Biology subjects

Chen, M. Y.

Publications and source records attributed to Chen, M. Y..

13 recordsLinked to original sources

bioRxiv2025

Myocyte Damage and Mass Loss Drives Increasing Water Content, Compliance, and Survival in Septic Cardiomyopathy

Introduction/PurposeDuring the septic cardiomyopathy, the mechanism and relationship to outcome of changes in left ventricular (LV) end diastolic volume (EDV) and ejection fraction (EF) remains obscure. We compared serial changes in LVEF and LVEDV to successive alterations in LV wall ultrastructure, water content, and total mass to investigate whether these measures can explain their basis. MethodsWe performed cardiac magnetic resonance imaging at 0,6,18,30,42,54, and 92h post-bacterial challenge in a large-animal model (n=57) that mimics human septic cardiomyopathy. LV tissue was obtained for electron microscopy (EM) upon death and 66h in sacrificed survivors. ResultsBetween 0-6h post-challenge, LV compliance and EDV reached its greatest decline. Non-survivors (n=18) exhibited significantly greater reductions in LVEDV, along with more myocyte edema, mitochondrial swelling and myofilament fragmentation on EM. This increased tissue damage may explain why non-survivors developed worse LV compliance and a greater decline in LVEDV, which persisted until death. From 6-30h, LVEDV significantly improved to baseline in non-survivors, while survivors experienced [~]20% increases (n=39). Concurrently, there was significant LV mass loss and increases in percent water content that were significantly associated with increases in LVEDV. This is consistent with a passive mechanism for rapidly improving LV compliance and EDV. Full recovery of EF required additional days. We hypothesize the prolonged significant mass loss over 5d reflects an active process for remodeling fragmented myofilaments, eliminating myocyte edema, and mitochondrial swelling, ultimately restoring contractile function. ConclusionThe septic cardiomyopathy constitutes a diffuse ultrastructural injury to myocytes with three phases. Initially, there is a decrease in LVEDV, and EF due to myocyte damage within 6h of bacterial challenge; next, the patient sees a passive LVEDV recovery from 6-30h, where LV mass loss increases relative wall percent water content, which facilitates wall compliance and LVEDV; and lastly, the patient sees mass loss beyond 30h consistent with an active repair mechanism of myocytes, returning systolic function to normal. Therefore, EDV changes are a pathophysiological biomarker for sepsis outcomes. A lower LVEDV indicates persistent unrepairable ultrastructure damage with worsening wall compliance and poorer outcomes. LVEDV dilation is a sign of near-full recovery of ultrastructure injury, augmenting wall compliance and improving outcomes. Clinical ImplicationsWe explain herein why septic cardiomyopathy findings dont have clinical implications like heart failure. Septic patients who exhibit signs of heart failure, low LVEF with high EDVs, are doing well - reflecting mild myocyte injury, effective damaged tissues clearance, increased relative LV wall water content, and compliance. This augments the LVEDV, lowering the LVEF. Septic patients who deteriorate rapidly, contrary to heart failure patients, show high/normal LVEF and low/normal LVEDV. Here, the myocyte damage is severe, leading to insufficient wall repair, and this decreased wall compliance persists, preventing the LV from dilating and making LVEDV low which ultimately raises the LVEF.

physiology↗

bioRxiv2025

Predicting bacterial-mediated entomopathogenicity through comparative genomics and statistical modeling

