Gene Copy Number Variation Research Articles

Structural variation in the pangenome of wild and domesticated barley.

Pangenomes are collections of annotated genome sequences of multiple individuals of a species1. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants2. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plantsto adapt to new selective regimes in agricultural ecosystems.

Characterization of the function and clinical value of ERCC family genes in lung adenocarcinoma

IntroductionERCC genes, responsible for encoding enzymes involved in base excision repair, have been implicated in various cancers, contributing to chemoresistance. However, a comprehensive analysis of the prognostic and therapeutic significance of this gene family in lung adenocarcinoma (LUAD) is lacking.MethodsThis study conducted a multidimensional assessment of ERCC family genes in LUAD using bioinformatic approaches, including mRNA expression level, gene methylation, and copy number variation (CNV), as well as their correlations with clinical outcome, gene set variations, and tumor-infiltrating lymphocytes (TILs). In addition, We evaluated the anti-tumor effects of ERCC8 in cell lines, demonstrating its clinical potential on an experimental level.ResultsOverall, the expression of ERCC genes exhibited a negative correlation with good prognosis, with ERCC6L and ERCC8 demonstrating the most reliable predictive performance. Gene methylation level and CNV increases of ERCC genes generally displayed negative and positive associations with their expression levels, respectively. Additionally, GSVA analysis suggested that ERCC expression was positively correlated with cell cycle and apoptosis pathways but negatively correlated to the TSC/mTOR pathway. Furthermore, the expression of ERCC genes exhibited a complex relationship with TILs and the response to anti-tumor drugs. The results of in vitro cellular experiments show that inhibiting ERCC8 can alleviate the malignant phenotype of LUAD cells.DiscussionOur study revealed the multifaceted biological and clinical significance of ERCC family members in LUAD. These findings provide new insights into the function of ERCC family genes in LUAD and their potential clinical applications.

Genotyping sequence-resolved copy-number variations using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes.

Copy-number variable (CNV) genes are important in evolution and disease, yet sequence variation in CNV genes is a blindspot for large-scale studies. We present a method, ctyper, that leverages pangenomes to produce copy-number maps with allele-specific sequences containing locally phased variants of CNV genes from NGS reads. We extensively characterized accuracy and efficiency on a database of 3,351 CNV genes including HLA , SMN , and CYP2D6 as well as 212 non-CNV medically-relevant challenging genes. The genotypes capture 96.5% of underlying variants in new genomes, requiring 0.9 seconds per gene. Expression analysis of ctyper genotypes explains more variance than known eQTL variants. Comparing allele-specific expression quantified divergent expression on 7.94% of paralogs and tissue-specific biases on 4.7% of paralogs. We found reduced expression of SMN-1 converted from SMN-2, which potentially affects diagnosis of spinal muscular atrophy, and increased expression of a duplicative translocation of AMY2B . Overall, ctyper enables biobank-scale genotyping of CNV and challenging genes.

Copy number variations in RNF216 and postsynaptic membrane-associated genes are associated with bipolar disorder: a case-control study in the Japanese population.

Bipolar disorder (BD) is a common psychiatric disorder characterized by alterations between manic/hypomanic and depressive states. Rare pathogenic copy number variations (CNVs) that overlap with exons of synaptic genes have been associated with BD. However, no study has comprehensively explored CNVs in synaptic genes associated with BD. Here, we evaluated the relationship between BD and rare CNVs that overlap with synaptic genes, not limited to exons, in the Japanese population. Using array comparative genome hybridization, we detected CNVs in 1839 patients with BD and 2760 controls. We used the Synaptic Gene Ontology database to identify rare CNVs that overlap with synaptic genes. Using gene-based analysis, we compared their frequencies between the BD and control groups. We also searched for synaptic gene sets related to BD. The significance level was set to a false discovery rate of 10%. The RNF216 gene was significantly associated with BD (odds ratio, 4.51 [95% confidence interval, 1.66-14.89], false discovery rate < 10%). The BD-associated CNV that corresponded with RNF216 also partially overlapped with the minimal critical region of the 7p22.1 microduplication syndrome. The integral component of the postsynaptic membrane (Gene Ontology:0099055) was significantly associated with BD. The CNV overlapping with the intron region of GRM5 in this gene set showed a nominal significant association between cases and controls (P < 0.05). We provide evidence that CNVs in RNF216 and postsynaptic membrane-related genes confer a risk of BD, contributing to a better understanding of the pathogenesis of BD.

