Targeting KRAS Mutant Cancers with a Covalent G12C-Specific Inhibitor.

KRASG12C was recently identified to be potentially druggable by allele-specific covalent targeting of Cys-12 in vicinity to an inducible allosteric switch II pocket (S-IIP). Success of this approach requires active cycling of KRASG12C between its active-GTP and inactive-GDP conformations as accessibility of the S-IIP is restricted only to the GDP-bound state. This strategy proved feasible for inhibiting mutant KRAS in vitro; however, it is uncertain whether this approach would translate to in vivo. Here, we describe structure-based design and identification of ARS-1620, a covalent compound with high potency and selectivity for KRASG12C. ARS-1620 achieves rapid and sustained in vivo target occupancy to induce tumor regression. We use ARS-1620 to dissect oncogenic KRAS dependency and demonstrate that monolayer culture formats significantly underestimate KRAS dependency in vivo. This study provides in vivo evidence that mutant KRAS can be selectively targeted and reveals ARS-1620 as representing a new generation of KRASG12C-specific inhibitors with promising therapeutic potential.

Metformin inhibition of mitochondrial ATP and DNA synthesis abrogates NLRP3 inflammasome activation and pulmonary inflammation.

Acute respiratory distress syndrome (ARDS), an inflammatory condition with high mortality rates, is common in severe COVID-19, whose risk is reduced by metformin rather than other anti-diabetic medications. Detecting of inflammasome assembly in post-mortem COVID-19 lungs, we asked whether and how metformin inhibits inflammasome activation while exerting its anti-inflammatory effect. We show that metformin inhibited NLRP3 inflammasome activation and interleukin (IL)-1ß production in cultured and alveolar macrophages along with inflammasome-independent IL-6 secretion, thus attenuating lipopolysaccharide (LPS)- and SARS-CoV-2-induced ARDS. By targeting electron transport chain complex 1 and independently of AMP-activated protein kinase (AMPK) or NF-κB, metformin blocked LPS-induced and ATP-dependent mitochondrial (mt) DNA synthesis and generation of oxidized mtDNA, an NLRP3 ligand. Myeloid-specific ablation of LPS-induced cytidine monophosphate kinase 2 (CMPK2), which is rate limiting for mtDNA synthesis, reduced ARDS severity without a direct effect on IL-6. Thus, inhibition of ATP and mtDNA synthesis is sufficient for ARDS amelioration.

Monolithic three-dimensional tier-by-tier integration via van der Waals lamination.

Two-dimensional (2D) semiconductors have shown great potential for monolithic three-dimensional (M3D) integration due to their dangling-bonds-free surface and the ability to integrate to various substrates without the conventional constraint of lattice matching1-10. However, with atomically thin body thickness, 2D semiconductors are not compatible with various high-energy processes in microelectronics11-13, where the M3D integration of multiple 2D circuit tiers is challenging. Here we report an alternative low-temperature M3D integration approach by van der Waals (vdW) lamination of entire prefabricated circuit tiers, where the processing temperature is controlled to 120 °C. By further repeating the vdW lamination process tier by tier, an M3D integrated system is achieved with 10 circuit tiers in the vertical direction, overcoming previous thermal budget limitations. Detailed electrical characterization demonstrates the bottom 2D transistor is not impacted after repetitively laminating vdW circuit tiers on top. Furthermore, by vertically connecting devices within different tiers through vdW inter-tier vias, various logic and heterogeneous structures are realized with desired system functions. Our demonstration provides a low-temperature route towards fabricating M3D circuits with increased numbers of tiers.

Two-dimensional Perovskitoids Enhance Stability in Perovskite Solar Cells.

