Genomic Features Research Articles

Pan-Chloroplast Genomes Reveal the Accession-Specific Marker for Gastrodia elata f. glauca

Gastrodia elata rhizomes have been applied as traditional medicinal materials for thousands of years. In China, G. elata f. elata (red flower and stem, Ge), G. elata f. viridis (green, Gv), and G. elata f. glauca (black, Gg) represent the primary cultivars in artificial cultivation. Although the annual output of G. elata amounts to 150,000 tons, only 20% is Gg. The long production period, low yield, and high quality of Gg led to its extremely high market prices. However, an effective method to identify this crude drug based solely on its morphological or chemical characteristics is lacking. In this study, the complete chloroplast genomes of three G. elata variants were sequenced using the Illumina HiSeq 2500 platform. Another 21 chloroplast genomes from Gastrodia species, which have published in previous reports, were combined and analyzed together. Our results showed that larger genomic sizes, fewer long tandem repeats, and more simple sequence repeats were the major features of the Gg chloroplast genomes. Phylogenetic analysis showed that the Gg samples were separately clustered in a subclade. Moreover, an accession-specific marker was successfully developed and validated for distinguishing additional rhizome samples. Our study provides investigations of the taxonomic relationships of Gastrodia species. The molecular marker will be useful for differentiating Gastrodia products on the market.

The Complete Mitochondrial Genome of Nephropsis grandis: Insights into the Phylogeny of Nephropidae Mitochondrial Genome.

The systematic phylogeny of Pleocyemata species, particularly within the family Nephropidae, remains incomplete. In order to enhance the taxonomy and systematics of Nephropidae within the evolutionary context of Pleocyemata, we embarked upon a comprehensive study aiming to elucidate the phylogenetic position of Nephropsis grandis. Consequently, we determined the complete mitochondrial DNA sequence for N. grandis. The circular genome spans a length of 15,344bp and exhibits a gene composition analogous to that observed in other metazoans, encompassing a comprehensive set of 37 genes. Additionally, the genome features an AT-rich region. The rRNAs exhibited the highest AT content among the 37 genes (70.41%), followed by tRNAs (67.42%) and protein-coding genes (PCGs) (62.76%). The absence of a dihydrouracil arm in trnS1 prevented the formation of the canonical cloverleaf secondary structure. Selective pressure analysis indicated that the PCGs underwent purifying selection. The Ka/Ks ratios for cox1, cox2, cox3, and cob were considerably lower compared to other PCGs, implying strong purifying selection acting upon these particular genes. The mitochondrial gene order in N. grandis was consistent with the reported order in ancestral Pleocyemata. Phylogenetic revealed that N. grandis forms a cluster with the genus Metanephrops, and this cluster further groups with Homarus and the genus Nephrops within the Nephropidae family. These findings provide robust support for N. grandis as an ancestral member of the Nephropidae family. This study highlights the significance of employing complete mitochondrial genomes in phylogenetic analysis and deepens our understanding of the evolution of the Nephropidae family.

Genomic characterization of parvovirus and beak and feather disease virus in cockatiel (Nymphicus hollandicus).

This study reveals the genomes of psittaciform chaphamaparvovirus 5 (PsChPV-5) and a beak and feather disease virus (BFDV), discovered in the fecal samples of cockatiels. The genomes of PsChPV-5 and BFDV are 4,366 and 2,009 base pairs long, respectively, each exhibiting the characteristic genomic structures of their respective genera.

Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese

Background: Lactiplantibacillus plantarum is a species found in a wide range of ecological niches, including vegetables and dairy products, and it may occur naturally in the human gastrointestinal tract. The precise mechanisms underlying the beneficial properties of these microbes to their host remain obscure. Although Lactic acid bacteria are generally regarded as safe, there are rare cases of the emergence of infections and antibiotic resistance by certain probiotics. Objective: An in silico whole genome sequence analysis of putative probiotic bacteria was set up to identify strains, predict desirable functional properties, and identify potentially detrimental antibiotic resistance and virulence genes. Methods: We characterized the genomes of three L. plantarum strains (54B, 54C, and 55A) isolated from Ethiopian traditional cottage cheese. Whole-genome sequencing was performed using Illumina MiSeq sequencing. The completeness and quality of the genome of L. plantarum strains were assessed through CheckM. Results: Analyses results showed that L. plantarum 54B and 54C are closely related but different strains. The genomes studied did not harbor resistance and virulence factors. They had five classes of carbohydrate-active enzymes with several important functions. Cyclic lactone autoinducer, terpenes, Type III polyketide synthases, ribosomally synthesized and post-translationally modified peptides-like gene clusters, sactipeptides, and all genes required for riboflavin biosynthesis were identified, evidencing their promising probiotic properties. Six bacteriocin-like structures encoding genes were found in the genome of L. plantarum 55A. Conclusions: The lack of resistome and virulome and their previous functional capabilities suggest the potential applicability of these strains in food industries as bio-preservatives and in the prevention and/or treatment of infectious diseases. The results also provide insights into the probiotic potential and safety of these three strains and indicate avenues for further mechanistic studies using these isolates.

