Thursday, August 26, 2010

Exercise, calorie restrictions can rejuvenate older nerve synapses, study finds

Harvard researchers have uncovered a mechanism through which caloric restriction and exercise delay some of the debilitating effects of aging by rejuvenating the connections between nerves and the muscles that they control.

The research, conducted in the labs of Joshua Sanes and Jeff Lichtman, both members of the Center for Brain Science at Harvard and professors of molecular and cellular biology, begins to explain prior findings that exercise and restricted-calorie diets help to stave off the mental and physical degeneration of aging.

Sanes said their research, conducted through laboratory mice genetically engineered so their nerve cells glow in fluorescent colors, shows that some of the debilitation of aging is caused by the deterioration of connections that nerves make with the muscles they control, structures called neuromuscular junctions. These microscopic links are remarkably similar to the synapses that connect neurons to form information-processing circuits in the brain.

In a healthy neuromuscular synapse, nerve endings and their receptors on muscle fibers are almost a perfect match, like two hands placed together, finger to finger, palm to palm. This lineup ensures maximum efficiency in transmitting the nerve’s signal from the brain to the muscle, which is what makes it contract during movement.

As people age, however, the neuromuscular synapses can deteriorate in several ways. Nerves can shrink, failing to cover the muscle’s receptors completely. Sanes said the intersections between the nerves and muscles can go from a continuous network that looks like a pretzel to one that resembles a bunch of beads — broken into discontinuous individual lumps, interfering with transmission of nerve impulses to the muscles. This loss of activity can result in wasting and eventually even death of muscle fibers.

The work showed that mice on a restricted-calorie diet largely avoid that age-related deterioration of their neuromuscular junctions, while those on a one-month exercise regimen when already elderly partially reverse the damage.

“With calorie restriction, we saw reversal of all of these things. With exercise, we saw a reversal of most, but not all,” Sanes said.

Because of the study’s structure — mice were on calorie-restricted diets for their whole lives, while those that exercised did so for just the month late in life — Sanes cautioned against drawing conclusions about the effectiveness of exercise versus calorie restriction in preventing or reversing synaptic damage. He noted that longer periods of exercise might have more profound effects, a possibility he and Lichtman are now testing.

The research, much of it conducted by postdoctoral fellows Gregorio Valdez, Juan Tapia, and Hyuno Kang, was published online by the journal Proceedings of the National Academy of Sciences and financed through grants from the National Institute on Aging, the National Institute of Neurological Disorders and Stroke, and the Ellison Medical Foundation.

Though much of the work in the Sanes and Lichtman labs focuses on understanding synapses in the brain, both scientists have investigated neuromuscular synapses for many years because they are far easier to study than brain synapses. Neuromuscular junctions are large enough to be viewed by light microscopy, and can be a jumping-off point for brain study, highlighting areas of inquiry and potential techniques.

“There’ve been quite a few reports that caloric restriction and exercise delay cognitive decline, but people don’t know much about the cellular reasons behind them,” Sanes said. “These findings in neuromuscular synapses make us curious to know whether similar effects might occur in brain synapses.”

Beyond the ease of study, neuromuscular junctions are important areas to understand because the gradual loss of muscle mass and strength, known to scientists as sarcopenia, is a problem in the elderly, debilitating otherwise healthy individuals who can lose their balance and break a hip or other bones, leading to a cascade of physical ills.

“The effects of exercise and caloric restriction on innervation may help explain their beneficial effects on sarcopenia,” Sanes said.

Lichtman and Sanes have been collaborating to study age-related changes in synapses for five years and began focusing on caloric restriction and exercise two years ago.

While the changes to the synapses through caloric restriction and exercise were clear in the images the researchers obtained, Sanes cautioned that their work was structural, not functional, and they have not yet tested how well the synapses worked.

Sanes said the research may help to advance research aimed at increasing the time that people spend healthy, termed “healthspan.”

“Caloric restriction and exercise have numerous, dramatic effects on our mental acuity and motor ability,” Sanes said. The research “gives us a hint that the way these extremely powerful lifestyle factors act is by attenuating or reversing the decline in our synapses.”

http://news.harvard.edu/gazette/story/2010/08/insights-on-healthy-aging/?utm_source=Harvard+University+List&utm_campaign=ae947977f7-Gazette_Newsletter6_03_2010&utm_medium=email

Cancer Drugs Force HIV to Mutate to Death- Voice of America News (08.24.10):: Joe DeCapua

Existing drugs approved to treat cancer and tested for anti-HIV activity proved potent in a new study, researchers report. After treatment, HIV mutated itself to death - and did so fairly quickly.
"Well, we were specifically looking for drugs that had already been approved by the [Food and Drug Administration] for other purposes," said study co-author professor Louis Mansky, director of the Institute for Molecular Virology at the University of Minnesota. "And we were screening to look for ones that may have been overlooked in the past for anti-HIV activity."
"HIV has this propensity for rapidly mutating and evolving," Mansky said. "And this is really in a lot of ways the main reason why there hasn't been an effective vaccine developed and why there's continual problems with drug resistance."
With a combination of cancer drugs decitabine and gemcitabine, Mansky and colleagues reported they were able to reduce HIV infectivity in tissue samples by 73 percent, though at concentrations that showed minimal antiviral activity when each drug was used alone. "Decreased infectivity coincided with a significant increase in mutation frequency and a shift in the HIV mutation spectrum," they reported.
"The drugs do not directly inhibit the virus from replicating," Mansky said. "What they do is to basically cause the virus to elevate its mutation rate. And through that process, allow it to continue to replicate and basically kill off its infectivity by this process of lethal mutagenesis, which is elevating the mutation rate to the point where the virus is no longer infectious."
Further research will involve animal studies, Mansky said, and proving that the drugs are not only efficacious but also safe. In addition, the cancer drugs, which are given intravenously, would need to be formulated as a pill.
The full study, "Exploiting Drug Repositioning for Discovery of a Novel HIV Combination Therapy," was published in the Journal of Virology (2010;84(18):9301-9309).

Wednesday, August 25, 2010

Myelosuppression by sunitinib is flt-3 genotype dependent

Sir,Myelosuppression is frequently observed during treatment with the multi tyrosine kinase inhibitors (TKIs) (Motzer et al, 2007; Bhojani et al, 2008). The frequency and severity of myelosuppression varies among the drug class with sunitinib being a relative myelotoxic compound leading to leukopenia and thrombocytopenia in 56–78% and 41–65% of the patients, respectively (Demetri et al, 2006; Motzer et al, 2007).

British Journal of Cancer 103, 757-758 (24 August 2010) | doi:10.1038/sj.bjc.6605813

Sex-specific exposure prevalence of established risk factors for oesophageal adenocarcinoma

Background:

There is an unexplained male predominance in the incidence of oesophageal adenocarcinoma, and the sex-specific distribution of its risk factors in the general population is not known.

Methods:

A random sample of Swedish citizens aged 40–79 years completed a questionnaire for assessment of the prevalence of five risk factors for oesophageal adenocarcinoma: reflux symptoms, body mass index, tobacco smoking habits, socioeconomic status, and use of non-steroidal anti-inflammatory drugs (NSAIDs). Logistic regression was used to calculate odds ratios (ORs) with 95% confidence intervals (CIs) to evaluate the association of these risk factors, separately and combined, with male sex, with women as reference.

Results:

Among 6969 invited people, 4906 (70.4%) completed the questionnaire. Adjusted prevalence estimates showed a negative association with male sex with regard to reflux disease (OR=0.70, 95% CI=0.58–0.84), whereas overweight (OR=1.98, 95%CI=1.72–2.27) and obesity (OR=1.22, 95% CI=1.01–1.47), previous smoking (OR=1.50, 95% CI=1.30–1.72), and no NSAID use (OR=1.35, 95% CI=1.15–1.49) were positively associated.

Conclusions:

Exposure to some but not all established risk factors for oesophageal adenocarcinoma seems to be more common in men than in women, but the differences are small and unlikely to explain the male predominance of this tumour.

British Journal of Cancer 103, 735-740 (24 August 2010) | doi:10.1038/sj.bjc.6605804

ANO1 amplification and expression in HNSCC with a high propensity for future distant metastasis and its functions in HNSCC cell lines

Background:

Head and neck squamous cell carcinoma (HNSCC) is associated with poor survival. To identify prognostic and diagnostic markers and therapeutic targets, we studied ANO1, a recently identified calcium-activated chloride channel (CaCC).

Methods:

High-resolution genomic and transcriptomic microarray analysis and functional studies using HNSCC cell line and CaCC inhibitors.

