Sample preparation and biostatistics for integrated genomics approaches

Genomics is based on the ability to determine the transcriptome, proteome, and metabolome of a cell. These technologies only have added value when they are integrated and based on robust and reproducible workflows. This chapter describes the experimental design, sampling, sample pretreatment, data evaluation, integration, and interpretation. The actual generation of the data is not covered in this chapter since it is highly depended on available equipment and infrastructure. The enormous amount of data generated by these technologies are integrated and interpreted inorder to generate leads for strain and process improvement. Biostatistics are becoming very important for the whole work flow therefore, some general recommendations how to set up experimental design and how to use biostatistics in enhancing the quality of the data and the selection of biological relevant leads for strain engineering and target identification are described.

Factors influencing concordance between clinical and ultrasound findings in rheumatoid arthritis

OBJECTIVE

Clinical joint examination (CJE) is less time-consuming than ultrasound (US) in rheumatoid arthritis (RA). Low concordance between CJE and US would indicate that the 2 tests provide different types of information. Knowledge of factors associated with CJE/US concordance would help to select patients and joints for US. Our objective was to identify factors associated with CJE/US concordance.

METHODS

Seventy-six patients with RA requiring tumor necrosis factor-α (TNF-α) antagonist therapy were included in a prospective, multicenter cohort. In each patient, 38 joints were evaluated. Synovitis was scored using CJE, B-mode US (B-US), and power Doppler US (PDUS). Joints whose kappa coefficient (κ) for agreement CJE/US was < 0.1 were considered discordant. Multivariate analysis was performed to identify factors independently associated with CJE/US concordance, defined as factors yielding p < 0.05 and OR > 2.

RESULTS

Concordance before TNF-α antagonist therapy varied across joints for CJE/US (κ = -0.08 to 0.51) and B-US/PDUS (κ = 0.30 to 0.67). CJE/US concordance was low at the metatarsophalangeal joints and shoulders (κ < 0.1). Before TNF-α antagonist therapy, a low 28-joint Disease Activity Score (DAS28) was associated with good CJE/B-US concordance, and no factors were associated with CJE/PDUS concordance. After TNF-α antagonist therapy, only the joint site was associated with CJE/B-US concordance; joint site and short disease duration were associated with CJE/PDUS concordance.

CONCLUSION

Concordance between CJE and US is poor overall. US adds information to CJE, most notably at the metatarsophalangeal joints and shoulders. Usefulness is decreased for B-US when DAS28 is low and for PDUS when disease duration is short.

Efficacy of rituximab in systemic manifestations of primary Sjogren's syndrome: results in 78 patients of the AutoImmune and Rituximab registry

OBJECTIVES

To evaluate the efficacy and safety of rituximab in patients with primary Sjögren's syndrome (pSS).

METHODS

The AutoImmune and Rituximab registry has included 86 patients with pSS treated with rituximab, prospectivey followed up every 6 months for 5 years.

RESULTS

Seventy-eight patients with pSS (11 men, 67 women), who already had at least one follow-up visit, were analysed. Median age was 59.8 years (29-83), median duration of disease was 11.9 years (3-32). Indications for treatment were systemic involvement for 74 patients and only severe glandular involvement in four patients. The median European Sjögren's Syndrome disease activity index (ESSDAI) was 11 (2-31). 17 patients were concomitantly treated with another immunosuppressant agent. Median follow-up was 34.9 months (6-81.4) (226 patient-years). Overall efficacy according to the treating physician was observed in 47 patients (60%) after the first cycle of rituximab. Median ESSDAI decreased from 11 (2-31) to 7.5 (0-26) (p<0.0001). Median dosage of corticosteroid decreased from 17.6 mg/day (3-60) to 10.8 mg/day (p=0.1). Forty-one patients were retreated with rituximab. Four infusion reactions and one delayed serum sickness-like disease resulted in rituximab discontinuation. Three serious infections (1.3/100 patient-years) and two cancer-related deaths occurred.

CONCLUSIONS

In common practice, the use of rituximab in pSS is mostly restricted to patients with systemic involvement. This prospective study shows good efficacy and tolerance of rituximab in patients with pSS and systemic involvement.

