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A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development

Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.

ABSTRACT

Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.

PMID:42189071 | DOI:10.1002/advs.75839

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A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development

Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.

ABSTRACT

Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.

PMID:42189071 | DOI:10.1002/advs.75839

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Low-Cost Labels, Reliable Choices: Rollout-Calibrated Hyper-Heuristics for Job Shop Scheduling

arXiv:2605.23957v1 Announce Type: new Abstract: Learning-assisted hyper-heuristics can select among dispatching rules while preserving the feasibility and interpretability of constructive Job Shop Scheduling Problem (JSSP) heuristics. Their main computational cost lies in label generation rather than model fitting, since each supervised label usually requires rolling out candidate rules from a partial schedule. We study this label-cost problem together with a reliability problem: a learned selector should not switch away from a strong default rule unless the predicted gain is credible. The proposed selector uses regret-normalized rollout labels, a contextual KNN uncertainty estimate, and a gate that acts only when the predicted improvement exceeds an uncertainty-adjusted margin. We also vary rollout depth and breadth to measure the cost-quality trade-off. On synthetic JSSP instances, the gated selector achieves the lowest mean RPD among learned selectors, remains close to the best fixed dispatching rule, and reduces Random-HH mean RPD by more than an order of magnitude.
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MobileGym: A Verifiable and Highly Parallel Simulation Platform for Mobile GUI Agent Research

arXiv:2605.26114v1 Announce Type: new Abstract: We present MobileGym, a browser-hosted, lightweight, fully controllable environment for everyday mobile use, targeting interaction fidelity without replicating proprietary backends. It enables two capabilities previously out of reach for everyday apps: verifiable outcome signals through deterministic state-based judging over structured JSON state, and scalable online RL through low-cost parallel rollouts. The full environment state is captured, configured, forked, and compared as structured JSON, and a single server can host hundreds of parallel instances, with about 400 MB memory per instance and about 3 s cold start. A layered state model and a declarative task-definition framework keep state programmability and task creation practical at scale, and a single programmatic judging mechanism delivers both deterministic evaluation verdicts and dense RL rewards. The accompanying MobileGym-Bench provides 416 parameterized task templates, including 256 test and 160 train templates, over 28 apps, with deterministic judges and a structured AnswerSheet protocol that avoids free-text matching failures. In a Sim-to-Real case study, GRPO on Qwen3-VL-4B-Instruct gains +12.8 percentage points on the 256-task test set, and on a 59-task real-device signal subset, real-device execution retains 95.1% of the simulation-side training gain. Project page: https://mobilegym.github.io.
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Turning Stale Gradients into Stable Gradients: Coherent Coordinate Descent with Implicit Landscape Smoothing for Lightweight Zeroth-Order Optimization

arXiv:2605.14373v2 Announce Type: replace-cross Abstract: Zeroth-Order (ZO) optimization is pivotal for scenarios where backpropagation is unavailable, such as memory-constrained on-device learning and black-box optimization. However, existing methods face a stark trade-off: they are either sample-inefficient (e.g., standard finite differences) or suffer from high variance due to randomized estimation (e.g., random subspace methods). In this work, we propose Coherent Coordinate Descent (CoCD), a deterministic, sample-efficient, and budget-aware ZO optimizer. Theoretically, we formalize the notion of gradient coherence and demonstrate that CoCD is equivalent to Block Cyclic Coordinate Descent (BCCD) with ``warm starts,'' effectively converting historical (stale) gradients from a liability into a computational asset. This mechanism enables $O(1)$ query complexity per step while maintaining global descent directions. Furthermore, we derive error bounds revealing a counter-intuitive insight: larger finite-difference step sizes can induce an implicit smoothing effect on the optimization landscape by reducing the effective smoothness constant, thereby improving convergence stability. Experiments on MLP, CNN, and ResNet architectures (up to 270k parameters) demonstrate that CoCD significantly outperforms BCCD in terms of sample efficiency and convergence loss/accuracy, and exhibits superior stability over randomized ZO methods. Our results suggest that deterministic, structure-aware updates offer a superior alternative to randomization for lightweight ZO optimization.
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AnyMo: Geometry-Aware Setup-Agnostic Modeling of Human Motion in the Wild