Spinal muscular atrophy carrier screening program: awareness and attitude of healthcare professionals in Turkey.

Spinal Muscular Atrophy (SMA) is an autosomal recessive disease caused by variants in the SMN1 gene, leading to progressive muscle weakness. The carrier frequency of SMN1 gene variants, including variant and copy number variations, is estimated to be around 1 in 50 people, while the global prevalence of SMA is 1-3 per 10,000 live births. In response to the increasing carrier proportion, especially due to consanguineous marriages, Turkey launched the SMA Carrier Screening Program in 2021. Notably, recent SMA cases have been observed in the children of healthcare workers who did not undergo carrier screening, prompting us to evaluate their awareness of this program. After receiving ethics approval, 1,322 healthcare professionals completed a 15-item survey based on the SMA Carrier Screening Guidelines. Of these, 5.8% were unaware of SMA, and 26% lacked information about the national screening program. Awareness of the screening program was significantly lower among secondary and tertiary healthcare professionals compared to primary healthcare professionals (p < 0.0001) and among non-physician healthcare professionals compared to physicians (p < 0.0001). Additionally, a serious lack of knowledge was observed concerning the parts of the screening covering the pregnancy period. Although there is generally high awareness of the SMA Carrier Screening Program among healthcare professionals, significant knowledge gaps exist. These findings highlight the need for increased efforts to more effectively deliver screening programs and continue the education of healthcare professionals. Education and awareness campaigns can enhance program awareness and effectiveness, reach wider audiences, and contribute to preventive measures for the health of future generations.

Single nucleus DNA sequencing of flow sorted archived frozen and formalin fixed paraffin embedded solid tumors.

Archived samples, including frozen and formalin fixed paraffin embedded (FFPE) tissues, are a vast resource of clinically annotated materials for the application of high-definition genomics to improve patient management and provide a molecular basis for the delivery of personalized cancer therapeutics. Notably, FFPE tissues are stable, provide repeat sampling of tissues of interest, and can be stored indefinitely at ambient temperature. The development of single cell DNA sequencing (scDNA-seq) technologies provides an unparalleled opportunity for the study of tumor heterogeneity and the identification of often rare subclonal cell populations that drive tumor evolution and progression to advanced therapy resistant disease. However, major limitations to the use of archived tissues for scDNA-seq include the low yields of intact cells in the presence of high levels of subcellular debris in biopsies, and the highly variable quantity and quality of the DNA extracted from samples of interest. The latter is of high significance for the use of FFPE tissues due to the presence of DNA-protein crosslinks. In addition, many samples, notably tumors arising in solid tissues, contain admixtures of reactive stroma, inflammatory cells, and necrosis in immediate contact with tumor cells. To expand their use for translational studies, we optimized flow sorting and sequencing of single nuclei from archived fresh frozen (FF) and FFPE tumor tissues. Our methods, which include isolation of intact nuclei suitable for library preparations, quality control (QC) metrics for each step, and a single cell sequencing bioinformatic processing and analysis pipeline, were validated with flow sorted nuclei from matching FF and FFPE ovarian cancer surgical samples and a sequencing panel of 553 amplicons targeting single nucleotide and copy number variants in genes of interest. Our flow sorting based protocol provides intact nuclei suitable for snDNA-seq from archival FF and FFPE tissues. Furthermore, we have developed QC steps that optimize the preparation and selection of samples for deep single cell clonal profiling. Our data processing pipeline captures rare subclones in tumors with highly variable genomes based on variants in genes of interest.

Unveiling the Power of Mitochondrial Fission and Fusion: A Five-Gene Signature for Personalized Prognosis in Gastric Cancer.

