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PubMed2026

A Practical Workflow for Spatial Transcriptomics Data Analysis: From Data Acquisition to Advanced Analyses.

Spatial transcriptomics (ST) profiles genome-wide gene expression while preserving the two-dimensional spatial context of mRNA molecules within tissue sections, enabling studies of tissue architecture and microenvironment-associated biology. However, ST analysis remains challenging because data import, quality control, integration, deconvolution, spatial statistics, and visualization often require multiple software environments and reproducible parameter choices. This protocol presents a practical computational workflow for public ST datasets in R, beginning with data acquisition and software setup and proceeding through Seurat-based data loading, quality control, normalization, multi-sample integration, clustering, and spatially variable gene analysis. The workflow then applies complementary deconvolution strategies, including reference-guided SPOTlight analysis and unsupervised STdeconvolve topic modeling, followed by Giotto-based spatial cell-cell communication analysis and interactive region-of-interest (ROI) selection using a custom Python Dash application. By emphasizing script-based execution, explicit parameter rationales, expected outputs, and troubleshooting checkpoints, the protocol provides an adaptable framework for standard array-based ST datasets and related platforms after dataset- and platform-specific parameter evaluation.

Spatial Transcriptomics↗
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↗
PubMed1980

X-ray microanalysis of colloidal-gold-labelled lysosomes in rat liver sinusoidal cells after incubation for acid phosphatase activity.

The lysosomal apparatus of the Kupffer and endothelial cells of the sinusoidal lining of the rat liver was found to take up colloidal-gold particles with a mean diameter of 5 nm, prepared according to a modified method. After incubation of the glutaraldehyde-perfusion-fixed tissue in a lead-containing medium for the demonstration of acid phosphatase activity, a reaction product was observed in the gold-loaded lysosomes. By X-ray microanalysis of such lysosomes, the presence of osmium, gold and lead was detected qualitatively in the unstained sections from the tissue, which after the incubation had been post-fixed with an OsO4-solution to which K4Fe(CN)6 had been added to enhance the contrast. The quantitative computer-assisted processing of the X-ray microanalytical data from such lysosomes enabled to determine the gold-to-lead ratio and the individual gold and lead peak intensities derived from both the M chi and L chi values in the spectra. On the basis of these results and those obtained similarly in control lysosomes containing either only gold or only lead phosphate precipitate, it was found that only the L chi values were reliable, whereas the M chi values from the same lysosomal spectra were unrealistic, due to deconvolution problems in the computer programs applied. Based upon the L chi values it was found that among the population of lysosomes in single Kupffer cells, studied after a 60-min interval between the injection of the gold colloid and fixation, three types of lysosomal contents could be quantitated by X-ray microanalysis, viz. one type with only gold, one with only lead, one with gold and lead, in various ratios. This quantitative approach might make it possible to detect variations in lysosomal composition associated with ageing.

Acid Phosphatase↗
PubMed2026

Association of MPO Expression with the Immune Microenvironment in Breast Cancer: Insights from Bioinformatics and Single-Cell Analyses.

Breast cancer remains a major cause of cancer-related mortality, and exploratory computational workflows can help prioritize immune-associated markers for further investigation. Here, we used the cancer genome atlas breast invasive carcinoma (TCGA-BRCA) bulk transcriptomic data and the public single-cell dataset GSE161529 to examine associations between myeloperoxidase (MPO) expression, clinical outcomes, immune infiltration, methylation, upstream-regulator annotations, single-cell expression patterns, virtual knockdown sensitivity outputs, drug-gene interaction retrieval, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) annotation. MPO expression was lower in breast cancer tissues than in adjacent non-tumor tissues. Higher MPO expression was associated with a longer progression-free interval, whereas its associations with overall survival and disease-specific survival were not statistically significant. Receiver operating characteristic (ROC) analysis suggested tumor-normal separation within the analyzed public dataset, but this should not be interpreted as clinical diagnostic validation. Immune deconvolution and enrichment analyses indicated that MPO expression mainly tracked with immune- and myeloid-related transcriptional features, rather than establishing tumor-intrinsic regulation of the immune microenvironment. At single-cell resolution, the MPO signal was sparse, with only 85 MPO-positive cells detected before k-nearest neighbor (KNN)-based neighborhood expansion. Detectable MPO signal and MPO-associated scores were interpreted cautiously because they may be influenced by sparse expression, cell-type annotation uncertainty, dropout, doublets, or ambient RNA. In silico virtual knockdown suggested candidate immune- and inflammatory-related transcriptional changes, but these results were considered exploratory and require validation. Drug-gene interaction database (DGIdb)-based drug-gene retrieval and ADMET annotation were used only as preliminary chemical annotations and were not interpreted as therapeutic evidence. Overall, this study provides a reproducible in silico workflow for generating hypotheses about MPO-associated immune/myeloid features in breast cancer, which require external cohort validation and experimental confirmation.