Two-dimensional (2D)/three-dimensional (3D) perovskite heterostructures have played a key role in advancing the performance of perovskite solar cells (PSCs)1,2. However, the migration of cations between 2D and 3D layers results in the disruption of octahedral networks that leads to degradation in performance over time3,4. We hypothesized that perovskitoids, with robust organic-inorganic networks enabled by edge- and face-sharing, could impede ion migration. We explored a set of perovskitoids of varying dimensionality, and found that cation migration within perovskitoid/perovskite heterostructures was suppressed compared to the 2D/3D perovskite case. Increasing the dimensionality of perovskitoids improves charge transport when they are interfaced with 3D perovskite surfaces - this the result of enhanced octahedral connectivity and out-of-plane orientation. The 2D perovskitoid (A6BfP)8Pb7I22 (A6BfP: N-aminohexyl-benz[f]-phthalimide) provides efficient passivation of perovskite surfaces and enables uniform large-area perovskite films. Devices based on perovskitoid/perovskite heterostructures achieve a certified quasi-steady-state power conversion efficiency of 24.6% for centimeter-area PSCs. We removed the fragile hole transport layers and showed stable operation of the underlying perovskitoid/perovskite heterostructure at 85°C for 1,250 hours for encapsulated large-area devices in an air ambient.

Inhibition of ASGR1 decreases lipid levels by promoting cholesterol excretion.

High cholesterol is a major risk factor for cardiovascular disease1. Currently, no drug lowers cholesterol through directly promoting cholesterol excretion. Human genetic studies have identified that the loss-of-function Asialoglycoprotein receptor 1 (ASGR1) variants associate with low cholesterol and a reduced risk of cardiovascular disease2. ASGR1 is exclusively expressed in liver and mediates internalization and lysosomal degradation of blood asialoglycoproteins3. The mechanism by which ASGR1 affects cholesterol metabolism is unknown. Here, we find that Asgr1 deficiency decreases lipid levels in serum and liver by stabilizing LXRα. LXRα upregulates ABCA1 and ABCG5/G8, which promotes cholesterol transport to high-density lipoprotein and excretion to bile and faeces4, respectively. ASGR1 deficiency blocks endocytosis and lysosomal degradation of glycoproteins, reduces amino-acid levels in lysosomes, and thereby inhibits mTORC1 and activates AMPK. On one hand, AMPK increases LXRα by decreasing its ubiquitin ligases BRCA1/BARD1. On the other hand, AMPK suppresses SREBP1 that controls lipogenesis. Anti-ASGR1 neutralizing antibody lowers lipid levels by increasing cholesterol excretion, and shows synergistic beneficial effects with atorvastatin or ezetimibe, two widely used hypocholesterolaemic drugs. In summary, this study demonstrates that targeting ASGR1 upregulates LXRα, ABCA1 and ABCG5/G8, inhibits SREBP1 and lipogenesis, and therefore promotes cholesterol excretion and decreases lipid levels.

Synthesis-on-substrate of quantum dot solids.

Perovskite light-emitting diodes (PeLEDs) with an external quantum efficiency exceeding 20% have been achieved in both green and red wavelengths1-5; however, the performance of blue-emitting PeLEDs lags behind6,7. Ultrasmall CsPbBr3 quantum dots are promising candidates with which to realize efficient and stable blue PeLEDs, although it has proven challenging to synthesize a monodispersed population of ultrasmall CsPbBr3 quantum dots, and difficult to retain their solution-phase properties when casting into solid films8. Here we report the direct synthesis-on-substrate of films of suitably coupled, monodispersed, ultrasmall perovskite QDs. We develop ligand structures that enable control over the quantum dots' size, monodispersity and coupling during film-based synthesis. A head group (the side with higher electrostatic potential) on the ligand provides steric hindrance that suppresses the formation of layered perovskites. The tail (the side with lower electrostatic potential) is modified using halide substitution to increase the surface binding affinity, constraining resulting grains to sizes within the quantum confinement regime. The approach achieves high monodispersity (full-width at half-maximum = 23 nm with emission centred at 478 nm) united with strong coupling. We report as a result blue PeLEDs with an external quantum efficiency of 18% at 480 nm and 10% at 465 nm, to our knowledge the highest reported among perovskite blue LEDs by a factor of 1.5 and 2, respectively6,7.