Genomic insights into genes expressed specifically during infancy highlight their dominant influence on the neuronal system

BackgroundElucidating the dynamics of gene expression across developmental stages, including the genomic characteristics of brain expression during infancy, is pivotal in deciphering human psychiatric and neurological disorders and providing insights into developmental disorders.ResultsLeveraging comprehensive human GWAS associations with temporal and spatial brain expression data, we discovered a distinctive co-expression cluster comprising 897 genes highly expressed specifically during infancy, enriched in functions related to the neuronal system. This gene cluster notably harbors the highest ratio of genes linked to psychiatric and neurological disorders. Through computational analysis, MYT1L emerged as a potential central transcription factor governing these genes. Remarkably, the infancy-specific expressed genes, including SYT1, exhibit prominent colocalization within human accelerated regions. Additionally, chromatin state analysis unveiled prevalent epigenetic markers associated with enhancer-specific modifications. In addition, this cluster of genes has demonstrated to be specifically highly expressed in cell-types including excitatory neurons, medial ganglionic eminence and caudal ganglionic eminence.ConclusionsThis study comprehensively characterizes the genomics and epigenomics of genes specifically expressed during infancy, identifying crucial hub genes and transcription factors. These findings offer valuable insights into early detection strategies and interventions for psychiatric and neurological disorders.

Expanded geographic distribution for two Legionella pneumophila sequence types of clinical concern.

Legionella pneumophila serogroup 1 sequence types (ST) 213 and 222, a single-locus variant of ST213, were first detected in the early 1990s in the Midwest United States (U.S.) and the late 1990s in the Northeast U.S. and Canada. Since 1992, these STs have increasingly been implicated in community-acquired sporadic and outbreak-associated Legionnaires' disease (LD) cases. We were interested in understanding the change in LD frequency due to these STs and identifying genetic features that differentiate these STs from one another. For the geographic area examined here (Mountain West to Northeast) and over the study period (1992-2020), ST213/222-associated LD cases identified by the Centers for Disease Control and Prevention increased by 0.15 cases per year, with ST213/222-associated LD cases concentrated in four states: Michigan (26%), New York (18%), Minnesota (16%), and Ohio (10%). Additionally, between 2002 and 2021, ST222 caused at least five LD outbreaks in the U.S.; no known outbreaks due to ST213 occurred in the U.S. during this time. We compared the genomes of 230 ST213/222 isolates and found that the mean of the average nucleotide identity (ANI) within each ST was high (99.92% for ST222 and 99.92% for ST213), with a minimum between ST ANI of 99.50% and a maximum of 99.87%, indicating low genetic diversity within and between these STs. While genomic features were identified (e.g., plasmids and CRISPR-Cas systems), no association explained the increasing geographic distribution and prevalence of ST213 and ST222. Yet, we provide evidence of the expanded geographical distribution of ST213 and ST222 in the U.S.IMPORTANCESince the 1990s, cases of Legionnaires' disease (LD) attributed to a pair of closely related Legionella pneumophila variants, ST213 and ST222, have increased in the U.S. Furthermore, between 2002 and 2021, ST222 caused at least five outbreaks of LD in the U.S., while ST213 has not been linked to any U.S. outbreak. We wanted to understand how the rate of LD cases attributed to these variants has changed over time and compare the genetic features of the two variants. Between 1992 and 2020, we determined an increase of 0.15 LD cases ascribed to ST213/222 per year in the geographic region studied. Our research shows that these STs are spreading within the U.S., yet most of the cases occurred in four states: Michigan, New York, Minnesota, and Ohio. Additionally, we found little genetic diversity within and between these STs nor could specific genetic features explain their geographic spread.

