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Development of a Serum Proteomic-Based Diagnostic Model for Lung Cancer Using Machine Learning Algorithms and Unveiling the Role of SLC16A4 in Tumor Progression and Immune Response

Biomolecules. 2025 Jul 26;15(8):1081. doi: 10.3390/biom15081081.

ABSTRACT

Early diagnosis of lung cancer is crucial for improving patient prognosis. In this study, we developed a diagnostic model for lung cancer based on serum proteomic data from the GSE168198 dataset using four machine learning algorithms (nnet, glmnet, svm, and XGBoost). The model's performance was validated on datasets that included normal controls, disease controls, and lung cancer data containing both. Furthermore, the model's diagnostic capability was further validated on an independent external dataset. Our analysis identified SLC16A4 as a key protein in the model, which was significantly downregulated in lung cancer serum samples compared to normal controls. The expression of SLC16A4 was closely associated with clinical pathological features such as gender, tumor stage, lymph node metastasis, and smoking history. Functional assays revealed that overexpression of SLC16A4 significantly inhibited lung cancer cell proliferation and induced cellular senescence, suggesting its potential role in lung cancer development. Additionally, correlation analyses showed that SLC16A4 expression was linked to immune cell infiltration and the expression of immune checkpoint genes, indicating its potential involvement in immune escape mechanisms. Based on multi-omics data from the TCGA database, we further discovered that the low expression of SLC16A4 in lung cancer may be regulated by DNA copy number variations and DNA methylation. In conclusion, this study not only established an efficient diagnostic model for lung cancer but also identified SLC16A4 as a promising biomarker with potential applications in early diagnosis and immunotherapy.

PMID:40867526 | PMC:PMC12383841 | DOI:10.3390/biom15081081

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From pilot to scale: Making agentic AI work in health care

Over the past 20 years building advanced AI systems—from academic labs to enterprise deployments—I’ve witnessed AI’s waves of success rise and fall. My journey began during the “AI Winter,” when billions were invested in expert systems that ultimately underdelivered. Flash forward to today: large language models (LLMs) represent a quantum leap forward, but their prompt-based adoption is similarly overhyped, as it’s essentially a rule-based approach disguised in natural language.

At Ensemble, the leading revenue cycle management (RCM) company for hospitals, we focus on overcoming model limitations by investing in what we believe is the next step in AI evolution: grounding LLMs in facts and logic through neuro-symbolic AI. Our in-house AI incubator pairs elite AI researchers with health-care experts to develop agentic systems powered by a neuro-symbolic AI framework. This bridges LLMs’ intuitive power with the precision of symbolic representation and reasoning.

Overcoming LLM limitations

LLMs excel at understanding nuanced context, performing instinctive reasoning, and generating human-like interactions, making them ideal for agentic tools to then interpret intricate data and communicate effectively. Yet in a domain like health care where compliance, accuracy, and adherence to regulatory standards are non-negotiable—and where a wealth of structured resources like taxonomies, rules, and clinical guidelines define the landscape—symbolic AI is indispensable.

By fusing LLMs and reinforcement learning with structured knowledge bases and clinical logic, our hybrid architecture delivers more than just intelligent automation—it minimizes hallucinations, expands reasoning capabilities, and ensures every decision is grounded in established guidelines and enforceable guardrails.

Creating a successful agentic AI strategy

Ensemble’s agentic AI approach includes three core pillars:

1. High-fidelity data sets: By managing revenue operations for hundreds of hospitals nationwide, Ensemble has unparallelled access to one of the most robust administrative datasets in health care. The team has decades of data aggregation, cleansing, and harmonization efforts, providing an exceptional environment to develop advanced applications.

To power our agentic systems, we’ve harmonized more than 2 petabytes of longitudinal claims data, 80,000 denial audit letters, and 80 million annual transactions mapped to industry-leading outcomes. This data fuels our end-to-end intelligence engine, EIQ, providing structured, context-rich data pipelines spanning across the 600-plus steps of revenue operations.

