Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis

Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.

Building a Harmonized Datamart by Integrating Cross-Institutional Systems of Clinical, Outcome, and Genomic Data: The Pediatric Patient Informatics Platform (PPIP)

PURPOSE

Siloed electronic medical data limits utility and accessibility. At the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, cross-institutional data were inconsistent and difficult to access. To unify data for clinical operations, administration, and research, we developed the Pediatric Patient Informatics Platform (PPIP), an integrated datamart harmonizing multiple source systems across two institutions into a common technology.

PATIENTS AND METHODS

Starting in 2009, user requirements were gathered and data sources were prioritized. Project teams, including biostatisticians, database developers, and an external contractor, were formed. Read-access to source systems was established. The 3-layer PPIP architecture was developed: STAGING, a near-exact copy of source data; INTEGRATION, where data were reorganized into domains; and, CONSUMPTION, where data were optimized for rapid retrieval. The diverse systems were integrated into a common IBM Netezza technology. Data filters were defined to accurately capture the Center's patients, and derived data items were created for harmonization across sources. An interactive online query tool, PPIP360, was developed using Microstrategy Analytics.

RESULTS

Driven by scientific objectives, the PPIP datamart was created, including 33,674 patients, 2,983 protocols, and 3.6 million patient visits from 14 source databases, 164 source tables, and 2,622 source data items. The PPIP360 has 605 data items and 33 metrics across 11 reports and dashboards. Dana-Farber and Boston Children's established a legal data-sharing agreement. The PPIP has supported hundreds of faculty, staff, and projects, including planning clinical trials and informing strategic planning.

CONCLUSION

The PPIP has successfully harmonized and integrated diagnostic, demographic, laboratory, treatment, clinical outcome, pathology, transplant, meta-protocol, and -omics data, for efficient, daily operational and research activities at Dana-Farber/Boston Children's Cancer and Blood Disorders Center, and future external sharing.

Addressing aquatic hazard classification for metals, metal compounds and alloys in marine systems

New International Maritime Organization regulations require shippers to classify all solid bulk cargo to indicate whether they are Harmful to the Marine Environment (HME). The objective of this work was to adapt the freshwater Transformation/Dissolution Protocol (T/DP) to marine water to provide a method to determine, when compared with marine Ecotoxicity Reference Values (ERVs), whether a metal-bearing substance is HME. The substances examined were: Cu2O powder; Ni metal powder; Co3O4 powder; and a Ni-Co-Fe alloy, as wire cuttings, which were the same substances examined in the freshwater T/D validation study and afforded comparisons of the reactivity, or measure of the rate and extent of metal release from the metal-bearing substances in freshwater versus marine conditions. The marine T/D method is suitable for conducting examinations of metal-bearing substances with a wide range of reactivities, from the relatively reactive Cu2O powder and the alloy to the Co3O4 powder, which was the least reactive.

Localization of CS and non-CS antigens in the sporogonic stages of Plasmodium yoelii

Monoclonal antibodies (MAbs) and colloidal gold probes were used to localize circumsporozoite (CS) protein and two unrelated polypeptides in developing oocysts and salivary gland sporozoites of the 17X (NL) strain of Plasmodium yoelii. MAbs NYS1, NYS2, and NYS3 recognized different epitopes of the P. yoelii CS protein and produced similar patterns of immunolabelling on developing oocysts and sporozoites. A small percentage of oocysts contained developing sporoblasts and sporozoites that did not exhibit surface reactivity to MAbs NYS1, NYS2 or NYS3, although internal labelling was associated with endoplasmic reticulum (ER). These sporozoites were still capable of completing development and invading salivary glands where they could be found adjacent to sporozoites with densely labelled surface coats. If these sporozoites are infective, their presence may explain in part the failure of CS vaccines to completely protect immunized animals against challenge. The non-CS antigen recognized by MAbs NYS4 did not become abundant until late in sporogony. Some gold labelling was associated with the surface of budding and mature sporozoites, but the antigen was most abundant within the cytoplasm and micronemes. A second non-CS antigen identified by NYS5 first appeared in 7-day-old oocysts, although labelling was sparse. Small quantities of antigen appeared on the sporoblast membrane, cytoplasmic clefts and ER of oocysts and was associated with micronemes and the surface of budding and mature sporozoites. As the role played by non-CS antigens in the biology of the parasite is not yet known, further characterization of their function is needed before their potential as vaccine candidates can be determined.

