Research Spotlight

Posted May 15th 2016

Moxifloxacin’s limited efficacy in the hollow-fiber model of mycobacterium abscessus disease.

Tawanda Gumbo M.D.

Tawanda Gumbo M.D.

Ferro, B. E., S. Srivastava, D. Deshpande, J. G. Pasipanodya, D. van Soolingen, J. W. Mouton, J. van Ingen and T. Gumbo (2016). “Moxifloxacin’s limited efficacy in the hollow-fiber model of mycobacterium abscessus disease.” Antimicrob Agents Chemother Apr 11 [Epub ahead of print].

Full text of this article.

Current regimens used to treat pulmonaryMycobacterium abscessusdisease have limited efficacy. There is an urgent need for new drugs and optimized combinations and doses. We performed hollow fiber system studies in whichM. abscessuswas exposed to moxifloxacin lung concentration-time profiles similar to human doses between 0 and 800 mg/day. The minimum bactericidal concentration and MIC were 8 and 2 mg/liter in ourM. abscessusstrain, suggesting bactericidal activity. Measurement of moxifloxacin concentrations in each hollow fiber system revealed an elimination rate (kel) of 0.11+/-0.05 hr-1(half-life of 9.8 h). Inhibitory sigmoid maximal effect (Emax) modeling revealed that the highest Emaxwas 3.15+/-1.84 log10CFU/ml on day 3, and the exposure mediating 50% of Emax(EC50) was a 0-24 hour area under the concentration time curve (AUC0-24) to MIC ratio of 41.99+/-31.78 (r2=0.99). The EC80was an AUC0-24/MIC of 102.11. However no moxifloxacin concentration killed the bacteria to burdens below the starting inoculum. There was re-growth beyond day 3 in all doses, with replacement by resistant subpopulation that had an MIC >32 mg/liter by the end of experiment. A quadratic function best described the relationship between AUC0-24/MIC and moxifloxacin-resistant subpopulation. Monte Carlo simulations of 10,000 patients revealed that the 400-800 mg/day doses would achieve or exceed the EC80in /=12.5% of patients. The moxifloxacin susceptibility breakpoint was 0.25 mg/liter, which means almost allM. abscessusclinical strains were moxifloxacin-resistant by these criteria. While moxifloxacin’s efficacy againstM. abscessuswas poor, formal combination therapy studies with moxifloxacin are still recommended.


Posted May 15th 2016

DNA methylation patterns as noninvasive biomarkers and targets of epigenetic therapies in colorectal cancer.

Ajay Goel Ph.D.

Ajay Goel Ph.D.

Hashimoto, Y., T. J. Zumwalt and A. Goel (2016). “DNA methylation patterns as noninvasive biomarkers and targets of epigenetic therapies in colorectal cancer.” Epigenomics Apr 22 [Epub ahead of print].

Full text of this article.

Aberrant DNA methylation is frequently detected in gastrointestinal tumors, and can therefore potentially be used to screen, diagnose, prognosticate, and predict colorectal cancers (CRCs). Although colonoscopic screening remains the gold standard for CRC screening, this procedure is invasive, expensive, and suffers from poor patient compliance. Methylated DNA is an attractive choice for a biomarker substrate because CRCs harbor hundreds of aberrantly methylated genes. Furthermore, abundance in extracellular environments and resistance to degradation and enrichment in serum, stool, and other noninvasive bodily fluids, allows quantitative measurements of methylated DNA biomarkers. This article describes the most important studies that investigated the efficacy of serum- or stool-derived methylated DNA as population-based screening biomarkers in CRC, details several mechanisms and factors that control DNA methylation, describes a better use of prevailing technologies that discover novel DNA methylation biomarkers, and illustrates the diversity of demethylating agents and their applicability toward clinical impact.


Posted May 15th 2016

A 380-gene meta-signature of active tuberculosis compared with healthy controls.

Virginia Pascual M.D.

Virginia Pascual M.D.

Blankley, S., C. M. Graham, J. Levin, J. Turner, M. P. Berry, C. I. Bloom, Z. Xu, V. Pascual, J. Banchereau, D. Chaussabel, R. Breen, G. Santis, D. M. Blankenship, M. Lipman and A. O’Garra (2016). “A 380-gene meta-signature of active tuberculosis compared with healthy controls.” Eur Respir J Apr 13 [Epub ahead of print].

Full text of this article.

Mycobacterium tuberculosis is estimated to have infected one third of the world’s population and continues to be a significant cause of mortality and morbidity [1]. There is a need for new and improved diagnostics or treatment-monitoring tools and blood-based mRNA diagnostics are a potential solution [2]. Gene expression microarray analysis of human blood has been widely used to profile the host transcriptional response in active tuberculosis (TB) to identify potential biomarkers and better understand the host immune response [2]. So far, there has been a relative lack of concordance in the actual genes being identified from the published studies [2, 3], although there has been agreement in some of the pathways identified. Interferon (IFN) signalling has been identified as a dominant signature in many of the individual studies [2, 4]; however, when significant gene lists were combined from eight publicly available TB datasets, TREM1 (triggering receptor expressed on myeloid cells 1) signalling became the most significant pathway [5].


