The Molecular Landscape of Gastric Cancers for Novel Targeted Therapies from Real-World Genomic Profiling

BACKGROUND

Panel-based comprehensive genomic profiling is used in clinical practice worldwide; however, large real-world datasets of patients with advanced gastric cancer are not well known.

OBJECTIVE

We investigated what differences exist in clinically relevant alterations for molecularly defined or age-stratified subgroups.

METHODS

This was a collaborative biomarker study of a real-world dataset from comprehensive genomic profiling testing (Foundation Medicine, Inc.). Hybrid capture was carried out on at least 324 cancer-related genes and select introns from 31 genes frequently rearranged in cancer. Overall, 4634 patients were available for analyses and were stratified by age (≥ 40/< 40 years), microsatellite instability status, tumor mutational burden status (high 10 ≥ /low < 10 Muts/Mb), Epstein-Barr virus status, and select gene alterations. We analyzed the frequency of alterations with a chi-square test with Yate's correction.

RESULTS

Genes with frequent alterations included TP53 (60.1%), ARID1A (19.6%), CDKN2A (18.2%), KRAS (16.6%), and CDH1 (15.8%). Differences in comprehensive genomic profiling were observed according to molecularly defined or age-stratified subgroups. Druggable genomic alterations were detected in 31.4% of patients; ATM (4.4%), BRAF V600E (0.4%), BRCA1 (1.5%), BRCA2 (2.9%), ERBB2 amplification (9.2%), IDH1 (0.2%), KRAS G12C (0.7%), microsatellite instability-high (4.8%), NTRK1/2/3 fusion (0.13%), PIK3CA mutation (11.4%), and tumor mutational burden-high (9.4%). CDH1 alterations and MET amplification were significantly more frequent in patients aged < 40 years (27.7 and 6.2%) than in those aged ≥ 40 years (14.7 and 4.0%).

CONCLUSIONS

Real-world datasets from clinical panel testing revealed the genomic landscape in gastric cancer by subgroup. These findings provide insights for the current therapeutic strategies and future development of treatments in gastric cancer.

Pan-Cancer Analysis of Copy-Number Features Identifies Recurrent Signatures and a Homologous Recombination Deficiency Biomarker to Predict Poly (ADP-Ribose) Polymerase Inhibitor Response

PURPOSE

Copy-number (CN) features reveal the molecular state of cancers and may have predictive and prognostic value in the treatment of cancer. We sought to apply published CN analysis methods to a large pan-cancer data set and characterize ubiquitous CN signatures across tumor types, including potential utility for treatment selection.

METHODS

We analyzed the landscape of CN features in 260,333 pan-cancer samples. We examined the association of 10 signatures with genomic alterations and clinical characteristics and trained a machine learning classifier using CN and insertion and deletion features to detect homologous recombination deficiency signature (HRDsig) positivity. Clinical outcomes were assessed using a real-world clinicogenomic database (CGDB) of comprehensive genomic profiling linked to deidentified, electronic health record-derived clinical data.

RESULTS

CN signatures were prevalent across cancer types and associated with diverse processes including focal tandem duplications, seismic amplifications, genome-wide loss of heterozygosity (gLOH), and HRD. Our novel HRDsig outperformed gLOH in predicting BRCAness and effectively distinguished biallelic BRCA and homologous recombination-repair wild-type (HRRwt) samples pan-tumor, demonstrating high sensitivity to detect biallelic BRCA in ovarian (93%) and other HRD-associated cancers (80%-87%). Pan-tumor prevalence of HRDsig was 6.4%. HRRwt cases represented a significant fraction of the HRDsig-positive cohort, likely reflecting a population with nongenomic mechanisms of HRD. In ovarian and prostate CGDBs, HRDsig identified more patients than gLOH and had predictive value for poly (ADP-ribose) polymerase inhibitor (PARPi) benefit.

CONCLUSION

Tumor CN profiles are informative, revealing diverse processes active in cancer. We describe the landscape of 10 CN signatures in a large pan-cancer cohort, including two associated with HRD. We trained a machine learning-based HRDsig that robustly identified BRCAness and associated with biallelic BRCA pan-tumor, and was predictive of PARPi benefit in real-world ovarian and prostate data sets.

Integrative Analysis of a Large Real-World Cohort of Small Cell Lung Cancer Identifies Distinct Genetic Subtypes and Insights into Histologic Transformation

Small cell lung cancer (SCLC) is a recalcitrant neuroendocrine carcinoma with dismal survival outcomes. A major barrier in the field has been the relative paucity of human tumors studied. Here we provide an integrated analysis of 3,600 "real-world" SCLC cases. This large cohort allowed us to identify new recurrent alterations and genetic subtypes, including STK11-mutant tumors (1.7%) and TP53/RB1 wild-type tumors (5.5%), as well as rare cases that were human papillomavirus-positive. In our cohort, gene amplifications on 4q12 are associated with increased overall survival, whereas CCNE1 amplification is associated with decreased overall survival. We also identify more frequent alterations in the PTEN pathway in brain metastases. Finally, profiling cases of SCLC containing oncogenic drivers typically associated with NSCLC demonstrates that SCLC transformation may occur across multiple distinct molecular cohorts of NSCLC. These novel and unsuspected genetic features of SCLC may help personalize treatment approaches for this fatal form of cancer.

SIGNIFICANCE

Minimal changes in therapy and survival outcomes have occurred in SCLC for the past four decades. The identification of new genetic subtypes and novel recurrent mutations as well as an improved understanding of the mechanisms of transformation to SCLC from NSCLC may guide the development of personalized therapies for subsets of patients with SCLC. This article is highlighted in the In This Issue feature, p. 1501.

Comprehensive genomic profiling and treatment patterns across ancestries in advanced prostate cancer: a large-scale retrospective analysis

BACKGROUND

Men of African ancestry experience the greatest burden of prostate cancer globally, but they are under-represented in genomic and precision medicine studies. Therefore, we sought to characterise the genomic landscape, comprehensive genomic profiling (CGP) utilisation patterns, and treatment patterns across ancestries in a large, diverse, advanced prostate cancer cohort, to determine the impact of genomics on ancestral disparities.

METHODS

In this large-scale retrospective analysis, the CGP-based genomic landscape was evaluated in biopsy sections from 11 741 patients with prostate cancer, with ancestry inferred using a single nucleotide polymorphism-based approach. Admixture-derived ancestry fractions for each patient were also interrogated. Independently, clinical and treatment information was retrospectively reviewed for 1234 patients in a de-identified US-based clinicogenomic database. Prevalence of gene alterations, including actionable gene alterations, was assessed across ancestries (n=11 741). Furthermore, real-world treatment patterns and overall survival was assessed in the subset of patients with linked clincogenomic information (n=1234).

FINDINGS

The CGP cohort included 1422 (12%) men of African ancestry and 9244 (79%) men of European ancestry; the clinicogenomic database cohort included 130 (11%) men of African ancestry and 1017 (82%) men of European ancestry. Men of African ancestry received more lines of therapy before CGP than men of European ancestry (median of two lines [IQR 0-8] vs one line [0-10], p=0·029). In genomic analyses, ancestry-specific mutational landscapes were observed, but the prevalence of alterations in AR, the DNA damage response pathway, and other actionable genes were similar across ancestries. Similar genomic landscapes were observed in analyses that accounted for admixture-derived ancestry fractions. After undergoing CGP, men of African ancestry were less likely to receive a clinical study drug compared with men of European ancestry (12 [10%] of 118 vs 246 [26%] of 938, p=0·0005).

