Abstract 2814: The mutational basis of cancer's vulnerability to ionizing radiation

Introduction: Large-scale sequencing efforts have established that cancer-associated genetic alterations are highly diverse, posing a challenge to the identification of variants that regulate complex phenotypes like radiation sensitivity. The impact of the vast majority of rare or common genetic variants on the sensitivity of cancers to radiotherapy remains largely unknown.

Methods: We developed a scalable gene editing and irradiation platform to assess the role of categories of variants in cells. Variants were prioritized based on genotype-phenotype associations from a previously completed large-scale cancer cell line radiation profiling study. Altogether, 488 alleles (396 unique SNVs) from 92 genes were generated and profiled in an immortalized lung cell line, BEAS-2B. We validated our results in other cell lines (TRT-HU1 and NCI-H520), in vivo via the use of both cell line and patient-derived murine xenografts, and in clinical cohorts.

Results: We show that resistance to radiation is characterized by substantial inter- and intra-gene allelic variation. Some genes (e.g. KEAP1) demonstrated significant intragenic allelic variation in the magnitude of conferred resistance and other genes (e.g. CTNNB1) displayed both resistance and sensitivity in a protein domain-dependent manner. We combined results from our platform with gene expression and metabolite features and identified the upregulation of amino acid transporters that facilitate oxidative reductive capacity and cell cycle deregulation as key regulators of radiation sensitivity.

Conclusions: Our results reveal new insights into the genetic determinants of tumor sensitivity to radiotherapy and nominate a multitude of cancer mutations that are predicted to impact treatment efficacy.

Citation Format: Priyanka Gopal, Mohamed E. Abazeed. The mutational basis of cancer's vulnerability to ionizing radiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2814.

Abstract 2229: Cell state transitions shape the intratumoral composition of small cell lung carcinoma

Introduction: Small cell lung carcinoma (SCLC) is characterized by rapid growth, early metastases, and initial response followed by almost invariable resistance to therapy. Studies to date have not determined the extent that diverse transcriptional programs drive SCLC and contribute to its lethality. We sought to characterize the intra-tumoral transcriptional heterogeneity of SCLC. We identify multivalent, distinct, and commutable transcriptional states that confer discrete functions in individual SCLC tumors.

Methods: We developed a biorepository of patient-derived xenografts (PDX) (n = 64) and matched PDX-derived ex vivo lines. We used multi-omic profiling (RNAseq, scRNAseq, and ATAC seq), single-cell fluorescence tracking of fate-defining transcription factor (TF)-driven states, and mathematical and statistical models (Markov chain) to study the topology of the SCLC transcriptional landscape and its plasticity. Human tumor material and associated clinical data were obtained after informed written consent on an IRB-approved prospective registry.

Results: We show that individual SCLC tumors are more heterogenous than previously appreciated, displaying distinctive equilibria in the proportion of cells within well-delimited cellular states (ASCL1, NEUROD1 and YAP1). We also show that transcriptional states undergo transitions, which we identified as a mechanism for maintaining cell state diversity. We measured the kinetics of state transitions using single-cell fluorescence tracking of ex vivo cultures and found that these measure were associated significantly with transition estimates using stochastic transition theory (i.e. Markov chains). ATAC-seq profiling indicated a role for the epigenome in the state diversity of SCLC. Namely, there was preferential promoter accessibility to Ascl1, NeuroD1, and Yap1 in a manner consistent with gene and protein expression in the respective subpopulations. Our results indicate that the transition rates between cell types in individual tumors were largely governed by tendencies to reach an equilibrium state that are critical for configuring intratumoral cell state proportions.

Conclusion: In conclusion, we demonstrate that TF driven cell states can transition to maintain an equilibrium in cell state proportions. Our work advances a model of cellular states and program diversity in SCLC and nominates new therapeutic strategies designed to limit the plasticity of this lethal cancer.

Citation Format: Priyanka Gopal, Aaron Petty, Kevin Rogacki, Titas Bera, Rohan Bareja, Craig Peacock, Mohamed Abazeed. Cell state transitions shape the intratumoral composition of small cell lung carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2229.

The Mutational Landscape of Cancer's Vulnerability to Ionizing Radiation

PURPOSE

Large-scale sequencing efforts have established that cancer-associated genetic alterations are highly diverse, posing a challenge to the identification of variants that regulate complex phenotypes like radiation sensitivity. The impact of the vast majority of rare or common genetic variants on the sensitivity of cancers to radiotherapy remains largely unknown.

EXPERIMENTAL DESIGN

We developed a scalable gene editing and irradiation platform to assess the role of categories of variants in cells. Variants were prioritized on the basis of genotype-phenotype associations from a previously completed large-scale cancer cell line radiation profiling study. Altogether, 488 alleles (396 unique single-nucleotide variants) from 92 genes were generated and profiled in an immortalized lung cell line, BEAS-2B. We validated our results in other cell lines (TRT-HU1 and NCI-H520), in vivo via the use of both cell line and patient-derived murine xenografts, and in clinical cohorts.

