEO confirmed that samples in the high-risk score group had a worse prognosis than those in the low-risk score group. We found significant differences between the high-risk and low-risk groups for 22 drugs (P < 0.05). In addition, we found differences in immune cell infiltration between the different risk score groups. Finally, through the risk assessment model, combined with multiple databases, THBS1, a high-risk and prognosis-related gene, was screened. We also found that THBS1 could promote the migration, invasion and proliferation of laryngeal cancer cells by constructing THBS1 knockout cell lines. In our study, we identified key fatty acid-related genes differentially expressed in laryngeal carcinoma that can be used to adequately predict prognosis using a comprehensive bioinformatic experimental approach. It was also found that THBS1, a high-risk and prognosis-related gene, may regulate the occurrence and development of laryngeal cancer through fatty acid metabolism, which has further helped us to explore the role of fatty acid metabolism genes in laryngeal cancer.

Effect of the m6ARNA gene on the prognosis of thyroid cancer, immune infiltration, and promising immunotherapy.

Accumulating evidence suggests that N6-methyladenosine (m6A) RNA methylation plays an important role in tumor proliferation and growth. However, its effect on the clinical prognosis, immune infiltration, and immunotherapy response of thyroid cancer patients has not been investigated in detail. Clinical data and RNA expression profiles of thyroid cancer were extracted from the Cancer Genome Atlas-thyroid carcinoma (TCGA-THCA) and preprocessed for consensus clustering. The risk model was constructed based on differentially expressed genes (DEGs) using Least Absolute Shrinkage and Selection Operator (LASSO) and Cox regression analyses. The associations between risk score and clinical traits, immune infiltration, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), immune infiltration, and immunotherapy were assessed. Immunohistochemistry was used to substantiate the clinical traits of our samples. Gene expression analysis showed that 17 genes, except YHTDF2, had significant differences (vs healthy control, P<0.001). Consensus clustering yielded 2 clusters according to their clinical features and estimated a poorer prognosis for Cluster 1 (P=0.03). The heatmap between the 2 clusters showed differences in T (P<0.01), N (P<0.001) and stage (P<0.01). Based on univariate Cox and LASSO regression, a risk model consisting of three high-risk genes (KIAA1429, RBM15, FTO) was established, and the expression difference between normal and tumor tissues of three genes was confirmed by immunohistochemical results of our clinical tissues. KEGG and GSEA analyses showed that the risk DEGs were related mainly to proteolysis, immune response, and cancer pathways. The levels of immune infiltration in the high- and low-risk groups were different mainly in iDCs (P<0.05), NK cells (P<0.05), and type-INF-II (P<0.001). Immunotherapy analysis yielded 30 drugs associated with the expression of each gene and 20 drugs associated with the risk score. Our risk model can act as an independent marker for thyroid cancer and provides promising immunotherapy targets for its treatment.

Association between cancer stem cell gene expression signatures and prognosis in head and neck squamous cell carcinoma

BackgroundVarious cancer stem cell (CSC) biomarkers and the genes encoding them in head and neck squamous cell carcinoma (HNSCC) have been identified and evaluated. However, the validity of these factors in the prognosis of HNSCC has been questioned and remains unclear. In this study, we examined the clinical significance of CSC biomarker genes in HNSCC, using five publicly available HNSCC cohorts.MethodsTo predict the prognosis of patients with HNSCC, we developed and validated the expression signatures of CSC biomarker genes whose mRNA expression levels correlated with at least one of the four CSC genes (CD44, MET, ALDH1A1, and BMI1).ResultsPatients in The Cancer Genome Atlas (TCGA) HNSCC cohort were classified into CSC gene expression-associated high-risk (CSC-HR; n = 285) and CSC gene expression-associated low-risk (CSC-LR; n = 281) subgroups. The 5-year overall survival and recurrence-free survival rates were significantly lower in the CSC-HR subgroup than in the CSC-LR subgroup (p = 0.04 and 0.02, respectively). The clinical significance of the CSC gene expression signature was validated using four independent cohorts. Analysis using Cox proportional hazards models showed that the CSC gene expression signature was an independent prognostic factor of non-oropharyngeal HNSCC which mostly indicates HPV (–) status. Furthermore, the CSC gene expression signature was associated with the prognosis of HNSCC patients who received radiotherapy.ConclusionThe CSC gene expression signature is associated with the prognosis of HNSCC and may help in personalized treatments for patients with HNSCC, especially in cases with HPV (–) status who were classified in more detail.