INTERPRETATION

Similar rates of gene alterations with therapy implications suggest that differences in actionable genes (including AR and DNA damage response pathway genes) might not be a main driver of disparities across ancestries in advanced prostate cancer. Later CGP utilisation and a lower rate of clinical trial enrolment observed in men of African ancestry could affect genomics, outcomes, and disparities.

FUNDING

American Society for Radiation Oncology, Department of Defense, Flatiron Health, Foundation Medicine, Prostate Cancer Foundation, and Sylvester Comprehensive Cancer Center.

Abstract 931: Comprehensive analysis of 3,600 small cell lung cancer cases reveals rare genetic subtypes and multiple mechanisms of histological transformation

Background: Small cell lung cancer (SCLC) is an aggressive neuroendocrine carcinoma with limited treatment options and extremely poor survival outcomes. A major barrier in the field has been the relative paucity of human tumors studied and lack of access to longitudinal samples to understand tumor evolution.

Methods: Here we provide a comprehensive analysis of 3,600 patients with SCLC who underwent targeted genomic profiling of at least 324 cancer-related genes as part of routine clinical care, including 678 cases with additional clinical and treatment information obtained from a US-based de-identified SCLC clinico-genomic database that originated from approximately 280 US cancer clinics. This large cohort allowed us to examine for new genetic subtypes, ancestry-associated genomic alterations, biopsy site-specific patterns, survival trends and histological transformation of SCLC from non-small cell lung cancer (NSCLC).

Results: Consistent with prior studies, SCLCs were predominantly TP53/RB1 altered. Yet, 5.5% of the cases in our cohort were TP53/RB1 wild-type tumors. These tumors often lacked a tobacco mutational signature, exhibited alternate mechanisms of p53/Rb pathway inactivation (e.g., CDKN2A, CCND1, MDM2), and had a high fraction of human papillomavirus-positive cases (12.7%). Another rare subtype of SCLCs included STK11-altered tumors (1.7%), which were observed more frequently in patients of African ancestry, and were associated with a decreased overall survival (OS) compared with the STK11 wild-type cohort. In our cohort, gene amplifications on 4q12 (KDR, KIT, PDGFRA) were associated with increased OS while CCNE1 amplification was associated with decreased OS. Interestingly, alterations in PTEN were more common in brain metastases compared to lung biopsies and liver metastases, suggesting its potentially unique role in brain metastases of SCLCs. Profiling of over 100 putative transformed SCLCs demonstrated that lineage plasticity may occur at variable lengths of time from the original NSCLC diagnosis and include multiple distinct molecular cohorts of NSCLC, beyond EGFR-mutant NSCLC (e.g., kinase fusion+ tumors: RET, ALK, ROS1, NTRK1).

Conclusion: Our work underscores the existence of genetic subtypes in SCLC, including rare subtypes with potential clinical utility. Findings from this study provide an improved understanding of genetic subtypes in SCLC and better inform mechanisms of transformation to SCLC from NSCLC, that may further guide the development of personalized therapies for subsets of patients with this fatal tumor.

Citation Format: Smruthy Sivakumar, Jay A. Moore, Meagan Montesion, Douglas I. Lin, Zoe Fleischmann, Ericka M. Ebot, Justin Newberg, Jennifer M. Mills, Priti S. Hegde, Garrett M. Frampton, Julien Sage, Christine M. Lovly. Comprehensive analysis of 3,600 small cell lung cancer cases reveals rare genetic subtypes and multiple mechanisms of histological transformation [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 931.

The Molecular Landscape of Pancreatobiliary Cancers for Novel Targeted Therapies From Real-World Genomic Profiling

BACKGROUND

Chemotherapies have limited efficacy in pancreatic cancer (PC) and biliary tract cancer (BTC), underscoring the need for new regimens. Recently, tumor-agnostic approaches have been developed for some targeted therapies in advanced solid tumors; however, the frequency of alterations by clinical and genomic background is unclear in PC and BTC.

METHODS

To assess the frequencies of druggable gene alterations and investigate new potential therapeutic targetable genomic alterations, advanced PC and BTC patients were tested with comprehensive genomic profiling at Foundation Medicine during the course of clinical care.

RESULTS

A total of 16 913 PC patients and 3031 BTC patients were available for analyses, and frequencies of genomic alterations were stratified by age (≥40 years or <40 years), microsatellite instability status, tumor mutational burden status (high ≥10 or low <10 Muts/Mb), and select genomic alterations. Alterations in BRCA2, BRAF, ERBB2, CDK12, PIK3CA, FGFR2, EGFR, and other potential targets were seen across cohorts, with enrichment observed within particular subsets such as in PC patients lacking a KRAS mutation. In BTC patients, the rate of ERBB2 amplification was statistically significantly higher in the tumor mutational burden-high population (23.3% vs 13.7%). Interestingly, CDK12 rearrangement was observed in BTC patients with ERBB2 amplification tumors. In patients younger than 40 years, FGFR2 rearrangement (4%) was observed in PC: GATA6 amplification (11.1%) and rearrangement of BRAF (2.8%)FGFR2 (5.6%) was observed in BTC patients.

CONCLUSIONS

We identified an appreciable frequency of immunotherapy biomarkers and targetable gene alterations in both PC and BTC, with notable frequencies in PC samples lacking KRAS mutations and children or adolescent and young adult populations, that should encourage comprehensive genomic profiling testing.

Genomic landscape in small intestine cancer from real-world data (RWD) of clinical genomic testing

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Background: Panel-based comprehensive genomic profiling (CGP) is used in clinical practice worldwide, however, large aggregated RWD of patients with advanced small intestine cancer have not been characterized. In particular, there has been limited data regarding examining CGP in pediatric/ Adolescent and Young Adult (AYA) small intestine cancer. For patient subgroups, it is unclear what clinically relevant alterations co-occur. Here, we investigated the genomic landscape of small intestine cancer patients, stratified by sub-group to help refine and discover new targets for improved cancer therapies in advanced small intestine cancer. Methods: This is a collaborative biomarker study using RWD paired with CGP testing (Foundation Medicine, Inc.). Hybrid capture was carried out on up to 395 cancer-related genes and select introns from up to 31 genes frequently rearranged in cancer. One thousand three hundred sixty-four patients were available for analyses and were stratified by age (≥40/ < 40), MSI status, tumor mutational burden (TMB) status (High ≥10/Low < 10Muts/Mb), and select gene alterations. Using a chi-square test with Yate’s correction, frequencies of alterations were analyzed according to clinical or genomic background. Results: Genes with frequent alterations including mutation, amplification, and rearrangement/fusion were TP53 (59.8%), KRAS (54.8%), APC (27.7%), CDKN2A (22.4%), and SMAD4 (20.2%). Genomic profiling according to age, MSI, and TMB status is shown in the following table. In pediatric/AYA patients, frequency of APC alterations was significantly low ( P< 0.001). In KRAS mutated tumors, codon 12 most abundant mutations were G12D (31.1%) followed by G12V (22.3%), G12C (6.2%), and G12R (5.1%), while G13D (13.8%) was the predominant mutation in codon 13. In TMB-High tumors, which were detected in 12% of patients, the mutation rate of KRAS was modestly lower compared to TMB-Low tumors (42.3% vs. 53.3%). Frequent genes with amplification were MYC (6.7%), MDM2 (5.9%), GATA6 (5.5%), CCND1 (3.4%), FGF19 (3.3%), and ERBB2 (2.3%). The number of any gene amplification was lower in MSI-High compared to TMB-High population. Conclusions: RWD from clinical panel testing revealed the genomic landscape in small intestine cancer and differences in CGP according to clinical or genomic background. These findings would provide insight on the direction of the future development of the treatment in advanced small intestine cancer.[Table: see text]

