Category Archives: Genome

Since 2010, there have been multiple new species added to the Listeria genus, many originally isolated from natural environments16. This paper describes the genotypic and phenotypic characterization of two new Listeria isolates obtained from soil samples collected in the Great Smoky Mountains National Park along the North Carolina-Tennessee border17. Evaluation of genotypic and phenotypic characteristics of L. swaminathanii strains will aid in the characterization of this novel species and contribute to our knowledge of the diversity of Listeria spp. Here, we describe the newly isolated strains, UTK C1-0015 and UTK C1-0024, and compare with the L. swaminathanii type strain (FSL L7-0020T) and other Listeria spp.

Both genomes were able to be assembled into complete closed genomes (contiguous sequences that comprise the entire genome). The genome of UTK C1-0015 consists of a 2.78Mb chromosome and 55Kb plasmid (total genome length of 2.84Mb) with a G+C content of 38.7%; UTK C1-0024 consists of a 2.95Mb chromosome with a G+C content of 38.6% (Table 1), which is consistent with FSL L7-0020T. Of the validly published type strains, the two isolates showed highest similarity to L. marthii (94.094.1%) (Fig.1); however, they were most closely related to L. swaminathanii FSL L7-0020T, with 98.798.8% ANI, indicating that they belong to the same species. Examination of the chromosomal alignment of the two isolates and the type strain shows that, overall, there is a high level of conservation across the entire chromosome, with no large rearrangements or deletions (Fig.2). However, there are some loci throughout that are present or absent in only one of the isolates.

ANI Similarity Dendrogram. Average nucleotide Identity (ANI) dendrogram of the recently isolated L. swaminathanii strains (bold), along with all described Listeria spp. type strains and representative from each of the L. monocytogenes lineages (indicated in parentheses). Horizontal distance represents ANI similarity (%) and vertical dashed lines indicate ANI values of 96 (yellow), 95 (orange), and 94% (red).

Chromosomal alignment of FSL L7-0020T, UTK C1-0024, and UTK C1-0015. Alignment shows three horizontal panels, one per strain. The colored portions inside each panel represents sequence similarity, with height corresponding to average conservation at that location. Regions that are conserved among all genomes are purple. Regions that are conserved among only two of the genomes are red (FSL L7-0020T and UTK C1-0024), green (FSL L7-0020T and UTK C1-0015), or yellow (UTK C1-0024 and UTK C1-0015). Regions without coloring were not aligned and likely contain loci that are present in only a single genome.

Both genomes contained the following antibiotic resistance genes: fosX, lin, norB, and sul. Virulence-associated genes involved with adherence (dltA, fbpA, lap, lapB, pdeE), bile-resistance (bsh, mdrM), immune modulation (lntA), intracellular survival (lplA1, oppA, pdeE, prsA2, purQ, svpA), invasion (iap, lpeA, pdeE), peptidoglycan modification (oatA, pdgA), regulation of transcription and translation (agrAC, cheAY, codY, fur, lisKR, stp, virRS), surface protein anchoring (lgt, lspA, srtAB), and teichoic acid biosynthesis (gltB, gtcA) were identified in both genomes, along with internalins inlGHJK, inlC2, and inlD (Supplementary Table S1). Genes associated with Listeria pathogenicity island LIPI-3 (llsABDGPXY) were only found in UTK C1-0024 (Supplementary Fig. S1), as well as gltA (teichoic acid biosynthesis). The internalin genes inlA and inlB and genes associated with Listeria pathogenicity islands LIPI-1, LIPI-2, or LIPI-4 were not detected in either.

A 56Kb plasmid was identified in UTK C1-0015. The plasmid has an Illumina read depth of 2.2 the overall median depth, indicating a copy number of two. The plasmid found in UTK C1-0015 shows a high similarity (86.03% nucleotide identity) to pLMIV from L. monocytogenes strain FSL J1-020846,47. However, pLMIV is approximately 21Kb longer than the plasmid found in UTK C1-0015; this is due to the presence of a region encoding four complete internalins and one internalin-like protein in pLMIV, this region is absent in the plasmid in UTK C1-0015 (Fig.3). Both plasmids are also similar to the plasmid in L. monocytogenes FSL J1-0158. Both FSL J1-0208 and FSL J1-0158 were originally isolated from clinical caprine sources46. Most genes in the plasmid found in UTK C1-0015 seem to encode proteins predicted to be involved in plasmid maintenance and conjugation46, with only a few putative cargo genes, most which are of unknown function and one encoding a DNA-methyltransferase.

Comparison of plasmid found in UTK C1-0015 to plasmids from FSL J1-020 and FSL J1-158. Comparison of the plasmids found in UTK C1-0015, FSL J1-020, and FSL J1-158, using pLMIV from J1-208 as the reference. The innermost black ring represents pLMIV. The middle rings represent FSL J1-158 (teal) and UTK C1-0015 (purple), with BLAST identity indicated by shading (see legend). The outermost ring contains gene annotations from pLMIV that are colored by functional category: green (plasmid replication and conjugation), red (internalins or internalin-related), blue (transposases or integrases), gray (hypothetical proteins), and black (other).

PHASTER and PhageBoost were used to predict prophage sequences in the genomes. The genome UTK C1-0024 was predicted to house a prophage integrated near a tRNA-Lys gene. Blastn results show the prophage from UTK C1-0024 has an 88.58% identity to Listeria phage A500 with 60% coverage. Prophages and other mobile genetic elements can contribute to genome diversity and have been used to distinguish epidemic clones of L. monocytogenes48,49,50. Strain UTK C1-0015 was predicted to house a partial monocin locus of eight open reading frames 51,52; structural genes such as those that code for the tail tape measure protein or tail fibers were absent from the locus. The monocin locus from strain UTK C1-0015 shares a 99.405% identity to the monocin locus from FSL L7-0020T (GCF_014229645.1). The UTK C1-0024 genome was predicted to house the full monocin locus of 18 open reading frames, similar to the monocin in L. monocytogenes strain 10403S (Fig.4). Blastp queries using the monocin locus from UTK C1-0015 and UTK C1-0024 return hits to L. marthii, L. cossartiae, L. innocua, L. farberi, and L. monocytogenes strains with 100% coverage and >89.90% identity, suggesting this is fairly dispersed across the sensu stricto clade of Listeria. Monocins are bacteriocins produced by the host that may be significant in establishing dominant strains in ecological niches, as they target closely related species, but remain inactive against the producing strain53.

