Proteomics evaluation of five economical commercial abundant protein depletion kits for enrichment of diseases-specific biomarkers from blood serum

Blood serum is arguably the most analyzed biofluid for disease prediction and diagnosis. Herein, we benchmarked five different serum abundant protein depletion (SAPD) kits with regard to the identification of disease-specific biomarkers in human serum using bottom-up proteomics. As expected, the IgG removal efficiency among the SAPD kits is highly variable, ranging from 70% to 93%. A pairwise comparison of database search results showed a 10%–19% variation in protein identification among the kits. Immunocapturing-based SAPD kits against IgG and albumin outperformed the others in the removal of these two abundant proteins. Conversely, non-antibody-based methods (i.e., kits using ion exchange resins) and kits leveraging a multi-antibody approach were proven to be less efficient in depleting IgG/albumin from samples but led to the highest number of identified peptides. Notably, our results indicate that different cancer biomarkers could be enriched up to 10% depending on the utilized SAPD kit compared with the undepleted sample. Additionally, functional analysis of the bottom-up proteomic results revealed that different SAPD kits enrich distinct disease- and pathway-specific protein sets. Overall, our study emphasizes that a careful selection of the appropriate commercial SAPD kit is crucial for the analysis of disease biomarkers in serum by shotgun proteomics.     

Adaptive characteristics of salt-induced myceloids of Arthrobacter globiformis

When Arthrobacter globiformis is grown in medium containing increased concentrations of NaCl or decreased levels of cations, the bacteria grow as clusters of branching myceloid cells. The sensitivities of salt-induced and citrate-induced myceloids to several environmental stresses were compared to those of normal exponential-phase bacilli and stationary-phase cocci. Salt-induced myceloids were more resistant than normal cells to ultraviolet light or heat shock at 45°C but not to osmotic upshock or pH 4.3; citrate-induced myceloids showed an intermediate rate of heat inactivation. Carbon or nitrogen starvation of myceloids in the absence of added NaCl or citrate led to their division into single cells. Both myceloids and the single cells derived from them were more resistant than normal bacteria to nitrogen starvation. Salt-induced and citrate-induced myceloids showed reduced metabolism of many different carbon compounds in Biolog GP plates. These studies suggest that the formation of multicellular structures by A. globiformis is an adaptive response which increases its potential for survival.     

Extracellular hyaline material in association with other cytologic features in aspirates from collagenous spherulosis and adenoid cystic carcinoma of the breast

OBJECTIVE: To reevaluate breast aspirates showing extracellular hyaline material (EHM) and globules to assess if clinicoradiologic and cytologic features could help in differentiating between benign and malignant lesions, especially collagenous spherulosis (CS) and adenoid cystic carcinoma (ACC). STUDY DESIGN: Fine needle aspiration was performed on 884 patients with breast lumps. The cytomorphologic features of 6 cases showing EHM, including classic hyaline globules (HGs), were analyzed in detail. Three cases also had hemorrhagic nipple discharge. Tissue diagnosis (4) and mammography (6) were available. RESULTS: Aspirate smears revealed high cellularity composed of monolayers: clusters of uniform, small cells; EHM; and HGs surrounded by similar cells. Benign naked nuclei and stromal fragments (4), nuclear pleomorphism (3), apocrine cells (2), foam cells (2), naked HGs (2) and spindle cells in proximity to HGs were also seen (4). Nipple discharge smears showed foam cells, erythrocytes (3) and epithelial cell clusters with hyaline material (1). The cytologic diagnosis was CS (4) and ACC (2). Histopathology confirmed the diagnosis of CS (2) and ACC (1). CONCLUSION: There may be a morphologic overlap between the cytomorphologic features of CS and ACC, leading to diagnostic errors. The presence of EHM and HGs in association with bland cellular features should be interpreted with caution to avoid erroneous diagnoses. Histopathology is mandatory in these cases because of their different prognostic implications.     

Does the neuropeptide somatostatin have therapeutic potential against schistosomiasis?

The neuropeptide hormone somatostatin is used to treat bleeding oesophageal varices and to reduce portal pressure, and can prevent progression to severe fibrosis in chronic liver disease. We believe that somatostatin can also have therapeutic potential against schistosomiasis, based on recent observations that severe morbidity symptoms are associated with low levels of host somatostatin in patients infected with Schistosoma mansoni. The administration of exogenous doses of this neuropeptide could therefore alleviate the pathology caused by schistosomiasis.     

