A modular master regulator landscape controls cancer transcriptional identity.

Despite considerable efforts, the mechanisms linking genomic alterations to the transcriptional identity of cancer cells remain elusive. Integrative genomic analysis, using a network-based approach, identified 407 master regulator (MR) proteins responsible for canalizing the genetics of individual samples from 20 cohorts in The Cancer Genome Atlas (TCGA) into 112 transcriptionally distinct tumor subtypes. MR proteins could be further organized into 24 pan-cancer, master regulator block modules (MRBs), each regulating key cancer hallmarks and predictive of patient outcome in multiple cohorts. Of all somatic alterations detected in each individual sample, >50% were predicted to induce aberrant MR activity, yielding insight into mechanisms linking tumor genetics and transcriptional identity and establishing non-oncogene dependencies. Genetic and pharmacological validation assays confirmed the predicted effect of upstream mutations and MR activity on downstream cellular identity and phenotype. Thus, co-analysis of mutational and gene expression profiles identified elusive subtypes and provided testable hypothesis for mechanisms mediating the effect of genetic alterations.

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes.

Silent mutations make some noise.

Synonymous mutations do not alter amino acids and are generally considered nonfunctional in cancer. Supek et al. now present a compelling analysis suggesting that such silent mutations can be oncogenic by altering transcript splicing and thereby affecting protein function.

The somatic genomic landscape of glioblastoma.

We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer.

Influence of Three Modification Methods on the Structure, Physicochemical, and Functional Properties of Insoluble Dietary Fiber from Rosa roxburghii Tratt Pomace.

Rosa roxburghii Tratt pomace is rich in insoluble dietary fiber (IDF). This study aimed to investigate the influence of three modification methods on Rosa roxburghii Tratt pomace insoluble dietary fiber (RIDF). The three modified RIDFs, named U-RIDF, C-RIDF, and UC-RIDF, were prepared using ultrasound, cellulase, and a combination of ultrasound and cellulase methods, respectively. The structure, physicochemical characteristics, and functional properties of the raw RIDF and modified RIDF were comparatively analyzed. The results showed that all three modification methods, especially the ultrasound-cellulase combination treatment, increased the soluble dietary fiber (SDF) content of RIDF, while also causing a transition in surface morphology from smooth and dense to wrinkled and loose structures. Compared with the raw RIDF, the modified RIDF, particularly UC-RIDF, displayed significantly improved water-holding capacity (WHC), oil-binding capacity (OHC), and swelling capacity (SC), with increases of 12.0%, 84.7%, and 91.3%, respectively. Additionally, UC-RIDF demonstrated the highest nitrite ion adsorption capacity (NIAC), cholesterol adsorption capacity (CAC), and bile salt adsorption capacity (BSAC). In summary, the combination of ultrasound and cellulase treatment proved to be an efficient approach for modifying IDF from RRTP, with the potential for developing a functional food ingredient.

An Increase in Peroxiredoxin 6 Expression Induces Neurotoxic A1 Astrocytes in the Lumbar Spinal Cord of Amyotrophic Lateral Sclerosis Mice Model.

Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disease with selective degeneration of motor neurons. It has been reported that an increase in the levels of inflammatory cytokines and glial cells such as reactive astrocytes is closely involved in the pathological progression of ALS. Recently, the levels of neuropathic cytotoxic (A1) astrocytes among reactive astrocytes have reportedly increased in the central nervous system of ALS mice, which induce motor neuron degeneration through the production of inflammatory cytokines and secretion of neuropathic factors. Hence, elucidating the induction mechanism of A1 astrocytes in ALS is important to understand the mechanism of disease progression in ALS. In this study, we observed that the expression of peroxiredoxin 6 (PRDX6), a member of the peroxiredoxin family, was markedly upregulated in astrocytes of the lumbar spinal cord of SOD1G93A mice model for ALS. Additionally, when PRDX6 was transiently transfected into the mouse astrocyte cell line C8-D1A and human astrocytoma cell line U-251 MG, the mRNA expression of complement C3 (a marker for A1 astrocyte phenotype) and inflammatory cytokines was increased. Furthermore, the mRNA expression of C3 and inflammatory cytokine was increased in C8-D1A and U-251 MG cells stably expressing PRDX6, and the increased mRNA expression was significantly suppressed by MJ33 (lithium[1-hexadecoxy-3-(2,2,2-trifluoroethoxy) propan-2-yl] methyl phosphate), an inhibitor of the phospholipase A2 activity of PRDX6. Our results suggest that the expression of PRDX6 in astrocytes plays an important role in the induction of A1 astrocytes and expression of inflammatory cytokines in the ALS mice model.

