Whole Genome Sequencing Research Articles

5-hydroxymethylcytosine as a liquid biopsy biomarker in colorectal cancer.

291 Background: 5-hydroxymethylcytosine (5hmC) is an epigenetic modification which regulates gene expression and is associated with active transcription. The optimization of 5hmC sequencing in cell-free DNA (cfDNA) could therefore enable assessment of gene activity through a liquid biopsy. We aimed to investigate the 5hmC landscape of colorectal cancer (CRC) in plasma-derived cfDNA to evaluate the potential of 5hmC modifications as a liquid biopsy-based biomarker of CRC. Methods: Genome-wide 5hmC modifications were analyzed with a low-input whole-genome 5hmC sequencing method based on selective chemical labeling in cfDNA from 72 CRC patients and 70 healthy samples. Differential 5hmC analysis between CRC and healthy samples was conducted using DESeq2 (padj < 0.05 and log2FC <= -1 and >=1). Low-pass whole genome sequencing (LP-WGS) was performed on all cfDNA samples. Tumor fraction was estimated using ichorCNA to classify samples into high ct-fraction (>=0.1) and low ct-fraction (<0.1) groups. Nucleosome profiling was performed on LP-WGS to reveal chromatin accessibility patterns. Elastic Net Regression (ENR) was applied to identify changes in 5hmC levels for classifying samples as cancerous or healthy. Results: Differential cfDNA 5hmC levels of 139 genes distinguished high ct-fraction CRC (n=16) and healthy samples (n=70). Although the remaining CRC samples (n=56) had similar ct-fractions as the healthy samples, as estimated by ichorCNA, we found a differentially hydroxymethylated gene signature could discriminate between these low ct-fraction CRC and healthy samples. Nucleosome profiling analysis with LP-WGS in cfDNA was used to identify active transcriptional drivers of the genes with increased 5hmC levels. The analysis revealed increased chromatin accessibility near the binding sites for the transcription factor caudal-related homeobox transcription factor 2 ( CDX2 ), a master transcriptional regulator of intestinal cell fate and cancer, in CRC patients relative to healthy samples. Corroborating this, CDX2 and its downstream targets had increased 5hmC levels in cfDNA in CRC relative to healthy samples, consistent with colorectal-derived tumor DNA in CRC plasma samples. Conclusions: Genes with differential 5hmC levels in cfDNA can discriminate CRC and healthy samples. Our 5hmC signature identified CRC samples that did not harbor copy number gains or losses; which is typically used to estimate ct-fraction and routinely included in targeted ctDNA sequencing assays. Integration of 5hmC and LP-WGS can be used to identify gene activation in disease. In the context of CRC, CDX2 displayed increased chromosome accessibility in the promoters of its target genes which in turn displayed increased 5hmC levels. Further studies are aimed at optimizing and validating 5hmC-based biomarkers throughout patient treatment.

Advancing molecular diagnostics of myotonic dystrophy type 1 using short-read whole genome sequencing.

Myotonic dystrophy type 1 (DM1) is a serious multisystem disorder caused by GCA repeat expansions in the DMPK gene. Early and accurate diagnosis, often requiring reliable DNA-diagnostic techniques, is critical for preventing life-threatening cardiac complications. Clinically, two main diagnostic challenges exist. Firstly, because of overlapping symptomatology with other conditions, conventional DNA-testing methods focusing on DM1 expansion detection ensure diagnostic results only in a small subset of patients, and frequently, further DNA-testing in remaining cases is necessary. Secondly, because of variable symptomatology and age of onset, not all DM1 patients are referred for DM1 genetic testing, leading to unrecognized but at-risk cases. When using conventional methods, the main technical problems are expanded-allele sizing and sensitivity to the presence of sequence interruptions. On a set of 50 individual genomes, including ten DM1 patients, we tested the performance of short-read whole-genome sequencing (WGS), one of the most up-to-date molecular testing methods. We identified all expansion-range DM1 alleles and characterized sequence interruptions in seven expansion-range/premutation-range alleles. Although neither the tested conventional methods, nor WGS allowed expanded-allele sizing, conventional methods provided higher sizing limits for normal-range alleles. Genotyping concordance rate was found to be 95-99%. WGS was found to be superior in elucidating the sequence structure of the motifs, even if they fall outside the sizing limit (from partial reads). In addition, WGS enables the identification of genetic modifiers in other genes and the detection of alternative diagnoses in DM1-negative patients by extension of the bioinformatic evaluation of the generated data.

