Influence Of Microenvironment Research Articles

Correlation of Vein-Rich Tumor Microenvironment of Intrahepatic Cholangiocarcinoma With Tertiary Lymphoid Structures and Patient Outcome

Intrahepatic cholangiocarcinoma (iCCA) is an aggressive cancer composed of large-duct and small-duct types. Understanding the tumor immune microenvironment and its related vascular system is important for developing novel and efficient therapies. We focused on tertiary lymphoid structure (TLS) as a hallmark of antitumor immunity and investigated the clinicopathologic significance of TLSs and the influence of vascular microenvironment on TLS formation in iCCAs. We examined 261 iCCA cases clinicopathologically and analyzed the vascular system using immunohistochemistry. Single-cell (102,685 cells) and bulk RNA (33 iCCA cases) sequencing analyses were performed using data sets downloaded from public databases, and endothelial cell characteristics in iCCA tissues and functional networks related to the tumor microenvironment were bioinformatically examined. High densities of both intratumoral and peritumoral TLSs were significantly associated with prolonged survival only in large-duct-type iCCA. Multivariate analyses showed that peritumoral TLS was a prognostic factor for the large-duct type. TLS-rich iCCA had a significantly higher vein density and tumor-infiltrating T-cell count than TLS-poor iCCA. Both the presence of TLSs and high vein endothelial cells in iCCA tissues were significantly associated with molecular networks representing active immune responses in transcriptomic analysis. Vein density was a prognostic factor in patients with large-duct and small-duct types. This suggests that TLS formation is involved in a microenvironment with high vein density, which represents an antitumor-directed immune microenvironment.

High Dimensional Clustering and Identification of Immune Cell Hybrid Populations in B-ALL across the Disease Continuum

Introduction: Nearly half of adults with acute lymphoblastic leukemia (ALL) will experience relapse of their disease, and those with relapsed ALL carry a worse prognosis than those who remain in remission. The influence of the tumor immune microenvironment (TME) on relapse and survival outcomes in ALL is not well understood. Mass cytometry (CyTOF) enables immune profiling based on single cell protein expression and can identify phenotypic diversity of cells in the TME that cannot reliably be detected by standard flow cytometry. Recently, T-cell/monocyte hybrid cells have been discovered in patients with uveal melanoma and latent tuberculosis infections. However, cells expressing CD19, a surface antigen expressed on B-ALL cells, and markers of other cells in the TME including T cells and tumor-associated macrophages (TAMs), have not been described in ALL or other hematologic malignancies. The presence of CD3/CD163 hybrid cells in the TME may have predictive and prognostic implications for adults with ALL, as TAMs play a role in suppressing antitumor immunity which can lead to T-cell exhaustion. In this study, we identify the presence of multilineage hybrid cells in peripheral blood (PB) and bone marrow (BM) samples of patients with B-ALL alongside accompanying evolution of the TME at each disease stage. Methods: PB (N=16) and BM aspirate (N=16) isolates were collected from patients with B-ALL at diagnosis, relapse, or remission, as well as from healthy donors (HDs, N=7) for comparison of cellular profiles. A 28-marker CYTOF panel was designed to evaluate cell surface and intracellular markers of interest in the myeloid compartment. Antibodies were purchased pre-conjugated or conjugated in house based on manufacturer guidelines (Standard BioTools). Samples were barcoded with palladium isotopes prior to staining to reduce the impact of batch effect, and were then analyzed on a first generation CyTOF system (Standard BioTools). Following background attenuation and singlet gating in FlowJo (BD), the CATALYST R package enabled deconvolution and visualization of single cell data, including dimensional reduction techniques (tSNE) and clustering of all cell populations. An iterative approach was taken to determine a stable configuration of clusters across sample populations to protect from over-fragmentation of data, further informed by K-means clustering using the elbow method. Heatmaps were then generated based on median scaled expression of markers contained in each cluster. Results: The CyTOF panel identified several different myeloid cell populations in newly diagnosed, relapsed, and remission samples in both PB and BM compared to HDs. Most interestingly, quantifiable levels of a cluster of cells co-expressing CD19, CD3 and CD163 as well as a second cluster of cells expressing CD19 and CD163 were detected in newly diagnosed and relapsed patients, but not in HDs. A single patient with the largest proportion of these cell populations in their PB at the time of relapse presented with an aggressive leukemia variant and relapsed multiple times prior to succumbing to illness. On investigation of BM aspirates, the triple positive hybrid population was found in a similar distribution amongst the newly diagnosed and relapsed patients, as well as affecting one patient who achieved remission. This patient also had a highly aggressive leukemia that was refractory to chemotherapy and immunotherapy, and only achieved this remission following CAR-T cell therapy. She subsequently underwent stem cell transplant and is in remission. Conclusions: Our findings add to the literature highlighting the utility of high parameter single cell capture techniques in detecting rare cell populations in the leukemic TME. Further, we identified two unique hybrid cell populations that are reliably detected across different disease stages in patients with B-ALL. Importantly, these populations persisted following stringent gating protocols to rule out doublets and debris. Although our sample size was too small to demonstrate a prognostic impact of these hybrid cell populations in patients with B-ALL, the identification of these populations alone is a significant finding. Further investigation and patient sample accrual are warranted to better understand the role of these cell types in tumor biology, which may pave the way towards new prognostic models that can leverage well-established immune monitoring techniques.

