A practical method to measure GFR in people with type 1 diabetes

AIMS

Improved early diagnostic methods are needed to identify risk for kidney disease in people with type 1 diabetes. We hypothesized that glomerular filtration rate (GFR) measured by iohexol clearance in dried blood spots (DBS) on filter paper would be comparable to plasma (gold-standard) and superior to estimated GFR (eGFR) and, second, that adjustment for ambient blood glucose would improve accuracy and precision of GFR measurement.

METHODS

GFR was measured by iohexol clearance in plasma, DBS, and as estimated by the CKD-Epidemiology Collaboration equations in 15 adults with type 1 diabetes at two visits, one euglycemic and one hyperglycemic.

RESULTS

GFR measured by DBS was more comparable and less biased than GFR cystatin C, serum creatinine, and both combined. GFR was higher during hyperglycemia. Correction for between visit glycemia statistically significantly reduced bias and mean squared error for GFR measured by DBS as compared to gold-standard during euglycemia.

CONCLUSIONS

Iohexol clearance measured with DBS performed better than eGFR methods. Correction for ambient blood glucose improved precision and accuracy of GFR measurement. This method is more convenient than the gold-standard GFR method and may improve screening and diagnostic capabilities in people with type 1 diabetes, especially when GFR is >60ml/min/1.73m(2).

SEPP: SATé-enabled phylogenetic placement

We address the problem of Phylogenetic Placement, in which the objective is to insert short molecular sequences (called query sequences) into an existing phylogenetic tree and alignment on full-length sequences for the same gene. Phylogenetic placement has the potential to provide information beyond pure "species identification" (i.e., the association of metagenomic reads to existing species), because it can also give information about the evolutionary relationships between these query sequences and to known species. Approaches for phylogenetic placement have been developed that operate in two steps: first, an alignment is estimated for each query sequence to the alignment of the full-length sequences, and then that alignment is used to find the optimal location in the phylogenetic tree for the query sequence. Recent methods of this type include HMMALIGN+EPA, HMMALIGN+pplacer, and PaPaRa+EPA.We report on a study evaluating phylogenetic placement methods on biological and simulated data. This study shows that these methods have extremely good accuracy and computational tractability under conditions where the input contains a highly accurate alignment and tree for the full-length sequences, and the set of full-length sequences is sufficiently small and not too evolutionarily diverse; however, we also show that under other conditions accuracy declines and the computational requirements for memory and time exceed acceptable limits. We present SEPP, a general "boosting" technique to improve the accuracy and/or speed of phylogenetic placement techniques. The key algorithmic aspect of this booster is a dataset decomposition technique in SATé, a method that utilizes an iterative divide-and-conquer technique to co-estimate alignments and trees on large molecular sequence datasets. We show that SATé-boosting improves HMMALIGN+pplacer, placing short sequences more accurately when the set of input sequences has a large evolutionary diameter and produces placements of comparable accuracy in a fraction of the time for easier cases. SEPP software and the datasets used in this study are all available for free at http://www.cs.utexas.edu/users/phylo/software/sepp/submission.

Matrix metalloprotease 1a deficiency suppresses tumor growth and angiogenesis

Matrix metalloprotease-1 (MMP1) is an important mediator of tumorigenesis, inflammation and tissue remodeling through its ability to degrade critical matrix components. Recent studies indicate that stromal-derived MMP1 may exert direct oncogenic activity by signaling through protease-activated receptor-1 (PAR1) in carcinoma cells; however, this has not been established in vivo. We generated an Mmp1a knockout mouse to ascertain whether stromal-derived Mmp1a affects tumor growth. Mmp1a-deficient mice are grossly normal and born in Mendelian ratios; however, deficiency of Mmp1a results in significantly decreased growth and angiogenesis of lung tumors. Coimplantation of lung cancer cells with wild-type Mmp1a(+/+) fibroblasts completely restored tumor growth in Mmp1a-deficient animals, highlighting the critical role of stromal-derived Mmp1a. Silencing of PAR1 expression in the lung carcinoma cells phenocopied stromal Mmp1a-deficiency, thus validating tumor-derived PAR1 as an Mmp1a target. Mmp1a secretion is controlled by the ability of its prodomain to facilitate autocleavage, whereas human MMP1 is efficiently secreted because of stable pro- and catalytic domain interactions. Taken together, these data demonstrate that stromal Mmp1a drives in vivo tumorigenesis and provide proof of concept that targeting the MMP1-PAR1 axis may afford effective treatments of lung cancer.