Humans↗
PubMed1981

Material from the internal surface of squid axon exhibits excess noise. Implications in modeling membrane noise.

A fluid material from a squid (Loligo pealei) axon was isolated by mechanical application of two types of microcapillary (1-3-mum Diam) to the internal surface of intact and cut-axon preparations. Current noise in the isolated material exceeded thermal levels and power spectra were 1/f in form in the frequency range 1.25-500 Hz with voltage-dependent intensities that were unrelated to specific ion channels. Whether conduction in this material is a significant source of excess noise during axon conduction remains to be determined. Nevertheless, a source of excess noise external to or within an ion channel may not be properly represented solely as an additive term to the spectrum of ion channel noise; a deconvolution of these spectral components may be required for modeling purposes.

Animals↗
PubMed1989

Regional pulmonary transit times in humans.

We measured the frequency distribution of erythrocyte (RBC) transit times in resected lobes of lungs in eight human subjects undergoing thoracotomy for peripheral lung tumors. RBC transit times were measured by the injection of radiolabeled blood flow and volume markers, which were counted in samples from the resected lung. In five of these subjects, the measurements from the resected lung were compared with preoperative measurements of the transit times of radiolabeled RBCs with a gamma camera-computer system. Time-activity curves from the cardiac chambers and the lung or its regions were obtained from which transit times were calculated by the centroid and deconvolution techniques. The reproducibility of transit times measured by this technique was assessed in another eight normal subjects, after sequential bolus injections of radiolabeled cells. The mean transit time of the upper lung region was longer (5.1 +/- 0.5 s) than that of the lower (4.1 +/- 0.6 s, P less than 0.05) in the preoperative study. Similarly, the mean transit time of the upper lung slice was longer (5.5 +/- 0.3 s) than that of the lower slice (3.8 +/- 0.3 s, P less than 0.05) in the resected lung specimens. We conclude that there was good agreement between these techniques and that there are long transit times in the upper regions of human lungs.

Blood Circulation Time↗
PubMed1995

Amplified nocturnal luteinizing hormone (LH) secretory burst frequency with selective attenuation of pulsatile (but not basal) testosterone secretion in healthy aged men: possible Leydig cell desensitization to endogenous LH signaling--a clinical research center study.

The specific mechanisms underlying the relative hypogonadism of aging remain to be elucidated fully. We used frequent venous sampling (every 2.5 min), sensitive and specific LH and testosterone assays, and deconvolution analysis of the endocrine time series to delineate the differences between healthy young (n = 10, age 21-34 yr) and aged (n = 8, age 62-74 yr) men in the nocturnal secretion of LH and testosterone and their half-lives. We found that elderly men vs. young men had more frequent bursts of LH secretion (1.4 vs. 0.9/h, P = 0.003), less testosterone secreted per testosterone secretory burst (9.2 vs. 17.0 nmol/L, P = 0.021), and less testosterone secreted per hour (10.7 vs. 25.0 nmol/L.h, P = 0.05). As the frequency of nocturnal LH secretory bursts increased, the frequency of testosterone bursts decreased (r = -0.746, P = 0.034). We conclude that healthy aging is associated with diminished nocturnal testosterone production attributable to 1) a decrement in the mass of testosterone released per burst and 2) an inadequate response by the pituitary gland to enhance testosterone production via an accelerated LH secretory pulse frequency. We speculate that this may reflect a partial desensitization of Leydig cells to LH.

Adult↗
PubMedDate not supplied

Three-dimensional chromatin distribution in neuroblastoma nuclei shown by confocal scanning laser microscopy.

