Breast tumours maintain a reservoir of subclonal diversity during expansion.

Our knowledge of copy number evolution during the expansion of primary breast tumours is limited1,2. Here, to investigate this process, we developed a single-cell, single-molecule DNA-sequencing method and performed copy number analysis of 16,178 single cells from 8 human triple-negative breast cancers and 4 cell lines. The results show that breast tumours and cell lines comprise a large milieu of subclones (7-22) that are organized into a few (3-5) major superclones. Evolutionary analysis suggests that after clonal TP53 mutations, multiple loss-of-heterozygosity events and genome doubling, there was a period of transient genomic instability followed by ongoing copy number evolution during the primary tumour expansion. By subcloning single daughter cells in culture, we show that tumour cells rediversify their genomes and do not retain isogenic properties. These data show that triple-negative breast cancers continue to evolve chromosome aberrations and maintain a reservoir of subclonal diversity during primary tumour growth.

iGWAS: Image-based genome-wide association of self-supervised deep phenotyping of retina fundus images.

Existing imaging genetics studies have been mostly limited in scope by using imaging-derived phenotypes defined by human experts. Here, leveraging new breakthroughs in self-supervised deep representation learning, we propose a new approach, image-based genome-wide association study (iGWAS), for identifying genetic factors associated with phenotypes discovered from medical images using contrastive learning. Using retinal fundus photos, our model extracts a 128-dimensional vector representing features of the retina as phenotypes. After training the model on 40,000 images from the EyePACS dataset, we generated phenotypes from 130,329 images of 65,629 British White participants in the UK Biobank. We conducted GWAS on these phenotypes and identified 14 loci with genome-wide significance (p<5×10-8 and intersection of hits from left and right eyes). We also did GWAS on the retina color, the average color of the center region of the retinal fundus photos. The GWAS of retina colors identified 34 loci, 7 are overlapping with GWAS of raw image phenotype. Our results establish the feasibility of this new framework of genomic study based on self-supervised phenotyping of medical images.

Uniform [13C,15N]-labeled and glycosylated IgG1 Fc expressed in Saccharomyces cerevisiae.

Despite the prevalence and importance of glycoproteins in human biology, methods for isotope labeling suffer significant limitations. Common prokaryotic platforms do not produce mammalian post-translation modifications that are essential to the function of many human glycoproteins, including immunoglobulin G1 (IgG1). Mammalian expression systems require complex media and thus introduce significant costs to achieve uniform labeling. Expression with Pichia is available, though expertise and equipment requirements surpass E. coli culture. We developed a system utilizing Saccharomyces cerevisiae, [13C]-glucose, and [15N]-ammonium chloride with complexity comparable to E. coli. Here we report two vectors for expressing the crystallizable fragment (Fc) of IgG1 for secretion into the culture medium, utilizing the ADH2 or DDI2 promoters. We also report a strategy to optimize the expression yield using orthogonal Taguchi arrays. Lastly, we developed two different media formulations, a standard medium which provides 86-92% 15N and 30% 13C incorporation into the polypeptide, or a rich medium which provides 98% 15N and 95% 13C incorporation as determined by mass spectrometry. This advance represents an expression and optimization strategy accessible to experimenters with the capability to grow and produce proteins for NMR-based experiments using E. coli.

A comprehensive assessment of selective amino acid 15N-labeling in human embryonic kidney 293 cells for NMR spectroscopy.

A large proportion of human proteins contain post-translational modifications that cannot be synthesized by prokaryotes. Thus, mammalian expression systems are often employed to characterize structure/function relationships using NMR spectroscopy. Here we define the selective isotope labeling of secreted, post-translationally modified proteins using human embryonic kidney (HEK)293 cells. We determined that alpha-[15N]- atoms from 10 amino acids experience minimal metabolic scrambling (C, F, H, K, M, N, R, T, W, Y). Two more interconvert to each other (G, S). Six others experience significant scrambling (A, D, E, I, L, V). We also demonstrate that tuning culture conditions suppressed V and I scrambling. These results define expectations for 15N-labeling in HEK293 cells.

Dual, Photo-Responsive and Redox-Active Supramolecular Foldamers.