Rare coexistence of keratinizing squamous metaplasia with xanthogranulomatous pyelonephritis. Report of a case with the role of immunocytochemistry in the differential diagnosis

BACKGROUND: Xanthogranulomatous pyelonephritis (XPN), a rare form ofchronicpyelonephritis, is commonly associated with lithiasis and rarely leads to keratinizing squamous metaplasia. Its manifestations closely mimic those of a renal neoplasm, leading to misdiagnosis of malignancy, often resulting in radical nephrectomy. The role of immunocytochemistry in the preoperative cytologic diagnosis is assessed in the present case report. CASE: A 20-year-old male presented with fever and an enlarging mass in the right renal angle. Ultrasonography revealed a heterogeneous mass in the renal pelvis. Fine needle aspiration cytology was advised to rule out malignancy. Aspiration smears from the mass showed many dissociated cells and clusters of them with abundant vacuolated cytoplasm, vesicular nuclei and prominent nucleoli in some cells. Many desquamated metaplastic squamous cells were also seen. The background was predominantly necrotic, with inflammatory cells. The cytologic possibility of XPN with squamous metaplasia vs. renal cell carcinoma was considered. Immunocytochemical markers, epithelial membrane antigen (EMA) and CD68 (histiocytic marker) were used to determine the nature of the suspicious vacuolated cells; these cells were immunoreactive for CD68 and negative for EMA, thus confirming the cytologic diagnosis of XPN with keratinizing squamous metaplasia. CONCLUSION: The case highlights the presence of metaplastic squamous cells in XPN in smears for the first time. Immunocytochemistry is an essential tool in the preoperative cytologic diagnosis of XPN. The patient can be managed conservatively with antibiotics.     

Plasmid-based genetic modification of human bone marrow-derived stromal cells: analysis of cell survival and transgene expression after transplantation in rat spinal cord

Background

Swine is an important agricultural commodity and biomedical model. Manipulation of the pig genome provides opportunity to improve production efficiency, enhance disease resistance, and add value to swine products. Genetic engineering can also expand the utility of pigs for modeling human disease, developing clinical treatment methodologies, or donating tissues for xenotransplantation. Realizing the full potential of pig genetic engineering requires translation of the complete repertoire of genetic tools currently employed in smaller model organisms to practical use in pigs.

Results

Application of transposon and recombinase technologies for manipulation of the swine genome requires characterization of their activity in pig cells. We tested four transposon systems- Sleeping Beauty, Tol2, piggyBac, and Passport in cultured porcine cells. Transposons increased the efficiency of DNA integration up to 28-fold above background and provided for precise delivery of 1 to 15 transgenes per cell. Both Cre and Flp recombinase were functional in pig cells as measured by their ability to remove a positive-negative selection cassette from 16 independent clones and over 20 independent genomic locations. We also demonstrated a Cre-dependent genetic switch capable of eliminating an intervening positive-negative selection cassette and activating GFP expression from episomal and genome-resident transposons.

Conclusion

We have demonstrated for the first time that transposons and recombinases are capable of mobilizing DNA into and out of the porcine genome in a precise and efficient manner. This study provides the basis for developing transposon and recombinase based tools for genetic engineering of the swine genome.     

Cytomorphologic spectrum of carcinoma ex pleomorphic adenoma

OBJECTIVE: To delineate the cytomorphologic features of carcinoma ex pleomorphic adenoma (CPA) and identify the diagnostic pitfalls. STUDY DESIGN: Smears of 14 cases suspected as CPA on fine needle aspiration over a period of 15 years were reviewed. Cytohistologic correlation was done in 10 cases. RESULTS: All cases had a salivary gland mass of 1-16 years' duration, with a rapid increase in size in 10 cases. Epithelial cells predominated over stroma in 11 of 14 cases. Group I showed unequivocal malignant cells admixed with benign epithelial and stromal components of pleomorphic adenoma (PA), which were considered diagnostic of CPA on review. The cytologic differential diagnosis in these cases included mucoepidermoid carcinoma, carcinosarcoma and metastatic adenocarcinoma. Group II comprised 7 cases suspected to be cellular PA with atypia or CPA. These showed mild to moderate degrees of pleomorphism, absence of unequivocal malignant cells, and a variable proportion of benign epithelial and stromal components. Four of them were histologically confirmed as CPA. CONCLUSION: Sampling error is an important cause of diagnostic pitfalls. Correlation with clinical data is essential in diagnosis of CPA on cytology. In a proper clinical setting, extensive fine needle aspiration sampling should be done initially. Any degree of nuclear atypia in PA should be documented, alerting the clinician and histopathologist to the possibility of CPA.     

