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Scalable generation and functional classification of genetic variants in inborn errors of immunity to accelerate clinical diagnosis and treatment

In lieu of traditional genetic variant testing approaches, an approach using scalable variant classification in primary human T cells with a clinically relevant readout can inform rapid diagnosis and treatment of inborn errors of immunity.

STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging

Single-cell transcriptomics analysis and multimodal profiling (STAMP) by imaging enables single-cell analysis of cells in suspension without the need for sequencing. The markedly reduced costs and flexible experimental designs support the profiling of millions of cells or the large-scale multiplexing of conditions, perturbations, and sample types.

Spatial joint profiling of DNA methylome and transcriptome in tissues

Nature, Published online: 03 September 2025; doi:10.1038/s41586-025-09478-x

DNA-methylation and gene-expression profiling of tissue sections at near single-cell resolution can be used to create detailed spatial maps showing how methylation and transcription interact to shape cell identity and tissue development.
  • ✇MIT Technology Review
  • Building the AI-enabled enterprise of the future MIT Technology Review Insights
    Artificial intelligence is fundamentally reshaping how the world operates. With its potential to automate repetitive tasks, analyze vast datasets, and augment human capabilities, the use of AI technologies is already driving changes across industries. In health care and pharmaceuticals, machine learning and AI-powered tools are advancing disease diagnosis, reducing drug discovery timelines by as much as 50%, and heralding a new era of personalized medicine. In supply chain and logistics,
     

Building the AI-enabled enterprise of the future

Artificial intelligence is fundamentally reshaping how the world operates. With its potential to automate repetitive tasks, analyze vast datasets, and augment human capabilities, the use of AI technologies is already driving changes across industries.

In health care and pharmaceuticals, machine learning and AI-powered tools are advancing disease diagnosis, reducing drug discovery timelines by as much as 50%, and heralding a new era of personalized medicine. In supply chain and logistics, AI models can help prevent or mitigate disruptions, allowing businesses to make informed decisions and enhance resilience amid geopolitical uncertainty. Across sectors, AI in research and development cycles may reduce time-to-market by 50% and lower costs in industries like automotive and aerospace by as much as 30%.

“This is one of those inflection points where I don’t think anybody really has a full view of the significance of the change this is going to have on not just companies but society as a whole,” says Patrick Milligan, chief information security officer at Ford, which is making AI an important part of its transformation efforts and expanding its use across company operations.

Given its game-changing potential—and the breakneck speed with which it is evolving—it is perhaps not surprising that companies are feeling the pressure to deploy AI as soon as possible: 98% say they feel an increased sense of urgency in the last year. And 85% believe they have less than 18 months to deploy an AI strategy or they will see negative business effects.

Companies that take a “wait and see” approach will fall behind, says Jeetu Patel, president and chief product officer at Cisco. “If you wait for too long, you risk becoming irrelevant,” he says. “I don’t worry about AI taking my job, but I definitely worry about another person that uses AI better than me or another company that uses AI better taking my job or making my company irrelevant.”

But despite the urgency, just 13% of companies globally say they are ready to leverage AI to its full potential. IT infrastructure is an increasing challenge as workloads grow ever larger. Two-thirds (68%) of organizations say their infrastructure is moderately ready at best to adopt and scale AI technologies.

Essential capabilities include adequate compute power to process complex AI models, optimized network performance across the organization and in data centers, and enhanced cybersecurity capabilities to detect and prevent sophisticated attacks. This must be combined with observability, which ensures the reliable and optimized performance of infrastructure, models, and the overall AI system by providing continuous monitoring and analysis of their behavior. Good quality, well-managed enterprise-wide data is also essential—after all, AI is only as good as the data it draws on. All of this must be supported by AI-focused company culture and talent development.

Download the report.

This content was produced by Insights, the custom content arm of MIT Technology Review. It was not written by MIT Technology Review’s editorial staff. It was researched, designed, and written entirely by human writers, editors, analysts, and illustrators. This includes the writing of surveys and collection of data for surveys. AI tools that may have been used were limited to secondary production processes that passed thorough human review.