We report on dual, light-responsive and redox-active foldamers that demonstrate reversible and robust stimuli-induced behaviour. Herein, UV/Vis, 1H NMR and circular dichroism (CD) spectroscopy and cyclic voltammetry have been used to establish the reversibility and highly robust nature of the light- and redox-driven behaviour of these new foldamers with minimal levels of fatigue observed even upon multiple cyclic treatments with irradiative/non-irradiative and oxidative/reductive conditions. This proof-of-concept work paves the way towards the creation of novel stimuli-responsive foldamers of increasing sophistication capable of demonstrating reversible and robust responses to multiple distinct stimuli.

Nanoscale ultrastructures increase the visual conspicuousness of signalling traits in obligate cleaner shrimps.

Signal theory predicts organisms should evolve signals that are conspicuous to intended receivers in natural signalling environments. Cleaner shrimps remove ectoparasites from reef fish clients and many signal their intent to clean by whipping long, white antennae. As white is a reliably conspicuous colour in aquatic environments, we hypothesized that selection has acted to increase broad-spectrum antennal reflectance in cleaners. Using scanning electron microscopy, optical models and reflectance measurements, we found that the antennae in three obligate cleaner species from two families (Palaemonidae and Lysmatidae) had thick (∼6 µm) chitinous layers or densely packed high refractive index spheres (300-400 nm diameter), which models show increase reflectance (400-700 nm). Two facultative and non-cleaning species had no visible antennae ultrastructure beyond the chitinous exoskeleton. Antennae reflectance was significantly higher in obligate cleaners than in facultative and non-cleaning species. Our results suggest that some obligate cleaners may have evolved ultrastructures that increase the conspicuousness of their antennae as signals.

Identification of cis-regulatory modules for adeno-associated virus-based cell-type-specific targeting in the retina and brain.

Adeno-associated viruses (AAVs) targeting specific cell types are powerful tools for studying distinct cell types in the central nervous system (CNS). Cis-regulatory modules (CRMs), e.g., enhancers, are highly cell-type-specific and can be integrated into AAVs to render cell type specificity. Chromatin accessibility has been commonly used to nominate CRMs, which have then been incorporated into AAVs and tested for cell type specificity in the CNS. However, chromatin accessibility data alone cannot accurately annotate active CRMs, as many chromatin-accessible CRMs are not active and fail to drive gene expression in vivo. Using available large-scale datasets on chromatin accessibility, such as those published by the ENCODE project, here we explored strategies to increase efficiency in identifying active CRMs for AAV-based cell-type-specific labeling and manipulation. We found that prescreening of chromatin-accessible putative CRMs based on the density of cell-type-specific transcription factor binding sites (TFBSs) can significantly increase efficiency in identifying active CRMs. In addition, generation of synthetic CRMs by stitching chromatin-accessible regions flanking cell-type-specific genes can render cell type specificity in many cases. Using these straightforward strategies, we generated AAVs that can target the extensively studied interneuron and glial cell types in the retina and brain. Both strategies utilize available genomic datasets and can be employed to generate AAVs targeting specific cell types in CNS without conducting comprehensive screening and sequencing experiments, making a step forward in cell-type-specific research.

Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina.

Transcription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is necessary. We analyzed how the expression of the homeobox TF, orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during development in the mouse retina. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs, respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages. We conclude that retinal cells use a cohort of TFs with different expression patterns and multiple CRMs with different chromatin configurations to regulate the expression of Otx2 precisely.

Metabolic15N labeling of the N-glycosylated immunoglobulin G1 Fc with an engineered Saccharomyces cerevisiae strain.

