SAMBLASTER: fast duplicate marking and structural variant read extraction

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)

Blackberries (Rubus spp.) are globally consumed and well known for their rich anthocyanin and antioxidant content and distinct flavors. Improving blackberries has been challenging due to genetic complexity of traits and limited genomic resources. The blackberry genome has been particularly challenging to assemble due to its polyploid nature. Here, we present the first chromosome-scale and haplotype-phased assembly for the primocane-fruiting, thornless tetraploid blackberry selection BL1 (Rubus L. subgenus Rubus Watson). The genome assembly was generated using Oxford Nanopore Technology and Hi-C scaffolding, resulting in a 919 Mb genome distributed across 27 pseudochromosomes, with an N50 of 35.73 Mb. This assembly covers >92% of the genome length and contains over 98% of complete BUSCOs. Approximately, 58% of the assembly consists of repetitive sequences, with long terminal repeats being the most abundant class. A total of 87,968 protein-coding genes were predicted, of which, 82% were functionally annotated. Genome mining and RNA-Seq analyses identified possible candidate genes and transcription factors related to thornlessness and the key structural genes and transcription factors for anthocyanin biosynthesis. Activator genes including PAP1 and TTG1 and repressor genes such as ANL2 and MYBPA1 play an important role in the fine tuning of anthocyanin production during blackberry development. Resequencing of seven tetraploid blackberry cultivars/selections with different horticultural characteristics revealed candidate genes that could impact fruiting habit and disease resistance/susceptibility. This tetraploid reference genome should provide a valuable resource for accelerating genetic analysis of blackberries and facilitating the development of new improved cultivars with enhanced horticultural and nutritional traits.

Rare damaging variants in the sex differences of congenital heart disease: an exome sequencing study

BACKGROUND

Congenital heart disease (CHD) exhibits a marked male predominance in birth prevalence, yet the genetic mechanisms underlying this sex disparity remain poorly understood. This study investigates the contribution of rare damaging variants on autosomes and the X chromosome to sex differences in foetal CHD.

METHODS

Parents of foetuses with CHD were recruited for the study. Rare damaging variants were identified by analysing whole-exome sequencing data from foetus-parental trios, and their contributions to sex differences were estimated through case-control studies. Functional enrichment analysis was conducted to assess functional differences in genetic variants between sexes.

FINDINGS

820 foetal probands with CHD were recruited, including 487 males and 333 females. We identified a significant enrichment of X-linked rare damaging variants, primarily driven by maternally inherited hemizygous variants (MIHVs) in male probands (OR = 1·84, P < 0·05), which accounted for 7·2% of male cases in our cohort. These variants were not found to be enriched in female probands. Additionally, X-linked rare damaging de novo variants (DNVs) were not enriched in either male or female probands (female probands: 1·8% versus female controls: 0·7%, P = 0·6789; no DNVs observed in males). Gene-level variant burden analysis revealed three X-linked CHD candidate genes: DCX, CACNA1F, and MAP3K15. Autosomal rare variants did not show significant differences in variant burdens between sexes. Notably, male probands showed specific functional enrichments in cilia-related pathways for autosomal recessive variants, as well as in chromatin remodelling and nervous system development pathways for autosomal DNVs.

INTERPRETATION

Male and female foetal CHD have significantly different genetic landscapes. The enrichment of X-linked rare damaging MIHVs in males provides a genetic explanation for the higher prevalence of CHD in males. This finding highlights the importance of incorporating sex-stratified approaches in clinical diagnostics and research.

FUNDING

Natural Science Foundation of China and Key research and development project of Hebei Province.

Lutetium-177-PSMA-617 or cabazitaxel in metastatic prostate cancer: circulating tumor DNA analysis of the randomized phase 2 TheraP trial

The prostate-specific membrane antigen (PSMA)-targeted radioligand [¹⁷⁷Lu]Lu-PSMA-617 is a new standard treatment for metastatic castration-resistant prostate cancer (mCRPC), but predictive genomic biomarkers informing its rational use are unknown. We performed detailed dissection of prostate cancer driver genes across 290 serial plasma cell-free DNA samples from 180 molecular imaging-selected patients with mCRPC from the randomized TheraP trial of [¹⁷⁷Lu]Lu-PSMA-617 (n = 97) versus cabazitaxel chemotherapy (n = 83). The primary endpoint was PSA50 biochemical response, with secondary endpoints of progression-free survival (PFS) and overall survival (OS). In this post-hoc biomarker analysis, a low pretreatment circulating tumor DNA (ctDNA) fraction predicted a superior biochemical response (100% versus 58%, P = 0.0067) and PFS (median 14.7 versus 6.0 months; hazard ratio 0.12, P = 2.5 × 10-4) on [¹⁷⁷Lu]Lu-PSMA-617 independent of predictive PSMA-positron emission tomography imaging parameters, although this benefit did not extend to OS. Deleterious PTEN alterations were associated with worse PFS and OS on cabazitaxel, whereas ATM defects were observed in select patients with favorable [¹⁷⁷Lu]Lu-PSMA-617 outcomes. Comparing pretreatment and progression ctDNA revealed population flux but no evidence that alterations in individual mCRPC genes (or FOLH1) are dominant causes of acquired [¹⁷⁷Lu]Lu-PSMA-617 or cabazitaxel resistance. Our results nominate new candidate biomarkers for [¹⁷⁷Lu]Lu-PSMA-617 selection and ultimately expand the mCRPC predictive biomarker repertoire. We anticipate our ctDNA fraction-aware analytical framework will aid future precision management strategies for [¹⁷⁷Lu]Lu-PSMA-617 and other PSMA-targeted therapeutics. ClinicalTrials.gov identifier: NCT03392428 .

Haplotype-resolved chromosome-level genome sequence of Elsholtzia splendens (Nakai ex F.Maek.)

Elsholtzia splendens, a perennial herb native to East Asia, is valued for its ornamental and medicinal uses, particularly in treating inflammatory and febrile conditions. Recent studies have highlighted its antibacterial, anti-inflammatory, antidepressant, antithrombotic, and lipid-lowering properties of its compounds. Additionally, E. splendens shows potential for phytoremediation owing to its ability to hyperaccumulate copper (Cu), lead (Pb), zinc (Zn), and cadmium (Cd). However, its role in remediation conflicts with its medicinal use because of the risk of heavy metal accumulation. Genome sequencing will be key to boosting beneficial compound production and reducing heavy metal risks. In this study, we generated a high-resolution, haplotype-resolved, chromosome-scale genome sequence of E. splendens using PacBio Revio long-read, Illumina short-read, and Hi-C sequencing technologies. The haplotype genome assemblies, spanned 275.4 and 265.0 Mbp with a scaffold N50 of 33.9 and 33.8 Mbp for haplotype 1 and 2, respectively. This assembly provides valuable insights into medicinal compound biosynthesis and supports genetic conservation efforts, facilitating future genetic and biotechnological applications of E. splendens for medicinal and ecological uses.

Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12

Nucleoporin 98 (NUP98) fusion oncoproteins are strong drivers of pediatric acute myeloid leukemia (AML) with poor prognosis. Here we show that NUP98 fusion-expressing AML harbors an epigenetic signature that is characterized by increased accessibility of hematopoietic stem cell genes and enrichment of activating histone marks. We employ an AML model for ligand-induced degradation of the NUP98::KDM5A fusion oncoprotein to identify epigenetic programs and transcriptional targets that are directly regulated by NUP98::KDM5A through CUT&Tag and nascent RNA-seq. Orthogonal genome-wide CRISPR/Cas9 screening identifies 12 direct NUP98::KDM5A target genes, which are essential for AML cell growth. Among these, we validate cyclin-dependent kinase 12 (CDK12) as a druggable vulnerability in NUP98::KDM5A-expressing AML. In line with its role in the transcription of DNA damage repair genes, small-molecule-mediated CDK12 inactivation causes increased DNA damage, leading to AML cell death. Altogether, we show that NUP98::KDM5A directly regulates a core set of essential target genes and reveal CDK12 as an actionable vulnerability in AML with oncogenic NUP98 fusions.

Cervicovaginal microbiome alters transcriptomic and epigenomic signatures across cervicovaginal epithelial barriers

Background

The cervicovaginal microbiome plays a critical role in women's health, with microbial communities dominated by Lactobacillus species considered optimal. In contrast, the depletion of lactobacilli and the presence of a diverse array of strict and facultative anaerobes, such as Gardnerella vaginalis, have been linked with adverse reproductive outcomes. Despite these associations, the molecular mechanisms by which host-microbial interactions modulate cervical and vaginal epithelial function remains poorly understood.