Bacterial genomes encode for vast functional diversity and have both beneficial and detrimental effects on insect hosts. However, connecting bacterial genotype to a host-associated phenotype can be experimentally time-consuming, particularly if insecticidal mechanisms are highly host-specific. To streamline the identification of virulence genes on a new host, we tested if merging existing mechanistic knowledge with in vivo tests on a small number of bacterial isolates could predict bacterial genes associated with entomopathogenesis. We used a model consisting of Drosophila melanogaster interactions with pathogenic and commensal genome-sequenced strains of Pseudomonas bacteria. We compiled a database of previously described insecticidal and biocontrol genes within the Pseudomonas genus and used comparative genomics to probe the distribution of these genes across Pseudomonas strains. We found natural variation in the presence of known insecticidal genes across the genus. We tested the insect-killing capacity of 13 Pseudomonas spp. strains against D. melanogaster and found natural variation in insecticidal activity. To identify bacterial genes associated with fly mortality, we employed two statistical models to correlate bacterial virulence with the presence of previously described insecticidal activity. To validate our predictions, we used a P. aeruginosa PAO1 transposon mutant library and identified 8 operons that are necessary for killing D. melanogaster. We show that by combining existing literature with phenotyping a small number of strains, we can identify genes necessary for insecticidal activity in a previously untested insect model. More broadly these findings illustrate a discovery pipeline for bacterial virulence mechanisms, accelerating the discovery of insect pest biocontrol mechanisms.

microbiology↗

bioRxiv2024

In vitro biofilm formation only partially predicts beneficial Pseudomonas fluorescens protection against rhizosphere pathogens

Plant roots form associations with both beneficial and pathogenic soil microorganisms. While members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a robust biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are necessary in vivo. Pseudomonas fluorescens WCS365 is a beneficial strain that is phylogenetically closely related to an opportunistic pathogen P. fluorescens N2C3 and confers robust protection against P. fluorescens N2C3 in the rhizosphere. We used this plant-mutualist-pathogen model to screen collections of P. fluorescens WCS365 increased attachment mutants (iam) and surface attachment defective (sad) transposon insertion mutants that form increased or decreased levels of biofilm on an abiotic surface, respectively. We found that while the P. fluorescens WCS365 mutants had altered biofilm formation in vitro, only a subset of these mutants, including those involved in large adhesion protein (Lap) biosynthesis, flagellin biosynthesis and O-antigen biosynthesis, lost protection against P. fluorescens N2C3. We found that the inability of P. fluorescens WCS365 mutants to grow in planta, and the inability to suppress pathogen growth, both partially contributed to loss of plant protection. We did not find a correlation between the extent of biofilm formed in vitro and pathogen protection in planta indicating that biofilm formation on abiotic surfaces may not fully predict pathogen exclusion in planta. Collectively, our work provides insights into mechanisms of biofilm formation and host colonization that shape the outcomes of host-microbe-pathogen interactions.

microbiology↗

bioRxiv2024

Optical Genome Mapping of the human reference iPSC line KOLF2.1J reveals new smaller structural variants in neurodevelopmental genes

The INDI consortium curated the KOLF2.1J human iPSC line to create a reference cell line for neurological disease modeling. However, despite careful assessments, two separate studies found using SNP arrays identified five structural variants (SVs) with sizes >100kbp. Two heterozygous SVs overlap the genes JARID2, DTNBP1, and ASTN2, raising concerns about KOLF2.1Js suitability as a reference line. To investigate further, we screened KOLF2.1J for SVs smaller than 100kbp using optical genome mapping (OGM) to produce a high-resolution karyotype. OGM, validated by qPCR, indicated that one of the five known SVs contained a previously undetected overlap with RYBP. RYBP plays regulatory roles in neuronal differentiation, PAX6 expression and Notch signaling. Furthermore, OGM identified 11 SVs smaller than 100kbp, whose overlaps include the genes PER2, CSMD1, and PALS1. In summary, these mutations should be considered by researchers when using KOLF2.1J as a reference iPSC line for designing studies and experiments.

cell biology↗

bioRxiv2024

Hemodynamics Affects Factor XI/XII Anticoagulation Efficacy in Patient-Specific Left Atrial Models