Chemoproteogenomic stratification of the missense variant cysteinome

Cancer genomes are rife with genetic variants; one key outcome of this variation is widespread gain-of-cysteine mutations. These acquired cysteines can be both driver mutations and sites targeted by precision therapies. However, despite their ubiquity, nearly all acquired cysteines remain unidentified via chemoproteomics; identification is a critical step to enable functional analysis, including assessment of potential druggability and susceptibility to oxidation. Here, we pair cysteine chemoproteomics—a technique that enables proteome-wide pinpointing of functional, redox sensitive, and potentially druggable residues—with genomics to reveal the hidden landscape of cysteine genetic variation. Our chemoproteogenomics platform integrates chemoproteomic, whole exome, and RNA-seq data, with a customized two-stage false discovery rate (FDR) error controlled proteomic search, which is further enhanced with a user-friendly FragPipe interface. Chemoproteogenomics analysis reveals that cysteine acquisition is a ubiquitous feature of both healthy and cancer genomes that is further elevated in the context of decreased DNA repair. Reference cysteines proximal to missense variants are also found to be pervasive, supporting heretofore untapped opportunities for variant-specific chemical probe development campaigns. As chemoproteogenomics is further distinguished by sample-matched combinatorial variant databases and is compatible with redox proteomics and small molecule screening, we expect widespread utility in guiding proteoform-specific biology and therapeutic discovery.

Comparative and Phylogenetic Analysis of Anthurium andraeanum Hybridization Based on Molecular and Morphological Traits

Hybridization is considered an important mode of species evolution, but the genetic evolutionary process of Anthurium andraeanum hybridization is still poorly characterized. In order to provide the molecular and morphological basis for phylogenetic analysis in A. andraeanum hybridization, we analyzed the morphological, nuclear genomic, and chloroplast genomic data of five A. andraeanum cultivars and explored the correlations between different traits and nuclear and chloroplast genome characteristics. A. andraeanum hybrid 1 is an A. andraeanum ‘Baron’ (♀) × A. andraeanum ‘Spice’ (♂) cross, and A. andraeanum hybrid 2 is an A. andraeanum ‘Cheers’ (♀) × A. andraeanum hybrid 1 (♂) cross. The A. andraeanum hybrids reflected their parents’ heterozygous features in their morphologies, nuclear genomes, and chloroplast genomes. The morphological traits in the F1 generation were widely separated, showing continuous variation. Based on cluster analysis, the five A. andraeanum cultivars could be divided into two groups. The ISSR analysis results were highly correlated with the spathe color. Among the five A. andraeanum cultivars, the composition and structure features of chloroplast genomes were completely the same or highly similar, respectively. Phylogenetic analysis based on complete chloroplast genome data showed that the genetic stability of the chloroplast is high in A. andraeanum, manifested as uniparental maternal inheritance, where the chloroplast genome composition and structural features of hybrids are highly similar to those of the maternal parent.

Characterization and phylogenetic analysis of the chloroplast genome of Diospyros aff. oleifera

The Diospyros genus (Ebenaceae) has significant economic value. During field surveys, we discovered a Diospyros specimen showing morphological overlap with both D. oleifera and D. kaki var. silvestris, provisionally named Diospyros aff. oleifera. To resolve its taxonomy, we sequenced and analyzed its chloroplast genome. The complete chloroplast genome is 157,732 bp with a quadripartite structure. mVISTA analysis revealed unique sequence variations compared to related species. Phylogenetic analysis using 75 protein-coding genes grouped it with D. oleifera, indicating their close relationship. Our findings suggest this specimen likely represents a novel, undescribed species. This study provides insights into Diospyros diversity and a foundation for future research.

Characterization of the viral genome of Omicron variants of SARS-CoV-2 circulating in Tripura, a remote frontier state in Northeastern India.

