Spatial Compartments Research Articles

Immunoproteomics reveal different characteristics for the prognostic markers of intratumoral-infiltrating CD3+ T lymphocytes and immunoscore in colorectal cancer

Tumor-infiltrating lymphocytes (TILs) and immunoscoring based on densities of CD3+ and CD8+ TILs are both favorable prognostic markers in colorectal cancer (CRC). However, determination of the molecular features of TILs, particularly their immunoproteomic signatures would require the development of large-scale in situ spatiotemporal technologies. Recently, a multiplex in situ digital spatial proteomic profiling (DSP) tool GeoMx DSP has been applied to identify biomarkers predictive of therapeutic responses and to understand disease mechanisms and progression. Taking advantage of this tool, we simultaneously characterized the spatial distribution and interactions of 42 immune proteins in tumor cells (TC), CD3+ T stromal TILs (sTILs), and CD20+ B sTILs using tissue microarrays, and further studied their associations with CD3+ T TILs and immunoscores in CRC. First, our data showed that well-known immune checkpoints, such as PD-L1, PD-L2, and LAG3, were expressed at low levels, whereas some other immune proteins, such as CD11c, CD68, STING, and CD44, were highly expressed. Second, eight spatial interactions were identified, including five interactions between TC and CD20+ B sTILs, two interactions between CD3+ T sTILs and CD20+ B sTILs, and one interaction among TC, CD3+ T sTILs, and CD20+ B sTILs. Third, the differential immune microlandscape in the spatial compartments was identified in tissues with positive CD3+ T intratumoral TILs and high immunoscores. Collectively, our study is the first to provide in situ spatial immune characteristics at the proteomic level. Moreover, our findings provide direct evidence supporting the infiltration of CD3+ T sTILs from stoma to TC and shed important insights into better understanding and treating CRC patients related to different immune prognostic markers.

Single-cell and spatial proteo-transcriptomic profiling reveals immune infiltration heterogeneity associated with neuroendocrine features in small cell lung cancer

Small cell lung cancer (SCLC) is an aggressive pulmonary neuroendocrine malignancy featured by cold tumor immune microenvironment (TIME), limited benefit from immunotherapy, and poor survival. The spatial heterogeneity of TIME significantly associated with anti-tumor immunity has not been systemically studied in SCLC. We performed ultra-high-plex Digital Spatial Profiling on 132 tissue microarray cores from 44 treatment-naive limited-stage SCLC tumors. Incorporating single-cell RNA-sequencing data from a local cohort and published SCLC data, we established a spatial proteo-transcriptomic landscape covering over 18,000 genes and 60 key immuno-oncology proteins that participate in signaling pathways affecting tumorigenesis, immune regulation, and cancer metabolism across 3 pathologically defined spatial compartments (pan-CK-positive tumor nest; CD45/CD3-positive tumor stroma; para-tumor). Our study depicted the spatial transcriptomic and proteomic TIME architecture of SCLC, indicating clear intra-tumor heterogeneity dictated via canonical neuroendocrine subtyping markers; revealed the enrichment of innate immune cells and functionally impaired B cells in tumor nest and suggested potentially important immunoregulatory roles of monocytes/macrophages. We identified RE1 silencing factor (REST) as a potential biomarker for SCLC associated with low neuroendocrine features, more active anti-tumor immunity, and prolonged survival.