RESULTS

We show that resistance to radiation is characterized by substantial inter- and intra-gene allelic variation. Some genes (e.g., KEAP1) demonstrated significant intragenic allelic variation in the magnitude of conferred resistance and other genes (e.g., CTNNB1) displayed both resistance and sensitivity in a protein domain-dependent manner. We combined results from our platform with gene expression and metabolite features and identified the upregulation of amino acid transporters that facilitate oxidative reductive capacity and cell-cycle deregulation as key regulators of radiation sensitivity.

CONCLUSIONS

Our results reveal new insights into the genetic determinants of tumor sensitivity to radiotherapy and nominate a multitude of cancer mutations that are predicted to impact treatment efficacy.

Multivalent state transitions shape the intratumoral composition of small cell lung carcinoma

Studies to date have not resolved how diverse transcriptional programs contribute to the intratumoral heterogeneity of small cell lung carcinoma (SCLC), an aggressive tumor associated with a dismal prognosis. Here, we identify distinct and commutable transcriptional states that confer discrete functional attributes in individual SCLC tumors. We combine an integrative approach comprising the transcriptomes of 52,975 single cells, high-resolution measurement of cell state dynamics at the single-cell level, and functional and correlative studies using treatment naïve xenografts with associated clinical outcomes. We show that individual SCLC tumors contain distinctive proportions of stable cellular states that are governed by bidirectional cell state transitions. Using drugs that target the epigenome, we reconfigure tumor state composition in part by altering individual state transition rates. Our results reveal new insights into how single-cell transition behaviors promote cell state equilibrium in SCLC and suggest that facile plasticity underlies its resistance to therapy and lethality.

H. pylori Pattern Gastritis with Negative Helicobacter Immunohistochemical Stain: Does A Specific Comment in Pathology Report Impact Clinical Management?

Introduction/Objective

The clinical significance of H. pylori (HP) pattern of gastritis with a negative Helicobacter IHC stain on gastric biopsy is unclear. Some pathologists report this pattern in cases that are highly suggestive of HP infection with a comment raising the possibility of HP infection; however, the subsequent clinical management of these patients has not been well described.

Methods/Case Report

We conducted a retrospective comparison study of patients with gastric biopsy between 2016 and 2019. Group 1 included patients with chronic active or chronic inactive gastritis and negative HP IHC with a comment stating the gastritis pattern is suggestive of HP. Group 2 included patients with chronic active or chronic inactive gastritis and negative HP IHC with no comment about HP pattern.

Results (if a Case Study enter NA)

We identified 60 patients in Group 1 which were compared to 63 patients in Group 2. Group 1 more frequently had history of HP (48.3% vs. 29.1%, p<0.05). After diagnosis, Group 1 more frequently received treatment (51.7% vs. 20.6%, p<0.001). Of those who received treatment, Group 1 more frequently received HP treatment (triple or quadruple therapy; 21.7% vs. 1.6%, p<0.001). History of HP did not affect whether a patient was treated (p>0.05). Following post-biopsy HP treatment, more patients in Group 1 received fecal antigen test (23.7% vs. 5.5%, p<0.01). Age, gender, NSAID and PPI use did not differ between groups.

Conclusion

Adding the diagnostic comment raising the possibility of HP for patients with HP pattern gastritis with negative HP IHC changes clinical management and it is independent of patients’ prior HP history.

Multivalent state transitions regulate the intratumoral composition of small cell lung carcinoma

e20587

Background: Small cell lung carcinoma (SCLC) is an aggressive, tobacco-associated tumor with neuroendocrine features characterized by rapid growth, metastatic progression, and initial response followed by almost invariable resistance to therapy. Studies to date have not resolved the extent that diverse transcriptional programs drive SCLC and contribute to its lethality. Methods: We combined one of the largest and most diverse inventories of patient-derived xenograft models of SCLC with an ex vivo culture system that maintains transcriptional fidelity with matched primary SCLC tumor to identify transcriptional state heterogeneity. Using the expression of the Ascl1, NeuroD1, and Yap1 as markers of well-conserved SCLC states, we developed a state-of-the-art fluorescent platform that can directly measure single-cell state transitions in a multi-layered ecosystem using tandemly integrated reporters. We modeled population dynamics using a discrete time Markov chain and directly measure single-cell state transitions. Results: We show significant cell-state heterogeneity in several SCLC primary tumors, patient-derived xenografts (PDX), and ex vivo cultures. These states comprise distinct subpopulations marked by the master regulatory transcription factors (TFs) Ascl1, NeuroD1, and Yap1. Ex vivo, the 3 TFs are associated with suspension aggregates of small neuroendocrine cells, pre-suspension (loosely adherent) aggregates, and large mesenchymal cells with visible cytoplasm and spindle-like membrane extensions, respectively. We have observed equilibria in cell-state proportions in SCLC tumors both in vivo (PDX) and ex vivo. In addition, we have shown that the “elasticity” of SCLC responses, measured as the extent of clinical response during chemotherapy followed by the time to relapse from the end of therapy, is dependent on tumor TF levels. These observations suggest that mechanistic modeling of intra-tumoral state dynamics is of high clinical relevance. Conclusions: Our integrative approach is poised to formulate and validate a unified model of cellular states and program diversity in SCLC. If successful, the characterization of malignant cell ontogenic programs, their plasticity, and the advancement of new therapies designed to combat plasticity by epigenetic reprogramming will create a new scientific canvas for the study of this highly lethal disease.