A tumor-associated heparan sulfate-related glycosaminoglycan promotes the generation of functional regulatory T cells.

Functional Tregs play a key role in tumor development and progression, representing a major barrier to anticancer immunity. The mechanisms by which Tregs are generated in cancer and the influence of the tumor microenvironment on these processes remain incompletely understood. Herein, by using NMR, chemoenzymatic structural assays and a plethora of in vitro and in vivo functional analyses, we demonstrate that the tumoral carbohydrate A10 (Ca10), a cell-surface carbohydrate derived from Ehrlich's tumor (ET) cells, is a heparan sulfate-related proteoglycan that enhances glycolysis and promotes the development of tolerogenic features in human DCs. Ca10-stimulated human DCs generate highly suppressive Tregs by mechanisms partially dependent on metabolic reprogramming, PD-L1, IL-10, and IDO. Ca10 also reprograms the differentiation of human monocytes into DCs with tolerogenic features. In solid ET-bearing mice, we found positive correlations between Ca10 serum levels, tumor size and splenic Treg numbers. Administration of isolated Ca10 also increases the proportion of splenic Tregs in tumor-free mice. Remarkably, we provide evidence supporting the presence of a circulating human Ca10 counterpart (Ca10H) and show, for the first time, that serum levels of Ca10H are increased in patients suffering from different cancer types compared to healthy individuals. Of note, these levels are higher in prostate cancer patients with bone metastases than in prostate cancer patients without metastases. Collectively, we reveal novel molecular mechanisms by which heparan sulfate-related structures associated with tumor cells promote the generation of functional Tregs in cancer. The discovery of this novel structural-functional relationship may open new avenues of research with important clinical implications in cancer treatment.

Regulation of T16H subcellular localization for promoting its catalytic efficiency in yeast cells.

To investigate the effect of subcellular localization on the transformation efficiency of heterologous expressed functional P450s in yeast. Microbial biotransformation offers a promising substitute for the direct extraction of natural products, but its viability in industrial applications depends on achieving high transformation efficiencies. To investigate the influence of subcellular microenvironments on the activity of heterologously expressed P450s, Catharanthus roseus tabersonine 16-hydroxylase (T16H) was chosen, and its subcellular localization was regulated by fusing organelle-localization signals. Interestingly, this manipulation had no effect on the gene expression levels of T16H, but resulted in varying conversion rates from tabersonine to 16-hydroxy tabersonine. Notably, the highest transformation efficiency was observed in yeast cells expressing peroxisome-localized T16H. Given the alkaline pH optimum for P450s, the alkaline peroxisomal lumen could be a suitable compartment for P450s reactions to achieve high transformation efficiency using yeast cells. Different organelle-localization of T16H in yeast cells resulted in varying conversion rates, suggesting that compartmentalizing the expression of target enzymes could be a viable approach to increase transformation efficiency in yeast.

