Abstract 5614: Genomic aberrations in circulating tumor DNA (ctDNA) and clinical outcomes from [177Lu]Lu-PSMA-617 in metastatic castration-resistant prostate cancer (mCRPC)

[177Lu]Lu-PSMA-617 (LuPSMA) radionuclide therapy improves overall survival in mCRPC, and was recently approved by the FDA. Nevertheless, owing to the heterogeneous nature of mCRPC, responses to LuPSMA therapy can be variable, and resistance is inevitable. As a result, biomarkers linked to clinical outcome with LuPSMA are urgently required. Using plasma ctDNA, we present the first comprehensive genomic analysis of a prospective cohort of mCRPC patients treated with LuPSMA. Targeted sequencing of 78 genes was performed on baseline plasma and matched buffy coat samples from patients who received LuPSMA on a prospective registry (NCT04769817). Reportable alterations included pathogenic single-nucleotide and copy number variants. Association between alterations and clinical outcomes were assessed using log rank, cox proportional, and chi-squared analyses. Clinical data collected included PSA decline by ≥50% or ≥90% (PSA50-response rate, PSA50-RR; and PSA90-RR), and PSA progression free survival (PSA-PFS). In total, 100 patients (median age 74 years, range 52-90) received a median of 4 cycles of LuPSMA. 83 patients had detectable ctDNA (median fraction 17%, range 0-94%) with PSA50-RR 50%, PSA90-RR 22%, and a median PSA-PFS of 7.2 months. Patients with an AR or PTEN aberration had significantly shorter PSA-PFS (HR 0.50 and 0.59, respectively; Table), as did patients with any PI3K pathway aberration (HR 0.56). Additionally, patients with a high ctDNA burden had significantly worse PSA-PFS (HR 0.42, Table). There were no significant differences in PSA-RR based on deleterious genomic changes. Our data reveal that aberrations in the AR and PI3K pathways, along with pre-treatment ctDNA fraction, whilst not linked to PSA-RR, are prognostic for durability of response to LuPSMA. If validated in larger cohorts, these data will help to optimise the use of LuPSMA by improving patient selection and enhancing prognostication.

Analysis of clinical endpoints based on deleterious genomic changes in ctDNA n PSA-PFS (months, wild type (wt) vs variant) PSA-PFS HR (95% CI, wt vs variant) PSA50-RR (wt vs variant) PSA90-RR (wt vs variant) Exonic AR variants 47 8.1 vs 6.0 p=0.005 0.50 (0.30-0.83) p=0.006 58% vs 40% p=0.09 23% vs 21% p=0.8 Any AR variant (intronic and upstream enhancer regions included) 49 8.1 vs 6.0 p=0.007 0.53 (0.31-0.83) p=0.008 60% vs 41% p=0.09 24% vs 20% p=0.7 RB1 variant 19 7.9 vs 5.5 p=0.2 0.67 (0.39-1.2) p=0.2 51% vs 42% p=0.5 23% vs 21% p=0.9 PTEN variant 25 7.8 vs 6.3 p=0.04 0.59 (0.36-1.00) p=0.045 50% vs 48% p=0.9 22% vs 24% p=0.8 TP53 variant 43 8.1 vs 6.7 p=0.1 0.67 (0.42-1.1) p=0.1 52% vs 47% p=0.6 20% vs 26% p=0.5 BRCA2 variant 10 7.7 vs 5.1 p=0.2 0.63 (0.29-1.30) p=0.2 51% vs 40% p=0.7 20% vs 40% p=0.1 PIK3CA variant 8 7.7 vs 4.1 p=0.08 0.48 (0.20-1.1) p=0.09 52% vs 13% p=0.06 23% vs 13% p=0.5 PI3K pathway variant 35 7.8 vs 5.5 p= 0.02 0.56 (0.34-0.91) p=0.02 55% vs 40% p=0.2 22% vs 23% p=0.9 ctDNA fraction ≥20% 43 9.0 vs 5.1 p=0.0002 0.42 (0.26-0.67) p<0.001 55% vs 42% p=0.2 21% vs 23% p=0.8

Citation Format: Heidi Fettke, Louise Kostos, James Buteau, Jason A. Steen, Elizabeth Medhurst, Mo B. Haskali, Declan Murphy, Maria Docanto, Patricia Bukczynska, Nicole Ng, Shahneen Sandhu, Siavash Foroughi, Luc Furic, Tu Nguyen-Dumont, Michael S. Hofman, Arun A. Azad. Genomic aberrations in circulating tumor DNA (ctDNA) and clinical outcomes from [177Lu]Lu-PSMA-617 in metastatic castration-resistant prostate cancer (mCRPC). [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 5614.

