Genomic Landscape Research Articles

Exploring the human genomic landscape: patterns of common homozygosity regions in a large middle eastern cohort.

Regions of Homozygosity (ROH) typically reflect normal demographic history of a human population, but may also relate to cryptic consanguinity, and, additionally, have been associated with specific medical conditions. The objective of this study was to investigate the location, size, and prevalence of common ROH segments in a Middle Eastern cohort. This retrospective study included 13 483 samples collected from all Chromosomal Microarray analyses (CMA) performed using Single Nucleotide Polymorphism (SNP) arrays at the genetic clinical laboratory of Rabin Medical Center between 2017-2023 (primary data set). An additional replication cohort including 100 842 samples from another SNP array platform, obtained from Maccabi Health Organization, was analyzed. Common ROH locations were defined as those ROH locations involving 1% or more of the samples. A total of 66 710 ROH segments, involving 13 035 samples (96.7%) were identified in the primary data set. Of the 4069 cytogenetic ROH locations, 68 were identified as common. The prevalence of non-common ROH was relatively high in affected individuals, and for acrocentric chromosomes, chromosomes associated with common trisomies, and non-imprinted chromosomes. In addition, differences in common ROH locations were observed between the primary and the replication cohorts. Our findings highlight the need for population-specific guidelines in determining ROH reporting cutoffs, considering factors such as population-specific prevalence and testing platform differences. Future research with larger, varied cohorts is essential to advance understanding of ROH's associations with medical conditions and to improve clinical practices accordingly.

Genomic and transcriptomic landscape of human gastrointestinal stromal tumors

Gastrointestinal stromal tumor (GISTs) are clinically heterogenous exhibiting varying degrees of disease aggressiveness in individual patients. We comprehensively describe the genomic and transcriptomic landscape of a cohort of 117 GISTs including 31 low-risk, 18 intermediate-risk, 29 high-risk, 34 metastatic and 5 neoadjuvant GISTs from 105 patients. GISTs have notably low tumor mutation burden but widespread copy number variations. Aggressive GISTs harbor remarkably more genomic aberrations than low-/intermediate-risk GISTs. Complex genomic alterations, chromothripsis and kataegis, occur selectively in aggressive GISTs. Despite the paucity of mutations, recurrent inactivating YLPM1 mutations are identified (10.3%, 7 of 68 patients), enriched in high-risk/metastatic GIST and functional study further demonstrates YLPM1 inactivation promotes GIST proliferation, growth and oxidative phosphorylation. Spatially and temporally separated GISTs from individual patients demonstrate complex tumor heterogeneity in metastatic GISTs. Finally, four prominent subtypes are proposed with different genomic features, expression profiles, immune characteristics, clinical characteristics and subtype-specific treatment strategies. This large-scale analysis depicts the landscape and provides further insights into GIST pathogenesis and precise treatment.

Driver mutations associated with signatures of platinum sensitivity in germ cell tumors

We sought to evaluate the genomic and transcriptomic landscapes in primary and metastatic germ cell tumors (GCTs; N = 138) to uncover factors that drive cisplatin resistance. Prevalence was calculated for platinum-resistant alterations (PRAs; KRAS, TP53, and KIT mutations, and MDM2 amplification) and high copy number amplifications (CNA ≥ 6 copies). Tumors were designated as chemo-naïve (PreC, N = 66) or post-chemotherapy (PostC, N = 17). A transcriptomic signature associated with platinum sensitivity (PSS, high suggests increased sensitivity) was applied. KIT mutations were observed in 14.5% of primary versus 1.8% of met and 0% of lymph. TP53 mutations were identified in 10% of primary GCTs versus 17% of met and 16.7% of lymph. MDM2 CNAs were similar between sites. PRA-positive PreC GCTs had significantly lower average PSS scores compared to PRA-negative tumors. Lower PSS scores in chemo-naïve tumors were associated with PRAs, suggesting a potential mechanism for platinum resistance.

Genomic Epidemiology of Human Respiratory Syncytial Virus, Minnesota, USA, July 2023-February 2024.