From 2020, with advent of COVID-19 pandemic, Tripura has experienced SARS-CoV-2 viral evolution in accordance with other parts of India. Since January 2022, the Omicron variant of SARS-CoV-2 virus became the predominant lineage circulating in India and neighboring countries. This study characterizes the viral genome of the omicron variant circulating in the state since its inception to June, 2023. The current study was performed on nasopharyngeal and oropharyngeal samples received from the various departments of AGMC, as well as eight district hospitals from Tripura. The positive samples with a cycle threshold value of 25 or less for the E and/or N gene were considered for whole genome sequencing using Illumina Miseq NGS platform. Majority of the sequences belonged to Clade 21L, with BA.5.2 being the major sub variant detected during the study period. Majority of the mutations were detected in the Spike protein region, including L24-, P25-, P26-, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, S477N, T478K, Q498R, Y505H, Q954H and N969K. All the sequences uniquely showed the mutations A27S and G142D in N terminal domain in Spike protein, not being reported from other Indian sequences like BA.5 variants. T9I, A63T and P13L were major substitutions in E, M and N protein regions respectively. Escape of mutants from vaccine induced immunity was mostly observed in BA.2 sub variants, majority endowed with the triplet mutation of K417N + E484K + N501Y. The current study indicates that Omicron variants circulating in the state of Tripura is comparable to other regions of India and the neighbouring country of Bangladesh. Genetic mutations increasing viral transmissibility have been identified in the circulating viral genomes.

Microbial community dynamics in blood, faeces and oral secretions of neotropical bats in Casanare, Colombia

Bats are known reservoirs for a wide range of pathogenic microorganisms, including viruses, bacteria, fungi, helminths, and protozoa, which can be transmitted and infect other zoonotic organisms. Various studies have utilised next-generation sequencing (NGS) to describe the pathogens associated with bats. Although most have characterised microbial communities in specific body fluids, few have analysed the composition and diversity of these microbial communities across different body fluids at the individual level. In this study, we employed two next-generation sequencing techniques: amplicon-based sequencing of the V4 hypervariable region of the 16S- and 18S-rRNA genes and viral metagenomics, to describe the prokaryotic, eukaryotic, and viral communities present in blood, faeces, and oral swab samples collected from two genera of bats (Carollia and Phyllostomus) in the department of Casanare, eastern Colombia. A total of 60 samples corresponding to the three bodily fluids were processed and analysed. The results indicated that the microbial communities across the body fluids were mainly composed of bacteria, fungi, protozoa, and various DNA and RNA viruses, showing a variability of microbial genera and species. The abundances, diversity metrics, and correlations of these microorganisms displayed patterns associated with bat genus and body fluids, suggesting that the ecological characteristics of these microbial communities may be influenced by the ecological and physiological traits of the bats. Additionally, we found similar community compositions of bacteria, some fungal genera, and viruses in the three body fluids, indicating a possible circulation of these microbes within the same bat. This could be due to microbial movement from the gut microbiota to other physiological systems or transmission via blood-feeding vectors. Furthermore, our results revealed the presence of various microbes of public health concern, including Bartonella spp., Mannheimia haemolytica, Rhodotorula spp., Piroplasmida spp., Toxoplasma gondii, Alphacoronavirus spp., and Bat circovirus. The abundance of these pathogenic microbial species across the three bodily fluids suggests potential transmission routes from bats to other organisms, which may contribute to the emergence of zoonotic disease outbreaks. These findings highlight the variability of microorganisms present within the same bat and the different pathogen-host interactions that may regulate the presence and transmission of these zoonotic microbes. Further research is required to elucidate the genomic features, ecological interactions, and biological activities of these microbial communities in bats.

Characterization of four Acidovorax phages and their potential in phage biocontrol for lamb's lettuce seed decontamination.