Whole genome sequencing characterization and comparative genome analysis of Acinetobacter baumannii JJAB01: A comprehensive insights on antimicrobial resistance and virulence genotype.

The emergence of antibiotic resistance has significantly elevated the threat posed by Acinetobacter baumannii as an opportunistic pathogen. A.baumannii, a notorious bacterium, poses a serious threat to health care, leading to severe nosocomial infections, particularly in immunocompromised individuals. Whole-Genome Sequencing studies are efficient in providing accurate genetic information, aiding in detecting outbreaks, surveillance of resistance, and controlling infection transmission. In this study, we investigated the whole genome of a clinical isolate A. baumannii JJAB01 which sourced from a urine sample of an Intensive Care Unit (ICU) patient. This strain showed resistance to 24 available antibiotics, signifying Extremely Drug Resistant (XDR) and high potential for pathogenicity. Whole Genome Sequencing was performed using Illumina, and the raw reads were evaluated using the FastQC tool. Genome assembly and annotation were performed with Unicycler and the RAST server. The JJAB01 genome is 4.07Mb with a GC content of 38.9%. A total of 51 and 31 virulence factors and antimicrobial-resistant (AMR) genes were predicted using the VFDB and CARD databases. Comparative genome studies were carried out on virulence factors, resistance genes, prophages, and Multi-Locus Sequence Typing (MLST) across twelve closely related A. baumannii genomes, including JJAB01, X4-584, X4-705, 2023CK-00423, 2023CK-00890, 2023CK-00127, 2022CK-00066, B20AB01, B20AB10, F20AB03, G20AB08, and X4-65. These computational investigations in this study emphasis the multidimensional nature of the ICU strain JJAB01 and its genetic similarity to other strains, thereby enhancing our understanding of drug resistance and the pathogenicity associated with A. baumannii infections.

LD-informed deep learning for Alzheimer's gene loci detection using WGS data.

The exponential growth of genomic datasets necessitates advanced analytical tools to effectively identify genetic loci from large-scale high throughput sequencing data. This study presents Deep-Block, a multi-stage deep learning framework that incorporates biological knowledge into its AI architecture to identify genetic regions as significantly associated with Alzheimer's disease (AD). The framework employs a three-stage approach: (1) genome segmentation based on linkage disequilibrium (LD) patterns, (2) selection of relevant LD blocks using sparse attention mechanisms, and (3) application of TabNet and Random Forest algorithms to quantify single nucleotide polymorphism (SNP) feature importance, thereby identifying genetic factors contributing to AD risk. The Deep-Block was applied to a large-scale whole genome sequencing (WGS) dataset from the Alzheimer's Disease Sequencing Project (ADSP), comprising 7416 non-Hispanic white (NHW) participants (3150 cognitively normal older adults (CN), 4266 AD). 30,218 LD blocks were identified and then ranked based on their relevance with Alzheimer's disease. Subsequently, the Deep-Block identified novel SNPs within the top 1500 LD blocks and confirmed previously known variants, including APOE rs429358 and rs769449. Expression Quantitative Trait Loci (eQTL) analysis across 13 brain regions provided functional evidence for the identified variants. The results were cross-validated against established AD-associated loci from the European Alzheimer's and Dementia Biobank (EADB) and the GWAS catalog. The Deep-Block framework effectively processes large-scale high throughput sequencing data while preserving SNP interactions during dimensionality reduction, minimizing bias and information loss. The framework's findings are supported by tissue-specific eQTL evidence across brain regions, indicating the functional relevance of the identified variants. Additionally, the Deep-Block approach has identified both known and novel genetic variants, enhancing our understanding of the genetic architecture and demonstrating its potential for application in large-scale sequencing studies. Growing genomic datasets require advanced tools to identify genetic loci in sequencing.Deep-Block, a novel AI framework, was used to process large-scale ADSP WGS data.Deep-Block identified both known and novel AD-associated genetic loci.rs429358 (APOE) was key; rs11556505 (TOMM40), rs34342646 (NECTIN2) were significant.The AI framework uses biological knowledge to enhance detection of Alzheimer's loci.

Imported seafood is a reservoir of Enterobacteriaceae carrying CTX-M-encoding genes of high clinical relevance.