Seasonal variation of distribution and removal of high-risk tetracycline resistance genes in constructed wetland.

Livestock wastewater is an important reservoir of antibiotic resistance genes (ARGs), with high environmental risks. We investigated the seasonal variations of distribution and removal of swine wastewater originated high-risk tetracycline resistance genes (TRGs) in horizontal subsurface flow constructed wetlands. The effects of exogenous addition of tetracycline (TC) and copper ion (Cu2+) on the abundance of TRGs in effluent with single and combined pollution of antibiotic and heavy metal were studied. The results showed that all the three high-risk TRGs (tetM, tetO and tetW) were detected in swine wastewater. Wetlands could effectively reduce the ARGs, with the absolute abundance of TRGs in effluent being decreased by 1.1-2.4 and 1.7-2.9 orders of magnitude in summer and winter compared with the influent, respectively. The abundance of TRGs in wetland soils showed the characte-ristics that the outflow side was lower than the inflow side, the non-rhizosphere area was lower than the rhizosphere area, and lower in winter than in summer. In summer and winter, single and combined pollution of TC and Cu2+ in swine wastewater would increase the abundance of TRGs in effluent compared with that in the control. The constructed wetland is suitable for controlling the environmental diffusion of ARGs in livestock wastewater.

40 (PB030) - Genome-wide mapping of cancer dependency and genetic modifiers of chemotherapy using a high-risk hepatoblastoma genetic model

A lack of genetic models hampers our understanding of hepatoblastoma pathogenesis and the development of new therapies for this neoplasm. We have developed a liver-specific MYC-driven murine model that faithfully recapitulates the pathological features of human hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of the human disease. Single-cell RNA-sequencing and spatial transcriptomics identified distinct subpopulations of hepatoblastoma cells. After deriving cell lines from the mouse model, we mapped the cancer dependency genes using CRISPR-Cas9 screening and identified druggable targets conserved in human hepatoblastoma.

A Large Case-Control Study Performed in Spanish Population Suggests That RECQL5 Is the Only RECQ Helicase Involved in Breast Cancer Susceptibility.

Simple SummaryAround 50% of the familial breast cancer (BC) cases are estimated to be caused by variants in low-, moderate-, and high-risk susceptibility genes; however, the other half is of unknown origin. The finding of new susceptibility genes is key to improve diagnosis, take preventive measures, and identify new therapies. In this context, previous studies have discussed whether the genes encoding for the RECQ helicase family could play a role in BC susceptibility, without very conclusive results. To clarify this, in this study, we sequenced the whole coding sequence of the RECQL1, BLM, WRN, RECQL4, and RECQL5 genes in 1993 Spanish BC familial cases and compared it with controls from gnomAD. No association was found for RECQL1, BLM, WRN, and RECQL4; however, we did find an association between RECQL5 and breast cancer as a moderate-risk gene, making it a perfect candidate for further studies.Around 50% of the familial breast cancer (BC) cases are estimated to be caused by germline variants in known low-, moderate-, and high-risk susceptibility genes, while the other half is of unknown genetic origin. In the present study, we wanted to evaluate the role of the RECQ helicases, some of which have been studied in the past as candidates, with unclear results about their role in the disease. Using next-generation sequencing (NGS) technology, we analyzed the whole coding sequence of BLM, RECQL1, RECQL4, RECQL5, and WRN in almost 2000 index cases from BC Spanish families that had previously tested negative for the known BC susceptibility genes (BRCAX) and compared the results with the controls extracted from gnomAD. Our results suggest that BLM, RECQL1, RECQL4, and WRN do not play a major role in BC susceptibility. However, in the combined analysis, joining the present results with those previously reported in a series of 1334 BC Spanish patients and controls, we found a statistically significant association between Loss of Function (LoF) variants in RECQL5 and BC risk, with an OR of 2.56 (p = 0.009; 95% CI, 1.18–4.98). Our findings support our previous work and places the RECQL5 gene as a new moderate-risk BC gene.

