Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer

Circulating tumor DNA (ctDNA) sequencing guides therapy decisions but has been studied mostly in small cohorts without sufficient follow-up to determine its influence on overall survival. We prospectively followed an international cohort of 1,127 patients with non-small-cell lung cancer and ctDNA-guided therapy. ctDNA detection was associated with shorter survival (hazard ratio (HR), 2.05; 95% confidence interval (CI), 1.74-2.42; P < 0.001) independently of clinicopathologic features and metabolic tumor volume. Among the 722 (64%) patients with detectable ctDNA, 255 (23%) matched to targeted therapy by ctDNA sequencing had longer survival than those not treated with targeted therapy (HR, 0.63; 95% CI, 0.52-0.76; P < 0.001). Genomic alterations in ctDNA not detected by time-matched tissue sequencing were found in 25% of the patients. These ctDNA-only alterations disproportionately featured subclonal drivers of resistance, including RICTOR and PIK3CA alterations, and were associated with short survival. Minimally invasive ctDNA profiling can identify heterogeneous drivers not captured in tissue sequencing and expand community access to life-prolonging therapy.

Tumor volume as a predictor of cell free DNA mutation detection in advanced non-small cell lung cancer

Background

Cell free DNA (cfDNA) is an exciting biomarker with applications across the cancer care continuum. Determinants of cfDNA shedding dynamics remain an active research area. We performed a detailed analysis of tumor volume and factors associated with detection of cfDNA mutations.

Methods

Patients with advanced non-small cell lung cancers (NSCLCs) were prospectively enrolled on a plasma biomarker protocol. Next generation sequencing (NGS) was performed using a validated, bias-corrected, hybrid-capture panel assay of lung cancer-associated genes. Volume of tumor in different subsites and total tumor volume were determined through manual volume delineation using PET/CT and brain magnetic resonance imaging (MRI) imaging. The primary endpoint was detection of cfDNA mutation; secondary endpoints were overall survival (OS) and variant allele frequency (VAF).

Results

There were 110 patients included, 78 of whom had at least one mutation detected. Median total tumor volume for the entire cohort, patients with mutation detected, and patients with no mutation detected were 66 mL (range, 2-1,383 mL), 76 mL (range, 5-1,383 mL), and 45 mL (range, 2-460 mL), respectively (P=0.002; mutation detected vs. not). The optimal total tumor volume threshold to predict increased probability of mutation detection was 65 mL (P=0.006). Total tumor volume greater than 65 mL was a significant predictor of mutation detection on multivariate analysis (OR: 4.30, P=0.003). Significant predictors of OS were age (HR: 1.04, P=0.002), detection of cfDNA mutation (HR: 2.11, P=0.024), and presence of bone metastases (HR: 1.66, P=0.047).

Conclusions

Total tumor volume greater than 65 mL was associated with cfDNA mutation detection in patients with advanced NSCLC.

Diverse alterations associated with resistance to KRAS(G12C) inhibition

Inactive state-selective KRAS(G12C) inhibitors^1-8 demonstrate a 30-40% response rate and result in approximately 6-month median progression-free survival in patients with lung cancer⁹. The genetic basis for resistance to these first-in-class mutant GTPase inhibitors remains under investigation. Here we evaluated matched pre-treatment and post-treatment specimens from 43 patients treated with the KRAS(G12C) inhibitor sotorasib. Multiple treatment-emergent alterations were observed across 27 patients, including alterations in KRAS, NRAS, BRAF, EGFR, FGFR2, MYC and other genes. In preclinical patient-derived xenograft and cell line models, resistance to KRAS(G12C) inhibition was associated with low allele frequency hotspot mutations in KRAS(G12V or G13D), NRAS(Q61K or G13R), MRAS(Q71R) and/or BRAF(G596R), mirroring observations in patients. Single-cell sequencing in an isogenic lineage identified secondary RAS and/or BRAF mutations in the same cells as KRAS(G12C), where they bypassed inhibition without affecting target inactivation. Genetic or pharmacological targeting of ERK signalling intermediates enhanced the antiproliferative effect of G12C inhibitor treatment in models with acquired RAS or BRAF mutations. Our study thus suggests a heterogenous pattern of resistance with multiple subclonal events emerging during G12C inhibitor treatment. A subset of patients in our cohort acquired oncogenic KRAS, NRAS or BRAF mutations, and resistance in this setting may be delayed by co-targeting of ERK signalling intermediates. These findings merit broader evaluation in prospective clinical trials.

SPACEWALK: A Remote Participation Study of ALK Resistance Leveraging Plasma Cell-Free DNA Genotyping

Introduction

Remote consent and enrollment offer a unique opportunity to provide rare cancer populations with access to clinical research. The genomic analysis of plasma cell-free DNA (cfDNA) permits remote characterization of the cancer genome. We hypothesized we could leverage these approaches to remotely study drug resistance in patients with metastatic ALK-positive NSCLC.

Methods

The SPACEWALK study (Study of Plasma Next-Generation Sequencing for Remote Assessment, Characterization, Evaluation of Patients With ALK Drug Resistance) enrolled patients with ALK-positive NSCLC and progression on a next-generation ALK inhibitor who could participate remotely. Plasma was collected for next-generation sequencing (NGS) of cfDNA before initiating subsequent therapy, with results returned and subsequent therapy studied.

Results

Of the 62 patients enrolled, an ALK fusion was detected in 27 (44%) with a median allelic fraction of 2.6%. Among these 27 patients, a potential resistance mechanism was identified in 17 patients (63%): eight cases (30%) had secondary ALK kinase domain resistance mutations, three cases (11%) had bypass track resistance, and six cases (22%) had both ALK resistance mutations and bypass resistance. The most frequently detected mechanism of bypass resistance was MET amplification. Repeat plasma NGS was performed in 14 patients after subsequent treatment was initiated, with seven (50%) patients exhibiting greater than 50% reductions in ALK fusion allelic fraction.

Conclusions

Through the leveraging of remote participation, plasma NGS offers an optimal mechanism for characterizing resistance to emerging targeted therapies in rare cancer populations, though sensitivity depends on adequate tumor DNA samples. Repeat cfDNA analysis on therapy may offer an objective monitoring approach to remotely study treatment response.

Clinical utility of next-generation sequencing-based ctDNA testing for common and novel ALK fusions

OBJECTIVES

Liquid biopsy for plasma circulating tumor DNA (ctDNA) next-generation sequencing (NGS) can detect ALK fusions, though data on clinical utility of this technology in the real world is limited.

MATERIALS AND METHODS

Patients with lung cancer without known oncogenic drivers or who had acquired resistance to therapy (n = 736) underwent prospective plasma ctDNA NGS. A subset of this cohort (n = 497) also had tissue NGS. We evaluated ALK fusion detection, turnaround time (TAT), plasma and tissue concordance, matching to therapy, and treatment response.

RESULTS

ctDNA identified an ALK fusion in 21 patients (3%) with a variety of breakpoints and fusion partners, including EML4, CLTC, and PON1, a novel ALK fusion partner. TAT for ctDNA NGS was shorter than tissue NGS (10 vs. 20 days; p < 0.001). Among ALK fusions identified by ctDNA, 93% (13/14, 95% CI 66%-99%) were concordant with tissue evaluation. Among ALK fusions detected by tissue NGS, 54% (13/24, 95% CI 33%-74%) were concordant with plasma ctDNA. ctDNA matched patients to ALK-directed therapy with subsequent clinical response, including four patients matched on the basis of ctDNA results alone due to inadequate or delayed tissue testing. Serial ctDNA analysis detected MET amplification (n = 2) and ALK G1202R mutation (n = 2) as mechanisms of acquired resistance to ALK-directed therapy.

