Feasibility and Relevance of an Intervention with Systematic Screening as a Base for Individualized Rehabilitation in Breast Cancer Patients: A Pilot Trial of the ReScreen Randomized Controlled Trial.

Background: A substantial proportion of women with breast cancer (BC) experience a wide range of long-term persistent and troublesome side effects related to the disease and its treatment. The ReScreen randomized controlled trial is conducted aiming to evaluate the effect of early screening of distress followed by individualized rehabilitation after primary BC treatment. Purpose: To examine recruitment, retention, distribution of distress, relevance of intervention and reported problems in a pilot trial of the ReScreen RCT. Patients and methods: Based on international research, a cutoff of ≥7 on the Distress Thermometer was used to identify women in need of extended support. Those who reported high distress were randomized to intervention group (IG, n = 9) or control group (CG, n = 9), while women with low distress formed an observational group (OG, n = 67). Self-reported data was collected at baseline, 2 weeks and 3, 6, 9, and 12 months after start of treatment. The participants were recruited from a BC unit in Sweden. Descriptive statistics were used for analyses. Results: Eighty-five patients consented to participate. The recruitment rate was 73%, answer frequency was 98%, 64%, 95%, and retention rate was 100%, 56%, 91% in the IG, CG and OG, respectively. Few systematic errors were identified. When exploring the distribution of distress, it was evident that the participants scoring ≥7 were fewer (21.2%) than reported in previous studies (34-43%). The most commonly problems reported were in line with previous reports of symptoms, including fatigue and worry. Conclusion: The satisfactory rates of inclusion and data collection and the few systematic errors indicate that the ReScreen study is feasible if well planned and executed. To identify patients in need of extended support, an adjustment of the cutoff in the main study is indicated. Based on self-reported problems, the intervention was found relevant in this context.

Barriers and facilitators for individualized rehabilitation during breast cancer treatment - a focus group study exploring health care professionals' experiences.

BACKGROUND: Breast cancer (BC) and related treatment are associated with the risk of developing a wide range of persistent disabling impairments. Despite extensive research in the field and an enhanced focus on BC rehabilitation, up to 34-43% of these patients are at risk of developing chronic distress. In addition, it is known that these patients repeatedly report unmet needs, which are strongly associated with reduced quality of life. However, despite knowledge that patients' needs for support during BC rehabilitation varies greatly, individualized rehabilitation is often lacking. Therefore, this study aimed to explore health care professionals' (HCPs) experiences of current rehabilitation practice and describe current barriers and facilitators for individualized rehabilitation for patients following BC treatment. METHODS: A total of 19 HCPs were included, representing various professions in BC care/rehabilitation within surgical, oncological and specialized cancer rehabilitation units at a university hospital in Sweden. Five semi structured focus group interviews were conducted and inductively analysed using conventional qualitative content analysis. RESULTS: Three categories were captured: (1) varying attitudes towards rehabilitation; (2) incongruence in how to identify and meet rehabilitation needs and (3) suboptimal collaboration during cancer treatment. The results showed a lack of consensus in how to optimize individualized rehabilitation. It also illuminated facilitators for individualized rehabilitation in terms of extensive competence related to long-term experience of working with patients with BC care/rehabilitation. Further, the analysis exposed barriers such as a great complexity in promoting individualized rehabilitation in a medically and treatment-driven health care system, which lacked structure and knowledge, and overarching collaboration for rehabilitation. CONCLUSION: This study suggests that the cancer trajectory is medically and treatment-driven and that rehabilitation plays a marginal role in today's BC trajectory. It also reveals that structures for systematic screening for needs, evidence-based guidelines for individualized rehabilitation interventions and structures for referring patients for advanced rehabilitation are lacking. To enable optimal and individualized recovery for BC patients', rehabilitation needs to be an integrated part of the cancer trajectory and run in parallel with diagnostics and treatment.

Integration of Transcriptomics and Antibody-Based Proteomics for Exploration of Proteins Expressed in Specialized Tissues.

A large portion of human proteins are referred to as missing proteins, defined as protein-coding genes that lack experimental data on the protein level due to factors such as temporal expression, expression in tissues that are difficult to sample, or they actually do not encode functional proteins. In the present investigation, an integrated omics approach was used for identification and exploration of missing proteins. Transcriptomics data from three different sources-the Human Protein Atlas (HPA), the GTEx consortium, and the FANTOM5 consortium-were used as a starting point to identify genes selectively expressed in specialized tissues. Complementing the analysis with profiling on more specific tissues based on immunohistochemistry allowed for further exploration of cell-type-specific expression patterns. More detailed tissue profiling was performed for >300 genes on complementing tissues. The analysis identified tissue-specific expression of nine proteins previously listed as missing proteins (POU4F1, FRMD1, ARHGEF33, GABRG1, KRTAP2-1, BHLHE22, SPRR4, AVPR1B, and DCLK3), as well as numerous proteins with evidence of existence on the protein level that previously lacked information on spatial resolution and cell-type-specific expression pattern. We here present a comprehensive strategy for identification of missing proteins by combining transcriptomics with antibody-based proteomics. The analyzed proteins provide interesting targets for organ-specific research in health and disease.

