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PubMed2026

AI-genomics synergy for drug repurposing in breast cancer: an interpretability-driven framework.

Breast cancer's genomic heterogeneity complicates drug discovery, making repurposing an attractive but challenging strategy. Advances in artificial intelligence now enable integration of multi-omics data to reveal drug-gene-disease relationships and generate subtype-specific repurposing hypotheses. In this Review, we examine AI-driven computational approaches from signature-based to multi-modal frameworks and propose an integrated interpretability-driven framework linking mechanistic validation with clinical translation toward more transparent and actionable precision oncology.

Journal Article↗
PubMed2026

Comparative evaluation of oxidative stress biomarkers F2-isoprostanes and 8-OHdG in Parkinson's disease and Type 2 Diabetes Mellitus: a systematic review and meta-analysis of human studies.

BACKGROUND: Oxidative stress is central to type 2 diabetes mellitus (T2DM) and Parkinson's disease (PD). However, the utility of biomarkers for lipid peroxidation (F2-isoprostanes) and DNA damage (8-OHdG) in the comorbidity of PD and T2DM remains unclear. METHODS: We conducted a systematic review and meta-analysis of 54 unique studies of human subjects aged &#x2265; 50&#x2009;years (n&#x2009;=&#x2009;7,521: 3,522 with T2DM, 722 with PD, and 3,277 controls), measuring biomarkers in serum, plasma, or leukocytes. Mixed-effects models quantified standardized differences (Hedges' g) across subgroups. RESULTS: In T2DM, F2-isoprostanes (g&#x2009;=&#x2009;1.60, 95% CI: 0.95-2.25) and 8-OHdG (g&#x2009;=&#x2009;2.64, 95% CI: 2.13-3.14) were markedly elevated (p&#x2009;<&#x2009;0.001). Stronger effects were observed in younger cohorts and serum/plasma samples, with complications like nephropathy exhibiting extreme oxidative stress (g&#x2009;=&#x2009;5.24). In PD, 8-OHdG was moderately elevated (g&#x2009;=&#x2009;0.78, 95% CI: 0.18-1.39; p&#x2009;=&#x2009;0.011), particularly in randomized controlled trials and plasma samples, whereas F2-isoprostanes were not significantly elevated (g&#x2009;=&#x2009;0.47, 95% CI: -0.43-1.38). High heterogeneity in T2DM (I2 > 90%) reflected methodological variability. CONCLUSION: Distinct profiles - both markers elevated in T2DM but only 8-OHdG in PD - underscore 8-OHdG's potential in PD-T2DM comorbidity. Future research should focus on standardized assays, multi-compartmental or multi-modal sampling, and longitudinal studies to clarify mechanisms and therapeutic targets.

Humans↗
PubMed2026

SIVA: diagonal integration of spatial multi-omics data via spatially informed variational autoencoders and anchor guidance.

MOTIVATION: Understanding cellular states and regulatory programs requires integrative analysis of multiple omics layers. Although recent spatial sequencing technologies allow molecular profiling of cells within their tissue context, paired spatial multi-omics assays are still limited by technical complexity and cost. This creates a pressing need for diagonal integration methods that enable joint analysis of unpaired spatial omics datasets. RESULTS: We propose SIVA, a deep generative framework based on Spatially-Informed Variational Autoencoders with Anchor Guidance, for diagonal integration of spatial multi-modal data. SIVA employs modality-specific variational autoencoders (VAEs) with a hybrid latent embedding that integrates Gaussian process and standard Gaussian priors, enabling joint modeling of spatially structured variation and dominant underlying data distributions across modalities. To facilitate cross-modal alignment in the absence of one-to-one cell correspondence, SIVA adopts a dual integration strategy combining global distribution alignment via Maximum Mean Discrepancy and local correspondence guidance using mutual nearest neighbor anchors. Extensive experiments across multiple cross-slice integration scenarios demonstrate that SIVA achieves robust and accurate integration of unpaired spatial omics datasets, consistently outperforming existing methods. AVAILABILITY AND IMPLEMENTATION: The source codes are available at https://github.com/PelenJiang/SIVA.