Improved renal allograft function and survival following nonspecific blood transfusions. I. Induction of soluble suppressor factors inhibiting the mitogenic response

A small number of blood transfusions (1-3) seems sufficient to improve the cadaveric renal allograft outcome, probably via induction of some nonspecific suppressive activity. This activity was assessed by the concanavalin A (Con A) enhancement method; when present, the response of freshly isolated patients' cells to a submitogenic dose of Con A was lowered, leading to a Con A ratio greater than 5, significantly (P less than 0.0001) higher than the one observed in normal controls or untransfused uremic patients. The correlation between this suppressive activity and graft outcome was determined. Thirty-five patients were studied over a 12-month period for graft function (creatinine level) and survival. Both parameters were significantly improved in the group of patients whose Con A ratio was greater than 5 after transfusions. A soluble suppressor factor, or factors, released into the supernatant of patients' lymphocytes cultured for 48 hr, seems responsible for this suppressive activity. Moreover this process is nonspecific, since it suppresses mitogenic response of cells isolated from normal untransfused volunteers, and could be observed when peripheral blood mononuclear cells were used, but not with purified adherent or nonadherent cells. Addition of indomethacin to the cells during the elaboration of the supernatant abolished this activity. However, amounts of PGE2 secreted into the supernatant during the 48 hr of culture could not be correlated with this suppressive activity. These findings suggest that induction of nonspecific immunosuppression by a few blood transfusions could predict a better kidney graft outcome.

Absence of correlation between the degree of alveolitis and antibody levels to Micropolysporum faeni

Specific IgG antibody (Ab) levels to Micropolysporum faeni (MF) antigen were measured in three study groups: 29 farmers of whom one had acute, two chronic and 26 with a past history of Farmer's lung disease (FLD), 91 clinically asymptomatic but exposed farmers and 23 unexposed donors. This study confirms the greater sensitivity of enzyme linked immunosorbent assay (ELISA) over double immunodiffusion (DID): 34 (37%) sera negative by DID were positive by ELISA and only two (4%) were positive by DID and negative by ELISA. Antibody levels to MF were higher in the serum of farmers whether symptomatic (113.2 +/- 196.1 u) or not (25.2 +/- 64.7 u) than in that of unexposed donors (1.05 +/- 1.46 u), (P less than 0.001). In a subgroup of farmers, antibody levels were compared in the serum and bronchoalveolar lavage (BAL) fluid; the levels were higher in the serum than in BAL fluids in all farmers except the only patient with acute FLD. A significant correlation was seen between Ab levels of the serum and BAL fluids. Finally, no correlation was seen between the serum antibody levels and the total number of cells or the percentage of lymphocytes found in BAL fluids, either in the subjects with a history of FLD or the asymptomatic group.

Abnormal bronchoalveolar lavage in asymptomatic dairy farmers. Study of lymphocytes

Bronchoalveolar lavage (BAL) was performed on 24 asymptomatic dairy farmers. Thirteen had serum precipitins to Micropolyspora faeni (MF) antigens (Group 1), and 11 were seronegative control subjects (Group 2). All were nonsmokers and had no history of previous lung disease. Thirteen of 24 subjects (9 in Group 1 and 4 in Group 2) had a high percentage of lymphocytes (greater than or equal to 20%) in their BAL. The T-lymphocyte subpopulations as estimated by OKT3, OKT4, and OKT8 monoclonal antibody reactivity were measured in peripheral blood lymphocytes; OKT3 = 58.5 +/- 15.6% for Group 1, and 58.5 +/- 8.7% for Group 2; OKT4 = 40.6 +/- 10.7% and 39.9 +/- 10.0%; OKT8 = 21.5 +/- 10.6% and 22.4 +/- 8.0%, respectively (p = NS). These lymphocyte characteristics were also similar when subjects with a high percentage of lymphocytes in BAL were compared to those with a normal percentage. Specific (MF-coated) chicken erythrocyte lymphocytotoxicity (Group 1, 45.2 +/- 29.5%, Group 2, 49.2 +/- 23.4%), and nonspecific lymphocytotoxicity (Group 1, 43.9 +/- 28.6%, Group 2, 37.9 +/- 18.0%) were also similar. We conclude that a large number of asymptomatic dairy farmers have an increased percentage of lymphocytes in their BAL ("alveolitis") and that peripheral blood lymphocytes in these subjects have normal subpopulations, as assessed by monoclonal antibodies, and normal lymphocytotoxicity.