Proteomics. Tissue-based map of the human proteome.

Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.

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.

Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).

A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few tissue-specific proteins and approximately half of the genes expressed in all the analyzed cells. The status for each gene with regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas ( www.proteinatlas.org ).

Production of tissue microarrays, immunohistochemistry staining and digitalization within the human protein atlas.

The tissue microarray (TMA) technology provides the means for high-throughput analysis of multiple tissues and cells. The technique is used within the Human Protein Atlas project for global analysis of protein expression patterns in normal human tissues, cancer and cell lines. Here we present the assembly of 1 mm cores, retrieved from microscopically selected representative tissues, into a single recipient TMA block. The number and size of cores in a TMA block can be varied from approximately forty 2 mm cores to hundreds of 0.6 mm cores. The advantage of using TMA technology is that large amount of data can rapidly be obtained using a single immunostaining protocol to avoid experimental variability. Importantly, only limited amount of scarce tissue is needed, which allows for the analysis of large patient cohorts (1 2). Approximately 250 consecutive sections (4 µm thick) can be cut from a TMA block and used for immunohistochemical staining to determine specific protein expression patterns for 250 different antibodies. In the Human Protein Atlas project, antibodies are generated towards all human proteins and used to acquire corresponding protein profiles in both normal human tissues from 144 individuals and cancer tissues from 216 different patients, representing the 20 most common forms of human cancer. Immunohistochemically stained TMA sections on glass slides are scanned to create high-resolution images from which pathologists can interpret and annotate the outcome of immunohistochemistry. Images together with corresponding pathology-based annotation data are made publically available for the research community through the Human Protein Atlas portal (www.proteinatlas.org) (Figure 1) (3 4). The Human Protein Atlas provides a map showing the distribution and relative abundance of proteins in the human body. The current version contains over 11 million images with protein expression data for 12.238 unique proteins, corresponding to more than 61% of all proteins encoded by the human genome.

Quality-by-design for biotechnology-related pharmaceuticals.

The following article is a report from a workshop on Quality-by-Design (QbD) held at the 7th European Symposium on Biochemical Engineering Science (7 September 2008, Faro, Portugal).The aim of the workshop was to provide an update on the present status of using QbD in biotechnology-related applications in the pharmaceutical industry. The report summarizes the essential parts of the presentations and covers the industrial, academic, and regulatory aspects of QbD. It concludes with recommendations for further work and development.

Design, synthesis, and multivariate quantitative structure-activity relationship of salicylanilides--potent inhibitors of type III secretion in Yersinia.

Analogues to the salicylanilide N-(4-Chlorophenyl)-2-acetoxy-3,5-diiodobenzamide, 1a, an inhibitor of type III secretion (T3S) in Yersinia, were selected, synthesized, and biologically evaluated in three cycles. First, a set of analogues with variations in the salicylic acid ring moiety was synthesized to probe possible structural variation. A basic structure-activity relationship was established and then used to cherry-pick compounds from a principal component analysis score plot of salicylanilides to generate a second set. A third set with increased likelihood of biological activity was designed using D-optimal onion design. A quantitative structure-activity relationship model using hierarchical partial least-square regression to latent structures (Hi-PLS) was computed using PLS score vectors of building blocks correlated to the % inhibition of T3S as a response. A PLS discriminant analysis (PLS-DA) model was derived using the same descriptor set as that for the Hi-PLS model. Both models were validated with an external test set.

Multivariate design and evaluation of a set of RGRPQ-derived innate immunity peptides.