Population-based estimates of age-specific cumulative risk of breast cancer for pathogenic variants in ATM

Background

Multigene panel tests for breast cancer predisposition routinely include ATM as it is now a well-established breast cancer predisposition gene.

Methods

We included ATM in a multigene panel test applied to the Australian Breast Cancer Family Registry (ABCFR), a population-based case–control–family study of breast cancer, with the purpose of estimating the prevalence and penetrance of heterozygous ATM pathogenic variants from the family data, using segregation analysis.

Results

The estimated breast cancer hazard ratio for carriers of pathogenic ATM variants in the ABCFR was 1.32 (95% confidence interval 0.45–3.87; P = 0.6). The estimated cumulative risk of breast cancer to age 80 years for heterozygous ATM pathogenic variant carriers was estimated to be 13% (95% CI 4.6–30).

Conclusions

Although ATM has been definitively identified as a breast cancer predisposition gene, further evidence, such as variant-specific penetrance estimates, are needed to inform risk management strategies for carriers of pathogenic variants to increase the clinical utility of population testing of this gene.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13058-022-01518-y.

Independent prognostic impact of plasma NCOA2 alterations in metastatic castration-resistant prostate cancer

BACKGROUND

The androgen receptor (AR) pathway-associated gene nuclear receptor coactivator 2 (NCOA2) has an established oncogenic role in early prostate cancer and likewise is a driver of metastatic disease and castration-resistant prostate cancer. However, its significance as a biomarker in metastatic castration-resistant prostate cancer (mCRPC), both alone and in conjunction with co-occurring AR alterations using a liquid biopsy approach has not been investigated.

METHODS

Ninety-one patients were included in this study, (n = 68 receiving an androgen receptor pathway inhibitor and n = 23 receiving taxane chemotherapy). Up to 30 ml of peripheral blood was collected before commencing treatment from each patient. Plasma cell-free DNA, along with a matched germline sample, underwent targeted next-generation sequencing using a validated, highly sensitive in-house prostate cancer panel. Variants in AR and NCOA2 were identified and correlated with clinical outcomes.

RESULTS

Plasma AR and NCOA2 aberrations were identified in 35% and 13% of the cohort, respectively, whilst 8% had concurrent AR and NCOA2 alterations. NCOA2 copy number gain and any NCOA2 aberration predicted for lower prostate-specific antigen (PSA) response rates. Likewise, median overall survival was shorter for NCOA2 gain (10.1 vs. 18.3 months; p = .004), remaining significant after adjusting for covariates including circulating tumor DNA fraction and tumor suppressor gene alterations. Importantly, dual AR and NCOA2 aberrations were also associated with inferior outcomes, including no PSA responses in patients treated with AR pathway inhibitors (0% vs. 64%; p = .02).

CONCLUSIONS

These data highlight the importance of identifying multiple markers of AR pathway modulation in mCRPC and represent the first instance of the assessment of plasma NCOA2 status as a prognostic biomarker for standard-of-care therapies. Further assessment is warranted to determine if NCOA2 aberrations are a marker of primary resistance to AR pathway inhibitors.