Atrial fibrillation (AF) disrupts the circulation of blood through the left atrium (LA), and may result in relative stasis in the left atrial appendage (LAA), increasing thromboembolic risk. Anticoagulant agents can lower this risk, but currently used agents target the common pathway central to the coagulation cascade, increasing bleeding risk. Anticoagulants such as factor XI/XII inhibitors target the initial phase of the intrinsic pathway, with a significantly lower associated bleeding risk. However, these agents efficacy in preventing thrombosis in patient-specific flow conditions is not fully understood. We hypothesized that patient-specific flow patterns in the LA and LAA not only influence the risk of thrombosis but also the effectiveness of anticoagulation agents. We simulated blood flow and the intrinsic coagulation pathway in patient-specific LA anatomies with and without factor XI/XII inhibition to test this hypothesis. We considered thirteen patients in sinus rhythm and AF, several of whom had an LAA clot or a history of transient ischemic attacks. We used computational fluid dynamics based on 4D CT imaging and a detailed 32-species coagulation system to run 247 simulations for 13 patients, systematically sweeping over a wide range of factor XI/XII inhibition levels. Implementing a novel multi-fidelity coagulation modeling approach accelerated computations by two orders of magnitude, enabling the large number of simulations performed. Our simulations provide spatiotemporally resolved maps of thrombin concentration throughout the LA, showing it peaks inside the LAA. Coagulation metrics based on peak LAA thrombin dynamics suggested patients could be classified as non-coagulating, moderately and severely coagulating cases. Severely coagulating cases had significantly slower flow and higher residence time than moderately coagulating patients inside the LAA, requiring stronger factor XI/XII inhibition to blunt thrombin growth. The methodology outlined in this study has the potential to enable personalized assessments of coagulation risk and tailor anticoagulation therapy based on medical imaging.

bioengineering↗

bioRxiv2024

Order among chaos: high throughput MYCroplanters can distinguish interacting drivers of host infection in a highly stochastic system

While microbiomes provide diverse benefits for their host, they are notoriously variable in structure and function. As a result, substantial experimental replication and scalability are required to identify the contributions of and interactions between microbiota, the host and the environment. Here, we describe a novel high throughput plant growth system (MYCroplanters) to test how multiple host, microbiota, and pathogen variables predict host health. Using an Arabidopsis-Pseudomonas host-microbiome-pathogen model, we found that host genotype and order of arrival predict competition outcome between strains in the rhizosphere, but pathogen and microbiota dose can overwhelm these effects. Regardless of host or inoculation conditions, final microbial community structure emerged as a consistent predictor of host health. We demonstrate that high-throughput tools like MYCroplanters can isolate interacting drivers of host health. Increasing the scale at which we can screen components of microbiome-mediated host benefits will facilitate building microbiome engineering solutions for medicine and agricultural applications.

ecology↗

bioRxiv2024

In a Canine Model of Septic Shock, Cardiomyopathy Occurs Independent of Catecholamine Surges and Cardiac Microvascular Ischemia