Genomic Profiling of Combined Hepatocellular Cholangiocarcinoma Reveals Genomics Similar to Either Hepatocellular Carcinoma or Cholangiocarcinoma

PURPOSE

Combined hepatocellular cholangiocarcinoma (cHCC-CCA) is a rare, aggressive primary liver carcinoma, with morphologic features of both hepatocellular carcinomas (HCC) and liver cholangiocarcinomas (CCA).

METHODS

The genomic profiles of 4,975 CCA, 1,470 HCC, and 73 cHCC-CCA cases arising from comprehensive genomic profiling in the course of clinical care were reviewed for genomic alterations (GA), tumor mutational burden, microsatellite instability status, genomic loss of heterozygosity, chromosomal aneuploidy, genomic ancestry, and hepatitis B virus status.

RESULTS

In cHCC-CCA, GA were most common in TP53 (65.8%), TERT (49.3%), and PTEN (9.6%), and 24.6% cHCC-CCA harbored potentially targetable GA. Other GA were predominantly associated with either HCC or CCA, including, but not limited to, TERT, FGFR2, IDH1, and presence of hepatitis B virus. On the basis of these features, a machine learning (ML) model was trained to classify a cHCC-CCA case as CCA-like or HCC-like. Of cHCC-CCA cases, 16% (12/73) were ML-classified as CCA-like and 58% (42/73) cHCC-CCA were ML-classified as HCC-like. The ML model classified more than 70% of cHCC-CCA as CCA-like or HCC-like on the basis of genomic profiles, without additional clinico-pathologic input.

CONCLUSION

These findings demonstrate the use of ML for classification as based on a targeted exome panel used during routine clinical care. Classification of cHCC-CCA by genomic features alone creates insights into the biology of the disease and warrants further investigation for relevance to clinical care.

Prediction and characterization of diffuse large B-cell lymphoma cell-of-origin subtypes using targeted sequencing

The aim of the present study was to determine cell of origin (COO) from a platform using a DNA-based method, COO DNA classifier (COODC). A targeted exome-sequencing platform that applies the mutational profile of a sample was used to classify COO subtype. Two major mutational signatures associated with COO were identified: Catalogue of Somatic Mutations in Cancer (COSMIC) signature 23 enriched in activated B-cell (ABC) and COSMIC signature 3, which suggested increased frequency in germinal center B-cell (GCB). Differential mutation signatures linked oncogenesis to mutational processes during B-cell activation, confirming the putative origin of GCB and ABC subtypes. Integrating COO with comprehensive genomic profiling enabled identification of features associated with COO and demonstrated the feasibility of determining COO without RNA.

Surgery school-who, what, when, and how: results of a national survey of multidisciplinary teams delivering group preoperative education

Background

Group education is increasing in popularity as a means of preparing patients for surgery. In recent years, these ‘surgery schools’ have evolved from primarily informing patients of what to expect before and after surgery, to providing support and encouragement for patients to ‘prehabilitate’ prior to surgery, through improving physical fitness, nutrition and emotional wellbeing.

Method

A survey aimed at clinicians delivering surgery schools was employed to capture a national overview of activity to establish research and practice priorities in this area. The survey was circulated online via the Enhanced Recovery after Surgery UK Society and the Centre for Perioperative Care mailing lists as well as social media.

Results

There were 80 responses describing 28 active and 4 planned surgery schools across the UK and Ireland. Schools were designed and delivered by multidisciplinary teams, contained broadly similar content and were well attended. Most were funded by the National Health Service. The majority included aspects of prehabilitation most commonly the importance of physical fitness. Seventy five percent of teams collected patient outcome data, but less than half collected data to establish the clinical effectiveness of the school. Few describe explicit inclusion of evidence-based behavior change techniques, but collaboration and partnerships with community teams, gyms and local charities were considered important in supporting patients to make changes in health behaviors prior to surgery.

Conclusion

It is recommended that teams work with patients when designing surgery schools and use evidence-based behavior change frameworks and techniques to inform their content. There is a need for high-quality research studies to determine the clinical effectiveness of this type of education intervention.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13741-021-00188-2.

Ancestral characterization of the genomic landscape, comprehensive genomic profiling utilization, and treatment patterns may inform disparities in advanced prostate cancer: A large-scale analysis

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Background: Prostate cancer (PCa) incidence, mortality, and outcomes vary widely across race/ethnicity. The underlying drivers of these differences are multifactorial, including systemic barriers that lead to wide variation in access to care including genomic and precision medicine. Men of African ancestry (AFR) are particularly underrepresented in genomic and precision medicine studies. Therefore, we sought to comprehensively assess patterns of gene alterations, comprehensive genomic profiling (CGP) utilization, and treatment patterns in a large, diverse advanced PCa cohort. Methods: 11,741 PCa patients with CGP, as part of routine clinical care (Foundation Medicine Inc., FMI) were evaluated for their genomic landscape. Predominant ancestry was inferred using a SNP-based approach (Connelly et al, AACR 2018). Independently, the US-based de-identified Flatiron Health (FH)-FMI clinico-genomic database (CGDB) of 897 evaluable PCa patients was also queried. Clinical characteristics and treatment selections were described for patients who received metastatic or castrate-resistant diagnosis between 1/2011 and 6/2020. Results: The FMI cohort included 1,422 (12%) men of AFR and 9,244 (79%) men of European ancestry (EUR). Median age was lower in AFR compared with EUR men (64 vs. 67, p < 0.001). TP53 and PTEN alterations and TMPRSS2-ERG rearrangements occurred less frequently in AFR than EUR men (35% vs. 43%, 21% vs. 33%, 15% vs. 33% respectively, p < 0.05). In contrast, alterations in SPOP (11.9% vs. 7.3%), CDK12 (10.0% vs. 5.2%), CCND1 (6.0% vs. 3.8%), KMT2D (7.7% vs. 5.1%), HGF (4.1% vs. 2.5%), and MYC (13.4% vs. 10.6%) were enriched in the AFR cohort (p < 0.05). Alteration frequency in BRCA1/2, AR, DNA damage response pathway genes, and actionable genes with therapy implications, were similar across ancestry. Of note, BRAF alterations were slightly enriched in AFR (5.0% vs. 3.2%, p < 0.05). In the CGDB cohort (79 AFR, 762 EUR), AFR men received a median of 2 lines of therapy prior to CGP, compared to 1 line for EUR men. Notably, the proportion of patients receiving immunotherapy and PARPi was similar across ancestry, however AFR men were less likely to receive clinical study drug compared with EUR men (11% vs 30%, p < 0.001), even among men with actionable alterations (1% vs 6%, p < 0.001). Conclusions: To our knowledge, this study encompasses the largest cohort, particularly of AFR men in a genomic study, that defines CGP utilization, the genomic landscape and therapeutic implications of CGP in PCa across ancestry. Overall, there were largely similar rates of actionable gene alterations across ancestry. Notably, AFR men were less likely to receive CGP earlier in their treatment course, and less likely to be treated on clinical trials, which could impact the genomic landscape, outcomes, and ultimately disparities.