The predominant protein expression host for NMR spectroscopy is Escherichia coli, however, it does not synthesize appropriate post-translation modifications required for mammalian protein function and is not ideal for expressing naturally secreted proteins that occupy an oxidative environment. Mammalian expression platforms can address these limitations; however, these are not amenable to cost-effective uniform 15 N labeling resulting from highly complex growth media requirements. Yeast expression platforms combine the simplicity of bacterial expression with the capabilities of mammalian platforms, however yeasts require optimization prior to isotope labeling. Yeast expression will benefit from methods to boost protein expression levels and developing labeling conditions to facilitate growth and high isotope incorporation within the target protein. In this work, we describe a novel platform based on the yeast Saccharomyces cerevisiae that simultaneously expresses the Kar2p chaperone and protein disulfide isomerase in the ER to facilitate the expression of secreted proteins. Furthermore, we developed a growth medium for uniform 15 N labeling. We recovered 2.2 mg/L of uniformly 15 N-labeled human immunoglobulin (Ig)G1 Fc domain with 90.6% 15 N labeling. NMR spectroscopy revealed a high degree of similarity between the yeast and mammalian-expressed IgG1 Fc domains. Furthermore, we were able to map the binding interaction between IgG1 Fc and the Z domain through chemical shift perturbations. This platform represents a novel cost-effective strategy for 15 N-labeled immunoglobulin fragments.

Influence of visual background on discrimination of signal-relevant colours in zebra finches (Taeniopygia guttata).

Colour signals of many animals are surrounded by a high-contrast achromatic background, but little is known about the possible function of this arrangement. For both humans and non-human animals, the background colour surrounding a colour stimulus affects the perception of that stimulus, an effect that can influence detection and discrimination of colour signals. Specifically, high colour contrast between the background and two given colour stimuli makes discrimination more difficult. However, it remains unclear how achromatic background contrast affects signal discrimination in non-human animals. Here, we test whether achromatic contrast between signal-relevant colours and an achromatic background affects the ability of zebra finches to discriminate between those colours. Using an odd-one-out paradigm and generalized linear mixed models, we found that higher achromatic contrast with the background, whether positive or negative, decreases the ability of zebra finches to discriminate between target and non-target stimuli. This effect is particularly strong when colour distances are small (less than 4 ΔS) and Michelson achromatic contrast with the background is high (greater than 0.5). We suggest that researchers should consider focal colour patches and their backgrounds as collectively comprising a signal, rather than focusing on solely the focal colour patch itself.

The value of adherence information during clinical pharmaceutical trials.

BACKGROUND/AIMS: The quality of the evidence used to evaluate a drug's safety and efficacy depends, in part, on how well participants adhere to the prescribed drug-taking regime. There are multiple approaches to measure adherence in clinical trials, varying in their cost and accuracy. We demonstrate a method for evaluating the cost-effectiveness of common adherence monitoring methods, considering the costs and data quality for drugs that differ in how forgiving they are of nonadherence. METHODS: We propose a simulation approach to estimate the value of evidence about adherence, considering both costs of collection and potential errors in interpreting clinical trial results. We demonstrate the approach with a simulated clinical trial of nitrendipine, a common calcium channel blocker. We consider two trial designs, one using pretrial adherence to "enrich" the trial sample and one without an enrichment strategy. We use scenarios combining high and low values of two key properties of a clinical trial: participant adherence and drug forgiveness. RESULTS: Under the conditions of these simulations, the most cost-effective adherence monitoring approach depends on both trial participant adherence and drug forgiveness. For example, the enrichment strategy is not cost-effective for the base scenario (high forgiveness and high adherence), but is for other scenarios. We also estimate the effects of evaluable patient analysis, a controversial procedure that excludes nonadherent participants from the analyses, after a trial is completed. CONCLUSIONS: Our proposed approach can guide drug regulators and developers in designing efficient clinical trials and assessing the impact of nonadherence on trial results. It can identify cost-effective adherence-monitoring methods, given available knowledge about the methods, drug, and patients' expected adherence.

Using implementation science frameworks to translate and adapt a pregnancy app for an emerging Latino community.

