Human Specimens Research Articles

Development and Evaluation of a Data Quality Management System for the Korea Biobank Network.

As the reliance on clinical epidemiological information from human specimens grows, so does the need for effective clinical information management systems, particularly for biobanks. Our study focuses on enhancing the Korea Biobank Network's (KBN) system with data quality verification features. By comparing the quality of data collected before and after these enhancements, we observed a notable improvement in data accuracy, with the error rate decreasing from 0.1198% to 0.0492%. This advancement underscores the importance of robust data quality management in supporting high-quality clinical research and sets a precedent for the development of clinical information management systems.

Mutant IDH Modulates Suppressive Myeloid Populations in Malignant Glioma.

Mutations in the isocitrate dehydrogenase (IDH) genes IDH1 and IDH2 have critical diagnostic and prognostic significance in diffuse gliomas. Neomorphic mutant IDH activity has been previously implicated in T-cell suppression; however, the effects of IDH mutations on intratumoral myeloid populations remain underexplored. In this study, we investigate the influence of IDH status on the myeloid compartment using human glioma specimens and preclinical models. We performed RNA sequencing and quantitative immunofluorescence on newly diagnosed, treatment-naive IDH-mutant grade 4 astrocytoma and IDH-wild-type (IDH-WT) glioblastoma (GBM) specimens. We also generated a syngeneic murine model, comparing transcriptomic and cell-level changes in paired isogenic glioma lines that differ only in IDH mutational status. Among patient samples, IDH-mutant tumors displayed an underrepresentation of suppressive myeloid transcriptional signatures, which was confirmed at the cellular level with decreased numbers of intratumoral M2-like macrophages and myeloid-derived suppressor cells. Introduction of the mutant IDH enzyme into murine glioma was sufficient to recapitulate the transcriptomic and cellular shifts observed in patient samples. We provide transcriptomic and cellular evidence that mutant IDH is associated with a quantitative reduction of suppressive myeloid cells in gliomas and that introduction of the mutant enzyme is sufficient to result in corresponding cellular changes using an in vivo preclinical model. These data advance our understanding of high-grade gliomas by identifying key myeloid cell populations that are reprogrammed by mutant IDH and may be targetable through therapeutic approaches.

ClearScope: a fully integrated light sheet theta microscope for sub-cellular resolution imaging without lateral size constraints.

Three-dimensional (3D) ex vivo imaging of cleared intact brains of animal models and large human and non-human primate postmortem brain specimens is important for understanding the physiological neural network connectivity patterns and the pathological alterations underlying neuropsychiatric and neurological disorders. Light-sheet microscopy has emerged as a highly effective imaging modality for rapid high-resolution imaging of large cleared samples. However, the orthogonal arrangements of illumination and detection optics in light sheet microscopy limits the size of specimen that can be imaged. Recently developed light sheet theta microscopy (LSTM) technology addressed this by utilizing a unique arrangement of two illumination light paths oblique to the detection light path, while allowing perpendicular arrangement of the detection light path relative to the specimen surface. Here, we report development of a next-generation, fully integrated, and user-friendly LSTM system for rapid sub-cellular resolution imaging uniformly throughout a large specimen without constraining the lateral (XY) size. In addition, we provide a seamlessly integrated workflow for image acquisition, data storage, pre- and post-processing, enhancement, and quantitative analysis. We demonstrate the system performance by high-resolution 3D imaging of intact mouse brains and human brain samples, and complete data analysis including digital neuron tracing, vessel reconstruction and design-based stereological analysis in 3D. This technically enhanced and user-friendly LSTM implementation will enable rapid quantitative mapping of molecular and cellular features of interests in diverse types of very large samples.

Dexamethasone induces trabecular meshwork cell myofibroblast transdifferentiation through ARHGEF26.

