Human Tissue-type Research Articles

Challenges and prospects of cell-free DNA in precision oncology

Cell-free DNA (cfDNA), predominantly derived from apoptotic or necrotic cells, is emerging as a potential biomarker due to non-invasiveness and cost-effectiveness1. Additionally, another type of cfDNA such as cell-free mitochondrial DNA (cf-mtDNA) that is released from cells under stress or damage condition, may play a key role in the immune system. Thus, the presence of cfDNA in the circulation of cancer patients with differential observations between the cancer and the healthy individuals may be used to improve diagnosis by liquid biopsies2. In the past decades, liquid biopsy has been significantly advanced, particularly in detecting cfDNA, which has opened a new research era in cancer diagnostics worldwide. However, there is a big hindrance in integrating cfDNA analysis with clinical diagnosis, For example, a high rate of false positives is caused by insensitive assays, which may be improved by refining the processing of sequencing data. That is due to the technical differences of feature analysis (e.g., fragmentomics and methylation patterns) and their heterogeneity limited the application of cfDNA in the clinics3–5. Currently, there are many efforts on the way to solve the problems. Especially, the top priority is to enhance assay sensitivity and specificity and to adapt analytical techniques in oncology.Nowadays, liquid biopsy technology based on circulating free DNA (cfDNA) brings new hope for future clinical applications such as minimally invasive early screening for tumors, with the key to effectiveness lying in the integration of next-generation sequencing (NGS) with advanced separation technologies. A comparison between the RNA expression datasets and the cfDNA fragment frequencies has revealed distinct genomic characteristics between cancer patients and healthy individuals. Research has found that there are specific fragmentation patterns of cfDNA in the promoter regions of some highly expressed genes6,7. Notably, cfSort is the first supervised tissue deconvolution approach powered by deep learning, leveraging a high-resolution methylation atlas from 521 non-cancer tissue samples across 29 major human tissue types. This model accurately identifies the origin of cfDNA, demonstrating the clinical value of sequencing data in disease diagnosis and treatment monitoring8. In this perspective, we outline the current trend of cfDNA research and highlight its potential limitations in oncology (Fig. 1). It provides valuable insights for cancer diagnosis and management which may help pave the way for the future adoption of cfDNA in oncology.

O-GlcNAcylation of ATP-citrate lyase couples glucose supply to lipogenesis for rapid tumor cell proliferation

Elevated lipid synthesis is one of the best-characterized metabolic alterations in cancer and crucial for membrane expansion. As a key rate-limiting enzyme in de novo fatty acid synthesis, ATP-citrate lyase (ACLY) is frequently up-regulated in tumors and regulated by posttranslational modifications (PTMs). Despite emerging evidence showing O-GlcNAcylation on ACLY, its biological function still remains unknown. Here, we observed a significant upregulation of ACLY O-GlcNAcylation in various types of human tumor cells and tissues and identified S979 as a major O-GlcNAcylation site. Importantly, S979 O-GlcNAcylation is required for substrate CoA binding and crucial for ACLY enzymatic activity. Moreover, it is sensitive to glucose fluctuation and decisive for fatty acid synthesis as well as tumor cell proliferation. In response to EGF stimulation, both S979 O-GlcNAcylation and previously characterized S455 phosphorylation played indispensable role in the regulation of ACLY activity and cell proliferation; however, they functioned independently from each other. In vivo, streptozocin treatment- and EGFR overexpression-induced growth of xenograft tumors was mitigated once S979 was mutated. Collectively, this work helps comprehend how cells interrogate the nutrient enrichment for proliferation and suggests that although mammalian cell proliferation is controlled by mitogen signaling, the ancient nutrition-sensing mechanism is conserved and still efficacious in the cells of multicellular organisms.

A novel homozygous nonsense variant of STX2 underlies non-obstructive azoospermia in a consanguineous Chinese family.

