Transcription factor induction of vascular blood stem cell niches in vivo.

The hematopoietic niche is a supportive microenvironment composed of distinct cell types, including specialized vascular endothelial cells that directly interact with hematopoietic stem and progenitor cells (HSPCs). The molecular factors that specify niche endothelial cells and orchestrate HSPC homeostasis remain largely unknown. Using multi-dimensional gene expression and chromatin accessibility analyses in zebrafish, we define a conserved gene expression signature and cis-regulatory landscape that are unique to sinusoidal endothelial cells in the HSPC niche. Using enhancer mutagenesis and transcription factor overexpression, we elucidate a transcriptional code that involves members of the Ets, Sox, and nuclear hormone receptor families and is sufficient to induce ectopic niche endothelial cells that associate with mesenchymal stromal cells and support the recruitment, maintenance, and division of HSPCs in vivo. These studies set forth an approach for generating synthetic HSPC niches, in vitro or in vivo, and for effective therapies to modulate the endogenous niche.

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC's functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.

3D Ultrasound-Guided Photoacoustic Imaging to Monitor the Effects of Suboptimal Tyrosine Kinase Inhibitor Therapy in Pancreatic Tumors.

Pancreatic cancer is a disease with an incredibly poor survival rate. As only about 20% of patients are eligible for surgical resection, neoadjuvant treatments that can relieve symptoms and shrink tumors for surgical resection become critical. Many forms of treatments rely on increased vulnerability of cancerous cells, but tumors or regions within the tumors that may be hypoxic could be drug resistant. Particularly for neoadjuvant therapies such as the tyrosine kinase inhibitors utilized to shrink tumors, it is critical to monitor changes in vascular function and hypoxia to predict treatment efficacy. Current clinical imaging modalities used to obtain structural and functional information regarding hypoxia or oxygen saturation (StO2) do not provide sufficient depth penetration or require the use of exogenous contrast agents. Recently, ultrasound-guided photoacoustic imaging (US-PAI) has garnered significant popularity, as it can noninvasively provide multiparametric information on tumor vasculature and function without the need for contrast agents. Here, we built upon existing literature on US-PAI and demonstrate the importance of changes in StO2 values to predict treatment response, particularly tumor growth rate, when the outcomes are suboptimal. Specifically, we image xenograft mouse models of pancreatic adenocarcinoma treated with suboptimal doses of a tyrosine kinase inhibitor cabozantinib. We utilize the US-PAI data to develop a multivariate regression model that demonstrates that a therapy-induced reduction in tumor growth rate can be predicted with 100% positive predictive power and a moderate (58.33%) negative predictive power when a combination of pretreatment tumor volume and changes in StO2 values pretreatment and immediately posttreatment was employed. Overall, our study indicates that US-PAI has the potential to provide label-free surrogate imaging biomarkers that can predict tumor growth rate in suboptimal therapy.

Mechanical phenotyping reveals unique biomechanical responses in retinoic acid-resistant acute promyelocytic leukemia.

All-trans retinoic acid (ATRA) is an essential therapy in the treatment of acute promyelocytic leukemia (APL), but nearly 20% of patients with APL are resistant to ATRA. As there are no biomarkers for ATRA resistance that yet exist, we investigated whether cell mechanics could be associated with this pathological phenotype. Using mechano-node-pore sensing, a single-cell mechanical phenotyping platform, and patient-derived APL cell lines, we discovered that ATRA-resistant APL cells are less mechanically pliable. By investigating how different subcellular components of APL cells contribute to whole-cell mechanical phenotype, we determined that nuclear mechanics strongly influence an APL cell's mechanical response. Moreover, decondensing chromatin with trichostatin A is especially effective in softening ATRA-resistant APL cells. RNA-seq allowed us to compare the transcriptomic differences between ATRA-resistant and ATRA-responsive APL cells and highlighted gene expression changes that could be associated with mechanical changes. Overall, we have demonstrated the potential of "physical" biomarkers in identifying APL resistance.

Node-Pore Sensing for Characterizing Cells and Extracellular Vesicles.

Node-Pore Sensing, NPS, is an extremely versatile and powerful technique for the analysis of cells and the detection of extracellular vesicles (EVs). NPS involves measuring the modulated current pulse caused by a cell transiting a microfluidic channel that has been segmented by a series of inserted nodes. As the current pulse reflects the number of nodes and segments of the channel, NPS can achieve exquisite sensitivity. Thus, when used as a Coulter counter, NPS can measure the sub-micron size increase of antibody-coated colloids to which EVs are specifically bound. By simply inserting between two nodes a "contraction" channel through which cells can squeeze, one can mechanically phenotype cells. We discuss the details of performing these two NPS applications.

Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications.

The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 -- 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should improve future clinical applications of mCN measurements.

High Rates of Mortality in Geriatric Patients Admitted for Inflammatory Bowel Disease Management.

GOAL: The goal of this study was to evaluate the inpatient mortality risk among geriatric patients with inflammatory bowel disease (IBD). BACKGROUND: The challenges of caring for elderly patients with IBD will increase with the aging of the US population. Given the complications of hospitalization, we set to examine if elderly patients age older than 65 were at higher risk of mortality. MATERIALS AND METHODS: All patients with ulcerative colitis (UC) or Crohn's disease (CD) in the National Inpatient Sample (NIS) from 2016 and 2017 as the primary diagnosis or secondary diagnosis with an IBD-related cause of admission were included. Outcomes for patients aged above 65 were compared with below 65 using multivariable survey-adjusted regression. CD and UC were analyzed separately. RESULTS: In 2016-2017, there were an estimated 162,800 admissions for CD and related complications compared with 96,450 for UC. In total, 30% of UC and 20% of CD admissions were geriatric. Geriatric status was associated with higher odds of mortality for CD [odds ratio (OR)=3.47, 95% confidence interval (CI): 2.72-4.44] and UC (OR=2.75, 95% CI: 2.16-3.49) after adjustment for comorbidities, admission type, hospital type, inpatient surgery, and IBD subtype. The cause of death was ∼80% infectious in both CD and UC in all groups. An average of 0.19 days (95% CI: 0.05-0.34) and $2467 (95% CI: 545-4388) increase was seen for geriatric CD patients. No significant change was seen for UC. CONCLUSIONS: Age over 65 was independently associated with higher odds of death in both UC and CD patients, even after appropriate adjustment. Further research is needed to optimize care for this growing patient population.

Multiplexed DNA-Directed Patterning of Antibodies for Applications in Cell Subpopulation Analysis.

Antibodies provide the functional biospecificity that has enabled the development of sensors, diagnostic tools, and assays in both laboratory and clinical settings. However, as multimarker screening becomes increasingly necessary due to the heterogeneity and complexity of human pathology, new methods must be developed that are capable of coordinating the precise assembly of multiple, distinct antibodies. To address this technological challenge, we engineered a bottom-up, high-throughput method in which DNA patterns, comprising unique 20-base pair oligonucleotides, are patterned onto a substrate using photolithography. These microfabricated surface patterns are programmed to hybridize with, and instruct the multiplexed assembly of, antibodies conjugated with the complementary DNA strands. We demonstrate that this simple, yet robust, approach preserves the antibody-binding functionality in two common applications: antibody-based cell capture and label-free surface marker screening. Using a simple proof-of-concept capture device, we achieved high purity separation of a breast cancer cell line, MCF-7, from a blood cell line, Jurkat, with capture purities of 77.4% and 96.6% when using antibodies specific for the respective cell types. We also show that antigen-antibody interactions slow cell trajectories in flow in the next-generation microfluidic node-pore sensing (NPS) device, enabling the differentiation of MCF-7 and Jurkat cells based on EpCAM surface-marker expression. Finally, we use a next-generation NPS device patterned with antibodies against E-cadherin, N-cadherin, and ß-integrin-three markers that are associated with epithelial-mesenchymal transitions-to perform label-free surface marker screening of MCF10A, MCF-7, and Hs 578T breast epithelial cells. Our high-throughput, highly versatile technique enables rapid development of customized, antibody-based assays across a host of diverse diseases and research thrusts.

Biomarkers for the Diagnosis of Allergic Bronchopulmonary Aspergillosis in Cystic Fibrosis: A Systematic Review and Meta-Analysis.

