Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale

BACKGROUND

Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples. In this case study, we present a proof-of-concept using read cloud sequencing to describe bacterial strain diversity in the gut microbiome of one hematopoietic cell transplantation patient over a 2-month time course and highlight temporal strain variation of gut microbes during therapy. The treatment was accompanied by diet changes and administration of multiple immunosuppressants and antimicrobials.

METHODS

We conducted short-read and read cloud metagenomic sequencing of DNA extracted from four longitudinal stool samples collected during the course of treatment of one hematopoietic cell transplantation (HCT) patient. After applying read cloud metagenomic assembly to discover strain-level sequence variants in these complex microbiome samples, we performed metatranscriptomic analysis to investigate differential expression of antibiotic resistance genes. Finally, we validated predictions from the genomic and metatranscriptomic findings through in vitro antibiotic susceptibility testing and whole genome sequencing of isolates derived from the patient stool samples.

RESULTS

During the 56-day longitudinal time course that was studied, the patient's microbiome was profoundly disrupted and eventually dominated by Bacteroides caccae. Comparative analysis of B. caccae genomes obtained using read cloud sequencing together with metagenomic RNA sequencing allowed us to identify differences in substrain populations over time. Based on this, we predicted that particular mobile element integrations likely resulted in increased antibiotic resistance, which we further supported using in vitro antibiotic susceptibility testing.

CONCLUSIONS

We find read cloud assembly to be useful in identifying key structural genomic strain variants within a metagenomic sample. These strains have fluctuating relative abundance over relatively short time periods in human microbiomes. We also find specific structural genomic variations that are associated with increased antibiotic resistance over the course of clinical treatment.

Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model

The diverse cellular milieu of the gastric tissue microenvironment plays a critical role in normal tissue homeostasis and tumor development. However, few cell culture model can recapitulate the tissue microenvironment and intercellular signaling in vitro. We used a primary tissue culture system to generate a murine p53 null gastric tissue model containing both epithelium and mesenchymal stroma. To characterize the microenvironment and niche signaling, we used single cell RNA sequencing (scRNA-Seq) to determine the transcriptomes of 4,391 individual cells. Based on specific markers, we identified epithelial cells, fibroblasts and macrophages in initial tissue explants during organoid formation. The majority of macrophages were polarized towards wound healing and tumor promotion M2-type. During the course of time, the organoids maintained both epithelial and fibroblast lineages with the features of immature mouse gastric stomach. We detected a subset of cells in both lineages expressing Lgr5, one of the stem cell markers. We examined the lineage-specific Wnt signaling activation, and identified that Rspo3 was specifically expressed in the fibroblast lineage, providing an endogenous source of the R-spondin to activate Wnt signaling. Our studies demonstrate that this primary tissue culture system enables one to study gastric tissue niche signaling and immune response in vitro.

Abstract 2715: Precision-designed, rapid and low-cost single molecule detection of mutations from circulating tumor DNA

Detecting and quantifying mutations from circulating tumor DNA (ctDNA) is a new approach for longitudinally monitoring cancer patients throughout the course of treatment. However, general limitations to the clinical utility of ctDNA include sample concentration, overall assay cost, and result turnaround time. We have developed a novel molecular assay that utilize single color digital droplet PCR (ddPCR) to both genotype and quantify the number of tumor derived DNA molecules in a given sample. Our assay routinely detects as few as three mutant DNA molecules per a reaction volume, can be tested efficiently for fewer than ten dollars per reaction, and generates useable mutation information within four hours. Additionally, the assay can be rapidly configured to detect different mutations specifically identified in any cancer patient. To demonstrate the single molecule sensitivity and specificity for clinically relevant hotspot mutations, we have validated the assay using multiple input sources including high quality cell line DNA, formalin-fixed paraffin embedded tissue (FFPET) DNA, and ctDNA. Our ddPCR assay utilizes a novel primer design that is not rely on fluorescent probes. The overall simplicity of assay design enables one to detect nearly any coding mutation; practically, this means that any cancer or DNA sample can be tested efficiently. We have created customized precision mutation assays for two individual cancer patients. After extracting ctDNA from 500µL of plasma we prepare a controlled mixed wild type and mutant standard curves which contain between 150-3 detectable mutant molecules of interest per reaction. We then assay the patient ctDNA sample in parallel to the controlled standard curve and generate clustering confidence intervals. We have designed precision mutation assays targeting KRAS A146V, AKT1 E17K, and TP53 R175H for Patient A as well as KRAS G12V and PIK3CA H1047R for Patient B. The results of our single-color precision mutation quantification assays support the original mutation findings from the primary tumors. In one case, from 1µL of un-amplified ctDNA equivalent to less than 0.5ng of DNA, we identified 4 mutant molecules per ddPCR reaction volume. We have verified the presence of hotspot mutations from un-amplified patient derived ctDNA and quantified the number of mutant molecules present in each ctDNA sample. This assay has many features that make it amenable to automation. We are currently developing a massively high throughput process to design assays for tens of thousands of mutations in a matter of weeks. Overall this is an extremely low cost, highly sensitive and scalable diagnostic technology. We anticipate that this technology will be a valuable tool for rapidly monitoring ctDNA longitudinally in cancer patients.