Self-consistent sharp interface theory of active condensate dynamics

Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active biomolecules which, after transient binding via molecular interactions, catalyze reactions among their substrates. Thereby, biomolecular condensates provide a spatial template for nonuniform concentration profiles of substrates. In turn, the concentration profiles of substrates, and their molecular interactions with enzymes, drive enzyme fluxes which can enable novel nonequilibrium dynamics. To analyze this generic class of systems, with a current focus on self-propelled droplet motion, we here develop a self-consistent sharp interface theory. In our theory, we diverge from the usual bottom-up approach, which involves calculating the dynamics of concentration profiles based on a given chemical potential gradient. Instead, reminiscent of control theory, we take the reverse approach by deriving the chemical potential profile and enzyme fluxes required to maintain a desired condensate form and dynamics. The chemical potential profile and currents of enzymes come with a corresponding power dissipation rate, which allows us to derive a thermodynamic consistency criterion for the passive part of the system (here, reciprocal enzyme-enzyme interactions). As a first-use case of our theory, we study the role of reciprocal interactions, where the transport of substrates due to reactions and diffusion is, in part, compensated by redistribution due to molecular interactions. More generally, our theory applies to mass-conserved active matter systems with moving phase boundaries. Published by the American Physical Society 2024

Spatial Heterogeneity of Immune Regulators Drives Dynamic Changes in Local Immune Responses, Affecting Disease Outcomes in Pancreatic Cancer.

Pancreatic ductal adenocarcinoma (PDAC) is considered a low-immunogenic (LI) tumor with a "cold" tumor microenvironment and is mostly unresponsive to immune checkpoint blockade therapies. In this study, we decipher the impact of intratumoral heterogeneity of immune determinants on antitumor responses. We performed spatial proteomic and transcriptomic analyses and multiplex immunofluorescence on multiple tumor regions, including tumor center (TC) and invasive front (IF), from 220 patients with PDAC, classified according to their transcriptomic immune signaling into high-immunogenic PDAC (HI-PDAC, n = 54) and LI PDAC (LI-PDAC, n = 166). Spatial compartments (tumor: pancytokeratin+/CD45- and leukocytes: pancytokeratin-/CD45+) were defined by fluorescence imaging. HI-PDAC exhibited higher densities of cytotoxic T lymphocytes with upregulation of T-cell priming-associated immune determinants, including CD40, ITGAM, glucocorticoid-induced TNF-related receptor, CXCL10, granzyme B, IFNG, and HLA-DR, which were significantly more prominent at the IF than at the TC. In contrast, LI-PDAC exhibited immune-evasive tumor microenvironments with downregulation of immune determinants and a negative gradient from TC to IF. Patients with HI-PDAC had significantly better outcomes but showed more frequently exhausted immune phenotypes. Our results indicate strategic differences in the regulation of immune determinants, leading to different levels of effectiveness of antitumor responses between HI and LI tumors and dynamic spatial changes, which affect the evolution of immune evasion and patient outcomes. This finding supports the coevolution of tumor and immune cells and may help define therapeutic vulnerabilities to improve antitumor immunity and harness the responsiveness to immune checkpoint inhibitors in patients with PDAC.

Fire Load of Combustibles in Studio-type Housing

The purpose of this study was to determine the fire load values for small-scale housing, specifically studio-type and small-type housing, and to gather fundamental data for fire safety design. To achieve this, we employed fire load-related theories from existing literature and previous studies, conducted a survey on the area and space of small-scale housing, and collected empirical data on the fire load of such housing. Additionally, through real-scale fire experiments, we determined the heat of combustion for furniture and electrical appliances. These experimental results were then compared with theoretical fire load values and empirical data to establish the fire load values of combustibles in small-scale housing. By comparing the empirical data with the results from real-scale experiments, we derived conclusions about the characteristics of areas based on the spatial configuration and compartments of small-scale housing, as well as the methods for inferring the heat of combustion and fire load of combustibles in these settings.

