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PubMed1994

Evaluation of the potential role of class II histocompatibility antigen HLA-DR in platelet/tumor cell interaction.

It has been reported that HLA-DR is a potent inducer of thrombin generation. Human colorectal cells (GEO, WiDr, DLD-1, and MIP) that lack the constitutive expression of HLA-DR cause platelet aggregation through a thrombin-dependent mechanism. Treatment with recombinant human gamma-interferon induced the expression of HLA-DR in the GEO, WiDr, and DLD-1 cells, whereas the MIP cell line remained HLA-DR negative. The concurrent analysis of tumor cell/platelet interaction after gamma-interferon treatment showed a decrease in platelet proaggregating activity of either the responsive GEO (highly expressing HLA-DR) or the unresponsive MIP (HLA-DR negative) cells. Furthermore, the DLD-1 (moderately expressing HLA-DR) cells showed an increase of proaggregating activity after gamma-interferon treatment, whereas WiDr (highly expressing HLA-DR) cells did not modify their activity. These results suggest a lack of a role of HLA-DR in the in vitro platelet proaggregating activity of human colorectal tumor cells.

Antibodies, Monoclonal↗

PubMed1995

Cooperative antiproliferative effects of 8-chloro-cyclic AMP and 528 anti-epidermal growth factor receptor monoclonal antibody on human cancer cells.

8-Chloro-cyclic AMP (8-Cl-cAMP), a site-selective cAMP analogue, is a specific inhibitor of type I cAMP-dependent protein kinase (PKAI) and induces growth inhibition in several human and rodent tumor cell lines. The anti-epidermal growth factor receptor (EGFR) mAb 528 is a blocking antibody able to inhibit the in vitro and in vivo growth of several human cancer cell lines that express functional EGFRs. Since enhanced levels of PKAI are generally found in tumor cells and an increase in PKAI expression is induced by transformation through a transforming growth factor alpha/EGFR autocrine pathway, we have evaluated whether treatment with mAb 528 in combination with 8-Cl-cAMP may have an additive or synergistic growth inhibitory effect on human cancer cells. A dose-dependent inhibition of monolayer cell growth was observed in two human colon cancer cell lines (GEO and CBS) and in a human breast cancer cell line (MDA-468) by treatment with either mAb 528 or 8-Cl-cAMP with 50% inhibitory concentration of 2-10 microgram/ml or 20-25 micrometer, respectively. The combined treatment with low noninhibitory doses of mAb 528 (0.25 microgram/ml) and with 8-Cl-cAMP had a more than additive growth inhibitory effect with a 3- to 5-fold reduction in the 8-Cl-cAMP 50% inhibitory concentration in all cell lines tested. This combined treatment was similarly effective in inhibiting the soft agar cloning efficiency of GEO cells. 8-Cl-cAMP treatment of GEO cells induced a dose-dependent increase in cell membrane-associated EGFRs with a maximum 3- to 4-fold increase within 48-72 h of treatment. These results suggest that a double blockade of the PKAI serine-threonine kinase-dependent and of the EGFR tyrosine kinase-dependent pathways is potentially useful in cancer therapy.

8-Bromo Cyclic Adenosine Monophosphate↗

PubMed2000

A novel MDM2 anti-sense oligonucleotide has anti-tumor activity and potentiates cytotoxic drugs acting by different mechanisms in human colon cancer.