We recently expanded the viral genomic surveillance program in Minnesota, USA, to include human respiratory syncytial virus. We performed whole-genome sequencing of 575 specimens collected at Minnesota healthcare facilities during July 2023-February 2024. Subgroups A and B differed in their genomic landscapes, and we identified 23 clusters of genetically identical genomes.

The genomic and epigenomic landscape of iridocorneal endothelial syndrome

The iridocorneal endothelial (ICE) syndrome is a rare but irreversibly blinding eye disease, whose etiology remains unknown and speculative. Characterization of its genomic and epigenomic landscape will benefit the development of etiology-based therapies. In this study, we recruited a cohort of 99 patients with ICE syndrome. Whole-genome sequencing was performed on 51 ICE patients and genome-wide DNA methylation profiling on 48 ICE patients. We then performed the mutational burden testing on genes and noncoding regulatory regions in the ICE cohort compared with control subjects (including 9197 East Asians from the gnomAD database and 350 normal Chinese from our in-house cohort). Copy number variance analysis was also performed. Hypomethylated and differentially methylated regions in ICE patients versus normal controls (45 normal Chinese from our in-house cohort) were explored. We identified RP1L1 (27/51, 53%) which emerged with a higher coding-altering mutational burden in the ICE syndrome cohort, whose mutations were mainly on chr8:10467637. We identified 41 regions exhibiting significant copy number variance. Specifically, regions at chr19:15783859-15791329 and chr3:75786061-75790887 showcased copy number loss in 39 and 19 out of 51 ICE patients, respectively. We also identified that 2717 differentially methylated regions and hypomethylation regions were predominantly found in ICE syndrome compared with normal samples (in 91.9% of 2717 differentially methylated regions). We also found 45 recurrent hypomethylation regions (identified in >10% ICE samples tested) that were differentially methylated (differential methylation < −0.1) between ICE syndrome and normal Chinese. Our study offers the first comprehensive genomic and epigenomic landscape of ICE syndrome, which will enhance the understanding of its etiology.

Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in Ganoderma.

Understanding the genomic diversity and functional implications of Ganoderma species is crucial for elucidating their evolutionary history and biotechnological potential. Here, we present the first pan-genomic analysis of Ganoderma spp., combining five newly sequenced genomes with ten publicly available genomes. Our comprehensive comparative study unveiled a rich genomic landscape, identifying core genes shared among all Ganoderma strains and species-specific gene sets. Additionally, we identified structural variants impacting the expression of key genes, including insights into the MSH4 gene involved in DNA repair and recombination processes, which exhibits a 440 bp insertion in the promoter region and a leucine-to-serine mutation in the gene body, potentially increasing spore production in the S3 strain. Overall, our study provides valuable insights into the genomic architecture and functional diversity of Ganoderma, paving the way for further research on its evolutionary dynamics, biotechnological applications and pharmaceutical potential.

Molecular subtypes and genomic landscape of undifferentiated and dedifferentiated endometrial cancer

Molecular subtypes and genomic landscape of undifferentiated and dedifferentiated endometrial cancer

Characterization of genomic profiling of Mexican women with breast cancer using Endopredict

PurposeIn the context of rising breast cancer incidence and mortality rates in Mexico, our study delves into the genomic landscape of Mexican women diagnosed with stage I-III breast cancer. MethodsEmploying the EndoPredict test for genomic analysis, our retrospective, cross-sectional study explores correlations between genomic expression and immunohistochemistry (IHC). ResultsAmong 50 female patients, risk stratification by IHC revealed 50% as high risk and 50% as low risk, with notable clinical and histological distinctions between the two groups. High-risk samples exhibited larger tumors, higher histological grades, and more positive lymph nodes. Immunohistochemistry results displayed a moderate concordance (kappa Cohen´s 0.48) with the EndoPredict test, emphasizing its clinical reliability over IHC. ConclusionsThe study advocates for the integration of genomic tools, particularly the EndoPredict test, in the management of breast cancer in Mexican women for enhanced precision in treatment decisions. Our findings contribute valuable insights to the evolving landscape of breast cancer diagnosis and management in the Mexican population.

A Comprehensive Exploration of Agents Targeting Tumor Microenvironment: Challenges and Future Perspectives.