BackgroundHigh levels of catecholamines are cardiotoxic and associated with stress-induced cardiomyopathies. Septic patients are routinely exposed to endogenously released and exogenously administered catecholamines, which may alter cardiac function and perfusion causing ischemia. Early during human septic shock, left ventricular ejection fraction (LVEF) decreases but normalizes in survivors over 7-10 days. Employing a septic shock model that reproduces these human septic cardiac findings, we investigated the effects of catecholamines on microcirculatory perfusion and cardiac function. MethodsPurpose-bred beagles received intrabronchial Staphylococcus aureus (n=30) or saline (n=6) challenges and septic animals recieved either epinephrine (1mcg/kg/min, n=15) or saline (n=15) infusions from 4 to 44 hours. Serial cardiac magnetic resonance imaging (CMR), invasive hemodynamics and laboratory data including catecholamine levels and troponins were collected over 92 hours. Adenosine-stress perfusion CMR was performed on eight of the fifteen septic epinephrine, and eight of the fifteen septic saline animals. High-dose sedation was titrated for comfort and suppress endogenous catecholamine release. ResultsCatecholamine levels were largely within the normal range throughout the study in animals receiving an intrabronchial bacteria or saline challenge. However, septic versus non-septic animals developed significant worsening of LV; EF, strain, and -aortic coupling that was not explained by differences in afterload, preload, or heart rate. In septic animals that received epinephrine versus saline infusions, plasma epinephrine levels increased 800-fold, pulmonary and systemic pressures significantly increased, and cardiac edema decreased. Despite this, septic animals receiving epinephrine versus saline during and after infusions, had no significant further worsening of LV; EF, strain, or -aortic coupling. Animals receiving saline had a sepsis-induced increase in microcirculatory reserve without troponin elevations. In contrast, septic animals receiving epinephrine had blunted microcirculatory perfusion and elevated troponin levels that persisted for hours after the infusion stopped. During infusion, septic animals that received epinephrine versus saline had significantly greater lactate, creatinine, and alanine aminotransferase levels. ConclusionsCardiac dysfunction during sepsis is not primarily due to elevated endogenous or exogenous catecholamines nor is it principally due to decreased microvascular perfusion-induced ischemia. However, epinephrine itself has potentially harmful long lasting ischemic effects during sepsis including impaired microvascular perfusion that persists after stopping the infusion. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIMyocardial depression of sepsis occurs without high levels of circulating catecholamines. C_LIO_LIWhereas large vessel coronary perfusion is known to be well maintained during sepsis, we show that during the myocardial depression of sepsis, in a model without exogenous catecholamine infusion, no perfusion abnormalities in the coronary microcirculation nor troponin elevations develop, indicating that the cardiac dysfunction of sepsis is not an ischemic injury. C_LIO_LIEpinephrine use during sepsis produces a form of injury tangential to the myocardial depression of sepsis. C_LIO_LIEpinephrine infusions depressed microcirculatory perfusion reserve and increased troponin I levels indicating a secondary prolonged mild ischemic effect on the myocardium. C_LI What are the clinical implications?O_LIProlonged high doses of epinephrine can secondarily contribute to perfusion abnormalities. C_LIO_LIDecoupling the septic heart from microvascular perfusion abnormalities and ischemia may lead to better strategies for managing shock associated with severe infections. In clinical practice in septic patients particularly potentially with coronary artery disease, commonly used vasopressors that are less associated with increased lactate production than epinephrine, alongside adjunct cardiac microcirculatory vasodilators, could help better maintain or improve cardiac performance during septic shock. C_LI

physiology↗

bioRxiv2024

Cardiac Magnetic Resonance Studies in a Large Animal Model that Simulates the Cardiac Abnormalities of Human Septic Shock