We determined the frequency, genotypes, phenotypes, and mobility of extended-spectrum β-lactamase (ESBL)-encoding genes in Enterobacteriaceae isolated from retail seafood products. Overall, 288 samples of fresh shrimps, catfish and seabass imported from Asia were collected from three supermarket chains in the UK (96 each). After enrichment in MacConkey broth supplemented with cefotaxime, total DNA was screened for the presence of CTX-M, SHV and TEM by real-time PCR. Positive samples were cultured on ESBL selective media and presumptive ESBL-producing isolates were confirmed by PCR and identified to the species level by MALDI-TOF-MS. CTX-M-positive isolates were further characterized by whole genome sequencing (WGS), antimicrobial susceptibility testing, and conjugation experiments. Approximately one in thirteen (7.6%) seafood products were contaminated with ESBL-producing Enterobacteriaceae. WGS analysis revealed the presence of CTX-M-15 (n=7), CTX-M-27 (n=7), and CTX-M-55 (n=7), CTX-M-14 (n=4) among Enterobacteriaceae isolated from shrimp (n=21) and catfish (n=4), and FONA-6 in two Serratia fonticola isolates from seabass. The higher rate of contamination in shrimp could be due to post-harvest contamination due to human handling or washing practices during processing. Half (n=13) of the CTX-M-producing isolates transferred blaCTX-M to laboratory E. coli via IncA/C (n=6), IncX2 (n=4), IncFIIK (n=1) or non-typeable plasmids (n=2). All plasmids contained additional resistance genes conferring resistance to antimicrobials used in aquaculture, indicating possible co-selection through the use these antimicrobials. The frequent occurrence of CTX-M-encoding genes of high clinical relevance in imported seafood, particularly shrimp, often on transferrable plasmids, underscores the need for ESBL surveillance on traded seafood, alongside quantitative risk assessment studies aimed at evaluating the potential health risks for consumers who are exposed to these bacteria via consumption of raw seafood.

Monitoring sewage and effluent water is an effective approach for the detection of the mobile colistin resistance genes (mcr) and associated bacterial hosts in the human population and environment in the USA.

Colistin, a last-resort antibiotic, is reserved for treating recalcitrant infections. Colistin has not been approved for agricultural use in the USA. Therefore, it has been suggested that the occurrence and spread of the mobile colistin resistance genes (mcr) were relatively limited in the USA. To evaluate the latter suggestion, we investigated the occurrence of mcr-positive Gram-negative bacterial isolates in sewage (a representative of the fecal microbial community of a human population) and environment (effluent and surface water) in Georgia, USA. Raw sewage and water samples were collected from major wastewater treatment plants and an associated water reservoir. The samples were screened on the selective chromogenic Rapid'E.coli2 agar supplemented with colistin. Colonies were investigated for mcr using gene-specific PCR analyses. The Kirby-Bauer disk diffusion and broth micro-dilution assays were used to determine susceptibility against different antibiotics. Whole Genome Sequencing (WGS) was used to investigate the resistome, virulome, and plasmidome of the mcr-positive isolates. Biofilm assays were used to evaluate the persistence of mcr. mcr-9-positive Serratia nevei strains were isolated from sewage, while mcr-3-positive Aeromonas jandaei strains were detected in effluent and surface water samples. The isolates were multidrug-resistant, and WGS analyses highlighted the detection of additional antibiotic resistance genes. Furthermore, mcr-9 was found to be located on an IncHI2 plasmid, while mcr-3 was on the chromosome. Also, mcr-9 persisted in 12-day old biofilms. Sewage analyses suggested that the plasmid-borne mcr-9 was potentially circulating in the human population, while the detection of mcr in effluent and surface waters highlighted a potential for environmental dissemination.

Clostridioides difficile hypervirulent strain ST1 isolated from clinical stool specimens obtained from three Provinces in South Africa