Results:

Amplification and overexpression of genes within the 11q13 amplicon are associated with the propensity for future distance metastasis of HPV-negative HNSCC. ANO1 was selected for functional studies based on high correlations, cell surface expression and CaCC activity. ANO1 overexpression in cells that express low endogenous levels stimulates cell movement, whereas downregulation in cells with high endogenous levels has the opposite effect. ANO1 overexpression also stimulates attachment, spreading, detachment and invasion, which could account for its effects on migration. CaCC inhibitors decrease movement, suggesting that channel activity is required for the effects of ANO1. In contrast, ANO1 overexpression does not affect cell proliferation.

Interpretation:

ANO1 amplification and expression could be markers for distant metastasis in HNSCC. ANO1 overexpression affects cell properties linked to metastasis. Inhibitors of CaCCs could be used to inhibit the tumourigenic properties of ANO1, whereas activators developed to increase CaCC activity could have adverse effects.

British Journal of Cancer 103, 715-726 (24 August 2010) | doi:10.1038/sj.bjc.6605823

Diagnosis of prostate cancer by detection of minichromosome maintenance 5 protein in urine sediments

Background:

The accuracy of prostate-specific antigen (PSA) testing in prostate cancer detection is constrained by low sensitivity and specificity. Dysregulated expression of minichromosome maintenance (Mcm) 2–7 proteins is an early event in epithelial multistep carcinogenesis and thus MCM proteins represent powerful cancer diagnostic markers. In this study we investigate Mcm5 as a urinary biomarker for prostate cancer detection.

Methods:

Urine was obtained from 88 men with prostate cancer and from two control groups negative for malignancy. A strictly normal cohort included 28 men with complete, normal investigations, no urinary calculi and serum PSA <2 ng ml–1. An expanded control cohort comprised 331 men with a benign final diagnosis, regardless of PSA level. Urine was collected before and after prostate massage in the cancer patient cohort. An immunofluorometric assay was used to measure Mcm5 levels in urine sediments.

Results:

The Mcm5 test detected prostate cancer with 82% sensitivity (confidence interval (CI)= 72–89%) and with a specificity ranging from 73 (CI=68–78%) to 93% (CI=76–99%). Prostate massage led to increased Mcm5 signals compared with pre-massage samples (median 3440 (interquartile range (IQR) 2280 to 5220) vs 2360 (IQR <1800 to 4360); P=0.009), and was associated with significantly increased diagnostic sensitivity (82 vs 60%; P=0.012).

Conclusions:

Urinary Mcm5 detection seems to be a simple, accurate and noninvasive method for identifying patients with prostate cancer. Large-scale prospective trials are now required to evaluate this test in diagnosis and screening.

British Journal of Cancer 103, 701-707 (24 August 2010) | doi:10.1038/sj.bjc.6605785

Whole blood-derived miRNA profiles as potential new tools for ovarian cancer screening

background:

Screening is an unsolved problem for ovarian cancer (OvCA). As late detection is equivalent to poor prognosis, we analysed whether OvCA patients show diagnostically meaningful microRNA (miRNA) patterns in blood cells.

methods:

Blood-borne whole miRNome profiles from 24 patients with OvCA and 15 age- and sex-matched healthy controls were biostatistically evaluated.

results:

Student's t-test revealed 147 significantly deregulated miRNAs before and 4 after Benjamini–Hochberg adjustment. Although these included miRNAs already linked to OvCA (e.g., miR-16, miR-155), others had never before been connected to specific diseases. A bioinformatically calculated miRNA profile allowed for discrimination between blood samples of OvCA patients and healthy controls with an accuracy of >76%. When only cancers of the serous subtype were considered and compared with an extended control group (n=39), accuracy, specificity and sensitivity all increased to >85%.

conclusion:

Our proof-of-principle study strengthens the hypothesis that neoplastic diseases generate characteristic miRNA fingerprints in blood cells. Still, the obtained OvCA-associated miRNA pattern is not yet sensitive and specific enough to permit the monitoring of disease progression or even preventive screening. Microarray-based miRNA profiling from peripheral blood could thus be combined with other markers to improve the notoriously difficult but important screening for OvCA.

British Journal of Cancer (2010) 103, 693–700. doi:10.1038/sj.bjc.6605833 www.bjcancer.com
Published online 3 August 2010

Identification of genes and pathways associated with cytotoxic T lymphocyte infiltration of serous ovarian cancer

Background:

Tumour-infiltrating lymphocytes (TILs) are predictors of disease-specific survival (DSS) in ovarian cancer. It is largely unknown what factors contribute to lymphocyte recruitment. Our aim was to evaluate genes and pathways contributing to infiltration of cytotoxic T lymphocytes (CTLs) in advanced-stage serous ovarian cancer.

Methods:

For this study global gene expression was compared between low TIL (n=25) and high TIL tumours (n=24). The differences in gene expression were evaluated using parametric T-testing. Selectively enriched biological pathways were identified with gene set enrichment analysis. Prognostic influence was validated in 157 late-stage serous ovarian cancer patients. Using immunohistochemistry, association of selected genes from identified pathways with CTL was validated.

Results:

The presence of CTL was associated with 320 genes and 23 pathways (P<0.05). In addition, 54 genes and 8 pathways were also associated with DSS in our validation cohort. Immunohistochemical evaluation showed strong correlations between MHC class I and II membrane expression, parts of the antigen processing and presentation pathway, and CTL recruitment.

Conclusion:

Gene expression profiling and pathway analyses are valuable tools to obtain more understanding of tumour characteristics influencing lymphocyte recruitment in advanced-stage serous ovarian cancer. Identified genes and pathways need to be further investigated for suitability as therapeutic targets.

British Journal of Cancer 103, 685-692 (24 August 2010) | doi:10.1038/sj.bjc.6605820

Targeting pancreatic and ovarian carcinomas using the auristatin-based anti-CD70 antibody–drug conjugate SGN-75

Background:

CD70 is an ideal target for antibody-based therapies because of its aberrant high expression in renal carcinomas and non-Hodgkin lymphomas and its highly restricted expression in normal tissues. The expression profiling of CD70 in carcinomas has been limited because of the lack of a CD70-specific reagent that works in formalin-fixed paraffin-embedded (FFPE) tissues.

Methods:

We generated murine monoclonal antibodies (mAbs) specific for CD70 and validated their specificity by western blot analysis and developed a protocol for immunohistochemistry on FFPE tissues. CD70+ tumour cell lines were used for testing the anti-tumour activity of the anti-CD70 antibody–drug conjugate, SGN-75.

Results:

We report novel detection of CD70 expression in multiple cancers including pancreatic (25%), larynx/pharynx (22%), melanoma (16%), ovarian (15%), lung (10%), and colon (9%). Our results show that pancreatic and ovarian tumour cell lines, which express high levels of endogenous or transfected CD70, are sensitive to the anti-tumour activity of SGN-75 in vitro and in vivo.

Conclusion:

Development of murine mAbs for robust and extensive screening of FFPE samples coupled with the detection of anti-tumour activity in novel indications provide rationale for expanding the application of SGN-75 for the treatment of multiple CD70 expressing cancers.

British Journal of Cancer 103, 676-684 (24 August 2010) | doi:10.1038/sj.bjc.6605816

BCL2 in breast cancer: a favourable prognostic marker across molecular subtypes and independent of adjuvant therapy received

Background:

Breast cancer is heterogeneous and the existing prognostic classifiers are limited in accuracy, leading to unnecessary treatment of numerous women. B-cell lymphoma 2 (BCL2), an antiapoptotic protein, has been proposed as a prognostic marker, but this effect is considered to relate to oestrogen receptor (ER) status. This study aimed to test the clinical validity of BCL2 as an independent prognostic marker.

Methods:

Five studies of 11 212 women with early-stage breast cancer were analysed. Individual patient data included tumour size, grade, lymph node status, endocrine therapy, chemotherapy and mortality. BCL2, ER, progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) levels were determined in all tumours. A Cox model incorporating the time-dependent effects of each variable was used to explore the prognostic significance of BCL2.

Results:

In univariate analysis, ER, PR and BCL2 positivity was associated with improved survival and HER2 positivity with inferior survival. For ER and PR this effect was time dependent, whereas for BCL2 and HER2 the effect persisted over time. In multivariate analysis, BCL2 positivity retained independent prognostic significance (hazard ratio (HR) 0.76, 95% confidence interval (CI) 0.66–0.88, P<0.001). BCL2 was a powerful prognostic marker in ER− (HR 0.63, 95% CI 0.54–0.74, P<0.001) and ER+ disease (HR 0.56, 95% CI 0.48–0.65, P<0.001), and in HER2− (HR 0.55, 95% CI 0.49–0.61, P<0.001) and HER2+ disease (HR 0.70, 95% CI 0.57–0.85, P<0.001), irrespective of the type of adjuvant therapy received. Addition of BCL2 to the Adjuvant! Online prognostic model, for a subset of cases with a 10-year follow-up, improved the survival prediction (P=0.0039).