BackgroundSeptic shock, in humans and in our well-established animal model, is associated with increases in biventricular end diastolic volume (EDV) and decreases in ejection fraction (EF). These abnormalities occur over 2 days and reverse within 10 days. Septic non-survivors do not develop an increase in EDV. The mechanism for this cardiac dysfunction and EDV differences is unknown. MethodsPurpose-bred beagles randomized to receive intrabronchial Staphylococcus aureus (n=27) or saline (n=6) were provided standard ICU care including sedation, mechanical ventilation, and fluid resuscitation to a pulmonary arterial occlusion pressure of over 10mmHg. No catecholamines were administered. Over 96h, cardiac magnetic resonance imaging, echocardiograms, and invasive hemodynamics were serially performed, and laboratory data was collected. Tissue was obtained at 66h from six septic animals. ResultsFrom 0-96h after bacterial challenge, septic animals vs. controls had significantly increased left ventricular wall edema (6%) and wall thinning with loss of mass (15%) which was more pronounced at 48h in non-survivors than survivors. On histology, edema was located predominantly in myocytes, the interstitium, and endothelial cells. Edema was associated with significantly worse biventricular function (lower EFs), ventricular-arterial coupling, and circumferential strain. In septic animals, from 0-24h, the EDV decreased from baseline and, despite cardiac filling pressures being similar, decreased significantly more in non-survivors. From 24-48h, all septic animals had increases in biventricular chamber sizes. Survivors biventricular EDVs were significantly greater than baseline and in non-survivors, where biventricular EDVs were not different from baseline. Preload, afterload, or HR differences did not explain these differential serial changes in chamber size. ConclusionSystolic and diastolic cardiac dysfunction during sepsis is associated with ventricular wall edema. Rather than differences in preload, afterload, or heart rate, structural alterations to the ventricular wall best account for the volume changes associated with outcome during sepsis. In non-survivors, from 0-24h, sepsis induces a more severe diastolic dysfunction, further decreasing chamber size. The loss of left ventricular mass with wall thinning in septic survivors may, in part explain, the EDV increases from 24-48h. However, these changes continued and even accelerated into the recovery phase consistent with a reparative process rather than ongoing injury. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIUtilizing multimodal imaging and hemodynamics, we demonstrate the cardiac changes of sepsis have injury and reparative phases. C_LIO_LIThe injury phase (0-24h) has EDV decreases more profound in non-survivors and is associated with worse ventricular compliance, myocardial edema, and diastolic dysfunction. C_LIO_LIThe recovery phase has left ventricular mass loss with wall thinning in survivors that explains the EDV increases (24-96h). These progressed into the EF recovery phase consistent with a reparative process removing damaged tissue. C_LIO_LIThis is the first controlled CMR sepsis study supporting ventricular wall edema is a fundamental aspect of sepsis pathophysiology and dry mass loss a reparative mechanism. C_LI What are the clinical implications?O_LIDespite optimizing filling pressures, the cardiac changes in ventricular wall structure and function associated with survival and non-survival in sepsis still occurred, thereby discounting fluid resuscitation as the major factor of therapeutic importance for cardiac function and survival. C_LIO_LIThe changes reported here have potential implications for sepsis treatment especially in the field of fluid resuscitation. These findings yield new understanding into the pathophysiology of sepsis cardiac dysfunction and allow for novel phenotyping and prognosticating of the syndrome with ventricular compliance and EDVs. This also offers potentially high yielding targets for research for new therapeutic approaches for sepsis and heart failure. C_LI

physiology↗

bioRxiv2023

Robust nuclease-dead S. aureus dCas9-mediated alpha-synuclein knockdown in substantia nigra in a humanized mouse model of Parkinson's disease

Parkinsons disease (PD) is becoming increasingly prevalent due to an aging society, which places a substantial disease burden on patients and their families and an annual cost estimated at 52 billion dollars. However, no approved disease modulatory therapies that halt disease progression are available. Alpha-synuclein is a critical therapeutic target found in aggregated form in Lewy bodies which is the diagnostic hallmark of PD. Familial autosomal dominant forms of PD can present with causative exonic point mutations, copy number multiplications, and non-coding risk variants in the alpha-synuclein gene. The disease onset, severity, and progression depend on the gene expression levels of the alpha-synuclein. Here, we demonstrate that Streptococcus aureus dCas9 (sadCas9)-mediated CRISPR interference (CRISPRi) reduces alpha-synuclein mRNA and protein levels in a humanized mouse model. The mechanism of action is based on the principle that a complementary single guide RNA (sgRNA) recruits the sadCas9 protein to the promoter region of alpha-synuclein and modulates target gene transcription, leading to reduced gene expression. We show robust downregulation of alpha-synuclein in neurons after unilateral stereotactic injection into the substantia nigra of adult mice 1 and 6 months after surgery. This work shows proof of concept that viral-mediated sadCas9 CRISPR interference can be a promising therapeutic strategy to reduce alpha-synuclein in vivo. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/556425v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@4d9247org.highwire.dtl.DTLVardef@beb419org.highwire.dtl.DTLVardef@21e0f9org.highwire.dtl.DTLVardef@391d5a_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOC synopsisThis study focuses on the development of an AAV9 nuclease-dead S. aureus CRISPR/Cas9 expression system designed to target the human SNCA promoter. The objective is to achieve downregulation of -synuclein (a-syn) expression. After performing surgery and introducing the expression system, the levels of a-syn were measured at 1 month and 6 months post-surgery. The results indicate a significant downregulation of a-syn at both time points. Furthermore, it was observed that the initial immune response to the system attenuated over time, reaching control levels at the 6-month mark. These findings suggest the potential of this expression system for long-term downregulation of a-syn and provide insights into the immune response dynamics associated with its use.