CONCLUSION

Our findings support a complementary role for ctDNA in detection of ALK fusions and other alterations at diagnosis and therapeutic resistance settings.

Acquired Resistance to KRASG12C Inhibition in Cancer

BACKGROUND

Clinical trials of the KRAS inhibitors adagrasib and sotorasib have shown promising activity in cancers harboring KRAS glycine-to-cysteine amino acid substitutions at codon 12 (KRAS^G12C). The mechanisms of acquired resistance to these therapies are currently unknown.

METHODS

Among patients with KRAS^G12C -mutant cancers treated with adagrasib monotherapy, we performed genomic and histologic analyses that compared pretreatment samples with those obtained after the development of resistance. Cell-based experiments were conducted to study mutations that confer resistance to KRAS^G12C inhibitors.

RESULTS

A total of 38 patients were included in this study: 27 with non-small-cell lung cancer, 10 with colorectal cancer, and 1 with appendiceal cancer. Putative mechanisms of resistance to adagrasib were detected in 17 patients (45% of the cohort), of whom 7 (18% of the cohort) had multiple coincident mechanisms. Acquired KRAS alterations included G12D/R/V/W, G13D, Q61H, R68S, H95D/Q/R, Y96C, and high-level amplification of the KRAS^G12C allele. Acquired bypass mechanisms of resistance included MET amplification; activating mutations in NRAS, BRAF, MAP2K1, and RET; oncogenic fusions involving ALK, RET, BRAF, RAF1, and FGFR3; and loss-of-function mutations in NF1 and PTEN. In two of nine patients with lung adenocarcinoma for whom paired tissue-biopsy samples were available, histologic transformation to squamous-cell carcinoma was observed without identification of any other resistance mechanisms. Using an in vitro deep mutational scanning screen, we systematically defined the landscape of KRAS mutations that confer resistance to KRAS^G12C inhibitors.

CONCLUSIONS

Diverse genomic and histologic mechanisms impart resistance to covalent KRAS^G12C inhibitors, and new therapeutic strategies are required to delay and overcome this drug resistance in patients with cancer. (Funded by Mirati Therapeutics and others; ClinicalTrials.gov number, NCT03785249.).

Abstract 709: The utility of plasma ctDNA for detection of KRAS G12C and other mutations in lung cancers

Background: KRAS is the most common oncogene in lung cancer, but has historically been considered undruggable. The recent development of mutant-selective KRAS G12C inhibitors has for the first time created potential therapeutic opportunities for this unmet need. Simultaneously, circulating tumor DNA (ctDNA) is increasingly being used to detect targetable oncogenes in patients with metastatic lung cancers. There is limited data regarding the utility of plasma ctDNA in specifically identifying KRAS G12C mutations.

Methods: Plasma was collected from 599 patients with lung cancer seen at Memorial Sloan Kettering Cancer Center between 10/2016 and 1/2019. ctDNA sequencing was performed using the ctDX-Lung Assay (Resolution Bioscience; Kirkland, WA). Tissue DNA sequencing was carried out using the MSK-IMPACT assay.

Results: Mutations in KRAS (KRAS+) were detected in 129 patients (21.5%). Of patients with KRAS+ lung cancers, 116 had metastatic disease at the time of plasma testing. Plasma testing was carried out within 90 days of metastatic diagnosis in 92 of the 116 metastatic KRAS+ patients (79.3%), of whom 66 patients had both plasma and tissue sequencing available for comparison. 59 of the 66 patients (89.4%) had not had systemic treatment at the time of plasma testing. Average turn-around-time (TAT) for ctDNA testing in this cohort of 66 patients was 10 days, while average TAT for tissue sequencing was 22 days. ctDNA detected a KRAS mutation in 48 of the 66 patients (72.7%). A G12C mutation was found in the tissue and/or blood from 29 patients (43.9%), while 37 patients (56.1%) had other KRAS mutations. In one patient with a G12C mutation detected on plasma testing, no KRAS mutation or other known oncogenic drivers were found on tissue testing, though with limited tumor cells in the tissue sample. 75.6% of the patients with G12C mutations had KRAS detectable in the plasma, as compared to 70.3% of patients with other KRAS mutations (p=0.6). Within the cohort of patients with paired tissue and plasma testing, at a median follow-up of 202 days post-metastatic diagnosis, survival was longer in those patients without detectable KRAS in the plasma as compared to those patients with detectable plasma KRAS (log rank (Mantel-Cox), p&lt;0.001, log rank HR 7.9, 95% CI: 3.7-16.8).

Conclusion: Plasma testing was able to rapidly detect KRAS G12C mutations in the majority of patients with this alteration, which may guide G12C inhibitor therapy. In our cohort, patients that shed KRAS mutant DNA into the plasma had shorter survival.

Citation Format: Yonina R. Murciano-Goroff, Kathryn C. Arbour, Michael D. Offin, Hai-Yan Y. Tu, Emily S. Lebow, Tristan S. Shaffer, Caterina Bertucci, Syed A. Hosseini, Kavita Garg, Lee P. Lim, Mark Li, Jason C. Chang, Jorge S. Reis-Filho, Pedram Razavi, James M. Isbell, Gregory J. Riely, David M. Hyman, Piro Lito, Bob T. Li. The utility of plasma ctDNA for detection of KRAS G12C and other mutations in lung cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 709.

Abstract 12: Characterizing KRAS G12C and other mutations in plasma ctDNA from patients with lung cancer

Background: KRAS is the most common oncogene in lung cancers, but despite decades of intense research, there are no FDA-approved drugs targeting these cancers. Recent recognition that KRAS G12C harbors a binding pocket near the mutant cysteine residue has enabled the development of a new class of allele-specific inhibitors that are currently in early-phase trials. However, the mutational landscape and clinical characteristics of KRAS G12C mutant lung cancers are not well understood. The clinical use of plasma circulating tumor DNA (ctDNA) provides an opportunity to characterize this disease.

Methods: Plasma was collected from 636 patients seen at Memorial Sloan Kettering Cancer Center between 11/2016 and 5/2019. ctDNA was extracted and analyzed using the validated 23-gene ctDx-Lung assay (Resolution Bioscience; Kirkland, WA). Categorical comparisons were carried out using Fisher’s exact test.

Results: 95 NSCLC patients were identified as having alterations in KRAS based on ctDNA analysis, of whom 93.7% were metastatic at the time of plasma testing. 81.8% and 80.6% of G12C and non-G12C patients were systemic treatment naive at the time of testing, respectively. 33 patients had KRAS G12C mutations (34.7%), and 62 had other KRAS mutations (65.3%), including mutations in G12D in 24 patients, G12V in 9 patients, Q61H in 5, G12A in 8, G12S in 7, G13C in 3, G13D in 2, G13V and G12F in one patient each, as well as both Q61L and G13C in 2 patients. 60.6% of KRAS G12C patients and 53.2% of KRAS non-G12C were female. 97% of patients with G12C mutations were former smokers as compared to 77.4% in the non-G12C group (p=0.02). Of patients with stage IV adenocarcinoma with plasma KRAS detection, 9 of 25 patients with G12C were alive at the time of data analysis (36%), while 28 of 53 (52.8%) patients with KRAS non-G12C disease were alive (p =0.23; days from metastatic diagnosis to data analysis: G12C patients: 113-608, median: 396.0; non-G12C patients: 79-2248, median: 427.5). For patients with KRAS G12C mutations, co-alterations were found in TP53 (n=12, 36.4%), as well as SNVs in ROS1 (n=2), and in ALK (n=1). In patients with non-G12C KRAS detected on plasma, co-alterations were found in TP53 (n=26, 41.9%), and PIK3CA (n=3), with additional concurrent alterations in RTKs, including one patient with EGFR K714N, one with EGFR L858R, one patient with an FGFR1 amplification, and one each with an FGFR1 and FGFR3 mutation. Alterations were also detected in MET R988C (n=1) and a MET exon 14 splice variation, with SNVs in RET (n=2), as well as in ALK, ROS1, and AKT1, with a MET as well as a RICTOR amplification in one patient each.