Conclusions:

BCL2 is an independent indicator of favourable prognosis for all types of early-stage breast cancer. This study establishes the rationale for introduction of BCL2 immunohistochemistry to improve prognostic stratification. Further work is now needed to ascertain the exact way to apply BCL2 testing for risk stratification and to standardise BCL2 immunohistochemistry for this application.

British Journal of Cancer 103, 668-675 (24 August 2010) | doi:10.1038/sj.bjc.6605736

In situ quantification of HER2–protein tyrosine kinase 6 (PTK6) protein–protein complexes in paraffin sections from breast cancer tissues

Background:

Protein tyrosine kinase 6 (PTK6; breast tumour kinase) is overexpressed in up to 86% of the invasive breast cancers, and its association with the oncoprotein human epidermal growth factor receptor 2 (HER2) was shown in vitro by co-precipitation. Furthermore, expression of PTK6 in tumours is linked with the expression of HER2.

Method and results:

In this study, we used the proximity ligation assay (PLA) technique on formalin-fixed paraffin sections from eighty invasive breast carcinoma tissue specimens to locate PTK6–HER2 protein–protein complexes. Proximity ligation assay signals from protein complexes were assessed quantitatively, and expression levels showed a statistically significant association with tumour size (P=0.015) and course of the cancer disease (P=0.012).

Conclusion:

Protein tyrosine kinase 6 forms protein complexes with HER2 in primary breast cancer tissues, which can be visualised by use of the PLA technique. Human epidermal growth factor receptor 2–PTK6 complexes are of prognostic relevance.

British Journal of Cancer 103, 663-667 (24 August 2010) | doi:10.1038/sj.bjc.6605836

Molecular basis of chemosensitivity of platinum pre-treated ovarian cancer to chemotherapy

Background:

Ovarian cancer shows considerable heterogeneity in its sensitivity to chemotherapy both clinically and in vitro. This study tested the hypothesis that the molecular basis of this difference lies within the known resistance mechanisms inherent to these patients' tumours.

Methods:

The chemosensitivity of a series of 31 ovarian tumours, all previously treated with platinum-based chemotherapy, was assessed using the ATP-based tumour chemosensitivity assay (ATP-TCA) and correlated with resistance gene expression measured by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) in a TaqMan Array following extraction of mRNA from formalin-fixed paraffin-embedded tissue. The results were standardised against a housekeeping gene (PBGD), and assessed by multiple linear regression.

Results:

Predictive multiple linear regression models were derived for four single agents (cisplatin, gemcitabine, topotecan, and treosulfan), and for the combinations of cisplatin+gemcitabine and treosulfan+gemcitabine. Particularly strong correlations were obtained for cisplatin, gemcitabine, topotecan, and treosulfan+gemcitabine. No individual gene expression showed direct correlation with activity in the ATP-TCA. Genes involved in DNA repair and apoptosis were strongly represented, with some drug pumps also involved.

Conclusion:

The chemosensitivity of ovarian cancer to drugs is related to the expression of genes involved in sensitivity and resistance mechanisms.

British Journal of Cancer 103, 656-662 (24 August 2010) | doi:10.1038/sj.bjc.6605817

Integrated preclinical and clinical development of mTOR inhibitors in pancreatic cancer

Background:

The purpose of this work was to determine the efficacy of inhibiting mammalian target of rapamycin (mTOR) in pancreatic cancer preclinical models and translate preclinical observations to the clinic.

Methods:

Temsirolimus (20 mg Kg−1 daily) was administered to freshly generated pancreatic cancer xenografts. Tumour growth inhibition was determined after 28 days. Xenografts were characterised at baseline by gene expression and comparative genomic hybridisation. Patients with advanced, gemcitabine-resistant pancreatic cancer were treated with sirolimus (5 mg daily). The primary end point was 6-month survival rate (6mSR). Correlative studies included immunohistochemistry assessment of pathway expression in baseline tumours, drug pharmacokinetics (PKs), response assessment by FDG-PET and pharmacodynamic effects in peripheral-blood mononuclear cells (PBMCs).

Results:

In all, 4 of 17 xenografts (23%) responded to treatment. Sensitive tumours were characterised by gene copy number variations and overexpression of genes leading to activation of the PI3K/Akt/mTOR pathway. Activation of p70S6K correlated with drug activity in the preclinical studies. Sirolimus was well tolerated in the clinic, showed predictable PKs, exerted pathway inhibition in post-treatment PBMCs and resulted in a 6mSR of 26%. No correlation, however, was found between activated p70S6K in tumour tissues and anti-tumour effects.

Conclusion:

Sirolimus activity in pancreatic cancer was marginal and not predicted by the selected biomarker.

British Journal of Cancer 103, 649-655 (24 August 2010) | doi:10.1038/sj.bjc.6605819

Quercetin induced apoptosis in association with death receptors and fludarabine in cells isolated from chronic lymphocytic leukaemia patients

Background:

Quercetin is a flavonoid naturally present in food and beverages belonging to the large class of phytochemicals with potential anti-cancer properties. Here, we investigated the ability of quercetin to sensitise primary cells from chronic lymphocytic leukaemia (CLL) to death receptor (DR) agonists, recombinant TNF-related-apoptosis-inducing ligand (rTRAIL) and anti-CD95, and to fludarabine, a widely used chemotherapeutic drug against CLL.

Methods:

Peripheral white blood cells were isolated from patients and incubated with medium containing 50 ng ml anti-CD95 agonist antibody; 10 ng ml recombinant TRAIL; 10–25 μM quercetin and 3.5–14 μM fludarabine. Neutral Red assay was used to measure cell viability, where as apoptosis was assessed by determining caspase-3 activity, exposure to Annexin V and PARP fragmentation.

Results:

Quercetin significantly enhanced anti-CD95- and rTRAIL-induced cell death as shown by decreased cell viability, increased caspase-3 and -9 activities, and positivity to Annexin V. In addition, association of quercetin with fludarabine increases the apoptotic response in CLL cells of about two-fold compared with quercetin monotreatment.

Conclusion:

This work shows that resistance to DR- and fludarabine-induced cell death in leukaemic cells isolated from CLL patients can be ameliorated or bypassed by the combined treatment with quercetin. Considering the low toxicity of the molecule, our study results are in favour of a potential use of quercetin in adjuvant chemotherapy in combination with other drugs.

 

British Journal of Cancer 103, 642-648 (24 August 2010) | doi:10.1038/sj.bjc.6605794

Zoledronic acid impairs myeloid differentiation to tumour-associated macrophages in mesothelioma

Suppressive immune cells present in tumour microenvironments are known to augment tumour growth and hamper efficacy of antitumour therapies. The amino-bisphosphonate Zoledronic acid (ZA) is considered as an antitumour agent, as recent studies showed that ZA prolongs disease-free survival in cancer patients. The exact mechanism is a topic of debate; it has been suggested that ZA targets tumour-associated macrophages (TAMs).

Methods:

We investigate the role of ZA on the myeloid differentiation to TAMs in murine mesothelioma in vivo and in vitro. Mice were intraperitoneally inoculated with a lethal dose of mesothelioma tumour cells and treated with ZA to determine the effects on myeloid differentiation and survival.

Results:

We show that ZA impaired myeloid differentiation. Inhibition of myeloid differentiation led to a reduction in TAMs, but the number of immature myeloid cells with myeloid-derived suppressor cell (MDSC) characteristics was increased. In addition, ZA affects the phenotype of macrophages leading to reduced level of TAM-associated cytokines in the tumour microenvironment. No improvement of survival was observed.

Conclusion:

We conclude that ZA leads to a reduction in macrophages and impairs polarisation towards an M2 phenotype, but this was associated with an increase in the number of immature myeloid cells, which might diminish the effects of ZA on survival.

British Journal of Cancer 103, 629-641 (24 August 2010) | doi:10.1038/sj.bjc.6605814

Tuesday, August 24, 2010

Creating and characterizing communities of human gut microbes in gnotobiotic mice

Microbiology laboratories are laden with flasks, plates and freezers stocks containing axenic cultures and their products. In contrast, virtually every other habitat on Earth is filled with microbial communities of varying degrees of complexity. In this context, microorganisms are interdependent components of ecosystems; deciphering this dynamic requires a move from microbial organisms studied in isolation to model microbial communities studied under conditions that mimic those encountered by their members in their native habitats. Here, we focus on model communities consisting of microbes that inhabit the human body habitat containing our largest collection of organisms—the gut. The adult human gastrointestinal tract is a microbial bioreactor, containing all three domains of life. This ecosystem is teeming with microorganisms at its distal end (1011–1012 cells ml−1 luminal contents in the colon) and less so at its proximal end (an estimated 103–104 cells ml−1 luminal contents in the duodenum). The gut microbiota affects myriad aspects of our systems physiology, ranging from processing and harvesting of macronutrients and micronutrients (and xenobiotics!) from our diets, to shaping the features of our innate and adaptive immune system. Recently, deep sampling of the fecal microbial community has revealed that each of us harbor a collection of a several hundred bacterial phylotypes (Qin et al., 2010; Turnbaugh et al., 2010). The exact set of microbes differs from person to person although there is a greater degree of similarity between family members (Turnbaugh et al., 2009a, 2010). A catalog of several million genes present in the fecal microbiome has been assembled from analysis of a 577-Gbp data set obtained from shotgun sequencing of fecal community DNA prepared from 124 Europeans (Qin et al., 2010) and a 10.1-Gbp data set generated from a set of deeply sampled obese monozygotic co-twins living in the United States (Turnbaugh et al., 2010). These data sets provide a starting point for making in silico predictions about functions that can be attributed to the gut microbiota. Measurements of expressed mRNAs (Turnbaugh et al., 2010), proteins (Verberkmoes et al., 2009), and metabolites (Hoverstad et al., 1984; Li et al., 2008;Martin et al., 2008) in gut samples represent a first step toward testing these predictions.