Autoencoder↗
PubMed2026

CodonMoE: DNA language models for codon-dependent mRNA prediction.

MOTIVATION: Genomic language models (gLMs) face a fundamental efficiency challenge: one must either maintain separate specialized models for each biological modality (DNA and RNA) or develop large multimodal architectures. Both approaches impose significant computational burdens-modality-specific models require redundant infrastructure despite inherent biological connections, while multi-modal architectures demand increased parameter counts and extensive cross-modality pretraining. RESULTS: To address this limitation, we introduce CodonMoE (Adaptive Mixture of Codon Reformative Experts), a lightweight adapter that transforms DNA language models into effective RNA analyzers without RNA-specific pretraining. Our theoretical analysis establishes CodonMoE as a universal approximator at the codon level, capable of mapping arbitrary functions from codon sequences to codon-dependent RNA properties given sufficient expert capacity. Across four RNA prediction tasks spanning stability, expression, and regulation, DNA models augmented with CodonMoE significantly outperform their unmodified counterparts, with the HyenaDNA+CodonMoE series achieving state-of-the-art results using 80% fewer parameters than specialized RNA models. By maintaining sub-quadratic complexity while achieving superior performance, our approach provides a principled path toward unifying genomic language modeling, leveraging more abundant DNA data and reducing computational overhead while preserving modality-specific performance advantages. AVAILABILITY AND IMPLEMENTATION: Source code for the method and to reproduce the results is available at https://github.com/Kingsford-Group/CodonMoE.

Codon↗
PubMed2026

DIVAS: an R package for identifying shared and individual variations of multiomics data.

MOTIVATION: Multiomics data integration aims to identify biological patterns shared across molecular modalities. Most existing methods detect either jointly shared variation, across all modalities, or individual variation, unique to a single modality, but overlook partially shared variation, shared by only a subset of modalities. This is a critical limitation, because many biological mechanisms manifest in some but not all molecular modalities. RESULTS: We present an open-source R package implementing data integration via analysis of subspaces (DIVAS), a framework for systematically identifying jointly shared, partially shared and individual variations across multiple data types. DIVAS combines angle-based subspace analysis with inference through rotational bootstrap, hierarchically searching all combinations of modalities to decompose multiomics data into interpretable components with scores and loadings. In simulations with a known sharing structure, DIVAS recovered every component across a wide range of noise levels, whereas existing methods did not. Applied to multi-modal COVID-19 data, it reveals partially shared immune and metabolic dysregulation patterns underpinning disease severity that conventional approaches would miss. AVAILABILITY AND IMPLEMENTATION: DIVAS is available at https://github.com/ByronSyun/DIVAS, with documentation and vignettes. The COVID-19 case study vignette is available at https://byronsyun.github.io/DIVAS_COVID19_CaseStudy/.

Multiomics↗
PubMed1992

The anatomy of phonological and semantic processing in normal subjects.

We assessed brain activation of nine normal right-handed volunteers in a positron emission tomography study designed to differentiate the functional anatomy of the two major components of auditory comprehension of language, namely phonological versus lexico-semantic processing. The activation paradigm included three tasks. In the reference task, subjects were asked to detect rising pitch within a series of pure tones. In the phonological task, they had to monitor the sequential phonemic organization of non-words. In the lexico-semantic task, they monitored concrete nouns according to semantic criteria. We found highly significant and different patterns of activation. Phonological processing was associated with activation in the left superior temporal gyrus (mainly Wernicke's area) and, to a lesser extent, in Broca's area and in the right superior temporal regions. Lexico-semantic processing was associated with activity in the left middle and inferior temporal gyri, the left inferior parietal region and the left superior prefrontal region, in addition to the superior temporal regions. A comparison of the pattern of activation obtained with the lexico-semantic task to that obtained with the phonological task was made in order to account for the contribution of lower stage components to semantic processing. No difference in activation was found in Broca's area and superior temporal areas which suggests that these areas are activated by the phonological component of both tasks, but activation was noted in the temporal, parietal and frontal multi-modal association areas. These constitute parts of a large network that represent the specific anatomic substrate of the lexico-semantic processing of language.

