title: Illumina HiSeq 2500 sequencing; Comprehensive transcriptome analysis of synovium and peripheral blood reveals major disease heterogeneity early in the RA disease process prior to therapeutic intervention
design: Comprehensive transcriptome analysis of synovium and peripheral blood reveals major disease heterogeneity early in the RA disease process prior to therapeutic intervention
library_construction_protocol: Ultrasound-guided synovial biopsies were selected from 90 consecutive individuals meeting the 1997 ACR classification criteria for early rheumatoid arthritis from the larger 325 Pathobiology of Early Arthritis Cohort (PEAC) funded by the Medical Research Council (MRC). RNA extracted from synovial biopsies and matching peripheral blood from 67 individuals was subject to RNA-sequencing. Onset (months): Refers to the time between the patient first displaying symptoms and their first rheumatologist appointment.<br><br>ESR (mm/hr): Refers to erythrocyte sedimentation rate (ESR). Results are reported in the distance in millimeters (mm) that red blood cells have descended in one hour (hr). A number of conditions can affect the properties of blood, thereby affecting how quickly red blood cells sink in a sample of blood, including inflammation.<br><br>CRP (mg/l): Refers to C-reactive protein (CRP), which can be measured in your blood, increases when there's inflammation in your body. <br><br>CCP (units/ml): Refers to levels of cyclic citrullinated peptide (CCP) antibodies.<br><br>RF (positive(1) or negative(0)): Refers to rheumatoid factor. Rheumatoid factors are proteins produced by your immune system that can attack healthy tissue in your body. A positive rheumatoid factor test result indicates that a high level of rheumatoid factor was detected in your blood. A higher level of rheumatoid factor in your blood is closely associated with autoimmune disease, particularly rheumatoid arthritis.<br><br>VAS (0-100mm): Refers to visual analogue scale. The scale is anchored by “no pain” (score of 0) and “pain as bad as it could be” or “worst imaginable pain” (score of 100). The pain VAS is self-completed by the respondent. The respondent is asked to place a line perpendicular to the VAS line at the point that represents their pain intensity<br><br>TENDER (0-28 joint count): Refers to the total number of tender joints. The rheumatologist counts the number of tender joints (out of the 28).<br><br>SWOLLEN (0-28 joint count): Refers to the total number of swollen joints. The rheumatologist counts the number of swollen joints (out of the 28).<br><br>HAQ (0-3 units): Refers to the Health Assessment Questionnaire Disability Index. This is an index measuring the quality of life related to health. It is a general index. This index considers how arthritis has an impact on everyday life. The questionnaire is designed to be completed by the patient himself, without the help of a doctor. The value of the HAQ-DI index can be interpreted in terms of three categories: from 0 to 1: mild difficulties to moderate disability, from 1 to 2: disability moderate to severe, from 2 to 3: severe to very severe disability.<br><br>Pathotype (myeloid, lymphoid, or fibroid): Refers to the pathotype in the synovium. In order to determine the degree of immune cell infiltration in the synovium cut sections underwent staining for B cells (CD20), T cells (CD3), macrophages (CD68) and plasma cells (CD138). Sections underwent SQ scoring (0-4) for CD3, CD20, CD68 lining (CD68L) and sublining (CD68SL) and CD138 number. CD20+ aggregates within synovial tissue were graded (1-3). Synovial biopsies were categorized into 3 separate synovial pathotypes according to the following criteria: i) Lymphoid (L) presence of grade 2-3 CD20+ aggregates, (CD20≥2) and/or CD138>2; ii) Myeloid (M) CD68SL≥2, CD20≤1 and/or CD3≥1, CD138≤2 and iii) Fibroid (F) CD68SL<2 and CD3, CD20, CD138<1. Total RNA was extracted from synovial tissue from an early arthritis patient cohort. Total RNA from synovial tissue was extracted using the Qiagen RNeasy mini kit as per manufacturer's protocol including the on-column DNase digestion. Where available, 1ug of total RNA was used as an input material for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Generated libraries were amplified with 10 cycles of PCR. Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA).
attributes.tag: Experimental Factor: pathotype
attributes.value: myeloid