Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes

Cellular behaviors emerge from layers of molecular interactions: proteins interact to form complexes, pathways, and phenotypes. We show that hierarchical networks of protein interactions can be defined from the statistical pattern of proteome variation measured across thousands of diverse bacteria and that these networks reflect the emergence of complex bacterial phenotypes. Our results are validated through gene-set enrichment analysis and comparison to existing experimentally derived databases. We demonstrate the biological utility of our approach by creating a model of motility in Pseudomonas aeruginosa and using it to identify a protein that affects pilus-mediated motility. Our method, SCALES (Spectral Correlation Analysis of Layered Evolutionary Signals), may be useful for interrogating genotype-phenotype relationships in bacteria.

The circadian clock regulates cisplatin-induced toxicity and tumor regression in melanoma mouse and human models

Cisplatin is one of the most commonly used chemotherapeutic drugs; however, toxicity and tumor resistance limit its use. Studies using murine models and human subjects have shown that the time of day of cisplatin treatment influences renal and blood toxicities. We hypothesized that the mechanisms responsible for these outcomes are driven by the circadian clock. We conducted experiments using wild-type and circadian disrupted Per1/2^-/- mice treated with cisplatin at selected morning (AM) and evening (PM) times. Wild-type mice treated in the evening showed an enhanced rate of removal of cisplatin-DNA adducts and less toxicity than the morning-treated mice. This temporal variation in toxicity was lost in the Per1/2^-/- clock-disrupted mice, suggesting that the time-of-day effect is linked to the circadian clock. Observations in blood cells from humans subjected to simulated day and night shift schedules corroborated this view. Per1/2^-/- mice also exhibited a more robust immune response and slower tumor growth rate, indicating that the circadian clock also influences the immune response to melanoma tumors. Our findings indicate that cisplatin chronopharmacology involves the circadian clock control of DNA repair as well as immune responses, and thus affects both cisplatin toxicity and tumor growth. This has important implications for chronochemotherapy in cancer patients, and also suggests that influencing the circadian clock (e.g., through bright light treatment) may be explored as a tool to improve patient outcomes.

The immunomodulatory, antitumor and antimetastatic responses of melanoma-bearing normal and alcoholic mice to sunitinib and ALT-803: a combinatorial treatment approach

ALT-803, a novel IL-15/IL-15 receptor alpha complex, and the tyrosine kinase inhibitor, sunitinib, were examined for their single and combined effects on the growth of subcutaneous B16BL6 melanoma and on lymph node and lung metastasis. The study was conducted in immunocompetent C57BL/6 mice drinking water (Water mice) and in mice that chronically consumed alcohol (Alcohol mice), which are deficient in CD8(+) T cells. Sunitinib inhibited melanoma growth and was more effective in Alcohol mice. ALT-803 did not alter tumor growth or survival in Water or Alcohol mice. Combined ALT-803 and sunitinib inhibited melanoma growth and increased survival, and these effects were greater than sunitinib alone in Water mice. ALT-803 and alcohol independently suppressed lymph node and lung metastasis, whereas sunitinib alone or in combination with ALT-803 increased lymph node and lung metastasis in Water and Alcohol mice. Initially, ALT-803 increased IFN-γ-producing CD8(+)CD44(hi) memory T cells and CD8(+)CD44(hi)CD62L(lo) effector memory T cells and sunitinib decreased immunosuppressive MDSC and T regulatory cells (Treg). However, the impact of these treatments diminished with time. Subcutaneous tumors from Water mice showed increased numbers of CD8(+) T cells, CD8(+)CD44(hi) T cells, NK cells, and MDSC cells and decreased Treg cells after ALT-803 treatment.

Abstract 1345: Antitumor and antimetastatic response of melanoma-bearing normal and alcoholic mice to Sunitinib and ALT-803 treatment

Chronic alcohol consumption (CAC) is a risk factor for melanoma as well as other cancers and can result in decreased patient survival. We previously showed that CAC increases the percentage of IFN-γ-producing CD8+ T cells exhibiting a memory phenotype (CD44hi) in the early stage of primary B16BL6 melanoma development; however, these cells rapidly decrease with continued tumor growth. CAC also results in decreased cells producing IL-15, a cytokine essential for sustained proliferation and survival of CD8+ T cells. In addition, myeloid derived suppressor cells (MDSC), which can inhibit CD8+ T cell proliferation and activation and thus suppress antitumor immune responses, also increase in the blood of melanoma-bearing mice during CAC. Herein, we examined the single and combined effects of ALT-803, a novel IL-15/IL-15 receptor alpha complex designed to increase CD8+ T cell proliferation and activation and Sunitinib, known to inhibit MDSC, on primary melanoma growth and metastasis in female C57BL/6 mice inoculated s.c. with B16BL6 melanoma and given continuous water or 20% w/v alcohol. Both drugs are being evaluated separately in human melanoma clinical trials. ALT-803 did not inhibit primary tumor growth or increase survival when given weekly at a dose of 0.2 mg/kg but did inhibit tumor growth and increase survival at a dosage of 1.5-2.0 mg/kg. Sunitinib (40 mg/kg daily) given alone and in combination with ALT-803 inhibited tumor growth compared to untreated water and alcohol controls. Sunitinib had a greater effect on tumor growth and final tumor weight in alcohol drinking mice compared to water drinking mice. Sunitinib increased survival and in combination with ALT-803 extended survival further. MDSC, which increased with tumor growth in untreated mice, were initially suppressed by Sunitinib; however, continued tumor growth overcame the initial suppressive effect. ALT-803 increased levels of CD8+ T cells, CD8+CD44hi T cells, and IFN-γ-producing CD8+ T cells. This effect decreased with continued tumor growth. ALT-803 inhibited and Sunitinib increased lymph node and lung metastasis in mice inoculated s.c. with melanoma. The Sunitinib effect on metastasis was not abrogated in combination with ALT-803. Further studies to investigate the mechanisms associated with these findings are warranted. Supported by NIH Grants K05AA017149 and R21AA022098 to GGM and HZ and NSF pre-doctoral fellowship DGE-1347973 to KAG.

Citation Format: Kari A. Gaither, Alexander A. Little, Alisha A. McBride, Savanna Castillo, Kiran K. Brar, Amity Platt, Zhaohui Zhu, Faya Zhang, Dung Luong, Hui Zhang, Gary G. Meadows. Antitumor and antimetastatic response of melanoma-bearing normal and alcoholic mice to Sunitinib and ALT-803 treatment. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1345. doi:10.1158/1538-7445.AM2015-1345

A three-state study of waterborne disease surveillance techniques

For a two-year period, the states of Colorado, Vermont and Washington tested the effectiveness of ten surveillance methods for identifying waterborne disease. Nine were active surveillance methods, soliciting illness reports; one was passive, relying on voluntary disease reporting. One waterborne disease outbreak was identified through use of the nine active methods, while 14 were reported through the passive surveillance method. The presence of coliform bacteria during routine water testing was not related to illness in the community.

Serotyping and serology studies of campylobacteriosis associated with consumption of raw milk

A community outbreak of 15 cases of gastroenteritis was traced to consumption of unpasteurized milk produced at one commercial dairy. Using two different testing schemes, we found that a Campylobacter jejuni isolate from an ill patient and an isolate from a sick cow were the same serotype. Bacteriological studies suggested that a single epidemic strain of Campylobacter jejuni caused this outbreak.