Biology subjects

Shin, S.

Publications and source records attributed to Shin, S..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

A Coxiella burnetii effector interacts with the host PAF1 complex and suppresses the innate immune response

Intracellular bacteria such as the pathogen Coxiella burnetii inject effector proteins into the host cell that promote productive infection. One common strategy of pathogen effectors is to suppress host immune responses to enable pathogen replication. The C. burnetii type IV secretion system translocates a large number of effectors into host cells that collectively promote intracellular bacterial replication, but the individual functions of most of these effectors are poorly understood. In this study, we describe a C. burnetii effector, CBU1314, that localizes to the nucleus and inhibits NF-{kappa}B-, MAPK-, and type I IFN-dependent gene expression. Mechanistically, we find that CBU1314 interacts with the PAF1 complex (PAF1C), a central host transcriptional complex that regulates expression of inflammatory genes in innate immune cells. Notably, we find that PAF1 promotes immune gene expression in response to various immune agonists and C. burnetii infection. Moreover, we find that PAF1 is critical for restricting intracellular C. burnetii replication. Overall, our findings uncover PAF1C as a host target of a C. burnetii effector and reveal new insight into how intracellular bacterial pathogens subvert cell- intrinsic innate defenses. SignificanceIntracellular bacteria often employ secreted effector proteins to modulate cellular processes and survive intracellularly. The study of these effectors can provide valuable insight into microbial pathogenesis and host biology. Here, we describe a Coxiella burnetii effector that inhibits multiple host signaling pathways and modulates the innate immune response. This effector interacts with the host PAF1 complex (PAF1C), a central regulator of transcription. Furthermore, we show that PAF1 is necessary for maximal gene expression downstream of various innate immune receptors and restricts bacterial replication during infection. Overall, our study elucidates the function of a C. burnetii effector in evading the immune response and provides insight into the role of PAF1C in cell-intrinsic defense against bacterial pathogens.

microbiology↗

bioRxiv2022

Systems modelling of TGF-β/Hippo signalling crosstalk uncovers molecular switches that coordinate YAP transcriptional complexes

The Hippo pathway is an evolutionarily conserved signaling network that integrates diverse cues to regulate cell fate and organ homeostasis. The central downstream pathway protein is the transcriptional co-activator Yes-associated protein (YAP). Although capable of inducing gene transcription, YAP cannot bind DNA directly. Instead, it mediates transcriptional activity through interaction with distinct DNA-binding transcriptional factors (TFs), including TEAD, SMAD, and p73, to form active and functionally opposing transcriptional complexes. Growing evidence in mammals demonstrates that YAP has a dual role and can either promote cell proliferation or apoptosis, which underpin its ability to function as both an oncogene or a tumour suppressor depending on the specific context. However, the mechanisms by which YAP coordinates its distinct transcriptional complexes and mediates context-dependent function remain poorly defined. This is in part due to the lack of systems-level studies that can decrypt the complexities of upstream signalling pathways and their crosstalk, which together dictate the transcriptional regulation at the YAP level. Here, we undertake an integrative systems-based approach combining computational network modelling and experimental studies to interrogate the dynamic formation of and transition between the YAP-SMAD and YAP-p73 transcriptional complexes, which control proliferative and apoptotic gene expression, respectively. We developed a new experimentally-validated mathematical model of the TGF-{beta}/Hippo signalling crosstalk and used this model to elucidate dynamic network behaviour. Our integrative studies uncovered previously unknown molecular switches that control the YAP-SMAD/p73 complexes in an on/off, switch-like manner. RASSF1A and ITCH were identified as major regulators of the switches, whereby a graded increase in ITCH expression can trigger YAP to abruptly switch from binding p73 to SMAD, swiftly promoting proliferative gene expression. Further, adjusting the model to reflect cell type-specific protein expression profiles using both in-house and publicly available experimental data enabled us to study the YAP switches under diverse and varied cellular contexts. Overall, our studies provide a new quantitative and systems-level understanding of the dynamic regulation of functionally opposing YAP transcriptional complexes in mammalian cells.