Clostridioides difficile infection is a serious healthcare-associated infection linked to antimicrobial use. The severity of the disease can be associated with hypervirulent ribotypes such as RT027. The study aimed to investigate the molecular epidemiology and genomic characteristics of C. difficile isolates from private and public healthcare settings in South Africa. One hundred clinical stool specimens were cultured on cycloserine-cefoxitin-fructose agar. Conventional multiplex polymerase chain reaction (M-PCR) assays were conducted for isolate identification and detection of toxin genes. Genomic characteristics of the isolates were determined using whole genome sequencing (WGS) and data was analysed using pubMLST, EnteroBase, Pathogenwatch and CARD. One hundred clinically presumptive C. difficile positive stool specimens were collected, of which 62% (62/100) were confirmed as C. difficile by M-PCR assay. Among the 62 identified C. difficile isolates, 97% (60/62) were toxigenic, with the most dominant toxin profile being A+B+CDT+according to the M-PCR assay. The results showed that 93% (40/43) of the WGS analysed C. difficile strains clustered into clades 1 to 5. These 40 strains were categorized into 16 sequence types (STs), with ST1 (clade 2) being the most prevalent, representing 45% (18/40), this strain is an RT027-associated strain previously epidemic hypervirulent strain. One major cluster (n=18) comprising ST1 strains was identified in Gauteng Province and all the isolates associated with this cluster showed the same resistome (antimicrobial resistance genes and mutations: CDD-1, aac (6')-Ie-aph (2″)-Ia, PnimBG and Thr82Ile). The study also identified one strain as ST11, this strain is well known for its zoonotic potential, and two strains were identified as ST37 known as an epidemic strain. Strains from public healthcare settings exhibited genetic similarity, while those from private settings showed greater genetic diversity. The study reported, for the first time, hypervirulent strains ST1 in Africa and ST11 in South Africa, with a minimum spanning tree indicating an ongoing ST1 outbreak.

Troponin C is required for copulation and ovulation in Nilaparvata lugens.

Troponin C (TnC) is a calcium-binding subunit of the troponin complex that regulates muscle contraction in animals. However, the physiological roles of TnC, especially in insect development and reproduction, remain largely unknown. We identified seven TnC genes encoding four EF-hand motif protein in the rice pest, the brown planthopper Nilaparvata lugens. This species has emerged as an ideal model insect to study gene functions because of the availability of its complete genome sequence and of the susceptibility to RNA interference (RNAi). RT-qPCR combined with in situ hybridization showed that TnCⅠ was highly expressed in the bursa copulatrix of ovaries. RNAi-mediated knockdown of TnCⅠ in 2nd- to 5th-instar nymphs generated significantly lethal deficits, and also led to copulation and ovulation failure in adult females, although males displayed appropriate mating behavior. These new findings provide insights into understanding the physiological functions of TnCⅠ in the survival of, and female reproductive success, in N. lugens. Thus, this gene could be used as a target to explore methods for pest control of this important species.

Personalized oncogenomic analysis of metastatic squamous cell carcinoma of the anus: Utilizing whole-genome sequencing to guide clinical decision-making.

11 Background: Metastatic squamous cell carcinoma of the anus (SCCA) is associated with significant morbidity and mortality. Due to its relative rarity, there is limited evidence to support systemic therapy regimens informed by genomic data. This study aims to utilize whole-genome and transcriptome sequencing to enhance the understanding of the genetic alterations driving metastatic SCCA and to identify potentially actionable therapeutic targets. Methods: This report examines nine cases of metastatic SCCA in patients enrolled in the Personalized Oncogenomics (POG) Program at the BC Cancer Agency. Comprehensive genomic profiling, including whole-genome and transcriptome analysis (WGTA) was conducted on fresh tumor biopsy or formalin fixed paraffin embedded (FFPE) tissue. Tumor genomic alterations were analyzed in detail including: SNVs, indels, copy number alterations, structural variants, mutation signatures, viral presence, tumor mutation burden (TMB), expression outliers, and immune cell scores. The somatic alterations were integrated with existing knowledge of drug-target interactions to identify actionable therapeutic targets. Results: Of the nine patients, eight were found to be HPV-positive, with one exhibiting high tumor mutational burden (TMB>10mut/Mb). Mutation signatures included seven cases with AID/APOBEC signatures (commonly seen with HPV), and one case with an ID2 DNA replication slippage signature. The PI3K/AKT/mTOR pathway was the most commonly affected signaling pathway (n=4), followed by FGFR amplification and overexpression (n=3), and RAS/RAF alterations ( BRAF mutation and KRAS overexpression, n=2). EGFR amplification was identified in two cases, one of which also exhibited EGFR overexpression. Additionally, FBXW7 mutations were present in two cases. Immunotherapy was recommended for all nine patients: eight based on HPV positivity, either alone or in combination with other alterations, such as high TMB, SWI/SNF complex alterations, and presence of immune infiltrating cells, and the remaining case based on a SWI/SNF complex mutation. Only two patients ultimately received immunotherapy, both of whom derived clinical benefit. One patient, treated with atezolizumab as part of the phase II CAPTIV-8 trial (NCT04273061), demonstrated progression-free survival (PFS) of 10 months (ongoing), while the other, treated with nivolumab, achieved a PFS of 6 months. Conclusions: Genomic analysis using WGTA supported the recommendation of immunotherapy for all patients in this cohort. Although only two patients received immunotherapy, both experienced clinical benefit, underscoring the potential of personalized genomic-guided treatment in metastatic SCCA.

