Additional Genes Research Articles

Transcriptome analysis reveals temporally regulated genetic networks during Drosophila border cell collective migration

BackgroundCollective cell migration underlies many essential processes, including sculpting organs during embryogenesis, wound healing in the adult, and metastasis of cancer cells. At mid-oogenesis, Drosophila border cells undergo collective migration. Border cells round up into a small group at the pre-migration stage, detach from the epithelium and undergo a dynamic and highly regulated migration at the mid-migration stage, and stop at the oocyte, their final destination, at the post-migration stage. While specific genes that promote cell signaling, polarization of the cluster, formation of protrusions, and cell-cell adhesion are known to regulate border cell migration, there may be additional genes that promote these distinct active phases of border cell migration. Therefore, we sought to identify genes whose expression patterns changed during border cell migration.ResultsWe performed RNA-sequencing on border cells isolated at pre-, mid-, and post-migration stages. We report that 1,729 transcripts, in nine co-expression gene clusters, are temporally and differentially expressed across the three migration stages. Gene ontology analyses and constructed protein-protein interaction networks identified genes expected to function in collective migration, such as regulators of the cytoskeleton, adhesion, and tissue morphogenesis, but also uncovered a notable enrichment of genes involved in immune signaling, ribosome biogenesis, and stress responses. Finally, we validated the in vivo expression and function of a subset of identified genes in border cells.ConclusionsOverall, our results identified differentially and temporally expressed genetic networks that may facilitate the efficient development and migration of border cells. The genes identified here represent a wealth of new candidates to investigate the molecular nature of dynamic collective cell migrations in developing tissues.

Diagnostic model based on key autophagy-related genes in intervertebral disc degeneration

BackgroundCurrent research on autophagy is mainly focused on intervertebral disc tissues and cells, while there is few on human peripheral blood sample. therefore, this study constructed a diagnostic model to identify autophagy-related markers of intervertebral disc degeneration (IVDD).MethodsGSE150408 and GSE124272 datasets were acquired from the Gene Expression Omnibus database, and differential expression analysis was performed. The IVDD-autophagy genes were obtained using Weighted Gene Coexpression Network Analysis, and a diagnostic model was constructed and validated, followed by Gene Set Variation Analysis (GSVA) and Gene Set Enrichment Analysis (GSEA). Meanwhile, miRNA–gene and transcription factor–gene interaction networks were constructed. In addition, drug-gene interactions and target genes of methylprednisolone and glucosamine were analyzed.ResultsA total of 1,776 differentially expressed genes were identified between IVDD and control samples, and the composition of the four immune cell types was significantly different between the IVDD and control samples. The Meturquoise and Mebrown modules were significantly related to immune cells, with significant differences between the control and IVDD samples. A diagnostic model was constructed using five key IVDD-autophagy genes. The area under the curve values of the model in the training and validation datasets were 0.907 and 0.984, respectively. The enrichment scores of the two pathways were significantly different between the IVDD and healthy groups. Eight pathways in the IVDD and healthy groups had significant differences. A total of 16 miRNAs and 3 transcription factors were predicted to be of great value. In total, 84 significantly related drugs were screened for five key IVDD-autophagy genes in the diagnostic model, and three common autophagy-related target genes of methylprednisolone and glucosamine were predicted.ConclusionThis study constructs a reliable autophagy-related diagnostic model that is strongly related to the immune microenvironment of IVD. Autophagy-related genes, including PHF23, RAB24, STAT3, TOMM5, and DNAJB9, may participate in IVDD pathogenesis. In addition, methylprednisolone and glucosamine may exert therapeutic effects on IVDD by targeting CTSD, VEGFA, and BAX genes through apoptosis, as well as the sphingolipid and AGE-RAGE signaling pathways in diabetic complications.

Identification of genes and blood co‐expression networks associated with cerebrovascular neuroimaging phenotypes

AbstractBackgroundA hallmark of Alzheimer’s disease is amyloid‐β (Aβ) deposition in the brain parenchyma as senile plaques which Aß frequently accompanies in the cerebral vasculature as cerebral amyloid angiopathy (CAA). Previous studies demonstrated that the cerebrovascular system is essential for Aβ clearance and interactions exist between cerebrovascular disease and AD. Neuroimaging data, including measures on small vessel disease, amyloid deposits, and microhemorrhages (MCH), can reflect both cerebrovascular disease and AD pathology, thereby serving as intermediate phenotypes of both conditions. We aim to identify genes and co‐expression networks in blood associated with these neuroimaging endophenotypes and the biological pathways enriched in these perturbed transcriptional networks.MethodWe conducted differential gene expression and Weighted Gene Co‐Expression Network analyses (WGCNA) on blood RNA sequencing data of 407 participants from the longitudinally followed Mayo Clinic Study of Aging cohort. The neuroimaging phenotypes include MCH, infarction, and amyloid deposits measured by Pittsburgh compound B positron emission tomography (PiB PET).ResultWGCNA analysis showed a nominally significant association (p<0.05) between several module eigengenes (MEs) and MCH and PiB PET. One module, M42, remained significantly associated with PiB PET after Bonferroni correction for all 43 modules tested. Pathway enrichment analysis of M42 identified two significant pathways (FDR‐adjusted p<0.05) including phosphodiesterase I activity and IgE binding. These pathways contain genes such as MS4A2 encoding the high‐affinity IgE receptor involved in the immune response. Similarly, ENPP2 in the phosphodiesterase I activity pathway represents an additional candidate gene previously implicated in Alzheimer’s disease.ConclusionWe generated co‐expression networks and identified one network module with a statistically significant association between brain amyloid deposits and blood transcriptome data. Further investigations of this network and its enriched pathways are necessary to understand their roles in amyloidosis, CAA, and neurodegeneration. Future studies will include seeking replication of these results in other datasets. Such studies can help elucidate the biological mechanisms of pathogenesis of cerebrovascular damage and amyloid deposits. In addition, in a clinical setting, blood levels of transcripts discovered in this study may serve as predictive or diagnostic biomarkers with mechanistic implications.

Integrative multi‐omics for normal brain aging and Alzheimer’s Disease in Drosophila

AbstractBackgroundNormal brain aging and Alzheimer’s Disease (AD) are both characterized by neurodegeneration and share many similarities. However, the mechanisms underlying both their similarities and differences remain largely unknown. Cell‐cell interactions mediate nearly all aspects of an organism’s physiology via cell‐surface proteins; as such, ∼70% of pharmaceutical drugs target cell‐surface proteins. Glial cells play many important roles in cell‐cell communication, plasticity, and immune function; thus, glial cell‐surface proteins present ideal novel biomarkers and drug targets. However, it remains difficult to profile glial cell‐surface proteins from intact brains, or to fully characterize gene expression changes during the progression of age‐related neurodegeneration. MethodTo investigate, we're fully characterizing how glial cells and their cell‐surface proteins differentially contribute to the progression of normal brain aging and AD, integrating state‐of‐the‐art in‐situ cell‐surface proteomics and high‐resolution single‐cell transcriptomics. Our study will be the first to apply in‐situ cell‐surface proteomics to glial cells in Drosophila, and the first to exhaustively profile and integrate the glial cell‐surface proteomes and single‐cell transcriptomes of both aging‐ and AD‐model flies. This will allow us to capture the “full picture” of how dysregulation of glial cell‐surface proteins differentially contributes to normal brain aging and AD, as changes in gene expression at the protein and mRNA levels often show considerable discrepancies.ResultIn total, our glial cell‐surface proteomics identified 872 proteins predicted to be involved in normal brain aging, and strong replicate correlations were observed. A Gene Ontology analysis revealed that most up‐regulated genes were associated with cell localization and transport, while most down‐regulated genes were associated with neural development, circuit organization, and neuroplasticity. We selected 48 candidate genes for further screening, based on which were the most up‐ and down‐regulated. Referencing our transcriptomic data, we found that 9/48 candidate genes identified by our cell‐surface proteomics also showed significant increases/decreases in expression levels, and selected 24 additional candidate genes for further screening.ConclusionCurrently, we are in the process of conducting several GOF/LOF genetic screens to investigate the effects of each candidate gene on lifespan. Based on preliminary data from our lifespan screens, we have identified 5 top candidate genes for further investigation.

