Journal: Therapeutic Advances in Gastroenterology

Article Title: Precision medicine and drug optimization in adult inflammatory bowel disease patients

doi: 10.1177/17562848231173331

Figure Lengend Snippet: Concept of precision medicine. Currently, our treatment approach is more the one shown in the left of the figure, where the same treatments are given to all patients. But with this ‘one-size-fits-all’ approach, some patients will show a clinical response, some will not and some may develop side effects. Using clinical factors and biomarkers (genetic, transcriptomic, proteomic, metabolomic, radiomic and microbiota) as well as predictive tools, precision medicine towards which there is a desire to evolve (on the right-hand side of the figure), could allow stratification of patients into high-risk patients, who would require a topdown strategy, and low-risk patients, for whom a step-up strategy would be more appropriate. It would also predict the response to treatment, allowing the administration of a certain type of drug only on those who will benefit, sparing side effects and expense for those who will not. 5-ASA, 5-aminosalicylic acid; JAK, Janus kinase; TNF-α, tumour-necrosis factor α; UST, ustekinumab; VDZ, vedolizumab.

Article Snippet: , Epigen. , Novel 25- and 23-feature panels of epigenetic biomarkers. CpGs of interest implicated genes involved in endothelial Cell–Cell adhesion and integrin-dependent T-Cell homing , LT , , LT , LT , , , , , , , , , , .

Techniques: Clinical Proteomics

Journal: Therapeutic Advances in Gastroenterology

Article Title: Precision medicine and drug optimization in adult inflammatory bowel disease patients

doi: 10.1177/17562848231173331

Figure Lengend Snippet: Parameters associated with unfavourable disease course at diagnosis including stricturing and penetrating disease in CD and colectomy in UC (except for acute severe UC).

Article Snippet: , Epigen. , Novel 25- and 23-feature panels of epigenetic biomarkers. CpGs of interest implicated genes involved in endothelial Cell–Cell adhesion and integrin-dependent T-Cell homing , LT , , LT , LT , , , , , , , , , , .

Techniques: Biomarker Discovery, Gene Expression, Expressing, Ligation, Computed Tomography

Journal: Therapeutic Advances in Gastroenterology

Article Title: Precision medicine and drug optimization in adult inflammatory bowel disease patients

doi: 10.1177/17562848231173331

Figure Lengend Snippet: Predictors of response or non-response to biologics and small molecule drugs at baseline in adult CD patients (for luminal disease). 104 – 107

Article Snippet: , Epigen. , Novel 25- and 23-feature panels of epigenetic biomarkers. CpGs of interest implicated genes involved in endothelial Cell–Cell adhesion and integrin-dependent T-Cell homing , LT , , LT , LT , , , , , , , , , , .

Techniques: Biomarker Discovery, Activity Assay, Variant Assay, Isolation, Concentration Assay, Mutagenesis, Gene Expression, Expressing, Clinical Proteomics, Immunohistochemistry, Diffusion-based Assay

Journal: Epigenetics

Article Title: Notch signaling genes

doi: 10.4161/epi.28597

Figure Lengend Snippet: Figure 4. Myogenesis-associated hypomethylation from 16 to 230 kb downstream of DLL1 . ( A ) Significantly hypomethylated (green) or hypermethylated (red) sites downstream of DLL1 . A long intergenic non-coding RNA (linc RNA) of 0.98 kb, ENST00000610240, which is based on expressed sequence tags (ESTs) found in many tissues, including skeletal muscle ( http://www.ensembl.org ), overlaps the central cluster of MbMt- and muscle-hypomethylated sites (tall orange box in center) and might have long-distance enhancer function as demonstrated for some other lncRNAs. ( B ) and ( C ), predicted chromatin states and C2C12-deduced MyoD-binding sites as in Figure 3 . Binding sites with signals >40 are indicated by a lollipop. ( D ) DNase-seq. ( E ) RNA-seq for the minus-strand with a vertical viewing range of 1 to 50. ( F ) An example of RRBS data tracks (Mb7) to indicate the coverage of the RRBS data. Thick- and thin-lined orange boxes, the positions of myogenic hypomethylated sites that overlapped enhancer-type chromatin and DHS in Mb and Mt and those that overlapped only a DHS seen in Mb and Mt, respectively. The region shown is chr6:170,357,260–170,608,718.

Article Snippet: Importantly, the central DHS seen in Mb and Mt at this enhancer-like region (as determined by histone modifications; ENCODE, Broad Institute) was retained in adult skeletal muscle ( , orange boxes).

Techniques: Sequencing, Binding Assay, RNA Sequencing