Results

In this study, we used RNA sequencing to characterize the transcriptional response of cervicovaginal epithelial cells exposed to the culture supernatants of common vaginal bacteria. Our findings revealed that G. vaginalis culture supernatants upregulate genes associated with an activated innate immune response and increased cell death. Conversely, Lactobacillus crispatus culture supernatants induced transcriptional changes indicative of epigenomic modeling in ectocervical epithelial cells. Epigenomic modification by L. crispatus, was confirmed by ATAC-sequencing, which demonstrated reduced chromatin accessibility.

Conclusions

These results provide new insights into host-microbe interactions within the lower reproductive tract and suggests that modulating the vaginal microbiome could offer innovative therapeutic strategies to improve reproductive health.

Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences

BACKGROUND

The lower Dipteran fungus gnat, Bradysia (aka Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during male meiosis I and both maternal X sister chromatids are retained in male meiosis II. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. In addition, there is gene amplification in larval polytene chromosomes, and the X polytene chromosome folds back on itself mediated by extremely long-range interactions between three loci. These developmentally normal events present opportunities to study chromosome behaviors that are unusual in other systems. Moreover, little is known about the centromeric and telomeric sequences of lower Dipterans in general, and there are recent claims of horizontally-transferred genes in fungus gnats. Overall, there is a pressing need to learn more about the fungus gnat chromosome sequences.

RESULTS

We produced the first chromosome-scale models of the X and autosomal chromosomes where each somatic chromosome is represented by a single scaffold. Extensive analysis supports the chromosome identity and structural accuracy of the scaffolds, demonstrating they are co-linear with historical polytene maps, consistent with evolutionary expectations, and have accurate centromere positions, chromosome lengths, and copy numbers. The positions of alleged horizontally-transferred genes in the nuclear chromosomes were broadly confirmed by genomic analyses of the chromosome scaffolds using Hi-C and single-molecule long-read datasets. The chromosomal context of repeats shows family-specific biases, such as retrotransposons correlated with the centromeres. Moreover, scaffold termini were enriched with arrays of retrotransposon-related sequence as well as nucleosome-length (~ 175 bp) satellite repeats. Finally, the Hi-C data captured Mb-scale physical interactions on the X chromosome that are seen in polytene spreads, and we characterize these interesting "fold-back regions" at the sequence level for the first time.

CONCLUSIONS

The chromosome scaffolds were shown to be of exceptional quality, including loci harboring horizontally-transferred genes. Repeat analyses demonstrate family-specific biases and telomere repeat candidates. Hi-C analyses revealed the sequences of ultra-long-range interactions on the X chromosome. The chromosome-scale scaffolds pave the way for further studies of the unusual chromosome movements in Bradysia coprophila.

CDK4 loss-of-function mutations cause microcephaly and short stature

Cell number is a major determinant of organism size in mammals. In humans, gene mutations in cell cycle components result in restricted growth through reduced cell numbers. Here we identified biallelic mutations in CDK4 as a cause of microcephaly and short stature. CDK4 encodes a key cell cycle kinase that associates with D-type cyclins during G1 of the cell cycle to promote S-phase entry and cell proliferation through retinoblastoma (RB) phosphorylation. CDK4 and CDK6 are believed to be functionally redundant and are targeted jointly by chemotherapeutic CDK4/6 inhibitors. Using molecular and cell biology approaches, we show that functional CDK4 protein is not detectable in cells with CDK4 mutations. Cells display impaired RB phosphorylation in G1, leading to G1/S-phase transition defects and reduced cell proliferation, consistent with complete loss of cellular CDK4 enzymatic activity. Together, these findings demonstrate that CDK4 is itself required for cell proliferation, human growth, and brain size determination during development.

Next-Generation Sequencing Identifies Novel Germline Mutations in Patients with Budd-Chiari Syndrome-Associated Hepatocellular Carcinoma

INTRODUCTION

Budd-Chiari syndrome-hepatocellular carcinoma (BCS-HCC) is uncommon and its molecular pathogenesis is poorly understood. In this study, we aimed to investigate the genomic landscape of BCS-HCC through whole exome sequencing (WES) to elucidate the cellular and molecular pathways involved in its pathogenesis.

METHODOLOGY

We enrolled BCS-HCC (n = 13) and BCS alone (n = 73) patients. WES was performed using the Twist Comprehensive Exome kit on the Illumina platform, followed by quality checks and analysis using the GATK pipeline. Pathogenic/likely pathogenic variants were filtered out from the exonic part of the annotated variant calling file. rsIDs and Cosmic IDs (catalogue of somatic mutations in cancer) were assigned using dbSNP and Cosmic ID databases. Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene ontology analysis were done for pathogenic gene variants.

RESULTS

We observed 1849 significant mutations in 305 genes in BCS-HCC patients, including missense, Indel, and frameshift mutations. Missense variants were more common than frameshift and indels in all subjects. The pathogenic mutations were found in 34 genes-cancer-causing (18 genes) and disease-causing (16 genes, both BCS or BCS-HCC) as per COSMIC cancer gene census. Pathogenic mutations were frequently observed in the mucin family genes including MUC3A, MUC4, MUC6, and MUC16 in BCS-HCC subjects. Changes in extracellular matrix and glycosylation were observed in gene ontology analysis of the genes having pathogenic variants.

CONCLUSION

Mutations in the mucin gene family including other cancer-causing genes were associated with BCS-HCC in our cohort. Larger, multicentric studies with regional and ethnic diversity are required to validate these findings.

The Genome of Lolium multiflorum Reveals the Genetic Architecture of Paraquat Resistance

Herbicide resistance in agricultural weeds has become one of the greatest challenges for sustainable crop production. The repeated evolution of herbicide resistance provides an excellent opportunity to study the genetic and physiological basis of the resistance phenotype and the evolutionary responses to human-mediated selection pressures. Lolium multiflorum is a ubiquitous weed that has evolved herbicide resistance repeatedly around the world in various cropping systems. We assembled and annotated a chromosome-scale genome for L. multiflorum and elucidated the genetic architecture of paraquat resistance by performing quantitative trait locus analysis, genome-wide association studies, genetic divergence analysis and transcriptome analyses from paraquat-resistant and -susceptible L. multiflorum plants. We identified two regions on chromosome 5 that were associated with paraquat resistance. These regions both showed evidence for positive selection among the resistant populations we sampled, but the effects of this selection on the genome differed, implying a complex evolutionary history. In addition, these regions contained candidate genes that encoded cellular transport functions, including a novel multidrug and toxin extrusion (MATE) protein and a cation transporter previously shown to interact with polyamines. Given that L. multiflorum is a weed and a cultivated crop species, the genomic resources generated will prove valuable to a wide spectrum of the plant science community. Our work contributes to a growing body of knowledge on the underlying evolutionary and ecological dynamics of rapid adaptation to strong anthropogenic selection pressure that could help initiate efforts to improve weed management practices in the long term for a more sustainable agriculture.

Application of Whole-Exome Sequencing (WES) for Prenatal Determination of Causes of Fetal Abnormalities

Fetal abnormalities are major issues in prenatal medicine. They affect the predicted pregnancy outcome and entail a risk of future recurrent adverse events in a particular couple. In order to clarify the possible outcomes of a specific pregnancy and subsequent ones, it is of the utmost importance to determine the causes of observed fetal abnormalities. Routine laboratory techniques sometimes fail to identify their cause because they are mainly intended for the detection of chromosomal disorders. Over recent years, single-gene disorders have increasingly been regarded as probable causes of fetal abnormalities, and next-generation sequencing (NGS) technologies have been adopted to detect them. This article provides the findings of applying whole-exome sequencing (WES) for prenatal diagnosis. It is aimed at identifying the causes of various fetus abnormalities with a normal molecular karyotype. The diagnostic value of this technique is shown based on the completeness of clinical patterns, abnormality types, and the ability to simultaneously examine the fetus and the parents. Consequently, WES revealed causative variants in 27.27% of cases, which encourages the consideration of applying this technique as part of a state-of-the-art multiple congenital malformation prenatal diagnosis algorithm.

Characterization of Extrachromosomal Circular DNA in Primary and Cisplatin-Resistant High-Grade Serous Ovarian Cancer

BACKGROUND

Cisplatin resistance is a major cause of tumor recurrence and mortality in high-grade serous ovarian cancer (HGSOC). Extrachromosomal circular DNA (eccDNA) has emerged as a critical factor in tumor evolution and drug resistance. However, the specific contribution of eccDNA to cisplatin resistance in HGSOC remains unclear.