GRAMD1/ASTER-mediated cholesterol transport promotes Smoothened cholesterylation at the endoplasmic reticulum.

Hedgehog (Hh) signaling pathway plays a pivotal role in embryonic development. Hh binding to Patched1 (PTCH1) derepresses Smoothened (SMO), thereby activating the downstream signal transduction. Covalent SMO modification by cholesterol in its cysteine-rich domain (CRD) is essential for SMO function. SMO cholesterylation is a calcium-accelerated autoprocessing reaction, and STIM1-ORAI1-mediated store-operated calcium entry promotes cholesterylation and activation of endosome-localized SMO. However, it is unknown whether the Hh-PTCH1 interplay regulates the activity of the endoplasmic reticulum (ER)-localized SMO. Here, we found that PTCH1 inhibited the COPII-dependent export of SMO from the ER, whereas Hh promoted this process. The RRxWxR amino acid motif in the cytosolic tail of SMO was essential for COPII recognition, ciliary localization, and signal transduction activity. Hh and PTCH1 regulated cholesterol modification of the ER-localized SMO, and SMO cholesterylation accelerated its exit from ER. The GRAMD1/ASTER sterol transport proteins facilitated cholesterol transfer to ER from PM, resulting in increased SMO cholesterylation and enhanced Hh signaling. Collectively, we reveal a regulatory role of GRAMD-mediated cholesterol transport in ER-resident SMO maturation and Hh signaling.

Promises and prospects of two-dimensional transistors.

Two-dimensional (2D) semiconductors have attracted tremendous interest as atomically thin channels that could facilitate continued transistor scaling. However, despite many proof-of-concept demonstrations, the full potential of 2D transistors has yet to be determined. To this end, the fundamental merits and technological limits of 2D transistors need a critical assessment and objective projection. Here we review the promise and current status of 2D transistors, and emphasize that widely used device parameters (such as carrier mobility and contact resistance) could be frequently misestimated or misinterpreted, and may not be the most reliable performance metrics for benchmarking 2D transistors. We suggest that the saturation or on-state current density, especially in the short-channel limit, could provide a more reliable measure for assessing the potential of diverse 2D semiconductors, and should be applied for cross-checking different studies, especially when milestone performance metrics are claimed. We also summarize the key technical challenges in optimizing the channels, contacts, dielectrics and substrates and outline potential pathways to push the performance limit of 2D transistors. We conclude with an overview of the critical technical targets, the key technological obstacles to the 'lab-to-fab' transition and the potential opportunities arising from the use of these atomically thin semiconductors.

Distribution control enables efficient reduced-dimensional perovskite LEDs.

Light-emitting diodes (LEDs) based on perovskite quantum dots have shown external quantum efficiencies (EQEs) of over 23% and narrowband emission, but suffer from limited operating stability1. Reduced-dimensional perovskites (RDPs) consisting of quantum wells (QWs) separated by organic intercalating cations show high exciton binding energies and have the potential to increase the stability and the photoluminescence quantum yield2,3. However, until now, RDP-based LEDs have exhibited lower EQEs and inferior colour purities4-6. We posit that the presence of variably confined QWs may contribute to non-radiative recombination losses and broadened emission. Here we report bright RDPs with a more monodispersed QW thickness distribution, achieved through the use of a bifunctional molecular additive that simultaneously controls the RDP polydispersity while passivating the perovskite QW surfaces. We synthesize a fluorinated triphenylphosphine oxide additive that hydrogen bonds with the organic cations, controlling their diffusion during RDP film deposition and suppressing the formation of low-thickness QWs. The phosphine oxide moiety passivates the perovskite grain boundaries via coordination bonding with unsaturated sites, which suppresses defect formation. This results in compact, smooth and uniform RDP thin films with narrowband emission and high photoluminescence quantum yield. This enables LEDs with an EQE of 25.6% with an average of 22.1 ±1.2% over 40 devices, and an operating half-life of two hours at an initial luminance of 7,200 candela per metre squared, indicating tenfold-enhanced operating stability relative to the best-known perovskite LEDs with an EQE exceeding 20%1,4-6.