Identifying the optimal post-surgical timing of molecular residual disease (MRD) detection in colorectal cancer (CRC) using an ultra-sensitive assay: Interim results from the VICTORI study.

275 Background: While detection of MRD using ctDNA is prognostic for recurrence in CRC, some patients still recur prior to MRD detection. VICTORI is prospectively investigating NeXT Personal, an ultra-sensitive NGS-based MRD assay, to profile patients with resected CRC. Methods: Patients with CRC treated with curative intent (all stages) are tested for MRD using NeXT Personal, a bespoke assay with up to ~1,800 tumor-informed single nucleotide variants (SNVs) identified from whole-genome sequencing. Plasma is collected prior to surgery, every 2 weeks post-surgery up to week 8 (MRD landmark window), and every 3 months for up to 3 years (surveillance). We present preliminary results on 397 samples from the first 62 patients. Results: A total of 62 patients (N=36 rectal [58%], N=26 colon [42%]; N=46 stage I-III [74%], N=16 stage IV [26%]) were included in our analysis. Baseline pre-surgical sensitivity (treatment naive) was 93.5% [N=29/31]. Pre-surgical positivity rate in patients who had received neoadjuvant therapy and had residual cancer at the time of surgery was 67% [N=16/24]. 60 patients were evaluable for clinical outcomes. At a median follow-up of 355 days, 15 patients (25%) had a recurrence. Of these, all patients were ctDNA-positive prior to recurrence (100%, 14/14; 1 pt excluded due to lack of samples prior to recurrence). ctDNA detection preceded clinical relapse by a median of 194 days [range: 5-397]); ctDNA for 78.6% (N=11/14) were first detected in the MRD landmark window. All landmark-positive recurrences occurred within one year of surgery. The 14 recurrent cancers with samples were first detected at a median ctDNA concentration of 28.7 parts per million (PPM) (range 2.4-111,120), with 64.3% (9/14) of those detections in the ultra-low range of <100 PPM. MRD detection at week 4 and week 8 had the greatest reduction in RFS (HR 12.86 [2.74-60.28], p=0.0012 week 4; HR 16.14 [3.52-74.09], p=0.0004 week 8), with weeks 4, 6 and 8 having similar higher prevalence of ctDNA detection (36.0% [18/50], 35.3% [18/51], 38.5% [20/52] respectively). Week 2 detection rate was 17.0% (8/46). cfDNA concentration was highest at week 2 (4.63ng/ml vs. 2.22 at baseline, p=0.00028) and 4 (3.68 vs. 2.22, p=0.0081), returning to baseline levels at week 6 (2.28 vs. 2.22, p=0.67) and 8 (2.48 vs. 2.22, p=0.64). Conclusions: In this interim report after a median ~1 year follow-up, NeXT Personal detected MRD for all patients prior to disease recurrence. Most initial MRD detection was in the ultra-sensitive range <100ppm and detection at 4-8 weeks after surgery was highly prognostic for recurrence.

Characterization of non-typhoidal Salmonella reveals the highly prevalent mcr-1-positive S. 1,4,[5],12:i:- within eggs are derived from chickens.