Posted May 15th 2016

Rhinovirus detection in symptomatic and asymptomatic children value of host transcriptome analysis.

Virginia Pascual M.D.

Virginia Pascual M.D.

Heinonen, S., T. Jartti, C. Garcia, S. Oliva, C. Smitherman, E. Anguiano, W. A. A. d. S. Piters, T. Vuorinen, O. Ruuskanen, B. Dimo, N. M. Suarez, V. Pascual, O. Ramilo and A. Mejias (2016). “Rhinovirus detection in symptomatic and asymptomatic children value of host transcriptome analysis.” American Journal of Respiratory and Critical Care Medicine 193(7): 772-782.

Full text of this article.

Rationale: Rhinoviruses (RVs) are a major cause of symptomatic respiratory tract infection in all age groups. However, RVs can frequently be detected in asymptomatic individuals. Objectives: To evaluate the ability of host transcriptional profiling to differentiate between symptomatic RV infection and incidental detection in children. Methods: Previously healthy children younger than 2 years old (n = 151) were enrolled at four study sites and classified into four clinical groups: RV-healthy control subjects (n = 37), RV+ asymptomatic subjects (n = 14), RV+ outpatients (n = 30), and RV+ inpatients (n = 70). Host responses were analyzed using whole-blood RNA transcriptional profiles. Measurements and Main Results: RV infection induced a robust transcriptional signature, which was validated in three independent cohorts and by quantitative real-time polymerase chain reaction with high prediction accuracy. The immune profile of symptomatic RV infection was characterized by overexpression of innate immunity and underexpression of adaptive immunity genes, whereas negligible changes were observed in asymptomatic RV+ subjects. Unsupervised hierarchical clustering identified two main clusters of subjects. The first included 93% of healthy control subjects and 100% of asymptomatic RV+ subjects, and the second comprised 98% of RV+ inpatients and 88% of RV+ outpatients. Genomic scores of healthy control subjects and asymptomatic RV+ children were similar and significantly lower than those of RV+ inpatients and outpatients (P< 0.0001). Conclusions: Symptomatic RV infection induced a robust and reproducible transcriptional signature, whereas identification of RV in asymptomatic children was not associated with significant systemic transcriptional immune responses. Transcriptional profiling represents a useful tool to discriminate between active infection and incidental virus detection.


Posted May 15th 2016

Expansion of inflammatory innate lymphoid cells in patients with common variable immune deficiency.

Virginia Pascual M.D.

Virginia Pascual M.D.

Cols, M., A. Rahman, P. J. Maglione, Y. Garcia-Carmona, N. Simchoni, H.-B. M. Ko, L. Radigan, A. Cerutti, D. Blankenship, V. Pascual and C. Cunningham-Rundles (2016). “Expansion of inflammatory innate lymphoid cells in patients with common variable immune deficiency.” Journal of Allergy and Clinical Immunology 137(4): 1206-NIL_1836.

Full text of this article.

Background: Common variable immunodeficiency (CVID) is an antibody deficiency treated with immunoglobulin; however, patients can have noninfectious inflammatory conditions that lead to heightened morbidity and mortality. Objectives: Modular analyses of RNA transcripts in whole blood previously identified an upregulation of many interferon-responsive genes. In this study we sought the cell populations leading to this signature. Methods: Lymphoid cells were measured in peripheral blood of 55 patients with CVID (31 with and 24 without inflammatory/autoimmune complications) by using mass cytometry and flow cytometry. Surface markers, cytokines, and transcriptional characteristics of sorted innate lymphoid cells (ILCs) were defined by using quantitative PCR. Gastrointestinal and lung biopsy specimens of subjects with inflammatory disease were stained to seek ILCs in tissues. Results: The linage-negative, CD127(+), CD161(+) lymphoid population containing T-box transcription factor, retinoic acid-related orphan receptor (ROR) gamma t, IFN-gamma, IL-17A, and IL-22, all hallmarks of type 3 innate lymphoid cells, were expanded in the blood of patients with CVID with inflammatory conditions (mean, 3.7% of PBMCs). ILCs contained detectable amounts of the transcription factors inhibitor of DNA binding 2, T-box transcription factor, and ROR gamma t and increased mRNA transcripts for IL-23 receptor (IL-23R) and IL-26, demonstrating inflammatory potential. In gastrointestinal and lung biopsy tissues of patients with CVID, numerous IFN-gamma+ROR gamma t(+)CD3(-) cells were identified, suggesting a role in these mucosal inflammatory states. Conclusions: An expansion of this highly inflammatory ILC population is a characteristic of patients with CVID with inflammatory disease; ILCs and the interferon signature are markers for the uncontrolled inflammatory state in these patients.