Conclusion: Patients with KRAS G12C mutations detected on plasma analysis were more likely to be smokers. Our data support the need for further analysis of co-alterations both in plasma and on tissue sequencing to aid the development of therapies for patients with KRAS mutations as well as to advance research on combinations of G12C inhibitors with other pathway inhibitors.

Citation Format: Yonina R. Murciano-Goroff, Emily S. Lebow, Hai-Yan Tu, Mark Li, Lee P. Lim, Kathryn C. Arbour, William Travis, David B. Solit, Marc Ladanyi, David R. Jones, Charles M. Rudin, Andres Martinez, Mackenzie L. Myers, Alexander Makhnin, Pedram Razavi, Michael D. Offin, James W. Isbell, Gregory J. Riely, David M. Hyman, Piro Lito, Bob T. Li. Characterizing KRAS G12C and other mutations in plasma ctDNA from patients with lung cancer [abstract]. In: Proceedings of the AACR Special Conference on Advancing Precision Medicine Drug Development: Incorporation of Real-World Data and Other Novel Strategies; Jan 9-12, 2020; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_1):Abstract nr 12.

Blood-Based Surveillance Monitoring of Circulating Tumor DNA From Patients With SCLC Detects Disease Relapse and Predicts Death in Patients With Limited-Stage Disease

Introduction

Most patients (70%) with limited-stage SCLC (LS-SCLC) who are treated with curative-intent therapy suffer disease relapse and cancer-related death. We evaluated circulating tumor DNA (ctDNA) as a predictor of disease relapse and death after definitive therapy in patients with LS-SCLC.

Methods

In our previous work, we developed a plasma-based ctDNA assay to sequence 14 genes (TP53, RB1, BRAF, KIT, NOTCH1-4, PIK3CA, PTEN, FGFR1, MYC, MYCL1, and MYCN) that are frequently mutated in SCLC. In this work, we evaluated 177 plasma samples from 23 patients with LS-SCLC who completed definitive chemoradiation (n = 21) or surgical resection (n = 2) and had an end-of-treatment blood collection (median 4 d, range 0–40 d from treatment completion) plus monthly surveillance blood sampling. Median overall survival (OS) and progression-free survival (PFS) were compared using a Wilcoxon test.

Results

The median OS among patients in whom we ever detected ctDNA after definitive treatment (n = 15) was 18.2 months compared with a median OS of greater than 48 months among patients in whom we never detected ctDNA after definitive treatment (n = 8; p = 0.081). The median PFS among patients in whom we ever detected ctDNA after definitive treatment was 9.1 months compared with a median PFS of greater than 48 months among patients in whom we never detected ctDNA after definitive treatment (p < 0.001).

Conclusions

Detection of ctDNA in patients with LS-SCLC after curative-intent therapy predicts disease relapse and death. Prospective trials using ctDNA as an integral biomarker for therapeutic selection should be considered in SCLC.

A Prospective Study of Circulating Tumor DNA to Guide Matched Targeted Therapy in Lung Cancers

BACKGROUND

Liquid biopsy for plasma circulating tumor DNA (ctDNA) next-generation sequencing (NGS) is commercially available and increasingly adopted in clinical practice despite a paucity of prospective data to support its use.

METHODS

Patients with advanced lung cancers who had no known oncogenic driver or developed resistance to current targeted therapy (n = 210) underwent plasma NGS, targeting 21 genes. A subset of patients had concurrent tissue NGS testing using a 468-gene panel (n = 106). Oncogenic driver detection, test turnaround time (TAT), concordance, and treatment response guided by plasma NGS were measured. All statistical tests were two-sided.

RESULTS

Somatic mutations were detected in 64.3% (135/210) of patients. ctDNA detection was lower in patients who were on systemic therapy at the time of plasma collection compared with those who were not (30/70, 42.9% vs 105/140, 75.0%; OR = 0.26, 95% CI = 0.1 to 0.5, P < .001). The median TAT of plasma NGS was shorter than tissue NGS (9 vs 20 days; P < .001). Overall concordance, defined as the proportion of patients for whom at least one identical genomic alteration was identified in both tissue and plasma, was 56.6% (60/106, 95% CI = 46.6% to 66.2%). Among patients who tested plasma NGS positive, 89.6% (60/67; 95% CI = 79.7% to 95.7%) were also concordant on tissue NGS and 60.6% (60/99; 95% CI = 50.3% to 70.3%) vice versa. Patients who tested plasma NGS positive for oncogenic drivers had tissue NGS concordance of 96.1% (49/51, 95% CI = 86.5% to 99.5%), and directly led to matched targeted therapy in 21.9% (46/210) with clinical response.

CONCLUSIONS

Plasma ctDNA NGS detected a variety of oncogenic drivers with a shorter TAT compared with tissue NGS and matched patients to targeted therapy with clinical response. Positive findings on plasma NGS were highly concordant with tissue NGS and can guide immediate therapy; however, a negative finding in plasma requires further testing. Our findings support the potential incorporation of plasma NGS into practice guidelines.

Monitoring Therapeutic Response and Resistance: Analysis of Circulating Tumor DNA in Patients With ALK+ Lung Cancer

INTRODUCTION

Despite initial effectiveness of ALK receptor tyrosine kinase inhibitors (TKIs) in patients with ALK+ NSCLC, therapeutic resistance will ultimately develop. Serial tracking of genetic alterations detected in circulating tumor DNA (ctDNA) can be an informative strategy to identify response and resistance. This study evaluated the utility of analyzing ctDNA as a function of response to ensartinib, a potent second-generation ALK TKI.

METHODS

Pre-treatment plasma was collected from 76 patients with ALK+ NSCLC who were ALK TKI-naive or had received prior ALK TKI, and analyzed for specific genetic alterations. Longitudinal plasma samples were analyzed from a subset (n = 11) of patients. Analysis of pre-treatment tumor biopsy specimens from 22 patients was compared with plasma.

RESULTS

Disease-associated genetic alterations were detected in 74% (56 of 76) of patients, the most common being EML4-ALK. Concordance of ALK fusion between plasma and tissue was 91% (20 of 22 blood and tissue samples). Twenty-four ALK kinase domain mutations were detected in 15 patients, all had previously received an ALK TKI; G1269A was the most prevalent (4 of 24). Patients with a detectable EML4-ALK variant 1 (V1) fusion had improved response (9 of 17 patients; 53%) to ensartinib compared to patients with EML4-ALK V3 fusion (one of seven patients; 14%). Serial changes in ALK alterations were observed during therapy.

CONCLUSIONS

Clinical utility of ctDNA was shown, both at pre-treatment by identifying a potential subgroup of ALK+ NSCLC patients who may derive more benefit from ensartinib and longitudinally by tracking resistance. Prospective application of this technology may translate to improved outcomes for NSCLC patients treated with ALK TKIs.