Bacterial black spot, caused by Acidovorax valerianellae, is responsible for significant yield losses in lamb's lettuce (Valerianella locusta) in many producing countries, especially Europe. Currently, no resistant varieties of V. locusta are available that effectively control the disease under field conditions. Bacteriophage-based biocontrol has been suggested as a sustainable and natural alternative strategy to combat bacterial pathogens. In this study, novel phages infecting A. valerianellae and Acidovorax cattleyae, Alfacinha1, Alfacinha3, Acica, and Aval, were isolated and characterized. Based on comparative genomics, these phages represent three new phage genera. Aval and Acica phages revealed genomic features characteristic of temperate lifestyle, encoding toxins likely associated with lysogenic conversion, which contrasts with Alfacinha1 and Alfacinha3. The latter was selected for application as a biocontrol agent during seed steeping. This phage reaches an 87% reduction in the A. valerianellae concentration on artificially infested seeds. Importantly, this reduction results in an increased germination rate from 58.9% to 93.3%. Moreover, the infected seedlings had a dramatic reduction in vigor index after 22 days of growth, whereas the phage-treated ones had a vigor index similar to the negative control, reinforcing the ability of bacteriophages to effectively reduce disease progression. We further evaluated the impact of lipopolysaccharides in phage suspensions on the development of seedlings. Here, we demonstrated that the presence of lipopolysaccharides do have an impact on seedling development, significantly reducing the number of roots developed. This study shows how genomic analyses and tailored bioassays represent an essential route to ensure safe phage application and demonstrates the potential of a phage-based biocontrol strategy against A. valerianellae.IMPORTANCEBacteria continue to globally cause serious damage to a variety of crops. One example is a bacterial black spot of lamb's lettuce caused by Acidovorax valerianellae. It has spread across Europe, resulting in economic losses of at least 10% in tonnage annually. Faced with the inefficiency of conventional control methods, an alternative and sustainable strategy based on the use of bacteriophages was pursued in this study. We present for the first time the isolation and characterization of A. valerianellae-specific phages. Moreover, we assessed their biocontrol potential in seed decontamination since the disease primarily spreads from seeds to seedlings. Interestingly, seed treatment with one of our phages reaches an 87% reduction in bacterial concentration. More importantly, this reduction results in an increased germination rate from 58.9% to 93.3%. Finally, our study demonstrated for the first time the need for removing endotoxins from phage suspensions as they impact plant development when used as a biocontrol agent.

Sodalis praecaptivus subsp. spalangiae subsp. nov., a nascent bacterial endosymbiont isolated from the parasitoid wasp, Spalangia cameroni.

An endosymbiotic bacterium of the genus Sodalis, designated as strain HZT, was cultured from the parasitoid wasp Spalangia cameroni, which develops on the pupae of various host flies. The bacterium was detected in S. cameroni developed on houseflies, Musca domestica, in a poultry facility in Hazon, northern Israel. After culturing, this bacterium displayed no surface motility on Luria-Bertani agar and was rod-shaped and irregular in size, ~10-30 nm in diameter and 5-20 µm in length. Phylogenetic analyses revealed that strain HZT is closely related to Sodalis praecaptivus strain HST, a free-living species of the genus Sodalis that includes many insect endosymbionts. Although these bacteria maintain >98% sequence identity in shared genes, genomic characterization revealed that strain HZT has undergone substantial reductive evolution, such that it lacks many gene functions that are maintained in S. praecaptivus strain HST. Based on the results of phylogenetic, genomic and chemotaxonomic analyses, we propose that this endosymbiont should be classified in a new subspecies as S. praecaptivus subsp. spalangiae subsp. nov. The type strain for this new subspecies is HZT (=ATCC TSD-398T=NCIMB 15482T). The subspecies Sodalis praecaptivus subsp. praecaptivus strain HST is created automatically with the type strain ATCC BAA-2554T (=DSMZ 27494T).

Contrast and Genomic Characterisation of Ancient and Recent Interspecific Introgression Between Deeply Diverged Moustache Toads (Leptobrachium).

Recent genomic analyses have provided new insights into the process of interspecific introgression and its consequences on species evolution. Most recent studies, however, focused on hybridization between recently radiated species, with few examining the genomic outcomes of ancient hybridization across deeply diverged species. Using whole genome data of moustache toads (Leptobrachium), we identified signals of three hybridization events among nine species that diverged at the Eocene. An ancient introgression from L. leishanense to the ancestral branch (C1) of L. liui introduced adaptive variants. The highly introgressed regions include genes with important functions in odorant detection and immune responses. These genes are preserved in all three descendent populations of L. liui_C1, and these regions likely have been positively selected over a long filtering process. A recent introgression occurred from L. huashen to L. tengchongense, with the introgressed regions being mostly neutral. Furthermore, one F1 hybrid individual was detected between sympatric L. ailaonicum and L. promustache. The signals of introgression largely disappeared after removing the hybrid individual, indicating an occasional hybridization but minimal introgression. Further examination of highly divergent but low introgressed genomic regions revealed both pre-mating isolation and genetic incompatibility as potential mechanisms of resisting introgression and maintaining species boundaries. Additionally, no large X-effect was found in these introgression events. Hybridization between deeply diverged amphibian species may be common, but detectable introgressions are likely less so, with recent introgression being mostly neutral and the rare ancient one potentially adaptive. Our findings complement recent genomic work, and together they provide a better understanding of the genomic characteristics of interspecific introgression and its significance in species adaptation and evolution.