Potential Role of Lymphocyte CD44 in Determining Treatment Selection Between Stereotactic Body Radiation Therapy and Surgery for Early-Stage Non-Small Cell Lung Cancer

Background: Stereotactic body radiotherapy (SBRT) versus surgery for operable early-stage non-small-cell lung cancer (ES-NSCLC) remains highly debated. Herein, we utilized spatial proteomics to identify whether any molecular biomarker(s) associate with the efficacy of either modality, in efforts to optimize treatment selection between surgery or SBRT for this population. Methods: We evaluated biopsy tissue samples from 44 ES-NSCLC patients treated with first-line SBRT (cohort 1) by GeoMx Digital Spatial Profiling (DSP) with a panel of 70 proteins in five spatial molecular compartments: tumor (panCK+), leukocyte (CD45+), lymphocyte (CD3+), macrophage (CD68+), and stroma (α-SMA+). To validate the findings in cohort 1, biopsy samples from 52 ES-NSCLC patients who received SBRT (cohort 2) and 62 ES-NSCLC patients who underwent surgery (cohort 3) were collected and analyzed by multiplex immunofluorescence (mIF). Results: In cohort 1, higher CD44 expression in the lymphocyte compartment was associated with poorer recurrence-free survival (RFS) (DSP: P<0.001; mIF: P<0.001) and higher recurrence rate (DSP: P=0.001; mIF: P=0.004). mIF data from cohort 2 validated these findings (P<0.05 for all). From cohort 3, higher lymphocyte CD44 predicted higher RFS after surgery (P=0.003). Inter-modality comparisons demonstrated that SBRT was associated with significantly higher RFS over surgery in CD44-low patients (P<0.001), but surgery was superior to SBRT in CD44-high cases (P=0.016). Conclusions: Lymphocyte CD44 may not only be a predictor of SBRT efficacy in this population, but also an important biomarker (pending validation by large prospective data) that could better sharpen selection for SBRT vs. surgery in ES-NSCLC.

Mizrahi Rap in Israel: Ethnicity and Intertextuality in the Cosmopolitan Post-Genre Era

Abstract This article uses ethnography and music analysis to compare the intertextuality of Mizrahi music and rap by two generations of hip hop artists in Israel. The perceived compatibility of the two genres is often motivated by apparent similarities between Mizrahiness and Blackness as two ethno-racial categories associated with disenfranchisement. We argue that varied musical approaches to combining Mizrahi music and rap reflect the ways that different generations have negotiated local and global cultural spaces. Early rappers in Israel, who regarded Mizrahi music and rap as two distinct genres, tended to compose a rather mechanistic juxtaposition between them that suggests a perceived ontological gap between the local and the global. Conversely, contemporary rappers have been socialized in and make use of a virtual and borderless musical environment, a realm that arguably breaks down the logic of coherent musical genres and the cultural and spatial compartments they once seemed to occupy. This is reflected in their typical compositional style, which merges the two genres into a seamless, indistinguishable form. The case of “Mizrahi rap” demonstrates how global trends are inscribed into local negotiations of ethnicity and how the perceived relatedness between ethnic and racial categories (i.e., Mizrahiness and Blackness) defines new conceptions of the global sphere itself.

Dose-Dependent Transcriptional Response to Ionizing Radiation Is Orchestrated with DNA Repair within the Nuclear Space.

Radiation therapy is commonly used to treat glioblastoma multiforme (GBM) brain tumors. Ionizing radiation (IR) induces dose-specific variations in transcriptional programs, implicating that they are tightly regulated and critical components in the tumor response and survival. Yet, our understanding of the downstream molecular events triggered by effective vs. non-effective IR doses is limited. Herein, we report that variations in the genetic programs are positively and functionally correlated with the exposure to effective or non-effective IR doses. Genome architecture analysis revealed that gene regulation is spatially and temporally coordinated with DNA repair kinetics. The radiation-activated genes were pre-positioned in active sub-nuclear compartments and were upregulated following the DNA damage response, while the DNA repair activity shifted to the inactive heterochromatic spatial compartments. The IR dose affected the levels of DNA damage repair and transcription modulation, but not the order of the events, which was linked to their spatial nuclear positioning. Thus, the distinct coordinated temporal dynamics of DNA damage repair and transcription reprogramming in the active and inactive sub-nuclear compartments highlight the importance of high-order genome organization in synchronizing the molecular events following IR.

Analysis of mitochondrial translation using click chemistry.