MDM2 is over-expressed in several human tumors. Its product is a negative-feedback regulator of p53, which interferes with the control of cell proliferation and apoptosis, interacting not only with p53 but also with retinoblastoma (Rb) and E2F. Moreover, mutations in the ARF-Ink4a locus may also allow MDM2 to override p53 functions. In this study, we have used a novel oligonucleotide anti-sense MDM2, with mixed-backbone structure and demonstrate that it causes inhibition of MDM2 expression, induction of both p53 and p21/WAF1 expression and a dose-dependent, growth-inhibitory effect in human GEO colon-cancer cells. We also show that anti-sense MDM2 has a co-operative growth-inhibitory effect with different classes of cytotoxic drugs acting by different mechanisms. Moreover, anti-sense MDM2 induces apoptosis and markedly enhances the apoptotic activity of different cytotoxic drugs. Finally, we show that anti-sense MDM2 has anti-tumor activity in vivo in nude mice bearing GEO xenografts and potentiates the anti-tumor effect of cytotoxic drugs. Indeed, despite the short treatment period, the combination of anti-sense MDM2 and cytotoxic drugs causes a marked delay in tumor growth and prolongation of mice survival, lasting several months after treatment cessation. The anti-tumor effect is associated with inhibition of MDM2 expression in tumor specimens of animals treated with anti-sense MDM2, alone or in combination with a cytotoxic drug. Our results provide the rationale for development of a novel mixed-backbone anti-sense MDM2 into a clinical setting in therapeutic combination strategies with conventional cytotoxic drugs.

Animals↗

PubMed2004

Involvement of phosphoinositide 3-kinase signaling pathway in chondrocytic differentiation of ATDC5 cells: application of a gene-trap mutagenesis.

Gene-trap mutagenesis is based on the notion that the random insertion of a trapping vector may disturb the function of inserted genes. Here, we applied this method to murine mesenchymal ATDC5 cells, which differentiate into mature chondrocytes in the presence of insulin. As the trap vector we used pPT1-geo, which lacks its own promoter and enhancer, but contains a lacZ-neo fusion gene as a reporter and selection marker driven by the promoter of the trapped gene. After pPT1-geo was introduced into ATDC5 cells by electroporation, the neomycin-resistant clones were screened for beta-galactosidase activity. The selected clones were cultured in differentiation medium to evaluate the chondrogenic phenotype. The clones no. 6-30 and 6-175, which exhibited impaired and accelerated mineralization, respectively, were subjected to further analysis. In clone no. 6-30 in which the gene coding for the p85alpha subunit of phosphoinositide 3-kinase (PI3K) was trapped, the expression of marker genes of early chondrocytes including collagen type II, aggrecan, and PTH/PTHrP receptor was delayed. The insulin-induced stimulation of growth was reduced in clone no. 6-30 compared with the parental ATDC5 cells. Moreover, treatment of parental ATDC5 cells with a specific inhibitor of PI3K, LY294002, phenocopied clone no. 6-30, suggesting the involvement of PI3K signaling in the chondrogenic differentiation of ATDC5 cells. Clone no. 6-175 with accelerated mineralization was revealed to have a gene homologous to human KIAA0312 trapped, whose function remains unclear. Taken together, the gene-trap in ATDC5 cells might be useful to identify the molecules involved in chondrogenic differentiation.

Animals↗

PubMed2026

Bioinformatics Analysis and Experimental Validation of Key Genes Associated With Hypoxia and Ischemia in Myocardial Infarction.

BACKGROUND: This study aimed to screen and identify core hypoxia-ischemia-related genes associated with myocardial infarction (MI). METHOD: Two transcriptomic datasets, GSE97320 and GSE48060, were retrieved from the Gene Expression Omnibus (GEO) database. After data integration and batch effect elimination, differential expression analysis was performed to screen differentially expressed genes (DEGs), and the corresponding visualization analysis was conducted. Hypoxia-ischemia-related genes were acquired from the GeneCards database; hypoxia-ischemia related genes (HIRGs) were subsequently identified by intersecting the retrieved genes with screened DEGs. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were implemented to explore the biological functions and underlying signaling pathways of HIRGs. A combination of protein-protein interaction (PPI) network analysis and random forest (RF) algorithm was applied to screen hub genes from HIRGs. The external GEO dataset GSE66360 was utilized to validate the expression patterns of candidate hub genes. Furthermore, an acute myocardial infarction (AMI) mouse model was established, and quantitative real-time polymerase chain reaction (qPCR) was performed to detect the mRNA expression levels of hub genes in myocardial tissues for in vivo validation. RESULTS: A total of 633 DEGs and 308 hypoxia-ischemia-related genes were screened in the present study, among which 21 overlapping HIRGs were obtained. PLAUR and IL1B were finally identified as two hub genes from HIRGs based on PPI network and random forest algorithm. The qPCR results revealed that the expression levels of PLAUR and IL1B were significantly upregulated in the AMI group compared with the sham operation group (p < 0.05). CONCLUSION: The present findings demonstrated that PLAUR and IL1B serve as pivotal genes involved in the pathological hypoxia-ischemia process of AMI. These two genes may act as novel biomarkers and promising therapeutic targets for the recognition and clinical intervention of hypoxia-ischemia injury following AMI.