Generating germ free mice via embryo transfer:-

Germ-free (GF) mice provide a complementary approach for characterizing the properties of the human gut microbiome. Methods for establishing and propagating inbred strains of mice under GF conditions were established >50 years ago by several groups. Re-derivation was based on caesarian section of a conventionally raised (microbe laden) mother, passaging the intact uterine horns containing the pups through a germicidal bath, and delivery of her pups in a GF isolator where they were suckled by a lactating foster mother (the original GF foster mothers were generated by caesarian delivery of litters, hand feeding of pups in an GF isolator with an autoclaved artificial liquid diet until a male and female reached reproductive maturity; colonies were established from these GF progenitors and their offspring distributed to other gnotobiotic facilities; for example seehttp://gordonlab.wustl.edu/SuppInfo/Reyniers_Sacksteder_1957.pdf). This approach requires precise timing and is also inefficient: in our experience, 0–5 wild-type pups survive to weaning age per re-derivation (n=100 C-sections performed between 1998 and 2007). Therefore, we have replaced this method with embryo transfer: embryos are harvested 1 day after mating, and transferred under sterile conditions to a pseudopregnant GF mother generated by mating to a vasectomized GF male. This technique yields 5–8 live born animals/25 embryos transferred/recipient mother (n>250 procedures). GF status is verified by PCR of feces using universal bacterial 16S rRNA gene primers and by culturing fecal and skin swabs under conditions that support growth of a broad range of anaerobic and aerobic bacterial species and fungi.

Studies of complex microbial communities  in gnotobiotic mice:-

GF mice can be colonized with microbial communities of varying complexity and origin at defined stages of their life. For example, gut microbial communities can be harvested from various body habitats of conventionally raised mice with defined genotypes and physiological phenotypes, and introduced into GF recipients (possessing a desired genotype) to determine how much of the donor phenotype is transferable to the resulting conventionalized mice via the microbiota. If complete or even partial phenotypic transfer occurs, follow-up studies can be performed to define composition of the donor community, the mechanisms by which the donor community impacts host physiology, and how the recipient affects the transplanted microbiota/microbiome. These types of studies have typically been performed using gut contents (Turnbaugh et al., 2006; Vijay-Kumar et al., 2010), but in principle can be extended to communities harvested from any body habitat.

We have developed procedures for subjecting GF and conventionalized mice to a variety of surgical and non-surgical manipulations while maintaining their gnotobiotic environments: these procedures include

(1) endurance training through swimming in a warmed sterile water tank placed within the isolator (a ‘gnotatorium’; Crawford et al., 2009); (2) using a plexiglass gnotobiotic transporter to bring mice to an irradiator for whole body irradiation; (3) bone marrow transplantation after whole body irradiation using marrow harvested from animals of varying genotypes (Crawford and Gordon, 2005); (4) using specialized transporters that fit inside a magnetic resonance imager to determine adiposity; and (5) techniques for generating aggregation chimeras using morula-stage embryos (for a discussion and illustration of why the stem cell hierarchy of intestinal crypts make chimeric mice such a powerful tool for studying cell autonomous versus non-autonomous regulation in the gut epithelium, see Wong et al., 2000).

We have also validated procedures for transplanting human fecal microbial communities into GF mouse recipients that are then fed diets that do or do not resemble those of the human donors (Turnbaugh et al., 2009b). We have found that a remarkable proportion of human fecal microbial diversity can be transferred in this manner even if the donor specimen had been frozen at −80 °C for 1–2 years (all bacterial phyla, up to 90% of class-level and genus-level taxa, and 60–90%of species level-phylotypes in donor samples are identifiable in recipient mice using 16S rRNA-based pyrosequencing). Once engrafted, the transplanted human microbial communities are remarkably stable, can be reliably transmitted across generations of animals, and exhibit well defined and reproducible biogeographical features along the length of the mouse gut (Turnbaugh et al., 2009b). Efficient intergenerational transfer of transplanted human fecal microbiota allows the microbiota and the host's innate/adaptive immune system to co-evolve beginning at birth in ‘second generation’ mice. ‘Humanized’ gnotobiotic mice can be used for proof-of-mechanism studies that cannot be readily conducted in humans where potentially confounding variables, including variations in host genotype, diet, and antibiotic consumption are notoriously difficult to control. A derivative of this procedure is to capture as much diversity as possible by culturing a donor's fecal microbiota, and then transferring this culture collectionen masse to wild-type or genetically engineered GF recipients (culturable ‘humanized’ mice).

Assembling defined model communities in vivo using gnotobiotic mice:-

As more members of the human gut microbiota are cultured and their genomes sequenced (Nelson et al., 2010), an opportunity exists to create model human gut communities in gnotobiotic mice where all community members and their complement of microbial genes are known. Members present in these synthetic human gut microbial communities can be selected from culture collections based on various criteria, including their consistent association with specific human physiologic or pathophysiologic states, their representation in a fecal microbiota that when transferred en masse confers a phenotype to recipient GF mice, their phylogenetic features, and/or by the results of in silico predictions of their functions based on inspection of their genomes. These communities can be used to address a number of basic questions in the field: for example (1) to what extent do priority effects, where established species are able to sequester limiting space or resources and are thereby able to exclude potential colonizers, determine community composition; (2) what is the strength of interspecific interactions (a key to generating predictive models of community structure and dynamics; Trosvik et al., 2010); (3) what are the genetic predictors of niche overlap; (4) how robust are the assembled communities to various environmental perturbations; and (5) what is the microbial host range of viruses and the determinants of viral lifecycles in various regions of the gut ecosystem (Reyes et al., 2010).

To date, these model communities have consisted of as few as 2 and as many as 15 members and have been used to explore some of the metabolic interactions that take place in the distal gut (both microbial–microbial and microbial–host; see Sonnenburg et al., 2006;Denou et al., 2009; Mahowald et al., 2009; Rey et al., 2010). These communities have also been extremely useful for technology development. For example, if the complete genome sequence of each member is known, then the relative abundance of each member can be used to infer the proportional representation of genes encoding various functions (for example metabolic and signaling pathways) in that community using quantitative metagenomic methods (Morgan et al., 2010). With the current capacity of the Illumina GAIIx DNA sequencer (~30 million reads per lane), relative and absolute species abundance is quantifiable for all microbes representing at least 0.01% of the community, while allowing greater than or equal to100 barcoded samples to be pooled in a single lane of the eight-lane flow cell for multiplex sequencing. These inexpensive assays of community member abundance support the large sample sizes needed for computational modeling of the responses of a defined (synthetic) community to various perturbations (including systematic alterations in macronutrient and micronutrient composition of the diet), across time.

Understanding how different gut communities modulate their gene expression in response to changes in diet, host physiological status, or invasion with microbial species is another key step in understanding the operations of the gut microbiota. RNA-Seq allows quantification of transcriptomes at high resolution and over a broad dynamic range. In the case of synthetic communities, where all the species and genes are known, this high-resolution data can be used to verify gene structure/operons, generate in silicoreconstructions of expressed metabolic pathways for each member in the community, and make predictions concerning the metabolic niches of each species. These predictions can be informed by RNA-Seq analysis of individual community members during monoculture under highly defined conditions (for example minimal medium supplemented with systematically varied carbon sources), then be validated using quantitative mass spectrometry-based analyses of products of microbial metabolism. These studies can prompt follow-up, hypothesis-based studies of metabolic niches where the investigator manipulates the species used to construct these model communities, or uses other approaches to perturb the activities of key members in ways that provide proof-of-principle tests for affecting community function and host physiology (for example devising ways to manipulate the hydrogen economy of the gut to affect the efficiency of fermentation and host energy extraction; Rey et al., 2010). In addition, gnotobiotic mice harboring defined collections of sequenced organisms provide an opportunity to further develop methods for extracting and characterizing, by LC-MS, the proteins expressed by their model microbiota (peptides can be readily mapped as all genes are known; Mahowald et al., 2009).