Depression severity mediates stigma and quality of life in clinically stable people with schizophrenia in rural China.

BACKGROUND: Depressive symptoms associated with schizophrenia are closely related to stigma and quality of life(QOL). There is, however, no thorough research on the connection between the three. This study sought to investigate the possible factors influencing depressive symptoms in people with schizophrenia (PWS) in rural Chaohu, China, and to further explore the role of depression severity in stigma and lifestyle quality. METHODS: Eight hundred twenty-one schizophrenia patients accomplished the entire scale, including the 9-item Patient Health Questionnaire (PHQ-9), the Social Impact Scale (SIS), and the World Health Organization on Quality of Life Brief Scale(WHOQOL-BREF). A straightforward mediation model was employed to determine if the intensity of the depression could act as a mediator between stigma and QOL. RESULTS: Two hundred seventy-nine schizophrenia patients (34%) had depressive symptoms (PHQ ≥ 10), and 542 patients (66%) did not (PHQ < 10). Logistic regression showed that marital status, job status, physical exercise, standard of living, and stigma contributed to the depressed symptoms of schizophrenia. Depression severity partially mediated the effect between stigma and QOL, with a mediating effect of 48.3%. CONCLUSIONS: This study discovered a significant incidence of depressed symptoms associated with schizophrenia, with depression severity serving as a mediator variable connecting stigma and QOL and partially moderating the association.

PCAT: an integrated portal for genomic and preclinical testing data of pediatric cancer patient-derived xenograft models.

Although cancer is the leading cause of disease-related mortality in children, the relative rarity of pediatric cancers poses a significant challenge for developing novel therapeutics to further improve prognosis. Patient-derived xenograft (PDX) models, which are usually developed from high-risk tumors, are a useful platform to study molecular driver events, identify biomarkers and prioritize therapeutic agents. Here, we develop PDX for Childhood Cancer Therapeutics (PCAT), a new integrated portal for pediatric cancer PDX models. Distinct from previously reported PDX portals, PCAT is focused on pediatric cancer models and provides intuitive interfaces for querying and data mining. The current release comprises 324 models and their associated clinical and genomic data, including gene expression, mutation and copy number alteration. Importantly, PCAT curates preclinical testing results for 68 models and 79 therapeutic agents manually collected from individual agent testing studies published since 2008. To facilitate comparisons of patterns between patient tumors and PDX models, PCAT curates clinical and molecular data of patient tumors from the TARGET project. In addition, PCAT provides access to gene fusions identified in nearly 1000 TARGET samples. PCAT was built using R-shiny and MySQL. The portal can be accessed at http://pcat.zhenglab.info or http://www.pedtranscriptome.org.

Deep learning of pharmacogenomics resources: moving towards precision oncology.

The recent accumulation of cancer genomic data provides an opportunity to understand how a tumor's genomic characteristics can affect its responses to drugs. This field, called pharmacogenomics, is a key area in the development of precision oncology. Deep learning (DL) methodology has emerged as a powerful technique to characterize and learn from rapidly accumulating pharmacogenomics data. We introduce the fundamentals and typical model architectures of DL. We review the use of DL in classification of cancers and cancer subtypes (diagnosis and treatment stratification of patients), prediction of drug response and drug synergy for individual tumors (treatment prioritization for a patient), drug repositioning and discovery and the study of mechanism/mode of action of treatments. For each topic, we summarize current genomics and pharmacogenomics data resources such as pan-cancer genomics data for cancer cell lines (CCLs) and tumors, and systematic pharmacologic screens of CCLs. By revisiting the published literature, including our in-house analyses, we demonstrate the unprecedented capability of DL enabled by rapid accumulation of data resources to decipher complex drug response patterns, thus potentially improving cancer medicine. Overall, this review provides an in-depth summary of state-of-the-art DL methods and up-to-date pharmacogenomics resources and future opportunities and challenges to realize the goal of precision oncology.