Exploring the role of brain DNA methylomic signatures on gene expression dynamics of frontotemporal lobar degeneration

AbstractBackgroundFrontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, which includes frontotemporal dementia and progressive supranuclear palsy. About 90% of the FTLD cases show either TDP‐43 or tau pathology (FTLD‐TDP or FTLD‐tau, respectively). Though aberrant brain DNA methylation has consistently been associated with Alzheimer’s disease and other neurodegenerative diseases, studies on FTLD are scarce. The main goal of this study was to investigate DNA methylation variation in FTLD bulk brain tissue and brain‐derived nuclei.MethodsWe used bulk frontal cortex genome‐wide DNA methylation profiles (Illumina 450K or EPIC microarrays) from three FTLD cohorts (N = 228). To identify unique and shared differentially methylated loci across FTLD subgroups/subtypes, we performed cohort‐specific epigenome‐wide association studies (EWAS) followed by a meta‐analysis. Additionally, we used weighted gene correlation network analysis to identify co‐methylation signatures associated with FTLD, FTLD pathological subtypes, and other disease‐related traits. To identify disturbed cell‐types and biological processes within disease associated signatures, we then carried out cell‐type and functional enrichment analyses. We also generated and have ongoing analysis of DNA methylation profiles (EPIC microarrays) of neuronal (NeuN+) and glial nuclei (NeuN‐) from FTLD‐TDP cases and controls (N = 40). Wherever possible, we also integrated additional DNA methylation, and gene and protein expression datasets.ResultsIn bulk tissue, the EWAS meta‐analysis identified four shared differentially methylated loci in FTLD, including hypomethylation in OTUD4, a gene we found to be upregulated (mRNA and protein) in FTLD. Two of the four meta‐analysis hits (mapping to OTUD4 and CEBPZ), were found to be co‐methylated within signatures strongly associated with FTLD. Disease‐associated signatures implicate transcription regulation, the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling, and specific brain cell‐types, including pyramidal neurons and oligodendrocytes, in FTLD. Preliminary analysis of the neuronal and glial datasets also revealed FTLD‐associated DNA methylation signatures, which will further inform on cell‐type‐specific changes in FTLD.ConclusionsOur findings identified novel FTLD‐associated loci, including OTUD4, and point to DNA methylation as an important mechanism in the dysregulation of biological processes relevant to the FTLD pathogenesis, such as RNA/stress granule formation.

An accelerated rate of Beta‐amyloid Measured with [C‐11]PiB in Down Syndrome compared to Neurotypical Populations

AbstractBackgroundDown syndrome (DS) is characterized by a higher risk and earlier onset of beta‐amyloid (Aβ) plaque accumulation and Alzheimer’s disease (AD). The triplication of chromosome 21 containing the amyloid precursor protein (APP) gene is implicated in this process and in this study we compare the accumulation rates of Aβ between DS and neurotypical (NT) populations quantified by longitudinal [C‐11]PiB imaged at the same site to minimize experimental variation.MethodsIndividuals with three or more [C‐11]PiB scans spanning eleven years our site with at least one Aβ+ (global SUVR>1.40) and Aβ‐ [C‐11]PiB scan were selected. 12 of 74 DS and 15 of 246 NT participants fit these criteria. An identical imaging procedure was conducted for all participants imaged on either an ECAT HR+ or Biograph mCT PET scanner 50‐70 minutes post‐injection. Reconstructed PET images were summed and spatially normalized into template space and converted into 50‐70min SUVR images using a cerebellar grey matter reference region. Global SUVR composed of grey matter regions from the AAL atlas was used as a metric for Aβ deposition. SUVR data were fit against age with a logistic growth curve (f(t) = NS+K/(1+e(‐r(t‐t50)))) to determine Aβ accumulation as subjects transitioned to Aβ+. The rate of accumulation was found using the slope of the curve at Aβ positivity threshold based on the model fit. Our model fixed NS = 1.12, the average baseline SUVR of all Aβ‐ subject scans (n = 491), and K = 1.28, the highest specific binding in any participant.ResultsPlotting [C‐11]PiB SUVR against age provides visual comparisons of cohorts (Fig 1) and transforming the x‐axis to amyloid chronicity (t = 0 at Aβ+) illustrates differences in accumulation rates between groups (Fig 2). The average rate of amyloid accumulation (ΔSUVR/yr) when becoming Aβ+ in the DS cohort is 0.071(0.021) versus 0.043(0.009) for NT (p = 4.31×10−4).ConclusionsAβ accumulation rate was higher in the DS cohort compared to NT. This is consistent with the additional APP gene copy in DS, and we observed an accumulation rate 65% faster in this cohort. There was a higher variability in the DS population requiring further investigation towards understanding the influence of genetic and lifestyle factors on Aβ deposition.

Progress in the Study of Significant Mutated Genes and Molecular Biological Factors in Cervical Tumors

Cervical cancer is the most prevalent gynecologic malignancy in developing countries, with incidence and mortality rates continuing to rise. Despite widespread research on cervical cancer, the specific mechanisms and synergistic factors underlying its occurrence remain unclear. In recent years, there has been a growing interest in the relationship between gene mutations and cervical cancer. Numerous studies have demonstrated that alterations in oncogenes, tumor suppressor genes, and related regulatory genes are closely associated with the development and progression of cervical cancer. The application of genome sequencing technology in malignant tumors has allowed for the identification of additional gene mutations in cervical cancer. By identifying significantly mutated genes, we can further target malignancy driver genes, which may be the key to uncovering the intrinsic mechanisms of sexual tumors. Therefore, a review of the current status of research on mutated genes in cervical cancer and factors associated with recurrence after treatment of early-stage cervical cancer can provide new insights for mechanistic studies, diagnosis, and targeted therapy of cervical cancer.