Mitochondrial fission and fusion play important roles in tumorigenesis, progression and therapy. Dysregulation of these processes may lead to tumor progression, and regulation of these processes may provide novel strategies for cancer therapy. The involvement of genes related to mitochondrial fission and fusion (MD) in gastric cancer (GC) remains poorly understood. The aim of this study was to establish an MD gene signature for GC patients and to investigate its association with prognosis, tumor microenvironment and treatment response in GC. We use the TCGA-GC database as the cohort, focusing specifically on genes associated with MD. We conducted identification and consistency clustering analysis of differentially expressed genes in MD, conducted MD gene mutation and copy number variation analysis, as well as correlation and functional enrichment analysis between MD gene cluster classification and immune infiltration. TCGA-GC and GSE15459 were used to construct training and validation cohorts for the model. We used various statistical methods, including Cox and Lasso regression, to develop the model. We validated the model using bulk transcriptome and single- cell transcriptome datasets (GSE13861, GSE26901, GSE66229, and GSE13450). We used GSEA enrichment, CIBERSORT algorithm, ESTIMATE, and TIDE to gain insight into the annotation of MD signature and the characterization of the tumor microenvironment. OncoPredict was used to analyze the relationship between the PRG signature and the drug sensitivity. We validated the expression of several key genes in MD signature on GC cell lines using quantitative real-time PCR (qRT-PCR). These MDs-related subtypes exhibited different prognosis and immune filtration patterns. A five-gene signature, comprising AGT, HCFC1, KIFC3, NOX4, and RIN1, was developed. There was a clear distinction in overall survival between low- and high-risk patients. The analyses showed further confirmation of the independent prognostic value of the gene signature. There was a notable correlation between the MD signature, immune infiltration and drug susceptibility. The expression levels of AGT, HCFC1, KIFC3, NOX4 and RIN1 mRNA were all increased in these GC cells. The MD signature has the capacity to significantly contribute to the prediction of personalized outcomes and the advancement of novel therapeutic strategies tailored for GC patients.

Genome architecture of the heavy metal tolerant and accumulator Hirschfeldia incana: Insights from genome sequencing, assembly, and comparative analysis

Hirschfeldia incana L., a member of the Brassicaceae family commonly found in Mediterranean regions, is known for its capacity to withstand and accumulate heavy metals, particularly lead (Pb) both in soil environments and hydroponic systems. This plant has been used as a model to study plant responses to heavy metals. Nonetheless, the molecular mechanisms underlying its tolerance and heavy metal accumulation are not fully understood, partly because of the limited knowledge about its genome. In this study, the genome of H. incana was sequenced, assembled, characterized, and annotated. Approximately 8.6 Gpb of data were generated using Oxford Nanopore Technology (ONT), resulting in a genome assembly of 390 Mb, comprising 5196 contigs with an N50 exceeding 131 kb. The genome had a BUSCO score of 97.2 %, with 38,454 genes and a repetition content of 38.25 %. Subsequently, the assembled genome was annotated using several databases including GO, InterPro, MetaCyc, PANTHER, Pfam, Reactome, SUPERFAMILY, and KEGG. This annotation yielded 22,661 GO terms and 143 KEGG maps. A comparative genomic analysis between H. incana and six Brassicaceae species (five hyperaccumulators of heavy metals and one non-hyperaccumulator) was also conducted. This analysis revealed that H. incana shares a substantial proportion of orthologous genes (89.7 % of orthogroups) with six Brassicaceae species. The generated phylogenetic tree suggests that H. incana is closely related to B. juncea, B. napus, and B. oleracea, indicating a common ancestry and potentially shared genetic factors contributing to hyperaccumulation in these species. Moreover, the copy number of twenty-nine genes involved in heavy metal tolerance and accumulation mechanisms in H. incana and six brassicaceae were assayed. This analysis revealed that H. incana and other hyperaccumulator species possess a higher copy number of genes related to heavy metal tolerance than the sensitive plant A. thaliana. Notably, the variation in gene copy numbers highlights their potential role in the adaptation of H. incana to heavy metal stress. This study provides a comprehensive genomic framework that enhance our understanding of H. incana adaptation to heavy metal stress, and offers valuable data for further genomic investigations of the molecular mechanisms of heavy metal tolerance and accumulation in plants.