The tumor microenvironment (TME) encompasses the complex and diverse surroundings in which tumors arise. Emerging insights highlight the TME's critical role in tumor development, progression, metastasis, and treatment response. Consequently, the TME has attracted significant research and clinical interest, leading to the identification of numerous novel therapeutic targets. Advances in molecular technologies now enable detailed genomic and transcriptional analysis of cancer cells and the TME and the integration of microenvironmental data to the tumor genomic landscape. This comprehensive review discusses current progress in targeting the TME for drug development, addressing associated challenges, strategies for modulating the pro-tumor microenvironment, and the discovery of new targets.

Urbanization affects population connectivity, reproductive success and phenotypic traits in the Mediterranean cliff species Brassica incana (Brassicaceae)

Biotic and abiotic changes induced by urbanization can highly affect the ecology and evolution of plant species. Indeed, urban development can have a major impact on plant population genomics, reproductive success and phenotypic traits hence influencing the adaptive strategies and the ecological functions of plant species within ecosystems. Through a holistic study of the impact of urbanization on the genetic and ecological dynamics of a Mediterranean plant species, we shed light on the mechanisms driving plant responses to urban environments. By focusing on 15 populations of the Mediterranean cliff species Brassica incana distributed along an urbanization gradient, we first analyzed the potential drivers of among-population genomic differentiation using a landscape genomics approach. Then, we provided a comprehensive understanding of the complex interplay among ecological factors (climate, herbivore damage, pollinator community), reproductive (relative fruit set and seed-ovule ratio) and phenotypic (glucosinolate content, flower number) traits involved in the response of B. incana populations to urban pressures using complementary Structural Equation Modeling (SEM) and correlative approaches. Our results show that urbanization reduces among-population connectivity by influencing the genomic differentiation among populations. Also, according to SEM analysis, urbanization showed direct and indirect (mediated by mean annual temperature) effects on both pollinator community and herbivory levels, and direct and indirect (mediated by honeybees and long-tongued bees) effects on plant reproductive success. Additionally, urban populations showed higher contents of a glucosinolate compound (glucobrassicin). Taken together, our findings suggest that urbanization can shape genomic differentiation, reproductive success and phenotypic variation. We showed that the impact of urbanization is rather complex and is likely mediated by the interplay between direct and indirect effects of abiotic and biotic conditions on B. incana. Overall, we documented how urban development can shape eco-evolutionary dynamics of a cliff species located in a densely inhabited Mediterranean area.

The Molecular Classification of Pheochromocytomas and Paragangliomas: Discovering the Genomic and Immune Landscape of Metastatic Disease.

Pheochromocytomas (PCCs) and paragangliomas (PGLs, together PPGLs) are the most hereditary tumors known. PPGLs were considered benign, but the fourth edition of the World Health Organisation (WHO) classification redefined all PPGLs as malignant neoplasms with variable metastatic potential. The metastatic rate differs based on histopathology, genetic background, size, and location of the tumor. The challenge in predicting metastatic disease lies in the absence of a clear genotype-phenotype correlation among the more than 20 identified genetic driver variants. Recent advances in molecular clustering based on underlying genetic alterations have paved the way for improved cluster-specific personalized treatments. However, despite some clusters demonstrating a higher propensity for metastatic disease, cluster-specific therapies have not yet been widely adopted in clinical practice. Comprehensive genomic profiling and transcriptomic analyses of large PPGL cohorts have identified potential new biomarkers that may influence metastatic potential. It appears that no single biomarker alone can reliably predict metastatic risk; instead, a combination of these biomarkers may be necessary to develop an effective prediction model for metastatic disease. This review evaluates current guidelines and recent genomic and transcriptomic findings, with the aim of accurately identifying novel biomarkers that could contribute to a predictive model for mPPGLs, thereby enhancing patient care and outcomes.