Adult↗
PubMed1992

Comparison of selenium and sulfur analogs in cancer prevention.

Several organoselenium compounds have been shown to have powerful anticarcinogenic activity. In view of certain similarities between selenium and sulfur biochemistry, we have evaluated the chemopreventive efficacy of three pairs of analogs using the 7,12-dimethylbenz[a]anthracene (DMBA)-induced mammary tumor model in rats. The compounds tested were selenocystamine/cysteamine, Semethylselenocysteine/S-methylcysteine, selenobetaine/sulfobetaine. In the first study, each agent was added to the basal AIN-76A diet and was given before and continued after DMBA treatment until the end. All three selenium compounds were active; a 50% inhibition was achieved at approximately 25 x 10(-6) mol/kg with Se-methylselenocysteine and selenobetaine and at approximately 40 x 10(-6) mol/kg with selenocystamine. In the sulfur series, only cysteamine and S-methylcysteine produced anticancer activity, and the levels required for comparable responses were 500- to 750-fold higher compared to the corresponding selenium analogs. Sulfobetaine was inactive even when present at near maximally tolerated levels. In the second study, Se-methylselenocysteine and S-methylcysteine were chosen for further examination during the initiation and post-initiation phases of mammary carcinogenesis. Se-Methylselenocysteine was effective when it was given either before or after DMBA administration. In contrast, S-methylcysteine was effective only after DMBA treatment. Thus, compared to the sulfur structural analogs, selenium compounds are much more active in cancer protection and may have a multi-modal mechanism in preventing cellular transformation as well as in delaying or inhibiting the expression of malignancy after carcinogen exposure.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1992

Pediatric genitourinary tumors.

Although genitourinary tumors make up only 10% of childhood cancers, with Wilms' tumor accounting for most, the study of these tumors has yielded a model of cancer development. Tremendous interinstitutional and international cooperation has improved the survival and lowered the morbidity of treatment. Advances in molecular biology and improvement in experimental techniques make this a tremendously exciting field, with discoveries being made almost routinely. Most importantly, however, the study of this group of tumors and the ensuing application of multi-modality therapy has saved the lives of thousands of children.

Adolescent↗
PubMed1992

Interferon-alpha and -gamma in combination with chemotherapeutic drugs: in vitro sensitivity studies in four human mesothelioma cell lines.

Mesothelioma is a tumor of the serous surfaces in the thorax and abdomen. This tumor has proved to be exceptionally resistant to treatment, although a variety of multi-modality therapies have been tried. We have used four human mesothelioma cell lines, originating from diffuse asbestos-related malignant (pleural) mesothelioma, to assess in vitro sensitivity to five chemotherapeutic drugs, to recombinant human interferon (IFN)-alpha and -gamma and to combined immuno-chemotherapy. The cytotoxic effects were assayed by vital dye exclusion. The drugs tested were etoposide, cisplatin, mitoxantrone, 4-epirubicin and vindesine. The combinations tested were etoposide+cisplatin, and etoposide+cisplatin+mitoxantrone. All the drugs and combinations were also tested with recombinant human (rHu) IFN-alpha 2C (rHuIFN-alpha), rHuIFN-gamma, and rHuIFN-alpha+rHuIFN-gamma. The cell lines were most sensitive to mitoxantrone, 4-epirubicin and vindesine (TC50 < or = 0.001 micrograms/ml), and least sensitive to etoposide and cisplatin (TC50 > or = 0.1 micrograms/ml) used singly. There was no improvement in sensitivity when the drugs were combined. To further investigate the lack of response to cisplatin treatment, we examined the binding of cisplatin to the mesothelioma cell DNA. The tumor cell DNA bound markedly less cisplatin than human fetal fibroblast DNA. Three cell lines were tested with rHuIFN-alpha and rHuIFN-gamma on their own or rHuIFN-alpha+rHuIFN-gamma. They were consistently sensitive to rHuIFN-alpha, but the sensitivity to rHuIFN-gamma varied with the cell lines. Finally, we tested two cell lines with the drugs singly and in combination, together with 0.01 micrograms/ml each of rHuIFN-alpha and rHuIFN-gamma.(ABSTRACT TRUNCATED AT 250 WORDS)

Antineoplastic Agents↗
PubMed2024

Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.

Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.

Journal Article↗
PubMed2026

The brain as an HIV reservoir: Recent findings using autopsy tissues from people with HIV.

HIV persistence within anatomical reservoirs remains the primary barrier to achieving an HIV cure. While antiretroviral therapy effectively suppresses plasma viremia, it does not eliminate integrated proviral genomes that persist in long-lived cellular compartments. The central nervous system (CNS) is a clinically important HIV reservoir, characterized by immune privilege and the persistence of tissue-resident infection despite effective antiretroviral therapy (ART). Evidence from postmortem studies reveals that HIV DNA, RNA, and even intact replication-competent proviruses remain detectable in brain tissue from virally suppressed people with HIV. Evidence derived primarily from in situ approaches and viable-cell studies supports myeloid-lineage reservoirs, particularly microglia and CNS-associated macrophages, as key cellular sources of persistence, while the extent and biological relevance of astrocyte infection remains debated. These reservoirs exhibit transcriptional activity and are associated with chronic neuroinflammation, which may contribute to HIV-associated neurocognitive disorders, despite systemic viral suppression. Here, we synthesize recent findings from autopsy brain studies, including work enabled by major biorepositories, such as the National NeuroHIV Tissue Consortium and rapid-autopsy programs, including the Last Gift, both of which are essential for studying HIV reservoirs in the CNS. We summarize methodologies for detecting and characterizing HIV in brain tissue, highlight heterogeneous patterns of regional distribution and compartmentalization, and review emerging links between CNS persistence and neuroinflammation. We conclude with priorities for harmonized tissue processing, multi-modal single-cell and spatial profiling, and coordinated cross-cohort analyses to clarify the contribution of CNS reservoirs to neuroHIV pathogenesis and systemic rebound.

Humans↗
PubMed2024

Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.

Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.

Journal Article↗
PubMed1976

Changes in cell age cohort composition of tumors and normal tissues by radiation and chemotherapy.

The cell cycle is now known to be important in normal and tumor tissue and to be altered by a variety of states and therapies. The fact that there is considerable normal variation in cell ages or age cohorts present in both normal and tumor tissues has only recently been widely appreciated. These differ in normal, malignant, young and adult tissues. They are also greatly perturbed by radiation or chemotherapeutic injury. How to combine multi-modality therapy to optimize tumor control using available agents while sparing normal tissues is a problem for the future of cancer therapy and radiation oncology.

Animals↗
PubMed1975

Philadelphia's community based drug abuse program: broader medical and social concepts.

