A Genomic Link From Heart Failure to Atrial Fibrillation Risk: FOG2 Modulates a TBX5/GATA4-Dependent Atrial Gene Regulatory Network.

BACKGROUND: The relationship between heart failure (HF) and atrial fibrillation (AF) is clear, with up to half of patients with HF progressing to AF. The pathophysiological basis of AF in the context of HF is presumed to result from atrial remodeling. Upregulation of the transcription factor FOG2 (friend of GATA2; encoded by ZFPM2) is observed in human ventricles during HF and causes HF in mice. METHODS: FOG2 expression was assessed in human atria. The effect of adult-specific FOG2 overexpression in the mouse heart was evaluated by whole animal electrophysiology, in vivo organ electrophysiology, cellular electrophysiology, calcium flux, mouse genetic interactions, gene expression, and genomic function, including a novel approach for defining functional transcription factor interactions based on overlapping effects on enhancer noncoding transcription. RESULTS: FOG2 is significantly upregulated in the human atria during HF. Adult cardiomyocyte-specific FOG2 overexpression in mice caused primary spontaneous AF before the development of HF or atrial remodeling. FOG2 overexpression generated arrhythmia substrate and trigger in cardiomyocytes, including calcium cycling defects. We found that FOG2 repressed atrial gene expression promoted by TBX5. FOG2 bound a subset of GATA4 and TBX5 co-bound genomic locations, defining a shared atrial gene regulatory network. FOG2 repressed TBX5-dependent transcription from a subset of co-bound enhancers, including a conserved enhancer at the Atp2a2 locus. Atrial rhythm abnormalities in mice caused by Tbx5 haploinsufficiency were rescued by Zfpm2 haploinsufficiency. CONCLUSIONS: Transcriptional changes in the atria observed in human HF directly antagonize the atrial rhythm gene regulatory network, providing a genomic link between HF and AF risk independent of atrial remodeling.

Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors.

Analyzing single-cell transcriptomes promises to decipher the plasticity, heterogeneity, and rapid switches in developmental cellular state transitions. Such analyses require the identification of gene markers for semi-stable transition states. However, there are nontrivial challenges such as unexplainable stochasticity, variable population sizes, and alternative trajectory constructions. By advancing current tipping-point theory-based models with feature selection, network decomposition, accurate estimation of correlations, and optimization, we developed BioTIP to overcome these challenges. BioTIP identifies a small group of genes, called critical transition signal (CTS), to characterize regulated stochasticity during semi-stable transitions. Although methods rooted in different theories converged at the same transition events in two benchmark datasets, BioTIP is unique in inferring lineage-determining transcription factors governing critical transition. Applying BioTIP to mouse gastrulation data, we identify multiple CTSs from one dataset and validated their significance in another independent dataset. We detect the established regulator Etv2 whose expression change drives the haemato-endothelial bifurcation, and its targets together in CTS across three datasets. After comparing to three current methods using six datasets, we show that BioTIP is accurate, user-friendly, independent of pseudo-temporal trajectory, and captures significantly interconnected and reproducible CTSs. We expect BioTIP to provide great insight into dynamic regulations of lineage-determining factors.

A fluorescent probe for detection of Hg2+ ions constructed by tetramethyl cucurbit[6]uril and 1,2-bis(4-pyridyl)ethene.

In this paper, tetramethyl cucurbit[6]uril (TMeQ[6]) and 1,2-bis(4-pyridyl)ethene (G) were used to construct a supramolecular fluorescent probe G@TMeQ[6]. The host-guest interaction between TMeQ[6] and G was investigated using 1H NMR spectroscopy, single-crystal X-ray diffraction and various experimental techniques. The results show that TMeQ[6] and G form an inclusion complex with a host-guest ratio of 1:1 and the equilibrium association constant (Ka) was 2.494 × 104 M-1. The G@TMeQ[6] fluorescent probe can sensitively recognize Hg2+ ions by fluorescence enhancement. The linear range is 0.33 × 10-5-1.65 × 10-5 mol·L-1, R2 = 0.9926, and the limit of detection is 4.12 × 10-8 mol·L-1. The fluorescent probe can be used to detect the concentration of Hg2+ ions in aqueous solution, and provides a theoretical basis for the development of new fluorescent probes for detecting heavy metal ions.

Transcriptional Patterning of the Ventricular Cardiac Conduction System.