Abstract A013: Leukemic stem cell differentiation visible at single-cell resolution in AML patients treated with BRG1/BRM inhibitor FHD-286

Abstract BAF chromatin remodeling complexes are critical to the regulation of cellular differentiation and are implicated in cancer as well as other diseases. FHD-286 is a first-in-class dual inhibitor of the BAF catalytic subunits BRM and BRG1 (SMARCA2/4) that is being developed for the treatment of advanced hematologic malignancies. We previously reported that exposure of acute myeloid leukemia (AML) cells to pharmacologically relevant concentrations of FHD-286 led to downregulation of leukemic stem cell (LSC) marker CD34, and upregulation of the myeloid maturation marker CD11b. Morphologic features of differentiation were also observed, suggesting that BAF functions to maintain AML cells in an undifferentiated state, and that FHD-286 may inhibit AML cell growth by reducing their capacity for stem cell renewal. Using single-cell transcriptomic data, we further assessed the impact of FHD-286 on differentiation markers of tumor cells from clinical AML patients. scRNA-seq data was obtained for 26 bone marrow aspirate samples from 11 AML and 2 myelodysplastic syndrome (MDS) patients from the Phase 1 clinical study evaluating FHD-286. Non-tumor cell types (T-cells, erythroid, B cells, megakaryocytes) were identified using published gene markers and removed from the dataset, leaving only tumor cells enriched for either LSC markers (CD34, CD123) or CD11b. We next identified differentially expressed genes between patient LSCs and CD11b+ cells. The top 50 genes associated with each cell group were taken as signature markers of stemness or differentiation, and their mean expression used as phenotypic scores for all patient tumor cells. Clustering analysis of the patient single-cell data showed that cells grouped according to cell type, treatment timepoint, and patient identity. Tumor cells expressing LSC markers CD34 and CD123 clustered separately from those expressing differentiation marker CD11b, and the relative percentage of CD11b+ tumor cells increased on treatment for 8 out of 12 patients dosed at >=5mg, consistent with preclinical AML models. Differential expression analysis revealed additional genes upregulated in either LSCs or CD11b+ cells, which were identified in literature as markers of stemness or myeloid differentiation, respectively. Single-cell LSC and differentiation signature scores showed a strongly statistically significant shift away from LSC identity and toward differentiation for 10 out of 12 patients. Single-cell RNA data from AML patients validates the preclinical observation that FHD-286 treatment induces changes in LSCs resembling differentiation towards a terminal myeloid cell state. This dataset further indicates that nearly all patients undergo some degree of tumor cell differentiation after treatment, suggesting broad on-target activity of FHD-286. Citation Format: GiNell Elliott, Jessica Wan, Kim Horrigan, Mike Collins, Astrid Thomsen, Ashley K Gartin, Ammar Adam, David L Lahr, Gabriel Sandoval, Sameul Agresta, Jessica Piel, Martin Hentemann. Leukemic stem cell differentiation visible at single-cell resolution in AML patients treated with BRG1/BRM inhibitor FHD-286 [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A013.

Expression analysis of genes encoding extracellular leucine-rich repeat proteins in Arabidopsis thaliana.

Leucine-rich repeat (LRR)-containing proteins have been identified in diverse species, including plants. The diverse intracellular and extracellular LRR variants are responsible for numerous biological processes. We analyzed the expression patterns of Arabidopsis thaliana extracellular LRR (AtExLRR) genes, 10 receptor-like proteins, and 4 additional genes expressing the LRR-containing protein by a promoter: β-glucuronidase (GUS) study. According to in silico expression studies, several AtExLRR genes were expressed in a tissue- or stage-specific and abiotic/hormone stress-responsive manner, indicating their potential participation in specific biological processes. Based on the promoter: GUS assay, AtExLRRs were expressed in different cells and organs. A quantitative real-time PCR investigation revealed that the expressions of AtExLRR3 and AtExLRR9 were distinct under various abiotic stress conditions. This study investigated the potential roles of extracellular LRR proteins in plant growth, development, and response to various abiotic stresses.

Altered Endogenous Expression of Alzheimer’s Risk Genes impacts Neural Morphology in a Large Cohort of Healthy study Participants

AbstractBackgroundDysregulation of white matter tracts (WMTs) in the brain is a common feature of Alzheimer’s Disease (AD) and is associated with declining cognitive function. Two neuroimaging measures, Fractional Anisotropy (FA) and isometric volume fraction (ISOVF) represent WM integrity through quantifying organization of axon bundles and changes in extracellular fluid within the fiber tracts (as occurs in inflammation or degeneration) respectively. Previous work examining the genetic basis of WMT changes in AD largely focused on SNP‐level associations. Here, we leverage transcriptome wide association studies (TWAS) and Mendelian randomization (MR) to interrogate the expression‐mediated influence of AD genes on WMT integrity.MethodWe first perform a multi‐tissue TWAS for AD by applying JTI‐PrediXcan to summary statistics from the largest AD GWAS meta‐analysis (Bellenguez, 2022). This approach leverages tissue‐specific eQTL models trained on data from the Genotype‐Tissue Expression project and enriched via Joint Tissue imputation to identify associations between genetically regulated gene expression (GReX) and AD (Barbeira, 2018). We apply prediction performance thresholds and correct for multiple testing. We perform similar TWAS using JTI‐PrediXcan on neuroimaging data from 33,000 participants in the UK Biobank to identify tissue‐specific associations between GReX and WMTs (FA and ISOVF) (Smith, 2021). We integrate these studies to identify AD‐associated genes associated with changes in FA or ISOVF. We quantify the GReX causal effect on WMTs through the MR protocol, MR‐JTI, which assumes gene expression as the exposure (Zhou, 2020).ResultOur AD TWAS identifies 59 genes. 14 occur at the APOE locus and we replicate 2 additional genes prioritized in the initial GWAS. FUMA analysis of our gene set implicates the brain as the primary tissue of downregulation (Watanabe, 2017). Neuroimaging analysis of these genes highlights 5 WMTs and 2 genes. GReX of CR1 is causally associated with ISOVF of the right acoustic radiation and superior longitudinal fasciculus. GReX of INO80E is causally associated with FA of the left inferior longitudinal fasciculus and the bilateral superior thalamic radiations.ConclusionBy integrating TWAS of AD and neuroimaging data, we identify multiple significant, tissue‐specific, causal associations between AD‐associated GReX and the integrity of key WMTs associated with cognitive function.

FastCAR: fast correction for ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets

Cell type-specific differential gene expression analyses based on single-cell transcriptome datasets are sensitive to the presence of cell-free mRNA in the droplets containing single cells. This so-called ambient RNA contamination may differ between samples obtained from patients and healthy controls. Current ambient RNA correction methods were not developed specifically for single-cell differential gene expression (sc-DGE) analyses and might therefore not sufficiently correct for ambient RNA-derived signals. Here, we show that ambient RNA levels are highly sample-specific. We found that without ambient RNA correction, sc-DGE analyses erroneously identify transcripts originating from ambient RNA as cell type-specific disease-associated genes. We therefore developed a computationally lean and intuitive correction method, Fast Correction for Ambient RNA (FastCAR), optimized for sc-DGE analysis of scRNA-Seq datasets generated by droplet-based methods including the 10XGenomics Chromium platform. FastCAR uses the profile of transcripts observed in libraries that likely represent empty droplets to determine the level of ambient RNA in each individual sample, and then corrects for these ambient RNA gene expression values. FastCAR can be applied as part of the data pre-processing and QC in sc-DGE workflows comparing scRNA-Seq data in a health versus disease experimental design. We compared FastCAR with two methods previously developed to remove ambient RNA, SoupX and CellBender. All three methods identified additional genes in sc-DGE analyses that were not identified in the absence of ambient RNA correction. However, we show that FastCAR performs better at correcting gene expression values attributed to ambient RNA, resulting in a lower frequency of false-positive observations. Moreover, the use of FastCAR in a sc-DGE workflow increases the cell-type specificity of sc-DGE analyses across disease conditions.