BACKGROUND: Digital mobile health (mHealth) applications are a popular form of prenatal education and care delivery in the U.S.; yet there are few Spanish language options for native speakers. Furthermore, existing applications do not consider cultural differences and disparities in healthcare access, including those specific to emerging Latino communities. OBJECTIVE: To adapt and translate an English-language pregnancy mobile health app to meet the language and cultural needs of Spanish-speaking Latino immigrants living in the United States. METHODS: We use a multi-step process, grounded in implementation science frameworks, to adapt and translate the contents of an existing pregnancy app. Interviews with stakeholders (n = 12) who advocate for the needs of pregnant individuals in an emerging Latino community were used to identify domains of possible disparities in access to prenatal care. We then conducted semi-structured interviews with peripartum Spanish-speaking Latino users (n = 14) to understand their perspectives within those domains. We identified a list of topics to create educational material for the modified app and implemented a systematic translation approach to ensure that the new version was acceptable for immigrants from different countries in Latin America. RESULTS: The interviews with stakeholders revealed seven critical domains that need to be addressed in an adapted prenatal app: language and communication, financial concerns, social support, immigration status, cultural differences, healthcare navigation, and connection to population-specific community resources that offer Spanish language services. The interviews with peripartum Spanish-speaking Latino women informed how the existing content in the app could be adjusted or built upon to address these issues, including providing information on accessing care offered in their native language and community support. Finally, we used a systematic approach to translate the existing application and create new content. CONCLUSION: This work illustrates a process to adapt an mHealth pregnancy app to the needs of an emerging Latino community, by incorporating culturally sensitive Spanish language content while focusing on addressing existing health disparities.

Risk heatmaps as visual displays: Opening movie studios after the COVID-19 shutdown.

Upon shutting down operations in early 2020 due to the COVID-19 pandemic, the movie industry assembled teams of experts to help develop guidelines for returning to operation. It resulted in a joint report, The Safe Way Forward, which was created in consultation with union members and provided the basis for negotiations with the studios. A centerpiece of the report was a set of heatmaps displaying SARS-CoV-2 risks for a shoot, as a function of testing rate, community infection prevalence, community transmission rate (R0), and risk measure (either expected number of cases or probability of at least one case). We develop and demonstrate a methodology for evaluating such complex displays, in terms of how well they inform potential users, in this case, workers deciding whether the risks of a shoot are acceptable. We ask whether individuals making hypothetical return-to-work decisions can (a) read display entries, (b) compare display entries, and (c) make inferences based on display entries. Generally speaking, respondents recruited through the Amazon MTurk platform could interpret the display information accurately and make coherent decisions, suggesting that heatmaps can communicate complex risks to lay audiences. Although these heatmaps were created for practical, rather than theoretical, purposes, these results provide partial support for theoretical accounts of visual information processing and identify challenges in applying them to complex settings.

Emerging biological therapies for the treatment of malignant pleural mesothelioma.

Introduction: Malignant pleural mesothelioma (MPM) has limited treatment options with minimal new therapy approvals for unresectable disease in the past 15 years. However, considerable work has occurred to develop immunotherapies and biomarker driven therapy to improve patient outcomes over this period.Areas covered: This review examines current standard of care systemic therapy in the first- and second line setting. The last 12 months has seen 2 significant trials (Checkmate 743 and CONFIRM) which provide evidence supporting the role of immunotherapy in the management of MPM. Further trials are underway to assess the role of combination chemoimmunotherapy and personalized therapy. Additionally, a large number of clinical trials are ongoing to assess the efficacy of oncoviral, dendritic cell, anti-mesothelin and chimeric antigen receptor T cell therapy in the treatment of MPM.Expert opinion: Recent Phase III trial results have established a role for immunotherapy in the management of MPM. The optimal sequencing and combination of chemotherapy and immunotherapy remains to be determined. Novel therapies for MPM are promising however efficacy remains to be determined and issues remain regarding access to and delivery of these therapies.

Assessing the predictive value of common gait measure for predicting falls in patients presenting with suspected normal pressure hydrocephalus.