Mismatch repair gene pathogenic germline variants in a population-based cohort of breast cancer

The advent of gene panel testing is challenging the previous practice of using clinically defined cancer family syndromes to inform single-gene genetic screening. Individual and family cancer histories that would have previously indicated testing of a single gene or a small number of related genes are now, increasingly, leading to screening across gene panels that contain larger numbers of genes. We have applied a gene panel test that included four DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6 and PMS2) to an Australian population-based case-control-family study of breast cancer. Altogether, eight pathogenic variants in MMR genes were identified: six in 1421 case-families (0.4%, 4 MSH6 and 2 PMS2) and two in 833 control-families (0.2%, one each of MLH1 and MSH2). This testing highlights the current and future challenges for clinical genetics in the context of anticipated gene panel-based population-based screening that includes the MMR genes. This testing is likely to provide additional opportunities for cancer prevention via cascade testing for Lynch syndrome and precision medicine for breast cancer treatment.

Population-based estimates of the age-specific cumulative risk of breast cancer for pathogenic variants in CHEK2: Findings from the Australian Breast Cancer Family Registry

551

Background: Case-control studies of breast cancer have consistently shown that pathogenic variants in CHEK2 are associated with about a 3-fold increased risk of breast cancer. Information about the recurrent protein truncating variant CHEK2c.1100delC dominates this estimate. There have been no formal estimates of age-specific cumulative risk of breast cancer for all CHEK2 pathogenic (including likely pathogenic) variants combined. Methods: We conducted a genetic screen of CHEK2 in an Australian population-based case-control-family study of breast cancer. This study is focused on disease at an early age and participants were unselected for family history. The age-specific cumulative risk (penetrance) of breast cancer was estimated using segregation analysis. Results: The estimated hazard ratio for carriers of pathogenic CHEK2 variants (combined) was 4.9 (95% CI 2.5-9.5; p < 0.0001) relative to non-carriers. The HR for carriers of the CHEK2 c.1100delC variant was estimated to be 3.5 (95% CI 1.02-11.6) and the HR for carriers of all other CHEK2 variants combined was estimated to be 5.7 (95% CI 2.5-12.9). The age-specific cumulative risk of breast cancer was estimated to be 18% (95% CI 11-30%) and 33% (95% CI 21-48%) to age 60 and 80 years, respectively. Conclusions: These findings provide important information for the clinical management of breast cancer risk for women carrying pathogenic variants in CHEK2.

Abstract PS7-04: Population-based estimates of breast cancer risk for germline pathogenic variants identified by gene-panel testing: An Australian perspective

BRA-STRAP is an Australia-wide study of breast cancer predisposition that brings together gene-panel data from 30,000 adult Australian women of all ages, across the breast cancer risk spectrum, with and without a diagnosis of breast cancer. The “BRA-STRAP panel” includes 24 genes* that are involved in, or putatively associated with, predisposition to breast and/or ovarian cancer. Despite insufficient evidence for clinical translation for some of these genes, all 24 are commonly included on panel tests for breast cancer predisposition.

We present findings from the population-based case-control sub-study of BRA-STRAP, which involved 1451 women diagnosed with breast cancer and 857 age-matched controls participating in the Australian Breast Cancer Family Registry (ABCFR), and 6101 healthy, elderly Australian women enrolled in the ASPREE study. These analyses focus on rare genetic variants predicted to lead to loss of function and/or classified as pathogenic/likely pathogenic (P/LP) in ClinVar. Odds ratios (ORs) for their associations with breast cancer were estimated by aggregating genetic variants for each gene.

For the women diagnosed with breast cancer, the median age at diagnosis (inter-quartile range, IQR) was 40.0 (14.0) years and the overall frequency of P/LP variant carriers across all genes was 156/1451 (10.8%). The median age (IQR) of the ABCFR and ASPREE controls were 39.4 (14.9) and 73.9 (5.8) years, respectively. The frequencies of P/LP variant carriers were 33/857 (3.9%) and 268/6101 (4.4%) in the ABCFR and ASPREE controls, respectively. We combined both control datasets and, after adjusting for age and other potential confounders, the ORs associated with P/LP variants in BRCA1 and BRCA2 were 4.1 [95% confidence interval (CI): 1.8-10.2] and 2.9 [95% CI: 1.5-6], respectively. We also found that the OR for P/LP variants in ATM was 4.0 [95% CI: 1.5-10.4] and the OR for P/LP variants in PALB2 was 2.2 [95% CI: 0.75-5.7] although this did not reach statistical significance.