TMIC-41. LATERAL VENTRICLE PROXIMITY OF GLIOBLASTOMA IS ASSOCIATED WITH LOCALIZED MALIGNANCY-PROMOTING MOLECULAR SIGNATURES IN IMAGE-GUIDED BIOPSIES

Abstract Glioblastoma (GBM) is the most devastating and common form of primary brain cancer in adults. Tumor location plays a significant role in patient prognosis; in particular, GBM tumors contacting the lateral ventricles (LVs) are more aggressive than LV-distal counterparts. This may be due to interaction of tumors with unique features of the LV microenvironment, including the cerebrospinal fluid (CSF) and neural progenitor cells (NPCs) of the subventricular zone. Despite LV contact having a role on tumor malignancy, studies using bulk tumor samples to identify molecular contributors to LV-contacting prognosis have been only moderately successful, in large part due to intratumoral heterogeneity. Here, we leverage intraoperative surgical navigation to collect matched biopsies of adult LV-contacting primary GBM at locations proximal (< 2 cm) and distal ( > 2 cm) from the LV. Matched samples were collected from ten patients with equal sex distribution and an age range of 46 to 81 years. RNA sequencing of biopsies revealed a localized transcriptional signature of gene expression in LV-proximal locations. These genes include those identified to be associated with GBM malignancy and upregulated in primary GBM cells by CSF exposure or co-culture with NPCs, such as SERPINA3, CD44, and CTSB, as well as many newly identified genes. Implicated biological pathways involved in this transcriptional signature involve inflammation, chemotaxis, Notch signaling, angiogenesis, integrin signaling, and more. The top 50 upregulated genes by LV-proximity of GBM were used to cluster patient transcriptomes from the TCGA GBM database and evaluate the contribution to patient outcome. This analysis revealed a cluster with significantly extended overall survival that displayed a general downregulation of LV-proximity genes. Ultimately, these studies provide evidence that regional tumoral analysis is essential in identifying molecular signatures associated with microenvironmental influence, and that LV-contacting GBM has regional gene expression changes in many genes associated with malignancy.

PATH-11. POOLED IN VIVO ASSAY TO CHARACTERIZE GLIOBLASTOMA INVASION AT THE SINGLE-CELL RESOLUTION

Abstract Tumor cell invasion is the main characteristic of glioblastoma and one of the obstacles to successful treatments. Nonetheless, molecular features of invading glioblastoma cells remain elusive and poorly characterized, such as their gene expression states and microenvironmental influences. Recently, we described cell state heterogeneity in glioblastoma by single-cell RNA-sequencing (scRNA-seq) and uncovered the contribution of immune cells to the heterogeneity. However, it is unclear whether the cell states observed in clinical specimens are implicated in invading glioblastoma cells in the surgically inaccessible brain parenchyma. It is also unclear whether the cell states are correlated to the non-immune microenvironment. As a tool for probing these questions, we developed an in vivo approach with mixtures of human glioblastoma spheroid lines for mouse intracranial xenografts. We validated this with 20 patient-derived models and identified, by scRNA-seq, in vivo models capable of infiltrating along the periphery of either neurons or blood vessels. We profiled and characterized programs, states, and clonality of invading glioblastoma cells by comparing cells from the contralateral invasive edge to their counterparts at the original bulk tumor. This comparative analysis showed evidence of a bi-directional transitioning model for cells residing in different spatial niches. Importantly, presence of an OPC-like state was significantly associated with invasion phenotype regardless of the infiltration routes. Our results suggest that cellular plasticity may be a prerequisite for the invasive phenotypes, urging further assessment to identify critical regulators of the cell states. In conclusion, this work describes pooled in vivo assays for the rapid interrogation of patient-derived xenografts, coupling the gene expression phenotypes with cellular functions such as invasion.