Myocardial Infarction↗

PubMed2007

A gas-inlet system coupled with a Knudsen cell mass spectrometer for high-temperature studies.

A gas-inlet system coupled with a Knudsen effusion mass spectrometer has been developed to study at high temperature the interaction of solids and vapors with reactive permanent gases, such as H(2) and O(2), directly introduced into the cell from external low-pressure reservoirs (pressure range: 10(-4) < p < 1 bar). By selecting the gas flow from the external reservoir the pressures of the gases inside the Knudsen cell can be quantitatively controlled over three orders of magnitude, approximately from 10(-8) to 5.10(-5) bar. Mixtures of two different gases can be introduced into the cell, controlling their partial pressures independently. The capabilities of the device have been tested with four gas-solid systems: PbO(s) + O(2)(g), GeO(2)(s) + O(2)(g), Ga(s) + H(2)(g) and Au(s) + H(2)(g), by studying the relevant high-temperature equilibria. The results obtained for the dissociation energies of the diatomic molecules PbO(g), GeO(g), GaH(g), and AuH(g) compare well with the literature data giving confidence in the reliability and versatility of the method. Preliminary experiments on the in situ formation of H(2)O(g) in the Knudsen cell by the introduction of controlled gaseous H(2)/O(2) mixtures are also presented.

Journal Article↗

PubMed1976

Homeostatic drive counteracting selection for positive and negative phototaxis and geotaxis in Drosophila pseudoobscura.

Tested in Hirsch-Hadler mazes, Drosophila pseudoobscura is on the average geoneutral and photoneutral. Strongly geo- and photopositive and geo- and photonegative populations can be obtained by artificial selection, but upon relaxation of the selection they tend to relapse toward neutrality. This genetic homeostasis is due to natural selection favoring neutrality. Experiments are described in which artificial selection for positivity and for negativity was deliberately made so weak that it only counterbalanced the nautral selection or "homeostatic drive" and the effects of cross-migration. Under these conditions, the behavior of the population artificially selected for positivity diverges only slightly from that of the population selected for negativity, but, at least in females, both populations move closer to neutrality.

Animals↗

PubMed1995

Disruption of the adenosine deaminase (ADA) gene using a dicistronic promoterless construct: production of an ADA-deficient homozygote ES cell line.

In man, deficiency of ADA activity is associated with an autosomal recessive form of severe combined immunodeficiency (SCID), a disease with profound defects both cellular and humoral immunity. Current treatments of ADA deficient patients include bone marrow transplantation, enzyme replacement and somatic gene therapy. The mechanism of the selective immune cell pathogenesis in ADA-SCIDS is, however, still poorly understood. Thus, the generation of an ADA deficient mouse model will be of considerable benefit to understand better the pathophysiology of the disorder and to improve the gene therapy treatments. We have disrupted the adenosine deaminase (ADA) gene in embryonic stem cells using a new efficient promoter trap gene-targeting approach. To this end, a dicistronic targeting construct containing a promoterless IRES beta geo cassette was used. This cassette allows, via the internal ribosomal entry site (IRES), the direct cap-independent translation of the beta geo reporter gene which encodes a protein with both beta-galactosidase and neomycin activities. After indentification of targeted clones by Southern blot, successful inactivation of the ADA gene was first confirmed by producing, from our heterozygote clones, an homozygote cell line. This line shows no ADA activity as judged by zymogram analysis. Second, we have been able to detect in the targeted clones, a specific beta galactosidase activity using a sensitive fluorogenic assay. The targeted ES cell clones are currently being injected into blastocysts to create an ADA deficient mouse model.

