Biology subjects

Earley, E. J.

Publications and source records attributed to Earley, E. J..

7 recordsLinked to original sources

bioRxiv2024

Ferroptosis regulates hemolysis in stored murine and human red blood cells

Red blood cell (RBC) metabolism regulates hemolysis during aging in vivo and in the blood bank. Here, we leveraged a diversity outbred mouse population to map the genetic drivers of fresh/stored RBC metabolism and extravascular hemolysis upon storage and transfusion in 350 mice. We identify the ferrireductase Steap3 as a critical regulator of a ferroptosis-like process of lipid peroxidation. Steap3 polymorphisms were associated with RBC iron content, in vitro hemolysis, and in vivo extravascular hemolysis both in mice and 13,091 blood donors from the Recipient Epidemiology and Donor evaluation Study. Using metabolite Quantitative Trait Loci analyses, we identified a network of gene products (FADS1/2, EPHX2 and LPCAT3) - enriched in donors of African descent - associated with oxylipin metabolism in stored human RBCs and related to Steap3 or its transcriptional regulator, the tumor protein TP53. Genetic variants were associated with lower in vivo hemolysis in thousands of single-unit transfusion recipients. HighlightsO_LISteap3 regulates lipid peroxidation and extravascular hemolysis in 350 diversity outbred mice C_LIO_LISteap3 SNPs are linked to RBC iron, hemolysis, vesiculation in 13,091 blood donors C_LIO_LImQTL analyses of oxylipins identified ferroptosis-related gene products FADS1/2, EPHX2, LPCAT3 C_LIO_LIFerroptosis markers are linked to hemoglobin increments in transfusion recipients C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/598512v1_ufig1.gif" ALT="Figure 1"> View larger version (117K): org.highwire.dtl.DTLVardef@150fec2org.highwire.dtl.DTLVardef@859c43org.highwire.dtl.DTLVardef@1d60156org.highwire.dtl.DTLVardef@f1b91e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma

Cancer immunotherapies have produced remarkable results in B-cell malignancies; however, optimal cell surface targets for many solid cancers remain elusive. Here, we present an integrative proteomic, transcriptomic, and epigenomic analysis of tumor specimens along with normal tissues to identify biologically relevant cell surface proteins that can serve as immunotherapeutic targets for neuroblastoma, an often-fatal childhood cancer of the developing nervous system. We apply this approach to human-derived cell lines (N=9) and cell/patient-derived xenograft (N=12) models of neuroblastoma. Plasma membrane-enriched mass spectrometry identified 1,461 cell surface proteins in cell lines and 1,401 in xenograft models, respectively. Additional proteogenomic analyses revealed 60 high-confidence candidate immunotherapeutic targets and we prioritized Delta-like canonical notch ligand 1 (DLK1) for further study. High expression of DLK1 directly correlated with the presence of a super-enhancer spanning the DLK1 locus. Robust cell surface expression of DLK1 was validated by immunofluorescence, flow cytometry, and immunohistochemistry. Short hairpin RNA mediated silencing of DLK1 in neuroblastoma cells resulted in increased cellular differentiation. ADCT-701, a DLK1-targeting antibody-drug conjugate (ADC), showed potent and specific cytotoxicity in DLK1-expressing neuroblastoma xenograft models. Moreover, DLK1 is highly expressed in several adult cancer types, including adrenocortical carcinoma (ACC), pheochromocytoma/paraganglioma (PCPG), hepatoblastoma, and small cell lung cancer (SCLC), suggesting potential clinical benefit beyond neuroblastoma. Taken together, our study demonstrates the utility of comprehensive cancer surfaceome characterization and credentials DLK1 as an immunotherapeutic target. HighlightsO_LIPlasma membrane enriched proteomics defines surfaceome of neuroblastoma C_LIO_LIMulti-omic data integration prioritizes DLK1 as a candidate immunotherapeutic target in neuroblastoma and other cancers C_LIO_LIDLK1 expression is driven by a super-enhancer C_LIO_LIDLK1 silencing in neuroblastoma cells results in cellular differentiation C_LIO_LIADCT-701, a DLK1-targeting antibody-drug conjugate, shows potent and specific cytotoxicity in DLK1-expressing neuroblastoma preclinical models C_LI

cancer biology↗

bioRxiv2023

Biological and Genetic Determinants of Red Blood Cell Glycolysis

Mature red blood cells (RBCs) lack mitochondria, and thus exclusively rely on glycolysis to generate adenosine triphosphate (ATP) during aging in vivo or storage in the blood bank. Here we leveraged 13,029 volunteers from the Recipient Epidemiology and Donor Evaluation Study to identify an association between end-of-storage levels of glycolytic metabolites and donor age, sex, and ancestry-specific genetic polymorphisms in regions encoding phosphofructokinase 1, platelet (detected in mature RBCs), hexokinase 1, ADP-ribosyl cyclase 1 and 2 (CD38/BST1). Gene-metabolite associations were validated in fresh and stored RBCs from 525 Diversity Outbred mice, and via multi-omics characterization of 1,929 samples from 643 human RBC units during storage. ATP and hypoxanthine levels - and the genetic traits linked to them - were associated with hemolysis in vitro and in vivo, both in healthy autologous transfusion recipients and in 5,816 critically ill patients receiving heterologous transfusions, suggesting their potential as markers to improve transfusion outcomes. eTOC and Highlights O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/557250v4_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@1a556b7org.highwire.dtl.DTLVardef@1e02b13org.highwire.dtl.DTLVardef@2bfab1org.highwire.dtl.DTLVardef@15787e3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBlood donor age and sex affect glycolysis in stored RBCs from 13,029 volunteers; C_LIO_LIAncestry, genetic polymorphisms in PFKP, HK1, CD38/BST1 influence RBC glycolysis; C_LIO_LIModeled PFKP effects relate to preventing loss of the total AXP pool in stored RBCs; C_LIO_LIATP and hypoxanthine are biomarkers of hemolysis in vitro and in vivo. C_LI