Mitochondria contain their own gene expression machinery, which synthesizes core subunits of the oxidative phosphorylation system. Monitoring mitochondrial translation within spatial compartments of cells is difficult. Here we describe a method to visualize mitochondrial translation within defined parts of cells, using a click chemistry approach. This method can be applied to different cell types such as neurons and allows detection of newly synthesized mitochondrial proteins in spatial resolution using microscopy techniques. Furthermore, using click chemistry, mitochondrial translation can also be monitored by standard SDS-PAGE. The described method avenues the analysis of newly synthesized mitochondrial encoded proteins in the cellular context, by avoiding the usage of radioactive components.

On the interface of enzyme and spatial confinement: The impacts of confinement rigidity, shape, and surface properties on the interplay of enzyme structure, dynamics, and function

Confining proteins in synthetic nanoscale spatial compartments has offered a cell-free avenue to understand enzyme structure–function relationships and complex cellular processes near the physiological conditions, an important branch of fundamental protein biophysics studies. Enzyme confinement has also provided advancement in biocatalysis by offering enhanced enzyme reusability, cost-efficiency, and substrate selectivity in certain cases for research and industrial applications. However, the primary research efforts in this area have been focused on the development of novel confinement materials and investigating protein adsorption/interaction with various surfaces, leaving a fundamental knowledge gap, namely, the lack of understanding of the confined enzymes (note that enzyme adsorption to or interactions with surfaces differs from enzyme confinement as the latter offers an enhanced extent of restriction to enzyme movement and/or conformational flexibility). In particular, there is limited understanding of enzymes' structure, dynamics, translocation (into biological pores), folding, and aggregation in extreme cases upon confinement, and how confinement properties such as the size, shape, and rigidity affect these details. The first barrier to bridge this gap is the difficulty in “penetrating” the “shielding” of the confinement walls experimentally; confinement could also lead to high heterogeneity and dynamics in the entrapped enzymes, challenging most protein-probing experimental techniques. The complexity is raised by the variety in the possible confinement environments that enzymes may encounter in nature or on lab benches, which can be categorized to rigid confinement with regular shapes, rigid restriction without regular shapes, and flexible/dynamic confinement which also introduces crowding effects. Thus, to bridge such a knowledge gap, it is critical to combine advanced materials and cutting-edge techniques to re-create the various confinement conditions and understand enzymes therein. We have spearheaded in this challenging area by creating various confinement conditions to restrict enzymes while exploring experimental techniques to understand enzyme behaviors upon confinement at the molecular/residue level. This review is to summarize our key findings on the molecular level details of enzymes confined in (i) rigid compartments with regular shapes based on pre-formed, mesoporous nanoparticles and Metal–Organic Frameworks/Covalent-Organic Frameworks (MOFs/COFs), (ii) rigid confinement with irregular crystal defects with shapes close to the outline of the confined enzymes via co-crystallization of enzymes with certain metal ions and ligands in the aqueous phase (biomineralization), and (iii) flexible, dynamic confinement created by protein-friendly polymeric materials and assemblies. Under each case, we will focus our discussion on (a) the way to load enzymes into the confined spaces, (b) the structural basis of the function and behavior of enzymes within each compartment environments, and (c) technical advances of our methodology to probe the needed structural information. The purposes are to depict the chemical physics details of enzymes at the challenging interface of natural molecules and synthetic compartment materials, guide the selection of enzyme confinement platforms for various applications, and generate excitement in the community on combining cutting-edge technologies and synthetic materials to better understand enzyme performance in biophysics, biocatalysis, and biomedical applications.