  • ✇Omics In Lung
  • Challenges in diagnosis of sarcoidosis Karol Bączek · Wojciech J Piotrowski · Francesco Bonella
    Curr Opin Immunol. 2025 Sep 1;97:102652. doi: 10.1016/j.coi.2025.102652. Online ahead of print.ABSTRACTPURPOSE OF REVIEW: Diagnosing sarcoidosis remains challenging. Histology findings and a variable clinical presentation can mimic other infectious, malignant, and autoimmune diseases. This review synthesizes current evidence on histopathology, sampling techniques, imaging modalities, and biomarkers and explores how emerging 'omics' and artificial intelligence tools may sharpen diagnostic accurac
     

Challenges in diagnosis of sarcoidosis

Curr Opin Immunol. 2025 Sep 1;97:102652. doi: 10.1016/j.coi.2025.102652. Online ahead of print.

ABSTRACT

PURPOSE OF REVIEW: Diagnosing sarcoidosis remains challenging. Histology findings and a variable clinical presentation can mimic other infectious, malignant, and autoimmune diseases. This review synthesizes current evidence on histopathology, sampling techniques, imaging modalities, and biomarkers and explores how emerging 'omics' and artificial intelligence tools may sharpen diagnostic accuracy.

RECENT FINDINGS: Within the typical granulomatous lesions, limited or 'burned-out' necrosis is an ancillary finding, which can be present in up to one-third of sarcoid biopsies, and demands a careful differential diagnostic work-up. Endobronchial ultrasound-guided transbronchial needle aspiration of lymph nodes has replaced mediastinoscopy as first-line sampling tool, while cryobiopsy is still under validation. Volumetric PET metrics such as total lung glycolysis and somatostatin-receptor tracers refine activity assessment; combined FDG PET/MRI improves detection of occult cardiac disease. Advanced bronchoalveolar lavage (BAL) immunophenotyping via flow cytometry and serum, BAL, and genetic biomarkers show to correlate with inflammatory burden but have low diagnostic value. Multi-omics signatures and Positron Emission Tomography with Computer Tomography radiomics, supported by deep-learning algorithms, show promising results for noninvasive diagnostic confirmation, phenotyping, and disease monitoring.

SUMMARY: No single test is conclusive for diagnosing sarcoidosis. An integrated, multidisciplinary strategy is needed. Large, multicenter, and multiethnic studies are essential to translate and validate data from emerging AI tools and -omics research into clinical routine.

PMID:40902264 | DOI:10.1016/j.coi.2025.102652

Enabling Digital Compassion in Digital Health Environments: Modified eDelphi Study to Identify Interprofessional Competencies and Technology Attributes

Background: Health care continues to advance through digital innovation, and technology-enabled processes and interventions are increasingly being introduced to deliver and expand access to care. In this evolving digital health ecosystem, health care professionals (HCPs), learners, and organizations may not be prepared or equipped with the knowledge, skills, and behaviors required to navigate these new digital tools while simultaneously sustaining and integrating compassionate care. Moreover, the tools may not be designed and implemented in a manner that facilitates digital compassion. Objective: This study aimed to identify (1) core digital compassion competencies for health professionals and (2) digital compassion health IT attributes. Methods: We conducted this study based on the Delphi method, a consensus-building technique using structured group communication that allows a group of experts to identify competencies and agree on items such as standards and attributes by achieving consensus on a given topic. To encourage enriched discussions, we used a modified eDelphi method, where the first round consisted of a group activity and focus group rather than a questionnaire. Due to COVID-19 pandemic restrictions, the first round was held online. Subsequent rounds consisted of questionnaires administered via email and a web-based survey. Using purposive sampling, participants were recruited from project partners and networks of the research team. A panel of experts across Canada in the fields of compassion, health professional or medical education, and technology was engaged to identify and prioritize professional domains and competency statements, as well as essential attributes for the development and deployment of digital technologies for compassionate care. Results: A total of 54 experts across Canada were recruited, representing diverse professions including patients or service users, HCPs, administrators, policy makers, health educators, data scientists, health technology designers, and software engineers. Overall, 9 focus groups were conducted and analyzed thematically. Seven domains of digital compassion were identified: (1) digital literacy, (2) patient preference, (3) collaboration and co-design, (4) therapeutic relationship, (5) ethical implications, (6) patient safety, and (7) technology safety. Technology attributes to facilitate digital compassion were also generated. We reached consensus after several subsequent rounds, resulting in 58 digital compassion competency statements and 15 technology attributes. Conclusions: This study identified a digital compassion framework consisting of competencies for HCPs and attributes for digital technologies that would enhance compassion in virtual care encounters. To promote a cultural shift where technologies are perceived to be not only efficient but also compassionate, practices of co-design, training, and ongoing evaluation and iteration must be prioritized within health care organizations. Future research should explore the adaptability of the professional competencies and technology attributes to specific medical specialties or in patient populations.