Adaptive copy number variations of ancient prokaryotic genes in marine fish colonization

During extensive evolution, higher eukaryotes have acquired numerous prokaryotic genes, some of which have experienced adaptive copy number variations (CNVs) in response to changing environments. The specific contribution of ancient prokaryotic genes to the evolutionary dynamics of marine fish remains unclear. In this study, we investigated ancient prokaryotic genes in 33 freshwater and 14 non-freshwater fish species. Non-freshwater fish exhibited a higher proportion of these genes (25.84 %) compared to freshwater fish (17.66 %), though functional categories showed similarity, suggesting genetic conservation. Comprehensive CNV analysis identified 24 genes with significantly higher copy numbers in non-freshwater fish, enriched in glycerolipid metabolism, immune regulation, and catechol O-methyltransferase activity. Eight of these genes displayed increased copy numbers in marine populations compared to Asian freshwater populations. These findings indicate that CNVs in genes related to glycerolipid metabolism, immune regulation, and methyltransferase activity may play crucial roles in marine adaptation at global and regional evolutionary scales.

EP.06F.03 Analysis of Copy Number Variations of MET, EGFR and ERBB2 Genes in a Lung Cancer Patient Series: Comparison of FISH with NGS

EP.06F.03 Analysis of Copy Number Variations of MET, EGFR and ERBB2 Genes in a Lung Cancer Patient Series: Comparison of FISH with NGS

β-Defensin gene copy number variation in cattle.

β-Defensins are peptides with antimicrobial roles, characterized by a conserved tertiary structure. Beyond antimicrobial functions, they exhibit diverse roles in both the immune response and fertility, including involvement in sperm maturation and function. Copy number variation (CNV) of β-defensin genes is extensive across mammals, including cattle, with possible implications for reproductive traits and disease resistance. In this study, we comprehensively catalogue 55 β-defensin genes in cattle. By constructing a phylogenetic tree to identify human orthologues and lineage-specific expansions, we identify 1 : 1 human orthologues for 35 bovine β-defensins. We also discover extensive β-defensin gene CNV across breeds, with DEFB103, in particular, showing extensive multi-allelic CNV. By comparing β-defensin expression levels in testis from calves and adult bulls, we find that 14 β-defensins, including DEFB103, increase in expression during sexual maturation. Analysis of β-defensin gene expression levels in the caput of adult bull epididymis, and β-defensin gene copy number, in 94 matched samples shows expression levels of four β-defensins are correlated with genomic copy numbers, including DEFB103. We therefore demonstrate extensive CNV in bovine β-defensin genes, in particular DEFB103, with potential functional consequences for fertility.

Mitochondrial genetic variations in leukemia: a comprehensive overview.

Leukemias are a group of heterogeneous hematological malignancies driven by diverse genetic variations, and the advent of genomic sequencing technologies facilitates the investigation of genetic abnormalities in leukemia. However, these sequencing-based studies mainly focus on nuclear DNAs. Increasing evidence indicates that mitochondrial dysfunction is an important mechanism of leukemia pathogenesis, which is closely related to the mitochondrial genome variations. Here, we provide an overview of current research progress concerning mitochondrial genetic variations in leukemia, encompassing gene mutations and copy number variations. We also summarize currently accessible mitochondrial DNA (mtDNA) sequencing methods. Notably, somatic mtDNA mutations may serve as natural genetic barcodes for lineage tracing and longitudinal assessment of clonal dynamics. Collectively, these findings enhance our understanding of leukemia pathogenesis and foster the identification of novel therapeutic targets and interventions.

Germline DNA Damage Repair Gene Alterations in Patients with Metachronous Breast and Colorectal Cancer.

A hereditary component of breast (BC) and colorectal cancer (CRC) has been described in approximately one-third of these tumor types. BC patients have an increased risk of developing CRC as a second primary tumor and vice versa. Germline genomic variants (NextSeq550, Illumina) were investigated in 24 unrelated BC and/or CRC patients and 7 relatives from 3 index patients. Fifty-six pathogenic or likely pathogenic variants were identified in 19 of 24 patients. We detected single-nucleotide variants (SNVs) in CRC predisposition genes (MLH1 and MUTYH) and other promising candidates (CDK5RAP3, MAD1L1, NOS3, and POLM). Eighteen patients presented SNVs or copy number variants (CNVs) in DNA damage repair genes. We also identified SNVs recently associated with BC or CRC predisposition (PABPC1, TYRO3, MAP3K1, SLC15A4, and LAMA1). The PABPC1c.1255C>T variant was detected in nine unrelated patients. Each patient presented at least one SNV/CNV in a candidate gene, and most had alterations in more than one gene, reinforcing a polygenic model for BC/CRC predisposition. A significant fraction of BC/CRC patients with a family history of these tumors harbored deleterious germline variants in DNA repair genes. Our findings can lead to strategies to improve the diagnosis, genetic counseling, and treatment of patients and their relatives.

