Genomic Studies Research Articles

Chromosome-level genome assembly of American sweetgum (Liquidambar styraciflua, Altingiaceae)

The deciduous American sweetgum (Liquidambar styraciflua, Altingiaceae) is a popular ornamental and economically valuable tree renowned for its sweet-smelling bark resin, abundant volatile substances, and spectacular fall leaf color. However, the absence of a reference genome hinders thorough investigations into the mechanisms underlying phenotypic variation, secondary metabolite synthesis and adaptation, both in this species and other Liquidambar members. In this study, we sequenced and constructed a chromosome-level assembly of the L. styraciflua genome, covering 662.48 Mb with a scaffold N50 of 39.54 Mb, by integrating PacBio, Illumina and chromosome conformation capture data. We identified 58.83% of the genome sequences as repetitive elements and 25,713 protein-coding genes, 97.28% of which were functionally annotated. The genome sequencing reads, assembly and annotation data have been deposited in publicly available repositories. This high-quality genome assembly provides valuable resources for further evolutionary and functional genomic studies in American sweetgum and other Liquidambar species.

Praziquantel resistance in schistosomes: a brief report

Schistosomiasis is a group of both acute and chronic parasitic trematode infections of the genus Schistosoma. Research into schistosomiasis has been minimal, leading to its classification as a neglected tropical disease, yet more than 140 million people are infected with schistosomes globally. There are no treatments available for early-stage infections, schistosomal dermatitis, or Katayama syndrome, other than symptomatic control with steroids and antihistamines, as the maturing organisms seem to be mostly resistant to typical antiparasitics. However, praziquantel (PZQ) has been the drug of choice for schistosomiasis for decades in the latter stages of the disease. Though it is effective against all three clinically relevant species, heavy reliance on PZQ has led to concerns of schistosome resistance, especially in areas that have implemented this drug in mass drug administration (MDA) programs. This article summarizes the available literature concerning the available evidence for and against a warranted concern for PZQ resistance, genomic studies in schistosomes, proposed mechanisms of resistance, and future research in alternative methods of schistosomiasis treatment.

Genome-wide investigation and analysis of U-box E3 ubiquitin-protein ligase gene family in kiwifruit (Actinidia chinensis) in response to the yeast antagonist, Wickerhamomyces anomalus

ABSTRACT Although the ubiquitin ligase U-box protein family is a vital component of plant development and stress response, the exact role of kiwifruit U-box genes family is not known. The study identified 73 putative U-box genes from the kiwifruit genome. Chromosomal localisation, phylogenetic analysis, physicochemical properties, gene structure, motifs, and promoters of these genes were analysed. Distribution of Actinidia chinensis PUB (AcPUB) genes exhibited varying densities across 27 chromosomes. The study found that U-box clusters were classified into groups I–VII in phylogenetic analyses of a variety of plants, including kiwifruit, Arabidopsis thaliana, and rice, with most of the genes in kiwifruit being related to rice. The conserved motif analyses revealed that all the AcPUB genes have typical U-box structural domains. Analysis of the cis-acting elements suggested that AcPUBs expression may be responsive to several hormones and stresses. RNA-Seq analysis showed that six kiwifruit U-box genes were differentially expressed after induction by Wickerhamomyces anomalus, suggesting a potential involvement of these U-box genes in the kiwifruit's response to W. anomalus, which might include mechanisms related to resistance. Overall, our findings provide valuable insights into the function and structure of U-box genes that will help develop new genomic technologies and study plant resistance.

