The gut microbiota in adults with cystic fibrosis compared to colorectal cancer

BACKGROUND

Gut dysbiosis is implicated in colorectal cancer (CRC) pathogenesis. Cystic fibrosis (CF) is associated with both gut dysbiosis and increased CRC risk. We therefore compared the faecal microbiota from individuals with CF to CRC and screening samples. We also assessed changes in CRC-associated taxa before and after triple CF transmembrane conductance regulator (CFTR) modulator therapy.

METHODS

Bacterial DNA amplification comprising V4 16S rRNA analysis was conducted on 84 baseline and 53 matched follow-up stool samples from adults with CF. These data were compared to an existing cohort of 430 CRC and 491 control gFOBT samples from the NHS Bowel Cancer Screening Programme. Data were also compared to 26 previously identified CRC-associated taxa from a published meta-analysis.

RESULTS

Faecal CF samples had a lower alpha diversity and clustered distinctly from both CRC and control samples, with no clear clinical variables explaining the variation. Compared to controls, CF samples had an increased relative abundance in 6 of the 20 enriched CRC-associated taxa and depletion of 2 of the 6 taxa which have been reported as reduced in CRC. Commencing triple modulator therapy had subtle influence on the relative abundance of CRC-associated microbiota (n = 23 paired CF samples).

CONCLUSIONS

CF stool samples were clearly dysbiotic, clustering distinctly from both CRC and control samples. Several bacterial shifts in CF samples resembled those observed in CRC. Studies assessing the impact of dietary or other interventions and the longer-term use of CFTR modulators on reducing this potentially pro-oncogenic milieu are needed.

Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer

PURPOSE

High tumor production of the EGFR ligands, amphiregulin (AREG) and epiregulin (EREG), predicted benefit from anti-EGFR therapy for metastatic colorectal cancer (mCRC) in a retrospective analysis of clinical trial data. Here, AREG/EREG IHC was analyzed in a cohort of patients who received anti-EGFR therapy as part of routine care, including key clinical contexts not investigated in the previous analysis.

EXPERIMENTAL DESIGN

Patients who received panitumumab or cetuximab ± chemotherapy for treatment of RAS wild-type mCRC at eight UK cancer centers were eligible. Archival formalin-fixed paraffin-embedded tumor tissue was analyzed for AREG and EREG IHC in six regional laboratories using previously developed artificial intelligence technologies. Primary endpoints were progression-free survival (PFS) and overall survival (OS).

RESULTS

A total of 494 of 541 patients (91.3%) had adequate tissue for analysis. A total of 45 were excluded after central extended RAS testing, leaving 449 patients in the primary analysis population. After adjustment for additional prognostic factors, high AREG/EREG expression (n = 360; 80.2%) was associated with significantly prolonged PFS [median: 8.5 vs. 4.4 months; HR, 0.73; 95% confidence interval (CI), 0.56-0.95; P = 0.02] and OS [median: 16.4 vs. 8.9 months; HR, 0.66 95% CI, 0.50-0.86; P = 0.002]. The significant OS benefit was maintained among patients with right primary tumor location (PTL), those receiving cetuximab or panitumumab, those with an oxaliplatin- or irinotecan-based chemotherapy backbone, and those with tumor tissue obtained by biopsy or surgical resection.

CONCLUSIONS

High tumor AREG/EREG expression was associated with superior survival outcomes from anti-EGFR therapy in mCRC, including in right PTL disease. AREG/EREG IHC assessment could aid therapeutic decisions in routine practice. See related commentary by Randon and Pietrantonio, p. 4021.

The risk of colorectal cancer in individuals with mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene: An English population-based study

BACKGROUND

Studies have demonstrated a higher risk of developing colorectal cancer (CRC) in individuals with Cystic Fibrosis (CF), and also a potentially increased risk in carriers of cystic fibrosis transmembrane conductance regulator (CFTR) mutations. Life expectancy for those with CF is rising, increasing the number at risk of developing CRC.

METHODS

The incidence of CRC amongst individuals with CF was calculated using data from CORECT-R and linked UK CF Registry and Secondary User Services (SUS) data. Crude, age-specific and age-standardised rates were compared to those without CF. The presence of CFTR mutations in individuals with CRC was assessed using 100,000 Genomes Project data.

FINDINGS

The crude incidence rate of CRC in the CF population was 0.29 per 1,000 person-years (28 cases). The CF population were significantly younger than those without (median age at CRC diagnosis 52 years versus 73 years; p<0·01). When age-adjusted, there was a 5-fold increased CRC incidence amongst individuals with CF compared to those without (SIR 5.0 95%CI 3.2-6.9). When compared to other population studies the overall prevalence of CFTR mutations in the CRC population was significantly higher than expected (p<0·01).

INTERPRETATION

CF is linked to an increased risk of CRC. The incidence of CFTR mutations in the CRC population is higher than would be expected, suggesting an association between CFTR function and CRC risk. Further research is needed to develop effective screening strategies for these populations.

FUNDING

Cancer Research UK (grants C23434/A23706 & C10674/A27140).

Analysis of an Indian colorectal cancer faecal microbiome collection demonstrates universal colorectal cancer-associated patterns, but closest correlation with other Indian cohorts

It is increasingly being recognised that changes in the gut microbiome have either a causative or associative relationship with colorectal cancer (CRC). However, most of this research has been carried out in a small number of developed countries with high CRC incidence. It is unknown if lower incidence countries such as India have similar microbial associations.Having previously established protocols to facilitate microbiome research in regions with developing research infrastructure, we have now collected and sequenced microbial samples from a larger cohort study of 46 Indian CRC patients and 43 healthy volunteers.When comparing to previous global collections, these samples resemble other Asian samples, with relatively high levels of Prevotella. Predicting cancer status between cohorts shows good concordance. When compared to a previous collection of Indian CRC patients, there was similar concordance, despite different sequencing technologies between cohorts.These results show that there does seem to be a global CRC microbiome, and that some inference between studies is reasonable. However, we also demonstrate that there is definite regional variation, with more similarities between location-matched comparisons. This emphasises the importance of developing protocols and advancing infrastructure to allow as many countries as possible to contribute to microbiome studies of their own populations.