Oral commensal Streptococcus gordonii proteolytically cleave the salivary PRP-1 polypeptide into an RGRPQ innate peptide. The Arg and Gln termini are crucial for RGRPQ-mediated ammonia production and proliferation by S. gordonii SK12 and adhesion inhibition and desorption by Actinomyces naeslundii T14V, respectively. Here we have applied (i) a multivariate approach using RGRPQ-related peptides varied at amino acids 2, 3, and 4 simultaneously and (ii) size and N- and C-terminal modifications of RGRPQ to generate structure activity information. While the N-terminal arginine motif mediated ammonia production independent of peptide size, other responses required more or less full-length peptide motifs. The motifs for adhesion inhibition and desorption were the same. The adhesion and proliferation motifs required similarly a hydrophobic/low polarity amino acid 4 but differentially a hydrophilic or hydrophobic character of amino acids 2/3, respectively; polar peptides with small/hydrophilic and hydrophilic amino acids 2 and 3, respectively, had high adhesion inhibition/desorption activity, and lipophilic peptides with large/hydrophobic amino acids 2 and 3 had high proliferation activity. Accordingly, while RIWWQ had increased proliferation but abolished adhesion/desorption activity, peptides designed with hydrophilic amino acids 2 and 3 were predicted to behave in the opposite way. Moreover, a RGRPQ mimetic for all three responses should mimic small hydrophilic, large nitrogen-containing, and hydrophobic/low polarity amino acids 2, 3, and 4, respectively. Peptides fulfilling these criteria were 1-1.6-fold improved in all three responses. Thus, both mimetics and peptides with differential proliferation and adhesion activities may be generated for evaluation in biofilm models.

Cadmium in food production systems: a health risk for sensitive population groups.

This paper gives an overview of the cadmium (Cd) situation in agricultural systems and human exposure in Sweden. Cadmium levels in agricultural soils (the plow layer) increase by 0.03% to 0.05% per year. Feed can give substantial contributions of Cd to local agricultural systems. Effects on human kidney function are indicated by some measurements already at today's exposure levels. If food products reach the maximum permissible levels given by the European Union, 10% to 25% of the Swedish population will be exposed to Cd levels above the provisional tolerable weekly intake (PTWI 7 microg Cd kg(-1) body weight). Sensitive groups in the population are individuals with low iron status (mainly women) and kidney disorders. Recent studies indicate that Cd plays a role in osteoporosis and that further research is needed to clarify if Cd is neurotoxic in early developmental stages. Firm actions have to be taken in order to stop a further increase of Cd in agricultural soils. Suggestions for prevention and measures are given in this paper.

A human protein atlas for normal and cancer tissues based on antibody proteomics.

Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, approximately 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.

Cadmium in food chain and health effects in sensitive population groups.

Even at the low exposure level of cadmium found in this study population living on farms in southern Sweden, there was an indication of effect on biochemical markers of renal function. Women had higher blood cadmium (BCd) and urinary cadmium (UCd) than men, which can be explained by higher absorption of Cd due to low iron status. In the present study, Cd in pig kidneys could not be used to predict human BCd or UCd even though cereals are a substantial part of both the human and the pig diet. The contribution of Cd from locally produced food to the total dietary intake in humans was relatively low and varied and the intake of Cd did not correlate with BCd or UCd. In contrast, Cd levels in pig kidney were significantly related to Cd levels in feed. However, there was no relationship between the locally produced cereals, constituting the main part of the feed, and Cd in pig kidneys. In pig feed, other non-locally produced ingredients contributed to a large part of the Cd in feed. The Cd in non-locally produced feed ingredients reaches the local circulation via excretion in faeces and application of manure to arable soils and will lead to increased levels in the crops. As indicated by experimental data from animals, neurochemical and neurobehavioral effects during development need to be further explored as sensitive endpoints for cadmium toxicity.

Cadmium in blood and urine--impact of sex, age, dietary intake, iron status, and former smoking--association of renal effects.

We studied determinants of cadmium status and kidney function in nonsmoking men and women living on farms in southern Sweden. Median blood Cd (BCd) was 1.8 nmol/L (range, 0.38-18) and median urinary Cd (UCd) was 0.23 nmol/mmol creatinine (range, 0.065-0.99). The intake of Cd per kilogram body weight did not significantly differ between sexes and did not correlate with BCd or UCd, which may be explained by a low and varying bioavailibility of Cd from food items. However, when a subgroup of the study population, couples of never-smoking men and women, were compared, a lower intake per kilogram body weight was found in the women, but the women had a 1.8 times higher BCd and a 1.4 times higher UCd. The higher female BCd and UCd may be explained by higher absorption due to low iron status. BCd and UCd both increased with age and were higher in the ex-smokers, who had stopped smoking more than 5 years before the study, compared to never-smokers. The contribution of locally produced food to the total Cd intake was relatively low and varied. Males living in areas with low soil Cd had lower UCd than the others. However, Cd levels in kidneys from pigs, fed locally produced cereals, did not predict BCd or UCd in humans at the same farms. The kidney function parameter ss2-microglobulin-creatinine clearance was related to UCd, whereas urinary protein-HC, N-acetyl-ss-glucoseaminidase or albumin-creatinine clearance was not when age was accounted for. Hence, even at the low exposure levels in this study population, there was an indication of effect on biochemical markers of renal function.