Enhanced Genomic Stability in Monomorphic Post-Transplant Lymphoproliferative Disorders Is Driven By Distinct Mechanisms Stratified By EBV Status

Introduction: We previously showed that HIV associated EBV negative (-) diffuse large B-cell lymphomas (DLBCL) of germinal center origins (GCB) have enhanced genomic stability and increased expression of DNA repair genes compared to their HIV negative counterparts (Maguire et al 2019). Given that immune deficiency can be induced virally or therapeutically, including the administration of immunosuppressive drugs post solid organ or hematopoietic stem cell transplant, we questioned whether these observations are specific to HIV or if they represent a more global immune impaired signature. Here we assessed the genomic stability of monomorphic DLBCL post-transplant lymphoproliferative disorders (PTLD) and the potential role of DNA repair. Methods: A total of 49 monomorphic DLBCL PTLDs (26 EBV(-), 23 EBV positive (+)) and 170 immune competent (IC) DLBCL (EBV status unknown) were studied. All were pathologically reviewed and samples with <60% tumor content were macro-dissected before RNA/DNA extraction. Cell of origin (COO) profiles were assessed using the DLBCL90 molecular assay which can distinguish primary mediastinal B-cell lymphoma (PMBL) from GCB, Activated B-cell (ABC) and unclassified (UNC) DLBCL (Ennishi et al 2019). NanoString gene expression profiling (GEP) was performed using the PanCancer Pathways panel and analyzed using NanoString nSolver Advanced Analysis. Copy number (CN) analysis was performed on a subset of samples (45 PTLD, 41 DLBCL) using the OncoScan CN assay and analyzed using Chromosome Analysis Suite (ChAS) v4.1. All p-values listed were Benjamini-Hochberg adjusted and Mann-Whitney tested for the GEP and CN data respectively. Results: In contrast to IC-DLBCL which are GCB enriched (50%), COO profiling revealed PTLD to be ABC enriched (43%). CN analyses revealed that the median CN/sample for PTLD (0.57, p<0.001), EBV(+)PTLD (0.25, p<0.001) and EBV(-)PTLD (0.80, p = 0.050) tumors were significantly less aberrant than IC-DLBCL (1.01). The data also showed that EBV(+)PTLD are less aberrant than EBV(-)PTLD tumors (0.25 vs 0.80, p<0.001). GEP pathway analysis identified DNA repair as downregulated in PTLD and EBV(+)PTLD but upregulated in EBV(-)PTLD compared IC-DLBCL. Nine DNA repair genes ( RAD51, CCNA2a, CHEK1b, POLR2Da, PCNAa, WHSC1a, GTF2H3a, ATM c, EP300 c) were differentially expressed (DE) in EBV(-)PTLD compared to IC-DLBCL (7 increased, 2 decreased, p ≤ 0.0425): where the most overexpressed gene RAD51, a critical mediator of Homologous Recombination (HR) and the Fanconi Anemia (FA) DNA repair pathways, was not DE in PTLD or EBV(+)PTLD compared to IC-DLBCL. Five a genes were increased in PTLD (p ≤ 0.0204) but not EBV(+)PTLD, 1 b was decreased in EBV(+)PTLD (p = 0.01) but not PTLD and 2 c were reduced in PTLD regardless of EBV status compared to IC-DLBCL (p ≤ 0.0024). Twenty-8 genes were DE in EBV(+)PTLD compared to IC-DLBCL. Of these, 23 were downregulated (p ≤ 0.0418) and included HR, FA and mismatch repair genes ( CHEK1, CHEK2, BRAC1/FANCS, FANCA, FANCB, FANCE, MSH2, MSH6). All but 2/23 were similarly expressed in PTLD compared to IC-DLBCL of which 11 were significant (p ≤ 0.0356). The five upregulated genes ( ZBTB32, DDB2, NBN, POLB, RBX1, p ≤ 0.0092) were also upregulated in PTLD (p ≤ 0.0042) but not EBV(-)PTLD compared to IC-DLBCL. Two additional genes ( SKP1, FBXW7) were also identified as increased in EBV(+)PTLD and PTLD (p ≤ 0.0204) compared to IC-DLBCL. In contrast, SKP1 was increased (p = 2.7E-4) and FBXW7 was decreased (p = 0.3610) in EBV(-)PTLD compared to IC-DLBCL. Together the protein products of RBX1, SKP1 and FBXW7 comprise the functional cores of a complete UPS complex, the SCF FBXW7 E3 ubiquitin ligase which have been reported to regulate the DNA damage response and promote genomic stability. Conclusions: Like HIV associated DLBCL, these results show that PTLD is more genomically stable than IC-DLBCL, and that genomic stability is further enhanced in EBV(+)PTLD which have increased expression of UPS related genes. In contrast, EBV(-)PTLD have increased expression of DNA damage repair genes, including RAD51. In summary, monomorphic DLBCL PTLD tumors have enhanced genomic stability that appears to be mediated by two distinct mechanisms stratified by EBV status. Further work is required to assess if this stratification of mechanisms is unique to PTLD or reflects a more global immune impaired EBV related signature.

Genomic Stability, DNA Repair and the SKP1-CUL1-F-Box Complex in HIV Associated Diffuse Large B-Cell Lymphoma

