Zhang, Yang

Malakoplakia is an inflammatory process related to defective macrophage response to bacterial infection. To further characterize the clinicopathologic manifestations of gastrointestinal malakoplakia, 26 cases were identified from 6 institutions. Hematoxylin and eosin-stained slides and available stains were reviewed, and pertinent clinicopathologic features analyzed. Sixteen patients were women (62%). Mean patient age was 64 (range: 24 to 83). Sites included the colorectum (n=23), appendix (n=1), and stomach (n=2). Clinical indications for tissue procurement included screening (n=14), tumor resection (n=5), diarrhea (n=1), adenoma surveillance (n=1), ulcerative colitis flare (n=1), abdominal pain (n=1), and appendicitis (1). All cases featured histiocytes with abundant, pale, eosinophilic cytoplasm focally containing Michaelis-Gutmann bodies. The process frequently involved the mucosa (n=19), with architectural distortion in 13 cases. Lymphoid aggregates were present in 18 cases, which were prominent or obscuring in 11 (all colon biopsies) and provoked concern for lymphoma in 2. Associated findings included adenocarcinoma (n=5), adenoma (n=2), gastric hyperplastic polyps (n=1), chemical gastritis (n=1), collagenous colitis (n=1), and active chronic colitis (n=2). In cases with available stains, Michaelis-Gutman bodies were highlighted by Periodic Acid-Schiff with diastase, Von Kossa, and iron stains. Although 2 cases were positive for Tropheryma whipplei antibody, no T. whipplei transcripts were detected on real-time polymerase chain reaction. All patients with available follow-up are alive and well with no additional instances of malakoplakia. Malakoplakia of the gastrointestinal tract is a benign, incidental finding. Although histologic features in the stomach and colon resections are similar to those at other sites, exuberant lymphocytic response in colon biopsies and immunoreactivity with T. whippleii antibody may provoke initial confusion and lead to unnecessary time and resource investment.

Background: Due to its ability to provide quantitative and dynamic information on tumor genesis and development by directly profiling protein expression, the proteomics has become intensely popular for characterizing the functional proteins driving the transformation of malignancy, tracing the large-scale protein alterations induced by anticancer drug, and discovering the innovative targets and first-in-class drugs for oncologic disorders. Objective: To quantify cancer proteomics data, the label-free quantification (LFQ) is frequently employed. However, low precision, poor reproducibility and inaccuracy of the LFQ of proteomics data have been recognized as the key “technical challenge” in the discovery of anticancer targets and drugs. In this paper, the recent advances and development in the computational perspective of LFQ in cancer proteomics were therefore systematically reviewed and analyzed. Methods: PubMed and Web of Science database were searched for label-free quantification approaches, cancer proteomics and computational advances. Results: First, a variety of popular acquisition techniques and state-of-the-art quantification tools are systematically discussed and critically assessed. Then, many processing approaches including transformation, normalization, filtering and imputation are subsequently discussed, and their impacts on improving LFQ performance of cancer proteomics are evaluated. Finally, the future direction for enhancing the computation-based quantification technique for cancer proteomics are also proposed. Conclusion: There is a dramatic increase in LFQ approaches in recent year, which significantly enhance the diversity of the possible quantification strategies for studying cancer proteomics.