Biology subjects

Tenson, T.

Publications and source records attributed to Tenson, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-cell analysis of pre-rRNA in Escherichia coli indicates distinct pathways of action for YbeX and YbeY proteins in ribosome biogenesis

The Escherichia coli protein YbeX/CorC is encoded in the same operon as the ribosome biogenesis factor YbeY, and its deletion leads to accumulation of 17S pre-rRNA and degradation intermediates of 16S rRNA under magnesium limitation. To further investigate the ybeX deletion phenotype, we used rRNA fluorescence in situ hybridization coupled with flow cytometry (rRNA-FISH-flow) to quantify 16S rRNA, 23S rRNA, and 17S pre-rRNA levels at single-cell resolution in{Delta} ybeX and{Delta} ybeY strains.{Delta} ybeX cells grown under limiting Mg2+ develop striking cell-to-cell heterogeneity in 17S pre-rRNA content during the transition to stationary phase, with up to 25-fold differences between individual cells. Upon regrowth from the stationary phase,{Delta} ybeX cultures display a bimodal distribution of 17S pre-rRNA, revealing two distinct subpopulations -- one retaining high levels of unprocessed pre-rRNA and the other with low levels -- whose relative proportions shift over time, until visible growth resumes. The stoichiometry between mature 16S and 23S rRNAs remains tight in both strains, indicating that the heterogeneity is specific to pre-rRNA processing, rather than a general disruption of ribosome homeostasis. The{Delta} ybeY mutant accumulates 17S pre-rRNA more uniformly across cells and primarily during exponential growth in rich medium, consistent with its direct role in 16S rRNA maturation. These single-cell data suggest that YbeX and YbeY affect ribosomal RNA metabolism through distinct mechanisms and that the extended lag phase of{Delta} ybeX is caused by a heterogeneous clearing of pre-ribosomal intermediates in individual cells.

molecular biology↗

bioRxiv2025

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

Viruses are among the most abundant and genetically diverse entities on Earth, yet the functions and evolutionary origins of most viral proteins remain poorly understood. Their rapid evolution often obscures evolutionary relationships, making it difficult to assign functions using sequence-based methods alone. Although conservation of protein fold can reveal deep homologies undetectable by sequence comparison, viral proteins remain vastly underrepresented in structural databases, limiting our ability to explore them at the structural level. Here, we address this gap by clustering all unique viral sequences from the NCBI RefSeq database and predicting the structures of [~]27,000 representative proteins using AlphaFold2, creating a large-scale viral structural resource, the Viral AlphaFold Database (VAD). We uncover [~]10,000 proteins belonging to clusters that share folds across viruses infecting bacteria, archaea, and eukaryotes, revealing shared protein folds across diverse host-infecting viruses. We also predict oligomeric states using AlphaFold2-based homodimer modelling, alongside structural comparisons to the Protein Data Bank, providing valuable new data on the potential for viral proteins to oligomerise. We further reveal that large regions of the viral protein universe remain functionally dark and report the discovery and experimental validation of a previously uncharacterised antiviral toxin-antitoxin (TA) system. VAD is a resource that provides a foundation for exploring viral structure-function relationships, including ancient folds that shape viral interactions across all life. Predicted structures used in this study are available at data-sharing.atkinson-lab.com/vad/.

molecular biology↗

bioRxiv2024

Antibacterial Compounds Against Non-Growing and Intracellular Bacteria

Slow- and non-growing bacterial populations, along with intracellular pathogens, often evade standard antibacterial treatments and are linked to persistent and recurrent infections. This necessitates the development of therapies specifically targeting nonproliferating bacteria. To identify compounds active against non-growing uropathogenic Escherichia coli (UPEC) we performed a drug-repurposing screen of 6,454 approved drugs and drug candidates. Using dilution-regrowth assays, we identified 39 compounds that either kill non-growing UPEC or delay its regrowth post-treatment. The hits include fluoroquinolones, macrolides, rifamycins, biguanide disinfectants, a pleuromutilin, and anti-cancer agents. 29 of the hits have not previously been recognized as active against non-growing bacteria. The hits were further tested against non-growing Pseudomonas aeruginosa and Staphylococcus aureus. Ten compounds - solithromycin, rifabutin, mitomycin C, and seven fluoroquinolones - have strong bactericidal activity against non-growing P. aeruginosa, killing >4 log10 of bacteria at 2.5 {micro}M. Solithromycin, valnemulin, evofosfamide, and satraplatin are unique in their ability to selectively target non-growing bacteria, exhibiting poor efficacy against growing bacteria. Finally, 31 hit compounds inhibit the growth of intracellular Shigella flexneri in a human enterocyte infection model, indicating their ability to permeate the cytoplasm of host cells. The identified compounds hold potential for treating persistent infections, warranting further comparative studies with current standard-of-care antibiotics.