2. Collaborative domain expertise: Partnering with revenue cycle domain experts at each step of innovation, our AI scientists benefit from direct collaboration with in-house RCM experts, clinical ontologists, and clinical data labeling teams. Together, they architect nuanced use cases that account for regulatory constraints, evolving payer-specific logic and the complexity of revenue cycle processes. Embedded end users provide post-deployment feedback for continuous improvement cycles, flagging friction points early and enabling rapid iteration.

This trilateral collaboration—AI scientists, health-care experts, and end users—creates unmatched contextual awareness that escalates to human judgement appropriately, resulting in a system mirroring decision-making of experienced operators, and with the speed, scale, and consistency of AI, all with human oversight.

3. Elite AI scientists drive differentiation: Ensemble’s incubator model for research and development is comprised of AI talent typically only found in big tech. Our scientists hold PhD and MS degrees from top AI/NLP institutions like Columbia University and Carnegie Mellon University, and bring decades of experience from FAANG companies [Facebook/Meta, Amazon, Apple, Netflix, Google/Alphabet] and AI startups. At Ensemble, they’re able to pursue cutting-edge research in areas like LLMs, reinforcement learning, and neuro-symbolic AI within a mission-driven environment.

The also have unparalleled access to vast amounts of private and sensitive health-care data they wouldn’t see at tech giants paired with compute and infrastructure that startups simply can’t afford. This unique environment equips our scientists with everything they need to test novel ideas and push the frontiers of AI research—while driving meaningful, real-world impact in health care and improving lives.

Strategy in action: Health-care use cases in production and pilot

By pairing the brightest AI minds with the most powerful health-care resources, we’re successfully building, deploying, and scaling AI models that are delivering tangible results across hundreds of health systems. Here’s how we put it into action:

Supporting clinical reasoning: Ensemble deployed neuro-symbolic AI with fine-tuned LLMs to support clinical reasoning. Clinical guidelines are rewritten into proprietary symbolic language and reviewed by humans for accuracy. When a hospital is denied payment for appropriate clinical care, an LLM-based system parses the patient record to produce the same symbolic language describing the patient’s clinical journey, which is matched deterministically against the guidelines to find the right justification and the proper evidence from the patient’s record. An LLM then generates a denial appeal letter with clinical justification grounded in evidence. AI-enabled clinical appeal letters have already improved denial overturn rates by 15% or more across Ensemble’s clients.

Building on this success, Ensemble is piloting similar clinical reasoning capabilities for utilization management and clinical documentation improvement, by analyzing real-time records, flagging documentation gaps, and suggesting compliance enhancements to reduce denial or downgrade risks.

Accelerating accurate reimbursement: Ensemble is piloting a multi-agent reasoning model to manage the complex process of collecting accurate reimbursement from health insurers. With this approach, a complex and coordinated system of autonomous agents work together to interpret account details, retrieve required data from various systems, decide account-specific next actions, automate resolution, and escalate complex cases to humans.

This will help reduce payment delays and minimize administrative burden for hospitals and ultimately improve the financial experience for patients.

Improving patient engagement: Ensemble’s conversational AI agents handle inbound patient calls naturally, routing to human operators as required. Operator assistant agents deliver call transcriptions, surface relevant data, suggest next-best actions, and streamline follow-up routines. According to Ensemble client performance metrics, the combination of these AI capabilities has reduced patient call duration by 35%, increasing one-call resolution rates and improving patient satisfaction by 15%.

The AI path forward in health care demands rigor, responsibility, and real-world impact. By grounding LLMs in symbolic logic and pairing AI scientists with domain experts, Ensemble is successfully deploying scalable AI to improve the experience for health-care providers and the people they serve.

This content was produced by Ensemble. It was not written by MIT Technology Review’s editorial staff.

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Global Hypomethylation as Minimal Residual Disease (MRD) Biomarker in Esophageal and Esophagogastric Junction Adenocarcinoma

Cancers (Basel). 2025 Aug 15;17(16):2668. doi: 10.3390/cancers17162668.