OBJECTIVE: To assess the predictive value of common measures validated to predict falls in other geriatric populations in patients presenting with suspected Normal Pressure Hydrocephalus (NPH). METHODS: One hundred ninety-five patients over the age of 60 who received the Fall Risk Questionnaire were retrospectively recruited from the CSF Disorders clinic within the departments of Neurosurgery and Neurology. Multiple logistic regression was used to create a model to predict falls for patients with suspected NPH using common measures: Timed Up & Go, Dual Timed Up & Go, 10 Meter Walk, MiniBESTest, 6-Minute Walk, Lower Extremity Function (Mobility), Fall Risk Questionnaire, and Functional Activities Questionnaire. RESULTS: The Fall Risk Questionnaire and age were shown to be the best predictors of falls. The model was 95.92% (Positive predictive value: 83.93%) sensitive and 47.92% specific (Negative predictive value: 77.78%). CONCLUSION: Patients presenting with suspected NPH are at an increased fall risk, 75% of the total patients and 89% of patients who responded to a temporary drain of CSF had at least one fall in the past 6 months. The Fall Risk Questionnaire and age were shown to be predictive of falls for patients with suspected NPH. The preliminary evidence indicates measures that have been validated to assess fall risk in other populations may not be valid for patients presenting with suspected NPH.

Mobile Remote Monitoring of Intimate Partner Violence Among Pregnant Patients During the COVID-19 Shelter-In-Place Order: Quality Improvement Pilot Study.

BACKGROUND: Intimate partner violence (IPV) is one of the leading causes of pregnancy-related death. Prenatal health care providers can offer critical screening and support to pregnant people who experience IPV. During the COVID-19 shelter-in-place order, mobile apps may offer such people the opportunity to continue receiving screening and support services. OBJECTIVE: We aimed to examine cases of IPV that were reported on a prenatal care app before and during the implementation of COVID-19 shelter-in-place mandates. METHODS: The number of patients who underwent voluntary IPV screening and the incidence rate of IPV were determined by using a prenatal care app that was disseminated to patients from a single, large health care system. We compared the IPV screening frequencies and IPV incidence rates of patients who started using the app before the COVID-19 shelter-in-place order, to those of patients who started using the app during the shelter-in-place order. RESULTS: We found 552 patients who started using the app within 60 days prior to the enforcement of the shelter-in-place order, and 407 patients who used the app at the start of shelter-in-place enforcement until the order was lifted. The incidence rates of voluntary IPV screening for new app users during the two time periods were similar (before sheltering in place: 252/552, 46%; during sheltering in place: 163/407, 40%). The overall use of the IPV screening tool increased during the shelter-in-place order. A slight, nonsignificant increase in the incidence of physical, sexual, and psychological violence during the shelter-in-place order was found across all app users (P=.56). Notably, none of the patients who screened positively for IPV had mentions of IPV in their medical charts. CONCLUSIONS: App-based screening for IPV is feasible during times when in-person access to health care providers is limited. Our results suggest that the incidence of IPV slightly increased during the shelter-in-place order. App-based screening may also address the needs of those who are unwilling or unable to share their IPV experiences with their health care provider.

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer.

Metastasis is a complex biological process that has been difficult to delineate in human colorectal cancer (CRC) patients. A major obstacle in understanding metastatic lineages is the extensive intra-tumor heterogeneity at the primary and metastatic tumor sites. To address this problem, we developed a highly multiplexed single-cell DNA sequencing approach to trace the metastatic lineages of two CRC patients with matched liver metastases. Single-cell copy number or mutational profiling was performed, in addition to bulk exome and targeted deep-sequencing. In the first patient, we observed monoclonal seeding, in which a single clone evolved a large number of mutations prior to migrating to the liver to establish the metastatic tumor. In the second patient, we observed polyclonal seeding, in which two independent clones seeded the metastatic liver tumor after having diverged at different time points from the primary tumor lineage. The single-cell data also revealed an unexpected independent tumor lineage that did not metastasize, and early progenitor clones with the "first hit" mutation in APC that subsequently gave rise to both the primary and metastatic tumors. Collectively, these data reveal a late-dissemination model of metastasis in two CRC patients and provide an unprecedented view of metastasis at single-cell genomic resolution.

Evidence that eye-facing photophores serve as a reference for counterillumination in an order of deep-sea fishes.