Abstract 1374: Building an effective concordance study: Plasma Next Generation Sequencing (NGS) for oncogenic fusion detection in non-small cell lung carcinoma (NSCLC)

Background: Non-invasive genotyping of cell-free DNA (cfDNA) is increasingly used in cancer care as tumor biopsies may be inadequate or unavailable. As clinical adaptation of liquid biopsies is driven in large part by commercial vendors that offer proprietary PCR or NGS-based tests, rigorous validation of these assays is essential to ensure maximum clinical benefit. Recent efforts to compare cfDNA diagnostics have not focused on clinically actionable mutations or used tumor to verify plasma results. The present study analyzes the concordance in reports of actionable gene fusions in NSCLC from two independent, commercial plasma NGS tests, compares the breakpoint characteristics between tissue and plasma, and highlights how differences in sequencing and bioinformatic analysis can be a source of false negatives.

Methods/Results: We studied a cohort of 169 NSCLC patients (pts) that had plasma analyzed by Guardant 360 between April 2016 and July 2018. In those with tumor positive ALK, ROS1, or RET fusions (n=16), banked cfDNA from a separate tube of plasma (69% collected within 2 weeks) underwent local testing and sequencing at DFCI using Resolution Bioscience's pre-production ctDx-Lung kit with remote bioinformatic variant calling performed by Resolution Bioscience; all parties involved were blinded to tumor genotype and Guardant results. Locked results were unblinded for post hoc analysis. The ctDx-lung kit detected 13 out 16 fusions (AF% range 80-0.3%), while Guardant360 detected 7 (AF% range 10-0.3%). Guardant360 tended to report lower AFs than ctDx-lung, though corroborating TP53 alterations were of similar AFs. Of the cases where both assays did not detect any fusions, no other shared SNVs were detected, possibly due to low shed of tumor DNA. Of the 13 cases where a fusion was detected in plasma by ctDx-lung, 4 rearrangements could be characterized as ‘non-productive’ due to opposite transcriptional orientations and comprised 50% (3/6) of the fusions not detected by Guardant360. Only one case detected by Guardant360 was ‘non-productive’. Of the 13 cases where a fusion was detected in plasma, 89% (8/9) of pts with productive fusions and 75% of pts (3/4) with ‘non-productive’ fusions responded to TKI therapies. Additional unblinding is ongoing to better understand false negative cases.

Conclusions: Here, we demonstrate that a rigorous approach to benchmarking plasma genotyping assays should 1) focus on actionable mutations, 2) use tumor as a gold standard for establishing true and false positives and negatives, and 3) include orthogonal validation to address assay design and bioinformatic analyses as sources of discordance. Our study further highlights the challenges of fusion detection and interpretation and the need for platform cross-comparisons to realize the potential of liquid biopsy to increase access to personalized cancer care.

Citation Format: Julianna G. Supplee, Marina S. Milan, Kristy T. Potts, Lynette M. Sholl, Tristan S. Shaffer, Lee P. Lim, Pasi A. Janne, Geoffrey R. Oxnard, Cloud P. Paweletz. Building an effective concordance study: Plasma Next Generation Sequencing (NGS) for oncogenic fusion detection in non-small cell lung carcinoma (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1374.

Longitudinal Cell-Free DNA Analysis in Patients with Small Cell Lung Cancer Reveals Dynamic Insights into Treatment Efficacy and Disease Relapse

INTRODUCTION

Patients with SCLC have a poor prognosis and limited treatment options. Because access to longitudinal tumor samples is very limited in patients with this disease, we chose to focus our studies on the characterization of plasma cell-free DNA (cfDNA) for rapid, noninvasive monitoring of disease burden.

METHODS

We developed a liquid biopsy assay that quantifies somatic variants in cfDNA. The assay detects single nucleotide variants, copy number alterations, and insertions or deletions in 14 genes that are frequently mutated in SCLC, including tumor protein p53 gene (TP53), retinoblastoma 1 gene (RB1), BRAF, KIT proto-oncogene receptor tyrosine kinase gene (KIT), notch 1 gene (NOTCH1), notch 2 gene (NOTCH2), notch 3 gene (NOTCH3), notch 4 gene (NOTCH4), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha gene (PIK3CA), phosphatase and tensin homolog gene (PTEN), fibroblast growth factor receptor 1 gene (FGFR1), v-myc avian myelocytomatosis viral oncogene homolog gene (MYC), v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog gene (MYCL1), and v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog gene (MYCN).

RESULTS

Over the course of 26 months of peripheral blood collection, we examined 140 plasma samples from 27 patients. We detected disease-associated mutations in 85% of patient samples with mutant allele frequencies ranging from 0.1% to 87%. In our cohort, 59% of the patients had extensive-stage disease, and the most common mutations occurred in TP53 (70%) and RB1 (52%). In addition to mutations in TP53 and RB1, we detected alterations in 10 additional genes in our patient population (PTEN, NOTCH1, NOTCH2, NOTCH3, NOTCH4, MYC, MYCL1, PIK3CA, KIT, and BRAF). The observed allele frequencies and copy number alterations tracked closely with treatment responses. Notably, in several cases analysis of cfDNA provided evidence of disease relapse before conventional imaging.

CONCLUSIONS

These results suggest that liquid biopsies are readily applicable in patients with SCLC and can potentially provide improved monitoring of disease burden, depth of response to treatment, and timely warning of disease relapse in patients with this disease.

Abstract 4949: Longitudinal monitoring of cell-free DNA in patients with small cell lung cancer reveals dynamic insights into treatment efficacy and disease relapse

Introduction: Small cell lung cancer (SCLC) is a highly lethal neuroendocrine malignancy that accounts for approximately 10-15% of all lung cancers and is responsible for approximately 30,000 deaths annually in the United States and 200,000 deaths worldwide every year1. There is an urgent need to develop novel treatment strategies for patients with this disease. We sought to improve the quality of patient care by establishing a liquid biopsy assay for rapid, noninvasive monitoring of disease burden.

Design: The SCLC assay relies on targeted next-generation DNA sequencing of cell-free DNA (cfDNA) collected from patient plasma. The assay targets a panel of 14 genes that are frequently mutated in SCLC2. We examined a total of 141 plasma samples from a cohort of 27 patients. 11 patients had limited stage SCLC and 16 patients had extensive stage SCLC. The analyzed plasma samples were collected during the course of patient treatment and included time points before and after chemotherapy or immunotherapy.

Results: We detected somatic, disease-associated mutations in the cfDNA of 78% of patient samples (21/27). The allele frequency of cfDNA ranged from ≤0.5% to ≥85%. The most commonly mutated genes were TP53 and RB1, which were found in 17/27 and 10/27 samples, respectively. We also detected single nucleotide variants in PIK3CA (3/27) and PTEN (1/27) as well as copy number variants in MYC and MYCL1 (2/27). The observed mutant allele frequencies in longitudinal samples tracked closely with treatment responses. Strikingly, we found instances where the assay detected the reappearance of tumor-associated markers several weeks before clinical evidence of relapse was detected.

Conclusions: cfDNA sequencing allows for improved monitoring of disease burden, depth of responses to treatment, and timely warning of disease relapse in patients with SCLC.