Male infertility is a widespread population health concern, causing various degrees of adverse fertility outcomes. We determined the genetic cause of an infertile male from a consanguineous family, expanding the mutant spectrum of male infertility. A non-obstructive azoospermia (NOA) patient was recruited, and histological type of human testicular tissue of the patient categorized as maturation arrest. We identified a novel loss-of-function variant of syntaxin 2 (STX2) (c.142C>T:p.Gln48*) by performing Whole-exome sequencing (WES) on the NOA patient from a consanguineous Chinese family. Sanger sequencing confirmed the p.Gln48* variant was maternally and paternally inherited. The variant was predicted to be deleterious and resulted in aberrant changes to structure and function of STX2 by In silico analysis. In summary, we reported for the first time that a nonsense variant occurred in the exon region of STX2 in an infertile male presenting with NOA, which was beneficial for diagnosis and therapies of NOA.

Electrical Conductivity Measurement in Human Liver Tissue: Assessment on Normal vs. Tumor Tissue and under In Vivo vs. Ex Vivo Conditions.

This study evaluated electrical conductivity in human liver tissue in the 3-1000 kHz frequency range to compare normal versus tumor tissues under in vivo versus ex vivo conditions. Previous informed consent was obtained from twenty patients undergoing liver resection in whom liver electrical conductivity was measured during surgery and after resection. We found higher electrical conductivity values in tumor tissues than in normal tissue in both in vivo (0.41 ± 0.10 vs. 0.13 ± 0.06 S/m) and ex vivo (0.27 ± 0.09 vs. 0.12 ± 0.07 S/m) conditions (at 3 kHz). The electric properties also showed a promising potential for distinguishing between different tissue types including metastasis, cholangiocarcinoma (CCA), hepatocellular carcinoma (HCC), hepatic cirrhosis, and normal liver (both in vivo and ex vivo). At 3 kHz, in vivo electrical conductivity for cholangiocarcinoma, HCC, and metastasis were 0.35, 0.42 ± 0.13, and 0.41 ± 0.08 S/m, respectively, which differed significantly from each other (p < 0.05). These findings could potentially improve liver disease diagnostics through electrical conductivity measurements and treatment techniques involving electric fields. Future research should focus on expanding the sample size to refine the categorization and comparison processes across diverse human liver tissue types.

DNA methylation correlates of chronological age in diverse human tissue types

BackgroundWhile the association of chronological age with DNA methylation (DNAm) in whole blood has been extensively studied, the tissue-specificity of age-related DNAm changes remains an active area of research. Studies investigating the association of age with DNAm in tissues such as brain, skin, immune cells, fat, and liver have identified tissue-specific and non-specific effects, thus, motivating additional studies of diverse human tissue and cell types.ResultsHere, we performed an epigenome-wide association study, leveraging DNAm data (Illumina EPIC array) from 961 tissue samples representing 9 tissue types (breast, lung, colon, ovary, prostate, skeletal muscle, testis, whole blood, and kidney) from the Genotype-Tissue Expression (GTEx) project. We identified age-associated CpG sites (false discovery rate < 0.05) in 8 tissues (all except skeletal muscle, n = 47). This included 162,002 unique hypermethylated and 90,626 hypomethylated CpG sites across all tissue types, with 130,137 (80%) hypermethylated CpGs and 74,703 (82%) hypomethylated CpG sites observed in a single tissue type. While the majority of age-associated CpG sites appeared tissue-specific, the patterns of enrichment among genomic features, such as chromatin states and CpG islands, were similar across most tissues, suggesting common mechanisms underlying cellular aging. Consistent with previous findings, we observed that hypermethylated CpG sites are enriched in regions with repressed polycomb signatures and CpG islands, while hypomethylated CpG sites preferentially occurred in non-CpG islands and enhancers. To gain insights into the functional effects of age-related DNAm changes, we assessed the correlation between DNAm and local gene expression changes to identify age-related expression quantitative trait methylation (age-eQTMs). We identified several age-eQTMs present in multiple tissue-types, including in the CDKN2A, HENMT1, and VCWE regions.ConclusionOverall, our findings will aid future efforts to develop biomarkers of aging and understand mechanisms of aging in diverse human tissue types.