Community genetics provides another powerful technology to dissect the operations of microbial communities and to identify potential avenues (targets) for microbiome-directed therapeutics. Addition or removal of organisms before gavaging the model microbiota into GF mice provides the simplest genetic perturbation to identify species that confer a benefit or detriment to other community members or the host. Another method is insertion sequencing, which combines genome-wide transposon mutagenesis with massively parallel sequencing (Goodman et al., 2009). In this approach, complex populations of tens of thousands of transposon mutants of a given sequenced community member are generated and simultaneously introduced into wild-type or genetically manipulated GF mice in the presence or absence of other (sequenced) microbes. The representation of each mutant in the input community is determined by targeted, sequencing of transposon-adjacent chromosomal DNA, and compared with their representation in the output community recovered from the mouse. Differences in mutant representation in input versus output communities indicate which microbial genes confer a fitness advantage as a function of whatever selective pressure is intentionally applied to the system (Goodman et al., 2009).

Creating more realisitc defined microbial communities: the challenges ahead:-

A look to the near future reveals a number of pressing needs. With genome sequences available for almost 200 human gut isolates from eight bacterial phyla and Archaea, our ability to move toward larger model communities in gnotobiotic mice is limited by our ability to grow microbes in parallel; therefore, we need to identify media capable of supporting growth of diverse sets of microbes, scale-up methods for growing anaerobic cultures in parallel (for example move from tubes to 96-well plates or microfluidic chips with individually addressable strains), and modify sequencing pipelines to allow for rapid assays of purity of single cell-derived cultures. The current set of sequenced human gut bacteria isolates are largely from different individuals. Using microbial communities obtained from a single individual is desirable for reasons described above, including the fact that co-existing microbial species have co-evolved, creating distinct collections of strain-level phylotypes. Thus, to move toward increasingly realistic communities, we need high-throughput methods to isolate and array in multi-well plates, single cell-derived cultures of hundreds of bacteria from a single individual. Sequencing capacity will likely be available to many individual laboratories in the next few years to generate draft genomes from hundreds of these arrayed organisms. In the context of human microbiome projects, the ultimate informative model microbiota would contain microbes isolated from single individuals that confer the donor's phenotype to the recipient gnotobiotic mice. The full model community ‘tool kit,’ both experimental and computational (including application of existing and new methods for modeling) could be applied to these communities in an attempt to expedite understanding of how their component organisms and genes confer a donor phenotype. However, for these efforts to benefit and build the field, we also need to create the infrastructure necessary to readily share both communities and their associated data between laboratories. The knowledge base for model microbial community biology (conditions for culturing its members, microbial genome sequences, quantitative data about community membership as a function of various perturbations, associated meta-transcriptome, meta-proteome, and metabolomic data sets; information about their impact on host physiology) requires systems for data deposition, annotation, and retrieval, which combine computer automation and error checking with as little human curation as necessary. Finally, currently license agreements, biological safety regulations, and shipping procedures are designed to distribute individual strains or multiple variants of the same strain. We must streamline the regulatory and infrastructure hurdles for multi-species distribution to ensure that the best model communities developed over the coming years have the opportunity to earn their ‘model’ designation as they follow the path ofEscherichia coli and Bacillus subtilis as facilitators of biological discovery.

The ISME Journal (2010) 4, 1094–1098; doi:10.1038/ismej.2010.110; published online 22 July 2010

Monday, August 16, 2010

A new family of microRNAs induces epithelial–mesenchymal transition and metastases formation by inhibiting DICER.

The expression level of microRNAs (miRNAs) is generally reduced in human cancers, but why this confers certain advantages to cancer cells is unknown. A group led by Stefano Piccolo has provided some answers to this question by identifying a new family of miRNAs that induces epithelial–mesenchymal transition (EMT) by inhibiting the expression of the microRNA regulator, DICER.

DICER processes miRNA precursors into mature miRNAs. These miRNAs control gene expression by binding to the 3′ untranslated region (UTR) of messenger RNAs (mRNAs). The authors identified an unusually long 3′ UTR in mRNAs that encode DICER, which could mean that some miRNAs bind to this region and control DICER expression through a feedback mechanism. Analysis of miRNA binding sites in the 3′ UTR of DICER1 mRNA revealed binding of the miR-103/107 family. Accordingly, in multiple cell lines, expression of miR-103 or miR-107 reduced DICER expression and as a consequence mature miRNAs were generally downregulated. This inverse correlation between miR-103 and miR-107 and DICER was also observed in patients with breast cancer who were at an increased risk of developing metastases.
The authors sought to analyse the metastatic potential of the miR-103/107 family by overexpressing miR-107 in non-metastatic mouse cells and transplanting these cells into the cleared mammary fat pads of severe combined immunodeficient mice. After several weeks, these mice developed multiple micrometastases in the lung. Treatment of mice with antagomiR-103/107, an antisense oligonucleotide that silences miR-103 and miR-107, reduced metastatic colonization and restored levels of mature miRNAs. Similarly, overexpression of DICER in a highly metastatic cell line reduced the ability of xenografts to form metastases. An analysis of chromosomal arrays from breast cancers revealed that tumours with a reduced copy number of the DICER1 locus had an increased probability of developing metastases. Therefore, DICER might be a limiting factor in the metastatic process.
How does DICER inhibition by miR-103/107 promote metastasis? Piccolo and collaborators observed how the epithelial morphology of the immortalized mammary cell lines MCF10 and NMuMG switched to a more fibroblast-like morphology when miR-107 was overexpressed, indicating an EMT. The miR200 family are known to be required to suppress EMT. The levels of miR200 expression were increased on treatment with antagomiR-103/107, reverting the phenotypic and migratory effects that were triggered by miR-107.
These results suggest a new pathway by which DICER inhibition promotes a less differentiated phenotype that favours metastasis formation.

Teresa Villanueva

References:Martello, G. et al. A MicroRNA targeting Dicer for metastasis control. Cell 141, 1195–1207 (2010)

Plasma membrane contributes to the formation of pre-autophagosomal structures

Autophagy is a catabolic process in which lysosomes degrade intracytoplasmic contents transported in double-membraned autophagosomes. Autophagosomes are formed by the elongation and fusion of phagophores, which derive from pre-autophagosomal structures. The membrane origins of autophagosomes are unclear and may involve multiple sources, including the endoplasmic reticulum and mitochondria. Here we show in mammalian cells that the heavy chain of clathrin interacts with Atg16L1 and is involved in the formation of Atg16L1-positive early autophagosome precursors. Atg16L1 associated with clathrin-coated structures, and inhibition of clathrin-mediated internalization decreased the formation of both Atg16L1-positive precursors and mature autophagosomes. We tested and demonstrated that the plasma membrane contributes directly to the formation of early Atg16L1-positive autophagosome precursors. This may be particularly important during periods of increased autophagosome formation, because the plasma membrane may serve as a large membrane reservoir that allows cells periods of autophagosome synthesis at levels many-fold higher than under basal conditions, without compromising other processes.

Nature Cell Biology 12, 747 - 757 (2010) Published online: 18 July 2010 doi:10.1038/ncb2078

The nuclear import of Frizzled2-C by Importins-β11 and α2 promotes postsynaptic development

Synapse-to-nucleus signaling is critical for synaptic development and plasticity. In Drosophila, the ligand Wingless causes the C terminus of its Frizzled2 receptor (Fz2-C) to be cleaved and translocated from the postsynaptic density to nuclei. The mechanism of nuclear import is unknown and the developmental consequences of this translocation are uncertain. We found that Fz2-C localization to muscle nuclei required the nuclear import factors Importin-β11 and Importin-α2 and that this pathway promoted the postsynaptic development of the subsynaptic reticulum (SSR), an elaboration of the postsynaptic plasma membrane. importin-β11 (imp-β11) and dfz2 mutants had less SSR, and some boutons lacked the postsynaptic marker Discs Large. These developmental defects in imp-β11 mutants could be overcome by expression of Fz2-C fused to a nuclear localization sequence that can bypass Importin-β11. Thus, Wnt-activated growth of the postsynaptic membrane is mediated by the synapse-to-nucleus translocation and active nuclear import of Fz2-C via a selective Importin-β11/α2 pathway.