biochemistry↗

bioRxiv2022

Neurostimulation Artifact Removal for Implantable Sensors Improves Signal Clarity and Decoding of Motor Volition

As the demand for prosthetic limbs with reliable and multi-functional control increases, recent advances in myoelectric pattern recognition and implanted sensors have proven considerably advantageous. Additionally, sensory feedback from the prosthesis can be achieved via stimulation of the residual nerves, enabling closed-loop control over the prosthesis. However, this stimulation can cause interfering artifacts in the electromyographic (EMG) signals which deteriorate the reliability and function of the prosthesis. Here, we implement two real-time stimulation artifact removal algorithms, Template Subtraction and {varepsilon}-Normalized Least Mean Squares, and investigate their performance in offline and real-time myoelectric pattern recognition in two transhumeral amputees implanted with nerve cuff and EMG electrodes. We show that both algorithms are capable of significantly improving signal-to-noise ratio and offline pattern recognition accuracy of artifact-corrupted EMG signals. Furthermore, both algorithms improved real-time decoding of motor intention during active neurostimulation. Although these outcomes are dependent on the user-specific sensor locations and neurostimulation settings, they nonetheless represent progress towards bi-directional neuromusculoskeletal prostheses capable of multifunction control and simultaneous sensory feedback.

neuroscience↗

bioRxiv2021

A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A

Sirtuin 6 (SIRT6) is a deacylase and mono-ADP ribosyl transferase (mADPr) enzyme involved in multiple cellular pathways implicated in the regulation of aging and metabolism. Targeted sequencing identified a SIRT6 allele containing two linked substitutions (N308K/A313S) as enriched in Ashkenazi Jewish (AJ) centenarians as compared to AJ control individuals. Characterization of this SIRT6 (centSIRT6) allele demonstrated it to be a stronger suppressor of LINE1 retrotransposons, confer enhanced stimulation of DNA double strand break repair, and more robust cancer cell killing compared to the wild type. Surprisingly, centSIRT6 displayed weaker deacetylase activity, but stronger mADPr activity, over a range of NAD+ concentrations and substrates. Additionally, centSIRT6 displayed a stronger interaction with Lamin A/C (LMNA), which correlated with enhanced ribosylation of LMNA. Our results suggest that enhanced SIRT6 function contributes to human longevity by improving genome maintenance via increased mADPr activity and enhanced interaction with LMNA.

molecular biology↗

bioRxiv2020

Artificial Joint Speed Feedback for Myoelectric Prosthesis Control

I.Accurate control of human limbs involves both feedforward and feedback signals. For prosthetic arms, feedforward control is commonly accomplished by recording myoelectric signals from the residual limb to predict the users intent, but augmented feedback signals are not explicitly provided in commercial devices. Previous studies have demonstrated inconsistent results when artificial feedback was provided in the presence of vision. We hypothesized that negligible benefits in past studies may have been due to artificial feedback with low precision compared to vision, which results in heavy reliance on vision during reaching tasks. Furthermore, we anticipated more reliable benefits from artificial feedback when providing information that vision estimates with high uncertainty - joint speed. In this study, we test an artificial sensory feedback system providing joint speed information and how it impacts performance and adaptation during a hybrid positional-and-myoelectric ballistic reaching task. We found modest improvement in overall reaching errors after perturbed control, and that high prosthesis control noise was compensated for by strategic overreaching with the positional control and underreaching with the myoelectric control. These results provide insights into the relevant factors influencing the improvements conferred by artificial sensory feedback.

neuroscience↗

bioRxiv2018

Joint Speed Discrimination and Augmentation For Prosthesis Feedback

Sensory feedback is critical in fine motor control, learning, and adaptation. However, robotic prosthetic limbs currently lack the feedback segment of the communication loop between user and device. Artificial sensory feedback can close this gap, but sometimes this improvement only persists when users cannot see their prosthesis. suggesting the provided feedback is redundant with vision. Thus, given the choice, users rely on vision over artificial feedback. To effectively augment vision, sensory feedback must provide information that vision cannot provide or provides poorly. Although vision is known to be less precise at estimating speed than position, no work has compared speed precision of biomimetic arm movements. In this study, we investigated the uncertainty of visual speed estimates as defined by different virtual arm movements. We found that uncertainty was greatest for visual estimates of joint speeds, compared to absolute or linear endpoint speeds. Furthermore, this uncertainty increased when the joint reference frame speed varied over time, potentially caused by an overestimation of joint speed. Finally, we demonstrate a joint-based sensory feedback paradigm capable of significantly reducing joint speed uncertainty when paired with vision. Ultimately, this work may lead to improved prosthesis control and capacity for motor learning.

neuroscience↗