Detection and quantification of microplastics in various types of human tumor tissues

Microplastics (MPs) have been detected in various human tissues. However, whether MPs can accumulate within tumors and how they affect the tumor immune microenvironment (TIME) and therapeutic responses remains unclear. This study aimed to determine the presence of MPs in tumors and their potential effects on the TIME. Sixty-one tumor samples were collected for analysis. The presence of MPs in tumors was qualitatively and quantitatively assessed using pyrolysis-gas chromatography-mass spectrometry. MPs were detected in 26 of the samples examined. Three types of MPs were identified: polystyrene, polyvinyl chloride, and polyethylene. In lung, gastric, colorectal, and cervical tumors, the MP detection rates were 80 %, 40 %, 50 %, and 17 % (7.1–545.9 ng/g), respectively. MPs were detected in 70 % of pancreatic tumors (18.4–427.1 ng/g) but not detected in esophageal tumors. In pancreatic cancer, the MP-infiltrated TIME exhibited a reduction in CD8+ T, natural killer, and dendritic cell counts, accompanied by substantial neutrophil infiltration. This study illustrates the potential presence of MPs in diverse tumors; varying adhesive affinities were observed among different tumor types. MPs may lead to a more adverse TIME in pancreatic tumors. Further investigations are warranted to assess whether MPs promote tumor progression and affect the efficacy of immunotherapy

Deciphering the fate of granulation tissue in the human inflammatory alveolar microenvironment using single-cell RNA sequencing

Objective: To investigate the cellular composition and heterogeneity of granulation tissue in human alveolar sockets and construct single-cell transcriptomic maps to elucidate the potential outcomes of natural resolution in the inflammatory microenvironment. Methods: Granulation tissues from 12 alveolar sockets undergoing tooth extraction due to periodontitis and scheduled for delayed site preservation or autologous tooth transplantation were collected in the Department of Oral and Maxillofacial Surgery, School of stomatology Fourth Military Medical University from September 2022 to August 2023. This study used HE staining and single-cell RNA sequencing (scRNA-seq) to observe the cellular composition and morphological changes of different types of granulation tissues. This approach enabled us to identify cellular sequence variations in the inflammatory dental alveolar granulation tissue within specific microenvironments, construct single-cell atlases for different types of human dental alveolar granulation tissues, and explore the spatiotemporal patterns of cell type distribution and key gene changes during the resolution process of inflammatory granulation tissue. Results: HE staining revealed extensive infiltration of inflammatory cells in the dental alveolar inflammatory granulation tissue. After allowing the inflammatory granulation tissue to naturally resolve for three weeks, its histological morphology was essentially consistent with that of reparative granulation tissue. ScRNA-seq captured a total of 20 448 cells from granulation tissues, and the gene expression quantification analysis revealed total gene counts of 33 835 for inflammatory granulation tissue, 36 058 for naturally resolved granulation tissue, and 34 719 for reparative granulation tissue. At the single-cell level, granulation tissue was annotated into ten cell subgroups, including vascular endothelial cells, mesenchymal stem cells, and fibroblasts. Differences were observed in the proportion of cell compositions between inflammatory and naturally resolved granulation tissues. Pseudo-temporal analysis illustrated two main outcomes in tissue resolution and healing, involving immune responses and angiogenesis. Among these, genes associated with inflammation regulation and immune response, such as Igbp5, Zfp36, and Hspa1b, as well as genes involved in extracellular matrix secretion and the formation of vessels and fibers such as Timp3, Postn, and Rgs5, showed significant differences in expression between the two types of granulation tissues. Conclusions: Inflammatory granulation tissue exhibits heterogeneity in cell composition, gene expression, and biological functions compared to naturally resolved granulation tissue. When the inflammatory granulation tissue in the alveolar socket is left undisturbed to undergo natural resolution, it displays a cellular composition similar to that of reparative granulation tissue at both the histological and single-cell levels. Moreover, it modulates the inflammatory response and the healing process through immune reactions and tissue remodeling.