Associations between antagonistic SNPs for neuropsychiatric disorders and human brain structure

A previously published genome-wide association study (GWAS) meta-analysis across eight neuropsychiatric disorders identified antagonistic single-nucleotide polymorphisms (SNPs) at eleven genomic loci where the same allele was protective against one neuropsychiatric disorder and increased the risk for another. Until now, these antagonistic SNPs have not been further investigated regarding their link to brain structural phenotypes. Here, we explored their associations with cortical surface area and cortical thickness (in 34 brain regions and one global measure each) as well as the volumes of eight subcortical structures using summary statistics of large-scale GWAS of brain structural phenotypes. We assessed if significantly associated brain structural phenotypes were previously reported to be associated with major neuropsychiatric disorders in large-scale case-control imaging studies by the ENIGMA consortium. We further characterized the effects of the antagonistic SNPs on gene expression in brain tissue and their association with additional cognitive and behavioral phenotypes, and performed an exploratory voxel-based whole-brain analysis in the FOR2107 study (n = 754 patients with major depressive disorder and n = 847 controls). We found that eight antagonistic SNPs were significantly associated with brain structural phenotypes in regions such as anterior parts of the cingulate cortex, the insula, and the superior temporal gyrus. Case-control differences in implicated brain structural phenotypes have previously been reported for bipolar disorder, major depressive disorder, and schizophrenia. In addition, antagonistic SNPs were associated with gene expression changes in brain tissue and linked to several cognitive-behavioral traits. In our exploratory whole-brain analysis, we observed significant associations of gray matter volume in the left superior temporal pole and left superior parietal region with the variants rs301805 and rs1933802, respectively. Our results suggest that multiple antagonistic SNPs for neuropsychiatric disorders are linked to brain structural phenotypes. However, to further elucidate these findings, future case-control genomic imaging studies are required.

Chromosome-level genome assembly of Huai pig (Sus scrofa)

Although advances in long-read sequencing technology and genome assembly techniques have facilitated the study of genomes, little is known about the genomes of unique Chinese indigenous breeds, including the Huai pig. Huai pig is an ancient domestic pig breed and is well-documented for its redder meat color and high forage tolerance compared to European domestic pigs. In the present study, we sequenced and assembled the Huai pig genome using PacBio, Hi-C, and Illumina sequencing technologies. The final highly contiguous chromosome-level Huai pig genome spans 2.53 Gb with a scaffold N50 of 138.92 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score for the assembled genome was 95.33%. Remarkably, 23,389 protein-coding genes were annotated in the Huai-pig genome, along with 45.87% repetitive sequences. Overall, this study provided new foundational resources for future genetic research on Chinese domestic pigs.

Chromosome-scale genome assembly of Astragalus membranaceus using PacBio and Hi-C technologies

Astragalus membranaceus (Fisch.) Bge (AM) is a medicinal herb plant belonging to the Leguminosae family. In this study, we present a chromosome-scale genome assembly of AM, aiming to enhance the molecular biology and functional studies of Astragali Radix. The genome size of AM is about 1.43 Gb, with a contig N50 value of 1.67 Mb. A total of 98.16% of the assembly anchored to 9 pseudochromosomes using Hi-C technology. The assembly completeness was estimated to be 97.27% using BUSCO with the long terminal repeat assembly index (LAI) of 16.22 and quality value (QV) of 48.58. Additionally, the genome contained 67.98% repetitive sequences. Genome annotation predicted 29,914 protein-coding genes, including 73 genes involved in the flavonoid biosynthetic pathway and 2,048 transcription factors. The high-quality genome assembly and gene annotation resources will greatly facilitate future functional genomic studies in Leguminosae species.

Characterization of two Plasmodium falciparum lipid transfer proteins of the Sec14/CRAL-TRIO family

Invasion of human red blood cells by the malaria parasite Plasmodium falciparum is followed by dramatic modifications of erythrocytes properties, including de novo formation of new membrane systems. Lipid transfer proteins from both the parasite and the host cell are most likely an important part of those membrane remodeling processes. Using bioinformatics and in silico structural analysis, we have identified five P. falciparum potential lipid transfer proteins containing cellular retinaldehyde binding – triple functional domain (CRAL-TRIO). Two of these proteins, C6KTD4, encoded by the PF3D7_0629900 gene and Q8II87, encoded by the PF3D7_1127600 gene, were studied in more detail. In vitro lipid transfer assays using recombinant C6KTD4 and Q8II87 confirmed that these proteins are indeed bona fide lipid transfer proteins. C6KTD4 transfers sterols, phosphatidylinositol 4,5 bisphosphate, and, to some degree, also phosphatidylcholine between two membrane compartments. Q8II87 possesses phosphatidylserine transfer activity in vitro. In the yeast model, the expression of P. falciparumQ8II87 protein partially complements the absence of Sec14p and its closest homologue, Sfh1p. C6KTD4 protein can substitute for the collective essential function of oxysterol-binding related proteins. According to published whole genome studies in P. falciparum, absence of C6KTD4 and Q8II87 proteins has severe consequences for parasite viability. Therefore, CRAL-TRIO lipid transfer proteins of P. falciparum are potential targets of novel antimalarials, in search for which the yeast model expressing these proteins could be a valuable tool.