Adenosine Deaminase↗

PubMed1995

An insertional mutation in the BTF3 transcription factor gene leads to an early postimplantation lethality in mice.

The gene that encodes the general transcription factor known as BTF3 was disrupted in mouse embryonic stem cells in a random mutagenesis screen for developmental genes with the ROSA beta-geo (Friedrich and Soriano, 1991) retroviral gene trap vector. The BTF3 mutation was transmitted through the germline of chimaeric mice. While the endogenous BTF3 gene is ubiquitously expressed, the expression pattern of the beta-galactosidase reporter gene present in the gene trap vector in BTF3 heterozygotes was restricted. Mice homozygous for the mutant allele died soon after implantation, around embryonic day 6.5. Thus, BTF3 is essential for postimplantation development. The isolation of the BTF3 sequences in this ROSA beta-geo insertion was facilitated by a relatively simple single lacZ primer reverse transcription PCR strategy.

Animals↗

PubMed2006

Data sharing - a case of shared databases and community use of on-line GIS support systems.

Data management is becoming increasingly simple and complex at the same time. The challenge is to effectively use the increasing number of tools available to manage increasing amounts of environmental information for purposes of data capture, analysis, display, sharing and storage. Government is no longer the main collector and provider of data. Community groups possess vast amounts of data collected through daily work of monitoring the environment in their local community. The chief concerns are data access, sharing, integrity and comparability. The capacity of groups to sustain data management is the key to making the sharing possible. The Southeast Environmental Association has been working with Environment Canada to develop a community, on-line database that will be linked to other geo-spatial data sets to allow instant access to geo-referenced data.

Canada↗

PubMed2006

Constructing an Index for the Subjective Well-being Under Neuroleptics scale (SWN), short form: applying structural equation modeling for testing reliability and validity of the index.

Structural equation modeling (SEM) has been widely used in psychology and sociology for testing validity of measurement instruments. However, this statistical technique has so far played minor role in quality-of-life research. The main objective of this paper is to demonstrate the potential of SEM for constructing and testing the validity of a Subjective Well-being under Neuroleptics (SWN) index for patients with schizophrenia. For these purposes, data from the GEO study (Gesundheitsökonomische Evaluation von Olanzapin in Deutschland; Health economics study of olanzapine in the treatment of schizophrenia in Germany) were used. The GEO is a prospective, comparative, noninterventional, observational study. A total of 646 participants treated with either olanzapine (n = 416) or haloperidol (n = 230) were enrolled in the study; 360 patients were available for factor analyses. The short (20-item) form of the SWN scale was administered to assess patients' perspectives on their quality of life. The structural equation models (SEMs) were then applied to construct 5- and 10-item indexes based on SWN. The data indicate that the 5-item index is the most time-saving approach for evaluating perceptions of well-being (and thus, quality of life) among patients with schizophrenia. The application of SEM showed no appreciable loss of validity of this index.

Adult↗

PubMed2026

Integrative pan-cancer analysis of transferrin reveals context-dependent prognostic associations and links to immune and metabolic disease-related programs.