Self-supervised learning for characterising histomorphological diversity and spatial RNA expression prediction across 23 human tissue types

As vast histological archives are digitised, there is a pressing need to be able to associate specific tissue substructures and incident pathology to disease outcomes without arduous annotation. Here, we learn self-supervised representations using a Vision Transformer, trained on 1.7 M histology images across 23 healthy tissues in 838 donors from the Genotype Tissue Expression consortium (GTEx). Using these representations, we can automatically segment tissues into their constituent tissue substructures and pathology proportions across thousands of whole slide images, outperforming other self-supervised methods (43% increase in silhouette score). Additionally, we can detect and quantify histological pathologies present, such as arterial calcification (AUROC = 0.93) and identify missing calcification diagnoses. Finally, to link gene expression to tissue morphology, we introduce RNAPath, a set of models trained on 23 tissue types that can predict and spatially localise individual RNA expression levels directly from H&E histology (mean genes significantly regressed = 5156, FDR 1%). We validate RNAPath spatial predictions with matched ground truth immunohistochemistry for several well characterised control genes, recapitulating their known spatial specificity. Together, these results demonstrate how self-supervised machine learning when applied to vast histological archives allows researchers to answer questions about tissue pathology, its spatial organisation and the interplay between morphological tissue variability and gene expression.

Airborne Aluminum as an Underestimated Source of Human Exposure: Quantification of Aluminum in 24 Human Tissue Types Reveals High Aluminum Concentrations in Lung and Hilar Lymph Node Tissues.

Aluminum (Al) is the most abundant metal in the earth's crust, and humans are exposed to Al through sources like food, cosmetics, and medication. So far, no comprehensive data on the Al distribution between and within human tissues were reported. We measured Al concentrations in 24 different tissue types of 8 autopsied patients using ICP-MS/MS (inductively coupled plasma-tandem mass spectrometry) under cleanroom conditions and found surprisingly high concentrations in both the upper and inferior lobes of the lung and hilar lymph nodes. Al/Si ratios in lung and hilar lymph node samples of 12 additional patients were similar to the ratios reported in urban fine dust. Histological analyses using lumogallion staining showed Al in lung erythrocytes and macrophages, indicating the uptake of airborne Al in the bloodstream. Furthermore, Al was continuously found in PM2.5 and PM10 fine dust particles over 7 years in Upper Austria, Austria. According to our findings, air pollution needs to be reconsidered as a major Al source for humans and the environment.

Association Study of Pleural Mesothelioma and Oncogenic Simian Virus 40 in the Crocidolite-Contaminated Area of Dayao County, Yunnan Province, Southwest China.

Background: In Dayao County, Chuxiong Yi Autonomous Prefecture, Yunnan Province, Southwest China, 5% of the surface is scattered with blue asbestos, which has a high incidence of pleural mesothelioma (PMe). Simian virus 40 (SV40) is a small circular double-stranded DNA polyomavirus that can cause malignant transformation of normal cells of various human and animal tissue types and promote tumor growth. In this study, we investigate whether oncogenic SV40 is associated with the occurrence of PMe in the crocidolite-contaminated area of Dayao County, Yunnan Province, Southwest China. Methods: Tumor tissues from 51 patients with PMe (40 of whom had a history of asbestos exposure) and pleural tissues from 12 non-PMe patients (including diseases such as pulmonary maculopathy and pulmonary tuberculosis) were collected. Three pairs of low-contamination risk primers (SVINT, SVfor2, and SVTA1) were used to detect the gene fragment of SV40 large T antigen (T-Ag) by polymerase chain reaction (PCR). The presence of SV40 T-Ag in PMe tumor tissues and PMe cell lines was detected by Western blotting and immunohistochemical staining with SV40-related antibodies (PAb 101 and PAb 416). Results: PCR, Western blotting, and immunohistochemical staining results showed that the Met5A cell line was positive for SV40 and contained the SV40 T-Ag gene and protein. In contrast, the various PMe cell lines NCI-H28, NCI-H2052, and NCI-H2452 were negative for SV40. PCR was negative for all three sets of low-contamination risk primers in 12 non-PMe tissues and 51 PMe tissues. SV40 T-Ag was not detected in 12 non-PMe tissues or 51 PMe tissues by immunohistochemical staining. Conclusion: Our data suggest that the occurrence of PMe in the crocidolite-contaminated area of Yunnan Province may not be related to SV40 infection and that crocidolite exposure may be the main cause of PMe. The Clinical Trial Registration number: 2020-YXLL20.