ABSTRACT

Background/Objectives: Esophageal and esophagogastric junction adenocarcinoma (EADC-EGJA), which mainly develops from Barrett's esophagus (BE), low-grade dysplasia (LGD), and high-grade dysplasia (HGD), has a poor prognosis and several unmet clinical needs, among which is the detection of minimal residual disease (MRD) after endoscopic/surgical resection. Long interspersed nuclear element-1 (LINE-1), a surrogate marker of global methylation, is considered an emerging biomarker for MRD monitoring. The aim of this study was to determine, by LINE-1 methylation analysis, at which carcinogenesis step global methylation is affected and whether this biomarker could be followed in longitudinal to monitor the disease behavior post-surgery. Methods: Cell-free DNA of 90 patients with non-dysplastic Barrett's esophagus (NDBE), HGD/early EADC-EGJA, or locally advanced/advanced EADC-EGJA were analyzed for LINE-1 methylation, by Methylation-Sensitive Restriction Enzyme droplet digital PCR (MSRE-ddPCR). Twenty-six patients were longitudinally studied by repetitive blood sampling. Results: Global hypomethylation increased during carcinogenesis, with significant difference between locally advanced/advanced EADC-EGJA and NDBE patients (p = 0.028). Longitudinal cases confirmed the rareness of hypomethylation in NDBE cases. The majority of HGD/early EADC-EGJA and locally advanced/advanced EADC-EGJA patients showed methylation changes after resection according to clinical status. Conclusions: This study suggests that global hypomethylation occurs just prior to cancer invasiveness and that it is a promising biomarker to monitor MRD.

PMID:40867295 | PMC:PMC12384112 | DOI:10.3390/cancers17162668

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GeneBits: ultra-sensitive tumour-informed ctDNA monitoring of treatment response and relapse in cancer patients

J Transl Med. 2025 Aug 27;23(1):964. doi: 10.1186/s12967-025-06993-3.

ABSTRACT

BACKGROUND: Circulating tumour DNA (ctDNA) in liquid biopsies has emerged as a powerful biomarker in cancer patients. Its relative abundance in cell-free DNA serves as a proxy for the overall tumour burden. Here we present GeneBits, a method for cancer therapy monitoring and relapse detection. GeneBits employs tumour-informed enrichment panels targeting 20-100 somatic single-nucleotide variants (SNVs) in plasma-derived DNA, combined with ultra-deep sequencing and unique molecular barcoding. In conjunction with the newly developed computational method umiVar, GeneBits enables accurate detection of molecular residual disease and early relapse identification.

RESULTS: To assess the performance of GeneBits and umiVar, we conducted benchmarking experiments using three different commercial cell-free DNA reference standards. These standards were tested with targeted next-generation sequencing (NGS) workflows from both IDT and Twist, allowing us to evaluate the consistency and accuracy of our approach across different oligo-enrichment strategies. GeneBits achieved comparable depth of coverage across all target sites, demonstrating robust performance independent of the enrichment kit used. For duplex reads with ≥ 4x UMI-family size, umiVar achieved exceptionally low error rates, ranging from 7.4×10-7 to 7.5×10-5. Even when including mixed consensus reads (duplex & simplex), error rates remained low, between 6.1×10-6 and 9×10-5. Furthermore, umiVar enabled variant detection at a limit of detection as low as 0.0017%, with no false positive calls in mutation-free reference samples. In a reanalysed melanoma cohort, variant allele frequency kinetics closely mirrored imaging results, confirming the clinical relevance of our method.

CONCLUSION: GeneBits and umiVar enable highly accurate therapy and relapse monitoring in plasma as well as identification of molecular residual disease within four weeks of tumour surgery or biopsy. By leveraging small, tumour-informed sequencing panels, GeneBits provides a targeted, cost-effective, and scalable approach for ctDNA-based cancer monitoring. The benchmarking experiments using multiple commercial cell-free DNA reference standards confirmed the high sensitivity and specificity of GeneBits and umiVar, making them valuable tools for precision oncology. UmiVar is available at https://github.com/imgag/umiVar .

PMID:40866952 | PMC:PMC12382282 | DOI:10.1186/s12967-025-06993-3

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