EPCO-05. SPATIOTEMPORAL MODELLING OF GLIOBLASTOMA FOR DRUG PREDICTION

Abstract Glioblastoma (GBM) is a lethal primary brain malignancy characterized by inevitable relapse. Understanding intra-tumoral heterogeneity and the microenvironmental influence on tumor progression is key to developing effective therapies. We employ 10X Genomics’ Visium Spatial Transcriptomics platform to study murine xenograft models of multi-regional and longitudinally derived cell lines from 4 GBM patients. This resource enables the study of tumor growth at spatial resolution and allows robust species-specific distinction of tumor and its microenvironment (TME). Using a matrix factorization approach, we delineate spatial gene expression programs (GEP) specific to the tumor and TME. We observe unique niches including progenitor cell-states along the leading edge (LE) of the tumor, oligodendrocyte-like (OC) and astrocytic-like (AC) states at the tumor core along with tumor-associated endothelial states. At early time-points, the homing of brain-resident microglia (MG), macrophages (BMDM), reactive astrocytes to the tumor site are observed. The invasiveness of GBM is a major obstacle, as these cells are therapeutically resistant and seed recurrence. Targeting the LE of GBM could therefore improve patient outcomes. Interestingly in our models, the LE state exhibits higher patient diversity; upregulation of ligand/receptor genes in secreted phosphoprotein, fibronectin, macrophage migration pathways highlighting prospective targets. Further, we analyzed protein-protein interaction networks of the LE programs, which revealed that upregulation of “hub genes” within the network significantly reduces patient survival. Further investigation of such program-specific vulnerabilities will help inform on combinatorial therapeutic strategies to control disease progression and paves the way for future testing of treatment response in both xenografts and syngeneic models.

CNSC-31. BESPOKE THREE- PHOTON MICROSCOPY AND ANALYSIS ENABLE DEEP INTRAVITAL BRAIN TUMOR IMAGING

Abstract Glioblastoma is the most common primary brain tumor with a poor prognosis due to its aggressive invasiveness, inevitable recurrence, and therapy resistance. One hallmark of the disease is its whole brain dissemination via preexisting brain structures like blood vessels or white matter tracts. While intravital glioblastoma imaging has been limited to the superficial cortical layers, we developed a method of three photon microscopy allowing the investigation of glioblastoma invasion and colonization in the white matter up to a depth of 1.2 mm over extended time periods. Our method, combining adaptive optics 3P imaging, customized deep learning- based denoising and machine learning segmentation, enables longitudinal volumetric multicolor imaging, being able to distinguish GBM cell signal from myelin structures as well as blood vessel signal. Thus, GBM cells and their interactions with and influence on the microenvironment within the white matter can be investigated longitudinally. We found that compared to cortical invasion, a majority of GBM cells in the corpus callosum are aligned with myelinated axonal tracts, showing the influence of the tumor microenvironment on GBM cell directionality. Also, we found that most GBM cells enter the corpus callosum via a perivascular route. We identified two blood vessel-related mechanisms that allow invasion orthogonal to the myelinated axonal tract direction. We discovered that white matter tract directionality did not change significantly in the early stages of GBM colonization. This might explain limitations of modern clinical imaging to depict white matter glioma infiltration. However, we found that the shape of THG discontinuities differs between GBM cells and other resident cells, which could potentially serve as an imaging biomarker. To summarize, this tailored three-photon microscopy methodology allows unprecedented intravital investigation of GBM invasion in the gray and white matter, enabling the discovery of novel (sub-)cellular mechanisms in cancer and its microenvironment deep in the brain.