Genomic landscape of adult testicular germ cell tumours in the 100,000 Genomes Project

Testicular germ cell tumours (TGCT), which comprise seminoma and non-seminoma subtypes, are the most common cancers in young men. In this study, we present a comprehensive whole genome sequencing analysis of adult TGCTs. Leveraging samples from participants recruited via the UK National Health Service and data from the Genomics England 100,000 Genomes Project, our results provide an extended description of genomic elements underlying TGCT pathogenesis. This catalogue offers a comprehensive, high-resolution map of copy number alterations, structural variation, and key global genome features, including mutational signatures and analysis of extrachromosomal DNA amplification. This study establishes correlations between genomic alterations and histological diversification, revealing divergent evolutionary trajectories among TGCT subtypes. By reconstructing the chronological order of driver events, we identify a subgroup of adult TGCTs undergoing relatively late whole genome duplication. Additionally, we present evidence that human leukocyte antigen loss is a more prevalent mechanism of immune disruption in seminomas. Collectively, our findings provide valuable insights into the developmental and immune modulatory processes implicated in TGCT pathogenesis and progression.

Putative mechanisms of primary resistance to EGFR-targeted therapies: A retrospective study

BackgroundsAdvanced lung adenocarcinoma (LUAD) patient with EGFR mutations often experience resistance to first-line epidermal growth factor tyrosine kinase inhibitors (EGFR-TKIs) therapy. Nonetheless, the mechanism and biomarkers of primary resistance remain unclear. Further exploration of independent prognostic factors will help clinicians identify patients who may not respond to EGFR-TKIs and select appropriate treatment strategies. MethodsA retrospective study involving 124 patients with stage IV LUAD harboring a common sensitizing EGFR mutation (exon 19 deletion or L858R mutation) who received EGFR-TKIs as first-line therapy was performed. All participants were tested by DNA-targeted sequencing in baseline samples, and there were 19 patients with progression-free survival (PFS) ≤ 3 months (cohort 1, C1, primary resistance), 22 patients with 3 < PFS < 8 months (cohort 2, C2, poor response) without known mutations associated with resistance, and 83 patients with PFS ≥ 8 months (cohort 3, C3, normal). ResultsThe most commonly mutated genes at baseline in patients prior to treatment within the entire study population. were TP53 (65 %), MYC (19 %), CDKN2A (12 %), MUC16 (12 %) and RBM10 (12 %). The baseline characteristics, except for the proportions of patients with EGFR L858R mutation and exon 19 deletion in C1 plus C2 compared to C3 (p = 0.036), were not significantly different among the cohorts. The frequencies of PIK3C2G, STK11, EPAS1, RARA and BTG2 variation were significantly higher in C1, the primary resistance group. Multivariate Cox analysis revealed that PIK3C2G (HR 15.70 95 % CI 3.24–76.05, p < 0.001), STK11 (HR 17.04, 95 % CI 3.68–78.92, p < 0.001), EPAS1 (HR 11.99, 95 % CI 2.57–56.03, p = 0.002), and BTG2 amplification (HR 9.53, 95 % CI 1.67–54.28, p = 0.011) were significantly associated with shorter PFS. ConclusionsThe genomic landscape varies significantly among patients with LUAD, which should be considered when making personalized treatment decisions. This information could provide insights into molecular changes and their effects on clinical treatment in diverse patients with LUAD harboring sensitizing EGFR mutations.

Genome sequencing in the management of myelodysplastic syndromes and related disorders.

Myeloid neoplasms originate from the clonal proliferation of hematopoietic stem cells, which is driven by the acquisition of somatic genetic mutations. Within these disorders, myelodysplastic syndromes (MDS) are specifically characterized by morphologic abnormalities (dysplasia) and impaired maturation of myeloid precursors (ineffective hematopoiesis), resulting in peripheral blood cytopenia. Several studies have advanced the field of MDS, with a few landmark papers leading to a paradigm shift, opening new avenues of research and enabling a molecular revolution. These seminal papers include the first description of the 5q- syndrome, the identification of somatic mutations of TET2 in myeloid neoplasms, the detection of common pathway mutations in the splicing machinery, and the discovery of clonal hematopoiesis. The somatic genomic landscape of MDS is now well-defined. Genes that are recurrently mutated include epigenetic regulators, as well as genes of RNA splicing machinery, transcription regulation, DNA repair control, cohesin complex, and signal transduction. Furthermore, several disorders with a germline genetic predisposition to MDS have been identified, collectively accounting for up to 15% of all MDS cases. Genomic profiling can significantly improve the diagnostic approach to MDS, allowing the identification of distinct nosologic entities such as SF3B1-mutant or TP53-mutant MDS. The Molecular International Prognostic Scoring System for MDS (IPSS-M) has already proven to be a valuable tool for individualized risk assessment and treatment decisions. In addition, the recently developed molecular taxonomy of MDS will likely facilitate the implementation of precision medicine approaches for these disorders. This will necessitate the establishment of specialized infrastructures within public health systems, involving close collaboration between healthcare institutions, academia, and the life sciences industry.

Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome.

The viral intra-host genetic diversitiesand interactions with the human genome during decades of persistence remain poorly characterized. In this study, we analyzed the variability and integration sites of persisting viruses in nine organs from thirteen individuals who died suddenly from non-viralcauses. The viruses studiedincluded parvovirus B19, six herpesviruses, Merkel cell (MCPyV) and JC polyomaviruses, totaling 127 genomes. The viral sequences across organs were remarkably conserved within each individual, suggesting that persistence stems from single dominant strains. This indicates that intra-host viral evolution, thus far inferred primarily from immunocompromised patients, is likely overestimated in healthy subjects. Indeed, we detected increased viral subpopulations in two individuals with putative reactivations, suggesting that replication status influences diversity. Furthermore, we identified asymmetrical mutationpatternsreflectingselective pressures exerted by the host. Strikingly, our analysis revealed non-clonal viral integrations even in individuals without cancer. These included MCPyV integrations and truncations resembling clonally expanded variants inMerkel cell carcinomas, as well as novel junctions between herpesvirus 6B and mitochondrial sequences, the significance of which remains to be evaluated. Our work systematically characterizes the genomic landscape of the tissue-resident virome, highlighting potential deviations occurring during disease.

The clinical outcome, pathologic spectrum, and genomic landscape for 454 cases of salivary mucoepidermoid carcinoma

Mucoepidermoid carcinoma (MEC) is the most common malignant salivary tumor. A complete understanding of the high heterogeneity of MEC in histology and genetics would help in accurate diagnosis and treatment. Therefore, We evaluated the clinical features, treatment outcomes, and pathological parameters of 454 MECs and analyzed their genomic features using whole-exome sequencing and whole-transcriptome sequencing. We found that MECs predominantly occurred in females and those in their 4th–5th decades. The parotid gland was the most frequently affected site. All patients underwent complete mass resection with lobectomy; 414 patients were alive without relapse at follow-up, after an average period of 62 months (1–116 months). The disease progressed after initial treatment in 40 patients. The lungs were the most common site of distant metastasis. For classical MECs, histologic gradings of the AFIP, modified Healey, and MSK systems were significantly associated with recurrence and lymph nodal metastasis; these gradings were significantly related to lymph nodal metastasis for the subtypes. Older age, minor salivary gland involvement, clinical symptoms, high TNM stage, high-grade tumor, and improper surgical modality were the main prognostic factors. BAP1 was the most frequently mutated gene in MEC. Mutations in CDKN2A, MET, and TP53 were more frequently found in aggressive tumor phenotypes. MAML2 rearrangement was observed in 42% of patients, and EWSR1 rearrangement in 8%. Specific genetic events (in TP53 and FBXW7) with CRTC1::MAML2 fusion superimposed might be associated with unfavorable prognosis. This study provides new insights into precision therapeutic strategies for MEC.

Hepatocellular-Carcinoma-Derived Organoids: Innovation in Cancer Research.

Hepatocellular carcinomas (HCCs) are highly heterogeneous malignancies. They are characterized by a peculiar tumor microenvironment and dense vascularization. The importance of signaling between immune cells, endothelial cells, and tumor cells leads to the difficult recapitulation of a reliable in vitro HCC model using the conventional two-dimensional cell cultures. The advent of three-dimensional organoid tumor technology has revolutionized our understanding of the pathogenesis and progression of several malignancies by faithfully replicating the original cancer genomic, epigenomic, and microenvironmental landscape. Organoids more closely mimic the in vivo environment and cell interactions, replicating factors such as the spatial organization of cell surface receptors and gene expression, and will probably become an important tool in the choice of therapies and the evaluation of tumor response to treatments. This review aimed to describe the ongoing and potential applications of organoids as an in vitro model for the study of HCC development, its interaction with the host's immunity, the analysis of drug sensitivity tests, and the current limits in this field.