RATIONALE: The heartbeat is organized by the cardiac conduction system (CCS), a specialized network of cardiomyocytes. Patterning of the CCS into atrial node versus ventricular conduction system (VCS) components with distinct physiology is essential for the normal heartbeat. Distinct node versus VCS physiology has been recognized for more than a century, but the molecular basis of this regional patterning is not well understood. OBJECTIVE: To study the genetic and genomic mechanisms underlying node versus VCS distinction and investigate rhythm consequences of failed VCS patterning. METHODS AND RESULTS: Using mouse genetics, we found that the balance between T-box transcriptional activator, Tbx5, and T-box transcriptional repressor, Tbx3, determined the molecular and functional output of VCS myocytes. Adult VCS-specific removal of Tbx5 or overexpression of Tbx3 re-patterned the fast VCS into slow, nodal-like cells based on molecular and functional criteria. In these cases, gene expression profiling showed diminished expression of genes required for VCS-specific fast conduction but maintenance of expression of genes required for nodal slow conduction physiology. Action potentials of Tbx5-deficient VCS myocytes adopted nodal-specific characteristics, including increased action potential duration and cellular automaticity. Removal of Tbx5 in vivo precipitated inappropriate depolarizations in the atrioventricular (His)-bundle associated with lethal ventricular arrhythmias. TBX5 bound and directly activated cis-regulatory elements at fast conduction channel genes required for fast physiological characteristics of the VCS action potential, defining the identity of the adult VCS. CONCLUSIONS: The CCS is patterned entirely as a slow, nodal ground state, with a T-box dependent, physiologically dominant, fast conduction network driven specifically in the VCS. Disruption of the fast VCS gene regulatory network allowed nodal physiology to emerge, providing a plausible molecular mechanism for some lethal ventricular arrhythmias.

Competitive Doping Chemistry for Nickel-Rich Layered Oxide Cathode Materials.

Chemical modification of electrode materials by heteroatom dopants is crucial for improving storage performance in rechargeable batteries. Electron configurations of different dopants significantly influence the chemical interactions inbetween and the chemical bonding with the host material, yet the underlying mechanism remains unclear. We revealed competitive doping chemistry of Group IIIA elements (boron and aluminum) taking nickel-rich cathode materials as a model. A notable difference between the atomic radii of B and Al accounts for different spatial configurations of the hybridized orbital in bonding with lattice oxygen. Density functional theory calculations reveal, Al is preferentially bonded to oxygen and vice versa, and shows a much lower diffusion barrier than BIII . In the case of Al-preoccupation, the bulk diffusion of BIII is hindered. In this way, a B-rich surface and Al-rich bulk is formed, which helps to synergistically stabilize the structural evolution and surface chemistry of the cathode.

P3/O3 Integrated Layered Oxide as High-Power and Long-Life Cathode toward Na-Ion Batteries.

Low-cost and stable sodium-layered oxides (such as P2- and O3-phases) are suggested as highly promising cathode materials for Na-ion batteries (NIBs). Biphasic hybridization, mainly involving P2/O3 and P2/P3 biphases, is typically used to boost their electrochemical performances. Herein, a P3/O3 intergrown layered oxide (Na2/3 Ni1/3 Mn1/3 Ti1/3 O2 ) as high-rate and long-life cathode for NIBs via tuning the amounts of Ti substitution in Na2/3 Ni1/3 Mn2/3- x Tix O2 (x = 0, 1/6, 1/3, 2/3) is demonstrated. The X-ray diffraction (XRD) Rietveld refinement and aberration-corrected scanning transmission electron microscopy show the co-existence of P3 and O3 phases, and density functional theory calculation corroborates the appearance of the anomalous O3 phase at the Ti substitution amount of 1/3. The P3/O3 biphasic cathode delivers an unexpected rate capability (≈88.7% of the initial capacity at a high rate of 5 C) and cycling stability (≈68.7% capacity retention after 2000 cycles at 1 C), superior to those of the sing phases P3-Na2/3 Ni1/3 Mn2/3 O2 , P3-Na2/3 Ni1/3 Mn1/2 Ti1/6 O2 , and O3-Na2/3 Ni1/3 Ti2/3 O2 . The highly reversible structural evolution of the P3/O3 integrated cathode observed by ex situ XRD, ex situ X-ray absorption spectra, and the rapid Na+ diffusion kinetics, underpin the enhancement. These results show the important role of P3/O3 biphasic hybridization in designing and engineering layered oxide cathodes for NIBs.

Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq.

Long noncoding RNAs (lncRNAs) localize in the cell nucleus and influence gene expression through a variety of molecular mechanisms. Chromatin-enriched RNAs (cheRNAs) are a unique class of lncRNAs that are tightly bound to chromatin and putatively function to locally cis-activate gene transcription. CheRNAs can be identified by biochemical fractionation of nuclear RNA followed by RNA sequencing, but until now, a rigorous analytic pipeline for nuclear RNA-seq has been lacking. In this study, we survey four computational strategies for nuclear RNA-seq data analysis and develop a new pipeline, Tuxedo-ch, which outperforms other approaches. Tuxedo-ch assembles a more complete transcriptome and identifies cheRNA with higher accuracy than other approaches. We used Tuxedo-ch to analyze benchmark datasets of K562 cells and further characterize the genomic features of intergenic cheRNA (icheRNA) and their similarity to enhancer RNAs (eRNAs). We quantify the transcriptional correlation of icheRNA and adjacent genes and show that icheRNA is more positively associated with neighboring gene expression than eRNA or cap analysis of gene expression (CAGE) signals. We also explore two novel genomic associations of cheRNA, which indicate that cheRNAs may function to promote or repress gene expression in a context-dependent manner. IcheRNA loci with significant levels of H3K9me3 modifications are associated with active enhancers, consistent with the hypothesis that enhancers are derived from ancient mobile elements. In contrast, antisense cheRNA (as-cheRNA) may play a role in local gene repression, possibly through local RNA:DNA:DNA triple-helix formation.

Evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development.

Codevelopment of the lungs and heart underlies key evolutionary innovations in the transition to terrestrial life. Cardiac specializations that support pulmonary circulation, including the atrial septum, are generated by second heart field (SHF) cardiopulmonary progenitors (CPPs). It has been presumed that transcription factors required in the SHF for cardiac septation, e.g., Tbx5, directly drive a cardiac morphogenesis gene-regulatory network. Here, we report instead that TBX5 directly drives Wnt ligands to initiate a bidirectional signaling loop between cardiopulmonary mesoderm and the foregut endoderm for endodermal pulmonary specification and, subsequently, atrial septation. We show that Tbx5 is required for pulmonary specification in mice and amphibians but not for swim bladder development in zebrafish. TBX5 is non-cell-autonomously required for pulmonary endoderm specification by directly driving Wnt2 and Wnt2b expression in cardiopulmonary mesoderm. TBX5 ChIP-sequencing identified cis-regulatory elements at Wnt2 sufficient for endogenous Wnt2 expression domains in vivo and required for Wnt2 expression in precardiac mesoderm in vitro. Tbx5 cooperated with Shh signaling to drive Wnt2b expression for lung morphogenesis. Tbx5 haploinsufficiency in mice, a model of Holt-Oram syndrome, caused a quantitative decrement of mesodermal-to-endodermal Wnt signaling and subsequent endodermal-to-mesodermal Shh signaling required for cardiac morphogenesis. Thus, Tbx5 initiates a mesoderm-endoderm-mesoderm signaling loop in lunged vertebrates that provides a molecular basis for the coevolution of pulmonary and cardiac structures required for terrestrial life.

Study on the interactions between melamine-cored Schiff bases with cucurbit[n]urils of different sizes and its application in detecting silver ions.

Three different complexes, TMeQ[6]-TBT, Q[7]-TBT, and Q[8]-TBT are constructed by three different cucurbiturils and synthesized by guest melamine-cored Schiff bases (TBT) through outer-surface interaction and host-guest interactions. TBT forms a TMeQ[6]-TBT complex with TMeQ[6] through outer-surface interaction, while Q[7]-TBT and Q[8]-TBT form complexes with Q[7,8] through host-guest interactions. Among them, Q[7]-TBT is selected as a UV detector for the detection of silver ions (Ag+). This work makes full use of the characteristics of each cucurbituril and melamine-cored Schiff base to construct a series of complexes and these are applied to metal detection.

Dynamic Evolution of a Cathode Interphase Layer at the Surface of LiNi0.5Co0.2Mn0.3O2 in Quasi-Solid-State Lithium Batteries.

