Development of Multigene Expression Signature Maps at the Protein Level from Digitized Immunohistochemistry Slides

Molecular classification of diseases based on multigene expression signatures is increasingly used for diagnosis, prognosis, and prediction of response to therapy. Immunohistochemistry (IHC) is an optimal method for validating expression signatures obtained using high-throughput genomics techniques since IHC allows a pathologist to examine gene expression at the protein level within the context of histologically interpretable tissue sections. Additionally, validated IHC assays may be readily implemented as clinical tests since IHC is performed on routinely processed clinical tissue samples. However, methods have not been available for automated n-gene expression profiling at the protein level using IHC data. We have developed methods to compute expression level maps (signature maps) of multiple genes from IHC data digitized on a commercial whole slide imaging system. Areas of cancer for these expression level maps are defined by a pathologist on adjacent, co-registered H&E slides, allowing assessment of IHC statistics and heterogeneity within the diseased tissue. This novel way of representing multiple IHC assays as signature maps will allow the development of n-gene expression profiling databases in three dimensions throughout virtual whole organ reconstructions

Comparing computer-generated and pathologist-generated tumour segmentations for immunohistochemical scoring of breast tissue microarrays

BACKGROUND: Tissue microarrays (TMAs) have become a valuable resource for biomarker expression in translational research. Immunohistochemical (IHC) assessment of TMAs is the principal method for analysing large numbers of patient samples, but manual IHC assessment of TMAs remains a challenging and laborious task. With advances in image analysis, computer-generated analyses of TMAs have the potential to lessen the burden of expert pathologist review. METHODS: In current commercial software computerised oestrogen receptor (ER) scoring relies on tumour localisation in the form of hand-drawn annotations. In this study, tumour localisation for ER scoring was evaluated comparing computer-generated segmentation masks with those of two specialist breast pathologists. Automatically and manually obtained segmentation masks were used to obtain IHC scores for thirty-two ER-stained invasive breast cancer TMA samples using FDA-approved IHC scoring software. RESULTS: Although pixel-level comparisons showed lower agreement between automated and manual segmentation masks (κ=0.81) than between pathologists' masks (κ=0.91), this had little impact on computed IHC scores (Allred; [Image: see text]=0.91, Quickscore; [Image: see text]=0.92). CONCLUSIONS: The proposed automated system provides consistent measurements thus ensuring standardisation, and shows promise for increasing IHC analysis of nuclear staining in TMAs from large clinical trials

Unusual primary HIV infection with colonic ulcer complicated by hemorrhagic shock: a case report

<p>Abstract</p> <p>Introduction</p> <p>Timely diagnosis of primary HIV infection is important to prevent further transmission of HIV. Primary HIV infection may take place without symptoms or may be associated with fever, pharyngitis or headache. Sometimes, the clinical presentation includes aseptic meningitis or cutaneous lesions. Intestinal ulceration due to opportunistic pathogens (cytomegalovirus, Epstein-Barr virus, <it>Toxoplasma gondii</it>) has been described in patients with AIDS. However, although invasion of intestinal lymphoid tissue is a prominent feature of human and simian lentivirus infections, colonic ulceration has not been reported in acute HIV infection.</p> <p>Case description</p> <p>A 42-year-old Caucasian man was treated with amoxicillin-clavulanate for pharyngitis. He did not improve, and a rash developed. History taking revealed a negative HIV antibody test five months previously and unprotected sex with a male partner the month before admission. Repeated tests revealed primary HIV infection with an exceptionally high HIV-1 RNA plasma concentration (3.6 × 10⁷copies/mL) and a low CD4 count (101 cells/mm³, seven percent of total lymphocytes). While being investigated, the patient had a life-threatening hematochezia. After angiographic occlusion of a branch of the ileocaecal artery and initiation of antiretroviral therapy, the patient became rapidly asymptomatic and could be discharged. Colonoscopy revealed a bleeding colonic ulcer. We were unable to identify an etiology other than HIV for this ulcer.</p> <p>Conclusion</p> <p>This case adds to the known protean manifestation of primary HIV infection. The lack of an alternative etiology, despite extensive investigations, suggests that this ulcer was directly caused by primary HIV infection. This conclusion is supported by the well-described extensive loss of intestinal mucosal CD4⁺T cells associated with primary HIV infection, the extremely high HIV viral load observed in our patient, and the rapid improvement of the ulcer after initiation of highly active antiretroviral therapy. This case also adds to the debate on treatment for primary HIV infection, especially in the context of severe symptoms and an extremely high viral load.</p