TOWARDS JUSTICE, EQUITY, AND COMMUNITY EMPOWERMENT IN GENOMICS STUDIES ON BEHAVIORAL, PSYCHIATRIC AND NEURODEVELOPMENTAL TRAITS

Genomics research on sensitive traits such as neurodevelopmental, psychiatric, and behavioral traits poses numerous conceptual, methodological, ethical, legal, and social challenges. Community engagement and participatory research have been proposed as tools to increase the relevance, rigor, and acceptability of research, including genetic and biomedical studies. Informed by a growing body of research and lessons learned from recent and ongoing efforts to engage communities affected by genomics studies, I set a vision for more just, equitable, and collaborative genomics where primary stakeholders are included in research and decision-making as peers and collaborators, not solely as objects of study. Further, considering recent debates, lapses, and successes, I propose frameworks to promote respectful and productive engagement, communication, and collaboration between diverse stakeholders.

"I Have Come Because I See You Care About Me": Recruiting Older Black Americans for Genomic Research.

The lack of diversity in genomic studies is a disparity that influences our understanding of human genomic variation and threatens equity in the benefits of precision medicine. Given our current genomic research with Black older adults, we conducted a qualitative study to elucidate participants' knowledge, attitudes, and beliefs about genomic research and research participation and what factors contribute to their willingness to participate and to gain insights into barriers that researchers may have in recruiting Black Americans. We conducted semistructured interviews (N=16) with previous genomic research participants, and an inductive thematic approach was used to code and interpret the data. The mean age was 70, 82% reported <$15,000 annual income, and 100% participated in genomic research. The results note that genomic research is poorly understood despite participation in prior genomic studies, and cultural beliefs about health and managing health impact an individual's research participation. Although not all participants identified with historical distrust, those who did report health system distrust also contributed distrust in research. Relationship building facilitates research participation, especially when perceived as personally relevant and meaningful. Participant incentives and convenience to engage in the study are less important if the personal benefits or relevance of the research are clear. Our results provide new context into the importance of relationship building and research literacy and highlight new considerations for engaging racially diverse populations in research.

Enhancer reprogramming underlies therapeutic utility of a SMARCA2 degrader in SMARCA4 mutant cancer.

Genomic studies have identified frequent mutations in subunits of the SWI/SNF (switch/sucrose non-fermenting) chromatin remodeling complex including SMARCA4 and ARID1A in non-small cell lung cancer (NSCLC). Genetic evidence indicates that the paralog SMARCA2 is synthetic lethal to SMARCA4 suggesting SMARCA2 is a valuable therapeutic target. However, the discovery of selective inhibitors of SMARCA2 has been challenging. Here, we utilized structure-activity relationship (SAR) studies to develop YD23, a potent and selective proteolysis targeting chimera (PROTAC) targeting SMARCA2. Mechanistically, we show that SMARCA2 degradation induces reprogramming of the enhancer landscape in SMARCA4-mutant cells with loss of chromatin accessibility at enhancers of genes involved in cell proliferation. Furthermore, we identified YAP/TEADas key partners to SMARCA2 in driving growth of SMARCA4-mutant cells. Finally, we show that YD23 has potent tumor growth inhibitory activity in SMARCA4-mutant xenografts. These findings provide the mechanistic basis for development of SMARCA2 degraders as synthetic lethal therapeutics against SMARCA4-mutant lung cancers.