Introduction: Previously we demonstrated that HIV associated diffuse large B-cell lymphomas (DLBCL) of Germinal Center B-cell subtype (GCB) are more proliferative, with enhanced genomic stability and increased expression of DNA repair genes, particularly Fanconi anemia (FA) and homologous recombination (HR) genes compared to their HIV negative counterparts (Maguire et al, 2019). It is unknown if this signature is unique to the GCB subtype or if it is also observed in Activated B-cell (ABC) and Unclassified (UNC) DLBCL. Herein we validate our HIV associated GCB DLBCL findings in a larger independent cohort and report for the first time the aberrational profile of molecularly profiled HIV associated ABC DLBCL compared to their HIV negative counterparts respectively. Methods: An independent cohort of 353 DLBCL FFPE cases was assembled, including 125 HIV-DLBCL samples. All samples underwent hematopathological review to confirm diagnosis and determine tumor content. Samples with <60% tumor content were macro-dissected before they were RNA/DNA extracted. Cell of origin (COO) profiles were assessed using the Lymph3Cx molecular assay which can distinguish primary mediastinal B-cell lymphoma (PMBL) like from GCB, ABC and UNC DLBCL (Mottok et al 2018). Copy number (CN) analyses were performed on samples with sufficient DNA (41 HIV neg, 32 HIV pos) using the OncoScan FFPE assay kit and the resulting data analyzed using Chromosome Analysis Suite (ChAS) v4.1 and the multisample viewer module of Reproductive Health Research Analysis Software (RHAS) v1.1. Additional digital gene expression profiling was performed using the Pan-Cancer panel (NanoString, Seattle, WA) customized to include 9 BCL2 family genes for a total of 739 genes and analyzed using the NanoString nSolver Advanced Analysis module. Results: GCB, ABC, UNC and PMBL-like proportions were 50%, 30%, 14% and 6% in HIV unassociated (HIV neg) and 50%, 23%, 25% and 2% in HIV pos tumors respectively, confirming both cohorts were GCB-enriched by molecular profiling. PMBL-like cases were excluded from further analyses. OncoScan CN analyses showed that HIV pos DLBCL were significantly less aberrant than HIV neg DLBCL (median CN per sample 0.56 vs 1.01, p<0.001). HIV pos GCB tumors were significantly less aberrant than both HIV neg GCB tumors (median CN per sample 0.50 vs 1.11, p<0.001), and HIV pos ABC tumors (median CN per sample 0.50 vs 0.81, p=0.009). HIV pos ABC tumors were also less aberrant than HIV neg ABC tumors, however, the difference was not significant overall (median CN per sample 0.81 vs 1.03, p=0.162) or for gain/amplifications (median CN per sample 0.38 vs 0.42, p=0.814), but was borderline significant for loss/deletions (median CN per sample 0.31 vs 0.47, p=0.06). GEP analyses identified Cell Cycle and DNA repair as the top two upregulated pathways in HIV pos GCB tumors compared to HIV neg GCB tumors. In contrast, Cell Cycle and DNA repair were downregulated in HIV pos ABC tumors compared to HIV neg ABC tumors. However, one gene ( RBX1) was identified as significantly upregulated in both pathways in HIV pos GCB (adjusted p-value 0.0215) and HIV pos ABC (adjusted p-value 0.0046) tumors compared to their HIV neg counterparts. A second gene ( SKP1) was also significantly upregulated in HIV pos GCB (adjusted p-value 3.94E-5) and HIV pos ABC (adjusted p-value 0.0031) tumors. Together RBX1 and SKP1 encode the two principal functional subunits of the SKP1, CUL1, F-box protein (SCF) complex which is part of the ubiquitin proteasome system (UPS) and has been reported as essential for maintaining genome and chromosome stability (Thompson et al 2021). Conclusions: These results demonstrate that HIV pos DLBCL tumors are less aberrant than their HIV neg counterparts irrespective of COO subtype. However, the degree of genomic stability differs by COO, with HIV pos GCB tumors being more genomically stable than HIV pos ABC tumors. Although both have enhanced expression of UPS related SCF genes ( RBX1, SKP1), only HIV pos GCB tumors have enhanced expression of key DNA repair genes as well including Fanconi Anemia ( BRCA2/FANCD1, FANCL) and mismatch repair ( MSH2, MSH6) genes (adjusted p-values of ≤ 0.0263). Given the reported role of SCF in genomic stability maintenance, the HIV pos COO CN differences could be due to the contributions of both DNA repair and SCF mechanisms in HIV pos GCB and mainly SCF mechanisms in HIV pos ABC tumors.

Pathogenic Mechanisms of DDX41 Mutations in the Development of Myeloid Malignancies

DDX41 is a newly identified leukemia predisposition gene encoding an RNA helicase, whose germline mutations are tightly associated with late-onset myeloid malignancies. Importantly, germline DDX41 mutations were also found in as many as ~7 % of sporadic cases of high-risk MDS, conferring the largest germline risk for myeloid malignancies. In typical cases, a germline loss-of-function allele (most commonly p.A500fs or p.D140fs, depending on the ethnicity) is compounded by a somatic missense mutation affecting the helicase domain in the remaining allele (p.R525H). However, the molecular mechanism by which DDX41 mutations lead to myeloid neoplasms have not fully been elucidated. To clarify the role of these distinct DDX41 alleles, we generated mice models carrying either or both of conditional/constitutive Ddx41 knock-out (KO) and conditional R525H knock-in (KI) alleles. Vav1-Cre mediated homozygous deletion of Ddx41 resulted in embryonic lethality, suggesting that Ddx41 is indispensable for normal hematopoiesis. Next, by crossing these mice and further breeding with Rosa26-CreERT2 transgenic mice, we engineered mice that were wild-type for Ddx41 ( Ddx41 +/+), heterozygous Ddx41 KO( Ddx41 +/-), homozygous Ddx41 KO( Ddx41 -/-), heterozygous for the Ddx41 R525H mutation ( Ddx41 R525H/+), or hemizygous for the Ddx41 R525H mutation( Ddx41 R525H/-), in which expression of the mutant allele was induced by tamoxifen administration. First, we assessed cell intrinsic effects of these Ddx41 alleles, using noncompetitive transplantation experiments. Shortly after tamoxifen administration, most of the recipient mice that were transplanted with BM from Ddx41 -/- or Ddx41 R525H/- mice died within a month after CreERT2 induction due to severe BM failure (BMF), which was not observed in mice transplanted with BM from Ddx41 +/+, Ddx41 +/- or Ddx41 R525H/+ mice. By contrast, the mice transplanted with Ddx41 +/- or Ddx41 R525H/+ BM showed significantly reduced WBC counts and anemia in long-term observation in both primary and serial transplantations. Some of the Ddx41 +/- or Ddx41 R525H/+ BM-transplanted mice exhibited MDS-like phenotypes, showing ineffective hematopoiesis with evidence of erythroid dysplasia. Transcriptome analysis revealed that stem cells (Kit +Sca-1 -Lin low cells) derived from Ddx41 R525H/- BM-transplanted mice exhibited a significant upregulation of genes involved in innate immunity, including interferon stimulated genes, compared with stem cells derived from Ddx41 +/+ BM-transplanted mice. In addition, snoRNA and ribosomal genes were significantly deregulated in stem cells from Ddx41 -/- and Ddx41 R525H/- BM-transplanted mice, which could result in abnormal ribosome biogenesis and protein synthesis in Ddx41 mutant cells. We also assessed the reconstitution capacity of whole BM cells from different Ddx41 mutant mice in competitive transplantation experiments. The donor chimerism of Ddx41 -/- and Ddx41 R525H/- BM-transplanted mice in PB was markedly reduced compared to Ddx41 +/+ BM-transplanted mice. In contrast, Ddx41 +/- and Ddx41 R525H/+ BM-transplanted micedid not show significant changes in competitive bone marrow reconstitution compared to Ddx41 +/+ BM-transplanted mice. Given that the MDS clones bearing DDX41 R525H somatic alleles are typically observed as a small subclone in patients, we next co-transplanted Ddx41 +/+- and Ddx41 525H/--derived BM cells with Ddx41 +/+- or Ddx41 +/--derived BM cells at the ratio of 1:9. Recipient mice showed significantly reduced WBC counts when Ddx41 +/+- or Ddx41 +/- were co-transplanted with Ddx41 525H/- -derived BM, suggesting that Ddx41 525H/--derived hematopoietic cells have negative effect on normal hematopoiesis. In summary, compound biallelic loss-of function and R525 alleles led to severe BM failure. Monoallelic Ddx41 loss-of function and R525H knock-in alleles, by contrast, are compatible with hematopoiesis but associated with an impairment of hematopoiesis and the development of MDS with ageing, where activated innate immunity, impaired RNA metabolism and ribosome functions may play important roles.