These results contribute to international efforts to refine the breast cancer risk estimates for genetic variants identified from population-based screening of unselected women using genes that are included on panel tests and thought to be potentially breast cancer predisposition genes.The case-control-family design of the ABCFR will also allow us to estimate the age specific cumulative risk (penetrance) of these genetic variants, which is important for genetic counselling and the clinical management of carrier families.

*ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, FANCM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, RECQL, STK11 and TP53

Citation Format: Tu Nguyen-Dumont, James Dowty, Katherine Tucker, Judy Kirk, Paul James, Alison Trainer, Ingrid Winship, Nicholas Pachter, Nicola Poplawski, Scott Grist, Daniel J Park, Anne-Laure Renault, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Jason A Steen, Derrick Theys, Amanda Rewse, Amanda Willis, April Morrow, Catherine Speechly, Rebecca Harris, Moeen Riaz, Robert Sebra, Eric Schadt, Paul Lacaze, John McNeil, John L Hopper, Melissa C Southey. Population-based estimates of breast cancer risk for germline pathogenic variants identified by gene-panel testing: An Australian perspective [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS7-04.

Fatal respiratory diphtheria caused by β-lactam-resistant Corynebacterium diphtheriae

BACKGROUND

Diphtheria is a potentially fatal respiratory disease caused by toxigenic Corynebacterium diphtheriae. Although resistance to erythromycin has been recognised, β-lactam resistance in toxigenic diphtheria has not been described. Here, we report a case of fatal respiratory diphtheria caused by toxigenic C. diphtheriae resistant to penicillin and all other β-lactam antibiotics and describe a novel mechanism of inducible carbapenem resistance associated with the acquisition of a mobile resistance element.

METHODS

Long-read whole genome sequencing was performed using Pacific Biosciences SMRT sequencing to determine the genome sequence of C. diphtheriae BQ11 and mechanism of β-lactam resistance. To investigate phenotypic inducibility of meropenem resistance, short read sequencing was performed using an Illumina NextSeq500 sequencer on the strain with and without exposure to meropenem.

RESULTS

BQ11 demonstrated high-level resistance to penicillin (benzylpenicillin MIC ≥ 256 μg/ml), β-lactam/β-lactamase inhibitors and cephalosporins (amoxicillin/clavulanic acid MIC ≥ 256 μg/mL; ceftriaxone MIC ≥ 8 μg/L). Genomic analysis of BQ11 identified acquisition of a novel transposon carrying the penicillin binding protein Pbp2c, responsible for resistance to penicillin and cephalosporins. When strain BQ11 was exposed to meropenem, selective pressure drove amplification of the transposon in a tandem array and led to a corresponding change from a low level to high level meropenem resistant phenotype.

CONCLUSIONS

We have identified a novel mechanism of inducible antibiotic resistance whereby isolates that appear to be carbapenem susceptible on initial testing can develop in vivo resistance to carbapenems with repeated exposure. This phenomenon could have significant implications for treatment of C. diphtheriae infection and may lead to clinical failure.

Rare germline genetic variants and risk of aggressive prostate cancer

Few genetic risk factors have been demonstrated to be specifically associated with aggressive prostate cancer (PrCa). Here, we report a case-case study of PrCa comparing the prevalence of germline pathogenic/likely pathogenic (P/LP) genetic variants in 787 men with aggressive disease and 769 with nonaggressive disease. Overall, we observed P/LP variants in 11.4% of men with aggressive PrCa and 9.8% of men with nonaggressive PrCa (two-tailed Fisher's exact tests, P = .28). The proportion of BRCA2 and ATM P/LP variant carriers in men with aggressive PrCa exceeded that observed in men with nonaggressive PrCa; 18/787 carriers (2.3%) and 4/769 carriers (0.5%), P = .004, and 14/787 carriers (0.02%) and 5/769 carriers (0.01%), P = .06, respectively. Our findings contribute to the extensive international effort to interpret the genetic variation identified in genes included on gene-panel tests, for which there is currently an insufficient evidence-base for clinical translation in the context of PrCa risk.