SPATIALLY‐RESOLVED TRANSCRIPTOMICS DEFINE CLINICALLY RELEVANT SUBSETS OF MACROPHAGES IN DIFFUSE LARGE B‐CELL LYMPHOMA

Introduction: Tumor-associated macrophages (TAMs) are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL) and are implicated in tumor progression and therapy resistance. Conventional immunohistochemistry-based studies have relied on the oversimplified M1/M2 classification of TAMs which does not fully capture the functional diversity of macrophage biology, thus potentially contributing to their inconsistent prognostic significance in DLBCL. Spatial whole-transcriptomic analysis allows in-depth investigation of specific cell types in different spatial regions within normal and malignant lymphoid tissues, enabling detailed macrophage phenotyping. Here, we employed spatial whole-transcriptomic analysis in the characterization of CD68+ cells of DLBCL and reactive lymphoid tissues (RLTs) to identify novel macrophage subsets with biological and clinical significance. Methods: Digital spatial profiling with whole-transcriptomic analysis of CD68+ cells was performed in 47 DLBCL and 17 RLTs, to define macrophage signatures (termed “MacroSigs”) of distinct lymphoid spatial niches and clinical scenarios. Eight independent DLBCL datasets (4594 patients) with complete transcriptomic and survival information were used for validation of these spatial-derived MacroSigs. Results: Digital spatial profiling revealed previously unrecognized transcriptomic differences between macrophages populating distinct spatial compartments in RLTs (light zone (LZ)/dark zone (DZ), germinal center (GC)/interfollicular (IF) regions), and in between disease states (RLTs and DLBCL with or without relapsed disease). This transcriptomic diversity of macrophages was categorized into eight MacroSigs. Spatial-derived MacroSigs associate with specific cell-of-origin (COO) subtypes of DLBCL, of particular interest being the IF-MacroSig enriched in the unclassified COO (p < 0.005, 6/8 datasets). MacroSigs of relapsed-DLBCL and DZ were prognostic for shorter overall survival in multiple datasets (p < 0.05 in 5/8 datasets; p < 0.05 in 8/8 datasets, respectively). Projection onto a macrophage single-cell RNA-sequencing atlas reveals the Non-relapse-DLBCL MacroSig to depict HES1/FOLR2-like macrophages, while relapse-DLBCL-MacroSig represents IL1B-like monocytes, with unique therapeutic vulnerabilities for each. The research was funded by: Work in ADJ’s laboratory is funded by a core grant from the Cancer Science Institute of Singapore, National University of Singapore through the National Research Foundation Singapore and the Singapore Ministry of Education under its Research Centres of Excellence initiative. CT was supported by the Italian Foundation for Cancer Research (AIRC) Investigator Grant IG ID.22145; 5 × 1000 Grant ID.22759. Keywords: aggressive B-cell non-Hodgkin lymphoma, diagnostic and prognostic biomarkers No conflicts of interests pertinent to the abstract.

Abstract 4293: Strategies and resources for applying a quantitative multiplex IHC imaging workflow to characterize immune contexture in solid tumors

Abstract Conventional immunohistochemistry (IHC) is a standardized diagnostic technique used in tissue pathology. However, the capacity to label only one marker per tissue section is a critical limitation. Multiplex immunohistochemistry (mIHC) is a powerful imaging technique used in basic, translational research and clinical settings to simultaneously detect the expression of multiple epitopes in a single formalin-fixed paraffin-embedded (FFPE) tissue section, allowing for characterization and quantification of cells while maintaining their spatial location. This technique allows for a comprehensive view of the immune milieu, expression patterns, and interactions between cell types that can help elucidate the complexity of the tumor-immune microenvironment (TiME). Multiplex imaging has emerged as a powerful tool to better understand tumor progression, response or resistance to therapy, and potentially identify predictive biomarkers. However, this technique requires careful tissue considerations and generates enormous amounts of hierarchical data, including single cell marker expressions, locations, and shape features, resulting in complex and challenging analyses. We previously published a validated platform using nine matched primary and recurrent head and neck squamous cell carcinoma (HNSCC) sections stained sequentially with a panel of 29 antibodies identifying malignant tumor cells, and 17 distinct leukocyte lineages and their functional states1. Here, we have optimized and consolidated important considerations, including tissue quality and QC steps necessary for generating high quality data from multiplex imaging studies. We demonstrate strategies for a streamline analytic pipeline using our quantitative workflow developed to characterize immune cells and infiltration patterns within spatial compartments of solid tumors in FFPE tissues, and herein, provide strategies and resources to practically adapt and utilize our analytic mIHC pipeline. 1. Banik, G., et al., Methods Enzymol., 2020 Citation Format: Shamilene Sivagnanam, Courtney M. Betts, Nell Kirchberger, Konjit Betre, Lisa M. Coussens. Strategies and resources for applying a quantitative multiplex IHC imaging workflow to characterize immune contexture in solid tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4293.