Abstract 1532: Improved reproducibility in multiplex immunofluorescence analysis of the tumor microenvironment using a novel quenching solution

Abstract Formalin-fixed, paraffin-embedded (FFPE) tissues are commonly used in histopathology because the fixed tissues are stable and easy to store. In the context of immunofluorescence detection, however, endogenous autofluorescence of FFPE tissues can significantly reduce or mask immunofluorescent signals. The autofluorescence of FFPE tissues is caused by a variety of factors, including the presence of endogenous fluorophores, tissue fixation, and processing. While there are several methods that can be used to quench autofluorescence in FFPE tissues, chemical quenchers, which absorb or scatter light, are most frequently used for multiplex IF. Examples of chemical quenchers commonly used in manual multiplex staining include Sudan Black B and TrueBlack; however, these are not chemically compatible for use on automated platforms such as the Leica Biosystems BOND RX. Due to the need for increased throughput and decreased hands-on time, automation has risen in popularity versus manual staining, leading to a need for a versatile quenching solution compatible with automation. Here we demonstrate that NovaPlex Quenching Solution (NPQS), a novel proprietary quenching agent, reduces the background caused by autofluorescence and enhances the signal of the Cell IDx UltraPlex multiplex immunofluorescent (mxIF) assay across tissue types. Qualitative studies showed a decrease in autofluorescent signal in FFPE mouse spleen stained with antibodies against B220/Foxp3/CD3e, suggesting the utility of NPQS in mouse models of cancer and immunity. Similarly, nonspecific background was decreased across FFPE human tissue types, including lung adenocarcinoma stained for CD8/Foxp3/CD3e/CD4 and tonsil stained for CD8/Foxp3/PD-1/CD4. Further statistical studies in FFPE human tonsil tissue stained with CD8/Foxp3/PD-1/CD4 showed there was no significant decrease in dye intensity across all four markers and channels, resulting in a significant increase in signal-to-noise ratio for both CD8 at 490nm and PD-1 at 650nm (p&amp;lt;0.05). These experiments using Cell IDx/LBS UltraPlex mxIF technology demonstrate an effective method to improve the signal-to-noise ratios of fluorophores without reducing signal intensity from any of the target proteins in these parallel multiplex immunofluorescent assays. Citation Format: Matt Levin, Jack Heath, April Schrank-Hacker, Shelby Dunn, Minh-Chau Vu, Imane Hamza, David Schwartz. Improved reproducibility in multiplex immunofluorescence analysis of the tumor microenvironment using a novel quenching solution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1532.

Role of HLA in cardiothoracic transplantation.

In current clinical practice, transplant clinicians create collaborative working relationships with histocompatibility laboratory scientists to identify the risk of long-term graft failure, which may assist in establishing strategies for treatment and surveillance. Transplant immunology research also focuses on optimizing human leukocyte antibody tissue typing and defines the most effective test for detecting the presence of donor-specific antibodies. Although several studies have been conducted, data on pediatric heart transplant recipients are limited. Epitope load information may be utilized to identify donors with permissible human leukocyte antibody mismatches to increase transplant success. Although current guidelines do not consider human leukocyte antibody epitope-based matching tools, these guidelines could be useful for identifying recipients at a high risk of donor-specific antibody production, which would be appropriate for routine donor-specific antibody screening to initiate early interventions to prevent antibody-mediated rejection. Human leukocyte antibody matching at the epitope level offers an effective approach for identifying acceptable mismatches in sensitized patients and provides information about epitope loads. In the future, eplet matching may be used to define the best immunosuppressive therapy protocol for cardiothoracic organ transplantation. This report provides an overview of the role of human leukocyte antibodies in heart and lung transplantation.

