rworkflows: automating reproducible practices for the R community

Despite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards sharing open-source software has been revolutionary, GitHub does not have any default built-in checks for minimal coding standards or software usability. This makes it difficult to assess the current quality R packages, or to consistently use them over time and across platforms. While GitHub-native solutions are technically possible, they require considerable time and expertise for each developer to write, implement, and maintain. To address this, we develop rworkflows; a suite of tools to make robust continuous integration and deployment ( https://github.com/neurogenomics/rworkflows ). rworkflows can be implemented by developers of all skill levels using a one-time R function call which has both sensible defaults and extensive options for customisation. Once implemented, any updates to the GitHub repository automatically trigger parallel workflows that install all software dependencies, run code checks, generate a dedicated documentation website, and deploy a publicly accessible containerised environment. By making the rworkflows suite free, automated, and simple to use, we aim to promote widespread adoption of reproducible practices across a continually growing R community.

Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer's disease dataset

Mathys et al. conducted the first single-nucleus RNA-seq (snRNA-seq) study of Alzheimer's disease (AD) (Mathys et al., 2019). With bulk RNA-seq, changes in gene expression across cell types can be lost, potentially masking the differentially expressed genes (DEGs) across different cell types. Through the use of single-cell techniques, the authors benefitted from increased resolution with the potential to uncover cell type-specific DEGs in AD for the first time. However, there were limitations in both their data processing and quality control and their differential expression analysis. Here, we correct these issues and use best-practice approaches to snRNA-seq differential expression, resulting in 549 times fewer DEGs at a false discovery rate of 0.05. Thus, this study highlights the impact of quality control and differential analysis methods on the discovery of disease-associated genes and aims to refocus the AD research field away from spuriously identified genes.

EpiCompare: R package for the comparison and quality control of epigenomic peak files

Summary

EpiCompare combines a variety of downstream analysis tools to compare, quality control and benchmark different epigenomic datasets. The package requires minimal input from users, can be run with just one line of code and provides all results of the analysis in a single interactive HTML report. EpiCompare thus enables downstream analysis of multiple epigenomic datasets in a simple, effective and user-friendly manner.

Availability and implementation

EpiCompare is available on Bioconductor (≥ v3.15): https://bioconductor.org/packages/release/bioc/html/EpiCompare.html; all source code is publicly available via GitHub: https://github.com/neurogenomics/EpiCompare; documentation website https://neurogenomics.github.io/EpiCompare; and EpiCompare DockerHub repository: https://hub.docker.com/repository/docker/neurogenomicslab/epicompare.

Transcriptomic analyses reveal neuronal specificity of Leigh syndrome associated genes

Leigh syndrome is a rare, inherited, complex neurometabolic disorder with genetic and clinical heterogeneity. Features present in affected patients range from classical stepwise developmental regression to ataxia, seizures, tremor, and occasionally psychiatric manifestations. Currently, more than 100 monogenic causes of Leigh syndrome have been identified, yet the pathophysiology remains unknown. Here, we sought to determine the cellular specificity within the brain of all genes currently associated with Leigh syndrome. Further, we aimed to investigate potential genetic commonalities between Leigh syndrome and other disorders with overlapping clinical features. Enrichment of our target genes within the brain was evaluated with co-expression (CoExp) network analyses constructed using existing UK Brain Expression Consortium data. To determine the cellular specificity of the Leigh associated genes, we employed expression weighted cell type enrichment (EWCE) analysis of single-cell RNA-Seq data. Finally, CoExp network modules demonstrating enrichment of Leigh syndrome associated genes were then utilised for synaptic gene ontology analysis and heritability analysis. CoExp network analyses revealed that Leigh syndrome associated genes exhibit the highest levels of expression in brain regions most affected on MRI in affected patients. EWCE revealed significant enrichment of target genes in hippocampal and somatosensory pyramidal neurons and interneurons of the brain. Analysis of CoExp modules enriched with our target genes revealed preferential association with pre-synaptic structures. Heritability studies suggested some common enrichment between Leigh syndrome and Parkinson disease and epilepsy. Our findings suggest a primary mitochondrial dysfunction as the underlying basis of Leigh syndrome, with associated genes primarily expressed in neuronal cells.