Infectious sacroiliitis: a retrospective, multicentre study of 39 adults

Background

Non-brucellar and non-tuberculous infectious sacroiliitis (ISI) is a rare disease, with misleading clinical signs that delay diagnosis. Most observations are based on isolated case reports or small case series. Our aim was to describe the clinical, bacteriological, and radiological characteristics of ISI, as well as the evolution of these arthritis cases under treatment.

Methods

This retrospective study included all ISI cases diagnosed between 1995 and 2011 in eight French rheumatology departments. ISI was diagnosed if sacroiliitis was confirmed bacteriologically or, in the absence of pathogenic agents, if clinical, biological, and radiological data was compatible with this diagnosis and evolution was favourable under antibiotic therapy.

Results

Overall, 39 cases of ISI were identified in adults, comprising 23 women and 16 men, with a mean age at diagnosis of 39.7 ± 18.1 years. The left sacroiliac joint (SI) was affected in 59% of cases, with five cases occurring during the post-partum period. Lumbogluteal pain was the most common symptom (36/39). Manipulations of the SI joint were performed in seven patients and were always painful. Mean score for pain using the visual analogue score was 7.3/10 at admission, while 16 patients were febrile at diagnosis. No risk factor was found for 30.7% of patients. A diagnosis of ISI was only suspected in five cases at admission. The mean time to diagnosis was long, being 43.3 ± 69.1 days on average. Mean C-reactive protein was 149.7 ± 115.3 mg/l, and leukocytosis (leukocytes ≥ 10 G/l) was uncommon (n = 15) (mean level of leukocytes 10.4 ± 3.5 G/l). Radiographs (n = 33) were abnormal in 20 cases, revealing lesions of SI, while an abdominopelvic computed tomography (CT) scan (n = 27) was abnormal in 21 cases, suggesting arthritis of the SI joints in 13 cases (48.1%) and a psoas abscess in eight. Bone scans (n = 14) showed hyperfixation of the SI in 13 cases. Magnetic resonance imaging (MRI) (n = 27), when focused on the SI (n = 25), directed towards the diagnosis to ISI in 25 cases. Pathogenic agents were isolated in 33 cases (84.6%) by means of articular puncture (n = 16), blood culture (n = 14), cytobacteriological examination of urine (n = 2), or puncture of the psoas (n = 1).

Gram-positive cocci were the mostly isolated common bacteria, with a predominance of staphylococci (n = 21). The most frequently isolated gram-negative bacillus was Pseudomonas aeruginosa (n = 3). Evolution was favourable in 37 out of 39 patients under prolonged antibiotic therapy (mean duration 3.01 ± 1.21 months).

Conclusion

Our series confirmed that the clinical manifestations of ISI usually lead to delayed diagnosis. Based on our results, we suggest performing an MRI of the spine and SI in clinical situations characterised by lumbogluteal pain and symptoms of an infectious disease, such as fever.

Lupus anticoagulant-hypoprothrombinemia syndrome: report of 8 cases and review of the literature

The lupus anticoagulant-hypoprothrombinemia syndrome (LAHS)--the association of acquired factor II deficiency and lupus anticoagulant--is a rare disease drastically different from antiphospholipid syndrome in that it may cause predisposition not only to thrombosis but also to severe bleeding. We performed a retrospective study of 8 patients with LAHS referred to 6 French tertiary care centers between January 2003 and February 2011, and a literature review retrieving all related articles published between 1960 and April 2011. Including our 8 new cases, LAHS has been reported in 74 cases. The disease mostly occurs in young adults, with a female to male sex ratio of 1.4. Associated conditions mostly include autoimmune diseases such as systemic lupus erythematosus and infectious diseases. Bleeding is a frequent feature (89% of cases), while arterial and/or venous thrombosis is less common (13%). Factor II level is severely decreased at diagnosis (median value, 11%; range, 1%-40%). LAHS associated with autoimmune diseases is more persistent than LAHS associated with infection, and hemorrhagic complications are more common. Corticosteroids should be considered the first-line treatment, but the thrombotic risk strongly increases during treatment because of the improvement of factor II level. Despite the fact that 50% of patients develop severe bleeding, the mortality rate is <5%, after a median follow-up of 13 months (range, 0.5-252 mo). LAHS associated with autoimmune diseases should be diagnosed and managed carefully because the disease is persistent and severe hemorrhagic complications are common.