References:

1. Society, A.C., Cancer Facts and Figures 2015. American Cancer Society, Atlanta, Ga, 2015.

2. George, J. et al., Comprehensive genomic profiles of small cell lung cancer, Nature 524:47

Citation Format: Christine M. Lovly, Karinna Almodovar, Wade T. Iams, Catherine B. Meador, Sally York, Leora Horn, Christopher K. Raymond, Jennifer Hernandez, Lee P. Lim. Longitudinal monitoring of cell-free DNA in patients with small cell lung cancer reveals dynamic insights into treatment efficacy and disease relapse [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4949. doi:10.1158/1538-7445.AM2017-4949

Stressful Life Events of Dental Students and Salivary Immunoglobulin A

To study the perceived sources of stressful events in dental students and the relationships between their self-perceived stress levels and salivary IgA. Undergraduates as well as postgraduates at the Faculty of Dentistry, National University of Singapore were surveyed one month after the new term. A 38-item dental environmental stress (DES) questionnaire, with subscales of academic work (AW), clinical factors (CF), faculty and administration factors (FA) and personal factors (PF), was used to identify the potential stressors in the dental environment. A 4-point perceived stress scale was used to rank their self-perceived stress levels. Enzyme linked immunosorbent assay method was used to determine the salivary IgA level. One hundred and thirty students (81.3% - valid response rate) participated in the study. Overall, students ranked AW with the highest score (mean 2.76), followed by CF (2.67), FA (2.24) and PF (2.16). Among the 38 items of DES questionnaire, 1st year students perceived “fear of being unable to catch up if behind” as the most stressful event (mean 3.30). For 2nd and 3rd year students, examination and grades had the highest scores (mean 3.28, 3.19, respectively). Completing graduation requirements was the most important stressor for 4th year students (mean 3.89). Postgraduates perceived atmosphere created by clinical faculty was most stressful to them (mean 3.05). The mean total perceived stress scores were highest (22.1) in 1st year students and lowest (21.0) in postgraduates, however, no significant different among various classes. First year students had the lowest IgA secretion rates (geometric mean [GM] 46.8 μg/min), significantly lower (p<0.05) than postgraduates (GM 79.4 μg/min). An inverse correlation was noted between perceived stress scale and log IgA secretion rates (r=-0.20, p=0.002.). AW was also significantly inversely correlated with salivary IgA (r=-0.18, p=0.04). Dental students in different academic years perceived different important stressors. Salivary IgA secretion rate correlated inversely with self perceived stress.

Bias-Corrected Targeted Next-Generation Sequencing for Rapid, Multiplexed Detection of Actionable Alterations in Cell-Free DNA from Advanced Lung Cancer Patients

PURPOSE

Tumor genotyping is a powerful tool for guiding non-small cell lung cancer (NSCLC) care; however, comprehensive tumor genotyping can be logistically cumbersome. To facilitate genotyping, we developed a next-generation sequencing (NGS) assay using a desktop sequencer to detect actionable mutations and rearrangements in cell-free plasma DNA (cfDNA).

EXPERIMENTAL DESIGN

An NGS panel was developed targeting 11 driver oncogenes found in NSCLC. Targeted NGS was performed using a novel methodology that maximizes on-target reads, and minimizes artifact, and was validated on DNA dilutions derived from cell lines. Plasma NGS was then blindly performed on 48 patients with advanced, progressive NSCLC and a known tumor genotype, and explored in two patients with incomplete tumor genotyping.

RESULTS

NGS could identify mutations present in DNA dilutions at ≥ 0.4% allelic frequency with 100% sensitivity/specificity. Plasma NGS detected a broad range of driver and resistance mutations, including ALK, ROS1, and RET rearrangements, HER2 insertions, and MET amplification, with 100% specificity. Sensitivity was 77% across 62 known driver and resistance mutations from the 48 cases; in 29 cases with common EGFR and KRAS mutations, sensitivity was similar to droplet digital PCR. In two cases with incomplete tumor genotyping, plasma NGS rapidly identified a novel EGFR exon 19 deletion and a missed case of MET amplification.

CONCLUSIONS

Blinded to tumor genotype, this plasma NGS approach detected a broad range of targetable genomic alterations in NSCLC with no false positives including complex mutations like rearrangements and unexpected resistance mutations such as EGFR C797S. Through use of widely available vacutainers and a desktop sequencing platform, this assay has the potential to be implemented broadly for patient care and translational research.

A screen in mice uncovers repression of lipoprotein lipase by microRNA-29a as a mechanism for lipid distribution away from the liver

Identification of microRNAs (miRNAs) that regulate lipid metabolism is important to advance the understanding and treatment of some of the most common human diseases. In the liver, a few key miRNAs have been reported that regulate lipid metabolism, but since many genes contribute to hepatic lipid metabolism, we hypothesized that other such miRNAs exist. To identify genes repressed by miRNAs in mature hepatocytes in vivo, we injected adult mice carrying floxed Dicer1 alleles with an adenoassociated viral vector expressing Cre recombinase specifically in hepatocytes. By inactivating Dicer in adult quiescent hepatocytes we avoided the hepatocyte injury and regeneration observed in previous mouse models of global miRNA deficiency in hepatocytes. Next, we combined gene and miRNA expression profiling to identify candidate gene/miRNA interactions involved in hepatic lipid metabolism and validated their function in vivo using antisense oligonucleotides. A candidate gene that emerged from our screen was lipoprotein lipase (Lpl), which encodes an enzyme that facilitates cellular uptake of lipids from the circulation. Unlike in energy-dependent cells like myocytes, LPL is normally repressed in adult hepatocytes. We identified miR-29a as the miRNA responsible for repressing LPL in hepatocytes, and found that decreasing hepatic miR-29a levels causes lipids to accumulate in mouse livers.

CONCLUSION

Our screen suggests several new miRNAs are regulators of hepatic lipid metabolism. We show that one of these, miR-29a, contributes to physiological lipid distribution away from the liver and protects hepatocytes from steatosis. Our results, together with miR-29a's known antifibrotic effect, suggest miR-29a is a therapeutic target in fatty liver disease.

Single-stranded microRNA mimics

miRNAs are ∼22-nt RNAs that bind to the Argonaute family of proteins and have important regulatory roles in plants and animals. Here, we show that miRNAs exhibit targeting activity in cells when delivered as single strands that are 5'-phosphorylated and that contain 2'-fluoro ribose modifications. Length preferences, chemical modification sensitivity, and genome-wide seed-based targeting all suggest that this activity is Ago-based. Activity could be enhanced by annealing of segmented passenger strands containing non-nucleic acid spacers. Furthermore, screening of randomly generated sequences identified pyrimidine rich 3' cassette sequences that increased single strand activity. These results provide an initial step in the development of single-stranded miRNA mimics for therapeutic use.

Persistence of seed-based activity following segmentation of a microRNA guide strand

microRNAs are ∼ 22 nucleotide regulatory RNAs that are processed into duplexes from hairpin structures and incorporated into Argonaute proteins. Here, we show that a nick in the middle of the guide strand of an miRNA sequence allows for seed-based targeting characteristic of miRNA activity. Insertion of an inverted abasic, a dye, or a small gap between the two segments still permits target knockdown. While activity from the seed region of the segmented miRNA is apparent, activity from the 3' half of the guide strand is impaired, suggesting that an intact guide backbone is required for contribution from the 3' half. miRNA activity was also observed following nicking of a miRNA precursor. These results illustrate a structural flexibility in miRNA duplexes and may have applications in the design of miRNA mimetics.

microRNAs regulate human embryonic stem cell division

microRNAs (miRNAs) regulate numerous physiological processes such as cell division and differentiation in many tissue types including stem cells. To probe the role that miRNAs play in regulating processes relevant to embryonic stem cell biology, we used RNA interference to silence DICER and DROSHA, the two main miRNA processing enzymes. Consistent with a role for miRNAs in maintaining normal stem cell division and renewal, we found that perturbation of miRNA pathway function in human embryonic stem cells (hESCs) attenuates cell proliferation. Normal cell growth can be partially restored by introduction of the mature miRNAs miR-195 and miR-372. These miRNAs regulate two tumor suppressor genes, respectively: WEE1, which encodes a negative G2/M kinase modulator of the CycB/CDK complex and CDKN1A, which encodes p21, a CycE/CDK cyclin dependent kinase inhibitor that regulates the G1/S transition. We show that in wild-type hESCs, WEE 1 levels control the rate of hESC division, whereas p21 levels must be maintained at a low level for hESC division to proceed. These data support a model for hESC cell cycle control in which miRNAs regulate negative cell cycle modulators at two phases of the cell cycle to ensure proper replenishment of the stem cell population.