Glucocorticoid use may cause elevated intraocular pressure, leading to the development of glucocorticoid-induced glaucoma (GIG). However, the mechanism of GIG development remains incompletely understood. In this study, we subjected primary human trabecular meshwork cells (TMCs) and mice to dexamethasone treatment to mimic glucocorticoid exposure. The myofibroblast transdifferentiation of TMCs was observed in cellular and mouse models, as well as in human trabecular mesh specimens. This was demonstrated by the cytoskeletal reorganization, alterations in cell morphology, heightened transdifferentiation markers, increased extracellular matrix deposition, and cellular dysfunction. Knockdown of Rho guanine nucleotide exchange factor 26 (ARHGEF26) expression ameliorated dexamethasone-induced changes in cell morphology and upregulation of myofibroblast markers, reversed dysfunction and extracellular matrix deposition in TMCs, and prevented the development of dexamethasone-induced intraocular hypertension. And, this process may be related to the TGF-β pathway. In conclusion, glucocorticoids induced the myofibroblast transdifferentiation in TMCs, which played a crucial role in the pathogenesis of GIG. Inhibition of ARHGEF26 expression protected TMCs by reversing myofibroblast transdifferentiation. This study demonstrated the potential of reversing the myofibroblast transdifferentiation of TMCs as a new target for treating GIG.

Astrocyte tau deposition in progressive supranuclear palsy is associated with dysregulation of MAPT transcription

Progressive supranuclear palsy (PSP) is a neurodegenerative disease characterized by 4R tau deposition in neurons as well as in astrocytes and oligodendrocytes. While astrocytic tau deposits are rarely observed in normal aging (so-called aging-related tau astrogliopathy, ARTAG) and Alzheimer’s disease (AD), astrocytic tau in the form of tufted astrocytes is a pathognomonic hallmark of PSP. Classical biochemical experiments emphasized tau synthesis in neurons in the central nervous system, suggesting that astrocytic tau inclusions might be derived from uptake of extracellular neuronal-derived tau. However, recent single-nucleus RNAseq experiments highlight the fact that MAPT, the gene encoding tau, is also expressed by astrocytes, albeit in lower amounts. We, therefore, revisited the question of whether astrocyte-driven expression of tau might contribute to astrocytic tau aggregates in PSP by performing fluorescent in situ hybridization/immunohistochemical co-localization in human postmortem brain specimens from individuals with PSP and AD with ARTAG as well as normal controls. We find that, in PSP but not in AD, tau-immunoreactive astrocytes have higher levels of MAPT mRNA compared to astrocytes that do not have tau aggregates. These results suggest that astrocytic responses in PSP are unique to this tauopathy and support the possibility that fundamental changes in PSP astrocyte-endogenous mRNA biology contribute to increased synthesis of tau protein and underlies the formation of the astrocytic tau deposits characteristic of PSP.

Targeting Cyclophilin A in the Cardiac Microenvironment Preserves Heart Function and Structure in Failing Hearts.

Cardiac hypertrophy is characterized by remodeling of the myocardium, which involves alterations in the ECM (extracellular matrix) and cardiomyocyte structure. These alterations critically contribute to impaired contractility and relaxation, ultimately leading to heart failure. Emerging evidence implicates that extracellular signaling molecules are critically involved in the pathogenesis of cardiac hypertrophy and remodeling. The immunophilin CyPA (cyclophilin A) has been identified as a potential culprit. In this study, we aimed to unravel the interplay between eCyPA (extracellular CyPA) and myocardial dysfunction and evaluate the therapeutic potential of inhibiting its extracellular accumulation to improve heart function. Employing a multidisciplinary approach encompassing in silico, in vitro, in vivo, and ex vivo experiments we studied a mouse model of cardiac hypertrophy and human heart specimen to decipher the interaction of CyPA and the cardiac microenvironment in highly relevant pre-/clinical settings. Myocardial expression of CyPA (immunohistology) and the inflammatory transcriptome (NanoString) was analyzed in human cardiac tissue derived from patients with nonischemic, noninflammatory congestive heart failure (n=187). These analyses were paralleled by a mouse model of Ang (angiotensin) II-induced heart failure, which was assessed by functional (echocardiography), structural (immunohistology, atomic force microscopy), and biomolecular (Raman spectroscopy) analyses. The effect of inhibiting eCyPA in the cardiac microenvironment was evaluated using a newly developed neutralizing anti-eCyPA monoclonal antibody. We observed a significant accumulation of eCyPA in both human and murine-failing hearts. Importantly, higher eCyPA expression was associated with poor clinical outcomes in patients (P=0.043) and contractile dysfunction in mice (Pearson correlation coefficient, -0.73). Further, myocardial expression of eCyPA was critically associated with an increase in myocardial hypertrophy, inflammation, fibrosis, stiffness, and cardiac dysfunction in vivo. Antibody-based inhibition of eCyPA prevented (Ang II)-induced myocardial remodeling and dysfunction in mice. Our study provides strong evidence of the pathogenic role of eCyPA in remodeling, myocardial stiffening, and dysfunction in heart failure. The findings suggest that antibody-based inhibition of eCyPA may offer a novel therapeutic strategy for nonischemic heart failure. Further research is needed to evaluate the translational potential of these interventions in human patients with cardiac hypertrophy.