cell biology↗

bioRxiv2022

Biocompatible polymers for scalable production of human neural organoids

The generation of neural organoids from human pluripotent stem cells holds great promise in modeling disease and screenings drugs, but current approaches are difficult to scale due to undesired organoid fusion. Here, we develop a scalable neural organoid platform by screening biocompatible polymers that prevent fusion of organoids cultured in suspension. We show that addition of one inexpensive polysaccharide enables straightforward screening of 298 FDA-approved drugs and teratogens for growth defects using over 2,400 cortical organoids.

neuroscience↗

bioRxiv2021

Position-specific secondary acylation determines detection of lipid A by murine TLR4 and caspase-11

Immune sensing of the Gram-negative bacterial membrane glycolipid lipopolysaccharide (LPS) is both a critical component of host defense against Gram-negative bacterial infection, and a contributor to hyper-inflammatory response, leading to sepsis and death. Innate immune activation by LPS is due to the lipid A moiety, an acylated di-glucosamine molecule that can activate inflammatory responses via the extracellular sensor TLR4/MD2 or the cytosolic sensor caspase-11 (Casp11). The number and length of acyl chains present on bacterial lipid A structures vary across bacterial species and strains, which affects the magnitude of TLR4 and Casp11 activation. TLR4 and Casp11 are thought to respond similarly to various lipid A structures, as tetra-acylated lipid A structures do not activate either sensor, whereas hexa-acylated structures activate both sensors. However, direct analysis of extracellular and cytosolic responses to the same sources and preparations of LPS/lipid A structures have been limited, and the precise features of lipid A that determine the differential activation of each receptor remain poorly defined. To address this question, we used rationally engineered lipid A isolated from a series of bacterial acyl-transferase mutants that produce novel, structurally defined molecules. Intriguingly, we find that the location of specific secondary acyl chains on lipid A resulted in differential recognition by TLR4- or Casp11, providing new insight into the structural features of lipid A required to activate either TLR4- or Casp11. Our findings indicate that TLR4 and Casp11 sense non-overlapping areas of lipid A chemical space, thereby constraining the ability of Gram-negative pathogens to evade innate immunity.

immunology↗

bioRxiv2021

Human TLR4 and noncanonical inflammasome differ in their ability to respond to distinct lipid A variants

Detection of Gram-negative bacterial lipid A by the extracellular sensor, MD-2/TLR4 or the intracellular inflammasome sensors, CASP4 and CASP5, induces robust inflammatory responses. The chemical structure of lipid A, specifically the phosphorylation and acylation state, varies across and within bacterial species, potentially allowing pathogens to evade or suppress host immunity. Currently, it is not clear how distinct alterations in the phosphorylation or acylation state of lipid A affect both human TLR4 and CASP4/5 activation. Using a panel of engineered lipooligosaccharides (LOS) derived from Yersinia pestis with defined lipid A structures that vary in their acylation or phosphorylation state, we identified that differences in phosphorylation state did not affect TLR4 or CASP4/5 activation. However, the acylation state differentially impacted TLR4 and CASP4/5 activation. Specifically, all of the examined tetra-, penta-, and hexa-acylated LOS variants activated CASP4/5-dependent responses, whereas TLR4 responded to penta- and hexa-acylated LOS but did not respond to tetra-acylated LOS or pentaacylated LOS lacking the secondary acyl chain at the 3 position. As expected, lipid A alone was sufficient for TLR4 activation; however, human macrophages required both lipid A and the core oligosaccharide to mount a robust CASP4/5 inflammasome response. Our findings show that human TLR4 and CASP4/5 detect both shared and non-overlapping LOS/lipid A structures, which enables the innate immune system to recognize a wider range of bacterial LOS/lipid A, thereby constraining the ability of pathogens to evade innate immune detection.

immunology↗

bioRxiv2021

Salmonella Typhimurium induces NAIP/NLRC4- and NLRP3/ASC-independent, caspase-1/4-dependent inflammasome activation in human intestinal epithelial cells