The association between drugs and vaccines commonly prescribed to older people and bullous pemphigoid: a case-control study.

Bullous pemphigoid (BP) is an autoimmune skin disease that affects mainly older people. Numerous drugs have been previously associated with BP based on case series and small hospital-based studies. More reliable and precise estimates of associations between a broad selection of drugs/vaccines and BP will enable greater awareness of potential increased risk of BP following certain medicines and help identify clinical, histological and genomic characteristics of drug-induced BP for different types of culprit drugs. Greater awareness could lead to earlier recognition or suspicion of BP and referral to a dermatologist for diagnosis. Earlier diagnosis may lead to less aggressive treatment and improved well-being. To determine the association between drugs/vaccines commonly prescribed to older people and BP risk. We conducted a population-based nested case-control study between 1998-2021 using electronic primary care records from the Clinical Practice Research Datalink. We matched BP cases with up to 5 controls. Exposures were drugs/vaccines commonly prescribed to older people. We used multivariable conditional logistic regression adjusting for multiple drug use. For antibiotics, we considered prescriptions may be prescribed for undiagnosed symptoms of BP which resemble skin infection (protopathic bias) in a sensitivity analysis. Antibiotics were the therapeutic group associated with the highest risk of BP (OR: 4.60; 95%CI 4.40-4.80). However, after adjusting for protopathic bias, the OR reduced to 2.08 (95%CI 1.99-2.17). After adjusting for protopathic bias, of all antibiotic classes and subclasses, penicillins and penicillinase-resistant penicillins had the strongest associations with BP risk (OR: 3.44; 95%CI 3.29-3.60; sensitivity analysis OR; 1.74; 1.66-1.84 and OR: 7.56; 95%CI 7.15-8.00; sensitivity analysis OR: 2.64; 95%CI 2.45-2.85, respectively). Other drugs strongly associated with increased risk were gliptins (OR: 2.77; 95% CI 2.37-3.23), and second-generation antipsychotics (OR: 2.58; 95%CI 2.20-3.03). Healthcare professionals need to be aware of BP risk in older people particularly when prescribing penicillinase-resistant penicillins, gliptins, and second-generation antipsychotic drugs to recognise and manage BP early. Due to the low prevalence of disease, we do not suggest avoidance of drugs/vaccines to prevent BP. Further research should consider recency, dosage, and duration of antibiotic treatments.

An integrated view of the structure and function of the human 4D nucleome.

The dynamic three-dimensional (3D) organization of the human genome (the "4D Nucleome") is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales. The data reveal a rich complexity of chromatin domains and their sub-nuclear positions, and over one hundred thousand structural loops and promoter-enhancer interactions. We developed 3D models of population-based and individual cell-to-cell variation in genome structure, establishing connections between chromosome folding, nuclear organization, chromatin looping, gene transcription, and DNA replication. We demonstrate the use of computational methods to predict genome folding from DNA sequence, uncovering potential effects of genetic variants on genome structure and function. Together, this comprehensive analysis contributes insights into human genome organization and enhances our understanding of connections between the regulation of genome function and 3D genome organization in general.

Adjuvant Modified FOLFIRINOX for Resected Pancreatic Adenocarcinoma (PDAC): Clinical Insights and Genomic Features from a Large Contemporary Cohort.

Adjuvant mFOLFIRINOX (mFFX) is standard of care for fit individuals with resected pancreatic ductal adenocarcinoma (PDAC). There are limited data on adjuvant mFFX outcomes outside clinical trials. Institutional databases queried to identify patients with resected PDAC who received ≥1 dose adjuvant mFFX. Primary endpoints: recurrence free survival (RFS), overall survival (OS). Secondary endpoints: clinical factors, genomic features associated with outcomes. RFS and OS were estimated with Kaplan-Meier. Cox proportional hazards regression model was used to associate clinico-genomic features correlated with survival outcomes. N = 147 identified between 01/2015-01/2023. Median age: 67 years; N = 57 (39%) >70 years. Unfavorable prognostic features: N = 52 (36%) N2 nodal status, N = 115 (78%) lymphovascular invasion), and N = 133 (90%) perineural invasion. Median time from surgery to start mFFX: 1.78 months (m) (IQR 1.45, 2.12). N = 124 (84%) completed 12 doses; N = 98 (67%) stopped oxaliplatin early for neuropathy (median 10 doses; range 4-12). Further dosing characteristics are summarized in Supplementary Table 3. With median follow up of 35.1 m, median RFS (mRFS) 26 m (95% CI 19, 39) and median OS (mOS) not reached. For >70 cohort, mRFS 23 m (95% CI 14, NR) and mOS 51 m (95% CI 37, NR). mFFX started <8 weeks from resection associated with improved RFS (HR 0.62; 95% CI 0.41, 0.96; p = .033) and OS (HR 0.53; 95% CI 0.3, 0.94; p = .030). KRAS mutation and whole genome doubling trended to shorter RFS and OS. Homologous recombination deficiency status did not confer improved survival outcomes. Adjuvant mFFX is effective and tolerable in resected PDAC in a non-trial setting, including for patients >70 years.