microbiology↗

bioRxiv2024

Nanomotion technology for testing azithromycin susceptibility of Salmonella enterica

Azithromycin is used to treat invasive salmonellosis, despite conflicting effective concentrations in vitro and in vivo. Resistance of Salmonella enterica to azithromycin is increasing. We demonstrate that nanomotion technology can be used for rapid phenotypic testing of Salmonellas susceptibility to azithromycin. Nanomotion changes under various culture conditions correlated with susceptibility measured by MIC determination, CFU counting, and fluorescent reporter-based estimates of intrabacterial azithromycin accumulation.

microbiology↗

bioRxiv2024

A history of repeated antibiotic usage leads to microbiota-dependent mucus defects

Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and lastingly changes the gut microbiota community. However, the physiological effects of repeated - but not recent - antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply-phenotyped Estonian Microbiome Cohort (EstMB) we here utilised human-to-mouse faecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex-vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilising bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterised by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our findings suggest that long-term antibiotic use in humans results in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.

microbiology↗

bioRxiv2024

A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis

Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless the ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in B. subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in an position analogous to that of S4-domain-containing RqcP, and that, similarly to RqcP, YlmH can co-habit with RqcH. Consistently, we show that YlmH can assume the role of RqcP in RQC in facilitating the addition of polyalanine tails to the truncated nascent polypeptides. While in B. subtilis the function of YlmH is redundant with RqcP, our taxonomic analysis reveals that in multiple bacterial phyla RqcP is absent, while YlmH and RqcH are present, suggesting that in these species the YlmH plays a central role in the RQC.

microbiology↗

bioRxiv2024

Mechanism of phage sensing and abortion by toxin-antitoxin-chaperone systems

Toxin-antitoxins (TAs) are prokaryotic two-gene systems comprised of a toxin neutralised by an antitoxin. Toxin-antitoxin-chaperone (TAC) systems additionally include a SecB-like chaperone that stabilises the antitoxin by recognising its chaperone addiction (ChAD) element. TACs have been shown to mediate antiphage defence, but the mechanisms of viral sensing and restriction are unexplored. We identify and characterise two Escherichia coli antiphage TAC systems containing HigBA and CmdTA TA units, HigBAC and CmdTAC. The HigBAC is triggered through recognition of the gpV major tail protein of phage {lambda}. Both the ChAD and gpV are recognised by the HigC chaperone through analogous aromatic molecular patterns, explaining the mechanism of activation. We show that the CmdT ADP-ribosyltransferase toxin modifies mRNA to shut down protein synthesis. We establish the modularity of TACs by creating a hybrid broad-spectrum antiphage system combining the CmdTA TA warhead with the HigC chaperone phage sensor. HighlightsE. coli HigBAC and CmdTAC are translation-targeting phage immunity TAC systems HigC chaperone recognises phage {lambda} major tail protein to trigger HigBAC toxicity CmdT ADP-ribosyltransferase toxin abrogates translation through modification of mRNA HigC combined with CmdTA yields hybrid broad-spectrum antiphage defence system

microbiology↗

bioRxiv2023

The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin and related phage defence systems

Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode two proteins: a toxin and a neutralising antitoxin. Using our tool NetFlax (standing for Network-FlaGs for toxins and antitoxins) we have performed a large-scale bioinformatic analysis of proteinaceous TAs, revealing interconnected clusters constituting a core network of TA-like gene pairs. To understand the structural basis of toxin neutralisation by antitoxins, we have predicted the structures of 3,419 complexes with AlphaFold2. Together with mutagenesis and functional assays, our structural predictions provide insights into the neutralising mechanism of the hyperpromiscuous Panacea antitoxin domain. In antitoxins composed of standalone Panacea, the domain mediates direct toxin neutralisation, while in multidomain antitoxins the neutralisation is mediated by other domains, such as PAD1, Phd-C and ZFD. We hypothesise that Panacea acts as a sensor that regulates TA activation. We have experimentally validated 16 new NetFlax TA systems. We used functional domain annotations and with metabolic labelling assays to predict their potential mechanisms of toxicity (such as disruption of membrane integrity, inhibition of cell division and abrogation of protein synthesis) as well as biological functions (such as antiphage defence). The interactive version of the NetFlax TA network that includes structural predictions can be accessed at http://netflax.webflags.se/. Significance statementToxin-antitoxin systems are enigmatic components of microbial genomes, with their biological functions being a conundrum of debate for decades. Increasingly, TAs are being found to have a role in defence against bacteriophages. By mapping and experimentally validating a core combinatorial network of TA systems and high-throughput prediction of structural interfaces, we uncover the evolutionary scale of TA partner swapping and discover new toxic effectors. We validate the predicted toxin:antitoxin complex interfaces of four TA systems, uncovering the evolutionary malleable mechanism of toxin neutralisation by Panacea-containing PanA antitoxins. We find TAs are evolutionarily related to several other phage defence systems, cementing their role as important molecular components of the arsenal of microbial warfare.