Effect of metformin and exenatide on pregnancy rate and pregnancy outcomes in overweight or obese infertility PCOS women: long-term follow-up of an RCT.

PURPOSE: The majority of Polycystic ovary syndrome (PCOS) are overweight or obese with increased infertility and high risk of pregnancy complications. We aim to compare efficacy of metformin and exenatide on spontaneous pregnancy rate, overall pregnancy rate after assisted reproductive technology treatment (ART) and pregnancy outcomes in overweight or obese infertility PCOS. METHODS: In this long-term follow-up study, 160 overweight or obese infertility Chinese PCOS were randomized to exenatide or metformin treatment for 12 weeks. Afterward, all were treated with metformin alone until pregnancy confirmed and followed until delivery. If patients failed spontaneous pregnancy during the second 12 weeks, ART could be offered until end of 64 weeks. The primary outcome was spontaneous pregnancy rate. RESULTS: At week 24, 29.2% of women in exenatide group conceived spontaneously while 14.7% in metformin group (p = 0.03). At week 64, total pregnancy rates were 79.2% in exenatide group and 76% in metformin group without significant difference (p = 0.65). Between two groups, there was no significant difference of pregnancy outcomes (p > 0.05). A stepwise logistic regression showed that spontaneous pregnancy was positively associated with body weight reduction and HOMA-IR improvement in either group. CONCLUSION: In overweight or obese infertility Chinese PCOS, 12 weeks pregestational exenatide treatment resulted in more spontaneous pregnancy likely due to greater weight reduction and improvement of insulin resistance compared with metformin treatment without obvious benefit on overall pregnancy rate after ART or pregnancy outcomes of successful conceived women. TRIAL REGISTRATION: This clinical trial was registered at Chinese Clinical Trials Registry (ChiCTR-IIR-16008084) on 13/3/2016.

sEMG-Based Gain-Tuned Compliance Control for the Lower Limb Rehabilitation Robot during Passive Training.

The lower limb rehabilitation robot is a typical man-machine coupling system. Aiming at the problems of insufficient physiological information and unsatisfactory safety performance in the compliance control strategy for the lower limb rehabilitation robot during passive training, this study developed a surface electromyography-based gain-tuned compliance control (EGCC) strategy for the lower limb rehabilitation robot. First, the mapping function relationship between the normalized surface electromyography (sEMG) signal and the gain parameter was established and an overall EGCC strategy proposed. Next, the EGCC strategy without sEMG information was simulated and analyzed. The effects of the impedance control parameters on the position correction amount were studied, and the change rules of the robot end trajectory, man-machine contact force, and position correction amount analyzed in different training modes. Then, the sEMG signal acquisition and feature analysis of target muscle groups under different training modes were carried out. Finally, based on the lower limb rehabilitation robot control system, the influence of normalized sEMG threshold on the robot end trajectory and gain parameters under different training modes was experimentally studied. The simulation and experimental results show that the adoption of the EGCC strategy can significantly enhance the compliance of the robot end-effector by detecting the sEMG signal and improve the safety of the robot in different training modes, indicating the EGCC strategy has good application prospects in the rehabilitation robot field.

A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival.

With the advent of high-throughput sequencing technologies, much progress has been made in the identification of somatic structural rearrangements in cancer genomes. However, characterization of the complex alterations and their associated mechanisms remains inadequate. Here, we report a comprehensive analysis of whole-genome sequencing and DNA copy number data sets from The Cancer Genome Atlas to relate chromosomal alterations to imbalances in DNA dosage and describe the landscape of intragenic breakpoints in glioblastoma multiforme (GBM). Gene length, guanine-cytosine (GC) content, and local presence of a copy number alteration were closely associated with breakpoint susceptibility. A dense pattern of repeated focal amplifications involving the murine double minute 2 (MDM2)/cyclin-dependent kinase 4 (CDK4) oncogenes and associated with poor survival was identified in 5% of GBMs. Gene fusions and rearrangements were detected concomitant within the breakpoint-enriched region. At the gene level, we noted recurrent breakpoints in genes such as apoptosis regulator FAF1. Structural alterations of the FAF1 gene disrupted expression and led to protein depletion. Restoration of the FAF1 protein in glioma cell lines significantly increased the FAS-mediated apoptosis response. Our study uncovered a previously underappreciated genomic mechanism of gene deregulation that can confer growth advantages on tumor cells and may generate cancer-specific vulnerabilities in subsets of GBM.