Female effects on offspring energetic status and consequences on early development in yolk feeding brown trout (Salmo trutta)

Energetic status can be defined as the interaction between energy stores and metabolic rate. In salmonids, it is variable and influences the timing of emergence, and therefore may have strong effects on both juvenile and maternal fitness. The aim of this study is to (i) describe the ontogeny of energy use for different brown trout clutches to understand how such a variability of energetic status is developed at the end of incubation and (ii) to estimate maternal influences over offspring physiological processes. Using individual measures of total mass and metabolism throughout ontogeny combined with a hierarchical Bayesian modeling approach, we successfully described clutch-specific (i) metabolic trajectories, (ii) use of yolk resources and the building of new tissues throughout ontogeny. Our results show that females laying large eggs have offspring with lower metabolic costs and higher yolk conversion efficiencies. Females also influence within clutch variance of metabolic and yolk consumption rates leading to potential developmental variations. These results are discussed with regard to their consequences on early life history through the critical period of emergence.

Elaboration and validation of a questionnaire (Qualisex) to assess the impact of rheumatoid arthritis on sexuality with patient involvement

OBJECTIVES

Rheumatoid arthritis (RA) may have consequences on sexual life. The objective was to develop and validate a questionnaire assessing the impact of RA on sexuality.

METHODS

First, 6 patients (5 women, 1 man) with RA, 2 rheumatologists and 1 sexologist elaborated during a one-day focus-group type meeting an exhaustive list of issues relating to impact of RA on sexuality. The list was reduced by merging similar issues, then according to the relative importance for patients of each issue. A questionnaire was developed with input from these patients, with particular attention on phrasing. Psychometric properties (missing data, correlations with other disease aspects, reliability) were assessed in a multi-centre study.

RESULTS

The list of 33 issues related to impact of RA on sexuality included psychological issues (9), couple/relationship issues (9), physical issues (7), and general aspects (5). A 10-question numeric rating scale questionnaire was constructed. Preliminary validation was obtained on 53 patients (44 women, mean age 50.7 years; mean disease duration 14.4 years). The mean score was 3.3±2.5, missing data were acceptable (13%). Qualisex results were correlated with disease activity and symptoms (r=0.50-0.65, p< 0.001); but not with demographics, depression or coping. Qualisex was reliable in 40 patients: the intra-class correlation coefficient was 0.83 (95% CI: 0.70-0.91).

CONCLUSIONS

A simple (10 questions) and valid tool investigating impact of RA on sexuality has been developed with the involvement of patients. This tool can be useful to assess this important aspect of quality of life.

The ability of synovitis to predict structural damage in rheumatoid arthritis: a comparative study between clinical examination and ultrasound

OBJECTIVES

To evaluate synovitis (clinical vs ultrasound (US)) to predict structural progression in rheumatoid arthritis (RA).

METHODS

Patients with RA.

STUDY DESIGN

Prospective, 2-year follow-up.

DATA COLLECTED

Synovitis (32 joints (2 wrists, 10 metacarpophalangeal, 10 proximal interphalangeal, 10 metatarsophalangeal)) at baseline and after 4 months of therapy by clinical, US grey scale (GS-US) and power doppler (PD-US); x-rays at baseline and at year 2.

ANALYSIS

Measures of association (OR) were tested between structural deterioration and the presence of baseline synovitis, or its persistence, after 4 months of therapy using generalised estimating equation analysis.

