Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer¹. Chronic lymphocytic leukaemia (CLL) is a highly informative model for cancer evolution as it undergoes substantial genetic diversification and evolution after therapy^2,3. The CLL epigenome is also an important disease-defining feature^4,5, and growing populations of cells in CLL diversify by stochastic changes in DNA methylation known as epimutations⁶. However, previous studies using bulk sequencing methods to analyse the patterns of DNA methylation were unable to determine whether epimutations affect CLL populations homogeneously. Here, to measure the epimutation rate at single-cell resolution, we applied multiplexed single-cell reduced-representation bisulfite sequencing to B cells from healthy donors and patients with CLL. We observed that the common clonal origin of CLL results in a consistently increased epimutation rate, with low variability in the cell-to-cell epimutation rate. By contrast, variable epimutation rates across healthy B cells reflect diverse evolutionary ages across the trajectory of B cell differentiation, consistent with epimutations serving as a molecular clock. Heritable epimutation information allowed us to reconstruct lineages at high-resolution with single-cell data, and to apply this directly to patient samples. The CLL lineage tree shape revealed earlier branching and longer branch lengths than in normal B cells, reflecting rapid drift after the initial malignant transformation and a greater proliferative history. Integration of single-cell bisulfite sequencing analysis with single-cell transcriptomes and genotyping confirmed that genetic subclones mapped to distinct clades, as inferred solely on the basis of epimutation information. Finally, to examine potential lineage biases during therapy, we profiled serial samples during ibrutinib-associated lymphocytosis, and identified clades of cells that were preferentially expelled from the lymph node after treatment, marked by distinct transcriptional profiles. The single-cell integration of genetic, epigenetic and transcriptional information thus charts the lineage history of CLL and its evolution with therapy.

Abstract 3247: Genome-wide cell-free DNA mutation integration for sensitive cancer detection

Solid malignancies are often diagnosed at a late stage with dismal prognosis. Even after cancer is diagnosed, we lack sensitive tools to guide difficult therapeutic decisions such as adjuvant therapy. Sensitive cancer detection by blood biopsy can therefore transform care by enabling early detection and residual disease monitoring.

Cell free DNA mutation detection has shown significant promise in its ability to survey the somatic genome and enable detection of cancer mutations in the peripheral blood. However, the combination of low tumor fraction and limiting number of DNA fragments in a typical plasma sample, restrict the probability of detecting early stage cancer in cfDNA through current deep targeted sequencing methods.

Focusing on non-small cell lung cancer (NSCLC), we reasoned that we would need to supplant depth of sequencing with breadth of sequencing to overcome the fundamental limitation of low input of cfDNA. To do so, we apply whole genome sequencing (WGS) that allows us to base sensitive detection on the cumulative signal provided by 10,000-30,000 somatic mutations observed in a substantial proportion of NSCLC. We developed an analytic method that integrates genome-wide mutation signal to obtain a tumor fraction (TF) estimate, and thus allow sensitive detection of residual disease and quantitative dynamic monitoring of disease burden. Benchmarking on artificial plasma showed TF detection sensitivity as low as 1:100,000, two orders of magnitude more sensitive than currently available methods.

To test this method, we performed WGS on resected NSCLC and matched germline samples of 8 NSCLC patients, as well as on matched pre- and post-surgery cfDNA. Patient-specific somatic mutations were identified in the tumor/normal pairs and used for the estimation of TF in the matched plasma samples. We detect pre-surgery circulating tumor DNA (ctDNA) in all of the early-stage pre-operative samples and in ~40% post-operative patients, correlated with post-operative disease progression.

In early cancer detection, tumor DNA is not available, requiring de-novo mutation detection in cfDNA. To do so, we first trained a convolutional neuronal network to distinguish between cancer altered sequencing reads and reads affected by sequencing errors. This was followed by genome-wide pattern matching to a specific genomic signature that mark lung cancer mutations (Tobacco signature) indicating the presence of ctDNA in the patient plasma. Applying this method to the pre-operative early stage lung cancer samples and plasma samples from 5 patients with benign nodules (CT-detected) showed an accurate discrimination between malignant and benign nodules, suggesting a potential role in improving the positive predictive value of lung cancer screening in at-risk populations.