High-order superlattices by rolling up van der Waals heterostructures.

Two-dimensional (2D) materials1,2 and the associated van der Waals (vdW) heterostructures3-7 have provided great flexibility for integrating distinct atomic layers beyond the traditional limits of lattice-matching requirements, through layer-by-layer mechanical restacking or sequential synthesis. However, the 2D vdW heterostructures explored so far have been usually limited to relatively simple heterostructures with a small number of blocks8-18. The preparation of high-order vdW superlattices with larger number of alternating units is exponentially more difficult, owing to the limited yield and material damage associated with each sequential restacking or synthesis step8-29. Here we report a straightforward approach to realizing high-order vdW superlattices by rolling up vdW heterostructures. We show that a capillary-force-driven rolling-up process can be used to delaminate synthetic SnS2/WSe2 vdW heterostructures from the growth substrate and produce SnS2/WSe2 roll-ups with alternating monolayers of WSe2 and SnS2, thus forming high-order SnS2/WSe2 vdW superlattices. The formation of these superlattices modulates the electronic band structure and the dimensionality, resulting in a transition of the transport characteristics from semiconducting to metallic, from 2D to one-dimensional (1D), with an angle-dependent linear magnetoresistance. This strategy can be extended to create diverse 2D/2D vdW superlattices, more complex 2D/2D/2D vdW superlattices, and beyond-2D materials, including three-dimensional (3D) thin-film materials and 1D nanowires, to generate mixed-dimensional vdW superlattices, such as 3D/2D, 3D/2D/2D, 1D/2D and 1D/3D/2D vdW superlattices. This study demonstrates a general approach to producing high-order vdW superlattices with widely variable material compositions, dimensions, chirality and topology, and defines a rich material platform for both fundamental studies and technological applications.

High-throughput measurement of elastic moduli of microfibers by rope coiling.

There are many fields where it is of interest to measure the elastic moduli of tiny fragile fibers, such as filamentous bacteria, actin filaments, DNA, carbon nanotubes, and functional microfibers. The elastic modulus is typically deduced from a sophisticated tensile test under a microscope, but the throughput is low and limited by the time-consuming and skill-intensive sample loading/unloading. Here, we demonstrate a simple microfluidic method enabling the high-throughput measurement of the elastic moduli of microfibers by rope coiling using a localized compression, where sample loading/unloading are not needed between consecutive measurements. The rope coiling phenomenon occurs spontaneously when a microfiber flows from a small channel into a wide channel. The elastic modulus is determined by measuring either the buckling length or the coiling radius. The throughput of this method, currently 3,300 fibers per hour, is a thousand times higher than that of a tensile tester. We demonstrate the feasibility of the method by testing a nonuniform fiber with axially varying elastic modulus. We also demonstrate its capability for in situ inline measurement in a microfluidic production line. We envisage that high-throughput measurements may facilitate potential applications such as screening or sorting by mechanical properties and real-time control during production of microfibers.

Integration of protein sequence and protein-protein interaction data by hypergraph learning to identify novel protein complexes.