Benchmarking of Approaches for Gene Copy-Number Variation Analysis and Its Utility for Genetic Aberration Detection in High-Grade Serous Ovarian Carcinomas.

Objective: The goal of this study was to compare the results of CNV detection by three different methods using 13 paired carcinoma samples, as well as to perform a statistical analysis of the agreement. Methods: CNV was studied using NanoString nCounter v2 Cancer CN Assay (Nanostring), Illumina Infinium CoreExome microarrays (CoreExome microarrays) and digital droplet PCR (ddPCR). Results: There was a good level of agreement (PABAK score > 0.6) between the CoreExome microarrays and the ddPCR results for finding CNVs. There was a moderate level of agreement (PABAK values ≈ 0.3-0.6) between the NanoString Assay results and microarrays or ddPCR. For 83 out of 87 target genes studied (95%), the agreement between the CoreExome microarrays and NanoString nCounter was characterized by PABAK values < 0.75, except for MAGI3, PDGFRA, NKX2-1 and KDR genes (>0.75). The MET, HMGA2, KDR, C8orf4, PAX9, CDK6, and CCND2 genes had the highest agreement among all three approaches. Conclusions: Therefore, to get a better idea of how to genotype an unknown CNV spectrum in tumor or normal tissue samples that are very different molecularly, it makes sense to use at least two CNV detection methods. One of them, like ddPCR, should be able to quantitatively confirm the results of the other.

The RAS/BRAF genes status in patients with colorectal cancer (review)

Colorectal cancer (CRC) is the third in prevalence among oncological diseases worldwide and second in the structure of oncological mortality. Genetic assessment of CRC is a necessary stage during selecting further treatment for patients. Many studies demonstrate a diverse distribution of mutations in the KRAS, NRAS, and BRAF genes in CRC. A critical literature review was conducted in order to systematize data on the mutational profile and genetic heterogeneity of these driver mutations in Russian patients with CRC. Articles were searched for in open databases. Totally 17 Russian studies and 3 English meta-analyses were analyzed for comparison with Russian data. Mutations in the KRAS, NRAS, and BRAF genes, according to Russian and international studies, are found in 40 %, 4 %, and 7 % in CRC patients, respectively. The frequency and specific localization of mutations may depend on the geographical location and nationality of the cohort. High intertumoral and intratumoral heterogeneity in CRC, especially in KRAS gene mutations, significantly influences the choice of further therapy and underscores the need for more detailed study of the mutational profile of the primary tumor, affected lymph nodes, and distant metastases. In Russia, several molecular genetic methods are used to determine somatic mutations in CRC with different sensitivity and specificity, the most common is real-time PCR. More accurate diagnostic methods include digital droplet PCR, Sanger sequencing, and next-generation sequencing, but each method has its limitations that must be considered when planning diagnostics and research. The promising directions in personalized oncology is the study of gene copy number variations, which may contribute to the development of new methods for treating CRC in the future. Despite the large number of studies, some aspects of the mutational profile of CRC in Russian studies remain poorly understood, which is why further research is needed on patients with colorectal cancer in Russia.

Deregulation and Shattering of Chromosomal Segments Containing Multiple Oncogenic Targets in the Pathogenesis of Diffuse Large B Cell Lymphoma, Not Otherwise Specified (DLBCL, NOS)

Diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS) is the most common type of non-Hodgkin lymphoma (NHL). Significant efforts have been focused on utilizing advanced genomic technologies to further subclassify DLBCL, NOS into clinically relevant subtypes. These efforts have led to the implementation of novel algorithms to support optimal risk-oriented therapy and improvement in the overall survival of DLBCL patients. The pathogenesis of DLBCL at the molecular level indicates copy number variation (CNV) as one of the major forms of genetic alterations in the somatic mutational landscape. Random deregulation that results in complex breaks of chromosomes and restructuring of shattered chromosomal segments is called chromothripsis. Gene expression changes influenced by chromothripsis have been reported in cancer and congenital diseases. This chaotic phenomenon results in complex CNV, gene fusions, and amplification and loss of tumor suppressor genes. We present herein a summary of the most clinically relevant genomic aberrations, with particular focus on copy number aberrations in a case that highlights DLBCL, NOS arising from relapsed Hodgkin lymphoma. The focus of our study was to understand the relationship between the clinical, morphological, and genomic abnormalities in DLBCL, NOS through multiple techniques for therapeutic considerations.

Adaptation to Environmental Stressors Conferred by Gene Copy Number Variation in Herbicide Resistant Amaranthus palmeri

Many rampant agricultural weeds have been found to contain gene copy number variation, a genetic adaptation that can facilitate the evolution of stress resistance. Amaranthus palmeri is a highly competitive and problematic agricultural weed in the United States which continues to naturalize, spreading northward to Canada. A.palmeri has gained attention due to its rapid evolution of herbicide resistance— a mechanism conferred by gene copy number variation of EPSPS. Researchers hypothesize that this gene is contained within an amplicon alongside other stress tolerance related genes. This raises the question of whether increased EPSPS gene copy number is associated with higher tolerance to environmental stressors, beyond herbicide stress. To prepare for addressing this hypothesis, I conducted a pilot project testing the ideal conditions for germination of A.palmeri. I planted 200 seeds divided between greenhouse and growth chamber environments. Many seeds benefit from a period of cold as a signal to break dormancy, thus, each category was further divided into two treatments: control and cold stratified (seeds were incubated in a –23 cold room for a week). I was interested in whether the increased consistency of temperature, light intensity, and photoperiod provided by a growth chamber, relative to a greenhouse, would increase germination rates. Results indicate that greenhouse grown seedlings had a 71% germination rate and within each treatment, 86% of cold stratified plants germinated while only 56% of the control group germinated. Whereas in the growth chamber, surprisingly only 26% of plants germinated with a breakdown of 22% cold stratified and 30% control. Thus, to germinate enough plants for a large-scale experiment, I chose to cold stratify seeds and grow them in the greenhouse for my undergraduate thesis. In this common garden experiment, I am currently growing 500 plants which will be divided into four stress treatment categories: control, salinity, drought, and salinity x drought. Using phenotypic measurements and digital droplet PCR (ddPCR) to quantify EPSPS gene copy number, I will test for a possible association between plants with a higher tolerance to these simulated environmental stressors and the presence of increased EPSPS gene copy number.

Deciphering genetic and nongenetic factors underlying tumour dormancy: insights from multiomics analysis of two syngeneic MRD models of melanoma and leukemia

BackgroundTumour dormancy, a resistance mechanism employed by cancer cells, is a significant challenge in cancer treatment, contributing to minimal residual disease (MRD) and potential relapse. Despite its clinical importance, the mechanisms underlying tumour dormancy and MRD remain unclear. In this study, we employed two syngeneic murine models of myeloid leukemia and melanoma to investigate the genetic, epigenetic, transcriptomic and protein signatures associated with tumour dormancy. We used a multiomics approach to elucidate the molecular mechanisms driving MRD and identify potential therapeutic targets.ResultsWe conducted an in-depth omics analysis encompassing whole-exome sequencing (WES), copy number variation (CNV) analysis, chromatin immunoprecipitation followed by sequencing (ChIP-seq), transcriptome and proteome investigations. WES analysis revealed a modest overlap of gene mutations between melanoma and leukemia dormancy models, with a significant number of mutated genes found exclusively in dormant cells. These exclusive genetic signatures suggest selective pressure during MRD, potentially conferring resistance to the microenvironment or therapies. CNV, histone marks and transcriptomic gene expression signatures combined with Gene Ontology (GO) enrichment analysis highlighted the potential functional roles of the mutated genes, providing insights into the pathways associated with MRD. In addition, we compared “murine MRD genes” profiles to the corresponding human disease through public datasets and highlighted common features according to disease progression. Proteomic analysis combined with multi-omics genetic investigations, revealed a dysregulated proteins signature in dormant cells with minimal genetic mechanism involvement. Pathway enrichment analysis revealed the metabolic, differentiation and cytoskeletal remodeling processes involved in MRD. Finally, we identified 11 common proteins differentially expressed in dormant cells from both pathologies.ConclusionsOur study underscores the complexity of tumour dormancy, implicating both genetic and nongenetic factors. By comparing genomic, transcriptomic, proteomic, and epigenomic datasets, our study provides a comprehensive understanding of the molecular landscape of minimal residual disease. These results provide a robust foundation for forthcoming investigations and offer potential avenues for the advancement of targeted MRD therapies in leukemia and melanoma patients, emphasizing the importance of considering both genetic and nongenetic factors in treatment strategies.Graphical

