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Qiu, S.

Publications and source records attributed to Qiu, S..

At least 91 records · Page 5Linked to original sources

Stable thalamocortical learning between medial-dorsal thalamus and cortical attractor networks captures cognitive flexibility

Primates and rodents are able to continually acquire, adapt, and transfer knowledge and skill, and lead to goal-directed behavior during their lifespan. For the case when context switches slowly, animals learn via slow processes. For the case when context switches rapidly, animals learn via fast processes. We build a biologically realistic model with modules similar to a distributed computing system. Specifically, we are emphasizing the role of thalamocortical learning on a slow time scale between the prefrontal cortex (PFC) and medial dorsal thalamus (MD). Previous work [1] has already shown experimental evidence supporting classification of cell ensembles in the medial dorsal thalamus, where each class encodes a different context. However, the mechanism by which such classification is learned is not clear. In this work, we show that such learning can be self-organizing in the manner of an automaton (a distributed computing system), via a combination of Hebbian learning and homeostatic synaptic scaling. We show that in the simple case of two contexts, the network with hierarchical structure can do context-based decision making and smooth switching between different contexts. Our learning rule creates synaptic competition [2] between the thalamic cells to create winner-take-all activity. Our theory shows that the capacity of such a learning process depends on the total number of task-related hidden variables, and such a capacity is limited by system size N. We also theoretically derived the effective functional connectivity as a function of an order parameter dependent on the thalamo-cortical coupling structure. Significance StatementAnimals need to adapt to dynamically changing environments and make decisions based on changing contexts. Here we propose a combination of neural circuit structure with learning mechanisms to account for such behaviors. Specifically, we built a reservoir computing network improved by a Hebbian learning rule together with a synaptic scaling learning mechanism between the prefrontal cortex and the medial-dorsal (MD) thalamus. This model shows that MD thalamus is crucial in such context-based decision making. I also make use of dynamical mean field theory to predict the effective neural circuit. Furthermore, theoretical analysis provides a prediction that the capacity of such a network increases with the network size and the total number of tasks-related latent variables.

neuroscience↗

Changes in nitrogen pools in the maize-soil system after urea or straw application to a typical intensive agricultural soil: A 15N tracer study

A 15N maize pot experiment was conducted to compare the N value of fertilizer alone and fertilizer combined with straw at an equivalent N rate. The four treatments were control (CK), 15N-urea, 15N-urea plus straw, and 15N-straw plus urea. Soil N pools, maize N and their 15N abundance were determined during maize growth. At maturity 26.0% of straw N was assimilated by maize in the urea plus straw treatment. From the eighth leaf stage to maturity, urea plus straw had a significantly (P < 0.05) higher concentration and percentage of exogenous substrate N present as soil total N (TN), particulate organic N (PON), and mineral associated total N (MTN) in bulk and rhizosphere soils than the urea-only treatment. From silking to maturity in the urea plus straw treatment, rhizosphere soil significantly (P < 0.05) increased the percentage of exogenous substrate N present as inorganic N (Inorg-N) and MTN, and significantly (P < 0.05) decreased that present as PON and microbial biomass N (MBN) compared with the bulk soil. From the eighth leaf stage to maturity, rhizosphere soil significantly (P < 0.05) increased the percentage of straw N present as Inorg-N and MTN except for MTN at the silking stage, and significantly decreased (P < 0.05) that present as PON compared with the bulk soil. Overall, straw was an available N source to the crop, and the increase in straw N availability needs to be considered from the interaction of fertilization practices and the crop rhizosphere.

plant biology↗

Large-scale Gradient Dysfunction of the Functional Connectome in Major Depression