BACKGROUND: Iron metabolism is closely linked to tumor biology, yet the pan-cancer significance of transferrin (TF), the major circulating iron-transport protein, remains insufficiently defined. Although TF has been implicated in cancer-related processes, its prognostic relevance, immune associations, and broader disease-related transcriptional context have not been systematically characterized across tumor types. OBJECTIVE: This study aimed to perform an integrative pan-cancer analysis of TF to characterize its expression patterns, clinical associations, immune context, pathway features, and pharmacogenomic correlations, and to explore whether TF-related signals extend to selected metabolic and chronic organ injury settings. METHODS: We used multiple public databases, including The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA), Gene Expression Omnibus (GEO), and Cancer Cell Line Encyclopedia (CCLE), to integrate transcriptomic, proteomic, and clinical data across 33 tumor types and selected non-malignant conditions. TF expression was evaluated across normal tissues, tumors, and cell lines, followed by survival analysis, immune infiltration analysis, TMB/MSI and methylation assessment, pathway enrichment, and drug-response correlation. Independent GEO cohorts of non-alcoholic steatohepatitis (NASH), heart failure (HF), and liver cirrhosis (LC) were used for cross-disease extension. Selected findings were further explored in OA/PA-treated hepatocytes, 786-O renal carcinoma cells, and AC16 cardiomyocytes. RESULTS: TF showed pronounced tissue specificity and cancer-type-dependent dysregulation. Across pan-cancer cohorts, the most consistent adverse survival associations were observed in kidney renal clear cell carcinoma (KIRC) and stomach adenocarcinoma (STAD), where TF remained associated with overall survival (OS) in multivariable analyses. TF expression was also correlated with cancer-type-specific immune infiltration patterns and selected drug-response profiles. Across independent NASH, HF, and LC datasets, TF expression was elevated and TF-associated pathways partially overlapped with those observed in cancer. In vitro experiments provided preliminary support that TF modulation is associated with proliferative phenotypes in KIRC cells and stress- and metabolism-related phenotypes in hepatocyte and cardiomyocyte models. CONCLUSION: These findings support TF as a context-dependent biomarker candidate in cancer, with the most consistent prognostic relevance observed in KIRC and STAD. Rather than establishing a unified mechanism across diseases, this study provides an integrative framework suggesting that TF is associated with malignant behavior, immune context, and selected metabolic stress-related programs, and warrants further mechanistic investigation.

Iron metabolism↗

PubMed2026

Machine learning-based integration develops a novel lysosome-related prognostic signature associated with prognosis and immune infiltration landscape in acute myeloid leukemia.

BACKGROUND: Lysosomes are essential for intracellular degradation and recycling, and changes in their function significantly contribute to tumor growth. Nonetheless, the exact role of lysosome-related genes (LRGs) in the pathogenesis of acute myeloid leukemia (AML) is still inadequately comprehended. METHODS: Differentially expressed LRGs (DE-LRGs) between AML and control groups were identified using AML-related data extracted from the Gene Expression Omnibus (GEO). The LRGs-related prognostic genes were identified and the risk model was established using univariate COX regression analysis and machine learning algorithms, based on the data obtained from The Cancer Genome Atlas (TCGA). Subsequently, we performed comprehensive analyses regarding clinical features, functional pathways, immune microenvironment, and chemotherapeutic drugs sensitivity between the high- and low-risk groups. Reverse transcription Quantitative polymerase chain reaction (RT-qPCR) and western blot were adopted to validate the expression of prognostic genes in human bone marrow-derived cell line HS-27 A and human AML cell line MOLM-13. RESULTS: Through comprehensive analysis, a risk model was developed utilizing ten LRGs (ATP6V0E2, CALCRL, TMEM165, GZMB, HCK, TCIRG1, CD1D, GPRASP1, ABCA1, and NAGA), and this model was further validated using GEO datasets. Significant differences in clinical characteristics, functional pathways, immune microenvironment characteristics, and chemotherapeutic drug sensitivity were observed between the two risk groups In vitro validation experiment illustrated that the expression trends of ATP6V0E2, TMEM165, and ABCA1 were consistent with our bioinformatics analysis. CONCLUSION: Our study demonstrates that lysosome-associated signature might forecast the prognosis of AML patients and offer guidance for subsequent immunotherapy and chemotherapy strategies.