METHODS

We performed whole-genome sequencing, Circle-Seq, and RNA-Seq in four pairs of primary and cisplatin-resistant (cisR) HGSOC cell lines to characterize genome-wide eccDNA distribution and features. Functional enrichment analyses were subsequently conducted on differentially expressed eccDNA-related genes.

RESULTS

In the SKOV3 cisR cell line, we identified a large extrachromosomal circular DNA (ecDNA) carrying the HIF1A gene, which regulates DNA repair, drug efflux, and epithelial-mesenchymal transition, contributing to cisplatin resistance. Using Circle-Seq, we detected a total of 161,062 eccDNAs, most of which were less than 1000 bp and distributed across all chromosomes. Notably, the number of eccDNAs on chromosome 21 differed significantly between the primary and cisR cell lines. Additionally, eccDNAs were predominantly located in non-coding repetitive elements. Functional analysis of eccDNA-related differentially expressed genes revealed that, compared to primary cell lines, cisR cell lines were associated with mitotic spindle assembly, regulation of vascular permeability, and cell differentiation. eccDNA-related genes involved in these pathways include MISP, WIPF1, RHOD, KRT80, and PLVAP.

CONCLUSIONS

Our findings suggest that eccDNAs, particularly ecDNA amplifications like HIF1A, contribute significantly to cisplatin resistance mechanisms in HGSOC. These insights highlight eccDNA as a potential target for overcoming therapeutic resistance and improving treatment outcomes in ovarian cancer.

Breast Cancer Is Increased in Women With Primary Ovarian Insufficiency

CONTEXT

DNA damage/repair gene variants are associated with both primary ovarian insufficiency (POI) and cancer risk.

OBJECTIVE

We hypothesized that a subset of women with POI and family members would have increased risk for cancer.

DESIGN

Case-control population-based study using records from 1995 to 2022.

SETTING

Two major Utah academic health care systems serving 85% of the state.

SUBJECTS

Women with POI (n = 613) were identified using International Classification of Diseases codes and reviewed for accuracy. Relatives were linked using the Utah Population Database.

INTERVENTION

Cancer diagnoses were identified using the Utah Cancer Registry.

MAIN OUTCOME MEASURES

The relative risk of cancer in women with POI and relatives was estimated by comparison to population rates. Whole genome sequencing was performed on a subset of women.

RESULTS

Breast cancer was increased in women with POI (OR, 2.20; 95% CI, 1.30-3.47; P = .0023) and there was a nominally significant increase in ovarian cancer. Probands with POI were 36.5 ± 4.3 years and 59.5 ± 12.7 years when diagnosed with POI and cancer, respectively. Causal and candidate gene variants for cancer and POI were identified. Among second-degree relatives of these women, there was an increased risk of breast (OR, 1.28; 95% CI, 1.08-1.52; P = .0078) and colon cancer (OR, 1.50; 95% CI, 1.14-1.94; P = .0036). Prostate cancer was increased in first- (OR, 1.64; 95% CI, 1.18-2.23; P = .0026), second- (OR, 1.54; 95% CI, 1.32-1.79; P < .001), and third-degree relatives (OR, 1.33; 95% CI, 1.20-1.48; P < .001).

CONCLUSION

Data suggest common genetic risk for POI and reproductive cancers. Tools are needed to predict cancer risk in women with POI and potentially to counsel about risks of hormone replacement therapy.

Estimating mutation rate and characterising single nucleotide de novo mutations in pigs

BACKGROUND

Direct estimates of mutation rates in humans have changed our understanding of evolutionary timing and de novo mutations (DNM) have been associated with several developmental disorders in humans. Livestock species, including pigs, can contribute to the study of DNM because of their ideal population structure and routine phenotype collection. In principle, there is the potential for livestock populations to quickly accumulate new genetic variants because of short generation intervals and high selection intensity. However, the impact of DNM on the fitness of individuals is not known and with current genomic selection programs they cannot contribute to estimated breeding values. The aims of our project were to detect and validate single nucleotide DNM in two commercial pig breeding lines, estimate the single nucleotide mutation rate, and characterise DNM.

RESULTS

We sequenced (150 bp paired end reads, 30X coverage) 46 pig trios from two commercial lines. Single nucleotide DNM were detected using a trio-aware method. We defined candidate DNM as single nucleotide variants (SNVs) found in heterozygous state in trio-offspring with both trio-parents homozygous for the reference allele. In this study, we estimate a lower threshold of the DNM rate in pigs of 6.3 × 10-9 per site per gamete. Our findings are consistent with those from other mammals and those published for a small number of livestock species. Most DNM we detected were in introns (47%) and intergenic regions (49%). The mutational spectrum in pigs differs from that in humans and we found several DNM predicted to have an effect on animal's fitness based on the base pair change and their location in the genome.

CONCLUSIONS

With this study, we have generated fundamental knowledge on mutation rate in a non-primate species and identified DNM that could have an impact on the fitness of individuals.

Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia

Bruton tyrosine kinase (BTK) inhibitors are effective for the treatment of chronic lymphocytic leukemia (CLL) due to BTK's role in B cell survival and proliferation. Treatment resistance is most commonly caused by the emergence of the hallmark BTK C481S mutation that inhibits drug binding. In this study, we aimed to investigate cancer subclones harboring a BTK C481S mutation and identify cells with co-occurring CLL driver mutations. In addition, we sought to determine whether BTK-mutated subclones exhibit distinct transcriptomic behavior when compared to other cancer subclones. To achieve these goals, we use scBayes, which integrates bulk DNA sequencing and single-cell RNA sequencing (scRNA-seq) data to genotype individual cells for subclone-defining mutations. Although the most common approach for scRNA-seq includes short-read sequencing, transcript coverage is limited due to the vast majority of the reads being concentrated at the priming end of the transcript. Here, we utilized MAS-seq, a long-read scRNA-seq technology, to substantially increase transcript coverage and expand the set of informative mutations to link cells to cancer subclones in six CLL patients who acquired BTK C481S mutations during BTK inhibitor treatment. In two patients who developed two independent BTK-mutated subclones, we find that most BTK-mutated cells have an additional CLL driver gene mutation. When examining subclone-specific gene expression, we find that in one patient, BTK-mutated subclones are transcriptionally distinct from the rest of the malignant B cell population with an overexpression of CLL-relevant genes.

TET2 gene mutation status associated with poor prognosis of transition zone prostate cancer: a retrospective cohort study based on whole exome sequencing and machine learning models

Background

Prostate cancer (PCa) in the transition zone (TZ) is uncommon and often poses challenges for early diagnosis, but its genomic determinants and therapeutic vulnerabilities remain poorly characterized.

Methods

Tumor mutational landscape was characterized in nine patients with TZ PCa, identifying somatic variants through whole-exome sequencing (WES). Novel candidate variants relevant to driver gene were selected using rare-variant burden analysis. Kaplan-Meier curves with log-rank testing and Cox regression models were applied to evaluate the prognostic significance of selected mutant driver gene and clinicopathological characteristics in a cohort of 132 patients with TZ PCa. Significant prognostic determinants were integrated into a validated nomogram for individualized prediction of 3-, 4-, and 5-year biochemical recurrence-free survival (BRFS) and overall survival (OS) probabilities. Eight machine learning algorithms were employed to develop BRFS and OS prediction models in a cohort.

Results

A total of 5,036 somatic single nucleotide variants (SNVs) and 587 somatic insertion and deletion (INDELs) were discovered. Among eight driver gene mutations which were verified through Sanger sequencing, TET2 gene, with high mutation frequency and potential targeted drug relevance (bromodomain inhibitors and DOT1L inhibitors) was selected for further validation. Retrospective cohort study demonstrated that TET2 mutant status was significantly associated with Gleason score (p = 0.004) and distant metastasis (p = 0.002). Furthermore, TET2 mutant status was significantly correlated with inferior BRFS and OS and served as an independent predictor. Comparative evaluation of eight algorithms revealed the GBM model achieved superior discriminative ability for BRFS (AUC for 3-year: 0.752, 4-year: 0.786, 5-year: 0.796). The predictive model based on the GBM machine learning algorithm achieved the best predictive performance for OS (AUC for 3-year: 0.838, 4-year: 0.915, 5-year: 0.868). The constructed predictive nomogram provided evidence that TET2 mutant status integration conferred statistically significant improvements in model accuracy and clinical predictive value.