Sparse modelling of cancer patients' survival based on genomic copy number alterations

Copy number alterations (CNA) are structural variation in the genome, in which some regions exhibit more or less than the normal two chromosomal copies. This genomic CNA profile provides critical information in tumour progression and is therefore informative for patients' survival. It is currently a statistical challenge to model patients' survival using their genomic CNA profiles while at the same time identify regions in the genome that are associated with patients' survival. Some methods have been proposed, including Cox proportional hazard (PH) model with ridge, lasso, or elastic net penalties. However, these methods do not take the general dependencies between genomic regions into account and produce results that are difficult to interpret. In this paper, we extend the elastic net penalty by introducing additional penalty that takes into account general dependencies between genomic regions. This new model produces smooth parameter estimates while simultaneously performs variable selection via sparse solution. The results indicate that the proposed method shows a better prediction performance than other models in our simulation study, while enabling us to investigate regions in the genome that are associated with the patients' survival with sensible interpretation. We illustrate the method using a real dataset from a lung cancer cohort and simulated data.

Characterisation of dysplastic liver nodules using low-pass DNA sequencing and detection of chromosome arm-level abnormalities in blood-derived cell-free DNA

High-grade dysplasia carries significant risk of transformation to hepatocellular carcinoma (HCC). Despite this, at the current standard of care, all non-malignant hepatic nodules including high-grade dysplastic nodules are managed similarly. This is partly related to difficulties in distinguishing high-risk pathology in the liver. We aimed to identify chromosome arm-level somatic copy number alterations (SCNAs) that characterise the transition of liver nodules along the cirrhosis-dysplasia-carcinoma axis. We validated our findings on an independent cohort using blood-derived cell-free DNA. A repository of non-cancer DNA sequences obtained from patients with HCC (n = 389) was analysed to generate cut-off thresholds aiming to minimise false-positive SCNAs. Tissue samples representing stages from the multistep process of hepatocarcinogenesis (n = 184) were subjected to low-pass whole genome sequencing. Chromosome arm-level SCNAs were identified in liver cirrhosis, dysplastic nodules, and HCC to assess their discriminative capacity. Samples positive for 1q+ or 8q+ arm-level duplications were likely to be either HCC or high-grade dysplastic nodules as opposed to low-grade dysplastic nodules or cirrhotic tissue with an odds ratio (OR) of 35.5 (95% CI 11.5-110) and 16 (95% CI 6.4-40.2), respectively (p < 0.0001). In an independent cohort of patients recruited from Nottingham, UK, at least two out of four alterations (1q+, 4q-, 8p-, and 8q+) were detectable in blood-derived cell-free DNA of patients with HCC (n = 22) but none of the control patients with liver cirrhosis (n = 9). Arm-level SCNAs on 1q+ or 8q+ are associated with high-risk liver pathology. These can be detected using low-pass sequencing of cell-free DNA isolated from blood, which may be a future early cancer screening tool for patients with liver cirrhosis. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Luminal Bioavailability of Orally Administered ω-3 PUFAs in the Distal Small Intestine, and Associated Changes to the Ileal Microbiome, in Humans with a Temporary Ileostomy

BACKGROUND

Oral administration of purified omega-3 (ω-3) PUFAs is associated with changes to the fecal microbiome. However, it is not known whether this effect is associated with increased PUFA concentrations in the gut.

OBJECTIVES

We investigated the luminal bioavailability of oral ω-3 PUFAs (daily dose 1 g EPA and 1g DHA free fatty acid equivalents as triglycerides in soft-gel capsules, twice daily) and changes to the gut microbiome, in the ileum.

METHODS

Ileostomy fluid (IF) and blood were obtained at baseline, after first capsule dosing (median 2 h), and at a similar time after final dosing on day 28, in 11 individuals (median age 63 y) with a temporary ileostomy. Fatty acids were measured by LC-tandem MS. The ileal microbiome was characterized by 16S rRNA PCR and Illumina sequencing.

RESULTS

There was a mean 6.0 ± 9.8-fold and 6.6 ± 9.6-fold increase in ileal EPA and DHA concentrations (primary outcome), respectively, at 28 d, which was associated with increased RBC ω-3 PUFA content (P ≤ 0.05). The first oral dose did not increase the ileal ω-3 PUFA concentration except in 4 individuals, who displayed high luminal EPA and DHA concentrations, which reduced to concentrations similar to the overall study population at day 28, suggesting physiological adaptation. Bacteroides, Clostridium, and Streptococcus were abundant bacterial genera in the ileum. Ileal microbiome variability over time and between individuals was large, with no consistent change associated with acute ω-3 PUFA dosing. However, high concentrations of EPA and DHA in IF on day 28 were associated with higher abundance of Bacteroides (r2 > 0.86, P < 0.05) and reduced abundance of other genera, including Actinomyces (r2 > 0.94, P < 0.05).

CONCLUSIONS

Oral administration of ω-3 PUFAs leads to increased luminal ω-3 PUFA concentrations and changes to the microbiome, in the ileum of individuals with a temporary ileostomy. This study is registered on the ISRCTN registry as ISRCTN14530452.

Abstract 2421: PTCH1 C-terminal domain truncations in colorectal cancer increase mitogenic signalling and autophagy

The canonical Hedgehog (Hh) signaling pathway, driving activation of SMO and GLI1, has been implicated in colorectal cancer (CRC) stemness and resistance to chemotherapy. We recently reported that the C-terminal domain (CTD) of the Hh receptor PTCH1 limits autophagic flux and ERK signaling by non-canonical mechanisms (independently of SMO/GLI1). Given that those novel functions are implicated in tumorigenesis, we explored the existence of PTCH1 CTD mutations in cancer specimens. Analysis of the TCGA Cancer Atlas database and the Genomics England 100,000 Genomes Project revealed relatively frequent somatic mutations in the CTD of PTCH1 in CRC: S1203(fs) and R1308(fs), which result in premature truncations of the CTD in about 4% of cases. PTCH1 CTD mutations were strongly associated with BRAF mutations (61% samples) and with right-sided disease (10/10 of samples with sidedness information). Co-immunoprecipitation analysis of truncated PTCH1(S1203*) and PTCH1(R1308*) showed loss of interaction with ATG101 and GRB2, required for regulation of autophagic flux and ERK signaling, respectively. To determine the pathogenic role of those mutations, we engineered SW620 metastatic CRC cell lines using CRISPR/Cas9 to create two clones with indel mutations between S1203 and R1308. Truncation of the CTD increased basal ERK and AKT phosphorylation levels, proliferation, invasion and migration compared to isogenic cells expressing wild type PTCH1. The mutant clones also showed persistent proliferation in the presence of glycolysis inhibitors and of the autophagy inducer rapamycin. Moreover, both clones displayed an enhanced autophagic flux by analysis of the LC3BI/II and p62 markers in the presence and absence of Bafilomycin A1. RNA-seq analysis revealed that the CTD truncation resulted in increase in GO terms of metabolic pathways, pathways in cancer, mTOR signaling pathway, PI3K-AKT pathway, MAPK signaling pathway and regulation of actin cytoskeleton, among others. The clones morphology changed together with a remarkable cadherin switch and loss of vimentin at RNA and protein level, suggestive of mesenchymal-epithelial transition, a process necessary for establishment of metastasis following cancer cell spread. Interestingly, one clone showed enhanced apoptosis in response to FOLFOX (5-fluorouracil/lecovorin/oxaliplatin), the most effective chemotherapy for metastatic CRC, as determined by cleaved PARP and Caspase 7 activity, compared to the parental cells. These findings reveal important tumor suppressor functions of the CTD of PTCH1 acting to suppress autophagy and mitogenic signaling, which are dysregulated by CTD mutations in a subset of colon cancer patients. Our results provide mechanistic insights of the effect of PTCH1 mutations in CRC and identify potential therapeutic vulnerabilities.