The mutational landscape of the sensitivity of cancer to ionizing radiation

3129

Background: The impact of common or rare gene mutations on the sensitivity of cancers to ionizing radiation remains largely unknown. We conducted a systematic, arrayed (single variant per well) profiling effort to identify gene mutations that alter cellular sensitivity to radiation and validated some of our findings using a clinical cohort of patients who received thoracic radiotherapy alone. Methods: Candidate mutations were prioritized on the basis of genotype-phenotype associations from our previously completed large-scale cancer cell line irradiation profiling study (doi: 10.1038/ncomms11428), location within conserved protein domains, and functional impact (MutationAssessor). We used site-directed mutagenesis to generate mutant clones (2 clones per variant) and transferred the ORFs into lentiviral vectors in SV40 lung primary immortalized cells (BEAS2B). For clinical validation, an IRB-approved study was used to identify patients treated with lung radiotherapy alone. 197 patients with primary (stage I–IV) or recurrent lung cancer and patients with other cancer types and solitary metastases or oligometastases to the lung were included. Death without evidence of local failure was treated as a competing event, and Fine and Gray regression modeling was used to examine potential predictors of local failure. Results: Over 600 cancer variants were tested in ̃1200 experimental replicates, comprising 91 genes. We identified known and new radioresistant and radiosensitive variants involved in several cellular functional categories including cellular signaling, cytoskeleton, cell cycle, apoptosis, DNA methylation, and DNA repair. Variants that conferred resistance in BEAS2B cells were significantly more likely to confer resistance in TERT-HU1 and NCI-H520 cells, suggesting that most functional variants are cellular context indifferent. Variants under somatic oncogenic selection (hotspot mutants) were significantly more likely to confer resistance to radiation. Several infrequent cancer variants ( < 1% prevalence in cancer), including those in ERBB3, SMAD4, TGFBR1, VHL, CTNNB1, and MAP2K1, conferred radiation resistance. Some genes (e.g. KEAP1) demonstrated significant intragenic allelic variation in the magnitude of conferred resistance and other genes (e.g. CTNNB1) displayed both resistance and sensitivity in a protein domain-dependent manner. KRAS (resistant; HR 2.23; P= 0.02) and CTNNB1 exon 3 (sensitive; HR 0.3; P = 0.04) mutants conferred resistance and sensitivity, respectively, to radiotherapy in our clinical cohort. Conclusions: We report on a large-scale profiling effort to identify mutant alleles that govern radiation survival. Our results reveal new insights into potentially actionable determinants of tumor sensitivity to radiotherapy and accelerate clinical validation of common and rare gene mutations that impact radiation sensitivity.

A Therapeutic Strategy for Preferential Targeting of TET2 Mutant and TET-dioxygenase Deficient Cells in Myeloid Neoplasms

TET2 is frequently mutated in myeloid neoplasms. Genetic TET2 deficiency leads to skewed myeloid differentiation and clonal expansion, but minimal residual TET activity is critical for survival of neoplastic progenitor and stem cells. Consistent with mutual exclusivity of TET2 and neomorphic IDH1/2 mutations, here we report that IDH1/2 mutant-derived 2-hydroxyglutarate is synthetically lethal to TET-dioxygenase deficient cells. In addition, a TET-selective small molecule inhibitor decreased cytosine hydroxymethylation and restricted clonal outgrowth of TET2 mutant, but not normal hematopoietic precursor cells in vitro and in vivo. While TET-inhibitor phenocopied somatic TET2 mutations, its pharmacologic effects on normal stem cells were, unlike mutations, reversible. Treatment with TET inhibitor suppressed the clonal evolution of TET2 mutant cells in murine models and TET2-mutated human leukemia xenografts. These results suggest that TET inhibitors may constitute a new class of targeted agents in TET2 mutant neoplasia.