Evolving Medical Students’ Digital Health Perceptions and Intentions: Insights From a Prepandemic and Postpandemic Survey Study

Background: The COVID-19 pandemic has underscored the importance of digital health (dHealth) technologies in medical practice. Despite this, medical curricula often provide limited exposure to these technologies. Objective: This study investigates the effects of the COVID-19 pandemic on medical students’ intentions to integrate dHealth technologies into their future practice. Methods: We employed a two-phase survey at the University of Montreal’s medical school to assess changes in perceptions before (N=184) and after (N=138) the pandemic. The survey used component-based structural equation modeling (SEM) and qualitative comparative analysis (QCA) to analyze our dataset. Results: Findings indicate limited exposure to dHealth technologies within the medical curriculum. However, there was a strong consensus on the necessity of formal dHealth training. A notable shift towards the acceptance of artificial intelligence (AI) and telehealth tools was observed, emphasizing the pandemic’s significant role in altering students' views on these technologies. Conclusions: The study advocates for the integration of formal dHealth training in medical curricula to better prepare future physicians for the demands of an increasingly digital healthcare landscape. The COVID-19 pandemic has significantly influenced medical students' perceptions, highlighting the urgent need to adapt medical education to include comprehensive dHealth training.

Protein lipoylation in cancer: metabolic reprogramming and therapeutic potential

Cell Death Discovery, Published online: 02 September 2025; doi:10.1038/s41420-025-02718-z

Protein lipoylation in cancer: metabolic reprogramming and therapeutic potential

Longitudinal liquid biopsy identifies an early predictive biomarker of immune checkpoint blockade response in head and neck squamous cell carcinoma

Nat Commun. 2025 Sep 1;16(1):8161. doi: 10.1038/s41467-025-63538-4.

ABSTRACT

Immune checkpoint blockade (ICB) has improved outcomes for patients with head and neck squamous cell carcinoma (HNSCC), but predictive biomarkers remain limited. Here, we use a time-resolved, multi-omic approach in a murine HNSCC model to characterize peripheral immune responses to ICB. Single-cell transcriptomics and T/B cell receptor analyses reveal early on-treatment expansion of effector memory T and B cell repertoires in responders, preceding tumor regression. These dynamic immune features inform a composite transcriptional signature that accurately predicts ICB response in independent human HNSCC cohorts. LiBIO outperforms existing biomarkers and generalizes to melanoma, non-small cell lung cancer, and breast cancer without retraining. These findings suggest that early treatment-induced changes in circulating immune repertoires reflect the host's capacity to mount an effective antitumor response. This work provides a framework for leveraging transient peripheral immune dynamics to develop non-invasive, high-fidelity biomarkers for response to immunotherapy across cancer types.

PMID:40890155 | PMC:PMC12402333 | DOI:10.1038/s41467-025-63538-4

Token Probabilities to Mitigate Large Language Models Overconfidence in Answering Medical Questions: Quantitative Study