Salmonella is one of the most common foodborne pathogens. Antimicrobial-resistant Salmonella isolates, especially those resistant to colistin, pose a significant threat to public health worldwide. However, data about the prevalence of mcr-positive Salmonella in animals was few and the dissemination of mcr-positive Salmonella from animals to food, especially eggs, has not been fully addressed. The role of houseflies in the Salmonella transmission has also not been clarified. Here, we analyzed the prevalence and resistance characteristics of mcr-positive Salmonella in 1707 samples of animals (commercial laying hens, broilers, waterfowls and swine), eggs and flies from 23 farms in four cities of China between July 2021 and October 2022. Pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) analyses of Salmonella from different sources were further performed. Among animals, waterfowls had the highest isolation rate of Salmonella (18.1%, 35/193), followed by swine (6.1%, 23/377), laying hens (4.2%, 21/505) and broilers (1.4%, 7/489). Two of the 53 flies (3.8%) carried Salmonella. The detection rate of Salmonella in eggs from farms was 26.7%. All mcr-1-positive Salmonella isolates were S. 1,4,[5],12:i:- and were only found in hens (0.2%) and eggs (11.1%). PFGE and WGS analyses showed that the mcr-1-positive S. 1,4,[5],12:i:- from commercial laying hens and eggs in the same farm had no single nucleotide polymorphism (SNP) variation, indicating that the mcr-1-positive S. 1,4,[5],12:i:- in eggs were derived from hens. The phylogenomic analysis also showed that the mcr-1-positive S. 1,4,[5],12:i:- isolates from hens and eggs were closely related to previously reported mcr-1-positive Salmonella from human in China, further confirming that such mcr-1-positive Salmonella in animals could transmit to humans via the food chain. Furthermore, the blaCTX-M-1G-positive S. Kentucky isolates from broiler and flies in the same farm had a limited number of variations (5-7 SNPs), proving the clonal transmission of Salmonella between broilers and flies. The S. Kentucky isolates carrying blaCTX-M-1G from broilers were also closely related to the S. Kentucky isolates from chicken meats and humans. Our findings suggest that Salmonella including those carrying mcr-1 in animals could transmit to eggs/meats and potentially trigger human infections. The houseflies can play an important role in the Salmonella transmission within farms. Salmonella carrying mcr in animals and animal products should be monitored regularly and control measures are urgently needed to reduce the dissemination of such pathogens.

A comprehensive safety assessment of a novel starter Weissella confusa M1 combining with whole-genome sequencing

A comprehensive safety assessment of a novel starter Weissella confusa M1 combining with whole-genome sequencing

Benefits of HIV-1 transmission cluster surveillance: a French retrospective observational study of the molecular and epidemiological co-evolution of recent circulating recombinant forms 94 and 132.

Molecular surveillance is an important tool for detecting chains of transmission and controlling the HIV epidemic. This can also improve our knowledge of molecular and epidemiological factors for the optimization of prevention. Our objective was to illustrate this by studying the molecular and epidemiological evolution of the cluster including the new circulating recombinant form (CRF) 94_cpx of HIV-1, detected in 2017 and targeted by preventive actions in 2018. In June 2022, 32 HIV-1 sequence databases from French laboratories were screened to identify all individuals who had acquired CRF94_cpx or a similar strain, whatever the date of diagnosis. Phylogenetic analyses were performed with the sequences identified, and biological parameters were collected at the time of diagnosis and after the start of treatment to analyse the evolution of the cluster. Full genomes were sequenced to characterize the new strains. We analysed 98 HIV-1 isolates: 63 were CRF94, three were unclassifiable, and the other 32 formed a new cluster containing a new recombinant, CRF132_94B, derived from CRF94 and a subtype B strain. At least 95% of the individuals in both the CRF94 and CRF132 clusters were men who have sex with men (MSM), most of whom had acquired HIV less than 12 months before diagnosis. The number of CRF94 diagnoses declined drastically after 2018, but CRF132 strains spread widely between 2020 and 2022, into a different area of Ile-de-France region and within a younger population nevertheless aware of pre-exposure prophylaxis. Higher viraemia, lower CD4 cell counts and delayed treatment efficacy suggested that CRF94 was more virulent than CRF132, possibly due to the F subtype fragment of the vif gene. These findings highlight the role of the MSM transmission cluster in spreading HIV and new variants. They show also the benefits of cluster surveillance for improving the targeting of preventive interventions, detecting the emergence of new strains and enriching our knowledge on virulence mechanisms. However, these investigations require support with sufficient resources dedicated to a regional or national programme to be responsive and effective.

Understanding the Emergence of Schizophrenia in the Light of Human Evolution: New Perspectives in Genetics.

Schizophrenia is a frequent and disabling disease. The persistence of the disorder despite its harmful consequences represents an evolutionary paradox. Based on recent discoveries in genetics, scientists have formulated the "price-to-pay" hypothesis: schizophrenia would be intimately related to human evolution, particularly to brain development and human-specific higher cognitive functions. The objective of the present work is to question scientific literature about the relationship between schizophrenia and human evolution from a genetic point of view. In the last two decades, research investigated the association between schizophrenia and a few genetic evolutionary markers: Human accelerated regions, segmental duplications, andhighly repetitive DNA such as the Olduvai domain. Other studies focused on the action of natural selection on schizophrenia-associated genetic variants, also thanks to the complete sequencing of archaic hominins' genomes (Neanderthal, Denisova). Results suggested that a connection between human evolution and schizophrenia may exist; nonetheless, much research is still needed, and it is possible that a definitive answer to the evolutionary paradox of schizophrenia will never be found.