Cellular and Genetic Determinants of the Sensitivity of Cancer to α-Particle Irradiation

Targeted α-particle-emitting radionuclides have great potential for the treatment of a broad range of cancers at different stages of progression. A platform that accurately measures cancer cellular sensitivity to α-particle irradiation could guide and accelerate clinical translation. Here, we performed high-content profiling of cellular survival following exposure to α-particles emitted from radium-223 (²²³Ra) using 28 genetically diverse human tumor cell lines. Significant variation in cellular sensitivity across tumor cells was observed. ²²³Ra was significantly more potent than sparsely ionizing irradiation, with a median relative biological effectiveness of 10.4 (IQR: 8.4-14.3). Cells that are the most resistant to γ radiation, such as Nrf2 gain-of-function mutant cells, were sensitive to α-particles. Combining these profiling results with genetic features, we identified several somatic copy-number alterations, gene mutations, and the basal expression of gene sets that correlated with radiation survival. Activating mutations in PIK3CA, a frequent event in cancer, decreased sensitivity to ²²³Ra. The identification of cellular and genetic determinants of sensitivity to ²²³Ra may guide the clinical incorporation of targeted α-particle emitters in the treatment of several cancer types. SIGNIFICANCE: These findings address limitations in the preclinical guidance and prediction of radionuclide tumor sensitivity by identifying intrinsic cellular and genetic determinants of cancer cell survival following exposure to α-particle irradiation.See related commentary by Sgouros, p. 5479.

Abstract 734: Large-scale radiogenomic profiling of patient derived xenografts (PDX)

The determinants of clinical failure after radiotherapy remains poorly understood. Although cancer derived cells grown in vitro have served as a valuable resource to identify tumor cell intrinsic determinants of radiation sensitivity, their propensity to undergo genetic selection due to non-native culture conditions reduces intratumoral heterogeneity and alters transcriptomic fidelity. We show that patient-derived xenografts (PDX) models recapitulate the genetic and transcriptomic features of the primary tumors from which they are derived. We extend this characterization to an extensive collection of PDXs derived from multiple cancer types. We propose our “10,000 mice” PDX effort, which seeks to profile up to 500 PDX across 20 cancer types with multiple single fraction doses of radiation (2, 4, 6, 8, 10 Gy). We establish the feasibility of our approach using a 3x1x1 experimental design (3 mice per PDX per dose of radiation). Initial treatment responses following single doses radiation revealed that tumors exhibit significant variation in their response to radiation. Responses in PDX correlated with clinical outcomes, mainly in patients treated with radiation or chemoradiation alone. We compare pre- and post-irradiation PDX and deoncstruct the phylogenetic architecture of tumors before and after treatment selection. We show that in a substantial proportion of the tumors profiled to date, treatment resistance is regulated by subclonal outgrowths. Taken together, our results demonstrate the feasibility of high-content profiling of PDX to identify determinants of radiation sensitivity.

Note: This abstract was not presented at the meeting.

Citation Format: Priyanka Gopal, Titas Bera, Craig Peacock, Mohamed Abazeed. Large-scale radiogenomic profiling of patient derived xenografts (PDX) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 734.

Case study: patient-derived clear cell adenocarcinoma xenograft model longitudinally predicts treatment response

There has been little progress in the use of patient-derived xenografts (PDX) to guide individual therapeutic strategies. In part, this can be attributed to the operational challenges of effecting successful engraftment and testing multiple candidate drugs in a clinically workable timeframe. It also remains unclear whether the ancestral tumor will evolve along similar evolutionary trajectories in its human and rodent hosts in response to similar selective pressures (i.e., drugs). Herein, we combine a metastatic clear cell adenocarcinoma PDX with a timely 3 mouse x 1 drug experimental design, followed by a co-clinical trial to longitudinally guide a patient's care. Using this approach, we accurately predict response to first- and second-line therapies in so far as tumor response in mice correlated with the patient's clinical response to first-line therapy (gemcitabine/nivolumab), development of resistance and response to second-line therapy (paclitaxel/neratinib) before these events were observed in the patient. Treatment resistance to first-line therapy in the PDX is coincident with biologically relevant changes in gene and gene set expression, including upregulation of phase I/II drug metabolism (CYP2C18, UGT2A, and ATP2A1) and DNA interstrand cross-link repair (i.e., XPA, FANCE, FANCG, and FANCL) genes. A total of 5.3% of our engrafted PDX collection is established within 2 weeks of implantation, suggesting our experimental designs can be broadened to other cancers. These findings could have significant implications for PDX-based avatars of aggressive human cancers.

Abstract 2194: Subclonal variation and evolutionary dynamics of BRAF mutations in cancer

Tumors have genetically distinct subclones that compete for space and resources and differentially resist efforts to make them extinct. We studied the intratumoral heterogeneity of BRAF mutations across several cancer types. We identified BRAF driver mutations as predominately clonal in some cancer types (e.g. melanoma) and subclonal in others (e.g. lung adenocarcinoma). Clonality corresponded to the amplification of BRAF and prevalence of V600 mutations in each cancer type. We mathematically and experimentally modeled the propagation and selection of tumors containing BRAF mutations and determined that the speed of clonal sweeps were associated with the extent of activation of MAPK signaling pathway and BRAF copy number. Consistent with these findings, tumors with "hard" sweeps were more likely to respond to BRAF and/or MEK inhibitors. Furthermore, some PDX models treated with cytotoxic therapy underwent BRAF mutant subclone expansion over time and this effect is mitigated by inhibitors of BRAF and/or MEK. Treatment strategies based on subclone composition resulted in significantly improved tumor control. Our study uncovers patterns of distinct BRAF clonal evolutionary trajectories and advances therapeutic strategies on the basis of BRAF mutation identity and subclone composition that merit testing in patients.