Counterillumination, the masking of an animal's silhouette with ventral photophores, is found in a number of mesopelagic taxa but is difficult to employ because it requires that the animal match the intensity of downwelling light without seeing its own ventral photophores. It has been proposed that the myctophid, Tarletonbeania crenularis, uses a photophore directed towards the eye, termed an eye-facing photophore, as a reference standard that it adjusts to match downwelling light. The potential use of this mechanism, however, has not been evaluated in other fishes. Here, we use micro-computed tomography, photography and dissection to evaluate the presence/absence of eye-facing photophores in three families of stomiiform fishes. We found that all sampled species with ventral photophores capable of counterillumination possess an eye-facing photophore that is pigmented on the anterior and lateral sides, thus preventing its use as a laterally directed signal, lure or searchlight. The two species that are incapable of counterillumination, Cyclothone obscura and Sigmops bathyphilus, lack an eye-facing photophore. After determining the phylogenetic distribution of eye-facing photophores, we used histology to examine the morphology of the cranial tissue in Argyropelecus aculeatus and determined that light from the eye-facing photophore passes through a transparent layer of tissue, then the lens, and finally strikes the accessory retina. Additionally, eight of the 14 species for which fresh specimens were available had an aphakic gap that aligned with the path of emitted light from the eye-facing photophore, while the remaining six had no aphakic gap. These findings, combined with records of eye-facing photophores from distantly related taxa, strongly suggest that eye-facing photophores serve as a reference for counterillumination in these fishes.

Tumor evolution: Linear, branching, neutral or punctuated?

Intratumor heterogeneity has been widely reported in human cancers, but our knowledge of how this genetic diversity emerges over time remains limited. A central challenge in studying tumor evolution is the difficulty in collecting longitudinal samples from cancer patients. Consequently, most studies have inferred tumor evolution from single time-point samples, providing very indirect information. These data have led to several competing models of tumor evolution: linear, branching, neutral and punctuated. Each model makes different assumptions regarding the timing of mutations and selection of clones, and therefore has different implications for the diagnosis and therapeutic treatment of cancer patients. Furthermore, emerging evidence suggests that models may change during tumor progression or operate concurrently for different classes of mutations. Finally, we discuss data that supports the theory that most human tumors evolve from a single cell in the normal tissue. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.

Standardized regression-based clinical change score cutoffs for normal pressure hydrocephalus.

BACKGROUND: Presently, for patients presenting with suspected Normal Pressure Hydrocephalus (NPH) who undergo temporary drainage of cerebrospinal fluid (CSF) there is no defined model to differentiate chance improvement form clinical significance change at the individual patient level. To address this lack of information we computed standard regression based clinical change models for the 10 Meter Walk Test, Timed Up & Go, Dual Timed Up & Go, 6-Minute Walk Test, Mini-Balance Evaluation Systems Test, Montreal Cognitive Assessment, and Symbol Digit Modalities using data from patients with suspected NPH that underwent temporary drainage of CSF. These clinically significant change modes can classify clinically significant improvement following temporary drainage of CSF at the individual patient level. This allows for physicians to differentiate a clinically significant improvement in symptoms from chance improvement. METHODS: Data was collected from 323 patients, over the age of 60, with suspected NPH that underwent temporary drainage of CSF with corresponding gait and cognitive testing. McSweeney Standardized Regression Based Clinical Change Models were computed for standard gait and cognitive measures: Timed Up & Go, Dual Timed Up & Go, 10 Meter Walk Test, MiniBESTest, 6-Minute Walk Test, Montreal Cognitive Assessment, and Symbol Digit Modalities Test. To assess the discriminate validity of the measures we used correlations, Chi2, and regression analyses. RESULTS: The clinical change models explained 69-91.8% of the variability in post-drain performance (p <  0.001). As patient scores became more impaired, the percent change required for improvement to be clinically significant increased for all measures. We found that the measures were not discriminate, the Timed Up & Go was highly related to the 10 Meter Walk Test (r = 0.85, R2 = 0.769-0.738, p <  0.001), MiniBESTest (r = - 0.67, R2 = 0.589-0.734, p <  0.001), and 6 Minute Walk Test (r = - 0.77, R2 = 0.71-0.734, p <  0.001). CONCLUSION: Standardized Regression Based Clinically Significant Change Models allow for physicians to use an evidence-based approach to differentiate clinically significant change from chance improvement at the individual patient level. The Timed Up & Go was shown to be predictive of detailed measures of gait velocity, balance, and endurance.