Conclusion

Our study elucidated the distinct genetic basis of prostate cancer in the transition zone and identified TET2 mutation as an independent prognostic determinant in TZ PCa. However, the limited sample size of this study necessitates cautious interpretation of these findings, and further validation in larger cohorts is warranted to confirm their generalizability.

Whole genome sequence of Coxiella burnetii Nine Mile II, clone 4, ∆cbu0533 mutant strain, an alternative for safer laboratory use

Here, we determined the genome sequence of the Coxiella burnetii Nine Mile II (NMII), RSA439, clone 4, ∆cbu0533 mutant strain. This strain was engineered as a potential laboratory replacement for the wild-type C. burnetii NMII, which can undergo lipopolysaccharide elongation in specific growth conditions due to cbu0533 mutation reversion.

Isolation and Characterization of the Adamantinomatous Craniopharyngioma Primary Cells with Cancer-Associated Fibroblast Features

Backgrounds: Adamantinomatous craniopharyngiomas (ACPs) are benign intracranial tumors that behave aggressively due to their location, infiltration of the surrounding nervous tissue and high capacity for recurrence. In this study, we aimed to construct ACP primary cell models for further investigation of tumorigenic and recurrent mechanisms. Methods: Primary cells were isolated from primary (one case) and recurrent (one case) ACP. Short tandem repeat (STR) analysis was used to clarify the identity of the ACP primary cells we isolated. Whole exome sequencing (WES), immunofluorescence (IF) and immunohistochemistry (IHC) were performed on primary cells and corresponding ACP tissues, to determine the mutational profile and to clarify the tissue origin and phenotypic of primary cells. Transcriptome RNA-seq was performed to obtain the gene expression characteristics of ACP primary cells. Subsequently, a heterotopic ACP xenograft mouse model was established to confirm the tumorigenesis capacity of ACP primary cells. Results: ACP primary cells were successfully cultured. The genetic variants were similar to the original tumor tissue, and they owned expression of cancer-associated fibroblast (CAF) markers (FSP1/S100A4, Vimentin) and nuclear translocation β-catenin. Meanwhile, they had an high level expression of extracellular matrix components (Fibronectin). The tumor formation ability of ACP primary cells was verified. The transcriptional signatures of ACP primary cells were also explored. Conclusions: We successfully isolated and characterized ACP primary cells that acquired multiple CAF features and demonstrated stable propagation through dozens of passages. These PDC models laid the foundation for further research on ACP.

Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees

Estimates of de novo mutation rates are essential for phylogenetic and demographic analyses, but their inference has previously been impeded by high error rates in sequence data and uncertainty in the fossil record. Here, we directly estimate de novo germline mutation rates for all extant members of Panthera, as well as the closely related outgroup Neofelis nebulosa, using pedigrees. We use a previously validated pipeline (RatesTools) to calculate mutation rates for each species and subsequently explore the impacts of the novel rates on historic effective population size estimates in each of these charismatic felids of conservation concern. Importantly, we find that the choice of reference genome, the data type and coverage, and the individual all impact estimates of the mutation rate, but these can be largely ameliorated through extensive manual curation. Despite these stochastic effects, manual validation of de novo mutation candidates permitted the reliable inference of pantherine mutation rates. We inferred that base pair mutation rates for all species fell between 3.6 × 10-9 and 7.6 × 10-9 per generation per base pair (mean 5.5 × 10-9 ± 1.7 × 10-9 across Pantherinae at a mean parental age of 5.5 years). Similar to other studies, we show a positive trend of mean parental age with mutation rate and our inferred rates are well within the expected range for other mammals.

Target-Enhanced Whole-Genome Sequencing Shows Clinical Validity Equivalent to Commercially Available Targeted Oncology Panel

PURPOSE

Cancer poses a significant global health challenge, demanding precise genomic testing for individualized treatment strategies. Targeted-panel sequencing (TPS) has improved personalized oncology but often lacks comprehensive coverage of crucial cancer alterations. Whole-genome sequencing (WGS) addresses this gap, offering extensive genomic testing. This study demonstrates the medical potential of WGS.

MATERIALS AND METHODS

This study evaluates target-enhanced WGS (TE-WGS), a clinical-grade WGS method sequencing both cancer and matched normal tissues. Forty-nine patients with various solid cancer types underwent both TE-WGS and TruSight Oncology 500 (TSO500), one of the mainstream TPS approaches.

RESULTS

TE-WGS detected all variants reported by TSO500 (100%, 498/498). A high correlation in variant allele fractions was observed between TE-WGS and TSO500 (r=0.978). Notably, 223 variants (44.8%) within the common set were discerned exclusively by TE-WGS in peripheral blood, suggesting their germline origin. Conversely, the remaining subset of 275 variants (55.2%) were not detected in peripheral blood using the TE-WGS, signifying them as bona fide somatic variants. Further, TE-WGS provided accurate copy number profiles, fusion genes, microsatellite instability, and homologous recombination deficiency scores, which were essential for clinical decision-making.

CONCLUSION

TE-WGS is a comprehensive approach in personalized oncology, matching TSO500's key biomarker detection capabilities. It uniquely identifies germline variants and genomic instability markers, offering additional clinical actions. Its adaptability and cost-effectiveness underscore its clinical utility, making TE-WGS a valuable tool in personalized cancer treatment.

TTLOC: A Tn5 transposase-based approach to localize T-DNA integration sites

Thermal asymmetric interlaced-polymerase chain reaction-based and whole-genome sequencing-based T-DNA localization approaches have been developed for the recovery of T-DNA integration sites (TISs). Nevertheless, a low-cost and high-throughput technique for the detection of TISs, which would facilitate the identification of genetically engineered plants, is in high demand for rapid crop breeding and plant synthetic biology. Here, we present Tn5 transposase-based T-DNA integration site localization (TTLOC), a Tn5-based approach for TIS localization. TTLOC employs specialized adaptor-assembled Tn5 transposases for genomic DNA tagmentation. TTLOC library construction is straightforward, involving only six steps that requires two and a half hours to complete. The resulting pooled library is compatible with next-generation sequencing, which enables high-throughput determination. We demonstrate the ability of TTLOC to recover 95 non-redundant TISs from 65 transgenic Arabidopsis (Arabidopsis thaliana) lines, and 37 non-redundant TISs from the genomes of transgenic rice (Oryza sativa), soybean (Glycine max), tomato (Solanum lycopersicum), potato (Solanum tuberosum), and from the large hexaploid wheat (Triticum aestivum) genome. TTLOC is a cost-effective method, as 1 to 2 Gb of raw data for each multiplexing library are sufficient for efficient TIS calling, independent of the genome size. Our results establish TTLOC as a promising strategy for evaluation of genome engineered plants and for selecting genome safe harbors for trait stacking in crop breeding and plant synthetic biology.

Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities

Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for phage-host interactions. Applied to three different microbiomes, the method unveiled over 1900 motifs that were deposited in REBASE. The motifs include a novel eight-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights into bacterial biology and biotechnological applications.

Single-cell and chromatin accessibility profiling reveals regulatory programs of pathogenic Th2 cells in allergic asthma

Lung pathogenic T helper type 2 (pTh2) cells are important in mediating allergic asthma, but fundamental questions remain regarding their heterogeneity and epigenetic regulation. Here we investigate immune regulation in allergic asthma by single-cell RNA sequencing in mice challenged with house dust mite, in the presence and absence of histone deacetylase 1 (HDAC1) function. Our analyses indicate two distinct highly proinflammatory subsets of lung pTh2 cells and pinpoint thymic stromal lymphopoietin (TSLP) and Tumour Necrosis Factor Receptor Superfamily (TNFRSF) members as important drivers to generate pTh2 cells in vitro. Using our in vitro model, we uncover how signalling via TSLP and a TNFRSF member shapes chromatin accessibility at the type 2 cytokine gene loci by modulating HDAC1 repressive function. In summary, we have generated insights into pTh2 cell biology and establish an in vitro model for investigating pTh2 cells that proves useful for discovering molecular mechanisms involved in pTh2-mediated allergic asthma.