BackgroundPatients with major depressive disorder (MDD) exhibit concurrent deficits in sensory processing and high-order cognitive functions such as self-awareness and rumination. Connectome mapping studies have suggested a principal primary-to-transmodal gradient in functional brain networks, supporting the spectrum from sensation to cognition. However, whether this principal connectome gradient is disrupted in patients with MDD and how this disruption is associated with gene expression profiles remain unclear. MethodsUsing a large cohort of resting-state functional magnetic resonance imaging data from 2,234 participants (1,150 patients with MDD and 1,084 healthy controls) recruited at 10 sites, we investigated MDD-related alterations in the principal connectome gradient. We further used Neurosynth and postmortem gene expression data to assess the cognitive functions and transcriptional profiles related to the gradient alterations in MDD, respectively. ResultsRelative to controls, patients with MDD exhibited abnormal global topography of the principal primary-to-transmodal gradient, as indicated by reduced explanation ratio, gradient range, and gradient variation (Cohens d = -0.16[~]-0.21). Focal alterations of gradient scores were mostly in the primary systems involved in sensory processing and in the transmodal systems implicated in high-order cognition. The transcriptional profiles explained 53.9% of the spatial variance in the altered gradient patterns, with the most correlated genes enriched in transsynaptic signaling and calcium ion binding. ConclusionsThese results highlight the dysfunction of the core connectome hierarchy in MDD and its linkage with gene expression profiles, providing insights into the neurobiological and molecular genetic underpinnings of sensory-cognitive deficits in this disorder.

neuroscience↗

Single-dose intranasal administration of AdCOVID elicits systemic and mucosal immunity against SARS-CoV-2 in mice

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the urgent need for effective preventive vaccination to reduce burden and spread of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) in humans. Intranasal vaccination is an attractive strategy to prevent COVID-19 as the nasal mucosa represents the first-line barrier to SARS-CoV-2 entry before viral spread to the lung. Although SARS-CoV-2 vaccine development is rapidly progressing, the current intramuscular vaccines are designed to elicit systemic immunity without conferring mucosal immunity. Here, we show that AdCOVID, an intranasal adenovirus type 5 (Ad5)-vectored vaccine encoding the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, elicits a strong and focused immune response against RBD through the induction of mucosal IgA, serum neutralizing antibodies and CD4+ and CD8+ T cells with a Th1-like cytokine expression profile. Therefore, AdCOVID, which promotes concomitant systemic and local mucosal immunity, represents a promising COVID-19 vaccine candidate.

immunology↗

Potentiating the anti-tumor response of tumor infiltrated T cells by NAD+ supplementation

Tumor immunotherapies have provided clinical benefits, yet great potential remains for optimizing therapeutic effects. Here, we show that low NAD+ levels restrict the function of tumor infiltrating T lymphocytes (TILs). TILs harvested from human ovarian tumor tissues showed decreased NAD+ levels compared with T cells from paired peripheral blood samples. The combination of whole-genome CRISPR and large-scale metabolic inhibitor screens implicated the NAD+ biosynthesis enzyme nicotinamide phosphoribosyltransferase (NAMPT) is required for T cell activation. Further isotopic labeling and LC-MS studies confirmed that NAD+ depletion suppressed mitochondrial energy biosynthesis in T cells. Excitingly, NAD+ supplementation significantly enhanced the tumor cell-killing efficacy of CAR-T cells ex vivo, and extended animal survive in both adoptive CAR-T model and immune checkpoint blockade treatment models in vivo. This study demonstrates an over-the-counter nutrient supplement NAD+ could robustly boost the efficacy of T cell-based immunotherapy and provides insights into the cellular basis of T cell metabolic reprogramming in treating cancers. One Sentence SummaryNAD+ supplementation during cancer immunotherapies significantly enhances T cell activation and tumor killing capacity.

immunology↗

Frequency-specific suppression of locomotor components by the white+ gene in Drosophila melanogaster adult flies