These results show that genome-wide mutation integration is a promising novel approach for ultra-sensitive early detection and residual disease monitoring.

Citation Format: Asaf Zviran, Steven T. Hill, Rafael Schulman, Minita Shah, Sunil Deochand, Gavin Ha, Sarah Reed, Denisse Rotem, Greg Gydush, Justin Rhoades, Kevin Huang, Will Liao, Dillon Maloney, Nathan Omans, Murtaza Malbari, Cathy F. Spinelli, Selena Kazancioglu, Nicolas Robine, Viktor Adalsteinsson, Brian Houck-Loomis, Nasser Altorki, Dan A. Landau. Genome-wide cell-free DNA mutation integration for sensitive cancer detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3247.

Self-assembly of precisely defined DNA nanotube superstructures using DNA origami seeds

We demonstrate a versatile process for assembling micron-scale filament architectures by controlling where DNA tile nanotubes nucleate on DNA origami assemblies. "Nunchucks," potential mechanical magnifiers of nanoscale dynamics consisting of two nanotubes connected by a dsDNA linker, form at yields sufficient for application and consistent with models.

A study of the workforce in emergency medicine

STUDY OBJECTIVE

Emergency medicine has progressed significantly since its initial recognition as a medical specialty. Relatively little factual information is known, however, regarding who or how many physicians practice emergency medicine. The purpose of this study is to determine the total number of physicians practicing clinical emergency medicine during a specified period, to describe certain characteristics of those individuals, and to estimate the total number of full-time equivalents (FTEs), as well as the total number of individuals needed to staff those FTEs.

METHODS

Data were gathered from a survey of a random sample of 2,062 hospitals drawn from a population of 5,220 hospitals reported by the American Hospital Association as having, or potentially having, an emergency department. The survey instrument addressed items such as descriptive data on the institution, enumeration of physicians in the ED, as well as the total number working during the period June 1, 1997, through June 14, 1997. Demographic data on the individuals were also collected.

RESULTS

A total of 942 hospitals responded (a 45.7% return rate). These hospitals reported a total of 5,872 physicians were working during the specified period, or an average of 7.48 persons scheduled per institution. The physicians were scheduled for a total of 297,062 hours. The average standard for FTE was 40 clinical hours per week. This equates to 3,713 FTEs or 4.96 FTEs per institution. The ratio of persons to FTEs was 1.51:1. With regard to demographics, 83% of the physicians were men and 81% were white. Their average age was 42 years. As to professional credentials, 58% were emergency medicine-residency trained and 53% were board certified in emergency medicine; 46% were certified by the American Board of Emergency Medicine.

CONCLUSION

Given that there are 4,945 hospitals with EDs and given that the data indicate there are 4.96 FTEs per ED, the total number of FTEs is projected to be 24,548 (standard error = 437). Given further that the data indicate a physician/FTE ratio of 1.51:1, we conclude that there are 36,990 persons (standard error = 683) needed to staff those FTEs. When adjusted for persons working at more than one ED, that number is reduced to 32,026.

Transferring patients from residency into practice

Recently graduated residents and their supervisors were questioned about the clinical wisdom of continuing to treat patients seen in training by transferring them to the residents' newly established private practices. Given the increasingly competitive market for psychotherapy patients, there will likely be a growing tendency for graduating residents to want to carry over patients from their training caseloads to their private practices. Questions arise concerning which patients should be offered such an option, how much to charge, whether such a practice should be encouraged, and whether transfer provides greater continuity of care. Residents were asked about their attitudes and about their clinical and supervisory experiences with such transfers. Supervisors were questioned about the indications and complexities of transfers and the specific issues that should be raised in teaching about this phenomenon. Results tended to support transferring patients from residents' training caseload to their private practices.