Citation Format: Christina M. Wood-Bouwens, Christine Handy, Billy Lau, Hanlee Ji. Precision-designed, rapid and low-cost single molecule detection of mutations from circulating tumor DNA [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 2715. doi:10.1158/1538-7445.AM2017-2715

Stress during Adolescence Alters Palatable Food Consumption in a Context-Dependent Manner

Food consumption and preferences may be shaped by exposure to stressful environments during sensitive periods in development, and even small changes in consumption can have important effects on long term health. Adolescence is increasingly recognized as a sensitive period, in which adverse experiences can alter development, but the specific programming effects that may occur during adolescence remain incompletely understood. The current study seeks to explore the effects of stress during late adolescence on consumption of a palatable, high-fat, high-sugar food in adulthood—under basal conditions, as well following acute stress. Male Long-Evans rats were exposed to a regimen of variable stress for seven days in late adolescence (PND 45–51). During the stress regimen, stressed animals gained significantly less weight than control animals, but weight in adulthood was unaffected by adolescent stress. Palatable food consumption differed between experimental groups, and the direction of effect depended on context; stressed rats ate significantly more palatable food than controls upon first exposure, but ate less following an acute stressor. Leptin levels and exploratory behaviors did not differ between stressed and non-stressed groups, suggesting that other factors regulate preference for a palatable food. Altered food consumption following adolescent stress suggests that rats remain sensitive to stress during late adolescence, and that adult feeding behavior may be affected by previous adverse experiences. Such programming effects highlight adolescence as a period of plasticity, with the potential to shape long term food consumption patterns and preferences.

Ipsilateral motor dysfunction from unilateral stroke: implications for the functional neuroanatomy of hemiparesis

BACKGROUND

Motor dysfunction in the contralateral hand has been well characterised after stroke. The ipsilateral hand has received less attention, yet may provide valuable insights into the structure of the motor system and the nature of the recovery process. By tracking motor function of both hands beginning in the acute stroke period in patients with cortical versus subcortical lesions, we sought to understand the functional anatomy of the ipsilateral deficit.

METHODS

We examined 30 patients with first-ever unilateral hemiparetic stroke, 23 with subcortical lesions affecting the corticospinal tract, seven with cortical involvement. Patients performed hand dynamometry and the 9-Hole Peg Test (9HPT) with each hand at 24-48 h, 1 week, 3 months and 1 year after stroke. Linear regression was used to compare the two different motor tasks in each hand. Repeated measures ANOVA was used to compare recovery rates of the two tasks in the first 3 months.

RESULTS

Ipsilateral 9HPT scores averaged z = -7.1, -3.6, -2.5 and -2.3 at the four time points whereas grip strength was unaffected. The initial degree of impairment of grip strength in the contralateral hand did not correlate with the degree of impairment of 9HPT in either the contralateral or ipsilateral hand (r = 0.001, p = 0.98), whereas the initial degree of impairment of 9HPT in the contralateral hand correlated with the degree of impairment of 9HPT in the ipsilateral hand (r = 0.79, p = 0.035). The rate of recovery also differed for the two tasks (p = 0.005).

CONCLUSION

Ipsilateral motor deficits are demonstrable immediately after stroke and extend into the subacute and chronic recovery period. Dissociation between grip strength and dexterity support the notion that dexterity and grip strength operate as anatomically and functionally distinct entities. Our findings in patients with subcortical lesions suggest that the model of white matter tract injury needs to be refined to reflect the influence of a subcortical lesion on bi-hemispheral cortical networks, rather than as a simple "severed cable" model of disruption of corticofugal fibres. Our data have implications for both stroke clinical trials and the development of new strategies for therapeutic intervention in stroke recovery.

On the uniqueness of the surface sources of evoked potentials

The uniqueness of a surface density of sources localized inside a spatial region R and producing a given electric potential distribution in its boundary B0 is revisited. The situation in which R is filled with various subregions, each one having a definite constant value for the electric conductivity is considered. It is argued that the knowledge of the potential in all B0 fully determines the surface-located sources for a general class of surfaces supporting them and also a wide type of those sources. The class of surfaces can be defined as a union of an arbitrary but finite number of open or closed surfaces. The only restriction upon them is that no one of the closed surfaces contains inside it another (nesting) of the closed or open ones. The types of sources are surface charge densities and double layer (dipolar) densities for the open surfaces and more restrictively, only surface charge densities for the closed ones. A two-dimensional analytically solvable example illustrating the drastic appearance of uniqueness after arbitrarily small holes are opened in nested surfaces is discussed.