Citation Format: Begoña Caballero-Ruiz, Cintli C. Morales-Alcala, Henry M. Wood, Gianluca Canettieri, Natalia A. Riobo-Del Galdo. PTCH1 C-terminal domain truncations in colorectal cancer increase mitogenic signalling and autophagy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2421.

Correction: Developing a Raman spectroscopy-based tool to stratify patient response to pre-operative radiotherapy in rectal cancer

Correction for 'Developing a Raman spectroscopy-based tool to stratify patient response to pre-operative radiotherapy in rectal cancer' by Chloe J. Kirkby et al., Analyst, 2021, 146, 581-589, DOI: .

Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy

PURPOSE

There is potential for fecal microbiome profiling to improve colorectal cancer screening. This has been demonstrated by research studies, but it has not been quantified at scale using samples collected and processed routinely by a national screening program.

EXPERIMENTAL DESIGN

Between 2016 and 2019, the largest of the NHS Bowel Cancer Screening Programme hubs prospectively collected processed guaiac fecal occult blood test (gFOBT) samples with subsequent colonoscopy outcomes: blood-negative [n = 491 (22%)]; colorectal cancer [n = 430 (19%)]; adenoma [n = 665 (30%)]; colonoscopy-normal [n = 300 (13%)]; nonneoplastic [n = 366 (16%)]. Samples were transported and stored at room temperature. DNA underwent 16S rRNA gene V4 amplicon sequencing. Taxonomic profiling was performed to provide features for classification via random forests (RF).

RESULTS

Samples provided 16S amplicon-based microbial profiles, which confirmed previously described colorectal cancer-microbiome associations. Microbiome-based RF models showed potential as a first-tier screen, distinguishing colorectal cancer or neoplasm (colorectal cancer or adenoma) from blood-negative with AUC 0.86 (0.82-0.89) and AUC 0.78 (0.74-0.82), respectively. Microbiome-based models also showed potential as a second-tier screen, distinguishing from among gFOBT blood-positive samples, colorectal cancer or neoplasm from colonoscopy-normal with AUC 0.79 (0.74-0.83) and AUC 0.73 (0.68-0.77), respectively. Models remained robust when restricted to 15 taxa, and performed similarly during external validation with metagenomic datasets.

CONCLUSIONS

Microbiome features can be assessed using gFOBT samples collected and processed routinely by a national colorectal cancer screening program to improve accuracy as a first- or second-tier screen. The models required as few as 15 taxa, raising the potential of an inexpensive qPCR test. This could reduce the number of colonoscopies in countries that use fecal occult blood test screening.

The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries

BACKGROUND

The incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facilities, and the difficulty of fresh or frozen stool storage/transport. Here, we aimed (1) to establish a broad representation of diverse developing countries (Argentina, Chile, India, and Vietnam); (2) to validate a 'resource-light' sample-collection protocol translatable in these settings using guaiac faecal occult blood test (gFOBT) cards stored and, importantly, shipped internationally at room temperature; (3) to perform initial profiling of the collective CRC-associated microbiome of these developing countries; and (4) to compare this quantitatively with established CRC biomarkers from developed countries.

METHODS

We assessed the effect of international storage and transport at room temperature by replicating gFOBT from five UK volunteers, storing two in the UK, and sending replicates to institutes in the four countries. Next, to determine the effect of prolonged UK storage, DNA extraction replicates for a subset of samples were performed up to 252 days apart. To profile the CRC-associated microbiome of developing countries, gFOBT were collected from 41 treatment-naïve CRC patients and 40 non-CRC controls from across the four institutes, and V4 16S rRNA gene sequencing was performed. Finally, we constructed a random forest (RF) model that was trained and tested against existing datasets from developed countries.

RESULTS

The microbiome was stably assayed when samples were stored/transported at room temperature and after prolonged UK storage. Large-scale microbiome structure was separated by country and continent, with a smaller effect from CRC. Importantly, the RF model performed similarly to models trained using external datasets and identified similar taxa of importance (Parvimonas, Peptostreptococcus, Fusobacterium, Alistipes, and Escherichia).

CONCLUSIONS

This study demonstrates that gFOBT, stored and transported at room temperature, represents a suitable method of faecal sample collection for amplicon-based microbiome biomarkers in developing countries and suggests a CRC-faecal microbiome association that is consistent between developed and developing countries.

Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA

Liquid biopsy testing utilising Next Generation Sequencing (NGS) is rapidly moving towards clinical adoption for personalised oncology. However, before NGS can fulfil its potential any novel testing approach must identify ways of reducing errors, allowing separation of true low-frequency mutations from procedural artefacts, and be designed to improve upon current technologies. Popular NGS technologies typically utilise two DNA capture approaches; PCR and ligation, which have known limitations and seem to have reached a development plateau with only small, stepwise improvements being made. To maximise the ultimate utility of liquid biopsy testing we have developed a highly versatile approach to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seq's strengths and versatility avoid the major limitations of both PCR- and ligation-based approaches. This technology is ligation free, simple, efficient, flexible, and streamlined, and it offers novel advantages that make it perfectly suited for use on highly challenging clinical material. Using reference and clinical materials, we demonstrate detection of known SNVs down to allele frequencies of 0.1% using as little as 20–25 ng of cfDNA, as well as the ability to detect fusions from RNA. We illustrate ATOM-Seq’s suitability for clinical testing by showing high concordance rates between paired cfDNA and FFPE clinical samples.

Developing a Raman spectroscopy-based tool to stratify patient response to pre-operative radiotherapy in rectal cancer

The use of Raman spectroscopy to stratify rectal cancer patient response to pre-operative radiotherapy, using routine pre-treatment biopsy samples.

Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli

Various species of the intestinal microbiota have been associated with the development of colorectal cancer1,2, but it has not been demonstrated that bacteria have a direct role in the occurrence of oncogenic mutations. Escherichia coli can carry the pathogenicity island pks, which encodes a set of enzymes that synthesize colibactin3. This compound is believed to alkylate DNA on adenine residues4,5 and induces double-strand breaks in cultured cells3. Here we expose human intestinal organoids to genotoxic pks+ E. coli by repeated luminal injection over five months. Whole-genome sequencing of clonal organoids before and after this exposure revealed a distinct mutational signature that was absent from organoids injected with isogenic pks-mutant bacteria. The same mutational signature was detected in a subset of 5,876 human cancer genomes from two independent cohorts, predominantly in colorectal cancer. Our study describes a distinct mutational signature in colorectal cancer and implies that the underlying mutational process results directly from past exposure to bacteria carrying the colibactin-producing pks pathogenicity island.

A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota

OBJECTIVE

Omega-3 polyunsaturated fatty acids (PUFAs) have anticolorectal cancer (CRC) activity. The intestinal microbiota has been implicated in colorectal carcinogenesis. Dietary omega-3 PUFAs alter the mouse intestinal microbiome compatible with antineoplastic activity. Therefore, we investigated the effect of omega-3 PUFA supplements on the faecal microbiome in middle-aged, healthy volunteers (n=22).

DESIGN

A randomised, open-label, cross-over trial of 8 weeks' treatment with 4 g mixed eicosapentaenoic acid/docosahexaenoic acid in two formulations (soft-gel capsules and Smartfish drinks), separated by a 12-week 'washout' period. Faecal samples were collected at five time-points for microbiome analysis by 16S ribosomal RNA PCR and Illumina MiSeq sequencing. Red blood cell (RBC) fatty acid analysis was performed by liquid chromatography tandem mass spectrometry.

RESULTS

Both omega-3 PUFA formulations induced similar changes in RBC fatty acid content, except that drinks were associated with a larger, and more prolonged, decrease in omega-6 PUFA arachidonic acid than the capsule intervention (p=0.02). There were no significant changes in α or β diversity, or phyla composition, associated with omega-3 PUFA supplementation. However, a reversible increased abundance of several genera, including Bifidobacterium, Roseburia and Lactobacillus was observed with one or both omega-3 PUFA interventions. Microbiome changes did not correlate with RBC omega-3 PUFA incorporation or development of omega-3 PUFA-induced diarrhoea. There were no treatment order effects.

CONCLUSION

Omega-3 PUFA supplementation induces a reversible increase in several short-chain fatty acid-producing bacteria, independently of the method of administration. There is no simple relationship between the intestinal microbiome and systemic omega-3 PUFA exposure.

TRIAL REGISTRATION NUMBER

ISRCTN18662143.

No Significant Association Between the Fecal Microbiome and the Presence of Irritable Bowel Syndrome-type Symptoms in Patients with Quiescent Inflammatory Bowel Disease

BACKGROUND

The microbiome is implicated in the pathogenesis of inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Whether a distinct microbiome profile is associated with the reporting of IBS-type symptoms in IBD patients is uncertain. We aimed to resolve this issue using a cross-sectional study design.

METHODS

Using clinical disease activity indices, the Rome III criteria for IBS and fecal calprotectin levels, we divided IBD patients into 4 groups: IBS-type symptoms, quiescent disease, occult inflammation, and active disease. A16S rRNA microbiome analysis was performed to determine whether any taxa were differentially abundant, and whether there were any differences in alpha or beta diversity in patients reporting IBS-type symptoms compared with those in the other 3 groups.

RESULTS

Of 270 patients included, 70 (25.9%) had IBS-type symptoms, 81 (30.0%) quiescent IBD, 66 (24.4%) occult inflammation, and 53 (19.6%) active IBD. At phylum level, there was a nonsignificant increase in the abundance of Actinobacteria in patients reporting IBS-type symptoms, but no other differences at any taxonomic level. When compared with patients reporting IBS-type symptoms, mean alpha diversity was greater in patients with quiescent disease, although this was nonsignificant (28.6 vs 31.7, P = 0.33), and similar to those with occult inflammation and active disease. Beta diversity variation among the 4 groups was significant for unweighted (P = 0.002) but not weighted (P = 0.21) UniFrac analysis.

CONCLUSIONS

Reporting IBS-type symptoms was not associated with distinct microbiome alterations. Unmeasured confounding could have impacted the significance of our findings.

Genomic analysis to assess disease progression and recurrence in patients with oral squamous cell carcinoma: - a preliminary study

We studied the progression from dysplasia to invasive carcinoma and subsequent second primaries or locoregional recurrences in 11 patients with recurrent squamous cell carcinoma (SCC). Between one and six samples were sequenced/patient. DNA samples were prepared, and libraries multiplexed to between 40 and 80 samples/lane of an Illumina HiSeq 3000 and sequenced with 2×100bp paired end sequencing. Copy number data were generated by CNAnorm (Bioconductor package). Samples of recurrent SCC showed unique patterns of descent when compared with earlier samples from the primary tumour, and three main patterns emerged. In four patients there was convincing evidence that the later lesion was descended directly from cells from the first, and in a further four there were no detectable genomic events between the two lesions. Three patients had some shared events between the early and later lesions, but although there were enough differences to deduce that the two lesions had a shared ancestor, they were not directly descended from each other. We present the patients' characteristics in detail, including the overall survival in each group. There was a distinct genomic pattern after a second episode of SCC in all the groups. A larger study that uses similar methods and a longer duration could provide reliable conclusions with respect to survival. With the use of new techniques, genomic data can be available to clinical teams during the planning of treatment.

Survival of Head and Neck Cancer Cells Relies upon LZK Kinase-Mediated Stabilization of Mutant p53

Head and neck squamous cell carcinoma (HNSCC) includes epithelial cancers of the oral and nasal cavity, larynx, and pharynx and accounts for ∼350,000 deaths per year worldwide. Smoking-related HNSCC is associated with few targetable mutations but is defined by frequent copy-number alteration, the most common of which is gain at 3q. Critical 3q target genes have not been conclusively determined for HNSCC. Here, we present data indicating that MAP3K13 (encoding LZK) is an amplified driver gene in HNSCC. Copy-number gain at 3q resulted in increased MAP3K13 mRNA in HNSCC tumor samples and cell lines. Silencing LZK reduced cell viability and proliferation of HNSCC cells with 3q gain but not control cell lines. Inducible silencing of LZK caused near-complete loss of colony-forming ability in cells harboring 3q gain. These results were validated in vivo by evidence that LZK silencing was sufficient to reduce tumor growth in a xenograft model of HNSCC. Our results establish LZK as critical for maintaining expression of mutant stabilized p53. Cancer Res; 77(18); 4961-72. ©2017 AACR.