Citation Format: Priyanka Gopal, Elif I. Sarihan, Mohamed E. Abazeed. Subclonal variation and evolutionary dynamics of BRAF mutations in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2194.

Abstract 1056: Cancer avatars are sensitive diagnosticians of the pleural space

The identification of malignant cells in pleural fluid has critical prognostic and therapeutic implications but is frequently a diagnostic challenge. The first step in determining the cause of a suspected malignant pleural effusion, thoracentesis, has an unsatisfying low sensitivity (~60-70%). Patient-derived xenografts (PDX) retain the principal characteristics of the tumor of origin. However, there has been little progress in the application of these models to guide diagnostic and staging strategies. We assessed the feasibility, cellular yield and comparative diagnostic accuracy of pleural-derived xenografts in patients with effusions.

An institutional review board-approved single-institution prospective registry of patients was used to identify patients undergoing diagnostic and/or therapeutic thoracentesis. Cells isolated from the pleural fluid of these patients were injected into NSG mice. A diagnosis of the cancer in the xenograft was confirmed by a staff pathologist with expertise in the correspondent cancer type.

All of the cases that were clinically positive for tumor cells in the pleural space demonstrated tumor engraftment. Samples taken from patients with known benign etiologies did not result in tumor engraftment. The developed xenografts provided ample tissue that can be made available for extensive molecular testing, even in cases where the cytological samples consisted of very few cells. Critically, two of 10 cases resulted in engraftment of the tumor despite no evidence of malignant cells on cytological examination, indicating a 20% improvement in the statistical power of pleural-based xenografting for the detection of malignancy.

Our study indicates that pleural-derived xenografts can enhance the sensitivity of malignant cell detection, reflecting the inherent limitations of cytological analyses of a few malignant cells. Moreover, the amplification of cellular material provides ample source material that can be used to satisfy the increasing demands for tissue-based molecular testing. To our knowledge, this is the first effort to effectively use patient-derived xenografts for the purpose of cancer staging and diagnosis.

Citation Format: Gwendolyn B. Kuzmishin, Priyanka Gopal, Mohamed E. Abazeed. Cancer avatars are sensitive diagnosticians of the pleural space [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1056.

A Histologic Basis for the Efficacy of SBRT to the lung

PURPOSE

Stereotactic body radiation therapy (SBRT) is the standard of care for medically inoperable patients with early-stage NSCLC. However, NSCLC is composed of several histological subtypes and the impact of this heterogeneity on SBRT treatments has yet to be established.

METHODS

We analyzed 740 patients with early-stage NSCLC treated definitively with SBRT from 2003 through 2015. We calculated cumulative incidence curves using the competing risk method and identified predictors of local failure using Fine and Gray regression.

RESULTS

Overall, 72 patients had a local failure, with a cumulative incidence of local failure at 3 years of 11.8%. On univariate analysis, squamous histological subtype, younger age, fewer medical comorbidities, higher body mass index, higher positron emission tomography standardized uptake value, central tumors, and lower radiation dose were associated with an increased risk for local failure. On multivariable analysis, squamous histological subtype (hazard ratio = 2.4 p = 0.008) was the strongest predictor of local failure. Patients with squamous cancers fail SBRT at a significantly higher rate than do those with adenocarcinomas or NSCLC not otherwise specified, with 3-year cumulative rates of local failure of 18.9% (95% confidence interval [CI]: 12.7-25.1), 8.7% (95% CI: 4.6-12.8), and 4.1% (95% CI: 0-9.6), respectively.

CONCLUSION

Our results demonstrate an increased rate of local failure in patients with squamous cell carcinoma. Standard approaches for radiotherapy that demonstrate efficacy for a population may not achieve optimal results for individual patients. Establishing the differential dose effect of SBRT across histological groups is likely to improve efficacy and inform ongoing and future studies that aim to expand indications for SBRT.

A genetic basis for the variation in the vulnerability of cancer to DNA damage

Radiotherapy is not currently informed by the genetic composition of an individual patient's tumour. To identify genetic features regulating survival after DNA damage, here we conduct large-scale profiling of cellular survival after exposure to radiation in a diverse collection of 533 genetically annotated human tumour cell lines. We show that sensitivity to radiation is characterized by significant variation across and within lineages. We combine results from our platform with genomic features to identify parameters that predict radiation sensitivity. We identify somatic copy number alterations, gene mutations and the basal expression of individual genes and gene sets that correlate with the radiation survival, revealing new insights into the genetic basis of tumour cellular response to DNA damage. These results demonstrate the diversity of tumour cellular response to ionizing radiation and establish multiple lines of evidence that new genetic features regulating cellular response after DNA damage can be identified.