Genomic alterations for novel targeted therapies in pancreatobiliary cancers from real-world data

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Background: Cancers of the pancreas and biliary tract remain one of the unfavorable malignant tumors with few driver genomic alterations. Tumor-agnostic approaches are promising for cancers with poor prognosis, with some potentially actionable alterations, such as BRCA1/2 mutations, ERBB2 amplification, MSI-High, or tumor mutational burden (TMB)-High. However, co-existing alterations, clinical significance of other genomic alterations, or frequency of alterations by clinical and genomic background are unclear. Here we investigated the genomic profile in a large cohort of advanced pancreatobiliary cancers to help refine and discover new targets for improved cancer therapies. Methods: Comprehensive genomic profiling was performed at Foundation Medicine, on patients with RWD tested during the course of routine clinical care. Hybrid capture was carried out on up to 395 cancer-related genes and select introns from up to 31 genes frequently rearranged in cancer. 16,913 pancreatic cancer (PC) patients and 3,031 biliary tract cancer (BTC) patients were available for analyses and were stratified by age (≥40/ < 40), MSI status, TMB status (High ≥10/Low < 10 Muts/Mb), and select gene alterations. Using a chi-square test with Yate’s correction, frequencies of genetic alterations were analyzed according to clinical or genomic background. Results: KRAS (84.8%), TP53 (73.3%), CDKN2A (51.2%), CDKN2B (26.5%), and SMAD4 (23.2%) were frequently altered in PC patients, versus TP53 (60.6%), CDKN2A (33.5%), KRAS (27.1%), CDKN2B (20.6%) and SMAD4 (16.9%) in BTC patients. The frequency of MSI-High and TMB-High in BTC was 1.2% and 5.7%, respectively, while these were lower in PC (0.48% and 2.1%, respectively). In PC patients, the KRAS alteration rate was significantly lower in both MSI-High (57.3%, P< 0.001) and TMB-High populations (51.3%, P< 0.001). In BTC patients, the rate of ERBB2 amplification was 6.4% in TMB-High and 8.6% in TMB-Low population. Interestingly, CDK12 rearrangement was observed in BTC patients with ERBB2 amplified tumors but not in those without ERBB2 amplified tumors. In patients of pediatric/adolescents and young adults ( < 40 years old), the mutation rate of KRAS/ TP53/ CDKN2A/ SMAD4 was lower, and FGFR2 rearrangement (4%) was observed in PC patients; GATA6 amplification (11.1%) and rearrangement of BRAF (2.8%), FGFR2 (5.6%) were observed in BTC patients. Conclusions: A large real-world dataset showed differences in genomic landscape according to clinical or genomic background, and some potential targets for the development of novel drugs in advanced pancreatobiliary cancers. These findings may lead to the improvement of cancer therapies in PC and BTC patients with poor prognosis.

Somatic HLA Class I Loss Is a Widespread Mechanism of Immune Evasion Which Refines the Use of Tumor Mutational Burden as a Biomarker of Checkpoint Inhibitor Response

Neoantigen presentation arises as a result of tumor-specific mutations and is a critical component of immune surveillance that can be abrogated by somatic LOH of the human leukocyte antigen class I (HLA-I) locus. To understand the role of HLA-I LOH in oncogenesis and treatment, we utilized a pan-cancer genomic dataset of 83,644 patient samples, a small subset of which had treatment outcomes with immune checkpoint inhibitors (ICI). HLA-I LOH was common (17%) and unexpectedly had a nonlinear relationship with tumor mutational burden (TMB). HLA-I LOH was frequent at intermediate TMB, yet prevalence decreased above 30 mutations/megabase, suggesting highly mutated tumors require alternate immune evasion mechanisms. In ICI-treated patients with nonsquamous non-small cell lung cancer, HLA-I LOH was a significant negative predictor of overall survival. Survival prediction improved when combined with TMB, suggesting TMB with HLA-I LOH may better identify patients likely to benefit from ICIs. SIGNIFICANCE: This work shows the pan-cancer landscape of HLA-I LOH, revealing an unexpected "Goldilocks" relationship between HLA-I LOH and TMB, and demonstrates HLA-I LOH as a significant negative predictor of outcomes after ICI treatment. These data informed a combined predictor of outcomes after ICI and have implications for tumor vaccine development.This article is highlighted in the In This Issue feature, p. 211.

Antibacterial activity of disulfiram and its metabolites

AIMS

Disulfiram (Antabuse™) and its metabolites formed in vivo were evaluated as antibacterial agents against thirty species of Gram-positive and Gram-negative bacteria. The synergistic potential of disulfiram (DSF) and metabolite diethyldithiocarbamate (DDTC) with approved antibiotics were also compared by isobologram (checkerboard) analysis.

METHODS AND RESULTS

Standard microdilution susceptibility testing showed that most DSF metabolites did not possess appreciable antibacterial activity except for DDTC in Bacillus anthracis. Checkerboard studies revealed similarities between the combination drug effects of DSF and DDTC with standard antibiotics.

CONCLUSIONS

It was concluded from the susceptibility data that the metabolites would not extend the antibacterial spectrum of DSF in vivo. The data also suggest that the DDTC by-product of DSF metabolism potentiates the antibacterial activity of DSF as both a standalone and combination agent.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides a greater understanding of the antibacterial effects of Antabuse and its metabolites. This research also demonstrates the potential application of DSF as an antibiotic adjuvant for the treatment of resistant staph infections.

Automated electrotransformation of Escherichia coli on a digital microfluidic platform using bioactivated magnetic beads

This paper reports on the use of a digital microfluidic platform to perform multiplex automated genetic engineering (MAGE) cycles on droplets containing Escherichia coli cells. Bioactivated magnetic beads were employed for cell binding, washing, and media exchange in the preparation of electrocompetent cells in the electrowetting-on-dieletric (EWoD) platform. On-cartridge electroporation was used to deliver oligonucleotides into the cells. In addition to the optimization of a magnetic bead-based benchtop protocol for generating and transforming electrocompetent E. coli cells, we report on the implementation of this protocol in a fully automated digital microfluidic platform. Bead-based media exchange and electroporation pulse conditions were optimized on benchtop for transformation frequency to provide initial parameters for microfluidic device trials. Benchtop experiments comparing electrotransformation of free and bead-bound cells are presented. Our results suggest that dielectric shielding intrinsic to bead-bound cells significantly reduces electroporation field exposure efficiency. However, high transformation frequency can be maintained in the presence of magnetic beads through the application of more intense electroporation pulses. As a proof of concept, MAGE cycles were successfully performed on a commercial EWoD cartridge using variations of the optimal magnetic bead-based preparation procedure and pulse conditions determined by the benchtop results. Transformation frequencies up to 22% were achieved on benchtop; this frequency was matched within 1% (21%) by MAGE cycles on the microfluidic device. However, typical frequencies on the device remain lower, averaging 9% with a standard deviation of 9%. The presented results demonstrate the potential of digital microfluidics to perform complex and automated genetic engineering protocols.