A Real World, Single-Centre Study of Young Adult Patients with Philadelphia Negative Myeloproliferative Neoplasms

Classical ‘Philadelphia negative’ myeloproliferative neoplasms (MPNs) are clonal haematopoietic disorders and include essential thrombocythaemia (ET), polycythaemia vera (PV) and myelofibrosis (MF). MPNs have a heterogenous phenotype with an inherent risk of thromboembolic and haemorrhagic complications, and risk of blastic transformation. MPNs are commonly diagnosed in the 6 th decade or later, although up to 20% of patients are diagnosed < 40 years. Current risk stratification and treatment guidance, however, is frequently extrapolated from older cohorts. Here, we present a comprehensive retrospective analysis of 107 MPN adolescent and young adult (AYA) patients diagnosed <40 years, representing 19.6% of the total outpatient MPN cohort at University College London Hospital. Median follow up was 78 months (range (r), 1 - 507). Table 1 displays clinicopathological details of the entire cohort. Median age at diagnosis was 32 years (r,13-40). There was a female preponderance (66%); 57.9% of patients were Caucasian. Most patients had a diagnosis of ET (57.9%), with 24.3% PV and 9.3% MF, respectively. The most common driver mutation was JAK2 V617F, observed in 60.7%, followed by CALR (15.9%) and MPL (1.9%); 17% of patients were classified as triple negative (TN). Where data was available (n=27), median variant allelic frequency (VAF) for JAK2 V617F was 19.7% (r, 4-75%) and for CALR 43% (r, 5.7 - 53). 9/107 (8.4%) of patients had additional pathogenic gene abnormalities, most commonly variants of NRAS (22.2%), TET2 (22.2%) and ASXL1 (22.2%). We observed a high thrombosis rate of 19.6% (21/107); the majority had a diagnosis of ET (61.9%).. In 80% of such cases, this was the heralding event leading to the MPN diagnosis. Venous thrombosis was more frequent than arterial thrombosis (68% vs 33%). In particular, there was a disproportionate number of venous thromboses at unusual sites including cerebral venous sinus and splanchnic venous thromboses, representing 40% and 33% of total events, respectively. Only 3 (2.8%) patients were found to have a co-existent thrombophilia. Younger age at diagnosis appeared to associate with a higher rate of thrombosis (60% in patients aged <20, 18.2% in patients aged 20-30, and 17.2% in patients aged 31-40). Thrombotic events were most common in those with a JAK2V617 mutation (23.4%), followed by those who were TN (20.0%). Only 5.9% of CALR mutated cases had a thrombotic event. In terms of cardiovascular risk factors, 13.0% (14/107) and 6.5% (7/107) of patients had diagnoses of hypertension and type 2 diabetes, respectively. Haemorrhagic events were reported in 8.4% (9/107) of patients; 3.7% (4/107) had grade 3 or 4 bleeding complications, requiring transfusion and/or surgical intervention. All who experienced haemorrhagic events were on treatment with an anti-platelet or anti-coagulant agent. 4.7% (5/107) were diagnosed with acquired von Willebrand's disease, of whom one experienced a grade 3 haemorrhagic event. No patients transformed during follow up. 33 patients reported pregnancies, with 7/33 (21%) reporting antenatal or perinatal medical complications. Over 50% (55/107) of patients were commenced on cytoreduction. Most common agents employed were pegylated interferon (45.5%; 25/55) and hydroxycarbamide (43.6%%; 24/55). No patients required combination therapy. 92/107 (86%) patients were treated with an antiplatelet agent and 9/107 (8.4%) were on anti-coagulant treatment with the majority (88.8%) receiving warfarin rather than a DOAC. AYA MPN patients have unique characteristics and heterogeneous clinico-biological features differentiating them from older MPN cohorts. Our data highlights a female preponderance, higher incidence of venous thrombosis (particularly atypical sites), and lower incidence of arterial thrombosis. Whilst traditionally younger patients are considered to have ‘low risk’ disease, this real-world study highlights a significant thrombosis rate of ~ 20% which may have associated morbidity considering the relatively longer duration of the disease course and need for cytoreductive therapy. Specific AYA MPN directed risk stratification and therapeutic algorithms are required to inform holistic and age-appropriate patient management.

Combined Deficiency of Chromosome 7 Myeloid Tumor Suppressors Enhances Chemotherapy Resistance

Monosomy 7 and del(7q) [-7/del(7q)] are recurrent in myeloid neoplasms and associated with chemoresistance. -7/del(7q) is identified in up to half of therapy-related myeloid neoplasms (t-MN), high-risk secondary malignancies arising after prior exposure to chemotherapy or radiation. -7/del(7q) is also detected in clonal hematopoiesis, suggesting chromosome 7 aberrations can be early events in disease etiology. Despite this prevalence, the pathogenesis of -7/del(7q) in leukemogenesis remains unclear. We previously reported that deficiency of the transcription factor CUX1, a 7q-encoded tumor suppressor gene, promotes hematopoietic stem and progenitor cell drug resistance and t-MN transformation. Herein, we determined the combined impact of CUX1 loss with additional 7q tumor suppressor genes. To this end, we established a CRISPR/Cas9-based murine model of del(7q) clonal hematopoiesis and drug resistance. After targeting four 7q genes simultaneously, combined deficiency of CUX1 and the histone methyltransferase EZH2 uniquely promoted clonal outgrowth under genotoxic pressure in vivo and in vitro. Mechanistically, clonal selection is due, in part, to decreased apoptosis after chemotherapy exposure. RNA-seq in the absence of genotoxic insult revealed that Cux1 and Ezh2 loss has an additive transcriptional impact that is enriched for -7/del(7q) patient-derived gene signatures. Overall, we reveal a previously unknown genetic interaction between the 7q genes CUX1 and EZH2, supporting the concept of 7q as a contiguous gene syndrome region . A refined understanding of the molecular pathways driving del(7q) pathogenesis and drug resistance will enable development of therapies designed to counter or prevent these high-risk malignancies. In addition, we report a tractable approach for interrogating the pathogenesis of aneuploid events more broadly in cancer.