Single-cell sequencing and establishment of an 8-gene prognostic model for pancreatic cancer patients.

BackgroundSingle-cell sequencing (SCS) technologies enable analysis of gene structure and expression data at single-cell resolution. However, SCS analysis in pancreatic cancer remains largely unexplored.MethodsWe downloaded pancreatic cancer SCS data from different databases and applied appropriate dimensionality reduction algorithms. We identified 10 cell types and subsequently screened differentially expressed marker genes of these 10 cell types using FindAllMarkers analysis. Also, we evaluated the tumor immune microenvironment based on ESTIMATE and MCP-counter. Statistical enrichment was evaluated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We used all candidate gene sets in KEGG database to perform gene set enrichment analysis. We used LASSO regression to reduce the number of genes in the pancreatic risk model by R package glmnet, followed by rtPCR to validate the expression of the signature genes in different pancreatic cancer cell lines.ResultsWe identified 15 cell subpopulations by dimension reduction and data clustering. We divided the 15 subpopulations into 10 distinct cell types based on marker gene expression. Then, we performed functional enrichment analysis for the 352 marker genes in pancreatic cancer cells. Based on RNA expression data and prognostic information from TCGA and GEO datasets, we identified 42 prognosis-related genes, including 5 protective genes and 37 high-risk genes, which we used to identified two molecular subtypes. C1 subtype was associated with a better prognosis, whereas C2 subtype was associated with a worse prognosis. Moreover, chemokine and chemokine receptor genes were differentially expressed between C1 and C2 subtypes. Functional and pathway enrichment uncovered functional differences between C1 and C2 subtype. We identified eight genes that could serve as potential biomarkers for prognosis prediction in pancreatic cancer patients. These genes were used to establish an 8-gene pancreatic cancer prognostic model.ConclusionsWe established an 8-gene pancreatic cancer prognostic model. This model can meaningfully predict prognosis and treatment response in pancreatic cancer patients.

Clinical Utility of Universal Germline Genetic Testing for Patients With Breast Cancer

National Comprehensive Cancer Network guidelines currently recommend germline testing for high-risk genes in selected patients with breast cancer. The clinical utility of recommending testing all patients with breast cancer with multigene panels is currently under consideration. To examine the implications of universal testing of patients with breast cancer with respect to clinical decision-making. Patients from a previously reported cohort were assessed as in-criteria or out-of-criteria according to the 2017 guidelines and underwent testing with a multigene germline panel between 2017 to 2018. Patients were women and men aged 18 to 90 years, with a new and/or previous diagnosis of breast cancer who had not undergone either single or multigene testing. Clinicians from 20 community and academic sites documented patient clinical information and changes to clinical recommendations made according to test findings. Association between prevalence of pathogenic or likely pathogenic germline variants and previously unreported clinical features, including scores generated by the BRCAPRO statistical model, was determined. Data were analyzed from April 2020 to May 2022. New and/or previous diagnosis of breast cancer. Disease management recommendations that were changed as a result of genetic testing results are reported. Clinicians were asked to assess changes to clinical management as a result of germline genetic testing for 952 patients. Informative clinician-reported recommendations were provided for 939 (467 in-criteria and 472 out-of-criteria) of the patients with breast cancer (936 [99.7%] female; 702 [74.8%] White; mean [SD] age at initial diagnosis, 57.6 [11.5] years). One or more changes were reported for 31 of 37 (83.8%) in-criteria patients and 23 of 34 (67.6%) out-of-criteria patients with a pathogenic or likely pathogenic variant. Recommendations were changed as a result of testing results for 14 of 22 (63.6%) out-of-criteria patients who had a variant in a breast cancer predisposition gene. Clinicians considered testing beneficial for two-thirds of patients with pathogenic or likely pathogenic variants and for one-third of patients with either negative results or variants of uncertain significance. There was no difference in variant rate between patients meeting the BRCAPRO threshold (≥10%) and those who did not (P = .86, Fisher exact test). No changes to clinical recommendations were made for most patients with negative results (345 of 349 patients [98.9%]) or variants of uncertain significance (492 of 509 patients [96.7%]). In this cohort study, germline genetic testing was used by clinicians to direct treatment for most out-of-criteria patients with breast cancer with pathogenic or likely pathogenic germline variants, including those with moderate-risk variants. Universal germline testing informs clinical decision-making and provides access to targeted treatments and clinical trials for all patients with breast cancer.

