Specific and general HLA-DR binding motifs: comparison of algorithms

Using panels of peptides well characterized for their ability to bind to HLA DR1, DRB1*1101, or DRB1*0401 molecules, algorithms were deduced to predict binding to these molecules. These algorithms consist of blocks of 8 amino acids containing an amino acid anchor (Tyr, Phe, Trp, Leu, Ile, or Val) at position i and different amino acid combinations at positions i+2 to i+7 depending on the class II molecule. The sensitivity (% of correctly predicted binder peptides) and specificity (% of correctly predicted non-binder peptides) of these algorithms, were tested against different independent panels of peptides and compared to other algorithms reported in the literature. Similarly, using a panel of 232 peptides able to bind to one or more HLA molecules as well as 43 non-binder peptides, we deduced a general motif for the prediction of binding to HLA-DR molecules. The sensitivity and specificity of this general motif was dependent on the threshold score used for the predictions. For a score of 0.1, the sensitivity and specificity were 84.7% and 69.8%, respectively. This motif was validated against several panels of binder and non-binder peptides reported in the literature, as well as against 35, 15-mer peptides from hepatitis C virus core protein, that were synthesized and tested in a binding assay against a panel of 19 HLA-DR molecules. The sensitivities and specificities against these panels of peptides were similar to those attained against the panels used to deduce the algorithm. These results show that comparison of binder and non-binder peptides, as well as correcting for the relative abundance of amino acids in proteins, is a useful approach to deduce performing algorithms to predict binding to HLA molecules

Long-term Oncological Outcome of Segmental Versus Extended Colectomy for Colorectal Cancer in Crohn's Disease: Results from an International Multicentre Study

Background and Aims Crohn's disease increases colorectal cancer risk, with high prevalence of synchronous and metachronous cancers. Current guidelines for colorectal cancer in Crohn's disease recommend pan-proctocolectomy. The aim of this study was to evaluate oncological outcomes of a less invasive surgical approach. Methods This was a retrospective database analysis of Crohn's disease patients with colorectal cancer undergoing surgery at selected European and US tertiary centres. Outcomes of segmental colectomy were compared with those of extended colectomy, total colectomy, and pan-proctocolectomy. Primary outcome was progression-free survival. Secondary outcomes included overall survival, synchronous and metachronous colorectal cancer, and major postoperative complications. Results Ninety-nine patients were included: 66 patients underwent segmental colectomy and 33 extended colectomy. Segmental colectomy patients were older [p = 0.0429], had less extensive colitis [p = 0.0002] and no preoperatively identified synchronous lesions [p = 0.0109]. Median follow-up was 43 [31-62] months. There was no difference in unadjusted progression-free survival [p = 0.2570] or in overall survival [p = 0.4191] between segmental and extended colectomy. Multivariate analysis adjusting for age, sex, ASA score, and AJCC staging, confirmed no difference for progression-free survival (hazard ratio [HR] 1.00, p = 0.9993) or overall survival [HR 0.77, p = 0.6654]. Synchronous and metachronous cancers incidence was 9% and 1.5%, respectively. Perioperative mortality was nil and major complications were comparable [7.58% vs 6.06%, p = 0.9998]. Conclusions Segmental colectomy seems to offer similar long-term outcomes to more extensive surgery. Incidence of synchronous and metachronous cancers appears much lower than previously described. Further prospective studies are warranted to confirm these results

"Near-TME" : proposed standardisation of the technique for proctectomy in male patients with ulcerative colitis

The aim of the present study was to describe in detail an approach to proctectomy in ulcerative colitis (UC), which can be standardized; near-total mesorectal excision (near-TME), to prevent injuries to autonomic pelvic nerves and subsequent sexual dysfunction. We demonstrate the technique ex vivo on a cadaver from a male patient in lithotomy position and on a sagittal section of a male pelvis. We also demonstrate the technique in vivo in two male patients diagnosed with UC, with no history of sexual dysfunction or bowel neoplasia. The study was performed at the Human Embryology and Anatomy Department. University of Valencia, Spain. The posterolateral dissection during a near-TME is similar to that of an oncologic TME, whereas the anterolateral is similar to that of a close rectal dissection. The near-TME technique preserves the superior hypogastric plexus, the hypogastric nerves, the nervi erigentes, the inferior hypogastric plexus, the pelvic plexus and the cavernous nerves. The near-TME technique is the standardisation of the technique for proctectomy in male patients with ulcerative colitis. Near-TME requires experience in pelvic surgery and an exhaustive knowledge of the embryological development and of the surgical anatomy of the pelvis. The online version contains supplementary material available at 10.1007/s10151-022-02579-

Specific and general HLA-DR binding motifs: comparison of algorithms

Using panels of peptides well characterized for their ability to bind to HLA DR1, DRB1*1101, or DRB1*0401 molecules, algorithms were deduced to predict binding to these molecules. These algorithms consist of blocks of 8 amino acids containing an amino acid anchor (Tyr, Phe, Trp, Leu, Ile, or Val) at position i and different amino acid combinations at positions i+2 to i+7 depending on the class II molecule. The sensitivity (% of correctly predicted binder peptides) and specificity (% of correctly predicted non-binder peptides) of these algorithms, were tested against different independent panels of peptides and compared to other algorithms reported in the literature. Similarly, using a panel of 232 peptides able to bind to one or more HLA molecules as well as 43 non-binder peptides, we deduced a general motif for the prediction of binding to HLA-DR molecules. The sensitivity and specificity of this general motif was dependent on the threshold score used for the predictions. For a score of 0.1, the sensitivity and specificity were 84.7% and 69.8%, respectively. This motif was validated against several panels of binder and non-binder peptides reported in the literature, as well as against 35, 15-mer peptides from hepatitis C virus core protein, that were synthesized and tested in a binding assay against a panel of 19 HLA-DR molecules. The sensitivities and specificities against these panels of peptides were similar to those attained against the panels used to deduce the algorithm. These results show that comparison of binder and non-binder peptides, as well as correcting for the relative abundance of amino acids in proteins, is a useful approach to deduce performing algorithms to predict binding to HLA molecules

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