An expanded genomic representation of the phylum cyanobacteria

Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a nonphotosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of population genomes from human gut and groundwater samples. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six diverse population genomes from gut and bioreactor samples supporting the inference that this lineage is nonphotosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer and extends the recognized functionality of members of this phylum.

ST2249-MRSA-III: a second major recombinant methicillin-resistant Staphylococcus aureus clone causing healthcare infection in the 1970s

Typing of healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) from Australia in the 1970s revealed a novel clone, ST2249-MRSA-III (CC45), present from 1973 to 1979. This clone was present before the Australian epidemic caused by the recombinant clone, ST239-MRSA-III. This study aimed to characterize the genome of ST2249-MRSA-III to establish its relationship to other MRSA clones. DNA microarray analysis was conducted and a draft genome sequence of ST2249 was obtained. The recombinant structure of the ST2249 genome was revealed by comparisons to publicly available ST239 and ST45 genomes. Microarray analysis of genomic DNA of 13 ST2249 isolates showed gross similarities with the ST239 chromosome in a segment around the origin of replication and with ST45 for the remainder of the chromosome. Recombination breakpoints were precisely determined by the changing pattern of nucleotide polymorphisms in the genome sequence of ST2249 isolate SK1585 compared with ST239 and ST45. One breakpoint was identified to the right of oriC, between sites 1014 and 1065 of the gene D484_00045. Another was identified to the left of oriC, between sites 1185 and 1248 of D484_01632. These results indicate that ST2249 inherited approximately 35.3% of its chromosome from an ST239-like parent and 64.7% from an ST45-like parent. ST2249-MRSA-III resulted from a major recombination between parents that resemble ST239 and ST45. Although only limited Australian archival material is available, the oldest extant isolate of ST2249 predates the oldest Australian isolate of ST239 by 3 years. It is therefore plausible that these two recombinant clones were introduced into Australia separately.

Pasteurella multocida Heddleston serovar 3 and 4 strains share a common lipopolysaccharide biosynthesis locus but display both inter- and intrastrain lipopolysaccharide heterogeneity

Pasteurella multocida is a Gram-negative multispecies pathogen and the causative agent of fowl cholera, a serious disease of poultry which can present in both acute and chronic forms. The major outer membrane component lipopolysaccharide (LPS) is both an important virulence factor and a major immunogen. Our previous studies determined the LPS structures expressed by different P. multocida strains and revealed that a number of strains belonging to different serovars contain the same LPS biosynthesis locus but express different LPS structures due to mutations within glycosyltransferase genes. In this study, we report the full LPS structure of the serovar 4 type strain, P1662, and reveal that it shares the same LPS outer core biosynthesis locus, L3, with the serovar 3 strains P1059 and Pm70. Using directed mutagenesis, the role of each glycosyltransferase gene in LPS outer core assembly was determined. LPS structural analysis of 23 Australian field isolates that contain the L3 locus revealed that at least six different LPS outer core structures can be produced as a result of mutations within the LPS glycosyltransferase genes. Moreover, some field isolates produce multiple but related LPS glycoforms simultaneously, and three LPS outer core structures are remarkably similar to the globo series of vertebrate glycosphingolipids. Our in-depth analysis showing the genetics and full range of P. multocida lipopolysaccharide structures will facilitate the improvement of typing systems and the prediction of the protective efficacy of vaccines.

In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?

OBJECTIVES

To obtain an expanded understanding of antibiotic resistance evolution in vivo, particularly in the context of vancomycin exposure.

METHODS

The whole genomes of six consecutive methicillin-resistant Staphylococcus aureus blood culture isolates (ST239-MRSA-III) from a single patient exposed to various antimicrobials (over a 77 day period) were sequenced and analysed.

RESULTS

Variant analysis revealed the existence of non-susceptible sub-populations derived from a common susceptible ancestor, with the predominant circulating clone(s) selected for by type and duration of antimicrobial exposure.

CONCLUSIONS

This study highlights the dynamic nature of bacterial evolution and that non-susceptible sub-populations can emerge from clouds of variation upon antimicrobial exposure. Diagnostically, this has direct implications for sample selection when using whole-genome sequencing as a tool to guide clinical therapy. In the context of bacteraemia, deep sequencing of bacterial DNA directly from patient blood samples would avoid culture 'bias' and identify mutations associated with circulating non-susceptible sub-populations, some of which may confer cross-resistance to alternate therapies.