Advantages and disadvantages of treatment of experimental ARDS by M2-polarized RAW 264.7 macrophages

Innate immunity reactions are core to any immunological process, including systemic inflammation and such extremes as acute respiratory distress syndrome (ARDS) and cytokine storm. Macrophages, the key cells of innate immunity, show high phenotypic plasticity: depending on microenvironmental cues, they can polarize into M1 (classically activated, pro-inflammatory) or M2 (alternatively activated, anti-inflammatory). The anti-inflammatory M2 macrophage polarization-based cell therapies constitute a novel prospective modality. Systemic administration of ‘educated’ macrophages is intended at their homing in lungs in order to mitigate the pro-inflammatory cytokine production and reduce the risks of ‘cytokine storm’ and related severe complications. Acute respiratory distress syndrome (ARDS) is the main mortality factor in pneumonia including SARS-CoV-associated cases. This study aimed to evaluate the influence of infusions of RAW 264.7 murine macrophage cell line polarized towards M2 phenotype on the development of LPS-induced ARDS in mouse model. The results indicate that the M2-polarized RAW 264.7 macrophage infusions in the studied model of ARDS promote relocation of lymphocytes from their depots in immune organs to the lungs. In addition, the treatment facilitates expression of M2-polarization markers Arg1, Vegfa and Tgfb and decreases of M1-polarization marker Cd38 in lung tissues, which can indicate the anti-inflammatory response activation. However, treatment of ARDS with M2-polarized macrophages didn't change the neutrophil numbers in the lungs. Moreover, the level of the Arg1 protein in lungs decreased throughtout the treatment with M2 macrophages, which is probably because of the pro-inflammatory microenvironment influence on the polarization of macrophages towards M1. Thus, the chemical polarization of macrophages is unstable and depends on the microenvironment. This adverse effect can be reduced through the use of primary autologous macrophages or some alternative methods of M2 polarization, notably siRNA-mediated.

Effect of the urban microenvironment on the indoor air temperature of the residential building stock in the Helsinki region

Due to climate change, there is an increased risk of apartment overheating. In Nordic countries, heatwaves have not been common in the past and hence apartments are not equipped with mechanical cooling systems, so wise urban design might be a solution. This study evaluated the influence of the urban microenvironment on residential building indoor air temperature via green view index (GVI), floor area ratio and distance from the sea. We analyzed a large dataset of over 2000 apartments in the Helsinki region during summers of 2018 and 2021, where severe heatwaves were presented, and combined it with the aforementioned parameters. In the method used, closely situated buildings were clustered into groups by the microenvironment parameters. The results showed consistent correlations between clustered groups and microenvironment parameters, where the best-performing group had an indoor air temperature of about 1 °C lower than the average during the summers and 0.7 °C lower during the severe heatwaves. Building groups with higher GVI demonstrated a greater ability to endure long heatwaves, where combined influence of other urban microenvironment factors was significantly reduced. A substantial influence of sea distance and floor area ratio was observed during short heatwaves in the middle and late summer. The indoor temperature difference of the groups was compared to the average outdoor temperature difference of group areas based on the Finnish Meteorological Institute HARMONIE-AROME weather model implemented with the SURFEX module. The results revealed a consistent correlation between predicted outdoor and indoor temperatures and their distribution of group-to-area differences.