Homo- and Co-Polycarbonates and Blends Derived from Diphenolic Acid

The properties of materials derived from diphenolic acid (4-(bis(hydroxyphenyl))pentanoic acid, DPA), such as polycarbonate homo- and co-polymers (with bisphenol A, BPA), have been determined. The influence of copolymer composition on the thermal properties of these materials has been determined. Blends of polycarbonates from BPA and from DPA appear to be compatible.

SU-F-BRCD-06: Multiple Anatomy Optimization of Accumulated Dose

PURPOSE

Multiple anatomy optimization (MAO) utilizing deformable dose accumulation on entire 4DCT data sets is implemented to overcome ambiguity between optimal dose defined on a single anatomy and optimal accumulated dose resulting from dose delivery to moving and deforming anatomy.

METHODS

Six lung cancer patients are planned using two methods of radiotherapy optimization: the internal target volume (ITV) envelope method and MAO, which simultaneously optimizes a single fluence for delivery to all 10 breathing phases such that the accumulated dose satisfies the plan objectives. Target dose is constrained to 70 Gy. The ITV-plan is optimized on a single breathing phase with the planning target volume defined as the ITV; the MAO target is the moving CTV. MAO is compared to single image ITV optimization based on the accumulated dose assuming equal monitor-units to each phase. Dose-volume differences between single image estimations and 10-image accumulation are examined.

RESULTS

Single image optimal dose distributions overestimate target V70 by 4.2%±3.1% (average, one standard deviation) and in five of six cases ipsilateral lung V20 is underestimated (1.4%±0.9%). For these five cases, MAO increases V70 by 2.8%±2.5% (maximum of 6% increase in V70) and reduces ipsilateral lung V20 by up to 3% (average decrease of 1.2%±1.3%). Contralateral lung V20, esophagus V25, and heart V30 are also reduced by up to 5%, 3%, and 3%. For the sixth case, lung tumor motion is on the order of the dose voxel size (3mm), and MAO did not improve upon the ITV plan.

CONCLUSIONS

Dose-volume optimization on a stationary image does not ensure accumulated dose coverage to the moving CTV. Multiple anatomy optimization can remove dose ambiguity and improve plan quality. P01CA11602 and Philips Medical Systems.

Patient safety incidents associated with obesity: a review of reports to the National Patient Safety Agency and recommendations for hospital practice

BACKGROUND

The incidence and prevalence of obesity are increasing world wide. In the UK, obesity governmental strategy has primarily focused on prevention measures, with less focus on the demands of treating obese patients in hospital. Increasing service demand by obese patients coupled with a lack of adequate provision for care of these patients may lead to an increase in patient safety incidents. By classifying patient safety incidents associated with obesity reported to the National Patient Safety Agency, this report aims to identify areas for improvement in the quality and safety of care of the obese patient.

METHODS

A search of the National Reporting and Learning System database was conducted for all incidents caused by or relating to obesity for the period 1 January 2005 to 31 August 2008. The keywords 'obesity', 'overweight', 'BMI' (body mass index), and 'bariatric' were used. The relevant free text fields of the resulting set of incidents were then searched for the terms designed to isolate incidents occurring in anaesthesia, critical care, and surgery. Reported incidents were analysed and subsequently categorised to identify incident themes. Levels of harm were also established.

RESULTS

555 patient safety incidents were identified; 388 met inclusion criteria for analysis. 148 incidents were related to assessment, diagnosis or treatment, 213 related to infrastructure and 27 related to staffing. The majority of incidents were classified as no or low harm. Three deaths were reported, all within the domain of anaesthesia.

CONCLUSIONS

This report identifies that the majority of safety incidents associated with obesity were related to infrastructure, suggesting that there is inadequate provision in place for the care of obese patients. While levels of harm were mostly low, the occurrence of incidents resulting in severe harm or death highlights the specific dangers associated with the care of the obese patient. A global approach to improving the safety of care delivery for obese patients is recommended, including obesity specific training, management structures, care pathways, and equipment provisioning.Further planning and development of operation policies is needed to ensure the safe delivery of healthcare to obese patients in the future.

Excellence in teaching for promotion and tenure in animal and dairy sciences at doctoral/research universities: a faculty perspective

In this study, animal or dairy sciences faculty from doctoral/research universities were surveyed to clarify teaching performance expectations for the purpose of promotion and tenure of assistant professors. A survey tool including 15 evaluation criteria was available online and at the registration desk of the 2005 Joint Annual Meeting of the American Dairy Science Association and the American Society of Animal Science. The analyzed data set included 47 faculty (41 tenured and 6 tenure-track) with a substantial teaching responsibility from 27 different departments in 25 states. Four criteria were perceived as currently overemphasized: student evaluation of the instructor, student evaluation of the course, authoring peer-reviewed publications, and authoring an undergraduate textbook or book chapter. Nevertheless, more than 50% of respondents reported that these criteria should be used. One criterion emerged as being currently underemphasized: documentation of personal assessment of one's own teaching by preparing a portfolio. The lack of consensus for the remaining 10 items may have reflected substantial differences in institutional practices. The significance of overemphasis or underemphasis of certain criteria varied substantially depending on the respondent's perceived institutional mission. When asked about recognition within their department, 68% of respondents indicated that efforts in teaching improvement were properly rewarded. Respondents doubted the meaningfulness and appropriateness of student ratings tools as currently used. Results also suggested that animal and dairy science faculty placed a higher value on criteria recognizing excellence in teaching based on intradepartmental recognition (e.g., interactions with close-up peers and students) rather than recognition within a broader community of scholars as evidenced by authorship or success in generating funding for teaching. Proposed improvements in the evaluation of teaching for promotion and tenure include 1) providing tenure-track faculty with written guidelines at the time of hiring; 2) ensuring that student ratings tools are reliable and valid; 3) carefully mentoring new faculty within the departmental and institutional culture; and 4) encouraging self-reflection and documentation of attempts to address pedagogical issues in one's own teaching. Educational leaders in doctoral/research universities should promote changes to enhance teaching performance of future faculty graduating from their institutions.

Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin

Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), probably because of the more open structure of (beta)-chitin. When exposed to different types of chitin, V. harveyi excreted several chitin-degrading proteins into the culture media. Some chitinases were present with all of the tested chitins, while others were unique to a particular chitin. We cloned and identified six separate chitinase genes from V. harveyi. These chitinases appear to be unique based on DNA restriction patterns, immunological data, and enzyme activity. This marine bacterium and probably others appear to synthesize separate chitinases for efficient utilization of different forms of chitin and chitin by-products.