The rehabilitation of drug dependent people has undergone drastic changes since first attempts were made to curb the abuse of illegal drugs. The isolated law-enforcement model proved to be of no use in this area. So, too, the medical model, the psychological model and the public health model proved disappointingly low in their results. During the last ten years, a so-called "metabolic replacement model" has had its upsurge, creating a controversy still under discussion. The Drug Abuse Rehabilitation Programs of the West Philadelphia Community Mental Health Consortium, Inc. have been in the forefront with its treatment models. Established in 1968 as a purely methadone maintenance program, it has evolved into becoming a model, applying community mental health principles. This paper will explore this model further, describing the mechanics of its changes. From a municipal hospital-based methadone dispensing station, the program has developed into a multi-modality project. Three decentralized drug-free outpatient services are located in the midst of the community where the drug abuse problem is more accute. Outreach is emphasized and case-funding is applied. A possibly unique river-front motel was just acquired for the development of a community-based treatment modality. The 94 rooms were converted into a first-floor alcoholism program which also has a "highway safety program" and an intermediate care facility for alcoholics. The second floor of this facility contains outpatient services for the treatment of drug addicts, including a methadone maintenance program, counselling, family therapy and group therapy. The place where most of the emphasis has been placed is the Work Rehabilitation Center (a novel approach whereby patients will spend up to six hours in "partial hospitalization"). Clients will be tested for vocational aptitude and four workshops will be developed on the premises - carpentry, automotive, electricity and clerical. A huge cafeteria with a semi-automatic kitchen will allow further training in cooking and kitchen aids. The third floor of this renovated motel will include highly sophisticated clinical research area where computer utilization is already giving us very meaningful data. Clinical research is rapidly developing, and new drugs for the rehabilitation of drug addicts will be used. Further comments on the usefulness of methadone as a tool will be included in this paper and general comments as to the outcome of treatment further explored.

Alcoholism↗
PubMed1978

Update of naltrexone treatment.

To summarize, then, our work with naltrexone in a multi-modality treatment program indicates that it appeals to about 5-10 percent of narcotic addicts--those who conciously want to obtain drug-free status. It does significantly attentuate the effect of narcotics to the extent that they lose their reinforcing properties, and it has minimal side effects. Although we treated a self-selected population, it is noteworthy that about 10 percent of those who remained on naltrexone for more than a week were still opiate free 6 months after cessation of treatment. For some it appeared to be a turning point in their lives. It was the first time in years that they could live in their neighborhood and not be either intoxicated or occupied with the pursuit of narcotics. Our behavioral studies have identified a number of conditioned psychophysiological responses associated with the self-injection ritual. So far, although we have succeeded in extinguishing some of these responses, this has not resulted in an improved clinical outcome. We are currently working on more comprehensive behavioral treatments, but the clinical significance of these conditioned responses is uncertain at present.

Adult↗
PubMedDate not supplied

C. parvum clinical protocols: prototypes and summary results in U. S. trials with Wellcome Coparvax.

Clinical investigations utilizing Wellcome C. parvum in cancer therapy number more than one hundred in multiple institutions. Multiple diseases in various stages are being attacked by multi-modality therapy, making the role of immunotherapy very difficult to assess. Fundamental laboratory observations have suggested ways of weaving non-specific with specific immunotherapy, and these with chemotherapy and radiation to yield maximum therapeutic benefit. Current protocols include examples of the critical interactions as well as instructive information on dosing, timing and adjunctive symptomatic therapies. Several protocols will be reviewed, especially where promising clinical results are expected. Important differences between systemic and regional administration are observed.

Clinical Trials as Topic↗
PubMed1979

Influence of varied stimuli on development of motor patterns in the premature infant.

The premature infant is at risk for both mortality and morbidity. His writhing contributes to weight loss, and his extrauterine environment does not contain the multi-modality patterned afferent stimuli that impinge upon the developing brain in utero. Sound is the most effective modality to achieve concurrent decrement in motility along with enhancement of cortical activity. It was anticipated that subjects exposed to 5 minutes of patterned sound 6 times a day would, by 36 weeks gestation, evidence: (a) less gross motor activity, (b) the normal predominance of upper over lower limb activity, and (c) beginning laterality. The sample consisted of 80 males and 73 females whose gestational age at birth was 26--33 weeks. By random assignment 52 subjects were exposed to the routine ambient noise of the isolette and nursery, 50 to a tape recording of their mother's voice, and 51 to an orchestral arrangement of Brahm's Lullaby. Limb activity was measured just prior to discharge by accelerometers worn unilaterally for a 24-hour period on the ankle and wrist prior to transfer to the alternate side for an additional 24 hours. No statistically significant differences were demonstrated among the limb patterns of the 3 groups. Large intragroup variation in gross activity precluded demonstration of between-group differences. The majority of subjects evidenced predominance of upper limb activity and laterality.

Acoustic Stimulation↗