Knocking down EGR1 inhibits nucleus pulposus cell senescence and mitochondrial damage through activation of PINK1-Parkin dependent mitophagy, thereby delaying intervertebral disc degeneration

Mitophagy plays a crucial role in maintaining the homeostasis of intervertebral disc (IVD). Early Growth Response 1 (EGR1), a conservative transcription factor, is commonly upregulated under oxidative stress conditions and participates in regulating cellular senescence, apoptosis, and inflammatory responses. However, the specific role of EGR1 in nucleus pulposus (NP) cell senescence and mitophagy remains unclear. In this study, through bioinformatics analysis and validation using human tissue specimens, we found that EGR1 is significantly upregulated in IVD degeneration (IDD). Further experimental results demonstrate that knockdown of EGR1 inhibits TBHP-induced NP cell senescence and mitochondrial dysfunction while promoting the activation of mitophagy. The protective effect of EGR1 knockdown on NP cell senescence and mitochondrion disappears upon inhibition of mitophagy with mdivi1. Mechanistic studies reveal that EGR1 suppresses NP cell senescence and mitochondrial dysfunction by modulating the PINK1-Parkin dependent mitophagy pathway. Additionally, EGR1 knockdown delays acupuncture-induced IDD in rats. In conclusion, our study demonstrates that under TBHP-induced oxidative stress, EGR1 knockdown mitigates NP cell senescence and mitochondrial dysfunction through the PINK1-Parkin dependent mitophagy pathway, thereby alleviating IDD.

Presoaking hamstring autograft with vancomycin does not jeopardize its biomechanical properties, including graft elongation, after cyclic loading.

Presoaking the graft with vancomycin before implantation has been shown to reduce the risk of postoperative infection after anterior cruciate ligament reconstruction (ACLR). However, the effects of presoaking on the graft biomechanical properties remain unclear. This study aimed to determine whether presoaking the graft with vancomycin affects the graft biomechanical properties and length after cyclic loading. Ten paired (20 specimens) gracilis and semitendinous tendons were harvested from fresh-frozen human cadaveric specimens. Two tendons were folded in half to make four strands, and the grafts were randomized into the vancomycin and control groups. The graft was exposed to the antibiotic solution for 15 min (5 mg/mL) and prepared by mixing 1 g of vancomycin with 200 mL of normal saline (NaCl 0.9%). The control group was soaked in normal saline for 15 min. The prepared grafts were attached to the actuator of a dynamic tensile-testing machine. All grafts were tested with 3000 cycles of cyclic loading followed by a pull-to-failure. The cyclic loading protocol consisted of position and load control blocks to simulate the graft in vivo in the postoperative phase after ACLR. Presoaking in vancomycin did not jeopardize the biomechanical properties of the graft. In addition, presoaking with vancomycin did not elongate the grafts. No significant differences were found in the mean Young's modulus and the mean total elongation of the graft of the specimen between the vancomycin group and the control group. Presoaking the graft with vancomycin jeopardized neither its biomechanical properties nor elongation even after cyclic loading in this in vitro study. It is suggested that vancomycin presoaking could be considered a safe and effective preventive measure for postoperative infections after ACLR. Not applicable.

Immunophenotypical Characterization of Limbal Mesenchymal Stromal Cell Subsets during In Vitro Expansion.