Nucleotide similarity of monocin regions. BLAST comparisons of monocin regions from L. monocytogenes 10403S, UTK C1-0015, UTK C1-0024, and the L. swaminathanii type strain FSL L7-0020T. Genes are represented by green arrows. The shaded regions represent nucleotide similarity (see scale at bottom right).

Listeria spp. grow at a wide range of temperatures from 0 to 45C7,8,14,16 and can survive at temperatures below freezing (7C)54. In the current study, we performed growth assessments at 4, 7, 22, 30, 37, and 41C. These temperatures were chosen to encompass the known growth temperature range, with 4 and 7C specifically included because some species are unable to grow well at low temperatures (<7C) 4. Strain UTK C1-0015 exhibited growth at all temperatures tested and strain UTK C1-0024 exhibited growth at all termperatures except 41 C (Supplementary Table S2). After 24h of incubation, UTK C1-0015 and UTK C1-0024 showed optimal growth at 30C (9.2 and 9.4 log10 CFU/mL), followed by at 37C (8.9 and 9.0 log10 CFU/mL). At 41C, UTK C1-0024 was enumerated daily for up to five days and no growth was observed, which is dissimilar to both UTK C1-0015 and FSL L7-0020T. At 4C, the concentration increases of UTK C1-0015 and UTK C1-0024 after 11 d (6.4 and 6.8 log10 CFU/mL, respectively) were higher than the increases seen in FSL L7-0020T (4.1 log10 CFU/mL)16.

Listeria spp. are Gram-positive rods7; this was confirmed for UTK C1-0015 and UTK C1-0024. Both isolates were observed to grow under aerobic and anaerobic conditions at 30C after 24h; this is another expected result, as Listeria spp. are facultative aerobes7. Both strains were oxidase negative (Supplementary Table S3), as expected7, indicating a lack of cytochrome c oxidase. Additionally, both were catalase positive, indicating they produce the catalase enzyme that converts hydrogen peroxide into oxygen gas and water; however, FSL L7-0020T is catalase negative16, a phenotype that has only been described in one other Listeria spp. (L. costaricensis)55. When kat gene from the reference, two isolates, and the type strain are aligned, there are nucleotide differences at 158 positions. 16 of the nucleotide differences differ between the type strain and one or both of the isolates. Four of those result in amino acid differences, with two between the type strain and both isolates. At amino acid position 72, the type strain has glutamic acid (polar, acidic) and the two isolates have lysine (polar, basic), a radical substitution. At amino acid position 92, the type strain has histidine and the other two arginine (both polar, basic), a conservative substitution. These amino acid differences may have an effect on the structure and function of the resulting protein, leading to the catalase-negative phenotype of FSL L7-0020T.

On MOX agar, UTK C1-0015 and UTK C1-0024 colonies were typical for Listeria spp.: gray to black colonies with sunken centers and black halos, indicating esculin hydrolysis. On Listeria CHROMagar, UTK C1-0015 and UTK C1-0024 were typical for Listeria spp.: blue colonies (indicating -glucosiadase enzyme activity), but lacking opaque white halos typical for L. monocytogenes and L. ivanovii (indicating no phosphoatidylinositol-specific phospholipase C [PI-PLC] activity) (Supplementary Table S3).

API test kits were used to characterize metabolic function of UTK C1-0015 and UTK C1-0024.

The Listeria API kit is designed for species-level identification Listeria spp. based on enzymatic tests and sugar fermentations. For this test, both strains generated a code of 6110 (Supplementary Table S3), consistent with FSL L7-0020T 16 and indicates an 80% (t-value of 0.62) ID to L. monocytogenes according to the APIweb database. The control strains, L. monocytogenes 10403S and L. innocua ATCC 33090, generated the expected codes of 6510 and 7510, respectively.

The API 20 E kit is designed for identification of Enterobacteriaceae and other non-fastidious Gram-negative rods; however, this kit contains tests that can be used for genus-level identification of Listeria spp. and has been used previously in the characterization of novel Listeria spp.10,16. For this test, UTK C1-0015 and UTK C1-0024 were positive for acetoin production (Voges Proskauer) and D-glucose and amygdalin fermentation, which is consistent with L. monocytogenes 10403S, L. innocua ATCC 33090, and FSL L7-0020T 16 (Supplementary Table S3). UTK C1-0015 and UTK C1-0024 were negative for all other tests, including indole, urease, and H2S production 16. All API 20 E results were consistent with FSL L7-0020T 16. Nitrogen reduction was evaluated using both the API 20E kits and nitrogen broth; both strains were negative.

The API 50 CH kit is designed for the study of carbohydrate and carbohydrate-derivative metabolism and API 50 CHB/E medium is designed for use with Bacillus and related genera, Enterobacteriaceae, and Vibrionaceae. Results for this test were consistent between UTK C1-0015, UTK C1-0024 and FSL L7-0020T (Supplementary Table S3), with four differences. UTK C1-0015 yielded a negative result for D-lactose, a result that differs from UTK C1-0024, FSL L7-0020T, and most sensu stricto Listeria species16. Both strains tested negative for glycerol and starch (amidon); this differed from the type strain16, which is positive for both. UTK C1-0024 was positive for d-trehalose fermentation, while UTK C1-0015 and the type strain were negative. Examination of the genomes shows that a locus containing three genes associated with trehalose fermentation (treR, treC, and treP) is present in UTK C1-0024, but absent in the two other genomes. In L. monocytogenes, trehalose has been shown to increase biofilm formation56. The API 50CH test is a qualitative test and interpretation of results can vary, which is one major limitation of qualitative tests.