A regulatory variant rs9379874 in T1D risk region 6p22.2 affects BTN3A1 expression regulating T cell function.

Genome-wide association studies (GWAS) have identified that 6p22.2 region is associated with type 1 diabetes (T1D) risk in the Chinese Han population. This study aims to reveal associations between this risk region and T1D subgroups and related clinical features, and further identify causal variant(s) and target gene(s) in this region. 2608 T1D and 4814 healthy controls were recruited from East, Central, and South China. Baseline data and genotyping for rs4320356 were collected. The most likely causal variant and gene were identified by bioinformatics analysis, dual-luciferase reporter assays, expression quantitative trait loci (eQTL), and functional annotation of the non-coding region within the 6p22.2 region. The leading variant rs4320356 in the 6p22.2 region was associated with T1D risk in the Chinese and Europeans. However, this variant was not significantly associated with islet function or autoimmunity. In silico analysis suggested rs9379874 was the most potential causal variant for T1D risk among thymus, spleen, and T cells, overlapping with the enhancer-related histone mark in multiple T cell subsets. Dual luciferase reporter assay and eQTL showed that the T allele of rs9379874 increased BTN3A1 expression by binding to FOXA1. Public single-cell RNA sequencing analysis indicated that BTN3A1 was related to T-cell activation, ATP metabolism, and cytokine metabolism pathways, which might contribute to T1D development. This study indicates that a functional variant rs9379874 regulates BTN3A1 expression, expanding the genomic landscape of T1D risk and offering a potential target for developing novel therapies.

RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape.

Rett syndrome (RTT) is a neurodevelopmental disorder occurring almost exclusively in females and leading to a variety of impairments and disabilities from mild to severe. In >95% cases, RTT is due to mutations in the X-linked gene MECP2, but the molecular mechanisms determining RTT are unknown at present, and the complexity of the system is challenging. To facilitate and provide guidance to the unraveling of those mechanisms, we developed a database resource for the visualization and analysis of the genomic landscape in the context of wild-type or mutated Mecp2 gene in the mouse model. Our resource allows for the exploration of differential dynamics of gene expression and the prediction of new potential MECP2 target genes to decipher the RTT disorder molecular mechanisms. Database URL: https://biomedinfo.di.unipi.it/rett-database/.

Integrating clinical and genomic landscape analysis of perineural invasion identify ACTA1 as an oncogene for oral squamous cell carcinoma.

Perineural invasion (PNI) has been shown to be a key pathological feature of several types of cancer, including oral squamous epithelial carcinoma (OSCC). However, the overall clinical and genomic landscape of PNI+ OSCC are still unclear, and the molecular mechanism of PNI remains to be further investigated. 279 OSCC samples were extracted from the TCGA database and grouped according to PNI. The clinicopathological information, prognostic and survival analyses were performed. The Cibersort algorithm and ESTIMATE algorithm was used to estimate the impacts on proportion of immune cells, immune score and stromal score by PNI. Immunotherapy prediction analysis was also performed. 167 differentially expressed genes were screened for functional enrichment analysis. Actin α1 (ACTA1) protein, which was significantly upregulated in the PNI+ group, was selected for validation in our OSCC patient's cohort (n = 70). We next analyzed the ratio and absolute number of key immunocytes in peripheral blood of OSCC patients according to Actin α1 expression by flow cytometry. PNI was more likely to occur in patients with advanced tumors and worse prognosis. Immunomodulation analyses showed that T cells follicular helper and cells were significantly lower, but M2 macrophages and total stromal score was significantly higher in PNI+ OSCC. Immunotherapy prediction analyses showed that PNI+ OSCC may be more sensitive to CTLA4 inhibitor treatment. 167 differentially expressed genes were identified and enriched in muscle structure and cell movement-related pathway. Among them, Actin α1 (ACTA1) was significantly upregulated in PNI+ advanced OSCC with worse clinical outcome whose had relatively low ratio of CD3+CD8+ circulating cytotoxic T cells. PNI+ OSCC patients with upregulated of Actin α1 could benefit from cytotoxic T cell-mediated immunotherapy.