The relationship between cell shape and function has long been of interest. However, although the behaviour of the cytoskeleton during the cell cycle has been studied extensively variations in the shape and three-dimensional substructure of the nucleus are less well documented. The spatial distribution of chromatin has previously been studied by a mathematical analysis of the optical densities of stained nuclei, allowing an indirect derivation of the three-dimensional distribution of chromatin. More direct information on chromatin organization can be obtained from electron-microscopic serial sections, although this is very laborious. Using an iterative deconvolution algorithm, Agard and Sedat achieved a degree of optical sectioning in conventional fluorescence microscopy and reconstructed the three-dimensional arrangement of polytene chromosomes. We report here on the three-dimensional structure of cultured mammalian cells as visualized by confocal scanning laser microscopy (CSLM). The exceptionally short depth of field of this imaging technique provides direct optical sectioning which, together with its higher resolution, makes CSLM extremely useful for studying the three-dimensional morphology of biological structures.

Anaphase↗
PubMed1984

A video image correlation technique for the measurement of electrophoretic mobility.

The electrophoretic movement of blood cells has been examined with a video image correlator using the signal from a 625 line monochrome television camera attached to the optical arrangement. The diffraction pattern of a cell produces a characteristic signal which can be detected and registered in any television scan line to form the data of the first image frame. Under the influence of an electric field, cells moved across the television field of view and after a short interval appeared on different scan lines. The detection and registering process was repeated, and a cross-correlation function between the first and second image frame was computed. This function was stored in an output buffer which was continuously updated as fresh functions were integrated with the existing contents. The mean electrophoretic mobility of a suspension of particles can be calculated from the peak position of the integrated correlation function. Using a triangle deconvolution procedure, the relative contributions of subpopulations of lymphocytes prepared from peripheral blood samples were examined.

Blood Cells↗
PubMed1992

Study of the structure of arrestin (S-antigen) from bovine photoreceptors by FTIR spectroscopy.

Fourier transform-infrared spectroscopy has been used for the study of the secondary structure of arrestin from bovine retina rod cells. Spectra have been obtained in H2O and in D2O media. Resolution enhancement of the amide I secondary structure-sensitive overlapped component bands has been achieved by means of Fourier self-deconvolution and Fourier derivation. In order to obtain a quantitative estimation of the proportion of amino acid residues involved in each type of secondary structure, bands at the resolved frequencies have been curve-fitted to the deconvolved amide I contour by means of a least-squares best-fitting iterative program. The analysis of the results suggests that the secondary structure of arrestin comprises 56-63% of extended strands, 12-19% of turns and bends, 15% of alpha-helices and 10% of undefined and irregular segments.

Amides↗
PubMed1990

A review of techniques and results obtained in one laboratory by an integrated system of methods designed for routine clinical flow cytometric DNA analysis.

Establishing flow cytometric DNA analysis as a clinical routine procedure requires adequate and proven guidelines, by which the data can be obtained and interpreted to directly influence management of the individual patient with a specific neoplasm. The present paper is intended as a contribution to such guidelines, of which only fragments are available today. We have previously described a system of methods, designed for routine flow cytometric DNA analysis. In the present status report our experience, based on approximately 18,000 samples (clinical and experimental) is summarised. Sample acquisition with fine-needle aspiration, storage at -80 degrees C, internal standardization by chicken (CRBC) and trout red blood cells (TRBC), staining with propidium iodide (PI), and analysis in the flow cytometer is recapitulated, with emphasis on previously unpublished aspects. The method of statistical analysis which has an integrating role is described in some detail. A lack of linearity between channel number and DNA content was determined experimentally, and the coefficient of variation (CV) was found to decrease with increasing channel number. The corrections in the algorithm of deconvolution made necessary by these findings are fundamental for estimating the end results. The zero point adjustment and procedures for changing from one batch of standards to another are described. A systematic approach to interpretation of DNA histograms is attempted and illustrated by data from clinical specimens of malignant lymphoma, breast cancer, small cell lung cancer, cancer of the oral cavity, and bladder cancer. Some problems are still unsolved and visual inspection is required to determine if the quality of the individual histogram is satisfactory. Inspection of the fluorescence/light scatter dot-plot provides additional information for the recognition of artifacts. The results stress that good quality DNA histograms with as small CVs as possible are important for interpretation of the data. It is essential that statistical methods are employed to extract the key end-point results. These are the number of subpopulations and their relative representation, and for each subpopulation the DNA index (DI) and the fractions of cells in the cell cycle phases. For the DNA data to have any rationally based impact on clinical decision making, it must be demonstrated that they have an independent prognostic value. Strategies for final evaluation are discussed. Multicenter trials on fresh material, to accrue quickly the number of patients necessary for firm conclusions, are suggested.