The complete lysis of red blood cells, hemolysis, is associated with pathogenicity in Listeria spp.7 On SBA, UTK C1-0015 and UTK C1-0024 were non-hemolytic, which is consistent with the non-hemolytic FSL L7-0020T 16 and the negative control L. innocua ATCC 33090. hemolysis is typically only observed in L. monocytogenes, L. ivanovii, and L. seeligeri7,45.

When observed microscopically, both UTK C1-0015 and UTK C1-0024 appeared motile at 25C and nonmotile at 37C (Supplementary Table S3). Motility at 25C was confirmed with MTM tubes; both strains were clearly motile after 5days of incubation as evidenced by an umbrella-shaped growth pattern, characteristic of motile Listeria spp. These results were consistent with FSL L7-0020T 16 and other sensu stricto species, with the exception of L. immobilis (non-motile at 25C10). In L. monocytogenes, motility genes like flagellin are expressed at lower temperatures like 25C, but become restricted at 37C57.

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Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species L. swaminathanii | Scientific Reports -...

DURHAM, N.C.--(BUSINESS WIRE)--BioSkryb Genomics, a biotech company developing advanced single-cell analysis tools, today announced the launch of the Early Access Program (EAP) for ResolveOME, a unified, single-cell workflow that amplifies the complete genome and full-length mRNA transcripts of the entire transcriptome from the same cell. This unification eliminated the need to split source material or interpret across datasets. Companies and researchers will have the opportunity to apply for the EAP at the upcoming Advances in Genome Biology and Technology (AGBT) 2022 General Meeting taking place June 6-9 in Orlando. The EAP will provide first access to BioSkrybs ResolveOME technology and BaseJumper, a bioinformatics platform to sort, analyze, and interpret very large single-cell analysis data sets.

The ability to deeply understand the factors influencing cell heterogeneity is key to unlocking insights into disease and developing new drugs and diagnostics, said Jay A.A. West, PhD, CEO and Cofounder of BioSkryb. We developed ResolveOME to deliver multiple tiers of dynamic molecular information to drive novel biological insights and deliver a more complete understanding of the relationship between genotype to phenotype.

BioSkryb recently released data demonstrating the use of ResolveOME to explore genetic drivers of tumor heterogeneity and treatment resistance. Employing even a relatively small number of individual cells ResolveOME has elucidated biomarkers of cellular variability in both the genome and transcriptome. The study highlights that both the genome and transcriptome are dynamic and plastic within individual cells, leading to a set of combinatorial alterations that affect cellular evolution. ResolveOME enables the unification of broad genomic and transcriptomic data from the same cell, driving a new understanding of the mechanisms of cellular function and differentiation.

While we are thrilled with the performance of the ResolveOME chemistry system, what continues to surprise us is the incredible plasticity of the genome, compared to the transcriptome. In addition, using full-length mRNA transcriptional profiles from the same cells, we are able to discern the biological impact, or penetrance, of these genome modifications. Discovering genomic variation in the absence of information about transcriptional consequence of that plasticity or, conversely, a transcriptional signature without understanding underlying genomic contributions, hinders the understanding of the molecular mechanisms of disease, explained Dr. West. ResolveOME provides a previously unattainable expansion of data capture and resolution, providing insights into tumor phenotype, immune evasion, and drug resistance which we expect will transform cancer drug discovery and development.

BioSkrybs ResolveOME and ResolveDNA products incorporate proprietary primary template-directed amplification (PTA) technology, which was created to address the inherent challenges of single-cell genomics by producing high-quality gene sequencing data. PTA technology employs controlled reaction parameters to uniformly amplify >95% of the genomes of single cells and low-input samples with high precision and sensitivity, resulting in the highest quality analyses available today for any single-cell genomic applications.

In addition to being the first to access ResolveOME, EAP partners will be enabled to leverage BaseJumper, which links a cells identity and genotype to identify and interpret molecular variability, said Gary Harton, PhD, Chief Scientific Officer of BioSkryb. While both ResolveDNA and Resolve provide an order of magnitude of improvement in sensitivity over conventional bulk sequencing methods, BaseJumper provides the ability to visualize the data in an intuitive layout which accelerates discoveries from single-cell genomics.

During AGBT 2022, BioSkryb scientific experts will be available in the Manatee Suite, located on the lower level of Signia by Hilton Orlando Bonnet Creek. A limited number of private BaseJumper demonstrations are available and can be reserved by emailing info@bioskryb.com.

About BioSkryb Genomics

BioSkryb Genomics is a venture-backed developer of genomic amplification technologies. BioSkryb develops single-cell whole genome amplification tools to study genomic heterogeneity aiding researchers and companies in the discovery of novel insights into human disease at the cellular level. BioSkryb is headquartered in Durham, North Carolina. For more information, visit http://www.bioskryb.com.

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BioSkryb Genomics Launches ResolveOME Early Access Program for Full Genome and Transcriptome Amplification From a Single Cell, in Conjunction With Its...

NEW YORK MGI Tech and King Abdullah International Medical Research Center (KAIMRC) said on Tuesday that they have signed a memorandum of understanding for a strategic collaboration in the areas of genomic science and biotechnology.

Financial and other terms of the collaboration were not disclosed.

The partnership will leverage BGI affiliate MGIs DNBSeq technology to improve KAIMRCs genome sequencing capacity and data quality across a wide range of applications, including human genome sequencing, transcriptome sequencing, infectious disease research, and microbial organism research, such as COVID-19 monitoring and epidemiology.