Mechanism investigation and experiment validation of capsaicin on uterine corpus endometrial carcinoma.

Background: Using bioinformatics analysis and experimental operations, we intend to analyze the potential mechanism of action of capsaicin target gene GATA1 in the treatment of uterine corpus endometrial carcinoma (UCEC) and develop a prognostic model for the disease to validate this model. Methods: By obtaining capsaicin and UCEC-related DR-DEGs, the prognosis-related gene GATA1 was screened. The survival analysis was conducted via establishing high and low expression groups of GATA1. Whether the GATA1 could be an independent prognostic factor for UCEC, it was also validated. The therapeutic mechanism of capsaicin-related genes in UCEC was further investigated using enrichment analysis and immune methods as well as in combination with single-cell sequencing data. Finally, it was validated by cell experiments. Results: GATA1, a high-risk gene associated with prognosis, was obtained by screening. Kaplan-Meier analysis showed that the survival of the high expression group was lower than that of low expression group. ROC curves showed that the prediction effect of the model was good and stable (1-year area under curve (AUC): 0.601; 2-years AUC: 0.575; 3-years AUC: 0.610). Independent prognosis analysis showed that the GATA1 can serve as an independent prognostic factor for UCEC. Enrichment analysis showed that “neuroactive Ligand - receptor interaction and TYPE I DIABETES MELLITUS” had a significant enrichment effect. Single-cell sequencing showed that the GATA1 was significantly expressed in mast cells. Cell experiments showed that the capsaicin significantly reduced the UCEC cell activity and migration ability, as well as inhibited the expression of GATA1. Conclusion: This study suggests that the capsaicin has potential value and application prospect in the treatment of UCEC. It provides new genetic markers for the prognosis of UCEC patients.

Hyperbaric Oxygen Therapy Alleviates Social Behavior Dysfunction and Neuroinflammation in a Mouse Model for Autism Spectrum Disorders.

Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental disorder (NDD) characterized by impaired social communication and repetitive behavior, among other symptoms. ASD is highly heritable, with SHANK3 being one of the high-risk genes for ASD. In recent years, knowledge has been growing regarding the neuroplasticity effect induced by hyperbaric oxygen therapy (HBOT) and its potential use for ASD. Here, we characterized the effect of HBOT on a mouse model for ASD with the human genetic condition of InsG3680 mutation in the Shank3 gene. As compared to placebo, HBOT improved social behavior and reduced neuroinflammation in the cortex of the InsG3680(+/+) mice. Specifically, HBOT induced upregulation of Insulin-like growth factor 1 (Igf1) expression levels and reduced the number of Iba1-positive cells in the mouse model for ASD compared to placebo control. Together, our research suggests that HBOT has the potential to improve the clinical outcome of ASD by ameliorating some of the core pathophysiological processes responsible for the development of the disorder.

Identification of novel cuproptosis-related lncRNA signatures to predict the prognosis and immune microenvironment of breast cancer patients.