Limbal mesenchymal stromal cells (LMSCs) reside in the limbal niche, supporting corneal integrity and facilitating regeneration. While mesenchymal stem/stromal cells (MSCs) are used in regenerative therapies, there is limited knowledge about LMSC subpopulations and their characteristics. This study characterized human LMSC subpopulations through the flow cytometric assessment of fifteen cell surface markers, including MSC, wound healing, immune regulation, ASC, endothelial, and differentiation markers. Primary LMSCs were established from remnant human corneal transplant specimens and passaged eight times to observe changes during subculture. The results showed the consistent expression of typical MSC markers and distinct subpopulations with the passage-dependent expression of wound healing, immune regulation, and differentiation markers. High CD166 and CD248 expressions indicated a crucial role in ocular surface repair. CD29 expression suggested an immunoregulatory role. Comparable pigment-epithelial-derived factor (PEDF) expression supported anti-inflammatory and anti-angiogenic roles. Sustained CD201 expression indicated maintained differentiation capability, while VEGFR2 expression suggested potential endothelial differentiation. LMSCs showed higher VEGF expression than fibroblasts and endothelial cells, suggesting a potential contribution to ocular surface regeneration through the modulation of angiogenesis and inflammation. These findings highlight the heterogeneity and multipotent potential of LMSC subpopulations during in vitro expansion, informing the development of standardized protocols for regenerative therapies and improving treatments for ocular surface disorders.

Proprioceptors of the human pericardium.

In the human organism, all functions are regulated and, therefore, require a feedback mechanism. This control involves a perception of the spatial tensile state of cardiac tissues. The presence and distribution of respective proprioceptive corpuscles have not been considered so far. Therefore, a comprehensive study of the entire human fibrous pericardium was conducted to describe the presence of proprioceptors, their density, and distribution patterns. Eight human pericardial specimens gained from our body donation program were used to create a three-dimensional map of proprioceptors in the pericardium based on their histological and immunohistochemical identification. The 3D map was generated as a volume-rendered 3D model based on magnetic resonance imaging of the pericardium, to which all identified receptors were mapped. To discover a systematic pattern in receptor distribution, statistical cluster analysis was conducted using the Scikit-learn library in Python. Ruffini-like corpuscles (RLCs) were found in all pericardia and assigned to three histological receptor localizations depending on the fibrous pericardium's layering, with no other corpuscular proprioceptors identified. Cluster analysis revealed that RLCs exhibit a specific topographical arrangement. The highest receptor concentrations occur at the ventricular bulges, where their size reaches its maximum in terms of diameter, and at the perivascular pericardial turn-up. The findings suggest that the pericardium is subject to proprioceptive control. RLCs record lateral shearing between the pericardial sublayers, and their distribution pattern enables the detection of distinct dilatation of the heart. Therefore, the pericardium might have an undiscovered function as a sensor with the RLCs as its anatomical correlate.

Characterizing bone density pattern and porosity in the human ossicular chain using synchrotron microtomography

The auditory ossicles amplify and transmit sound from the environment to the inner ear. The distribution of bone mineral density is crucial for the proper functioning of sound transmission as the ossicles are suspended in an air-filled chamber. However, little is known about the distribution of bone mineral density along the human ossicular chain and within individual ossicles. To investigate this, we analyzed fresh-frozen human specimens using synchrotron-based phase-contrast microtomography. In addition, we analyzed the volume and porosity of the ossicles. The porosity for the auditory ossicles lies, on average, between 1.92% and 9.85%. The average volume for the mallei is 13.85 ± 2.15 mm3, for the incudes 17.62 ± 4.05 mm3 and 1.24 ± 0.29 mm3 for the stapedes. The bone density distribution showed a similar pattern through all samples. In particular, we found high bone mineralization spots on the anterior crus of the stapes, its footplate, and along areas that are crucial for the transmission of sound. We could also see a correlation between low bone mineral density and holey areas where the bone is only very thin or missing. Our study identified a similar pattern of bone density distribution within all samples: regions exposed to lower forces generally show higher bone density. Further, we observed that the stapes shows high bone mineral density along the anterior crus and its footplate, which may indicate its importance in transmitting sound waves to the inner ear.