Articulatory dynamics of loud and normal speech

A comparison was made between normal and loud productions of bilabial stops and stressed vowels. Simultaneous recordings of lip and jaw movement and the accompanying audio signal were made for four native speakers of Swedish. The stimuli consisted of 12 Swedish vowels appearing in an /i'b_b/ frame and were produced with both normal and increased vocal effort. The displacement, velocity, and relative timing associated with the individual articulators as well as their coarticulatory interactions were studied together with changes in acoustic segmental duration. It is shown that the production of loud as compared with normal speech is characterized by amplification of normal movement patterns that are predictable for the above articulatory parameters. In addition, it was observed that the acoustic durations of bilabial stops were shortened, whereas stressed vowels were lengthened during loud speech production. Two interpretations of the data are offered, viewing loud articulatory behavior as a response to production demands and perceptual constraints, respectively.

Comparative evaluation of the API 20S and AutoMicrobic gram-positive identification systems for non-beta-hemolytic streptococci and aerococci

The API 20S system (Analytab Products, Plainview, N.Y.) and the AutoMicrobic Gram-Positive Identification system (GPI; Vitek Systems, Hazelwood, Mo.) were evaluated for their capacity to identify the non-beta-hemolytic streptococci and aerococci to the species level. The 20S system identified 86% (six of seven strains) of nonhemolytic group B streptococci, whereas 100% of the same group B streptococcal strains were correctly identified by the GPI system. With both systems 99% (134 of 135 strains) of four species of group D enterococcus strains and 92% (24 of 26 strains) of the Aerococcus spp. strains were identified. The 20S system identified 84% (41 of 49 strains) of three species of group D non-enterococcus strains. The GPI system identified 96% of the same group D non-enterococcus strains. The 20S system identified 84% (190 of 226 strains) of 10 species of viridans streptococci; however, supplemental conventional tests were required to identify 49% (110 of the 226 strains) of the viridans strains to the species level. The GPI system identified 79% of the same viridans streptococci without the need for supplemental tests. Both systems identified 84% (161 of 192 strains) of the seven most commonly occurring viridans Streptococcus spp. The 20S system identified 82% (75 of 92 strains) and the GPI system identified 84% (54 of 64 strains) of Streptococcus pneumoniae.

Effect of different media on determination of novobiocin resistance for differentiation of coagulase-negative staphylococci

Species identification of coagulase-negative staphylococci often requires the determination of novobiocin susceptibility. Although previous investigators have recommended the use of P agar for this purpose, most clinical laboratories do not routinely utilize this medium. For this reason, studies were performed to compare novobiocin susceptibility results obtained with 11 different species of staphylococci (10 isolates of each species), using P agar, Trypticase soy agar with 5% sheep blood, and Mueller-Hinton agar. Tests performed on 70 susceptible isolates (minimal inhibitory concentration less than 1.6 micrograms/ml) resulted in zones of inhibition around 5-micrograms novobiocin disks ranging from 19.6 to 33.9, 16.2 to 26.6, and 21.3 to 36.4 mm on P agar, Trypticase soy agar with 5% sheep blood, and Mueller-Hinton agar, respectively. Forty resistant isolates (minimal inhibitory concentration greater than or equal to 1.6 micrograms/ml) exhibited zones of inhibition ranging from 6.0 to 11.3 mm on P agar, 6.0 to 11.6 mm on Trypticase soy agar with 5% sheep blood, and 6.0 to 13.5 mm on Mueller-Hinton agar. Using the established cut off of 16 mm to define novobiocin resistance for the identification of coagulase-negative staphylococci, we correctly identified 100% of the strains tested, regardless of the media utilized.

A two-dose dexamethasone suppression test in patients with psychiatric illness

After exposure to a low and high dose dexamethasone regime, 11 of 34 acute psychiatric inpatients demonstrated abnormal dexamethasone suppression characterized by morning and/or mid-afternoon escape from suppression. This abnormality of suppression was found in primary depression, in mania, and in acute schizophrenia. In primary depression, the presence of abnormal dexamethasone suppression failed to discriminate "endogenous" depressed from "other depressed" subjects. Because nonsuppression to a high dose of dexamethasone is also found in patients with ectopic ACTH secretion and in patients with autonomous adrenal tumors, caution is necessary in the interpretation of nonsuppression which persists after recovery from psychiatric illness. As patients with Cushing's syndrome of uncertain etiology may be referred to a psychiatrist for a diagnostic evaluation, the psychological correlates of abnormal dexamethasone suppression need to be established with greater certainty.