Whole genome sequence analysis of the first Australian OXA-48-producing outbreak-associated Klebsiella pneumoniae isolates: the resistome and in vivo evolution

Whole genome sequencing was used to characterize the resistome of intensive care unit (ICU) outbreak-associated carbapenem-resistant K. pneumoniae isolates. Importantly, and of particular concern, the carbapenem-hydrolyzing β-lactamase gene bla_OXA-48 and the extended-spectrum β-lactamase gene bla_CTX-M-14, were identified on a single broad host-range conjugative plasmid. This represents the first report of bla_OXA-48 in Australia and highlights the importance of resistance gene surveillance, as such plasmids can silently spread amongst enterobacterial populations and have the potential to drastically limit treatment options. Furthermore, the in vivo evolution of these isolates was also examined after 18 months of intra-abdominal carriage in a patient that transited through the ICU during the outbreak period. Reflecting the clonality of K. pneumoniae, only 11 single nucleotide polymorphisms (SNPs) were accumulated during this time-period and many of these were associated with genes involved in tolerance/resistance to antibiotics, metals or organic solvents, and transcriptional regulation. Collectively, these SNPs are likely to be associated with changes in virulence (at least to some extent) that have refined the in vivo colonization capacity of the original outbreak isolate.

In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery

Over the past decade, technological advances in whole genome amplification, microfluidics, flow sorting, and high-throughput sequencing have led to the development of single-cell genomics. Single-cell genomic approaches are typically applied to anonymous microbial cells with only morphology providing clues to their identity. However, targeted separation of microorganisms based on phylogenetic markers, such as the 16S rRNA gene, is beginning to emerge in the single-cell genomics field. Here, we describe an in-solution fluorescence in situ hybridization (FISH) protocol which can be combined with fluorescence-activated cell sorting (FACS) for separation of single cells or populations of interest from environmental samples. Sequencing of DNA obtained from sorted cells can be used for the recovery of draft quality genomes, and when performed in parallel with deep metagenomics, can be used to validate and further scaffold metagenomic assemblies. We illustrate in this chapter the feasibility of this FISH-FACS approach by describing the targeted recovery of a novel anaerobic methanotrophic archaeon.

MicroRNAs and their isomiRs function cooperatively to target common biological pathways

Background

Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for these molecules.

Results

To assess the biological relevance of isomiRs, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline called miRNA-MATE to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. A large proportion of isomiRs potentially derive from AGO2 cleavage independent of Dicer. We isolated polyribosome-associated mRNA, captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies allow us to experimentally determine genome-wide mRNA targets, and these experiments showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs.

Conclusions

Together, these results find isomiRs to be biologically relevant and functionally cooperative partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur when the specificity of miRNA targeting is mediated by only 6 to 11 nucleotides.

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

Background

The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models.

Results

To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs.

Conclusion

The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events.

Tracheal tube forces on the posterior larynx: index of laryngeal loading

Most tracheal tubes sold today are arcuate in shape while the human airway is S-shaped. In situ, the tubes exert different forces on the posterior larynx, depending on their stiffness. Laryngeal damage after prolonged intubation is recognized as the result of these forces. The authors tested 8 types of size 8.0 tracheal tubes to determine the magnitude of laryngeal loading in a model approximating the geometry of the human airway. The force each tube exerted on the posterior larynx was measured in conditions simulating both, immediately after intubation and after prolonged intubation of 24 h. The force was converted into an integer number, an index of laryngeal loading, that can be used to compare various types of tracheal tubes. The airway model and test procedure can be utilized by manufactures, designers, and others to provide valuable information on tracheal tube performance and to develop improved tracheal tubes in the future. The results indicate that the polyvinylchloride tubes (PVC) and the silicone rubber tubes had the lowest index of laryngeal loading after long-term conditioning and would be preferable for prolonged intubation. The red rubber tube had the highest index of laryngeal loading after long-term conditioning, yet its stiffness would facilitate intubation.