(micro)Genomic medicine: microRNAs as therapeutics and biomarkers

Genomic studies have shown that a microRNA(miRNA) can post-transcriptionally regulate hundreds of other genes, providing challenges and opportunities for therapeutic development. Profiling studies have placed several miRNAs within transcriptional pathways linked to disease, and oligonucleotide therapeutics are being developed that modulate miRNA activity. The involvement of miRNAs in diverse genetic pathways across human tissues suggests that miRNAs will also be useful as biomarkers for disease and tissue injury.

Global survey of genomic imprinting by transcriptome sequencing

Genomic imprinting restricts gene expression to a paternal or maternal allele. To date, approximately 90 imprinted transcripts have been identified in mouse, of which the majority were detected after intense interrogation of clusters of imprinted genes identified by phenotype-driven assays in mice with uniparental disomies [1]. Here we use selective priming and parallel sequencing to measure allelic bias in whole transcriptomes. By distinguishing parent-of-origin bias from strain-specific bias in embryos derived from a reciprocal cross of mice, we constructed a genome-wide map of imprinted transcription. This map was able to objectively locate over 80% of known imprinted loci and allowed the detection and confirmation of six novel imprinted genes. Even in the intensely studied embryonic day 9.5 developmental stage that we analyzed, more than half of all imprinted single-nucleotide polymorphisms did not overlap previously discovered imprinted transcripts; a large fraction of these represent novel noncoding RNAs within known imprinted loci. For example, a previously unnoticed, maternally expressed antisense transcript was mapped within the Grb10 locus. This study demonstrates the feasibility of using transcriptome sequencing for mapping of imprinted gene expression in physiologically normal animals. Such an approach will allow researchers to study imprinting without restricting themselves to individual loci or specific transcripts.

MicroRNA targeting specificity in mammals: determinants beyond seed pairing

Mammalian microRNAs (miRNAs) pair to 3'UTRs of mRNAs to direct their posttranscriptional repression. Important for target recognition are approximately 7 nt sites that match the seed region of the miRNA. However, these seed matches are not always sufficient for repression, indicating that other characteristics help specify targeting. By combining computational and experimental approaches, we uncovered five general features of site context that boost site efficacy: AU-rich nucleotide composition near the site, proximity to sites for coexpressed miRNAs (which leads to cooperative action), proximity to residues pairing to miRNA nucleotides 13-16, positioning within the 3'UTR at least 15 nt from the stop codon, and positioning away from the center of long UTRs. A model combining these context determinants quantitatively predicts site performance both for exogenously added miRNAs and for endogenous miRNA-message interactions. Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets.

A microRNA component of the p53 tumour suppressor network

A global decrease in microRNA (miRNA) levels is often observed in human cancers, indicating that small RNAs may have an intrinsic function in tumour suppression. To identify miRNA components of tumour suppressor pathways, we compared miRNA expression profiles of wild-type and p53-deficient cells. Here we describe a family of miRNAs, miR-34a-c, whose expression reflected p53 status. Genes encoding miRNAs in the miR-34 family are direct transcriptional targets of p53, whose induction by DNA damage and oncogenic stress depends on p53 both in vitro and in vivo. Ectopic expression of miR-34 induces cell cycle arrest in both primary and tumour-derived cell lines, which is consistent with the observed ability of miR-34 to downregulate a programme of genes promoting cell cycle progression. The p53 network suppresses tumour formation through the coordinated activation of multiple transcriptional targets, and miR-34 may act in concert with other effectors to inhibit inappropriate cell proliferation.

Relationship between markers of metabolic control and inflammation on severity of periodontal disease in patients with diabetes mellitus

AIM

The aim of this study was to investigate the relationship between markers of metabolic control and inflammation and periodontal disease parameters in patients with diabetes.

MATERIAL & METHODS

One hundred and eighty one adult patients with diabetes attending treatment at two diabetes centres were invited to participate in the study. Periodontal examination included full-mouth assessment for probing depths and bleeding on probing (BOP). Blood analyses were carried out for glycated haemoglobin, (HbA1c), high-sensitivity C reactive protein, (hsCRP) and lipid profile comprising total cholesterol, low-density lipoprotein cholesterol (LDL chol), high-density lipoprotein cholesterol (HDL chol) and triglycerides.

RESULTS

Upon multivariate analysis, periodontal disease severity in terms of increased percentage of BOP and mean percentage of sites with probing depths > or = 5 mm were found to be associated with inadequate glycaemic control as measured by HbA1c (p<0.01). HsCRP was also found to be a significant predictor for mean percentage of sites with probing depths > or = 5 mm (p<0.05). After controlling for age, gender, smoking habits and number of teeth, positive correlations were found between HbA1c and percentage sites with probing depths > or = 5 mm, percentage sites BOP, total cholesterol, LDL chol and triglycerides (p<0.05). Using the adjusted differences, subjects with acceptable glycaemic control (HbA1c < 8%) showed a lower percentage of sites with BOP and probing depths > or = 5 mm (p<0.05) when compared with those having inadequate glycaemic control. There was also a trend towards lower blood cholesterol in the well-controlled group.

CONCLUSION

The level of glycaemic control as measured by HbA1c emerged as the most consistent risk factor associated with the extent and severity of periodontal disease in this study cohort.

The widespread impact of mammalian MicroRNAs on mRNA repression and evolution

Thousands of mammalian messenger RNAs are under selective pressure to maintain 7-nucleotide sites matching microRNAs (miRNAs). We found that these conserved targets are often highly expressed at developmental stages before miRNA expression and that their levels tend to fall as the miRNA that targets them begins to accumulate. Nonconserved sites, which outnumber the conserved sites 10 to 1, also mediate repression. As a consequence, genes preferentially expressed at the same time and place as a miRNA have evolved to selectively avoid sites matching the miRNA. This phenomenon of selective avoidance extends to thousands of genes and enables spatial and temporal specificities of miRNAs to be revealed by finding tissues and developmental stages in which messages with corresponding sites are expressed at lower levels.

Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs

There has been a surge of interest in the biology of microRNAs and the technology of RNA interference. We describe a simple, robust, inexpensive assay for quantitative analysis of microRNAs and short-interfering RNAs. The method relies on primer extension conversion of RNA to cDNA by reverse transcription followed by quantitative, real-time PCR. Technical parameters critical to the success of the assay are presented. Measurements of microRNA levels are sensitive, with most assays allowing measurements in the femtomolar range, which corresponds to tens of copies per cell or less. The assay has a high dynamic range and provides linear readout over differences in microRNA concentrations that span 6-7 orders of magnitude. The assay is capable of discriminating between related microRNA family members that differ by subtle sequence differences. We used the method for quantitative analysis of six microRNAs across 12 tissue samples. The data confirm striking variation in the patterns of expression of these noncoding regulatory RNAs.

Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs

MicroRNAs (miRNAs) are a class of noncoding RNAs that post-transcriptionally regulate gene expression in plants and animals. To investigate the influence of miRNAs on transcript levels, we transfected miRNAs into human cells and used microarrays to examine changes in the messenger RNA profile. Here we show that delivering miR-124 causes the expression profile to shift towards that of brain, the organ in which miR-124 is preferentially expressed, whereas delivering miR-1 shifts the profile towards that of muscle, where miR-1 is preferentially expressed. In each case, about 100 messages were downregulated after 12 h. The 3' untranslated regions of these messages had a significant propensity to pair to the 5' region of the miRNA, as expected if many of these messages are the direct targets of the miRNAs. Our results suggest that metazoan miRNAs can reduce the levels of many of their target transcripts, not just the amount of protein deriving from these transcripts. Moreover, miR-1 and miR-124, and presumably other tissue-specific miRNAs, seem to downregulate a far greater number of targets than previously appreciated, thereby helping to define tissue-specific gene expression in humans.

Periodontal disease -- the emergence of a risk for systemic conditions: pre-term low birth weight

This paper addresses the problem of adverse pregnancy outcome in relation to periodontal disease. There is compelling evidence that a link exists between pre-term low birth weight (PLBW) and periodontitis. Although 25% to 50% of PLBW deliveries occur without any known aetiology, there is increasing evidence that infection may play a significant role in pre-term delivery. A model explaining the plausible relationship is proposed based upon the concept of infection leading to a cascade of inflammatory reactions associated with pre-term labour and periodontal disease. Current evidence has pointed to an interest in dental intervention studies to control periodontal disease as one of the potential strategies to reduce pre-term labour. This paper reviews the potential association between periodontal infection and adverse pregnancy outcomes.

Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification

MicroRNAs are approximately 22-nucleotide (nt) RNAs processed from foldback segments of endogenous transcripts. Some are known to play important gene regulatory roles during animal and plant development by pairing to the messages of protein-coding genes to direct the post-transcriptional repression of these messages. Previously, we developed a computational method called MiRscan, which scores features related to the foldbacks, and used this algorithm to identify new miRNA genes in the nematode Caenorhabditis elegans. In the present study, to identify sequences that might be involved in processing or transcriptional regulation of miRNAs, we aligned sequences upstream and downstream of orthologous nematode miRNA foldbacks. These alignments showed a pronounced peak in sequence conservation about 200 bp upstream of the miRNA foldback and revealed a highly significant sequence motif, with consensus CTCCGCCC, that is present upstream of almost all independently transcribed nematode miRNA genes. Scoring the pattern of upstream/downstream conservation, the occurrence of this sequence motif, and orthology of host genes for intronic miRNA candidates, yielded substantial improvements in the accuracy of MiRscan. Nine new C. elegans miRNA gene candidates were validated using a PCR-sequencing protocol. As previously seen for bacterial RNA genes, sequence features outside of the RNA secondary structure can therefore be very useful for the computational identification of eukaryotic noncoding RNA genes. The total number of confidently identified nematode miRNAs now approaches 100. The improved analysis supports our previous assertion that miRNA gene identification is nearing completion in C. elegans with apparently no more than 20 miRNA genes now remaining to be identified.

The microRNAs of Caenorhabditis elegans

MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to identify miRNA genes conserved in more than one genome. Applying this program, known as MiRscan, together with molecular identification and validation methods, we have identified most of the miRNA genes in the nematode Caenorhabditis elegans. The total number of validated miRNA genes stands at 88, with no more than 35 genes remaining to be detected or validated. These 88 miRNA genes represent 48 gene families; 46 of these families (comprising 86 of the 88 genes) are conserved in Caenorhabditis briggsae, and 22 families are conserved in humans. More than a third of the worm miRNAs, including newly identified members of the lin-4 and let-7 gene families, are differentially expressed during larval development, suggesting a role for these miRNAs in mediating larval developmental transitions. Most are present at very high steady-state levels-more than 1000 molecules per cell, with some exceeding 50,000 molecules per cell. Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species.

Prediction of plant microRNA targets

We predict regulatory targets for 14 Arabidopsis microRNAs (miRNAs) by identifying mRNAs with near complementarity. Complementary sites within predicted targets are conserved in rice. Of the 49 predicted targets, 34 are members of transcription factor gene families involved in developmental patterning or cell differentiation. The near-perfect complementarity between plant miRNAs and their targets suggests that many plant miRNAs act similarly to small interfering RNAs and direct mRNA cleavage. The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory transcripts from daughter cell lineages.

An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans

Two small temporal RNAs (stRNAs), lin-4 and let-7, control developmental timing in Caenorhabditis elegans. We find that these two regulatory RNAs are members of a large class of 21- to 24-nucleotide noncoding RNAs, called microRNAs (miRNAs). We report on 55 previously unknown miRNAs in C. elegans. The miRNAs have diverse expression patterns during development: a let-7 paralog is temporally coexpressed with let-7; miRNAs encoded in a single genomic cluster are coexpressed during embryogenesis; and still other miRNAs are expressed constitutively throughout development. Potential orthologs of several of these miRNA genes were identified in Drosophila and human genomes. The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals.

A computational analysis of sequence features involved in recognition of short introns

Splicing of short introns by the nuclear pre-mRNA splicing machinery is thought to proceed via an "intron definition" mechanism, in which the 5' and 3' splice sites (5'ss, 3'ss, respectively) are initially recognized and paired across the intron. Here, we describe a computational analysis of sequence features involved in recognition of short introns by using available transcript data from five eukaryotes with complete or nearly complete genomic sequences. The information content of five different transcript features was measured by using methods from information theory, and Monte Carlo simulations were used to determine the amount of information required for accurate recognition of short introns in each organism. We conclude: (i) that short introns in Drosophila melanogaster and Caenorhabditis elegans contain essentially all of the information for their recognition by the splicing machinery, and computer programs that simulate splicing specificity can predict the exact boundaries of approximately 95% of short introns in both organisms; (ii) that in yeast, the 5'ss, branch signal, and 3'ss can accurately identify intron locations but do not precisely determine the location of 3' cleavage in every intron; and (iii) that the 5'ss, branch signal, and 3'ss are not sufficient to accurately identify short introns in plant and human transcripts, but that specific subsets of candidate intronic enhancer motifs can be identified in both human and Arabidopsis that contribute dramatically to the accuracy of splicing simulators.

Computational inference of homologous gene structures in the human genome

With the human genome sequence approaching completion, a major challenge is to identify the locations and encoded protein sequences of all human genes. To address this problem we have developed a new gene identification algorithm, GenomeScan, which combines exon-intron and splice signal models with similarity to known protein sequences in an integrated model. Extensive testing shows that GenomeScan can accurately identify the exon-intron structures of genes in finished or draft human genome sequence with a low rate of false-positives. Application of GenomeScan to 2.7 billion bases of human genomic DNA identified at least 20,000-25,000 human genes out of an estimated 30,000-40,000 present in the genome. The results show an accurate and efficient automated approach for identifying genes in higher eukaryotic genomes and provide a first-level annotation of the draft human genome.