Salmonella enterica serovar Typhimurium is a gram-negative pathogen that causes diseases ranging from gastroenteritis to systemic infection and sepsis. Salmonella uses type III secretion systems (T3SSs) to inject effectors into host cells. While these effectors are necessary for bacterial invasion and intracellular survival, intracellular delivery of T3SS products also enables detection of Salmonella by cytosolic immune sensors. Upon detecting translocated Salmonella ligands, these sensors form multimeric complexes called inflammasomes, which activate caspases that lead to proinflammatory cytokine release and pyroptosis. In particular, the Salmonella T3SS needle, inner rod, and flagellin proteins activate the NAIP/NLRC4 inflammasome in murine intestinal epithelial cells (IECs), which leads to restriction of bacterial replication and extrusion of infected IECs into the intestinal lumen, thereby preventing systemic dissemination of Salmonella. While these processes are studied quite well in mice, the role of the NAIP/NLRC4 inflammasome in human IECs remains unknown. Unexpectedly, we found the NAIP/NLRC4 inflammasome is dispensable for early inflammasome responses to Salmonella in both human intestinal epithelial cell lines and organoids. Additionally, the NLRP3 inflammasome and the adaptor protein ASC are not required for inflammasome activation in Caco-2 cells. Instead, we observed a partial requirement for caspase-1, and a necessity for caspase-4 and GSDMD pore-forming activity in mediating inflammasome responses to Salmonella in Caco-2 cells. These findings suggest that unlike murine IECs, human IECs do not rely on NAIP/NLRC4, and also do not use NLRP3/ASC. Instead, they primarily use caspases-1 and -4 to mediate early inflammasome responses to SPI-1-expressing Salmonella.

microbiology↗

bioRxiv2021

Integrative Modelling of Signalling Network Dynamics Identifies Cell Type-selective 1 Therapeutic Strategies for FGFR4-driven Cancers

Oncogenic FGFR4 signalling represents a potential therapeutic target in various cancer types, including triple negative breast cancer (TNBC) and hepatocellular carcinoma (HCC). However, resistance to FGFR4 single-agent therapy remains a major challenge, emphasizing the need for effective combinatorial treatments. Our study sought to develop a comprehensive computational model of FGFR4 signalling and provide network-level insights into resistance mechanisms driven by signalling dynamics. Our integrated approach, combining computational network modelling with experimental validation, uncovered potent AKT reactivation following FGFR4 targeting in the TNBC cell line MDA-MB-453. By systematically simulating the model to analyse the effects of co-targeting specific network nodes, we were able to predict, and subsequently confirm through experimental validation, the strong synergy of co-targeting FGFR4 and AKT or specific ErbB kinases, but not PI3K. Incorporating protein expression data from hundreds of cancer cell lines, we then adapted our model to diverse cellular contexts. This revealed that while AKT rebound is common, it is not a general phenomenon. ERK reactivation, for example, occurs in certain cell types, including the FGFR4-driven HCC cell line Hep3B, where there is a synergistic effect of co-targeting FGFR4 and MEK, but not AKT. In summary, our study offers key insights into drug-induced network remodelling and the role of protein expression heterogeneity in targeted therapy responses. We underscore the utility of computational network modelling for designing cell type-selective combination therapies and enhancing precision cancer treatment. SignificanceThis study underscores the potential of computational predictive modelling in deciphering mechanisms of cancer cell resistance to targeted therapies and in designing more effective, cancer type-specific combination treatments.

systems biology↗

bioRxiv2021

A Developmentally Prometastatic Niche to Hepatoblastoma in Neonatal Liver mediated by the Cxcl1/Cxcr2 Axis

Background and RationaleHepatoblastoma (HB) is the most common pediatric liver cancer. Its predominant occurrence in very young children led us to investigating whether the neonatal liver provides a protumorigenic niche to HB development. MethodsHB development was compared between orthotopic transplantation models established in postnatal day 5 and 60 mice (P5Tx and P60Tx models). Single-cell RNA-sequencing was performed using tumor and liver tissues from both models and the top candidate cell types and genes identified are investigated for their roles in HB cell growth, migration, and survival. ResultsWe found that various HB cell lines including HepG2 cells were consistently and considerably more tumorigenic and metastatic in the P5Tx model than in the P60Tx models. Sc-RNAseq of the P5Tx and P60Tx HepG2 models revealed that the P5Tx tumor was more hypoxic and had a larger number of activated hepatic stellate cells (aHSCs) in the tumor-surrounding liver which express significantly higher levels of Cxcl1 than those from the P60Tx model. We found these differences were developmentally present in normal P5 and P60 liver. We showed that the Cxcl1/Cxcr2 axis mediated HB cell migration and was critical to HB cell survival under hypoxia. Treating HepG2 P60Tx model with recombinant CXCL1 protein induced intrahepatic and pulmonary metastasis and CXCR2 knockout in HepG2 cells abolished their metastatic potential in the P5Tx model. Lastly, we showed that in metastatic HB patient tumors there was a similar larger population of aHSCs in the tumor-surrounding liver than in localized tumors, and tumor hypoxia was uniquely associated with HB patient prognosis among pediatric cancers. ConclusionWe demonstrated that the neonatal liver provides a prometastatic niche to HB development via the Cxcl1/Cxcr2 axis.

