Transcriptional adaptation of Mycobacterium tuberculosis that survives prolonged multi-drug treatment in mice.

To address the ongoing global tuberculosis crisis, there is a need for shorter, more effective treatments. A major reason why tuberculosis requires prolonged treatment is that, following a short initial phase of rapid killing, the residual Mycobacterium tuberculosis withstands drug killing. Because existing methods lack sensitivity to quantify low-abundance mycobacterial RNA in drug-treated animals, cellular adaptations of drug-exposed bacterial phenotypes in vivo remain poorly understood. Here, we used a novel RNA-seq method called SEARCH-TB to elucidate the Mycobacterium tuberculosis transcriptome in mice treated for up to 28 days with standard doses of isoniazid, rifampin, pyrazinamide, and ethambutol. We compared murine results with in vitro SEARCH-TB results during exposure to the same regimen. Treatment suppressed genes associated with growth, transcription, translation, synthesis of rRNA proteins, and immunogenic secretory peptides. Bacteria that survived prolonged treatment appeared to transition from ATP-maximizing respiration toward lower-efficiency pathways and showed modification and recycling of cell wall components, large-scale regulatory reprogramming, and reconfiguration of efflux pump expression. Although the pre-treatment in vivo and in vitro transcriptomes differed profoundly, genes differentially expressed following treatment in vivo and in vitro were similar, with differences likely attributable to immunity and drug pharmacokinetics in mice. These results reveal cellular adaptations of Mycobacterium tuberculosis that withstand prolonged drug exposure in vivo, demonstrating proof of concept that SEARCH-TB is a highly granular pharmacodynamic readout. The surprising finding that differential expression is concordant in vivo and in vitro suggests that insights from transcriptional analyses in vitro may translate to the mouse. IMPORTANCE A major reason that curing tuberculosis requires prolonged treatment is that drug exposure changes bacterial phenotypes. The physiologic adaptations of Mycobacterium tuberculosis that survive drug exposure in vivo have been obscure due to low sensitivity of existing methods in drug-treated animals. Using the novel SEARCH-TB RNA-seq platform, we elucidated Mycobacterium tuberculosis phenotypes in mice treated for with the global standard 4-drug regimen and compared them with the effect of the same regimen in vitro. This first view of the transcriptome of the minority Mycobacterium tuberculosis population that withstands treatment in vivo reveals adaptation of a broad range of cellular processes, including a shift in metabolism and cell wall modification. Surprisingly, the change in gene expression induced by treatment in vivo and in vitro was largely similar. This apparent "portability" from in vitro to the mouse provides important new context for in vitro transcriptional analyses that may support early preclinical drug evaluation.

Transcriptional adaptation of drug-tolerant Mycobacterium tuberculosis in mice.

Transcriptome evaluation of Mycobacterium tuberculosis in the lungs of laboratory animals during long-term treatment has been limited by extremely low abundance of bacterial mRNA relative to eukaryotic RNA. Here we report a targeted amplification RNA sequencing method called SEARCH-TB. After confirming that SEARCH-TB recapitulates conventional RNA-seq in vitro, we applied SEARCH-TB to Mycobacterium tuberculosis-infected BALB/c mice treated for up to 28 days with the global standard isoniazid, rifampin, pyrazinamide, and ethambutol regimen. We compared results in mice with 8-day exposure to the same regimen in vitro. After treatment of mice for 28 days, SEARCH-TB suggested broad suppression of genes associated with bacterial growth, transcription, translation, synthesis of rRNA proteins and immunogenic secretory peptides. Adaptation of drug-stressed Mycobacterium tuberculosis appeared to include a metabolic transition from ATP-maximizing respiration towards lower-efficiency pathways, modification and recycling of cell wall components, large-scale regulatory reprogramming, and reconfiguration of efflux pumps expression. Despite markedly different expression at pre-treatment baseline, murine and in vitro samples had broadly similar transcriptional change during treatment. The differences observed likely indicate the importance of immunity and pharmacokinetics in the mouse. By elucidating the long-term effect of tuberculosis treatment on bacterial cellular processes in vivo, SEARCH-TB represents a highly granular pharmacodynamic monitoring tool with potential to enhance evaluation of new regimens and thereby accelerate progress towards a new generation of more effective tuberculosis treatment.

lmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models.