A comparison between over-the-shoulder and computer-derived measurement procedures in assessing student performance in radar air traffic control

On July 18, 1980, the air traffic control Radar Training Facility (RTF) at Oklahoma City was formally dedicated. The RTF can use the computer system in making automated measures of how well a student is moving air traffic. The purpose of this study was to compare the computer-derived automated measures with over-the-shoulder evaluation methods. Subjects were 48 recent nonradar Federal Aviation Administration (FAA) Academy air traffic control graduates who were employed at the National Aviation Facilities Experimental Center (NAFEC; renamed FAA Technical Center) in Atlantic City, NJ, on the Dynamic Simulation Facility. Two sets of measures were taken: 20 computer-derived measures and an over-the-shoulder evaluation of student performance by experts in air traffic control. The results of the study show that the automated measures predict a success criterion at least as well as an over-the-shoulder evaluation and that the automated measures are far more reliable. The study further demonstrated that the factor structures of the two sets of measures were very similar except in two areas where direct observation was necessary for evaluation.

The levels of serum enzymes, plasma proteins and lipids in normal infants and small children

A group of 291 children aged 3 weeks to 6 1/2 years was examined at a public maternal and child health center and 260 of them - who were considered to be healthy - were included in the present study. By venipuncture, serum was obtained for the analysis of 6 enzymes, and plasma for the estimation of 9 proteins and for lipid analyses. In different age groups, high levels were found for alkaline phosphatase, lactate dehydrogenase, aspartate aminotransferase, alanine aminotransferase, creatine kinase and gamma-glutamyl transferase. Haptoglobin, alpha 1-antitrypsin, prealbumin and transferrin were present at low concentrations during the first months of life. Transferrin rose later in childhood to above adult levels. Only immunoglobulin M showed a sex difference, with higher values for girls. Breast-fed infants had higher (non-fasting) concentrations of cholesterol and triglycerides than formula-fed babies, and they also had higher levels of aspartate aminotransferase and alanine aminotransferase.

Irreversible thermodynamics of an isometric twitch, time-dependent general formulation

We used the phenomenological laws of irreversible thermodynamics, to derive a system of coupled differential equations describing the time course of the mechanochemical coupling underlying an isometric twitch. Our general description is concerned only with the fundamental process of energy transduction taking place within an idealized unit element of muscle and does not include the description of associated processes such as the excitation-contraction coupling and the mechanical or external coupling that, in bulk muscle, lead to or mediate the fundamental process. The values of the initial conditions and of four parameters are required to solve for the time course of the process. Two of the parameters have a clear physical interpretation and, for the specific case of muscular contraction involving hydrolysis of ATP, their values can be readily estimated from available experimental data. The interpretation of the two other parameters is more speculative, but, from their strong interdependence with the other parameters, their values can be also approximated. Solution of the coupled differential equations yields results consistent with the typical experimental time course of an isometric twitch.

Health device legislation: an overview of the law and its impact on respiratory care

The Medical Device Amendments of 1976 were intended to protect the public from unsafe and ineffective medical devices. The Food and Drug Administration (FDA) has general authority from this law to regulate medical devices but now must establish specific regulations to do so. In this process all devices are being classified in Class I (general controls), Class II (performance standards), or Class III (premarket approval). General controls impose relatively fewer restrictions, while premarket approval can require very strict laboratory and clinical testing. Classification panels have been grouping medical devices into these three classes. The Anesthesiology Device Classification Panel and the Pulmonary Function and Respiratory Therapy Subcommittee have recommended classifications for more than 200 types of devices. After comments from the public, the FDA will publish final device classifications, probably in 1979. The Medical Device Amendments also provide for release of safety and effectiveness data to the public, for tracing of devices in the field in case of recalls or problems, and for assistance to small manufacturers in complying with the law. The Medical Device Amendments should help to improve medical devices, but official regulations cannot accomplish everything. Users must also do their part by employing preventive maintenance and applying devices knowledgeably and safely.