The partners also envision establishing a high-throughput sequencing center in Riyadh, Saudi Arabia-based KAIMRC, which will house MGIs sequencing platforms, laboratory automation, and bioinformatics products. MGI, based in Shenzhen, China, will also join forces with KAIMRC for business development, marketing, public communications, and genomics education.

MGI is an invaluable strategic partner in our journey towards establishing state-of-the-art genomic sequencing capabilities in Saudi Arabia, Ahmed Alaskar, executive director of KAIMRC, said in a statement. Precision medicine is the future of healthcare, and this partnership paves the way for new and innovative approaches in this field.

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MGI Tech, King Abdullah International Medical Research Center Partner on Genomic Research - GenomeWeb

A plan to develop plant varieties and animal breeds that are better suited to the UAEs environmental conditions has been unveiled by Abu Dhabi's government.

The Abu Dhabi Agricultural Genome Programme will involve scientific research centres carrying out work to create the new varieties and breeds.

It will also see the setting up of a database of genetic resources and a store of actual material, an approach that, elsewhere, has often resulted in the creation of seed banks.

The initiative has been launched by the Abu Dhabi Authority for Agriculture and Food Safety (ADAFSA) and is part of the authoritys 2022 to 2025 strategic plan to enhance food security.

As well as enhancing food security a key aim in a country that is a net importer of food officials also want agriculture to make an increased contribution to Abu Dhabi emirates GDP.

In a statement, the Abu Dhabi Government Media Office said the programme would improve agricultural production and meet the challenges of the emirates climatic and environmental conditions.

The plant varieties and fish and animal breeds developed through the programme will be particularly suited to the UAEs climate, which is characterised by high temperatures, low rainfall and, in some cases, high salinity levels in soil.

In line with this, ADAFSA said in the statement that tolerance of drought and high salinity would be a key aim of breeding programmes.

Sheikh Mansour bin Zayed, pictured with now President Sheikh Mohamed earlier this year, said the genome will better equip the country for future food production. Photo: Twitter

An additional aim is to develop plants, fish and farm animals that are resistant to disease. Better disease resistance, which has for many decades been a priority of, in particular, plant-breeding programmes around the world, can improve yields and reduce the cost of production.

Sheikh Mansour bin Zayed, Deputy Prime Minister, Minister of Presidential Affairs and ADAFSAs chairman, said the programme would help to train Emiratis in agricultural genetic research. Sheikh Mansour said the initiative was part of the UAEs move towards global leadership in food security.

Also as part of its efforts to improve the supply of locally grown food, last month ADAFSA awarded two contracts, worth Dh310 million in total, for the creation of a hydroponic farm in the Abu Dhabi region and a conventional farm in Al Ain.

Hydroponic farms, which have previously been set up in the UAE and neighbouring countries including Saudi Arabia, involve growing crops in nutrient solutions instead of soil. While often energy intensive, the approach reduces water consumption.

Updated: June 01, 2022, 7:06 PM

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New genome project to improve UAE agriculture and food - The National

It has not been a month since a confirmed case of monkeypox was reported in the United Kingdom (UK) and there are more than 400 infections in, at least, 20 countries outside Africaincluding Canada, Portugal, Spain and the UK. This is the largest outbreak of the virus outside Africa.

Notably, monkeypox is generally confined to African countries and the increasing number of cases in different countries has alarmed scientists. In many of the clusters of cases, there is no apparent link, which raises the possibility of local transmission of the virus going undetected.

Now, scientists and researchers are busy digging up the matter and are focussed on certain questions. Notably, scientists have sequenced the genome of the virus, collected from countries outside Africa, including Belgium, France, Germany and the United States.

The sequencing revealed that the viral strain in these countries was similar to that commonly found in West Africa. Its worth noting that the west African strain has a death rate of even less than 1%, especially among the poor and rural population. On the other hand, the strain commonly prevalent in Central Africa is of concern, which can cause fatality with a rate of 10%.

Researchers are still searching for a definitive lead about how exactly the outbreaks started outside Africa. There may be a travel link but it has not been zeroed down yet. In earlier outbreaks outside Africa in 2018 and 2019, researchers could find a definitive link to travel history to Africa.

Experts also put forward the other hypothesisthe virus was already in circulation among people and animals outside Africa and went undetected. However, the possibility of such a situation is not strong as the virus forms visible skin lesions like the chickenpox virus and physicians would have suspected it readily.

Researchers are also looking at the possibility of some genetic changes accrued by the virus over time which might offer them the capability of spreading so fast outside Africa, which is not that easy. Understanding whether there is a genetic basis for the viruss unprecedented spread outside Africa will be incredibly difficult, said computational virologist of the University of Alabama, Birmingham Elliot Lefkowitz.

Scientists are still struggling to decipher what changes in the Central African strain made it more virulent even after 17 years of the two strains were detected. One of the reasons for this too difficult task, according to Lefkowitz, is the sheer size of the pox virus. For example, the genome of the pox virus is six times larger than SARS-CoV-2, the coronavirus that drives the pandemic. This implies that it is nearly six times tougher to analyse the pox virus compared to the coronavirus. Alongside, the limited resource availability of genome surveillance of the pox virus in Africa is also relatable, said experts.

Scientists are also looking at whether the virus is spreading differently than it did in the previous outbreaks. The monkeypox virus is well known to spread through close contact with lesions, bodily fluids or the respiratory droplets of infected people or animals. This is different than the coronavirus, which can spread also via droplets but more worryingly through the air. This makes the coronavirus spread readily and to more distances. Along with it, researchers are also looking at whether sexual activity has something to do with the spreading ability of the virus.