The classic eye-color gene white+ (w+) in Drosophila melanogaster (fruitfly) has unexpected behavioral consequences. How w+ affect locomotion of adult flies is largely unknown. Here, we show that w+ selectively suppresses locomotor components at relatively high frequencies (> 0.1 Hz). The wildtype Canton-S male flies walked intermittently in circular arenas while the white-eyed w1118 flies walked continuously. Through careful control of genetic and cytoplasmic backgrounds, we found that w+ was associated with intermittent walking. w+-carrying male flies had smaller median values of path length per second (PPS) and reduced 5-min path length compared with w1118-carrying males. Additionally, flies carrying 2-4 genomic copies of mini-white+ (mw+) showed reduced median PPSs and decreased 5-min path length compared with w1118 flies, and the suppression was dependent on the copy number of mw+. Fourier transform of the time series (i.e. PPSs over time) indicated that w+/mw+ specifically suppressed the locomotor components at relatively high frequencies (> 0.1 Hz). Lastly, the downregulation of w+ in neurons but not glial cells resulted in an increased percentage of high-frequency locomotor components. We concluded that w+ suppressed the locomotion of adult flies by selectively reducing the high-frequency locomotor components.

genetics↗

Development and validation of a deep learning framework for Alzheimers disease classification

Alzheimers disease (AD) is the primary cause of dementia worldwide (1), with an increasing morbidity burden that may outstrip diagnosis and management capacity as the population ages. Current methods integrate patient history, neuropsychological testing and magnetic resonance imaging (MRI) to identify likely cases, yet effective practices remain variably-applied and lacking in sensitivity and specificity (2). Here we report an explainable deep learning strategy that delineates unique AD signatures from multimodal inputs of MRI, age, gender, and mini-mental state examination (MMSE) score. Our framework linked a fully convolutional network (FCN) to a multilayer perceptron (MLP) to construct high resolution maps of disease probability from local brain structure. This enabled precise, intuitive visualization of individual AD risk en route to accurate diagnosis. The model was trained using clinically-diagnosed AD and cognitively normal (NC) subjects from the Alzheimers Disease Neuroimaging Initiative (ADNI) dataset (n=417) (3), and validated on three independent cohorts: the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL, n=382) (4), the Framingham Heart Study (FHS, n=102) (5), and the National Alzheimers Coordinating Center (NACC, n=582) (6). Model performance was consistent across datasets, with mean accuracy values of 0.966, 0.948, 0.815, and 0.916 for ADNI, AIBL, FHS and NACC, respectively. Moreover, our approach exceeded the diagnostic performance of a multi-institutional team of practicing neurologists (n=11), and high-risk cerebral regions predicted by the model closely tracked postmortem histopathological findings. This framework provides a clinically-adaptable strategy for using routinely available imaging techniques such as MRI to generate nuanced neuroimaging signatures for AD diagnosis, as well as a generalizable approach for linking deep learning to pathophysiological processes in human disease.

neuroscience↗

Molecular profiling of lymphovascular invasive cancer cells in TNBC using G&T-seq

Lymphovascular invasion (LVI) is a critical step in the metastatic process but have received relatively little attention due to the technical challenges associated with their isolation. In this study, we used laser capture microdissection (LCM) to isolate 97 cancer cell clusters from pathological frozen sections within lymphatic vessels, primary tumor tissue, and axillary lymph nodes of a triple negative breast cancer (TNBC) patient. Simultaneous genome and transcriptome amplification and sequencing (G&T-seq) performed on these clusters permitted a comprehensive depiction of the genomic and transcriptional profiles of cancer cells associated with LVI. Combination phylogeny analysis pointed to three evolutionarily distinct pathways of tumor clone development and metastasis in this patient, each of which was associated with a unique mRNA signature, and correlated to disparate overall survival outcomes. Moreover, hub gene evaluation found extensive down regulation of ribosomal protein mRNA to be a potential marker of poor prognosis in breast cancer patients.

cancer biology↗

Satellite Imaging of Global Urbanicity relate to Adolescent Brain Development and Behavior