H-gene-mediated resistance to Hessian fly exhibits features of penetration resistance to fungi

Features shared by host-specific phytophagous insects and biotrophic plant pathogens include gene-for-gene interactions and the ability to induce susceptibility in plants. The Hessian fly shows both. To protect against Hessian fly, grasses have H genes. Avirulent larvae die on H-gene-containing resistant plants but the cause of death is not known. Imaging techniques were used to examine epidermal cells at larval attack sites, comparing four resistant wheat genotypes (H6, H9, H13, and H26) to a susceptible genotype. Present in both resistant and susceptible plants attacked by larvae were small holes in the tangential cell wall, with the size of the holes (0.1 microm in diameter) matching that of the larval mandible. Absent from attacked resistant plants were signs of induced susceptibility, including nutritive tissue and ruptured cell walls. Present in attacked resistant plants were signs of induced resistance, including cell death and fortification of the cell wall. Both presumably limit larval access to food, because the larva feeds on the leaf surface by sucking up liquids released from ruptured cells. Resistance was associated with several subcellular responses, including elaboration of the endoplasmic reticulum-Golgi complex and associated vesicles. Similar responses are observed in plant resistance to fungi, suggesting that "vesicle-associated penetration resistance" also functions against insects.

Synthesis and characterization of fluorescent displacers for online monitoring of displacement chromatography

One of the major impediments to the implementation of displacement chromatography for the purification of biomolecules is the need to collect fractions from the column effluent for time-consuming offline analysis. The ability to employ direct online monitoring of displacement chromatography would have significant implications for applications ranging from analytical to preparative bioseparations. To this end, a set of novel fluorescent displacers were rationally designed using known chemically selective displacers as a template. Fluorescent cores were functionalized with different charge moieties, creating a homologous library of displacers. These compounds were then tested on two protein pairs, alpha-chymotrypsinogen A/ribonuclease A and cytochrome c/lysozyme, using batch and column displacement experiments. Of the synthesized displacers, two were found to be highly selective while one was determined to be a high-affinity displacer. Column displacements using one of the selective displacers yielded complete separation of both protein pairs while facilitating direct online detection using UV and fluorescence detection. Saturation transfer difference NMR was also carried out to investigate the binding of the fluorescent displacers to proteins. The results indicated a selective binding between the selective displacers and alpha-chymotrypsinogen A, while no binding was observed for ribonuclease A, confirming that protein-displacer binding is responsible for the selectivity in these systems. This work demonstrates the utility of fluorescent displacers to enable online monitoring of displacer breakthroughs while also acting as efficient displacers for protein purification.

A simple radon chamber for educational use

Radon chambers are typically able to maintain a constant, known concentration of radon by pumping a constant activity concentration of radon gas into the chamber. A radon chamber has been designed by placing a radon source inside the chamber volume and allowing radon to build up inside the chamber. Because the radon concentration is not constant, calculations have been made to determine the integrated equivalent constant radon concentration in MBqhm for up to 4 d. The chamber, made by placing a radium dial inside an incubator, has interior dimensions of 87.6 cm x 55.9 cm x 51.4 cm for a total volume of 0.25 m. The chamber can produce an integrated equivalent constant radon activity concentration level of 0.013 MBq h m over the initial 24 h, 0.043 MBq h m over the initial 48 h, 0.078 MBq h m over the initial 72 h, and 0.118 MBq h m over the initial 96 h. The chamber can also demonstrate, for educational purposes, the kinetics of the build-up of a radioactive gas in an enclosed environment as well as the kinetics of washout and leakage.

Soybean hulls as an alternative feed for horses

Soybean hulls have been successfully fed to ruminant animals as an economical substitute for hay. This feedstuff is a source of highly digestible fiber that does not contain starch. The purpose of this trial was to evaluate soybean hulls as a replacement fiber in horse diets. Four cecally cannulated Quarter Horse geldings, aged 6 to 10 yr and averaging 502 kg, were used in a 4 x 4 Latin square design with 21-d periods. Diets consisted of alfalfa/bromegrass hay (14.4% CP, 58.1% NDF, 39.1% ADF; DM basis) with the replacement of either 0, 25, 50, or 75% (as-fed basis) unpelleted soybean hulls (13.1% CP, 60.6% NDF, 43.7% ADF; DM basis). Diets were offered at 1.8% of BW (DM) daily and body weights were measured weekly. Cecal samples (90 min after feeding) and total fecal collections (3 d) were taken at the end of each treatment period. Fecal collection bags were emptied every 6 h and 10% of the total amount was frozen for later analysis. Total cecal VFA production increased linearly (P = 0.02) from 70 mM to 109 mM as proportions of soybean hulls in diets increased. Proportions of propionate increased linearly (P < 0.01) with means of 15.7, 18.0, 16.6, and 21.9 mol/100 mol total VFA for the 0, 25, 50, and 75% soybean hulls diets respectively. Proportions of butyrate decreased linearly (P < 0.01) from 5.3 to 3.9 mol/100 mol total VFA. The acetate:propionate ratio decreased linearly (P = 0.02) and cubically (P = 0.03) with means of 4.9, 4.2, 4.9, and 3.3. Apparent digestibility of DM (P = 0.95), OM (P = 0.70), NDF (P = 0.34), ADF (P = 0.31), cellulose (P = 0.93), and hemicellulose (P = 0.25) did not differ among treatments. Apparent digestibility of N decreased linearly (P < 0.01) as concentrations of soybean hulls increased in the diet, and this response was associated with increased cecal fermentation and microbial biomass production. Cecal pH decreased linearly (P = 0.01) from 7.00 to 6.45 as the level of soybean hulls increased, but there was no change (P = 0.68 for the linear effect) for cecal ammonia (mean concentration of 3.85 mM). Soybean hulls stimulate cecal fermentation and are a suitable replacement for hay in equine diets.

Botulinum toxin injection inhibits myogenic tone and sympathetic nerve function in the porcine internal anal sphincter

OBJECTIVE

Botulinum toxin is an effective treatment for anal fissure, though there is a lack of agreement over the optimal site for its injection. This reflects our current ignorance of its mechanism, and whether it has any action on the nerves of the internal anal sphincter (IAS). This study set out to resolve this issue through use of a pig model.

MATERIALS AND METHODS

Eight pigs were studied in pairs: one of each pair received a botulinum toxin injection into the anal sphincter, whilst the other acted as its control. Manometry was performed every two weeks under anaesthesia. Pigs were slaughtered at between four and six weeks after injection and the properties of the IAS compared in vitro.

RESULTS

Whilst maximum anal resting pressure (MARP) increased slowly in control pigs during the experimental period, reflecting weight gain, a fall was observed in treated pigs. In vitro, IAS strips from control pigs generated 400 mg of spontaneous tone per gram of tissue (+/- 45; standard error), compared to 250 (+/- 25) mg/g tissue from treated pigs (P < 0.01). Electric Field Stimulation at 50 Hz produced 150 (+/- 22) mg contraction/gram tissue in IAS strips from control pigs compared to 53 (+/- 13) mg/g tissue in treated pigs (P < 0.0005). This contractile response was blocked by guanethidine.