Differential ligand-signaling network of CCL19/CCL21-CCR7 system

Chemokine (C-C motif) receptor 7 (CCR7), a class A subtype G-Protein Coupled Receptor (GPCR), is involved in the migration, activation and survival of multiple cell types including dendritic cells, T cells, eosinophils, B cells, endothelial cells and different cancer cells. Together, CCR7 signaling system has been implicated in diverse biological processes such as lymph node homeostasis, T cell activation, immune tolerance, inflammatory response and cancer metastasis. CCL19 and CCL21, the two well-characterized CCR7 ligands, have been established to be differential in their signaling through CCR7 in multiple cell types. Although the differential ligand signaling through single receptor have been suggested for many receptors including GPCRs, there exists no resource or platform to analyse them globally. Here, first of its kind, we present the cell-type-specific differential signaling network of CCL19/CCL21-CCR7 system for effective visualization and differential analysis of chemokine/GPCR signaling.

Database URL:http:// www. netpath. org/ pathways? path_ id= NetPath_ 46.

Effect of chronic hypoxia on RAGE and its soluble forms in lungs and plasma of mice

The receptor for advanced glycation end products (RAGE) is a multi-ligand receptor. Alternative splicing and enzymatic shedding produce soluble forms that protect against damage by ligands including Advanced Glycation End products (AGEs). A link between RAGE and oxygen levels is evident from studies showing RAGE-mediated injury following hyperoxia. The effect of hypoxia on pulmonary RAGE expression and circulating sRAGE levels is however unknown. Therefore mice were exposed to chronic hypoxia for 21 d and expression of RAGE, sheddases in lungs and circulating sRAGE were determined. In addition, accumulation of AGEs in lungs and expression of the AGE detoxifying enzyme GLO1 and receptors were evaluated. In lung tissue gene expression of total RAGE, variants 1 and 3 were elevated in mice exposed to hypoxia, whereas mRAGE and sRAGE protein levels were decreased. In the hypoxic group plasma sRAGE levels were enhanced. Although the levels of pro-ADAM10 were elevated in lungs of hypoxia exposed mice, the relative amount of the active form was decreased and gelatinase activity unaffected. In the lungs, the RAGE ligand HMGB1 was decreased and of the AGEs, only LW-1 was increased by chronic hypoxia. Gene expression of AGE receptors 2 and 3 was significantly upregulated. Chronic hypoxia is associated with downregulation of pulmonary RAGE protein levels, but a relative increase in sRAGE. These alterations might be part of the adaptive and protective response mechanism to chronic hypoxia and are not associated with AGE formation except for the fluorophore LW-1 which emerges as a novel marker of tissue hypoxia.

Preparation, characterization and analytical application of an electrochemical laccase biosensor towards low level determination of isoprenaline in human serum samples

A novel electrochemical biosensor has been developed based on the immobilization of multiwalled carbon nanotubes (MWCNT) followed by sol–gel entrapment of laccase (Lac) enzyme on to the GCE.

Meta-analysis: underutilisation and disparities of treatment among patients with hepatocellular carcinoma in the United States

BACKGROUND

Despite wide availability of treatment options for hepatocellular carcinoma (HCC), several studies have suggested underutilisation in clinical practice.

AIMS

To quantify utilisation rates for HCC treatment among patients with HCC in the United States, and to summarise patterns of association between utilisation rates and patient socio-demographic characteristics.

METHODS

We performed a systematic literature review using the Medline database from January 1989 to March 2013. Two investigators independently extracted data on patient populations, study methods and results using standardised forms. Pooled treatment rates for any treatment and curative treatment, with 95% confidence intervals, were calculated. Prespecified subgroup analysis was performed to identify patient-level correlates of treatment utilisation.

RESULTS

We identified 24 studies that met inclusion criteria. The pooled rates of any treatment and curative treatment were 52.8% (95% CI 52.2-53.4%) and 21.8% (95% CI 21.4-22.1%) respectively. Among patients diagnosed at an early stage, the pooled curative treatment rate was 59.0% (95% CI 58.1-59.9%). Elderly, non-Caucasians and patients of low socioeconomic status had lower treatment rates than their counterparts.

CONCLUSIONS

Rates of HCC treatment in the United States, including curative treatment rates among patients detected at an early stage, are disappointingly low. Future efforts should focus on identifying appropriate intervention targets to increase treatment rates and reduce socio-demographic disparities.

Differential roles of C4 and betaC1 in mediating suppression of post-transcriptional gene silencing: evidence for transactivation by the C2 of Bhendi yellow vein mosaic virus, a monopartite begomovirus

Bhendi yellow vein mosaic disease (BYVMD) is caused by the association of a DNA beta satellite with a begomovirus component. The begomovirus component has two promoters, one in the virion sense (V-sense) and the other in the complementary sense (C-sense) in the intergenic region (IR). To study the promoter activities of V-sense and C-sense promoters, mGFP gene fusion was made downstream to the promoters. Transient and stable expressions in N. benthamiana leaves showed significant GFP expression under C-sense promoter whereas the expression under the V-sense promoter was very weak in the absence of the transactivator C2. Untransformed N. benthamiana plants were agroinfiltrated with binary vector constructs containing V-sense-GFP alone or along with C1, C2, C4, V1, V2 or betaC1 (in both sense and antisense orientations) to understand the roles of these gene products in transactivation and/or suppression of post-transcriptional gene silencing (PTGS). The results showed strong suppression of gene silencing activities for C4 and betaC1 but a weak activity for C2. The suppression activities were also confirmed using gfp-silenced GFP16c/GFPi plants by agroinfiltration and agroinoculation. The expression of C4 and betaC1 as transgenes produced abnormal phenotypic growth compared to the other viral genes mentioned above, further supporting their suppressor function.