Background: Chatbots have demonstrated promising capabilities in Medicine, scoring passing grades for board examinations across various specialties. However, their tendency to express high levels of confidence in their responses, even when incorrect, poses a limitation to their utility in clinical settings. Objective: To examine whether token probabilities outperform chatbots' Expressed Confidence levels in predict-ing the accuracy of their responses to medical questions. Methods: Seven large languages models (LLMs), comprising both commercial (GPT-3.5, GPT-4 and GPT-4o) and open-source (Llama 3-8b, Llama 3-70b, Phi-3-Mini, and Phi-3-Medium), were prompted to respond to a set of 2,522 questions from the US Medical Licensing Examination (MedQA database). Addition-ally, the models rated their confidence from 0 to 100 and the token probability of each response was extracted. The models’ success rates were measured, and the predictive performances of both Ex-pressed Confidence and Response Token Probability in predicting response accuracy were evaluated using Area Under the Receiver Operating Characteristic Curve (AUROC), Adapted Calibration Error (ACE) and Brier score. Sensitivity analyses were conducted using additional questions sourced from other databases in English (MedMCQA, n=2,797), Chinese (MedQA Main-land China, n=3,413 and Taiwan, n=2,808), and French (FrMedMCQA, n=1,079). Results: Overall, mean accuracy ranged from 52.7%[50.8-54.7] for Phi-3-Mini to 87.6%[86.2-88.9] for GPT-4o. Across the US Medical Licensing Examination questions, all chatbots consistently expressed high levels of confidence in their responses (ranging from 90[90-90] for Llama 3-70B to 100[100–100] for GPT-3.5). However, Expressed Confidence failed to predict response accuracy (AUROC ranging from 0.52[0.50-0.53] for Phi 3 Mini to 0.68[0.65-0.71] for GPT-4o). In contrast, the Response Token Probability consistently outperformed Expressed Confidence for predicting response accuracy (AU-ROC ranging from 0.67[0.65-0.69] for Phi-3-Mini to 0.83[0.81-0.85] for Llama 3-70B, all p-values

Integration of Environmental Data Into Electronic Health Records for Clinical and Public Health Decision Making: A Viewpoint on Expanding Development in the United States

Electronic health records are often extracted and combined with environmental data to conduct research or public health surveillance. However, to date, electronic health record systems do not integrate environmental data to aid real-time decisions that could mitigate the health impacts of environmental hazards, including the impacts of climate change. Pursuing this goal requires the enhancement of health record systems and the modification of financial incentives driving healthcare innovation and delivery.

An eyecare foundation model for clinical assistance: a randomized controlled trial

Nature Medicine, Published online: 28 August 2025; doi:10.1038/s41591-025-03900-7

Trained and validated on multimodal data from 14.5 million images from multicountry datasets, a foundation model is shown to increase diagnostic and referral accuracy of clinicians when used as an assistant in a trial involving 16 ophthalmologists and 668 patients.

Multiomics Insights into the Mechanism and Enhanced Efficacy of Tumor Treating Fields (TTFields) Therapy in Glioblastoma

J Proteome Res. 2025 Sep 1. doi: 10.1021/acs.jproteome.5c00424. Online ahead of print.

ABSTRACT

Glioma is an aggressive brain tumor that requires challenging treatments. Tumor Treating Fields (TTFields), an FDA-approved therapy for glioblastoma (GBM), pleural mesothelioma, and platinum-refractory metastatic nonsmall cell lung cancer (in combination with PD-1/PD-L1 inhibitors or docetaxel), employs specific frequency electric fields to disrupt cell division and enhance treatment efficacy. However, their molecular mechanisms remain unclear. This study aimed to elucidate these mechanisms and optimize the therapeutic potential of TTFields through quantitative proteomics, phosphoproteomics, and glycoproteomics. Pathway analysis of the proteomics revealed that TTFields impact the cell cycle, DNA repair, autophagy, and DNA replication. Phosphoproteomic studies further demonstrated a marked decline in the activity of key kinases ABL1 and PDK1, while glycoproteomics highlighted disruptions in cell adhesion and ECM-receptor interactions. Notably, proteomic analysis identified an upregulation of PARP1 and BRD4 protein levels, suggesting a previously unrecognized resistance mechanism. Consistently, combining TTFields with inhibitors targeting these proteins significantly enhanced the treatment efficacy in U87 cells. Thus, this study uncovers comprehensive molecular mechanisms underlying TTFields' effects on GBM cells and supports the development of concomitant therapies to enhance treatment efficacy.

PMID:40889189 | DOI:10.1021/acs.jproteome.5c00424

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