A rapid and validated GC-MS/MS method for simultaneous quantification of serum Myo- and D-chiro-inositol isomers

BackgroundMyo-inositol (MI) and D-chiro-inositol (DCI) are two paramount isomers of inositol, both vital in glucose and steroid metabolism. Deficits in MI, DCI or MI/DCI ratio are expressly concerned with several pathological process, whereas MI and DCI lack practical measurement for human specimen. MethodsTo quantify MI and DCI in serum samples simultaneously, a gas chromatography tandem mass spectrometry (GC-MS/MS) method was established. The process flow was optimized in ion source, derivative agent volume and reaction time. The performance characteristics were verified by commercial standards and clinical serums. ResultsThis method was confirmed to be sensitive (LOD ≤ 30 ng/mL of MI, ≤3 ng/mL of DCI) and reproducible (RSD < 6 % for repeated analyses). Quantitative determinations performed good linearity within the measurement range of 0.500–10.00 and 0.005–0.500 μg/mL for MI and DCI respectively (R2 > 0.999). The recoveries of MI and DCI were 97.11–99.35 % and 107.82–113.09 %, respectively. This method was successfully applied to 114 clinical specimens. No significant matrix effect was observed in serum samples under current conditions.

Sequential correction of sagittal vertical alignment and lumbar lordosis in adult flatback deformity

BackgroundFlatback deformity, or lumbar hypolordosis, can cause sagittal imbalance, causing back pain, fatigue, and functional limitation. Surgical correction through osteotomies and interbody fusion techniques can restore sagittal balance and relieve pain. This study investigated sagittal vertical alignment (SVA) and lumbar lordosis correction achieved through sequential procedures on human spine specimens. MethodsHuman T10-sacrum specimens were stratified into 2 groups: degenerative flatback specimens had smaller L1-S1 lordosis compared to the iatrogenic group (26.1°±15.0° vs. 47.8°±19.3°, p<.05). Specimens were mounted in the apparatus in simulated standing posture with a nominal sacral slope of 45 degrees and subjected to a 400N compressive follower preload. Sequential correction of degenerative lumbar flatback deformity involved: anterior lumbar interbody fusion (ALIF) at L5-S1, ALIF at L4-5, lateral lumbar interbody fusion (LLIF) at L2-3 and L3-4, and posterior column osteotomy (PCO) at L2-3 and L3-4. In iatrogenic specimens, flatback deformity was created by performing a posterior in-situ immobilization using pedicle screw instrumentation at L4-L5-S1 followed by distraction across the pedicle screws. We then performed LLIF at L2-3 and L3-4, followed by PCO at L2-3 and L3-4. ResultsStatistically significant incremental corrections were noted in SVAs and lordosis after L5-S1 ALIF, L4-5 ALIF, and PCO in degenerative flatback specimens. For the iatrogenic group, statistically significant worsening was noted in measures of standing alignment after L4-L5-S1 hypolordotic fusion. Subsequent LLIF at L2-3 and L3-4 did not significantly improve sagittal alignment. However, after PCO at L2-3 and L3-4, final alignment parameters were not significantly different than preoperative baseline values prior to hypolordotic fusion. ConclusionsALIF cages in the lower lumbar segments significantly improved sagittal alignment in degenerative flatback specimens. In the upper lumbar segments, LLIF cages alone were ineffective at enhancing lumbar lordosis. LLIF cages in conjunction with PCO improved alignment parameters in degenerative and iatrogenic flatback deformities.

Pathogenic Leptospira Detection in Environmental Contaminant Water Sources by Highly Performance Antibody Absorption Polystyrene Agglutinating Particles

AbstractLeptospirosis is a re‐emerging bacterial zoonotic disease that affects both humans and animals, with a significantly higher incidence in tropical and sub‐tropical regions. Disease control, epidemiology, and surveillance rely on a One Health approach, as accurate detection can be applied to humans, animals, and the environment. This study represents the first attempt to develop a method for detecting the pathogenic Leptospira santarosai serovar Shermani based on the latex agglutination reaction. The serological activity of the antibody is examined to achieve a high titer of antibody before adsorption onto polystyrene particles. Using a pH medium of 6.8–7.8, total antibody adsorption of up to 3 mg m−2 is achieved. Particle agglutination is observed after incubating the antibody‐adsorbed PS with leptospiral culture for 4 min, revealing a detection limit of 1.7 × 102 leptospires mL−1. Interestingly, the detection limit increased by 1000 times when observing agglutination using spectrophotometer. The test exhibits high specificity with Shermani and shows negligible cross‐agglutination with non‐pathogenic Leptospira and water‐borne bacteria. Agglutination testing in collected water samples from natural sources demonstrates a good correlation with culture technique. This simple and rapid leptospires agglutination detection method can be applied as a screening test in environmental, human, and animal specimens.