arXiv:2605.22715v2 Announce Type: replace-cross Abstract: As wearable and mobile devices become increasingly embedded in daily life, they offer a practical way to continuously sense human motion in the wild. But inertial signals are highly dependent on the sensing setup, including body location, mounting position, sensor orientation, device hardware, and sampling protocol. This setup dependence makes it difficult to learn motion representations that transfer across devices and datasets, and limits the broader use of wearable IMUs beyond closed-set recognition. We introduce AnyMo, a geometry-aware framework for setup-agnostic human motion modeling. AnyMo uses physics-grounded IMU simulation over dense body-surface placements to generate diverse and plausible synthetic signals, pre-trains a graph encoder from paired synthetic placement views and masked partial observations, tokenizes multi-position IMU into full-body motion tokens, and aligns these tokens with an LLM for motion-language understanding. We evaluate AnyMo on three complementary tasks: zero-shot activity recognition across 14 unseen downstream datasets, cross-modal retrieval, and wearable IMU motion captioning, where it improves average Accuracy/F1/R@2 by 11.7\%/11.6\%/22.6\% on HAR, increases zero-shot IMU-to-text and text-to-IMU retrieval MRR by 15.9\% and 28.6\%, respectively, and improves zero-shot captioning BERT-F1 by 18.8\%. These results support AnyMo as a generalist model for wearable motion understanding in the wild. Project page: https://baiyuchen.com/project/AnyMo.
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Cuproptosis causes meiotic metaphase I arrest by disrupting mitochondrial functions in oocytes

Cell Death Discovery, Published online: 23 May 2026; doi:10.1038/s41420-026-03168-x

Cuproptosis causes meiotic metaphase I arrest by disrupting mitochondrial functions in oocytes
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High-salt diet in macrophage-associated metabolic disorders: Mechanisms and therapeutic implications

Chin Med J (Engl). 2026 May 19. doi: 10.1097/CM9.0000000000004098. Online ahead of print.

ABSTRACT

High-salt diet (HSD) has emerged as a prevalent environmental factor that exacerbates chronic inflammation and insulin resistance in obesity-associated type 2 diabetes (T2D) by modulating macrophage polarization, metabolic reprogramming, and epigenetic imprinting. Current evidence demonstrates that HSD activates p38/mitogen-activated protein kinase (MAPK), nuclear factor kappa-B (NF-κB), and NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome signaling pathways, by which it drives macrophage polarization toward a proinflammatory M1 phenotype while inducing a glycolysis-dominant metabolic shift, thereby establishing a persistent "metabolic memory". Moreover, HSD orchestrates metabolic memory in macrophages through coordinated epigenetic machinery, including histone modifications (Trimethylation of histone H3 at lysine 4 [H3K4me3] and Acetylation of histone H3 at lysine 27 [H3K27ac]), DNA methylation, and noncoding RNAs (e.g., long non-coding RNA MALAT1 and miR-155), leading to sustained inflammatory phenotypes. In multiple metabolic organs (e.g., adipose tissue, liver, pancreas, and gut), the HSD-macrophage axis aggravates systemic insulin resistance through shared proinflammatory signaling and other tissue-specific mechanisms. Most importantly, therapeutic strategies targeting the NLRP3 inflammasome, metabolic pathways, and epigenetic alterations offer novel approaches for managing metabolic inflammation. Future investigations are encouraged to leverage lineage tracing, single-cell sequencing, and spatial multi-omics technologies to advance the development of precision medicine for macrophage-associated metabolic disorders.

PMID:42156155 | DOI:10.1097/CM9.0000000000004098

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The 2025 lung cancer landscape: advances in screening, molecular taxonomy and therapeutic strategy: a narrative review

Transl Lung Cancer Res. 2026 Mar 23;15(3):62. doi: 10.21037/tlcr-2025-1-1477. Epub 2026 Mar 18.

ABSTRACT

BACKGROUND AND OBJECTIVE: In 2025, lung cancer research advanced rapidly across the disease continuum, from population-level risk assessment and screening to mechanistic studies of early carcinogenesis and therapeutic innovation in perioperative and metastatic settings. A key shift moved beyond a smoking-centred paradigm toward a multidimensional risk framework reflecting the growing burden among never-smokers and the roles of air pollution, occupational exposures, and systemic metabolic-inflammatory states. This narrative review aims to synthesize influential 2025 evidence across prevention, diagnosis, treatment, and survivorship, and to identify convergent themes and translational gaps relevant to clinical practice and policy.

METHODS: We performed a narrative synthesis of influential lung cancer studies published in major international journals in 2025. Evidence was organized along a clinically oriented pathway spanning carcinogenesis and screening, precision diagnosis, treatment optimization in resectable and advanced disease, and survivorship, emphasizing practice-informing trials, high-impact translational research, and implementation-relevant technologies.