BACKGROUND: Studies that utilize RNA Sequencing (RNA-Seq) in conjunction with designs that introduce dependence between observations (e.g. longitudinal sampling) require specialized analysis tools to accommodate this additional complexity. This R package contains a set of utilities to fit linear mixed effects models to transformed RNA-Seq counts that properly account for this dependence when performing statistical analyses. RESULTS: In a simulation study comparing lmerSeq and two existing methodologies that also work with transformed RNA-Seq counts, we found that lmerSeq was comprehensively better in terms of nominal error rate control and statistical power. CONCLUSIONS: Existing R packages for analyzing transformed RNA-Seq data with linear mixed models are limited in the variance structures they allow and/or the transformation methods they support. The lmerSeq package offers more flexibility in both of these areas and gave substantially better results in our simulations.

A comparison of methods for multiple degree of freedom testing in repeated measures RNA-sequencing experiments.

BACKGROUND: As the cost of RNA-sequencing decreases, complex study designs, including paired, longitudinal, and other correlated designs, become increasingly feasible. These studies often include multiple hypotheses and thus multiple degree of freedom tests, or tests that evaluate multiple hypotheses jointly, are often useful for filtering the gene list to a set of interesting features for further exploration while controlling the false discovery rate. Though there are several methods which have been proposed for analyzing correlated RNA-sequencing data, there has been little research evaluating and comparing the performance of multiple degree of freedom tests across methods. METHODS: We evaluated 11 different methods for modelling correlated RNA-sequencing data by performing a simulation study to compare the false discovery rate, power, and model convergence rate across several hypothesis tests and sample size scenarios. We also applied each method to a real longitudinal RNA-sequencing dataset. RESULTS: Linear mixed modelling using transformed data had the best false discovery rate control while maintaining relatively high power. However, this method had high model non-convergence, particularly at small sample sizes. No method had high power at the lowest sample size. We found a mix of conservative and anti-conservative behavior across the other methods, which was influenced by the sample size and the hypothesis being evaluated. The patterns observed in the simulation study were largely replicated in the analysis of a longitudinal study including data from intensive care unit patients experiencing cardiogenic or septic shock. CONCLUSIONS: Multiple degree of freedom testing is a valuable tool in longitudinal and other correlated RNA-sequencing experiments. Of the methods that we investigated, linear mixed modelling had the best overall combination of power and false discovery rate control. Other methods may also be appropriate in some scenarios.

Refractory neutrophilic asthma and ciliary genes.

BACKGROUND: Refractory asthma (RA) remains poorly controlled, resulting in high health care utilization despite guideline-based therapies. Patients with RA manifest higher neutrophilia as a result of increased airway inflammation and subclinical infection, the underlying mechanisms of which remain unclear. OBJECTIVE: We sought to characterize and clinically correlate gene expression differences between refractory and nonrefractory (NR) asthma to uncover molecular mechanisms driving group distinctions. METHODS: Microarray gene expression of paired airway epithelial brush and endobronchial biopsy samples was compared between 60 RA and 30 NR subjects. Subjects were hierarchically clustered to identify subgroups of RA, and biochemical and clinical traits (airway inflammatory molecules, respiratory pathogens, chest imaging) were compared between groups. Weighted gene correlation network analysis was used to identify coexpressed gene modules. Module expression scores were compared between groups using linear regression, controlling for age, sex, and body mass index. RESULTS: Differential gene expression analysis showed upregulation of proneutrophilic and downregulation of ciliary function genes/pathways in RA compared to NR. A subgroup of RA with downregulated ciliary gene expression had increased levels of subclinical infections, airway neutrophilia, and eosinophilia as well as higher chest imaging mucus burden compared to other RA, the dominant differences between RA and NR. Weighted gene correlation network analysis identified gene modules related to ciliary function, which were downregulated in RA and were associated with lower pulmonary function and higher airway wall thickness/inflammation, markers of poorer asthma control. CONCLUSIONS: Identification of a novel ciliary-deficient subgroup of RA suggests that diminished mucociliary clearance may underlie repeated asthma exacerbations despite adequate treatment, necessitating further exploration of function, mechanism, and therapeutics.