Nature Neuroscience 13, 935 - 943 (2010) Published online: 4 July 2010doi:10.1038/nn.2593


http://www.nature.com/neuro/journal/v13/n8/full/nn.2593.html

Saturday, August 14, 2010

Simplified Automated Image Analysis for Detection and Phenotyping of Mycobacterium tuberculosis on Porous Supports by Monitoring Growing Microcolonies

Even with the advent of nucleic acid (NA) amplification technologies the culture of mycobacteria for diagnostic and other applications remains of critical importance. Notably microscopic observed drug susceptibility testing (MODS), as opposed to traditional culture on solid media or automated liquid culture, has shown potential to both speed up and increase the provision of mycobacterial culture in high burden settings. This study explored the growth of Mycobacterial tuberculosis microcolonies, imaged by automated digital microscopy, cultured on porous aluminium oxide (PAO) supports. Repeated imaging during colony growth greatly simplifies "computer vision" and presumptive identification of microcolonies was achieved here using existing publically available algorithms. The researchers’ system thus allowed the growth of individual microcolonies to be monitored and critically, also to change the media during the growth phase without disrupting the microcolonies. Transfer of identified microcolonies onto selective media allowed the researchers, within 1-2 bacterial generations, to rapidly detect the drug susceptibility of individual microcolonies, eliminating the need for time consuming subculturing or the inoculation of multiple parallel cultures. Monitoring the phenotype of individual microcolonies as they grow has immense potential for research, screening, and ultimately M. tuberculosisdiagnostic applications. The method described is particularly appealing with respect to speed and automation.


PLoS One. 2010 Jun 8; Volume 5, Number 6: e11008. 

Role of 4-1BB Receptor in the Control Played by CD8(+) T Cells on IFN-Gamma Production by Mycobacterium tuberculosis Antigen-Specific CD4(+) T Cells


Antigen-specific IFN-gamma producing CD4(+) T cells are the main mediators of protection against Mycobacterium tuberculosisinfection both under natural conditions and following vaccination. However these cells are responsible for lung damage and poor vaccine efficacy when not tightly controlled. Discovering new tools to control nonprotective antigen-specific IFN-gamma production without affecting protective IFN-gamma is a challenge in TB research. Immunization with DNA encoding Ag85B, a candidate vaccine antigen of Mycobacterium tuberculosis, elicited in mice a low but protective CD4(+) T cell-mediated IFN-gamma response, while in mice primed with DNA and boosted with Ag85B protein a massive increase in IFN-gamma response was associated with loss of protection. Both protective and non-protective Ag85B-immunization generated antigen-specific CD8(+) T cells, which suppressed IFN-gamma-secreting CD4(+) T cells. However, ex vivo ligation of 4-1BB, a member of TNF-receptor super-family, reduced the massive, non-protective IFN-gamma responses by CD4(+) T cells in protein-boosted mice without affecting the low protective IFN-gamma-secretion in mice immunized with DNA. This selective inhibition was due to the induction of 4-1BB exclusively on CD8(+) T cells of DNA-primed and protein-boosted mice following Ag85B protein stimulation. The 4-1BB-mediated IFN-gamma inhibition did not require soluble IL-10, TGF-beta, XCL-1 and MIP-1beta. In vivo Ag85B stimulation induced 4-1BB expression on CD8(+) T cells and in vivo 4-1BB ligation reduced the activation, IFN-gamma production and expansion of Ag85B-specific CD4(+) T cells of DNA-primed and protein-boosted mice. Antigen-specific suppressor CD8(+) T cells are elicited through immunization with the mycobacterial antigen Ag85B. Ligation of 4-1BB receptor further enhanced their suppressive activity on IFN-gamma-secreting CD4(+) T cells. The selective expression of 4-1BB only on CD8(+) T cells in mice developing a massive, non-protective IFN-gamma response opens novel strategies for intervention in TB pathology and vaccination through T-cell co-stimulatory-based molecular targeting.

 PLoS One. 2010 Jun 8; Volume 5, Number 6: e11019. 

Contrasting Transcriptional Responses of a Virulent and an Attenuated Strain of Mycobacterium tuberculosis Infecting Macrophages

H37Rv and H37Ra are well-described laboratory strains of Mycobacterium tuberculosis derived from the same parental strain, H37, that show dramatically different pathogenic phenotypes. In this study, the transcriptomes of the two strains during axenic growth in broth and during intracellular growth within murine bone-marrow macrophages were compared by whole genome expression profiling. The researchers identified and compared adaptations of either strain upon encountering an intracellular environment, and also contrasted the transcriptomes of the two strains while inside macrophages. In the former comparison, both strains induced genes that would facilitate intracellular survival including those involved in mycobactin synthesis and fatty acid metabolism. However, this response was stronger and more extensive for H37Rv than for H37Ra. This was manifested as the differential expression of a greater number of genes and an increased magnitude of expression for these genes in H37Rv. In comparing intracellular transcriptional signatures, fifty genes were found to be differentially expressed between the strains. Of these fifty, twelve were under control of the PhoPR regulon. Further differences between strains included genes whose products were members of the ESAT-6 family of proteins, or were associated with their secretion. Along with the recent identification of single nucleotide polymorphisms in H37Ra when compared to H37Rv, the researchers’ demonstration of differential expression of PhoP-regulated and ESX-1 region-related genes during macrophage infection further highlighted the significance of these genes in the attenuation of H37Ra.


 PLoS One. 2010 Jun 10; Volume 5, Number 6: e11066. 

Helminth Coinfection Does Not Affect Therapeutic Effect of a DNA Vaccine in Mice Harboring Tuberculosis

Helminthiasis and TB coincide geographically and there is much interest in exploring how concurrent worm infections might alter immune responses against bacilli and might necessitate altered therapeutic approaches. A DNA vaccine that codifies heat shock protein Hsp65 from M. leprae (DNAhsp65) has been used in therapy during experimental TB. This study focused on the impact of the co-existence of worms and TB on the therapeutic effects of DNAhsp65. Mice were infected with Toxocara canis or withSchistosoma mansoni, followed by coinfection with M. tuberculosis and treatment with DNAhsp65. While T. canis infection did not increase vulnerability to pulmonary TB, S. mansoni enhanced susceptibility to TB as shown by higher numbers of bacteria in the lungs and spleen, which was associated with an increase in Th2 and regulatory cytokines. However, in coinfected mice, the therapeutic effect of DNAhsp65 was not abrogated, as indicated by colony forming units and analysis of histopathological changes. In vitro studies indicated that Hsp65-specific IFN-gamma production was correlated with vaccine-induced protection in coinfected mice. Moreover, in S. mansoni-coinfected mice, DNA treatment inhibited in vivo TGF-beta and IL-10 production, which could be associated with long-term protection. The researchers have demonstrated that the therapeutic effects of DNAhsp65 in experimental TB infection are persistent in the presence of an unrelated Th2 immune response induced by helminth infections.


PLoS Neglected Tropical Diseases. 2010 Jun 8; Volume 4, Number 6: e700. 

Usefulness of the Paralens Fluorescent Microscope Adaptor for the Identification of Mycobacteria in Both Field and Laboratory Settings;

The presence of acid-fast bacilli (AFB) in laboratories has traditionally been demonstrated using the fluorochrome method, which requires a fluorescent microscope, or the Ziehl-Neelsen (ZN) method employing light microscopy. Low sensitivity of the ZN method and high costs of fluoroscopy make the need for a more effective means of diagnosis a top priority, especially in developing countries where the burden of TB is high. The QBC ParaLens attachment (QBC Diagnostic Inc., Port Matilda, PA) is a substitute for conventional fluoroscopy in the identification of AFB. To evaluate the efficacy of the ParaLens LED (light-emitting diode) system, the authors performed a two-part study, looking at usefulness, functionality, and durability in urban/rural health clinics around the world, as well as in a controlled state public health laboratory setting. In the field, the ParaLens was durable and functioned well with various power sources and lighting conditions. Results from the state laboratory indicated agreement between standard fluorescent microscopy and fluorescent microscopy using the ParaLens. This adaptor is a welcome addition to laboratories in resource-limited settings as a useful alternative to conventional fluoroscopy for detection of mycobacterial species.
The Open Microbiology Journal. 2010 Apr 30; Volume 4: 30-3.

Evaluation of Seven Tests for the Rapid Detection of Multidrug-Resistant Tuberculosis in Uganda;

This study evaluated head-to-head rapid tests for drug susceptibility testing (DST) of Mycobacterium tuberculosis against rifampicin (RMP) and isoniazid (INH) in a resource-limited setting. Thirty-one well-characterized strains of M. tuberculosis were tested with the nitrate reductase assay (NRA), microscopic observation drug susceptibility (MODS), MGIT 960 (Mycobacterium Growth Indicator Tube 960), Genotype MTBDRplus, Alamar blue, MTT, and resazurin assays at the National TB Reference Laboratory and Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda. The proportion method on Löwenstein-Jensen medium was used as the reference test. NRA correctly identified the resistant strains, with 100% sensitivity and specificity. MGIT 960 detected all multidrug-resistant strains but missed one RMP-monoresistant strain. Genotype MTBDRplus detected all RMP-resistant strains, but the sensitivity for detection of INH resistance was lower (88%). Sensitivity and specificity ranged from 86% to 100% for MODS and from 57% to 100% for the Alamar blue, MTT, and resazurin assays. Test results were obtained within 2-14 days. In the study setting, NRA, MGIT 960, and Genotype MTBDRplus gave excellent detection of multidrug-resistant TB, with significantly shorter time to results compared to conventional testing.
The International Journal of Tuberculosis and Lung Disease. 2010 Jul; Volume 14, Number 7: 890-5.