The genomic road to invasion-examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples

BACKGROUND

It is frequently assumed that pre-invasive lesions are simpler precursors of cancer and will contain a limited subset of the genomic changes seen in their associated invasive disease. Driver mutations are thought to occur early, but it is not known how many of these are present in pre-invasive lesions. These assumptions need to be tested with the increasing focus on both personalised cancer treatments and early detection methodologies.

METHODS

We examined genomic copy number changes in 256 pre-invasive and invasive samples from 69 oral cancer patients. Forty-eight samples from 16 patients were further examined using exome sequencing.

RESULTS

Evidence of a shared ancestor of both dysplasia and carcinoma was seen in all but one patient. One-third of dysplasias showed independent copy number events. The remainder had a copy number pattern that was similar to or simpler than that of the carcinoma. All dysplasias examined contained somatic mutations absent in the related carcinoma. Previously observed copy number changes and TP53 mutations were very frequently observed, and almost always shared between dysplasia and carcinoma. Other gene changes were more sporadic. Pathway analysis confirmed that each patient's disease developed in a different way. Examining the numbers of shared mutations and the rate of accumulation of mutations showed evidence that all samples contain a population of sub-clones, with little evidence of selective advantage of a subset of these.

CONCLUSIONS

These findings suggest that most of the genomic changes driving oral cancer occur in the pre-cancerous state by way of gradual random accumulation rather than a dramatic single event.

Comparing mutation calls in fixed tumour samples between the affymetrix OncoScan® array and PCR based next-generation sequencing

BACKGROUND

The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platform is designed to produce actionable mutation calls in archival material.

METHODS

We compared calls made using the OncoScan platform with calls made using a custom designed PCR panel followed by next-generation sequencing (NGS), in order to benchmark the sensitivity and specificity of the OncoScan calls in a large cohort of fixed tumour samples. 392 fixed, clinical samples were sequenced, encompassing 641 PCR regions, 403 putative positive calls and 1528 putative negative calls.

RESULTS

A small number of mutations could not be validated, either due to large indels or pseudogenes impairing parts of the NGS pipeline. For the remainder, if calls were filtered according to simple quality metrics, both sensitivity and specificity for the OncoScan platform were over 98%. This applied even to samples with poorer sample quality and lower variant allele frequency (5-10%) than product claims indicated.

CONCLUSIONS

This benchmarking study will be useful to users and potential users of this platform, who wish to compare technologies or interpret their own results.

Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing

Aims

With a growing interest in the influence the gut microbiome has on the development of colorectal cancer (CRC), we investigated the feasibility and stability of isolating and typing microbial DNA from guaiac faecal occult blood test (gFOBt) cards. This has the future potential to screen the microbial populations present in confirmed colorectal neoplasia cases with aims to predict the presence and development of CRC.

Methods

Fresh stool samples from three healthy volunteers were applied to gFOBt cards. DNA was extracted from both the cards and fresh stool samples. A series of additional cards were prepared from one volunteer, and extracted at time points between 2 weeks and 3 years. The V4 region of the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq at 2×250 bp read lengths. Data were analysed using QIIME software.

Results

Samples were grouped both by volunteer and by type (fresh or gFOBt), and compared a variety of ways: visual inspection of taxa, α and β diversity, intraclass correlation. In all comparisons, samples grouped by volunteer, and not by sample type. The different time points showed no appreciable differences with increased storage time.

Conclusions

This study has demonstrated that there is good concordance between microbial DNA isolated from fresh stool sample, and from the matched gFOBt card. Samples stored for up to 3 years showed no detrimental effect on measureable microbial DNA. This study has important future implications for investigating microbial influence on CRC development and other pathologies.

Past and future impact of next-generation sequencing in head and neck cancer

Progress in sequencing technology is intrinsically linked to progress in understanding cancer genomics. The purpose of this review was to discuss the development from Sanger sequencing to next-generation sequencing (NGS) technology. We highlight the technical considerations for understanding reports using NGS. We discuss the findings of studies in head and neck cancer using NGS as well as The Cancer Genome Atlas. Finally we discuss future routes for research utilizing this methodology and the potential impact of this. © 2015 Wiley Periodicals, Inc. Head Neck 38: E2395-E2402, 2016.

A novel genomic signature reclassifies an oral cancer subtype

Verrucous carcinoma of the oral cavity (OVC) is considered a subtype of classical oral squamous cell carcinoma (OSCC). Diagnosis is problematic, and additional biomarkers are needed to better stratify patients. To investigate their molecular signature, we performed low-coverage copy number (CN) sequencing on 57 OVC and exome and RNA sequencing on a subset of these and compared the data to the same OSCC parameters. CN results showed that OVC lacked any of the classical OSCC patterns such as gain of 3q and loss of 3p and demonstrated considerably fewer genomic rearrangements compared to the OSCC cohort. OVC and OSCC samples could be clearly differentiated. Exome sequencing showed that OVC samples lacked mutations in genes commonly associated with OSCC (TP53, NOTCH1, NOTCH2, CDKN2A and FAT1). RNA sequencing identified genes that were differentially expressed between the groups. In silico functional analysis showed that the mutated and differentially expressed genes in OVC samples were involved in cell adhesion and keratinocyte proliferation, while those in the OSCC cohort were enriched for cell death and apoptosis pathways. This is the largest and most detailed genomic and transcriptomic analysis yet performed on this tumour type, which, as an example of non-metastatic cancer, may shed light on the nature of metastases. These three independent investigations consistently show substantial differences between the cohorts. Taken together, they lead to the conclusion that OVC is not a subtype of OSCC, but should be classified as a distinct entity.

Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data

MOTIVATION

The role of personalized medicine and target treatment in the clinical management of cancer patients has become increasingly important in recent years. This has made the task of precise histological substratification of cancers crucial. Increasingly, genomic data are being seen as a valuable classifier. Specifically, copy number alteration (CNA) profiles generated by next-generation sequencing (NGS) can become a determinant for tumours subtyping. The principle purpose of this study is to devise a model with good prediction capability for the tumours histological subtypes as a function of both the patients covariates and their genome-wide CNA profiles from NGS data.

