Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer.

Macrophages represent an important component of the tumor microenvironment and play a complex role in cancer progression. These cells are characterized by a high degree of plasticity, and they alter their phenotype in response to local environmental cues. Whereas the M1/M2 classification of macrophages has been widely used, the complexity of macrophage phenotypes has not been well studied, particularly in lung cancer. In this study we employed an orthotopic immunocompetent model of lung adenocarcinoma in which murine lung cancer cells are directly implanted into the left lobe of syngeneic mice. Using multimarker flow cytometry, we defined and recovered several distinct populations of monocytes/macrophages from tumors at different stages of progression. We used RNA-seq transcriptional profiling to define distinct features of each population and determine how they change during tumor progression. We defined an alveolar resident macrophage population that does not change in number and expresses multiple genes related to lipid metabolism and lipid signaling. We also defined a population of tumor-associated macrophages that increase dramatically with tumor and selectively expresses a panel of chemokine genes. A third population, which resembles tumor-associated monocytes, expresses a large number of genes involved in matrix remodeling. By correlating transcriptional profiles with clinically prognostic genes, we show that specific monocyte/macrophage populations are enriched in genes that predict outcomes in lung adenocarcinoma, implicating these subpopulations as critical determinants of patient survival. Our data underscore the complexity of monocytes/macrophages in the tumor microenvironment, and they suggest that distinct populations play specific roles in tumor progression.

Rational Design of a Parthenolide-based Drug Regimen That Selectively Eradicates Acute Myelogenous Leukemia Stem Cells.

Although multidrug approaches to cancer therapy are common, few strategies are based on rigorous scientific principles. Rather, drug combinations are largely dictated by empirical or clinical parameters. In the present study we developed a strategy for rational design of a regimen that selectively targets human acute myelogenous leukemia (AML) stem cells. As a starting point, we used parthenolide, an agent shown to target critical mechanisms of redox balance in primary AML cells. Next, using proteomic, genomic, and metabolomic methods, we determined that treatment with parthenolide leads to induction of compensatory mechanisms that include up-regulated NADPH production via the pentose phosphate pathway as well as activation of the Nrf2-mediated oxidative stress response pathway. Using this knowledge we identified 2-deoxyglucose and temsirolimus as agents that can be added to a parthenolide regimen as a means to inhibit such compensatory events and thereby further enhance eradication of AML cells. We demonstrate that the parthenolide, 2-deoxyglucose, temsirolimus (termed PDT) regimen is a potent means of targeting AML stem cells but has little to no effect on normal stem cells. Taken together our findings illustrate a comprehensive approach to designing combination anticancer drug regimens.

SomVarIUS: somatic variant identification from unpaired tissue samples.

MOTIVATION: Somatic variant calling typically requires paired tumor-normal tissue samples. Yet, paired normal tissues are not always available in clinical settings or for archival samples. RESULTS: We present SomVarIUS, a computational method for detecting somatic variants using high throughput sequencing data from unpaired tissue samples. We evaluate the performance of the method using genomic data from synthetic and real tumor samples. SomVarIUS identifies somatic variants in exome-seq data of ∼150 × coverage with at least 67.7% precision and 64.6% recall rates, when compared with paired-tissue somatic variant calls in real tumor samples. We demonstrate the utility of SomVarIUS by identifying somatic mutations in formalin-fixed samples, and tracking clonal dynamics of oncogenic mutations in targeted deep sequencing data from pre- and post-treatment leukemia samples. AVAILABILITY AND IMPLEMENTATION: SomVarIUS is written in Python 2.7 and available at http://www.sjdlab.org/resources/ CONTACT: subhajyoti.de@ucdenver.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.

Cancer-associated somatic mutations outside protein-coding regions remain largely unexplored. Analyses of the TERT locus have indicated that non-coding regulatory mutations can be more frequent than previously suspected and play important roles in oncogenesis. Using a computational method called SASE-hunter, developed here, we identified a novel signature of accelerated somatic evolution (SASE) marked by a significant excess of somatic mutations localized in a genomic locus, and prioritized those loci that carried the signature in multiple cancer patients. Interestingly, even when an affected locus carried the signature in multiple individuals, the mutations contributing to SASE themselves were rarely recurrent at the base-pair resolution. In a pan-cancer analysis of 906 samples from 12 tumor types, we detected SASE in the promoters of several genes, including known cancer genes such as MYC, BCL2, RBM5 and WWOX. Nucleotide substitution patterns consistent with oxidative DNA damage and local somatic hypermutation appeared to contribute to this signature in selected gene promoters (e.g. MYC). SASEs in selected cancer gene promoters were associated with over-expression, and also correlated with the age of onset of cancer, aggressiveness of the disease and survival. Taken together, our work detects a hitherto under-appreciated and clinically important class of regulatory changes in cancer genomes.

Aerobic oxysulfonylation of alkenes using thiophenols: an efficient one-pot route to ß-ketosulfones.

We have developed a highly efficient synthetic route to ß-ketosulfones via AgNO3 catalyzed oxysulfonylation of alkenes using thiophenols in the presence of air (O2) and K2S2O8 as eco-friendly oxidants. Thiophenols have been used as sulfonylation precursors for the first time in a dioxygen activation based radical process. Moreover, the protocol also offers a new and convenient method for the synthesis of ß-hydroxysulfides at room temperature without the use of any initiator.

Impact of Direct Acting Antiviral Drugs in Treatment Naïve HCV Cirrhosis on Fibrosis and Severity of Liver Disease: A Real Life Experience from a Tertiary Care Center of North India.

BACKGROUND/AIMS: Treatment of chronic hepatitis C infection with direct-acting antiviral (DAA) drugs has been highly effective, but data regarding benefit in advanced liver disease is relatively scarce in Indian patients. The aim of this study was to determine the effects of DAA in patients with HCV related cirrhosis (compensated/decompensated) who achieved sustained virological response post-therapy at 12 weeks (SVR12). METHODS: Sixty-three patients with HCV related cirrhosis treated with sofosbuvir based regimen were evaluated. Data regarding baseline demographics, the severity of liver disease and treatment regimen were collected. The primary end point was to evaluate the effect of treatment (SVR12) on the severity of liver disease with the secondary end point being to observe for any adverse events related to treatment. RESULTS: Treatment naïve patients with HCV cirrhosis either due to genotype 1 or genotype 3 were divided into two groups: group A (compensated cirrhosis), group B (decompensated cirrhosis). SVR12 in group A was 91.66% (33/37) and in group, B was 73.17% (30/41). Baseline mean liver stiffness measurement (LSM) in group A was 16.81 ± 3.57 kPa which decreased to 11.19 ± 1.75 kPa at SVR12 (P-value <0.0001). Baseline mean APRI and FIB-4 score in group A were 1.228 ± 0.499 and 2.61 ± 1.06 and in group B were 2.156 ± 1.10 and 5.71 ± 2.06 respectively which decrease to 0.415 ± 0.115 and 1.25 ± 0.46 in group A, to 0.759 ± 0.275 and 2.60 ± 1.12 in group B following SVR12 (P value <0.0001). Mean MELD-Na improved from baseline 9.93 ± 2.04, 20.70 ± 4.52 to 7.21 ± 0.92, 14.23 ± 4.51 respectively in group A and B at SVR12 (P-value <0.0001). Child-Turcotte-Pugh score improved by 1 in 27.27% (9/33) and ≥2 in 76.67% (23/30) of patients in group A and group B respectively. CONCLUSION: There was a significant improvement in severity of liver disease as depicted by the decrease in LSM and other noninvasive marker of fibrosis in patients who achieved SVR12 on DAA therapy.