DNA↗
PubMed1989

Physiological attributes of endogenous bioactive luteinizing hormone secretory bursts in man.

The exact nature of glandular secretory events is difficult to discern in vivo, since underlying patterns of hormone release are confounded by metabolic clearance. Moreover, conventional immunoassay does not always agree with bioassay. Here, we have used the rat interstitial cell testosterone in vitro bioassay of luteinizing hormone (LH) to measure serial LH concentrations in the normal adult human male. The resultant bioactive LH time series were analyzed by a deconvolution model in which circulating hormone concentrations are controlled by the operation of four finite, nonzero, and determinable parameters: 1) the location(s); 2) the amplitude(s), and 3) the half-duration(s) of underlying secretory bursts, acted on by 4) endogenous exponential clearance kinetics. A macroscopic secretory burst was modeled in the algebraic form of a Gaussian distribution of instantaneous molecular secretory rates. The physiological implications of this model were examined by analyzing bioactive LH pulsatility in eight men sampled every 10 min for 6 h. Multiple-parameter deconvolution disclosed endogenous bioactive LH half-lives of 53 +/- 5.4 min (range 38-76 min), in agreement with earlier independent estimates of 65 +/- 4.9 (42-87) min in four LH-deficient men given a 35 micrograms iv bolus of human LH. Calculated endogenous production rates of bioactive LH (0.48 +/- 0.06 mIU.min-1.ml-1) were also in accord with values estimated previously from steady-state infusions of LH. Deconvolution further indicated that underlying bioactive LH secretory bursts had half-durations of only 12.2 +/- 1.5 min, occurred at intervals of 56 +/- 1.3 min, and achieved amplitudes of 2.1 +/- 0.26 mIU.min-1.ml-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2025

Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture.

MOTIVATION: The wide range of cellular complexity created by multicellular organisms is due in large part to the intricate and synergistic interplay of regulatory complexes throughout the eukaryotic genome. These regulatory elements "enhance" specific gene programs and have been shown to operate in diverse networks that are distinct across cell states of the same organism. Attempts to characterize and predict enhancers have typically focused on leveraging information-dense DNA sequence in parallel with epigenomic assays. We examined the viability of enhancer prediction using only a minimal set of epigenomic datasets without direct DNA information. RESULTS: We demonstrate that chromatin datasets are sufficient to identify enhancers genome-wide with high accuracy. By training networks leveraging data from multiple cell types simultaneously, we generated a cell-type invariant enhancer prediction platform that utilized only the patterns of protein binding for inference. We also showed the utility of swarm-based adversarial attacks [adversarial particle swarm optimization (APSO)] to deconvolute trained genomic neural networks for the first time. Critically, unlike saliency mapping or other game-theory based approaches, APSO is completely network-architecture independent and can be applied to any prediction engine to derive the features that drive inference. AVAILABILITY AND IMPLEMENTATION: All software and code for data downloading, processing, enhancer inference, eXplainable AI (XAI), and complete figure generation are publicly available on GitHub at https://github.com/EpiGenomicsCode/ChromEnhancer and Zenodo at https://doi.org/10.5281/zenodo.15652797.

Enhancer Elements, Genetic↗
PubMed2025

Deconvoluting clonal and cellular architecture in IDH-mutant acute myeloid leukemia.

Isocitrate dehydrogenase 1/2 (IDH) mutations are early initiating events in acute myeloid leukemia (AML). The complex clonal architecture and cellular heterogeneity in IDH-mutant AML underlies the heterogeneous clinical presentation and outcomes. Integrating single-cell genotyping and transcriptomics, we demonstrate a stem-like and inflammatory phenotype of IDH-mutant AML and identify clone-specific programs associated with NPM1, NRAS, and SRSF2 co-mutations. Furthermore, these clones had distinct responses to treatment with combination IDH inhibitors and chemotherapy, including elimination, reconstitution of myeloid differentiation, or retention within progenitor populations. At relapse after IDH inhibitor monotherapy, we identify upregulated stemness, inflammation, mitochondrial metabolism, and anti-apoptotic factors, as well as downregulated major histocompatibility complex (MHC) class II antigen presentation. At the pre-leukemic stage, we observe upregulation of IDH2-associated pathways, including inflammation. We deliver a detailed phenotyping of IDH-mutant AML and a framework for dissecting contributions of recurrently mutated genes in AML at diagnosis and following therapy, with implications for precision medicine.