Dynamic investigation of hypoxia-induced L-lactylation

The recently identified histone modification lysine lactylation can be stimulated by L-lactate and glycolysis. Although the chemical group added upon lysine lactylation was originally proposed to be the L-enantiomer of lactate (KL-la), two isomeric modifications, lysine D-lactylation (KD-la) and N-ε-(carboxyethyl) lysine (Kce), also exist in cells, with their precursors being metabolites of glycolysis. The dynamic regulation and differences among these three modifications in response to hypoxia remain poorly understood. In this study, we demonstrate that intracellular KL-la, but not KD-la or Kce, is up-regulated in response to hypoxia. Depletion of glyoxalase enzymes, GLO1 and GLO2, had minimal impact on KD-la, Kce, or hypoxia-induced KL-la. Conversely, blocking glycolytic flux to L-lactate under hypoxic conditions by knocking out lactate dehydrogenase A/B completely abolished the induction of KL-la but increased KD-la and Kce. We further observed a correlation between the level of KL-la and hypoxia-inducible factor 1 alpha (HIF-1α) expression under hypoxic conditions and when small molecules were used to stabilize HIF-1α in the normoxia condition. Our result demonstrated that there is a strong correlation between HIF-1α and KL-la in lung cancer tissues and that patient samples with higher grade tend to have higher KL-la levels. Using a proteomics approach, we quantified 66 KL-la sites that were up-regulated by hypoxia and demonstrated that p300/CBP contributes to hypoxia-induced KL-la. Collectively, our study demonstrates that KL-la, rather than KD-la or Kce, is the prevailing lysine lactylation in response to hypoxia. Our results therefore demonstrate a link between KL-la and the hypoxia-induced adaptation of tumor cells.

Identification of CNTN2 as a genetic modifier of PIGA-CDG in a family with incomplete penetrance and in Drosophila

Loss-of-function mutations in the X chromosome gene PIGA lead to phosphatidylinositol glycan class A congenital disorder of glycosylation (PIGA-CDG), an ultra-rare CDG typically presenting with seizures, hypotonia, and neurodevelopmental delay. We identified two brothers (probands) with PIGA-CDG, presenting with epilepsy and mild developmental delay. Both probands carry PIGA c.395C>G (p.Ser132Cys), an ultra-rare variant predicted to be damaging. Strikingly, the maternal grandfather and a great uncle also carry the same PIGA variant, but neither presents with symptoms associated with PIGA-CDG. We hypothesized that genetic modifiers might contribute to this reduced penetrance. Using whole-genome sequencing and pedigree analysis, we identified possible susceptibility variants found in the probands and not in the carriers and possible protective variants found in the carriers and not in the probands. Candidate genetic modifier variants included heterozygous, damaging variants in three genes involved directly in glycosylphosphatidylinositol (GPI)-anchor biosynthesis and additional variants in other glycosylation pathways or encoding GPI-anchored proteins. Using a Drosophila eye-based model, we tested modifiers identified through genome sequencing. Loss of CNTN2, a predicted protective modifier that encodes a GPI-anchored protein responsible for neuron/glial interactions, rescues loss of PIGA in the eye-based model, as we predict in the family. Further testing found that the loss of CNTN2 also rescues PIGA-CDG-specific phenotypes, including seizures and climbing defects in Drosophila neurological models of PIGA-CDG. Using pedigree information, genome sequencing, and in vivo testing, we identified CNTN2 as a strong candidate modifier that could explain the incomplete penetrance in this family. Identifying and studying rare disease modifier genes in families may lead to therapeutic targets.

Ide Copy Number Variant Does Not Influence Stroke Severity in 2 C57BL/6J Mouse Models nor in Humans: An Exploratory Study

BACKGROUND

Contrary to the common belief, the most commonly used laboratory C57BL/6J mouse inbred strain presents a distinctive genetic and phenotypic variability, and for several traits, the genotype-phenotype link remains still unknown. Recently, we characterized the most important stroke survival factor such as brain collateral plasticity in 2 brain ischemia C57BL/6J mouse models (bilateral common carotid artery stenosis and middle cerebral artery occlusion) and observed a Mendelian-like fashion of inheritance of the posterior communicating artery (PcomA) patency. Interestingly, a copy number variant (CNV) spanning Ide locus was reported to segregate in an analogous Mendelian-like pattern in the C57BL/6J colonies of the Jackson Laboratory. Given IDE critical role in vascular plasticity, we hypothesized Ide CNV may have explained PcomA variability in C57BL/6J inbred mice.

METHODS

We applied a combination of techniques (T2-weighted magnetic resonance imaging, time-of-flight angiography, cerebral blood flow imaging, and histology) to characterize the collaterome in 77 C57BL/6J bilateral common carotid artery stenosis, middle cerebral artery occlusion, naive, and sham mice and performed on these Taqman genotyping, exome sequencing, and RNA sequencing. We then investigated the hypothesis that IDE structural variants (CNVs, gain/loss of function mutations) may have influenced the cerebrovascular phenotype in a large cohort of 454 040 cases and controls (UK Biobank, Genomics England).

RESULTS

We detected an Ide CNV in a bilateral common carotid artery stenosis mouse with 2 patent PcomAs (minor allele frequency, 1.3%), not segregating with the PcomA patency phenotype. In addition, 2 heterozygous IDE CNVs, resulting in loss of function were found in 1 patient with hereditary ataxia, a patient with hereditary congenital heart disease, and 2 healthy individuals (minor allele frequency 9×10-6). Moreover, we report 4 IDE loss of function point mutations (p.Leu5X, p.Met394ValfsX29, p.Pro14SerfsX26, p.Leu889X, minor allele frequency 0.02%) present also in controls or inherited from healthy parents.

CONCLUSIONS

Ide CNV and loss of function variants are rare, do not crucially influence PcomA variability in C57BL/6J inbred mice, and do not cause a vascular phenotype in humans.

A deep-learning model for quantifying circulating tumour DNA from the density distribution of DNA-fragment lengths

The quantification of circulating tumour DNA (ctDNA) in blood enables non-invasive surveillance of cancer progression. Here we show that a deep-learning model can accurately quantify ctDNA from the density distribution of cell-free DNA-fragment lengths. We validated the model, which we named 'Fragle', by using low-pass whole-genome-sequencing data from multiple cancer types and healthy control cohorts. In independent cohorts, Fragle outperformed tumour-naive methods, achieving higher accuracy and lower detection limits. We also show that Fragle is compatible with targeted sequencing data. In plasma samples from patients with colorectal cancer, longitudinal analysis with Fragle revealed strong concordance between ctDNA dynamics and treatment responses. In patients with resected lung cancer, Fragle outperformed a tumour-naive gene panel in the prediction of minimal residual disease for risk stratification. The method's versatility, speed and accuracy for ctDNA quantification suggest that it may have broad clinical utility.

p85β acts as a transcription cofactor and cooperates with BCLAF1 in the nucleus

p85β is a regulatory subunit of the phosphoinositide 3-kinase (PI3K). Emerging evidence suggests that p85β goes beyond its role in the PI3K and is functional in the nucleus. In this study, we discover that nuclear p85β is enriched at gene loci and regulates gene transcription and that this regulatory role contributes to the oncogenic potential of nuclear p85β. A multi-omics approach reveals the physical interaction and functional cooperativity between nuclear p85β and a transcription factor BCLAF1. We observe genome-wide co-occupancy of p85β and BCLAF1 at gene targets associated with transcriptional responses. Intriguingly, the targetome includes BCLAF1 of which transcription is activated by p85β and BCLAF1, indicating a positive autoregulation. While BCLAF1 recruits p85β to BCLAF1 loci, p85β facilitates the assembly of BCLAF1, the scaffold protein TRIM28 and the zinc finger transcription factor ZNF263, which together act in concert to activate BCLAF1 transcription. Collectively, this study provides functional evidence and mechanistic basis to support a role of nuclear p85β in modulating gene transcription.

Evolutionary adaptation to hyperstable microtubules selectively targets tubulins and is empowered by the spindle assembly checkpoint

Microtubules are polymers required for chromosome segregation. Their drug-induced hyperstabilization impairs chromosome segregation and is an established anti-cancer therapy. How cells respond to microtubule hyperstabilization, however, is incompletely understood. To study this, we evolved budding yeast cells expressing a microtubule-hyperstabilizing tubulin mutant and isolated adapted strains. Aneuploidy of specific chromosomes carrying the microtubule regulators STU2 and VIK1/KAR3 was the first observable adaptation. In the longer run, aneuploidies were outcompeted by mutations in α- or β-tubulin, partially overlapping with mutations in cancer patients. Thus, compensation of microtubule hyperstabilization follows a restrained and reproducible path where new mutations combine with the original offending mutation on the same carrier. While partly compensatory, several mutations failed to re-establish fully normal microtubule dynamics. Sustained growth relied on the mitotic checkpoint, indicating that extended mitotic timing limits the genomic instability caused by reduced microtubule dynamics. Our results predict a potential vulnerability of cells resistant to microtubule-hyperstabilizing agents.