Urbanicity, the impact of living in urban areas, is among the greatest environmental challenges for mental health. While urbanicity might be distinct in different sociocultural conditions and geographic locations, there are likely to exist common features shared in different areas of the globe. Understanding these common and specific relations of urbanicity with human brain and behavior will enable to assess the impact of urbanicity on mental disorders, especially in childhood and adolescence, where prevention and early interventions are likely to be most effective.\n\nWe constructed from satellite-based remote sensing data a factor for urbanicity that was highly correlated with population density ground data. This factor, UrbanSat was utilized in the Chinese CHIMGEN sample (N=831) and the longitudinal European IMAGEN cohort (N=810) to investigate if exposure to urbanicity during childhood and adolescence is associated with differences in brain structure and function in young adults, and if these changes are linked to behavior.\n\nUrbanicity was found negatively correlated with medial prefrontal cortex volume and positively correlated with cerebellar vermis volume in young adults from both China and Europe. We found an increased correlation of urbanicity with functional network connectivity within- and between- brain networks in Chinese compared to European participants. Urbanicity was highly correlated with a measure of perceiving a situation from the perspective of others, as well as symptoms of depression in both datasets. These correlations were mediated by the structural and functional brain changes observed. Susceptibility to urbanicity was greatest in two developmental windows during mid-childhood and adolescence.\n\nUsing innovative technology, we were able to probe the relationship between urban upbringing with brain change and behavior in different sociocultural conditions and geographic locations. Our findings help to identify shared and distinct determinants of adolescent brain development and mental health in different regions of the world, thus contributing to targeted prevention and early-intervention programs for young people in their unique environment. Our approach may be relevant for public health, policy and urban planning globally.

neuroscience↗

Expression of heat shock protein 70 is insufficient to extend Drosophila melanogaster longevity

It has been known for over 20 years that Drosophila melanogaster flies with twelve additional copies of the hsp70 gene encoding the 70 kDa heat shock protein lives longer after a non-lethal heat treatment. Since the heat treatment also induces the expression of additional heat shock proteins, the biological effect can be due either to HSP70 acting alone or in combination. This study used the UAS/GAL4 system to determine whether hsp70 is sufficient to affect the longevity and the resistance to thermal, oxidative or desiccation stresses of the whole organism. We observed that HSP70 expression in the nervous system or muscles has no effect on longevity or stress resistance but ubiquitous expression reduces the life span of males. We also observed that the down-regulation of Hsp70 using RNAi did not affect longevity.

genetics↗

Directed robust generation of functional retinal ganglion cells from Muller glia

Glaucoma and optic neuropathies cause progressive and irreversible degeneration of retinal ganglion cells (RGCs) and the optic nerve and are currently without any effective treatment. Previous research into cell replacement therapy of these neurodegenerative diseases has been stalled due to the limited capability for grafted RGCs to integrate into the retina and project properly along the long visual pathway to reach their brain targets. In vivo RGC regeneration would be a promising alternative approach but mammalian retinas lack regenerative capacity even though cold-blood vertebrates such as zebrafish have the full capacity to regenerate a damaged retina using Muller glia (MG) as retinal stem cells. Nevertheless, mammalian MG undergo limited neurogenesis when stimulated by retinal injury. Therefore, a fundamental question that remains to be answered is whether MG can be induced to efficiently regenerate functional RGCs for vision restoration in mammals. Here we show that without stimulating proliferation, the transcription factor (TF) Math5 together with a Brn3 TF family member are able to reprogram mature mouse MG into RGCs with exceedingly high efficiency while either alone has no or limited capacity. The reprogrammed RGCs extend long axons that make appropriate intra-retinal and extra-retinal projections through the entire visual pathway including the optic nerve, optic chiasm and optic tract to innervate both image-forming and non-image-forming brain targets. They exhibit typical neuronal electrophysiological properties and improve visual responses in two glaucoma mouse models: Brn3b null mutant mice and mice with the optic nerve crushed (ONC). Together, our data provide evidence that mammalian MG can be reprogrammed by defined TFs to achieve robust in vivo regeneration of functional RGCs as well as a promising new therapeutic approach to restore vision to patients with glaucoma and other optic neuropathies.

neuroscience↗

A Single-Cell Immune Atlas of Triple Negative Breast Cancer Reveals Novel Immune Cell Subsets