A theoretical study of hydrogen-bonded molecular clusters of sulfuric acid and organic acids with amides.

Amides, a series of significant atmospheric nitrogen-containing volatile organic compounds (VOCs), can participate in new particle formation (NPF) throught interacting with sulfuric acid (SA) and organic acids. In this study, we investigated the molecular interactions of formamide (FA), acetamide (AA), N-methylformamide (MF), propanamide (PA), N-methylacetamide (MA), and N,N-dimethylformamide (DMF) with SA, acetic acid (HAC), propanoic acid (PAC), oxalic acid (OA), and malonic acid (MOA). Global minimum of clusters were obtained through the association of the artificial bee colony (ABC) algorithm and density functional theory (DFT) calculations. The conformational analysis, thermochemical analysis, frequency analysis, and topological analysis were conducted to determine the interactions of hydrogen-bonded molecular clusters. The heterodimers formed a hepta or octa membered ring through four different types of hydrogen bonds, and the strength of the bonds are ranked in the following order: SOH•••O > COH•••O > NH•••O > CH•••O. We also evaluated the stability of the clusters and found that the stabilization effect of amides with SA is weaker than that of amines with SA but stronger than that of ammonia (NH3) with SA in the dimer formation of nucleation process. Additionally, the nucleation capacity of SA with amides is greater than that of organic acids with amides.

TumorFusions: an integrative resource for cancer-associated transcript fusions.

Gene fusion represents a class of molecular aberrations in cancer and has been exploited for therapeutic purposes. In this paper we describe TumorFusions, a data portal that catalogues 20 731 gene fusions detected in 9966 well characterized cancer samples and 648 normal specimens from The Cancer Genome Atlas (TCGA). The portal spans 33 cancer types in TCGA. Fusion transcripts were identified via a uniform pipeline, including filtering against a list of 3838 transcript fusions detected in a panel of 648 non-neoplastic samples. Fusions were mapped to somatic DNA rearrangements identified using whole genome sequencing data from 561 cancer samples as a means of validation. We observed that 65% of transcript fusions were associated with a chromosomal alteration, which is annotated in the portal. Other features of the portal include links to SNP array-based copy number levels and mutational patterns, exon and transcript level expressions of the partner genes, and a network-based centrality score for prioritizing functional fusions. Our portal aims to be a broadly applicable and user friendly resource for cancer gene annotation and is publicly available at http://www.tumorfusions.org.

Circulating zinc-α2-glycoprotein is reduced in women with polycystic ovary syndrome, but can be increased by exenatide or metformin treatment.

The study was to investigate circulating zinc-α2-glycoprotein (ZAG) concentrations in women with PCOS, and changes in ZAG levels after exenatide or metformin treatment. One hundred eighty-two women with polycystic ovary syndrome (PCOS) who met the 2003 Rotterdam diagnostic criteria and 150 controls without PCOS were recruited. We partitioned women with PCOS into groups according to body mass index or blood glucose concentrations, determined serum ZAG, anthropometric parameters, metabolic and endocrine indicators, and inflammatory markers, and statistically analyzed the results. Eighty-two overweight/obese subjects of the recruited women with PCOS were then randomly assigned to groups administered either 12 weeks of exenatide injection (10 µg b.i.d.) or oral metformin (1,000 mg b.i.d.). Circulating ZAG levels were determined after 12 weeks of treatment. The results showed that circulating ZAG was significantly lower in PCOS women than in healthy women (p < 0.01). Overweight/obese women and those with higher blood glucose levels had lower circulating ZAG. After 12 weeks of exenatide or metformin treatment, there were significant increases (p < 0.01) in circulating ZAG in both treatment groups (the exenatide baseline level was 46.54 ± 2.38 ng/mL vs. 56.41 ± 2.02 ng/mL after treatment, p < 0.01; metformin baseline was 47.81 ± 2.14 ng/mL vs. 55.67 ± 2.01 ng/mL after treatment, p < 0.01), however there was no statistical difference between the 2 treatments (p > 0.05). Circulating ZAG is closely related to PCOS and could be an important adipokine involved in the occurrence and development of PCOS. ZAG might possibly be applicable as a new observational indicator in the treatment of PCOS.