BackgroundCuproptosis is a new modality of cell death regulation that is currently considered as a new cancer treatment strategy. Nevertheless, the prognostic predictive value of cuproptosis-related lncRNAs in breast cancer (BC) remains unknown. Using cuproptosis-related lncRNAs, this study aims to predict the immune microenvironment and prognosis of BC patients. and develop new therapeutic strategies that target the disease.MethodsThe Cancer Genome Atlas (TCGA) database provided the RNA-seq data along with the corresponding clinical and prognostic information. Univariate and multivariate Cox regression analyses were performed to acquire lncRNAs associated with cuproptosis to establish predictive features. The Kaplan-Meier method was used to calculate the overall survival rate (OS) in the high-risk and low-risk groups. High risk and low risk gene sets were enriched to explore functional discrepancies among risk teams. The mutation data were analyzed using the “MAFTools” r-package. The ties of predictive characteristics and immune status had been explored by single sample gene set enrichment analysis (ssGSEA). Last, the correlation between predictive features and treatment condition in patients with BC was analyzed. Based on prognostic risk models, we assessed associations between risk subgroups and immune scores and immune checkpoints. In addition, drug responses in at-risk populations were predicted.ResultsWe identified a set of 11 Cuproptosis-Related lncRNAs (GORAB-AS1, AC 079922.2, AL 589765.4, AC 005696.4, Cytor, ZNF 197-AS1, AC 002398.1, AL 451085.3, YTH DF 3-AS1, AC 008771.1, LINC 02446), based on which to construct the risk model. In comparison to the high-risk group, the low-risk patients lived longer (p < 0.001). Moreover, cuproptosis-related lncRNA profiles can independently predict prognosis in BC patients. The AUC values for receiver operating characteristics (ROC) of 1-, 3-, and 5-year risk were 0.849, 0.779, and 0.794, respectively. Patients in the high-risk group had lower OS than those in the low-risk group when they were divided into groups based on various clinicopathological variables. The tumor burden mutations (TMB) correlation analysis showed that high TMB had a worse prognosis than low-TMB, and gene mutations were found to be different in high and low TMB groups, such as PIK3CA (36% versus 32%), SYNE1 (4% versus 6%). Gene enrichment analysis indicated that the differential genes were significantly concentrated in immune-related pathways. The predictive traits were significantly correlated with the immune status of BC patients, according to ssGSEA results. Finally, high-risk patients showed high sensitivity in anti-CD276 immunotherapy and conventional chemotherapeutic drugs such as imatinib, lapatinib, and pazopanib.ConclusionWe successfully constructed of a cuproptosis-related lncRNA signature, which can independently predict the prognosis of BC patients and can be used to estimate OS and clinical treatment outcomes in BRCA patients. It will serve as a foundation for further research into the mechanism of cuproptosis-related lncRNAs in breast cancer, as well as for the development of new markers and therapeutic targets for the disease.

Family-based exome sequencing identifies candidate genes related to keratoconus in Chinese families.

Background: Keratoconus (KC) is a complex corneal disorder with a strong genetic component. The present study aimed to identify candidate genes related to KC in Chinese families. Methods: Family-based exome sequencing was performed in ten patients suffering from KC who belong to five families with two affected members in each. The candidate rare variants were identified with multi-step bioinformatics analysis. The STRING website was used to perform the protein interaction of the identified genes. Results: Our analyses identified 32 candidate rare variants in 13 genes by family-based exome sequencing. The molecular analyses of identified genes showed that EPCAM directly interacted with CTNNB1 of the Hippo signaling pathway and focal adhesion pathway, and directly interacted with CTNNB1, CDH1 of the WNT signaling pathway. SHROOM3 directly interacted with ROCK2, ROCK1 of the focal adhesion pathway. SYNE1 directly interacted with MUSK of the extracellular matrix organization pathway. TEK directly interacted with VEGFA, SHC1, PIK3R1, GRB2 of the focal adhesion pathway. TTN directly interacted with CAPN3 of the extracellular matrix organization pathway. Conclusion: The EPCAM, SHROOM3, SYNE1, TEK, and TTN genes were potential high-risk candidate pathogenic genes of familial KC. The findings might significantly improve our understanding of the genetic etiology of the disease, providing novel insights on KC pathogenesis.

1391P Tumor-first mutation-specific risk approach to trigger germline testing in castration-resistant prostate cancer