Beyond nest size: the clinicopathological spectrum of large nested melanocytic tumours and the value of comparative genomic hybridisation and messenger RNA expression analysis

Large nested melanomas (LNMs) are a rare subtype of naevoid melanoma consisting of large junctional melanocytic nests that are more common in older individuals and/or associated with sun damage. However, the presence of large melanocytic nests alone does not lead to a diagnosis of malignancy, ​as they can also be found in melanocytic naevi. LNMs are challenging because they lack most classic histological features of malignancy and require thorough clinicopathological evaluation. This ambiguity calls for a critical reassessment of the current diagnostic criteria for the subclassification of benign or malignant within the spectrum of large nested melanocytic tumours (LNMTs). Eighteen LNMTs and six special-site melanocytic naevi (SSMNs) ​were studied using different approaches: clinical features, dermoscopy, histopathology, immunohistochemistry, array comparative genomic hybridisation (aCGH) and messenger RNA (mRNA) sequencing analysis, with the aim of identifying novel and reproducible criteria for the recognition of LNMs.Careful clinicopathological evaluation of the 18 LNMTs led to the diagnosis of seven LNMs and 11 large nested melanocytic naevi (LNMNs). Lentiginous spread and nest bridging were significantly associated with LNMs after Holm–Bonferroni correction. Asymmetry, largest nest size, poor lateral demarcation, the number of colours and dermoscopic structures, and preferentially expressed antigen in melanoma (PRAME) immunostaining were more common in LNMs but did not reach statistical significance. Four of seven LNMs and nine of 11 LNMNs lacked the BRAF V600E mutation. Regarding aCGH, no LNMN or SSMN cases had ≥3 copy number variations (CNVs), in contrast to 50% of LNM cases. Importantly, LNM and LNMN could be distinguished by differential mRNA expression of nine genes. Our study demonstrates that there is a spectrum of LNMTs and that the clinicopathological diagnosis of LNM, for which we support the term ‘late-onset nested naevoid melanomas’, can be significantly strengthened by the presence of lentiginous pattern, nest bridging, gene CNV and differential mRNA expression.

BCORL1, POF1B, and USP9X copy number variation in women withidiopathic diminished ovarian reserve.

To analyze the copy number variation (CNV) in the X-linked genes BCORL1, POF1B, and USP9X in idiopathic diminished ovarian reserve (DOR). This case-control study included 47 women, 26 with DOR and 21 in the control group. Age, weight, height, BMI, and FSH level were evaluated, as well as antral follicle count (AFC), oocyte retrieval after controlled ovarian stimulation, and metaphase II (MII) oocytes. The CNVs of BCORL1, USP9X, and POF1B genes were measured by quantitative real time PCR (qPCR) using two reference genes, the HPRT1 (X-linked) and MFN2 (autosomal). Protein-protein interaction network and functional enrichment analysis were performed using the STRING database. The mean age was 36.52 ± 4.75 in DOR women and 35.38 ± 4.14 in control. Anthropometric measures did not differ between the DOR and control groups. DOR women presented higher FSH (p = 0.0025) and lower AFC (p < .0001), oocyte retrieval after COS (p = 0.0004), and MII oocytes (p < .0001) when compared to the control group. BCORL1 and POF1B did not differ in copy number between DOR and control. However, DOR women had more copies of USP9X than the control group (p = 0.028). The increase in the number of copies of the USP9X gene may lead to overexpression in idiopathic DOR and contribute to altered folliculogenesis and oocyte retrieval.