RESULTS

We investigate a logistic regression for modelling tumour histological subtypes as a function of the patients' covariates and their CNA profiles, in a mixed model framework. The covariates, such as age and gender, are considered as fixed predictors and the genome-wide CNA profiles are considered as random predictors. We illustrate the application of this model in lung and oral cancer datasets, and the results indicate that the tumour histological subtypes can be modelled with a good fit. Our cross-validation indicates that the logistic regression exhibits the best prediction relative to other classification methods we considered in this study. The model also exhibits the best agreement in the prediction between smooth-segmented and circular binary-segmented CNA profiles.

AVAILABILITY AND IMPLEMENTATION

An R package to run a logistic regression is available in http://www1.maths.leeds.ac.uk/~arief/R/CNALR/.

CONTACT

a.gusnanto@leeds.ac.uk

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Estimating optimal window size for analysis of low-coverage next-generation sequence data

MOTIVATION

Current high-throughput sequencing has greatly transformed genome sequence analysis. In the context of very low-coverage sequencing (<0.1×), performing 'binning' or 'windowing' on mapped short sequences ('reads') is critical to extract genomic information of interest for further evaluation, such as copy-number alteration analysis. If the window size is too small, many windows will exhibit zero counts and almost no pattern can be observed. In contrast, if the window size is too wide, the patterns or genomic features will be 'smoothed out'. Our objective is to identify an optimal window size in between the two extremes.

RESULTS

We assume the reads density to be a step function. Given this model, we propose a data-based estimation of optimal window size based on Akaike's information criterion (AIC) and cross-validation (CV) log-likelihood. By plotting the AIC and CV log-likelihood curve as a function of window size, we are able to estimate the optimal window size that minimizes AIC or maximizes CV log-likelihood. The proposed methods are of general purpose and we illustrate their application using low-coverage next-generation sequence datasets from real tumour samples and simulated datasets.

AVAILABILITY AND IMPLEMENTATION

An R package to estimate optimal window size is available at http://www1.maths.leeds.ac.uk/∼arief/R/win/.

Abstract PD3-3: Next generation sequencing shows clonal selection after treatment with anastrozole or fulvestrant in a randomized trial of postmenopausal patients with large operable or locally-advanced hormone-receptor-positive breast cancer

Background: Unlike chemotherapy, endocrine therapy is not clastogenic or mutagenic, so genetic changes arising during treatment are unlikely to be secondary events provoked by iatrogenic DNA damage. Endocrine therapy for breast cancer is thus a clean setting in which to explore the evolution of tumour genomes under treatment, and the changes seen are likely to be biologically meaningful. To identify such changes we have analysed pre and post treatment biopsies from a clinical trial that compared two endocrine therapies.

Patients and methods: DNA was extracted from pre and post treatment samples from 20 patients enrolled in the HORGEN trial. Postmenopausal patients with large operable or locally-advanced hormone-receptor-positive breast cancer were randomly assigned to receive either neoadjuvant anastrozole or fulvestrant for 6 months in this multicenter randomized phase II study. Low depth next generation sequencing was used to generate DNA copy number profiles for each sample.

Results: The copy number profiles were similar before and after treatment in 10 cases. In three cases new amplicons appeared. In one case the amplicon contained the ESR1 gene, in another the FOXA1 gene, and in the third the NCOA3 gene. In the remaining seven cases where the profiles changed after treatment, the differences affected whole chromosomal arms. In six of these cases the profiles became simpler, indicating that clones with gains and losses of chromosomal arms had been counterselected by the treatment.

Conclusions: Differences between the pre and post treatment biopsies were surprisingly frequent and informative. Genes directly implicated in estrogen signalling were amplified in three cases. This suggests that specific amplicons confer resistance to endocrine therapy. From a clinical perspective, their appearance in a post treatment biopsy probably indicates that the treatment should be changed. A possible explanation for the chromosomal arm changes after treatment, a phenomenon we have dubbed the “wandering arms” phenotype, is that endocrine therapy deprives tumour cells of signals that are necessary for the survival of clones with copy number changes affecting whole chromosomal arms.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD3-3.

IMSA: integrated metagenomic sequence analysis for identification of exogenous reads in a host genomic background

Metagenomics, the study of microbial genomes within diverse environments, is a rapidly developing field. The identification of microbial sequences within a host organism enables the study of human intestinal, respiratory, and skin microbiota, and has allowed the identification of novel viruses in diseases such as Merkel cell carcinoma. There are few publicly available tools for metagenomic high throughput sequence analysis. We present Integrated Metagenomic Sequence Analysis (IMSA), a flexible, fast, and robust computational analysis pipeline that is available for public use. IMSA takes input sequence from high throughput datasets and uses a user-defined host database to filter out host sequence. IMSA then aligns the filtered reads to a user-defined universal database to characterize exogenous reads within the host background. IMSA assigns a score to each node of the taxonomy based on read frequency, and can output this as a taxonomy report suitable for cluster analysis or as a taxonomy map (TaxMap). IMSA also outputs the specific sequence reads assigned to a taxon of interest for downstream analysis. We demonstrate the use of IMSA to detect pathogens and normal flora within sequence data from a primary human cervical cancer carrying HPV16, a primary human cutaneous squamous cell carcinoma carrying HPV 16, the CaSki cell line carrying HPV16, and the HeLa cell line carrying HPV18.

Next-generation sequencing for simultaneous determination of human papillomavirus load, subtype, and associated genomic copy number changes in tumors

Human papillomavirus (HPV) infection in cases of squamous cell carcinoma of the oropharynx is a powerful predictive and prognostic biomarker. We describe how the use of next-generation sequencing can provide a novel method for the detection of HPV in DNA isolated from formalin-fixed paraffin-embedded tissues. Using this methodology in a cohort of 44 head and neck tumors, we identified the samples that contained HPV sequences, the viral subtype involved, and a direct readout of viral load. Specificity of HPV detection by sequencing compared to traditional detection methods using either PCR or p16 immunohistochemistry was 100%. Sensitivity was 50% when either compared to PCR [confidence interval (CI) = 29% to 71%] or 75% when compared to p16 (CI = 47% to 91%). In addition, we demonstrate the ability of next-generation sequencing to detect other HPV subtypes that would not have been detected by traditional methods, and we demonstrated the ability to apply this method to any tumor and any virus in a panel of eight human cancer cell lines. This methodology also provides a tumor genomic copy number karyogram, and in the samples analyzed here, a lower level of chromosome instability was detected in HPV-positive tumors compared to HPV-negative tumors, as observed in previous studies. Thus, the use of next-generation sequencing for the detection of HPV provides a multiplicity of data with clinical significance in a single test.