The prevalence of hereditary prostate cancer (PCa) in the Netherlands appears lower than previously reported, and routine germline testing is not advocated as standard of care. Current referral strategies are based on a positive family history (FH) for high-risk penetrating cancer predisposition genes, on presence of metastatic disease (DISCOVER-study), or on a tumor-first approach in patients (pts) with castration-resistant PCa (CRPC) with cascade germline testing in those with an alteration in predefined genes. Here we compare referral based on FH with the tumor-first approach. The PROMPT trial (NCT04746300) prospectively studies the impact of routine molecular tumor profiling with broad next-generation sequencing (NGS) in recently diagnosed CRPC pts. All results were discussed within the Radboudumc Molecular Tumor Board to guide precision medicine and for germline testing by geneticists per protocol. FH was taken at screening. The presence of familial and hereditary PCa by Dutch criteria for included pts was retrospectively assessed. High-risk homologous recombination deficiency (HRD) genes studied were BRCA1, BRCA2 and PALB2. Data on ATM and CHEK2 (lower-risk) will also be presented. In the 307 evaluable pts at least one pathogenic HRD alteration was found in 24 pts (8%), in BRCA1 (n=1), BRCA2 (n=21) and PALB2 (n=2) respectively. 17 pts (6%) were referred for germline testing; in 11 pts a germline variant was found. In 7/11 families the genetic predisposition was unknown, with pts not fulfilling Dutch referral criteria. FH was reported in 305 pts. Based on FH 53 pts would have been eligible for referral to clinical genetics and germline testing. In these pts, 48 pts did not have a pathogenic aberration in BRCA1/BRCA2 or PALB2 in tumor DNA. Based on reported FH, 18% of the pts would meet the Dutch criteria for genetic testing. In the majority of them the chance of a germline mutation is estimated to be low based on tumor test results, and 7 families with a germline mutation would have been missed. A tumor-first approach for high risk genes led to referral of 6%, with a germline variant in 53% of pts. Routine tumor-first DNA testing in CRPC efficiently identifies pts eligible for germline testing.

Abstract PO014: Genome-wide mapping of oncogenic pathways and genetic modifiers of chemotherapy using a high-risk hepatoblastoma genetic model

Abstract Lack of relevant animal models and cell lines of hepatoblastoma hampers our understanding pathogenesis of and identifying therapeutic targets for this neoplasm. We report a liver-specific MYC-driven hepatoblastoma murine model that faithfully recapitulates the pathological features of mixed fetal and embryonal hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of human disease. Single-cell RNA-sequencing (scRNA-seq) and spatiotranscriptomics identified distinct subpopulations of hepatoblastoma cells. After deriving cell lines from the mouse model, we mapped the cancer dependency genes using CRISPR-Cas9 screening and identified druggable targets shared with human hepatoblastoma (i.e., CDK7, CDK9, PRMT1, PRMT5). Our screen also revealed oncogenes and tumor suppressor genes in hepatoblastoma that engage multiple, druggable cancer signaling pathways. Chemotherapy is the mainstay for human hepatoblastoma treatment. A genetic mapping of doxorubicin response by CRISPR-Cas9 screening identified modifiers whose loss-of-function synergizes and antagonizes with the effect of chemotherapy. The combination of PRKDC inhibition and chemotherapy greatly enhances therapeutic efficacy. Our studies have provided and characterized useful resources including disease models and identified potential therapeutic targets of high-risk hepatoblastoma. Citation Format: Jun Yang. Genome-wide mapping of oncogenic pathways and genetic modifiers of chemotherapy using a high-risk hepatoblastoma genetic model [abstract]. In: Proceedings of the AACR Special Conference: Advances in the Pathogenesis and Molecular Therapies of Liver Cancer; 2022 May 5-8; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(17_Suppl):Abstract nr PO014.

Characterization of genetic predisposition to molecular subtypes of breast cancer in Brazilian patients.