Prevalence and type of ocular disease in a population of aged captive nondomestic felids.

OBJECTIVES: Report of prevalence and type of ocular disease in a captive population of nondomestic felids. METHODS: Medical records of 202 cats from 1993 to 2018 were reviewed. Species, age at diagnosis, sex, ocular examination abnormalities, systemic/physical examination abnormalities, type of examination (visual, sedated, or anesthetized), ocular structures affected, other diagnostics, therapy, and resolution of ocular disease were recorded. RESULTS: A total of 202 nondomestic felids including 18 different species (bobcat, caracal, cougar, Fishing cat, Geoffroy's cat, jaguar, jungle cat, leopard, leopard cat, liger, lion, lynx, ocelot, Sand cat, Savannah cat, serval, snow leopard, and tiger) from a rescue facility were evaluated. Forty-six ocular lesions were diagnosed in 33 (16.3%) cats from 8 different species (bobcat, caracal, cougar, leopard, lion, ocelot, serval, and tiger) with a mean age of 16 ± 5.9 years at time of diagnosis. Ocular lesions included corneal disease (37%) (ulcerations, perforations, keratitis, corneal scars), cataracts (23.9%), hyphema (8.7%), lens luxation (6.5%), retinal detachment (6.5%), uveitis (4.3%), conjunctival disease (4.3%), retinal degeneration (2.1%), glaucoma (2.1%), and optic neuritis (2.1%). Therapies included medical (topical antibiotics, anti-inflammatories, serum, etc.) and/or surgical management (enucleation, intracapsular lens extraction, corneoconjunctival transposition, and corneal burr debridement). CONCLUSIONS: To the authors' knowledge, this is the first report of the prevalence of ocular disease in a population of captive nondomestic felids. It is difficult to diagnose and treat ocular disease in nondomestic cats due to challenges related to handling, diagnostics, and therapeutics in nondomestic species. Ocular disease seen in this population is similar to that found in domestic cat populations.

Keratometry, biometry, and prediction of intraocular lens power in adult tigers (Panthera tigris).

OBJECTIVE: To calculate the necessary pseudophakic intraocular lens (IOL) power to approximate emmetropia in adult tigers. ANIMALS: 17 clinically normal adult tigers. PROCEDURES: 33 eyes of 17 clinically normal adult tigers underwent routine ophthalmic examination and B-scan ultrasonography while anesthetized for unrelated procedures. Specific ultrasound data (globe measurements and corneal curvature) and estimated postoperative IOL positions were utilized to calculate predicted IOL power by use of Retzlaff and Binkhorst theoretical formulas. Applanation tonometry and refraction were also performed. RESULTS: Mean ± SD axial globe length was 29.36 ± 0.82 mm, preoperative anterior chamber depth was 7.00 ± 0.74 mm, and crystalline lens thickness was 8.72 ± 0.56 mm. Mean net refractive error (n = 33 eyes) was +0.27 ± 0.30 diopters (D). By use of the Retzlaff formula, mean predicted IOL power for the postoperative anterior chamber depth (PACD), PACD - 2 mm, and PACD + 2 mm was 43.72 ± 4.84 D, 37.62 ± 4.19 D, and 51.57 ± 5.72 D, respectively. By use of the Binkhorst equation, these values were 45.11 ± 4.91 D, 38.84 ± 4.25 D, and 53.18 ± 5.81 D, respectively. Mean intraocular pressure for all eyes was 14.7 ± 2.69 mm Hg. CLINICAL RELEVANCE: The calculated tiger IOL was lower than reported values for adult domestic felids. Further studies evaluating actual PACD and pseudophakic refraction would help determine the appropriate IOL power to achieve emmetropia in this species.

Ensconsin-dependent changes in microtubule organization and LINC complex-dependent changes in nucleus-nucleus interactions result in quantitatively distinct myonuclear positioning defects.