KEY CONTENT AND FINDINGS: Lineage tracing, single-cell and spatial omics, and evolutionary inference refined concepts of field cancerization, clonal selection, and copy-number-driven fitness. In small-cell lung cancer, evidence further supported neuronal coupling and synapse-like programs as potentially tractable vulnerabilities. Clinically, low-dose computed tomography (CT) strategies and data-informed nodule thresholds aimed to balance under-detection against over-surveillance harms. In diagnostics, artificial intelligence (AI) models increasingly inferred molecular features from routine histopathology ("virtual molecular testing") and should be regarded as decision support requiring prospective validation, population calibration, and explicit failure-mode reporting. Multimodal approaches integrating imaging with circulating tumor DNA (ctDNA) improved feasibility in tissue-limited settings, but clinical utility remains contingent on assay standardization and pathway-level implementation. In resectable disease, longer follow-up consolidated neoadjuvant chemo-immunotherapy for selected patients, while ctDNA kinetics emerged as a candidate biomarker for response-adaptive escalation and de-escalation. In advanced non-small cell lung cancer (NSCLC), phase III evidence for antibody-drug conjugates and bispecific antibodies began reshaping sequencing, while highlighting challenges in toxicity, access, affordability, and immature overall survival in several programs.

CONCLUSIONS: The 2025 landscape reflects coordinated progress in risk conceptualization, biology, diagnostics, and therapeutics, yet gaps in validation, standardization, and real-world deliverability persist. Priorities include prospective evaluation of AI- and ctDNA-enabled pathways, toxicity-informed sequencing, and equitable implementation aligned with health-system capacity.

PMID:41982682 | PMC:PMC13071762 | DOI:10.21037/tlcr-2025-1-1477

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Integrative fragmentomic and mutational signature profile of plasma cfDNA for early lung cancer detection

NPJ Precis Oncol. 2026 Apr 15. doi: 10.1038/s41698-026-01416-y. Online ahead of print.

ABSTRACT

Detecting lung cancer effectively in the general population is essential for optimizing treatment outcomes and improving the 5-year survival rate. While low-dose computed tomography (LDCT) is the current standard, it has limitations in broader populations. We developed a blood-based multi-omics model using whole-genome cell-free DNA (cfDNA) features to distinguish lung cancer from non-cancer individuals. This study included 1600 patients and an equal number of non-cancer controls, divided into training and validation cohorts. The model achieved an area under the curve (AUC) of 95.59% for the training cohort and 95.74% for the validation cohort. The model consistently performed well across various cancer stages and histological subtypes. To further validate the performance of the model, an external validation cohort was utilized. Notably, it also effectively differentiated non-cancer samples from cancer samples in the external validation cohort, with 85.9% sensitivity and 94.78% specificity. Importantly, in simulated population screenings, our ctDNA assay outperformed both LDCT and a previously established method. This suggests its potential utility in wider lung cancer screening programs, possibly complementing the LDCT approach. In conclusion, our ctDNA assay emerges as a promising and highly sensitive tool for the early detection and categorization of lung cancer.

PMID:41986614 | DOI:10.1038/s41698-026-01416-y

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A Multimodal Foundation Model of Spatial Transcriptomics and Histology for Biological Discovery and Clinical Prediction

arXiv:2604.03630v1 Announce Type: new Abstract: Spatial transcriptomics (ST) enables gene expression mapping within anatomical context but remains costly and low-throughput. Hematoxylin and eosin (H\&E) staining offers rich morphology yet lacks molecular resolution. We present \textbf{\ours} (\textbf{S}patial \textbf{T}ranscriptomics and hist\textbf{O}logy \textbf{R}epresentation \textbf{M}odel), a foundation model trained on 1.2 million spatially resolved transcriptomic profiles with matched histology across 18 organs. Using a hierarchical architecture integrating morphological features, gene expression, and spatial context, STORM bridges imaging and omics through robust molecular--morphological representations. STORM enhances spatial domain discovery, producing biologically coherent tissue maps, and outperforms existing methods in predicting spatial gene expression from H\&E images across 11 tumor types. The model is platform-agnostic, performing consistently across Visium, Xenium, Visium HD, and CosMx. Applied to 23 independent cohorts comprising 7,245 patients, STORM significantly improves immunotherapy response prediction and prognostication over established biomarkers, providing a scalable framework for spatially informed discovery and clinical precision medicine.
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FactReview: Evidence-Grounded Reviews with Literature Positioning and Execution-Based Claim Verification