Intensive understanding of the surface mechanism of cathode materials, such as structural evolution and chemical and mechanical stability upon charging/discharging, is crucial to design advanced solid-state lithium batteries (SSLBs) of tomorrow. Here, via in situ atomic force microscopy monitoring, we explore the dynamic evolution process at the surface of LiNi0.5Co0.2Mn0.3O2 cathode particles inside a working SSLB. The dynamic formation process of the cathode interphase layer, with an inorganic-organic hybrid structure, was real-time imaged, as well as the evolution of its mechanical property by in situ scanning of the Derjaguin-Muller-Toporov modulus. Moreover, different components of the cathode interphase layer, such as LiF, Li2CO3, and specific organic species, were identified in detailat different stages of cycling, which can be directly correlated with the impedance buildup of the battery. In addition, the transition metal migration and the formation of new phases can further exacerbate the degradation of the SSLB. A relatively stable cathode interphase is key to improving the performance of SSLBs. Our findings provide deep insights into the dynamic evolution of surface morphology, chemical components and mechanical properties of the cathode interphase layer, which are pivotal for the performance optimization of SSLBs.

Highly efficient electrochemical gas reduction on a three-dimensional foam electrode: mechanism and application for the determination of hazardous mercury in complex matrix.

For the first time a nickel foam electrode (NFE) is applied in the field of electrochemical vapor generation (EVG) to carry out the electrochemical vapor phase conversion of mercury. Systematical electrochemical and morphological research has demonstrated that the specific surface area of the NFE was several times larger than that of the metal/non-metal electrode with the same geometric size. At the same time, the 3D porous channel composed of multi-layer nickel wire ensures the full contact between reactant and interface. The evident enhancement of spectral signals on a Ni electrode (283%), compared with Pt (27%) and graphite (109%), confirmed that the NFE effectively enhances the yield of mercury reduction. The NFE exhibits low limit of detection (0.017 µg L-1) and a wide linear range (0.2-20 µg L-1) with recoveries of actual samples in the range 87.8-117% towards Hg2+. Although the NFE has no advantage in electronic transmission and catalytic performance, its excellent stability, especially anti-interference and other characteristics, is sufficient for the analysis of hazardous mercury in complex matrix including certified reference materials and real samples.

CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs.

Motivation: Long intergenic noncoding RNAs (lincRNAs) have risen to prominence in cancer biology as new biomarkers of disease. Those lincRNAs transcribed from active cis-regulatory elements (enhancers) have provided mechanistic insight into cis-acting regulation; however, in the absence of an enhancer hallmark, computational prediction of cis-acting transcription of lincRNAs remains challenging. Here, we introduce a novel transcriptomic method: a cis-regulatory lincRNA-gene associating metric, termed 'CisPi'. CisPi quantifies the mutual information between lincRNAs and local gene expression regarding their response to perturbation, such as disease risk-dependence. To predict risk-dependent lincRNAs in neuroblastoma, an aggressive pediatric cancer, we advance this scoring scheme to measure lincRNAs that represent the minority of reads in RNA-Seq libraries by a novel side-by-side analytical pipeline. Results: Altered expression of lincRNAs that stratifies tumor risk is an informative readout of oncogenic enhancer activity. Our CisPi metric therefore provides a powerful computational model to identify enhancer-templated RNAs (eRNAs), eRNA-like lincRNAs, or active enhancers that regulate the expression of local genes. First, risk-dependent lincRNAs revealed active enhancers, over-represented neuroblastoma susceptibility loci, and uncovered novel clinical biomarkers. Second, the prioritized lincRNAs were significantly prognostic. Third, the predicted target genes further inherited the prognostic significance of these lincRNAs. In sum, RNA-Seq alone is sufficient to identify disease-associated lincRNAs using our methodologies, allowing broader applications to contexts in which enhancer hallmarks are not available or show limited sensitivity. Availability and implementation: The source code is available on request. The prioritized lincRNAs and their target genes are in the Supplementary Material. Supplementary information: Supplementary data are available at Bioinformatics online.

Correction: Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation.

[This corrects the article DOI: 10.1371/journal.pgen.1004604.].

De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects.