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

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

Bla SED-1 beta-lactamase-producing Citrobacter sedlakii isolated from horses and genomic comparison with human-derived isolates.

We aim to detect beta-lactamase-producing Citrobacter sedlakii from horses and compare the genomic characteristics with isolates from humans.Methods and Result: We characterized phenotypically and genotypically nine C. sedlakii isolates from the feces of horses and then compared them to human-derived isolates using whole genome sequencing and phylogenomic methods. Seven isolates (7/9) were ampicillin-resistant, while at least one isolate was resistant to ceftriaxone, gentamicin, meropenem, and streptomycin. All nine isolates were carriers of the chromosomal-mediated blaSED-1 beta-lactamase gene which confer resistance to ampicillin. One isolate was positive for the mcr-9 gene that confers resistance to colistin, and another isolate had the aac(6')-lid gene that confers resistance to aminoglycosides. Seven isolates (7/9) were carriers of genes that confer metal resistance to copper, silver, and arsenic. Phylogenetically, two horse-derived isolates clustered together with two human-derived isolates from the NDARO database. The results from our study provide insight into the antimicrobial susceptibility of C. sedlakii in horses which was previously lacking, and the specific beta-lactamase gene mediating resistance.

Integrating single cell and bulk RNA sequencing data identifies RBM17 as a novel response biomarker for immunotherapy in bladder cancer.

Checkpoint inhibitors (CPIs) have been widely applied in the treatment of patients with bladder cancer (BLCA). However, there is still unmet need to dissect response predict biomarkers. To uncover CPI response-related marker genes in cancer cells, we utilized SCISSOR, integrating single-cell RNA and bulk RNA sequencing data. Transcriptomic and clinical data from IMvigor210, UNC-108, and BCAN/HCRN datasets were collected to evaluate and validate the identified biomarkers and signatures. Additionally, we analyzed TCGA-BLCA and local-BLCA RNA-seq data to investigate alternative splicing events (ASEs). Cell viability was assessed in T24 and UMUC3 cells with RBM17 upregulation or downregulation. Through SCISSOR analysis, we discovered that the expression levels of RBM17, TAP1, and PSMB8 were significantly associated with CPI response. Since PSMB8 displayed a highly positive correlation with TAP1, we developed a CPI response score (CRS) signature based on the expression profiles of RBM17 and TAP1. The CRS demonstrated robust predictive capacity in IMvigor210, UNC-108, and BCAN/HCRN datasets and was associated with higher tumor mutational burden (TMB), PD-L1 expression, and unique genomic features. Notably, RBM17 was not linked to the clinical outcomes of BLCA patients but positively correlated with BLCA cell proliferation in vitro. In the meantime, RBM17 was correlated with higher activity in core biological pathways, including antigen processing machinery, CD8 + T effector cells, cell cycle, DNA damage repair, epithelial-mesenchymal transition, histone regulation, and immune checkpoints. Moreover, the high-RBM17 group showed enrichment of LumU/Ba/sq subtypes but fewer FGFR3 alterations. Lastly, RBM17 significantly upregulated ASEs in BLCA samples, leading to higher neoantigen levels, a more inflamed tumor microenvironment, and improved CPI response. RBM17 is associated with higher ASEs and neoantigen levels, thereby potentiating the efficacy of CPI in BLCA. The established predictive signature, utilizing only two genes, has the potential to streamline clinical applications, providing a cost-effective alternative to expensive genomic, transcriptomic, and biological feature tests.