Impact of consumption of different levels of Bifidobacterium lactis HN019 on the intestinal microflora of elderly human subjects

BACKGROUND

Age-related changes in the physiology and intestinal function of the elderly render them more susceptible to gut-related illnesses. Probiotic dietary supplementation has been shown to enhance the health indices in the elderly.

OBJECTIVE

To determine the effect of three different doses [5 x 109 CFU/day (high), 1.0 x 109 CFU/day (medium) and 6.5 x 107 CFU/day (low)] of Bifidobacterium lactis HN019 (DR10TM) on the intestinal flora of elderly human subjects and the dose response effect.

DESIGN

Randomised, double-blind and placebo-controlled human dietary intervention study consisting of four groups of 20 elderly (over 60 years old) volunteers. Each volunteer consumed 250 mL per day of reconstituted skim milk (RSM) which either did not contain any probiotic supplement (placebo group) or contained B. lactis HN019 at different levels (low, medium and high dose groups). The study comprised three stages: a 2-week pre-intervention (without any supplement), followed by 4 weeks of test feeding (dietary intervention) and then a 2-week washout period.

RESULTS

After dietary intervention, statistically significant increases in bifidobacteria, lactobacilli and enterococci were observed. At the end of the 4-week feeding period the mean number of bifidobacteria recorded in the placebo group were 9.31 +/- 0.01 log CFU/g of faeces. In the high, medium and low dose groups the bifidobacteria levels were significantly (p < 0.006) higher (9.88 +/- 0.1, 9.75 +/- 0.14 and 9.74 +/- 0.11 log CFU/g of faeces, respectively), when compared to the respective pre-intervention levels. There were no significant differences (p superior 0.05) between the responses of the different dose groups, indicating that even the lowest dose tested augmented the changes in bifidobacteria. Similar trends were observed for lactobacilli and enterococci. In contrast, the counts of enterobacteria were reduced in all the probiotic dose groups.

CONCLUSION

The present study showed that dietary supplementation with B. lactis HN019 significantly increased the number of resident bifidobacteria and reduced the enterobacteria counts. In addition, enterococci and lactobacilli were also increased. Based on this study and already published clinical evidence (4, 5, 8, 9) we conclude that, B. lactis HN019 is a suitable probiotic for elderly human subjects and even the lowest dose (6.5 x 107 CFU/day) tested is able to confer desired changes in the intestinal microflora.

Probiotic research in Australia, New Zealand and the Asia-Pacific region

Although the epicentres of probiotic research in the past decade have been Japan and Europe, researchers in the Asia-Pacific region have actively contributed to the growing understanding of the intestinal microbial ecosystem, and interactions between gut bacteria, diet and health of the human host. A number of new probiotic strains have been developed in the region that have been demonstrated to have beneficial impacts on health in animal and human trials, including improved protection against intestinal pathogens and modulation of the immune system. Probiotics targeted to animals, including aquaculture, feature heavily in many Asian countries. Developments in probiotic technologies have included microencapsulation techniques, antimicrobial production in fermented meats, and synbiotic combinations. In particular, the impact of resistant starch on the intestinal environment and fermentation by intestinal bacteria has been intensively studied and new probiotic strains selected specifically for synbiotic combinations with resistant starch. This paper provides an overview of probiotic research within Australia, New Zealand and a number of Asian countries, and lists scientists in the Asia-Pacific region involved in various aspects of probiotic research and development.

A mutation that prevents glucosylation of the lipid-linked oligosaccharide precursor leads to underglycosylation of secreted yeast invertase

A mutant of Saccharomyces cerevisiae with the genotype mnn1 mnn2 mnn9 gls1 synthesizes mannoproteins with oligosaccharides having the composition Glc3Man10Glc-NAc2- owing to the mnn9 defect, which prevents synthesis of the outer chain, the mnn1 defect, which prevents branching of the core, and the gls1 mutation, which prevents deglucosylation of the resultant glycoprotein as a consequence of a defective glucosidase-I [Tsai, P.-K., Ballou, L., Esmon, B., Schekman, R. & Ballou, C. E. (1984) Proc. Natl. Acad. Sci. USA 81, 6340-6343]. (The mnn2 defect is not expressed in presence of the mnn9 mutation.) This strain spontaneously forms new colonies in which gls1 is suppressed owing to a defect in synthesis of dolichol phosphoglucose, the glucosylation substrate. The new mutant, designated mnn1 mnn2 mnn9 gls1 dpg1, synthesizes and secretes invertase (EC 3.2.1.26) that has a higher mobility on native gel electrophoresis than that made by the parent strain, the consequence of a reduction in both the size and the number of carbohydrate chains. The mannoprotein chains have the mnn1 mnn9 structure (Man10Glc-NAc2-), and the invertase is resolved by gel electrophoresis in sodium dodecyl sulfate into two major and two minor bands that represent homologs with about 4-7 carbohydrate units, in contrast to about 8-11 chains in the parent strain. Thus, the inability to glucosylate the lipid-linked precursor reduces the efficiency of glycosylation of the protein chains. The genetic defect is in synthesis of the glucose donor dolichol phosphoglucose, but the mutation is nonallelic with the reported alg5-1 mutation, which has a similar phenotype [Runge, K. W., Huffaker, T. C. & Robbins, P. W. (1984) J. Biol. Chem. 259, 412-417].