Congenital heart disease (CHD) has a complex genetic etiology, and recent studies suggest that high penetrance de novo mutations may account for only a small fraction of disease. In a multi-institutional cohort surveyed by exome sequencing, combining analysis of 987 individuals (discovery cohort of 59 affected trios and 59 control trios, and a replication cohort of 100 affected singletons and 533 unaffected singletons) we observe variation at novel and known loci related to a specific cardiac malformation the atrioventricular septal defect (AVSD). In a primary analysis, by combining developmental coexpression networks with inheritance modeling, we identify a de novo mutation in the DNA binding domain of NR1D2 (p.R175W). We show that p.R175W changes the transcriptional activity of Nr1d2 using an in vitro transactivation model in HUVEC cells. Finally, we demonstrate previously unrecognized cardiovascular malformations in the Nr1d2tm1-Dgen knockout mouse. In secondary analyses we map genetic variation to protein-interaction networks suggesting a role for two collagen genes in AVSD, which we corroborate by burden testing in a second replication cohort of 100 AVSDs and 533 controls (p = 8.37e-08). Finally, we apply a rare-disease inheritance model to identify variation in genes previously associated with CHD (ZFPM2, NSD1, NOTCH1, VCAN, and MYH6), cardiac malformations in mouse models (ADAM17, CHRD, IFT140, PTPRJ, RYR1 and ATE1), and hypomorphic alleles of genes causing syndromic CHD (EHMT1, SRCAP, BBS2, NOTCH2, and KMT2D) in 14 of 59 trios, greatly exceeding variation in control trios without CHD (p = 9.60e-06). In total, 32% of trios carried at least one putatively disease-associated variant across 19 loci,suggesting that inherited and de novo variation across a heterogeneous group of loci may contribute to disease risk.

Trapping Lithium into Hollow Silica Microspheres with a Carbon Nanotube Core for Dendrite-Free Lithium Metal Anodes.

Li metal anodes, which have attracted much attention for their high specific capacity and low redox potential, face a great challenge in realizing their practical application. The fatal issue of dendrite formation gives rise to internal short circuit and safety hazards and needs to be addressed. Here we propose a rational strategy of trapping Li within microcages to confine the deposition morphology and suppress dendrite growth. Microcages with a carbon nanotube core and porous silica sheath were prepared and proved to be effective for controlling the electrodeposition behavior. In addition, the insulative coating layer prevents concentrated electron flow and decreases the possibility of "hot spots" formation. Because of the Li trapper and uniform electron distribution, the electrode with delicate structure exhibits a dendrite-free morphology after plating 2 mA h cm-2 of Li. As the dendrite growth is suppressed, the as-obtained electrode maintains a high plating/stripping efficiency of 99% over 200 cycles. This work delivers new insights into the design of rational Li metal anodes and hastens the practical application of Li metal batteries.

Cilia gene mutations cause atrioventricular septal defects by multiple mechanisms.

Atrioventricular septal defects (AVSDs) are a common severe form of congenital heart disease (CHD). In this study we identified deleterious non-synonymous mutations in two cilia genes, Dnah11 and Mks1, in independent N-ethyl-N-nitrosourea-induced mouse mutant lines with heritable recessive AVSDs by whole-exome sequencing. Cilia are required for left/right body axis determination and second heart field (SHF) Hedgehog (Hh) signaling, and we find that cilia mutations affect these requirements differentially. Dnah11avc4 did not disrupt SHF Hh signaling and caused AVSDs only concurrently with heterotaxy, a left/right axis abnormality. In contrast, Mks1avc6 disrupted SHF Hh signaling and caused AVSDs without heterotaxy. We performed unbiased whole-genome SHF transcriptional profiling and found that cilia motility genes were not expressed in the SHF whereas cilia structural and signaling genes were highly expressed. SHF cilia gene expression predicted the phenotypic concordance between AVSDs and heterotaxy in mice and humans with cilia gene mutations. A two-step model of cilia action accurately predicted the AVSD/heterotaxyu phenotypic expression pattern caused by cilia gene mutations. We speculate that cilia gene mutations contribute to both syndromic and non-syndromic AVSDs in humans and provide a model that predicts the phenotypic consequences of specific cilia gene mutations.

An Abnormal 3.7†Volt O3-Type Sodium-Ion Battery Cathode.