Utility of repeat fine needle aspiration in acute suppurative lesions. Follow-up of 263 cases

OBJECTIVE: To determine the clinical value of repeat fine needle aspiration (FNA) as a follow-up strategy in the management of patients in India, clinically suspected of having tuberculosis (TB) but showing a cytologic picture of acute suppuration. STUDY DESIGN: Repeat aspirates from 263 patients presenting with lymph node or soft tissue masses were analyzed. The previous FNA of these cases had shown acute inflammatory exudate but no epithelioid granuloma or acid-fast bacilli (AFB). RESULTS: The repeat FNA helped to detect 55% additional cases of TB within a period of 8 weeks; 67% of them were diagnosed in the second and third weeks. Diagnostic yield rose to 59% after the third FNA. AFB were detected in 34 (13.3%) cases that showed a low bacterial load. In addition, nontubercular lesions, such as epidermal inclusion cyst (4), cysticercosis (3), sialadenitis (2) and metastatic carcinoma (8), were diagnosed. CONCLUSION: All cases showing acute suppuration without granulomas or AFB on the first FNA should be reevaluated by follow-up FNA and staining for AFB. This will enhance the diagnostic yield of tuberculosis in developing countries, where molecular diagnostics are too costly or unavailable. This procedure is cost effective as compared to biopsy and culture. In addition to tuberculosis, many unexpected nontubercular lesions may also be unmasked. Repeat FNA reduces sampling and screening errors, improves sensitivity and helps to study the evolution of epithelioid granulomas.     

Morphologic spectrum of papillary carcinoma of the thyroid: role of cytology in identifying the variants

OBJECTIVE: To evaluate the efficacy of fine needle aspiration cytology (FNAC) in the diagnosis of morphologic variants of papillary carcinoma of the thyroid (PCT) and to determine the reasons for misdiagnosis in discrepant cases on cytology. STUDY DESIGN: Fine needle aspiration smears from 158 histologically proven cases of PCT were blindly reviewed and an attempt made to subclassify them into different variants on the basis of various architectural and morphologic features. Cytohistologic correlation was performed to assess the efficacy of cytology in correctly identifying these variants. RESULTS: In cases with satisfactory aspirates, the diagnosis of papillary carcinoma was correctly made in 112 of 139 (80.5%) histologically proven cases of PCT. Subclassification was correct in 87 of 96 (90.6%) cases of classic papillary carcinoma and in 25 of 43 (58.1%) of the other variants of PCT with adequate aspirates. Cytohistologic agreement was 100% in columnar cell variant (CCV) and high grade variant (HGV). Although there was overlap in the morphologic features of tall cell variant (TCV) and Hürthle cell variant, cytology correctly identified 60% and 76.4% of these cases, respectively. The accuracy of cytology was limited in diagnosing follicular variant as only 50% of these cases could be correctly typed on cytology. Nodular fascitis-like stroma and diffuse sclerosis variants could not be diagnosed on cytology. CONCLUSION: Though FNAC is of limited value in typing the variants of PCT due to overlapping morphologic features, it can provide clues to the diagnosis in certain aggressive variants such as TCV, CCV and HGV. Early diagnosis in these cases can assist clinicians with management.     

Do N-glycoproteins have preference for specific sequons?

Protein N-glycosylation requires the presence of asparagine (N) in the consensus tri-peptide NXS/T (where X is any amino acid, S is serine and T is threonine). Several factors affect the glycosylation potential of NXS/T sequons and one such factor is the type of amino acid at position X. While proline was shown to negatively affect N-glycosylation, the nature of other amino acids at this position is not clear. Using Markov chain analysis of tri-peptide NXS/T from viral, archaeal and eukaryotic proteins as well as experimentally confirmed N-glycosylated sequons from eukaryotic proteins, we show here that the occurrence of most sequon types differ significantly from the expected probability. Sequon types with F, G, I, S, T and V amino acids are consistently preferred while those with P and charged amino acids are under-represented in all four groups. Further, proteins contained far fewer number of possible sequon types (maximum 20 types for NXS or NXT taken separately) for any given number of sequons, which may be explained based on random sampling. Consistent with the present finding, majority of the over-represented sequons found in two important viral envelope glycoproteins (hemagglutinin of influenza A H3N2 and glycoprotein120 of HIV-1) are indeed preferred sequon types, which may provide a selective advantage. Accordingly, although there seems to be some preference for sequons, this preference may not be unique to N-glycosylation.