Ways to increase the regenerative potential of mesenchymal stromal cells

The ability of mesenchymal stromal cells (MSCs) to migrate into tissue defects and stimulate regeneration makes them a valuable resource for cell therapy. However, in many cases, in vitro cultivation and the influence of the pathological microenvironment in the patient’s body reduce the viability and therapeutic efficacy of MSCs, so their regenerative potential needs to be strengthened. Preconditioning with hormones, cytokines, various chemical or physical factors, cultivation in a three-dimensional environment or at a reduced oxygen content improves the ability of MSCs to colonize damaged tissue, survive in it, and produce regulatory molecules for regeneration. The same goals can be achieved by genetic modification of MSCs. In addition, with the help of transfected MSCs, it is possible to deliver genes necessary for the treatment of hereditary or oncological diseases into the tissue. Finally, an alternative to avoid a decrease in the therapeutic potential of subsequently transplanted MSCs during cultivation can be stimulation of the migration of endogenous patient cells from tissue niches through the systemic circulation to the area of damage. The development of these approaches opens the way to increasing the efficiency of using MSCs in regenerative medicine.

Comprehensive bioinformatics analysis of the role of VWF in the tumor microenvironment of malignant mesothelioma.

To explore the influence and effect of tumor microenvironment on the development of malignant mesothelioma using machine learning methods. 87 open cases were downloaded from the Cancer Genome Atlas database including transcriptome data, clinical data, and mutation data. The immune, stromal, and estimate scores were calculated for each case by using the ESTIMATE algorithm, and then the cases were grouped according to high and low stromal scores to predict all-cause survival in malignant mesothelioma cases. Their mutation data were analyzed to reveal the differences in mutated genes between the 2 groups, and then the von Willebrand factor (VWF) and FCRL3 genes were identified according to the intersection of DEGs and high-frequency mutated genes. Lastly, the correlation between VWF and the immune checkpoint of 22 kinds of immune cells was analyzed by using the CIBERSORT package of R software. A significant difference was found in the survival time of patients between the high and low stromal score groups. High expression of the VWF gene was negatively correlated with the prognosis of malignant mesothelioma, and the expression of VWF was positively correlated with naive B cells and activated CD4 memory T cells and negatively correlated with NK cells. The results revealed that high expression of VWF may involve in the development of malignant mesothelioma, and the anti-CTLA4 immune checkpoint treatment may have certain efficacy.

Interleukin-6 Inhibits Expression of miR-204-5p, a Regulator of Oligodendrocyte Differentiation: Involvement of miR-204-5p in the Prevention of Chemical-Induced Oligodendrocyte Impairment.

Oligodendrocytes (OLs) form myelin sheaths around axons in the central nervous system (CNS) facilitate the propagation of action potentials. The studies have shown that the differentiation and maturation of OLs involve microRNA (miR) regulation. The recent findings have addressed that miR-204 regulates OL differentiation in culture. In this study, through in situ hybridization in combination with immunohistochemistry, we showed that microRNA-204-5p in the corpus callosum was mainly expressed in OLs immunoreactive with adenomatous polyposis coli (APC), an OL marker. We also found miR-204-5p expression in mature OLs was suppressed by the addition of interleukin-6 (IL-6). Moreover, IL-6-induced inhibition of miR-204-5p expression was blocked by the addition of the inhibitors specific for p38 mitogen-activated protein kinase (p38MAPK) or phosphatidylinositol 3-kinase (PI3K) pathway. We further utilized a rat model by feeding cuprizone (CPZ)-containing diet for 3 weeks to induce demyelination and gliosis in the corpus callosum, as well as the upregulation of IL-6 gene expression significantly. Despite that miR-204-5p expression in the corpus callosum was not altered after feeding by CPZ for 3 weeks, its expression was increased and IL-6 transcription was decreased in the corpus callosum of the recovery group that was fed by CPZ for the first 2 weeks and by the regular diet for one more week. Our data demonstrate that miR-204-5p expression in OLs declined under the influence of the inflamed microenvironment. The findings that an increase in miR-204-5p and declined IL-6 expression observed in the recovery group might be involved with OL repair in the corpus callosum, and also shed light on a potential role for miR-204-5p in OL homeostasis following the white matter injury.

CellNeighborEX: deciphering neighbor-dependent gene expression from spatial transcriptomics data.