Nuclear movement is a fundamental process of eukaryotic cell biology. Skeletal muscle presents an intriguing model to study nuclear movement because its development requires the precise positioning of multiple nuclei within a single cytoplasm. Furthermore, there is a high correlation between aberrant nuclear positioning and poor muscle function. Although many genes that regulate nuclear movement have been identified, the mechanisms by which these genes act are not known. Using Drosophila melanogaster muscle development as a model system and a combination of live-embryo microscopy and laser ablation of nuclei, we have found that clustered nuclei encompass at least two phenotypes that are caused by distinct mechanisms. Specifically, Ensconsin is necessary for productive force production to drive any movement of nuclei, whereas Bocksbeutel and Klarsicht are necessary to form distinct populations of nuclei that move to different cellular locations. Mechanistically, Ensconsin regulates the number of growing microtubules that are used to move nuclei, whereas Bocksbeutel and Klarsicht regulate interactions between nuclei.

MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments.

BACKGROUND: As the barriers to incorporating RNA sequencing (RNA-Seq) into biomedical studies continue to decrease, the complexity and size of RNA-Seq experiments are rapidly growing. Paired, longitudinal, and other correlated designs are becoming commonplace, and these studies offer immense potential for understanding how transcriptional changes within an individual over time differ depending on treatment or environmental conditions. While several methods have been proposed for dealing with repeated measures within RNA-Seq analyses, they are either restricted to handling only paired measurements, can only test for differences between two groups, and/or have issues with maintaining nominal false positive and false discovery rates. In this work, we propose a Bayesian hierarchical negative binomial generalized linear mixed model framework that can flexibly model RNA-Seq counts from studies with arbitrarily many repeated observations, can include covariates, and also maintains nominal false positive and false discovery rates in its posterior inference. RESULTS: In simulation studies, we showed that our proposed method (MCMSeq) best combines high statistical power (i.e. sensitivity or recall) with maintenance of nominal false positive and false discovery rates compared the other available strategies, especially at the smaller sample sizes investigated. This behavior was then replicated in an application to real RNA-Seq data where MCMSeq was able to find previously reported genes associated with tuberculosis infection in a cohort with longitudinal measurements. CONCLUSIONS: Failing to account for repeated measurements when analyzing RNA-Seq experiments can result in significantly inflated false positive and false discovery rates. Of the methods we investigated, whether they model RNA-Seq counts directly or worked on transformed values, the Bayesian hierarchical model implemented in the mcmseq R package (available at https://github.com/stop-pre16/mcmseq ) best combined sensitivity and nominal error rate control.

Pathogenicity and selective constraint on variation near splice sites.

Mutations that perturb normal pre-mRNA splicing are significant contributors to human disease. We used exome sequencing data from 7833 probands with developmental disorders (DDs) and their unaffected parents, as well as more than 60,000 aggregated exomes from the Exome Aggregation Consortium, to investigate selection around the splice sites and quantify the contribution of splicing mutations to DDs. Patterns of purifying selection, a deficit of variants in highly constrained genes in healthy subjects, and excess de novo mutations in patients highlighted particular positions within and around the consensus splice site of greater functional relevance. By using mutational burden analyses in this large cohort of proband-parent trios, we could estimate in an unbiased manner the relative contributions of mutations at canonical dinucleotides (73%) and flanking noncanonical positions (27%), and calculate the positive predictive value of pathogenicity for different classes of mutations. We identified 18 patients with likely diagnostic de novo mutations in dominant DD-associated genes at noncanonical positions in splice sites. We estimate 35%-40% of pathogenic variants in noncanonical splice site positions are missing from public databases.

Lyplal1 is dispensable for normal fat deposition in mice.