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

MOTIVATION

Comparison of read depths from next-generation sequencing between cancer and normal cells makes the estimation of copy number alteration (CNA) possible, even at very low coverage. However, estimating CNA from patients' tumour samples poses considerable challenges due to infiltration with normal cells and aneuploid cancer genomes. Here we provide a method that corrects contamination with normal cells and adjusts for genomes of different sizes so that the actual copy number of each region can be estimated.

RESULTS

The procedure consists of several steps. First, we identify the multi-modality of the distribution of smoothed ratios. Then we use the estimates of the mean (modes) to identify underlying ploidy and the contamination level, and finally we perform the correction. The results indicate that the method works properly to estimate genomic regions with gains and losses in a range of simulated data as well as in two datasets from lung cancer patients. It also proves a powerful tool when analysing publicly available data from two cell lines (HCC1143 and COLO829).

AVAILABILITY

An R package, called CNAnorm, is available at http://www.precancer.leeds.ac.uk/cnanorm or from Bioconductor.

CONTACT

a.gusnanto@leeds.ac.uk

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A computational index derived from whole-genome copy number analysis is a novel tool for prognosis in early stage lung squamous cell carcinoma

Squamous cell carcinoma of the lung is remarkable for the extent to which the same chromosomal abnormalities are detected in individual tumours. We have used next generation sequencing at low coverage to produce high resolution copy number karyograms of a series of 89 non-small cell lung tumours specifically of the squamous cell subtype. Because this methodology is able to create karyograms from formalin-fixed paraffin-embedded material, we were able to use archival stored samples for which survival data were available and correlate frequently occurring copy number changes with disease outcome. No single region of genomic change showed significant correlation with survival. However, adopting a whole-genome approach, we devised an algorithm that relates to total genomic damage, specifically the relative ratios of copy number states across the genome. This algorithm generated a novel index, which is an independent prognostic indicator in early stage squamous cell carcinoma of the lung.

Detecting copy number aberrations (CNA) in cancer genomes using high-throughput sequencing technologies

The karyotype of human tumors are often aneuploid: besides these numerical deviations, there are often structural rearrangements within individual chromosomes such as amplifications, deletions and translocations. In the resulting genome, profound and complex alterations in the underlying gene network and dosage occur, giving rise to the observed malignant phenotype. To understand how these events contribute to the biology of a tumor cell, a first crucial step is to be able to detect variation in chromosomal structure and, in particular, copy number. The recent development in technology, such as array comparative genomic hybridization (aCGH), SNP microarray and, more recently, high throughput sequencing, made it feasible to detect copy number aberrations (CNA).

Using these techniques it is possible to obtain, for thousands of regions across the genome, a numerical value proportional to the chromosome copy number for each of the accessed regions. Comparing DNA from tumor to normal samples, it is possible to identify copy number aberrations across the genome.

However, the methodology used to calculate CNA from the raw data usually makes one or both of the following assumptions:

• The starting material consists of genetically homogeneous cells.

• The overall size of a tumor genome is very similar to the size of the normal genome.

The first assumption is completely reasonable when dealing with cell lines, but the same cannot be said when the DNA analyzed is isolated from patients’ tumors. Infiltrations with stromal or endothelial cells are, in fact, largely inevitable.

The second assumption, that has a strong impact on the normalization step, is often not correct. Given the scale, extent and severity of chromosomal structural changes, the overall genetic material of a cancer cell might be significantly different (usually larger) than a normal one. Therefore, assuming that the total size of a cancer genome is comparable to the size of the normal genome, might lead to artifacts and misleading results.

Some methods do not strictly require assumptions on the size of the genome, but they rely on the ability to detect SNP variants and distinguish between the two alleles of a heterozygous region. They can then infer when two, three, four or more copies are present. Although high throughput sequencing could also detect SNP variants, a very high read coverage would be required, making the technology far too expensive at present.

Here, we propose a method to obtain CNA from high throughput sequencing that avoids the two assumptions mentioned above.

The method counts the number of reads mapped to a region of fixed length both in tumor and normal DNAs from the same patient. For each region, the ratio between number of reads from the tumor sample and the normal sample depends mainly on three factors:

• The average number of copies (including stromal contamination) of a given chromosomal region in the two samples.

• The overall depth of coverage (total number of reads) of the two samples.

• Sampling error.

The goal is to detect, for each chromosomal region, the underlying ratio between number of copies in the tumor genome versus the normal genome, despite the noise due to different depth of coverage and the sampling error. For each chromosomal region, we first calculate the ratio of read counts between tumor and normal. This way we balance out various biases due to biological and technical issues (i.e. GC content, aligning artifacts). Second, to reduce the sampling error with minimal effect on the resolution, we use a segmentation algorithm on the obtained ratio. At this point, we look at the distribution of ratio in all chromosomal regions and we fit a model of several normal distributions with equally spaced means. The ratio from each region can thus be assigned to one of these distributions and underlying CNA estimated.

We are testing the algorithm on a series of simulated and real samples to access the strength of the proposed method.

Confirmation of linear system theory prediction: Changes in Herrnstein's k as a function of changes in reinforcer magnitude

Eight human subjects pressed a lever on a range of variable-interval schedules for 0.25 cent to 35.0 cent per reinforcement. Herrnstein's hyperbola described seven of the eight subjects' response-rate data well. For all subjects, the y-asymptote of the hyperbola increased with increasing reinforcer magnitude and its reciprocal was a linear function of the reciprocal of reinforcer magnitude. These results confirm predictions made by linear system theory; they contradict formal properties of Herrnstein's account and of six other mathematical accounts of single-alternative responding.

Confirmation of linear system theory prediction: Rate of change of Herrnstein's kappa as a function of response-force requirement

Four human subjects worked on all combinations of five variable-interval schedules and five reinforcer magnitudes ( cent/reinforcer) in each of two phases of the experiment. In one phase the force requirement on the operandum was low (1 or 11 N) and in the other it was high (25 or 146 N). Estimates of Herrnstein's kappa were obtained at each reinforcer magnitude. The results were: (1) response rate was more sensitive to changes in reinforcement rate at the high than at the low force requirement, (2) kappa increased from the beginning to the end of the magnitude range for all subjects at both force requirements, (3) the reciprocal of kappa was a linear function of the reciprocal of reinforcer magnitude for seven of the eight data sets, and (4) the rate of change of kappa was greater at the high than at the low force requirement by an order of magnitude or more. The second and third findings confirm predictions made by linear system theory, and replicate the results of an earlier experiment (McDowell & Wood, 1984). The fourth finding confirms a further prediction of the theory and supports the theory's interpretation of conflicting data on the constancy of Herrnstein's kappa.