Introduction BRCA1 and BRCA2 germline pathogenic variants (GPVs) account for most of the 5-10% of breast cancer (BC) that is attributable to inherited genetic variants. BRCA1 GPVs are associated with the triple negative subtype, whereas BRCA2 GPVs are likely to result in higher grade, estrogen-receptor positive BCs. The contribution of other genes of high and moderate risk for BC has not been well defined and risk estimates to specific BC subtypes is lacking, especially for an admixed population like Brazilian.ObjectiveThe aim of this study is to evaluate the value of a multigene panel in detecting germline mutations in cancer-predisposing genes for Brazilian BC patients and its relation with molecular subtypes and the predominant molecular ancestry.Patients and methodsA total of 321 unrelated BC patients who fulfilled NCCN criteria for BRCA1/2 testing between 2016-2018 were investigated with a 94-genes panel. Molecular subtypes were retrieved from medical records and ancestry-specific variants were obtained from off-target reads obtained from the sequencing data.ResultsWe detected 83 GPVs in 81 patients (positivity rate of 25.2%). Among GPVs, 47% (39/83) were identified in high-risk BC genes (BRCA1/2, PALB2 and TP53) and 18% (15/83) in moderate-penetrance genes (ATM, CHEK2 and RAD51C). The remainder of the GPVs (35% - 29/83), were identified in lower-risk genes. As for the molecular subtypes, triple negative BC had a mutation frequency of 31.6% (25/79), with predominance in BRCA1 (12.6%; 10/79). Among the luminal subtypes, except Luminal B HER2-positive, 18.7% (29/155) had GPV with BRCA1/2 genes contributing 7.1% (11/155) and non-BRCA1/2 genes, 12.9% (20/155). For Luminal B HER2-positive subtype, 40% (16/40) had GPVs, with a predominance of ATM gene (15% - 6/40) and BRCA2 with only 2.5% (1/40). Finally, HER2-enriched subtype presented a mutation rate of 30.8% (4/13) with contribution of BRCA2 of 7.5% (1/13) and non-BRCA1/2 of 23% (3/13). Variants of uncertain significance (VUS) were identified in 77.6% (249/321) of the patients and the number of VUS was increased in patients with Asian and Native American ancestry.ConclusionThe multigene panel contributed to identify GPVs in genes other than BRCA1/2, increasing the positivity of the genetic test from 9.6% (BRCA1/2) to 25.2% and, considering only the most clinically relevant BC predisposing genes, to 16.2%. These results indicate that women with clinical criteria for hereditary BC may benefit from a multigene panel testing, as it allows identifying GPVs in genes that directly impact the clinical management of these patients and family members.

Corpse decomposition of freshwater economic fish leads to similar resistomes and the enrichment of high-risk antibiotic resistance genes in different water types

Animal carcass decay produces many poisonous metabolites and chemical pollutants, which pose potential ecological risks to the aquatic environment and human health. However, the effects of animal cadaver decomposition on high-risk antibiotic resistance genes (ARGs) and potential pathogens in different water types are still unknown. In this study, fifteen freshwater economic fish (Carassius auratus) corpses were put into three types of water (i.e., pond water, tap water, and domestic sewage) for a 100-day decomposition. Next generation sequencing and HT-qPCR were used to illustrate how corpse decomposition affected microbial communities and ARG profiles. Our results revealed that fish corpse degradation caused similar resistomes and microbiome in different water types. MLSB (Macrolide-Lincosamide-Streptogramin B), β-lactamase, sulfonamide, tetracycline resistance genes and transposase genes in the experimental groups were increased. Among them, tetracycline resistance genes were enriched by 224 to 136,218-fold during the process of corpse degradation. Furthermore, high-risk ARGs (ermB, floR and dfrA1), which resist to MLSB, multidrug and sulfonamide respectively, were significantly enriched in the cadaver groups and had co-occurrence patterns with opportunistic pathogens, such as Bacteroidetes, which was more than 37 times in carcass groups than that in control groups. The study is able to draw a general conclusion that cadaver decomposition of freshwater economic fish deteriorates the aquatic environment by affecting high-risk ARGs and pathogenic microorganisms regardless of water types, which poses potential threats to human health. Therefore, timely management and treatment of animal carcasses is of great significance to the protection of water environment.

Unravelling genetic variants of a swedish family with high risk of prostate cancer

BackgroundProstate cancer is the most prevalent cancer in men worldwide. It is a polygenic disease with a substantial proportion of heritability. Identification of novel candidate biomarkers is crucial for clinical cancer prevention and the development of therapeutic strategies. Here, we describe the analysis of rare and common genetic variants that can predispose to the development of prostate cancer.MethodsWhole-genome sequencing was performed on germline DNA of five Swedish siblings which were diagnosed with prostate cancer. The high-risk variants were identified setting the minor allele frequency < 0.01, CADD > 10 and if tested in PRACTICAL, OR > 1.5, while the low-risk variants were identified minor allele frequency > 0.01, CADD > 10 and if tested in PRACTICAL, OR > 1.1.ResultsWe identified 38 candidate high-risk gene variants and 332 candidate low-risk gene variants, where 2 and 14 variants were in coding regions, respectively, that were shared by the brothers with prostate cancer.ConclusionsThis study expanded the knowledge of potential risk factor candidates involved in hereditary and familial prostate cancer. Our findings can be beneficial when applying targeted screening in families with a high risk of developing the disease.