Dental trauma management awareness of Singapore pre-school teachers

The purpose of this study was to assess the awareness of pre-school teachers concerning the management of traumatized teeth. A questionnaire survey of teachers' backgrounds, attitudes/practices and knowledge was distributed to all teachers who attended a dental education program organized by the Singapore Dental Health Foundation. Of a total of 291 teachers surveyed, 29% had received tertiary education, while the rest (71%) had received secondary education. The mean teaching experience was 6.8 +/- 6.9 years. About a quarter had previous experience in handling dental trauma. Sixty-three percent admitted having no knowledge of dental trauma; 79% were unsatisfied with their level of knowledge in this area; 95% were keen to have further education in dental trauma; 65% thought dental trauma emergency should be dealt with as soon as possible. Concerning knowledge, during-office hour emergency services were more familiar (84%) than after-office hour emergency services (15%), as was the concept of management of avulsed teeth (71%) compared to that of fractured teeth (51%). Knowledge about optimal storage media for avulsed permanent teeth was especially poor--being as low as 15%. Using multiple logistic regression analysis, it was found that teaching experience significantly influenced the respondents' self-assessed knowledge and their level of satisfaction with their knowledge (P = 0.012). Teachers with more teaching experience had better knowledge about the replantation of permanent teeth (P = 0.003). It is recommended that public education targeted at teachers should be carried out to increase dental trauma management awareness.

Survey of dental fees charged by dentists in Singapore

A survey on dental fees was conducted among all private dental clinics registered with the Medical Audit and Accreditation Unit of the Ministry of Health in Singapore. Replies were received from 74 dental clinics. Analysis of results showed that there was a general increase in the median of fees charged in 1998 compared to the fees listed in the Minimum Fee Schedule issued by the Singapore Dental Association in 1994. 93% of the respondents indicated that there is a need to revise the Minimum Fee Schedule.

Challenges and relevance of problem-based learning in dental education

The rôle of PBL as an innovative approach in medical education has been well documented. There has been an emerging trend of incorporating PBL into the dental curriculum. The potential advantages of PBL as a mode of learning encompass the enhancement of an integrated approach in solving dental-treatment-related problems, the development of critical thinking and problem solving skills and the encouragement of independent life-long learning. PBL was introduced into the dental curriculum as a pilot project in the Faculty of Dentistry, National University of Singapore in summer 1996. An example of a case-based study was illustrated and the learning objectives of the study were highlighted. Initial feedback from students indicated a positive attitude to this mode of learning in terms of cognitive, affective and psychomotor skills. Strategies to enhance learning in the PBL environment include time allocation for self-study, availability of resource materials and use of appropriate assessment methods. Problems that remain to be resolved include the choice of appropriate outcome assessment measures to evaluate the effectiveness of PBL as a mode of learning in undergraduate dental education.

Patient and parental awareness of the importance of immediate management of traumatised teeth

The purpose of this study was to assess patient and parental awareness of the importance of immediate management of traumatised teeth. A three-part questionnaire comprising questions on demographic data, attitude and knowledge was distributed to patients or accompanying parents who presented to the principal author for treatment in an 8-week period. One hundred and fifty-seven respondents with a mean age of 31.1 years participated in the study. Only 30% of the respondents recalled having had previous experience of dental trauma. The majority of the respondents, especially those with a higher educational background, had a positive attitude, expressing enthusiasm for public education on emergency management of dental trauma (85%). The availability of an emergency service during office hours was known by 71% of the respondents while only 26% were aware of the after-office-hour emergency service. Participants generally had a better concept of management of avulsed teeth (63%) compared to that of fractured teeth (35%). Knowledge on some critical aspects of the handling of avulsed teeth was poor (6%). Using multiple logistic regression analysis, it was found that the respondents' attitude tended to be influenced by their educational background (P = 0.08). In addition, subjects with higher education were more knowledgeable regarding the emergency service available during office hours (P = 0.05) and the concept of management of fractured teeth (P = 0.02). Educational background appeared to influence the level of awareness of the importance of immediate management of traumatised teeth.

Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats

The fibronectin EIIIB exon is alternatively spliced in a cell-type-specific manner, and TGCATG repeats in the intron downstream of EIIIB have been implicated in this regulation. Analysis of the intron sequence from several vertebrates shows that the pattern of repeats in the 3' half of the intron is evolutionarily conserved. Point mutations in certain highly conserved repeats greatly reduce EIIIB inclusion, suggesting that a multicomponent complex may recognize the repeats. Expression of the SR protein SRp40, SRp20, or ASF/SF2 stimulates EIIIB inclusion. Studies of the interplay between mutations in the repeats and SRp40-stimulated inclusion suggest that the repeats are recognized in many, if not all, cell types, and that EIIIB inclusion may be regulated by quantitative changes in multiple factors.

Comparison of modes of oral hygiene instruction in improving gingival health

195 Hong Kong Chinese employees from a single company participated in a 10-month longitudinal study on the effects of various modes of delivery of oral hygiene messages on their gingival health. Subjects were allocated to one of the following modes of oral hygiene education: (1) personal instruction; (2) self-education manual; (3) video; (4) a combination of 2 or more of these modes of instruction. Scaling or any other form of periodontal treatment was not given throughout the study period. Full mouth clinical examinations were carried out using a Williams Periodontal probe to examine for the presence or absence of plaque and bleeding on probing from the gingival sulcus. At 2 weeks, 4 months and 10 months, results showed significant reductions in the mean % of plaque and bleeding when compared with baseline. No significant differences were found between the groups given the various modes of oral hygiene education. The study does confirm the effectiveness of oral hygiene alone in improving gingival health, but the lack of difference in the outcome of various oral hygiene education approaches indicates that the mode of instruction is not crucially important to the end result. However, it has to be acknowledged that improvement in oral hygiene may be related to factors other than the oral hygiene programme itself. The findings have significant implications in oral health promotion programmes to improve the periodontal status of the local community.

Comparison of various modalities of "simple" periodontal therapy on oral cleanliness and bleeding

550 Chinese employees of both sexes aged 25-44 from an industrial organisation participated in a 16-month longitudinal study. Subjects were divided into 4 groups: an oral hygiene group (group A), a scaling group (group B), an oral hygiene + scaling group (group C) and a control (group D). The experimental subjects were examined at baseline, 2 weeks, 4 months, 10 months and 16 months. After 10 months, group A received scaling while group B was given oral hygiene instruction for the 1st time. The control group did not receive any treatment until completion of the programme. At 16 months, all 3 experimental groups had significantly lower plaque and bleeding scores than the control. The plaque and bleeding levels of the experimental groups were lower at all review appointments when compared with baseline. Some variations in the clinical parameters were found between groups at 2 weeks, 4 months and 10 months. The scaling + oral hygiene group showed the best response. Although a proportion of subjects showed a substantial improvement in bleeding scores following scaling, the significant resource implications in providing such treatment has to be considered in planning community health programmes to promote periodontal health, wherein oral hygiene education must still have the highest priority.

Chinese health beliefs and oral health practices among the middle-aged and the elderly in Hong Kong

The purpose of this paper was to study possible relationships between traditional Chinese health beliefs and health practices in adult Chinese in a modernized society. The study populations comprised 398 35-44-yr-old and 559 65-74-yr-old Hong Kong Chinese. The respondents were categorized into three groups with weak, moderate, or strong Chinese beliefs on the basis of interview questions on the causes of gum disease. Chinese preventive practices and Chinese pain practices were defined according to respondents' reported use of recommended traditional cures. Questions on generally accepted oral practices were phrased in terms of frequency of daily brushing of teeth, use of toothpicks the previous day, and whether or not teeth were flossed the previous day. Around one-third of the respondents had weak, almost one-half had moderate, and around one-quarter expressed strong Chinese health beliefs. No significant differences in Chinese health beliefs were found between men and women in either age group, or between the age groups. In the 35-44 age group, more of those with a higher education were in the "weak" Chinese health belief category, whereas, conversely, more of those with a lower education expressed stronger Chinese health beliefs (P < 0.05). Women in both age groups reported significantly more frequent brushing. Toothpicks were used by around three-quarters of both age groups, but flossing was extremely rare.(ABSTRACT TRUNCATED AT 250 WORDS)