cancer biology↗

bioRxiv2021

Transitioning to confined spaces impacts bacterial swimming and escape response

Symbiotic bacteria often navigate complex environments before colonizing privileged sites in their host organism. Chemical gradients are known to facilitate directional taxis of these bacteria, guiding them towards their eventual destination. However, less is known about the role of physical features in shaping the path the bacteria take and defining how they traverse a given space. The flagellated marine bacterium Vibrio fischeri,which forms a binary symbiosis with the Hawaiian bobtail squid, Euprymna scolopes, must navigate tight physical confinement, squeezing through a bottleneck constricting to ~2 m in width on the way to its eventual home. Using microfluidic in vitro experiments, we discovered that V. fischeri cells alter their behavior upon entry into confined space, straightening their swimming paths and promoting escape from confinement. Using a computational model, we attributed this escape response to two factors: reduced directional fluctuation and a refractory period between reversals. Additional experiments in asymmetric capillary tubes confirmed that V. fischeri quickly escape from tapered ends, even when drawn into the ends by chemoattraction. This avoidance was apparent down to a limit of confinement approaching the diameter of the cell itself, resulting in a balance between chemoattraction and evasion of physical confinement. Our findings demonstrate that non-trivial distributions of swimming bacteria can emerge from simple physical gradients in the level of confinement. Tight spaces may serve as an additional, crucial cue for bacteria while they navigate complex environments to enter specific habitats. Significance StatementSymbiotic bacteria that navigate to and through specific host tissues often face tight physical confinement. This work reveals that confinement-associated changes in swimming can dramatically alter taxis, shaping bacterial localization in conjuncture with other motility-directing cues. This work helps explain how bacteria can avoid getting stuck in confined areas while transiting to privileged spaces, adding confinement as an environmental cue that symbiotic bacteria use to shape their motility behavior.

biophysics↗

bioRxiv2021

INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants

Genome-wide association studies have revealed many non-coding variants associated with complex traits. However, model organism studies have largely remained as an untapped resource for unveiling the effector genes of non-coding variants. We develop INFIMA, Integrative Fine-Mapping, to pinpoint causal SNPs for Diversity Outbred (DO) mice eQTL by integrating founder mice multi-omics data including ATAC-seq, RNA-seq, footprinting, and in silico mutation analysis. We demonstrate INFIMAs superior performance compared to alternatives with human and mouse chromatin conformation capture datasets. We apply INFIMA to identify novel effector genes for GWAS variants associated with diabetes. The results of the application are available at http://www.statlab.wisc.edu/shiny/INFIMA/

bioinformatics↗

bioRxiv2021

Human NAIP/NLRC4 and NLRP3 inflammasomes detect Salmonella type III secretion system activities to restrict intracellular bacterial replication

Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that uses two distinct type III secretion systems (T3SSs), termed Salmonella pathogenicity island (SPI)-1 and SPI-2, to deliver virulence factors into the host cell. The SPI-1 T3SS enables Salmonella to invade host cells, while the SPI-2 T3SS facilitates Salmonellas intracellular survival. In mice, a family of cytosolic immune sensors, including NAIP1, NAIP2, and NAIP5/6, recognizes the SPI-1 T3SS needle, inner rod, and flagellin proteins, respectively. Ligand recognition triggers assembly of the NAIP/NLRC4 inflammasome, which mediates caspase-1 activation, IL-1 family cytokine secretion, and pyroptosis of infected cells. In contrast to mice, humans encode a single NAIP that broadly recognizes all three ligands. The role of NAIP/NLRC4 or other inflammasomes during Salmonella infection of human macrophages is unclear. We find that although the NAIP/NLRC4 inflammasome is essential for detecting SPI-1 T3SS ligands in human macrophages, it is partially required for responses to infection, as Salmonella also activated the NLRP3 and CASP4/5 inflammasomes. Importantly, we demonstrate that combinatorial NAIP/NLRC4 and NLRP3 inflammasome activation restricts Salmonella replication in human macrophages. In contrast to SPI-1, the SPI-2 T3SS inner rod is not sensed by human or murine NAIPs, which is thought to allow Salmonella to evade host recognition and replicate intracellularly. Intriguingly, we find that human NAIP detects the SPI-2 T3SS needle protein. Critically, in the absence of both flagellin and the SPI-1 T3SS, the NAIP/NLRC4 inflammasome still restricted intracellular Salmonella replication. These findings reveal that recognition of Salmonella SPI-1 and SPI-2 T3SSs and engagement of both the NAIP/NLRC4 and NLRP3 inflammasomes control Salmonella infection in human macrophages. Author summarySalmonella enterica serovar Typhimurium is a gastrointestinal bacterial pathogen that causes diarrheal disease and is a major cause of morbidity and mortality worldwide. Salmonella uses molecular syringe-like machines called type III secretion systems (T3SSs) to inject virulence factors into host cells. These T3SSs enable Salmonella to infect and survive within host cells such as macrophages. However, host cells contain a family of cytosolic immune receptors, termed NAIPs, that recognize T3SS and flagellin components. Upon detecting these components, NAIPs recruit the adaptor protein NLRC4 to form signaling complexes called inflammasomes. Inflammasomes activate host proteases called caspases that mount robust immune responses against the invading pathogen. While mice encode multiple NAIPs that have been extensively studied, much remains unknown about how the single human NAIP mediates inflammasome responses to Salmonella in macrophages. Our study reveals that while NAIP is necessary to detect individual T3SS ligands in human macrophages, it is only partially required for inflammasome responses to Salmonella infection. We found that the NLRP3 and CASP4/5 inflammasomes are also activated, and the combination of NAIP- and NLRP3-mediated recognition limits intracellular Salmonella replication in human macrophages. Our results demonstrate that human macrophages employ multiple inflammasomes to mount robust host defense against Salmonella infection.

microbiology↗

bioRxiv2021

Robust IgM responses following vaccination are associated with prevention of Mycobacterium tuberculosis infection in macaques

Development of an effective tuberculosis (TB) vaccine has suffered from an incomplete understanding of the correlates of protection against Mycobacterium tuberculosis (Mtb). However, recent work has shown that compared to standard intradermal Bacille Calmette-Guerin (BCG) vaccination, intravenous (IV) BCG vaccination provides nearly complete protection against TB in rhesus macaques. While studies have focused on cellular immunity in this setting, the antibody response elicited by IV BCG vaccination remains incompletely defined. Using an agnostic antibody profiling approach, here we show that IV BCG drives superior antibody responses in the plasma and the bronchoalveolar lavage fluid (BAL). While IV BCG immunization resulted in the expansion of a robust IgM, IgG, IgA, Fc-receptor binding antibodies, and antibody effector functions in the BAL, IgM titers were among the strongest markers of reduced bacterial burden in the plasma and BAL of BCG immunized animals. Moreover, IgM immunity was also enriched among animals receiving protective vaccination with an attenuated Mtb strain. Finally, a LAM-specific IgM monoclonal antibody reduced Mtb survival in vitro. Collectively, these data highlight the potential importance of IgM responses as a marker and as a functional mediator of protection against TB.

immunology↗

bioRxiv2021

Vaccination with SARS-CoV-2 Spike Protein and AS03 Adjuvant Induces Rapid Anamnestic Antibodies in the Lung and Protects Against Virus Challenge in Nonhuman Primates