The complete chloroplast genome sequence of Cathetus clarkei Hook.f.1890 R.W.Bouman, 2022 (Phyllanthaceae)

Cathetus clarkei, a significant folk medicinal plant, is utilized to treat a variety of ailments. In this study, we reported the complete chloroplast genome sequence of this species. The length of the complete chloroplast genome was 155,810 bp, included a pair of inverted repeat (IR) regions (26,340 bp), a large single-copy region (LSC, 84,853 bp), and a small single-copy region (SSC, 18,277 bp). It comprised 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The total GC content was 36.8%. The phylogenetic tree revealed that C. clarkei had a close relationship with P. cochinchinensis, followed by P. reticulatus. This study provides a reference for important medicinal plants within the Phyllanthaceae, and we can gain a deeper understanding of how the species adapts to changes in the environment, helping us to identify and protect it.

Clinical and genomic features of the morphological subtypes in advanced pancreatic cancer.

765 Background: In resected pancreatic cancer (PDA), morphology from routine histopathology slides provides a rapid inexpensive biomarker that predicts overall survival and correlates with transcriptomic subtypes. In this study, we evaluated clinical and genomic associations of morphological subtypes in resected and advanced disease and validated the consistency of subtypes in patient-derived organoids (PDO) and mouse xenografts (PDXs) during in vitro and in vivo modeling. Methods: Our cohort included PDA tumor tissues from 152 resectable (stage I/II) and 228 advanced cases (Stage III/IV). Hematoxylin and eosin-stained slides were blindly reviewed by two pathologists and classified into subtypes based on Kalimuthu (1). Morphological subtypes were correlated with clinical and genomic data from whole-genome and transcriptome sequencing. Histological preparations from PDOs and PDXs obtained from pancreatic resections and metastases were reviewed using the same criteria. Results: Morphological subtypes were significantly associated with clinical patterns. Locally advanced PDA exhibited the highest proportion of glandular tumors. Metastatic tumors were enriched for non-glandular morphologies. The non-glandular morphologies were significantly associated with lower survival rates in both resected and advanced tumors. Furthermore, morphological subtypes were significantly associated with unique genomic alterations. Compared to glandular tumors, non-glandular tumors were associated with increased KRAS copy number, KRAS imbalances, and polyploid genomes. In advanced settings, glandular and non-glandular tumors mostly exhibited classical and basal-like transcriptional subtypes, respectively. Squamous tumors had the highest mutation burden and the highest proportion of Basal A signature (2). Using differential gene expression, we identified transcriptional signatures of the morphological subtypes. PDOs and PDXs maintained the morphological subtypes, although non-glandular tumors had a lower success rate for PDO establishment. Conclusions: Morphological subtypes have distinct clinical and genomic associations across all stages of pancreatic cancer, which can be consistently modeled both in vitro and in vivo . These results demonstrate that morphological subtyping offers a rapid and biologically-relevant classification of PDA that could be used for drug development and stratification to predict therapy selection. 1. Gut; 69:317-328 (2020). 2. Nat Gen; 52:231-240 (2020).

Detection and Whole-Genome Analysis of tigecycline resistant Escherichia coli in poultry and meat samples in Türkiye.

The emergence and dissemination of tigecyline resistant Enterobacterales (TRE) in animals is a critical issue. This study aimed to investigate the presence of TRE in the gut of healthy avians as well as meat samples. A total of 940 ceacal samples from 94 commercial poultry flocks were collected at slaughter and a total of 335 meat samples [(chicken (n = 159), turkey (n = 4) and beef/lamb (n = 172)] were collected from supermarkets and butcher shops. Out of 960 samples, 146 (19.21 %) samples from chicken farms and 24 (13.3 %) from turkey farms were positive for TRE. Forty-nine Escherichia coli isolates were determined to carry the tet(X4) gene by PCR and exhibited multi-drug resistance. Whole-genome short-read sequencing (WGS) on all tet(X4) positive E. coli isolates and long-read sequencing on a selection of five isolates were carried out. WGS identified four ST types (ST206 being the most dominant, ST609, ST744 and ST189), indicating significant homogeneity among tigecyline resistant E. coli strains. In 47 isolates, the tet(X4) gene was transferrable to E. coli EC600 and it was found to be located on the IncX1 plasmid. Additionally, all tet(X4)-positive E. coli isolates also harbored other resistance genes, including floR, aadA2 and tet(A). In this study, the identification of tet(X4) carrying E. coli in healthy chicken and meats suggests the likely source of food-producing animals for humans. Therefore, active surveillance of critical priority lineages of TRE should focus on to contain the potential public health risk.