microbiology↗

bioRxiv2023

Involvement of the putative metal efflux protein YbeX in ribosomal metabolism

YbeX of Escherichia coli, a member of CorC protein family, is a putative Co2+/ Mg2+ efflux factor. Here, we describe several{Delta} ybeX phenotypes and report an involvement of YbeX in ribosomal metabolism. E. coli lacking ybeX has a longer lag phase on outgrowth from the stationary phase. This phenotype is heterogeneous at the individual cell level and can be rescued by supplementing the growth media with magnesium.{Delta} ybeX strain is sensitive to elevated growth temperatures and to several ribosome-targeting antibiotics, which have a common ability to induce the cold shock response in E. coli.{Delta} ybeX cells accumulate distinct 16S rRNA degradation intermediates present in both 30S particles and 70S ribosomes. We propose that a function of YbeX is maintaining the magnesium homeostasis in the cell, which is needed for proper ribosomal assembly.

microbiology↗

bioRxiv2023

What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds

Driven by the development and upscaling of fast genome sequencing and assembly pipelines, the number of protein-coding sequences deposited in public protein sequence databases is increasing exponentially. Recently, the dramatic success of deep learning-based approaches applied to protein structure prediction has done the same for protein structures. We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database. These models cover most of the catalogued natural proteins, including those difficult to annotate for function or putative biological role based on standard, homology-based approaches. In this work, we quantified how much of such "dark matter" of the natural protein universe was structurally illuminated by AlphaFold2 and modelled this diversity as an interactive sequence similarity network that can be navigated at https://uniprot3d.org/atlas/AFDB90v4. In the process, we discovered multiple novel protein families by searching for novelties from sequence, structure, and semantic perspectives. We added a number of them to Pfam, and experimentally demonstrate that one of these belongs to a novel superfamily of translation-targeting toxin-antitoxin systems, TumE-TumA. This work highlights the role of large-scale, evolution-driven protein comparison efforts in combination with structural similarities, genomic context conservation, and deep-learning based function prediction tools for the identification of novel protein families, aiding not only annotation and classification efforts but also the curation and prioritisation of target proteins for experimental characterisation.

bioinformatics↗

bioRxiv2022

Synthetic oxepanoprolinamide iboxamycin is highly active against human pathogen Listeria monocytogenes

Listeriosis is a dangerous food-borne bacterial disease caused by the Gram-positive Bacillota (Firmicute) bacterium Listeria monocytogenes. In this report, we show that the synthetic lincosamide iboxamycin is highly active against L. monocytogenes and can overcome the intrinsic lincosamide resistance mediated by VgaL/Lmo0919, a member of ABCF ATPase resistance determinants that act by directly removing the antibiotic from the ribosome. While iboxamycin is not bactericidal against L. monocytogenes, it displays a pronounced postantibiotic effect, which is a valuable pharmacokinetic feature. Experiments in L. monocytogenes infection models are necessary to further assess the potential of iboxamycin as a novel drug for treatment of listeriosis. We demonstrate that VmlR ARE ABCF of Bacillota bacterium Bacillus subtilis grants significant (33-fold increase in MIC) protection from iboxamycin, while LsaA ABCF of Enterococcus faecalis grants an 8-fold protective effect. Furthermore, the VmlR-mediated iboxamycin resistance is cooperative with that mediated by the Cfr 23S rRNA methyltransferase resistance determinant, resulting in up to a 512-fold increase in MIC. Therefore, emergence and spread of ABCF ARE variants capable of defeating next-generation lincosamides in the clinic is possible and should be closely monitored.

microbiology↗

bioRxiv2022

Broad-spectrum mono- and combinational drug therapies for global viral pandemic preparedness