Understanding the transfer and persistence of antimicrobial resistance in aquaculture using a model teleost gut system

BACKGROUND

The development, progression, and dissemination of antimicrobial resistance (AMR) are determined by interlinked human, animal, and environmental drivers, which pose severe risks to human and livestock health. Conjugative plasmid transfer drives the rapid dissemination of AMR among bacteria. In addition to the judicious use and implementation of stewardship programs, mitigating the spread of antibiotic resistance requires an understanding of the dynamics of AMR transfer among microbial communities, as well as the role of various microbial taxa as potential reservoirs that promote long-term AMR persistence. Here, we employed Hi-C, a high-throughput, culture-free technique, combined with qPCR, to monitor carriage and transfer of a multidrug-resistent (MDR) plasmid within an Atlantic salmon in vitro gut model during florfenicol treatment, a benzenesulfonyl antibiotic widely deployed in fin-fish aquaculture.

RESULTS

Microbial communities from the pyloric ceaca of three healthy adult farmed salmon were inoculated into three bioreactors simulating the teleost gut, which were developed for the SalmoSim gut system. The model system was then inoculated with the Escherichia coli strain ATCC 25922 carrying the plasmid pM07-1 and treated with florfenicol at a concentration of 150 mg/L in fish feed media for 5 days prior to the washout/recovery phase. Hi-C and metagenomic sequencing identified numerous transfer events, including those involving gram-negative and gram-positive taxa, and, crucially, the transfer and persistence of the plasmid continued once florfenicol treatment was withdrawn.

CONCLUSIONS

Our findings highlight the role of the commensal teleost gut flora as a reservoir for AMR even once antimicrobial selective pressure has been withdrawn. Our system also provides a model to study how different treatment regimens and interventions may be deployed to mitigate AMR persistence.

Circulating cell-free DNA methylation profiles as noninvasive multiple sclerosis biomarkers: A proof-of-concept study

In multiple sclerosis (MS), there is a critical need for non-invasive biomarkers to concurrently classify disease subtypes, evaluate disability severity, and predict long-term progression. In this proof-of-concept study, we performed low-coverage whole-genome bisulfite sequencing (WGBS) on 75 plasma cell-free DNA (cfDNA) samples and assessed the clinical utility of cfDNA methylation as a single assay for distinguishing MS patients from non-MS controls, identifying MS subtypes, estimating disability severity, and predicting disease trajectories. We identified thousands of differentially methylated CpGs and hundreds of differentially methylated regions (DMRs) that significantly distinguished MS from controls, separated MS subtypes, and stratified disability severity levels. These DMRs were highly enriched in immunologically and neurologically relevant regulatory elements (e.g., active promoters and enhancers) and contained motifs associated with neuronal function and T-cell differentiation. To distinguish MS subtypes and severity groups, we achieved area-under-the-curve (AUC) values ranging from 0.67 to 0.81 using DMRs and 0.70 to 0.82 using inferred tissue-of-origin patterns from cfDNA methylation, significantly outperforming benchmark neurofilament light chain (NfL) and glial fibrillary acidic protein (GFAP) in the same cohort. Finally, a linear mixed-effects model identified "prognostic regions" where baseline cfDNA methylation levels were associated with disease progression and predicted future disability severity (AUC=0.81) within a 4-year evaluation window. As we plan to generate higher-depth WGBS data and validation in independent cohorts, the present findings suggest the potential clinical utility of circulating cfDNA methylation profiles as promising noninvasive biomarkers in MS diagnosis and prognosis.

Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus

BACKGROUND

India harbors the world's largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome.

RESULTS

Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics 'linked-read' technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb, comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 Mb was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs encompassing ~ 2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis. The protein-coding genes were found in various prominent quantitative trait locus (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance.

CONCLUSIONS

This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.

Germline pathogenic variation impacts somatic alterations and patient outcomes in pediatric CNS tumors

The contribution of rare pathogenic/likely pathogenic (P/LP) germline variants to pediatric central nervous system (CNS) tumor development remains understudied. Here, we characterized the prevalence and clinical significance of germline P/LP variants in cancer predisposition genes across 830 CNS tumor patients from the Pediatric Brain Tumor Atlas (PBTA). We identified germline P/LP variants in 24.2% (201/830) of patients and the majority (154/201) lacked clinical reporting of genetic tumor syndromes. Among P/LP carriers, 30.7% had putative somatic second hits or loss of function tumor alterations. Finally, we linked pathogenic germline variation with novel somatic events and patient survival to highlight the impact of germline variation on tumorigenesis and patient outcomes.

Dispensable genome and segmental duplications drive the genome plasticity in Fusarium solani

Fusarium solani is a species complex encompassing a large phylogenetic clade with diverse members occupying varied habitats. We recently reported a unique opportunistic F. solani associated with unusual dark galls in sugarbeet. We assembled the chromosome-level genome of the F. solani sugarbeet isolate strain SB1 using Oxford Nanopore and Hi-C sequencing. The average size of F. solani genomes is 54 Mb, whereas SB1 has a larger genome of 59.38 Mb, organized into 15 chromosomes. The genome expansion of strain SB1 is due to the high repeats and segmental duplications within its three potentially accessory chromosomes. These chromosomes are absent in the closest reference genome with chromosome-level assembly, F. vanettenii 77-13-4. Segmental duplications were found in three chromosomes but are most extensive between two specific SB1 chromosomes, suggesting that this isolate may have doubled its accessory genes. Further comparison of the F. solani strain SB1 genome demonstrates inversions and syntenic regions to an accessory chromosome of F. vanettenii 77-13-4. The pan-genome of 12 publicly available F. solani isolates nearly reached gene saturation, with few new genes discovered after the addition of the last genome. Based on orthogroups and average nucleotide identity, F. solani is not grouped by lifestyle or origin. The pan-genome analysis further revealed the enrichment of several enzymes-coding genes within the dispensable (accessory + unique genes) genome, such as hydrolases, transferases, oxidoreductases, lyases, ligases, isomerase, and dehydrogenase. The evidence presented here suggests that genome plasticity, genetic diversity, and adaptive traits in Fusarium solani are driven by the dispensable genome with significant contributions from segmental duplications.

A chromosome-level genome assembly of the Peruvian Algarrobo (Neltuma pallida) provides insights on its adaptation to its unique ecological niche

The dry forests of northern Peru are dominated by the legumous tree Neltuma pallida which is adapted to hot arid and semiarid conditions in the tropics. Despite having been successfully introduced in multiple other areas around the world, N. pallida is currently threatened in its native area, where it is invaluable for the dry forest ecosystem and human subsistence. A major tool for enhancing ecosystem conservation and understanding the adaptive properties of N. pallida to dry forest ecosystems is the construction of a reference genome sequence. Here, we report on a high-quality reference genome for N. pallida. The final genome assembly size is 403.7 Mb, consisting of 14 pseudochromosomes and 63 scaffolds with an N50 size of 26.2 Mb and a 34.3% GC content. Use of Benchmarking Universal Single Copy Orthologs revealed 99.2% complete orthologs. Long terminal repeat elements dominated the repetitive sequence content which was 51.2%. Genes were annotated using N. pallida transcripts, plant protein sequences, and ab initio predictions resulting in 22,409 protein-coding genes encoding 24,607 gene models. Comparative genomic analysis showed evidence of rapidly evolving gene families related to disease resistance, transcription factors, and signaling pathways. The chromosome-scale N. pallida reference genome will be a useful resource for understanding plant evolution in extreme and highly variable environments.

Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and gliomagenesis

Histone lysine lactylation is a physiologically and pathologically relevant epigenetic pathway that can be stimulated by the Warburg effect-associated L-lactate. Nevertheless, the mechanism by which cells use L-lactate to generate lactyl-coenzyme A (CoA) and how this process is regulated remains unknown. Here, we report the identification of guanosine triphosphate (GTP)-specific SCS (GTPSCS) as a lactyl-CoA synthetase in the nucleus. The mechanism was elucidated through the crystallographic structure of GTPSCS in complex with L-lactate, followed by mutagenesis experiments. GTPSCS translocates into the nucleus and interacts with p300 to elevate histone lactylation but not succinylation. This process depends on a nuclear localization signal in the GTPSCS G1 subunit and acetylation at G2 subunit residue K73, which mediates the interaction with p300. GTPSCS/p300 collaboration synergistically regulates histone H3K18la and GDF15 expression, promoting glioma proliferation and radioresistance. GTPSCS represents the inaugural enzyme to catalyze lactyl-CoA synthesis for epigenetic histone lactylation and regulate oncogenic gene expression in glioma.

Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System

Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.

Genotypes and clinical phenotypes of pediatric patients with NOG variants: Middle ear surgical outcomes from a Tertiary Center in South Korea

OBJECTIVE

Although NOG variants are linked to congenital stapes fixation and conductive hearing loss (CHL), little is known about middle ear surgery outcomes and the characteristics of accompanying inner ear anomalies. We explored auditory phenotypes in patients with NOG variants, with a focus on the outcomes of middle ear surgery.

METHODS

This study included 11 patients from five unrelated Korean families harboring NOG variants. Genomic investigations were conducted using whole-exome sequencing and whole-genome sequencing. The clinical phenotypes, including pre- and postoperative audiological profiles, radiological abnormalities, and other comorbidities, were analyzed.

RESULTS

The average age at genetic testing was 8.2 years (range, 0-13 years). Two previously reported NOG variants (c.509C > T:p.Pro170Leu and c.252dup:p.Glu85ArgfsTer97) and three novel NOG variants, including the c.187G > T: p.Glu63Ter and two cryptic large deletion within the 17q22.2 region, were identified. All patients exhibited non-progressive CHL. Inner ear anomalies were documented in two patients, with variations such as cochlea and vestibular dysplasia. In this study, seven ears of four patients underwent stapedotomy, resulting in a significantly reduced air-bone gap of 10.18 ± 1.48 dB (P = 0.016), with sustained improvement. Conversely, patients carrying p.Pro170Leu variant, which is associated with poor outcomes for middle ear surgery, were excluded from surgical consideration.

CONCLUSION

We expanded the spectrum of genotypes and auditory phenotypes associated with NOG variants. Surgical intervention for CHL underlying NOG variants elicits favorable outcomes. However, clinicians should consider the potential for poor prognosis in certain NOG variants. Collectively, identifying NOG variants could guide the treatment strategies to improve CHL.

TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states

Mutations in cancer risk genes increase susceptibility, but not all carriers develop cancer. Indeed, while DNA mutations are necessary drivers of cancer, only a small subset of mutated cells go on to cause the disease. To date, the mechanisms underlying individual cancer susceptibility remain unclear. Here, we took advantage of a unique mouse model of intrinsic developmental heterogeneity (Trim28+/D9) to investigate whether early-life epigenetic variation influences cancer susceptibility later in life. We found that heterozygosity of Trim28 is sufficient to generate two distinct early-life epigenetic states associated with differing cancer susceptibility. These developmentally primed states exhibit differential methylation patterns at typically silenced heterochromatin, detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential, frequently mutated in human cancers and correlated with poor prognosis. This study provides genetic evidence that intrinsic developmental heterogeneity can prime individual, lifelong cancer susceptibility.

Chromosome-level and haplotype-resolved genome assembly of Bougainvillea glabra

Bougainvillea glabra Choisy, a common perennial shrub or climbing vine in tropical and subtropical areas, has significant ornamental and ecological value due to its showy floriferous blooms and adaptability to multiple environmental stresses. In this study, based on PacBio and Hi-C sequencing data, we presented the haplotype-resolved, and chromosome-level assembled genomes for B. glabra (2n = 34). We obtained two haplotypes with genome size of 2,855,692,602 bp and 2,889,511,499 bp, N50 of 165 Mbp and 167 Mbp, and both anchored to 17 chromosomes with anchor ratio of 97.07% and 97.55%, respectively. Through the BUSCO evaluation process, the two assembled haplotypes both exhibited the high score of 96%. By combining the high-confidence different evidence of genome structure annotation pipeline we annotated each haplotype containing ~33,000 predicted genes, of which 86% were functionally annotated by different databases. These high-quality haplotypes assembly and annotation results will serve as a great genomic resource to explore the ornamental traits and environmental adaptability and accelerate improvement in future.

DNA hypomethylation promotes UHRF1-and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states

Mono-ubiquitination of lysine 18 on histone H3 (H3K18ub), catalyzed by UHRF1, is a DNMT1 docking site that facilitates replication-coupled DNA methylation maintenance. Its functions beyond this are unknown. Here, we genomically map simultaneous increases in UHRF1-dependent H3K18ub and SUV39H1/H2-dependent H3K9me3 following DNMT1 inhibition. Mechanistically, transient accumulation of hemi-methylated DNA at CpG islands facilitates UHRF1 recruitment and E3 ligase activity toward H3K18. Notably, H3K18ub enhances SUV39H1/H2 methyltransferase activity and, in colon cancer cells, nucleates new H3K9me3 domains at CpG island promoters of DNA methylation-silenced tumor suppressor genes (TSGs). Disrupting UHRF1 enzyme activity prevents H3K9me3 accumulation while promoting PRC2-dependent H3K27me3 as a tertiary layer of gene repression in these regions. By contrast, disrupting H3K18ub-dependent SUV39H1/H2 activity enhances the transcriptional activating and antiproliferative effects of DNMT1 inhibition. Collectively, these findings reveal roles for UHRF1 and H3K18ub in regulating a hierarchy of repressive histone methylation signaling and rationalize a combination strategy for epigenetic cancer therapy.

Functional genomics implicates ebony in the black pupae phenotype of tephritid fruit flies

The remarkable diversity of insect pigmentation offers a captivating avenue for studying evolution and genetics. In tephritids, understanding the molecular basis of mutant traits is also crucial for applied entomology, enabling the creation of genetic sexing strains through genome editing, thus facilitating sex-sorting before sterile insect releases. Here, we present evidence from classical and modern genetics showing that the black pupae (bp) phenotype in the GUA10 strain of Anastrepha ludens is caused by a large deletion at the ebony locus, removing the gene's entire coding region. Targeted knockout of ebony induced analogous bp phenotypes across six major tephritid agricultural pests, demonstrating that disruption of Ebony alone is sufficient to produce the mutant trait in distantly related species. This functional characterization further allowed a deeper exploration of Ebony's role in pigmentation and development across life stages in diverse species. Our findings offer key insights for molecular engineering of sexing strains based on the bp marker and for future evolutionary developmental biology studies in tephritids.

Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide nicking enzyme epitope targeted DNA sequencing

Gene expression is regulated by chromatin DNA methylation and other features, including histone post-translational modifications (PTMs), chromatin remodelers and transcription factor occupancy. A complete understanding of gene regulation will require the mapping of these chromatin features in small cell number samples. Here we describe a novel genome-wide chromatin profiling technology, named as Nicking Enzyme Epitope targeted DNA sequencing (NEED-seq). NEED-seq offers antibody-targeted controlled nicking by Nt.CviPII-pGL fusion to study specific protein-DNA complexes in formaldehyde fixed cells, allowing for both visual and genomic resolution of epitope bound chromatin. When applied to nuclei, NEED-seq yielded genome-wide profile of chromatin-associated proteins and histone PTMs. Additionally, NEED-seq of lamin B1 and B2 demonstrated their association with heterochromatin. Lamin B1- and B2-associated domains (LAD) segregated to three different states, and states with stronger LAD correlated with heterochromatic marks. Hi-C analysis displayed A and B compartment with equal lamin B1 and B2 distribution, although methylated DNA remained high in B compartment. LAD clustering with Hi-C resulted in subcompartments, with lamin B1 and B2 partitioning to facultative and constitutive heterochromatin, respectively, and were associated with neuronal development. Thus, lamin B1 and B2 show structural and functional partitioning in mammalian nucleus.

Dominant negative variants in ITPR3 impair T cell Ca2+ dynamics causing combined immunodeficiency

The importance of calcium (Ca2+) as a second messenger in T cell signaling is exemplified by genetic deficiencies of STIM1 and ORAI1, which abolish store-operated Ca2+ entry (SOCE) resulting in combined immunodeficiency (CID). We report five unrelated patients with de novo missense variants in ITPR3, encoding a subunit of the inositol 1,4,5-trisphosphate receptor (IP3R), which forms a Ca2+ channel in the endoplasmic reticulum (ER) membrane responsible for the release of ER Ca2+ required to trigger SOCE, and for Ca2+ transfer to other organelles. The patients presented with CID, abnormal T cell Ca2+ homeostasis, incompletely penetrant ectodermal dysplasia, and multisystem disease. Their predominant T cell immunodeficiency is characterized by significant T cell lymphopenia, defects in late stages of thymic T cell development, and impaired function of peripheral T cells, including inadequate NF-κB- and NFAT-mediated, proliferative, and metabolic responses to activation. Pathogenicity is not due to haploinsufficiency, rather ITPR3 protein variants interfere with IP3R channel function leading to depletion of ER Ca2+ stores and blunted SOCE in T cells.