Abstract 46: High-plex spatial transcriptomic characterization of canine tumor tissue

Abstract Background: Combination therapy to treat hematological and solid malignancies including chemotherapy, radiation, targeted and immunotherapy all hold huge potential for eliciting clinical responses. Informative pre-clinical testing of these approaches can be greatly facilitated using immune competent animals with spontaneous tumors. Pet dogs are immunologically outbred, immune competent and develop spontaneous tumors such as non Hodgkin’s lymphoma, glioblastoma, osteosarcoma, urothelial carcinoma and melanoma that share remarkable clinical, biological and genetic features with their human counterparts. As such, pre clinical testing of therapeutic approaches in dogs with cancer promises to accurately inform human clinical trial design. For this comparative approach to provide maximum information to accelerate human clinical translation of novel combination therapies and identify correlative biomarkers of therapeutic response, it is necessary to develop research tools for deep interrogation of the canine tumor microenvironment (TME). Here we present spatial transcriptomic analysis of multiple canine tumor and tissue types using GeoMx® digital spatial profiler (DSP) Canine Cancer Atlas (CCA) panel. Methods: FFPE slides or tissue microarrays were used to profile tumor and normal tissue from canines. Each slide was stained with tissue specific immunofluorescent antibodies, including Pan-cytokeratin, CD45, Vimentin, IBA1, CD3, and/or CD68. Regions of interest were selected to assess the TME and normal tissue as possible. Slides were then run on the DSP using the CCA panel that contains 1900-canine specific genes using standard DSP methods. Results: We were able to spatially detect over 1700 genes across multiple tissue types from canines, including osteosarcoma, glioblastoma, melanoma and normal tissues. Genes were detected in spatial compartments including malignant tumor, tumor stroma and normal tissue. Conclusions: Together the GeoMx CCA allow for interrogation of the TME of multiple tumor types and has the potential to inform spatial biomarkers for response to therapy, as well as translate the effectiveness of these therapies to humans. Citation Format: Sarah E. Church, Cheryl London, Christine M. Toedebusch, Ben Sutton, Sarah Weigel, Erin Piazza. High-plex spatial transcriptomic characterization of canine tumor tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 46.

Abstract ED7-2: Multiplex spatial proteomic profiling

Abstract Multiplex spatial analysis is touted as a potential solution for tissue biomarkers for prognostic and companion diagnostic applications. Spatial analysis infers maintaining the location of a biomolecule so that both its amount and context can contribute to the information obtained. Immunohistochemistry (IHC) is the archetypal method of spatial profiling and the only application that has made it to the clinic. In this session, we will discuss technologies based on IHC, but that allow assessment of at least two, and as many as 100 or more proteins within the cell or molecular compartment that maintains spatial context. The simplest and most common approach is multiplex immunofluorescence, followed by a number of next generation techniques that use alternative labeling of the antibodies or cycling strategies or both to generate spatially informed data. Excluding Mass spectrometry-based methods, still in early stages, the highest “plex” method for protein is digital spatial profiling. Digital spatial profiling (DSP) uses a molecular method to define spatial compartments which is different from other high-plex methods that use cell segmentation, an image analysis method that largely depends on the presence of a cell nucleus in the image. As a result, the DSP method allows assessment of both cellular and non-cellular stromal compartments. DSP and other high-plex methods that will be discussed are thought to be best used as biomarker discovery tools, that might find biomarkers that can be measured with a more traditional approach for assessment in the clinic. Citation Format: David Rimm. Multiplex spatial proteomic profiling [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr ED7-2.