Multidimensional dynamics of the proteome in the neurodegenerative and aging mammalian brain

The amount of any given protein in the brain is determined by the rates of its synthesis and destruction, which are regulated by different cellular mechanisms. Here, we combine metabolic labeling in live mice with global proteomic profiling to simultaneously quantify both the flux and amount of proteins in mouse models of neurodegeneration. In multiple models, protein turnover increases were associated with increasing pathology. This method distinguishes changes in protein expression mediated by synthesis from those mediated by degradation. In the App^NL-F knockin mouse model of Alzheimer’s disease, increased turnover resulted from imbalances in both synthesis and degradation, converging on proteins associated with synaptic vesicle recycling (Dnm1, Cltc, Rims1) and mitochondria (Fis1, Ndufv1). In contrast to disease models, aging in wild-type mice caused a widespread decrease in protein recycling associated with a decrease in autophagic flux. Overall, this simple multidimensional approach enables a comprehensive mapping of proteome dynamics and identifies affected proteins in mouse models of disease and other live animal test settings.

•

Multidimensional proteomic screen to detect imbalances in mouse models of disease.

•

Increased proteome turnover in multiple symptomatic neurodegeneration mouse models.

•

Healthy aging is associated with a global decrease in protein turnover.

MungeSumstats: A Bioconductor package for the standardisation and quality control of many GWAS summary statistics

Motivation

Genome‐wide association studies (GWAS) summary statistics have popularized and accelerated genetic research. However, a lack of standardization of the file formats used has proven problematic when running secondary analysis tools or performing meta-analysis studies.

Results

To address this issue, we have developed MungeSumstats, a Bioconductor R package for the standardization and quality control of GWAS summary statistics. MungeSumstats can handle the most common summary statistic formats, including variant call format (VCF) producing a reformatted, standardized, tabular summary statistic file, VCF or R native data object.

Availability and implementation

MungeSumstats is available on Bioconductor (v 3.13) and can also be found on Github at: https://neurogenomics.github.io/MungeSumstats.

Supplementary information

Supplementary data are available at Bioinformatics online.

Extrapituitary GH in the chicken: underestimation of immunohistochemical staining by Carnoy's fixation

GH has previously been shown to be present in peripheral extrapituitary tIssues of chick embryos, but the cellular distribution of GH immunoreactivity is still uncertain because of differing immunohistochemical findings. The possibility that this uncertainty reflects differences in fixation of the embryonic tIssues was assessed by comparing GH immunoreactivity in tIssues fixed in 4% (w/v) paraformaldehyde or Carnoy's fluid (60% ethanol (v/v); 30% chloroform (v/v); 10% acetic acid (v/v)). A widespread distribution of GH immunoreactivity was seen in paraformaldehyde-fixed tIssues, although it was particularly intense in the spinal cord, dorsal and ventral root ganglia, notochord, myotome, epidermis, crop, heart, lung and humerus. In marked contrast, GH immunoreactivity in embryonic tIssues fixed with Carnoy's was more discrete and mainly restricted to marginal and mantle layers of the spinal cord, spinal nerves, the ventral root ganglia and the extensor nerve of the anterior limb bud. Since these are neural derivatives, Carnoy's fixation appears to preferentially result in neural GH staining, whereas GH staining in neural and non-neural tIssues is seen after paraformaldehyde fixation. Carnoy's, because it is a precipitive fixative, may only fix large GH moieties, whereas GH in peripheral tIssues includes numerous molecular variants, many of which are of relatively small size. Paraformaldehyde, because it is a cross-linking fixative, preferentially fixes peptides and small proteins, and it may therefore fix more GH moieties than Carnoy's fluid. Carnoy's fixation appears to underestimate GH immunoreactivity in immunohistochemical studies on the cellular distribution of GH-like proteins in embryonic chicks.

Growth hormone in the nervous system: autocrine or paracrine roles in retinal function?

Growth hormone (GH) is primarily produced in the pituitary gland, although GH gene expression also occurs in the central and autonomic nervous systems. GH-immunoreactive proteins are abundant in the brain, spinal cord, and peripheral nerves. The appearance of GH in these tissues occurs prior to the ontogenic differentiation of the pituitary gland and prior to the presence of GH in systemic circulation. Neural GH is also present in neonates, juveniles, and adults and is independent of changes in pituitary GH secretion. Neural GH is therefore likely to have local roles in neural development or neural function, especially as GH receptors (GHRs) are widespread in the nervous system. In recent studies, GH mRNA and GH immunoreactive proteins have been identified in the neural retina of embryonic chicks. GH immunoreactivity is present in the optic cup of chick embryos at embryonic day (ED) 3 of the 21-d incubation period. It is widespread in the neural retina by ED 7 but also present in the nonpigmented retina, choroid, sclera, and cornea. This immunoreactivity is associated with proteins in the neural retina comparable in size with those in the adult pituitary gland, although it is primarily associated with 15-16 kDa moieties rather than with the full-length molecule of approximately 22 kDa. These small GH moieties may reflect proteolytic fragments of "monomer" GH and (or) the presence of different GH gene transcripts, since full-length and truncated GH cDNAs are present in retinal tissue extracts. The GH immunoreactivity in the retina persists throughout embryonic development but is not present in juvenile birds (after 6 weeks of age). This immunoreactivity is also associated with the presence of GH receptor (GHR) immunoreactivity and GHR mRNA in ocular tissues of chick embryos. The retina is thus an extrapituitary site of GH gene expression during early development and is probably an autocrine or paracrine site of GH action. The marked ontogenic pattern of GH immunoreactivity in the retina suggests hitherto unsuspected roles for GH in neurogenesis or ocular development.