Triple-negative breast cancer (TNBC) represents the most aggressive breast cancer subtype, which recently attracts great interest for immune therapeutic development. In this context, in-depth understanding of TNBC immune landscape is highly demanded. Here we report single-cell RNA sequencing results of 9683 tumor-infiltrated immune cells isolated from 14 treatment naive TNBC tumors, where 22 immune cell subsets, including T cells, macrophages, B cells, and DCs have been characterized. We identify a new T cell subset, CD8+CXCL8+ naive T cell, which associates with poor survival. A novel immune cell subset comprised of TCR+ macrophages, is found to be widely distributed in TNBC tumors. Further analyses reveal an up-regulation of molecules associated with TCR signaling and cytotoxicity in these immune cells, indicating TCR signaling activation. Altogether, our study provides a valuable resource to understand the immune ecosystem of TNBC. The novel immune cell subsets reported herein might be functionally important in cancer immunity.\n\nSIGNIFICANCEThis work demonstrates a single-cell transcriptome atlas of immune cells in treatment naive TNBC tumors, revealing novel immune cell subsets. This study provides a valuable resource to understand the immune ecosystem of TNBC, which will be helpful for the immunotherapeutic strategy design of TNBC.

immunology↗

Assessment of the optimum fertilizer rates and planting density for soybean production in China

Fertilization rate and planting density are important factors affecting crop yield. A large number of soybean [Glycine max (L.) Merr] field experimental data (1998-2017) were collected through different database sources to evaluate the optimum fertilizer rate and planting density for high yield of spring and summer soybean in China. The yield of spring and summer soybean gradually increased over year, with their average yields were 2610 and 2724 kg ha-1, respectively. Based on the fitted quadratic curve, the optimal rate of nitrogen (N), phosphorus (P), and potassium (K) fertilizers for high yield of summer soybean was 96 kg N ha-1, 80 kg P2O5 ha-1, and 126 kg K2O ha-1, and the corresponding yields were 3038, 2801 and 2305 kg ha-1, respectively. The optimal rate of N, P and K fertilizers for spring soybean was 71 kg N ha-1, 108 kg P2O5 ha-1 and 74 kg K2O ha-1, and the corresponding yields were 2932, 2834 and 2678 kg ha-1, respectively. The optimum density was 27x104 and 34x104 plants ha-1 under high yield for summer and spring soybean, respectively. Stepwise regression analysis showed that the P fertilizer had the greatest influence on the spring soybean yield followed by K fertilizer and planting density. For summer soybean, population density had the major effect on yield followed by P fertilizer. Overall, the P fertilization and planting density should be payed attention to increase soybean yield in different regions of China.

plant biology↗

The common neoantigens in colorectal cancer are predicted and validated to be presented or immunogenic

Colorectal cancer (CRC) is a malignant cancer with high incidence and mortality in the world, as the result of the traditional treatments. Immunotherapy targeting neoantigens can induce durable tumor regression in cancer patients, but is almost limited to individual treatment, resulting from the unique neoantigens. Many shared oncogenic mutations are detected, but whether the common neoantigens can be identified in CRC is unknown. Using the somatic mutations data from 321 CRC patients combined with a filter standard and 7 predicted algorithms, we screened and obtained 25 HLA-A*11:01 restricted common neoantigens with high binding affinity (IC50<50 nM) and presentation score (>0.9). Except the positive epitope KRAS_G12V8-16, 11 out of 25 common neoantigens were proved to be naturally processed and presented on constructed K562 cell surface by mass spectroscopy (MS), and 11 out of 25 common neoantigens specifically induced in vitro pre-stimulated cytotoxic lymphocyte (CTL) to secrete IFN-{gamma}. However, only 2 out of 25 common neoantigens were simultaneously presented and immunogenic. Moreover, using cell-sorting technology combined with single-cell RNA sequencing, the immune repertoire profiles of C1orf170_S418G413-421 and KRAS_G12V8-16-specific CTL were clarified. Therefore, common neoantigens with presentation and immunogenicity could be found in CRC, which would be developed as the universal targets for CRC immunotherapy.