Cells have evolved their communication methods to sense their microenvironments and send biological signals. In addition to communication using ligands and receptors, cells use diverse channels including gap junctions to communicate with their immediate neighbors. Current approaches, however, cannot effectively capture the influence of various microenvironments. Here, we propose a novel approach to investigate cell neighbor-dependent gene expression (CellNeighborEX) in spatial transcriptomics (ST) data. To categorize cells based on their microenvironment, CellNeighborEX uses direct cell location or the mixture of transcriptome from multiple cells depending on ST technologies. For each cell type, CellNeighborEX identifies diverse gene sets associated with partnering cell types, providing further insight. We found that cells express different genes depending on their neighboring cell types in various tissues including mouse embryos, brain, and liver cancer. Those genes are associated with critical biological processes such as development or metastases. We further validated that gene expression is induced by neighboring partners via spatial visualization. The neighbor-dependent gene expression suggests new potential genes involved in cell-cell interactions beyond what ligand-receptor co-expression can discover.

Advances in the use of cell-membrane encapsulated nanoparticles to target tumor drugs

<p style="text-align: justify;">Cancer treatment faces multiple challenges, including tumor heterogeneity, drug resistance, microenvironment influence, treatment side effects, and treatment cost. The heterogeneity of the tumor makes the effect of the same treatment vary in different patients, so the development of personalized treatment strategies is crucial. In addition, resistance of tumor cells to therapeutic drugs is a major challenge, and new strategies to overcome resistance are needed. As a cutting-edge field of science and technology, nanotechnology has brought great potential and opportunities for tumor treatment. Nanoparticle drug delivery systems improve drug efficacy and reduce side effects through precise targeted delivery and controlled release. Cell-membrane coated nanoparticles show great promise in tumor therapy. Nanoparticles coated with cell membranes have good biocompatibility, can reduce the obstacles of immune rejection and cell uptake, improve the accumulation and retention of drugs in tumor tissues, and have good drug delivery ability, drug stability and control release ability. This review discusses advances in the use of cell-membrane coated nanoparticles to target tumor drugs.</p>

Unraveling molecular networks in thymic epithelial tumors: deciphering the unique signatures.

Thymic epithelial tumors (TETs) are a rare and diverse group of neoplasms characterized by distinct molecular signatures. This review delves into the complex molecular networks of TETs, highlighting key aspects such as chromosomal abnormalities, molecular subtypes, aberrant gene mutations and expressions, structural gene rearrangements, and epigenetic changes. Additionally, the influence of the dynamic tumor microenvironment on TET behavior and therapeutic responses is examined. A thorough understanding of these facets elucidates TET pathogenesis, offering avenues for enhancing diagnostic accuracy, refining prognostic assessments, and tailoring targeted therapeutic strategies. Our review underscores the importance of deciphering TETs' unique molecular signatures to advance personalized treatment paradigms and improve patient outcomes. We also discuss future research directions and anticipated challenges in this intriguing field.

First person – Rebeka Tomasin

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Rebeka Tomasin is first author on ‘ A molecular landscape of quiescence and proliferation highlights the role of Pten in mammary gland acinogenesis’, published in JCS. Rebeka conducted the research described in this article while a postdoc in Alexandre Bruni-Cardoso's lab at the Institute of Chemistry, University of São Paulo, São Paulo, Brazil. She is now a postdoc in the lab of Cyrus Ghajar at the Fred Hutchinson Cancer Research Center, Seattle, USA, investigating microenvironmental influences on cell behavior in normal tissue and across cancer progression.