neuroscience↗

bioRxiv2023

Innate immunity can distinguish beneficial from pathogenic rhizosphere microbiota

For optimal growth and development, hosts depend on their ability to promote healthy symbiotic interactions while restricting pathogen growth. To ask whether hosts can distinguish phylogenetically similar pathogens and beneficial bacteria, we used two closely related plant-associated strains of Pseudomonas fluorescens where one is beneficial and the other exhibits toxin-dependent virulence. We show that while the two strains co-exist in vitro, the beneficial outcompetes that pathogen in planta. Using several readouts for plant innate immunity, we found that the beneficial and pathogenic strains elicit mechanistically distinct immune responses that occur in distinct root compartments. We show that while both the pathogenic and beneficial bacterial have plant recognizable MAMPs, the pathogen uniquely induces MAMP-independent immune responses. We found that the pathogen induces both a toxin-independent and a unique toxin-dependent defense response that remains intact in immune signaling mutants including bak1/bkk1 and npr1/4D. We conclude that hosts can distinguish between phylogenetically similar microbes.

plant biology↗

bioRxiv2022

Multiplex imaging of human induced pluripotent stem cell-derived neurons with CO-Detection by indEXing (CODEX) technology

BackgroundHuman induced pluripotent stem cell (iPSC) models have been hailed as a breakthrough for understanding disease and developing new therapeutics. The major advantage of iPSC-derived neurons is that they carry the genetic background of the donor, and as such could be more predictive for clinical translation. However, the development of these cell models is time-consuming and expensive and it is thus critical to maximize biomarker readout from every model that is developed. One option is to use a highly multiplexed biomarker imaging assay, like CO-Detection by indEXing (CODEX), which allows detection of 50+ targets in situ at single-cell resolution. New MethodThis paper describes the development of CODEX in neuronal cell cultures derived from human iPSCs. ResultsWe differentiated human iPSCs into mixed neuronal and glial cultures on glass coverslips. We then developed and optimized a panel of 21 antibodies to phenotype iPSC-derived neuronal subtypes of cortical, dopaminergic, and striatal neurons, as well as astrocytes, and pre-and postsynaptic proteins. Comparison with existing methodsCompared to standard immunocytochemistry, CODEX oligoconjugated fluorophores circumvent antibody host interactions and allow for highly customized multiplexing. ConclusionWe show that CODEX can be applied to iPSC neuronal cultures and developed fixation and staining protocols for the neurons to sustain the multiple wash-stain cycles of the technology. Furthermore, we demonstrate both cellular and subcellular resolution imaging of multiplexed biomarkers in the same samples. CODEX is a powerful technique that complements other single-cell omics technologies for in-depth phenotype analysis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/479039v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@68d49dorg.highwire.dtl.DTLVardef@5ea424org.highwire.dtl.DTLVardef@16a763forg.highwire.dtl.DTLVardef@7950fc_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOC_FLOATNO CODEX(R) Multiplex Imaging in human iPSC neurons [A-D] Schematic drawings of the tools and steps used for Co-Detection by indEXing (CODEX) imaging. [A] Target-specific antibodies are conjugated to unique DNA oligonucleotide barcodes. Fluorescent reporter (excitation wavelength at 488 nm, 550 nm, or 647 nm/Cy5) carrying the complementary DNA (to the barcode) enables barcode-specific binding of the reporter to the antibody and detection by fluorescence microscopy. [B] Neuronal cell cultures are prepared for the CODEX staining and imaging by several fixation steps with different PFA concentrations followed by incubation with 100% acetone. Residual acetone is removed by drying the sample. After rehydration with PBS, autofluorescence is quenched by exposure to broad-spectrum LED light. Following a pre-staining fixation step, the sample is incubated with a mix of all conjugated primary antibodies. Excessive, unbound antibodies are removed by a washing step, leaving only the bound antibodies followed by a final post-staining fixation. [C] The CODEX Instrument Manager performs the multicycle run and controls the microscope software for automated addition of reporters, imaging, and washing of the samples (pre-stained with primary antibodies) to remove reporters from each cycle. After imaging, bound reporters are removed without damaging the tissue using a solvent, and the next set of reporters (conjugated to different barcodes) are added. [D] CODEX(R) Processor processes raw files and performs stitching, deconvolution, background subtraction, and cell segmentation. The processed images can be viewed and analyzed with the CODEX(R) Multiplex Analysis Viewer (MAV) plugin using Fiji software. C_FIG