Layered O3-type sodium oxides (NaMO2 , M=transition metal) commonly exhibit an O3-P3 phase transition, which occurs at a low redox voltage of about 3 V (vs. Na+ /Na) during sodium extraction and insertion, with the result that almost 50 % of their total capacity lies at this low voltage region, and they possess insufficient energy density as cathode materials for sodium-ion batteries (NIBs). Therefore, development of high-voltage O3-type cathodes remains challenging because it is difficult to raise the phase-transition voltage by reasonable structure modulation. A new example of O3-type sodium insertion materials is presented for use in NIBs. The designed O3-type Na0.7 Ni0.35 Sn0.65 O2 material displays a highest redox potential of 3.7 V (vs. Na+ /Na) among the reported O3-type materials based on the Ni2+ /Ni3+ couple, by virtue of its increased Ni-O bond ionicity through reduced orbital overlap between transition metals and oxygen within the MO2 slabs. This study provides an orbital-level understanding of the operating potentials of the nominal redox couples for O3-NaMO2 cathodes. The strategy described could be used to tailor electrodes for improved performance.

Foxf genes integrate tbx5 and hedgehog pathways in the second heart field for cardiac septation.

The Second Heart Field (SHF) has been implicated in several forms of congenital heart disease (CHD), including atrioventricular septal defects (AVSDs). Identifying the SHF gene regulatory networks required for atrioventricular septation is therefore an essential goal for understanding the molecular basis of AVSDs. We defined a SHF Hedgehog-dependent gene regulatory network using whole genome transcriptional profiling and GLI-chromatin interaction studies. The Forkhead box transcription factors Foxf1a and Foxf2 were identified as SHF Hedgehog targets. Compound haploinsufficiency for Foxf1a and Foxf2 caused atrioventricular septal defects, demonstrating the biological relevance of this regulatory network. We identified a Foxf1a cis-regulatory element that bound the Hedgehog transcriptional regulators GLI1 and GLI3 and the T-box transcription factor TBX5 in vivo. GLI1 and TBX5 synergistically activated transcription from this cis-regulatory element in vitro. This enhancer drove reproducible expression in vivo in the posterior SHF, the only region where Gli1 and Tbx5 expression overlaps. Our findings implicate Foxf genes in atrioventricular septation, describe the molecular underpinnings of the genetic interaction between Hedgehog signaling and Tbx5, and establish a molecular model for the selection of the SHF gene regulatory network for cardiac septation.

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.

UNLABELLED: Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores. It is designed to isolate systematic disturbances and common biological underpinnings from next-generation sequencing (NGS) data. Seq2pathway offers Bioconductor users enhanced capability in discovering collective pathway effects caused by both coding genes and cis-regulation of non-coding elements. AVAILABILITY AND IMPLEMENTATION: The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html. CONTACT: xyang2@uchicago.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia.

BACKGROUND: Genes that regulate stem cell function are suspected to exert adverse effects on prognosis in malignancy. However, diverse cancer stem cell signatures are difficult for physicians to interpret and apply clinically. To connect the transcriptome and stem cell biology, with potential clinical applications, we propose a novel computational "gene-to-function, snapshot-to-dynamics, and biology-to-clinic" framework to uncover core functional gene-sets signatures. This framework incorporates three function-centric gene-set analysis strategies: a meta-analysis of both microarray and RNA-seq data, novel dynamic network mechanism (DNM) identification, and a personalized prognostic indicator analysis. This work uses complex disease acute myeloid leukemia (AML) as a research platform. RESULTS: We introduced an adjustable "soft threshold" to a functional gene-set algorithm and found that two different analysis methods identified distinct gene-set signatures from the same samples. We identified a 30-gene cluster that characterizes leukemic stem cell (LSC)-depleted cells and a 25-gene cluster that characterizes LSC-enriched cells in parallel; both mark favorable-prognosis in AML. Genes within each signature significantly share common biological processes and/or molecular functions (empirical p = 6e-5 and 0.03 respectively). The 25-gene signature reflects the abnormal development of stem cells in AML, such as AURKA over-expression. We subsequently determined that the clinical relevance of both signatures is independent of known clinical risk classifications in 214 patients with cytogenetically normal AML. We successfully validated the prognosis of both signatures in two independent cohorts of 91 and 242 patients respectively (log-rank p < 0.0015 and 0.05; empirical p < 0.015 and 0.08). CONCLUSION: The proposed algorithms and computational framework will harness systems biology research because they efficiently translate gene-sets (rather than single genes) into biological discoveries about AML and other complex diseases.