The regulatory effect of histamine on the immune response: III. Defect on in vitro IgE production in atopics

Spontaneous in vitro production of IgE was found higher in a group of untreated grass sensitive atopic patients than in normal volunteers when assessed at the cellular level with a reverse hemolytic plaque assay. This study also confirmed the increase of IgE synthesis after pokeweed mitogen stimulation in non-atopic donors and its decrease in atopic patients. Moreover, in this work we looked for a potential defect in immunoregulatory functions in atopic patients toward the in vitro IgE production. Indeed, histamine is known to activate suppressor cells capable, in turn, of suppressing IgG and IgE production from normal cells. In atopic patients, histamine could activate cells capable of suppressing IgG production but not IgE. Furthermore, similar findings were found when Concanavalin A-induced suppressor cells were examined. These findings suggest (a) a defective regulatory function towards IgE in atopic patients and (b) that the same subpopulation of suppressor cells seems to be activated by histamine and ConA and defective in atopic patients.

Blood transfusions in renal dialysis patients. Effect on cellular immune response

The effect of blood transfusions, given in low number (less than 5), on the immune response of renal dialysis patients was studied. A significantly lowered response of lymphocytes to mitogen stimulation was observed in patients after as few as one, two or three transfusions, depending on the patient. This led to an increased delta 48/delta 0 ratio reflected by the enhanced response of the cells following delayed addition of suboptimal dose of mitogen. There was no modification of the ratio of helper/inducer to suppressor/cytotoxic T cells subsets (OKT4/OKT8). The use of such simple in vitro tests in a strict protocol of transfusions could allow an adequate follow-up thereby limiting the risks of sensitization. These results demonstrate that important phenomena affecting patients' immune response are turned on following even a low number of transfusions in the majority of uremic patients. This could probably be related to the beneficial effects of blood transfusions on the kidney allograft survival already described.

Étude polarographique du niobium dans les mélanges eau – fluorure d'hydrogène

Solubilization in hydrogen fluoride is required for the analysis of some minerals. A method of analysis directly applicable to water – hydrogen fluoride mixtures was worked out.However, in 50% hydrofluoric acid niobium is soluble as [Formula: see text] complex, which can be reduced with a polarographic electrode at a potential of −0.880 V vs. E.C.S. For concentrations lower than 45% in HF, the niobium complex is hydrated and exists as a non-reducible ion [Formula: see text].

Detection of immunoglobulin-secreting lymphocytes by the use of a hemolytic plaque assay in liquid phase

This paper describes a modification of the reverse hemolytic plaque assay allowing the enumeration of immunoglobulin (Ig)-secreting lymphocytes at rest or after in vitro stimulation. Ig-secreting cells are mixed with anti-Ig coated sheep red blood cells, developing anti-Ig antiserum and complement in liquid medium. This mixture is pipetted between two slides and the hemolytic plaques are numerated after incubation at 37 degrees C. The class of Ig secreted can be determined using a monospecific developing antiserum. This technique is easier to perform and more economical than the previously described method using agarose without loss of sensitivity, the number of plaques detected being about the same and the kinetic of their appearance comparable.

[In vitro stimulation of human T and B lymphocytes by lipopolysaccharide (LPS)]

The appearance of cells (CFC) having the property to cluster several layers of sheep red blood cells around themselves has been used in our laboratory as a marker for T cell activation. In this study, enumeration of stimulated T cells was carried out by this technique, whereas enumeration of B cells was carried out with surface Ig staining using fluorescein-labelled anti-Ig antibodies or F(ab)2 anti-Ig. Lymphocytes were stimulated in vitro for various lengths of time with the polyclonal mitogen PWM, the specific antigen Varidase and LPS added at culture initiation or 16 hours after beginning of culture. Our results confirm that human lymphocytes preincubated for 16 hours before addition of LPS give rise to higher numbers of CFC and blast cells, In all cases, less than half of these blasts reacted with the F(ab)2 anti-Ig, This suggests that under these conditions, LPS is not a mitogen specific for human B cells.