Development of the Interosseous Muscles of the Human Hand: Morphological and Functional Aspects of the Terminal Insertion.

To date, there have been no studies conducted on the development of interosseous muscles (IO) in the human hand. This study aimed to investigate the development of these muscles in order to clarify their terminal insertions and their relationship with the metacarpophalangeal joints. Serial sections of 25 human specimens (9 embryos and 16 fetuses) between the 7th and 14th weeks of development, sourced from the Collection of the Department of Anatomy and Embryology at UCM Faculty of Medicine, were analyzed bilaterally using a conventional optical microscope. Our findings revealed that, during the 7th week of development, the metacarpophalangeal interzone mesenchyme extended into the extensor apparatus of the fingers. Furthermore, we observed that the joint capsule and the tendon of the IO derive from the articular interzone mesenchyme. By the end of the 7th week, corresponding to Carnegie stage 21, the myotendinous junction appeared, initiating cavitation of the metacarpophalangeal joint. During the fetal period, the terminal insertions of the IO were identified: both the dorsal interosseous (DI) and palmar interosseous (PI) muscles insert into the metacarpophalangeal joint capsule and establish a connection with the volar plate located at the base of the proximal phalanx and the extensor apparatus. Some muscle fibers also attach to the joint capsule at the level of the proximal synovial cul-de-sac. The functional implications of these findings are discussed within this work. This study provides the first detailed description of the development of the interosseous muscles in the human hand.

Characteristics and comparative genome analysis of Yersinia enterocolitica and related species associated with human infections in Switzerland 2019–2023

PurposeWe aimed to characterise Yersinia enterocolitica from human clinical specimens in Switzerland using epidemiological, microbiological and whole-genome sequencing (WGS) data. MethodsIsolates (n = 149) were collected between January 2019 and December 2023. Epidemiological data was noted and strains were characterized by biochemical and serological typing, antimicrobial susceptibility testing (AST), and WGS-based analysis. ResultsMost of the isolates (86%) were from stool specimens and 52% were from male patients. The patients' median age was 28 years (range < 1–94 years). Typing assigned the isolates to bioserotype 4/O:3 (44%), biotype 1A (34%), bioserotype 2/O:9 (21%), and bioserotype 3/O:3 (1%). WGS identified Y. enterocolitica (n = 147), Y. alsatica (n = 1) and Y. proxima (n = 1). Seven isolates were multidrug resistant (MDR) and harboured plasmid pAB829 carrying aph(3″)-Ib, aph(6)-Id, and tet(Y) (n = 1), pAC120 carrying aph(6)-Id and tet(A) (n = 2), or a 12.6 kb Tn2670-like transposon containing catA1, aadA12, sul1, and qacEΔ1 (n = 4). Virulence factors (VFs) included ail (n = 99), invB, (n = 145), ystA (n = 99), ystB (n = 48) and pYV-associated VFs (n = 93). MLST and cgMLST analysis showed that BT 1A strains consisted of several STs and were highly diverse, whereas BT 2/O:9 strains were all ST12 and clustered closely, and BT 4/O:3 strains mostly belonged to ST18 but were more diverse. SNP analysis revealed two highly clonal BT 4/O:3 subpopulations with wide spatio-temporal distribution. ConclusionsY. enterocolitica BT 1A, BT 2/O:9 and BT 4/O:3 are frequently associated with human yersiniosis in Switzerland. WGS-based subtyping of Y. enterocolitica is a powerful tool to explore the genetic diversity and the pathogenic potential of human isolates.