immunology↗

EPIC: MHC-I epitope prediction integrating mass spectrometry derived motifs and tissue-specific expression profiles

BackgroundAccurate prediction of epitopes presented by human leukocyte antigen (HLA) is crucial for personalized cancer immunotherapies targeting T cell epitopes. Mass spectrometry (MS) profiling of eluted HLA ligands, which provides high-throughput measurements of HLA associated peptides in vivo, can be used to faithfully model the presentation of epitopes on the cell surface. In addition, gene expression profiles measured by RNA-seq data in a specific cell/tissue type can significantly improve the performance of epitope presentation prediction. However, although large amount of high-quality MS data of HLA-bound peptides is being generated in recent years, few provide matching RNA-seq data, which makes incorporating gene expression into epitope prediction difficult. MethodsWe collected publicly available HLA peptidome and matching RNA-seq data of 34 cell lines derived from various sources. We built position score specific matrixes (PSSMs) for 21 HLA-I alleles based on these MS data, then used logistic regression (LR) to model the relationship among PSSM score, gene expression and peptide length to predict whether a peptide could be presented in each of the cell line. We further built a universal LR model, termed Epitope Presentation Integrated Prediction (EPIP), based on more than 180,000 unique HLA ligands collected from public sources and ~3,000 HLA ligands generated by ourselves, to predict epitope presentation for 66 common HLA-I alleles. ResultsWhen evaluating EPIP on large, independent HLA eluted ligand datasets, it performed substantially better than other popular methods, including MixMHCpred (v2.0), NetMHCpan (v4.0), and MHCflurry (v1.2.2), with an average 0.1% positive predictive value (PPV) of 52.01%, compared to 37.24%, 36.96%, 24.90% and 23.76% achieved by MixMHCpred, NetMHCpan-4.0 (EL), NetMHCpan-4.0 (BA) and MHCflurry, respectively. It is also comparable to EDGE, a recent deep learning-based model that is not publicly available, on predicting epitope presentation and selecting immunogenic cancer neoantigens. However, the simplicity and flexibility of EPIP makes it easier to be applied in diverse situations, and we demonstrated this by generating MS data for the HCC4006 cell line and adding the support of HLA-A*33:03 to EPIP. EPIP is publicly available as a web tool < http://epip.genomics.cn/>. Conclusionswe have developed an easy to use, publicly available epitope prediction tool, EPIP, that incorporates information from both MS and RNA-seq data, and demonstrated its superior performance over existing public methods.

bioinformatics↗

Predicting bilateral knee pain from MR imaging using deep neural networks

Background and objectiveIt remains difficult to characterize pain in knee joints with osteoarthritis solely by radiographic findings. We sought to understand how advanced machine learning methods such as deep neural networks can be used to analyze raw MRI scans and predict bilateral knee pain, independent of other risk factors. MethodsWe developed a deep learning framework to associate information from MRI slices taken from the left and right knees of subjects from the Osteoarthritis Initiative with bilateral knee pain. Model training was performed by first extracting features from two-dimensional (2D) sagittal intermediate-weighted turbo spin echo slices. The extracted features from all the 2D slices were subsequently combined to directly associate using a fused deep neural network with the output of interest as a binary classification problem. ResultsThe deep learning model resulted in predicting bilateral knee pain on test data with 70.1% mean accuracy, 51.3% mean sensitivity, and 81.6% mean specificity. Systematic analysis of the predictions on the test data revealed that the model performance was consistent across subjects of different Kellgren-Lawrence grades. ConclusionThe study demonstrates a proof of principle that a machine learning approach can be applied to associate MR images with bilateral knee pain. SIGNIFICANCE AND INNOVATIONKnee pain is typically considered as an early indicator of osteoarthritis (OA) risk. Emerging evidence suggests that MRI changes are linked to pre-clinical OA, thus underscoring the need for building image-based models to predict knee pain. We leveraged a state-of-the-art machine learning approach to associate raw MR images with bilateral knee pain, independent of other risk factors.

bioengineering↗

Molecular profiles and mutation burden analysis in Chinese patients with gastric carcinoma