Genotype imputation in human genomic studies.

Imputation is a method that supplies missing information about genetic variants that could not be directly genotyped with DNA microarrays or low-coverage sequencing. Imputation plays a critical role in genome-wide association studies (GWAS). It leads to a significant increase in the number of studied variants, which improves the resolution of the method and enhances the comparability of data obtained in different cohorts and/or by using different technologies, which is important for conducting meta-analyses. When performing imputation, genotype information from the study sample, in which only part of the genetic variants are known, is complemented using the standard (reference) sample, which has more complete genotype data (most often the results of whole-genome sequencing). Imputation has become an integral part of human genomic research due to the benefits it provides and the increasing availability of imputation tools and reference sample data. This review focuses on imputation in human genomic research. The first section of the review provides a description of technologies for obtaining information about human genotypes and characteristics of these types of data. The second section describes the imputation methodology, lists the stages of its implementation and the corresponding programs, provides a description of the most popular reference panels and methods for assessing the quality of imputation. The review concludes with examples of the use of imputation in genomic studies of samples from Russia. This review shows the importance of imputation, provides information on how to carry it out, and systematizes the results of its application using Russian samples.

Current Management and Therapy of Severe Aortic Stenosis and Future Perspective.

Intervention for severe aortic stenosis (AS) has dramatically progressed since the introduction of transcatheter aortic valve replacement (TAVR). Decades ago, controversies existed regarding comparing clinical outcomes between TAVR and surgical aortic valve replacement (SAVR) in various risk profiles. Recently, we discussed the durability of transcatheter heart valves and their lifetime management after aortic valve replacement (AVR). Regarding the management of AS, we discuss the appropriate timing of intervention for severe aortic stenosis, especially in asymptomatic patients. In spite of dramatic progression of intervention for AS, there are no established medications available to prevent or slow the progression of AS at present. Basic research and genome studies have suggested several targets associated with the progression of aortic valve calcification. Randomized controlled trials evaluating the efficacy of medications to prevent AS progression are ongoing, which might lead to new strategies for AS management. In this review, we summarize the current management of AS and the drugs expected to prevent the progression of AS.

Novel Genes of the Male Reproductive System: Potential Roles in Male Reproduction and as Non-hormonal Male Contraceptive Targets.

The development of novel non-hormonal male contraceptives represents a pivotal frontier in reproductive health, driven by the need for safe, effective, and reversible contraceptive methods. This comprehensive review explores the genetic underpinnings of male fertility, emphasizing the crucial roles of specific genes and structural variants (SVs) identified through advanced sequencing technologies such as long-read sequencing (LRS). LRS has revolutionized the detection of structural variants and complex genomic regions, offering unprecedented precision and resolution over traditional next-generation sequencing (NGS). Key genetic targets, including those implicated in spermatogenesis and sperm motility, are highlighted, showcasing their potential as non-hormonal contraceptive targets. The review delves into the systematic identification and validation of male reproductive tract-specific genes, utilizing advanced transcriptomics and genomics studies with validation using novel knockout mouse models. We discuss the innovative application of small molecule inhibitors, developed through platforms like DNA-encoded chemistry technology (DEC-Tec), which have shown significant promise in preclinical models. Notable examples include inhibitors targeting serine/threonine kinase 33 (STK33), soluble adenylyl cyclase (sAC), cyclin-dependent kinase 2 (CDK2), and bromodomain testis associated (BRDT), each demonstrating nanomolar affinity and potential for reversible and specific inhibition of male fertility. This review also honors the contributions of Dr. David L. Garbers whose foundational work has paved the way for these advancements. The integration of genomic, proteomic, and chemical biology approaches, supported by interdisciplinary collaboration, is poised to transform male contraceptive development. Future perspectives emphasize the need for continued innovation and rigorous testing to bring these novel contraceptives from the laboratory to clinical application, promising a new era of male reproductive health management.

