Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer^1-3. The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.

Spatial Characterization of the Human Centrosome Proteome Opens Up New Horizons for a Small but Versatile Organelle

After a century of research, the human centrosome continues to fascinate. Based on immunofluorescence and confocal microscopy, an extensive inventory of the protein components of the human centrosome, and the centriolar satellites, with the important contribution of over 300 novel proteins localizing to these compartments is presented. A network of candidate centrosome proteins involved in ubiquitination, including six interaction partners of the Kelch-like protein 21, and an additional network of protein phosphatases, together supporting the suggested role of the centrosome as an interactive hub for cell signaling, is identified. Analysis of multi-localization across cellular organelles analyzed within the Human Protein Atlas (HPA) project shows how multi-localizing proteins are particularly overrepresented in centriolar satellites, supporting the dynamic nature and wide range of functions for this compartment. In summary, the spatial dissection of the human centrosome and centriolar satellites described here provides a comprehensive knowledgebase for further exploration of their proteomes.

The human secretome

The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immunoassays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.

Vimentin Diversity in Health and Disease

Vimentin is a protein that has been linked to a large variety of pathophysiological conditions, including cataracts, Crohn's disease, rheumatoid arthritis, HIV and cancer. Vimentin has also been shown to regulate a wide spectrum of basic cellular functions. In cells, vimentin assembles into a network of filaments that spans the cytoplasm. It can also be found in smaller, non-filamentous forms that can localise both within cells and within the extracellular microenvironment. The vimentin structure can be altered by subunit exchange, cleavage into different sizes, re-annealing, post-translational modifications and interacting proteins. Together with the observation that different domains of vimentin might have evolved under different selection pressures that defined distinct biological functions for different parts of the protein, the many diverse variants of vimentin might be the cause of its functional diversity. A number of review articles have focussed on the biology and medical aspects of intermediate filament proteins without particular commitment to vimentin, and other reviews have focussed on intermediate filaments in an in vitro context. In contrast, the present review focusses almost exclusively on vimentin, and covers both ex vivo and in vivo data from tissue culture and from living organisms, including a summary of the many phenotypes of vimentin knockout animals. Our aim is to provide a comprehensive overview of the current understanding of the many diverse aspects of vimentin, from biochemical, mechanical, cellular, systems biology and medical perspectives.

Inflammatory response in dogs with spontaneous cranial cruciate ligament rupture

The inflammatory response in 73 dogs with spontaneous rupture of the cranial cruciate ligament was studied. Collagen I and II antibodies (CI, CII), antinuclear antibodies (ANA) and anti-neutrophil cytoplasmic antibodies (ANCA) in synovial fluid (SF) and serum were analysed, as well as serum thyroxine (T4) and free thyroxine (fT4). The type and degree of synovitis did not affect the concentration of antibodies to CI&II. The histological findings of the synovial membranes in 47 dogs were graded as mild non-specific synovitis in 21%, moderate nonspecific synovitis in 32%, moderate lymphoplasmacytic synovitis in 36% and nodular lymphoplasmacytic synovitis in 11% of the dogs. Of 45 dogs four had lower than normal concentration of T4 and fT4. There was not any evidence of a primary autoimmune response.

A subcellular map of the human proteome

Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.

Gene-specific correlation of RNA and protein levels in human cells and tissues

An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.

Assessing the consistency of public human tissue RNA-seq data sets

Sequencing-based gene expression methods like RNA-sequencing (RNA-seq) have become increasingly common, but it is often claimed that results obtained in different studies are not comparable owing to the influence of laboratory batch effects, differences in RNA extraction and sequencing library preparation methods and bioinformatics processing pipelines. It would be unfortunate if different experiments were in fact incomparable, as there is great promise in data fusion and meta-analysis applied to sequencing data sets. We therefore compared reported gene expression measurements for ostensibly similar samples (specifically, human brain, heart and kidney samples) in several different RNA-seq studies to assess their overall consistency and to examine the factors contributing most to systematic differences. The same comparisons were also performed after preprocessing all data in a consistent way, eliminating potential bias from bioinformatics pipelines. We conclude that published human tissue RNA-seq expression measurements appear relatively consistent in the sense that samples cluster by tissue rather than laboratory of origin given simple preprocessing transformations. The article is supplemented by a detailed walkthrough with embedded R code and figures.

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics

Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to ∼80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.

Identification of a new HLA-Cw*05 allele, HLA-Cw*0505*

We have identified a new human leukocyte antigen-C allele in a Caucasian potential stem-cell donor. The new allele is identical to the other Cw*05 alleles in exon 2 but differs from Cw*0501 and *0503 at nucleotide position 379 in exon 3, where a C is substituted with a G. This results in an amino acid substitution from leucine to valine at residue 103 in alpha2 helix.

Ability to work and owner satisfaction following surgical repair of common calcanean tendon injuries in working dogs in New Zealand

AIM

To report the long-term outcome (return to work and owner satisfaction) following surgical treatment of common calcanean tendon (Achilles tendon) injuries in working dogs in New Zealand.

METHODS

Ten New Zealand Huntaway or Heading dogs (working Collies) with complete or partial tears of the common calcanean tendon, were treated using locking-loop suturing and casting, with (7) or without (3), a calcaneo-tibial screw. All dogs were actively in work on sheep or cattle farms at the time of injury, and return to work was the desired outcome. Ability to work and owner satisfaction were investigated using a telephone questionnaire at a mean followup interval of 14.6 months.