Leukemia, Myeloid, Acute↗
PubMed1990

Estimation of in vivo reticuloendothelial system phagocytic activity in rats by direct blood clearance techniques and nuclear scintigraphy.

There has been considerable interest in the examination of reticuloendothelial system phagocytic blockade. In this study, the kinetics of phospholipid liposome-mediated and intraperitoneal silica-mediated phagocytic blockade were examined using five methods of analysis of in vivo 99mTc-labeled albumin clearance and reticuloendothelial cell uptake. Two direct blood sampling techniques revealed significant impairment in 99mTc-labeled albumin clearance after treatment with silica (P less than 0.05), while liposome treatment was not associated with such impairment. A method utilizing nuclear scintigraphy for the determination of blood clearance was incapable of detecting silica-mediated blockade but demonstrated significant impairment by liposomes at 2 hr (P less than 0.001), 6 hr (P less than 0.05), and 24 hr (P less than 0.001). Gamma camera imaging methods for determination of hepatic uptake demonstrated significant (P less than 0.05) and reversible impairment of 99mTc-labeled albumin uptake by liposomes. The most promising of these techniques utilizes deconvolutional analysis of liver region of interest time-activity curves to correct for continuously changing blood concentrations of tracer and for intracellular tracer processing and catabolism. Measurements of reticuloendothelial system phagocytic activity should include methods that take into account the observed discrepancies between blood clearance determinations and reticuloendothelial cell uptake.

Albumins↗
PubMed1980

Electron probe microanalysis of biological soft tissues: principle and technique.

Electron probe microanalysis is a method based upon X-ray spectrometry used for analyzing the chemical element content of very small amounts of material. The concentration of electrolytes in the microenvironment of cells, in cells, and in intracellular organelles can be measured. The main difficulties in using this method in biological soft tissue lie in sample preparation and in proper interpretation of the data. Best tissue preparation seems to be to quench the sample and to analyze it either freeze dried in thin or ultrathin sections, or frozen hydrated in thin sections or bulk samples. In all cases analysis should be performed using a cold stage and an ultra clean vacuum in order to minimize mass loss due to beam damage and mass gain due to contamination trapping. Interpretation of the data relies upon the knowledge of both the localization of the volume excited by the electron beam and the origin of the continuum and characteristic X-ray signals received by the X-ray spectrometer. This knowledge can be complicated by two facts: 1) when the electron beam is used in an analytical mode, viewing of the analyzed microarea can be lost, and 2) the X-ray signals received by the spectrometer can originate not only from the volume directly excited by the electron beam but from areas that can be far apart, excited by the electron beam tail, scattered electrons or secondary fluorescence, particularly when using energy dispersive spectrometers. Theoretical quantitation of the results is well developed. Practical quantitation could be complicated by the possibility of mass gain, mass loss, standard inhomogeneity, non-uniformity of sample thickness, possibility of shrinkage during freeze drying and, when using energy dispersive spectrometry, by the low signal over background for low atomic number elements (Na), the possibility of overlap of characteristic X-ray lines, and the use of complex and empirical methods for background stripping and peak deconvolution. All these difficulties can be overcome, making electron probe microanalysis one of the most powerful tools available to the biologist.

Animals↗
PubMed1987

Quantitative renal blood flow in urinary tract obstruction.

Technetium-labeled red blood cell scintigraphy using a bolus injection was used to obtain a noninvasive quantitative measurement of renal blood flow. The method used is an adaptation of the one used for calculating cerebral blood flow which involves deconvolution of the first pass of the isotope through the kidneys. The relative renal blood flow of 18 normal patients and 18 patients with unilateral urinary tract obstruction was performed. All patients with obstruction, but one, were reexamined after surgery. There was a significant difference between the normal and partially obstructed patients (p less than 0.001) and between those with partial and complete obstruction (p less than 0.01). After surgery a statistically observable improvement in the relative renal blood flow was obtained.

Adolescent↗