Abstract PR06: Uncovering nuclear expulsion: chromatin-bound signals from dying cancer cells accelerate metastatic outgrowth through S100A4-RAGE pathway

Abstract Tumor cells are highly heterogeneous, exhibiting diverse responses when exposed to different environments. We have recently observed this heterogeneity in tumor cell apoptosis by which some tumor cell die for the benefits of the population’s survival. Majority of tumor cells undergo apoptosis in response to immune surveillance, various treatments, and a hostile microenvironment, both in circulation and at metastatic organ sites. However, the full range of apoptotic signals, or "last words," that dying cells communicate to the surviving cancer cell community remains incompletely understood. While apoptotic cell death is often perceived as a favorable therapeutic outcome, tumor cells can exploit it to enhance their metastatic capabilities, leading to poor prognoses in certain cancers. Here, we present a remarkable discovery of an altered apoptotic program in tumor cells characterized by nuclear expulsion and citrullinated chromatin, promoting metastatic outgrowth in the lungs in a Padi4-dependent manner. We further identified a calcium spike during apoptosis as the trigger for Padi4 activation, resulting in rapid chromatin de-condensation, nuclear content expulsion, followed by the generation of nuclear expulsion products (NEPs). This process was observed in various types of human cancer tissues. Profiling of proteins bound to the NEP complex unveiled an enrichment of receptor for advanced glycation end-products (RAGE) pathway proteins, such as S100a4 in mouse NEPs and high-mobility group-binding (HMGB) proteins in human NEPs. These chromatin-bound RAGE ligands activated RAGE receptors in neighboring surviving tumor cells, leading to Erk pathway activation. This, in turn, promotes proliferation through the RAGE-MAPK pathway. A nuclear expulsion signature was associated with worse prognoses in cancer patients, underscoring the clinical efficacy in the context of apoptosis-inducing treatments. As we continue our investigations, we are particularly interested in understanding how dying tumor cell-derived NEPs from chemotherapy may affect therapy outcomes. Taken together, our studies uncover a novel mechanism by which tumor cells come together as a community and that the apoptotic tumor cells help live tumor cells metastasize. This insight is likely a step forward to understand the mechanisms of metastatic spread, treatment resistance and relapse. Citation Format: Wooyong Park, Justin M Gray, Ronald J Holewinski, Thorkell Andresson, Jae Young So, Carmelo M Carmona-Rivera, Mariana J Kaplan, Steven D Cappell, Li Yang. Uncovering nuclear expulsion: chromatin-bound signals from dying cancer cells accelerate metastatic outgrowth through S100A4-RAGE pathway [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr PR06.

A New Method for the Production of High-Concentration Collagen Bioinks with Semiautonomic Preparation.

It is believed that 3D bioprinting will greatly help the field of tissue engineering and regenerative medicine, as live patient cells are incorporated into the material, which directly creates a 3D structure. Thus, this method has potential in many types of human body tissues. Collagen provides an advantage, as it is the most common extracellular matrix present in all kinds of tissues and is, therefore, very natural for cells and the organism. Hydrogels with highly concentrated collagen make it possible to create 3D structures without additional additives to crosslink the polymer, which could negatively affect cell proliferation and viability. This study established a new method for preparing highly concentrated collagen bioinks, which does not negatively affect cell proliferation and viability. The method is based on two successive neutralizations of the prepared hydrogel using the bicarbonate buffering mechanisms of the 2× enhanced culture medium and pH adjustment by adding NaOH. Collagen hydrogel was used in concentrations of 20 and 30 mg/mL dissolved in acetic acid with a concentration of 0.05 and 0.1 wt.%. The bioink preparation process is automated, including colorimetric pH detection and adjustment. The new method was validated using bioprinting and subsequent cultivation of collagen hydrogels with incorporated stromal cells. After 96 h of cultivation, cell proliferation and viability were not statistically significantly reduced.