Acute myeloid leukemia↗

PubMed1983

Gravitational effects on plant growth hormone concentration.

Numerous studies, particularly those of H. Dolk in the 1930's, established by means of bio-assay, that more growth hormone diffused from the lower, than from the upper side of a gravity-stimulated plant shoot. Now, using an isotope dilution assay, with 4,5,6,7 tetradeutero indole-3-acetic acid as internal standard, and selected ion monitoring-gas chromatography-mass spectrometry as the method of determination, we have confirmed Dolk's finding and established that the asymmetrically distributed hormone is, in fact, indole-3-acetic acid (IAA). This is the first physico-chemical demonstration that there is more free IAA on the lower sides of a geo-stimulated plant shoot. We have also shown that free IAA occurs primarily in the conductive vascular tissues of the shoot, whereas IAA esters predominate in the growing cortical cells. Now, using an especially sensitive gas chromatographic isotope dilution assay we have found that the hormone asymmetry also occurs in the non-vascular tissue. Currently, efforts are directed to developing isotope dilution assays, with picogram sensitivity, to determine how this asymmetry of IAA distribution is attained so as to better understand how the plant perceives the geo-stimulus.

Avena↗

PubMed1992

Sensitivity of nuclear c-myc levels and induction to differentiation-inducing agents in human colon tumor cell lines.

Six human colon tumor cell lines were analyzed for their constitutive levels of the c-myc protein. The nuclear proto-oncogene, c-myc, was detected as an expressed product in all of the human colon tumor cell lines analyzed. The poorly differentiated cell lines HCT116, RKO and C showed c-myc levels that averaged 2-fold greater than their well-differentiated counterparts, i.e., GEO, CBS and FET. When c-myc levels and responses to serum induction were analyzed in the presence of inducers of differentiation, i.e., dimethylformamide, retinoic acid, sodium butyrate and TGF-beta, distinct patterns of sensitivity and resistance emerged. Nuclear c-myc levels were reduced in all the colon cell phenotypes treated with dimethylformamide or sodium butyrate. Only the well-differentiated human colon tumor cell lines were responsive to transforming growth factor-beta. Only one of the human colon tumor cell lines (GEO) responded to retinoic acid. Increased levels of c-myc protein were found to correlate well with greater growth rates and with poor differentiation class. Similarly, a parallel sensitivity to down-regulation of c-myc levels and attenuation of c-myc induction curves for inducers of differentiation were observed in growth sensitive human colon tumor cell lines.

Butyrates↗

PubMed2004

Environmental concentrations of boron, LAS, EDTA, NTA and Triclosan simulated with GREAT-ER in the river Itter.

A computer simulation of the environmental concentrations of some typical consumer-product ingredients was performed using the geo-referenced exposure model GREAT-ER (Geo-referenced Regional Environmental Assessment Tool for European Rivers) in the river Itter. Boron and LAS were chosen as typical detergent ingredients along with EDTA, NTA and Triclosan as examples of household and cosmetic product ingredients. The simulations were based on consumption figures of the respective chemical in consumer products in the year 2000. For EDTA, the consumption figure used for the calculation had to be extended to commercial products since the EDTA-use in domestic products could not account for the measured concentrations alone. The resulting PEC (Predicted Environmental Concentration) for all investigated compounds showed very good accordance to the measured concentrations in the Itter which were monitored in the same year. The concentrations did not deviate more than by a factor of 3. GREAT-ER's calculated 90th-percentile was never exceeded by the monitoring result thus reflecting a reasonable accuracy.

Arylsulfonates↗

PubMed2026

Pan-cancer multi-omics machine learning defines a lactylation-associated immune-excluded tumor state with proteomic and experimental corroboration.