CONCLUSION

Botulinum toxin has a significant action on the IAS. It reduces myogenic tone and contractile responses of this tissue to sympathetic nerve stimulation. Further studies are required to clarify its mechanism of action more precisely.

By-product feeds for meat goats: effects on digestibility, ruminal environment, and carcass characteristics

Crossbred wether goats (n = 24; 50% Boer, 6 per diet) initially averaging 27.4+/-0.4 kg were fed either wheat middlings (wheat midds), soybean hulls (soyhulls), or corn gluten feed at 1% BW (as-fed) along with orchardgrass hay (10.7% CP) offered to ad-libitum consumption for 72 d followed by 5 d total fecal collection. The Control (hay) diet was supplemented with 5.7% soybean meal to bring total dietary protein to 12.5%, by-products were brought to a higher Ca:P ratio with limestone or dicalcium phosphate to make total dietary Ca:P 1.5:1, and soybean meal was added to soyhulls to bring them up to 17% CP (wheat midds = 17% and corn gluten feed = 21% CP). Total DMI (916 g/d+/-57 or 3.2%+/-0.2 BW) did not differ (P > 0.92) among treatments. Initial BW (P = 0.25), final BW (P = 0.48), and ADG (P = 0.56) did not differ for the four treatments. Carcass weight was greater (P = 0.05) for goats fed soyhulls (16.0 kg) or wheat midds (15.6 kg) as compared with goats fed the hay diet (14.5 kg), with carcass weight from goats fed corn gluten feed being intermediate (15.3 kg, SEM = 0.3 kg). Carcass grade did not differ (P = 0.80) and averaged 5.42+/-0.4. Dressing percentage tended (P = 0.12) to be lower for goats fed the hay diet (46.4%) compared with soyhull (48.3%), corn gluten feed (48.3%), or wheat midd (48.8%) diets (SEM = 0.7). Ruminal pH was highest (P < 0.01) for goats fed the hay diet (6.52) and lowest for goats fed wheat midds (6.23) with soyhull (6.41) and corn gluten feed diets (6.35) being intermediate (SEM = 0.05). Digestibility of DM (70.1+/-2.5%), OM (70.3+/-2.6%,), CP (75.5+/-2.0%), GE (68.5+/-2.7%), NDF (68.1+/-3.0%), ADF (65.4+/-3.4%), cellulose (70.1+/-2.9%), and lignin (31.1+/-8.2%) did not differ (P > 0.15). Total ruminal VFA did not differ (86.0+/-6.1 mM, P = 0.59), but acetate:propionate ratio was higher (P < 0.01) for hay (3.1) and soyhull diets (3.3) than for corn gluten feed (2.4) and wheat midd diets (2.4, SEM = 0.11). Ruminal ammonia (mg/100 mL) was lower (P < 0.01) for goats fed hay (15.4) and soyhull diets (11.6) than those fed corn gluten feed (25.2) and wheat midd diets (23.0, SEM = 1.35). Ruminal pH was lower for goats fed the byproducts, but remained above 6. Serum urea nitrogen (mg/100 mL) averaged 21.0+/-1.0 (P = 0.11) with soyhulls tending to be lowest (19.3) and corn gluten feed tending to be highest (22.8). Soyhulls, corn gluten feed, and wheat midds appear to be viable feed ingredients for meat goat diets.

Stationary phase effects on the dynamic affinity of low-molecular-mass displacers

In this paper, the selectivity of a variety of cation-exchange stationary phases was investigated using a homologous series of displacer molecules based on pentaerythritol. These displacers were derived from pentaerythritol and contained either four trimethyl ammonium groups [pentaerythrityl-(trimethylammonium chloride)4, PE(TMA)4], benzene rings [pentaerythrityl-(benzyl dimethylammonium chloride)4, PE(DMABzCl)4], heptyl groups [pentaerythrityl-(heptyl dimethylammonium iodide)4, PE(DMAHepI)4] or cyclohexyl groups [pentaerythrityl-(cyclohexyl dimethylammonium iodide)4, PE(DMACyI)4]. This series enabled us to probe the secondary interactions that can play a role in the affinity of low-molecular-mass displacers for different stationary phases. The relative affinities of these displacers were examined using a displacer ranking plot based on the steric mass action (SMA) isotherm model. While hydrophobicity and aromaticity played important roles in generating the affinity to the hydrophilized polystyrene-divinylbenzene (Source 15S) and polymethacrylate-based (Toyopearl 650M) resins, these secondary interactions had a minimal impact on the selectivity in agarose resins coated with dextran (SP Sepharose XL), "gel in a shell" (S Ceramic HyperD F), and monolithic (Bio-Rad Uno S6) cation-exchange materials. Further, the results with a tentacular stationary phase (Fractogel EMD) suggest that the alkyl chains on PE(DMAHepI)4 play an important role in increasing the affinity, possibly because of strong interactions between the alkyl moiety and the polymer matrix as well as between the charged groups and the polyelectrolyte tentacles. The results of this study provide insight into the design of high affinity, low-molecular-mass displacers for different cation-exchange stationary phase materials.

Net absorption and utilization of nitrogenous compounds across ruminal, intestinal, and hepatic tissues of growing beef steers fed dry-rolled or steam-flaked sorghum grain

Our objectives were to determine effects of grain processing on splanchnic (gut tissues and liver) N metabolism and whole-body N balance by growing steers and to ascertain the relative contributions of ruminal and intestinal tissues to net absorption and utilization of N-containing nutrients. Seven beef steers (348 kg initial BW), surgically implanted with appropriate catheters, were fed diets containing 77% steam-flaked (SF) or dry-rolled (DR) sorghum grain. Blood flows and net output or uptake of ammonia N, urea N, and alpha-amino N (estimate of amino acids) were measured across portal-drained viscera (PDV or gut tissues) and intestinal, ruminal, hepatic, and splanchnic tissues (PDV + hepatic). The experimental design was a crossover between DR and SF diets, with six samplings of blood at 2-h intervals on 2 d for each steer. Nitrogen intake (139 +/- 3 g/d), output in urine (43 +/- 2 g/d), and retention (40 +/- 3 g/d) were similar for both processing treatments. When steers were fed SF sorghum compared to DR sorghum, N retention as a percentage of N intake was numerically greater (P < 0.12), output of fecal N was numerically lower (P < 0.13), and urinary urea N was lower (P < 0.04). For SF vs DR, net uptake of alpha-amino N by liver was higher (P < 0.04; 20 vs 9 g/d) and was numerically lower (P < 0.16) for ruminal tissues (15 vs 33 g/d). Feeding steers SF compared to DR tended to increase net transfer (cycling) of blood urea N to PDV (57 vs 41 g/d; P < 0.07), increased cycling to intestinal tissues (15 vs 6 g/d; P < 0.05), and numerically increased transfer to ruminal tissues (42 vs 32 g/d; P < 0.12) but did not alter other net output or uptake of N across splanchnic tissues. Total urea N transfer (blood + saliva) was similar for both treatments. Net uptake of alpha-amino N by ruminal tissues was about 30% of the net amount of alpha-amino N absorbed across the intestinal tissues. In summary, most of the blood urea N cycled from the liver to gut tissues was transferred to ruminal tissues for potential microbial protein synthesis, and the net ruminal utilization of alpha-amino N was about 30% of that absorbed from intestinal tissues. Feeding growing steers SF compared to DR sorghum diets numerically increased whole-body N retention (percentage of N intake) by about 15% and tended to increase transfer of blood urea N to the gut by about 40%, which could increase the supply of high-quality microbial protein for absorption.