BACKGROUND: Allergic bronchopulmonary aspergillosis (ABPA) is a hypersensitivity reaction to Aspergillus fumigatus and impacts 10% of individuals with cystic fibrosis (CF). A diagnosis of ABPA is challenging to establish in CF owing to overlapping clinical and radiologic features with CF lung disease. Recent studies have identified blood tests, imaging, and other biomarkers that may be useful for diagnosis. OBJECTIVE: To summarize biomarkers that can aid in the diagnosis of ABPA in CF patients and to quantify their diagnostic accuracy through meta-analysis. METHODS: We searched MEDLINE, EMBASE, and the Cochrane Controlled Register of Trials and included studies that used a laboratory technique or imaging modality in CF patients diagnosed with ABPA. Pooled sensitivity and specificity were calculated using a hierarchical summary receiver operating characteristic model. RESULTS: We identified 791 articles, of which 29 met our eligibility criteria and 9 were included in the meta-analysis. Hyperattenuating mucus on computed tomography (CT) scan (n = 3 studies; pooled sensitivity 62% and specificity 92%) and serum specific immunoglobulin E against recombinant Aspergillus funigatus antigens f4 (n = 6; 69%, 89%) and f6 (n = 6; 39%, 97%) demonstrated high specificity. Based on single studies, serum thymus and activation regulated chemokine (92%, 94%), stimulated basophil expression of CD203c (94%, 74%), the inverted mucoid impaction signal on magnetic resonance imaging (94%, 100%), and skin prick test with recombinant Aspergillus fumigatus f4 and/or f6 (100%, 100%) showed high sensitivity and specificity. CONCLUSIONS: Recent studies have found promising biomarkers for diagnosing ABPA in CF. Further research is needed to improve our understanding of their utility in diagnosis and disease monitoring.

Evidence for treatment of lower limb in-stent restenosis with drug eluting balloons.

INTRODUCTION: Restenosis by myointimal hyperplasia after peripheral arterial angioplasty or stenting often limits long term patency. Drug-eluting balloons (DEBs) which inhibit the proliferation of neo-intimal growth of vascular smooth muscle cells may prevent restenosis. The aim of this paper was to examine the evidence in published literature on the use of DEBs in the treatment of peripheral arterial in-stent restenosis (ISR). EVIDENCE ACQUISITION: A systematic literature review was undertaken of all published literature on the treatment of peripheral ISR with drug eluting balloon using Medline and cross-referenced. All published papers on the use of DEBs in peripheral arterial disease (PAD) were used. Cochrane Central Register of Controlled Trials and electronic databases were also searched for on-going studies. EVIDENCE SYNTHESIS: There were no level 1 or 2 evidence published on this subject. The number of high-quality publications is few, and consequently a sufficient analysis is not possible. Recently data from non-randomized cohort studies showed encouraging results with DEB as treatment modality for ISR, whether used alone or as combined strategies. CONCLUSIONS: Evidence from the published literature suggests that DEBs are safe in preventing peripheral ISR. Despite strong corporate pressure for the use of DEBs, there is only circumstantial evidence that this is a useful modality for ISR. Results from on-going studies may allow further meta-analysis for efficiency and cost-effectiveness.

Outcomes in lower GI bleeding comparing weekend with weekday admission.

BACKGROUND AND AIMS: Acute lower gastrointestinal bleeding (LGIB) is a common indication for hospitalization potentially requiring urgent intervention, which may not be readily available at weekends and off-hours. The aim of this study was to examine the association between weekend admission for LGIB and mortality, time to colonoscopy, length of stay, and hospital charges. METHODS: The 2016 U.S. National Inpatient Sample (NIS) dataset was queried for admissions with a primary diagnosis of LGIB. Outcomes for weekend versus weekday admissions were compared using survey-adjusted chi-squared or bivariate correlation. Multivariable regression was then used to compare primary outcomes adjusting for the Elixhauser mortality score (a validated measure of comorbidities), colonoscopy, transfusion, shock, and hospital type. RESULTS: An estimated 124,620 patients were admitted for LGIB in 2016. Comparing weekend with weekday admissions, there was no difference in unadjusted mortality (0.9% vs 1.0%, P = .636). Colonoscopy within the first day (28.6% vs 23.0%, P < .001) and transfusion (34.0% vs 31.5%, P < .001) were more common with weekday admissions; no differences in colonoscopy rate (60.7% vs 60.9%, P = .818), angiography rate (2.7% vs 2.7%, P = .976), mean days to colonoscopy (2.0 vs 2.0, P = .233), or length of stay (4.2 vs 4.1 days, P = .068) were seen. There was no difference in multivariable adjusted mortality rates (odds ratio, 1.11; 95% confidence interval, 0.81-1.54; P = .495) based on the above factors. CONCLUSIONS: Early colonoscopy (within the first day) is more common for weekday admissions, but overall outcomes are not affected by weekend admission for LGIB compared with weekday admissions.

Stress-induced tunneling nanotubes support treatment adaptation in prostate cancer.