Coarsening dynamics can explain meiotic crossover patterning in both the presence and absence of the synaptonemal complex.

The shuffling of genetic material facilitated by meiotic crossovers is a critical driver of genetic variation. Therefore, the number and positions of crossover events must be carefully controlled. In Arabidopsis, an obligate crossover and repression of nearby crossovers on each chromosome pair are abolished in mutants that lack the synaptonemal complex (SC), a conserved protein scaffold. We use mathematical modelling and quantitative super-resolution microscopy to explore and mechanistically explain meiotic crossover pattering in Arabidopsis lines with full, incomplete, or abolished synapsis. For zyp1 mutants, which lack an SC, we develop a coarsening model in which crossover precursors globally compete for a limited pool of the pro-crossover factor HEI10, with dynamic HEI10 exchange mediated through the nucleoplasm. We demonstrate that this model is capable of quantitatively reproducing and predicting zyp1 experimental crossover patterning and HEI10 foci intensity data. Additionally, we find that a model combining both SC- and nucleoplasm-mediated coarsening can explain crossover patterning in wild-type Arabidopsis and in pch2 mutants, which display partial synapsis. Together, our results reveal that regulation of crossover patterning in wild-type Arabidopsis and SC-defective mutants likely acts through the same underlying coarsening mechanism, differing only in the spatial compartments through which the pro-crossover factor diffuses.

Spatially restricted tumour-associated and host-associated immune drivers correlate with the recurrence sites of pancreatic cancer

ObjectiveMost patients with pancreatic ductal adenocarcinoma (PDAC) will experience recurrence after resection. Here, we investigate spatially organised immune determinants of PDAC recurrence.DesignPDACs (n=284; discovery cohort) were classified according to recurrence...

PS-BPB05-1: DUAL DISRUPTION OF ENDOTHELIAL NITRIC OXIDE SYNTHASE AND APOE GENE ACCELERATES KIDNEY FIBROSIS AND AGING AFTER INJURY

Objective: Advances in medical science have made it possible to control diseases such as cancer, autoimmune diseases, and infectious diseases, extending the lifespan of affected people around the world. On the other hand, the number of patients with Chronic Kidney Disease (CKD) is increasing worldwide, and hypertension is a key factor. Suppression of CKD is important for extending healthy life expectancy. In this study, we will clarify the effects of the interaction between hypertension and atherosclerosis on renal fibrosis and aging. Design and method: Wild type (WT) mouse, apolipoprotein E-/- (ApoE KO) mouse, and endothelial nitric oxide synthase (eNOS)-/- ; ApoE-/- (DKO) mouse were obtained by crossing eNOS+/- mouse and ApoE+/- mouse. Unilateral ureteral obstruction (UUO) was performed on 8–10 weeks old male mice after blood pressure and lipid profile were measured. Mice were sacrificed 10 days after UUO. The degree of renal tubular injury, fibrosis and kidney senescence were evaluated. Results: DKO mice exhibited the most pronounced blood pressure and lipid abnormalities among the three groups, with a significant elevation of blood pressure, total cholesterol, and low HDL cholesterol compared to WT mice. DKO mice manifested elevated blood pressure, higher total cholesterol and lower HDL than WT mice. Compared with WT mice, ApoE KO and DKO mice showed sustained kidney injury molecule-1 expression and kidney fibrosis was significantly higher in ApoEKO and DKO mice. mRNA expression of genes related to kidney fibrosis was the highest in DKO mice. The mRNA expression of Zinc alpha2 Glycoprotein and heme oxygenase-1 were significantly decreased in DKO mice. Furthermore, mRNA expression of p53, p21 and p16 were increased both in ApoEKO and DKO mice, with DKO mice being the highest. Senescence associated beta-gal positive tubule area was significantly increased in DKO. Increased DNA damage and target of rapamycin autophagy spatial coupling compartments (TASCCs, Sci Transl Med. 2019;11(476):eaav4754. J Clin Invest. 2019;129(11):4797- 4816.) formation was found in DKO mice. Conclusion: Mice at high risk for cardiovascular disease developed kidney fibrosis and aging even in the young mice after injury. Vulnerability to oxidative stress due to endothelial cell dysfunction promotes fibrosis and aging. Managing lifestyle-related diseases including hypertension from a young age is important for CKD prevention.