BACKGROUND: Histone lactylation links lactate metabolism to chromatin regulation, but whether lactylation-program-associated transcriptional patterns delineate recurrent pan-cancer tumor states remains unclear. METHODS: We integrated mRNA, lncRNA, and miRNA profiles from 9712 TCGA tumors across 33 cancer types with GTEx references, six GEO cohorts, IMvigor210, and an institutional clear-cell renal cell carcinoma (ccRCC) cohort used for exploratory DIA-NN proteomic corroboration. Random-effects co-expression meta-analysis, multi-omics consensus clustering, regulon inference, immune deconvolution, TIDE, oncoPredict, and SHAP-based machine learning were applied. hsa-miR-431-5p was functionally evaluated as a proof-of-concept CS2-associated miRNA in bladder cancer models. RESULTS: LacCoEx-Atlas comprised 398,491 lactylation-related co-expression pairs across 24,667 RNA features under a random-effects framework (median I² = 88.6%). Consensus clustering identified two subtypes: CS2 showed glycolytic-mesenchymal-immune-excluded features, M2 macrophage enrichment, CD8⁺ T-cell depletion, elevated HDAC4/NSD3/KDM6B activity, and worse survival, whereas CS1 showed oxidative, sirtuin-active programs. CS2 had fewer predicted ICI responders (18.3% vs. 52.0%) and a lower observed ORR in IMvigor210 (15.3% vs. 24.0%). oncoPredict identified NU7441 as a hypothesis-generating CS2-associated sensitivity signal (Hedges' g = 1.17). DIA-NN proteomics in 50 ccRCC specimens provided exploratory support for CS2-associated hypoxia, ECM degradation, and metastasis programs. The 10-feature mRNA LARItools model achieved an apparent AUC of 0.9413, while a separate multi-omics model achieved 0.971; neither was independently validated. LARItools reproduced prognostic separation across six GEO cohorts. miR-431-5p promoted malignant phenotypes and EMT in bladder cancer cells, with concordant CMU4h expression findings. CONCLUSIONS: Lactylation-program-associated transcriptional patterns delineate a recurrent immune-excluded pan-cancer tumor state associated with adverse prognosis, reduced predicted immunotherapy responsiveness, exploratory single-cancer protein-level support, and testable DNA damage response-targeting hypotheses. LacCoEx-Atlas and LARItools provide open resources for lactylation-program-associated tumor-state stratification and future translational research.

Humans↗

PubMed2026

Machine learning-enabled multi-omics discovery of prognostic biomarkers and signaling targets in pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) remains difficult to subtype using single omics layers. We conducted an exploratory investigation integrating reverse-phase protein array (RPPA) and DNA methylation data from the cancer genome atlas (TCGA)- pancreatic adenocarcinoma (PAAD) to assess the feasibility of multi-omics subtyping, alongside a supervised machine learning analysis of a small gene expression omnibus (GEO) transcriptomic cohort (n = 26) to identify candidate diagnostic genes. RPPA-based K-means clustering suggested a weak, possible two-subtype structure (silhouette ≈ 0.16) that remained unassociated with overall survival (log-rank p = 0.113) and lacked independent prognostic value. An independently performed similarity network fusion (SNF) analysis integrating RPPA and methylation data showed low concordance with RPPA-derived subtypes (Adjusted Rand Index (ARI) = 0.014), indicating limited convergence between molecular modalities. Supervised machine learning analysis of the GEO cohort using a fully nested leave-one-out cross-validation pipeline achieved a mean (area under the curve) AUC of 0.896 across four classifiers and identified four-fold-stable candidate genes (ESCO2, COL17A1, BCL2L14, and SOWAHB). However, this gene panel demonstrated limited external validity across two independent PDAC cohorts (log-rank p = 0.438 for both GSE62452 and GSE28735), indicating limited generalizability despite robust internal performance. Collectively, these findings provide limited evidence for a robust, prognostically significant multi-omics subtype or a validated diagnostic gene signature; instead, this study serves as a hypothesis-generating resource and highlights the importance of rigorous cross-validation and independent external validation in small-sample transcriptomic biomarker discovery.

Humans↗