RESULTS

Structural deterioration was observed in 9% of the 1888 evaluated joints in 59 patients. Baseline synovitis increased the risk of structural progression: OR=2.01 (1.36-2.98) p<0.001 versus 1.61 (1.06-2.45) p=0.026 versus 1.75 (1.18-2.58) p=0.005 for the clinical versus US-GS versus US-PD evaluation, respectively. In the joints with normal baseline examination (clinical or US), an increased probability for structural progression in the presence of synovitis for the other modality was also observed (OR=2.16 (1.16-4.02) p=0.015 and 3.50 (1.77-6.95) p<0.001 for US-GS and US-PD and 2.79 (1.35-5.76) p=0.002) for clinical examination. Persistent (vs disappearance) synovitis after 4 months of therapy was also predictive of subsequent structural progression.

CONCLUSIONS

This study confirms the validity of synovitis for predicting subsequent structural deterioration irrespective of the modality of examination of joints, but also suggests that both clinical and ultrasonographic examinations may be relevant to optimally evaluate the risk of subsequent structural deterioration.

Positivity for anti-cyclic citrullinated peptide is associated with a better response to abatacept: data from the 'Orencia and Rheumatoid Arthritis' registry

OBJECTIVES

Very limited data are available regarding the efficacy of abatacept (ABA) in real life. The aims of this study were to determine the efficacy of ABA in rheumatoid arthritis and predicting factors of efficacy in common practice.

METHODS

The Orencia and Rheumatoid Arthritis" (ORA) prospective registry, promoted by the French Society of Rheumatology, has included 1003 patients with RA.

RESULTS

773 patients had already fulfilled the 6-month follow-up visit. Only 21.3% of patients would have fulfilled inclusion criteria used in pivotal controlled trials. The European League Against Rheumatism (EULAR) response, was observed in 330 (59.1%) of the 558 assessed patients (good response: 20.4%, moderate response: 38.7%) and was similar in patients who did and in patients who did not fulfill inclusion criteria of controlled trials. Among EULAR responders, initial 28-joint disease activity score (5.4 (4.7-6.5) in responders vs 4.9 (4.0-6.0) in non responders, p< 0.0001), the proportion of rheumatoid factor (75.6% vs 66.7%, p= 0.03) and the proportion of anti-cyclic citrullinated peptide antibody (anti-CCP)-positivity (75.9% vs 62.2%, p= 0.001) were significantly higher. In multivariate analysis adjusted on initial 28-joint disease activity score and CRP, anti-CCP positivity was associated with EULAR response (OR=1.9;95% CI=1.2 to 2.9, p=0.007), but not rheumatoid factor (OR=1.0;95% CI=0.6 to 1.6, p=0.9). Anti-CCP positivity was also significantly associated with a higher ABA retention rate at 6 months.

CONCLUSIONS

Real life efficacy of ABA in the ORA registry was similar as that reported in clinical trials. Anti-CCP positivity was associated with a better response to ABA, independently from disease activity.

Is IL-6 an appropriate target to treat spondyloarthritis patients refractory to anti-TNF therapy? A multicentre retrospective observational study

INTRODUCTION

The aim of this study was to evaluate, under real-life conditions, the safety and efficacy of tocilizumab in patients having failed anti-TNFα therapy for spondyloarthritis.

METHODS

French rheumatologists and internal-medicine practitioners registered on the Club Rhumatismes et Inflammations website were asked to report on patients given tocilizumab (4 or 8 mg/kg) to treat active disease meeting Assessment of SpondyloArthritis International Society (ASAS) criteria for axial or peripheral spondyloarthritis, after anti-TNFα treatment failure. Safety and efficacy after 3 and 6 months were assessed retrospectively using standardised questionnaires.

RESULTS

Data were obtained for 21 patients, 13 with axial spondyloarthritis (46% men; median age, 42 years; disease duration, 11 years; HLA-B27-positive, 92.3%) and eight with peripheral spondyloarthritis (25% men; median age, 40 years; disease duration, 10 years; HLA-B27-positive, 62.5%). No patients with axial disease had at least a 20 mm decrease in the BASDAI, nor a BASDAI50 response or major ASAS-endorsed disease activity score improvements after 3 or 6 months; an ASAS-endorsed disease activity score clinically important improvement was noted at month 3 in five of 13 patients and at month 6 in one of four patients. A good DAS28 response was achieved in four patients with peripheral disease, including one in EULAR remission at month 3. Four patients were still taking tocilizumab at month 6, including one in EULAR remission and one with a good DAS28 response. Tocilizumab was well tolerated, with no serious adverse events. Initially elevated acute-phase reactants declined during tocilizumab therapy.