Whole genome and transcriptome analysis of pancreatic acinar cell carcinoma elucidates mechanisms of homologous recombination deficiency and unravels novel relevant fusion events.

Pancreatic acinar cell carcinoma (PACC) is a rare pancreatic tumor with a heterogeneous clinical course and, except for radical surgery, limited treatment options. We present a comprehensive study encompassing whole-genome and RNA sequencing of 7 tumor samples from 3 metastatic PACC patients to further delineate its genomic landscape and potential therapeutic implications. Our findings reveal distinct signatures of homologous recombination deficiency (HRD) in patients harboring pathogenic germline BRCA1/2 and FANCL mutations, demonstrating favorable responses to poly (ADP-ribose) polymerase 1 (PARP) inhibitors with prolonged disease-free intervals. Additionally, we first describe structural variants in PACC, including BRCA1::TRIM47 fusion and another variant impacting FANCC, both events related to HRD, and we also identify alterations in the mitogen-activated protein kinase (MAPK) pathway, including RAF1 duplication as well as novel BRAF::SORBS2 and MAP7D2::SND1 gene fusions, offering potential targets for therapy. Our study underscores the importance of genome and transcriptome-wide profiling of PACC, to help guide personalized treatment strategies to improve patient outcomes.

Constructing mRNA-meth-miRNA single-sample networks to reveal the molecular interaction patterns induced by lunar orbital stressors in rice (Oryzasativa).

To explore the bio-effects during Moon exploration missions, we utilized the Chang'E 5 probe to carry the seeds of Oryza. Sativa L., which were later returned to Earth after 23 days in lunar orbit and planted in an artificial climate chamber. Compared to the control group, rice seeds that underwent spaceflight showed inhibited growth and development when planted on the ground. Then we collected samples and employed RNA sequencing (RNA-Seq) and whole-genome bisulfite sequencing (WGBS) in the tillering and heading stages of rice. To gain a comprehensive understanding of the dysregulation in molecular interaction patterns during Moon exploration, a bioinformatics pipeline based on mRNA-meth-miRNA Single-Sample Networks (SSNs) was developed. Specifically, we constructed four SSNs for each sample at the mRNA, DNA methylation (promoter and gene bodies), and miRNA levels. By combining with the Protein-Protein Interaction (PPI) network, SSNs can character individual-specific gene interaction patterns. Under spaceflight conditions, distinct interaction patterns emerge across various omics levels. However, the molecules driving changes at each omics level predominantly regulate consistent biological functions, such as metabolic processes, DNA damage and repair, cell cycle, developmental processes, etc. In the tillering stage, pathways such as ubiquitin mediated proteolysis, nucleotide excision repair, and nucleotide metabolism are significantly enriched. Moreover, we identified 18 genes that played key/hub roles in the dysregulation of multi-omics molecular interaction patterns, and observed their involvement in regulating the above biological processes. As aforementioned, our multi-omics SSNs method can reveal the molecular interaction patterns under deep space exploration.

Molecular characteristics and pathogenicity analysis of infectious laryngotracheitis virus isolated in China from 2015 to 2019.

The aim of this study was to investigate the molecular characteristics and pathogenicity of recently isolated ILTV strains from China, thereby augmenting our understanding of its prevalence. The complete genome sequences of seven ILTV strains obtained from China between 2015 and 2019 were determined by high-throughput sequencing. Phylogenetic analysis showed that six isolates (SD2015, GD2017, SYB2018, HB201812, HB201806, and TJ2019) were classified together with CEO vaccine strains, while only one isolates LN2018 belonged to the wild-type cluster. Recombination analysis revealed compelling evidence of probable recombination events existing in SD2015, HB201806, and LN2018. Compared to TJ2019 and LN2018, chickens infected with HB201806 exhibited more severe conjunctivitis symptoms and tracheal damage, as well as higher viral load and viral shedding in the trachea. These findings will provide valuable references for further understanding the epidemiological status of ILTV and developing effective control measures.