RESULTS

Overall, 7/10 dogs returned to full or substantial levels of work. Post-operative complications occurred in two dogs that did not return to full or substantial levels of work. Moderate persistent lameness (score 3 on a scale of 0-5) was present in 2/7 dogs that returned to full or substantial levels of work, equating to a 71% good-to-excellent functional outcome within this group. Seven owners felt the financial investment in opting for surgical repair was worthwhile. A screw and cast method of rigid immobilisation was thought to be superior to casting alone.

CONCLUSIONS

Surgical treatment of common calcanean tendon injury in working dogs carries a good prognosis if an appropriate tenorrhaphy technique is used and rigid immobilisation is achieved for 6 weeks. Care must be taken to limit post-operative complications.

CLINICAL RELEVANCE

This study justifies the use of surgical repair of such injuries in the working dog even when return to work is the only acceptable outcome.

Identification of a new HLA-DPB1 allele,HLA-DPB1*9001

During routine typing of a potential bone marrow donor, a new HLA DPB1 allele was identified. The new allele, officially named HLA DPB1*9001, differs from HLA DPB1*01011 in the second hypervariable region, where a single nucleotide substitution in position 191 changes the codon 35 from TAC to TTC with a predicted amino acid change from Tyr to Phe.

Two new HLA Cw* alleles, Cw*0105 and Cw*1405, detected by sequence based typing

During recent years, the view of the relative importance of the HLA Cw locus has undergone substantial change. From being an HLA locus with both limited polymorphism and biological significance there are now more than a hundred different alleles known and the biological importance of HLA Cw, both as a transplantation antigen and as a receptor for NK cells, is well established. Sequence based typing has been shown to be a powerful tool, especially for HLA Cw typing. Here we describe two new HLA Cw* alleles found during routine typing of potential bone marrow donors and hematological patients. The HLA Cw*0105 differs from Cw*0102 at positions 361 and 368 in exon 3 leading to a Trp to Arg and Cys to Ser substitution, respectively. HLA Cw*1405 differs from Cw*14021 by a single nucleotide substitution at position 368. This mutation results in an amino acid substitution of Phe for Tyr.

Identification of a novel HLA DRB1 exon 2 sequence, DRB1*1345

Five different haplotypes in the human HLA D region are recognized based on their gene composition. The HLA DR52 associated DRB1 alleles include DRB1*03/08/11/12/13/14 and are characterized by the YST sequence motif in the codons 10-12 but vary in other polymorphic regions. The mechanisms generating the extensive variability are not entirely clear. Some alleles have probably arisen from point mutations, but most polymorphism has probably been caused by intralocus gene conversion, and the distinction between the ancient serologically defined groups is more and more difficult. This report describes the identification of a novel DRB1* allele - DRB1*1345 - found in a kidney transplant recipient from East Africa. The new allele shows the closest resemblance to DRB1*1114 and DRB1*1323. It differs from both those alleles at codons 57, 58 and 60, where the new allele carries the 'A-H' sequence motif common to DRB1*14 alleles such as 1401/04/07/10/16/25. This motif is only found in one other DRB1*13 allele namely DRB1*1343.

Surgical treatment of degenerative lumbosacral stenosis in dogs

OBJECTIVE

To study the epidemiology, clinical findings, and long-term outcome of surgical treatment of degenerative lumbosacral stenosis (DLSS) in dogs.

STUDY DESIGN

Retrospective study.

SAMPLE POPULATION

131 client-owned dogs with DLSS.

METHODS

The medical records of dogs with DLSS treated by dorsal laminectomy and dorsal fenestration were reviewed. The clinical diagnosis had been verified by diskography, epidurography or myelography, or a combination thereof.

RESULTS

The German shepherd breed was over-represented (56.5%), and males were more often affected than females (2:1). Historically, reluctance or pain when jumping, rising from a prone position, or climbing stairs (92.4%) and signs of pain or stiffness during extensive physical activity (85.5%) were the most frequent concerns. The most common physical and neurologic examination findings were pain in the lumbosacral area during hyperextension (97.7%) and on direct digital palpation (84.7%). A total of 93.2% of the dogs were improved clinically within the follow-up period (mean 26 +/- 17 months). Recurrence of clinical signs resembling DLSS was reported by the owner or diagnosed by clinical examination in 17.6% of the dogs with a mean onset of signs at 18 +/- 13 months postoperatively.

CONCLUSIONS

Surgical treatment of DLSS with dorsal laminectomy and fenestration generally resulted in good to excellent clinical outcome.

Lymphangioma in the metacarpal pad of a dog

A five-year-old English springer spaniel was presented with a three year history of metacarpal ulceration causing lameness. The lesion was initially thought to be caused by a foreign body, but subsequently diagnosed as lymphangioma. The dog was surgically treated with resection of the metacarpal pad and transposition of the second digital pad. A severe infection developed 11 days postoperatively but was managed with antibiotics and intensive wound therapy. The surgical technique was successful, considerable adaptation of the transposed pad occurred and the dog returned to full weightbearing on the leg. However, one year later another area of new ulceration developed on the dorsomedial aspect of the paw. This, too, was resected but recurred after a short time and the owner elected for euthanasia of the dog.