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

The use of next-generation sequencing technologies to produce genomic copy number data has recently been described. Most approaches, however, reply on optimal starting DNA, and are therefore unsuitable for the analysis of formalin-fixed paraffin-embedded (FFPE) samples, which largely precludes the analysis of many tumour series. We have sought to challenge the limits of this technique with regards to quality and quantity of starting material and the depth of sequencing required. We confirm that the technique can be used to interrogate DNA from cell lines, fresh frozen material and FFPE samples to assess copy number variation. We show that as little as 5 ng of DNA is needed to generate a copy number karyogram, and follow this up with data from a series of FFPE biopsies and surgical samples. We have used various levels of sample multiplexing to demonstrate the adjustable resolution of the methodology, depending on the number of samples and available resources. We also demonstrate reproducibility by use of replicate samples and comparison with microarray-based comparative genomic hybridization (aCGH) and digital PCR. This technique can be valuable in both the analysis of routine diagnostic samples and in examining large repositories of fixed archival material.

Cloning of the CYP51 gene from the eyespot pathogen Tapesia yallundae indicates that resistance to the DMI fungicide prochloraz is not related to sequence changes in the gene encoding the target site enzyme

Resistance to sterol 14 alpha-demethylase inhibitor (DMI) fungicides has been correlated with mutations in the CYP51 gene encoding the target enzyme eburicol 14 alpha-demethylase. CYP51 was isolated from the eyespot pathogen Tapesia yallundae revealing a predicted 526-amino acid product exhibiting homology to other fungal CYP51s. CYP51 was sequenced from four field isolates sensitive or resistant to the DMI fungicide prochloraz and partially sequenced from two further isolates and eight progeny from a cross between prochloraz-sensitive and -resistant parents. Two alleles of the gene were detected termed CYP51-1 and CYP51-2. No correlation was found between sequence change and fungicide sensitivity. Therefore prochloraz resistance involved a mechanism other than mutation in the target site gene.

Differences in visuospatial judgement in reading-disabled and normal children

Both visual and verbal impairments have been reported in two independent streams of research into the etiology of dyslexia or reading-disability. To address the question of the presence of either abnormality in reading-disabled children, visuospatial and phonological ability were assessed and contrasted in 39 Normal and 26 Reading-disabled children. To assess whether these deficits are unique to dyslexia, scores were also compared to those of a group of 12 Poor Readers ("garden-variety" backward readers with low IQs). The Benton Judgement of Line Orientation Test was used for its simplicity and clinical reliability: Reading-disabled subjects performed significantly worse than Normal readers (but similar to Poor Readers). Reading-disabled subjects performed worse for lines in the left-hemifield compared to Normal subjects and also had a greater tendency to scan the task in reverse order (left-to-right) from the usual right-to-left scanning pattern observed in the Normal group when performing this test. When both verbal and visuospatial variables were combined in a multiple regression analysis, 71% of reading variance could be accounted for. These results suggest that Reading-disabled children not only have poor phonological awareness, but they also show visuospatial deficits. However, poor performance on both these tasks was also observed in the group of Poor Readers, suggesting that these deficits are not unique to children with specific reading disability. The results lend further evidence to the hypothesis that reading disability cannot solely be attributed to left-hemisphere dysfunction resulting in phonological impairment. There are other behavioral deficits, possibly caused by a common mechanism, some of which, like visuospatial ability, can be measured by simple behavioral tests such as the Judgment of Line Orientation Test.

Temporal and spatial processing in reading disabled and normal children

The ability to process temporal and spatial visual stimuli was studied to investigate the role these functions play in the reading process. Previous studies of this type have often been confounded by memory involvement, or did not take into account the evidence which suggests a visual transient deficient in some dyslexics. Normal (n = 39), reading disabled (n = 26), and backward reading children (n=12) were compared on a visual computer game, which consisted of a temporal and a analogous spatial dot counting task. Reading disabled children performed significantly worse than normal children on the Temporal Dot Task, but were only mildly impaired on the Spatial Dot Task, Backward readers were not significantly better than the reading disabled group on either task, suggesting that poor poor visual temporal processing is not specific to dyslexia. In a group of 93 children, a regression model including age, verbal IQ, phonological awareness, and visual temporal processing ability, predicted 73% of the variance of reading ability. The results suggest that dyslexics perform worse in tasks that require fast, sequential processing and that this impairment may be partially responsible for their reading difficulties.

Differences in eye movements and reading problems in dyslexic and normal children

It has been suggested that eye movement abnormalities seen in dyslexics are attributable to their language problems. In order to investigate this claim, we studied eye movements in dyslexic children, during several non-reading tasks. Dyslexic children were compared to normal and backward readers on measures of fixation, vergence amplitude, saccade and smooth pursuit. The results were compared to the children's phonological ability. Dyslexic children (n = 26) had significantly worse eye movement stability during fixation of small targets than normal children (n = 39). Vergence amplitudes were lower for dyslexics than for controls. A qualitative assessment of saccadic eye movements revealed that dyslexics exhibit fixation instability at the end of saccades. Assessment of smooth pursuit revealed poor smooth pursuit in the dyslexic group, particularly when pursuing a target moving from left to right. Dyslexic children also performed significantly worse than normal children on a test of phonological awareness (Pig Latin). Eye movement results were studied in the light of the findings on phonological awareness: dyslexics with small vergence amplitudes also always have poor phonemic awareness. However, poor fixation control is found in dyslexics with or without poor phonological ability. The backward reading children performed similar to the dyslexics on all tests, suggesting that the deficiencies observed in this study are not specific to children with dyslexia. The problems experienced by the children (revealed by a questionnaire) are in agreement with those measured in terms of eye movement recordings and phonemic awareness. Sex, handedness, IQ or the presence of attention deficit disorder (ADD) did not appear to influence the children's performances on any of the eye movement tasks. The presence of oculomotor abnormalities in a non-reading task strongly suggests that the underlying deficit in the control of eye movements seen in dyslexics is not caused by language problems alone.

The management of infants for cardiac surgery under deep hypothermia

Deep hypothermia is now employed for open heart surgery in infants. The method of surface cooling infants to 25° C and then by-pass cooling down to 15–20° C prior to exsanguination is described. This provides a still heart and ideal operating conditions. The infants are re-warmed on by-pass. Some of the physiological effects of hypothermia and the methods employed to counteract these are discussed. The aims are to reduce temperature gradients, improve cerebral oxygen supply, avoid arrhythmias and secure haemostasis.

The experience in 33 operations is outlined. Seventeen patients were under one year of age.