Atypical Stem Cell, Pre-B-Cell, T-Cell and Myeloid Gene Expression Characterizes Early Waldenstrom's Macroglobulinemia Clones Which Diminishes with Advancing Disease and Has Therapeutic Implications

Background: In previous studies using multi-omic data for 253 treatment-naive patients with Waldenstrom's Macroglobulinemia (WM), we identified three subtypes of WM: B-cell like (BCL), Plasma cell like (PCL), and an intermediate clone enriched for early/smoldering WM from which the other two evolved (Hunter et al, ASH 2022). The BCL and PCL subtypes show distinct mutation and transcriptional signatures, as well as clinical characteristics. Diffusion pseudo-time (DPT) analysis suggests all patient tumors, regardless of subtype have a shared evolutionary path and can be divided into Early and Late DPT determined stages that mirror disease progression. Additional analysis of DPT suggests it represents a continuous process akin to clonal evolution. We therefore sought to further characterize the DPT signal in MYD88 mutated WM. Methods: RNASeq was performed on CD19-selected bone marrow (BM) samples from 249 of the 253 treatment-naive WM patients who were MYD88 mutated, as well as 13 paired CD19+CD27- and CD19+CD27+ selected healthy donor (HD) peripheral blood samples. Whole exome sequencing of CD19-selected BM cells along with CD19-depleted peripheral blood mononuclear controls was also performed for 215 of the WM samples. To assess BM histology, slides from 66 BM paraffin blocks from these WM patients were analyzed. Results: WM patients had median age of 66 (range 31-95 years), BM involvement of 50% (5-95%) and serum IgM level of 3,162 (104-10,321 mg/dL). The median follow-up for the study cohort was 8.8 (range 0.2 - 33.8 years). Patients were stratified into 5 cohorts by DPT values. Analysis of BM involvement by DPT cohorts revealed a stepwise increase with the median involvement rising from 20% in the lowest to 80% in the highest cohort (p<0.0001). Increasing DPT predicted for shorter time from biopsy to first therapy (p=0.0003) but was not predictive of time from diagnosis to first therapy consistent with DPT alignment by stage of WM development. RNASeq analysis revealed high expression of genes atypical of mature B-cells that diminished with increasing DPT ( Figure 1). Among these were the myeloid chemo-attractants CXCL1, CXCL8 and CXCL12 which fell from a median of 4.4, 67.2 and 41.1 to 0.1, 3.6 and 0.8 transcripts per million (TpM) in the lowest and highest DPT cohorts, respectively (p<0.0001). Accordingly, all the top 20 gene ontology (GO) terms associated with DPT were related to activation, degranulation, and migration of myeloid cells and leukocytes. Pathological review of the 66 BM slides ranked by DPT, showed increased early myeloid cells and eosinophils clustering near small lymphoid aggregates, and as DPT increased, increased lymphocytes and mast cells with decreased myeloid cell involvement was observed. By RNASeq, pre-B-cell genes including MYB, the VDJ recombination genes RAG1, RAG2 and DNTT as well as the surrogate light chain genes IGLL1 and VPREB1 fell from 22.5, 10, 13.5, 61.1, 144 and 38.3 to 2.2, 1, 1.1, 9.1, 12.2 and 4.3 TpM, respectively (p<0.0001). T-cell and myeloid genes including CD4, CD8A, FCGR3A (CD16), CD14 and CD33 also decreased with increased DPT from 67.6, 7.1, 80.5, 200, and 23.2 to 2.4, 0.9, 1.7, 3.6 and 0.7 TpM, respectively (p<0.0005). A subclonal stem cell signature was also detected, including CD34 and KIT (CD117), which fell from 1.67 and 0.64 to 0.15 and 0.06 TpM, respectively (0<0.0001). CD34, KIT, preBCR, CD4, CD8A, FCGR3A, CEACAM8 (CD66b), and CD33 expression was confirmed by CD19+ light chain restricted flow cytometry in WM but not in HD samples. In addition, the MB and plasma blast genes PRDM1 and XBP1 were elevated in all samples regardless of DPT, consistent with a putative memory B-cell origin. Progression free survival (PFS) in response to proteasome inhibitors revealed strong stratification by subtype (p=0.001), as well as inferior PFS with BTK-inhibitors in low DPT patients (p= 0.044; Figure 2), suggesting less BTK dependence in the early DPT clones. Consistent with this finding, gene set enrichment identified increased BCR signaling with increased DPT. Conclusions: This analysis suggests that stem cell program reactivation and atypical marker expression characterize early WM clones that are ultimately replaced by clones exhibiting more typical B-cell markers with disease progression. The findings may be relevant to treatment selection and provide a framework for investigating subtype and early/late evolutionary staging in the treatment approach to WM.

Evaluation of Couples at Risk for Hemoglobin Disorders in Italy: The Results of an 18-Month Retrospective Observational Single-Center Study

Background: Hemoglobinopathies are genetic disorders caused by mutations in the genes encoding globin chains. These conditions are the most common monogenic disorders worldwide, resulting in significant morbidity and mortality among those affected by the most severe forms. Antenatal evaluation for thalassemia and sickle cell disease (SCD) enables couples to know their reproductive risk, thus allowing an informed reproductive choice. However, in certain areas, couples do not often receive the appropriate counseling at the appropriate time. Aim: The aim of this study is to describe the characteristics of couples referred to our tertiary referral center in Milan, Italy, for evaluation of hemoglobinopathy risk and their management. Methods: in our Institution, a diagnostic-therapeutic pathway involving the Hemoglobinopathies unit, the Medical Genetic unit, and the central laboratory has been implemented. Subjects referred to the Institution, and their partner, underwent the following laboratory tests: complete blood count, hemolysis and iron parameters, vitamin pattern, and hemoglobin (Hb) pattern by high-performance liquid chromatography (HPLC). The couples were then evaluated by a hemoglobinopathy expert, and those at risk for Hb disorders were offered a molecular analysis. Couples were then referred to the geneticist to receive the results of the molecular analysis, discuss the genetic risk for the fetus and, in case of high risk, discuss possible reproductive choices (i.e., prenatal diagnosis, pre-implantation diagnosis). We retrospectively collected and analyzed couples' data referred to our center from the 1 st of July 2021 to the 31 st of December 2022. Results: Three hundred and fifty-one couples were evaluated for hemoglobinopathies over 18 months. The median age was 34 years, with a tendency for younger age in female partners; 67% (234/351) of the women were already pregnant at the time of evaluation (median gestational age 18 weeks, range 7-37), while 33% (117/351) were referred for preconception counseling. Individuals from more than 48 different countries were screened, and the most represented countries of origin included: Italy (50%), Nigeria (6%), Bangladesh (4%), and Ivory Coast (4%), underpinning a vastly diverse genomic background. The referral was triggered by either evidence of microcytic anemia (58%) or HPLC anomalies (42%), including Hb variants, HbA2 anomalies, or elevated HbF in at least one partner. 55% of the referrals did not require additional testing. The remaining 45% (158/351) underwent advanced molecular tests to determine the nature of the Hb defect, guided by the results of the first-level panel. Among these, 33 couples (12% of the total) were found to be at risk for transmission of severe clinical forms of β-thalassemia, sickle cell anemia, or compound β-disorder heterozygosity (HbS/β-thal, HbC/HbS). One additional couple (0.4%) was at risk for HbH disease. In addition, 4 couples (1.5%) were found to be at risk for thalassemia intermedia combining a β-thalassemia mutation and α-gene triplication. Of the above, all 34 couples underwent invasive fetal evaluation: 24 women underwent chorionic villous sampling, while 10 received amniocentesis. A diagnosis of thalassemia in the fetus was reported in 6/34 (18%) cases and 3 (9%) of SCD. Interestingly, during the 18 months of observation, among the evaluated adult subjects, we found 4 cases of non-transfusion dependent thalassemia (NTDT) and 1 of HbS/β-thal in otherwise healthy subjects. All 4 cases of NTDT resulted from α-gene triplication paired with a β-thalassemia heterozygous defect. Furthermore, α triplication was found alone in 4 subjects without additional Hb gene defects. Overall, α triplication was detected in 9 out of 154 (5.8%) individuals who underwent HBA gene analysis. Conclusion: The median gestational age at presentation was high, leading to a limited time for couples to receive the appropriate counseling to make an informed reproductive choice. Increasing awareness across all involved specialists remains the mainstay for an effective prevention program to promptly identify at-risk couples and offer counseling at the right time. In addition, the relatively high incidence of α triplication in our population of asymptomatic and hematologically normal subjects and the new diagnosis of 4 NTDT warrants further studies to confirm the prevalence of α triplication in the general population.