The Differential Translation Capabilities of the Human DHFR2 Gene Indicates a Developmental and Tissue-Specific Endogenous Protein of Low Abundance

A functional role has been ascribed to the human dihydrofolate reductase 2 (DHFR2) gene based on the enzymatic activity of recombinant versions of the predicted translated protein. However, the invivo function is still unclear. The high amino acid sequence identity (92%) between DHFR2 and its parental homolog, DHFR, makes analysis of the endogenous protein challenging. This paper describes a targeted mass spectrometry proteomics approach in several human cell lines and tissue types to identify DHFR2-specific peptides as evidence of its translation. We show definitive evidence that the DHFR2 activity in the mitochondria is in fact mediated by DHFR, and not DHFR2. Analysis of Ribo-seq data and an experimental assessment of ribosome association using a sucrose cushion showed that the two main Ensembl annotated mRNA isoforms of DHFR2, 201 and 202, are differentially associated with the ribosome. This indicates a functional role at both the RNA and protein level. However, we were unable to detect DHFR2 protein at a detectable level in most cell types examined despite various RNA isoforms of DHFR2 being relatively abundant. We did detect a DHFR2-specific peptide in embryonic heart, indicating that the protein may have a specific role during embryogenesis. We propose that the main functionality of the DHFR2 gene in adult cells is likely to arise at the RNA level.

An N-glycome tissue atlas of 15 human normal and cancer tissue types determined by MALDI-imaging mass spectrometry

N-glycosylation is an abundant post-translational modification of most cell-surface proteins. N-glycans play a crucial role in cellular functions like protein folding, protein localization, cell–cell signaling, and immune detection. As different tissue types display different N-glycan profiles, changes in N-glycan compositions occur in tissue-specific ways with development of disease, like cancer. However, no comparative atlas resource exists for documenting N-glycome alterations across various human tissue types, particularly comparing normal and cancerous tissues. In order to study a broad range of human tissue N-glycomes, N-glycan targeted MALDI imaging mass spectrometry was applied to custom formalin-fixed paraffin-embedded tissue microarrays. These encompassed fifteen human tissue types including bladder, breast, cervix, colon, esophagus, gastric, kidney, liver, lung, pancreas, prostate, sarcoma, skin, thyroid, and uterus. Each array contained both normal and tumor cores from the same pathology block, selected by a pathologist, allowing more in-depth comparisons of the N-glycome differences between tumor and normal and across tissue types. Using established MALDI-IMS workflows and existing N-glycan databases, the N-glycans present in each tissue core were spatially profiled and peak intensity data compiled for comparative analyses. Further structural information was determined for core fucosylation using endoglycosidase F3, and differentiation of sialic acid linkages through stabilization chemistry. Glycan structural differences across the tissue types were compared for oligomannose levels, branching complexity, presence of bisecting N-acetylglucosamine, fucosylation, and sialylation. Collectively, our research identified the N-glycans that were significantly increased and/or decreased in relative abundance in cancer for each tissue type. This study offers valuable information on a wide scale for both normal and cancerous tissues, serving as a reference for future studies and potential diagnostic applications of MALDI-IMS.

Tissue-specific and tissue-agnostic effects of genome sequence variation modulating blood pressure

Genome-wide association studies (GWASs) have identified numerous variants associated with polygenic traits and diseases. However, with few exceptions, a mechanistic understanding of which variants affect which genes in which tissues to modulate trait variation is lacking. Here, we present genomic analyses to explain trait heritability of blood pressure (BP) through the genetics of transcriptional regulation using GWASs, multiomics data from different tissues, and machine learning approaches. Approximately 500,000 predicted regulatory variants across four tissues explain 33.4% of variant heritability: 2.5%, 5.3%, 7.7%, and 11.8% for kidney-, adrenal-, heart-, and artery-specific variants, respectively. Variation in the enhancers involved shows greater tissue specificity than in the genes they regulate, suggesting that gene regulatory networks perturbed by enhancer variants in a tissue relevant to a phenotype are the major source of interindividual variation in BP. Thus, our study provides an approach to scan human tissue and cell types for their physiological contribution to any trait.