Design and Evaluation of an Acoustic Modem for a Small Autonomous Unmanned Vehicle.

Design of underwater acoustic (UWA) modems for compact-sized, underwater platforms such as autonomous underwater vehicles (AUVs) is challenging because of the practical requirement to keep an engineering balance between the performance and the system overhead. Considering this type of mobile communication scenario, Doppler spread as well as the multipath draws substantial attention in implementing the system's design and engineering. Specifically, for a small AUV, the large computational complexity of real-time resampling for the classic Doppler correction poses significant difficulty for the limited capability of the low-cost processor. In this paper, by adopting an adjustable AD (analog-to-digital) sampling rate, a Doppler compensation approach is proposed to enable low-complexity hardware implementation. Based on this, a direct sequence spread spectrum (DSSS) acoustic modem is designed for a low-cost, small-sized AUV. Meanwhile, the performance evaluation of this acoustic modem is conducted in terms of the robustness upon varying Doppler as well as AUV integration. Finally, experimental results performed on a commercial, small-sized AUV under different speeds are reported to verify the effectiveness of the proposed acoustic modem.

Quantum Chemical and Kinetic Study on Radical/Molecule Formation Mechanism of Pre-Intermediates for PCTA/PT/DT/DFs from 2-Chlorothiophenol and 2-Chlorophenol Precursors.

Polychlorinated phenoxathiins (PCPTs), polychlorinated dibenzothiophenes (PCDTs), and polychlorinated thianthrenes (PCTAs) are sulfur analogues of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/DFs). Chlorothiophenols (CTPs) and chlorophenols (CPs) are key precursors for the formation of PCTA/PT/DTs, which can react with H or OH to form chloro(thio)phenoxy radical, sulfydryl/hydroxyl-substituted phenyl radicals, and (thio)phenoxyl diradicals. However, previous radical/radical PCTA/DT formation mechanisms in the literature failed to explain the higher concentration of PCDTs than that of PCTAs under the pyrolysis or combustion conditions. In this work, a detailed thermodynamics and kinetic calculations were carried out to investigate the pre-intermediate formation for PCTA/PT/DTs from radical/molecule coupling of the 2-C(T)P with their key radical species. Our study showed that the radical/molecule coupling mechanism explains the gas-phase formation of PCTA/PT/DTs in both thermodynamic and kinetic perspectives. The S/C coupling modes to form thioether-(thio)enol intermediates are preferable over the O/C coupling modes to form ether-(thio)enol intermediates. Thus, although the radical/molecule coupling of chlorophenoxy radical with 2-C(T)P has no effect on the PCDD/PT formation, the radical/molecule coupling of chlorothiophenoxy radical with 2-C(T)P plays an important role in the PCTA/PT formation. Most importantly, the pre-PCDT intermediates formation pathways from the couplings of sulfydryl/hydroxyl-substituted phenyl radical with 2-C(T)P and (thio)phenoxyl diradicals with 2-C(T)P are more favorable than pre-PCTA/PT intermediates formation pathways from the coupling of chlorothiophenoxy radical with 2-C(T)P, which provides reasonable explanation for the high PCDT-to-PCTA ratio in the environment.

The Gas-Phase Formation Mechanism of Dibenzofuran (DBF), Dibenzothiophene (DBT), and Carbazole (CA) from Benzofuran (BF), Benzothiophene (BT), and Indole (IN) with Cyclopentadienyl Radical.