Extrapituitary beta TSH and GH in early chick embryos

Somatotropes and thyrotropes are thought to be derived from the same cellular lineage and the expression of both growth hormone (GH) and thyrotropin (beta TSH) is thought to be dependent upon the same (Pit-1) transcription factor. The presence and comparative distribution of GH- and beta TSH-immunoreactivity in early chick embryos, was therefore investigated, especially as extrapituitary GH-immunoreactive cells are present in some peripheral tissues of early chick embryos prior to the ontogenic differentiation of the pituitary gland. At the end of the first trimester of incubation (embryonic day (ED) 7), GH-immunoreactivity was widespread in the head, particularly in neural tissue. Strong labeling was found in the diencephalon and mesencephalon and in neural ganglia and the trigeminal nerve. beta TSH-immunoreactivity was also present in these tissues, although restricted to the ependymal cells lining the diocoele and mesocoele and absent from mantle layers. It was also present in the cellular layer lining the otic vesicle, which was devoid of GH staining. In contrast, Rathke's pouch, the primordial pituitary gland was without GH- or beta TSH-staining. Control sections incubated with preabsorbed antisera or with pre-immune serum were completely devoid of staining. In the trunk, the epidermal cells were stained for beta TSH, but not for GH. Intense GH-immunoreactivity was present in the ventral and dorsal horns of the spinal cord and was particularly strong in the outer marginal layer. In contrast, beta TSH-immunoreactivity was again restricted to ependymal cells lining the spinal canal, which were devoid of GH-immunoreactivity. Strong GH staining was also present in the dorsal and ventral root ganglia, both of which lacked significant beta TSH staining. In non-neural tissues, both GH and beta TSH staining was present in the crop, although in topographically different cells. beta TSH-immunoreactivity was also present in the cells lining the bronchial ducts and the adluminal linings of the pleural and pericardial cavities. GH-immunoreactivity, in contrast, was absent from the lung but present in the surrounding intracostal muscles and in the Müllerian duct. Both GH- and beta TSH-immunoreactivity was present in liver hepatocytes. These results clearly show, for the first time, the presence of TSH-immunoreactivity in central and peripheral tissues of the ED7 chick embryo, prior to the differentiation of pituitary thyrotropes. They also show that beta TSH- and GH-immunoreactive cells are differentially located within embryonic tissues.

Dealing with the uncertainty of developing a cancer

Based on a personal experience in a genetic counselling consultation, this article proposes a personal reflection about the different ways in which individuals from high-risk families are living and dealing with the uncertainty of one day developing a cancer. The psychological reactions of the individuals concerned are described before exploring actual issues of genetic testing--such as the reasons for testing--but also technical and familial limits. This paper also presents the limits existing in follow-up and prevention for the carriers of susceptibility genes and insists on the importance of counselling before genetic testing and the necessity of further multidisciplinary research in this field. The original text was presented in French during the Eleventh MASCC International Symposium on Supportive Care in Cancer, at Nice, in February 1999.

Is preoperative cardiac evaluation for abdominal aortic aneurysm repair necessary?

PURPOSE

It is reported that 25% to 50% of patients with abdominal aortic aneurysms (AAA) have severe coronary artery disease (CAD) and should undergo an aggressive cardiac workup before AAA repair. In contrast, it has been our policy that patients referred for AAA repairs undergo no cardiac testing before surgery.

METHODS

This report reviews the last 113 consecutive patients who underwent elective AAA repair by the senior author using this policy. Seventy-four patients (group A) had only an electrocardiogram before surgery. The remaining 39 patients (group B) were referred having already had additional testing that included a thallium stress test (n = 20), echocardiogram (n = 18), multiple gated acquisition (MUGA) scan (n = 3), cardiac catheterization (n = 8), or some combination of these.