Tocqueville revisited. The meaning of American prosperity

Why is business so admired in the United States and so often denigrated in Europe? How has America created 30 million new jobs in the last 20 years while the European Union, with a bigger population, only managed 5 million? What is feeding America's apparently inexhaustible appetite for growth and its recent dramatic improvements in productivity? In 1831, French philosopher Alexis de Tocqueville came to America to examine its prison system and returned with a vision of democracy so profound it has become part of our cultural heritage. More than a century and a half later, renowned British business philosopher Charles Handy retraces Tocqueville's intellectual journey, this time focusing not on democracy but on capitalism. The result is an eye-opening look at some of the fundamental assumptions underpinning business in America today. It is America's optimism that Handy finds most striking, the unquestioned belief that tomorrow can--and should--be made better than today. He contrasts this with the Spaniards when they came to the New World: No haya novedades, those Spaniards would say, "Let nothing new arise." The energy engendered by American optimism, coupled with the Puritan belief in work and in the nobility of earned wealth (as opposed to Europe's furtive attitude toward its nobility's inherited wealth) lies, in Handy's view, at the heart of America's success. Will American capitalism, born as it was from a property-owning democracy, now adapt to a dematerialized world, where property is intellectual rather than physical? Handy draws no absolute conclusions, but rather lays out the challenges that must be overcome for tomorrow to indeed continue to be better than today in this still-young country.

Looking ahead: implications of the present

On its seventy-fifth anniversary, HBR asked five of the business world's most insightful thinkers to comment on the challenges taking shape for executives as they move into the next century. In "The Future That Has Already Happened," Peter Drucker examines the effects of the increasing underpopulation of the world's developed countries. With growing imbalances in labor resources worldwide, he writes, executives in the developed countries will need to improve the productivity of knowledge and of knowledge workers to maintain a competitive advantage. Esther Dyson's article "Mirror, Mirror on the Wall" reveals the mind shift executives will need to make in a networked world, where companies will be known for what they do rather than for what they say. Executives will have to respond openly and intelligently to feedback about their organizations. The old language of property and ownership no longer serves executives, writes Charles Handy in "The Citizen Corporation." The corporation should be thought of no longer as property but as a community, where members are regarded as citizens. Technology has given executives more information than today's machines can help them understand, explains Paul Saffo in "Are You Machine Wise?" Machine-wise executives will know when to turn their computers off and take their own counsel, he writes. Peter Senge's article "Communities of Leaders and Learners" urges executives to reject the myth of leaders as isolated heroes and instead to build a community of leaders. Sustained institutional learning, he writes, requires organizations to reintegrate their typically fragmented learning processes.

The new equation

What the formula doesn't say is what happens to the other half of all workers, the half no longer needed. Nor does it make clear that as well as being paid twice as much, the favored half will also have to work twice as hard. Hence the paradox that half of the people have money but no time, and the other half have time but no money.

Balancing corporate power: a new Federalist paper

In an effort to govern their increasingly complex organizations, chief executives in some of today's largest corporations are turning to one of the world's oldest political philosophies-federalism. Given that organizations are seen more and more as minisocieties, the prospect of applying political principles to management makes a great deal of sense. Federalism is particularly appropriate because it offers a well-recognized system for dealing with paradoxes of power and control: the need to make things big by keeping them small; to encourage autonomy but within bounds; and to combine variety and shared purpose, individuality and partnership, local and global. As London Business School professor Charles Handy explains it, federalism responds to these paradoxes by balancing power among those in the center of the organization, those in the centers of expertise, and those in the center of the action--the operating businesses. The centers of federal organizations meet regularly, but they do not need to live together. Doing so would concentrate too much power in one place, whereas federalism gets its strength and energy from spreading responsibility across many decision points. Guided by five principles, federalism avoids the risks of autocracy and the overcontrol of a central bureaucracy. It ensures a measure of democracy and creates a "dispersed center" that is more a network than a place. That's why Asea Brown Boveri CEO Percy Barnevik calls his sprawling "multi-domestic" enterprise of 1,100 separate companies and 210,000 employees a federation. It succeeds because the independent bits, be they individuals, clusters, or business units, know they are part of the greater whole.

Through the organizational looking glass: you can't plan tomorrow's organizations with today's assumptions

It's hard to imagine what our industrial society would be like if, for instance, there were no factories. How would things get produced, how would business survive? But are we, in fact, an industrial society? Are factories going to be the prime production place for a society that is conserving energy and doesn't need to travel to work because the silicon chip makes it more efficient to work at home? Who knows what the impact of energy conservation and women in the work force will be on future organizations? One thing we can be sure of, this author writes, is that whatever tomorrow brings, today's assumptions probably cannot account for it. We are, he asserts, entering a period of discontinuous change where the assumptions we have been working with as a society and in organizations are no longer necessarily true. He discusses three assumptions he sees fading--what causes efficiency, what work is, and what value organizational hierarchy has--and then gives some clues as to what our new assumptions might be. Regardless of what our assumptions actually are, however, our organizations and society will require leaders willing to take enormous risks and try unproved ways to cope with them.