Desiccation tolerance and reduced antibiotic resistance: Key drivers in ST239-III to ST22-IV MRSA clonal replacement at a Malaysian teaching hospital

Molecular surveillance of methicillin-resistant Staphylococcus aureus (MRSA) isolated from Hospital Canselor Tuanku Muhriz (HCTM), a Malaysian teaching hospital revealed clonal replacement events of SCCmec type III-SCCmercury to SCCmec type IV strains before the year 2017; however, the reasons behind this phenomenon are still unclear. This study aimed to identify factors associated with the clonal replacement using genomic sequencing and phenotypic investigations (antibiogram profiling, growth rate and desiccation tolerance determination, survival in vancomycin sub-minimum inhibitory concentration (MIC) determination) of representative HCTM MRSA strains isolated in four-year intervals from 2005 – 2017 (n = 16). HCTM Antimicrobial Stewardship (AMS) and Infection Prevention and Control (IPC) policies were also reviewed. Phylogenetic analyses revealed the presence of 3 major MRSA lineages: ST239-III, ST22-IV and ST6-IV; MRSAs with the same STs shared similar core and accessory genomes. Majority of the ST239-III strains isolated in earlier years of the surveillance (2005, 2009 and 2013) were resistant to many antibiotics and harboured multiple AMR and virulence genes compared to ST22-IV and ST6-IV strains (isolated in 2013 and 2017). Interestingly, ST22-IV and ST6-IV MRSAs grew significantly faster and were more resistant to desiccation than ST239-III (p < 0.05), even though the later clone survived better post-vancomycin exposure. Intriguingly, ST22-IV was outcompeted by ST239-III in broth co-cultures; though it survived better when desiccated together with ST239-III. Higher desiccation tolerance and fewer carriage of AMR genes by ST22-IV, together with reduction of antibiotic selection pressure in HCTM (due to AMS and IPC policies) during 2005 – 2017 may have provided the clone a competitive edge in replacing the previously dominant ST239-III in HCTM. This study highlights the importance of MRSA surveillance for a clearer picture of circulating clones and clonal changes. To our knowledge, this is the first genomic epidemiology study of MRSA in Malaysia, which will serve as baseline genomic data for future surveillance.

Computational Insights into Kaempferol and Luteolin: Potential Mitigators of the Omicron B.1.1.529 SARS-CoV-2 Variant

Abstract The coronavirus disease 2019 (COVID-19) has been circulating in the local and global population. Among the SARS-CoV-2 variants, the Omicron strain tends to be detected in the recent genomic surveillance studies. Despite being a manageable disease, recovered patients may experience post-COVID-19 conditions such as cough (50.6%), fatigue (45.8%), and memory loss (37.4%). While developing an updated vaccine for COVID-19 is time-consuming, the in-silico discovery of phytoconstituents that bind to the SARS-CoV-2 receptor binding domain (RBD), may provide insights on the potential of edible plants as complementary treatments. This study aimed to investigate and compare the ligand-protein interactions of phytoconstituents and COVID-19 treatment drug, remdesivir, to the SARS-CoV-2 spike protein. The molecular docking results indicated that kaempferol and luteolin could potentially mitigate COVID-19, as they exhibited higher RBD-binding affinities than remdesivir.

Wastewater monitoring of human and avian influenza A viruses in Northern Ireland: a genomic surveillance study