Isolation and structure of glucan from regenerating spheroplasts of Candida albicans

Regenerating spheroplasts of Candida albicans formed organized glucan nets in liquid culture. The nets consisted of interwoven microfibrils about 50 nm wide, but of an undetermined length. Partial acid hydrolysis of the polysaccharide showed the presence of chains of beta(1----3)- and beta(1----6)-linked glucose residues, but no intrachain beta(1----3) and beta(1----6) linkages. Periodate oxidation and GLC of the methylated glucan indicated a highly branched polymer (9.5% branch points). Sequential enzymic degradation of the isolated nets confirmed the presence of chains of beta(1----3)- and beta(1----6)-linked glucose residues. Degradation by (1----3)-beta- and (1----6)-beta-glucanase released 23% (w/w) and 30% (w/w) respectively of the carbohydrate as glucose equivalents. The residual material was degraded by chitinase. Equal amounts of N-acetylglucosamine and glucose equivalents were detected in the chitinase hydrolysate, suggesting a possible linkage between glucan and chitin. Our data indicate that the cell wall of C. albicans contains at least two highly branched glucans with predominantly beta(1----3) or beta(1----6) linkages.

Metabolism of [14C]glucose by regenerating spheroplasts of Candida albicans

Spheroplasts of Candida albicans were regenerated in [14C]glucose and buffered magnesium sulphate (0.1 M-Tris/HCl; 0.5 M-MgSO4, pH 7.2) at 35 degrees C. Uptake of glucose by spheroplasts was faster than that by intact yeast cells. After 6 h, 65% of the glucose taken up by the yeast appeared as CO2 and 30% was incorporated into the cellular material. With spheroplasts, 55% of the glucose taken up was expired as CO2, 25% was excreted into the medium as other metabolites and 20% was incorporated into the cells. The regenerating spheroplasts excreted 14C-labelled carbohydrates into the medium which were fractionated on a Sephadex G-15 column. Acid hydrolysis of the low molecular-weight fraction yielded the following sugars: mannose (75.7%), fucose (3.8%), arabinose (3%), galactose (2.1%) and an unidentified monosaccharide (14%). Spheroplasts did not incorporate mannoprotein into the regenerated wall. The wall carbohydrate from regenerated spheroplasts was fractionated on the basis of solubility in sodium hydroxide. The alkali-insoluble fraction was analysed by sequential enzyme hydrolysis; 40% of the incorporated counts were associated with beta (1----3)-linked glucan and 50% with a mixed glucan comprising beta (1----3)- and beta (1----6)-linkages and chitin.

Enzymes of N-acetylglucosamine metabolism during germ-tube formation in Candida albicans

The enzymes of N-acetyl-D-glucosamine (GlcNAc) metabolism, GlcNAc-6-phosphate deacetylase and GlcN-6-phosphate deaminase were found to be inducible in Candida albicans. The pattern of induction for these enzymes was the same under conditions of germ-tube formation (37 degrees C) and where yeast cells metabolized GlcNAc with no change in morphology (28 degrees C); this indicates that these enzymes are not control points in the dimorphic development of C. albicans. During induction there was a 40-and 25-fold increase in specific activity for the deacetylase and the deaminase, respectively, and the maximum specific activity correspond to the time when all the GlcNAc had been metabolized. The presence of lomofungin (an inhibitor of transcription) or trichodermin (an inhibitor of translation) in cell suspensions of C. albicans containing GlcNAc prevented the increase in specific activity of these enzymes. 2-Deoxyglucose inhibited germ-tube formation, partially inhibited the induction of the deacetylase (43%) and the deaminase (60%), but did not affect the growth of C. albicans on either Glc or GlcNAc. GlcN-6-phosphate was a competitive inhibitor of the deacetylase with a Ki of 1.4 mM while the other product of the reaction, acetate, did not inhibit the enzyme. The Km value for GlcN-6-phosphate on GlcN-6-phosphate deaminase was 0.24 mM. Incubation of starved yeast cells with GlcNAc produced a four-fold increase in the specific activity of UDP-GlcNAc-pyrophosphorylase at either 28 degrees C or 37 degrees C.