RESULTS

There was no statistical difference between group A and group B with regard to age, sex, tobacco use or history of coronary artery disease, diabetes mellitus, stroke (CVA), hypertension, peripheral vascular disease, or chronic obstructive pulmonary disease. Group B more commonly had a history of myocardial infarction (41% vs 19%, p < 0.03) and congestive heart failure (23% vs 7%, p < 0.03). During surgery there was no significant differences in blood loss, transfusion requirements, or operative times. There were no myocardial infarctions in group A and two (5.1%) in group B, which was not significantly different. Other complications, such as CVA, renal failure, pulmonary failure, pneumonia, wound infection, and hemorrhage, were not significantly different between the two groups. Postoperative hospital stay was not significantly different. There were three deaths in the entire series (2.7%), and only one in group B was cardiac-related in a patient with known end-stage cardiac disease and a symptomatic 8 cm AAA.

CONCLUSIONS

These data indicate that most patients with AAA can safely undergo repair with no cardiac workup and that cardiac workup before AAA repair contributes little information that impacts on treatment or final clinical outcome. We conclude that cardiac testing in preparation for AAA repair is not usually necessary and that intraoperative hemodynamic management may be the most important variable in determining outcome.

In vitro generation of human cytolytic T-cells specific for peptides derived from the HER-2/neu protooncogene protein

The development of T-cell therapy for the treatment of human malignancy has been hindered, in large part, by a lack of identifiable tumor antigens. Studies to identify potential T-cell targets in humans have been difficult because of practical problems limiting the use of in vivo immunization and a lack of reproducible in vitro priming methods. Oncogenic proteins are involved in malignant transformation and maintenance of the transformed phenotype and theoretically are potential targets to T-cell therapy. HER-2/neu protein is a protooncogene product overexpressed in a variety of human malignancies and is associated with malignant transformation and aggressive disease in human breast cancer. Previous studies have shown that some patients with breast cancer have existent helper/inducer T-cell immunity to p185HER-2/neu protein and peptides. The current study represents initial attempts to identify candidate cytotoxic T-lymphocyte (CTL) epitopes. Synthetic peptides were constructed identical to HER-2/neu protein segments with amino acid motifs similar to the published motif for HLA-2.1-binding peptides. Four peptides were synthesized and two were shown to be avid binders to HLA-A2.1. Two of the four peptides could be shown to elicit peptide-specific CTL by primary in vitro immunization in a culture system using peripheral blood lymphocytes from a normal individual homozygous for HLA-A2. p185HER-2/neu protooncogene protein contains immunogenic epitopes capable of generating human CD8+ CTL. The identification of candidate CTL epitopes will allow studies to determine whether some cancer patients have existent CTL immunity to HER-2/neu protein. The demonstrated ability to generate human peptide-specific CTL in vitro allows screening of other oncogenic proteins to identify candidate T-cell epitopes potentially useful for future immunotherapy studies.

Defining the surgical personality: a preliminary study

Noting that noncognitive factors may be more predictive of success in a medical career than is intellectual ability or cognitive performance, we undertook a study to determine whether a surgical personality exists and to delineate the temperament and personality traits that contribute to its definition. The Krug Adult Personality Inventory, the Strelau Temperament Inventory, and Barclay's adjective checklist were administered to 110 physicians, 35 in a "controllable lifestyle" specialty, 28 in primary care, and 47 in surgery or a surgery subspecialty. In addition, participants completed a stress inventory. Results showed that surgeons form a distinct and homogeneous group based on temperament and personality traits. We suggest that noncognitive factors can be of use to medical educators in the selection, counseling, training, and evaluation of medical personnel.

Existent T-cell and antibody immunity to HER-2/neu protein in patients with breast cancer

The HER-2/neu protooncogene is amplified and overexpressed in 20-40% of invasive breast cancers. HER-2/neu protein overexpression is associated with aggressive disease and is an independent predictor of poor prognosis in several subsets of patients. The protein may also be related to cancer formation, with overexpression being detectable in 50-60% of ductal carcinomas in situ. It has been suggested that it might be possible to develop specific T-cell therapy directed against proteins involved in malignant transformation. One question is whether normal proteins that are overexpressed are appropriate targets for therapeutic immune attack. This report demonstrates that some patients with HER-2/neu-positive breast cancers have both existent CD4+ helper/inducer T-cell immunity and antibody-mediated immunity to HER-2/neu protein. Initial studies performed on 20 premenopausal breast cancer patients identified antibodies to HER-2/neu in 11 individuals. Similar antibody responses have been found in some normal individuals. The patient with the greatest antibody response was studied in detail. In addition to a humoral immune response this patient had evidence of a significant proliferative T-cell response to the HER-2/neu protein and peptides. Similar T-cell responses have been detected in additional patients. It has been assumed that patients would be immunologically tolerant to HER-2/neu as a self-protein and that immunity might be difficult to generate. If immunity could be generated, the result might be destructive autoimmunity. The current data support the notion that HER-2/neu-specific immunity might be used in therapy without destroying normal tissue but also raises questions as to the role of existent immunity in immune surveillance and cancer progression.