Adjuvanted soluble protein vaccines have been used extensively in humans for protection against various viral infections based on their robust induction of antibody responses. Here, soluble prefusion-stabilized spike trimers (preS dTM) from the severe acute respiratory syndrome coronavirus (SARS-CoV-2) were formulated with the adjuvant AS03 and administered twice to nonhuman primates (NHP). Binding and functional neutralization assays and systems serology revealed that NHP developed AS03-dependent multi-functional humoral responses that targeted multiple spike domains and bound to a variety of antibody FC receptors mediating effector functions in vitro. Pseudovirus and live virus neutralizing IC50 titers were on average greater than 1000 and significantly higher than a panel of human convalescent sera. NHP were challenged intranasally and intratracheally with a high dose (3x106 PFU) of SARS-CoV-2 (USA-WA1/2020 isolate). Two days post-challenge, vaccinated NHP showed rapid control of viral replication in both the upper and lower airways. Notably, vaccinated NHP also had increased spike-specific IgG antibody responses in the lung as early as 2 days post challenge. Moreover, vaccine-induced IgG mediated protection from SARS-CoV-2 challenge following passive transfer to hamsters. These data show that antibodies induced by the AS03-adjuvanted preS dTM vaccine are sufficient to mediate protection against SARS-CoV-2 and support the evaluation of this vaccine in human clinical trials.

immunology↗

bioRxiv2021

Adjuvanting a subunit SARS-CoV-2 nanoparticle vaccine to induce protective immunity in non-human primates

The development of a portfolio of SARS-CoV-2 vaccines to vaccinate the global population remains an urgent public health imperative. Here, we demonstrate the capacity of a subunit vaccine under clinical development, comprising the SARS-CoV-2 Spike protein receptor binding domain displayed on a two-component protein nanoparticle (RBD-NP), to stimulate robust and durable neutralizing antibody (nAb) responses and protection against SARS-CoV-2 in non-human primates. We evaluated five different adjuvants combined with RBD-NP including Essai O/W 1849101, a squalene-in-water emulsion; AS03, an alpha-tocopherol-containing squalene-based oil-in-water emulsion used in pandemic influenza vaccines; AS37, a TLR-7 agonist adsorbed to Alum; CpG 1018-Alum (CpG-Alum), a TLR-9 agonist formulated in Alum; or Alum, the most widely used adjuvant. All five adjuvants induced substantial nAb and CD4 T cell responses after two consecutive immunizations. Durable nAb responses were evaluated for RBD-NP/AS03 immunization and the live-virus nAb response was durably maintained up to 154 days post-vaccination. AS03, CpG-Alum, AS37 and Alum groups conferred significant protection against SARS-CoV-2 infection in the pharynges, nares and in the bronchoalveolar lavage. The nAb titers were highly correlated with protection against infection. Furthermore, RBD-NP when used in conjunction with AS03 was as potent as the prefusion stabilized Spike immunogen, HexaPro. Taken together, these data highlight the efficacy of the RBD-NP formulated with clinically relevant adjuvants in promoting robust immunity against SARS-CoV-2 in non-human primates.

immunology↗

bioRxiv2021

Red Blood Cells Function as DNA Sensors

Erythrocytes have long been mistaken as exclusively inert oxygen carriers lacking immune function. Here we show that red blood cells (RBCs) serve as immune sensors through surface expression of the nucleic acid-sensing toll-like receptor 9 (TLR9), a classically endosomal receptor that initiates immune responses following the detection of unmethylated CpG motifs present in pathogen and mitochondrial DNA. Mammalian RBCs express TLR9 on their surface and bind CpG-containing bacterial, malarial, and mitochondrial DNA. Erythrocyte-bound CpG DNA increases during infection, and CpG-carrying RBCs trigger accelerated erythrophagocytosis and innate immune activation characterized by RBC-TLR9 dependent local and systemic cytokine production. Thus, RBC nucleic acid detection and capture regulates red cell clearance and immune responses and provides evidence for RBCs as innate immune sentinels during pathologic states. One Sentence SummaryThe ability of RBCs to detect and bind cell-free nucleic acids contributes to immunity during acute inflammatory states.

immunology↗

bioRxiv2020

Estimation of Kinematics from Inertial Measurement Units Using a Combined Deep Learning and Optimization Framework