Protein-protein interactions (PPIs) are the basis of many important biological processes, with protein complexes being the key forms implementing these interactions. Understanding protein complexes and their functions is critical for elucidating mechanisms of life processes, disease diagnosis and treatment and drug development. However, experimental methods for identifying protein complexes have many limitations. Therefore, it is necessary to use computational methods to predict protein complexes. Protein sequences can indicate the structure and biological functions of proteins, while also determining their binding abilities with other proteins, influencing the formation of protein complexes. Integrating these characteristics to predict protein complexes is very promising, but currently there is no effective framework that can utilize both protein sequence and PPI network topology for complex prediction. To address this challenge, we have developed HyperGraphComplex, a method based on hypergraph variational autoencoder that can capture expressive features from protein sequences without feature engineering, while also considering topological properties in PPI networks, to predict protein complexes. Experiment results demonstrated that HyperGraphComplex achieves satisfactory predictive performance when compared with state-of-art methods. Further bioinformatics analysis shows that the predicted protein complexes have similar attributes to known ones. Moreover, case studies corroborated the remarkable predictive capability of our model in identifying protein complexes, including 3 that were not only experimentally validated by recent studies but also exhibited high-confidence structural predictions from AlphaFold-Multimer. We believe that the HyperGraphComplex algorithm and our provided proteome-wide high-confidence protein complex prediction dataset will help elucidate how proteins regulate cellular processes in the form of complexes, and facilitate disease diagnosis and treatment and drug development. Source codes are available at https://github.com/LiDlab/HyperGraphComplex.

Discovery of metal-binding proteins by thermal proteome profiling.

Metal-binding proteins (MBPs) have various and important biological roles in all living species and many human diseases are intricately linked to dysfunctional MBPs. Here, we report a chemoproteomic method named 'metal extraction-triggered agitation logged by thermal proteome profiling' (METAL-TPP) to globally profile MBPs in proteomes. The method involves the extraction of metals from MBPs using chelators and monitoring the resulting protein stability changes through thermal proteome profiling. Applying METAL-TPP to the human proteome with a broad-spectrum chelator, EDTA, revealed a group of proteins with reduced thermal stability that contained both previously known MBPs and currently unannotated MBP candidates. Biochemical characterization of one potential target, glutamine-fructose-6-phosphate transaminase 2 (GFPT2), showed that zinc bound the protein, inhibited its enzymatic activity and modulated the hexosamine biosynthesis pathway. METAL-TPP profiling with another chelator, TPEN, uncovered additional MBPs in proteomes. Collectively, this study developed a robust tool for proteomic discovery of MBPs and provides a rich resource for functional studies of metals in cell biology.

van der Waals Contact for Two-Dimensional Transition Metal Dichalcogenides.

Two-dimensional (2D) transition metal dichalcogenides (TMDs) have emerged as highly promising candidates for next-generation electronics owing to their atomically thin structures and surfaces devoid of dangling bonds. However, establishing high-quality metal contacts with TMDs presents a critical challenge, primarily attributed to their ultrathin bodies and delicate lattices. These distinctive characteristics render them susceptible to physical damage and chemical reactions when conventional metallization approaches involving "high-energy" processes are implemented. To tackle this challenge, the concept of van der Waals (vdW) contacts has recently been proposed as a "low-energy" alternative. Within the vdW geometry, metal contacts can be physically laminated or gently deposited onto the 2D channel of TMDs, ensuring the formation of atomically clean and electronically sharp contact interfaces while preserving the inherent properties of the 2D TMDs. Consequently, a considerable number of vdW contact devices have been extensively investigated, revealing unprecedented transport physics or exceptional device performance that was previously unachievable. This review presents recent advancements in vdW contacts for TMD transistors, discussing the merits, limitations, and prospects associated with each device geometry. By doing so, our purpose is to offer a comprehensive understanding of the current research landscape and provide insights into future directions within this rapidly evolving field.

miR-345-3p Modulates M1/M2 Macrophage Polarization to Inhibit Inflammation in Bone Infection via Targeting MAP3K1 and NF-κB Pathway.