Broadly effective antiviral therapies must be developed to be ready for clinical trials, which should begin soon after the emergence of new life-threatening viruses. Here, we pave the way towards this goal by analyzing conserved druggable virus-host interactions, mechanisms of action and immunomodulatory properties of broad-spectrum antivirals (BSAs), routes of BSA delivery, and BSA interactions with other antivirals. Based on the analysis we developed scoring systems, which allowed us to predict novel BSAs and BSA-containing drug combinations (BCCs). Thus, we have developed a new strategy to broaden the spectrum of BSA indications and predict novel mono-and combinational therapies that can help better prepare for imminent future viral outbreaks. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/476444v2_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@7fee8dorg.highwire.dtl.DTLVardef@1069131org.highwire.dtl.DTLVardef@2632bforg.highwire.dtl.DTLVardef@1cdcbf0_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Active components of commonly prescribed medicines affect influenza A virus-host cell interaction: a pilot study

BackgroundEvery year, millions of people are hospitalized, and thousands die from influenza A virus (FLUAV) infection. Most cases of hospitalizations and death occur among elderly. Many of these elderly patients are reliant on medical treatment of underlying chronic diseases, such as arthritis, diabetes, and hypertension. We hypothesized that the commonly prescribed medicines for treatment of underlying chronic diseases can affect host responses to FLUAV infection, and thus contribute to morbidity and mortality associated with influenza. Therefore, the aim of this study was to examine whether commonly prescribed medicines could affect host responses to virus infection in vitro. MethodsWe first identified 45 active compounds of commonly prescribed medicines. Then we constructed a drug-target interaction network and identified potential implication of these interactions for FLUAV-host cell interplay. Finally, we tested the effect of 45 drugs on viability, transcription and metabolism of mock- and FLUAV-infected human retinal pigment epithelial (RPE) cells. ResultsIn silico drug-target interaction analysis revealed that many drugs, such as atorvastatin, candesartan, and hydroxocobalam, could target and modulate FLUAV-host cell interaction. In vitro experiments showed that these and other compounds at non-cytotoxic concentrations differently affected transcription and metabolism of mock- and FLUAV-infected cells. ConclusionMany commonly prescribed drugs modulate FLUAV-host cell interactions in silico and in vitro and, therefore, could affect their interplay in vivo, thus, contributing to morbidity and mortality of patients with influenza virus infections.

pharmacology and toxicology↗

bioRxiv2021

Nafamostat-interferon-alpha combination suppresses SARS-CoV-2 infection in vitro and in vivo

SARS-CoV-2 and its vaccine/immune-escaping variants continue to pose a serious threat to public health due to a paucity of effective, rapidly deployable, and widely available treatments. Here, we address these challenges by combining Pegasys (IFNa) and nafamostat to effectively suppress SARS-CoV-2 infection in cell culture and hamsters. Our results indicate that Serpin E1 is an important mediator of the antiviral activity of IFNa and that both Serpin E1 and camostat can target the same cellular factor TMPRSS2, which plays a critical role in viral replication. The low doses of the drugs in combination may have several clinical advantages, including fewer adverse events and improved patient outcome. Thus, our study may provide a proactive solution for the ongoing pandemic and potential future coronavirus outbreaks, which is still urgently required in many parts of the world.

microbiology↗

bioRxiv2021

Panacea: a hyperpromiscuous antitoxin protein domain for the neutralisation of diverse toxin domains

Toxin-Antitoxin (TA) gene pairs are ubiquitous in microbial chromosomal genomes and plasmids, as well as bacteriophages. They act as regulatory switches, with the toxin limiting the growth of bacteria and archaea by compromising diverse essential cellular targets, and the antitoxin counteracting the toxic effect. To uncover previously uncharted TA diversity across microbes and bacteriophages, we analysed the conservation of genomic neighbourhoods using our computational tool FlaGs (for Flanking Genes), which allows high-throughput detection of TA-like operons. Focussing on the widespread but poorly experimentally characterised antitoxin domain DUF4065, our in silico analyses indicated that DUF4065-containing proteins serve as broadly distributed antitoxin components in putative TA-like operons with dozens of different toxic domains with multiple different folds. Given the versatility of DUF4065, we have renamed the domain to Panacea (and proteins containing the domain, PanA) after the Greek goddess of universal remedy. We have experimentally validated nine PanA-neutralised TA pairs. While the majority of validated PanA-neutralised toxins act as translation inhibitors or membrane disruptors, a putative nucleotide cyclase toxin from a Burkholderia prophage compromises replication and translation, as well as inducing RelA-dependent accumulation of the nucleotide alarmone (p)ppGpp. We find that Panacea-containing antitoxins form a complex with their diverse cognate toxins, characteristic of the direct neutralisation mechanisms employed by Type II TA systems. Finally, through directed evolution we have selected PanA variants that can neutralise non-cognate TA toxins, thus experimentally demonstrating the evolutionary plasticity of this hyperpromiscuous antitoxin domain. SignificanceToxin-antitoxin systems are enigmatic and diverse elements of bacterial and bacteriophage genomes. We have uncovered remarkable versatility of an antitoxin protein domain, that has evolved to neutralise dozens of different toxin domains. We find that antitoxins carrying this domain - Panacea - form complexes with their cognate toxins, indicating a direct neutralisation mechanism, and that Panacea can be evolved to neutralise a non-cognate and non-homologous toxin with just two amino acid substitutions. This raises the possibility that this domain could be an adaptable universal, or semi-universal protein neutraliser with significant biotechnological and medical potential.