The other major issue is how to contain the outbreaks before they create a worldwide panic. Importantly, vaccines against the small pox have been found effective against monkeypox as well. The other positive part of these pox vaccines is that they can offer protection when administered even within four days of infection. This is due to the long incubation period of the virus, which is not the situation with the COVID-19 vaccines.

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Monkeypox Genome 6 Times Tougher to Analyse than SARS-CoV-2 - NewsClick

Eight proteins that may serve as potential therapeutic targets for treating heart failure have been identified in a meta-analysis of population-based proteomic studies. This study may not only inform new heart failure treatments, wrote the authors of the analysis, but their methods can provide a roadmap for discovering drug targets in other diseases using proteomic and genomic data.

Heart failure is a growing cause of hospitalizations and deaths in the United States. In 2014, there were an estimated 80,000 deaths in the US from heart failure and another 230,000 deaths from heart failure with another co-morbidity. Moreover, a study published in the American Journal of Medicine in 2020 found that the mean predicted 10-year risk of heart failure increased from two percent to three percent of the population between 1999 and 2016. Despite being highly prevalent, the mechanisms of heart failure are incompletely understood.

To elucidate the causes of heart failure and reveal potential therapeutic targets, Thomas Lumbers from the University College London and collaborators used data from four population-based studies as part of the SCALLOP (Systematic and Combined AnaLysis of Olink Proteins) consortium in a meta-analysis to uncover therapeutic targets for heart failure. Through the examination of 90 cardiovascular proteins in the plasma of 3,019 participants (among whom there were 732 heart failure events), a total of 44 proteins were observationally associated with heart failure.

An additional dataset from a separate study of 30,000 individuals was used to identify 75 proteins with one or more cis-genetic instruments, and the overlap between the 44 and 75 proteins from the respective cohorts resulted in 40 heart-failure-associated proteins available for evaluation with the epidemiological technique of Mendelian randomization. A total of 120 combinations of instrument selection parameters were evaluated to improve the precision of the derived causal estimates.

Mendelian randomization is a technique developed to utilize the wealth of available genetic information as a kind of natural randomized clinical trial. Genes are randomly assorted during meiosis; differences between the different parental alleles mimic a randomized clinical trial with cases and controls replaced by a difference in the alleles distributed to the offspring. These differences will influence the level of the circulating protein in question, serving as a life-long exposure to the individual which can then be connected to the phenotype of interest (that is, the presence or absence of disease).

As an example, a genetic variant associated with higher LDL cholesterol levels that is also associated with a higher risk of coronary heart disease would provide supportive evidence for a causal effect of LDL cholesterol on coronary heart disease.

Each individuals genome, with its millions of individual variants mapped into haplotype blocks, together with phenotypic data relating to the disease being studied, can then be combined with data from hundreds or thousands of other individuals. This wealth of genomic data and phenotype data enables a statistical analysis of particular genetic instruments in terms of the relative concentration of a collection of circulating plasma proteins. This provides a shortlist of proteins that are highly likely to be causative in the disease phenotype of interest, which then can be manipulated through pharmaceutical intervention to mitigate the disease in question.

Interest in using Mendelian randomization is growing rapidly. A proportional search for the term Mendelian randomization via the tool PubMed by Year yields the following graph as a proxy for the popularity of this method, with some 1,288 uses in 2021 and 899 in 2020.

Using this technique, Lumbers and colleagues identified eight proteins with strong evidence of causality for heart failure: three risk factor proteins, CSF-1, Gal-3, and KIM-1; and five protective proteins, ADM, CHI3L1, CTSL1, FGF-23, and MMP-12. The ChEMBL public drug discovery database and a clinical trial registry were consulted for ongoing drug development and estimated druggability of the proteins involved. The only protein not rated for druggability is KIM-1, and the remaining seven targets are of interest for future drug development.

One protein target, fibroblast growth factor 23 (FGF-23) already has an on-market approved therapy for X-linked hypophosphatemia. In addition, colony-stimulating factor-1 (CSF-1) and matrix metallopeptidase-12 (MMP-12) are in early Phase I/II clinical trials for various disease indications including asthma, hypertension, and stomach neoplasms. Importantly the two protein targets adrenomedullin (ADM) and galactin-3 (Gal-3) provide confirmatory evidence for the development and evaluation of pharmaceuticals targeting these proteins that are currently in clinical trials for heart failure.

The authors concluded their paper by saying, Proteomewide studies incorporating both direct association with target outcomes and genetic-based inference through [Mendelian randomization] are likely to provide important new tools for therapeutic target discovery and prioritization.

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Therapeutic Targets for Heart Failure Identified With Plasma Proteome and Genome Analysis - GenomeWeb

IRVINE, Calif.--(BUSINESS WIRE)--Genomic Testing Cooperative, LCA (GTC) announced that it will be presenting at the American Society of Clinical Oncology (ASCO) 2022 annual meeting data showcasing its new innovative approach to liquid biopsy testing that combines both cell-free-DNA (cfDNA) with cell-free RNA (cfRNA), Liquid Trace. Liquid Trace tests both cfDNA and cfRNA not only improves sensitivity of the liquid biopsy but also provides transcriptome data that is enriched by various tumor markers (CA125, CA 15-3, CEA, etc) and makes it possible to perform liquid immunoprofiling by evaluating levels of CD19, CD20, CD33, CD4, CD8, etc.

This data will be presented in two posters:

GTC will also present validation data of its innovative artificial Intelligence (AI) approach that uses targeted transcriptome to classify and aid in the differential diagnosis between 47 different diagnoses of hematologic and solid tumors. This AI is particularly powerful in the differential diagnosis between various types of lymphoma and Hodgkin disease and solid tumors of unknown origin. This data will be presented in the following poster:

Our new Liquid Trace test represents a significant leap in the science of liquid biopsy. Cells in various tissues contain the same DNA, but RNA makes the difference between skin and brain tissue. Analyzing RNA is the next step in the advancement of genomics. GTC is committed to combining the science of RNA with AI to bring this type of innovation to everyday practice of molecular testing in tissue biopsy as well as in liquid biopsy, stated Dr. Maher Albitar, founder, chief medical officer, and chief executive officer of GTC. These advances were possible because of the collaborative (Co-Op) business model that was adapted by GTC. Collaboration between various Co-Op members accelerates innovation and advances genomics. We are grateful for the support and collaborative efforts of various members of the Co-Op.