Myocardial contractile reserve and indices of contractility

A close examiniation of several indices of contractility derived from the ventricular pressure was made using an isolated canine heart preparation. The repsonses to single intracoronary injections of calcium chloride as well as to increasing doses of this agent were tested. From the latter, calcium dose-transient-response curves intended to reveal the extent of myocardial/contractile reserve were constructed. Indices included various extrapolations to maximal velocity of shortening at zero load, maximal value of the quotient of the first derivative and ventricular pressure, time-tension index, energy averaged power density, and power averaged rate of generation of power density. Indices were compared over the same cardiac cycles before and after administration of calcium. Most indices showed increments from 10 to 20%, except power density functions which had increments of 40 and 70%, respectively. Calcium dose-response curves were linear for most indices, but, again, the power density functions showed the steepest slopes. After severe coronary occlusion, the curves for most indices flattened and lost linearity and, presumably, this was due to loss of myocardial contractile reserve. For milder occlusions, only the power density functions showed significant flattening. The conceptual framework of a contractile myocardial reserve appears supported by these results.

Interaction between marihuana and altitude on a complex behavioral task in baboons

Marihuana, or its principal active ingredient, delta-9-tetra-hydrocannabinal (delta9-THC), impairs performance on complex behavioral tasks in animals and man. Although there exists some evidence that altitude-induced hypoxia potentiates the physiological effects of marihuana, the interaction between altitude and marihuana on behavioral tasks has not been established. In the absence of evidence that use of marihuana is less frequent among members of the aviation community than among the general population, it was necessary to evaluate the effects on performance of any interaction between hypoxia and marihuana. Two baboons were trained to perform on a delayed matching-to-sample task at ground level and altitudes of 2438 and 3658 m (8000 and 12000 ft). The animals were orally administered doses of delta9-THC, ranging from 0.25 to 2.0 mg/kg, 2 h prior to experimental sessions at each altitude. No effects on accuracy of matching performance were observed for any of the drug doses or altitudes used. Amount of work output, as measured by number of trials completed and speed of responding, was not affected by delta9-THC at ground level but was markedly reduced by the higher drug doses at the 2438- and 3658-m altitudes. This interaction suggests that the behavioral impairment produced by marihuana can be potentiated by hypoxia.

Predictive validities of several clinical color vision tests for aviation signal light gun performance

Scores on the American Optical Company (AOC) test (1965 edition), Dvorine test, Farnsworth Lantern test, Color Threshold Tester, Farnsworth-Munsell 100-Hue test, Farnsworth Panel D-15 test, and Schmidt-Haensch Anomaloscope were obtained from 137 men with color-defective vision and 128 men with normal color vision. The validity of each of these tests in predicting scores on the aviation signal light gun was assessed by using daytime and nighttime administrations of the light gun as the criteria. Two "best sets" of plates from the AOC and Dvorine tests were selected by calculating a multiple regression equation in a stepwise manner with the nighttime and then the daytime administration of the signal light gun test as the criteria. Based on a graphic presentation of the miss and false alarm rates for each test at various possible cut scores, suggestions were made regarding the use of each test and the selection of optimal pass/fail scores.

Spontaneous reversal of portal blood flow: the case for and against its occurrence in patients with cirrhosis of the liver

Because of its presumed serious clinical significance, we made an analysis of the evidence for and against the occurrence of spontaneous reversal of portal flow in cirrhosis of the liver. We examined the evidence obtained from manometric studies, radioactive tracer studies, radiologic studies, and actual measurements of magnitude and direction of portal blood flow. Concerning manometric studies, we introduced a physical analysis, based on first principles, which demonstrates that the occluded portal pressures cannot be used to construct a hydraulic gradient for portal flow. Similarly, we examined the weakness of the evidence derived from radioactive tracer and radiologic studies and, in the latter, the drastically opposite results reported by different investigators. Finally, we found that actual measurements of magnitude and direction of portal flow provide impressive evidence against the occurrence of spontaneous reversal of portal flow in cirrhosis. We conclude that unless new and convincing evidence is provided, it may not serve the best interests of medicine and of our patients to continue accepting spontaneous reversal of portal flow in cirrhosis as if it were a proven phenomenon.