arXiv:2604.04074v2 Announce Type: new Abstract: Peer review in machine learning is under growing pressure from rising submission volume and limited reviewer time. Most LLM-based reviewing systems read only the manuscript and generate comments from the paper's own narrative. This makes their outputs sensitive to presentation quality and leaves them weak when the evidence needed for review lies in related work or released code. We present FactReview, an evidence-grounded reviewing system that combines claim extraction, literature positioning, and execution-based claim verification. Given a submission, FactReview identifies major claims and reported results, retrieves nearby work to clarify the paper's technical position, and, when code is available, executes the released repository under bounded budgets to test central empirical claims. It then produces a concise review and an evidence report that assigns each major claim one of five labels: Supported, Supported by the paper, Partially supported, In conflict, or Inconclusive. In a case study on CompGCN, FactReview reproduces results that closely match those reported for link prediction and node classification, yet also shows that the paper's broader performance claim across tasks is not fully sustained: on MUTAG graph classification, the reproduced result is 88.4%, whereas the strongest baseline reported in the paper remains 92.6%. The claim is therefore only partially supported. More broadly, this case suggests that AI is most useful in peer review not as a final decision-maker, but as a tool for gathering evidence and helping reviewers produce more evidence-grounded assessments. The code is public at https://github.com/DEFENSE-SEU/Review-Assistant.
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Combee: Scaling Prompt Learning for Self-Improving Language Model Agents

arXiv:2604.04247v1 Announce Type: new Abstract: Recent advances in prompt learning allow large language model agents to acquire task-relevant knowledge from inference-time context without parameter changes. For example, existing methods (like ACE or GEPA) can learn system prompts to improve accuracy based on previous agent runs. However, these methods primarily focus on single-agent or low-parallelism settings. This fundamentally limits their ability to efficiently learn from a large set of collected agentic traces. It would be efficient and beneficial to run prompt learning in parallel to accommodate the growing trend of learning from many agentic traces or parallel agent executions. Yet without a principled strategy for scaling, current methods suffer from quality degradation with high parallelism. To improve both the efficiency and quality of prompt learning, we propose Combee, a novel framework to scale parallel prompt learning for self-improving agents. Combee speeds up learning and enables running many agents in parallel while learning from their aggregate traces without quality degradation. To achieve this, Combee leverages parallel scans and employs an augmented shuffle mechanism; Combee also introduces a dynamic batch size controller to balance quality and delay. Evaluations on AppWorld, Terminal-Bench, Formula, and FiNER demonstrate that Combee achieves up to 17x speedup over previous methods with comparable or better accuracy and equivalent cost.
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ART: Adaptive Relational Transformer for Pedestrian Trajectory Prediction with Temporal-Aware Relations

arXiv:2604.03649v1 Announce Type: cross Abstract: Accurate prediction of real-world pedestrian trajectories is crucial for a wide range of robot-related applications. Recent approaches typically adopt graph-based or transformer-based frameworks to model interactions. Despite their effectiveness, these methods either introduce unnecessary computational overhead or struggle to represent the diverse and time-varying characteristics of human interactions. In this work, we present an Adaptive Relational Transformer (ART), which introduces a Temporal-Aware Relation Graph (TARG) to explicitly capture the evolution of pairwise interactions and an Adaptive Interaction Pruning (AIP) mechanism to reduce redundant computations efficiently. Extensive evaluations on ETH/UCY and NBA benchmarks show that ART delivers state-of-the-art accuracy with high computational efficiency.
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GISTBench: Evaluating LLM User Understanding via Evidence-Based Interest Verification

arXiv:2603.29112v1 Announce Type: new Abstract: We introduce GISTBench, a benchmark for evaluating Large Language Models' (LLMs) ability to understand users from their interaction histories in recommendation systems. Unlike traditional RecSys benchmarks that focus on item prediction accuracy, our benchmark evaluates how well LLMs can extract and verify user interests from engagement data. We propose two novel metric families: Interest Groundedness (IG), decomposed into precision and recall components to separately penalize hallucinated interest categories and reward coverage, and Interest Specificity (IS), which assesses the distinctiveness of verified LLM-predicted user profiles. We release a synthetic dataset constructed on real user interactions on a global short-form video platform. Our dataset contains both implicit and explicit engagement signals and rich textual descriptions. We validate our dataset fidelity against user surveys, and evaluate eight open-weight LLMs spanning 7B to 120B parameters. Our findings reveal performance bottlenecks in current LLMs, particularly their limited ability to accurately count and attribute engagement signals across heterogeneous interaction types.
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Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis

Oncogene, Published online: 01 April 2026; doi:10.1038/s41388-026-03754-4

Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis
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Dual function of DOT1L suppresses tumor cell-intrinsic immunogenicity in hepatocellular carcinoma

Oncogene, Published online: 31 March 2026; doi:10.1038/s41388-026-03744-6

Dual function of DOT1L suppresses tumor cell-intrinsic immunogenicity in hepatocellular carcinoma
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PERMA: Benchmarking Personalized Memory Agents via Event-Driven Preference and Realistic Task Environments

arXiv:2603.23231v1 Announce Type: new Abstract: Empowering large language models with long-term memory is crucial for building agents that adapt to users' evolving needs. However, prior evaluations typically interleave preference-related dialogues with irrelevant conversations, reducing the task to needle-in-a-haystack retrieval while ignoring relationships between events that drive the evolution of user preferences. Such settings overlook a fundamental characteristic of real-world personalization: preferences emerge gradually and accumulate across interactions within noisy contexts. To bridge this gap, we introduce PERMA, a benchmark designed to evaluate persona consistency over time beyond static preference recall. Additionally, we incorporate (1) text variability and (2) linguistic alignment to simulate erratic user inputs and individual idiolects in real-world data. PERMA consists of temporally ordered interaction events spanning multiple sessions and domains, with preference-related queries inserted over time. We design both multiple-choice and interactive tasks to probe the model's understanding of persona along the interaction timeline. Experiments demonstrate that by linking related interactions, advanced memory systems can extract more precise preferences and reduce token consumption, outperforming traditional semantic retrieval of raw dialogues. Nevertheless, they still struggle to maintain a coherent persona across temporal depth and cross-domain interference, highlighting the need for more robust personalized memory management in agents. Our code and data are open-sourced at https://github.com/PolarisLiu1/PERMA.
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FAAR: Format-Aware Adaptive Rounding for NVFP4

arXiv:2603.22370v1 Announce Type: cross Abstract: Deploying large language models (LLMs) on edge devices requires extremely low-bit quantization. Ultra-low precision formats such as NVFP4 offer a promising solution for reducing memory footprint and accelerating computation. However, existing quantization methods typically rely on conventional rounding strategies and fail to account for the non-uniformity of the NVFP4 numerical grid, resulting in suboptimal rounding decisions and amplified quantization errors. To address this, we propose Format-Aware Adaptive Rounding (FAAR), a learnable rounding strategy tailored for the NVFP4 format. Unlike conventional quantization paradigms, FAAR explicitly incorporates the non-uniform NVFP4 grid into the optimization process. By adaptively adjusting rounding decisions guided by loss gradients, our method effectively approximates the theoretically optimal quantization. To complement FAAR, we introduce a 2-stages Format Alignment (2FA) fine-tuning scheme that aligns LLM parameters layer-by-layer to the NVFP4 numerical space, further narrowing the performance gap. Remarkably, this learnable optimization incurs a minimal training overhead of only 4 GPU hours on Llama3-1B. Extensive experiments demonstrate the effectiveness of our approach. Compared with Round-to-Nearest (RTN), our method reduces perplexity on WikiText-2 from 14.28 to 12.60 on Llama3-1B and from 23.06 to 21.27 on Qwen3-1.7B. Additionally, our method consistently outperforms state-of-the-art approaches across various zero-shot downstream tasks.
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MSR-HuBERT: Self-supervised Pre-training for Adaptation to Multiple Sampling Rates

arXiv:2603.23048v1 Announce Type: cross Abstract: Self-supervised learning (SSL) has advanced speech processing. However, existing speech SSL methods typically assume a single sampling rate and struggle with mixed-rate data due to temporal resolution mismatch. To address this limitation, we propose MSRHuBERT, a multi-sampling-rate adaptive pre-training method. Building on HuBERT, we replace its single-rate downsampling CNN with a multi-sampling-rate adaptive downsampling CNN that maps raw waveforms from different sampling rates to a shared temporal resolution without resampling. This design enables unified mixed-rate pre-training and fine-tuning. In experiments spanning 16 to 48 kHz, MSRHuBERT outperforms HuBERT on speech recognition and full-band speech reconstruction, preserving high-frequency detail while modeling low-frequency semantic structure. Moreover, MSRHuBERT retains HuBERT's mask-prediction objective and Transformer encoder, so existing analyses and improvements that were developed for HuBERT can apply directly.
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