Visit GTC at booth #4117 at ASCO for more details and highlights on this work and on how to become a member of the Co-Op. The abstracts presented at ASCO will be made available on GTCs website after the ASCO meeting.

About Genomic Testing Cooperative, LCA

Genomic Testing Cooperative (GTC) is a privately-owned molecular testing company located in Irvine, CA. The company operates based on a cooperative (Co-Op) business model. Members of the co-op hold type A shares with voting rights. The company offers its patron members a full suite of comprehensive genomic profiling based mainly on next generation sequencing. Molecular alterations are identified based on rigorous testing with the aid of specially developed algorithms to increase accuracy and efficiency. The clinical relevance of the detected alterations is pulled from numerous databases using internally developed software. Relevance of findings to diagnosis, prognosis, selecting therapy, and predicting outcome are reported to members. The Co-Op model allows GTC to make the testing and information platform available to members at a lower cost because of a lower overhead. For more information, please visit https://genomictestingcooperative.com/.

Forward-Looking Statements

All of the statements, expectations and assumptions contained in this press release are forward-looking statements. Such forward-looking statements are based on the GTC managements current expectations and includes statements regarding the value of comprehensive genomic profiling, RNA profiling, DNA profiling, algorithms, therapy, the ability of testing to provide clinically useful information. All information in this press release is as of the date of the release, and GTC undertakes no duty to update this information unless required by law.

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Genomic Testing Cooperative to Reveal Liquid Trace at ASCO, a Liquid Biopsy Test that Combines Cell-Free DNA with Targeted Transcriptome, and to...

ExtramuralBy Adeline Lopez

NIEHS-funded researchers developed a high-throughput approach, called single-molecule mutation sequencing (SMM-seq), to characterize point mutations in normal cells. Point mutations occur when a single building block of DNA and its complement are added, deleted, or changed during replication. Linked to a variety of diseases, including cancer, point mutations have been difficult to study because they can be unique for each cell and occur at low frequencies.

SMM-seq includes a two-step library preparation protocol. First, an amplification process creates long single-stranded DNA molecules that contain multiple copies of each DNA fragment strung together. These copies are independent replicas of the original DNA fragment, reducing potential for errors to spread. Then, the long single-stranded DNA are individually amplified and converted into a sequencing library.

During this step, the team introduced unique molecular identifiers to each end of the DNA. These identifiers allowed the team to recognize matches to the original DNA fragment, filter out inherited mutations, and identify new mutations when comparing results against a single nucleotide polymorphisms database. They carried out proof-of-principle tests to detect both age-associated mutations and those following low-dose exposure to a compound known to cause mutations.

According to the authors, SMM-seq can detect both induced and naturally acquired point mutations in normal cells and tissues with high accuracy while being significantly more cost-effective than traditional methods. Paired with their structural variant search assay, this method is well suited to comprehensively assess genome integrity in large-scale human studies, according to the researchers.

Citation:Maslov AY, Makhortov S, Sun S, Heid J, Dong X, Lee M, Vijg J. 2022. Single-molecule, quantitative detection of low-abundance somatic mutations by high-throughput sequencing. Sci Adv 8(14):eabm3259.

NIEHS-funded researchers developed a new approach to leverage machine learning to predict biological abdominal age from magnetic resonance images (MRIs) of the liver and pancreas. Unlike chronological age, biological age can be altered by lifestyle habits and our environment. By predicting abdominal age and identifying risk factors for accelerated aging, the team hoped to reveal clues to delay the onset of age-related diseases, such as fatty liver disease and type 2 diabetes.

The team built an abdominal age predictor by training a sophisticated machine learning method on 45,552 liver MRIs and 36,784 pancreas MRIs collected from UK Biobank participants aged 37-82 years old. Then they looked to see whether certain genes, genetic variants, biomarkers, diseases, or environmental and socioeconomic variables were associated with accelerated abdominal aging.

The team reported that abdominal age is a complex trait involving genetics, clinical attributes, disease, and environmental and socioeconomic factors. For example, predictions were driven by anatomical features in both liver and pancreas as well as their surrounding organs and tissues. They also identified that the gene EFEMP1, markers related to poor liver and metabolic function, and poor general health were associated with increased abdominal aging, as were sedentary behavior, diet, and smoking. The opposite was true for higher socioeconomic status.

According to the authors, their approach can be used to assess abdominal aging or the effectiveness of rejuvenating therapies. They suggested that the genes they identified may point to new therapeutic gene targets and new instruments to study causality.

Citation:Le Goallec A, Diai S, Collin S, Prost JB, Vincent T, Patel CJ. 2022. Using deep learning to predict abdominal age from liver and pancreas magnetic resonance images. Nat Commun 13(1):1979.

NIEHS-funded researchers designed a genetic sensor, called PRISM, to detect DNA damage response in brain cells and visualize neurodegeneration relevant to Parkinson's Disease (PD).

The DNA damage response pathway allows brain cells to detect and repair damage in DNA, but persistent genotoxic stress to brain cells triggers an overactivation of the pathway, leading to premature cell aging and cell death associated with neurodegeneration.

The sensor leverages the properties of a virus often used in gene therapy. Host cells fight against the viral genetic sensor using DNA damage response pathways, enabling the team to trace the fate of neurons exposed to genotoxic stress. It also uses a genetic marker with high mutation rates as an indicator of genetic instability, allowing the researchers to explore DNA damage repair in cells.