Influenza Aviruses (IAVs) are significant pathogens of humans and other animals. Although endemic in humans and birds, novel IAV strains can emerge, jump species, and cause epidemics, like the latest variant of H5N1. Wastewater-based epidemiology (WBE) has been shown capable of detecting human IAVs. We aimed to assess whether whole-genome sequencing (WGS) of IAVs from wastewater is possible and can be used to discriminate between circulating strains of human and any non-human IAVs, such as those of avian origin. Using a pan-IAV RT-quantitative PCR assay, six wastewater treatment works (WWTWs) across Northern Ireland were screened from Aug 1to Dec 5, 2022. Ananopore WGS approach was used to sequence RT-qPCR-positive samples. Phylogenetic analysis of sequences relative to currently circulating human and non-human IAVs was performed. Forcomparative purposes, clinical data (PCR test results) were supplied by The Regional Virus Laboratory, Belfast Health and Social Care Trust (Belfast, Northern Ireland, UK). We detected a dynamic IAV signal in wastewater from Sept 5, 2022, onwards across Northern Ireland, which did not show a clear positive relationship with the clinical data obtained for the region. Meta (mixed strain) whole-genome sequences were generated from wastewater samples displaying homology to only human and avian IAVstrains. The relative proportion of IAV reads of human versus avian origin differed across time and sample site. Adiversity in subtypes and lineages was detected (eg, H1N1, H3N2, and several avian). Avian segment 8related to those found in recent H5N1 clade 2.3.4.4b was identified. WBE affords a means to monitor circulating human and avian IAV strains and provide crucial genetic information. As such, WBE can provide rapid, cost-effective, year-round One Health surveillance to help control IAV epidemic and pandemic-related threats. However, optimisation of WBE protocols are necessary to ensure observed wastewater signals not only correlate with clinical case data, but yield information on the wider environmental pan-influenz-ome. Department of Health for Northern Ireland.

Cardiovascular risk according to genetic predisposition to gout, lifestyle and metabolic health across prospective European and Korean cohorts

ObjectiveRecent studies have reported that gout is associated with a risk of cardiovascular disease (CVD) later in life. However, the predictive value of genetic predisposition to gout combined with lifestyle...

A genome-wide Association study of the Count of Codeine prescriptions

Opioid prescription records in existing electronic health record (EHR) databases are a potentially useful, high-fidelity data source for opioid use-related risk phenotyping in genetic analyses. Prescriptions for codeine derived from EHR records were used as targeting traits by screening 16 million patient-level medication records. Genome-wide association analyses were then conducted to identify genomic loci and candidate genes associated with different count patterns of codeine prescriptions. Both low- and high-prescription counts were captured by developing 8 types of phenotypes with selected ranges of prescription numbers to reflect potentially different levels of opioid risk severity. We identified one significant locus associated with low-count codeine prescriptions (1, 2 or 3 prescriptions), while up to 7 loci were identified for higher counts (≥ 4, ≥ 5, ≥6, or ≥ 7 prescriptions), with a strong overlap across different thresholds. We identified 9 significant genomic loci with all-count phenotype. Further, using the polygenic risk approach, we identified a significant correlation (Tau = 0.67, p = 0.01) between an externally derived polygenic risk score for opioid use disorder and numbers of codeine prescriptions. As a proof-of-concept study, our research provides a novel and generalizable phenotyping pipeline for the genomic study of opioid-related risk traits.

Pure Squamous Cell Carcinoma of the Prostate With a Complete Remission to Gemcitabine-Cisplatin: Case Presentation and Literature Review

Abstract Squamous cell carcinoma of prostate is a very rare condition and little is known regarding the appropriate managment. Here we reported our patient with pure squamous cell carcinoma of prostate who had complete remission with gemcitabine and cisplatin treatment which last 5 months. Based on his genomic study of prostate cancer, he enrolled to our clinical trial and now receiveing mTOR pathway inhibtor. We also briefly reviewed previous cases of metastatic squamous cell carcinoma of prostate and their managment.

Application Of Genomic Signal Processing To Detect Cancer Cells

In the field of signal processing, a new area of research has been introduced namely genomic signal processing (GSP). GSP processes genes, proteins, and DNA sequences using various hidden signals. As some genetic abnormalities turn into cancer diseases, proper understanding, and analysis of genes and proteins may lead to a new horizon in cancer genomic study. In genomic signal processing, identifying and classifying the diseased gene is a great challenge to researchers. Hence in the present paper, the crucial job of gene identification and classification is attempted for cancer detection. Our project is implemented in MATLAB R2019a using the bioinformatics toolbox. Where the DNA sequences obtained from the NCBI are processed and numerically mapped before extracting the exons using the period-3 property which is done using an anti-notch filter and STFT. Digital filters are used for noise reduction and increased accuracy.