CONCLUSION

In patients having failed anti-TNFα therapy, tocilizumab decreased acute-phase reactants but failed to substantially improve axial spondyloarthritis and was inconsistently effective in peripheral spondyloarthritis.

[Lyme disease with hepatitis and corticosteroids: a case report]

INTRODUCTION

Abnormalities of liver function tests have been occasionally described in large series of Lyme disease, but only one case of hepatitis directly related to infection have been described in literature.

CASE REPORT

A 78-year-old-man, with a past medical history of polymyalgia rheumatica (PMR) who had discontinued corticosteroids two years before, presented a transient acute fever and liver cholestasis and cytolysis after an exposure to tick bites. A few days later, cervical pain occurred and corticosteroids were resumed as a PMR relapse was suspected. Hematogenous dissemination with acute meningoradiculitis and multiple erythema migrans led to conclude to a stage 2 Lyme disease.

CONCLUSION

Although hepatitis complicating the course of Lyme disease has been described in literature, the marked inflammation in our patient led us to investigate the possibility of a co-infection. Also, we discuss the responsibility of corticosteroids in clinical worsening of Lyme disease if they are prescribed without concomitant antibiotics.

Efficacy of resistance exercises in rheumatoid arthritis: meta-analysis of randomized controlled trials

OBJECTIVE

To evaluate the efficacy of resistance exercises in RA patients.

METHODS

A systematic literature search was done using Pubmed, Embase and Cochrane databases through November 2009 and in abstracts presented at rheumatology scientific meetings over the past 3 years. Randomized controlled trials (RCTs) comparing resistance exercise based therapy with interventions without resistance exercise for the treatment of RA patients were included. Outcomes studied were post-intervention disability on the HAQ, functional capacity assessed by walking speed, pain on the visual analogue scale (VAS), joint count, isometric, isokinetic and grip strength. Efficacy was assessed by weighted mean differences (WMDs) and tolerance was assessed by relative risk (RR). Data were pooled using the inverse of variance model, and heterogeneity was tested.

RESULTS

Ten RCTs, including 547 patients, met the study inclusion criteria. The mean (S.D.) Jadad score was 2.3 (0.6). Resistance exercises significantly improved isokinetic strength (WMD = 23.7%, P < 0.001), isometric strength (WMD = 35.8%, P < 0.001), grip strength (WMD = 26.4%, P < 0.001) and HAQ (WMD = -0.22, P < 0.001). Exercise also had a positive impact on the 50-foot walking test (WMD = -1.90 s, P < 0.001) and ESR (WMD = -5.17, P = 0.005). Withdrawals [RR = 0.95, 95% confidence interval (CI) 0.61, 1.48] and adverse events (RR = 1.08, 95% CI 0.72, 1.63) were well balanced in both groups. Patient and exercise characteristics did not influence the results. Subgroup analysis revealed a trend towards higher efficacy associated with high-intensity programmes.

CONCLUSION

Resistance exercise in RA is safe, and the improvement in most outcomes was statistically significant and possibly clinically relevant for RA disability.

A tool to identify recent or present rheumatoid arthritis flare from both patient and physician perspectives: the 'FLARE' instrument

INTRODUCTION

There is a lack of consensus about the definition of flare of rheumatoid arthritis (RA) and a measurement tool.

OBJECTIVES

To develop a self-administered tool integrating the perspectives of the patient and the rheumatologist, enabling the detection of present or recent-past RA flare.

METHODS

The patient perspective was explored by semistructured individual interviews of patients with RA. Two health psychologists conducted a content analysis to extract items best describing flare from the interviews. The physician's perspective was explored through a Delphi exercise conducted among a panel of 13 rheumatologists. A comprehensive list of items produced in the first round was reduced in a four-round Delphi process to select items cited by at least 75% of the respondents. The identified elements were assembled in domains-each converted into a statement-to constitute the final self-administered Flare Assessment in Rheumatoid Arthritis (FLARE) questionnaire.