The team tested the effectiveness and sensitivity of the sensor to detect genetic toxicity in mice treated with paraquat, an herbicide associated with PD risk; mice modified to overexpress a protein known to be involved in the onset and progression of PD; and the brains of patients with PD.

Exposure to paraquat heightened genetic toxicity in neurons. Neurons involved with dopamine transmission in the brain were most affected in cells, mice, and patients with PD. Loss of dopamine is a hallmark of PD. Neurons had subtle structural and cellular changes that may increase their vulnerability and affect function before cell death.

According to the researchers, PRISM successfully labeled genetic stress in neurons and may offer a useful tool for further understanding the underlying mechanisms by which environmental factors lead to neurodegeneration and exploring new therapies.

Citation:El-Saadi MW, Tian X, Grames M, Ren M, Keys K, Li H, Knott E, Yin H, Huang S, Lu XH. 2022. Tracing brain genotoxic stress in Parkinson's disease with a novel single-cell genetic sensor. Sci Adv 8(15):eabd1700.

Prenatal exposure to chemical mixtures worsens working memory in adolescents, according to NIEHS-funded researchers. Working memory is the ability to keep information in ones mind and mentally manipulate it. Although prenatal exposure to individual chemicals may adversely affect working memory among children, few studies have explored the association of co-exposure to multiple chemicals with this outcome in adolescence, a time when working memory develops substantially.

The researchers evaluated prenatal exposure to individual chemicals and their mixture in relation to working memory among 373 adolescents living near a Superfund site in New Bedford, Massachusetts. Specifically, they compared dichlorodiphenyldichloroethylene (DDE), hexachlorobenzene (HCB), and 51 polychlorinated biphenyls measured in cord serum, and lead and manganese measured in cord blood with verbal and symbolic working memory. Their statistical analysis also looked for differences between males and females and between groups with higher or lower social disadvantage.

The team found worse verbal working memory among adolescents with higher exposure to manganese and the chemical mixture. There were no significant differences between males and females, but greater social disadvantage during prenatal development combined with higher exposure to HCB and DDE worsened working memory scores.

Given that working memory undergoes considerable development during adolescence and deficiencies may be associated with psychiatric and behavioral disorders, further research should examine the effect of environmental exposures on working memory in this age group, as well as social and economic stressors that may alter susceptibility, according to the team.

Citation:Oppenheimer AV, Bellinger DC, Coull BA, Weisskopf MG, Korrick SA. 2022. Prenatal exposure to chemical mixtures and working memory among adolescents. Environ Res 205:112436.

(Adeline Lopez is a science writer for MDB Inc., a contractor for the NIEHS Division of Extramural Research and Training.)

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June 2022: Extramural Papers of the Month - Environmental Factor Newsletter

Researchers from the RI-MUHC and the McGill Genome Centre examine differences in ICU patients who recovered or died from COVID-19 and identify candidate drugs to treat severe disease.

Montreal, June 1, 2022 -Despite the availability of highly efficacious vaccines, SARS-CoV-2 still causes serious medical complications. The lack of an effective drug treatment for hospitalized patients with severe COVID-19 has contributed to the more than six million deaths worldwide since the beginning of the pandemic, including more than 50,000 deaths in May 2022 alone. To address this therapeutical gap, a team of researchers from the Research Institute of the McGill University Health Centre (RI-MUHC), the Canadian Centre for Computational Genomics (C3G), and the McGill Genome Centre studied host biological responses of patients hospitalized with severe COVID-19, looking for differences between patients who recovered and those who succumbed to the disease. They found that certain cellular pathways were overactivated at the time of intensive care unit (ICU) admission in the deceased patients. The researchers then identified three existing drugs targeting these pathways. Their study, published inScience Advances, provides the required preclinical data to support the testing of these drugs tacrolimus, zotatifin and nintedanib in controlled clinical studies.

We identified overactivation of messenger RNA metabolism, RNA splicing and interferon signalling pathways in patients who would not survive, says Vinicius Fava, PhD, a research associate at the RI-MUHC, co-first author of the study. The identification by different assays of these differentially activated pathways in the cells of COVID-19 survivors and deceased patients suggests that they are determinants of prognosis and makes them promising targets for pharmacological intervention at the earliest point of hospitalization of critically ill patients.

Understanding physiology of immune cells in severe COVID-19

The researchers performed a series of cellular and genomic analyses on seven patients hospitalized in the ICU of the McGill University Health Centre, in Montreal, Canada, at the start of the pandemic, between March and April 2020. These patients, of whom three died and four recovered, had the same level of disease severity on the WHO ordinal scale at the time of ICU admission.

The team of researchers characterized the transcriptome (expression of messenger RNA molecule) and the epigenetic landscape (alterations in the DNA structure that affect the ability of cells to regulate gene expression) of the patients immune cells at different timepoints: at their admission, at day 5 and at day 15 post admission, to monitor disease evolution. They compared the data between the deceased patients, those who survived and six healthy individuals.

Specifically, the team used single-cell RNA sequencing to understand the cellular composition and the physiological state of Peripheral Blood Mononuclear Cells (PBMCs) following hospitalization. PBMCs are critical components of the immune system that mediate the response to pathogens entering the human body. The analyses focused on three major PBMC cell populations: B cells, myeloid cells and Tcells. The team found significant differences in proportions of T cells and myeloid cells between patients who exhibited critical versus moderate symptoms. Critically ill patients at day 5 and day 15 showed a significant reduction of T cells (P=0.006) and a significant increase of myeloid cells (P=0.04), suggesting that COVID-19 severity has an impact on PBMC proportions.

Our results show a strong correlation of PBMC composition with disease progression. Critically ill patients with poor prognosis showed a significant reduction of T cells and a significant increase of monocytes, consistent with previously reported findings in patients suffering from severe COVID-19, write the authors of the study.