Infection after fracture fixation (IAFF), a complex infectious disease, causes inflammatory destruction of bone tissue and poses a significant clinical challenge. miR-345-3p is a biomarker for tibial infected nonunion; however, the comprehensive mechanistic role of miR-345-3p in IAFF is elusive. In this study, we investigated the role of miR-345-3p in IAFF pathogenesis through in vivo and in vitro experiments. In vivo, in a rat model of IAFF, miR-345-3p expression was downregulated, accompanied by increased M1 macrophage infiltration and secretion of proinflammatory factors. In vitro, LPS induced differentiation of primary rat bone marrow-derived macrophages into M1 macrophages, which was attenuated by miR-345-3p mimics. miR-345-3p promoted M1 to M2 macrophage transition-it reduced the expression of cluster of differentiation (CD) 86, inducible NO synthase, IL-1ß, and TNF-α but elevated those of CD163, arginase-1, IL-4, and IL-10. MAPK kinase kinase 1 (MAP3K1), a target mRNA of miR-345-3p, was overexpressed in the bone tissue of IAFF rats compared with that in those of the control rats. The M1 to M2 polarization inhibited MAP3K1 signaling pathways in vitro. Conversely, MAP3K1 overexpression promoted the transition from M2 to M1. miR-345-3p significantly inhibited NF-κB translocation from the cytosol to the nucleus in a MAP3K1-dependent manner. In conclusion, miR-345-3p promotes the polarization of M1 macrophages to the M2 phenotype by inhibiting the MAP3K1 and NF-κB pathways. These findings provide insight into the pathogenesis and immunotherapeutic strategies for IAFF and offer potential new targets for subsequent research.

Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals.

The ongoing outbreak of coronavirus disease 2019 (COVID-19) has spread rapidly on a global scale. Although it is clear that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is transmitted through human respiratory droplets and direct contact, the potential for aerosol transmission is poorly understood1-3. Here we investigated the aerodynamic nature of SARS-CoV-2 by measuring viral RNA in aerosols in different areas of two Wuhan hospitals during the outbreak of COVID-19 in February and March 2020. The concentration of SARS-CoV-2 RNA in aerosols that was detected in isolation wards and ventilated patient rooms was very low, but it was higher in the toilet areas used by the patients. Levels of airborne SARS-CoV-2 RNA in the most public areas was undetectable, except in two areas that were prone to crowding; this increase was possibly due to individuals infected with SARS-CoV-2 in the crowd. We found that some medical staff areas initially had high concentrations of viral RNA with aerosol size distributions that showed peaks in the submicrometre and/or supermicrometre regions; however, these levels were reduced to undetectable levels after implementation of rigorous sanitization procedures. Although we have not established the infectivity of the virus detected in these hospital areas, we propose that SARS-CoV-2 may have the potential to be transmitted through aerosols. Our results indicate that room ventilation, open space, sanitization of protective apparel, and proper use and disinfection of toilet areas can effectively limit the concentration of SARS-CoV-2 RNA in aerosols. Future work should explore the infectivity of aerosolized virus.

A droplet-based electricity generator with high instantaneous power density.

Extensive efforts have been made to harvest energy from water in the form of raindrops1-6, river and ocean waves7,8, tides9 and others10-17. However, achieving a high density of electrical power generation is challenging. Traditional hydraulic power generation mainly uses electromagnetic generators that are heavy, bulky, and become inefficient with low water supply. An alternative, the water-droplet/solid-based triboelectric nanogenerator, has so far generated peak power densities of less than one watt per square metre, owing to the limitations imposed by interfacial effects-as seen in characterizations of the charge generation and transfer that occur at solid-liquid1-4 or liquid-liquid5,18 interfaces. Here we develop a device to harvest energy from impinging water droplets by using an architecture that comprises a polytetrafluoroethylene film on an indium tin oxide substrate plus an aluminium electrode. We show that spreading of an impinged water droplet on the device bridges the originally disconnected components into a closed-loop electrical system, transforming the conventional interfacial effect into a bulk effect, and so enhancing the instantaneous power density by several orders of magnitude over equivalent devices that are limited by interfacial effects.

General synthesis of two-dimensional van der Waals heterostructure arrays.