Demographic history and genetic variation of the Armenian population

We introduce a sizable (n = 34) whole-genome dataset on Armenians, a population inhabiting the region in West Asia known as the Armenian highlands. Equipped with this genetic data, we conducted a whole-genome study of Armenians and deciphered their fine-scale population structure and complex demographic history. We demonstrated that the Armenian populations from western, central, and eastern parts of the highlands are relatively homogeneous. The Sasun, a population in the south that had been argued to have received a major genetic contribution from Assyrians, was instead shown to have derived its slightly divergent genetic profile from a bottleneck that occurred in the recent past. We also investigated the debated question on the genetic origin of Armenians and failed to find any significant support for historical suggestions by Herodotus of their Balkan-related ancestry. We checked the degree of continuity of modern Armenians with ancient inhabitants of the eastern Armenian highlands and detected a genetic input into the region from a source linked to Neolithic Levantine Farmers at some point after the Early Bronze Age. Additionally, we cataloged an abundance of new mutations unique to the population, including a missense mutation predicted to cause familial Mediterranean fever, an autoinflammatory disorder highly prevalent in Armenians. Thus, we highlight the importance of further genetic and medical studies of this population.

Pan-phylum genomes of hornworts reveal conserved autosomes but dynamic accessory and sex chromosomes

Hornworts, one of the three bryophyte phyla, show some of the deepest divergences in extant land plants, with some families separated by more than 300 million years. Previous hornwort genomes represented only one genus, limiting the ability to infer evolution within hornworts and their early land plant ancestors. Here we report ten new chromosome-scale genomes representing all hornwort families and most of the genera. We found that, despite the deep divergence, synteny was surprisingly conserved across all hornwort genomes, a pattern that might be related to the absence of whole-genome duplication. We further uncovered multiple accessory and putative sex chromosomes that are highly repetitive and CpG methylated. In contrast to autosomes, these chromosomes mostly lack syntenic relationships with one another and are evolutionarily labile. Notable gene retention and losses were identified, including those responsible for flavonoid biosynthesis, stomata patterning and phytohormone reception, which have implications in reconstructing the evolution of early land plants. Together, our pan-phylum genomes revealed an array of conserved and divergent genomic features in hornworts, highlighting the uniqueness of this deeply diverged lineage.

Proximity-Ligation Metagenomic Sequence Analysis Reveals That the Antibiotic Resistome Makes Significant Transitions During Municipal Wastewater Treatment

Shotgun and proximity-ligation metagenomic sequencing were used to generate thousands of metagenome assembled genomes (MAGs) from the untreated wastewater, activated sludge bioreactors, and anaerobic digesters from two full-scale municipal wastewater treatment facilities. Analysis of the antibiotic resistance genes (ARGs) in the pool of contigs from the shotgun metagenomic sequences revealed significantly different relative abundances and types of ARGs in the untreated wastewaster compared to the activated sludge bioreactors or the anaerobic digesters (p < 0.05). In contrast, these results were statistically similar when comparing the ARGs in the pool of MAGs, suggesting that proximity-ligation metagenomic sequencing is particularly useful for pairing ARGs with their hosts but less adept at discerning quantitative differences in ARG types and relative abundances. For example, numerous MAGs of the genera Acinetobacter, Enterococcus, Klebsiella and Pseudomonas were identified in the untreated wastewater, many of which harboured plasmid-borne and/or chromosomal-borne ARGs; none of these MAGs, however, were detected in the activated sludge bioreactors or anaerobic digesters. In conclusion, this research demonstrates that the antibiotic resistome undergoes significant transitions in both the relative abundance and the host organisms during the municipal wastewater treatment process.

Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A-menin to bivalent promoters

Members of the KMT2C/D-KDM6A complex are recurrently mutated in urothelial carcinoma and in histologically normal urothelium. Here, using genetically engineered mouse models, we demonstrate that Kmt2c/d knockout in the urothelium led to impaired differentiation, augmented responses to growth and inflammatory stimuli and sensitization to oncogenic transformation by carcinogen and oncogenes. Mechanistically, KMT2D localized to active enhancers and CpG-poor promoters that preferentially regulate the urothelial lineage program and Kmt2c/d knockout led to diminished H3K4me1, H3K27ac and nascent RNA transcription at these sites, which leads to impaired differentiation. Kmt2c/d knockout further led to KMT2A-menin redistribution from KMT2D localized enhancers to CpG-high and bivalent promoters, resulting in derepression of signal-induced immediate early genes. Therapeutically, Kmt2c/d knockout upregulated epidermal growth factor receptor signaling and conferred vulnerability to epidermal growth factor receptor inhibitors. Together, our data posit that functional loss of Kmt2c/d licenses a molecular 'field effect' priming histologically normal urothelium for oncogenic transformation and presents therapeutic vulnerabilities.

Myotonia Congenita in Australian Merino Sheep with a Missense Variant in CLCN1

Myotonia congenita is a hereditary, non-dystrophic skeletal muscle disorder associated with muscle stiffness due to delayed muscle relaxation after contraction. We review myotonia congenita in domesticated animals and humans and investigated suspected myotonia congenita in a flock of Merino sheep in Australia. In 2020, a property in New South Wales reported a four-year history of lambs that would fall on disturbance before rapidly recovering, with 13 affected sheep identified in 2020. Episodes were associated with a short period of tetanic spasms and a stiff gait upon rising. Lambs were otherwise normal between episodes, although over time, lost body condition and occasionally died from misadventure. An inherited condition was considered from limited pedigree information and a preliminary diagnosis of myotonia congenita was made based on clinical presentation. Biochemistry from four sheep found variable, but typically mild increases in creatine kinase (CK) and aspartate aminotransferase (AST). Modified electromyography on six affected sheep found irregular electrical activity within the muscle. For four sheep, there were no consistent significant abnormalities on post mortem examination and histopathology-typical for this condition. A review of the Online Mendelian Inheritance in Man (OMIM) and Online Mendelian Inheritance in Animals (OMIA) databases was conducted to summarise information about myotonia congenita in humans and eight non-human species of animals. Comparing the characteristic clinical presentation, pathology and electromyography data of affected Merino sheep to similar conditions in other species assisted the identification of likely candidate genes. Whole genome sequencing of two affected lambs detected a missense variant in CLCN1 (NC_056057.1:g.107930611C>T; XM_004008136.5:c.844C>T; XP_004008185.4:p.(P282S)), with a predicted deleterious effect on protein function. An SNP genotyping assay was developed, and the variant segregated with the disease in 12 affected sheep and obligate carrier rams under an assumed recessive mode of inheritance. Identifying a likely causal variant and developing a diagnostic test allows screening of suspected affected or carrier Merino sheep for early intervention to reduce propagation of the variant within flocks.

Genome-Wide Structural Variation Analysis and Breed Comparison of Local Domestic Ducks in Shandong Province, China

Structural variations in the duck genome significantly impact the environmental adaptability and phenotypic diversity of duck populations. Characterizing these SVs in local domestic duck breeds from Shandong province offers valuable insights for breed selection and the development of new breeds. This study aimed to profile the genomic SVs in three local duck breeds (Matahu duck, Weishan partridge duck, and Wendeng black duck) and explore their differential distributions. A total of 21,673 SVs were detected using LUMPY (v0.2.13) and DELLY (v1.0.3) software, with 46% located in intergenic regions, 33% in intronic regions, and frameshift deletions being the most prevalent in exonic regions (3%). SVs distribution showed a decreasing trend with shorter chromosome lengths. Population structure analysis revealed distinct genetic profiles, with Matahu and Weishan partridge ducks showing closer affinities and the Wendeng black duck having a more homogeneous genetic background, likely due to geographic isolation. Functional annotation identified genes related to nervous system development, mitosis, spindle assembly, and energy metabolism. Notable genes included PLXNA4, NRP2, SEMA3A, PTEN, MYBL2, ADK, and COX4I1. Additionally, genes such as PRKG1, GABRA2, and FSHR were linked to energy metabolism and reproductive activity. The study provides a comprehensive analysis of SVs, revealing significant genetic differentiation and identifying genes associated with economically important traits, offering valuable resources for the genetic improvement and breeding of local duck breeds.