Genome-wide association studies (GWAS) have detected association between variants in or near the Lysophospholipase-like 1 (LYPLAL1) locus and metabolic traits, including central obesity, fatty liver and waist-to-hip ratio. LYPLAL1 is also known to be upregulated in the adipose tissue of obese patients. However, the physiological role of LYPLAL1 is not understood. To investigate the function of Lyplal1 in vivo we investigated the phenotype of the Lyplal1tm1a(KOMP)Wtsi homozygous mouse. Body composition was unaltered in Lyplal1 knockout mice as assessed by dual-energy X-ray absorptiometry (DEXA) scanning, both on normal chow and on a high-fat diet. Adipose tissue distribution between visceral and subcutaneous fat depots was unaltered, with no change in adipocyte cell size. The response to both insulin and glucose dosing was normal in Lyplal1tm1a(KOMP)Wtsi homozygous mice, with normal fasting blood glucose concentrations. RNAseq analysis of liver, muscle and adipose tissue confirmed that Lyplal1 expression was ablated with minimal additional changes in gene expression. These results suggest that Lyplal1 is dispensable for normal mouse metabolic physiology and that despite having been maintained through evolution Lyplal1 is not an essential gene, suggesting possible functional redundancy. Further studies will be required to clarify its physiological role.

Genomic variation in the vomeronasal receptor gene repertoires of inbred mice.

BACKGROUND: Vomeronasal receptors (VRs), expressed in sensory neurons of the vomeronasal organ, are thought to bind pheromones and mediate innate behaviours. The mouse reference genome has over 360 functional VRs arranged in highly homologous clusters, but the vast majority are of unknown function. Differences in these receptors within and between closely related species of mice are likely to underpin a range of behavioural responses. To investigate these differences, we interrogated the VR gene repertoire from 17 inbred strains of mice using massively parallel sequencing. RESULTS: Approximately half of the 6222 VR genes that we investigated could be successfully resolved, and those that were unambiguously mapped resulted in an extremely accurate dataset. Collectively VRs have over twice the coding sequence variation of the genome average; but we identify striking non-random distribution of these variants within and between genes, clusters, clades and functional classes of VRs. We show that functional VR gene repertoires differ considerably between different Mus subspecies and species, suggesting these receptors may play a role in mediating behavioural adaptations. Finally, we provide evidence that widely-used, highly inbred laboratory-derived strains have a greatly reduced, but not entirely redundant capacity for differential pheromone-mediated behaviours. CONCLUSIONS: Together our results suggest that the unusually variable VR repertoires of mice have a significant role in encoding differences in olfactory-mediated responses and behaviours. Our dataset has expanded over nine fold the known number of mouse VR alleles, and will enable mechanistic analyses into the genetics of innate behavioural differences in mice.

Comparison of single time-point [111-In] pentetreotide SPECT/CT with dual time-point imaging of neuroendocrine tumors.

PURPOSE: to determine whether single time-point single-photon emission computed tomography-computed tomography (SPECT/CT) somatostatin receptor imaging can replace traditional dual time-point planar and SPECT somatostatin receptor scintigraphy for evaluation of neuroendocrine tumors. MATERIALS AND METHODS: twenty-four patients (9 males, 15 females; mean age: 56 years; range: 14-82 years) underwent [111-In] pentetreotide scintigraphy, with planar whole-body images acquired at 24 and 48 hours after injection and abdominal SPECT/CT at 24 hours postinjection. Two blinded readers independently interpreted each study, using single time-point (24 hours planar and SPECT/CT) and separately using dual time-point (24- and 48-hours planar, and 24-hour SPECT without CT) image information. Consensus interpretations were compared with surgical pathology, or clinical and radiologic follow-up for at least 12 months. RESULTS: Interobserver agreement was excellent (κ = 0.86) for single time-point imaging, and good (κ = 0.56) with dual time-point imaging. After consensus review, single time-point imaging identified pathologic lesions in 11 of 12 subjects with diagnosis of NET at follow-up, and in 0 of 12 subjects without NET (sensitivity 92%; specificity 100%). Dual time-point imaging performed similarly, but missed an additional NET case (sensitivity 83%; specificity 100%). After review of SPECT/CT, the readers considered that additional 48 hours imaging was not necessary in the majority of cases, indicating high degree of confidence with the single time-point imaging. CONCLUSION: [111-In] pentetreotide SPECT/CT imaging at 24 hours identifies pathologic disease sites and distinguishes physiologic activity equally well compared to traditional strategies using 2 imaging days. Routine use of SPECT/CT will allow single time-point imaging without loss of diagnostic accuracy, enhancing patient convenience, and clinical throughput.