microbiology↗

bioRxiv2021

RelA-SpoT Homologue toxins pyrophosphorylate the CCA end of tRNA to inhibit protein synthesis

RelA-SpoT Homolog (RSH) enzymes control bacterial physiology through synthesis and degradation of the nucleotide alarmone (p)ppGpp. We recently discovered multiple families of Small Alarmone Synthetase (SAS) RSH acting as toxins of toxin-antitoxin (TA) modules, with the FaRel subfamily of toxSAS abrogating bacterial growth by producing an analogue of (p)ppGpp, (pp)pApp. Here we probe the mechanism of growth arrest employed by four experimentally unexplored subfamilies of toxSAS: FaRel2, PhRel, PhRel2 and CapRel. Surprisingly, all these toxins specifically inhibit protein synthesis. To do so, they transfer a pyrophosphate moiety from ATP to the tRNA 3' CCA. The modification inhibits both tRNA aminoacylation and the sensing of cellular amino acid starvation by the ribosome-associated RSH RelA. Conversely, we show that some Small Alarmone Hydrolase (SAH) RSH enzymes can reverse the pyrophosphorylation of tRNA to counter the growth inhibition by toxSAS. Collectively, we establish RSHs as a novel class of RNA-modifying enzymes.

microbiology↗

bioRxiv2021

Synergistic interferon alpha-based drug combinations inhibit SARS-CoV-2 and other viral infections in vitro

There is an urgent need for new antivirals with powerful therapeutic potential and tolerable side effects. In the present study, we found that recombinant human interferon-alpha (IFNa) triggers intrinsic and extrinsic cellular antiviral responses, as well as reduces replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro. Although IFNa alone was insufficient to completely abolish SARS-CoV-2 replication, combinations of IFNa with remdesivir or other antiviral agents (EIDD-2801, camostat, cycloheximide, or convalescent serum) showed strong synergy and effectively inhibited SARS-CoV-2 infection in human lung epithelial Calu-3 cells. Furthermore, we showed that the IFNa-remdesivir combination suppressed virus replication in human lung organoids, and that its single prophylactic dose attenuated SARS-CoV-2 infection in lungs of Syrian hamsters. Transcriptome and metabolomic analyses showed that the combination of IFNa-remdesivir suppressed virus-mediated changes in infected cells, although it affected the homeostasis of uninfected cells. We also demonstrated synergistic antiviral activity of IFNa2a-based combinations against other virus infections in vitro. Altogether, our results indicate that IFNa2a-based combination therapies can achieve higher efficacy while requiring lower dosage compared to monotherapies, making them attractive targets for further pre-clinical and clinical development.

microbiology↗

bioRxiv2021

A field-wide assessment of differential high throughput sequencing reveals widespread bias

Here we assess inferential quality in the field of differential expression profiling by high throughput sequencing, based on analysis of datasets submitted 2008-2020 to the NCBI GEO data repository. We take advantage of the parallel differential expression testing over thousands of genes, whereby each experiment leads to a large set of p values, the distribution of which can indicate the validity of assumptions behind the test. Moreover, from a well-behaved p value set{pi} 0, the fraction of genes that are not differentially expressed, can be estimated. We found that only 25% of experiments resulted in theoretically expected p value histogram shapes, although there is a marked improvement over time. Uniform p value histogram shapes, indicative of < 100 true effects, were extremely few. Furthermore, although many HT-seq workflows assume that most genes are not differentially expressed we found 37% of experiments to have{pi} 0-s of less than 0.5, as if most genes changed their expression level. Restricting our analysis to studies involving cancer or transcription factors, expected to lead to real changes in expression of many genes, did not result in meaningfully different distributions of{pi} 0-s. Both the fractions of different p value histogram types and the{pi} 0 values are strongly associated with the differential expression analysis program used by the original authors. While we could double the proportion of theoretically expected p value distributions by removing low-count features from analysis, this treatment did not remove the association with the analysis program. Taken together, our results indicate widespread bias in differential expression profiling field.

bioinformatics↗