In contrast, at the time of hospital admission, the researchers detected significant changes in the expression of genes in key molecular pathways that are associated with epigenetic changes in monocytes, a type of white blood cells that transform into macrophages, i.e., cells capable of travelling to an area where an infection is present to kill the pathogen and control proliferation.

This study confirms the pivotal role of monocytes in COVID-19 severity and disease prognosis, as well as the involvement of interferon pathways in the development of COVID-19, says David Langlais, PhD, Assistant Professor in McGills School of Biomedical Sciences based at the McGill Genome Centre and co-senior author of the study. It also suggests that variations in transcriptional activity, and the accompanying epigenomics changes, mostly occurred at an early stage of COVID-19 disease, dictating how the disease will evolve in terms of severity and final outcome.

Repurposing the right drug for the right target

The researchers used various approaches to identify drugs that could suppress the cellular pathways overactivated in monocytes of patients who succumbed to COVID-19.

The initial approach resulted in more than 1500 candidate drugs, which were narrowed down to 53 candidate drugs/compounds previously used to treat cancers and/or inflammatory conditions. Using drug-protein and protein-protein interaction databases, the team was finally able to identify three promising candidate drugs (tacrolimus, zotatifin, and nintedanib) that act on the targeted pathways.

Our work demonstrates the power of combining transcriptomic and epigenomic analyses to identify biological factors that influence the evolution of COVID-19 hospitalization and the survival of patients with severe disease, says Erwin Schurr, PhD, a scientist in the Infectious Diseases and Immunity in Global Health Program at the RI-MUHC and Professor at McGills Department of Medicine, and co-senior author. We are looking forward to clinical trials that hopefully will confirm the efficacy of the three drugs to reduce mortality of severely ill COVID-19 patients.

About the study

The study A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19 was conducted by Vinicius M. Fava, Mathieu Bourgey, Pubudu M. Nawarathna, Marianna Orlova, Pauline Cassart, Donald C. Vinh, Matthew Pellan Cheng, Guillaume Bourque, Erwin Schurr and David Langlais.

DOI: 10.1126/sciadv.abm2510

Funding for this study was provided by the Canadian Institutes of Health Research (CIHR) and the McGill University Interdisciplinary Infection and Immunity Initiative (MI4), thanks to the generosity of multiple donors to the MUHC Foundation COVID-19 Emergency Fund.

The researchers are grateful to the patients who have participated in this study.

Media contacts

Fabienne LandryCommunications coordinator, Research, MUHC[emailprotected]

Cynthia Lee

Media Relations, Universit McGill / McGill University

[emailprotected]

514-398-6754

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New study: Montreal researchers identify three drugs that could reduce mortality in severely ill COVID-19 patients - McGill University Health Centre

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Int J Fertil Steril. 2022 Apr;16(2):70-75. doi: 10.22074/IJFS.2021.527076.1098. Epub 2022 May 8.

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters cells through angiotensin converting enzyme 2 (ACE2), which expression of its gene increases during pregnancy that is resulted in an enhanced level of the ACE2 enzyme. It might enhance the risk of SARS-CoV-2 infection and its complications in the pregnant women. Although, pregnancy hypertensive disorders and severe infection with SARS-CoV-2 are correlated with high comorbidity, these two entities should be discriminated from each other. Also, there is a concern about the risk of preeclampsia and consequently severe coronavirus disease 2019 (COVID-19) development in the pregnant women. So, to answer these questions, in the present review the literature was surveyed. It seems there is higher severity of COVID-19 among pregnant women than non-pregnant women and more adverse pregnancy outcomes among pregnant women infected with SARS-CoV-2. In addition, an association between COVID-19 with preeclampsia and the role of preeclampsia and gestational hypertension as risk factors for SARS-CoV-2 infection and its complications is suggested. However, infection of the placenta and the SARS-CoV-2 vertical transmission is rare. Various mechanisms could explain the role of COVID-19 in the risk of preeclampsia and association between preeclampsia and COVID-19. Suggested mechanisms are included decreased ACE2 activity and imbalance between Ang II and Ang-(1-7) in preeclampsia, association of both of severe forms of COVID-19 and pregnancy hypertensive disorders with comorbidity, and interaction between immune system, inflammatory cytokines and the renin angiotensin aldosterone system and its contribution to the hypertension pathogenesis. It is concluded that preeclampsia and gestational hypertension might be risk factors for SARS-CoV-2 infection and its complications.Infertility is one of the major problems faced in medicine. There are numerous factors that play a role in infertility. For example, numerous studies mention the impact of the quantity and quality of mitochondria in sexual gametes. This is a narrative review of the effects of the mitochondrial genome on fertility. We searched the PubMed, Science Direct, SID, Google Scholar, and Scopus databases for articles related to Fertility, Infertility, Miscarriage, Mitochondria, Sperm, mtDNA, Oocytes and other synonymous keywords from 2000 to 2020. The mitochondrial genome affects infertility in both male and female gametes; in sperm, it mainly releases free radicals. In the oocyte, a mutation in this genome can affect the amount of energy required after fertilisation, leading to gestation failure. In both cases, infertile cells have substantially less mitochondrial DNA (mtDNA) copies. The effects of mtDNA on gamete fertility occur via changes in oxidative phosphorylation and cellular energy production. Also, a reduction in the number of mtDNA copies is directly associated with sex cell infertility. Therefore, evaluation of the mitochondrial genome can be an excellent diagnostic option for couples who have children with neonatal disorders, infertile couples who seek assisted reproductive treatment, and those in whom assisted reproductive techniques have failed.

PMID:35639654 | DOI:10.22074/IJFS.2021.527076.1098

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Effects of The Mitochondrial Genome on Germ Cell Fertility: A Review of The Literature - DocWire News