RESULTS

The content of 99 patient interviews was analysed, and 10 domains were identified: joint swelling or pain, night pain, fatigue and different emotional consequences, as well as analgesic intake. The Delphi process for physicians identified eight domains related to objective RA symptoms and drug intake, of which only four were common to domains for patients. Finally, 13 domains were retained in the FLARE questionnaire, formulated as 13 statements with a Likert-scale response modality of six answers ranging from 'absolutely true' to 'completely untrue'.

CONCLUSION

Two different methods, for patient and physician perspectives, were used to develop the FLARE self-administered questionnaire, which can identify past or present RA flare.

TNF alpha antagonist therapy and safety monitoring

OBJECTIVES

To develop and/or update fact sheets about TNFα antagonists treatments, in order to assist physicians in the management of patients with inflammatory joint disease.

METHODS

1. selection by a committee of rheumatology experts of the main topics of interest for which fact sheets were desirable; 2. identification and review of publications relevant to each topic; 3. development and/or update of fact sheets based on three levels of evidence: evidence-based medicine, official recommendations, and expert opinion. The experts were rheumatologists and invited specialists in other fields, and they had extensive experience with the management of chronic inflammatory diseases, such as rheumatoid. They were members of the CRI (Club Rhumatismes et Inflammation), a section of the Société Francaise de Rhumatologie. Each fact sheet was revised by several experts and the overall process was coordinated by three experts.

RESULTS

Several topics of major interest were selected: contraindications of TNFα antagonists treatments, the management of adverse effects and concomitant diseases that may develop during these therapies, and the management of everyday situations such as pregnancy, surgery, and immunizations. After a review of the literature and discussions among experts, a consensus was developed about the content of the fact sheets presented here. These fact sheets focus on several points: 1. in RA and SpA, initiation and monitoring of TNFα antagonists treatments, management of patients with specific past histories, and specific clinical situations such as pregnancy; 2. diseases other than RA, such as juvenile idiopathic arthritis; 3. models of letters for informing the rheumatologist and general practitioner; 4. and patient information.

CONCLUSION

These TNFα antagonists treatments fact sheets built on evidence-based medicine and expert opinion will serve as a practical tool for assisting physicians who manage patients on these therapies. They will be available continuously at www.cri-net.com and updated at appropriate intervals.

Mutations of the cystic fibrosis gene in patients with bronchiectasis associated with rheumatoid arthritis

OBJECTIVES

In cystic fibrosis, mutations of the CFTR gene lead to diffuse bronchiectasis (DB). DB is also associated with other diseases including rheumatoid arthritis (RA) in which the role of genetic factors in the predisposition to DB remains unclear.

METHODS

A family-based association study was carried out to determine whether the frequency of CFTR mutations was higher in patients with RA-associated DB and to determine whether a causal relationship could be established between the variant and the disease by evaluating its cosegregation with DB within families. Families of probands with RA-DB were included if one first-degree relative had RA and/or DB. The controls comprised healthy subjects requesting genetic counselling because their partner had cystic fibrosis.

RESULTS

The frequency of CFTR mutations was higher in family members with RA-DB or DB only than in unaffected relatives (p<0.005 for each comparison) and in unrelated healthy controls (p<0.001 for each comparison) but not in family members with RA only. CFTR mutations were more frequent in family members with RA-DB than in those with RA only (OR 5.30, 95% CI 2.48 to 11.33; p<5×10(-5)). They cosegregated with RA-DB in the families (sib-TDT=10.82, p=0.005).

CONCLUSIONS

RA-DB should be added to the list of phenotypes in which CFTR mutations are pathogenic. CFTR mutation is the first genetic defect linked to an extra-articular feature of RA to be described. CFTR mutations in patients with RA appear to be an important marker of the risk of associated DB, which has been linked to a less favourable prognosis.