Tunneling nanotubes (TNTs) are actin-based membranous structures bridging distant cells for intercellular communication. We define roles for TNTs in stress adaptation and treatment resistance in prostate cancer (PCa). Androgen receptor (AR) blockade and metabolic stress induce TNTs, but not in normal prostatic epithelial or osteoblast cells. Co-culture assays reveal enhanced TNT formation between stressed and unstressed PCa cells as well as from stressed PCa to osteoblasts. Stress-induced chaperones clusterin and YB-1 localize within TNTs, are transported bi-directionally via TNTs and facilitate TNT formation in PI3K/AKT and Eps8-dependent manner. AR variants, induced by AR antagonism to mediate resistance to AR pathway inhibition, also enhance TNT production and rescue loss of clusterin- or YB-1-repressed TNT formation. TNT disruption sensitizes PCa to treatment-induced cell death. These data define a mechanistic network involving stress induction of chaperone and AR variants, PI3K/AKT signaling, actin remodeling and TNT-mediated intercellular communication that confer stress adaptative cell survival.

Symptom Assessment in Patients with Advanced Cancer: Are the Most Severe Symptoms the Most Bothersome?

Objective: We investigated correspondence between symptom severity and symptom bothersomeness in patients with advanced cancer. Background: Symptom severity is commonly assessed in clinical cancer settings, but bothersomeness of these symptoms is less often measured. Methods: Participants with advanced cancer enrolled in a cluster-randomized trial of early palliative care completed the Edmonton Symptom Assessment System (ESAS) and the quality of life at the end of life (QUAL-E) measure as part of their baseline assessment. For each symptom, we examined the correspondence between the symptom being indicated as most severe on the ESAS and rated as most bothersome on the QUAL-E. Results: For the 386 patients who completed relevant sections of the ESAS and QUAL-E, tiredness (32.8%), sleep (23.8%), and appetite (20.2%) were most frequently rated as most severe, whereas pain (28.9%) and tiredness (24.3%) were most frequently indicated as most bothersome. The most bothersome and most severe symptom corresponded in 42%. Pain and/or tiredness were consistently among the top three most bothersome symptoms, whereas appetite was frequently rated the most severe symptom but was rarely perceived as the most bothersome. The probability that patients rating a symptom as most severe would also rate it as most bothersome was highest for pain (66%), nausea (58%), and tiredness (40%). Discussion: ESAS symptom severity does not necessarily indicate patients' most bothersome symptom; regardless of severity, pain and tiredness are most frequently perceived as most bothersome. Further research should investigate the clinical benefits of patients also indicating their three most bothersome ESAS symptoms.

Visco-Node-Pore Sensing: A Microfluidic Rheology Platform to Characterize Viscoelastic Properties of Epithelial Cells.

Viscoelastic properties of cells provide valuable information regarding biological or clinically relevant cellular characteristics. Here, we introduce a new, electronic-based, microfluidic platform-visco-node-pore sensing (visco-NPS)-which quantifies cellular viscoelastic properties under periodic deformation. We measure the storage (G') and loss (G″) moduli (i.e., elasticity and viscosity, respectively) of cells. By applying a wide range of deformation frequencies, our platform quantifies the frequency dependence of viscoelastic properties. G' and G″ measurements show that the viscoelastic properties of malignant breast epithelial cells (MCF-7) are distinctly different from those of non-malignant breast epithelial cells (MCF-10A). With its sensitivity, visco-NPS can dissect the individual contributions of different cytoskeletal components to whole-cell mechanical properties. Moreover, visco-NPS can quantify the mechanical transitions of cells as they traverse the cell cycle or are initiated into an epithelial-mesenchymal transition. Visco-NPS identifies viscoelastic characteristics of cell populations, providing a biophysical understanding of cellular behavior and a potential for clinical applications.

Developments in label-free microfluidic methods for single-cell analysis and sorting.

Advancements in microfluidic technologies have led to the development of many new tools for both the characterization and sorting of single cells without the need for exogenous labels. Label-free microfluidics reduce the preparation time, reagents needed, and cost of conventional methods based on fluorescent or magnetic labels. Furthermore, these devices enable analysis of cell properties such as mechanical phenotype and dielectric parameters that cannot be characterized with traditional labels. Some of the most promising technologies for current and future development toward label-free, single-cell analysis and sorting include electronic sensors such as Coulter counters and electrical impedance cytometry; deformation analysis using optical traps and deformation cytometry; hydrodynamic sorting such as deterministic lateral displacement, inertial focusing, and microvortex trapping; and acoustic sorting using traveling or standing surface acoustic waves. These label-free microfluidic methods have been used to screen, sort, and analyze cells for a wide range of biomedical and clinical applications, including cell cycle monitoring, rapid complete blood counts, cancer diagnosis, metastatic progression monitoring, HIV and parasite detection, circulating tumor cell isolation, and point-of-care diagnostics. Because of the versatility of label-free methods for characterization and sorting, the low-cost nature of microfluidics, and the rapid prototyping capabilities of modern microfabrication, we expect this class of technology to continue to be an area of high research interest going forward. New developments in this field will contribute to the ongoing paradigm shift in cell analysis and sorting technologies toward label-free microfluidic devices, enabling new capabilities in biomedical research tools as well as clinical diagnostics. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.