Search for photon-linelike signatures from dark matter annihilations with H.E.S.S

Gamma-ray line signatures can be expected in the very-high-energy (E(γ)>100 GeV) domain due to self-annihilation or decay of dark matter (DM) particles in space. Such a signal would be readily distinguishable from astrophysical γ-ray sources that in most cases produce continuous spectra that span over several orders of magnitude in energy. Using data collected with the H.E.S.S. γ-ray instrument, upper limits on linelike emission are obtained in the energy range between ∼ 500 GeV and ∼ 25 TeV for the central part of the Milky Way halo and for extragalactic observations, complementing recent limits obtained with the Fermi-LAT instrument at lower energies. No statistically significant signal could be found. For monochromatic γ-ray line emission, flux limits of (2 × 10(-7) -2 × 10(-5)) m(-2) s(-1) sr(-1) and (1 × 10(-8) -2 × 10(-6)) m(-2) s(-1)sr(-1) are obtained for the central part of the Milky Way halo and extragalactic observations, respectively. For a DM particle mass of 1 TeV, limits on the velocity-averaged DM annihilation cross section ⟨σv⟩(χχ → γγ) reach ∼ 10(-27) cm(3)s(-1), based on the Einasto parametrization of the Galactic DM halo density profile.

Abstract P4-08-08: HOXC10, a homeobox protein overexpressed in breast cancer, modulates the response to chemotherapy treatment

Background: Breast cancer is the second leading cause of cancer deaths in women worldwide. Although chemotherapy is effective, resistance to drugs develops over time and can account for treatment failure in over 90% of metastatic breast cancer patients. HOX genes are homeobox-containing transcription factors well-known for their role in morphogenesis. and during carcinogenesis and metastasis. The goal of this study is to understand the role of HOXC10 in breast cancer and mainly in response to chemotherapy.

Methods: Using a tiling array of all four HOX clusters in a panel of primary and metastatic breast cancer tissues, we identified HOXC10 as being among the highly overexpressed genes in breast cancer. Then using a panel of cell lines that either stably overexpress exogenous HOXC10 or cell lines with stably downregulated endogenous HOXC10 (mediated by shRNA), we investigated the role of HOXC10 in proliferation, response to chemotherapy treatment and repair of DNA damage.

Results: HOXC10 is overexpressed in 67% of primary breast tumors (n = 31), in 82% of the metastatic tissues (n = 49) and in most breast cancer cell lines (n = 48). In vitro and in vivo investigation confirmed that HOXC10 plays an oncogenic role in breast cancer. Further, knockdown of HOXC10 in a panel of breast cancer cell lines slowed their proliferation and arrested them at the G1 phase, by inactivating the RB/E2F pathway, decreasing the number of new origins and eventually reducing the polyploidy population.

Cell survival assays after different chemotherapeutic drug treatment showed that overexpression of the exogenous HOXC10 in MCF10A led to less susceptibility to most drugs. This was partially due to a protection from apoptosis by upregulating and activating the anti-apoptotic machinery such as the NF-kb pathway. Further investigation revealed the involvement of HOXC10 in DNA repair (and not initial response), especially after DNA crosslink damage. Interestingly, the binding of HOXC10 to CDK7 in a region outside its homeodomain activates CDK7 activity towards RNA polymerase II mainly in response to DNA damage. Since HOX genes are difficult to target therapeutically, one potential approach to overcome chemoresistance in HOXC10 overexpressing cells is by including CDK7 inhibitors (already in clinical trials).

All these results were confirmed in the SUM159 model which stably expresses a HOXC10-shRNA.

Finally, HOXC10 was found to be significantly overexpressed in MCF7 isogenic cell lines gradually selected to be resistant to some chemotherapeutic drugs. By knocking down HOXC10 in these sublines, resistance to the drug was reduced. Further, SUM159 and MDAMD231 xenografts that were treated with chemotherapy over weeks and that show partial to no response tend to have a higher expression of HOXC10.

Conclusion: This study shows that HOXC10, a homeobox protein previously shown to be regulated during the cell cycle and to have a positive effect on proliferation, is overexpressed in the majority of breast cancers. This upregulation may have clinical implications since cells with higher expression of HOXC10 tend to have more genomic instability and activation of anti-apoptotic and DNA repair pathways, which eventually modulate the response to some chemotherapy drugs.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-08-08.

Abstract P2-09-01: Reactivation of epigenetically silenced retinoic acid receptor-beta for therapy of breast cancer- from molecular mechanism to potential clinical applications

Background: Triple negative breast cancer (TNBC) is a subgroup of breast cancer that is characterized by a lack of expression of targets for validated targeted therapies. Although responses to chemotherapy are observed, resistance develops rapidly. Genomic and molecular profiling of TNBC has identified multiple contributors to their uncontrolled growth including epigenetic dysregulation of genes important for normal cell growth and differentiation. Recent studies have shown that histone deacetylase (HDAC) inhibitors reverse the epigenetic profile of tumors, resulting in the re-expression of silenced genes encoding proteins such as ERα, EGFR, and RARβ. Entinostat is an oral, class 1 isoform selective HDACi recently shown in a phase 2 study to be active in ER+ breast cancer. Clinical trials with entinostat in HER2+ and TNBC are also in progress. We hypothesized that combining epigenetic therapy using entinostat, with differentiation therapy using a retinoic acid receptor agonist- All Trans Retinoic Acid (ATRA) will provide an effective strategy for impeding the growth of TNBC and potentially sensitize tumors to commonly used chemotherapies (doxorubicin, carboplatin, paclitaxel).