Analysis the Relationship between Clonal Hematopoiesis and Cardiovascular Events in Chronic Myeloid Leukemia Based on Next-Generation Sequencing Technology

B ackground With the development and clinical application of high-throughput sequencing technologies and cytogenetics, the genetic complexity of hematopoiesis is better understood. Studies have found that there are gene mutations in hematopoietic stem cells that leading to subsequent clonal hematopoiesis (CH) phenomenon. Moreover, several recent studies have linked the occurrence of cardiovascular events with CH, and individuals with CH had a doubled risk of coronary heart disease and a fourfold increased risk of myocardial infarction. CH also exists in CML, and with the widespread application of second- and third-generation TKIs, the occurrence of cardiovascular adverse events had become one of the difficulties in the management of CML patients. Therefore, analyzing the relationship between additional gene mutations and cardiovascular adverse events in CML patients based on Next-Generation Sequencing (NGS) technology will provide new directions and ideas for the precise management of CML patients. O bjective Analyzing the relationship between clonal hematopoiesis and cardiovascular events in CML patients based on NGS technology. Method Using NGS technology to find hematological tumor-related gene mutations in CML patients, and analyzing their relationship with cardiovascular adverse events in CML patients. R esult A total of 149 CML patients were tested by NGS in this study, and were detected 152 clinically significant mutations. The mutations mainly involved genes related to epigenetic and activated signaling pathways, most of which were detected only in patients with drug resistance/intolerance to tyrosine kinase inhibitors (TKIs). The genes with higher mutation frequency were FAT1, GSTM1, ABL1, CUX1, EP300, ASXL1, TET2, CEBPA and so on. In this study, a total of 40 patients had cardiovascular events during treatment. When analyzing the risk factors of cardiovascular events in CML patients, it was found that patients with cardiovascular events were older [the median age were 58 (23-74) years vs 39 (16-73) years, P<0.001], and the duration of taking second-generation TKIs was also longer [the median time were 38 (0-102) months vs 16 (0-66) months, P=0.001]. When analyzing the relationship between gene mutations and cardiovascular events in CML, it was found that ASXL1, DNMT3A, EZH2 and other genes were more frequently detected in CML patients with cardiovascular events. Among them，DNMT3A mutation was associated with the occurrence of cardiovascular events in CML patients (RR 23.3, P=0.003). In addition, we also found that CCND1, CYP2C19 and NTRK2 gene mutations were only detected in patients without cardiovascular events significantly. C onclusion CML patients with cardiovascular events are older, take second-generation TKIs for a longer time, and have a higher incidence of DNMT3A gene mutation; CCND1, CYP2C19, NTRK2 gene mutation may be a protective factor for cardiovascular events in CML patients.

A Large Cohort Study of 412 Patients with SRSF2/TET2 Co-Mutated Myeloid Neoplasms: The Molecular Landscape and Clinical Outcomes

Introduction: Serine and arginine-rich splicing factor 2 ( SRSF2) and tet methylcytosine dioxygenase 2 ( TET2) are early mutations that drive the development of myeloid neoplasms and monocytosis. SRSF2/ TET2 co-mutations are most common in chronic myelomonocytic leukemia (CMML). However, they can also be seen in myelodysplastic syndrome (MDS), acute myeloid leukemia from CMML (AML-CMML), other AML (AML-Other, mostly de novo AML), and myeloproliferative neoplasms (MPN). Previous studies have investigated these co-mutations in myeloid diseases separately and as a subset (CMML) or small subset (MDS or AML) of the patients. Additionally, these studies mainly compared the clinical difference between patients with and without these double mutations. A large cohort study of patients with both mutations, irrespective of the morphologic diagnosis, has not been reported. Methods: Out of the Moffitt NextGen sequencing database of more than 8000 patients, we identified 412 patients with both SRSF2 and TET2 mutations and with diagnosed or suspected myeloid neoplasms. The demographics and clinical parameters were collected. Overall survival (OS) was defined as the time from sequencing to the last visit at Moffitt or death. Two experienced hematopathologists confirmed the final diagnosis according to the 5 th edition of the World Health Organization classification of hematological malignancies. Chi-squared tests of independence were used to compare the association between gene mutation and diagnosis, and a post hoc test based on adjusted standardized residuals was used. Cox proportional hazards models were used to compare the OS within and across diagnoses and included gender, age, gene mutation, and diagnosis (when comparing across diagnoses) as covariates. Results: Of the 412 patients, 284 (69%) were male, 128 (31%) were female, and the average age was 75 years. The five most common diagnoses, in descending order, were CMML (41%), AML-Others (23%), MDS (12%), AML-CMML (9%), and MPN (6%). The ten most common additional mutated genes, in descending order, were ASXL1 (44%), RUNX1 (28%), CUX1 (13%), JAK2 (13%), CBL (11%), TP53 (10%), SETBP1 (9%), KRAS (9%), STAG2 (9%), and NRAS (9%). A comparison of the top 5 diagnoses and the top 10 additional gene mutations showed an association between diagnosis and gene mutation (chi2 = 131, 36 df, p=.000). A post hoc test showed CBL mutations were less frequent in patients with AML-Others (p=.029), STAG2 mutations were less common in CMML patients (p=.007), and STAG2 mutations were more frequent in patients with MDS (p=.000). Among all patients, RUNX1 mutation (HR=2.4, 95% CI [1.3, 4.4], p=.005), ASXL1 mutation (HR=2.3, 95% CI [1.3, 4.2], p=.005), and CBL mutation (HR=2.0, 95% CI [1.0, 3.8], p=.048) were associated with lower OS. Among patients diagnosed with CMML, KRAS mutation (HR=4.1, 95% CI [1.5, 11.3], p=.006) and ASXL1 mutation (HR=3.3, 95% CI [1.4, 8.3], p=.009]) were associated with lower OS. Among patients with low-grade myeloid diseases (CMML and MDS), ASXL1 mutation (HR=2.6, 95% CI [1.2, 5.9], p=.021) was associated with lower OS. For the five most frequently co-mutated genes ( ASXL1, RUNX1, CUX1, JAK2, and CBL), no difference in OS was found between patients with CMML vs MDS, or AML-CMML vs AML-Others. Conclusions: SRSF2 and TET2 co-mutations occurred in various myeloid diseases, including CMML, AML transformed from CMML, other types of AML, MDS, and MPN. RUNX1, ASXL1, and CBL, were commonly mutated and associated with lower OS compared to patients with only SRSF2 and TET2 mutations. When comparing OS for patients diagnosed with low-grade diseases (CMML or MDS), ASXL1 mutation was associated with an increased risk of death. No difference in OS was found between CMML vs MDS, or AML-CMML vs AML-Others when co-mutation with ASXL1, RUNX1, CUX1, JAK2, or CBL was present.