Clonal expansion and compartmentalized maintenance of rhesus macaque NK cell subsets.

Natural killer (NK) cells recognize and eliminate infected and malignant cells. Their life histories are poorly understood, particularly in humans, due to lack of informative models and endogenous clonal markers. Here, we apply transplantation of barcoded rhesus macaque hematopoietic cells to interrogate the landscape of NK cell production, expansion, and life histories at a clonal level long term and after proliferative challenge. We identify oligoclonal populations of rhesus CD56-CD16+ NK cells that are characterized by marked expansions and contractions over time yet remained long-term clonally uncoupled from other hematopoietic lineages, including CD56+CD16- NK cells. Individual or groups of CD56-CD16+ expanded clones segregated with surface expression of specific killer immunoglobulin-like receptors. These clonally distinct NK cell subpopulation patterns persisted for more than 4 years, including after transient in vivo anti-CD16-mediated depletion and subsequent regeneration. Profound and sustained interleukin-15-mediated depletion was required to generate new oligoclonal CD56-CD16+ NK cells. Together, our results indicate that linear NK cell production from multipotent hematopoietic progenitors or less mature CD56+CD16- cells is negligible during homeostasis and moderate proliferative stress. In such settings, peripheral compartmentalized self-renewal can maintain the composition of distinct, differentiated NK cell subpopulations.

Generation of mouse-zebrafish hematopoietic tissue chimeric embryos for hematopoiesis and host-pathogen interaction studies.

Xenografts of the hematopoietic system are extremely useful as disease models and for translational research. Zebrafish xenografts have been widely used to monitor blood cancer cell dissemination and homing due to the optical clarity of embryos and larvae, which allow unrestricted in vivo visualization of migratory events. Here, we have developed a xenotransplantation technique that transiently generates hundreds of hematopoietic tissue chimeric embryos by transplanting murine bone marrow cells into zebrafish blastulae. In contrast to previous methods, this procedure allows mammalian cell integration into the fish developmental hematopoietic program, which results in chimeric animals containing distinct phenotypes of murine blood cells in both circulation and the hematopoietic niche. Murine cells in chimeric animals express antigens related to (i) hematopoietic stem and progenitor cells, (ii) active cell proliferation and (iii) myeloid cell lineages. We verified the utility of this method by monitoring zebrafish chimeras during development using in vivo non-invasive imaging to show novel murine cell behaviors, such as homing to primitive and definitive hematopoietic tissues, dynamic hematopoietic cell and hematopoietic niche interactions, and response to bacterial infection. Overall, transplantation into the zebrafish blastula provides a useful method that simplifies the generation of numerous chimeric animals and expands the range of murine cell behaviors that can be studied in zebrafish chimeras. In addition, integration of murine cells into the host hematopoietic system during development suggests highly conserved molecular mechanisms of hematopoiesis between zebrafish and mammals.This article has an associated First Person interview with the first author of the paper.

Droplet digital PCR shows the D-Loop to be an error prone locus for mitochondrial DNA copy number determination.

Absolute quantification of mitochondrial DNA copy number (mCN) provides important insights in many fields of research including cancer, cardiovascular and reproductive health. Droplet digital PCR (ddPCR) natively reports absolute copy number, and we have developed a single-dye, multiplex assay to measure rat mCN that is accurate, precise and affordable. We demonstrate simple methods to optimize this assay and to determine nuclear reference pseudogene copy number to extend the range of mCN that can be measured with this assay. We evaluated two commonly used mitochondrial DNA reference loci to determine mCN, the ND1 gene and the D-Loop. Harnessing the absolute measures of ddPCR, we found that the D-Loop amplifies with a copy number of ~1.0-1.5 relative to other sites on the mitochondrial genome. This anomalous copy number varied significantly between rats and tissues (aorta, brain, heart, liver, soleus muscle). We advocate for avoiding the D-Loop as a mitochondrial reference in future studies of mCN. Further, we report a novel approach to quantifying immunolabelled mitochondrial DNA that provides single-cell estimates of mCN that closely agree with the population analyses by ddPCR. The combination of these assays represents a cost-effective and powerful suite of tools to study mCN.