Low Uptake of Antiretroviral Therapy after Admission with Human Immunodeficiency Virus and Tuberculosis in KwaZulu-Natal, South Africa

A prospective cohort study was conducted among HIV- infected inpatients with TB or other opportunistic infections (OIs) in South Africa to estimate subsequent antiretroviral therapy (ART) uptake and survival. Logistic regression modeling explored associations between baseline characteristics and starting ART, and ART exposure-adjusted incidence of death was estimated over 6 months of follow-up. Among 49 participants enrolled, median CD4 cell count at hospital discharge was 42 cells/microl and the most common presenting OIs were TB (76%), Pneumocystis pneumonia (8%), chronic diarrhea (8%), cryptococcal meningitis (6%), and Toxoplasma gondii (4%). By 6 months, only 20 (45%) patients had initiated ART, and four (8%) were lost to follow-up. ART uptake was independently associated with previous use of traditional medicine (OR 7.2, 95%CI 1.4-55.1) and with less advanced HIV infection (baseline CD4 count per 50 cells/microl increase OR 1.4, 95%CI 0.9-2.2). A total of 14 (31%) patients died before initiating ART; the monthly incidence of death did not decrease over the 6-month interval. The high mortality observed within the 6 months following hospitalization with TB or other acute OIs indicate that mechanisms are needed to expedite ART for patients after an acquired immune-deficiency syndrome defining illness.
The International Journal of Tuberculosis and Lung Disease. 2010 Jul; Volume 14, Number 7: 903-8.

Human Immunodeficiency Virus Increases the Risk of Tuberculosis Due to Recent Re-infection in Individuals with Latent Infection


HIV-associated TB disease can follow reactivation of latent Mycobacterium tuberculosis infection or recent (re-)infection with M. tuberculosis. If contemporary TB cases share identical M. tuberculosis strains (i.e., are “clustered”), the episode is likely to have followed recent (re-)infection, irrespective of evidence of previous latent infection. Individuals experiencing a first TB episode between 1996 and 2008 in Karonga District, Northern Malawi, were included if information on M. tuberculosis infection status (from tuberculin tests) before 1990 and a DNA fingerprint from the TB episode were available. The researchers explored differences in proportion clustered by prior M. tuberculosis infection status and HIV status, adjusting for age, sex, bacille Calmette-Guérin scar status, and time since tuberculin testing. Of 79 HIV-negative TB cases, those with previous M. tuberculosis infection were much less likely to be clustered than cases without prior infection (29% vs. 77%, adjusted OR = 0.15, 95%CI 0.04-0.59). Among 119 HIV-infected TB cases, clustering was similar in both groups (88% vs. 84%, adjusted OR = 1.85, 95%CI 0.41-8.29). HIV infection appears to increase the risk of TB following recent re-infection in patients with latent M. tuberculosis infection. Results add to the mounting evidence that HIV-associated TB mainly follows recent M. tuberculosis infection.
 The International Journal of Tuberculosis and Lung Disease. 2010 Jul; Volume 14, Number 7: 909-15. 

Human Leukocyte Antigen Typing in Tuberculous Rheumatism: Poncet's Disease

Tuberculous rheumatism (Poncet's disease) is a reactive polyarthropathy associated with extra-pulmonary and pulmonary tuberculosis (TB) without evidence of mycobacterial infection of the involved joints. As all patients with TB do not present with this peculiar clinical feature, a genetic susceptibility is suspected. OBJECTIVE: To determine the major histocompatibility complex (MHC) class I and II alleles in Mexican mestizo patients with Poncet's disease. DESIGN: In this case-control study of 16 Mexican mestizo patients diagnosed with Poncet's disease and 99 ethnically matched healthy controls, high resolution human leukocyte antigen (HLA) typing was performed for HLA-A, B, DR and DQ by polymerase chain reaction. HLA-DRB1 and HLA-DQB1 subtypes were performed by sequence-specific oligonucleotide probe hybridization. RESULTS: A significantly increased frequency of HLA-B27 (corrected P = 0.01) and DQB1*0301 (corrected P = 0.0009) alleles and decreased frequency of HLA-DQB1*0302 (corrected P = 0.00001) were identified in patients compared to healthy controls. CONCLUSION: These data suggest that genes located within the MHC may play a role in the susceptibility to Poncet's disease in patients diagnosed with TB.
The International Journal of Tuberculosis and Lung Disease. 2010 Jul; Volume 14, Number 7: 916-20. 

Unmasking Immune Reconstitution Inflammatory Syndrome” Presentation of Tuberculosis Following Combination Antiretroviral Therapy Initiation in HIV-Infected Patients;

This study determined characteristics and risk factors for unmasking TB-associated immune reconstitution inflammatory syndrome (IRIS) following initiation of combination antiretroviral therapy (cART) in HIV-infected patients, which have not yet been assessed to date. In the retrospective single-center cohort study, medical records of HIV-infected patients diagnosed with TB following cART initiation were reviewed. Cases of unmasking IRIS were identified using provisional consensus definitions. Characteristics of patients with and without unmasking TB-IRIS were compared. A case-control design was used to identify risk factors for unmasking TB-IRIS in patients initiating cART. Among 47 patients on cART at TB diagnosis, 11 experienced unmasking IRIS (23%). They had lower CD4% (9 vs. 14, P=0.02), higher HIV-RNA load at baseline (5.2 vs. 4.0 log, P=0.005), and a stronger CD4% increase with HIV-RNA decline after 1 month on cART (+7 vs. +3 log, P=0.02, and -3.2 vs. -0.8 log, P=0.005) than the 36 remaining patients without unmasking IRIS. In the case-control study, risk factors for unmasking IRIS were African country of origin (65 vs. 18%, P=0.007), higher baseline HIV-RNA load (5.2 vs. 4.7 log, P=0.01), stronger CD4% increase (+7 vs. +2, P=0.0001), and HIV-RNA decline of more than 3 log after 1 month on cART (73 vs. 27%, P=0.02). Patients with African origins, advanced HIV infection, or a strong response to cART are at greater risk of unmasking TB-IRIS.
AIDS. 2010 Jun 19; Volume 24, Number 10: 1519-25.

Survival Mechanisms of Pathogenic Mycobacterium tuberculosis H37Rv

Mycobacterium tuberculosis H(37)Rv is a highly successful pathogen and its success fully relies on its ability to utilize macrophages for its replication and, more importantly, the macrophage should remain viable to host the Mycobacterium. Despite the fact that these phagocytes are usually very effective in internalizing and clearing most of the bacteria, M. tuberculosis H(37)Rv has evolved a number of very effective survival strategies, including: (a) the inhibition of phagosome-lysosome fusion; (b) the inhibition of phagosome acidification; (c) the recruitment and retention of tryptophan-aspartate containing coat protein on phagosomes to prevent their delivery to lysosomes; and (d) the expression of members of the host-induced repetitive glycine-rich protein family of proteins. However, the mechanisms by which M. tuberculosis H(37)Rv enters the host cell, circumvents host defenses and spreads to neighboring cell are not completely understood. Therefore, a better understanding of host-pathogen interaction is essential if the global tuberculosis pandemic is ever to be controlled. This review addresses some of the pathogenic strategies of the M. tuberculosis H(37)Rv that aids in its survival and pathogenicity.


FEBS J. 2010 Jun;277(11):2416-27.

Work on For New Vaccine to Fight TB (India)


Dr. Javed N. Agrewala of the Institute of Microbial Technology (IMTECH), Chandigarh, recently described ongoing research to create a new TB vaccine by supplementing memory-enhancing cells called cytokines. These cells will enhance the human immune response making BCG vaccine last longer, thus leading to a drastic reduction in TB cases and TB transmission. He noted that although the prospect is promising, the vaccine is in its experimental stages. Dr. Agrewala explained that there is a need for this new vaccine because BCG mainly offers limited protection for children. By adulthood, the immune memory has died, and the adult is not protected from TB. Dr. D.N. Rao of the All India Institute of Medical Sciences added that by integrating nanoparticles and creating drugs and vaccines, the result will be super drugs. After being taken, the nanoparticles will slowly release the drug into the body so that dosage and frequency can be decreased. The doctors were guest lecturers at a national conference on CME in immunology, organized by the Central Indian Institute of Medical Science.