Methods: Combination studies of entinostat combined with ATRA with and without non-toxic doses (half clinical) of chemotherapy were carried out in vitro and in xenograft models of TNBC. Expression of RARb and downstream effectors were measured in cell lines and tumors from xenograft studies.

Results: Nontoxic (half clinical) doses of doxorubicin when combined with entinostat and ATRA in vitro and in vivo exerted the best response when compared with combinations using paclitaxel and carboplatin. Re-expression of the silenced RARβ and downstream effectors was observed in the cell lines treated in vitro and in tumor xenografts of MDA-MB-231 and SUM159 cells in vivo. To gain insight into mechanism of action for the entinostat – doxorubicin combinations we examined the expression of enzyme targets of doxorubicin and determined that entinostat treatment reduced the expression of topoisomerase (Topo) II enzymes. Besides its conventional role in cell replication and division, Topo II has an important function in regulating transcription, especially in the nuclear receptor pathways such as ER and RAR. Our results demonstrated that Topo IIβ has a dual role in regulating the expression of RARβ. Inhibition of Topo IIβ in a time- and dose dependent manner up-regulated the expression of RARβ and its downstream genes. However, completely eliminating Topo IIβ decreased expression of RARβ.

Conclusions: Our detailed study provides a new approach to treating TNBC using combinations of nontoxic doses of chemotherapeutic drugs with epigenetic therapy, and a deeper understanding of the molecular pathways involved in this response. These results suggest that combination of entinostat and a retinoic acid receptor agonist with low dose doxorubicin will provide an effective strategy for treatment of TNBC.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-09-01.

Longitudinal analysis of integrase N155H variants in heavily treated patients failing raltegravir-based regimens

OBJECTIVES

The mechanism of raltegravir (RAL)-resistant evolutions has not already been elucidated. Because the emergence of RAL resistance is usually initiated by the N155H mutant, we assessed the role of minor N155H-mutated variants in circulating RNA and archived DNA in five heavily treated patients experiencing long-term RAL therapy failure and harbouring three different resistance profiles determined by standard genotyping.

METHODS

Allele-specific polymerase chain reaction (AS-PCR) was used to detect N155H mutants in longitudinal stored plasma and whole-blood samples before, during and after RAL-based regimens in five patients infected with the HIV-1 B subtype.

RESULTS

No minor N155H-mutated variant was found by AS-PCR in either plasma or whole-blood samples collected at baseline and after RAL withdrawal in any of the five patients. During RAL failure, the mutation N155H was detected at different levels in three patients displaying the N155H pathway and gradually declined when the double mutant Q148H+G140S was selected in one patient. In two patients with the Q148H resistance pathway, no N155H variant was identified by AS-PCR in either viral RNA or DNA.

CONCLUSIONS

The N155H mutation present at various levels from minority to majority showed no relationship with the three RAL-associated resistance profiles, suggesting that this mutant may not play a role in determining different resistance profiles. Moreover, pre-existing N155H is very infrequent and, if selected during RAL failure, the N155H mutant disappears quickly after RAL withdrawal.

A review of unmet needs in obesity management

The prevalence of obesity continues to escalate in the USA; however, there is no consensus regarding the optimal therapy for obesity. For the vast majority of severely obese patients, conventional medical therapies (i.e., diet, exercise, behavioral counseling) often fail over the long term. Existing pharmacotherapy adjunctive to behavioral therapy has limited effectiveness and an imperfect safety record. In contrast, bariatric surgery has a high degree of weight loss efficacy, yet only a small fraction of the qualifying obese population undergoes these procedures because of the associated perioperative risks and potential late complications. In addition, the role of bariatric surgery is unclear in certain patient populations, such as patients with lower body mass index (BMI, 30-35 kg/m(2)), the high-risk super-super obese patients (BMI > 60), the morbidly obese adolescent, and obese patients requiring weight reduction in preparation for other procedures, such as orthopedic, transplant, or vascular surgeries. In these circumstances, there is a need for an effective but less invasive treatment to bridge the gap between medical and surgical therapy. This review examines current treatment outcomes, identifies prominent areas of unmet clinical needs, and provides an overview of two minimally invasive "temporary procedures for weight loss" that may eventually address some of the unmet needs in obesity management.