Regional estimation of current and future forest biomass

The 90,674 wildland fires that burned 2.9 million ha at an estimated suppression cost of $1.6 billion in the United States during the 2000 fire season demonstrated that forest fuel loading has become a hazard to life, property, and ecosystem health as a result of past fire exclusion policies and practices. The fire regime at any given location in these regions is a result of complex interactions between forest biomass, topography, ignitions, and weather. Forest structure and biomass are important aspects in determining current and future fire regimes. Efforts to quantify live and dead forest biomass at the local to regional scale has been hindered by the uncertainty surrounding the measurement and modeling of forest ecosystem processes and fluxes. The interaction of elevated CO2 with climate, soil nutrients, and other forest management factors that affect forest growth and fuel loading will play a major role in determining future forest stand growth and the distribution of species across the southern United States. The use of satellite image analysis has been tested for timely and accurate measurement of spatially explicit land use change and is well suited for use in inventory and monitoring of forest carbon. The incorporation of Landsat Thematic Mapper data coupled with a physiologically based productivity model (PnET), soil water holding capacity, and historic and projected climatic data provides an opportunity to enhance field plot based forest inventory and monitoring methodologies. We use periodic forest inventory data from the USDA Forest Service's Forest Inventory and Analysis (FIA) project to obtain estimates of forest area and type to generate estimates of carbon storage for evergreen, deciduous, and mixed forest classes for use in an assessment of remotely sensed forest cover at the regional scale for the southern United States. The displays of net primary productivity (NPP) generated from the PnET model show areas of high and low forest carbon storage potential and their spatial relationship to other landscape features for the southern United States. At the regional scale, predicted annual NPP in 1992 ranged from 836 to 2181 g/m2/year for evergreen forests and 769-2634 g/m2/year for deciduous forests with a regional mean for all forest land of 1448 g/m2/year. Prediction of annual NPP in 2050 ranged from 913 to 2076 g/m2/year for evergreen forest types to 1214-2376 g/m2/year for deciduous forest types with a regional mean for all forest land of 1659 g/m2/year. The changes in forest productivity from 1992 to 2050 are shown to display potential areas of increased or decreased forest biomass. This methodology addresses the need for spatially quantifying forest carbon in the terrestrial biosphere to assess forest productivity and wildland fire fuels.

Quenching of biotinylated aequorin bioluminescence by dye-labeled avidin conjugates: application to homogeneous bioluminescence resonance energy transfer assays

[see reaction]. Avidin conjugates containing the covalently attached dyes QSY-7 and dabcyl were prepared and shown to quench the bioluminescence of biotinylated aequorin. Quenching efficiency was shown to be dependent on both the label-to-avidin ratio and the concentration of the avidin conjugate. These properties were exploited to develop a homogeneous bioluminescence resonance energy transfer (BRET) assay for biotin.

Design of Acridinium-9-carboxamides and Anti-acridinium Antibodies for Chemiluminescent Signal Enhancement

A novel system of signal enhancement is presented in which every labeled antibody is capable of generating a signal. Three chemiluminescent acridinium-9-carboxamide haptens (1, 2, and 3) which incorporated differences in charge and location of the linker were designed and synthesized. Anti-acridinium polyclonal antibodies for each hapten were screened using surface plasmon resonance instrumentation to determine specificity for each hapten. Anti-acridinium 2 antibodies were found to be non-cross-reactive to acridinium 1. This property was exploited to design secondary antibody conjugates which would bind to primary antibodies labeled with 2 yet could still be labeled with the structurally similar acridinium 1. Consequently, both layers contributed to the overall chemiluminescent signal. This format is an advance over other signal amplification formats which employ non-signal-generating, labeled antibodies to construct multilayered systems.

Factors influencing blood flow patterns in the human right coronary artery

Evidence suggests that atherogenesis is linked to local hemodynamic factors such as wall shear stress. We investigated the velocity and wall shear stress patterns within a human right coronary artery (RCA), an important site of atherosclerotic lesion development. Emphasis was placed on evaluating the effect of flow waveform and inlet flow velocity profile on the hemodynamics in the proximal, medial, and distal arterial regions. Using the finite-element method, velocity and wall shear stress patterns in a rigid, anatomically realistic model of a human RCA were computed. Steady flow simulations (ReD=500) were performed with three different inlet velocity profiles; pulsatile flow simulations utilized two different flow waveforms (both with Womersley parameter=1.82, mean ReD=233), as well as two of the three inlet profiles. Velocity profiles showed Dean-like secondary flow features that were remarkably sensitive to the local curvature of the RCA model. Particularly noteworthy was the "rotation" of these Dean-like profiles, which produced large local variations in wall shear stress along the sidewalls of the RCA model. Changes in the inlet velocity profiles did not produce significant changes in the arterial velocity and wall shear stress patterns. Pulsatile flow simulations exhibited remarkably similar cycle-average wall shear stress distributions regardless of waveform and inlet velocity profile. The oscillatory shear index was very small and was attributed to flow reversal in the waveform, rather than separation. Cumulatively, these results illustrate that geometric effects (particularly local three-dimensional curvature) dominate RCA hemodynamics, implying that studies attempting to link hemodynamics with atherogenesis should replicate the patient-specific RCA geometry.

8 french transradial coronary interventions: clinical outcome and late effects on the radial artery and hand function

BACKGROUND

Limited information is available on the effects of 8 French (Fr) transradial procedures on radial patency. In addition, the effects of radial procedures and radial occlusion on hand function are unknown.

METHODS

Two groups were recruited: twenty-four patients who had undergone 26 transradial 8 Fr interventions and 16 patients who had undergone 16 transradial 6 Fr procedures. At 1 year, radial patency, hand strength and hand endurance were measured.

RESULTS

No major adverse cardiac events or vascular complications were noted in either group. Late radial occlusion was noted in 2/18 (11%) 8 Fr patients and 3/16 (19%) 6 Fr patients (p = ns). There were no differences in the 8 Fr group between the catheterized and uncatheterized radial arteries for diameter (3.2 +/- 1.1 mm versus 3.3 +/- 0.7 mm, respectively; p = NS) or volumetric flow (55 +/- 51 ml/minute versus 57 +/- 45 ml/minute, respectively; p = NS). No differences in hand strength or hand endurance were seen between the catheterized and uncatheterized arms in the 8 Fr group, between the 8 Fr and 6 Fr groups, or between occluded and non-occluded patients.

CONCLUSION

Transradial use of 8 Fr guiding catheters appears to be feasible and safe in highly selected patients, albeit associated with a low incidence of silent radial occlusion. Additionally, neither the use of 8 Fr sheaths nor the presence of radial artery occlusion appear to adversely affect hand strength or endurance.