The goal of this work was to investigate the molecular profiles and mutation burden in Chinese patients with gastric carcinoma (GC). In total, we performed whole exome sequencing (WES) on 74 GC patients with tumor and adjacent normal formalin-fixed, paraffin-embedded (FFPE) tissue samples. The mutation spectrum of these samples showed a high concordance with TCGA and other studies on GC. We found the alterations of 17 DNA repair genes (including BRCA2, POLE and MSH3, etc.) were strongly correlated with the tumor mutation burden (TMB) and tumor neoantigen burden (TNB) of GC patients. Patients with mutations of these genes tend to have high TMB (median of TMB = 12.77, p=2.3e-6) and TNB (median of TNB = 5.97, p= 2.8e-3). In addition, younger GC patients (age < 60) have lower TMB (p = 0.0021) and TNB (p = 0.034) than older patients (age >= 60). Furthermore, we found a list of 18 genes and two genomic regions (1p36.21 and Xq26.3) were associated with peritoneal metastasis (PM) of GC, and patients with amplification of 1p36.21 and Xq26.3 have a worse prognosis (p=0.002, 0.01, respectively). Our analysis provides GC patients with potential markers for single and combination therapies.

cancer biology↗

5-Hydroxymethylcytosines from Circulating Cell-free DNA as Diagnostic and Prognostic Markers for Hepatocellular Carcinoma

The lack of highly sensitive and specific diagnostic biomarkers is a major contributor to the poor outcomes of patients with hepatocellular carcinoma (HCC), the second-most common cause of cancer deaths worldwide. We sought to develop a clinically convenient and minimally-invasive approach that can be deployed at scale for the sensitive, specific, and highly reliable diagnosis of HCC, and to evaluate the potential prognostic value of this approach. The study cohort comprised of 2,728 subjects, including HCC patients (n = 1,208), controls (n = 965) (572 healthy individuals and 393 patients with benign lesions), as well as patients with chronic hepatitis B infection (CHB) (n =291), liver cirrhosis (LC) (n = 110), and cholangiocarcinoma (CCC) (n = 154), was recruited from three major liver cancer hospitals in Shanghai, China, from July 2016 to November 2017. Circulating cell-free DNA (cfDNA) were collected from plasma samples from these individuals before surgery or any radical treatment. Applying our 5hmC-Seal technique, the summarized 5-hydroxymethylcytosine (5hmC) profiles in cfDNA were obtained. Molecular annotation analysis suggested that the profiled 5hmC loci in cfDNA were enriched with liver tissue-derived regulatory markers (e.g., H3K4me1). We showed that a weighted diagnostic score (wd-score) based on 117 genes detected using the summarized 5hmC profiles in cfDNA accurately distinguished HCC patients from controls (AUC = 95.1%; 95% CI, 93.6-96.5%) in the validation set, markedly outperformed -fetoprotein (AFP) with superior sensitivity. The wd-scores, which not only detected early BCLC stages (e.g., Stage 0: AUC = 96.2%; 95% CI,94.1-98.4%) and small tumors (e.g., < 2 cm: AUC = 95.7%; 95% CI: 93.6-97.7%), also showed high capacity for distinguishing HCC from non-cancer patients with CHB/LC (AUC = 80.2%; 95% CI, 75.8-84.6%). Moreover, the prognostic value of 5hmC markers in cfDNA was evaluated for HCC recurrence, showing that a weighted prognostic score (wp-score) based on 16 marker genes predicted the recurrence risk (HR = 6.67; 95% CI, 2.81-15.82, p < 0.0001) in 555 patients who have been followed up after surgery. In conclusion, we have developed and validated a robust 5hmC-based diagnostic model that can be applied routinely with clinically feasible amount of cfDNA (e.g., from ~2-5 mL of plasma). Applying this new approach in the clinic could significantly improve the clinical outcomes of HCC patients, for example by early detection of those patients with surgically resectable tumors or as a convenient disease surveillance tool for recurrence.

cancer biology↗