The Times of India, http://timesofindia.indiatimes.com/, August 10, 2010

Nano Particles for Effective TB Treatment (India)

Researchers in Pune, India, are working to make the existing TB drugs in nano form, which can increase the efficiency of a dose by 10 times. The aim is to lower the minimum inhibitory concentration (MIC) and method of administration. The process involves coating the medicine on metal oxide nano particles by forming a colloidal suspension, resulting in a 30 nano-meter-thick coating on each nano particle of 40 nano meter diameter. According to Tejeshree Bhave, principal investigator at the Defense Institute of Advanced Technology (DIAT), they have patented the coating method. Also, by making the drug available in nano form, the surface to volume ratio is increased, which means more of the medicine is available for fighting the disease. The project is a multi-institutional initiative with DIAT, King Edward Memorial Hospital (KEM), and the Department of Biotechnology (DBT). The scientists are also changing the method of administration from oral consumption by providing nano carriers, which can be injected or inhaled. As a result, the drug enters the bloodstream directly, increasing its effectiveness.


Indianexpress.com, www.indianexpress.com, August 8, 2010, by Pranav Kulkarni

Innovative Portable Microscope Detects TB Cheaply, Accurately (United States)


The ability of the Global Focus, a $240 battery-operated fluorescent microsocope, to detect TB   was compared to that of a Nikon E400 fluorescence microscope that cost over $40,000. The study was conducted according to the International Union Against TB and Lung Disease (IUATLD) guidelines, using TB bacilli from sputum smears obtained from clinical specimens collected in a remote area of Iran. Concordant results were obtained in 56 of 64 specimens (87.5 percent concordance).   When samples were evaluated as positive or negative, results with both microscopes agreed except for one specimen, resulting in a 98.4 percent concordance rate. The Global Focus is a compact, lightweight, low-cost, inverted bright field and fluorescence microscope, with up to 1000x magnification. According to the authors, the microscope may be a useful diagnostic tool to expand TB testing at the point of care in low-resource settings. This article was published online at PLoS ONE 5(8): e11890. doi:10.1371/journal.pone.0011890.           

TMC.net, www.tmcnet.com, August 6, 2010, by J.M. Graham

Identification of wild-type Mycobacterium tuberculosis isolates and point mutations associated with isoniazid resistance

Isoniazid resistance in Mycobacterium tuberculosis (MBT) is associated with point mutations in codon 315 of the katG gene. Two PCR technique were developed for detection of point mutations in codon 315. Most frequent point mutations (AGC → ACC and AGC → AGA) were identified in codon 315 by using two sets of primers, either of which included an additional competitive blocking primer with a 3′-terminal phosphate group in order to prevent nonspecific amplification. PCR with a set of two primers, one of which contained five locked nucleic acid monomers (LNA), permits one to detect any of six known mutations in codon 315 ofkatG and, thereby, discriminate between isoniazid-sensitive and resistant MBT isolates. The structure and purity of the 17-nt long LNA-containing oligonucleotides were characterized by MALDI-TOF mass spectrometry; and the 17 bp duplex formed by two LNA-containing complementary oligonucleotides was analyzed by thermal denaturation.



Volume 44, Number 4559-567DOI: 10.1134/S0026893310040096

Insight into crucial inhibitor–enzyme interaction of arylamides as novel direct inhibitors of the enoyl ACP reductase (InhA) from Mycobacterium tuberculosis: computer-aided molecular design

The enoyl ACP reductase enzyme (InhA) involved in the type II fatty acid biosynthesis pathway of Mycobacterium tuberculosis is an attractive target enzyme for antitubercular drug development. Arylamide derivatives are a novel class of InhA inhibitors used to overcome the drug-resistance problem of isoniazid, the frontline drug for tuberculosis treatment. Their remarkable property of inhibiting the InhA enzyme directly without requiring any coenzyme, makes them especially appropriate for the design of new antibacterials. In order to find a sound binding conformation for the different arylamide analogs, molecular docking experiments were performed with subsequent QSAR investigations. The X-ray conformation of one arylamide within its cocrystallized complex with InhA was used as a starting conformation for the docking experiments. The results thus obtained are perfectly consistent (rmsd = 0.73 Å) with the results from X-ray analysis. A thorough investigation of the arylamide binding modes with InhA provided ample information about structural requirements for appropriate inhibitor–enzyme interactions. Three different QSAR models were established using two three-dimensional (CoMFA and CoMSIA) and one two-dimensional (HQSAR) techniques. With statistically ensured models, the QSAR results obtained had high correlation coefficients between molecular structure properties of 28 arylamide derivatives and their biological activity. Molecular fragment contributions to the biological activity of arylamides could be obtained from the HQSAR model. Finally, a graphic interpretation designed in different contour maps provided coincident information about the ligand–receptor interaction thus offering guidelines for syntheses of novel analogs with enhanced biological activity.



DOI: 10.1007/s00706-010-0359-4

Mycobacterium tuberculosis lipoprotein LprG (Rv1411c) binds triacylated glycolipid agonists of Toll-like receptor 2

Knockout of lprG results in decreased virulence of Mycobacterium tuberculosis (MTB) in mice. MTB lipoprotein LprG has TLR2 agonist activity, which is thought to be dependent on its N-terminal triacylation. Unexpectedly, here we find that nonacylated LprG retains TLR2 activity. Moreover, we show LprG association with triacylated glycolipid TLR2 agonists lipoarabinomannan, lipomannan and phosphatidylinositol mannosides (which share core structures). Binding of triacylated species was specific to LprG (not LprA) and increased LprG TLR2 agonist activity; conversely, association of glycolipids with LprG enhanced their recognition by TLR2. The crystal structure of LprG in complex with phosphatidylinositol mannoside revealed a hydrophobic pocket that accommodates the three alkyl chains of the ligand. In conclusion, we demonstrate a glycolipid binding function of LprG that enhances recognition of triacylated MTB glycolipids by TLR2 and may affect glycolipid assembly or transport for bacterial cell wall biogenesis.


Nature Structural & Molecular Biology
Published online: 8 August 2010 | doi:10.1038/nsmb.1869

Thursday, August 12, 2010

Ikaros and Aiolos Inhibit Pre-B-Cell Proliferation by Directly Suppressing c-Myc Expression

Pre-B- cell expansion is driven by signals from the interleukin-7 receptor and the pre-B-cell receptor and is dependent on
cyclin D3 and c-Myc. We have shown previously that interferon regulatory factors 4 and 8 induce the expression of Ikaros
and Aiolos to suppress pre-B- cell proliferation
. However, the molecular mechanisms through which Ikaros and Aiolos
exert their growth inhibitory effect remain to be determined. Here, we provide evidence that Aiolos and Ikaros bind to the
c-Myc promoter in vivo and directly suppress c-Myc expression in pre-B cells. We further show that downregulation of c-
Myc is critical for the growth- inhibitory effect of Ikaros and Aiolos. Ikaros and Aiolos also induce expression of p27 and
downregulate cyclin D3 in pre-B cells , and the growth- inhibitory effect of Ikaros and Aiolos is compromised in the absence
of p27. A time course analysis further reveals that downregulation of c-Myc by Ikaros and Aiolos precedes p27 induction
and cyclin D3 downregulation. Moreover, downregulation of c-Myc by Ikaros and Aiolos is necessary for the induction of
p27 and downregulation of cyclin D3. Collectively, our studies identify a pre-B- cell receptor signaling induced inhibitory
network, orchestrated by Ikaros and Aiolos, which functions to terminate pre-B-cell expansion.

Molecular and Cellular Biology, September 2010, p. 4149-4158, Vol. 30, No. 17
0270-7306/10/$12.00+0 doi:10.1128/MCB.00224-10

How we approach patient evaluation for hematopoietic stem cell transplantation

The evaluation of patients for hematopoietic stem cell transplantation is a complex process. The decision to recommend transplantation is not simply dependent on patient diagnosis; instead it is a specialized analytic decision process intricately dependent on a number of variables including patient age, performance status, medical comorbidities, family support structure, socioeconomic viability and motivation to participate in self-care, to name a few. The process of pre-transplant patient evaluation has substantial variability across different transplant centers, owing to lack of formal published guidelines. This review summarizes the process of pre-transplant patient evaluation and workup, and aims to describe components of a well-organized and evidenced-based patient selection process for SCT.

Bone Marrow Transplantation 45, 1259-1268 (August 2010) | doi:10.1038/bmt.2010.94

Wednesday, August 11, 2010

Impact of discontinuing fluoroquinolone prophylaxis on early mortality after allogeneic marrow or peripheral blood SCT with myeloablative conditioning

Oral fluoroquinolones (FQs) or other antibiotics are commonly used as antibacterial prophylaxis after cytotoxic chemotherapy for malignant neoplasms, although significant practice variations have been reported among centers and countries.1 Despite such practical variations, the efficacy of oral FQ as a prophylactic agent has not been fully evaluated in the SCT setting.

Bone Marrow Transplantation 45, 1369-1371 (August 2010) | doi:10.1038/bmt.2009.344