The difficulty of estimating joint kinematics remains a critical barrier toward widespread use of inertial measurement units in biomechanics. Traditional sensor-fusion filters are largely reliant on magnetometer readings, which may be disturbed in uncontrolled environments. Careful sensor-to-segment alignment and calibration strategies are also necessary, which may burden users and lead to further error in uncontrolled settings. We introduce a new framework that combines deep learning and top-down optimization to accurately predict lower extremity joint angles directly from inertial data, without relying on magnetometer readings. We trained deep neural networks on a large set of synthetic inertial data derived from a clinical marker-based motion-tracking database of hundreds of subjects. We used data augmentation techniques and an automated calibration approach to reduce error due to variability in sensor placement and limb alignment. On left-out subjects, lower extremity kinematics could be predicted with a mean ({+/-} STD) root mean squared error of less than 1.27 {degrees} ({+/-} 0.38 {degrees}) in flexion/extension, less than 2.52 {degrees} ({+/-} 0.98 {degrees}) in ad/abduction, and less than 3.34 {degrees} ({+/-} 1.02 {degrees}) internal/external rotation, across walking and running trials. Errors decreased exponentially with the amount of training data, confirming the need for large datasets when training deep neural networks. While this framework remains to be validated with true inertial measurement unit (IMU) data, the results presented here are a promising advance toward convenient estimation of gait kinematics in natural environments. Progress in this direction could enable large-scale studies and offer an unprecedented view into disease progression, patient recovery, and sports biomechanics.

bioengineering↗

bioRxiv2020

Translatome-based classification reveals a dual metabolic dependency of a new tumor subtype of pancreatic cancer.

Molecular profiling of Pancreatic Ductal Adenocarcinoma (PDA), based on transcriptomic analyses, identifies two main prognostic subtypes (basal-like and classical), but does not allow personalized first-line treatment. To date, tumors have not been profiled based on protein synthesis rates, yet the step of mRNA translation is highly deregulated in both PDA cancer cells and their microenvironment. Using a collection of twenty-seven pancreatic Patient-Derived Xenografts (PDX), we performed genome-wide analysis of translated mRNA (translatome). Unsupervised bioinformatics analysis revealed a new tumor subtype harboring a low protein synthesis rate, but associated with a robust translation of mRNAs encoding effectors of the integrated stress response (ISR), including the transcription factor ATF4. Functional characterization of the "ISR-activated" human cancer cells revealed a high resistance to drugs, low autophagic capacities, and importantly, metabolic impairments in the serine synthesis and transsulfuration pathways. Overall, our study highlights the strength of translatomic profiling on PDA, which here revealed an unforeseen drug-resistant cancer cell phenotype, whose auxotrophy to both serine and cysteine may be amenable to targeted therapy.

cancer biology↗

bioRxiv2020

Topical heterogeneity in affective touch: Does it impact body image?

Recent evidence suggests that altered responses to affective touch - a pleasant interoceptive stimulus associated with activation of the C-Tactile (CT) system, may contribute to the aetiology and maintenance of mental conditions characterised by body image disturbances (e.g., Anorexia Nervosa). Here, we investigated whether tactile pleasantness and intensity differ across body sites, and if individual differences in dysmorphic appearance concerns and body awareness might be associated to touch perceptions across body sites. To this end, we measured perceived pleasantness and intensity of gentle, dynamic stroking touches applied to the palm, forearm, face, abdomen and back of 30 female participants (mean age: 25.87{+/-}1.17yrs) using CT-optimal (3 cm/s) and non-CT optimal (0.3 and 30 cm/s) stroking touch. As expected, participants rated CT-targeted touch as more pleasant compared to the two non-CT optimal stroking touch at all body sites. Nevertheless, CT-targeted touch applied to the abdomen elicited the lowest pleasantness ratings compared to all other body sites and to the two non-CT optimal stroking touch. Individual differences in body awareness and dysmorphic concerns significantly predicted preference for CT-optimal over non-CT optimal stroking touch applied to the forearm and the back. These findings begin to elucidate the link between CT sensitivity, dysmorphic appearance concerns and body awareness, which may have implications for future research looking to inform early interventions. Addressing impaired processing of affective interoceptive stimuli, such as CT-targeted touch, may be the key to current treatment approaches available for those populations at risk of disorders characterised by body image disturbance.

neuroscience↗