neuroscience↗

bioRxiv2019

Regional dynamics of fractal dimension of the LV endocardium from cine CT images

We present a method to leverage the high fidelity of CT to quantify regional left ventricular function using topography variation of the endocardium as a surrogate measure of strain. 4DCT images of 10 normal and 10 abnormal subjects, acquired with standard clinical protocols, were used. The topography of the endocardium was characterized by its regional values of fractal dimension (FD), computed using a box-counting algorithm developed in-house. The average FD in each of the 16 American Heart Association segments was calculated for each subject as a function of time over the cardiac cycle. The normal subjects showed a peak systolic percentage change in FD of 5.9% {+/-} 2% in all free-wall segments, while the abnormal cohort experienced a change of 2% {+/-} 1.2% (p < 0.00001). Septal segments, being smooth, did not undergo large changes in FD. Additionally, a principal component analysis was performed on the temporal profiles of FD to highlight the possibility for unsupervised classification of normal and abnormal function. The method developed is free from manual contouring and does not require any feature tracking or registration algorithms. The FD values in the free wall segments correlated well with radial strain and with endocardial regional shortening measurements.

bioengineering↗

bioRxiv2018

Nuclear export of chimeric mRNAs depends on an lncRNA-triggered autoregulatory loop

Aberrant chromosomal translocations leading to tumorigenesis have been ascribed to the heterogeneously oncogenic functions. However, how fusion transcripts exporting remains to be declared. Here, we showed that the nuclear speckle-specific long non coding RNA MALAT1 controls chimeric mRNA export processes and regulates myeloid progenitor cell differentiation in malignant hematopoiesis. We demonstrated that MALAT1 regulates chimeric mRNAs export in an m6A-dependent manner and thus controls hematopoietic cell differentiation. Specifically, reducing MALAT1 or m6A methyltransferases and the reader YTHDC1 result in the universal retention of distinct oncogenic gene mRNAs in nucleus. Mechanically, MALAT1 hijacks both the chimeric mRNAs and fusion proteins in nuclear speckles during chromosomal translocations and mediates the colocalization of oncogenic fusion proteins with METTL14. MALAT1 and fusion protein complexes serve as a functional loading bridge for the interaction of chimeric mRNA and METTL14. This study demonstrated a universal mechanism of chimeric mRNA transport that involves lncRNA-fusion protein-m6A autoregulatory loop for controlling myeloid cell differentiation. Targeting the lncRNA-triggered autoregulatory loop to disrupt chimeric mRNA transport might represent a new common paradigm for treating blood malignancies.

cancer biology↗