A deep learning-based pipeline for analyzing the influences of interfacial mechanochemical microenvironments on spheroid invasion using differential interference contrast microscopic images

Metastasis is the leading cause of cancer-related deaths. During this process, cancer cells are likely to navigate discrete tissue-tissue interfaces, enabling them to infiltrate and spread throughout the body. Three-dimensional (3D) spheroid modeling is receiving more attention due to its strengths in studying the invasive behavior of metastatic cancer cells. While microscopy is a conventional approach for investigating 3D invasion, post-invasion image analysis, which is a time-consuming process, remains a significant challenge for researchers. In this study, we presented an image processing pipeline that utilized a deep learning (DL) solution, with an encoder-decoder architecture, to assess and characterize the invasion dynamics of tumor spheroids. The developed models, equipped with feature extraction and measurement capabilities, could be successfully utilized for the automated segmentation of the invasive protrusions as well as the core region of spheroids situated within interfacial microenvironments with distinct mechanochemical factors. Our findings suggest that a combination of the spheroid culture and DL-based image analysis enable identification of time-lapse migratory patterns for tumor spheroids above matrix-substrate interfaces, thus paving the foundation for delineating the mechanism of local invasion during cancer metastasis.

Influence of leachate microenvironment on the occurrence of phthalate esters in landfills

Phthalate esters (PAEs) are added to various products as plasticizers. Plastic waste containing PAEs enters landfills as they age with use. However, the influence of microenvironmental changes on the occurrence of PAEs during landfill stabilization is still unknown. In this study, we evaluated the relationship between the physical and chemical properties of leachate, the structure of bacterial communities and the chemical structure of dissolved organic matter (DOM), and the occurrence of PAEs and the mechanism underlying their responses to changes. Landfill leachate in different stabilization states had high Cl− and NH4+ contents and its metal element (Cr, Pb, and Zn) contents generally decreased with the increase in landfill ages. Proteobacteria, Bacteroidetes, and Firmicutes were important phyla and had an average relative abundance of 68.63%. The lignin/carboxylate-rich alicyclic molecule structure was the main component of DOM (56%–64%). Of the 6-priority controlled PAEs in leachate, di-n-butyl phthalate was the most abundant (1046 μg L−1), while butyl phthalate was not detected. The results showed that pH, the relative abundance of Chloroflexi, and the value of SUVA254 can directly influence the occurrence of PAEs in leachate. The positive and negative effects vary depending on the PAE content and molecular weight. DBP and DEHP have higher environmental risks in the aquatic system. These results are intended to provide a scientific basis for the evolutionary characterization of the microenvironment in complex environmental systems and the control of novel contaminants, such as PAEs.

The matrix microenvironment influences but does not dominate tissue-specific stem cell lineage differentiation

Mesenchymal stem cells (MSCs) play a pivotal role in tissue engineering and regenerative medicine, with their clinical application often hindered by cell senescence during ex vivo expansion. Recent studies suggest that MSC-deposited decellularized extracellular matrix (dECM) offers a conducive microenvironment that fosters cell proliferation and accentuates stem cell differentiation. However, the ability of this matrix environment to govern lineage differentiation of tissue-specific stem cells remains ambiguous. This research employs human adipose-derived MSCs (ADSCs) and synovium-derived MSCs (SDSCs) as models for adipogenesis and chondrogenesis differentiation pathways, respectively. Genetically modified dECM (GMdECM), produced by SV40LT-transduced immortalized cells, was studied for its influence on cell differentiation. Both types of immortalized cells displayed a reduction in chondrogenic ability but an enhancement in adipogenic potential. ADSCs grown on ADSC-deposited dECM showed stable chondrogenic potential but increased adipogenic capacity; conversely, SDSCs expanded on SDSC-generated dECM displayed elevated chondrogenic capacity and diminished adipogenic potential. This cell-dependent response was confirmed through GMdECM expansion, with SDSCs showing enhanced chondrogenesis. However, ADSCs did not exhibit improved chondrogenic potential on GMdECM, suggesting that the matrix microenvironment does not dictate the final differentiation path of tissue-specific stem cells. Potential molecular mechanisms, such as elevated basement membrane protein expression in GMdECMs and dynamic TWIST1 expression during expansion and chondrogenic induction, may underpin the strong chondrogenic differentiation of GMdECM-expanded SDSCs.