Benzofuran (BF), benzothiophene (BT), indole (IN), dibenzofuran (DBF), dibenzothiophene (DBT), and carbazole (CA) are typical heterocyclic aromatic compounds (NSO-HETs), which can coexist with polycyclic aromatic hydrocarbons (PAHs) in combustion and pyrolysis conditions. In this work, quantum chemical calculations were carried out to investigate the formation of DBF, DBT, and CA from the reactions of BF, BT, and IN with a cyclopentadienyl radical (CPDyl) by using the hybrid density functional theory (DFT) at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. The rate constants of crucial elementary steps were deduced over 600-1200 K, using canonical variational transition state theory with a small-curvature tunneling contribution (CVT/SCT). This paper showed that the production of DBF, DBT, and CA from the reactions of BF, BT, and IN with CPDyl involved six elementary steps: the addition reaction, ring closure, the first H shift, C-C cleavage, the second H shift, and elimination of CH3 or H. The cleavage of the C-C bond was regarded as the rate-determining step for each pathway due to the extremely high barrier. The 1-methyl substituted products were more easily formed than the 4-methyl substituted products. The main products were DBF and 1-methyl-DBF, DBT and 1-methyl-DBT, and CA and 1-methyl-CA for reactions of BF, BT, and IN with CPDyl, respectively. The ranking of DBF, DBT, and CA formation potential was as follows: DBT and methyl-DBT formation > DBF and methyl-DBF formation > CA, and methyl-CA formation. Comparison with the reaction of naphthalene with CPDyl indicated that the reactions of CPDyl attacking a benzene ring and a furan/thiophene/pyrrole ring could be inferred to be comparable under high temperature conditions.

Mechanistic and Kinetic Study on Self-/Cross- Condensation of PCTA/DT Formation Mechanisms from Three Types of Radicals of 2,4-Dichlorothiophenol.

Chlorothiophenols (CTPs) are known to be key and direct precursors of polychlorinated thianthrene/dibenzothiophenes (PCTA/DTs). Self/cross-coupling of the chlorothiophenoxy radicals (CTPRs), sulfydryl-substituted phenyl radicals and thiophenoxyl diradicals evolving from CTPs are initial and important steps for PCTA/DT formation. In this study, quantum chemical calculations were carried out to investigate the homogenous gas-phase formation of PCTA/DTs from self/cross-coupling of 2,4-dichlorothiophenoxy radical (R1), 2-sulfydryl-3,5-dichlorophenyl radical (R2) and 3,5-dichlorothiophenoxyl diradical (DR) at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. The rate constants of crucial elementary steps were deduced over 600-1200 K, using canonical variational transition state theory with a small curvature tunneling contribution. For the formation of PCTAs, the S•/σ-C• condensation with both thiophenolic sulfur in one radical and ortho carbon in the other radical bonded to single electron is the most efficient sulfur-carbon coupling mode, and the ranking of the PCTA formation potential is DR + DR > R2 + DR > R1 + DR > R1 + R2 > R1 + R1. For the formation of PCDTs, the σ-C•/σ-C• coupling with both ortho carbon in the two radicals bonded to single electron is the energetically favored carbon-carbon coupling mode, and the ranking of the PCDT formation potential is: R2 + DR > R2 + R2 > R1 + DR > R1 + R2 > R1 + R1. The PCTA/DTs could be produced from R1, R2 and DR much more readily than PCDD/DFs from corresponding oxygen substituted radicals.

Profiles of brain metastases: Prioritization of therapeutic targets.

We sought to compare the tumor profiles of brain metastases from common cancers with those of primary tumors and extracranial metastases in order to identify potential targets and prioritize rational treatment strategies. Tumor samples were collected from both the primary and metastatic sites of nonsmall cell lung cancer, breast cancer and melanoma from patients in locations worldwide, and these were submitted to Caris Life Sciences for tumor multiplatform analysis, including gene sequencing (Sanger and next-generation sequencing with a targeted 47-gene panel), protein expression (assayed by immunohistochemistry) and gene amplification (assayed by in situ hybridization). The data analysis considered differential protein expression, gene amplification and mutations among brain metastases, extracranial metastases and primary tumors. The analyzed population included: 16,999 unmatched primary tumor and/or metastasis samples: 8,178 nonsmall cell lung cancers (5,098 primaries; 2,787 systemic metastases; 293 brain metastases), 7,064 breast cancers (3,496 primaries; 3,469 systemic metastases; 99 brain metastases) and 1,757 melanomas (660 primaries; 996 systemic metastases; 101 brain metastases). TOP2A expression was increased in brain metastases from all 3 cancers, and brain metastases overexpressed multiple proteins clustering around functions critical to DNA synthesis and repair and implicated in chemotherapy resistance, including RRM1, TS, ERCC1 and TOPO1. cMET was overexpressed in melanoma brain metastases relative to primary skin specimens. Brain metastasis patients may particularly benefit from therapeutic targeting of enzymes associated with DNA synthesis, replication and/or repair.