Population balance modeling of unstirred cooling crystallization on an integrated belt filter

The successive unit operations of cooling crystallization, cake filtration and contact drying are joined in one apparatus, the modular integrated belt filter, for small-scale downstream processing. This modular equipment offers high flexibility without external solid transport. After prior studies on equipment setup and functionality, this contribution focuses on understanding and influencing unstirred cooling crystallization in small layers with the aid of population balance modeling.An unstirred cooling crystallization is dominated by sedimentation effects. Thus, particle size distributions (PSD) are modeled for discrete spatial compartments based on orthogonal collocation on finite elements. Model validation regarding temperature profile and yield is conducted for two material systems featuring high (sucrose/water) and low viscosity (ascorbic acid/water). With a high impact on sedimentation, viscosity influences product quantity (yield) and quality (PSD). For both material systems, the effects of operating parameters on yield and PSD are determined through a parameter study based on surrogate models to derive optimal operating conditions.

SnapShot: Chromosome organization

Chromosomes in higher eukaryotes are folded at different length scales into loop extrusion domains, spatial compartments, and chromosome territories and exhibit interactions with nuclear structures such as the lamina. Microscopic methods can probe this structure by measuring positions of chromosomes in the nuclear space in individual cells, while sequencing-based contact capture approaches can report the frequency of contacts of different regions within these structural layers. To view this SnapShot, open or download the PDF.

Niche‐specific transcriptional reprogramming leads to pro‐angiogenic neutrophil specialization in colon cancer

Robust neutrophil (PMN) tissue accumulation is an important clinical feature in active Ulcerative Colitis (UC) lesions and in colorectal cancer (CRC). Using murine colitis‐associated CRC model, we observed prominent and persistent PMN accumulation as the inflamed colon tissue progressed from colonic ulceration to CRC. Given the emerging evidence of PMN phenotypic and functional heterogeneity in homeostatic and pathologic conditions, we analyzed the transcriptomic landscape of these immune cells in blood and tissue during the transition from inflammatory ulceration to CRC. Principal component analysis effectively stratified neutrophils across different conditions into three discrete clusters that marked distinct spatial compartments of peripheral blood, inflamed colon tissue and the CRC tumor niche. Importantly, combinatory analyses of pathway overrepresentation, protein‐network mapping, and gene‐ontology scoring revealed a robust enrichment of biological pathways involved in vasculature development and angiogenesis uniquely in PMNs associated with the advanced CRC niche. These findings were validated in vivo as we found that temporary PMN depletion profoundly reduced tumor vascularity, vessel branching, and penetration depth of the tumor vessels. Moreover, we identified Spp1 (OPN) and Mmp14(MT1‐MMP) to be highly induced transcriptionally in PMNs as they left the circulation and entered the tumor niche, where Spp1 and Mmp14 directly promoted tumor angiogenesis. TCGA data mining and validation in UC/CRC patient cohorts further confirmed significant upregulation of Spp1 and Mmp14in high‐grade CRC, but not in UC patients. In conclusion, the current study identified a niche‐specific compartmentalization of PMN transcriptional programing, highlighting the novel PMN plasticity. Our findings further established the contribution of CRC‐associated PMNs via Spp1/Mmp14 activity to the formation of a complex tumor vasculature and subsequent neoplastic progression from inflammatory colitis to advanced CRC.