Unveiling novel double-negative prostate cancer subtypes through single-cell RNA sequencing analysis

Recent advancements in single-cell RNA sequencing (scRNAseq) have facilitated the discovery of previously unrecognized subtypes within prostate cancer (PCa), offering new insights into cancer heterogeneity and progression. In this study, we integrated scRNAseq data from multiple studies, comprising publicly available cohorts and data generated by our research team, and established the Human Prostate Single cell Atlas (HuPSA) and Mouse Prostate Single cell Atlas (MoPSA) datasets. Through comprehensive analysis, we identified two novel double-negative PCa populations: KRT7 cells characterized by elevated KRT7 expression and progenitor-like cells marked by SOX2 and FOXA2 expression, distinct from NEPCa, and displaying stem/progenitor features. Furthermore, HuPSA-based deconvolution re-classified human PCa specimens, validating the presence of these novel subtypes. We then developed a user-friendly web application, “HuPSA–MoPSA” (https://pcatools.shinyapps.io/HuPSA-MoPSA/), for visualizing gene expression across all newly established datasets. Our study provides comprehensive tools for PCa research and uncovers novel cancer subtypes that can inform clinical diagnosis and treatment strategies.

Rapid identification of SARS CoV-2 omicron sub-variant JN.1 (BA.2.86.1.1) with mass spectrometry

ObjectiveThe rapid detection and differentiation of strains of the BA.2.86 lineage including the new sub-variant JN.1 (BA.2.86.1.1) is demonstrated employing selected ion monitoring (SIM) and high resolution mass spectrometry. MethodsA study of a preliminary set of BA.2.86 lineage positive specimens, identified BA.2.86 and BA.2.86.1.1 peptide markers in 62.5 % and 29.1 % of samples. ResultsPeptide-specific markers in the surface spike protein associated with the L455S mutation are confidently detected with high sensitivity in protein and virus digests.The virus was thus confidently assigned in over 91 % of positive specimens. ConclusionsA rise in the global prevalence of the JN.1 (BA.2.86.1.1) immune evasive sub-variant, that emerged in late 2023, requires that new strategies and protocols to detect such strains in human specimens are accelerated and implemented.

Histopathological analysis potential for unveiling hormone signaling in endocrine-related tumors.

Elucidating the mechanisms of action of steroid hormones will contribute to the development of therapeutic strategies for hormone-dependent tumors. Recent advances in genetic engineering have revealed the complex and diverse mechanisms of steroid hormone signaling; however, these techniques are limited to in vitro or animal experiments. It is believed that verifying hormone signals elucidated using human pathological tissue specimens will directly aid in treatment and diagnosis. However, pathological tissue specimens are generally formalin-fixed paraffin-embedded (FFPE), and protein/gene analyses of FFPE tissues are limited. Protein detection using immunohistochemistry with specific antibodies in FFPE tissues is a classical technique essential for diagnosis and treatment decisions in various types of cancer. In steroid hormone signaling, the expression and localization of receptors, hormone-related enzymes, and proteins encoded by response genes can be clarified using immunohistochemistry. Although protein-protein interactions such as receptor dimers and DNA-binding proteins are mainly detected in vitro, they can be examined in FFPE tissues using in situ proximity ligation assays and southwestern histochemistry, respectively. Using these detection methods, including immunohistochemistry, it is possible to analyze each hormone signaling pathway in hormone-related tumors histopathologically. Although FFPE tissues still suffer from gene and protein denaturation, their advantages include the ability to retrospectively study target factors/signals and obtain spatial information through microscopy. This review describes a visualization method for elucidating steroid hormone signaling in hormone-dependent tumors using FFPE tissues.

The m6A reader IGF2BP2 promotes ESCC progression by stabilizing HDGF mRNA.

This study aimed to explore the role of IGF2BP2 in esophageal squamous cell carcinoma (ESCC) progression. The Cancer Genome Atlas (TCGA) dataset, transcriptome sequencing, and the Gene Expression Omnibus (GEO) dataset were used to detect the expression of m6A-associated genes in ESCC. The in vitro and in vivo assays were used to explore the role of IGF2BP2 in ESCC. IGF2BP2 was significantly overexpressed in human ESCC specimens, which was confirmed by analyzing the GEO dataset. IGF2BP2 overexpression was correlated with poor prognosis in patients with ESCC. Altering the expression of IGF2BP2 influenced the proliferation, migration, and invasion of ESCC cells in vitro and tumorigenicity in vivo. IGF2BP2 could bind to and stabilize hepatoma-derived growth factor (HDGF) transcripts in ESCC in an m6A-dependent manner and promote HDGF expression. These findings indicate that the novel IGF2BP2-HDGF axis is pivotal for ESCC cancer progression and can serve as a target for developing therapeutics.