Protein PRDM16 and its importance for adipose tissue (literature review)

Currently, in Russia and in the world, there is an increase in the proportion of overweight and obese people among the population, which contributes to an increase in the number of socially significant diseases. Obesity is associated with the predominance of the proportion of fat mass in the component composition of the body. Based on this, increased attention is paid to a comprehensive study of the functioning of all types of human adipose tissue, which is necessary for the further use of this knowledge in the fight against obesity. This article provides an overview of the literature data on the structure and properties of the PRDM16 gene, the features of its functioning in brown, white and beige adipose tissue. The influence of the PRDM16 gene on the activation of brown adipogenesis and the formation of beige adipocytes in white adipose tissue, which contribute to increased heat production of cells by means of non-contractile thermogenesis and improvement of metabolic parameters of the body, is considered. Data on the role of PRDM16 protein in the treatment of obesity, type 2 diabetes mellitus and other human diseases associated with it are analyzed. The results on the methods of effective activation of brown and beige adipocytes and the use of these methods in the treatment of obesity are presented.

Features of damage to the leather substitute when fired from the “FORT 12R” and “AE 790G1” pistols from different distances

Annotation. Examination of damage caused by firearms is always a difficult challenge for a forensic scientist. The reason for this is the unpredictability of the interaction of the trace-receiving surface with the ammunition, additional factors of the shot and residual components of the shot, which in turn is caused by the specific design of different types of firearms and the composition of different types of ammunition, which is also combined with various factors affecting pre-wound ballistics (weather factors, etc.), wound ballistics (different types of human body tissue, different materials of obstacles, their presence, etc.). All these factors require detailed study. The purpose of the study is to compare the features of damage to the leatherette as a complex “clothing + non-biological human body simulator” when shot from different distances using the “Fort 12R” and “AE 790G” pistols. The experimental study was conducted by manufacturing ballistic gelatin blocks, which were covered with leatherette and fired at close range, 25 and 50 cm using “Fort 12R” and “AE 790G1” pistols. The analysis of all fired samples of leatherette revealed the formation of a minus-tissue type defect, with the formation of a round (mostly at close range for both pistols) or oval shape (at 25 and 50 cm for both pistols). Gap formation is characteristic of point-blank shots for both pistols and the Fort 12R at 25 cm. All shot distances and both pistols are characterized by the deposition of residual shot components in the form of half-burnt or unburned powder particles. The dimensions of the defect are approximately the same, but when using Fort 12R, the formation of larger defects was recorded at all shot distances. Thus, during the visual examination, when comparing the samples of leatherette from all the studied distances, significant differences were found between all the studied groups, in particular, between the respective groups of pistols, which makes it possible to identify the pistol already during the visual examination of the sample.

Chemical Epigenetic Regulation of Adeno-Associated Virus Delivered Transgenes.

Adeno-associated virus (AAV) is a powerful gene therapy vector that has been used in several FDA-approved therapies as well as in multiple clinical trials. This vector has high therapeutic versatility with the ability to deliver genetic payloads to a variety of human tissue types, yet there is currently a lack of transgene expression control once the virus is administered. There are also times when transgene expression is too low for the desired therapeutic outcome, necessitating high viral dose administration resulting in possible immunological complications. Herein, we validate a chemically controllable AAV transgene expression technology in vitro that utilizes bifunctional molecules known as chemical epigenetic modifiers (CEMs). These compounds employ endogenous epigenetic machinery to specifically enhance transgene expression of episomal DNA. A recombinant AAV (rAAV) was designed to both deliver the reporter transgene as well as deliver a synthetic zinc finger (ZFs) protein fused to FK506 binding protein (FKBP). These synthetic ZFs target a DNA-binding array sequence upstream of the promoter expressing the AAV transgene to specifically enhance AAV transgene expression in the presence of a CEM. The transcriptional activating compound CEM87 functions by recruiting the epigenetic transcription activator bromodomain-containing protein 4 (BRD4), increasing AAV transgene activity up to fivefold in a dose-dependent manner in HEK293T cells. The highest levels of transgene product activity are seen 24 h following CEM87 treatment. Additionally, the CEM87-mediated enhancement of different transgene products with either Luciferase or green fluorescent protein (GFP) was observed in multiple cell lines and enhancement of transgene expression was capsid serotype independent. The impact of CEM87 activity can be disrupted through drug removal or chemical recruitment site competition with FK506, thus demonstrating the reversibility of the impact of CEM87 on transgene expression. Collectively, this chemically controllable rAAV transgene technology provides temporal gene expression control that could increase the safety and efficiency of AAV-based research and therapies.