Two-dimensional van der Waals heterostructures (vdWHs) have attracted considerable interest1-4. However, most vdWHs reported so far  are created by an arduous micromechanical exfoliation and manual restacking process5, which-although versatile for proof-of-concept demonstrations6-16 and fundamental studies17-30-is clearly not scalable for practical technologies. Here we report a general synthetic strategy for two-dimensional vdWH arrays between metallic transition-metal dichalcogenides (m-TMDs) and semiconducting TMDs (s-TMDs). By selectively patterning nucleation sites on monolayer or bilayer s-TMDs, we precisely control the nucleation and growth of diverse m-TMDs with designable periodic arrangements and tunable lateral dimensions at the predesignated spatial locations, producing a series of vdWH arrays, including VSe2/WSe2, NiTe2/WSe2, CoTe2/WSe2, NbTe2/WSe2, VS2/WSe2, VSe2/MoS2 and VSe2/WS2. Systematic scanning transmission electron microscopy studies reveal nearly ideal vdW interfaces with widely tunable moiré superlattices. With the atomically clean vdW interface, we further show that the m-TMDs function as highly reliable synthetic vdW contacts for the underlying WSe2 with excellent device performance and yield, delivering a high ON-current density of up to 900 microamperes per micrometre in bilayer WSe2 transistors. This general synthesis of diverse two-dimensional vdWH arrays provides a versatile material platform for exploring exotic physics and promises a scalable pathway to high-performance devices.

PancanQTLv2.0: a comprehensive resource for expression quantitative trait loci across human cancers.

Expression quantitative trait locus (eQTL) analysis is a powerful tool used to investigate genetic variations in complex diseases, including cancer. We previously developed a comprehensive database, PancanQTL, to characterize cancer eQTLs using The Cancer Genome Atlas (TCGA) dataset, and linked eQTLs with patient survival and GWAS risk variants. Here, we present an updated version, PancanQTLv2.0 (https://hanlaboratory.com/PancanQTLv2/), with advancements in fine-mapping causal variants for eQTLs, updating eQTLs overlapping with GWAS linkage disequilibrium regions and identifying eQTLs associated with drug response and immune infiltration. Through fine-mapping analysis, we identified 58 747 fine-mapped eQTLs credible sets, providing mechanic insights of gene regulation in cancer. We further integrated the latest GWAS Catalog and identified a total of 84 592 135 linkage associations between eQTLs and the existing GWAS loci, which represents a remarkable ∼50-fold increase compared to the previous version. Additionally, PancanQTLv2.0 uncovered 659516 associations between eQTLs and drug response and identified 146948 associations between eQTLs and immune cell abundance, providing potentially clinical utility of eQTLs in cancer therapy. PancanQTLv2.0 expanded the resources available for investigating gene expression regulation in human cancers, leading to advancements in cancer research and precision oncology.

A full-proteome, interaction-specific characterization of mutational hotspots across human cancers.

Rapid accumulation of cancer genomic data has led to the identification of an increasing number of mutational hotspots with uncharacterized significance. Here we present a biologically informed computational framework that characterizes the functional relevance of all 1107 published mutational hotspots identified in approximately 25,000 tumor samples across 41 cancer types in the context of a human 3D interactome network, in which the interface of each interaction is mapped at residue resolution. Hotspots reside in network hub proteins and are enriched on protein interaction interfaces, suggesting that alteration of specific protein-protein interactions is critical for the oncogenicity of many hotspot mutations. Our framework enables, for the first time, systematic identification of specific protein interactions affected by hotspot mutations at the full proteome scale. Furthermore, by constructing a hotspot-affected network that connects all hotspot-affected interactions throughout the whole-human interactome, we uncover genome-wide relationships among hotspots and implicate novel cancer proteins that do not harbor hotspot mutations themselves. Moreover, applying our network-based framework to specific cancer types identifies clinically significant hotspots that can be used for prognosis and therapy targets. Overall, we show that our framework bridges the gap between the statistical significance of mutational hotspots and their biological and clinical significance in human cancers.